-- dump date 20140619_113353 -- class Genbank::misc_feature -- table misc_feature_note -- id note 907240000001 Initiator Replication protein; Region: Rep_3; pfam01051 907240000002 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 907240000003 putative RNA binding site [nucleotide binding]; other site 907240000004 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 907240000005 homopentamer interface [polypeptide binding]; other site 907240000006 active site 907240000007 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 907240000008 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 907240000009 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 907240000010 active site clefts [active] 907240000011 zinc binding site [ion binding]; other site 907240000012 dimer interface [polypeptide binding]; other site 907240000013 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 907240000014 active site 907240000015 dimer interface [polypeptide binding]; other site 907240000016 pantoate--beta-alanine ligase; Region: panC; TIGR00018 907240000017 Pantoate-beta-alanine ligase; Region: PanC; cd00560 907240000018 active site 907240000019 ATP-binding site [chemical binding]; other site 907240000020 pantoate-binding site; other site 907240000021 HXXH motif; other site 907240000022 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240000023 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 907240000024 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 907240000025 ring oligomerisation interface [polypeptide binding]; other site 907240000026 ATP/Mg binding site [chemical binding]; other site 907240000027 stacking interactions; other site 907240000028 hinge regions; other site 907240000029 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 907240000030 oligomerisation interface [polypeptide binding]; other site 907240000031 mobile loop; other site 907240000032 roof hairpin; other site 907240000033 DNA primase, catalytic core; Region: dnaG; TIGR01391 907240000034 CHC2 zinc finger; Region: zf-CHC2; pfam01807 907240000035 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 907240000036 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 907240000037 active site 907240000038 metal binding site [ion binding]; metal-binding site 907240000039 interdomain interaction site; other site 907240000040 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 907240000041 ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide; Region: ThiI; cd01712 907240000042 Ligand Binding Site [chemical binding]; other site 907240000043 TrbC/VIRB2 family; Region: TrbC; cl01583 907240000044 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 907240000045 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 907240000046 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 907240000047 Walker A motif; other site 907240000048 ATP binding site [chemical binding]; other site 907240000049 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 907240000050 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 907240000051 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; cd00588 907240000052 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 907240000053 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 907240000054 active site 907240000055 phosphorylation site [posttranslational modification] 907240000056 intermolecular recognition site; other site 907240000057 dimerization interface [polypeptide binding]; other site 907240000058 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 907240000059 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 907240000060 dimer interface [polypeptide binding]; other site 907240000061 active site 907240000062 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 907240000063 catalytic residues [active] 907240000064 substrate binding site [chemical binding]; other site 907240000065 lipid A 1-phosphatase; Reviewed; Region: PRK09597 907240000066 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 907240000067 active site 907240000068 lipid A phosphoethanolamine transferase; Reviewed; Region: PRK09598 907240000069 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 907240000070 Sulfatase; Region: Sulfatase; pfam00884 907240000071 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240000072 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 907240000073 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 907240000074 dimer interface [polypeptide binding]; other site 907240000075 active site 907240000076 citrylCoA binding site [chemical binding]; other site 907240000077 NADH binding [chemical binding]; other site 907240000078 cationic pore residues; other site 907240000079 oxalacetate/citrate binding site [chemical binding]; other site 907240000080 coenzyme A binding site [chemical binding]; other site 907240000081 catalytic triad [active] 907240000082 isocitrate dehydrogenase; Validated; Region: PRK07362 907240000083 isocitrate dehydrogenase; Reviewed; Region: PRK07006 907240000084 Protein of unknown function (DUF1523); Region: DUF1523; pfam07509 907240000085 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 907240000086 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 907240000087 Ligand Binding Site [chemical binding]; other site 907240000088 Uncharacterized conserved protein [Function unknown]; Region: COG2127 907240000089 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 907240000090 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 907240000091 Walker A motif; other site 907240000092 ATP binding site [chemical binding]; other site 907240000093 Walker B motif; other site 907240000094 arginine finger; other site 907240000095 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 907240000096 Walker A motif; other site 907240000097 ATP binding site [chemical binding]; other site 907240000098 Walker B motif; other site 907240000099 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 907240000100 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 907240000101 tetramerization interface [polypeptide binding]; other site 907240000102 active site 907240000103 hypothetical protein; Provisional; Region: PRK03762 907240000104 PDZ domain; Region: PDZ_2; pfam13180 907240000105 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 907240000106 Type IV secretory pathway, TrbL components [Intracellular trafficking and secretion]; Region: TrbL; COG3846 907240000107 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 907240000108 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 907240000109 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 907240000110 VirB7 interaction site; other site 907240000111 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 907240000112 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 907240000113 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 907240000114 Substrate binding site; other site 907240000115 Cupin domain; Region: Cupin_2; cl17218 907240000116 GDP-mannose 4,6-dehydratase; Region: gmd; TIGR01472 907240000117 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 907240000118 NADP-binding site; other site 907240000119 homotetramer interface [polypeptide binding]; other site 907240000120 substrate binding site [chemical binding]; other site 907240000121 homodimer interface [polypeptide binding]; other site 907240000122 active site 907240000123 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 907240000124 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 907240000125 NADP binding site [chemical binding]; other site 907240000126 active site 907240000127 putative substrate binding site [chemical binding]; other site 907240000128 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 907240000129 dimerization interface [polypeptide binding]; other site 907240000130 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 907240000131 ATP binding site [chemical binding]; other site 907240000132 Acylphosphatase; Region: Acylphosphatase; pfam00708 907240000133 [NiFe] hydrogenase maturation protein HypF; Region: hypF; TIGR00143 907240000134 HypF finger; Region: zf-HYPF; pfam07503 907240000135 HypF finger; Region: zf-HYPF; pfam07503 907240000136 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 907240000137 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957 907240000138 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 907240000139 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 907240000140 DNA methylase; Region: N6_N4_Mtase; pfam01555 907240000141 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 907240000142 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 907240000143 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 907240000144 DNA methylase; Region: N6_N4_Mtase; pfam01555 907240000145 Tsp45I type II restriction enzyme; Region: Tsp45I; pfam06300 907240000146 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 907240000147 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 907240000148 cofactor binding site; other site 907240000149 DNA binding site [nucleotide binding] 907240000150 substrate interaction site [chemical binding]; other site 907240000151 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 907240000152 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 907240000153 S-adenosylmethionine binding site [chemical binding]; other site 907240000154 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 907240000155 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 907240000156 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 907240000157 Na binding site [ion binding]; other site 907240000158 Proline dehydrogenase; Region: Pro_dh; pfam01619 907240000159 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 907240000160 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 907240000161 Glutamate binding site [chemical binding]; other site 907240000162 NAD binding site [chemical binding]; other site 907240000163 catalytic residues [active] 907240000164 Proteins of 100 residues with WXG; Region: WXG100; cl02005 907240000165 A nuclease of the HNH/ENDO VII superfamily with conserved WHH; Region: WHH; pfam14414 907240000166 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 907240000167 potential frameshift: common BLAST hit: gi|108562492|ref|YP_626808.1| ATP-binding protein 907240000168 Urease accessory protein UreH [Posttranslational modification, protein turnover, chaperones]; Region: UreH; COG0829 907240000169 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 907240000170 G1 box; other site 907240000171 GTP/Mg2+ binding site [chemical binding]; other site 907240000172 G2 box; other site 907240000173 Switch I region; other site 907240000174 G3 box; other site 907240000175 Switch II region; other site 907240000176 G4 box; other site 907240000177 G5 box; other site 907240000178 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 907240000179 UreF; Region: UreF; pfam01730 907240000180 urease accessory protein UreE; Provisional; Region: ureE; PRK13261 907240000181 UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The...; Region: UreE; cd00571 907240000182 dimer interface [polypeptide binding]; other site 907240000183 catalytic residues [active] 907240000184 AmiS/UreI family transporter; Region: AmiS_UreI; pfam02293 907240000185 urease subunit beta; Provisional; Region: ureB; PRK13985 907240000186 Urease alpha-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, fungi and plants. Their primary role is to allow the use of...; Region: Urease_alpha; cd00375 907240000187 subunit interactions [polypeptide binding]; other site 907240000188 active site 907240000189 flap region; other site 907240000190 urease subunit alpha; Provisional; Region: PRK13986 907240000191 Urease gamma-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use...; Region: Urease_gamma; cd00390 907240000192 alpha-gamma subunit interface [polypeptide binding]; other site 907240000193 beta-gamma subunit interface [polypeptide binding]; other site 907240000194 Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of...; Region: Urease_beta; cd00407 907240000195 gamma-beta subunit interface [polypeptide binding]; other site 907240000196 alpha-beta subunit interface [polypeptide binding]; other site 907240000197 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 907240000198 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14324 907240000199 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 907240000200 active site 907240000201 substrate binding site [chemical binding]; other site 907240000202 metal binding site [ion binding]; metal-binding site 907240000203 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 907240000204 peptide chain release factor 1; Validated; Region: prfA; PRK00591 907240000205 This domain is found in peptide chain release factors; Region: PCRF; smart00937 907240000206 RF-1 domain; Region: RF-1; pfam00472 907240000207 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240000208 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 907240000209 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 907240000210 dimer interface [polypeptide binding]; other site 907240000211 putative CheW interface [polypeptide binding]; other site 907240000212 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 907240000213 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 907240000214 23S rRNA interface [nucleotide binding]; other site 907240000215 L3 interface [polypeptide binding]; other site 907240000216 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl17341 907240000217 Predicted dehydrogenase [General function prediction only]; Region: COG0579 907240000218 NLPC_P60 stabilising domain, N term; Region: N_NLPC_P60; pfam12912 907240000219 SH3 domain of the SH3b1 type; Region: SH3_6; pfam12913 907240000220 SH3 domain of SH3b2 type; Region: SH3_7; pfam12914 907240000221 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 907240000222 NlpC/P60 family; Region: NLPC_P60; pfam00877 907240000223 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 907240000224 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 907240000225 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 907240000226 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 907240000227 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 907240000228 DNA binding residues [nucleotide binding] 907240000229 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 907240000230 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 907240000231 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 907240000232 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 907240000233 Protein of unknown function (DUF511); Region: DUF511; pfam04373 907240000234 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 907240000235 DNA methylase; Region: N6_N4_Mtase; pfam01555 907240000236 potential frameshift: common BLAST hit: gi|254778815|ref|YP_003056920.1| Alpha-1,2-fucosyltransferase 907240000237 2-hydroxyacid dehydrogenase; Provisional; Region: PRK08410 907240000238 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 907240000239 NAD binding site [chemical binding]; other site 907240000240 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 907240000241 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 907240000242 pyridoxal 5'-phosphate binding site [chemical binding]; other site 907240000243 catalytic residue [active] 907240000244 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 907240000245 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 907240000246 dimer interface [polypeptide binding]; other site 907240000247 putative CheW interface [polypeptide binding]; other site 907240000248 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases and ATP sulphurylases. The domain forms a apha/beta/apha fold which binds to Adenosine group; Region: Alpha_ANH_like; cd01986 907240000249 Ligand Binding Site [chemical binding]; other site 907240000250 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240000251 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 907240000252 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 907240000253 metal-binding site 907240000254 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 907240000255 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 907240000256 dimerization interface [polypeptide binding]; other site 907240000257 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 907240000258 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 907240000259 dimer interface [polypeptide binding]; other site 907240000260 putative CheW interface [polypeptide binding]; other site 907240000261 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 907240000262 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 907240000263 active site 907240000264 metal binding site [ion binding]; metal-binding site 907240000265 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 907240000266 S-ribosylhomocysteinase; Provisional; Region: PRK02260 907240000267 cystathionine gamma-synthase/cystathionine beta-lyase; Validated; Region: PRK06176 907240000268 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 907240000269 homodimer interface [polypeptide binding]; other site 907240000270 substrate-cofactor binding pocket; other site 907240000271 pyridoxal 5'-phosphate binding site [chemical binding]; other site 907240000272 catalytic residue [active] 907240000273 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 907240000274 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 907240000275 dimer interface [polypeptide binding]; other site 907240000276 pyridoxal 5'-phosphate binding site [chemical binding]; other site 907240000277 catalytic residue [active] 907240000278 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 907240000279 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 907240000280 nucleotide binding site [chemical binding]; other site 907240000281 NEF interaction site [polypeptide binding]; other site 907240000282 SBD interface [polypeptide binding]; other site 907240000283 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 907240000284 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 907240000285 dimer interface [polypeptide binding]; other site 907240000286 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 907240000287 heat-inducible transcription repressor; Provisional; Region: PRK03911 907240000288 hypothetical protein; Provisional; Region: PRK05834 907240000289 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 907240000290 flagellin B; Provisional; Region: PRK13588 907240000291 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 907240000292 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 907240000293 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 907240000294 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 907240000295 DNA topoisomerase I; Validated; Region: PRK05582 907240000296 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 907240000297 active site 907240000298 interdomain interaction site; other site 907240000299 putative metal-binding site [ion binding]; other site 907240000300 nucleotide binding site [chemical binding]; other site 907240000301 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 907240000302 domain I; other site 907240000303 DNA binding groove [nucleotide binding] 907240000304 phosphate binding site [ion binding]; other site 907240000305 domain II; other site 907240000306 domain III; other site 907240000307 nucleotide binding site [chemical binding]; other site 907240000308 catalytic site [active] 907240000309 domain IV; other site 907240000310 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 907240000311 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 907240000312 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 907240000313 Fe-S oxidoreductases [Energy production and conversion]; Region: COG0731 907240000314 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 907240000315 FeS/SAM binding site; other site 907240000316 Helicobacter pylori protein of unknown function (DUF874); Region: DUF874; pfam05917 907240000317 phosphoenolpyruvate synthase; Validated; Region: PRK06464 907240000318 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 907240000319 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 907240000320 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 907240000321 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK12305 907240000322 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 907240000323 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 907240000324 active site 907240000325 dimer interface [polypeptide binding]; other site 907240000326 motif 1; other site 907240000327 motif 2; other site 907240000328 motif 3; other site 907240000329 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 907240000330 anticodon binding site; other site 907240000331 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 907240000332 translation initiation factor IF-3; Region: infC; TIGR00168 907240000333 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 907240000334 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 907240000335 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 907240000336 23S rRNA binding site [nucleotide binding]; other site 907240000337 L21 binding site [polypeptide binding]; other site 907240000338 L13 binding site [polypeptide binding]; other site 907240000339 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240000340 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 907240000341 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 907240000342 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 907240000343 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 907240000344 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 907240000345 threonine/serine transporter TdcC; Provisional; Region: PRK13629; cl17672 907240000346 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]; Region: AroG; COG3200 907240000347 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 907240000348 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 907240000349 catalytic triad [active] 907240000350 Uncharacterized conserved protein [Function unknown]; Region: COG1556 907240000351 iron-sulfur cluster-binding protein; Region: TIGR00273 907240000352 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 907240000353 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 907240000354 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 907240000355 Cysteine-rich domain; Region: CCG; pfam02754 907240000356 Cysteine-rich domain; Region: CCG; pfam02754 907240000357 L-lactate transport; Region: lctP; TIGR00795 907240000358 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 907240000359 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 907240000360 L-lactate transport; Region: lctP; TIGR00795 907240000361 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 907240000362 DNA glycosylase MutY; Provisional; Region: PRK13910 907240000363 minor groove reading motif; other site 907240000364 helix-hairpin-helix signature motif; other site 907240000365 substrate binding pocket [chemical binding]; other site 907240000366 active site 907240000367 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 907240000368 DNA binding and oxoG recognition site [nucleotide binding] 907240000369 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 907240000370 Sodium:sulfate symporter transmembrane region; Region: Na_sulph_symp; pfam00939 907240000371 transmembrane helices; other site 907240000372 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 907240000373 Low-spin heme binding site [chemical binding]; other site 907240000374 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 907240000375 D-pathway; other site 907240000376 Putative water exit pathway; other site 907240000377 Binuclear center (active site) [active] 907240000378 K-pathway; other site 907240000379 Putative proton exit pathway; other site 907240000380 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 907240000381 cytochrome c oxidase, cbb3-type, subunit II; Region: ccoO; TIGR00781 907240000382 cytochrome c oxidase, cbb3-type, CcoQ subunit, epsilon-Proteobacterial; Region: cbb3_Q_epsi; TIGR02736 907240000383 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 907240000384 Cytochrome c; Region: Cytochrom_C; pfam00034 907240000385 Cytochrome c; Region: Cytochrom_C; pfam00034 907240000386 Family of unknown function (DUF4006); Region: DUF4006; pfam13179 907240000387 Predicted periplasmic solute-binding protein [General function prediction only]; Region: COG2107 907240000388 recombinase A; Provisional; Region: recA; PRK09354 907240000389 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 907240000390 hexamer interface [polypeptide binding]; other site 907240000391 Walker A motif; other site 907240000392 ATP binding site [chemical binding]; other site 907240000393 Walker B motif; other site 907240000394 enolase; Provisional; Region: eno; PRK00077 907240000395 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 907240000396 dimer interface [polypeptide binding]; other site 907240000397 metal binding site [ion binding]; metal-binding site 907240000398 substrate binding pocket [chemical binding]; other site 907240000399 AMIN domain; Region: AMIN; pfam11741 907240000400 Shikimate kinase [Amino acid transport and metabolism]; Region: AroK; COG0703 907240000401 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 907240000402 ADP binding site [chemical binding]; other site 907240000403 magnesium binding site [ion binding]; other site 907240000404 putative shikimate binding site; other site 907240000405 Cache domain; Region: Cache_1; pfam02743 907240000406 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 907240000407 A4GalT_like proteins catalyze the addition of galactose or glucose residues to the lipooligosaccharide (LOS) or lipopolysaccharide (LPS) of the bacterial cell surface; Region: GT8_A4GalT_like; cd04194 907240000408 Ligand binding site; other site 907240000409 metal-binding site 907240000410 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 907240000411 Sel1-like repeats; Region: SEL1; smart00671 907240000412 Sel1-like repeats; Region: SEL1; smart00671 907240000413 Sel1-like repeats; Region: SEL1; smart00671 907240000414 Sel1-like repeats; Region: SEL1; smart00671 907240000415 Sel1-like repeats; Region: SEL1; smart00671 907240000416 hypothetical protein; Provisional; Region: PRK12378 907240000417 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS; cd00384 907240000418 dimer interface [polypeptide binding]; other site 907240000419 active site 907240000420 Schiff base residues; other site 907240000421 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 907240000422 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 907240000423 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 907240000424 dimer interface [polypeptide binding]; other site 907240000425 phosphorylation site [posttranslational modification] 907240000426 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 907240000427 ATP binding site [chemical binding]; other site 907240000428 Mg2+ binding site [ion binding]; other site 907240000429 G-X-G motif; other site 907240000430 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 907240000431 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 907240000432 active site 907240000433 phosphorylation site [posttranslational modification] 907240000434 intermolecular recognition site; other site 907240000435 dimerization interface [polypeptide binding]; other site 907240000436 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 907240000437 DNA binding site [nucleotide binding] 907240000438 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 907240000439 Peptidase family U32; Region: Peptidase_U32; pfam01136 907240000440 peptide chain release factor 2; Region: prfB; TIGR00020 907240000441 This domain is found in peptide chain release factors; Region: PCRF; smart00937 907240000442 RF-1 domain; Region: RF-1; pfam00472 907240000443 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 907240000444 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 907240000445 dimer interface [polypeptide binding]; other site 907240000446 putative functional site; other site 907240000447 putative MPT binding site; other site 907240000448 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 907240000449 Etoposide-induced protein 2.4 (EI24); Region: EI24; pfam07264 907240000450 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 907240000451 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 907240000452 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 907240000453 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 907240000454 intersubunit interface [polypeptide binding]; other site 907240000455 active site 907240000456 zinc binding site [ion binding]; other site 907240000457 Na+ binding site [ion binding]; other site 907240000458 elongation factor P; Validated; Region: PRK00529 907240000459 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 907240000460 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 907240000461 RNA binding site [nucleotide binding]; other site 907240000462 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 907240000463 RNA binding site [nucleotide binding]; other site 907240000464 pseudaminic acid synthase; Region: PseI; TIGR03586 907240000465 NeuB family; Region: NeuB; pfam03102 907240000466 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 907240000467 NeuB binding interface [polypeptide binding]; other site 907240000468 putative substrate binding site [chemical binding]; other site 907240000469 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 907240000470 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 907240000471 Walker A/P-loop; other site 907240000472 ATP binding site [chemical binding]; other site 907240000473 Q-loop/lid; other site 907240000474 ABC transporter signature motif; other site 907240000475 Walker B; other site 907240000476 D-loop; other site 907240000477 H-loop/switch region; other site 907240000478 apolipoprotein N-acyltransferase; Reviewed; Region: PRK12291 907240000479 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 907240000480 active site 907240000481 catalytic triad [active] 907240000482 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 907240000483 Colicin V production protein; Region: Colicin_V; pfam02674 907240000484 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 907240000485 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 907240000486 dimer interface [polypeptide binding]; other site 907240000487 putative anticodon binding site; other site 907240000488 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 907240000489 motif 1; other site 907240000490 active site 907240000491 motif 2; other site 907240000492 motif 3; other site 907240000493 serine hydroxymethyltransferase; Reviewed; Region: PRK13034 907240000494 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 907240000495 dimer interface [polypeptide binding]; other site 907240000496 active site 907240000497 glycine-pyridoxal phosphate binding site [chemical binding]; other site 907240000498 folate binding site [chemical binding]; other site 907240000499 AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis...; Region: AE_Prim_S_like; cd00525 907240000500 nucleotide binding site [chemical binding]; other site 907240000501 AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis...; Region: AE_Prim_S_like; cl01287 907240000502 Sporulation related domain; Region: SPOR; cl10051 907240000503 Uncharacterized conserved protein [Function unknown]; Region: COG1479 907240000504 Protein of unknown function DUF262; Region: DUF262; pfam03235 907240000505 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 907240000506 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 907240000507 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 907240000508 PLD-like domain; Region: PLDc_2; pfam13091 907240000509 putative active site [active] 907240000510 catalytic site [active] 907240000511 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 907240000512 PLD-like domain; Region: PLDc_2; pfam13091 907240000513 putative active site [active] 907240000514 catalytic site [active] 907240000515 fumarate reductase iron-sulfur subunit; Provisional; Region: frdB; PRK13552 907240000516 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 907240000517 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 907240000518 fumarate reductase flavoprotein subunit; Provisional; Region: PRK08626 907240000519 L-aspartate oxidase; Provisional; Region: PRK06175 907240000520 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 907240000521 fumarate reductase cytochrome b-556 subunit; Provisional; Region: PRK13553 907240000522 Quinol:fumarate reductase (QFR) Type B subfamily, transmembrane subunit; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinone...; Region: QFR_TypeB_TM; cd00581 907240000523 Iron-sulfur protein interface; other site 907240000524 proximal heme binding site [chemical binding]; other site 907240000525 distal heme binding site [chemical binding]; other site 907240000526 dimer interface [polypeptide binding]; other site 907240000527 triosephosphate isomerase; Provisional; Region: PRK14567 907240000528 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 907240000529 substrate binding site [chemical binding]; other site 907240000530 dimer interface [polypeptide binding]; other site 907240000531 catalytic triad [active] 907240000532 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08415 907240000533 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 907240000534 NAD binding site [chemical binding]; other site 907240000535 homotetramer interface [polypeptide binding]; other site 907240000536 homodimer interface [polypeptide binding]; other site 907240000537 substrate binding site [chemical binding]; other site 907240000538 active site 907240000539 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Region: lipid_A_lpxD; TIGR01853 907240000540 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 907240000541 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 907240000542 trimer interface [polypeptide binding]; other site 907240000543 active site 907240000544 UDP-GlcNAc binding site [chemical binding]; other site 907240000545 lipid binding site [chemical binding]; lipid-binding site 907240000546 Phage holin family (Lysis protein S); Region: Phage_holin_3; cl04938 907240000547 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5410 907240000548 DEAD-like helicases superfamily; Region: DEXDc; smart00487 907240000549 Phage portal protein, SPP1 Gp6-like; Region: Phage_prot_Gp6; pfam05133 907240000550 Protein of unknown function (DUF4043); Region: DUF4043; pfam13252 907240000551 Protein of unknown function (DUF1353); Region: DUF1353; pfam07087 907240000552 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 907240000553 S-adenosylmethionine synthetase; Validated; Region: PRK05250 907240000554 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 907240000555 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 907240000556 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 907240000557 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 907240000558 active site 907240000559 multimer interface [polypeptide binding]; other site 907240000560 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 907240000561 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 907240000562 fatty acid/phospholipid synthesis protein PlsX; Region: plsX; TIGR00182 907240000563 3-oxoacyl-(acyl-carrier-protein) synthase III; Region: fabH; TIGR00747 907240000564 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 907240000565 dimer interface [polypeptide binding]; other site 907240000566 active site 907240000567 CoA binding pocket [chemical binding]; other site 907240000568 AAA domain; Region: AAA_21; pfam13304 907240000569 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cd00267 907240000570 Walker B; other site 907240000571 D-loop; other site 907240000572 H-loop/switch region; other site 907240000573 antiporter inner membrane protein; Provisional; Region: PRK11670 907240000574 Domain of unknown function DUF59; Region: DUF59; pfam01883 907240000575 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 907240000576 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 907240000577 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 907240000578 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 907240000579 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 907240000580 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 907240000581 heat shock protein 90; Provisional; Region: PRK05218 907240000582 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 907240000583 ATP binding site [chemical binding]; other site 907240000584 Mg2+ binding site [ion binding]; other site 907240000585 G-X-G motif; other site 907240000586 TPR repeat; Region: TPR_11; pfam13414 907240000587 Sel1-like repeats; Region: SEL1; smart00671 907240000588 Sel1-like repeats; Region: SEL1; smart00671 907240000589 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 907240000590 TPR motif; other site 907240000591 binding surface 907240000592 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 907240000593 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 907240000594 metal binding site [ion binding]; metal-binding site 907240000595 dimer interface [polypeptide binding]; other site 907240000596 glucose-inhibited division protein A; Region: gidA; TIGR00136 907240000597 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 907240000598 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 907240000599 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 907240000600 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 907240000601 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 907240000602 transmembrane helices; other site 907240000603 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 907240000604 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 907240000605 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: Dxr; TIGR00243 907240000606 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 907240000607 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 907240000608 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 907240000609 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 907240000610 substrate binding site [chemical binding]; other site 907240000611 Helix-turn-helix domain; Region: HTH_28; pfam13518 907240000612 cysteine desulfurase, NifS family, epsilon proteobacteria type; Region: nifS_epsilon; TIGR03403 907240000613 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 907240000614 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 907240000615 catalytic residue [active] 907240000616 Fe-S cluster assembly protein NifU; Region: NifU_proper; TIGR02000 907240000617 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 907240000618 trimerization site [polypeptide binding]; other site 907240000619 active site 907240000620 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 907240000621 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 907240000622 DNA repair protein RadA; Region: sms; TIGR00416 907240000623 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 907240000624 Walker A motif/ATP binding site; other site 907240000625 ATP binding site [chemical binding]; other site 907240000626 Walker B motif; other site 907240000627 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 907240000628 Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: MsrA; COG0225 907240000629 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229 907240000630 SelR domain; Region: SelR; pfam01641 907240000631 Predicted permeases [General function prediction only]; Region: COG0730 907240000632 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240000633 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 907240000634 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 907240000635 Sulfate transporter family; Region: Sulfate_transp; pfam00916 907240000636 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240000637 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 907240000638 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 907240000639 Ligand binding site; other site 907240000640 oligomer interface; other site 907240000641 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 907240000642 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 907240000643 hypothetical protein; Provisional; Region: PRK04081 907240000644 Glutathionylspermidine synthase [Amino acid transport and metabolism]; Region: Gsp; COG0754 907240000645 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 907240000646 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 907240000647 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 907240000648 binding surface 907240000649 TPR motif; other site 907240000650 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 907240000651 binding surface 907240000652 TPR motif; other site 907240000653 Sel1-like repeats; Region: SEL1; smart00671 907240000654 Sel1-like repeats; Region: SEL1; smart00671 907240000655 Cytochrome c; Region: Cytochrom_C; cl11414 907240000656 Porphobilinogen deaminase [Coenzyme metabolism]; Region: HemC; COG0181 907240000657 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 907240000658 domain interfaces; other site 907240000659 active site 907240000660 prolyl-tRNA synthetase, family II; Region: proS_fam_II; TIGR00409 907240000661 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 907240000662 dimer interface [polypeptide binding]; other site 907240000663 motif 1; other site 907240000664 active site 907240000665 motif 2; other site 907240000666 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 907240000667 putative deacylase active site [active] 907240000668 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 907240000669 active site 907240000670 motif 3; other site 907240000671 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 907240000672 anticodon binding site; other site 907240000673 glutamyl-tRNA reductase; Region: hemA; TIGR01035 907240000674 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 907240000675 tRNA; other site 907240000676 putative tRNA binding site [nucleotide binding]; other site 907240000677 putative NADP binding site [chemical binding]; other site 907240000678 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 907240000679 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 907240000680 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 907240000681 substrate binding pocket [chemical binding]; other site 907240000682 chain length determination region; other site 907240000683 substrate-Mg2+ binding site; other site 907240000684 catalytic residues [active] 907240000685 aspartate-rich region 1; other site 907240000686 active site lid residues [active] 907240000687 aspartate-rich region 2; other site 907240000688 Domain of unknown function (DUF2018); Region: DUF2018; pfam09442 907240000689 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 907240000690 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 907240000691 dimerization interface [polypeptide binding]; other site 907240000692 DPS ferroxidase diiron center [ion binding]; other site 907240000693 ion pore; other site 907240000694 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 907240000695 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 907240000696 dimer interface [polypeptide binding]; other site 907240000697 phosphorylation site [posttranslational modification] 907240000698 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 907240000699 ATP binding site [chemical binding]; other site 907240000700 Mg2+ binding site [ion binding]; other site 907240000701 G-X-G motif; other site 907240000702 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 907240000703 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 907240000704 helicase 45; Provisional; Region: PTZ00424 907240000705 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 907240000706 ATP binding site [chemical binding]; other site 907240000707 Mg++ binding site [ion binding]; other site 907240000708 motif III; other site 907240000709 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 907240000710 nucleotide binding region [chemical binding]; other site 907240000711 ATP-binding site [chemical binding]; other site 907240000712 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 907240000713 SPFH domain / Band 7 family; Region: Band_7; pfam01145 907240000714 Protein of unknown function (DUF2393); Region: DUF2393; pfam09624 907240000715 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 907240000716 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 907240000717 Walker A/P-loop; other site 907240000718 ATP binding site [chemical binding]; other site 907240000719 Q-loop/lid; other site 907240000720 ABC transporter signature motif; other site 907240000721 Walker B; other site 907240000722 D-loop; other site 907240000723 H-loop/switch region; other site 907240000724 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 907240000725 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 907240000726 Walker A/P-loop; other site 907240000727 ATP binding site [chemical binding]; other site 907240000728 Q-loop/lid; other site 907240000729 ABC transporter signature motif; other site 907240000730 Walker B; other site 907240000731 D-loop; other site 907240000732 H-loop/switch region; other site 907240000733 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 907240000734 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 907240000735 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 907240000736 dimer interface [polypeptide binding]; other site 907240000737 conserved gate region; other site 907240000738 putative PBP binding loops; other site 907240000739 ABC-ATPase subunit interface; other site 907240000740 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240000741 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240000742 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 907240000743 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 907240000744 GDP-binding site [chemical binding]; other site 907240000745 ACT binding site; other site 907240000746 IMP binding site; other site 907240000747 Flagellar FliJ protein; Region: FliJ; pfam02050 907240000748 Uncharacterized conserved protein [Function unknown]; Region: COG3334 907240000749 RIP metalloprotease RseP; Region: TIGR00054 907240000750 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 907240000751 active site 907240000752 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 907240000753 exodeoxyribonuclease VII, large subunit; Region: xseA; TIGR00237 907240000754 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 907240000755 generic binding surface II; other site 907240000756 generic binding surface I; other site 907240000757 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 907240000758 DNA methylase; Region: N6_N4_Mtase; pfam01555 907240000759 DNA methylase; Region: N6_N4_Mtase; pfam01555 907240000760 potential frameshift: common BLAST hit: gi|208434208|ref|YP_002265874.1| type II DNA modification enzyme 907240000761 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 907240000762 DNA methylase; Region: N6_N4_Mtase; pfam01555 907240000763 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 907240000764 Clp amino terminal domain; Region: Clp_N; pfam02861 907240000765 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 907240000766 Walker A motif; other site 907240000767 ATP binding site [chemical binding]; other site 907240000768 Walker B motif; other site 907240000769 arginine finger; other site 907240000770 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 907240000771 Walker A motif; other site 907240000772 ATP binding site [chemical binding]; other site 907240000773 Walker B motif; other site 907240000774 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 907240000775 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 907240000776 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; pfam02683 907240000777 Dihydroorotase and related cyclic amidohydrolases [Nucleotide transport and metabolism]; Region: PyrC; COG0044 907240000778 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 907240000779 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 907240000780 active site 907240000781 chlorohydrolase; Provisional; Region: PRK08418 907240000782 Metallo-dependent hydrolases, subgroup D is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_D; cd01312 907240000783 active site 907240000784 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14339 907240000785 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 907240000786 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 907240000787 FeS/SAM binding site; other site 907240000788 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 907240000789 putative acyl-acceptor binding pocket; other site 907240000790 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 907240000791 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]; Region: COG2956 907240000792 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 907240000793 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 907240000794 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 907240000795 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 907240000796 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 907240000797 putative active site [active] 907240000798 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 907240000799 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 907240000800 putative acyl-acceptor binding pocket; other site 907240000801 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 907240000802 tRNA-guanine family transglycosylase; Region: tgt_general; TIGR00449 907240000803 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3400 907240000804 TrkA-C domain; Region: TrkA_C; pfam02080 907240000805 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 907240000806 active site 907240000807 dimer interface [polypeptide binding]; other site 907240000808 metal binding site [ion binding]; metal-binding site 907240000809 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 907240000810 Mechanosensitive ion channel; Region: MS_channel; pfam00924 907240000811 radical SAM methylthiotransferase, MiaB/RimO family; Region: TIGR00089 907240000812 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 907240000813 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 907240000814 FeS/SAM binding site; other site 907240000815 ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]; Region: HflB; COG0465 907240000816 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 907240000817 Walker B motif; other site 907240000818 arginine finger; other site 907240000819 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 907240000820 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907240000821 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907240000822 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 907240000823 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907240000824 Autotransporter beta-domain; Region: Autotransporter; pfam03797 907240000825 diaminopimelate decarboxylase; Region: lysA; TIGR01048 907240000826 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 907240000827 active site 907240000828 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 907240000829 substrate binding site [chemical binding]; other site 907240000830 catalytic residues [active] 907240000831 dimer interface [polypeptide binding]; other site 907240000832 Chorismate mutase [Amino acid transport and metabolism]; Region: PheA; COG1605 907240000833 Uncharacterized conserved protein [Function unknown]; Region: COG4866 907240000834 aminodeoxychorismate synthase; Provisional; Region: PRK07508 907240000835 chorismate binding enzyme; Region: Chorismate_bind; cl10555 907240000836 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and...; Region: PLPDE_IV; cl00224 907240000837 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 907240000838 substrate-cofactor binding pocket; other site 907240000839 pyridoxal 5'-phosphate binding site [chemical binding]; other site 907240000840 catalytic residue [active] 907240000841 acylamide amidohydrolase; Provisional; Region: amiE; PRK13286 907240000842 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 907240000843 multimer interface [polypeptide binding]; other site 907240000844 active site 907240000845 catalytic triad [active] 907240000846 dimer interface [polypeptide binding]; other site 907240000847 flagellar hook-associated protein FlgL; Validated; Region: flgL; PRK08412 907240000848 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 907240000849 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 907240000850 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 907240000851 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 907240000852 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 907240000853 peptide binding site [polypeptide binding]; other site 907240000854 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 907240000855 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 907240000856 dimer interface [polypeptide binding]; other site 907240000857 conserved gate region; other site 907240000858 putative PBP binding loops; other site 907240000859 ABC-ATPase subunit interface; other site 907240000860 dipeptide transporter; Provisional; Region: PRK10913 907240000861 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 907240000862 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 907240000863 dimer interface [polypeptide binding]; other site 907240000864 conserved gate region; other site 907240000865 putative PBP binding loops; other site 907240000866 ABC-ATPase subunit interface; other site 907240000867 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 907240000868 nickel import ATP-binding protein NikD; Region: nickel_nikD; TIGR02770 907240000869 Walker A/P-loop; other site 907240000870 ATP binding site [chemical binding]; other site 907240000871 Q-loop/lid; other site 907240000872 ABC transporter signature motif; other site 907240000873 Walker B; other site 907240000874 D-loop; other site 907240000875 H-loop/switch region; other site 907240000876 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 907240000877 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 907240000878 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 907240000879 Walker A/P-loop; other site 907240000880 ATP binding site [chemical binding]; other site 907240000881 Q-loop/lid; other site 907240000882 ABC transporter signature motif; other site 907240000883 Walker B; other site 907240000884 D-loop; other site 907240000885 H-loop/switch region; other site 907240000886 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 907240000887 GTPase CgtA; Reviewed; Region: obgE; PRK12299 907240000888 GTP1/OBG; Region: GTP1_OBG; pfam01018 907240000889 Obg GTPase; Region: Obg; cd01898 907240000890 G1 box; other site 907240000891 GTP/Mg2+ binding site [chemical binding]; other site 907240000892 Switch I region; other site 907240000893 G2 box; other site 907240000894 G3 box; other site 907240000895 Switch II region; other site 907240000896 G4 box; other site 907240000897 G5 box; other site 907240000898 Alginate lyase; Region: Alginate_lyase; pfam05426 907240000899 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 907240000900 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 907240000901 inhibitor-cofactor binding pocket; inhibition site 907240000902 pyridoxal 5'-phosphate binding site [chemical binding]; other site 907240000903 catalytic residue [active] 907240000904 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 907240000905 Predicted amidohydrolase [General function prediction only]; Region: COG0388 907240000906 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 907240000907 active site 907240000908 catalytic triad [active] 907240000909 dimer interface [polypeptide binding]; other site 907240000910 Catalytic domain of Helicobacter pylori peptidoglycan deacetylase (HpPgdA) and similar proteins; Region: CE4_HpPgdA_like; cd10938 907240000911 active site 907240000912 catalytic site [active] 907240000913 Zn binding site [ion binding]; other site 907240000914 tetramer interface [polypeptide binding]; other site 907240000915 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 907240000916 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 907240000917 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 907240000918 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 907240000919 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 907240000920 Major Facilitator Superfamily; Region: MFS_1; pfam07690 907240000921 putative substrate translocation pore; other site 907240000922 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 907240000923 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 907240000924 Walker A/P-loop; other site 907240000925 ATP binding site [chemical binding]; other site 907240000926 Q-loop/lid; other site 907240000927 ABC transporter signature motif; other site 907240000928 Walker B; other site 907240000929 D-loop; other site 907240000930 H-loop/switch region; other site 907240000931 heme oxygenase, HugZ family; Region: heme_ox_HugZ; TIGR04109 907240000932 Protein of unknown function (DUF2470); Region: DUF2470; pfam10615 907240000933 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 907240000934 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 907240000935 arginyl-tRNA synthetase; Region: argS; TIGR00456 907240000936 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 907240000937 active site 907240000938 HIGH motif; other site 907240000939 KMSK motif region; other site 907240000940 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 907240000941 tRNA binding surface [nucleotide binding]; other site 907240000942 anticodon binding site; other site 907240000943 twin arginine-targeting protein translocase, TatA/E family; Region: tatAE; TIGR01411 907240000944 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 907240000945 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 907240000946 catalytic site [active] 907240000947 G-X2-G-X-G-K; other site 907240000948 Daxx Family; Region: Daxx; pfam03344 907240000949 nuclease NucT; Provisional; Region: PRK13912 907240000950 Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar proteins; Region: PLDc_Nuc_like; cd09116 907240000951 putative active site [active] 907240000952 catalytic site [active] 907240000953 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240000954 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 907240000955 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK00249 907240000956 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 907240000957 ligand binding site; other site 907240000958 tetramer interface; other site 907240000959 Spore coat polysaccharide biosynthesis protein, predicted glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: spsG; COG3980 907240000960 pseudaminic acid biosynthesis N-acetyl transferase; Region: PseH; TIGR03585 907240000961 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 907240000962 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 907240000963 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 907240000964 NAD synthetase; Provisional; Region: PRK13980 907240000965 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 907240000966 homodimer interface [polypeptide binding]; other site 907240000967 NAD binding pocket [chemical binding]; other site 907240000968 ATP binding pocket [chemical binding]; other site 907240000969 Mg binding site [ion binding]; other site 907240000970 active-site loop [active] 907240000971 ketol-acid reductoisomerase; Provisional; Region: PRK05479 907240000972 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 907240000973 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 907240000974 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 907240000975 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 907240000976 Switch I; other site 907240000977 Switch II; other site 907240000978 cell division topological specificity factor MinE; Region: minE; TIGR01215 907240000979 DNA protecting protein DprA; Region: dprA; TIGR00732 907240000980 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 907240000981 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 907240000982 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 907240000983 Sel1-like repeats; Region: SEL1; smart00671 907240000984 Sel1-like repeats; Region: SEL1; smart00671 907240000985 Sel1-like repeats; Region: SEL1; smart00671 907240000986 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 907240000987 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 907240000988 active site 907240000989 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 907240000990 DHH family; Region: DHH; pfam01368 907240000991 DHHA1 domain; Region: DHHA1; pfam02272 907240000992 CTP synthetase; Validated; Region: pyrG; PRK05380 907240000993 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 907240000994 Catalytic site [active] 907240000995 active site 907240000996 UTP binding site [chemical binding]; other site 907240000997 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 907240000998 active site 907240000999 putative oxyanion hole; other site 907240001000 catalytic triad [active] 907240001001 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 907240001002 flagellar basal-body M-ring protein/flagellar hook-basal body protein (fliF); Region: fliF; TIGR00206 907240001003 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 907240001004 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 907240001005 flagellar motor switch protein FliG; Region: fliG; TIGR00207 907240001006 FliG C-terminal domain; Region: FliG_C; pfam01706 907240001007 flagellar assembly protein H; Validated; Region: fliH; PRK06669 907240001008 Flagellar assembly protein FliH; Region: FliH; pfam02108 907240001009 1-deoxy-D-xylulose-5-phosphate synthase; Region: dxs; TIGR00204 907240001010 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 907240001011 TPP-binding site; other site 907240001012 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 907240001013 PYR/PP interface [polypeptide binding]; other site 907240001014 dimer interface [polypeptide binding]; other site 907240001015 TPP binding site [chemical binding]; other site 907240001016 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 907240001017 GTP-binding protein LepA; Provisional; Region: PRK05433 907240001018 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 907240001019 G1 box; other site 907240001020 putative GEF interaction site [polypeptide binding]; other site 907240001021 GTP/Mg2+ binding site [chemical binding]; other site 907240001022 Switch I region; other site 907240001023 G2 box; other site 907240001024 G3 box; other site 907240001025 Switch II region; other site 907240001026 G4 box; other site 907240001027 G5 box; other site 907240001028 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 907240001029 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 907240001030 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 907240001031 Domain of unknown function (DUF3883); Region: DUF3883; pfam13020 907240001032 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgG; COG4786 907240001033 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 907240001034 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 907240001035 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 907240001036 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 907240001037 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 907240001038 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 907240001039 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 907240001040 Inactivated superfamily I helicase [DNA replication, recombination, and repair]; Region: COG3893 907240001041 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 907240001042 transketolase, bacterial and yeast; Region: tktlase_bact; TIGR00232 907240001043 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 907240001044 TPP-binding site [chemical binding]; other site 907240001045 dimer interface [polypeptide binding]; other site 907240001046 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 907240001047 PYR/PP interface [polypeptide binding]; other site 907240001048 dimer interface [polypeptide binding]; other site 907240001049 TPP binding site [chemical binding]; other site 907240001050 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 907240001051 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 907240001052 riboflavin kinase/FMN adenylyltransferase; Region: ribF; TIGR00083 907240001053 active site 907240001054 Riboflavin kinase; Region: Flavokinase; pfam01687 907240001055 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 907240001056 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 907240001057 RNA binding surface [nucleotide binding]; other site 907240001058 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 907240001059 S-adenosylmethionine binding site [chemical binding]; other site 907240001060 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 907240001061 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 907240001062 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 907240001063 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 907240001064 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 907240001065 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 907240001066 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 907240001067 Walker A/P-loop; other site 907240001068 ATP binding site [chemical binding]; other site 907240001069 Q-loop/lid; other site 907240001070 ABC transporter signature motif; other site 907240001071 Walker B; other site 907240001072 D-loop; other site 907240001073 H-loop/switch region; other site 907240001074 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 907240001075 Predicted endonuclease distantly related to archaeal Holliday junction resolvase and Mrr-like restriction enzymes [Defense mechanisms]; Region: COG1787 907240001076 Restriction endonuclease; Region: Mrr_cat; pfam04471 907240001077 Predicted ATPases [General function prediction only]; Region: COG1106 907240001078 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 907240001079 Walker A/P-loop; other site 907240001080 ATP binding site [chemical binding]; other site 907240001081 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 907240001082 Q-loop/lid; other site 907240001083 ABC transporter signature motif; other site 907240001084 Walker B; other site 907240001085 D-loop; other site 907240001086 H-loop/switch region; other site 907240001087 High-affinity nickel permease [Inorganic ion transport and metabolism]; Region: HoxN; COG3376 907240001088 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cd00596 907240001089 active site 907240001090 Zn binding site [ion binding]; other site 907240001091 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 907240001092 metal-binding site [ion binding] 907240001093 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 907240001094 metal-binding site [ion binding] 907240001095 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 907240001096 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 907240001097 Soluble P-type ATPase [General function prediction only]; Region: COG4087 907240001098 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 907240001099 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 907240001100 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 907240001101 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 907240001102 Walker A motif; other site 907240001103 ATP binding site [chemical binding]; other site 907240001104 Walker B motif; other site 907240001105 arginine finger; other site 907240001106 Peptidase family M41; Region: Peptidase_M41; pfam01434 907240001107 ribosomal protein L11 methyltransferase; Region: prmA; TIGR00406 907240001108 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 907240001109 S-adenosylmethionine binding site [chemical binding]; other site 907240001110 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 907240001111 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 907240001112 active site 907240001113 phosphorylation site [posttranslational modification] 907240001114 intermolecular recognition site; other site 907240001115 dimerization interface [polypeptide binding]; other site 907240001116 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240001117 rRNA small subunit methyltransferase G; Region: GidB; pfam02527 907240001118 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 907240001119 S-adenosylmethionine binding site [chemical binding]; other site 907240001120 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 907240001121 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 907240001122 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 907240001123 sec-independent translocase; Provisional; Region: PRK04098 907240001124 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 907240001125 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 907240001126 Walker A motif; other site 907240001127 ATP binding site [chemical binding]; other site 907240001128 Walker B motif; other site 907240001129 arginine finger; other site 907240001130 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 907240001131 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 907240001132 oligomerization interface [polypeptide binding]; other site 907240001133 active site 907240001134 metal binding site [ion binding]; metal-binding site 907240001135 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240001136 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240001137 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 907240001138 septum formation inhibitor; Reviewed; Region: minC; PRK00556 907240001139 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 907240001140 UDP-3-0-acyl N-acetylglucosamine deacetylase; Region: lpxC; TIGR00325 907240001141 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 907240001142 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 907240001143 homoserine kinase; Region: thrB; TIGR00191 907240001144 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 907240001145 Predicted nucleic-acid-binding protein implicated in transcription termination [Transcription]; Region: COG2740 907240001146 translation initiation factor IF-2; Region: IF-2; TIGR00487 907240001147 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 907240001148 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 907240001149 G1 box; other site 907240001150 putative GEF interaction site [polypeptide binding]; other site 907240001151 GTP/Mg2+ binding site [chemical binding]; other site 907240001152 Switch I region; other site 907240001153 G2 box; other site 907240001154 G3 box; other site 907240001155 Switch II region; other site 907240001156 G4 box; other site 907240001157 G5 box; other site 907240001158 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 907240001159 Translation-initiation factor 2; Region: IF-2; pfam11987 907240001160 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 907240001161 Ribosome-binding factor A; Region: RBFA; cl00542 907240001162 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG0779 907240001163 Sm and related proteins; Region: Sm_like; cl00259 907240001164 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 907240001165 putative oligomer interface [polypeptide binding]; other site 907240001166 putative RNA binding site [nucleotide binding]; other site 907240001167 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 907240001168 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 907240001169 putative active site [active] 907240001170 putative metal binding site [ion binding]; other site 907240001171 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 907240001172 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 907240001173 active site 907240001174 intermolecular recognition site; other site 907240001175 dimerization interface [polypeptide binding]; other site 907240001176 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 907240001177 DNA binding site [nucleotide binding] 907240001178 Predicted phosphohydrolase (DHH superfamily) [General function prediction only]; Region: COG2404 907240001179 DHH family; Region: DHH; pfam01368 907240001180 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 907240001181 FHIPEP family; Region: FHIPEP; pfam00771 907240001182 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 907240001183 16S/18S rRNA binding site [nucleotide binding]; other site 907240001184 S13e-L30e interaction site [polypeptide binding]; other site 907240001185 25S rRNA binding site [nucleotide binding]; other site 907240001186 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 907240001187 O-Antigen ligase; Region: Wzy_C; pfam04932 907240001188 Dehydroquinase class II; Region: DHquinase_II; pfam01220 907240001189 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 907240001190 trimer interface [polypeptide binding]; other site 907240001191 active site 907240001192 dimer interface [polypeptide binding]; other site 907240001193 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 907240001194 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 907240001195 Similar to Prolidase and Aminopeptidase P. The members of this subfamily presumably catalyse hydrolysis of Xaa-Pro dipeptides and/or release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP-like; cd01092 907240001196 active site 907240001197 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 907240001198 catalytic center binding site [active] 907240001199 ATP binding site [chemical binding]; other site 907240001200 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 907240001201 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 907240001202 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 907240001203 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 907240001204 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 907240001205 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 907240001206 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 907240001207 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 907240001208 DNA binding residues [nucleotide binding] 907240001209 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 907240001210 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 907240001211 flagellar motor switch protein FliY; Validated; Region: PRK08432 907240001212 flagellar motor switch protein FliN; Region: fliN; TIGR02480 907240001213 Beta-galactosidase, beta subunit [Carbohydrate transport and metabolism]; Region: EbgC; COG2731 907240001214 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4731 907240001215 ferric uptake regulator; Provisional; Region: fur; PRK09462 907240001216 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 907240001217 metal binding site 2 [ion binding]; metal-binding site 907240001218 putative DNA binding helix; other site 907240001219 metal binding site 1 [ion binding]; metal-binding site 907240001220 dimer interface [polypeptide binding]; other site 907240001221 structural Zn2+ binding site [ion binding]; other site 907240001222 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]; Region: MGS1; COG2256 907240001223 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 907240001224 Walker A motif; other site 907240001225 ATP binding site [chemical binding]; other site 907240001226 Walker B motif; other site 907240001227 arginine finger; other site 907240001228 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 907240001229 Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Region: HTH_HspR; cd04766 907240001230 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 907240001231 DNA binding residues [nucleotide binding] 907240001232 putative dimer interface [polypeptide binding]; other site 907240001233 chaperone protein DnaJ; Provisional; Region: PRK14299 907240001234 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 907240001235 HSP70 interaction site [polypeptide binding]; other site 907240001236 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 907240001237 substrate binding site [polypeptide binding]; other site 907240001238 dimer interface [polypeptide binding]; other site 907240001239 5'-3' exonuclease; Provisional; Region: PRK14976 907240001240 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 907240001241 putative active site [active] 907240001242 Helix-hairpin-helix class 2 (Pol1 family) motifs; Region: HhH2; smart00279 907240001243 DNA binding site [nucleotide binding] 907240001244 metal binding site [ion binding]; metal-binding site 907240001245 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 907240001246 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 907240001247 active site 907240001248 dimerization interface [polypeptide binding]; other site 907240001249 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 907240001250 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 907240001251 substrate binding site; other site 907240001252 dimer interface; other site 907240001253 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 907240001254 homotrimer interaction site [polypeptide binding]; other site 907240001255 zinc binding site [ion binding]; other site 907240001256 CDP-binding sites; other site 907240001257 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 907240001258 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 907240001259 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 907240001260 protein binding site [polypeptide binding]; other site 907240001261 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 907240001262 protein binding site [polypeptide binding]; other site 907240001263 S-methylmethionine transporter; Provisional; Region: PRK11387 907240001264 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase; Region: pgsA; TIGR00560 907240001265 7-alpha-hydroxysteroid dehydrogenase; Provisional; Region: PRK08416 907240001266 1-cyclohexenylcarbonyl_coenzyme A_reductase (ChcA)_like, classical (c) SDRs; Region: ChcA_like_SDR_c; cd05359 907240001267 putative NAD(P) binding site [chemical binding]; other site 907240001268 active site 907240001269 dihydrodipicolinate synthase; Region: dapA; TIGR00674 907240001270 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 907240001271 dimer interface [polypeptide binding]; other site 907240001272 active site 907240001273 catalytic residue [active] 907240001274 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 907240001275 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 907240001276 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 907240001277 dihydroorotate dehydrogenase, subfamily 2; Region: pyrD_sub2; TIGR01036 907240001278 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 907240001279 quinone interaction residues [chemical binding]; other site 907240001280 active site 907240001281 catalytic residues [active] 907240001282 FMN binding site [chemical binding]; other site 907240001283 substrate binding site [chemical binding]; other site 907240001284 Polyphosphate kinase [Inorganic ion transport and metabolism]; Region: Ppk; COG0855 907240001285 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 907240001286 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 907240001287 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 907240001288 putative domain interface [polypeptide binding]; other site 907240001289 putative active site [active] 907240001290 catalytic site [active] 907240001291 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 907240001292 putative active site [active] 907240001293 putative domain interface [polypeptide binding]; other site 907240001294 catalytic site [active] 907240001295 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 907240001296 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 907240001297 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 907240001298 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 907240001299 Methyltransferase domain; Region: Methyltransf_26; pfam13659 907240001300 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 907240001301 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 907240001302 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 907240001303 ATP binding site [chemical binding]; other site 907240001304 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 907240001305 putative Mg++ binding site [ion binding]; other site 907240001306 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 907240001307 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 907240001308 putative metal binding site [ion binding]; other site 907240001309 CoB--CoM heterodisulfide reductase, subunit B; Region: CoB_CoM_SS_B; TIGR03288 907240001310 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 907240001311 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_5; cd09610 907240001312 active site 907240001313 Zn binding site [ion binding]; other site 907240001314 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 907240001315 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 907240001316 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240001317 ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ModA; COG0725 907240001318 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 907240001319 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 907240001320 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 907240001321 dimer interface [polypeptide binding]; other site 907240001322 conserved gate region; other site 907240001323 putative PBP binding loops; other site 907240001324 ABC-ATPase subunit interface; other site 907240001325 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 907240001326 putative bacteriocin export ABC transporter, lactococcin 972 group; Region: L_ocin_972_ABC; TIGR03608 907240001327 Walker A/P-loop; other site 907240001328 ATP binding site [chemical binding]; other site 907240001329 Q-loop/lid; other site 907240001330 ABC transporter signature motif; other site 907240001331 Walker B; other site 907240001332 D-loop; other site 907240001333 H-loop/switch region; other site 907240001334 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 907240001335 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 907240001336 active site 907240001337 HIGH motif; other site 907240001338 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 907240001339 active site 907240001340 KMSKS motif; other site 907240001341 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240001342 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 907240001343 ADP-heptose:LPS heptosyl transferase I; Provisional; Region: PRK10964; cl15782 907240001344 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 907240001345 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 907240001346 G1 box; other site 907240001347 putative GEF interaction site [polypeptide binding]; other site 907240001348 GTP/Mg2+ binding site [chemical binding]; other site 907240001349 Switch I region; other site 907240001350 G2 box; other site 907240001351 G3 box; other site 907240001352 Switch II region; other site 907240001353 G4 box; other site 907240001354 G5 box; other site 907240001355 BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a...; Region: BipA_TypA_II; cd03691 907240001356 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 907240001357 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 907240001358 Catalytic GIY-YIG domain of coliphage T4 non-specific endonuclease II, type II restriction endonuclease R.Hpy188I, and similar proteins; Region: GIY-YIG_EndoII_Hpy188I_like; cd10436 907240001359 GIY-YIG motif/motif A; other site 907240001360 active site 907240001361 DNA binding site [nucleotide binding] 907240001362 catalytic site [active] 907240001363 metal binding site [ion binding]; metal-binding site 907240001364 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 907240001365 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 907240001366 cofactor binding site; other site 907240001367 DNA binding site [nucleotide binding] 907240001368 substrate interaction site [chemical binding]; other site 907240001369 potential frameshift: common BLAST hit: gi|254779149|ref|YP_003057254.1| putative non-functional type II restriction endonuclease 907240001370 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 907240001371 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 907240001372 putative heme binding pocket [chemical binding]; other site 907240001373 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 907240001374 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 907240001375 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 907240001376 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 907240001377 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 907240001378 TrkA-N domain; Region: TrkA_N; pfam02254 907240001379 TrkA-C domain; Region: TrkA_C; pfam02080 907240001380 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 907240001381 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 907240001382 phospho-N-acetylmuramoyl-pentapeptide-transferase; Region: mraY; TIGR00445 907240001383 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 907240001384 Mg++ binding site [ion binding]; other site 907240001385 putative catalytic motif [active] 907240001386 putative substrate binding site [chemical binding]; other site 907240001387 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03815 907240001388 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 907240001389 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 907240001390 Protein of unknown function (DUF493); Region: DUF493; pfam04359 907240001391 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 907240001392 active site 907240001393 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 907240001394 Na2 binding site [ion binding]; other site 907240001395 putative substrate binding site 1 [chemical binding]; other site 907240001396 Na binding site 1 [ion binding]; other site 907240001397 putative substrate binding site 2 [chemical binding]; other site 907240001398 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 907240001399 Na2 binding site [ion binding]; other site 907240001400 putative substrate binding site 1 [chemical binding]; other site 907240001401 Na binding site 1 [ion binding]; other site 907240001402 putative substrate binding site 2 [chemical binding]; other site 907240001403 potential frameshift: common BLAST hit: gi|108562900|ref|YP_627216.1| phospholipase A1 907240001404 DNA polymerase III, beta subunit; Region: dnan; TIGR00663 907240001405 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 907240001406 putative DNA binding surface [nucleotide binding]; other site 907240001407 dimer interface [polypeptide binding]; other site 907240001408 beta-clamp/translesion DNA polymerase binding surface; other site 907240001409 beta-clamp/clamp loader binding surface; other site 907240001410 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 907240001411 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 907240001412 Mg2+ binding site [ion binding]; other site 907240001413 G-X-G motif; other site 907240001414 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 907240001415 anchoring element; other site 907240001416 dimer interface [polypeptide binding]; other site 907240001417 ATP binding site [chemical binding]; other site 907240001418 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 907240001419 active site 907240001420 putative metal-binding site [ion binding]; other site 907240001421 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 907240001422 R.Pab1 restriction endonuclease; Region: RE_R_Pab1; pfam09522 907240001423 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 907240001424 Peptidase family M23; Region: Peptidase_M23; pfam01551 907240001425 nudix-type nucleoside diphosphatase, YffH/AdpP family; Region: TIGR00052 907240001426 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 907240001427 dimer interface [polypeptide binding]; other site 907240001428 ADP-ribose binding site [chemical binding]; other site 907240001429 active site 907240001430 nudix motif; other site 907240001431 metal binding site [ion binding]; metal-binding site 907240001432 FAD binding domain; Region: FAD_binding_4; pfam01565 907240001433 glycolate oxidase, subunit GlcD; Region: glcD; TIGR00387 907240001434 dihydrodipicolinate reductase; Region: dapB; TIGR00036 907240001435 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 907240001436 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 907240001437 glutamine synthetase, type I; Region: GlnA; TIGR00653 907240001438 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 907240001439 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 907240001440 Uncharacterized conserved protein [Function unknown]; Region: COG1479 907240001441 Protein of unknown function DUF262; Region: DUF262; pfam03235 907240001442 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 907240001443 Uncharacterized conserved protein [Function unknown]; Region: COG3586 907240001444 ribosomal protein L9; Region: L9; TIGR00158 907240001445 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 907240001446 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 907240001447 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 907240001448 active site 907240001449 HslU subunit interaction site [polypeptide binding]; other site 907240001450 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 907240001451 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 907240001452 Walker A motif; other site 907240001453 ATP binding site [chemical binding]; other site 907240001454 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 907240001455 Walker B motif; other site 907240001456 arginine finger; other site 907240001457 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 907240001458 GTPase [General function prediction only]; Region: Era; COG1159 907240001459 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 907240001460 G1 box; other site 907240001461 GTP/Mg2+ binding site [chemical binding]; other site 907240001462 Switch I region; other site 907240001463 G2 box; other site 907240001464 Switch II region; other site 907240001465 G3 box; other site 907240001466 G4 box; other site 907240001467 G5 box; other site 907240001468 KH domain; Region: KH_2; pfam07650 907240001469 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 907240001470 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 907240001471 Sel1-like repeats; Region: SEL1; smart00671 907240001472 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 907240001473 Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion]; Region: VirD4; COG3505 907240001474 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer...; Region: TraG_VirD4; cd01126 907240001475 Walker A motif; other site 907240001476 ATP binding site [chemical binding]; other site 907240001477 Walker B motif; other site 907240001478 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 907240001479 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 907240001480 ATP binding site [chemical binding]; other site 907240001481 Walker A motif; other site 907240001482 hexamer interface [polypeptide binding]; other site 907240001483 Walker B motif; other site 907240001484 CagZ; Region: CagZ; pfam09053 907240001485 DC-EC Repeat; Region: CagY_M; pfam07337 907240001486 DC-EC Repeat; Region: CagY_M; pfam07337 907240001487 DC-EC Repeat; Region: CagY_M; pfam07337 907240001488 DC-EC Repeat; Region: CagY_M; pfam07337 907240001489 DC-EC Repeat; Region: CagY_M; pfam07337 907240001490 DC-EC Repeat; Region: CagY_M; pfam07337 907240001491 DC-EC Repeat; Region: CagY_M; pfam07337 907240001492 DC-EC Repeat; Region: CagY_M; pfam07337 907240001493 DC-EC Repeat; Region: CagY_M; pfam07337 907240001494 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 907240001495 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 907240001496 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 907240001497 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 907240001498 VirB7 interaction site; other site 907240001499 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 907240001500 Cag pathogenicity island protein Cag12; Region: Cag12; pfam13117 907240001501 prolyl-tRNA synthetase; Provisional; Region: PRK08661 907240001502 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 907240001503 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 907240001504 CagA exotoxin; Region: CagA; pfam03507 907240001505 CagA exotoxin; Region: CagA; pfam03507 907240001506 AAA domain; Region: AAA_12; pfam13087 907240001507 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 907240001508 transcription termination factor Rho; Provisional; Region: rho; PRK09376 907240001509 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 907240001510 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 907240001511 RNA binding site [nucleotide binding]; other site 907240001512 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 907240001513 multimer interface [polypeptide binding]; other site 907240001514 Walker A motif; other site 907240001515 ATP binding site [chemical binding]; other site 907240001516 Walker B motif; other site 907240001517 Ribosomal protein L31; Region: Ribosomal_L31; pfam01197 907240001518 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 907240001519 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 907240001520 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 907240001521 acetyl-CoA carboxylase, carboxyl transferase, alpha subunit; Region: accA; TIGR00513 907240001522 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 907240001523 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK08439 907240001524 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 907240001525 dimer interface [polypeptide binding]; other site 907240001526 active site 907240001527 acyl carrier protein; Provisional; Region: acpP; PRK00982 907240001528 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 907240001529 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 907240001530 NAD(P) binding site [chemical binding]; other site 907240001531 active site 907240001532 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 907240001533 Predicted membrane protein [Function unknown]; Region: COG3059 907240001534 diaminopimelate epimerase; Region: DapF; TIGR00652 907240001535 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 907240001536 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 907240001537 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 907240001538 Domain of unknown function DUF20; Region: UPF0118; pfam01594 907240001539 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 907240001540 FeS/SAM binding site; other site 907240001541 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 907240001542 GTP-binding protein YchF; Reviewed; Region: PRK09601 907240001543 YchF GTPase; Region: YchF; cd01900 907240001544 G1 box; other site 907240001545 GTP/Mg2+ binding site [chemical binding]; other site 907240001546 Switch I region; other site 907240001547 G2 box; other site 907240001548 Switch II region; other site 907240001549 G3 box; other site 907240001550 G4 box; other site 907240001551 G5 box; other site 907240001552 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 907240001553 multifunctional aminopeptidase A; Provisional; Region: PRK00913 907240001554 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 907240001555 interface (dimer of trimers) [polypeptide binding]; other site 907240001556 Substrate-binding/catalytic site; other site 907240001557 Zn-binding sites [ion binding]; other site 907240001558 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 907240001559 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 907240001560 active site 907240001561 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 907240001562 ribose 5-phosphate isomerase B; Region: rpiB; TIGR01120 907240001563 Peptidase family M50; Region: Peptidase_M50; pfam02163 907240001564 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 907240001565 active site 907240001566 putative substrate binding region [chemical binding]; other site 907240001567 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 907240001568 signal peptidase I; Provisional; Region: PRK10861 907240001569 Catalytic site [active] 907240001570 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 907240001571 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14191 907240001572 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 907240001573 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 907240001574 homodimer interface [polypeptide binding]; other site 907240001575 NADP binding site [chemical binding]; other site 907240001576 substrate binding site [chemical binding]; other site 907240001577 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 907240001578 Sulfatase; Region: Sulfatase; pfam00884 907240001579 Predicted neuraminidase (sialidase) [Carbohydrate transport and metabolism]; Region: COG4692 907240001580 BNR repeat-like domain; Region: BNR_2; pfam13088 907240001581 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 907240001582 active site 907240001583 substrate binding pocket [chemical binding]; other site 907240001584 dimer interface [polypeptide binding]; other site 907240001585 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 907240001586 TonB family C-terminal domain; Region: tonB_Cterm; TIGR01352 907240001587 flagellar motor switch protein; Validated; Region: PRK08433 907240001588 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 907240001589 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 907240001590 minor groove reading motif; other site 907240001591 helix-hairpin-helix signature motif; other site 907240001592 substrate binding pocket [chemical binding]; other site 907240001593 active site 907240001594 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 907240001595 Fe2+ transport system protein A [Inorganic ion transport and metabolism]; Region: FeoA; COG1918 907240001596 Protein of unknown function; Region: DUF3971; pfam13116 907240001597 AsmA-like C-terminal region; Region: AsmA_1; pfam13109 907240001598 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 907240001599 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 907240001600 dimerization interface [polypeptide binding]; other site 907240001601 2-oxoglutarate-acceptor oxidoreductase subunit OorD; Reviewed; Region: oorD; PRK09626 907240001602 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 907240001603 2-oxoglutarate-acceptor oxidoreductase subunit OorA; Reviewed; Region: oorA; PRK09627 907240001604 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 907240001605 dimer interface [polypeptide binding]; other site 907240001606 PYR/PP interface [polypeptide binding]; other site 907240001607 TPP binding site [chemical binding]; other site 907240001608 substrate binding site [chemical binding]; other site 907240001609 2-oxoglutarate-acceptor oxidoreductase subunit OorB; Reviewed; Region: oorB; PRK09628 907240001610 Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR...; Region: TPP_OGFOR; cd03375 907240001611 TPP-binding site [chemical binding]; other site 907240001612 2-oxoglutarate-acceptor oxidoreductase subunit OorC; Reviewed; Region: oorC; PRK08441 907240001613 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 907240001614 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG5610 907240001615 haloacid dehalogenase superfamily, subfamily IA, variant 1 with third motif having Dx(3-4)D or Dx(3-4)E; Region: HAD-SF-IA-v1; TIGR01549 907240001616 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 907240001617 tumor necrosis factor alpha-inducing protein; Reviewed; Region: PRK12303 907240001618 Transglycosylase; Region: Transgly; pfam00912 907240001619 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 907240001620 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 907240001621 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 907240001622 Aminotransferase class I and II; Region: Aminotran_1_2; pfam00155 907240001623 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 907240001624 catalytic residue [active] 907240001625 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 907240001626 dimer interface [polypeptide binding]; other site 907240001627 putative CheW interface [polypeptide binding]; other site 907240001628 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 907240001629 potential frameshift: common BLAST hit: gi|15645225|ref|NP_207395.1| multidrug resistance protein (spaB) 907240001630 flagellin A; Reviewed; Region: PRK12584 907240001631 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 907240001632 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 907240001633 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 907240001634 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 907240001635 3-methyladenine DNA glycosylase; Provisional; Region: PRK13913 907240001636 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 907240001637 minor groove reading motif; other site 907240001638 helix-hairpin-helix signature motif; other site 907240001639 active site 907240001640 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 907240001641 substrate binding site [chemical binding]; other site 907240001642 active site 907240001643 Outer membrane efflux protein; Region: OEP; pfam02321 907240001644 Outer membrane efflux protein; Region: OEP; pfam02321 907240001645 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 907240001646 HlyD family secretion protein; Region: HlyD_3; pfam13437 907240001647 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 907240001648 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240001649 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 907240001650 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907240001651 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907240001652 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907240001653 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907240001654 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 907240001655 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907240001656 Autotransporter beta-domain; Region: Autotransporter; pfam03797 907240001657 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 907240001658 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 907240001659 Walker A/P-loop; other site 907240001660 ATP binding site [chemical binding]; other site 907240001661 Q-loop/lid; other site 907240001662 ABC transporter signature motif; other site 907240001663 Walker B; other site 907240001664 D-loop; other site 907240001665 H-loop/switch region; other site 907240001666 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 907240001667 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 907240001668 nucleotide binding pocket [chemical binding]; other site 907240001669 K-X-D-G motif; other site 907240001670 catalytic site [active] 907240001671 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 907240001672 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 907240001673 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 907240001674 Dimer interface [polypeptide binding]; other site 907240001675 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; cd00588 907240001676 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 907240001677 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 907240001678 active site 907240001679 phosphorylation site [posttranslational modification] 907240001680 intermolecular recognition site; other site 907240001681 dimerization interface [polypeptide binding]; other site 907240001682 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 907240001683 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 907240001684 dimer interface [polypeptide binding]; other site 907240001685 anticodon binding site; other site 907240001686 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 907240001687 homodimer interface [polypeptide binding]; other site 907240001688 motif 1; other site 907240001689 active site 907240001690 motif 2; other site 907240001691 GAD domain; Region: GAD; pfam02938 907240001692 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 907240001693 active site 907240001694 motif 3; other site 907240001695 adenylate kinase; Reviewed; Region: adk; PRK00279 907240001696 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 907240001697 AMP-binding site [chemical binding]; other site 907240001698 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 907240001699 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 907240001700 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cl01298 907240001701 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 907240001702 Glycosyltransferase involved in LPS biosynthesis [Cell envelope biogenesis, outer membrane]; Region: COG3306 907240001703 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 907240001704 dimer interface [polypeptide binding]; other site 907240001705 substrate binding site [chemical binding]; other site 907240001706 metal binding sites [ion binding]; metal-binding site 907240001707 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 907240001708 ATPase domain of DNA mismatch repair MUTS family; Region: MUTSac; smart00534 907240001709 Walker A/P-loop; other site 907240001710 ATP binding site [chemical binding]; other site 907240001711 Q-loop/lid; other site 907240001712 ABC transporter signature motif; other site 907240001713 Walker B; other site 907240001714 D-loop; other site 907240001715 H-loop/switch region; other site 907240001716 Smr domain; Region: Smr; pfam01713 907240001717 UDP-N-acetylmuramate--alanine ligase; Region: murC; TIGR01082 907240001718 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 907240001719 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 907240001720 hypothetical protein; Provisional; Region: PRK05839 907240001721 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 907240001722 pyridoxal 5'-phosphate binding site [chemical binding]; other site 907240001723 homodimer interface [polypeptide binding]; other site 907240001724 catalytic residue [active] 907240001725 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 907240001726 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 907240001727 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 907240001728 Tetrahydrodipicolinate N-succinyltransferase [Amino acid transport and metabolism]; Region: DapD; COG2171 907240001729 Putative 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (THP succinyltransferase), C-terminal left-handed parallel alpha-helix (LbH) domain: This group is composed of mostly uncharacterized proteins containing an N-terminal...; Region: LbH_THP_succinylT_putative; cd04649 907240001730 putative trimer interface [polypeptide binding]; other site 907240001731 putative CoA binding site [chemical binding]; other site 907240001732 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 907240001733 Sel1-like repeats; Region: SEL1; smart00671 907240001734 Sel1-like repeats; Region: SEL1; smart00671 907240001735 Sel1 repeat; Region: Sel1; cl02723 907240001736 Sel1-like repeats; Region: SEL1; smart00671 907240001737 Uncharacterized conserved protein [Function unknown]; Region: COG1479 907240001738 Protein of unknown function DUF262; Region: DUF262; pfam03235 907240001739 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 907240001740 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 907240001741 hydrogenase (NiFe) small subunit (hydA); Region: hydA; TIGR00391 907240001742 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 907240001743 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 907240001744 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 907240001745 Ni,Fe-hydrogenase I cytochrome b subunit [Energy production and conversion]; Region: HyaC; COG1969 907240001746 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 907240001747 nickel binding site [ion binding]; other site 907240001748 putative substrate-binding site; other site 907240001749 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240001750 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 907240001751 Ligand Binding Site [chemical binding]; other site 907240001752 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 907240001753 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 907240001754 active site 907240001755 NTP binding site [chemical binding]; other site 907240001756 metal binding triad [ion binding]; metal-binding site 907240001757 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 907240001758 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 907240001759 hydrophobic ligand binding site; other site 907240001760 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 907240001761 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 907240001762 potential frameshift: common BLAST hit: gi|15611653|ref|NP_223304.1| NAD(P)H-flavin oxidoreductase 907240001763 glutamylglutaminyl-tRNA synthetase; Provisional; Region: PRK12410 907240001764 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 907240001765 active site 907240001766 HIGH motif; other site 907240001767 nucleotide binding site [chemical binding]; other site 907240001768 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 907240001769 active site 907240001770 KMSKS motif; other site 907240001771 YGGT family; Region: YGGT; pfam02325 907240001772 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 907240001773 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 907240001774 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 907240001775 N-acetyl-D-glucosamine binding site [chemical binding]; other site 907240001776 catalytic residue [active] 907240001777 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 907240001778 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 907240001779 active site 907240001780 tetramer interface; other site 907240001781 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 907240001782 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 907240001783 hinge; other site 907240001784 active site 907240001785 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 907240001786 Aspartase; Region: Aspartase; cd01357 907240001787 active sites [active] 907240001788 tetramer interface [polypeptide binding]; other site 907240001789 Uracil-DNA glycosylases (UDG) and related enzymes; Region: UDG_like; cl00483 907240001790 ligand binding site [chemical binding]; other site 907240001791 active site 907240001792 Glycosyltransferase family 10 (fucosyltransferase); Region: Glyco_transf_10; pfam00852 907240001793 Homeobox associated leucine zipper; Region: HALZ; pfam02183 907240001794 Homeobox associated leucine zipper; Region: HALZ; cl02577 907240001795 phosphoserine phosphatase SerB; Region: serB; TIGR00338 907240001796 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 907240001797 motif II; other site 907240001798 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 907240001799 Ferritin-like domain; Region: Ferritin; pfam00210 907240001800 ferroxidase diiron center [ion binding]; other site 907240001801 hypothetical protein; Provisional; Region: PRK08444 907240001802 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 907240001803 FeS/SAM binding site; other site 907240001804 potential frameshift: common BLAST hit: gi|15611667|ref|NP_223318.1| protective surface antigen D15 907240001805 hypothetical protein; Provisional; Region: PRK08445 907240001806 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 907240001807 FeS/SAM binding site; other site 907240001808 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 907240001809 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 907240001810 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 907240001811 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 907240001812 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 907240001813 GatB domain; Region: GatB_Yqey; smart00845 907240001814 SurA N-terminal domain; Region: SurA_N; pfam09312 907240001815 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]; Region: COG2956 907240001816 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]; Region: COG1439 907240001817 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 907240001818 RNA/DNA hybrid binding site [nucleotide binding]; other site 907240001819 active site 907240001820 ribonuclease III; Reviewed; Region: rnc; PRK00102 907240001821 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 907240001822 dimerization interface [polypeptide binding]; other site 907240001823 active site 907240001824 metal binding site [ion binding]; metal-binding site 907240001825 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 907240001826 dsRNA binding site [nucleotide binding]; other site 907240001827 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 907240001828 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 907240001829 Tetramer interface [polypeptide binding]; other site 907240001830 active site 907240001831 FMN-binding site [chemical binding]; other site 907240001832 Protein of unknown function (DUF2603); Region: DUF2603; pfam10788 907240001833 oxygen-independent coproporphyrinogen III oxidase; Region: hemN; TIGR00538 907240001834 HemN C-terminal domain; Region: HemN_C; pfam06969 907240001835 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 907240001836 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 907240001837 Cysteine-rich domain; Region: CCG; pfam02754 907240001838 Cysteine-rich domain; Region: CCG; pfam02754 907240001839 Restriction endonuclease; Region: Mrr_cat_2; pfam13156 907240001840 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 907240001841 ATP binding site [chemical binding]; other site 907240001842 putative Mg++ binding site [ion binding]; other site 907240001843 Predicted helicase [General function prediction only]; Region: COG4889 907240001844 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 907240001845 nucleotide binding region [chemical binding]; other site 907240001846 ATP-binding site [chemical binding]; other site 907240001847 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 907240001848 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240001849 aspartate aminotransferase; Provisional; Region: PRK05764 907240001850 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 907240001851 pyridoxal 5'-phosphate binding site [chemical binding]; other site 907240001852 homodimer interface [polypeptide binding]; other site 907240001853 catalytic residue [active] 907240001854 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 907240001855 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 907240001856 active site 907240001857 DNA binding site [nucleotide binding] 907240001858 Int/Topo IB signature motif; other site 907240001859 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 907240001860 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 907240001861 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 907240001862 DNA binding site [nucleotide binding] 907240001863 active site 907240001864 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 907240001865 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 907240001866 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 907240001867 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 907240001868 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK08447 907240001869 ATP cone domain; Region: ATP-cone; pfam03477 907240001870 Class I ribonucleotide reductase; Region: RNR_I; cd01679 907240001871 active site 907240001872 dimer interface [polypeptide binding]; other site 907240001873 catalytic residues [active] 907240001874 effector binding site; other site 907240001875 R2 peptide binding site; other site 907240001876 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14359 907240001877 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 907240001878 Substrate binding site; other site 907240001879 Mg++ binding site; other site 907240001880 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 907240001881 active site 907240001882 substrate binding site [chemical binding]; other site 907240001883 CoA binding site [chemical binding]; other site 907240001884 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 907240001885 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 907240001886 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 907240001887 N-terminal plug; other site 907240001888 ligand-binding site [chemical binding]; other site 907240001889 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 907240001890 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 907240001891 G1 box; other site 907240001892 GTP/Mg2+ binding site [chemical binding]; other site 907240001893 Switch I region; other site 907240001894 G2 box; other site 907240001895 G3 box; other site 907240001896 Switch II region; other site 907240001897 G4 box; other site 907240001898 G5 box; other site 907240001899 Nucleoside recognition; Region: Gate; pfam07670 907240001900 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 907240001901 Nucleoside recognition; Region: Gate; pfam07670 907240001902 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 907240001903 active site 907240001904 catalytic site [active] 907240001905 substrate binding site [chemical binding]; other site 907240001906 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 907240001907 potential frameshift: common BLAST hit: gi|15611696|ref|NP_223347.1| putative type II DNA modification enzyme (methyltransferase) 907240001908 potential frameshift: common BLAST hit: gi|15611696|ref|NP_223347.1| putative type II DNA modification enzyme (methyltransferase) 907240001909 potential frameshift: common BLAST hit: gi|15611697|ref|NP_223348.1| putative type II restriction enzyme 907240001910 Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcxC; COG4647 907240001911 Acetone carboxylase gamma subunit; Region: Acetone_carb_G; pfam08882 907240001912 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 907240001913 Hydantoinase B/oxoprolinase; Region: Hydantoinase_B; pfam02538 907240001914 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 907240001915 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 907240001916 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 907240001917 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3528 907240001918 Short chain fatty acid transporter; Region: SCFA_trans; pfam02667 907240001919 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 907240001920 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 907240001921 putative acyltransferase; Provisional; Region: PRK05790 907240001922 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 907240001923 dimer interface [polypeptide binding]; other site 907240001924 active site 907240001925 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 907240001926 DNA gyrase subunit A; Validated; Region: PRK05560 907240001927 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 907240001928 CAP-like domain; other site 907240001929 active site 907240001930 primary dimer interface [polypeptide binding]; other site 907240001931 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 907240001932 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 907240001933 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 907240001934 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 907240001935 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 907240001936 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 907240001937 Response regulator receiver domain; Region: Response_reg; pfam00072 907240001938 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 907240001939 active site 907240001940 phosphorylation site [posttranslational modification] 907240001941 intermolecular recognition site; other site 907240001942 dimerization interface [polypeptide binding]; other site 907240001943 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 907240001944 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 907240001945 Walker A motif; other site 907240001946 ATP binding site [chemical binding]; other site 907240001947 Walker B motif; other site 907240001948 arginine finger; other site 907240001949 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 907240001950 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 907240001951 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 907240001952 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 907240001953 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240001954 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 907240001955 16S rRNA (cytosine(1402)-N(4))-methyltransferase; Region: TIGR00006 907240001956 Uncharacterized conserved protein [Function unknown]; Region: COG1912 907240001957 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240001958 Competence protein ComGF [Intracellular trafficking and secretion]; Region: ComGF; COG4940 907240001959 Predicted hydrolases of HD superfamily [General function prediction only]; Region: COG1896 907240001960 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 907240001961 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 907240001962 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 907240001963 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 907240001964 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 907240001965 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 907240001966 Walker A/P-loop; other site 907240001967 ATP binding site [chemical binding]; other site 907240001968 Q-loop/lid; other site 907240001969 ABC transporter signature motif; other site 907240001970 Walker B; other site 907240001971 D-loop; other site 907240001972 H-loop/switch region; other site 907240001973 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 907240001974 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 907240001975 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 907240001976 Walker A motif; other site 907240001977 ATP binding site [chemical binding]; other site 907240001978 Walker B motif; other site 907240001979 arginine finger; other site 907240001980 Lysine efflux permease [General function prediction only]; Region: COG1279 907240001981 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 907240001982 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 907240001983 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240001984 anaerobic c4-dicarboxylate membrane transporter family protein; Region: Dcu; TIGR00770 907240001985 Anaerobic C4-dicarboxylate transporter [General function prediction only]; Region: DcuB; COG2704 907240001986 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 907240001987 active site 907240001988 homotetramer interface [polypeptide binding]; other site 907240001989 homodimer interface [polypeptide binding]; other site 907240001990 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240001991 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 907240001992 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 907240001993 FMN binding site [chemical binding]; other site 907240001994 active site 907240001995 catalytic residues [active] 907240001996 substrate binding site [chemical binding]; other site 907240001997 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 907240001998 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 907240001999 Ligand Binding Site [chemical binding]; other site 907240002000 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 907240002001 G1 box; other site 907240002002 GTP/Mg2+ binding site [chemical binding]; other site 907240002003 G2 box; other site 907240002004 Switch I region; other site 907240002005 G3 box; other site 907240002006 Switch II region; other site 907240002007 G4 box; other site 907240002008 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 907240002009 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 907240002010 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 907240002011 FeS/SAM binding site; other site 907240002012 Predicted phosphoribosyltransferases [General function prediction only]; Region: COG2236 907240002013 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 907240002014 active site 907240002015 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 907240002016 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 907240002017 catalytic residue [active] 907240002018 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 907240002019 tetramer interfaces [polypeptide binding]; other site 907240002020 binuclear metal-binding site [ion binding]; other site 907240002021 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 907240002022 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 907240002023 ATP-grasp domain; Region: ATP-grasp_4; cl17255 907240002024 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 907240002025 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 907240002026 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 907240002027 FHIT (fragile histidine family): FHIT proteins, related to the HIT family carry a motif HxHxH/Qxx (x, is a hydrophobic amino acid), On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified into...; Region: FHIT; cd01275 907240002028 nucleotide binding site/active site [active] 907240002029 HIT family signature motif; other site 907240002030 catalytic residue [active] 907240002031 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 907240002032 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 907240002033 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 907240002034 active site 907240002035 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 907240002036 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 907240002037 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 907240002038 RNA binding surface [nucleotide binding]; other site 907240002039 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 907240002040 active site 907240002041 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cl00065 907240002042 Fibronectin type 3 domain-containing protein [General function prediction only]; Region: COG3401 907240002043 Interdomain contacts; other site 907240002044 Cytokine receptor motif; other site 907240002045 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 907240002046 Interdomain contacts; other site 907240002047 Cytokine receptor motif; other site 907240002048 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 907240002049 Interdomain contacts; other site 907240002050 Cytokine receptor motif; other site 907240002051 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 907240002052 S-adenosylmethionine binding site [chemical binding]; other site 907240002053 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 907240002054 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 907240002055 Walker A/P-loop; other site 907240002056 ATP binding site [chemical binding]; other site 907240002057 Q-loop/lid; other site 907240002058 ABC transporter signature motif; other site 907240002059 Walker B; other site 907240002060 D-loop; other site 907240002061 H-loop/switch region; other site 907240002062 putative protein insertion permease FtsX; Region: ftsX; TIGR00439 907240002063 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 907240002064 Peptidase family M23; Region: Peptidase_M23; pfam01551 907240002065 flagellar protein FlaG; Provisional; Region: PRK08452 907240002066 flagellar capping protein; Validated; Region: fliD; PRK08453 907240002067 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 907240002068 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 907240002069 flagellar biosynthetic protein FliS; Region: fliS; TIGR00208 907240002070 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 907240002071 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 907240002072 putative ATP binding site [chemical binding]; other site 907240002073 putative substrate interface [chemical binding]; other site 907240002074 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 907240002075 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 907240002076 putative active site; other site 907240002077 catalytic triad [active] 907240002078 putative dimer interface [polypeptide binding]; other site 907240002079 Predicted permease [General function prediction only]; Region: COG2056 907240002080 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 907240002081 Predicted membrane protein [Function unknown]; Region: COG1288; cl17886 907240002082 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Thermotoga marina NorM; Region: MATE_NorM_like; cd13137 907240002083 putative efflux protein, MATE family; Region: matE; TIGR00797 907240002084 phosphodiesterase; Provisional; Region: PRK12704 907240002085 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cd00105 907240002086 nucleic acid binding region [nucleotide binding]; other site 907240002087 G-X-X-G motif; other site 907240002088 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 907240002089 Zn2+ binding site [ion binding]; other site 907240002090 Mg2+ binding site [ion binding]; other site 907240002091 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212; cl00360 907240002092 signal recognition particle-docking protein FtsY; Region: ftsY; TIGR00064 907240002093 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 907240002094 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 907240002095 LrgB-like family; Region: LrgB; cl00596 907240002096 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 907240002097 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 907240002098 FeS/SAM binding site; other site 907240002099 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 907240002100 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 907240002101 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 907240002102 GTP binding site; other site 907240002103 flagellar biosynthetic protein FlhB; Region: flhB; TIGR00328 907240002104 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 907240002105 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 907240002106 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 907240002107 active site 907240002108 metal binding site [ion binding]; metal-binding site 907240002109 Nitronate monooxygenase; Region: NMO; pfam03060 907240002110 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 907240002111 FMN binding site [chemical binding]; other site 907240002112 substrate binding site [chemical binding]; other site 907240002113 putative catalytic residue [active] 907240002114 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 907240002115 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 907240002116 active site 907240002117 HIGH motif; other site 907240002118 dimer interface [polypeptide binding]; other site 907240002119 KMSKS motif; other site 907240002120 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 907240002121 RNA binding surface [nucleotide binding]; other site 907240002122 (p)ppGpp synthetase, RelA/SpoT family; Region: spoT_relA; TIGR00691 907240002123 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 907240002124 Zn2+ binding site [ion binding]; other site 907240002125 Mg2+ binding site [ion binding]; other site 907240002126 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 907240002127 synthetase active site [active] 907240002128 NTP binding site [chemical binding]; other site 907240002129 metal binding site [ion binding]; metal-binding site 907240002130 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 907240002131 DNA-directed RNA polymerase, subunit K/omega [Transcription]; Region: RpoZ; COG1758 907240002132 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 907240002133 putative nucleotide binding site [chemical binding]; other site 907240002134 uridine monophosphate binding site [chemical binding]; other site 907240002135 homohexameric interface [polypeptide binding]; other site 907240002136 Predicted periplasmic solute-binding protein [General function prediction only]; Region: COG1427 907240002137 aconitate hydratase 2; Region: acnB; TIGR00117 907240002138 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change in...; Region: AcnB_Swivel; cd01576 907240002139 substrate binding site [chemical binding]; other site 907240002140 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 907240002141 substrate binding site [chemical binding]; other site 907240002142 ligand binding site [chemical binding]; other site 907240002143 FOG: Transposase [DNA replication, recombination, and repair]; Region: COG5659 907240002144 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 907240002145 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 907240002146 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 907240002147 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 907240002148 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 907240002149 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 907240002150 nucleotide binding region [chemical binding]; other site 907240002151 ATP-binding site [chemical binding]; other site 907240002152 SEC-C motif; Region: SEC-C; pfam02810 907240002153 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 907240002154 FtsX-like permease family; Region: FtsX; pfam02687 907240002155 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 907240002156 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 907240002157 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 907240002158 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 907240002159 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; cl00207 907240002160 metal-binding site [ion binding] 907240002161 heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase; Region: ATPase-IB2_Cd; TIGR01512 907240002162 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 907240002163 Soluble P-type ATPase [General function prediction only]; Region: COG4087 907240002164 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 907240002165 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 907240002166 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 907240002167 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 907240002168 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 907240002169 active site 907240002170 catalytic residues [active] 907240002171 metal binding site [ion binding]; metal-binding site 907240002172 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 907240002173 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 907240002174 oligomer interface [polypeptide binding]; other site 907240002175 active site residues [active] 907240002176 trigger factor; Provisional; Region: tig; PRK01490 907240002177 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 907240002178 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 907240002179 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240002180 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 907240002181 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 907240002182 trimer interface [polypeptide binding]; other site 907240002183 dimer interface [polypeptide binding]; other site 907240002184 putative active site [active] 907240002185 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 907240002186 MPT binding site; other site 907240002187 trimer interface [polypeptide binding]; other site 907240002188 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 907240002189 MoaE homodimer interface [polypeptide binding]; other site 907240002190 MoaD interaction [polypeptide binding]; other site 907240002191 active site residues [active] 907240002192 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 907240002193 MoaE interaction surface [polypeptide binding]; other site 907240002194 MoeB interaction surface [polypeptide binding]; other site 907240002195 thiocarboxylated glycine; other site 907240002196 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cd00641 907240002197 dimerization interface [polypeptide binding]; other site 907240002198 active site 907240002199 Domain of unknown function (DUF3943); Region: DUF3943; pfam13084 907240002200 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09314 907240002201 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: ribB; TIGR00506 907240002202 GTP cyclohydrolase II [Coenzyme metabolism]; Region: RibA; COG0807 907240002203 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 907240002204 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 907240002205 potential frameshift: common BLAST hit: gi|208434718|ref|YP_002266384.1| iron (III) dicitrate transport protein 907240002206 holo-[acyl-carrier-protein] synthase; Region: acpS; TIGR00516 907240002207 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK08455 907240002208 RNA methyltransferase, RsmD family; Region: TIGR00095 907240002209 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 907240002210 Uncharacterized conserved protein [Function unknown]; Region: COG1565 907240002211 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 907240002212 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism]; Region: ThiF; COG0476 907240002213 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 907240002214 ATP binding site [chemical binding]; other site 907240002215 substrate interface [chemical binding]; other site 907240002216 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 907240002217 flagellar motor protein MotA; Validated; Region: PRK08456 907240002218 flagellar motor protein MotB; Reviewed; Region: motB; PRK08457 907240002219 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 907240002220 ligand binding site [chemical binding]; other site 907240002221 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 907240002222 dimer interface [polypeptide binding]; other site 907240002223 conserved gate region; other site 907240002224 ABC-ATPase subunit interface; other site 907240002225 Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane]; Region: OpuBC; COG1732 907240002226 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 907240002227 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 907240002228 Walker A/P-loop; other site 907240002229 ATP binding site [chemical binding]; other site 907240002230 Q-loop/lid; other site 907240002231 ABC transporter signature motif; other site 907240002232 Walker B; other site 907240002233 D-loop; other site 907240002234 H-loop/switch region; other site 907240002235 excinuclease ABC, C subunit; Region: uvrC; TIGR00194 907240002236 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 907240002237 GIY-YIG motif/motif A; other site 907240002238 active site 907240002239 catalytic site [active] 907240002240 putative DNA binding site [nucleotide binding]; other site 907240002241 metal binding site [ion binding]; metal-binding site 907240002242 UvrB/uvrC motif; Region: UVR; pfam02151 907240002243 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 907240002244 homoserine dehydrogenase; Provisional; Region: PRK06349 907240002245 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 907240002246 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 907240002247 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 907240002248 Uncharacterized protein family UPF0102; Region: UPF0102; pfam02021 907240002249 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 907240002250 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 907240002251 catalytic residues [active] 907240002252 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 907240002253 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 907240002254 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 907240002255 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 907240002256 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 907240002257 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 907240002258 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 907240002259 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 907240002260 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 907240002261 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 907240002262 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 907240002263 active site 907240002264 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 907240002265 indole acetimide hydrolase; Validated; Region: PRK07488 907240002266 dephospho-CoA kinase; Region: TIGR00152 907240002267 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 907240002268 CoA-binding site [chemical binding]; other site 907240002269 ATP-binding [chemical binding]; other site 907240002270 spermidine synthase; Provisional; Region: speE; PRK00536 907240002271 spermidine synthase; Provisional; Region: PRK00811 907240002272 GTP-binding protein Der; Reviewed; Region: PRK00093 907240002273 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 907240002274 G1 box; other site 907240002275 GTP/Mg2+ binding site [chemical binding]; other site 907240002276 Switch I region; other site 907240002277 G2 box; other site 907240002278 Switch II region; other site 907240002279 G3 box; other site 907240002280 G4 box; other site 907240002281 G5 box; other site 907240002282 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 907240002283 G1 box; other site 907240002284 GTP/Mg2+ binding site [chemical binding]; other site 907240002285 Switch I region; other site 907240002286 G2 box; other site 907240002287 G3 box; other site 907240002288 Switch II region; other site 907240002289 G4 box; other site 907240002290 G5 box; other site 907240002291 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 907240002292 IHF dimer interface [polypeptide binding]; other site 907240002293 IHF - DNA interface [nucleotide binding]; other site 907240002294 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3018 907240002295 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3018 907240002296 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 907240002297 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 907240002298 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 907240002299 NAD(P) binding site [chemical binding]; other site 907240002300 homodimer interface [polypeptide binding]; other site 907240002301 substrate binding site [chemical binding]; other site 907240002302 active site 907240002303 phosphopantothenoylcysteine decarboxylase / phosphopantothenate--cysteine ligase; Region: coaBC_dfp; TIGR00521 907240002304 Flavoprotein; Region: Flavoprotein; pfam02441 907240002305 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 907240002306 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 907240002307 active site 907240002308 thiamine phosphate binding site [chemical binding]; other site 907240002309 pyrophosphate binding site [ion binding]; other site 907240002310 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 907240002311 dimer interface [polypeptide binding]; other site 907240002312 substrate binding site [chemical binding]; other site 907240002313 ATP binding site [chemical binding]; other site 907240002314 4-methyl-5-beta-hydroxyethylthiazole (Thz) kinase catalyzes the phosphorylation of the hydroxylgroup of Thz. A reaction that allows cells to recycle Thz into the thiamine biosynthesis pathway, as an alternative to its synthesis from cysteine, tyrosine...; Region: THZ_kinase; cd01170 907240002315 substrate binding site [chemical binding]; other site 907240002316 multimerization interface [polypeptide binding]; other site 907240002317 ATP binding site [chemical binding]; other site 907240002318 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 907240002319 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 907240002320 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 907240002321 ATP binding site [chemical binding]; other site 907240002322 putative Mg++ binding site [ion binding]; other site 907240002323 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 907240002324 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 907240002325 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 907240002326 type I restriction system adenine methylase (hsdM); Region: hsdM; TIGR00497 907240002327 HsdM N-terminal domain; Region: HsdM_N; pfam12161 907240002328 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 907240002329 S-adenosylmethionine binding site [chemical binding]; other site 907240002330 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 907240002331 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 907240002332 active site 907240002333 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2958 907240002334 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 907240002335 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 907240002336 Walker A/P-loop; other site 907240002337 ATP binding site [chemical binding]; other site 907240002338 Q-loop/lid; other site 907240002339 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 907240002340 ABC transporter; Region: ABC_tran_2; pfam12848 907240002341 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 907240002342 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05458 907240002343 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 907240002344 active site 907240002345 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 907240002346 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 907240002347 dimer interface [polypeptide binding]; other site 907240002348 active site 907240002349 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 907240002350 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 907240002351 putative ribose interaction site [chemical binding]; other site 907240002352 putative ADP binding site [chemical binding]; other site 907240002353 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 907240002354 active site 907240002355 nucleotide binding site [chemical binding]; other site 907240002356 HIGH motif; other site 907240002357 KMSKS motif; other site 907240002358 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 907240002359 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 907240002360 NAD(P) binding site [chemical binding]; other site 907240002361 active site 907240002362 D,D-heptose 1,7-bisphosphate phosphatase; Region: GmhB_yaeD; TIGR00213 907240002363 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 907240002364 active site 907240002365 motif I; other site 907240002366 motif II; other site 907240002367 Uncharacterized conserved protein [Function unknown]; Region: COG2836 907240002368 pantothenate kinase; Reviewed; Region: PRK13333 907240002369 PQQ-like domain; Region: PQQ_2; pfam13360 907240002370 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 907240002371 trimer interface [polypeptide binding]; other site 907240002372 active site 907240002373 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 907240002374 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 907240002375 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 907240002376 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 907240002377 lipid-A-disaccharide synthase; Region: lpxB; TIGR00215 907240002378 hydrogenase nickel incorporation protein; Provisional; Region: hypA; PRK00564 907240002379 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 907240002380 flagellar hook protein FlgE; Validated; Region: flgE; PRK08425 907240002381 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 907240002382 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 907240002383 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 907240002384 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 907240002385 CDP-diacylglycerol pyrophosphatase, bacterial type; Region: cdh; TIGR00672 907240002386 alkylphosphonate utilization operon protein PhnA; Region: phnA; TIGR00686 907240002387 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 907240002388 PhnA protein; Region: PhnA; pfam03831 907240002389 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 907240002390 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 907240002391 tetramer interface [polypeptide binding]; other site 907240002392 heme binding pocket [chemical binding]; other site 907240002393 NADPH binding site [chemical binding]; other site 907240002394 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 907240002395 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 907240002396 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 907240002397 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 907240002398 active site 907240002399 putative DNA-binding cleft [nucleotide binding]; other site 907240002400 dimer interface [polypeptide binding]; other site 907240002401 Uncharacterized conserved protein [Function unknown]; Region: COG1432 907240002402 LabA_like proteins; Region: LabA_like; cd06167 907240002403 putative metal binding site [ion binding]; other site 907240002404 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 907240002405 Holliday junction DNA helicase, RuvA subunit; Region: ruvA; TIGR00084 907240002406 RuvA N terminal domain; Region: RuvA_N; pfam01330 907240002407 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 907240002408 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 907240002409 MviN-like protein; Region: MVIN; pfam03023 907240002410 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 907240002411 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 907240002412 active site 907240002413 HIGH motif; other site 907240002414 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 907240002415 KMSKS motif; other site 907240002416 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 907240002417 tRNA binding surface [nucleotide binding]; other site 907240002418 anticodon binding site; other site 907240002419 Vacuolating cyotoxin; Region: VacA; pfam02691 907240002420 Autotransporter beta-domain; Region: Autotransporter; pfam03797 907240002421 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 907240002422 A4GalT_like proteins catalyze the addition of galactose or glucose residues to the lipooligosaccharide (LOS) or lipopolysaccharide (LPS) of the bacterial cell surface; Region: GT8_A4GalT_like; cd04194 907240002423 Ligand binding site; other site 907240002424 metal-binding site 907240002425 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 907240002426 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 907240002427 Walker A/P-loop; other site 907240002428 ATP binding site [chemical binding]; other site 907240002429 Q-loop/lid; other site 907240002430 ABC transporter signature motif; other site 907240002431 Walker B; other site 907240002432 D-loop; other site 907240002433 H-loop/switch region; other site 907240002434 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 907240002435 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 907240002436 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 907240002437 ABC-ATPase subunit interface; other site 907240002438 dimer interface [polypeptide binding]; other site 907240002439 putative PBP binding regions; other site 907240002440 short chain dehydrogenase; Validated; Region: PRK06182 907240002441 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 907240002442 NADP binding site [chemical binding]; other site 907240002443 active site 907240002444 steroid binding site; other site 907240002445 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 907240002446 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041 907240002447 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 907240002448 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041 907240002449 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240002450 Hydrogenase formation hypA family; Region: HypD; cl12072 907240002451 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 907240002452 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 907240002453 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypC; COG0298 907240002454 hydrogenase accessory protein HypB; Region: hypB; TIGR00073 907240002455 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 907240002456 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 907240002457 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 907240002458 propionate/acetate kinase; Provisional; Region: PRK12379 907240002459 BioD-like N-terminal domain of phosphotransacetylase [General function prediction only]; Region: Pta; COG0857 907240002460 phosphotransacetylase; Reviewed; Region: eutD; PRK09653 907240002461 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 907240002462 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK05842 907240002463 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 907240002464 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 907240002465 flagellar hook protein FlgE; Validated; Region: flgE; PRK05841 907240002466 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 907240002467 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 907240002468 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 907240002469 S-adenosylmethionine binding site [chemical binding]; other site 907240002470 potential frameshift: common BLAST hit: gi|15611914|ref|NP_223565.1| putative ATP-dependent helicase 907240002471 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240002472 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240002473 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 907240002474 potential frameshift: common BLAST hit: gi|15611918|ref|NP_223569.1| putative IRON-regulated outer membrane protein 907240002475 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 907240002476 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 907240002477 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 907240002478 ATP-grasp domain; Region: ATP-grasp_4; cl17255 907240002479 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 907240002480 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 907240002481 ATP-grasp domain; Region: ATP-grasp_4; cl17255 907240002482 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 907240002483 IMP binding site; other site 907240002484 dimer interface [polypeptide binding]; other site 907240002485 interdomain contacts; other site 907240002486 partial ornithine binding site; other site 907240002487 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 907240002488 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 907240002489 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 907240002490 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 907240002491 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 907240002492 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907240002493 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907240002494 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 907240002495 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907240002496 Autotransporter beta-domain; Region: Autotransporter; pfam03797 907240002497 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240002498 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cd00491 907240002499 active site 1 [active] 907240002500 dimer interface [polypeptide binding]; other site 907240002501 hexamer interface [polypeptide binding]; other site 907240002502 active site 2 [active] 907240002503 recombination protein RecR; Region: recR; TIGR00615 907240002504 RecR protein; Region: RecR; pfam02132 907240002505 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 907240002506 putative active site [active] 907240002507 putative metal-binding site [ion binding]; other site 907240002508 tetramer interface [polypeptide binding]; other site 907240002509 tRNA pseudouridine synthase, TruD family; Region: tRNA_TruD_broad; TIGR00094 907240002510 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 907240002511 Permutation of conserved domain; other site 907240002512 active site 907240002513 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 907240002514 heat shock protein HtpX; Provisional; Region: PRK02870 907240002515 GTP cyclohydrolase I; Region: folE; TIGR00063 907240002516 GTP cyclohydrolase I; Provisional; Region: PLN03044 907240002517 active site 907240002518 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 907240002519 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 907240002520 substrate binding pocket [chemical binding]; other site 907240002521 chain length determination region; other site 907240002522 substrate-Mg2+ binding site; other site 907240002523 catalytic residues [active] 907240002524 aspartate-rich region 1; other site 907240002525 active site lid residues [active] 907240002526 aspartate-rich region 2; other site 907240002527 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 907240002528 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism]; Region: COG0720 907240002529 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 907240002530 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Region: rSAM_QueE_Ecoli; TIGR04322 907240002531 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 907240002532 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 907240002533 Coenzyme A binding pocket [chemical binding]; other site 907240002534 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240002535 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 907240002536 metabolite-proton symporter; Region: 2A0106; TIGR00883 907240002537 putative substrate translocation pore; other site 907240002538 Uncharacterized conserved protein [Function unknown]; Region: COG1479 907240002539 Protein of unknown function DUF262; Region: DUF262; pfam03235 907240002540 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 907240002541 dimer interface [polypeptide binding]; other site 907240002542 conserved gate region; other site 907240002543 putative PBP binding loops; other site 907240002544 ABC-ATPase subunit interface; other site 907240002545 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 907240002546 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 907240002547 substrate binding pocket [chemical binding]; other site 907240002548 membrane-bound complex binding site; other site 907240002549 hinge residues; other site 907240002550 alanine racemase; Region: alr; TIGR00492 907240002551 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 907240002552 active site 907240002553 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 907240002554 dimer interface [polypeptide binding]; other site 907240002555 substrate binding site [chemical binding]; other site 907240002556 catalytic residues [active] 907240002557 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 907240002558 amino acid carrier protein; Region: agcS; TIGR00835 907240002559 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 907240002560 Streptococcal 67 kDa myosin-cross-reactive antigen like family; Region: Strep_67kDa_ant; cl17487 907240002561 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 907240002562 homotrimer interaction site [polypeptide binding]; other site 907240002563 putative active site [active] 907240002564 potential protein location (hypothetical protein HPGAM_04885 [Helicobacter pylori Gambia94/24]) that overlaps RNA (tRNA-G) 907240002565 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 907240002566 TIGR01210 family protein; Region: TIGR01210 907240002567 Uncharacterized conserved protein [Function unknown]; Region: COG1576 907240002568 acetyl-CoA carboxylase, carboxyl transferase, beta subunit; Region: accD; TIGR00515 907240002569 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 907240002570 putative recombination protein RecO; Provisional; Region: PRK13908 907240002571 Uncharacterized protein (competence- and mitomycin-induced) [General function prediction only]; Region: CinA; COG1546 907240002572 NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family...; Region: NfsB_like_nitroreductase; cd02149 907240002573 dimer interface [polypeptide binding]; other site 907240002574 FMN binding site [chemical binding]; other site 907240002575 prolipoprotein diacylglyceryl transferase; Region: lgt; TIGR00544 907240002576 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 907240002577 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 907240002578 active site 907240002579 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 907240002580 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 907240002581 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 907240002582 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 907240002583 Putative zinc ribbon domain; Region: DUF164; pfam02591 907240002584 dinuclear metal center protein, YbgI/SA1388 family; Region: YbgI_SA1388; TIGR00486 907240002585 Uncharacterized conserved protein [Function unknown]; Region: COG0327 907240002586 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 907240002587 dimer interface [polypeptide binding]; other site 907240002588 motif 1; other site 907240002589 active site 907240002590 motif 2; other site 907240002591 motif 3; other site 907240002592 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 907240002593 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 907240002594 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 907240002595 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 907240002596 Dynamin family; Region: Dynamin_N; pfam00350 907240002597 G1 box; other site 907240002598 GTP/Mg2+ binding site [chemical binding]; other site 907240002599 G2 box; other site 907240002600 Switch I region; other site 907240002601 G3 box; other site 907240002602 Switch II region; other site 907240002603 G4 box; other site 907240002604 G5 box; other site 907240002605 potential frameshift: common BLAST hit: gi|298736077|ref|YP_003728602.1| putative tRNA modification GTPase TrmE 907240002606 Protein of unknown function (DUF3240); Region: DUF3240; pfam11582 907240002607 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 907240002608 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 907240002609 Outer membrane efflux protein; Region: OEP; pfam02321 907240002610 Outer membrane efflux protein; Region: OEP; pfam02321 907240002611 glycyl-tRNA synthetase, tetrameric type, beta subunit; Region: glyS; TIGR00211 907240002612 phosphoglyceromutase; Provisional; Region: PRK05434 907240002613 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; Region: pgm_bpd_ind; TIGR01307 907240002614 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C subunit; Region: gatC; TIGR00135 907240002615 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK05964 907240002616 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 907240002617 inhibitor-cofactor binding pocket; inhibition site 907240002618 pyridoxal 5'-phosphate binding site [chemical binding]; other site 907240002619 catalytic residue [active] 907240002620 SurA N-terminal domain; Region: SurA_N_3; cl07813 907240002621 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 907240002622 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 907240002623 cell division protein FtsA; Region: ftsA; TIGR01174 907240002624 Cell division protein FtsA; Region: FtsA; smart00842 907240002625 Cell division protein FtsA; Region: FtsA; pfam14450 907240002626 cell division protein FtsZ; Validated; Region: PRK09330 907240002627 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 907240002628 nucleotide binding site [chemical binding]; other site 907240002629 SulA interaction site; other site 907240002630 Mechanosensitive ion channel; Region: MS_channel; pfam00924 907240002631 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 907240002632 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 907240002633 AAA-like domain; Region: AAA_10; pfam12846 907240002634 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 907240002635 Topoisomerase IA [DNA replication, recombination, and repair]; Region: TopA; COG0550 907240002636 TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli...; Region: TOPRIM_TopoIA; cd01028 907240002637 active site 907240002638 interdomain interaction site; other site 907240002639 putative metal-binding site [ion binding]; other site 907240002640 nucleotide binding site [chemical binding]; other site 907240002641 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 907240002642 domain I; other site 907240002643 DNA binding groove [nucleotide binding] 907240002644 phosphate binding site [ion binding]; other site 907240002645 domain II; other site 907240002646 domain III; other site 907240002647 nucleotide binding site [chemical binding]; other site 907240002648 catalytic site [active] 907240002649 domain IV; other site 907240002650 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 907240002651 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 907240002652 VirB7 interaction site; other site 907240002653 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 907240002654 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 907240002655 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 907240002656 Walker A motif; other site 907240002657 hexamer interface [polypeptide binding]; other site 907240002658 ATP binding site [chemical binding]; other site 907240002659 Walker B motif; other site 907240002660 Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion]; Region: VirD4; COG3505 907240002661 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 907240002662 Walker A motif; other site 907240002663 ATP binding site [chemical binding]; other site 907240002664 TraM recognition site of TraD and TraG; Region: TraG-D_C; pfam12696 907240002665 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 907240002666 potential frameshift: common BLAST hit: gi|210134648|ref|YP_002301087.1| relaxase 907240002667 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 907240002668 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 907240002669 P-loop; other site 907240002670 Magnesium ion binding site [ion binding]; other site 907240002671 potential frameshift: common BLAST hit: gi|208434933|ref|YP_002266599.1| adenine specific DNA methyltransferase 907240002672 potential frameshift: common BLAST hit: gi|210134636|ref|YP_002301075.1| VirB6 type IV secretion protein 907240002673 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 907240002674 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 907240002675 active site 907240002676 catalytic residues [active] 907240002677 DNA binding site [nucleotide binding] 907240002678 Int/Topo IB signature motif; other site 907240002679 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 907240002680 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]; Region: COG1724 907240002681 Arginine decarboxylase (spermidine biosynthesis) [Amino acid transport and metabolism]; Region: SpeA; COG1166 907240002682 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 907240002683 active site 907240002684 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 907240002685 catalytic residues [active] 907240002686 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 907240002687 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 907240002688 This family is most closely related to the GT1 family of glycosyltransferases. UDP-glucose-diacylglycerol glucosyltransferase (UGDG; also known as 1,2-diacylglycerol 3-glucosyltransferase) catalyzes the transfer of glucose from UDP-glucose to 1; Region: GT1_UGDG_like; cd03817 907240002689 putative ADP-binding pocket [chemical binding]; other site 907240002690 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 907240002691 Methyltransferase domain; Region: Methyltransf_23; pfam13489 907240002692 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 907240002693 S-adenosylmethionine binding site [chemical binding]; other site 907240002694 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 907240002695 methionyl-tRNA synthetase; Reviewed; Region: PRK12267 907240002696 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 907240002697 active site 907240002698 HIGH motif; other site 907240002699 KMSKS motif; other site 907240002700 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 907240002701 anticodon binding site; other site 907240002702 tRNA binding surface [nucleotide binding]; other site 907240002703 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 907240002704 dimer interface [polypeptide binding]; other site 907240002705 putative tRNA-binding site [nucleotide binding]; other site 907240002706 Mycolic acid cyclopropane synthetase; Region: CMAS; pfam02353 907240002707 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 907240002708 S-adenosylmethionine binding site [chemical binding]; other site 907240002709 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 907240002710 Mechanosensitive ion channel; Region: MS_channel; pfam00924 907240002711 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 907240002712 GMP synthase; Reviewed; Region: guaA; PRK00074 907240002713 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 907240002714 AMP/PPi binding site [chemical binding]; other site 907240002715 candidate oxyanion hole; other site 907240002716 catalytic triad [active] 907240002717 potential glutamine specificity residues [chemical binding]; other site 907240002718 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 907240002719 ATP Binding subdomain [chemical binding]; other site 907240002720 Ligand Binding sites [chemical binding]; other site 907240002721 Dimerization subdomain; other site 907240002722 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_DMSOR-BSOR-TMAOR; cd02769 907240002723 molybdopterin guanine dinucleotide-containing S/N-oxide reductases; Region: bisC_fam; TIGR00509 907240002724 molybdopterin cofactor binding site [chemical binding]; other site 907240002725 substrate binding site [chemical binding]; other site 907240002726 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_CT_DMSOR-BSOR-TMAOR; cd02793 907240002727 molybdopterin cofactor binding site; other site 907240002728 Protein of unknown function (DUF3972); Region: DUF3972; pfam13118 907240002729 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 907240002730 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 907240002731 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 907240002732 catalytic residue [active] 907240002733 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 907240002734 nucleotide binding site/active site [active] 907240002735 HIT family signature motif; other site 907240002736 catalytic residue [active] 907240002737 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 907240002738 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 907240002739 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 907240002740 dimer interface [polypeptide binding]; other site 907240002741 motif 1; other site 907240002742 active site 907240002743 motif 2; other site 907240002744 motif 3; other site 907240002745 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 907240002746 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 907240002747 putative tRNA-binding site [nucleotide binding]; other site 907240002748 tRNA synthetase B5 domain; Region: B5; pfam03484 907240002749 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 907240002750 dimer interface [polypeptide binding]; other site 907240002751 motif 1; other site 907240002752 motif 3; other site 907240002753 motif 2; other site 907240002754 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 907240002755 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 907240002756 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 907240002757 hinge; other site 907240002758 active site 907240002759 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 907240002760 LytB protein; Region: LYTB; pfam02401 907240002761 ribosomal protein S1; Region: rpsA; TIGR00717 907240002762 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 907240002763 RNA binding site [nucleotide binding]; other site 907240002764 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 907240002765 RNA binding site [nucleotide binding]; other site 907240002766 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 907240002767 RNA binding site [nucleotide binding]; other site 907240002768 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 907240002769 RNA binding site [nucleotide binding]; other site 907240002770 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; cd00164 907240002771 RNA binding site [nucleotide binding]; other site 907240002772 D-3-phosphoglycerate dehydrogenase; Region: PGDH; TIGR01327 907240002773 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 907240002774 ligand binding site [chemical binding]; other site 907240002775 NAD binding site [chemical binding]; other site 907240002776 dimerization interface [polypeptide binding]; other site 907240002777 catalytic site [active] 907240002778 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 907240002779 putative L-serine binding site [chemical binding]; other site 907240002780 menaquinone biosynthesis decarboxylase, SCO4490 family; Region: mena_SCO4490; TIGR03701 907240002781 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 907240002782 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 907240002783 catalytic residue [active] 907240002784 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 907240002785 putative active site [active] 907240002786 putative metal binding site [ion binding]; other site 907240002787 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 907240002788 putative CheA interaction surface; other site 907240002789 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 907240002790 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 907240002791 active site 907240002792 phosphorylation site [posttranslational modification] 907240002793 intermolecular recognition site; other site 907240002794 dimerization interface [polypeptide binding]; other site 907240002795 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 907240002796 putative binding surface; other site 907240002797 active site 907240002798 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 907240002799 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 907240002800 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 907240002801 ATP binding site [chemical binding]; other site 907240002802 Mg2+ binding site [ion binding]; other site 907240002803 G-X-G motif; other site 907240002804 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 907240002805 Response regulator receiver domain; Region: Response_reg; pfam00072 907240002806 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 907240002807 active site 907240002808 phosphorylation site [posttranslational modification] 907240002809 intermolecular recognition site; other site 907240002810 dimerization interface [polypeptide binding]; other site 907240002811 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 907240002812 putative CheA interaction surface; other site 907240002813 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 907240002814 dimer interface [polypeptide binding]; other site 907240002815 catalytic triad [active] 907240002816 peroxidatic and resolving cysteines [active] 907240002817 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 907240002818 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 907240002819 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 907240002820 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 907240002821 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 907240002822 S-adenosylmethionine binding site [chemical binding]; other site 907240002823 primosome assembly protein PriA; Validated; Region: PRK05580 907240002824 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 907240002825 ATP binding site [chemical binding]; other site 907240002826 putative Mg++ binding site [ion binding]; other site 907240002827 helicase superfamily c-terminal domain; Region: HELICc; smart00490 907240002828 Sporulation related domain; Region: SPOR; pfam05036 907240002829 Peptidase family M48; Region: Peptidase_M48; pfam01435 907240002830 HemK family putative methylases; Region: hemK_fam; TIGR00536 907240002831 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 907240002832 glutamate dehydrogenase; Provisional; Region: PRK09414 907240002833 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 907240002834 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 907240002835 NAD(P) binding site [chemical binding]; other site 907240002836 Glycosyltransferase family 10 (fucosyltransferase); Region: Glyco_transf_10; pfam00852 907240002837 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 907240002838 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 907240002839 SoxW family; SoxW is a bacterial periplasmic TRX, containing a redox active CXXC motif, encoded by a genetic locus (sox operon) involved in thiosulfate oxidation. Sulfur bacteria oxidize sulfur compounds to provide reducing equivalents for carbon dioxide...; Region: SoxW; cd02951 907240002840 catalytic residues [active] 907240002841 ferrochelatase; Region: hemH; TIGR00109 907240002842 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 907240002843 C-terminal domain interface [polypeptide binding]; other site 907240002844 active site 907240002845 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 907240002846 active site 907240002847 N-terminal domain interface [polypeptide binding]; other site 907240002848 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 907240002849 RNA methyltransferase, RsmE family; Region: TIGR00046 907240002850 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240002851 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 907240002852 trimer interface [polypeptide binding]; other site 907240002853 active site 907240002854 acetyl-CoA carboxylase, biotin carboxyl carrier protein; Region: BCCP; TIGR00531 907240002855 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 907240002856 carboxyltransferase (CT) interaction site; other site 907240002857 biotinylation site [posttranslational modification]; other site 907240002858 biotin carboxylase; Validated; Region: PRK08462 907240002859 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 907240002860 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 907240002861 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 907240002862 Methyltransferase domain; Region: Methyltransf_26; pfam13659 907240002863 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 907240002864 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 907240002865 inhibitor-cofactor binding pocket; inhibition site 907240002866 pyridoxal 5'-phosphate binding site [chemical binding]; other site 907240002867 catalytic residue [active] 907240002868 potential protein location (hypothetical protein HPGAM_05600 [Helicobacter pylori Gambia94/24]) that overlaps RNA (tRNA-L) 907240002869 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 907240002870 dimer interface [polypeptide binding]; other site 907240002871 putative radical transfer pathway; other site 907240002872 diiron center [ion binding]; other site 907240002873 tyrosyl radical; other site 907240002874 protein-L-isoaspartate(D-aspartate) O-methyltransferase; Region: pimt; TIGR00080 907240002875 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 907240002876 S-adenosylmethionine binding site [chemical binding]; other site 907240002877 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 907240002878 Predicted permeases [General function prediction only]; Region: COG0795 907240002879 tRNA pseudouridine(38-40) synthase; Region: hisT_truA; TIGR00071 907240002880 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 907240002881 dimerization interface 3.5A [polypeptide binding]; other site 907240002882 active site 907240002883 UDP-glucose-4-epimerase GalE; Region: galE; TIGR01179 907240002884 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 907240002885 NAD binding site [chemical binding]; other site 907240002886 homodimer interface [polypeptide binding]; other site 907240002887 active site 907240002888 substrate binding site [chemical binding]; other site 907240002889 potential protein location (hypothetical protein HPGAM_05630 [Helicobacter pylori Gambia94/24]) that overlaps RNA (tRNA-I) 907240002890 classical (c) SDR, subgroup 5; Region: SDR_c5; cd05346 907240002891 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 907240002892 putative NAD(P) binding site [chemical binding]; other site 907240002893 homodimer interface [polypeptide binding]; other site 907240002894 homotetramer interface [polypeptide binding]; other site 907240002895 active site 907240002896 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 907240002897 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 907240002898 binding surface 907240002899 TPR motif; other site 907240002900 Sel1-like repeats; Region: SEL1; smart00671 907240002901 Sel1-like repeats; Region: SEL1; smart00671 907240002902 Sel1-like repeats; Region: SEL1; smart00671 907240002903 Entner-Doudoroff aldolase; Region: eda; TIGR01182 907240002904 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 907240002905 active site 907240002906 intersubunit interface [polypeptide binding]; other site 907240002907 catalytic residue [active] 907240002908 phosphogluconate dehydratase; Validated; Region: PRK09054 907240002909 6-phosphogluconate dehydratase; Region: edd; TIGR01196 907240002910 Glucose-6-phosphate 1-dehydrogenase [Carbohydrate transport and metabolism]; Region: Zwf; COG0364 907240002911 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 907240002912 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 907240002913 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 907240002914 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 907240002915 putative active site [active] 907240002916 glucokinase, proteobacterial type; Region: glk; TIGR00749 907240002917 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 907240002918 nucleotide binding site [chemical binding]; other site 907240002919 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 907240002920 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 907240002921 putative NAD(P) binding site [chemical binding]; other site 907240002922 putative substrate binding site [chemical binding]; other site 907240002923 catalytic Zn binding site [ion binding]; other site 907240002924 structural Zn binding site [ion binding]; other site 907240002925 dimer interface [polypeptide binding]; other site 907240002926 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 907240002927 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 907240002928 active site 907240002929 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 907240002930 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 907240002931 active site 907240002932 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240002933 pyruvate flavodoxin oxidoreductase subunit gamma; Validated; Region: PRK05844 907240002934 pyruvate/ketoisovalerate ferredoxin oxidoreductase subunit gamma; Provisional; Region: PRK14029 907240002935 pyruvate flavodoxin oxidoreductase subunit delta; Reviewed; Region: porD; PRK09625 907240002936 4Fe-4S binding domain; Region: Fer4; pfam00037 907240002937 pyruvate flavodoxin oxidoreductase subunit alpha; Reviewed; Region: porA; PRK09622 907240002938 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 907240002939 dimer interface [polypeptide binding]; other site 907240002940 PYR/PP interface [polypeptide binding]; other site 907240002941 TPP binding site [chemical binding]; other site 907240002942 substrate binding site [chemical binding]; other site 907240002943 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 907240002944 pyruvate ferredoxin oxidoreductase subunit beta; Provisional; Region: PRK11865 907240002945 Thiamine pyrophosphate (TPP family), PFOR porB-like subfamily, TPP-binding module; composed of proteins similar to the beta subunit (porB) of the Helicobacter pylori four-subunit pyruvate ferredoxin oxidoreductase (PFOR), which are also found in archaea...; Region: TPP_PFOR_porB_like; cd03376 907240002946 TPP-binding site [chemical binding]; other site 907240002947 putative dimer interface [polypeptide binding]; other site 907240002948 adenylosuccinate lyase; Provisional; Region: PRK08470 907240002949 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 907240002950 tetramer interface [polypeptide binding]; other site 907240002951 active site 907240002952 Adenylosuccinate lyase C-terminus; Region: ADSL_C; smart00998 907240002953 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240002954 excinuclease ABC subunit B; Provisional; Region: PRK05298 907240002955 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 907240002956 ATP binding site [chemical binding]; other site 907240002957 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 907240002958 putative Mg++ binding site [ion binding]; other site 907240002959 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 907240002960 nucleotide binding region [chemical binding]; other site 907240002961 ATP-binding site [chemical binding]; other site 907240002962 Ultra-violet resistance protein B; Region: UvrB; pfam12344 907240002963 UvrB/uvrC motif; Region: UVR; pfam02151 907240002964 DNA recombination protein RmuC; Provisional; Region: PRK10361 907240002965 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 907240002966 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 907240002967 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 907240002968 binding surface 907240002969 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 907240002970 TPR motif; other site 907240002971 Sel1-like repeats; Region: SEL1; smart00671 907240002972 Sel1-like repeats; Region: SEL1; smart00671 907240002973 Sel1-like repeats; Region: SEL1; smart00671 907240002974 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 907240002975 gamma-glutamyltranspeptidase; Region: g_glut_trans; TIGR00066 907240002976 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK08471 907240002977 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 907240002978 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 907240002979 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 907240002980 cofactor binding site; other site 907240002981 DNA binding site [nucleotide binding] 907240002982 substrate interaction site [chemical binding]; other site 907240002983 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 907240002984 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 907240002985 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 907240002986 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 907240002987 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 907240002988 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 907240002989 ligand binding site [chemical binding]; other site 907240002990 translocation protein TolB; Provisional; Region: tolB; PRK04043 907240002991 TolB amino-terminal domain; Region: TolB_N; pfam04052 907240002992 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 907240002993 TonB C terminal; Region: TonB_2; pfam13103 907240002994 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 907240002995 TolR protein; Region: tolR; TIGR02801 907240002996 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 907240002997 ATP synthase, F1 epsilon subunit (delta in mitochondria); Region: ATP_synt_epsi; TIGR01216 907240002998 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 907240002999 gamma subunit interface [polypeptide binding]; other site 907240003000 epsilon subunit interface [polypeptide binding]; other site 907240003001 LBP interface [polypeptide binding]; other site 907240003002 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 907240003003 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 907240003004 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 907240003005 alpha subunit interaction interface [polypeptide binding]; other site 907240003006 Walker A motif; other site 907240003007 ATP binding site [chemical binding]; other site 907240003008 Walker B motif; other site 907240003009 inhibitor binding site; inhibition site 907240003010 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 907240003011 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 907240003012 core domain interface [polypeptide binding]; other site 907240003013 delta subunit interface [polypeptide binding]; other site 907240003014 epsilon subunit interface [polypeptide binding]; other site 907240003015 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 907240003016 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 907240003017 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 907240003018 beta subunit interaction interface [polypeptide binding]; other site 907240003019 Walker A motif; other site 907240003020 ATP binding site [chemical binding]; other site 907240003021 Walker B motif; other site 907240003022 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 907240003023 F0F1 ATP synthase subunit delta; Provisional; Region: PRK13431 907240003024 F0F1 ATP synthase subunit B; Validated; Region: PRK08475 907240003025 F0F1 ATP synthase subunit B'; Validated; Region: PRK08476 907240003026 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 907240003027 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 907240003028 ParB-like nuclease domain; Region: ParB; smart00470 907240003029 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 907240003030 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 907240003031 P-loop; other site 907240003032 Magnesium ion binding site [ion binding]; other site 907240003033 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 907240003034 Magnesium ion binding site [ion binding]; other site 907240003035 biotin--protein ligase; Provisional; Region: PRK08477 907240003036 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 907240003037 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 907240003038 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 907240003039 putative active site [active] 907240003040 substrate binding site [chemical binding]; other site 907240003041 putative cosubstrate binding site; other site 907240003042 catalytic site [active] 907240003043 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 907240003044 substrate binding site [chemical binding]; other site 907240003045 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4694 907240003046 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4487 907240003047 Uncharacterized protein conserved in bacteria (DUF2130); Region: DUF2130; pfam09903 907240003048 LabA_like proteins; Region: LabA_like; cd06167 907240003049 putative metal binding site [ion binding]; other site 907240003050 Uncharacterized conserved protein [Function unknown]; Region: COG1432 907240003051 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 907240003052 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 907240003053 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK14593 907240003054 RimM N-terminal domain; Region: RimM; pfam01782 907240003055 PRC-barrel domain; Region: PRC; pfam05239 907240003056 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837 907240003057 KH domain; Region: KH_4; pfam13083 907240003058 G-X-X-G motif; other site 907240003059 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 907240003060 signal recognition particle protein; Provisional; Region: PRK10867 907240003061 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 907240003062 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 907240003063 P loop; other site 907240003064 GTP binding site [chemical binding]; other site 907240003065 Signal peptide binding domain; Region: SRP_SPB; pfam02978 907240003066 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 907240003067 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 907240003068 active site 907240003069 HIGH motif; other site 907240003070 nucleotide binding site [chemical binding]; other site 907240003071 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 907240003072 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 907240003073 active site 907240003074 KMSKS motif; other site 907240003075 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 907240003076 anticodon binding site; other site 907240003077 flagellar assembly protein FliW; Provisional; Region: PRK13283 907240003078 undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase; Region: murG; TIGR01133 907240003079 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 907240003080 active site 907240003081 homodimer interface [polypeptide binding]; other site 907240003082 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240003083 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240003084 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 907240003085 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 907240003086 potential frameshift: common BLAST hit: gi|15612151|ref|NP_223803.1| putative cAMP-induced cell filamentation protein 907240003087 metal-binding heat shock protein; Provisional; Region: PRK00016 907240003088 flavodoxin FldA; Validated; Region: PRK09267 907240003089 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 907240003090 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 907240003091 Uncharacterized protein, possibly involved in nitrogen fixation [Inorganic ion transport and metabolism]; Region: FixS; COG3197 907240003092 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 907240003093 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 907240003094 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 907240003095 Major Facilitator Superfamily; Region: MFS_1; pfam07690 907240003096 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 907240003097 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 907240003098 active site 907240003099 dimer interface [polypeptide binding]; other site 907240003100 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 907240003101 dimer interface [polypeptide binding]; other site 907240003102 active site 907240003103 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 907240003104 carbon starvation protein A; Provisional; Region: PRK15015 907240003105 Carbon starvation protein CstA; Region: CstA; pfam02554 907240003106 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 907240003107 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 907240003108 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 907240003109 dimer interface [polypeptide binding]; other site 907240003110 conserved gate region; other site 907240003111 putative PBP binding loops; other site 907240003112 ABC-ATPase subunit interface; other site 907240003113 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 907240003114 dimer interface [polypeptide binding]; other site 907240003115 conserved gate region; other site 907240003116 putative PBP binding loops; other site 907240003117 ABC-ATPase subunit interface; other site 907240003118 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 907240003119 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 907240003120 Walker A/P-loop; other site 907240003121 ATP binding site [chemical binding]; other site 907240003122 Q-loop/lid; other site 907240003123 ABC transporter signature motif; other site 907240003124 Walker B; other site 907240003125 D-loop; other site 907240003126 H-loop/switch region; other site 907240003127 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 907240003128 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 907240003129 substrate binding pocket [chemical binding]; other site 907240003130 membrane-bound complex binding site; other site 907240003131 hinge residues; other site 907240003132 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 907240003133 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 907240003134 putative substrate translocation pore; other site 907240003135 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 907240003136 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240003137 purine-nucleoside phosphorylase, family 1 (deoD); Region: deoD; TIGR00107 907240003138 phosphopentomutase; Provisional; Region: PRK05362 907240003139 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 907240003140 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 907240003141 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 907240003142 Nucleoside recognition; Region: Gate; pfam07670 907240003143 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 907240003144 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 907240003145 Major Facilitator Superfamily; Region: MFS_1; pfam07690 907240003146 putative substrate translocation pore; other site 907240003147 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 907240003148 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 907240003149 Ligand Binding Site [chemical binding]; other site 907240003150 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 907240003151 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 907240003152 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 907240003153 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 907240003154 putative arabinose transporter; Provisional; Region: PRK03545 907240003155 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 907240003156 putative substrate translocation pore; other site 907240003157 Carbonic anhydrase [Inorganic ion transport and metabolism]; Region: Cah; COG3338 907240003158 Carbonic anhydrase alpha, prokaryotic-like subfamily. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon...; Region: alpha_CA_prokaryotic_like; cd03124 907240003159 active site 907240003160 zinc binding site [ion binding]; other site 907240003161 Helicobacter pylori protein of unknown function (DUF874); Region: DUF874; pfam05917 907240003162 aspartate-semialdehyde dehydrogenase (peptidoglycan organisms); Region: asd_B; TIGR01296 907240003163 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 907240003164 Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: HisS; COG0124 907240003165 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 907240003166 dimer interface [polypeptide binding]; other site 907240003167 motif 1; other site 907240003168 active site 907240003169 motif 2; other site 907240003170 motif 3; other site 907240003171 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 907240003172 anticodon binding site; other site 907240003173 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 907240003174 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 907240003175 putative active site [active] 907240003176 elongation factor G; Reviewed; Region: PRK00007 907240003177 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 907240003178 G1 box; other site 907240003179 putative GEF interaction site [polypeptide binding]; other site 907240003180 GTP/Mg2+ binding site [chemical binding]; other site 907240003181 Switch I region; other site 907240003182 G2 box; other site 907240003183 G3 box; other site 907240003184 Switch II region; other site 907240003185 G4 box; other site 907240003186 G5 box; other site 907240003187 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 907240003188 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 907240003189 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 907240003190 30S ribosomal protein S7; Validated; Region: PRK05302 907240003191 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 907240003192 S17 interaction site [polypeptide binding]; other site 907240003193 S8 interaction site; other site 907240003194 16S rRNA interaction site [nucleotide binding]; other site 907240003195 streptomycin interaction site [chemical binding]; other site 907240003196 23S rRNA interaction site [nucleotide binding]; other site 907240003197 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 907240003198 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 907240003199 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 907240003200 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 907240003201 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 907240003202 RPB11 interaction site [polypeptide binding]; other site 907240003203 RPB12 interaction site [polypeptide binding]; other site 907240003204 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 907240003205 RPB3 interaction site [polypeptide binding]; other site 907240003206 RPB1 interaction site [polypeptide binding]; other site 907240003207 RPB11 interaction site [polypeptide binding]; other site 907240003208 RPB10 interaction site [polypeptide binding]; other site 907240003209 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 907240003210 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 907240003211 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 907240003212 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 907240003213 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 907240003214 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 907240003215 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 907240003216 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 907240003217 DNA binding site [nucleotide binding] 907240003218 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 907240003219 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 907240003220 core dimer interface [polypeptide binding]; other site 907240003221 peripheral dimer interface [polypeptide binding]; other site 907240003222 L10 interface [polypeptide binding]; other site 907240003223 L11 interface [polypeptide binding]; other site 907240003224 putative EF-Tu interaction site [polypeptide binding]; other site 907240003225 putative EF-G interaction site [polypeptide binding]; other site 907240003226 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 907240003227 23S rRNA interface [nucleotide binding]; other site 907240003228 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 907240003229 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 907240003230 mRNA/rRNA interface [nucleotide binding]; other site 907240003231 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 907240003232 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 907240003233 23S rRNA interface [nucleotide binding]; other site 907240003234 L7/L12 interface [polypeptide binding]; other site 907240003235 putative thiostrepton binding site; other site 907240003236 L25 interface [polypeptide binding]; other site 907240003237 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 907240003238 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 907240003239 putative homodimer interface [polypeptide binding]; other site 907240003240 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 907240003241 heterodimer interface [polypeptide binding]; other site 907240003242 homodimer interface [polypeptide binding]; other site 907240003243 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 907240003244 elongation factor Tu; Reviewed; Region: PRK00049 907240003245 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 907240003246 G1 box; other site 907240003247 GEF interaction site [polypeptide binding]; other site 907240003248 GTP/Mg2+ binding site [chemical binding]; other site 907240003249 Switch I region; other site 907240003250 G2 box; other site 907240003251 G3 box; other site 907240003252 Switch II region; other site 907240003253 G4 box; other site 907240003254 G5 box; other site 907240003255 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 907240003256 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 907240003257 Antibiotic Binding Site [chemical binding]; other site 907240003258 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 907240003259 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 907240003260 Walker A/P-loop; other site 907240003261 ATP binding site [chemical binding]; other site 907240003262 Q-loop/lid; other site 907240003263 ABC transporter signature motif; other site 907240003264 Walker B; other site 907240003265 D-loop; other site 907240003266 H-loop/switch region; other site 907240003267 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 907240003268 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 907240003269 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG3392 907240003270 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; pfam02086 907240003271 Helicobacter pylori IceA2 protein; Region: IceA2; pfam05862 907240003272 serine O-acetyltransferase; Region: cysE; TIGR01172 907240003273 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 907240003274 trimer interface [polypeptide binding]; other site 907240003275 active site 907240003276 substrate binding site [chemical binding]; other site 907240003277 CoA binding site [chemical binding]; other site 907240003278 F0F1 ATP synthase subunit C; Validated; Region: PRK08482 907240003279 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 907240003280 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 907240003281 oligomer interface [polypeptide binding]; other site 907240003282 RNA binding site [nucleotide binding]; other site 907240003283 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 907240003284 oligomer interface [polypeptide binding]; other site 907240003285 RNA binding site [nucleotide binding]; other site 907240003286 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 907240003287 putative nucleic acid binding region [nucleotide binding]; other site 907240003288 G-X-X-G motif; other site 907240003289 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 907240003290 RNA binding site [nucleotide binding]; other site 907240003291 Predicted phosphoribosyltransferases [General function prediction only]; Region: COG1926 907240003292 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 907240003293 Organic solvent tolerance protein; Region: OstA_C; pfam04453 907240003294 Predicted membrane protein/domain [Function unknown]; Region: COG1714 907240003295 phosphoribosylamine--glycine ligase; Region: purD; TIGR00877 907240003296 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 907240003297 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 907240003298 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 907240003299 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 907240003300 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 907240003301 Walker A/P-loop; other site 907240003302 ATP binding site [chemical binding]; other site 907240003303 Q-loop/lid; other site 907240003304 ABC transporter signature motif; other site 907240003305 Walker B; other site 907240003306 D-loop; other site 907240003307 H-loop/switch region; other site 907240003308 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cd00475 907240003309 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 907240003310 catalytic residue [active] 907240003311 putative FPP diphosphate binding site; other site 907240003312 putative FPP binding hydrophobic cleft; other site 907240003313 dimer interface [polypeptide binding]; other site 907240003314 putative IPP diphosphate binding site; other site 907240003315 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 907240003316 FAD binding domain; Region: FAD_binding_4; pfam01565 907240003317 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 907240003318 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 907240003319 active site residue [active] 907240003320 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 907240003321 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 907240003322 active site 907240003323 camphor resistance protein CrcB; Provisional; Region: PRK14204 907240003324 coproporphyrinogen III oxidase; Provisional; Region: PRK08446 907240003325 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 907240003326 FeS/SAM binding site; other site 907240003327 HemN C-terminal domain; Region: HemN_C; pfam06969 907240003328 Cytochrome c553 [Energy production and conversion]; Region: COG2863 907240003329 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 907240003330 putative active site [active] 907240003331 Ap4A binding site [chemical binding]; other site 907240003332 nudix motif; other site 907240003333 putative metal binding site [ion binding]; other site 907240003334 aspartate kinase; Reviewed; Region: PRK06635 907240003335 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 907240003336 putative nucleotide binding site [chemical binding]; other site 907240003337 putative catalytic residues [active] 907240003338 putative Mg ion binding site [ion binding]; other site 907240003339 putative aspartate binding site [chemical binding]; other site 907240003340 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 907240003341 putative allosteric regulatory site; other site 907240003342 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 907240003343 putative allosteric regulatory residue; other site 907240003344 DNA replication regulator; Region: HobA; pfam12163 907240003345 DNA polymerase III subunit delta'; Validated; Region: PRK08485 907240003346 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 907240003347 dihydropteroate synthase; Region: DHPS; TIGR01496 907240003348 substrate binding pocket [chemical binding]; other site 907240003349 dimer interface [polypeptide binding]; other site 907240003350 inhibitor binding site; inhibition site 907240003351 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 907240003352 EamA-like transporter family; Region: EamA; pfam00892 907240003353 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 907240003354 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2952 907240003355 Carbamoylphosphate synthase small subunit [Amino acid transport and metabolism / Nucleotide transport and metabolism]; Region: CarA; COG0505 907240003356 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; pfam00988 907240003357 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 907240003358 catalytic site [active] 907240003359 subunit interface [polypeptide binding]; other site 907240003360 formamidase; Provisional; Region: amiF; PRK13287 907240003361 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 907240003362 multimer interface [polypeptide binding]; other site 907240003363 active site 907240003364 catalytic triad [active] 907240003365 dimer interface [polypeptide binding]; other site 907240003366 Maf-like protein; Region: Maf; pfam02545 907240003367 Maf-like protein; Reviewed; Region: PRK04056 907240003368 putative active site [active] 907240003369 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 907240003370 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 907240003371 motif 1; other site 907240003372 active site 907240003373 motif 2; other site 907240003374 motif 3; other site 907240003375 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 907240003376 DHHA1 domain; Region: DHHA1; pfam02272 907240003377 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2841 907240003378 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240003379 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 907240003380 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 907240003381 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 907240003382 dimer interface [polypeptide binding]; other site 907240003383 ssDNA binding site [nucleotide binding]; other site 907240003384 tetramer (dimer of dimers) interface [polypeptide binding]; other site 907240003385 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 907240003386 DNA polymerase III subunit delta; Validated; Region: PRK08487 907240003387 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 907240003388 Exoribonuclease R [Transcription]; Region: VacB; COG0557 907240003389 RNB domain; Region: RNB; pfam00773 907240003390 shikimate 5-dehydrogenase; Region: aroE; TIGR00507 907240003391 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 907240003392 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 907240003393 shikimate binding site; other site 907240003394 NAD(P) binding site [chemical binding]; other site 907240003395 Bacterial SH3 domain; Region: SH3_3; pfam08239 907240003396 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 907240003397 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 907240003398 dimer interface [polypeptide binding]; other site 907240003399 conserved gate region; other site 907240003400 putative PBP binding loops; other site 907240003401 ABC-ATPase subunit interface; other site 907240003402 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 907240003403 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_14; cd08497 907240003404 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 907240003405 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 907240003406 active site 907240003407 HIGH motif; other site 907240003408 dimer interface [polypeptide binding]; other site 907240003409 KMSKS motif; other site 907240003410 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 907240003411 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 907240003412 S-adenosylmethionine binding site [chemical binding]; other site 907240003413 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 907240003414 ribosome recycling factor; Reviewed; Region: frr; PRK00083 907240003415 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 907240003416 hinge region; other site 907240003417 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 907240003418 active site 907240003419 RDD family; Region: RDD; pfam06271 907240003420 NAD-dependent protein deacetylases, SIR2 family [Transcription]; Region: SIR2; COG0846 907240003421 SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which...; Region: SIRT5_Af1_CobB; cd01412 907240003422 NAD+ binding site [chemical binding]; other site 907240003423 substrate binding site [chemical binding]; other site 907240003424 Zn binding site [ion binding]; other site 907240003425 NADH dehydrogenase subunit A; Validated; Region: PRK08489 907240003426 NADH dehydrogenase subunit B; Validated; Region: PRK06411 907240003427 NADH dehydrogenase subunit C; Provisional; Region: PRK08491 907240003428 NADH dehydrogenase subunit C; Provisional; Region: PRK08491 907240003429 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 907240003430 NADH dehydrogenase subunit D; Validated; Region: PRK06075 907240003431 NADH dehydrogenase I, D subunit; Region: NuoD; TIGR01962 907240003432 NADH dehydrogenase subunit G; Validated; Region: PRK08493 907240003433 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 907240003434 catalytic loop [active] 907240003435 iron binding site [ion binding]; other site 907240003436 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 907240003437 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 907240003438 molybdopterin cofactor binding site; other site 907240003439 Domain of unknown function (DUF4350); Region: DUF4350; pfam14258 907240003440 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 907240003441 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 907240003442 NADH-quinone oxidoreductase, chain I; Region: NuoI; TIGR01971 907240003443 4Fe-4S binding domain; Region: Fer4; cl02805 907240003444 4Fe-4S binding domain; Region: Fer4; pfam00037 907240003445 NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion]; Region: NuoJ; COG0839 907240003446 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 907240003447 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 907240003448 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 907240003449 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 907240003450 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 907240003451 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 907240003452 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 907240003453 proton-translocating NADH-quinone oxidoreductase, chain N; Region: NDH_I_N; TIGR01770 907240003454 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 907240003455 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 907240003456 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 907240003457 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 907240003458 active site 907240003459 substrate binding site [chemical binding]; other site 907240003460 metal binding site [ion binding]; metal-binding site 907240003461 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 907240003462 substrate binding site [chemical binding]; other site 907240003463 active site 907240003464 catalytic residues [active] 907240003465 heterodimer interface [polypeptide binding]; other site 907240003466 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 907240003467 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 907240003468 pyridoxal 5'-phosphate binding site [chemical binding]; other site 907240003469 catalytic residue [active] 907240003470 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional; Region: PRK09427 907240003471 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 907240003472 active site 907240003473 ribulose/triose binding site [chemical binding]; other site 907240003474 phosphate binding site [ion binding]; other site 907240003475 substrate (anthranilate) binding pocket [chemical binding]; other site 907240003476 product (indole) binding pocket [chemical binding]; other site 907240003477 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 907240003478 active site 907240003479 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 907240003480 anthranilate phosphoribosyltransferase; Region: trpD; TIGR01245 907240003481 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 907240003482 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 907240003483 Glutamine amidotransferase class-I; Region: GATase; pfam00117 907240003484 glutamine binding [chemical binding]; other site 907240003485 catalytic triad [active] 907240003486 anthranilate synthase component I; Provisional; Region: PRK13564 907240003487 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 907240003488 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 907240003489 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 907240003490 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 907240003491 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 907240003492 active site 907240003493 motif I; other site 907240003494 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 907240003495 motif II; other site 907240003496 Uncharacterized conserved protein [Function unknown]; Region: COG2353 907240003497 thiaminase II; Region: salvage_TenA; TIGR04306 907240003498 Nicotinamide mononucleotide transporter [Coenzyme metabolism]; Region: PnuC; COG3201 907240003499 Thiamine pyrophosphokinase [Coenzyme metabolism]; Region: THI80; COG1564 907240003500 Thiamine pyrophosphokinase; Region: TPK; cd07995 907240003501 active site 907240003502 dimerization interface [polypeptide binding]; other site 907240003503 thiamine binding site [chemical binding]; other site 907240003504 Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]; Region: RplQ; COG0203 907240003505 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 907240003506 alphaNTD homodimer interface [polypeptide binding]; other site 907240003507 DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type; Region: rpoA; TIGR02027 907240003508 alphaNTD - beta interaction site [polypeptide binding]; other site 907240003509 alphaNTD - beta' interaction site [polypeptide binding]; other site 907240003510 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 907240003511 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 907240003512 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 907240003513 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 907240003514 RNA binding surface [nucleotide binding]; other site 907240003515 30S ribosomal protein S11; Validated; Region: PRK05309 907240003516 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 907240003517 30S ribosomal protein S13; Region: bact_S13; TIGR03631 907240003518 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 907240003519 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 907240003520 rRNA binding site [nucleotide binding]; other site 907240003521 predicted 30S ribosome binding site; other site 907240003522 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 907240003523 active site 907240003524 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 907240003525 SecY translocase; Region: SecY; pfam00344 907240003526 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 907240003527 ribosomal protein S5, bacterial/organelle type; Region: rpsE_bact; TIGR01021 907240003528 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 907240003529 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 907240003530 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 907240003531 23S rRNA interface [nucleotide binding]; other site 907240003532 5S rRNA interface [nucleotide binding]; other site 907240003533 L27 interface [polypeptide binding]; other site 907240003534 L5 interface [polypeptide binding]; other site 907240003535 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 907240003536 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 907240003537 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 907240003538 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08061 907240003539 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 907240003540 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 907240003541 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 907240003542 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 907240003543 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 907240003544 RNA binding site [nucleotide binding]; other site 907240003545 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 907240003546 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 907240003547 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 907240003548 putative translocon interaction site; other site 907240003549 23S rRNA interface [nucleotide binding]; other site 907240003550 signal recognition particle (SRP54) interaction site; other site 907240003551 L23 interface [polypeptide binding]; other site 907240003552 trigger factor interaction site; other site 907240003553 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 907240003554 23S rRNA interface [nucleotide binding]; other site 907240003555 5S rRNA interface [nucleotide binding]; other site 907240003556 putative antibiotic binding site [chemical binding]; other site 907240003557 L25 interface [polypeptide binding]; other site 907240003558 L27 interface [polypeptide binding]; other site 907240003559 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 907240003560 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 907240003561 G-X-X-G motif; other site 907240003562 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 907240003563 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 907240003564 putative translocon binding site; other site 907240003565 protein-rRNA interface [nucleotide binding]; other site 907240003566 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 907240003567 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 907240003568 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 907240003569 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 907240003570 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 907240003571 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 907240003572 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 907240003573 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 907240003574 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 907240003575 AAA domain; Region: AAA_14; pfam13173 907240003576 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 907240003577 RNA/DNA hybrid binding site [nucleotide binding]; other site 907240003578 active site 907240003579 fumarate hydratase; Reviewed; Region: fumC; PRK00485 907240003580 Class II fumarases; Region: Fumarase_classII; cd01362 907240003581 active site 907240003582 tetramer interface [polypeptide binding]; other site 907240003583 YtkA-like; Region: YtkA; pfam13115 907240003584 Outer membrane efflux protein; Region: OEP; pfam02321 907240003585 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 907240003586 HlyD family secretion protein; Region: HlyD_3; pfam13437 907240003587 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 907240003588 Predicted branched-chain amino acid permeases (azaleucine resistance) [Amino acid transport and metabolism]; Region: AzlD; COG1687 907240003589 AzlC protein; Region: AzlC; cl00570 907240003590 chaperone protein DnaJ; Provisional; Region: PRK14288 907240003591 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 907240003592 HSP70 interaction site [polypeptide binding]; other site 907240003593 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 907240003594 substrate binding site [polypeptide binding]; other site 907240003595 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 907240003596 Zn binding sites [ion binding]; other site 907240003597 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 907240003598 dimer interface [polypeptide binding]; other site 907240003599 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 907240003600 tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase; Region: trmU; TIGR00420 907240003601 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 907240003602 Ligand Binding Site [chemical binding]; other site 907240003603 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 907240003604 HSP70 interaction site [polypeptide binding]; other site 907240003605 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 907240003606 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 907240003607 active site 907240003608 (T/H)XGH motif; other site 907240003609 nickel responsive regulator; Provisional; Region: PRK00630 907240003610 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 907240003611 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 907240003612 tonB-system energizer ExbB, group 2; Region: exbB2; TIGR02805 907240003613 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 907240003614 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 907240003615 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 907240003616 TonB family C-terminal domain; Region: tonB_Cterm; TIGR01352 907240003617 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240003618 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 907240003619 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 907240003620 Mg2+ transporter Helicobacter pylori CorA-like subgroup; Region: HpCorA-like; cd12836 907240003621 Cl binding site [ion binding]; other site 907240003622 oligomer interface [polypeptide binding]; other site 907240003623 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 907240003624 Phosphoglycerate kinase; Region: PGK; pfam00162 907240003625 substrate binding site [chemical binding]; other site 907240003626 hinge regions; other site 907240003627 ADP binding site [chemical binding]; other site 907240003628 catalytic site [active] 907240003629 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 907240003630 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 907240003631 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 907240003632 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 907240003633 ligand binding site [chemical binding]; other site 907240003634 active site 907240003635 UGI interface [polypeptide binding]; other site 907240003636 catalytic site [active] 907240003637 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 907240003638 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 907240003639 putative acyl-acceptor binding pocket; other site 907240003640 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 907240003641 C-terminal peptidase (prc); Region: prc; TIGR00225 907240003642 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 907240003643 protein binding site [polypeptide binding]; other site 907240003644 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 907240003645 Catalytic dyad [active] 907240003646 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 907240003647 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 907240003648 DNA methylase; Region: N6_N4_Mtase; pfam01555 907240003649 potential frameshift: common BLAST hit: gi|108563726|ref|YP_628042.1| adenine specific DNA methyltransferase 907240003650 Predicted helicase [General function prediction only]; Region: COG4889 907240003651 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK05848 907240003652 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 907240003653 dimerization interface [polypeptide binding]; other site 907240003654 active site 907240003655 Quinolinate synthetase A protein; Region: NadA; cl00420 907240003656 phosphatidylserine decarboxylase; Provisional; Region: PRK03934 907240003657 prenyltransferase; Reviewed; Region: ubiA; PRK12874 907240003658 UbiA prenyltransferase family; Region: UbiA; pfam01040 907240003659 Predicted membrane metal-binding protein [General function prediction only]; Region: ComEC; COG0658 907240003660 Competence protein; Region: Competence; pfam03772 907240003661 replicative DNA helicase; Provisional; Region: PRK08506 907240003662 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 907240003663 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 907240003664 Walker A motif; other site 907240003665 ATP binding site [chemical binding]; other site 907240003666 Walker B motif; other site 907240003667 DNA binding loops [nucleotide binding] 907240003668 yjeF N-terminal region; Region: yjeF_nterm; TIGR00197 907240003669 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 907240003670 putative substrate binding site [chemical binding]; other site 907240003671 putative ATP binding site [chemical binding]; other site 907240003672 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 907240003673 His Kinase A (phospho-acceptor) domain; Region: HisKA; pfam00512 907240003674 dimer interface [polypeptide binding]; other site 907240003675 phosphorylation site [posttranslational modification] 907240003676 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 907240003677 ATP binding site [chemical binding]; other site 907240003678 Mg2+ binding site [ion binding]; other site 907240003679 G-X-G motif; other site 907240003680 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 907240003681 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 907240003682 active site 907240003683 phosphorylation site [posttranslational modification] 907240003684 intermolecular recognition site; other site 907240003685 dimerization interface [polypeptide binding]; other site 907240003686 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 907240003687 DNA binding site [nucleotide binding] 907240003688 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 907240003689 DNA methylase; Region: N6_N4_Mtase; pfam01555 907240003690 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 907240003691 DNA methylase; Region: N6_N4_Mtase; pfam01555 907240003692 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 907240003693 DNA methylase; Region: N6_N4_Mtase; pfam01555 907240003694 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 907240003695 DNA methylase; Region: N6_N4_Mtase; pfam01555 907240003696 DEAD-like helicases superfamily; Region: DEXDc; smart00487 907240003697 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 907240003698 rod shape-determining protein MreC; Region: MreC; pfam04085 907240003699 rod shape-determining protein MreB; Provisional; Region: PRK13927 907240003700 MreB and similar proteins; Region: MreB_like; cd10225 907240003701 nucleotide binding site [chemical binding]; other site 907240003702 Mg binding site [ion binding]; other site 907240003703 putative protofilament interaction site [polypeptide binding]; other site 907240003704 RodZ interaction site [polypeptide binding]; other site 907240003705 endopeptidase Clp ATP-binding regulatory subunit (clpX); Region: clpX; TIGR00382 907240003706 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 907240003707 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 907240003708 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 907240003709 Walker A motif; other site 907240003710 ATP binding site [chemical binding]; other site 907240003711 Walker B motif; other site 907240003712 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 907240003713 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 907240003714 acyl-[acyl-carrier-protein]--UDP-N- acetylglucosamine O-acyltransferase; Region: lipid_A_lpxA; TIGR01852 907240003715 active site 907240003716 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 907240003717 flagellar assembly protein FliW; Provisional; Region: PRK13282 907240003718 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 907240003719 ATP-dependent protease La; Region: lon; TIGR00763 907240003720 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 907240003721 Walker A motif; other site 907240003722 ATP binding site [chemical binding]; other site 907240003723 Walker B motif; other site 907240003724 arginine finger; other site 907240003725 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 907240003726 prephenate dehydrogenase; Validated; Region: PRK08507 907240003727 Prephenate dehydrogenase; Region: PDH; pfam02153 907240003728 DNA/RNA endonuclease G, NUC1 [Nucleotide transport and metabolism]; Region: NUC1; COG1864 907240003729 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 907240003730 active site 907240003731 substrate binding site [chemical binding]; other site 907240003732 Mg2+ binding site [ion binding]; other site 907240003733 Type III restriction/modification enzyme methylation subunit; Region: TypeIII_RM_meth; pfam12564 907240003734 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 907240003735 DNA methylase; Region: N6_N4_Mtase; pfam01555 907240003736 DNA methylase; Region: N6_N4_Mtase; pfam01555 907240003737 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3421 907240003738 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 907240003739 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 907240003740 biotin synthase; Provisional; Region: PRK08508 907240003741 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 907240003742 FeS/SAM binding site; other site 907240003743 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 907240003744 YihY family inner membrane protein; Region: yihY_not_rbn; TIGR00765 907240003745 Uncharacterized conserved protein [Function unknown]; Region: COG1479 907240003746 Protein of unknown function DUF262; Region: DUF262; pfam03235 907240003747 Protein of unknown function DUF262; Region: DUF262; pfam03235 907240003748 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 907240003749 7-cyano-7-deazaguanine reductase; Region: QueF-II; TIGR03139 907240003750 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 907240003751 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 907240003752 tRNA dimethylallyltransferase; Region: miaA; TIGR00174 907240003753 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 907240003754 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 907240003755 active site 907240003756 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13904 907240003757 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 907240003758 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 907240003759 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08472 907240003760 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 907240003761 Walker A motif/ATP binding site; other site 907240003762 Walker B motif; other site 907240003763 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]; Region: VirB11; COG0630 907240003764 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 907240003765 ATP binding site [chemical binding]; other site 907240003766 Walker A motif; other site 907240003767 hexamer interface [polypeptide binding]; other site 907240003768 Walker B motif; other site 907240003769 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 907240003770 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 907240003771 active site 907240003772 HIGH motif; other site 907240003773 nucleotide binding site [chemical binding]; other site 907240003774 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 907240003775 active site 907240003776 KMSKS motif; other site 907240003777 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 907240003778 tRNA binding surface [nucleotide binding]; other site 907240003779 anticodon binding site; other site 907240003780 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 907240003781 RNA binding surface [nucleotide binding]; other site 907240003782 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 907240003783 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 907240003784 S-adenosylmethionine binding site [chemical binding]; other site 907240003785 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 907240003786 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 907240003787 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 907240003788 KpsF/GutQ family protein; Region: kpsF; TIGR00393 907240003789 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 907240003790 putative active site [active] 907240003791 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 907240003792 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14462 907240003793 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 907240003794 FeS/SAM binding site; other site 907240003795 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 907240003796 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 907240003797 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 907240003798 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 907240003799 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 907240003800 active site 907240003801 catalytic residues [active] 907240003802 DNA binding site [nucleotide binding] 907240003803 Int/Topo IB signature motif; other site 907240003804 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 907240003805 Type IV secretory pathway, TrbL components [Intracellular trafficking and secretion]; Region: TrbL; COG3846 907240003806 Protein of unknown function (DUF3991); Region: DUF3991; pfam13154 907240003807 Toprim-like; Region: Toprim_2; pfam13155 907240003808 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 907240003809 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 907240003810 P-loop; other site 907240003811 Magnesium ion binding site [ion binding]; other site 907240003812 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 907240003813 Topoisomerase IA [DNA replication, recombination, and repair]; Region: TopA; COG0550 907240003814 TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli...; Region: TOPRIM_TopoIA; cd01028 907240003815 active site 907240003816 interdomain interaction site; other site 907240003817 putative metal-binding site [ion binding]; other site 907240003818 nucleotide binding site [chemical binding]; other site 907240003819 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 907240003820 domain I; other site 907240003821 DNA binding groove [nucleotide binding] 907240003822 phosphate binding site [ion binding]; other site 907240003823 domain II; other site 907240003824 domain III; other site 907240003825 nucleotide binding site [chemical binding]; other site 907240003826 catalytic site [active] 907240003827 domain IV; other site 907240003828 potential frameshift: common BLAST hit: gi|308185126|ref|YP_003929259.1| adenine specific DNA methyltransferase 907240003829 Type IV secretory system Conjugative DNA transfer; Region: T4SS-DNA_transf; pfam02534 907240003830 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 907240003831 Walker A motif; other site 907240003832 ATP binding site [chemical binding]; other site 907240003833 Walker B motif; other site 907240003834 Replication regulatory protein RepB; Region: RepB-RCR_reg; cl11673 907240003835 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 907240003836 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 907240003837 Walker A motif; other site 907240003838 hexamer interface [polypeptide binding]; other site 907240003839 ATP binding site [chemical binding]; other site 907240003840 Walker B motif; other site 907240003841 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 907240003842 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 907240003843 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 907240003844 VirB7 interaction site; other site 907240003845 VirB8 protein; Region: VirB8; cl01500 907240003846 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 907240003847 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 907240003848 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 907240003849 Walker A motif; other site 907240003850 ATP binding site [chemical binding]; other site 907240003851 Walker B motif; other site 907240003852 TrbC/VIRB2 family; Region: TrbC; pfam04956 907240003853 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 907240003854 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 907240003855 formyltetrahydrofolate deformylase; Region: PurU; TIGR00655 907240003856 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 907240003857 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 907240003858 active site 907240003859 substrate binding site [chemical binding]; other site 907240003860 cosubstrate binding site; other site 907240003861 catalytic site [active] 907240003862 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 907240003863 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 907240003864 tandem repeat interface [polypeptide binding]; other site 907240003865 oligomer interface [polypeptide binding]; other site 907240003866 active site residues [active] 907240003867 TIR domain; Region: TIR_2; pfam13676 907240003868 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cd00317 907240003869 active site 907240003870 carbon storage regulator; Provisional; Region: PRK00568 907240003871 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK04181 907240003872 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 907240003873 SmpB-tmRNA interface; other site 907240003874 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 907240003875 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 907240003876 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 907240003877 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 907240003878 ribonuclease P protein component, eubacterial; Region: rnpA; TIGR00188 907240003879 hypothetical protein; Provisional; Region: PRK14374 907240003880 membrane protein insertase; Provisional; Region: PRK01318 907240003881 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 907240003882 Predicted RNA-binding protein [General function prediction only]; Region: Jag; COG1847 907240003883 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 907240003884 tRNA modification GTPase TrmE; Region: mnmE_trmE_thdF; TIGR00450 907240003885 Circularly permuted YlqF-related GTPases; Region: YlqF_related_GTPase; cl17249 907240003886 GTP/Mg2+ binding site [chemical binding]; other site 907240003887 G5 box; other site 907240003888 trmE is a tRNA modification GTPase; Region: trmE; cd04164 907240003889 G1 box; other site 907240003890 G1 box; other site 907240003891 GTP/Mg2+ binding site [chemical binding]; other site 907240003892 Switch I region; other site 907240003893 Switch I region; other site 907240003894 G2 box; other site 907240003895 G2 box; other site 907240003896 Switch II region; other site 907240003897 G3 box; other site 907240003898 G3 box; other site 907240003899 Switch II region; other site 907240003900 G4 box; other site 907240003901 G5 box; other site 907240003902 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 907240003903 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240003904 LPP20 lipoprotein; Region: LPP20; pfam02169 907240003905 Collagen-binding surface adhesin SpaP (antigen I/II family) [General function prediction only]; Region: FlgN; COG3417 907240003906 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 907240003907 catalytic residues [active] 907240003908 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 907240003909 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 907240003910 RNA binding surface [nucleotide binding]; other site 907240003911 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 907240003912 active site 907240003913 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; Region: PHP_PolIIIA_DnaE3; cd12113 907240003914 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 907240003915 active site 907240003916 PHP Thumb interface [polypeptide binding]; other site 907240003917 metal binding site [ion binding]; metal-binding site 907240003918 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 907240003919 generic binding surface I; other site 907240003920 generic binding surface II; other site 907240003921 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 907240003922 Heat shock protein [Posttranslational modification, protein turnover, chaperones]; Region: HslJ; COG3187 907240003923 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 907240003924 mce related protein; Region: MCE; pfam02470 907240003925 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 907240003926 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 907240003927 Walker A/P-loop; other site 907240003928 ATP binding site [chemical binding]; other site 907240003929 Q-loop/lid; other site 907240003930 ABC transporter signature motif; other site 907240003931 Walker B; other site 907240003932 D-loop; other site 907240003933 H-loop/switch region; other site 907240003934 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 907240003935 conserved hypothetical integral membrane protein; Region: TIGR00056 907240003936 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240003937 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 907240003938 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 907240003939 homodimer interface [polypeptide binding]; other site 907240003940 substrate-cofactor binding pocket; other site 907240003941 catalytic residue [active] 907240003942 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240003943 DNA polymerase I; Region: pola; TIGR00593 907240003944 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 907240003945 active site 907240003946 metal binding site 1 [ion binding]; metal-binding site 907240003947 putative 5' ssDNA interaction site; other site 907240003948 metal binding site 3; metal-binding site 907240003949 metal binding site 2 [ion binding]; metal-binding site 907240003950 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 907240003951 putative DNA binding site [nucleotide binding]; other site 907240003952 putative metal binding site [ion binding]; other site 907240003953 3'-5' exonuclease; Region: 35EXOc; smart00474 907240003954 active site 907240003955 substrate binding site [chemical binding]; other site 907240003956 catalytic site [active] 907240003957 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 907240003958 active site 907240003959 DNA binding site [nucleotide binding] 907240003960 catalytic site [active] 907240003961 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 907240003962 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 907240003963 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 907240003964 thymidylate kinase; Validated; Region: tmk; PRK00698 907240003965 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 907240003966 TMP-binding site; other site 907240003967 ATP-binding site [chemical binding]; other site 907240003968 Phosphopantetheine adenylyltransferase [Coenzyme metabolism]; Region: CoaD; COG0669 907240003969 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 907240003970 active site 907240003971 (T/H)XGH motif; other site 907240003972 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 907240003973 Flavoprotein; Region: Flavoprotein; pfam02441 907240003974 flagellar basal body P-ring biosynthesis protein FlgA; Reviewed; Region: flgA; PRK08515 907240003975 flagella basal body P-ring formation protein FlgA; Region: flgA_cterm; TIGR03170 907240003976 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 907240003977 Part of AAA domain; Region: AAA_19; pfam13245 907240003978 Family description; Region: UvrD_C_2; pfam13538 907240003979 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 907240003980 binding surface 907240003981 TPR motif; other site 907240003982 seryl-tRNA synthetase; Provisional; Region: PRK05431 907240003983 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 907240003984 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 907240003985 dimer interface [polypeptide binding]; other site 907240003986 active site 907240003987 motif 1; other site 907240003988 motif 2; other site 907240003989 motif 3; other site 907240003990 Predicted amidohydrolase [General function prediction only]; Region: COG0388 907240003991 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 907240003992 active site 907240003993 catalytic triad [active] 907240003994 dimer interface [polypeptide binding]; other site 907240003995 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK14065 907240003996 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 907240003997 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 907240003998 S-adenosylmethionine binding site [chemical binding]; other site 907240003999 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 907240004000 uncharacterized protein, YigZ family; Region: IMPACT_YIGZ; TIGR00257 907240004001 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 907240004002 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 907240004003 ABC-2 type transporter; Region: ABC2_membrane; cl17235 907240004004 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 907240004005 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 907240004006 HlyD family secretion protein; Region: HlyD_3; pfam13437 907240004007 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 907240004008 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 907240004009 Domain of unknown function DUF21; Region: DUF21; pfam01595 907240004010 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 907240004011 Transporter associated domain; Region: CorC_HlyC; smart01091 907240004012 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 907240004013 Phosphate transporter family; Region: PHO4; pfam01384 907240004014 NifU-like domain; Region: NifU; pfam01106 907240004015 UDP-N-acetylmuramyl-tripeptide synthetase; Region: murE; TIGR01085 907240004016 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 907240004017 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 907240004018 Transaldolase-like proteins from plants and bacteria; Region: Transaldolase_like; cd00955 907240004019 putative active site [active] 907240004020 transaldolase; Provisional; Region: PRK03903 907240004021 catalytic residue [active] 907240004022 ribosomal protein L25, Ctc-form; Region: ctc_TL5; TIGR00731 907240004023 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 907240004024 5S rRNA interface [nucleotide binding]; other site 907240004025 CTC domain interface [polypeptide binding]; other site 907240004026 L16 interface [polypeptide binding]; other site 907240004027 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 907240004028 putative active site [active] 907240004029 catalytic residue [active] 907240004030 Predicted permeases [General function prediction only]; Region: COG0795 907240004031 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 907240004032 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG3392 907240004033 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 907240004034 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 907240004035 AlwI restriction endonuclease; Region: RE_AlwI; pfam09491 907240004036 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240004037 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3399 907240004038 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 907240004039 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 907240004040 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 907240004041 metal-binding site [ion binding] 907240004042 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 907240004043 Soluble P-type ATPase [General function prediction only]; Region: COG4087 907240004044 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 907240004045 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 907240004046 S-adenosylmethionine binding site [chemical binding]; other site 907240004047 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 907240004048 catalytic motif [active] 907240004049 Zn binding site [ion binding]; other site 907240004050 Pyrimidine reductase, riboflavin biosynthesis [Coenzyme metabolism]; Region: RibD; COG1985 907240004051 RibD C-terminal domain; Region: RibD_C; cl17279 907240004052 sodium--glutamate symport carrier (gltS); Region: gltS; TIGR00210 907240004053 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 907240004054 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 907240004055 NAD(P) binding pocket [chemical binding]; other site 907240004056 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 907240004057 4Fe-4S binding domain; Region: Fer4_5; pfam12801 907240004058 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 907240004059 acyl-phosphate glycerol 3-phosphate acyltransferase; Region: TIGR00023 907240004060 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 907240004061 homooctamer interface [polypeptide binding]; other site 907240004062 active site 907240004063 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 907240004064 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 907240004065 Selenocysteine synthase [seryl-tRNASer selenium transferase] [Amino acid transport and metabolism]; Region: SelA; COG1921 907240004066 L-seryl-tRNA selenium transferase; Region: SelA; pfam03841 907240004067 transcription elongation factor NusA; Provisional; Region: nusA; PRK12328 907240004068 NusA N-terminal domain; Region: NusA_N; pfam08529 907240004069 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 907240004070 RNA binding site [nucleotide binding]; other site 907240004071 homodimer interface [polypeptide binding]; other site 907240004072 NusA-like KH domain; Region: KH_5; pfam13184 907240004073 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 907240004074 G-X-X-G motif; other site 907240004075 potential frameshift: common BLAST hit: gi|298735510|ref|YP_003728031.1| putative type IIS restriction/modification enzyme 907240004076 Restriction endonuclease [Defense mechanisms]; Region: COG3587 907240004077 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 907240004078 ATP binding site [chemical binding]; other site 907240004079 putative Mg++ binding site [ion binding]; other site 907240004080 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 907240004081 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 907240004082 DNA methylase; Region: N6_N4_Mtase; pfam01555 907240004083 DNA methylase; Region: N6_N4_Mtase; cl17433 907240004084 ATP-dependent DNA helicase RecG; Region: recG; TIGR00643 907240004085 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 907240004086 ssDNA binding site; other site 907240004087 generic binding surface II; other site 907240004088 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 907240004089 ATP binding site [chemical binding]; other site 907240004090 putative Mg++ binding site [ion binding]; other site 907240004091 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 907240004092 nucleotide binding region [chemical binding]; other site 907240004093 ATP-binding site [chemical binding]; other site 907240004094 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240004095 Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Ape1-like_AP-endo; cd09087 907240004096 active site 907240004097 putative catalytic site [active] 907240004098 DNA binding site [nucleotide binding] 907240004099 putative phosphate binding site [ion binding]; other site 907240004100 metal binding site A [ion binding]; metal-binding site 907240004101 AP binding site [nucleotide binding]; other site 907240004102 metal binding site B [ion binding]; metal-binding site 907240004103 potential protein location (hypothetical protein HPGAM_08050 [Helicobacter pylori Gambia94/24]) that overlaps RNA (tRNA-F) 907240004104 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 907240004105 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 907240004106 Walker A motif; other site 907240004107 ATP binding site [chemical binding]; other site 907240004108 Walker B motif; other site 907240004109 arginine finger; other site 907240004110 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 907240004111 DnaA box-binding interface [nucleotide binding]; other site 907240004112 Nucleoside phosphorylase [Nucleotide transport and metabolism]; Region: Pfs; COG0775 907240004113 Protein of unknown function (DUF2443); Region: DUF2443; pfam10398 907240004114 glucosamine--fructose-6-phosphate aminotransferase (isomerizing); Region: glmS; TIGR01135 907240004115 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 907240004116 glutaminase active site [active] 907240004117 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 907240004118 dimer interface [polypeptide binding]; other site 907240004119 active site 907240004120 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 907240004121 dimer interface [polypeptide binding]; other site 907240004122 active site 907240004123 Predicted alternative thymidylate synthase [Nucleotide transport and metabolism]; Region: THY1; COG1351 907240004124 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 907240004125 HsdM N-terminal domain; Region: HsdM_N; pfam12161 907240004126 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 907240004127 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 907240004128 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 907240004129 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 907240004130 ATP binding site [chemical binding]; other site 907240004131 putative Mg++ binding site [ion binding]; other site 907240004132 Protein of unknown function DUF45; Region: DUF45; pfam01863 907240004133 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 907240004134 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 907240004135 N-terminal plug; other site 907240004136 ligand-binding site [chemical binding]; other site 907240004137 Arginase family; Region: Arginase; cd09989 907240004138 active site 907240004139 Mn binding site [ion binding]; other site 907240004140 oligomer interface [polypeptide binding]; other site 907240004141 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 907240004142 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 907240004143 hexamer interface [polypeptide binding]; other site 907240004144 ligand binding site [chemical binding]; other site 907240004145 putative active site [active] 907240004146 NAD(P) binding site [chemical binding]; other site 907240004147 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 907240004148 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 907240004149 putative NAD(P) binding site [chemical binding]; other site 907240004150 putative substrate binding site [chemical binding]; other site 907240004151 catalytic Zn binding site [ion binding]; other site 907240004152 structural Zn binding site [ion binding]; other site 907240004153 dimer interface [polypeptide binding]; other site 907240004154 Uncharacterized conserved protein [Function unknown]; Region: COG1479 907240004155 Protein of unknown function DUF262; Region: DUF262; pfam03235 907240004156 Protein of unknown function DUF262; Region: DUF262; pfam03235 907240004157 Uncharacterized conserved protein [Function unknown]; Region: COG1479 907240004158 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 907240004159 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907240004160 NAD kinase [Coenzyme metabolism]; Region: nadF; COG0061 907240004161 ATP-NAD kinase; Region: NAD_kinase; pfam01513 907240004162 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 907240004163 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 907240004164 Walker A/P-loop; other site 907240004165 ATP binding site [chemical binding]; other site 907240004166 Q-loop/lid; other site 907240004167 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 907240004168 ABC transporter signature motif; other site 907240004169 Walker B; other site 907240004170 D-loop; other site 907240004171 H-loop/switch region; other site 907240004172 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]; Region: COG1293 907240004173 Domain of unknown function (DUF814); Region: DUF814; pfam05670 907240004174 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 907240004175 binding surface 907240004176 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 907240004177 TPR motif; other site 907240004178 Sel1-like repeats; Region: SEL1; smart00671 907240004179 Sel1-like repeats; Region: SEL1; smart00671 907240004180 Sel1-like repeats; Region: SEL1; smart00671 907240004181 DNA polymerase III subunit epsilon; Provisional; Region: PRK08517 907240004182 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 907240004183 active site 907240004184 catalytic site [active] 907240004185 substrate binding site [chemical binding]; other site 907240004186 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 907240004187 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 907240004188 substrate binding site [chemical binding]; other site 907240004189 hexamer interface [polypeptide binding]; other site 907240004190 metal binding site [ion binding]; metal-binding site 907240004191 FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in...; Region: FIG; cl00289 907240004192 active site 907240004193 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 907240004194 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 907240004195 active site 907240004196 phosphorylation site [posttranslational modification] 907240004197 intermolecular recognition site; other site 907240004198 dimerization interface [polypeptide binding]; other site 907240004199 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 907240004200 DNA binding site [nucleotide binding] 907240004201 elongation factor Ts; Provisional; Region: tsf; PRK09377 907240004202 UBA/TS-N domain; Region: UBA; pfam00627 907240004203 Elongation factor TS; Region: EF_TS; pfam00889 907240004204 Elongation factor TS; Region: EF_TS; pfam00889 907240004205 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 907240004206 rRNA interaction site [nucleotide binding]; other site 907240004207 S8 interaction site; other site 907240004208 putative laminin-1 binding site; other site 907240004209 putative recombination protein RecB; Provisional; Region: PRK13909 907240004210 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 907240004211 pH-dependent sodium/proton antiporter; Provisional; Region: nhaA; PRK14856 907240004212 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 907240004213 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 907240004214 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 907240004215 protein-export membrane protein SecF; Region: 3a0501s07; TIGR00966 907240004216 Protein export membrane protein; Region: SecD_SecF; pfam02355 907240004217 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 907240004218 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 907240004219 HIGH motif; other site 907240004220 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 907240004221 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 907240004222 active site 907240004223 KMSKS motif; other site 907240004224 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 907240004225 tRNA binding surface [nucleotide binding]; other site 907240004226 anticodon binding site; other site 907240004227 Lipopolysaccharide-assembly; Region: LptE; pfam04390 907240004228 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 907240004229 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 907240004230 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 907240004231 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 907240004232 Peptidase family M23; Region: Peptidase_M23; pfam01551 907240004233 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 907240004234 Peptidase family M23; Region: Peptidase_M23; pfam01551 907240004235 Integral membrane protein CcmA involved in cell shape determination [Cell envelope biogenesis, outer membrane]; Region: CcmA; COG1664 907240004236 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 907240004237 transcription-repair coupling factor (mfd); Region: mfd; TIGR00580 907240004238 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 907240004239 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 907240004240 ATP binding site [chemical binding]; other site 907240004241 putative Mg++ binding site [ion binding]; other site 907240004242 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 907240004243 nucleotide binding region [chemical binding]; other site 907240004244 ATP-binding site [chemical binding]; other site 907240004245 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 907240004246 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 907240004247 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 907240004248 [2Fe-2S] cluster binding site [ion binding]; other site 907240004249 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 907240004250 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 907240004251 intrachain domain interface; other site 907240004252 interchain domain interface [polypeptide binding]; other site 907240004253 heme bH binding site [chemical binding]; other site 907240004254 Qi binding site; other site 907240004255 heme bL binding site [chemical binding]; other site 907240004256 Qo binding site; other site 907240004257 interchain domain interface [polypeptide binding]; other site 907240004258 intrachain domain interface; other site 907240004259 Qi binding site; other site 907240004260 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 907240004261 Qo binding site; other site 907240004262 Cytochrome c1 [Energy production and conversion]; Region: CYT1; COG2857 907240004263 Cytochrome c; Region: Cytochrom_C; pfam00034 907240004264 Cytochrome c; Region: Cytochrom_C; cl11414 907240004265 potential frameshift: common BLAST hit: gi|109946700|ref|YP_663928.1| putative metal-dependent hydrolase fragment 1 907240004266 Sulfatase; Region: Sulfatase; cl17466 907240004267 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 907240004268 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 907240004269 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 907240004270 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK03907 907240004271 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 907240004272 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 907240004273 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 907240004274 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 907240004275 Cell cycle protein; Region: FTSW_RODA_SPOVE; pfam01098 907240004276 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 907240004277 Periplasmic binding protein TroA_d. 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_d; cd01141 907240004278 putative ligand binding site [chemical binding]; other site 907240004279 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 907240004280 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 907240004281 dimer interface [polypeptide binding]; other site 907240004282 decamer (pentamer of dimers) interface [polypeptide binding]; other site 907240004283 catalytic triad [active] 907240004284 peroxidatic and resolving cysteines [active] 907240004285 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 907240004286 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 907240004287 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 907240004288 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 907240004289 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 907240004290 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 907240004291 G1 box; other site 907240004292 GTP/Mg2+ binding site [chemical binding]; other site 907240004293 Switch I region; other site 907240004294 G2 box; other site 907240004295 G3 box; other site 907240004296 Switch II region; other site 907240004297 G4 box; other site 907240004298 G5 box; other site 907240004299 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1934 907240004300 OstA-like protein; Region: OstA; pfam03968 907240004301 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 907240004302 motif II; other site 907240004303 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 907240004304 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 907240004305 Sporulation related domain; Region: SPOR; pfam05036 907240004306 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 907240004307 N-acetyl-D-glucosamine binding site [chemical binding]; other site 907240004308 catalytic residue [active] 907240004309 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 907240004310 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 907240004311 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 907240004312 active site 907240004313 riboflavin synthase, alpha subunit; Region: ribE; TIGR00187 907240004314 Lumazine binding domain; Region: Lum_binding; pfam00677 907240004315 Lumazine binding domain; Region: Lum_binding; pfam00677 907240004316 flhB C-terminus-related protein; Region: flhB_rel; TIGR00789 907240004317 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 907240004318 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 907240004319 Walker A/P-loop; other site 907240004320 ATP binding site [chemical binding]; other site 907240004321 Q-loop/lid; other site 907240004322 ABC transporter signature motif; other site 907240004323 Walker B; other site 907240004324 D-loop; other site 907240004325 H-loop/switch region; other site 907240004326 NIL domain; Region: NIL; pfam09383 907240004327 ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]; Region: AbcD; COG2011 907240004328 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 907240004329 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 907240004330 active site 907240004331 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 907240004332 This subfamily is composed of uncharacterized bacterial glycosyltransferases in the MraY-like family. This family contains both eukaryotic and prokaryotic UDP-D-N-acetylhexosamine:polyprenol phosphate D-N-acetylhexosamine-1-phosphate transferases, which...; Region: GT_MraY_like; cd06912 907240004333 Mg++ binding site [ion binding]; other site 907240004334 putative catalytic motif [active] 907240004335 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 907240004336 active site 907240004337 hydrophilic channel; other site 907240004338 dimerization interface [polypeptide binding]; other site 907240004339 catalytic residues [active] 907240004340 active site lid [active] 907240004341 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 907240004342 4-hydroxythreonine-4-phosphate dehydrogenase; Provisional; Region: pdxA; PRK03946 907240004343 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 907240004344 metallohydrolase, glycoprotease/Kae1 family; Region: gcp_kae1; TIGR00329 907240004345 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 907240004346 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 907240004347 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 907240004348 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4735 907240004349 hypothetical protein; Provisional; Region: PRK10236 907240004350 Domain of unknown function (DUF3944); Region: DUF3944; pfam13099 907240004351 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4735