-- dump date 20140619_113116 -- class Genbank::misc_feature -- table misc_feature_note -- id note 1055527000001 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 1055527000002 putative RNA binding site [nucleotide binding]; other site 1055527000003 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 1055527000004 homopentamer interface [polypeptide binding]; other site 1055527000005 active site 1055527000006 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 1055527000007 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 1055527000008 potential frameshift: common BLAST hit: gi|208433980|ref|YP_002265646.1| beta-carbonicanhydrase 1055527000009 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 1055527000010 active site 1055527000011 dimer interface [polypeptide binding]; other site 1055527000012 pantoate--beta-alanine ligase; Region: panC; TIGR00018 1055527000013 Pantoate-beta-alanine ligase; Region: PanC; cd00560 1055527000014 active site 1055527000015 ATP-binding site [chemical binding]; other site 1055527000016 pantoate-binding site; other site 1055527000017 HXXH motif; other site 1055527000018 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527000019 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 1055527000020 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 1055527000021 ring oligomerisation interface [polypeptide binding]; other site 1055527000022 ATP/Mg binding site [chemical binding]; other site 1055527000023 stacking interactions; other site 1055527000024 hinge regions; other site 1055527000025 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 1055527000026 oligomerisation interface [polypeptide binding]; other site 1055527000027 mobile loop; other site 1055527000028 roof hairpin; other site 1055527000029 DNA primase, catalytic core; Region: dnaG; TIGR01391 1055527000030 CHC2 zinc finger; Region: zf-CHC2; pfam01807 1055527000031 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 1055527000032 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 1055527000033 active site 1055527000034 metal binding site [ion binding]; metal-binding site 1055527000035 interdomain interaction site; other site 1055527000036 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 1055527000037 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 1055527000038 Ligand Binding Site [chemical binding]; other site 1055527000039 TrbC/VIRB2 family; Region: TrbC; cl01583 1055527000040 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 1055527000041 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1055527000042 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 1055527000043 Walker A motif; other site 1055527000044 ATP binding site [chemical binding]; other site 1055527000045 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 1055527000046 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 1055527000047 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 1055527000048 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 1055527000049 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 1055527000050 active site 1055527000051 phosphorylation site [posttranslational modification] 1055527000052 intermolecular recognition site; other site 1055527000053 dimerization interface [polypeptide binding]; other site 1055527000054 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 1055527000055 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 1055527000056 dimer interface [polypeptide binding]; other site 1055527000057 active site 1055527000058 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1055527000059 catalytic residues [active] 1055527000060 substrate binding site [chemical binding]; other site 1055527000061 lipid A 1-phosphatase; Reviewed; Region: PRK09597 1055527000062 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 1055527000063 active site 1055527000064 lipid A phosphoethanolamine transferase; Reviewed; Region: PRK09598 1055527000065 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 1055527000066 Sulfatase; Region: Sulfatase; pfam00884 1055527000067 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527000068 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 1055527000069 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 1055527000070 dimer interface [polypeptide binding]; other site 1055527000071 active site 1055527000072 citrylCoA binding site [chemical binding]; other site 1055527000073 NADH binding [chemical binding]; other site 1055527000074 cationic pore residues; other site 1055527000075 oxalacetate/citrate binding site [chemical binding]; other site 1055527000076 coenzyme A binding site [chemical binding]; other site 1055527000077 catalytic triad [active] 1055527000078 isocitrate dehydrogenase; Validated; Region: PRK07362 1055527000079 isocitrate dehydrogenase; Reviewed; Region: PRK07006 1055527000080 Protein of unknown function (DUF1523); Region: DUF1523; pfam07509 1055527000081 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 1055527000082 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 1055527000083 Ligand Binding Site [chemical binding]; other site 1055527000084 Uncharacterized conserved protein [Function unknown]; Region: COG2127 1055527000085 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 1055527000086 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 1055527000087 Walker A motif; other site 1055527000088 ATP binding site [chemical binding]; other site 1055527000089 Walker B motif; other site 1055527000090 arginine finger; other site 1055527000091 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 1055527000092 Walker A motif; other site 1055527000093 ATP binding site [chemical binding]; other site 1055527000094 Walker B motif; other site 1055527000095 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 1055527000096 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 1055527000097 tetramerization interface [polypeptide binding]; other site 1055527000098 active site 1055527000099 hypothetical protein; Provisional; Region: PRK03762 1055527000100 PDZ domain; Region: PDZ_2; pfam13180 1055527000101 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 1055527000102 Type IV secretory pathway, TrbL components [Intracellular trafficking and secretion]; Region: TrbL; COG3846 1055527000103 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 1055527000104 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 1055527000105 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 1055527000106 VirB7 interaction site; other site 1055527000107 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 1055527000108 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 1055527000109 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 1055527000110 Substrate binding site; other site 1055527000111 Cupin domain; Region: Cupin_2; cl17218 1055527000112 GDP-mannose 4,6-dehydratase; Region: gmd; TIGR01472 1055527000113 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 1055527000114 NADP-binding site; other site 1055527000115 homotetramer interface [polypeptide binding]; other site 1055527000116 substrate binding site [chemical binding]; other site 1055527000117 homodimer interface [polypeptide binding]; other site 1055527000118 active site 1055527000119 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 1055527000120 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 1055527000121 NADP binding site [chemical binding]; other site 1055527000122 active site 1055527000123 putative substrate binding site [chemical binding]; other site 1055527000124 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 1055527000125 dimerization interface [polypeptide binding]; other site 1055527000126 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 1055527000127 ATP binding site [chemical binding]; other site 1055527000128 Acylphosphatase; Region: Acylphosphatase; pfam00708 1055527000129 [NiFe] hydrogenase maturation protein HypF; Region: hypF; TIGR00143 1055527000130 HypF finger; Region: zf-HYPF; pfam07503 1055527000131 HypF finger; Region: zf-HYPF; pfam07503 1055527000132 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 1055527000133 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957 1055527000134 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 1055527000135 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 1055527000136 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 1055527000137 DNA methylase; Region: N6_N4_Mtase; pfam01555 1055527000138 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 1055527000139 potential frameshift: common BLAST hit: gi|210134248|ref|YP_002300687.1| type II R-M system restriction endonuclease 1055527000140 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 1055527000141 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 1055527000142 cofactor binding site; other site 1055527000143 DNA binding site [nucleotide binding] 1055527000144 substrate interaction site [chemical binding]; other site 1055527000145 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 1055527000146 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 1055527000147 S-adenosylmethionine binding site [chemical binding]; other site 1055527000148 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 1055527000149 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 1055527000150 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 1055527000151 Na binding site [ion binding]; other site 1055527000152 Proline dehydrogenase; Region: Pro_dh; pfam01619 1055527000153 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 1055527000154 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 1055527000155 Glutamate binding site [chemical binding]; other site 1055527000156 NAD binding site [chemical binding]; other site 1055527000157 catalytic residues [active] 1055527000158 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 1055527000159 Proteins of 100 residues with WXG; Region: WXG100; cl02005 1055527000160 A nuclease of the HNH/ENDO VII superfamily with conserved WHH; Region: WHH; pfam14414 1055527000161 SMI1 / KNR4 family; Region: SMI1_KNR4; smart00860 1055527000162 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 1055527000163 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 1055527000164 Urease accessory protein UreH [Posttranslational modification, protein turnover, chaperones]; Region: UreH; COG0829 1055527000165 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 1055527000166 G1 box; other site 1055527000167 GTP/Mg2+ binding site [chemical binding]; other site 1055527000168 G2 box; other site 1055527000169 Switch I region; other site 1055527000170 G3 box; other site 1055527000171 Switch II region; other site 1055527000172 G4 box; other site 1055527000173 G5 box; other site 1055527000174 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 1055527000175 UreF; Region: UreF; pfam01730 1055527000176 urease accessory protein UreE; Provisional; Region: ureE; PRK13261 1055527000177 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 1055527000178 dimer interface [polypeptide binding]; other site 1055527000179 catalytic residues [active] 1055527000180 AmiS/UreI family transporter; Region: AmiS_UreI; pfam02293 1055527000181 urease subunit beta; Provisional; Region: ureB; PRK13985 1055527000182 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 1055527000183 subunit interactions [polypeptide binding]; other site 1055527000184 active site 1055527000185 flap region; other site 1055527000186 urease subunit alpha; Provisional; Region: PRK13986 1055527000187 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 1055527000188 alpha-gamma subunit interface [polypeptide binding]; other site 1055527000189 beta-gamma subunit interface [polypeptide binding]; other site 1055527000190 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 1055527000191 gamma-beta subunit interface [polypeptide binding]; other site 1055527000192 alpha-beta subunit interface [polypeptide binding]; other site 1055527000193 lipoprotein signal peptidase; Region: lspA; TIGR00077 1055527000194 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14324 1055527000195 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 1055527000196 active site 1055527000197 substrate binding site [chemical binding]; other site 1055527000198 metal binding site [ion binding]; metal-binding site 1055527000199 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 1055527000200 peptide chain release factor 1; Validated; Region: prfA; PRK00591 1055527000201 This domain is found in peptide chain release factors; Region: PCRF; smart00937 1055527000202 RF-1 domain; Region: RF-1; pfam00472 1055527000203 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 1055527000204 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527000205 Cache domain; Region: Cache_1; pfam02743 1055527000206 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1055527000207 dimer interface [polypeptide binding]; other site 1055527000208 putative CheW interface [polypeptide binding]; other site 1055527000209 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 1055527000210 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 1055527000211 23S rRNA interface [nucleotide binding]; other site 1055527000212 L3 interface [polypeptide binding]; other site 1055527000213 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl17341 1055527000214 Predicted dehydrogenase [General function prediction only]; Region: COG0579 1055527000215 NLPC_P60 stabilising domain, N term; Region: N_NLPC_P60; pfam12912 1055527000216 SH3 domain of the SH3b1 type; Region: SH3_6; pfam12913 1055527000217 SH3 domain of SH3b2 type; Region: SH3_7; pfam12914 1055527000218 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 1055527000219 NlpC/P60 family; Region: NLPC_P60; pfam00877 1055527000220 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 1055527000221 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1055527000222 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1055527000223 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1055527000224 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 1055527000225 DNA binding residues [nucleotide binding] 1055527000226 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 1055527000227 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 1055527000228 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 1055527000229 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 1055527000230 potential protein location (hypothetical protein HPELS_00470 [Helicobacter pylori ELS37]) that overlaps RNA (tRNA-S) 1055527000231 DpnII restriction endonuclease; Region: DpnII; pfam04556 1055527000232 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 1055527000233 Methyltransferase domain; Region: Methyltransf_26; pfam13659 1055527000234 DNA methylase; Region: N6_N4_Mtase; pfam01555 1055527000235 potential frameshift: common BLAST hit: gi|254778815|ref|YP_003056920.1| Alpha-1,2-fucosyltransferase 1055527000236 2-hydroxyacid dehydrogenase; Provisional; Region: PRK08410 1055527000237 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 1055527000238 NAD binding site [chemical binding]; other site 1055527000239 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 1055527000240 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 1055527000241 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1055527000242 catalytic residue [active] 1055527000243 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1055527000244 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1055527000245 dimer interface [polypeptide binding]; other site 1055527000246 putative CheW interface [polypeptide binding]; other site 1055527000247 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 1055527000248 Ligand Binding Site [chemical binding]; other site 1055527000249 potential frameshift: common BLAST hit: gi|254778822|ref|YP_003056927.1| outer membrane protein; signal peptide 1055527000250 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 1055527000251 metal-binding site 1055527000252 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 1055527000253 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 1055527000254 dimerization interface [polypeptide binding]; other site 1055527000255 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1055527000256 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1055527000257 dimer interface [polypeptide binding]; other site 1055527000258 putative CheW interface [polypeptide binding]; other site 1055527000259 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 1055527000260 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 1055527000261 active site 1055527000262 metal binding site [ion binding]; metal-binding site 1055527000263 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 1055527000264 S-ribosylhomocysteinase; Provisional; Region: PRK02260 1055527000265 cystathionine gamma-synthase/cystathionine beta-lyase; Validated; Region: PRK06176 1055527000266 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 1055527000267 homodimer interface [polypeptide binding]; other site 1055527000268 substrate-cofactor binding pocket; other site 1055527000269 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1055527000270 catalytic residue [active] 1055527000271 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 1055527000272 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 1055527000273 dimer interface [polypeptide binding]; other site 1055527000274 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1055527000275 catalytic residue [active] 1055527000276 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 1055527000277 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 1055527000278 nucleotide binding site [chemical binding]; other site 1055527000279 NEF interaction site [polypeptide binding]; other site 1055527000280 SBD interface [polypeptide binding]; other site 1055527000281 GrpE; Region: GrpE; pfam01025 1055527000282 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 1055527000283 dimer interface [polypeptide binding]; other site 1055527000284 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 1055527000285 heat-inducible transcription repressor; Provisional; Region: PRK03911 1055527000286 hypothetical protein; Provisional; Region: PRK05834 1055527000287 intersubunit interface [polypeptide binding]; other site 1055527000288 active site 1055527000289 Zn2+ binding site [ion binding]; other site 1055527000290 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 1055527000291 flagellin B; Provisional; Region: PRK13588 1055527000292 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 1055527000293 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 1055527000294 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 1055527000295 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 1055527000296 DNA topoisomerase I; Validated; Region: PRK05582 1055527000297 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 1055527000298 active site 1055527000299 interdomain interaction site; other site 1055527000300 putative metal-binding site [ion binding]; other site 1055527000301 nucleotide binding site [chemical binding]; other site 1055527000302 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 1055527000303 domain I; other site 1055527000304 DNA binding groove [nucleotide binding] 1055527000305 phosphate binding site [ion binding]; other site 1055527000306 domain II; other site 1055527000307 domain III; other site 1055527000308 nucleotide binding site [chemical binding]; other site 1055527000309 catalytic site [active] 1055527000310 domain IV; other site 1055527000311 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1055527000312 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1055527000313 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1055527000314 Fe-S oxidoreductases [Energy production and conversion]; Region: COG0731 1055527000315 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 1055527000316 FeS/SAM binding site; other site 1055527000317 Helicobacter pylori protein of unknown function (DUF874); Region: DUF874; pfam05917 1055527000318 Helicobacter pylori protein of unknown function (DUF874); Region: DUF874; pfam05917 1055527000319 phosphoenolpyruvate synthase; Validated; Region: PRK06464 1055527000320 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 1055527000321 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 1055527000322 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 1055527000323 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK12305 1055527000324 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 1055527000325 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 1055527000326 active site 1055527000327 dimer interface [polypeptide binding]; other site 1055527000328 motif 1; other site 1055527000329 motif 2; other site 1055527000330 motif 3; other site 1055527000331 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 1055527000332 anticodon binding site; other site 1055527000333 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 1055527000334 translation initiation factor IF-3; Region: infC; TIGR00168 1055527000335 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 1055527000336 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 1055527000337 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 1055527000338 23S rRNA binding site [nucleotide binding]; other site 1055527000339 L21 binding site [polypeptide binding]; other site 1055527000340 L13 binding site [polypeptide binding]; other site 1055527000341 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527000342 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 1055527000343 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 1055527000344 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 1055527000345 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 1055527000346 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 1055527000347 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 1055527000348 threonine/serine transporter TdcC; Provisional; Region: PRK13629; cl17672 1055527000349 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]; Region: AroG; COG3200 1055527000350 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1055527000351 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 1055527000352 catalytic triad [active] 1055527000353 Uncharacterized conserved protein [Function unknown]; Region: COG1556 1055527000354 iron-sulfur cluster-binding protein; Region: TIGR00273 1055527000355 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 1055527000356 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 1055527000357 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 1055527000358 Cysteine-rich domain; Region: CCG; pfam02754 1055527000359 Cysteine-rich domain; Region: CCG; pfam02754 1055527000360 L-lactate transport; Region: lctP; TIGR00795 1055527000361 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 1055527000362 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 1055527000363 L-lactate transport; Region: lctP; TIGR00795 1055527000364 DNA glycosylase MutY; Provisional; Region: PRK13910 1055527000365 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1055527000366 minor groove reading motif; other site 1055527000367 helix-hairpin-helix signature motif; other site 1055527000368 substrate binding pocket [chemical binding]; other site 1055527000369 active site 1055527000370 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 1055527000371 DNA binding and oxoG recognition site [nucleotide binding] 1055527000372 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 1055527000373 Sodium:sulfate symporter transmembrane region; Region: Na_sulph_symp; pfam00939 1055527000374 transmembrane helices; other site 1055527000375 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 1055527000376 Low-spin heme binding site [chemical binding]; other site 1055527000377 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 1055527000378 D-pathway; other site 1055527000379 Putative water exit pathway; other site 1055527000380 Binuclear center (active site) [active] 1055527000381 K-pathway; other site 1055527000382 Putative proton exit pathway; other site 1055527000383 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 1055527000384 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 1055527000385 cytochrome c oxidase, cbb3-type, CcoQ subunit, epsilon-Proteobacterial; Region: cbb3_Q_epsi; TIGR02736 1055527000386 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 1055527000387 Cytochrome c; Region: Cytochrom_C; pfam00034 1055527000388 Cytochrome c; Region: Cytochrom_C; pfam00034 1055527000389 Family of unknown function (DUF4006); Region: DUF4006; pfam13179 1055527000390 Predicted periplasmic solute-binding protein [General function prediction only]; Region: COG2107 1055527000391 recombinase A; Provisional; Region: recA; PRK09354 1055527000392 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 1055527000393 hexamer interface [polypeptide binding]; other site 1055527000394 Walker A motif; other site 1055527000395 ATP binding site [chemical binding]; other site 1055527000396 Walker B motif; other site 1055527000397 enolase; Provisional; Region: eno; PRK00077 1055527000398 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 1055527000399 dimer interface [polypeptide binding]; other site 1055527000400 metal binding site [ion binding]; metal-binding site 1055527000401 substrate binding pocket [chemical binding]; other site 1055527000402 AMIN domain; Region: AMIN; pfam11741 1055527000403 Shikimate kinase [Amino acid transport and metabolism]; Region: AroK; COG0703 1055527000404 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 1055527000405 ADP binding site [chemical binding]; other site 1055527000406 magnesium binding site [ion binding]; other site 1055527000407 putative shikimate binding site; other site 1055527000408 Cache domain; Region: Cache_1; pfam02743 1055527000409 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 1055527000410 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 1055527000411 Ligand binding site; other site 1055527000412 metal-binding site 1055527000413 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1055527000414 Sel1-like repeats; Region: SEL1; smart00671 1055527000415 Sel1-like repeats; Region: SEL1; smart00671 1055527000416 Sel1-like repeats; Region: SEL1; smart00671 1055527000417 Sel1-like repeats; Region: SEL1; smart00671 1055527000418 Sel1-like repeats; Region: SEL1; smart00671 1055527000419 hypothetical protein; Provisional; Region: PRK12378 1055527000420 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 1055527000421 dimer interface [polypeptide binding]; other site 1055527000422 active site 1055527000423 Schiff base residues; other site 1055527000424 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1055527000425 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 1055527000426 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 1055527000427 dimer interface [polypeptide binding]; other site 1055527000428 phosphorylation site [posttranslational modification] 1055527000429 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 1055527000430 ATP binding site [chemical binding]; other site 1055527000431 Mg2+ binding site [ion binding]; other site 1055527000432 G-X-G motif; other site 1055527000433 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1055527000434 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 1055527000435 active site 1055527000436 phosphorylation site [posttranslational modification] 1055527000437 intermolecular recognition site; other site 1055527000438 dimerization interface [polypeptide binding]; other site 1055527000439 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 1055527000440 DNA binding site [nucleotide binding] 1055527000441 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 1055527000442 Peptidase family U32; Region: Peptidase_U32; pfam01136 1055527000443 peptide chain release factor 2; Region: prfB; TIGR00020 1055527000444 This domain is found in peptide chain release factors; Region: PCRF; smart00937 1055527000445 RF-1 domain; Region: RF-1; pfam00472 1055527000446 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 1055527000447 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 1055527000448 dimer interface [polypeptide binding]; other site 1055527000449 putative functional site; other site 1055527000450 putative MPT binding site; other site 1055527000451 Flagellar biosynthesis pathway, component FliR [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FliR; COG1684 1055527000452 Etoposide-induced protein 2.4 (EI24); Region: EI24; pfam07264 1055527000453 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 1055527000454 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 1055527000455 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 1055527000456 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 1055527000457 intersubunit interface [polypeptide binding]; other site 1055527000458 active site 1055527000459 zinc binding site [ion binding]; other site 1055527000460 Na+ binding site [ion binding]; other site 1055527000461 elongation factor P; Validated; Region: PRK00529 1055527000462 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 1055527000463 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 1055527000464 RNA binding site [nucleotide binding]; other site 1055527000465 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 1055527000466 RNA binding site [nucleotide binding]; other site 1055527000467 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 1055527000468 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 1055527000469 cofactor binding site; other site 1055527000470 DNA binding site [nucleotide binding] 1055527000471 substrate interaction site [chemical binding]; other site 1055527000472 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 1055527000473 potential frameshift: common BLAST hit: gi|169795375|ref|YP_001713168.1| phage related protein 1055527000474 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 1055527000475 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 1055527000476 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 1055527000477 Probable transposase; Region: OrfB_IS605; pfam01385 1055527000478 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 1055527000479 Probable transposase; Region: OrfB_IS605; pfam01385 1055527000480 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 1055527000481 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 1055527000482 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4487 1055527000483 Uncharacterized protein conserved in bacteria (DUF2130); Region: DUF2130; pfam09903 1055527000484 PHP-associated; Region: PHP_C; pfam13263 1055527000485 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1055527000486 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 1055527000487 Walker A/P-loop; other site 1055527000488 ATP binding site [chemical binding]; other site 1055527000489 Q-loop/lid; other site 1055527000490 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 1055527000491 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 1055527000492 Probable transposase; Region: OrfB_IS605; pfam01385 1055527000493 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 1055527000494 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 1055527000495 AAA domain; Region: AAA_21; pfam13304 1055527000496 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 1055527000497 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 1055527000498 putative active site [active] 1055527000499 substrate binding site [chemical binding]; other site 1055527000500 putative cosubstrate binding site; other site 1055527000501 catalytic site [active] 1055527000502 Formyl transferase, C-terminal domain; Region: Formyl_trans_C; pfam02911 1055527000503 biotin--protein ligase; Provisional; Region: PRK08477 1055527000504 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 1055527000505 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 1055527000506 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 1055527000507 P-loop; other site 1055527000508 Magnesium ion binding site [ion binding]; other site 1055527000509 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 1055527000510 Magnesium ion binding site [ion binding]; other site 1055527000511 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 1055527000512 ParB-like nuclease domain; Region: ParB; smart00470 1055527000513 F0F1 ATP synthase subunit B'; Validated; Region: PRK08476 1055527000514 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1055527000515 F0F1 ATP synthase subunit B; Validated; Region: PRK08475 1055527000516 F0F1 ATP synthase subunit delta; Provisional; Region: PRK13431 1055527000517 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 1055527000518 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1055527000519 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 1055527000520 beta subunit interaction interface [polypeptide binding]; other site 1055527000521 Walker A motif; other site 1055527000522 ATP binding site [chemical binding]; other site 1055527000523 Walker B motif; other site 1055527000524 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1055527000525 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 1055527000526 core domain interface [polypeptide binding]; other site 1055527000527 delta subunit interface [polypeptide binding]; other site 1055527000528 epsilon subunit interface [polypeptide binding]; other site 1055527000529 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 1055527000530 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1055527000531 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 1055527000532 alpha subunit interaction interface [polypeptide binding]; other site 1055527000533 Walker A motif; other site 1055527000534 ATP binding site [chemical binding]; other site 1055527000535 Walker B motif; other site 1055527000536 inhibitor binding site; inhibition site 1055527000537 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1055527000538 ATP synthase, F1 epsilon subunit (delta in mitochondria); Region: ATP_synt_epsi; TIGR01216 1055527000539 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 1055527000540 gamma subunit interface [polypeptide binding]; other site 1055527000541 epsilon subunit interface [polypeptide binding]; other site 1055527000542 LBP interface [polypeptide binding]; other site 1055527000543 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 1055527000544 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 1055527000545 TolR protein; Region: tolR; TIGR02801 1055527000546 TonB C terminal; Region: TonB_2; pfam13103 1055527000547 translocation protein TolB; Provisional; Region: tolB; PRK04043 1055527000548 TolB amino-terminal domain; Region: TolB_N; pfam04052 1055527000549 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1055527000550 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 1055527000551 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1055527000552 ligand binding site [chemical binding]; other site 1055527000553 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 1055527000554 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1055527000555 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 1055527000556 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 1055527000557 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 1055527000558 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 1055527000559 cofactor binding site; other site 1055527000560 DNA binding site [nucleotide binding] 1055527000561 substrate interaction site [chemical binding]; other site 1055527000562 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK08471 1055527000563 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1055527000564 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 1055527000565 gamma-glutamyltranspeptidase; Region: g_glut_trans; TIGR00066 1055527000566 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1055527000567 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 1055527000568 binding surface 1055527000569 TPR motif; other site 1055527000570 Sel1-like repeats; Region: SEL1; smart00671 1055527000571 Sel1-like repeats; Region: SEL1; smart00671 1055527000572 Sel1-like repeats; Region: SEL1; smart00671 1055527000573 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 1055527000574 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 1055527000575 excinuclease ABC subunit B; Provisional; Region: PRK05298 1055527000576 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 1055527000577 ATP binding site [chemical binding]; other site 1055527000578 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 1055527000579 putative Mg++ binding site [ion binding]; other site 1055527000580 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 1055527000581 nucleotide binding region [chemical binding]; other site 1055527000582 ATP-binding site [chemical binding]; other site 1055527000583 Ultra-violet resistance protein B; Region: UvrB; pfam12344 1055527000584 UvrB/uvrC motif; Region: UVR; pfam02151 1055527000585 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527000586 adenylosuccinate lyase; Provisional; Region: PRK08470 1055527000587 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 1055527000588 tetramer interface [polypeptide binding]; other site 1055527000589 active site 1055527000590 Adenylosuccinate lyase C-terminus; Region: ADSL_C; smart00998 1055527000591 pyruvate ferredoxin oxidoreductase subunit beta; Provisional; Region: PRK11865 1055527000592 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 1055527000593 TPP-binding site [chemical binding]; other site 1055527000594 putative dimer interface [polypeptide binding]; other site 1055527000595 pyruvate flavodoxin oxidoreductase subunit alpha; Reviewed; Region: porA; PRK09622 1055527000596 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 1055527000597 dimer interface [polypeptide binding]; other site 1055527000598 PYR/PP interface [polypeptide binding]; other site 1055527000599 TPP binding site [chemical binding]; other site 1055527000600 substrate binding site [chemical binding]; other site 1055527000601 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1055527000602 pyruvate flavodoxin oxidoreductase subunit delta; Reviewed; Region: porD; PRK09625 1055527000603 4Fe-4S binding domain; Region: Fer4; pfam00037 1055527000604 pyruvate flavodoxin oxidoreductase subunit gamma; Validated; Region: PRK05844 1055527000605 pyruvate/ketoisovalerate ferredoxin oxidoreductase subunit gamma; Provisional; Region: PRK14029 1055527000606 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527000607 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 1055527000608 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 1055527000609 active site 1055527000610 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 1055527000611 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 1055527000612 active site 1055527000613 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 1055527000614 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 1055527000615 putative NAD(P) binding site [chemical binding]; other site 1055527000616 putative substrate binding site [chemical binding]; other site 1055527000617 catalytic Zn binding site [ion binding]; other site 1055527000618 structural Zn binding site [ion binding]; other site 1055527000619 dimer interface [polypeptide binding]; other site 1055527000620 glucokinase, proteobacterial type; Region: glk; TIGR00749 1055527000621 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 1055527000622 nucleotide binding site [chemical binding]; other site 1055527000623 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 1055527000624 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 1055527000625 putative active site [active] 1055527000626 Glucose-6-phosphate 1-dehydrogenase [Carbohydrate transport and metabolism]; Region: Zwf; COG0364 1055527000627 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 1055527000628 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 1055527000629 phosphogluconate dehydratase; Validated; Region: PRK09054 1055527000630 6-phosphogluconate dehydratase; Region: edd; TIGR01196 1055527000631 Entner-Doudoroff aldolase; Region: eda; TIGR01182 1055527000632 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 1055527000633 active site 1055527000634 intersubunit interface [polypeptide binding]; other site 1055527000635 catalytic residue [active] 1055527000636 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1055527000637 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 1055527000638 binding surface 1055527000639 TPR motif; other site 1055527000640 Sel1-like repeats; Region: SEL1; smart00671 1055527000641 Sel1-like repeats; Region: SEL1; smart00671 1055527000642 Sel1-like repeats; Region: SEL1; smart00671 1055527000643 classical (c) SDR, subgroup 5; Region: SDR_c5; cd05346 1055527000644 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 1055527000645 putative NAD(P) binding site [chemical binding]; other site 1055527000646 homodimer interface [polypeptide binding]; other site 1055527000647 homotetramer interface [polypeptide binding]; other site 1055527000648 active site 1055527000649 potential protein location (hypothetical protein HPELS_01205 [Helicobacter pylori ELS37]) that overlaps RNA (tRNA-I) 1055527000650 UDP-glucose-4-epimerase GalE; Region: galE; TIGR01179 1055527000651 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 1055527000652 NAD binding site [chemical binding]; other site 1055527000653 homodimer interface [polypeptide binding]; other site 1055527000654 active site 1055527000655 substrate binding site [chemical binding]; other site 1055527000656 tRNA pseudouridine(38-40) synthase; Region: hisT_truA; TIGR00071 1055527000657 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 1055527000658 dimerization interface 3.5A [polypeptide binding]; other site 1055527000659 active site 1055527000660 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1055527000661 Predicted permeases [General function prediction only]; Region: COG0795 1055527000662 protein-L-isoaspartate(D-aspartate) O-methyltransferase; Region: pimt; TIGR00080 1055527000663 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 1055527000664 S-adenosylmethionine binding site [chemical binding]; other site 1055527000665 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 1055527000666 dimer interface [polypeptide binding]; other site 1055527000667 putative radical transfer pathway; other site 1055527000668 diiron center [ion binding]; other site 1055527000669 tyrosyl radical; other site 1055527000670 potential protein location (hypothetical protein HPELS_01235 [Helicobacter pylori ELS37]) that overlaps RNA (tRNA-L) 1055527000671 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 1055527000672 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 1055527000673 inhibitor-cofactor binding pocket; inhibition site 1055527000674 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1055527000675 catalytic residue [active] 1055527000676 potential frameshift: common BLAST hit: gi|254779640|ref|YP_003057746.1| type II restriction endonuclease 1055527000677 potential frameshift: common BLAST hit: gi|254779639|ref|YP_003057745.1| adenine methyltransferase 1055527000678 biotin carboxylase; Validated; Region: PRK08462 1055527000679 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1055527000680 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 1055527000681 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 1055527000682 acetyl-CoA carboxylase, biotin carboxyl carrier protein; Region: BCCP; TIGR00531 1055527000683 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 1055527000684 carboxyltransferase (CT) interaction site; other site 1055527000685 biotinylation site [posttranslational modification]; other site 1055527000686 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1055527000687 trimer interface [polypeptide binding]; other site 1055527000688 active site 1055527000689 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527000690 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 1055527000691 RNA methyltransferase, RsmE family; Region: TIGR00046 1055527000692 ferrochelatase; Region: hemH; TIGR00109 1055527000693 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 1055527000694 C-terminal domain interface [polypeptide binding]; other site 1055527000695 active site 1055527000696 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 1055527000697 active site 1055527000698 N-terminal domain interface [polypeptide binding]; other site 1055527000699 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 1055527000700 catalytic residues [active] 1055527000701 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 1055527000702 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 1055527000703 potential frameshift: common BLAST hit: gi|254779629|ref|YP_003057735.1| Alpha1,3-fucosyltransferase 1055527000704 Glycosyltransferase family 10 (fucosyltransferase); Region: Glyco_transf_10; pfam00852 1055527000705 glutamate dehydrogenase; Provisional; Region: PRK09414 1055527000706 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 1055527000707 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 1055527000708 NAD(P) binding site [chemical binding]; other site 1055527000709 HemK family putative methylases; Region: hemK_fam; TIGR00536 1055527000710 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 1055527000711 Peptidase family M48; Region: Peptidase_M48; pfam01435 1055527000712 Sporulation related domain; Region: SPOR; pfam05036 1055527000713 primosome assembly protein PriA; Validated; Region: PRK05580 1055527000714 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 1055527000715 ATP binding site [chemical binding]; other site 1055527000716 putative Mg++ binding site [ion binding]; other site 1055527000717 helicase superfamily c-terminal domain; Region: HELICc; smart00490 1055527000718 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 1055527000719 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 1055527000720 S-adenosylmethionine binding site [chemical binding]; other site 1055527000721 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 1055527000722 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 1055527000723 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 1055527000724 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 1055527000725 dimer interface [polypeptide binding]; other site 1055527000726 catalytic triad [active] 1055527000727 peroxidatic and resolving cysteines [active] 1055527000728 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 1055527000729 putative CheA interaction surface; other site 1055527000730 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 1055527000731 putative binding surface; other site 1055527000732 active site 1055527000733 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 1055527000734 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 1055527000735 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 1055527000736 ATP binding site [chemical binding]; other site 1055527000737 Mg2+ binding site [ion binding]; other site 1055527000738 G-X-G motif; other site 1055527000739 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 1055527000740 Response regulator receiver domain; Region: Response_reg; pfam00072 1055527000741 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 1055527000742 active site 1055527000743 phosphorylation site [posttranslational modification] 1055527000744 intermolecular recognition site; other site 1055527000745 dimerization interface [polypeptide binding]; other site 1055527000746 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 1055527000747 putative CheA interaction surface; other site 1055527000748 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 1055527000749 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 1055527000750 active site 1055527000751 phosphorylation site [posttranslational modification] 1055527000752 intermolecular recognition site; other site 1055527000753 dimerization interface [polypeptide binding]; other site 1055527000754 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 1055527000755 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 1055527000756 putative active site [active] 1055527000757 putative metal binding site [ion binding]; other site 1055527000758 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 1055527000759 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1055527000760 catalytic residue [active] 1055527000761 menaquinone biosynthesis decarboxylase, SCO4490 family; Region: mena_SCO4490; TIGR03701 1055527000762 D-3-phosphoglycerate dehydrogenase; Region: PGDH; TIGR01327 1055527000763 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 1055527000764 ligand binding site [chemical binding]; other site 1055527000765 NAD binding site [chemical binding]; other site 1055527000766 dimerization interface [polypeptide binding]; other site 1055527000767 catalytic site [active] 1055527000768 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 1055527000769 putative L-serine binding site [chemical binding]; other site 1055527000770 ribosomal protein S1; Region: rpsA; TIGR00717 1055527000771 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 1055527000772 RNA binding site [nucleotide binding]; other site 1055527000773 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 1055527000774 RNA binding site [nucleotide binding]; other site 1055527000775 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 1055527000776 RNA binding site [nucleotide binding]; other site 1055527000777 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 1055527000778 RNA binding site [nucleotide binding]; other site 1055527000779 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 1055527000780 RNA binding site [nucleotide binding]; other site 1055527000781 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 1055527000782 LytB protein; Region: LYTB; pfam02401 1055527000783 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 1055527000784 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 1055527000785 hinge; other site 1055527000786 active site 1055527000787 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 1055527000788 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 1055527000789 putative tRNA-binding site [nucleotide binding]; other site 1055527000790 tRNA synthetase B5 domain; Region: B5; pfam03484 1055527000791 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 1055527000792 dimer interface [polypeptide binding]; other site 1055527000793 motif 1; other site 1055527000794 motif 3; other site 1055527000795 motif 2; other site 1055527000796 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 1055527000797 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 1055527000798 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 1055527000799 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 1055527000800 dimer interface [polypeptide binding]; other site 1055527000801 motif 1; other site 1055527000802 active site 1055527000803 motif 2; other site 1055527000804 motif 3; other site 1055527000805 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 1055527000806 nucleotide binding site/active site [active] 1055527000807 HIT family signature motif; other site 1055527000808 catalytic residue [active] 1055527000809 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 1055527000810 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 1055527000811 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1055527000812 catalytic residue [active] 1055527000813 Protein of unknown function (DUF3972); Region: DUF3972; pfam13118 1055527000814 potential frameshift: common BLAST hit: gi|15645035|ref|NP_207205.1| biotin sulfoxide reductase (bisC) 1055527000815 GMP synthase; Reviewed; Region: guaA; PRK00074 1055527000816 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 1055527000817 AMP/PPi binding site [chemical binding]; other site 1055527000818 candidate oxyanion hole; other site 1055527000819 catalytic triad [active] 1055527000820 potential glutamine specificity residues [chemical binding]; other site 1055527000821 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 1055527000822 ATP Binding subdomain [chemical binding]; other site 1055527000823 Ligand Binding sites [chemical binding]; other site 1055527000824 Dimerization subdomain; other site 1055527000825 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 1055527000826 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1055527000827 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1055527000828 Mycolic acid cyclopropane synthetase; Region: CMAS; pfam02353 1055527000829 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 1055527000830 S-adenosylmethionine binding site [chemical binding]; other site 1055527000831 methionyl-tRNA synthetase; Reviewed; Region: PRK12267 1055527000832 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 1055527000833 active site 1055527000834 HIGH motif; other site 1055527000835 KMSKS motif; other site 1055527000836 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 1055527000837 anticodon binding site; other site 1055527000838 tRNA binding surface [nucleotide binding]; other site 1055527000839 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 1055527000840 dimer interface [polypeptide binding]; other site 1055527000841 putative tRNA-binding site [nucleotide binding]; other site 1055527000842 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 1055527000843 potential frameshift: common BLAST hit: gi|298735965|ref|YP_003728490.1| tRNA (mo5U34)-methyltransferase 1055527000844 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cd03440 1055527000845 active site 2 [active] 1055527000846 active site 1 [active] 1055527000847 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1055527000848 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 1055527000849 putative ADP-binding pocket [chemical binding]; other site 1055527000850 Arginine decarboxylase (spermidine biosynthesis) [Amino acid transport and metabolism]; Region: SpeA; COG1166 1055527000851 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 1055527000852 active site 1055527000853 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1055527000854 catalytic residues [active] 1055527000855 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 1055527000856 Uncharacterized conserved protein [Function unknown]; Region: COG1479 1055527000857 Protein of unknown function DUF262; Region: DUF262; pfam03235 1055527000858 Protein of unknown function DUF262; Region: DUF262; pfam03235 1055527000859 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 1055527000860 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1055527000861 cell division protein FtsZ; Validated; Region: PRK09330 1055527000862 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 1055527000863 nucleotide binding site [chemical binding]; other site 1055527000864 SulA interaction site; other site 1055527000865 cell division protein FtsA; Region: ftsA; TIGR01174 1055527000866 Cell division protein FtsA; Region: FtsA; smart00842 1055527000867 Cell division protein FtsA; Region: FtsA; pfam14450 1055527000868 SurA N-terminal domain; Region: SurA_N_3; cl07813 1055527000869 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 1055527000870 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 1055527000871 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK05964 1055527000872 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 1055527000873 inhibitor-cofactor binding pocket; inhibition site 1055527000874 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1055527000875 catalytic residue [active] 1055527000876 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C subunit; Region: gatC; TIGR00135 1055527000877 phosphoglyceromutase; Provisional; Region: PRK05434 1055527000878 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; Region: pgm_bpd_ind; TIGR01307 1055527000879 glycyl-tRNA synthetase, tetrameric type, beta subunit; Region: glyS; TIGR00211 1055527000880 Outer membrane efflux protein; Region: OEP; pfam02321 1055527000881 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 1055527000882 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 1055527000883 Protein of unknown function (DUF3240); Region: DUF3240; pfam11582 1055527000884 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 1055527000885 G1 box; other site 1055527000886 GTP/Mg2+ binding site [chemical binding]; other site 1055527000887 Predicted GTPases (dynamin-related) [General function prediction only]; Region: COG0699 1055527000888 G2 box; other site 1055527000889 Switch I region; other site 1055527000890 G3 box; other site 1055527000891 Switch II region; other site 1055527000892 G4 box; other site 1055527000893 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 1055527000894 G1 box; other site 1055527000895 GTP/Mg2+ binding site [chemical binding]; other site 1055527000896 G2 box; other site 1055527000897 Switch I region; other site 1055527000898 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 1055527000899 G3 box; other site 1055527000900 Switch II region; other site 1055527000901 G4 box; other site 1055527000902 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 1055527000903 Dynamin family; Region: Dynamin_N; pfam00350 1055527000904 G1 box; other site 1055527000905 GTP/Mg2+ binding site [chemical binding]; other site 1055527000906 G2 box; other site 1055527000907 Switch I region; other site 1055527000908 G3 box; other site 1055527000909 Switch II region; other site 1055527000910 G4 box; other site 1055527000911 G5 box; other site 1055527000912 DNA polymerase II large subunit; Provisional; Region: PRK14714 1055527000913 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 1055527000914 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 1055527000915 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 1055527000916 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 1055527000917 dimer interface [polypeptide binding]; other site 1055527000918 motif 1; other site 1055527000919 active site 1055527000920 motif 2; other site 1055527000921 motif 3; other site 1055527000922 dinuclear metal center protein, YbgI/SA1388 family; Region: YbgI_SA1388; TIGR00486 1055527000923 Uncharacterized conserved protein [Function unknown]; Region: COG0327 1055527000924 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 1055527000925 Putative zinc ribbon domain; Region: DUF164; pfam02591 1055527000926 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 1055527000927 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 1055527000928 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 1055527000929 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1055527000930 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1055527000931 active site 1055527000932 prolipoprotein diacylglyceryl transferase; Region: lgt; TIGR00544 1055527000933 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 1055527000934 dimer interface [polypeptide binding]; other site 1055527000935 FMN binding site [chemical binding]; other site 1055527000936 competence/damage-inducible protein CinA C-terminal domain; Region: cinA_cterm; TIGR00199 1055527000937 putative recombination protein RecO; Provisional; Region: PRK13908 1055527000938 acetyl-CoA carboxylase, carboxyl transferase, beta subunit; Region: accD; TIGR00515 1055527000939 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 1055527000940 Uncharacterized conserved protein [Function unknown]; Region: COG1576 1055527000941 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 1055527000942 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 1055527000943 homotrimer interaction site [polypeptide binding]; other site 1055527000944 putative active site [active] 1055527000945 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 1055527000946 Streptococcal 67 kDa myosin-cross-reactive antigen like family; Region: Strep_67kDa_ant; cl17487 1055527000947 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 1055527000948 amino acid carrier protein; Region: agcS; TIGR00835 1055527000949 alanine racemase; Region: alr; TIGR00492 1055527000950 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 1055527000951 active site 1055527000952 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1055527000953 dimer interface [polypeptide binding]; other site 1055527000954 substrate binding site [chemical binding]; other site 1055527000955 catalytic residues [active] 1055527000956 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 1055527000957 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 1055527000958 substrate binding pocket [chemical binding]; other site 1055527000959 membrane-bound complex binding site; other site 1055527000960 hinge residues; other site 1055527000961 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 1055527000962 dimer interface [polypeptide binding]; other site 1055527000963 conserved gate region; other site 1055527000964 putative PBP binding loops; other site 1055527000965 ABC-ATPase subunit interface; other site 1055527000966 Uncharacterized conserved protein [Function unknown]; Region: COG1479 1055527000967 Protein of unknown function DUF262; Region: DUF262; pfam03235 1055527000968 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 1055527000969 metabolite-proton symporter; Region: 2A0106; TIGR00883 1055527000970 putative substrate translocation pore; other site 1055527000971 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527000972 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1055527000973 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 1055527000974 Coenzyme A binding pocket [chemical binding]; other site 1055527000975 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 1055527000976 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 1055527000977 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Region: rSAM_QueE_Ecoli; TIGR04322 1055527000978 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism]; Region: COG0720 1055527000979 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 1055527000980 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 1055527000981 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 1055527000982 substrate binding pocket [chemical binding]; other site 1055527000983 chain length determination region; other site 1055527000984 substrate-Mg2+ binding site; other site 1055527000985 catalytic residues [active] 1055527000986 aspartate-rich region 1; other site 1055527000987 active site lid residues [active] 1055527000988 aspartate-rich region 2; other site 1055527000989 GTP cyclohydrolase I; Region: folE; TIGR00063 1055527000990 GTP cyclohydrolase I; Provisional; Region: PLN03044 1055527000991 active site 1055527000992 heat shock protein HtpX; Provisional; Region: PRK02870 1055527000993 tRNA pseudouridine synthase, TruD family; Region: tRNA_TruD_broad; TIGR00094 1055527000994 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 1055527000995 Permutation of conserved domain; other site 1055527000996 active site 1055527000997 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 1055527000998 recombination protein RecR; Region: recR; TIGR00615 1055527000999 RecR protein; Region: RecR; pfam02132 1055527001000 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 1055527001001 putative active site [active] 1055527001002 putative metal-binding site [ion binding]; other site 1055527001003 tetramer interface [polypeptide binding]; other site 1055527001004 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 1055527001005 active site 1 [active] 1055527001006 dimer interface [polypeptide binding]; other site 1055527001007 hexamer interface [polypeptide binding]; other site 1055527001008 active site 2 [active] 1055527001009 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527001010 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 1055527001011 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 1055527001012 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 1055527001013 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 1055527001014 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1055527001015 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 1055527001016 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 1055527001017 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 1055527001018 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 1055527001019 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 1055527001020 potential frameshift: common BLAST hit: gi|254779520|ref|YP_003057626.1| carbamoyl phosphate synthase large subunit 1055527001021 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 1055527001022 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 1055527001023 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 1055527001024 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 1055527001025 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1055527001026 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527001027 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527001028 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 1055527001029 Part of AAA domain; Region: AAA_19; pfam13245 1055527001030 Family description; Region: UvrD_C_2; pfam13538 1055527001031 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 1055527001032 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 1055527001033 S-adenosylmethionine binding site [chemical binding]; other site 1055527001034 flagellar hook protein FlgE; Validated; Region: flgE; PRK05841 1055527001035 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1055527001036 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK05842 1055527001037 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 1055527001038 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 1055527001039 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 1055527001040 potential frameshift: common BLAST hit: gi|15611908|ref|NP_223559.1| phosphotransacetylase 1055527001041 potential frameshift: common BLAST hit: gi|15611908|ref|NP_223559.1| phosphotransacetylase 1055527001042 Acetokinase family; Region: Acetate_kinase; cl17229 1055527001043 Acetokinase family; Region: Acetate_kinase; cl17229 1055527001044 Acetokinase family; Region: Acetate_kinase; cl17229 1055527001045 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 1055527001046 hydrogenase accessory protein HypB; Region: hypB; TIGR00073 1055527001047 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 1055527001048 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypC; COG0298 1055527001049 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 1055527001050 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 1055527001051 Hydrogenase formation hypA family; Region: HypD; cl12072 1055527001052 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527001053 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041 1055527001054 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 1055527001055 short chain dehydrogenase; Provisional; Region: PRK06914 1055527001056 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 1055527001057 NADP binding site [chemical binding]; other site 1055527001058 active site 1055527001059 steroid binding site; other site 1055527001060 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 1055527001061 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 1055527001062 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 1055527001063 ABC-ATPase subunit interface; other site 1055527001064 dimer interface [polypeptide binding]; other site 1055527001065 putative PBP binding regions; other site 1055527001066 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 1055527001067 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 1055527001068 Walker A/P-loop; other site 1055527001069 ATP binding site [chemical binding]; other site 1055527001070 Q-loop/lid; other site 1055527001071 ABC transporter signature motif; other site 1055527001072 Walker B; other site 1055527001073 D-loop; other site 1055527001074 H-loop/switch region; other site 1055527001075 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 1055527001076 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 1055527001077 Ligand binding site; other site 1055527001078 metal-binding site 1055527001079 Vacuolating cyotoxin; Region: VacA; pfam02691 1055527001080 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1055527001081 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 1055527001082 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1055527001083 active site 1055527001084 HIGH motif; other site 1055527001085 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1055527001086 KMSKS motif; other site 1055527001087 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1055527001088 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 1055527001089 MviN-like protein; Region: MVIN; pfam03023 1055527001090 Holliday junction DNA helicase, RuvA subunit; Region: ruvA; TIGR00084 1055527001091 RuvA N terminal domain; Region: RuvA_N; pfam01330 1055527001092 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 1055527001093 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 1055527001094 Uncharacterized conserved protein [Function unknown]; Region: COG1432 1055527001095 LabA_like proteins; Region: LabA_like; cd06167 1055527001096 putative metal binding site [ion binding]; other site 1055527001097 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 1055527001098 active site 1055527001099 putative DNA-binding cleft [nucleotide binding]; other site 1055527001100 dimer interface [polypeptide binding]; other site 1055527001101 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 1055527001102 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 1055527001103 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 1055527001104 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 1055527001105 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 1055527001106 tetramer interface [polypeptide binding]; other site 1055527001107 heme binding pocket [chemical binding]; other site 1055527001108 NADPH binding site [chemical binding]; other site 1055527001109 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 1055527001110 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 1055527001111 PhnA protein; Region: PhnA; pfam03831 1055527001112 CDP-diacylglycerol pyrophosphatase, bacterial type; Region: cdh; TIGR00672 1055527001113 flagellar hook protein FlgE; Validated; Region: flgE; PRK08425 1055527001114 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 1055527001115 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 1055527001116 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 1055527001117 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1055527001118 hydrogenase nickel incorporation protein; Provisional; Region: hypA; PRK00564 1055527001119 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 1055527001120 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 1055527001121 lipid-A-disaccharide synthase; Region: lpxB; TIGR00215 1055527001122 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 1055527001123 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 1055527001124 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1055527001125 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1055527001126 trimer interface [polypeptide binding]; other site 1055527001127 active site 1055527001128 PQQ-like domain; Region: PQQ_2; pfam13360 1055527001129 pantothenate kinase; Reviewed; Region: PRK13333 1055527001130 Uncharacterized conserved protein [Function unknown]; Region: COG2836 1055527001131 D,D-heptose 1,7-bisphosphate phosphatase; Region: GmhB_yaeD; TIGR00213 1055527001132 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 1055527001133 active site 1055527001134 motif I; other site 1055527001135 motif II; other site 1055527001136 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1055527001137 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 1055527001138 NAD(P) binding site [chemical binding]; other site 1055527001139 active site 1055527001140 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 1055527001141 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 1055527001142 putative ribose interaction site [chemical binding]; other site 1055527001143 putative ADP binding site [chemical binding]; other site 1055527001144 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 1055527001145 active site 1055527001146 nucleotide binding site [chemical binding]; other site 1055527001147 HIGH motif; other site 1055527001148 KMSKS motif; other site 1055527001149 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 1055527001150 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 1055527001151 dimer interface [polypeptide binding]; other site 1055527001152 active site 1055527001153 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05458 1055527001154 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 1055527001155 active site 1055527001156 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 1055527001157 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1055527001158 Walker A/P-loop; other site 1055527001159 ATP binding site [chemical binding]; other site 1055527001160 Q-loop/lid; other site 1055527001161 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1055527001162 ABC transporter; Region: ABC_tran_2; pfam12848 1055527001163 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1055527001164 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2958 1055527001165 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 1055527001166 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 1055527001167 active site 1055527001168 type I restriction system adenine methylase (hsdM); Region: hsdM; TIGR00497 1055527001169 HsdM N-terminal domain; Region: HsdM_N; pfam12161 1055527001170 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 1055527001171 S-adenosylmethionine binding site [chemical binding]; other site 1055527001172 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1055527001173 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 1055527001174 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1055527001175 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 1055527001176 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 1055527001177 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 1055527001178 ATP binding site [chemical binding]; other site 1055527001179 putative Mg++ binding site [ion binding]; other site 1055527001180 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 1055527001181 substrate binding site [chemical binding]; other site 1055527001182 multimerization interface [polypeptide binding]; other site 1055527001183 ATP binding site [chemical binding]; other site 1055527001184 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 1055527001185 dimer interface [polypeptide binding]; other site 1055527001186 substrate binding site [chemical binding]; other site 1055527001187 ATP binding site [chemical binding]; other site 1055527001188 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 1055527001189 thiamine phosphate binding site [chemical binding]; other site 1055527001190 active site 1055527001191 pyrophosphate binding site [ion binding]; other site 1055527001192 phosphopantothenoylcysteine decarboxylase / phosphopantothenate--cysteine ligase; Region: coaBC_dfp; TIGR00521 1055527001193 Flavoprotein; Region: Flavoprotein; pfam02441 1055527001194 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 1055527001195 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 1055527001196 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 1055527001197 NAD(P) binding site [chemical binding]; other site 1055527001198 homodimer interface [polypeptide binding]; other site 1055527001199 substrate binding site [chemical binding]; other site 1055527001200 active site 1055527001201 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 1055527001202 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3018 1055527001203 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3018 1055527001204 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 1055527001205 IHF dimer interface [polypeptide binding]; other site 1055527001206 IHF - DNA interface [nucleotide binding]; other site 1055527001207 GTP-binding protein Der; Reviewed; Region: PRK00093 1055527001208 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 1055527001209 G1 box; other site 1055527001210 GTP/Mg2+ binding site [chemical binding]; other site 1055527001211 Switch I region; other site 1055527001212 G2 box; other site 1055527001213 Switch II region; other site 1055527001214 G3 box; other site 1055527001215 G4 box; other site 1055527001216 G5 box; other site 1055527001217 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 1055527001218 G1 box; other site 1055527001219 GTP/Mg2+ binding site [chemical binding]; other site 1055527001220 Switch I region; other site 1055527001221 G2 box; other site 1055527001222 G3 box; other site 1055527001223 Switch II region; other site 1055527001224 G4 box; other site 1055527001225 G5 box; other site 1055527001226 spermidine synthase; Provisional; Region: speE; PRK00536 1055527001227 spermidine synthase; Provisional; Region: PRK00811 1055527001228 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 1055527001229 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 1055527001230 CoA-binding site [chemical binding]; other site 1055527001231 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit; Region: gatA; TIGR00132 1055527001232 indole acetimide hydrolase; Validated; Region: PRK07488 1055527001233 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 1055527001234 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 1055527001235 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 1055527001236 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 1055527001237 active site 1055527001238 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 1055527001239 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 1055527001240 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 1055527001241 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 1055527001242 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 1055527001243 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1055527001244 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1055527001245 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 1055527001246 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 1055527001247 catalytic residues [active] 1055527001248 Predicted endonuclease distantly related to archaeal Holliday junction resolvase [DNA replication, recombination, and repair]; Region: COG0792 1055527001249 homoserine dehydrogenase; Provisional; Region: PRK06349 1055527001250 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 1055527001251 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 1055527001252 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 1055527001253 excinuclease ABC, C subunit; Region: uvrC; TIGR00194 1055527001254 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 1055527001255 GIY-YIG motif/motif A; other site 1055527001256 active site 1055527001257 catalytic site [active] 1055527001258 putative DNA binding site [nucleotide binding]; other site 1055527001259 metal binding site [ion binding]; metal-binding site 1055527001260 UvrB/uvrC motif; Region: UVR; pfam02151 1055527001261 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 1055527001262 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1055527001263 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1055527001264 Walker A/P-loop; other site 1055527001265 ATP binding site [chemical binding]; other site 1055527001266 Q-loop/lid; other site 1055527001267 ABC transporter signature motif; other site 1055527001268 Walker B; other site 1055527001269 D-loop; other site 1055527001270 H-loop/switch region; other site 1055527001271 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 1055527001272 dimer interface [polypeptide binding]; other site 1055527001273 conserved gate region; other site 1055527001274 ABC-ATPase subunit interface; other site 1055527001275 Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane]; Region: OpuBC; COG1732 1055527001276 flagellar motor protein MotB; Reviewed; Region: motB; PRK08457 1055527001277 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1055527001278 ligand binding site [chemical binding]; other site 1055527001279 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 1055527001280 flagellar motor protein MotA; Validated; Region: PRK08456 1055527001281 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism]; Region: ThiF; COG0476 1055527001282 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 1055527001283 ATP binding site [chemical binding]; other site 1055527001284 substrate interface [chemical binding]; other site 1055527001285 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1055527001286 Uncharacterized conserved protein [Function unknown]; Region: COG1565 1055527001287 RNA methyltransferase, RsmD family; Region: TIGR00095 1055527001288 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 1055527001289 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK08455 1055527001290 holo-[acyl-carrier-protein] synthase; Region: acpS; TIGR00516 1055527001291 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 1055527001292 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 1055527001293 N-terminal plug; other site 1055527001294 ligand-binding site [chemical binding]; other site 1055527001295 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 1055527001296 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 1055527001297 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09314 1055527001298 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: ribB; TIGR00506 1055527001299 GTP cyclohydrolase II [Coenzyme metabolism]; Region: RibA; COG0807 1055527001300 Domain of unknown function (DUF3943); Region: DUF3943; pfam13084 1055527001301 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 1055527001302 dimerization interface [polypeptide binding]; other site 1055527001303 active site 1055527001304 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 1055527001305 MoaE interaction surface [polypeptide binding]; other site 1055527001306 MoeB interaction surface [polypeptide binding]; other site 1055527001307 thiocarboxylated glycine; other site 1055527001308 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 1055527001309 MoaE homodimer interface [polypeptide binding]; other site 1055527001310 MoaD interaction [polypeptide binding]; other site 1055527001311 active site residues [active] 1055527001312 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 1055527001313 MPT binding site; other site 1055527001314 trimer interface [polypeptide binding]; other site 1055527001315 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 1055527001316 trimer interface [polypeptide binding]; other site 1055527001317 dimer interface [polypeptide binding]; other site 1055527001318 putative active site [active] 1055527001319 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 1055527001320 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527001321 trigger factor; Provisional; Region: tig; PRK01490 1055527001322 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1055527001323 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 1055527001324 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 1055527001325 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 1055527001326 oligomer interface [polypeptide binding]; other site 1055527001327 active site residues [active] 1055527001328 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 1055527001329 active site 1055527001330 catalytic residues [active] 1055527001331 metal binding site [ion binding]; metal-binding site 1055527001332 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 1055527001333 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 1055527001334 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 1055527001335 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 1055527001336 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 1055527001337 metal-binding site [ion binding] 1055527001338 heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase; Region: ATPase-IB2_Cd; TIGR01512 1055527001339 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1055527001340 Soluble P-type ATPase [General function prediction only]; Region: COG4087 1055527001341 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1055527001342 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 1055527001343 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1055527001344 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1055527001345 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 1055527001346 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1055527001347 FtsX-like permease family; Region: FtsX; pfam02687 1055527001348 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 1055527001349 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 1055527001350 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 1055527001351 nucleotide binding region [chemical binding]; other site 1055527001352 ATP-binding site [chemical binding]; other site 1055527001353 SEC-C motif; Region: SEC-C; pfam02810 1055527001354 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 1055527001355 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 1055527001356 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1055527001357 FOG: Transposase [DNA replication, recombination, and repair]; Region: COG5659 1055527001358 aconitate hydratase 2; Region: acnB; TIGR00117 1055527001359 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 1055527001360 substrate binding site [chemical binding]; other site 1055527001361 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 1055527001362 substrate binding site [chemical binding]; other site 1055527001363 ligand binding site [chemical binding]; other site 1055527001364 Predicted periplasmic solute-binding protein [General function prediction only]; Region: COG1427 1055527001365 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 1055527001366 putative nucleotide binding site [chemical binding]; other site 1055527001367 uridine monophosphate binding site [chemical binding]; other site 1055527001368 homohexameric interface [polypeptide binding]; other site 1055527001369 DNA-directed RNA polymerase, subunit K/omega [Transcription]; Region: RpoZ; COG1758 1055527001370 (p)ppGpp synthetase, RelA/SpoT family; Region: spoT_relA; TIGR00691 1055527001371 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1055527001372 Zn2+ binding site [ion binding]; other site 1055527001373 Mg2+ binding site [ion binding]; other site 1055527001374 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 1055527001375 synthetase active site [active] 1055527001376 NTP binding site [chemical binding]; other site 1055527001377 metal binding site [ion binding]; metal-binding site 1055527001378 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 1055527001379 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 1055527001380 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 1055527001381 active site 1055527001382 HIGH motif; other site 1055527001383 dimer interface [polypeptide binding]; other site 1055527001384 KMSKS motif; other site 1055527001385 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 1055527001386 RNA binding surface [nucleotide binding]; other site 1055527001387 Nitronate monooxygenase; Region: NMO; pfam03060 1055527001388 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 1055527001389 FMN binding site [chemical binding]; other site 1055527001390 substrate binding site [chemical binding]; other site 1055527001391 putative catalytic residue [active] 1055527001392 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 1055527001393 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 1055527001394 active site 1055527001395 metal binding site [ion binding]; metal-binding site 1055527001396 potential frameshift: common BLAST hit: gi|308184555|ref|YP_003928688.1| flagellar biosynthesis protein FlhB 1055527001397 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 1055527001398 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 1055527001399 GTP binding site; other site 1055527001400 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 1055527001401 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 1055527001402 FeS/SAM binding site; other site 1055527001403 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 1055527001404 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 1055527001405 signal recognition particle-docking protein FtsY; Region: ftsY; TIGR00064 1055527001406 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 1055527001407 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 1055527001408 phosphodiesterase; Provisional; Region: PRK12704 1055527001409 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 1055527001410 nucleic acid binding region [nucleotide binding]; other site 1055527001411 G-X-X-G motif; other site 1055527001412 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1055527001413 Zn2+ binding site [ion binding]; other site 1055527001414 Mg2+ binding site [ion binding]; other site 1055527001415 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Thermotoga marina NorM; Region: MATE_NorM_like; cd13137 1055527001416 putative efflux protein, MATE family; Region: matE; TIGR00797 1055527001417 Predicted permease [General function prediction only]; Region: COG2056 1055527001418 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 1055527001419 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 1055527001420 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 1055527001421 putative active site; other site 1055527001422 catalytic triad [active] 1055527001423 putative dimer interface [polypeptide binding]; other site 1055527001424 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 1055527001425 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 1055527001426 putative ATP binding site [chemical binding]; other site 1055527001427 putative substrate interface [chemical binding]; other site 1055527001428 flagellar biosynthetic protein FliS; Region: fliS; TIGR00208 1055527001429 flagellar capping protein; Validated; Region: fliD; PRK08453 1055527001430 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 1055527001431 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 1055527001432 flagellar protein FlaG; Provisional; Region: PRK08452 1055527001433 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1055527001434 Peptidase family M23; Region: Peptidase_M23; pfam01551 1055527001435 potential frameshift: common BLAST hit: gi|254779275|ref|YP_003057380.1| ABC-type transport system, permease component; cell division 1055527001436 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1055527001437 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1055527001438 Walker A/P-loop; other site 1055527001439 ATP binding site [chemical binding]; other site 1055527001440 Q-loop/lid; other site 1055527001441 ABC transporter signature motif; other site 1055527001442 Walker B; other site 1055527001443 D-loop; other site 1055527001444 H-loop/switch region; other site 1055527001445 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 1055527001446 S-adenosylmethionine binding site [chemical binding]; other site 1055527001447 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 1055527001448 Fibronectin type 3 domain-containing protein [General function prediction only]; Region: COG3401 1055527001449 Interdomain contacts; other site 1055527001450 Cytokine receptor motif; other site 1055527001451 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 1055527001452 Interdomain contacts; other site 1055527001453 Cytokine receptor motif; other site 1055527001454 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 1055527001455 Interdomain contacts; other site 1055527001456 Cytokine receptor motif; other site 1055527001457 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1055527001458 S4 RNA-binding domain; Region: S4; smart00363 1055527001459 RNA binding surface [nucleotide binding]; other site 1055527001460 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1055527001461 active site 1055527001462 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 1055527001463 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 1055527001464 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 1055527001465 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1055527001466 active site 1055527001467 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 1055527001468 nucleotide binding site/active site [active] 1055527001469 HIT family signature motif; other site 1055527001470 catalytic residue [active] 1055527001471 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 1055527001472 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1055527001473 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1055527001474 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 1055527001475 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 1055527001476 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1055527001477 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 1055527001478 tetramer interfaces [polypeptide binding]; other site 1055527001479 binuclear metal-binding site [ion binding]; other site 1055527001480 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 1055527001481 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1055527001482 catalytic residue [active] 1055527001483 Predicted phosphoribosyltransferases [General function prediction only]; Region: COG2236 1055527001484 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1055527001485 active site 1055527001486 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 1055527001487 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1055527001488 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 1055527001489 FeS/SAM binding site; other site 1055527001490 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 1055527001491 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 1055527001492 cofactor binding site; other site 1055527001493 DNA binding site [nucleotide binding] 1055527001494 substrate interaction site [chemical binding]; other site 1055527001495 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 1055527001496 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 1055527001497 cofactor binding site; other site 1055527001498 DNA binding site [nucleotide binding] 1055527001499 substrate interaction site [chemical binding]; other site 1055527001500 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 1055527001501 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 1055527001502 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 1055527001503 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 1055527001504 Ligand Binding Site [chemical binding]; other site 1055527001505 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 1055527001506 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 1055527001507 FMN binding site [chemical binding]; other site 1055527001508 active site 1055527001509 catalytic residues [active] 1055527001510 substrate binding site [chemical binding]; other site 1055527001511 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527001512 anaerobic c4-dicarboxylate membrane transporter family protein; Region: Dcu; TIGR00770 1055527001513 Anaerobic C4-dicarboxylate transporter [General function prediction only]; Region: DcuB; COG2704 1055527001514 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 1055527001515 active site 1055527001516 homodimer interface [polypeptide binding]; other site 1055527001517 homotetramer interface [polypeptide binding]; other site 1055527001518 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527001519 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 1055527001520 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 1055527001521 Lysine efflux permease [General function prediction only]; Region: COG1279 1055527001522 DNA polymerase III subunits gamma and tau; Validated; Region: PRK08451 1055527001523 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 1055527001524 Walker A motif; other site 1055527001525 ATP binding site [chemical binding]; other site 1055527001526 Walker B motif; other site 1055527001527 arginine finger; other site 1055527001528 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 1055527001529 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 1055527001530 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 1055527001531 Walker A/P-loop; other site 1055527001532 ATP binding site [chemical binding]; other site 1055527001533 Q-loop/lid; other site 1055527001534 ABC transporter signature motif; other site 1055527001535 Walker B; other site 1055527001536 D-loop; other site 1055527001537 H-loop/switch region; other site 1055527001538 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 1055527001539 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 1055527001540 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 1055527001541 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 1055527001542 Fic family protein [Function unknown]; Region: COG3177 1055527001543 Fic/DOC family; Region: Fic; pfam02661 1055527001544 Competence protein ComGF [Intracellular trafficking and secretion]; Region: ComGF; COG4940 1055527001545 Predicted hydrolases of HD superfamily [General function prediction only]; Region: COG1896 1055527001546 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527001547 Uncharacterized conserved protein [Function unknown]; Region: COG1912 1055527001548 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 1055527001549 16S rRNA (cytosine(1402)-N(4))-methyltransferase; Region: TIGR00006 1055527001550 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527001551 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 1055527001552 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1055527001553 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1055527001554 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 1055527001555 Response regulator receiver domain; Region: Response_reg; pfam00072 1055527001556 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 1055527001557 active site 1055527001558 phosphorylation site [posttranslational modification] 1055527001559 intermolecular recognition site; other site 1055527001560 dimerization interface [polypeptide binding]; other site 1055527001561 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 1055527001562 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 1055527001563 Walker A motif; other site 1055527001564 ATP binding site [chemical binding]; other site 1055527001565 Walker B motif; other site 1055527001566 arginine finger; other site 1055527001567 DNA gyrase subunit A; Validated; Region: PRK05560 1055527001568 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 1055527001569 CAP-like domain; other site 1055527001570 active site 1055527001571 primary dimer interface [polypeptide binding]; other site 1055527001572 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1055527001573 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1055527001574 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1055527001575 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1055527001576 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1055527001577 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1055527001578 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 1055527001579 putative acyltransferase; Provisional; Region: PRK05790 1055527001580 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 1055527001581 dimer interface [polypeptide binding]; other site 1055527001582 active site 1055527001583 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 1055527001584 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 1055527001585 Short chain fatty acid transporter; Region: SCFA_trans; pfam02667 1055527001586 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3528 1055527001587 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 1055527001588 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 1055527001589 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 1055527001590 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 1055527001591 Hydantoinase B/oxoprolinase; Region: Hydantoinase_B; pfam02538 1055527001592 Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcxC; COG4647 1055527001593 Acetone carboxylase gamma subunit; Region: Acetone_carb_G; pfam08882 1055527001594 CfrBI restriction endonuclease; Region: RE_CfrBI; pfam09516 1055527001595 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 1055527001596 DNA methylase; Region: N6_N4_Mtase; pfam01555 1055527001597 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 1055527001598 active site 1055527001599 catalytic site [active] 1055527001600 substrate binding site [chemical binding]; other site 1055527001601 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 1055527001602 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 1055527001603 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 1055527001604 G1 box; other site 1055527001605 GTP/Mg2+ binding site [chemical binding]; other site 1055527001606 Switch I region; other site 1055527001607 G2 box; other site 1055527001608 G3 box; other site 1055527001609 Switch II region; other site 1055527001610 G4 box; other site 1055527001611 G5 box; other site 1055527001612 Nucleoside recognition; Region: Gate; pfam07670 1055527001613 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 1055527001614 Nucleoside recognition; Region: Gate; pfam07670 1055527001615 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 1055527001616 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 1055527001617 N-terminal plug; other site 1055527001618 ligand-binding site [chemical binding]; other site 1055527001619 potential frameshift: common BLAST hit: gi|210134891|ref|YP_002301330.1| flagellar biosynthesis protein FliP 1055527001620 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14359 1055527001621 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 1055527001622 Substrate binding site; other site 1055527001623 Mg++ binding site; other site 1055527001624 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 1055527001625 active site 1055527001626 substrate binding site [chemical binding]; other site 1055527001627 CoA binding site [chemical binding]; other site 1055527001628 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK08447 1055527001629 ATP cone domain; Region: ATP-cone; pfam03477 1055527001630 Class I ribonucleotide reductase; Region: RNR_I; cd01679 1055527001631 active site 1055527001632 dimer interface [polypeptide binding]; other site 1055527001633 catalytic residues [active] 1055527001634 effector binding site; other site 1055527001635 R2 peptide binding site; other site 1055527001636 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 1055527001637 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 1055527001638 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 1055527001639 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 1055527001640 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 1055527001641 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 1055527001642 DNA binding site [nucleotide binding] 1055527001643 active site 1055527001644 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 1055527001645 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 1055527001646 active site 1055527001647 DNA binding site [nucleotide binding] 1055527001648 Int/Topo IB signature motif; other site 1055527001649 aspartate aminotransferase; Provisional; Region: PRK05764 1055527001650 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 1055527001651 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1055527001652 homodimer interface [polypeptide binding]; other site 1055527001653 catalytic residue [active] 1055527001654 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527001655 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 1055527001656 Predicted helicase [General function prediction only]; Region: COG4889 1055527001657 Predicted helicase [General function prediction only]; Region: COG4889 1055527001658 Restriction endonuclease; Region: Mrr_cat; pfam04471 1055527001659 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 1055527001660 ATP binding site [chemical binding]; other site 1055527001661 putative Mg++ binding site [ion binding]; other site 1055527001662 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 1055527001663 nucleotide binding region [chemical binding]; other site 1055527001664 ATP-binding site [chemical binding]; other site 1055527001665 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 1055527001666 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 1055527001667 Cysteine-rich domain; Region: CCG; pfam02754 1055527001668 Cysteine-rich domain; Region: CCG; pfam02754 1055527001669 oxygen-independent coproporphyrinogen III oxidase; Region: hemN; TIGR00538 1055527001670 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 1055527001671 FeS/SAM binding site; other site 1055527001672 HemN C-terminal domain; Region: HemN_C; pfam06969 1055527001673 Protein of unknown function (DUF2603); Region: DUF2603; pfam10788 1055527001674 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 1055527001675 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 1055527001676 Tetramer interface [polypeptide binding]; other site 1055527001677 active site 1055527001678 FMN-binding site [chemical binding]; other site 1055527001679 ribonuclease III; Reviewed; Region: rnc; PRK00102 1055527001680 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 1055527001681 dimerization interface [polypeptide binding]; other site 1055527001682 active site 1055527001683 metal binding site [ion binding]; metal-binding site 1055527001684 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 1055527001685 dsRNA binding site [nucleotide binding]; other site 1055527001686 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 1055527001687 RNA/DNA hybrid binding site [nucleotide binding]; other site 1055527001688 active site 1055527001689 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]; Region: COG2956 1055527001690 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]; Region: COG1439 1055527001691 SurA N-terminal domain; Region: SurA_N; pfam09312 1055527001692 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 1055527001693 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 1055527001694 GatB domain; Region: GatB_Yqey; smart00845 1055527001695 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1055527001696 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1055527001697 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1055527001698 hypothetical protein; Provisional; Region: PRK08445 1055527001699 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 1055527001700 FeS/SAM binding site; other site 1055527001701 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 1055527001702 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1055527001703 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1055527001704 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1055527001705 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1055527001706 Surface antigen; Region: Bac_surface_Ag; pfam01103 1055527001707 hypothetical protein; Provisional; Region: PRK08444 1055527001708 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 1055527001709 FeS/SAM binding site; other site 1055527001710 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 1055527001711 Ferritin-like domain; Region: Ferritin; pfam00210 1055527001712 ferroxidase diiron center [ion binding]; other site 1055527001713 phosphoserine phosphatase SerB; Region: serB; TIGR00338 1055527001714 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 1055527001715 motif II; other site 1055527001716 Glycosyltransferase family 10 (fucosyltransferase); Region: Glyco_transf_10; pfam00852 1055527001717 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_2; cd10034 1055527001718 putative uracil binding site [chemical binding]; other site 1055527001719 putative active site [active] 1055527001720 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 1055527001721 Aspartase; Region: Aspartase; cd01357 1055527001722 active sites [active] 1055527001723 tetramer interface [polypeptide binding]; other site 1055527001724 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 1055527001725 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 1055527001726 hinge; other site 1055527001727 active site 1055527001728 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 1055527001729 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 1055527001730 active site 1055527001731 tetramer interface; other site 1055527001732 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1055527001733 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 1055527001734 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1055527001735 catalytic residue [active] 1055527001736 YGGT family; Region: YGGT; pfam02325 1055527001737 glutamylglutaminyl-tRNA synthetase; Provisional; Region: PRK12410 1055527001738 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1055527001739 active site 1055527001740 HIGH motif; other site 1055527001741 nucleotide binding site [chemical binding]; other site 1055527001742 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1055527001743 active site 1055527001744 KMSKS motif; other site 1055527001745 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 1055527001746 dimer interface [polypeptide binding]; other site 1055527001747 FMN binding site [chemical binding]; other site 1055527001748 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 1055527001749 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 1055527001750 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_4; cd07822 1055527001751 putative hydrophobic ligand binding site [chemical binding]; other site 1055527001752 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 1055527001753 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 1055527001754 active site 1055527001755 NTP binding site [chemical binding]; other site 1055527001756 metal binding triad [ion binding]; metal-binding site 1055527001757 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 1055527001758 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 1055527001759 Ligand Binding Site [chemical binding]; other site 1055527001760 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527001761 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 1055527001762 nickel binding site [ion binding]; other site 1055527001763 putative substrate-binding site; other site 1055527001764 Ni,Fe-hydrogenase I cytochrome b subunit [Energy production and conversion]; Region: HyaC; COG1969 1055527001765 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 1055527001766 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 1055527001767 hydrogenase (NiFe) small subunit (hydA); Region: hydA; TIGR00391 1055527001768 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 1055527001769 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 1055527001770 Uncharacterized conserved protein [Function unknown]; Region: COG1479 1055527001771 Protein of unknown function DUF262; Region: DUF262; pfam03235 1055527001772 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 1055527001773 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1055527001774 Sel1-like repeats; Region: SEL1; smart00671 1055527001775 Sel1-like repeats; Region: SEL1; smart00671 1055527001776 Sel1 repeat; Region: Sel1; cl02723 1055527001777 Sel1-like repeats; Region: SEL1; smart00671 1055527001778 Tetrahydrodipicolinate N-succinyltransferase [Amino acid transport and metabolism]; Region: DapD; COG2171 1055527001779 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 1055527001780 putative trimer interface [polypeptide binding]; other site 1055527001781 putative CoA binding site [chemical binding]; other site 1055527001782 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 1055527001783 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 1055527001784 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 1055527001785 hypothetical protein; Provisional; Region: PRK05839 1055527001786 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 1055527001787 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1055527001788 homodimer interface [polypeptide binding]; other site 1055527001789 catalytic residue [active] 1055527001790 UDP-N-acetylmuramate--alanine ligase; Region: murC; TIGR01082 1055527001791 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1055527001792 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1055527001793 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1055527001794 MutS2 family protein; Region: mutS2; TIGR01069 1055527001795 ATPase domain of DNA mismatch repair MUTS family; Region: MUTSac; smart00534 1055527001796 Walker A/P-loop; other site 1055527001797 ATP binding site [chemical binding]; other site 1055527001798 Q-loop/lid; other site 1055527001799 ABC transporter signature motif; other site 1055527001800 Walker B; other site 1055527001801 D-loop; other site 1055527001802 H-loop/switch region; other site 1055527001803 Smr domain; Region: Smr; pfam01713 1055527001804 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 1055527001805 dimer interface [polypeptide binding]; other site 1055527001806 substrate binding site [chemical binding]; other site 1055527001807 metal binding sites [ion binding]; metal-binding site 1055527001808 Glycosyltransferase involved in LPS biosynthesis [Cell envelope biogenesis, outer membrane]; Region: COG3306 1055527001809 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 1055527001810 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 1055527001811 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 1055527001812 adenylate kinase; Reviewed; Region: adk; PRK00279 1055527001813 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 1055527001814 AMP-binding site [chemical binding]; other site 1055527001815 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 1055527001816 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 1055527001817 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 1055527001818 dimer interface [polypeptide binding]; other site 1055527001819 anticodon binding site; other site 1055527001820 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 1055527001821 homodimer interface [polypeptide binding]; other site 1055527001822 motif 1; other site 1055527001823 active site 1055527001824 motif 2; other site 1055527001825 GAD domain; Region: GAD; pfam02938 1055527001826 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 1055527001827 active site 1055527001828 motif 3; other site 1055527001829 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 1055527001830 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 1055527001831 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 1055527001832 active site 1055527001833 phosphorylation site [posttranslational modification] 1055527001834 intermolecular recognition site; other site 1055527001835 dimerization interface [polypeptide binding]; other site 1055527001836 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 1055527001837 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 1055527001838 nucleotide binding pocket [chemical binding]; other site 1055527001839 K-X-D-G motif; other site 1055527001840 catalytic site [active] 1055527001841 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 1055527001842 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 1055527001843 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 1055527001844 Dimer interface [polypeptide binding]; other site 1055527001845 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1055527001846 ABC transporter signature motif; other site 1055527001847 Walker B; other site 1055527001848 D-loop; other site 1055527001849 H-loop/switch region; other site 1055527001850 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 1055527001851 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 1055527001852 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 1055527001853 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 1055527001854 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 1055527001855 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 1055527001856 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 1055527001857 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1055527001858 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527001859 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 1055527001860 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1055527001861 HlyD family secretion protein; Region: HlyD_3; pfam13437 1055527001862 Outer membrane efflux protein; Region: OEP; pfam02321 1055527001863 Outer membrane efflux protein; Region: OEP; pfam02321 1055527001864 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 1055527001865 substrate binding site [chemical binding]; other site 1055527001866 active site 1055527001867 3-methyladenine DNA glycosylase; Provisional; Region: PRK13913 1055527001868 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1055527001869 minor groove reading motif; other site 1055527001870 helix-hairpin-helix signature motif; other site 1055527001871 active site 1055527001872 flagellin A; Reviewed; Region: PRK12584 1055527001873 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 1055527001874 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 1055527001875 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 1055527001876 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 1055527001877 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1055527001878 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1055527001879 ABC transporter; Region: ABC_tran; pfam00005 1055527001880 Q-loop/lid; other site 1055527001881 ABC transporter signature motif; other site 1055527001882 Walker B; other site 1055527001883 D-loop; other site 1055527001884 H-loop/switch region; other site 1055527001885 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1055527001886 dimer interface [polypeptide binding]; other site 1055527001887 putative CheW interface [polypeptide binding]; other site 1055527001888 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 1055527001889 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 1055527001890 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1055527001891 catalytic residue [active] 1055527001892 Transglycosylase; Region: Transgly; pfam00912 1055527001893 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 1055527001894 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1055527001895 tumor necrosis factor alpha-inducing protein; Reviewed; Region: PRK12303 1055527001896 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 1055527001897 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG5610 1055527001898 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 1055527001899 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 1055527001900 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 1055527001901 2-oxoglutarate-acceptor oxidoreductase subunit OorB; Reviewed; Region: oorB; PRK09628 1055527001902 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 1055527001903 TPP-binding site [chemical binding]; other site 1055527001904 2-oxoglutarate-acceptor oxidoreductase subunit OorA; Reviewed; Region: oorA; PRK09627 1055527001905 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 1055527001906 dimer interface [polypeptide binding]; other site 1055527001907 PYR/PP interface [polypeptide binding]; other site 1055527001908 TPP binding site [chemical binding]; other site 1055527001909 substrate binding site [chemical binding]; other site 1055527001910 2-oxoglutarate-acceptor oxidoreductase subunit OorD; Reviewed; Region: oorD; PRK09626 1055527001911 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 1055527001912 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 1055527001913 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 1055527001914 dimerization interface [polypeptide binding]; other site 1055527001915 Protein of unknown function; Region: DUF3971; pfam13116 1055527001916 AsmA-like C-terminal region; Region: AsmA_1; pfam13109 1055527001917 Fe2+ transport system protein A [Inorganic ion transport and metabolism]; Region: FeoA; COG1918 1055527001918 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 1055527001919 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1055527001920 minor groove reading motif; other site 1055527001921 helix-hairpin-helix signature motif; other site 1055527001922 substrate binding pocket [chemical binding]; other site 1055527001923 active site 1055527001924 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 1055527001925 flagellar motor switch protein; Validated; Region: PRK08433 1055527001926 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 1055527001927 TonB family C-terminal domain; Region: tonB_Cterm; TIGR01352 1055527001928 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 1055527001929 active site 1055527001930 substrate binding pocket [chemical binding]; other site 1055527001931 dimer interface [polypeptide binding]; other site 1055527001932 Predicted neuraminidase (sialidase) [Carbohydrate transport and metabolism]; Region: COG4692 1055527001933 BNR repeat-like domain; Region: BNR_2; pfam13088 1055527001934 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 1055527001935 Sulfatase; Region: Sulfatase; pfam00884 1055527001936 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14191 1055527001937 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 1055527001938 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 1055527001939 homodimer interface [polypeptide binding]; other site 1055527001940 NADP binding site [chemical binding]; other site 1055527001941 substrate binding site [chemical binding]; other site 1055527001942 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 1055527001943 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 1055527001944 Catalytic site [active] 1055527001945 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 1055527001946 Peptidase family M50; Region: Peptidase_M50; pfam02163 1055527001947 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 1055527001948 active site 1055527001949 putative substrate binding region [chemical binding]; other site 1055527001950 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 1055527001951 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 1055527001952 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1055527001953 active site 1055527001954 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 1055527001955 multifunctional aminopeptidase A; Provisional; Region: PRK00913 1055527001956 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 1055527001957 interface (dimer of trimers) [polypeptide binding]; other site 1055527001958 Substrate-binding/catalytic site; other site 1055527001959 Zn-binding sites [ion binding]; other site 1055527001960 GTP-binding protein YchF; Reviewed; Region: PRK09601 1055527001961 YchF GTPase; Region: YchF; cd01900 1055527001962 G1 box; other site 1055527001963 GTP/Mg2+ binding site [chemical binding]; other site 1055527001964 Switch I region; other site 1055527001965 G2 box; other site 1055527001966 Switch II region; other site 1055527001967 G3 box; other site 1055527001968 G4 box; other site 1055527001969 G5 box; other site 1055527001970 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 1055527001971 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 1055527001972 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 1055527001973 Domain of unknown function DUF20; Region: UPF0118; pfam01594 1055527001974 diaminopimelate epimerase; Region: DapF; TIGR00652 1055527001975 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1055527001976 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1055527001977 Predicted membrane protein [Function unknown]; Region: COG3059 1055527001978 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 1055527001979 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 1055527001980 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1055527001981 NAD(P) binding site [chemical binding]; other site 1055527001982 active site 1055527001983 acyl carrier protein; Provisional; Region: acpP; PRK00982 1055527001984 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK08439 1055527001985 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 1055527001986 dimer interface [polypeptide binding]; other site 1055527001987 active site 1055527001988 acetyl-CoA carboxylase, carboxyl transferase, alpha subunit; Region: accA; TIGR00513 1055527001989 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 1055527001990 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 1055527001991 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 1055527001992 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 1055527001993 Predicted methyltransferases [General function prediction only]; Region: COG0313 1055527001994 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 1055527001995 putative SAM binding site [chemical binding]; other site 1055527001996 putative homodimer interface [polypeptide binding]; other site 1055527001997 Ribosomal protein L31; Region: Ribosomal_L31; pfam01197 1055527001998 transcription termination factor Rho; Provisional; Region: rho; PRK09376 1055527001999 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 1055527002000 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 1055527002001 RNA binding site [nucleotide binding]; other site 1055527002002 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 1055527002003 multimer interface [polypeptide binding]; other site 1055527002004 Walker A motif; other site 1055527002005 ATP binding site [chemical binding]; other site 1055527002006 Walker B motif; other site 1055527002007 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 1055527002008 AAA domain; Region: AAA_12; pfam13087 1055527002009 CagA exotoxin; Region: CagA; pfam03507 1055527002010 AAA domain; Region: AAA_12; pfam13087 1055527002011 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 1055527002012 GTPase [General function prediction only]; Region: Era; COG1159 1055527002013 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 1055527002014 G1 box; other site 1055527002015 GTP/Mg2+ binding site [chemical binding]; other site 1055527002016 Switch I region; other site 1055527002017 G2 box; other site 1055527002018 Switch II region; other site 1055527002019 G3 box; other site 1055527002020 G4 box; other site 1055527002021 G5 box; other site 1055527002022 KH domain; Region: KH_2; pfam07650 1055527002023 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 1055527002024 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 1055527002025 Walker A motif; other site 1055527002026 ATP binding site [chemical binding]; other site 1055527002027 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 1055527002028 Walker B motif; other site 1055527002029 arginine finger; other site 1055527002030 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1055527002031 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 1055527002032 active site 1055527002033 HslU subunit interaction site [polypeptide binding]; other site 1055527002034 ribosomal protein L9; Region: L9; TIGR00158 1055527002035 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 1055527002036 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 1055527002037 Uncharacterized conserved protein [Function unknown]; Region: COG1479 1055527002038 Protein of unknown function DUF262; Region: DUF262; pfam03235 1055527002039 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 1055527002040 Uncharacterized conserved protein [Function unknown]; Region: COG3586 1055527002041 glutamine synthetase, type I; Region: GlnA; TIGR00653 1055527002042 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 1055527002043 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1055527002044 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1055527002045 Sel1-like repeats; Region: SEL1; smart00671 1055527002046 DNA topoisomerase I; Validated; Region: PRK06599 1055527002047 Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion]; Region: VirD4; COG3505 1055527002048 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 1055527002049 Walker A motif; other site 1055527002050 ATP binding site [chemical binding]; other site 1055527002051 Walker B motif; other site 1055527002052 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 1055527002053 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 1055527002054 ATP binding site [chemical binding]; other site 1055527002055 Walker A motif; other site 1055527002056 hexamer interface [polypeptide binding]; other site 1055527002057 Walker B motif; other site 1055527002058 CagZ; Region: CagZ; pfam09053 1055527002059 DC-EC Repeat; Region: CagY_M; pfam07337 1055527002060 DC-EC Repeat; Region: CagY_M; pfam07337 1055527002061 DC-EC Repeat; Region: CagY_M; pfam07337 1055527002062 DC-EC Repeat; Region: CagY_M; pfam07337 1055527002063 DC-EC Repeat; Region: CagY_M; pfam07337 1055527002064 DC-EC Repeat; Region: CagY_M; pfam07337 1055527002065 DC-EC Repeat; Region: CagY_M; pfam07337 1055527002066 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 1055527002067 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 1055527002068 Protein of unknown function (DUF3807); Region: DUF3807; pfam12720 1055527002069 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 1055527002070 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 1055527002071 VirB7 interaction site; other site 1055527002072 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 1055527002073 Cag pathogenicity island protein Cag12; Region: Cag12; pfam13117 1055527002074 prolyl-tRNA synthetase; Provisional; Region: PRK08661 1055527002075 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 1055527002076 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1055527002077 dihydrodipicolinate reductase; Region: dapB; TIGR00036 1055527002078 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 1055527002079 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 1055527002080 FAD binding domain; Region: FAD_binding_4; pfam01565 1055527002081 glycolate oxidase, subunit GlcD; Region: glcD; TIGR00387 1055527002082 Protein-interacting Bro1-like domain of mammalian Alix and related domains; Region: BRO1_Alix_like; cl14649 1055527002083 nudix-type nucleoside diphosphatase, YffH/AdpP family; Region: TIGR00052 1055527002084 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 1055527002085 dimer interface [polypeptide binding]; other site 1055527002086 ADP-ribose binding site [chemical binding]; other site 1055527002087 active site 1055527002088 nudix motif; other site 1055527002089 metal binding site [ion binding]; metal-binding site 1055527002090 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1055527002091 Peptidase family M23; Region: Peptidase_M23; pfam01551 1055527002092 R.Pab1 restriction endonuclease; Region: RE_R_Pab1; pfam09522 1055527002093 TrbC/VIRB2 family; Region: TrbC; pfam04956 1055527002094 potential frameshift: common BLAST hit: gi|298736044|ref|YP_003728569.1| type IV secretion system protein VirB4 1055527002095 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 1055527002096 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 1055527002097 VirB7 interaction site; other site 1055527002098 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 1055527002099 phosphodiesterase; Provisional; Region: PRK12704 1055527002100 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 1055527002101 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 1055527002102 Walker A motif; other site 1055527002103 hexamer interface [polypeptide binding]; other site 1055527002104 ATP binding site [chemical binding]; other site 1055527002105 Walker B motif; other site 1055527002106 Type IV secretory system Conjugative DNA transfer; Region: T4SS-DNA_transf; pfam02534 1055527002107 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 1055527002108 Walker A motif; other site 1055527002109 ATP binding site [chemical binding]; other site 1055527002110 Walker B motif; other site 1055527002111 Methyltransferase domain; Region: Methyltransf_26; pfam13659 1055527002112 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 1055527002113 DEAD-like helicases superfamily; Region: DEXDc; smart00487 1055527002114 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 1055527002115 ATP binding site [chemical binding]; other site 1055527002116 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 1055527002117 helicase superfamily c-terminal domain; Region: HELICc; smart00490 1055527002118 nucleotide binding region [chemical binding]; other site 1055527002119 ATP-binding site [chemical binding]; other site 1055527002120 Topoisomerase IA [DNA replication, recombination, and repair]; Region: TopA; COG0550 1055527002121 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 1055527002122 active site 1055527002123 metal binding site [ion binding]; metal-binding site 1055527002124 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 1055527002125 domain I; other site 1055527002126 DNA binding groove [nucleotide binding] 1055527002127 phosphate binding site [ion binding]; other site 1055527002128 domain II; other site 1055527002129 domain III; other site 1055527002130 nucleotide binding site [chemical binding]; other site 1055527002131 catalytic site [active] 1055527002132 domain IV; other site 1055527002133 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 1055527002134 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 1055527002135 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 1055527002136 P-loop; other site 1055527002137 Magnesium ion binding site [ion binding]; other site 1055527002138 Protein of unknown function (DUF3991); Region: DUF3991; pfam13154 1055527002139 Toprim-like; Region: Toprim_2; pfam13155 1055527002140 Type IV secretory pathway, TrbL components [Intracellular trafficking and secretion]; Region: TrbL; COG3846 1055527002141 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 1055527002142 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 1055527002143 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 1055527002144 active site 1055527002145 catalytic residues [active] 1055527002146 DNA binding site [nucleotide binding] 1055527002147 Int/Topo IB signature motif; other site 1055527002148 potential frameshift: common BLAST hit: gi|308185146|ref|YP_003929279.1| relaxase 1055527002149 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 1055527002150 Toprim-like; Region: Toprim_2; pfam13155 1055527002151 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1055527002152 Peptidase family M23; Region: Peptidase_M23; pfam01551 1055527002153 R.Pab1 restriction endonuclease; Region: RE_R_Pab1; pfam09522 1055527002154 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 1055527002155 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 1055527002156 Mg2+ binding site [ion binding]; other site 1055527002157 G-X-G motif; other site 1055527002158 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 1055527002159 anchoring element; other site 1055527002160 dimer interface [polypeptide binding]; other site 1055527002161 ATP binding site [chemical binding]; other site 1055527002162 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 1055527002163 active site 1055527002164 putative metal-binding site [ion binding]; other site 1055527002165 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1055527002166 DNA polymerase III, beta subunit; Region: dnan; TIGR00663 1055527002167 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 1055527002168 putative DNA binding surface [nucleotide binding]; other site 1055527002169 dimer interface [polypeptide binding]; other site 1055527002170 beta-clamp/translesion DNA polymerase binding surface; other site 1055527002171 beta-clamp/clamp loader binding surface; other site 1055527002172 The outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of acylester bonds in phospholipids using calcium as a cofactor. The enzyme has a fold of transmembrane beta-barrels and is widespread among...; Region: OMPLA; cd00541 1055527002173 dimerization interface [polypeptide binding]; other site 1055527002174 substrate binding site [chemical binding]; other site 1055527002175 active site 1055527002176 calcium binding site [ion binding]; other site 1055527002177 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 1055527002178 Na2 binding site [ion binding]; other site 1055527002179 putative substrate binding site 1 [chemical binding]; other site 1055527002180 Na binding site 1 [ion binding]; other site 1055527002181 putative substrate binding site 2 [chemical binding]; other site 1055527002182 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 1055527002183 Na2 binding site [ion binding]; other site 1055527002184 putative substrate binding site 1 [chemical binding]; other site 1055527002185 Na binding site 1 [ion binding]; other site 1055527002186 putative substrate binding site 2 [chemical binding]; other site 1055527002187 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 1055527002188 active site 1055527002189 Protein of unknown function (DUF493); Region: DUF493; pfam04359 1055527002190 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03815 1055527002191 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1055527002192 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1055527002193 phospho-N-acetylmuramoyl-pentapeptide-transferase; Region: mraY; TIGR00445 1055527002194 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 1055527002195 Mg++ binding site [ion binding]; other site 1055527002196 putative catalytic motif [active] 1055527002197 putative substrate binding site [chemical binding]; other site 1055527002198 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 1055527002199 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 1055527002200 Cation transport protein; Region: TrkH; cl17365 1055527002201 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 1055527002202 TrkA-N domain; Region: TrkA_N; pfam02254 1055527002203 TrkA-C domain; Region: TrkA_C; pfam02080 1055527002204 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 1055527002205 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1055527002206 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1055527002207 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 1055527002208 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 1055527002209 putative heme binding pocket [chemical binding]; other site 1055527002210 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 1055527002211 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 1055527002212 cofactor binding site; other site 1055527002213 DNA binding site [nucleotide binding] 1055527002214 substrate interaction site [chemical binding]; other site 1055527002215 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 1055527002216 GIY-YIG motif/motif A; other site 1055527002217 DNA binding site [nucleotide binding] 1055527002218 active site 1055527002219 catalytic site [active] 1055527002220 metal binding site [ion binding]; metal-binding site 1055527002221 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 1055527002222 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 1055527002223 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 1055527002224 G1 box; other site 1055527002225 putative GEF interaction site [polypeptide binding]; other site 1055527002226 GTP/Mg2+ binding site [chemical binding]; other site 1055527002227 Switch I region; other site 1055527002228 G2 box; other site 1055527002229 G3 box; other site 1055527002230 Switch II region; other site 1055527002231 G4 box; other site 1055527002232 G5 box; other site 1055527002233 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 1055527002234 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 1055527002235 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 1055527002236 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 1055527002237 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 1055527002238 Methyltransferase domain; Region: Methyltransf_26; pfam13659 1055527002239 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527002240 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 1055527002241 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1055527002242 active site 1055527002243 HIGH motif; other site 1055527002244 nucleotide binding site [chemical binding]; other site 1055527002245 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1055527002246 active site 1055527002247 KMSKS motif; other site 1055527002248 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 1055527002249 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1055527002250 Walker A/P-loop; other site 1055527002251 ATP binding site [chemical binding]; other site 1055527002252 Q-loop/lid; other site 1055527002253 ABC transporter signature motif; other site 1055527002254 Walker B; other site 1055527002255 D-loop; other site 1055527002256 H-loop/switch region; other site 1055527002257 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 1055527002258 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 1055527002259 dimer interface [polypeptide binding]; other site 1055527002260 conserved gate region; other site 1055527002261 putative PBP binding loops; other site 1055527002262 ABC-ATPase subunit interface; other site 1055527002263 ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ModA; COG0725 1055527002264 molybdenum ABC transporter, periplasmic molybdate-binding protein; Region: modA; TIGR01256 1055527002265 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527002266 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 1055527002267 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 1055527002268 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 1055527002269 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_5; cd09610 1055527002270 active site 1055527002271 Zn binding site [ion binding]; other site 1055527002272 CoB--CoM heterodisulfide reductase, subunit B; Region: CoB_CoM_SS_B; TIGR03288 1055527002273 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 1055527002274 putative metal binding site [ion binding]; other site 1055527002275 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 1055527002276 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 1055527002277 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 1055527002278 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 1055527002279 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 1055527002280 ATP binding site [chemical binding]; other site 1055527002281 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 1055527002282 putative Mg++ binding site [ion binding]; other site 1055527002283 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 1055527002284 Methyltransferase domain; Region: Methyltransf_26; pfam13659 1055527002285 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1055527002286 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 1055527002287 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1055527002288 Polyphosphate kinase [Inorganic ion transport and metabolism]; Region: Ppk; COG0855 1055527002289 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 1055527002290 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 1055527002291 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 1055527002292 putative domain interface [polypeptide binding]; other site 1055527002293 putative active site [active] 1055527002294 catalytic site [active] 1055527002295 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 1055527002296 putative active site [active] 1055527002297 putative domain interface [polypeptide binding]; other site 1055527002298 catalytic site [active] 1055527002299 dihydroorotate dehydrogenase, subfamily 2; Region: pyrD_sub2; TIGR01036 1055527002300 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 1055527002301 quinone interaction residues [chemical binding]; other site 1055527002302 active site 1055527002303 catalytic residues [active] 1055527002304 FMN binding site [chemical binding]; other site 1055527002305 substrate binding site [chemical binding]; other site 1055527002306 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1055527002307 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1055527002308 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1055527002309 dihydrodipicolinate synthase; Region: dapA; TIGR00674 1055527002310 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 1055527002311 dimer interface [polypeptide binding]; other site 1055527002312 active site 1055527002313 catalytic residue [active] 1055527002314 7-alpha-hydroxysteroid dehydrogenase; Provisional; Region: PRK08416 1055527002315 1-cyclohexenylcarbonyl_coenzyme A_reductase (ChcA)_like, classical (c) SDRs; Region: ChcA_like_SDR_c; cd05359 1055527002316 putative NAD(P) binding site [chemical binding]; other site 1055527002317 active site 1055527002318 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase; Region: pgsA; TIGR00560 1055527002319 S-methylmethionine transporter; Provisional; Region: PRK11387 1055527002320 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 1055527002321 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1055527002322 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 1055527002323 protein binding site [polypeptide binding]; other site 1055527002324 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 1055527002325 protein binding site [polypeptide binding]; other site 1055527002326 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 1055527002327 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 1055527002328 substrate binding site; other site 1055527002329 dimer interface; other site 1055527002330 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 1055527002331 homotrimer interaction site [polypeptide binding]; other site 1055527002332 zinc binding site [ion binding]; other site 1055527002333 CDP-binding sites; other site 1055527002334 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 1055527002335 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 1055527002336 active site 1055527002337 dimerization interface [polypeptide binding]; other site 1055527002338 5'-3' exonuclease; Provisional; Region: PRK14976 1055527002339 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 1055527002340 putative active site [active] 1055527002341 Helix-hairpin-helix class 2 (Pol1 family) motifs; Region: HhH2; smart00279 1055527002342 DNA binding site [nucleotide binding] 1055527002343 metal binding site [ion binding]; metal-binding site 1055527002344 chaperone protein DnaJ; Provisional; Region: PRK14299 1055527002345 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 1055527002346 HSP70 interaction site [polypeptide binding]; other site 1055527002347 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 1055527002348 substrate binding site [polypeptide binding]; other site 1055527002349 dimer interface [polypeptide binding]; other site 1055527002350 Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Region: HTH_HspR; cd04766 1055527002351 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 1055527002352 DNA binding residues [nucleotide binding] 1055527002353 putative dimer interface [polypeptide binding]; other site 1055527002354 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]; Region: MGS1; COG2256 1055527002355 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 1055527002356 Walker A motif; other site 1055527002357 ATP binding site [chemical binding]; other site 1055527002358 Walker B motif; other site 1055527002359 arginine finger; other site 1055527002360 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 1055527002361 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 1055527002362 metal binding site 2 [ion binding]; metal-binding site 1055527002363 putative DNA binding helix; other site 1055527002364 metal binding site 1 [ion binding]; metal-binding site 1055527002365 dimer interface [polypeptide binding]; other site 1055527002366 structural Zn2+ binding site [ion binding]; other site 1055527002367 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4731 1055527002368 Beta-galactosidase, beta subunit [Carbohydrate transport and metabolism]; Region: EbgC; COG2731 1055527002369 flagellar motor switch protein FliY; Validated; Region: PRK08432 1055527002370 flagellar motor switch protein FliN; Region: fliN; TIGR02480 1055527002371 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 1055527002372 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 1055527002373 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 1055527002374 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1055527002375 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 1055527002376 DNA binding residues [nucleotide binding] 1055527002377 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 1055527002378 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 1055527002379 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 1055527002380 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 1055527002381 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 1055527002382 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 1055527002383 catalytic center binding site [active] 1055527002384 ATP binding site [chemical binding]; other site 1055527002385 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 1055527002386 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 1055527002387 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 1055527002388 active site 1055527002389 Dehydroquinase class II; Region: DHquinase_II; pfam01220 1055527002390 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 1055527002391 trimer interface [polypeptide binding]; other site 1055527002392 active site 1055527002393 dimer interface [polypeptide binding]; other site 1055527002394 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 1055527002395 O-Antigen ligase; Region: Wzy_C; pfam04932 1055527002396 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 1055527002397 16S/18S rRNA binding site [nucleotide binding]; other site 1055527002398 S13e-L30e interaction site [polypeptide binding]; other site 1055527002399 25S rRNA binding site [nucleotide binding]; other site 1055527002400 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 1055527002401 FHIPEP family; Region: FHIPEP; pfam00771 1055527002402 Predicted phosphohydrolase (DHH superfamily) [General function prediction only]; Region: COG2404 1055527002403 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; cl00687 1055527002404 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1055527002405 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 1055527002406 active site 1055527002407 intermolecular recognition site; other site 1055527002408 dimerization interface [polypeptide binding]; other site 1055527002409 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 1055527002410 DNA binding site [nucleotide binding] 1055527002411 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 1055527002412 putative active site [active] 1055527002413 putative metal binding site [ion binding]; other site 1055527002414 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 1055527002415 acetyl-CoA synthetase; Provisional; Region: PRK00174 1055527002416 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 1055527002417 active site 1055527002418 CoA binding site [chemical binding]; other site 1055527002419 acyl-activating enzyme (AAE) consensus motif; other site 1055527002420 AMP binding site [chemical binding]; other site 1055527002421 acetate binding site [chemical binding]; other site 1055527002422 Uncharacterized BCR, YhbC family COG0779; Region: DUF150; pfam02576 1055527002423 Sm and related proteins; Region: Sm_like; cl00259 1055527002424 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 1055527002425 putative oligomer interface [polypeptide binding]; other site 1055527002426 putative RNA binding site [nucleotide binding]; other site 1055527002427 Ribosome-binding factor A; Region: RBFA; cl00542 1055527002428 translation initiation factor IF-2; Region: IF-2; TIGR00487 1055527002429 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 1055527002430 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 1055527002431 G1 box; other site 1055527002432 putative GEF interaction site [polypeptide binding]; other site 1055527002433 GTP/Mg2+ binding site [chemical binding]; other site 1055527002434 Switch I region; other site 1055527002435 G2 box; other site 1055527002436 G3 box; other site 1055527002437 Switch II region; other site 1055527002438 G4 box; other site 1055527002439 G5 box; other site 1055527002440 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 1055527002441 Translation-initiation factor 2; Region: IF-2; pfam11987 1055527002442 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 1055527002443 Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation; Region: YlxR; cl00189 1055527002444 putative RNA binding cleft [nucleotide binding]; other site 1055527002445 homoserine kinase; Region: thrB; TIGR00191 1055527002446 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 1055527002447 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214 1055527002448 UDP-3-0-acyl N-acetylglucosamine deacetylase; Region: lpxC; TIGR00325 1055527002449 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 1055527002450 septum formation inhibitor; Reviewed; Region: minC; PRK00556 1055527002451 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 1055527002452 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1055527002453 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527002454 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527002455 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 1055527002456 oligomerization interface [polypeptide binding]; other site 1055527002457 active site 1055527002458 metal binding site [ion binding]; metal-binding site 1055527002459 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 1055527002460 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 1055527002461 Walker A motif; other site 1055527002462 ATP binding site [chemical binding]; other site 1055527002463 Walker B motif; other site 1055527002464 arginine finger; other site 1055527002465 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 1055527002466 sec-independent translocase; Provisional; Region: PRK04098 1055527002467 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 1055527002468 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 1055527002469 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 1055527002470 rRNA small subunit methyltransferase G; Region: GidB; pfam02527 1055527002471 16S rRNA (guanine(527)-N(7))-methyltransferase GidB; Region: gidB; TIGR00138 1055527002472 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527002473 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 1055527002474 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 1055527002475 active site 1055527002476 phosphorylation site [posttranslational modification] 1055527002477 intermolecular recognition site; other site 1055527002478 dimerization interface [polypeptide binding]; other site 1055527002479 ribosomal protein L11 methyltransferase; Region: prmA; TIGR00406 1055527002480 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 1055527002481 S-adenosylmethionine binding site [chemical binding]; other site 1055527002482 FtsH Extracellular; Region: FtsH_ext; pfam06480 1055527002483 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 1055527002484 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 1055527002485 Walker A motif; other site 1055527002486 ATP binding site [chemical binding]; other site 1055527002487 Walker B motif; other site 1055527002488 arginine finger; other site 1055527002489 Peptidase family M41; Region: Peptidase_M41; pfam01434 1055527002490 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 1055527002491 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 1055527002492 potential frameshift: common BLAST hit: gi|210134570|ref|YP_002301009.1| copper-transporting ATPase 1055527002493 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 1055527002494 metal-binding site [ion binding] 1055527002495 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cd00596 1055527002496 active site 1055527002497 Zn binding site [ion binding]; other site 1055527002498 High-affinity nickel permease [Inorganic ion transport and metabolism]; Region: HoxN; COG3376 1055527002499 Predicted ATPases [General function prediction only]; Region: COG1106 1055527002500 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1055527002501 Walker A/P-loop; other site 1055527002502 ATP binding site [chemical binding]; other site 1055527002503 Predicted endonuclease distantly related to archaeal Holliday junction resolvase and Mrr-like restriction enzymes [Defense mechanisms]; Region: COG1787 1055527002504 Restriction endonuclease; Region: Mrr_cat; pfam04471 1055527002505 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1055527002506 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1055527002507 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1055527002508 Walker A/P-loop; other site 1055527002509 ATP binding site [chemical binding]; other site 1055527002510 Q-loop/lid; other site 1055527002511 ABC transporter signature motif; other site 1055527002512 Walker B; other site 1055527002513 D-loop; other site 1055527002514 H-loop/switch region; other site 1055527002515 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1055527002516 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 1055527002517 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 1055527002518 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 1055527002519 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 1055527002520 S4 RNA-binding domain; Region: S4; smart00363 1055527002521 RNA binding surface [nucleotide binding]; other site 1055527002522 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 1055527002523 S-adenosylmethionine binding site [chemical binding]; other site 1055527002524 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 1055527002525 riboflavin kinase/FMN adenylyltransferase; Region: ribF; TIGR00083 1055527002526 active site 1055527002527 Riboflavin kinase; Region: Flavokinase; smart00904 1055527002528 transketolase, bacterial and yeast; Region: tktlase_bact; TIGR00232 1055527002529 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 1055527002530 TPP-binding site [chemical binding]; other site 1055527002531 dimer interface [polypeptide binding]; other site 1055527002532 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 1055527002533 PYR/PP interface [polypeptide binding]; other site 1055527002534 dimer interface [polypeptide binding]; other site 1055527002535 TPP binding site [chemical binding]; other site 1055527002536 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1055527002537 Inactivated superfamily I helicase [DNA replication, recombination, and repair]; Region: COG3893 1055527002538 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 1055527002539 potential frameshift: common BLAST hit: gi|298736700|ref|YP_003729230.1| DNA segregation ATPase FtsK/SpoIIIE 1055527002540 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 1055527002541 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 1055527002542 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgG; COG4786 1055527002543 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 1055527002544 Domain of unknown function (DUF3883); Region: DUF3883; pfam13020 1055527002545 GTP-binding protein LepA; Provisional; Region: PRK05433 1055527002546 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 1055527002547 G1 box; other site 1055527002548 putative GEF interaction site [polypeptide binding]; other site 1055527002549 GTP/Mg2+ binding site [chemical binding]; other site 1055527002550 Switch I region; other site 1055527002551 G2 box; other site 1055527002552 G3 box; other site 1055527002553 Switch II region; other site 1055527002554 G4 box; other site 1055527002555 G5 box; other site 1055527002556 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 1055527002557 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 1055527002558 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 1055527002559 1-deoxy-D-xylulose-5-phosphate synthase; Region: dxs; TIGR00204 1055527002560 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 1055527002561 TPP-binding site; other site 1055527002562 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 1055527002563 PYR/PP interface [polypeptide binding]; other site 1055527002564 dimer interface [polypeptide binding]; other site 1055527002565 TPP binding site [chemical binding]; other site 1055527002566 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1055527002567 flagellar assembly protein H; Validated; Region: fliH; PRK06669 1055527002568 Flagellar assembly protein FliH; Region: FliH; pfam02108 1055527002569 flagellar motor switch protein FliG; Region: fliG; TIGR00207 1055527002570 FliG C-terminal domain; Region: FliG_C; pfam01706 1055527002571 flagellar basal-body M-ring protein/flagellar hook-basal body protein (fliF); Region: fliF; TIGR00206 1055527002572 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 1055527002573 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 1055527002574 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 1055527002575 active site 1055527002576 CTP synthetase; Validated; Region: pyrG; PRK05380 1055527002577 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 1055527002578 Catalytic site [active] 1055527002579 active site 1055527002580 UTP binding site [chemical binding]; other site 1055527002581 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 1055527002582 active site 1055527002583 putative oxyanion hole; other site 1055527002584 catalytic triad [active] 1055527002585 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 1055527002586 DHH family; Region: DHH; pfam01368 1055527002587 DHHA1 domain; Region: DHHA1; pfam02272 1055527002588 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1055527002589 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1055527002590 active site 1055527002591 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1055527002592 Sel1-like repeats; Region: SEL1; smart00671 1055527002593 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 1055527002594 DNA protecting protein DprA; Region: dprA; TIGR00732 1055527002595 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 1055527002596 cell division topological specificity factor MinE; Region: minE; TIGR01215 1055527002597 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 1055527002598 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 1055527002599 Switch I; other site 1055527002600 Switch II; other site 1055527002601 ketol-acid reductoisomerase; Provisional; Region: PRK05479 1055527002602 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 1055527002603 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 1055527002604 NAD synthetase; Provisional; Region: PRK13980 1055527002605 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 1055527002606 homodimer interface [polypeptide binding]; other site 1055527002607 NAD binding pocket [chemical binding]; other site 1055527002608 ATP binding pocket [chemical binding]; other site 1055527002609 Mg binding site [ion binding]; other site 1055527002610 active-site loop [active] 1055527002611 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 1055527002612 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 1055527002613 pseudaminic acid biosynthesis N-acetyl transferase; Region: PseH; TIGR03585 1055527002614 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1055527002615 Spore coat polysaccharide biosynthesis protein, predicted glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: spsG; COG3980 1055527002616 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 1055527002617 ligand binding site; other site 1055527002618 tetramer interface; other site 1055527002619 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 1055527002620 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK00249 1055527002621 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527002622 nuclease NucT; Provisional; Region: PRK13912 1055527002623 Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar proteins; Region: PLDc_Nuc_like; cd09116 1055527002624 putative active site [active] 1055527002625 catalytic site [active] 1055527002626 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 1055527002627 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 1055527002628 catalytic site [active] 1055527002629 G-X2-G-X-G-K; other site 1055527002630 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 1055527002631 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 1055527002632 arginyl-tRNA synthetase; Region: argS; TIGR00456 1055527002633 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 1055527002634 active site 1055527002635 HIGH motif; other site 1055527002636 KMSK motif region; other site 1055527002637 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1055527002638 tRNA binding surface [nucleotide binding]; other site 1055527002639 anticodon binding site; other site 1055527002640 heme oxygenase, HugZ family; Region: heme_ox_HugZ; TIGR04109 1055527002641 Protein of unknown function (DUF2470); Region: DUF2470; pfam10615 1055527002642 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 1055527002643 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 1055527002644 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1055527002645 putative substrate translocation pore; other site 1055527002646 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 1055527002647 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 1055527002648 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 1055527002649 Catalytic domain of Helicobacter pylori peptidoglycan deacetylase (HpPgdA) and similar proteins; Region: CE4_HpPgdA_like; cd10938 1055527002650 active site 1055527002651 catalytic site [active] 1055527002652 Zn binding site [ion binding]; other site 1055527002653 tetramer interface [polypeptide binding]; other site 1055527002654 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 1055527002655 Predicted amidohydrolase [General function prediction only]; Region: COG0388 1055527002656 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 1055527002657 active site 1055527002658 catalytic triad [active] 1055527002659 dimer interface [polypeptide binding]; other site 1055527002660 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 1055527002661 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 1055527002662 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 1055527002663 inhibitor-cofactor binding pocket; inhibition site 1055527002664 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1055527002665 catalytic residue [active] 1055527002666 Alginate lyase; Region: Alginate_lyase; pfam05426 1055527002667 GTPase CgtA; Reviewed; Region: obgE; PRK12299 1055527002668 GTP1/OBG; Region: GTP1_OBG; pfam01018 1055527002669 Obg GTPase; Region: Obg; cd01898 1055527002670 G1 box; other site 1055527002671 GTP/Mg2+ binding site [chemical binding]; other site 1055527002672 Switch I region; other site 1055527002673 G2 box; other site 1055527002674 G3 box; other site 1055527002675 Switch II region; other site 1055527002676 G4 box; other site 1055527002677 G5 box; other site 1055527002678 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 1055527002679 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1055527002680 Walker A/P-loop; other site 1055527002681 ATP binding site [chemical binding]; other site 1055527002682 Q-loop/lid; other site 1055527002683 ABC transporter signature motif; other site 1055527002684 Walker B; other site 1055527002685 D-loop; other site 1055527002686 H-loop/switch region; other site 1055527002687 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 1055527002688 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1055527002689 nickel import ATP-binding protein NikD; Region: nickel_nikD; TIGR02770 1055527002690 Walker A/P-loop; other site 1055527002691 ATP binding site [chemical binding]; other site 1055527002692 Q-loop/lid; other site 1055527002693 ABC transporter signature motif; other site 1055527002694 Walker B; other site 1055527002695 D-loop; other site 1055527002696 H-loop/switch region; other site 1055527002697 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 1055527002698 dipeptide transporter; Provisional; Region: PRK10913 1055527002699 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 1055527002700 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 1055527002701 dimer interface [polypeptide binding]; other site 1055527002702 conserved gate region; other site 1055527002703 putative PBP binding loops; other site 1055527002704 ABC-ATPase subunit interface; other site 1055527002705 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 1055527002706 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 1055527002707 dimer interface [polypeptide binding]; other site 1055527002708 conserved gate region; other site 1055527002709 putative PBP binding loops; other site 1055527002710 ABC-ATPase subunit interface; other site 1055527002711 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 1055527002712 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 1055527002713 peptide binding site [polypeptide binding]; other site 1055527002714 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 1055527002715 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 1055527002716 flagellar hook-associated protein FlgL; Validated; Region: flgL; PRK08412 1055527002717 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 1055527002718 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 1055527002719 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 1055527002720 Probable transposase; Region: OrfB_IS605; pfam01385 1055527002721 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 1055527002722 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 1055527002723 acylamide amidohydrolase; Provisional; Region: amiE; PRK13286 1055527002724 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 1055527002725 multimer interface [polypeptide binding]; other site 1055527002726 active site 1055527002727 catalytic triad [active] 1055527002728 dimer interface [polypeptide binding]; other site 1055527002729 aminodeoxychorismate synthase; Provisional; Region: PRK07508 1055527002730 chorismate binding enzyme; Region: Chorismate_bind; cl10555 1055527002731 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 1055527002732 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 1055527002733 substrate-cofactor binding pocket; other site 1055527002734 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1055527002735 catalytic residue [active] 1055527002736 Uncharacterized conserved protein [Function unknown]; Region: COG4866 1055527002737 Chorismate mutase [Amino acid transport and metabolism]; Region: PheA; COG1605 1055527002738 diaminopimelate decarboxylase; Region: lysA; TIGR01048 1055527002739 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 1055527002740 active site 1055527002741 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1055527002742 substrate binding site [chemical binding]; other site 1055527002743 catalytic residues [active] 1055527002744 dimer interface [polypeptide binding]; other site 1055527002745 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 1055527002746 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 1055527002747 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 1055527002748 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1055527002749 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 1055527002750 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 1055527002751 ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]; Region: HflB; COG0465 1055527002752 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 1055527002753 Walker B motif; other site 1055527002754 arginine finger; other site 1055527002755 radical SAM methylthiotransferase, MiaB/RimO family; Region: TIGR00089 1055527002756 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1055527002757 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 1055527002758 FeS/SAM binding site; other site 1055527002759 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1055527002760 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1055527002761 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 1055527002762 active site 1055527002763 dimer interface [polypeptide binding]; other site 1055527002764 metal binding site [ion binding]; metal-binding site 1055527002765 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3400 1055527002766 TrkA-C domain; Region: TrkA_C; pfam02080 1055527002767 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 1055527002768 tRNA-guanine family transglycosylase; Region: tgt_general; TIGR00449 1055527002769 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 1055527002770 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 1055527002771 putative acyl-acceptor binding pocket; other site 1055527002772 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 1055527002773 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 1055527002774 putative active site [active] 1055527002775 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 1055527002776 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 1055527002777 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 1055527002778 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 1055527002779 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 1055527002780 putative acyl-acceptor binding pocket; other site 1055527002781 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1055527002782 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14339 1055527002783 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 1055527002784 FeS/SAM binding site; other site 1055527002785 chlorohydrolase; Provisional; Region: PRK08418 1055527002786 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 1055527002787 active site 1055527002788 Dihydroorotase and related cyclic amidohydrolases [Nucleotide transport and metabolism]; Region: PyrC; COG0044 1055527002789 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 1055527002790 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 1055527002791 active site 1055527002792 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 1055527002793 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; pfam02683 1055527002794 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 1055527002795 Clp amino terminal domain; Region: Clp_N; pfam02861 1055527002796 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 1055527002797 Walker A motif; other site 1055527002798 ATP binding site [chemical binding]; other site 1055527002799 Walker B motif; other site 1055527002800 arginine finger; other site 1055527002801 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 1055527002802 Walker A motif; other site 1055527002803 ATP binding site [chemical binding]; other site 1055527002804 Walker B motif; other site 1055527002805 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 1055527002806 potential frameshift: common BLAST hit: gi|15611318|ref|NP_222969.1| type II DNA modification (methyltransferase 1055527002807 potential frameshift: common BLAST hit: gi|308182436|ref|YP_003926563.1| Endonuclease MjaVIP 1055527002808 potential frameshift: common BLAST hit: gi|308182436|ref|YP_003926563.1| Endonuclease MjaVIP 1055527002809 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 1055527002810 DNA methylase; Region: N6_N4_Mtase; pfam01555 1055527002811 DNA methylase; Region: N6_N4_Mtase; pfam01555 1055527002812 exodeoxyribonuclease VII, large subunit; Region: xseA; TIGR00237 1055527002813 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 1055527002814 generic binding surface II; other site 1055527002815 generic binding surface I; other site 1055527002816 RIP metalloprotease RseP; Region: TIGR00054 1055527002817 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 1055527002818 active site 1055527002819 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 1055527002820 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 1055527002821 putative substrate binding region [chemical binding]; other site 1055527002822 Uncharacterized conserved protein [Function unknown]; Region: COG3334 1055527002823 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 1055527002824 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 1055527002825 GDP-binding site [chemical binding]; other site 1055527002826 ACT binding site; other site 1055527002827 IMP binding site; other site 1055527002828 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527002829 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527002830 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 1055527002831 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 1055527002832 dimer interface [polypeptide binding]; other site 1055527002833 conserved gate region; other site 1055527002834 putative PBP binding loops; other site 1055527002835 ABC-ATPase subunit interface; other site 1055527002836 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 1055527002837 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1055527002838 Walker A/P-loop; other site 1055527002839 ATP binding site [chemical binding]; other site 1055527002840 Q-loop/lid; other site 1055527002841 ABC transporter signature motif; other site 1055527002842 Walker B; other site 1055527002843 D-loop; other site 1055527002844 H-loop/switch region; other site 1055527002845 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 1055527002846 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1055527002847 Walker A/P-loop; other site 1055527002848 ATP binding site [chemical binding]; other site 1055527002849 Q-loop/lid; other site 1055527002850 ABC transporter signature motif; other site 1055527002851 Walker B; other site 1055527002852 D-loop; other site 1055527002853 H-loop/switch region; other site 1055527002854 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 1055527002855 Protein of unknown function (DUF2393); Region: DUF2393; pfam09624 1055527002856 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1055527002857 SPFH domain / Band 7 family; Region: Band_7; pfam01145 1055527002858 helicase 45; Provisional; Region: PTZ00424 1055527002859 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 1055527002860 ATP binding site [chemical binding]; other site 1055527002861 Mg++ binding site [ion binding]; other site 1055527002862 motif III; other site 1055527002863 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 1055527002864 nucleotide binding region [chemical binding]; other site 1055527002865 ATP-binding site [chemical binding]; other site 1055527002866 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 1055527002867 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 1055527002868 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1055527002869 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 1055527002870 dimer interface [polypeptide binding]; other site 1055527002871 phosphorylation site [posttranslational modification] 1055527002872 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 1055527002873 ATP binding site [chemical binding]; other site 1055527002874 Mg2+ binding site [ion binding]; other site 1055527002875 G-X-G motif; other site 1055527002876 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 1055527002877 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 1055527002878 dimerization interface [polypeptide binding]; other site 1055527002879 DPS ferroxidase diiron center [ion binding]; other site 1055527002880 ion pore; other site 1055527002881 Domain of unknown function (DUF2018); Region: DUF2018; pfam09442 1055527002882 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 1055527002883 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 1055527002884 substrate binding pocket [chemical binding]; other site 1055527002885 chain length determination region; other site 1055527002886 substrate-Mg2+ binding site; other site 1055527002887 catalytic residues [active] 1055527002888 aspartate-rich region 1; other site 1055527002889 active site lid residues [active] 1055527002890 aspartate-rich region 2; other site 1055527002891 glutamyl-tRNA reductase; Region: hemA; TIGR01035 1055527002892 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 1055527002893 tRNA; other site 1055527002894 putative tRNA binding site [nucleotide binding]; other site 1055527002895 putative NADP binding site [chemical binding]; other site 1055527002896 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 1055527002897 prolyl-tRNA synthetase, family II; Region: proS_fam_II; TIGR00409 1055527002898 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 1055527002899 dimer interface [polypeptide binding]; other site 1055527002900 motif 1; other site 1055527002901 active site 1055527002902 motif 2; other site 1055527002903 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 1055527002904 putative deacylase active site [active] 1055527002905 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 1055527002906 active site 1055527002907 motif 3; other site 1055527002908 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 1055527002909 anticodon binding site; other site 1055527002910 Porphobilinogen deaminase [Coenzyme metabolism]; Region: HemC; COG0181 1055527002911 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 1055527002912 domain interfaces; other site 1055527002913 active site 1055527002914 Cytochrome c; Region: Cytochrom_C; cl11414 1055527002915 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1055527002916 Sel1-like repeats; Region: SEL1; smart00671 1055527002917 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 1055527002918 binding surface 1055527002919 TPR motif; other site 1055527002920 Sel1-like repeats; Region: SEL1; smart00671 1055527002921 Sel1-like repeats; Region: SEL1; smart00671 1055527002922 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 1055527002923 Glutathionylspermidine synthase [Amino acid transport and metabolism]; Region: Gsp; COG0754 1055527002924 hypothetical protein; Provisional; Region: PRK04081 1055527002925 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 1055527002926 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 1055527002927 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 1055527002928 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 1055527002929 Ligand binding site; other site 1055527002930 oligomer interface; other site 1055527002931 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527002932 potential protein location (hypothetical protein HPELS_05620 [Helicobacter pylori ELS37]) that overlaps RNA (tRNA-N) 1055527002933 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 1055527002934 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 1055527002935 Sulfate transporter family; Region: Sulfate_transp; pfam00916 1055527002936 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527002937 Predicted permeases [General function prediction only]; Region: COG0730 1055527002938 Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: MsrA; COG0225 1055527002939 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229 1055527002940 SelR domain; Region: SelR; pfam01641 1055527002941 DNA repair protein RadA; Region: sms; TIGR00416 1055527002942 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 1055527002943 Walker A motif/ATP binding site; other site 1055527002944 ATP binding site [chemical binding]; other site 1055527002945 Walker B motif; other site 1055527002946 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 1055527002947 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 1055527002948 Fe-S cluster assembly protein NifU; Region: NifU_proper; TIGR02000 1055527002949 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 1055527002950 trimerization site [polypeptide binding]; other site 1055527002951 active site 1055527002952 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 1055527002953 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 1055527002954 cysteine desulfurase, NifS family, epsilon proteobacteria type; Region: nifS_epsilon; TIGR03403 1055527002955 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 1055527002956 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1055527002957 catalytic residue [active] 1055527002958 Helix-turn-helix domain; Region: HTH_28; pfam13518 1055527002959 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 1055527002960 substrate binding site [chemical binding]; other site 1055527002961 Beta-1,4-N-acetylgalactosaminyltransferase (CgtA); Region: CgtA; pfam06306 1055527002962 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: Dxr; TIGR00243 1055527002963 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 1055527002964 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 1055527002965 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 1055527002966 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 1055527002967 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 1055527002968 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 1055527002969 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 1055527002970 transmembrane helices; other site 1055527002971 glucose-inhibited division protein A; Region: gidA; TIGR00136 1055527002972 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1055527002973 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 1055527002974 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 1055527002975 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 1055527002976 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 1055527002977 metal binding site [ion binding]; metal-binding site 1055527002978 dimer interface [polypeptide binding]; other site 1055527002979 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1055527002980 Sel1-like repeats; Region: SEL1; smart00671 1055527002981 Sel1-like repeats; Region: SEL1; smart00671 1055527002982 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 1055527002983 TPR motif; other site 1055527002984 binding surface 1055527002985 heat shock protein 90; Provisional; Region: PRK05218 1055527002986 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 1055527002987 ATP binding site [chemical binding]; other site 1055527002988 Mg2+ binding site [ion binding]; other site 1055527002989 G-X-G motif; other site 1055527002990 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1055527002991 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 1055527002992 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 1055527002993 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 1055527002994 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 1055527002995 antiporter inner membrane protein; Provisional; Region: PRK11670 1055527002996 Domain of unknown function DUF59; Region: DUF59; pfam01883 1055527002997 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 1055527002998 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1055527002999 AAA domain; Region: AAA_21; pfam13304 1055527003000 Walker A/P-loop; other site 1055527003001 ATP binding site [chemical binding]; other site 1055527003002 AAA ATPase domain; Region: AAA_15; pfam13175 1055527003003 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cd00267 1055527003004 Walker B; other site 1055527003005 D-loop; other site 1055527003006 H-loop/switch region; other site 1055527003007 3-oxoacyl-(acyl-carrier-protein) synthase III; Region: fabH; TIGR00747 1055527003008 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 1055527003009 dimer interface [polypeptide binding]; other site 1055527003010 active site 1055527003011 CoA binding pocket [chemical binding]; other site 1055527003012 putative phosphate acyltransferase; Provisional; Region: PRK05331 1055527003013 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 1055527003014 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 1055527003015 active site 1055527003016 multimer interface [polypeptide binding]; other site 1055527003017 S-adenosylmethionine synthetase; Validated; Region: PRK05250 1055527003018 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 1055527003019 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 1055527003020 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 1055527003021 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Region: lipid_A_lpxD; TIGR01853 1055527003022 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 1055527003023 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 1055527003024 trimer interface [polypeptide binding]; other site 1055527003025 active site 1055527003026 UDP-GlcNAc binding site [chemical binding]; other site 1055527003027 lipid binding site [chemical binding]; lipid-binding site 1055527003028 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08415 1055527003029 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 1055527003030 NAD binding site [chemical binding]; other site 1055527003031 homotetramer interface [polypeptide binding]; other site 1055527003032 homodimer interface [polypeptide binding]; other site 1055527003033 substrate binding site [chemical binding]; other site 1055527003034 active site 1055527003035 triosephosphate isomerase; Provisional; Region: PRK14567 1055527003036 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 1055527003037 substrate binding site [chemical binding]; other site 1055527003038 dimer interface [polypeptide binding]; other site 1055527003039 catalytic triad [active] 1055527003040 fumarate reductase cytochrome b-556 subunit; Provisional; Region: PRK13553 1055527003041 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 1055527003042 Iron-sulfur protein interface; other site 1055527003043 proximal heme binding site [chemical binding]; other site 1055527003044 distal heme binding site [chemical binding]; other site 1055527003045 dimer interface [polypeptide binding]; other site 1055527003046 fumarate reductase flavoprotein subunit; Provisional; Region: PRK08626 1055527003047 L-aspartate oxidase; Provisional; Region: PRK06175 1055527003048 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 1055527003049 fumarate reductase iron-sulfur subunit; Provisional; Region: frdB; PRK13552 1055527003050 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 1055527003051 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 1055527003052 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 1055527003053 PLD-like domain; Region: PLDc_2; pfam13091 1055527003054 putative active site [active] 1055527003055 catalytic site [active] 1055527003056 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 1055527003057 PLD-like domain; Region: PLDc_2; pfam13091 1055527003058 putative active site [active] 1055527003059 catalytic site [active] 1055527003060 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 1055527003061 Sporulation related domain; Region: SPOR; cl10051 1055527003062 Domain of unknown function (DUF1882); Region: DUF1882; pfam08966 1055527003063 serine hydroxymethyltransferase; Reviewed; Region: PRK13034 1055527003064 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 1055527003065 dimer interface [polypeptide binding]; other site 1055527003066 active site 1055527003067 glycine-pyridoxal phosphate binding site [chemical binding]; other site 1055527003068 folate binding site [chemical binding]; other site 1055527003069 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 1055527003070 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 1055527003071 dimer interface [polypeptide binding]; other site 1055527003072 putative anticodon binding site; other site 1055527003073 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 1055527003074 motif 1; other site 1055527003075 active site 1055527003076 motif 2; other site 1055527003077 motif 3; other site 1055527003078 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 1055527003079 Colicin V production protein; Region: Colicin_V; pfam02674 1055527003080 apolipoprotein N-acyltransferase; Reviewed; Region: PRK12291 1055527003081 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 1055527003082 active site 1055527003083 catalytic triad [active] 1055527003084 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1055527003085 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1055527003086 Walker A/P-loop; other site 1055527003087 ATP binding site [chemical binding]; other site 1055527003088 Q-loop/lid; other site 1055527003089 ABC transporter signature motif; other site 1055527003090 Walker B; other site 1055527003091 D-loop; other site 1055527003092 H-loop/switch region; other site 1055527003093 pseudaminic acid synthase; Region: PseI; TIGR03586 1055527003094 NeuB family; Region: NeuB; pfam03102 1055527003095 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 1055527003096 NeuB binding interface [polypeptide binding]; other site 1055527003097 putative substrate binding site [chemical binding]; other site 1055527003098 potential frameshift: common BLAST hit: gi|15611234|ref|NP_222885.1| putative restriction enzyme 1055527003099 Probable transposase; Region: OrfB_IS605; pfam01385 1055527003100 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 1055527003101 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 1055527003102 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 1055527003103 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 1055527003104 Probable transposase; Region: OrfB_IS605; pfam01385 1055527003105 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 1055527003106 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 1055527003107 Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair]; Region: COG2452 1055527003108 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cd04761 1055527003109 DNA binding residues [nucleotide binding] 1055527003110 Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members contain a DNA binding domain with homology to MerR/SoxR located N-terminal to the catalytic domain. Serine recombinases catalyze site-specific recombination of...; Region: SR_IS607_transposase_like; cd03769 1055527003111 catalytic residues [active] 1055527003112 catalytic nucleophile [active] 1055527003113 Uncharacterized conserved protein [Function unknown]; Region: COG1432 1055527003114 LabA_like proteins; Region: LabA_like; cd06167 1055527003115 putative metal binding site [ion binding]; other site 1055527003116 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 1055527003117 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 1055527003118 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK14593 1055527003119 RimM N-terminal domain; Region: RimM; pfam01782 1055527003120 PRC-barrel domain; Region: PRC; pfam05239 1055527003121 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837 1055527003122 KH domain; Region: KH_4; pfam13083 1055527003123 G-X-X-G motif; other site 1055527003124 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 1055527003125 signal recognition particle protein; Provisional; Region: PRK10867 1055527003126 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 1055527003127 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 1055527003128 P loop; other site 1055527003129 GTP binding site [chemical binding]; other site 1055527003130 Signal peptide binding domain; Region: SRP_SPB; pfam02978 1055527003131 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 1055527003132 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1055527003133 active site 1055527003134 HIGH motif; other site 1055527003135 nucleotide binding site [chemical binding]; other site 1055527003136 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1055527003137 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 1055527003138 active site 1055527003139 KMSKS motif; other site 1055527003140 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 1055527003141 anticodon binding site; other site 1055527003142 flagellar assembly protein FliW; Provisional; Region: PRK13283 1055527003143 undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase; Region: murG; TIGR01133 1055527003144 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 1055527003145 active site 1055527003146 homodimer interface [polypeptide binding]; other site 1055527003147 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527003148 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527003149 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 1055527003150 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 1055527003151 Protein involved in cell division [Cell division and chromosome partitioning]; Region: Fic; COG2184 1055527003152 Fic/DOC family; Region: Fic; cl00960 1055527003153 metal-binding heat shock protein; Provisional; Region: PRK00016 1055527003154 flavodoxin FldA; Validated; Region: PRK09267 1055527003155 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 1055527003156 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 1055527003157 Uncharacterized protein, possibly involved in nitrogen fixation [Inorganic ion transport and metabolism]; Region: FixS; COG3197 1055527003158 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 1055527003159 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1055527003160 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1055527003161 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 1055527003162 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 1055527003163 active site 1055527003164 dimer interface [polypeptide binding]; other site 1055527003165 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 1055527003166 dimer interface [polypeptide binding]; other site 1055527003167 active site 1055527003168 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1055527003169 carbon starvation protein A; Provisional; Region: PRK15015 1055527003170 Carbon starvation protein CstA; Region: CstA; pfam02554 1055527003171 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 1055527003172 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1055527003173 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 1055527003174 dimer interface [polypeptide binding]; other site 1055527003175 conserved gate region; other site 1055527003176 putative PBP binding loops; other site 1055527003177 ABC-ATPase subunit interface; other site 1055527003178 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 1055527003179 dimer interface [polypeptide binding]; other site 1055527003180 conserved gate region; other site 1055527003181 putative PBP binding loops; other site 1055527003182 ABC-ATPase subunit interface; other site 1055527003183 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 1055527003184 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 1055527003185 Walker A/P-loop; other site 1055527003186 ATP binding site [chemical binding]; other site 1055527003187 Q-loop/lid; other site 1055527003188 ABC transporter signature motif; other site 1055527003189 Walker B; other site 1055527003190 D-loop; other site 1055527003191 H-loop/switch region; other site 1055527003192 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 1055527003193 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 1055527003194 substrate binding pocket [chemical binding]; other site 1055527003195 membrane-bound complex binding site; other site 1055527003196 hinge residues; other site 1055527003197 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 1055527003198 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 1055527003199 putative substrate translocation pore; other site 1055527003200 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 1055527003201 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527003202 purine-nucleoside phosphorylase, family 1 (deoD); Region: deoD; TIGR00107 1055527003203 phosphopentomutase; Provisional; Region: PRK05362 1055527003204 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 1055527003205 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 1055527003206 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 1055527003207 Nucleoside recognition; Region: Gate; pfam07670 1055527003208 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 1055527003209 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 1055527003210 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1055527003211 putative substrate translocation pore; other site 1055527003212 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 1055527003213 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 1055527003214 Ligand Binding Site [chemical binding]; other site 1055527003215 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 1055527003216 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 1055527003217 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 1055527003218 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 1055527003219 putative arabinose transporter; Provisional; Region: PRK03545 1055527003220 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 1055527003221 putative substrate translocation pore; other site 1055527003222 Carbonic anhydrase [Inorganic ion transport and metabolism]; Region: Cah; COG3338 1055527003223 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 1055527003224 active site 1055527003225 zinc binding site [ion binding]; other site 1055527003226 Helicobacter pylori protein of unknown function (DUF874); Region: DUF874; pfam05917 1055527003227 Helicobacter pylori protein of unknown function (DUF874); Region: DUF874; pfam05917 1055527003228 aspartate-semialdehyde dehydrogenase (peptidoglycan organisms); Region: asd_B; TIGR01296 1055527003229 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 1055527003230 Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: HisS; COG0124 1055527003231 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 1055527003232 dimer interface [polypeptide binding]; other site 1055527003233 motif 1; other site 1055527003234 active site 1055527003235 motif 2; other site 1055527003236 motif 3; other site 1055527003237 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 1055527003238 anticodon binding site; other site 1055527003239 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 1055527003240 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 1055527003241 putative active site [active] 1055527003242 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 1055527003243 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 1055527003244 active site 1055527003245 catalytic tetrad [active] 1055527003246 elongation factor G; Reviewed; Region: PRK00007 1055527003247 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 1055527003248 G1 box; other site 1055527003249 putative GEF interaction site [polypeptide binding]; other site 1055527003250 GTP/Mg2+ binding site [chemical binding]; other site 1055527003251 Switch I region; other site 1055527003252 G2 box; other site 1055527003253 G3 box; other site 1055527003254 Switch II region; other site 1055527003255 G4 box; other site 1055527003256 G5 box; other site 1055527003257 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 1055527003258 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 1055527003259 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 1055527003260 30S ribosomal protein S7; Validated; Region: PRK05302 1055527003261 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 1055527003262 S17 interaction site [polypeptide binding]; other site 1055527003263 S8 interaction site; other site 1055527003264 16S rRNA interaction site [nucleotide binding]; other site 1055527003265 streptomycin interaction site [chemical binding]; other site 1055527003266 23S rRNA interaction site [nucleotide binding]; other site 1055527003267 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 1055527003268 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 1055527003269 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 1055527003270 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 1055527003271 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 1055527003272 RPB11 interaction site [polypeptide binding]; other site 1055527003273 RPB12 interaction site [polypeptide binding]; other site 1055527003274 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 1055527003275 RPB3 interaction site [polypeptide binding]; other site 1055527003276 RPB1 interaction site [polypeptide binding]; other site 1055527003277 RPB11 interaction site [polypeptide binding]; other site 1055527003278 RPB10 interaction site [polypeptide binding]; other site 1055527003279 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 1055527003280 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 1055527003281 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 1055527003282 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 1055527003283 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 1055527003284 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 1055527003285 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 1055527003286 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 1055527003287 DNA binding site [nucleotide binding] 1055527003288 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 1055527003289 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 1055527003290 core dimer interface [polypeptide binding]; other site 1055527003291 peripheral dimer interface [polypeptide binding]; other site 1055527003292 L10 interface [polypeptide binding]; other site 1055527003293 L11 interface [polypeptide binding]; other site 1055527003294 putative EF-Tu interaction site [polypeptide binding]; other site 1055527003295 putative EF-G interaction site [polypeptide binding]; other site 1055527003296 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 1055527003297 23S rRNA interface [nucleotide binding]; other site 1055527003298 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 1055527003299 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 1055527003300 mRNA/rRNA interface [nucleotide binding]; other site 1055527003301 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 1055527003302 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 1055527003303 23S rRNA interface [nucleotide binding]; other site 1055527003304 L7/L12 interface [polypeptide binding]; other site 1055527003305 putative thiostrepton binding site; other site 1055527003306 L25 interface [polypeptide binding]; other site 1055527003307 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 1055527003308 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 1055527003309 putative homodimer interface [polypeptide binding]; other site 1055527003310 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 1055527003311 heterodimer interface [polypeptide binding]; other site 1055527003312 homodimer interface [polypeptide binding]; other site 1055527003313 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 1055527003314 elongation factor Tu; Reviewed; Region: PRK00049 1055527003315 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 1055527003316 G1 box; other site 1055527003317 GEF interaction site [polypeptide binding]; other site 1055527003318 GTP/Mg2+ binding site [chemical binding]; other site 1055527003319 Switch I region; other site 1055527003320 G2 box; other site 1055527003321 G3 box; other site 1055527003322 Switch II region; other site 1055527003323 G4 box; other site 1055527003324 G5 box; other site 1055527003325 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 1055527003326 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 1055527003327 Antibiotic Binding Site [chemical binding]; other site 1055527003328 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1055527003329 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 1055527003330 Walker A/P-loop; other site 1055527003331 ATP binding site [chemical binding]; other site 1055527003332 Q-loop/lid; other site 1055527003333 ABC transporter signature motif; other site 1055527003334 Walker B; other site 1055527003335 D-loop; other site 1055527003336 H-loop/switch region; other site 1055527003337 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 1055527003338 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG3392 1055527003339 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; pfam02086 1055527003340 ICEA Protein; Region: ICEA; pfam05315 1055527003341 ICEA Protein; Region: ICEA; pfam05315 1055527003342 ICEA Protein; Region: ICEA; pfam05315 1055527003343 serine O-acetyltransferase; Region: cysE; TIGR01172 1055527003344 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 1055527003345 trimer interface [polypeptide binding]; other site 1055527003346 active site 1055527003347 substrate binding site [chemical binding]; other site 1055527003348 CoA binding site [chemical binding]; other site 1055527003349 F0F1 ATP synthase subunit C; Validated; Region: PRK08482 1055527003350 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 1055527003351 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 1055527003352 oligomer interface [polypeptide binding]; other site 1055527003353 RNA binding site [nucleotide binding]; other site 1055527003354 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 1055527003355 oligomer interface [polypeptide binding]; other site 1055527003356 RNA binding site [nucleotide binding]; other site 1055527003357 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 1055527003358 putative nucleic acid binding region [nucleotide binding]; other site 1055527003359 G-X-X-G motif; other site 1055527003360 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 1055527003361 RNA binding site [nucleotide binding]; other site 1055527003362 Predicted phosphoribosyltransferases [General function prediction only]; Region: COG1926 1055527003363 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 1055527003364 Organic solvent tolerance protein; Region: OstA_C; pfam04453 1055527003365 Predicted membrane protein/domain [Function unknown]; Region: COG1714 1055527003366 phosphoribosylamine--glycine ligase; Region: purD; TIGR00877 1055527003367 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 1055527003368 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 1055527003369 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 1055527003370 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 1055527003371 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 1055527003372 Walker A/P-loop; other site 1055527003373 ATP binding site [chemical binding]; other site 1055527003374 Q-loop/lid; other site 1055527003375 ABC transporter signature motif; other site 1055527003376 Walker B; other site 1055527003377 D-loop; other site 1055527003378 H-loop/switch region; other site 1055527003379 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 1055527003380 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 1055527003381 catalytic residue [active] 1055527003382 putative FPP diphosphate binding site; other site 1055527003383 putative FPP binding hydrophobic cleft; other site 1055527003384 dimer interface [polypeptide binding]; other site 1055527003385 putative IPP diphosphate binding site; other site 1055527003386 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 1055527003387 FAD binding domain; Region: FAD_binding_4; pfam01565 1055527003388 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 1055527003389 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 1055527003390 active site residue [active] 1055527003391 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 1055527003392 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 1055527003393 active site 1055527003394 camphor resistance protein CrcB; Provisional; Region: PRK14204 1055527003395 coproporphyrinogen III oxidase; Provisional; Region: PRK08446 1055527003396 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 1055527003397 FeS/SAM binding site; other site 1055527003398 HemN C-terminal domain; Region: HemN_C; pfam06969 1055527003399 Cytochrome c553 [Energy production and conversion]; Region: COG2863 1055527003400 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 1055527003401 putative active site [active] 1055527003402 Ap4A binding site [chemical binding]; other site 1055527003403 nudix motif; other site 1055527003404 putative metal binding site [ion binding]; other site 1055527003405 aspartate kinase; Reviewed; Region: PRK06635 1055527003406 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 1055527003407 putative nucleotide binding site [chemical binding]; other site 1055527003408 putative catalytic residues [active] 1055527003409 putative Mg ion binding site [ion binding]; other site 1055527003410 putative aspartate binding site [chemical binding]; other site 1055527003411 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 1055527003412 putative allosteric regulatory site; other site 1055527003413 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 1055527003414 putative allosteric regulatory residue; other site 1055527003415 DNA replication regulator; Region: HobA; pfam12163 1055527003416 DNA polymerase III subunit delta'; Validated; Region: PRK08485 1055527003417 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 1055527003418 dihydropteroate synthase; Region: DHPS; TIGR01496 1055527003419 substrate binding pocket [chemical binding]; other site 1055527003420 dimer interface [polypeptide binding]; other site 1055527003421 inhibitor binding site; inhibition site 1055527003422 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 1055527003423 EamA-like transporter family; Region: EamA; pfam00892 1055527003424 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 1055527003425 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2952 1055527003426 Carbamoylphosphate synthase small subunit [Amino acid transport and metabolism / Nucleotide transport and metabolism]; Region: CarA; COG0505 1055527003427 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; pfam00988 1055527003428 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 1055527003429 catalytic site [active] 1055527003430 subunit interface [polypeptide binding]; other site 1055527003431 formamidase; Provisional; Region: amiF; PRK13287 1055527003432 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 1055527003433 multimer interface [polypeptide binding]; other site 1055527003434 active site 1055527003435 catalytic triad [active] 1055527003436 dimer interface [polypeptide binding]; other site 1055527003437 Maf-like protein; Reviewed; Region: PRK04056 1055527003438 putative active site [active] 1055527003439 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 1055527003440 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 1055527003441 motif 1; other site 1055527003442 active site 1055527003443 motif 2; other site 1055527003444 motif 3; other site 1055527003445 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 1055527003446 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2841 1055527003447 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527003448 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 1055527003449 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 1055527003450 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 1055527003451 dimer interface [polypeptide binding]; other site 1055527003452 ssDNA binding site [nucleotide binding]; other site 1055527003453 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1055527003454 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 1055527003455 DNA polymerase III subunit delta; Validated; Region: PRK08487 1055527003456 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 1055527003457 Exoribonuclease R [Transcription]; Region: VacB; COG0557 1055527003458 RNB domain; Region: RNB; pfam00773 1055527003459 shikimate 5-dehydrogenase; Region: aroE; TIGR00507 1055527003460 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 1055527003461 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 1055527003462 shikimate binding site; other site 1055527003463 NAD(P) binding site [chemical binding]; other site 1055527003464 Bacterial SH3 domain homologues; Region: SH3b; smart00287 1055527003465 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 1055527003466 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 1055527003467 dimer interface [polypeptide binding]; other site 1055527003468 conserved gate region; other site 1055527003469 putative PBP binding loops; other site 1055527003470 ABC-ATPase subunit interface; other site 1055527003471 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 1055527003472 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 1055527003473 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 1055527003474 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 1055527003475 active site 1055527003476 HIGH motif; other site 1055527003477 dimer interface [polypeptide binding]; other site 1055527003478 KMSKS motif; other site 1055527003479 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 1055527003480 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 1055527003481 S-adenosylmethionine binding site [chemical binding]; other site 1055527003482 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 1055527003483 ribosome recycling factor; Reviewed; Region: frr; PRK00083 1055527003484 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 1055527003485 hinge region; other site 1055527003486 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1055527003487 active site 1055527003488 RDD family; Region: RDD; pfam06271 1055527003489 NAD-dependent protein deacetylases, SIR2 family [Transcription]; Region: SIR2; COG0846 1055527003490 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 1055527003491 NAD+ binding site [chemical binding]; other site 1055527003492 substrate binding site [chemical binding]; other site 1055527003493 Zn binding site [ion binding]; other site 1055527003494 NADH dehydrogenase subunit A; Validated; Region: PRK08489 1055527003495 NADH dehydrogenase subunit B; Validated; Region: PRK06411 1055527003496 NADH dehydrogenase subunit C; Provisional; Region: PRK08491 1055527003497 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 1055527003498 NADH dehydrogenase subunit D; Validated; Region: PRK06075 1055527003499 NADH dehydrogenase I, D subunit; Region: NuoD; TIGR01962 1055527003500 NADH dehydrogenase subunit G; Validated; Region: PRK08493 1055527003501 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 1055527003502 catalytic loop [active] 1055527003503 iron binding site [ion binding]; other site 1055527003504 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 1055527003505 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 1055527003506 molybdopterin cofactor binding site; other site 1055527003507 Domain of unknown function (DUF4350); Region: DUF4350; pfam14258 1055527003508 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 1055527003509 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 1055527003510 NADH-quinone oxidoreductase, chain I; Region: NuoI; TIGR01971 1055527003511 4Fe-4S binding domain; Region: Fer4; cl02805 1055527003512 4Fe-4S binding domain; Region: Fer4; pfam00037 1055527003513 NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion]; Region: NuoJ; COG0839 1055527003514 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 1055527003515 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 1055527003516 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 1055527003517 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 1055527003518 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1055527003519 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 1055527003520 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1055527003521 proton-translocating NADH-quinone oxidoreductase, chain N; Region: NDH_I_N; TIGR01770 1055527003522 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1055527003523 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 1055527003524 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 1055527003525 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 1055527003526 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 1055527003527 active site 1055527003528 substrate binding site [chemical binding]; other site 1055527003529 metal binding site [ion binding]; metal-binding site 1055527003530 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 1055527003531 substrate binding site [chemical binding]; other site 1055527003532 active site 1055527003533 catalytic residues [active] 1055527003534 heterodimer interface [polypeptide binding]; other site 1055527003535 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 1055527003536 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 1055527003537 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1055527003538 catalytic residue [active] 1055527003539 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional; Region: PRK09427 1055527003540 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 1055527003541 active site 1055527003542 ribulose/triose binding site [chemical binding]; other site 1055527003543 phosphate binding site [ion binding]; other site 1055527003544 substrate (anthranilate) binding pocket [chemical binding]; other site 1055527003545 product (indole) binding pocket [chemical binding]; other site 1055527003546 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 1055527003547 active site 1055527003548 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 1055527003549 anthranilate phosphoribosyltransferase; Region: trpD; TIGR01245 1055527003550 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 1055527003551 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 1055527003552 Glutamine amidotransferase class-I; Region: GATase; pfam00117 1055527003553 glutamine binding [chemical binding]; other site 1055527003554 catalytic triad [active] 1055527003555 anthranilate synthase component I; Provisional; Region: PRK13564 1055527003556 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 1055527003557 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 1055527003558 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 1055527003559 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 1055527003560 putative active site [active] 1055527003561 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 1055527003562 active site 1055527003563 motif I; other site 1055527003564 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 1055527003565 motif II; other site 1055527003566 Uncharacterized conserved protein [Function unknown]; Region: COG2353 1055527003567 thiaminase II; Region: salvage_TenA; TIGR04306 1055527003568 Nicotinamide mononucleotide transporter [Coenzyme metabolism]; Region: PnuC; COG3201 1055527003569 Thiamine pyrophosphokinase [Coenzyme metabolism]; Region: THI80; COG1564 1055527003570 Thiamine pyrophosphokinase; Region: TPK; cd07995 1055527003571 active site 1055527003572 dimerization interface [polypeptide binding]; other site 1055527003573 thiamine binding site [chemical binding]; other site 1055527003574 Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]; Region: RplQ; COG0203 1055527003575 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 1055527003576 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 1055527003577 alphaNTD homodimer interface [polypeptide binding]; other site 1055527003578 alphaNTD - beta interaction site [polypeptide binding]; other site 1055527003579 alphaNTD - beta' interaction site [polypeptide binding]; other site 1055527003580 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 1055527003581 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 1055527003582 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 1055527003583 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 1055527003584 RNA binding surface [nucleotide binding]; other site 1055527003585 30S ribosomal protein S11; Validated; Region: PRK05309 1055527003586 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 1055527003587 30S ribosomal protein S13; Region: bact_S13; TIGR03631 1055527003588 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 1055527003589 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 1055527003590 rRNA binding site [nucleotide binding]; other site 1055527003591 predicted 30S ribosome binding site; other site 1055527003592 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 1055527003593 active site 1055527003594 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 1055527003595 SecY translocase; Region: SecY; pfam00344 1055527003596 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 1055527003597 ribosomal protein S5, bacterial/organelle type; Region: rpsE_bact; TIGR01021 1055527003598 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 1055527003599 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 1055527003600 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 1055527003601 23S rRNA interface [nucleotide binding]; other site 1055527003602 5S rRNA interface [nucleotide binding]; other site 1055527003603 L27 interface [polypeptide binding]; other site 1055527003604 L5 interface [polypeptide binding]; other site 1055527003605 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 1055527003606 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1055527003607 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 1055527003608 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08061 1055527003609 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 1055527003610 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 1055527003611 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 1055527003612 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 1055527003613 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 1055527003614 RNA binding site [nucleotide binding]; other site 1055527003615 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 1055527003616 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 1055527003617 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 1055527003618 putative translocon interaction site; other site 1055527003619 23S rRNA interface [nucleotide binding]; other site 1055527003620 signal recognition particle (SRP54) interaction site; other site 1055527003621 L23 interface [polypeptide binding]; other site 1055527003622 trigger factor interaction site; other site 1055527003623 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 1055527003624 23S rRNA interface [nucleotide binding]; other site 1055527003625 5S rRNA interface [nucleotide binding]; other site 1055527003626 putative antibiotic binding site [chemical binding]; other site 1055527003627 L25 interface [polypeptide binding]; other site 1055527003628 L27 interface [polypeptide binding]; other site 1055527003629 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 1055527003630 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 1055527003631 G-X-X-G motif; other site 1055527003632 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 1055527003633 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 1055527003634 putative translocon binding site; other site 1055527003635 protein-rRNA interface [nucleotide binding]; other site 1055527003636 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 1055527003637 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 1055527003638 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 1055527003639 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 1055527003640 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 1055527003641 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 1055527003642 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 1055527003643 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 1055527003644 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 1055527003645 AAA domain; Region: AAA_14; pfam13173 1055527003646 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 1055527003647 RNA/DNA hybrid binding site [nucleotide binding]; other site 1055527003648 active site 1055527003649 SIR2-like domain; Region: SIR2_2; pfam13289 1055527003650 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 1055527003651 Walker A motif; other site 1055527003652 ATP binding site [chemical binding]; other site 1055527003653 fumarate hydratase; Reviewed; Region: fumC; PRK00485 1055527003654 Class II fumarases; Region: Fumarase_classII; cd01362 1055527003655 active site 1055527003656 tetramer interface [polypeptide binding]; other site 1055527003657 YtkA-like; Region: YtkA; pfam13115 1055527003658 Outer membrane efflux protein; Region: OEP; pfam02321 1055527003659 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 1055527003660 HlyD family secretion protein; Region: HlyD_3; pfam13437 1055527003661 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 1055527003662 Predicted branched-chain amino acid permeases (azaleucine resistance) [Amino acid transport and metabolism]; Region: AzlD; COG1687 1055527003663 AzlC protein; Region: AzlC; cl00570 1055527003664 chaperone protein DnaJ; Provisional; Region: PRK14288 1055527003665 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 1055527003666 HSP70 interaction site [polypeptide binding]; other site 1055527003667 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 1055527003668 substrate binding site [polypeptide binding]; other site 1055527003669 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 1055527003670 Zn binding sites [ion binding]; other site 1055527003671 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 1055527003672 dimer interface [polypeptide binding]; other site 1055527003673 tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase; Region: trmU; TIGR00420 1055527003674 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 1055527003675 Ligand Binding Site [chemical binding]; other site 1055527003676 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 1055527003677 HSP70 interaction site [polypeptide binding]; other site 1055527003678 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 1055527003679 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 1055527003680 active site 1055527003681 (T/H)XGH motif; other site 1055527003682 nickel responsive regulator; Provisional; Region: PRK00630 1055527003683 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 1055527003684 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 1055527003685 tonB-system energizer ExbB, group 2; Region: exbB2; TIGR02805 1055527003686 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 1055527003687 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 1055527003688 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 1055527003689 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 1055527003690 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527003691 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 1055527003692 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 1055527003693 Mg2+ transporter Helicobacter pylori CorA-like subgroup; Region: HpCorA-like; cd12836 1055527003694 Cl binding site [ion binding]; other site 1055527003695 oligomer interface [polypeptide binding]; other site 1055527003696 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 1055527003697 Phosphoglycerate kinase; Region: PGK; pfam00162 1055527003698 substrate binding site [chemical binding]; other site 1055527003699 hinge regions; other site 1055527003700 ADP binding site [chemical binding]; other site 1055527003701 catalytic site [active] 1055527003702 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 1055527003703 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 1055527003704 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 1055527003705 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 1055527003706 ligand binding site [chemical binding]; other site 1055527003707 active site 1055527003708 UGI interface [polypeptide binding]; other site 1055527003709 catalytic site [active] 1055527003710 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1055527003711 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1055527003712 putative acyl-acceptor binding pocket; other site 1055527003713 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 1055527003714 C-terminal peptidase (prc); Region: prc; TIGR00225 1055527003715 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 1055527003716 protein binding site [polypeptide binding]; other site 1055527003717 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 1055527003718 Catalytic dyad [active] 1055527003719 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 1055527003720 DNA methylase; Region: N6_N4_Mtase; pfam01555 1055527003721 Predicted helicase [General function prediction only]; Region: COG4889 1055527003722 Predicted helicase [General function prediction only]; Region: COG4889 1055527003723 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK05848 1055527003724 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 1055527003725 dimerization interface [polypeptide binding]; other site 1055527003726 active site 1055527003727 quinolinate synthetase complex, A subunit; Region: nadA; TIGR00550 1055527003728 phosphatidylserine decarboxylase; Provisional; Region: PRK03934 1055527003729 prenyltransferase; Reviewed; Region: ubiA; PRK12874 1055527003730 UbiA prenyltransferase family; Region: UbiA; pfam01040 1055527003731 Predicted membrane metal-binding protein [General function prediction only]; Region: ComEC; COG0658 1055527003732 Competence protein; Region: Competence; pfam03772 1055527003733 replicative DNA helicase; Provisional; Region: PRK08506 1055527003734 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 1055527003735 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 1055527003736 Walker A motif; other site 1055527003737 ATP binding site [chemical binding]; other site 1055527003738 Walker B motif; other site 1055527003739 DNA binding loops [nucleotide binding] 1055527003740 yjeF N-terminal region; Region: yjeF_nterm; TIGR00197 1055527003741 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 1055527003742 putative substrate binding site [chemical binding]; other site 1055527003743 putative ATP binding site [chemical binding]; other site 1055527003744 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1055527003745 His Kinase A (phospho-acceptor) domain; Region: HisKA; pfam00512 1055527003746 dimer interface [polypeptide binding]; other site 1055527003747 phosphorylation site [posttranslational modification] 1055527003748 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 1055527003749 ATP binding site [chemical binding]; other site 1055527003750 Mg2+ binding site [ion binding]; other site 1055527003751 G-X-G motif; other site 1055527003752 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1055527003753 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 1055527003754 active site 1055527003755 phosphorylation site [posttranslational modification] 1055527003756 intermolecular recognition site; other site 1055527003757 dimerization interface [polypeptide binding]; other site 1055527003758 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 1055527003759 DNA binding site [nucleotide binding] 1055527003760 potential frameshift: common BLAST hit: gi|15612507|ref|NP_224160.1| type II restriction enzyme 1055527003761 potential frameshift: common BLAST hit: gi|15645978|ref|NP_208158.1| type IIS restriction enzyme R protein (MBOIIR) 1055527003762 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 1055527003763 DNA methylase; Region: N6_N4_Mtase; pfam01555 1055527003764 potential frameshift: common BLAST hit: gi|109946808|ref|YP_664036.1| modification methylase mjai 1055527003765 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 1055527003766 DNA methylase; Region: N6_N4_Mtase; pfam01555 1055527003767 DNA methylase; Region: N6_N4_Mtase; pfam01555 1055527003768 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 1055527003769 DEAD-like helicases superfamily; Region: DEXDc; smart00487 1055527003770 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 1055527003771 rod shape-determining protein MreC; Region: MreC; pfam04085 1055527003772 rod shape-determining protein MreB; Provisional; Region: PRK13927 1055527003773 MreB and similar proteins; Region: MreB_like; cd10225 1055527003774 nucleotide binding site [chemical binding]; other site 1055527003775 Mg binding site [ion binding]; other site 1055527003776 putative protofilament interaction site [polypeptide binding]; other site 1055527003777 RodZ interaction site [polypeptide binding]; other site 1055527003778 endopeptidase Clp ATP-binding regulatory subunit (clpX); Region: clpX; TIGR00382 1055527003779 ClpX C4-type zinc finger; Region: zf-C4_ClpX; smart00994 1055527003780 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 1055527003781 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 1055527003782 Walker A motif; other site 1055527003783 ATP binding site [chemical binding]; other site 1055527003784 Walker B motif; other site 1055527003785 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1055527003786 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 1055527003787 acyl-[acyl-carrier-protein]--UDP-N- acetylglucosamine O-acyltransferase; Region: lipid_A_lpxA; TIGR01852 1055527003788 active site 1055527003789 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 1055527003790 flagellar assembly protein FliW; Provisional; Region: PRK13282 1055527003791 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 1055527003792 ATP-dependent protease La; Region: lon; TIGR00763 1055527003793 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 1055527003794 Walker A motif; other site 1055527003795 ATP binding site [chemical binding]; other site 1055527003796 Walker B motif; other site 1055527003797 arginine finger; other site 1055527003798 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 1055527003799 prephenate dehydrogenase; Validated; Region: PRK08507 1055527003800 Prephenate dehydrogenase; Region: PDH; pfam02153 1055527003801 DNA/RNA endonuclease G, NUC1 [Nucleotide transport and metabolism]; Region: NUC1; COG1864 1055527003802 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 1055527003803 active site 1055527003804 substrate binding site [chemical binding]; other site 1055527003805 Mg2+ binding site [ion binding]; other site 1055527003806 Type III restriction/modification enzyme methylation subunit; Region: TypeIII_RM_meth; pfam12564 1055527003807 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 1055527003808 DNA methylase; Region: N6_N4_Mtase; pfam01555 1055527003809 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3421 1055527003810 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 1055527003811 ATP binding site [chemical binding]; other site 1055527003812 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 1055527003813 putative Mg++ binding site [ion binding]; other site 1055527003814 biotin synthase; Provisional; Region: PRK08508 1055527003815 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 1055527003816 FeS/SAM binding site; other site 1055527003817 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 1055527003818 YihY family inner membrane protein; Region: yihY_not_rbn; TIGR00765 1055527003819 Uncharacterized conserved protein [Function unknown]; Region: COG1479 1055527003820 Protein of unknown function DUF262; Region: DUF262; pfam03235 1055527003821 Protein of unknown function DUF262; Region: DUF262; pfam03235 1055527003822 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 1055527003823 7-cyano-7-deazaguanine reductase; Region: QueF-II; TIGR03139 1055527003824 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 1055527003825 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 1055527003826 IPP transferase; Region: IPPT; pfam01715 1055527003827 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 1055527003828 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 1055527003829 Ligand binding site; other site 1055527003830 metal-binding site 1055527003831 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 1055527003832 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 1055527003833 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 1055527003834 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 1055527003835 Probable transposase; Region: OrfB_IS605; pfam01385 1055527003836 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 1055527003837 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13904 1055527003838 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 1055527003839 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 1055527003840 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08472 1055527003841 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 1055527003842 Walker A motif/ATP binding site; other site 1055527003843 Walker B motif; other site 1055527003844 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 1055527003845 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 1055527003846 ATP binding site [chemical binding]; other site 1055527003847 Walker A motif; other site 1055527003848 hexamer interface [polypeptide binding]; other site 1055527003849 Walker B motif; other site 1055527003850 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 1055527003851 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1055527003852 active site 1055527003853 HIGH motif; other site 1055527003854 nucleotide binding site [chemical binding]; other site 1055527003855 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1055527003856 active site 1055527003857 KMSKS motif; other site 1055527003858 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 1055527003859 tRNA binding surface [nucleotide binding]; other site 1055527003860 anticodon binding site; other site 1055527003861 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 1055527003862 RNA binding surface [nucleotide binding]; other site 1055527003863 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 1055527003864 dimethyladenosine transferase; Region: ksgA; TIGR00755 1055527003865 S-adenosylmethionine binding site [chemical binding]; other site 1055527003866 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 1055527003867 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1055527003868 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 1055527003869 KpsF/GutQ family protein; Region: kpsF; TIGR00393 1055527003870 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 1055527003871 putative active site [active] 1055527003872 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 1055527003873 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14462 1055527003874 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 1055527003875 FeS/SAM binding site; other site 1055527003876 formyltetrahydrofolate deformylase; Region: PurU; TIGR00655 1055527003877 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 1055527003878 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 1055527003879 active site 1055527003880 substrate binding site [chemical binding]; other site 1055527003881 cosubstrate binding site; other site 1055527003882 catalytic site [active] 1055527003883 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 1055527003884 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1055527003885 tandem repeat interface [polypeptide binding]; other site 1055527003886 oligomer interface [polypeptide binding]; other site 1055527003887 active site residues [active] 1055527003888 TIR domain; Region: TIR_2; pfam13676 1055527003889 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 1055527003890 active site 1055527003891 carbon storage regulator; Provisional; Region: PRK00568 1055527003892 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK04181 1055527003893 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 1055527003894 SmpB-tmRNA interface; other site 1055527003895 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 1055527003896 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 1055527003897 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 1055527003898 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 1055527003899 ribonuclease P protein component, eubacterial; Region: rnpA; TIGR00188 1055527003900 hypothetical protein; Provisional; Region: PRK14374 1055527003901 membrane protein insertase; Provisional; Region: PRK01318 1055527003902 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 1055527003903 potential frameshift: common BLAST hit: gi|298735583|ref|YP_003728106.1| spoIIIJ-associated protein 1055527003904 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 1055527003905 tRNA modification GTPase TrmE; Region: mnmE_trmE_thdF; TIGR00450 1055527003906 Circularly permuted YlqF-related GTPases; Region: YlqF_related_GTPase; cl17249 1055527003907 GTP/Mg2+ binding site [chemical binding]; other site 1055527003908 G4 box; other site 1055527003909 G5 box; other site 1055527003910 trmE is a tRNA modification GTPase; Region: trmE; cd04164 1055527003911 G1 box; other site 1055527003912 G1 box; other site 1055527003913 GTP/Mg2+ binding site [chemical binding]; other site 1055527003914 Switch I region; other site 1055527003915 Switch I region; other site 1055527003916 G2 box; other site 1055527003917 G2 box; other site 1055527003918 Switch II region; other site 1055527003919 G3 box; other site 1055527003920 G3 box; other site 1055527003921 Switch II region; other site 1055527003922 G4 box; other site 1055527003923 G5 box; other site 1055527003924 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 1055527003925 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527003926 LPP20 lipoprotein; Region: LPP20; pfam02169 1055527003927 Collagen-binding surface adhesin SpaP (antigen I/II family) [General function prediction only]; Region: FlgN; COG3417 1055527003928 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 1055527003929 catalytic residues [active] 1055527003930 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 1055527003931 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 1055527003932 RNA binding surface [nucleotide binding]; other site 1055527003933 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 1055527003934 active site 1055527003935 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; Region: PHP_PolIIIA_DnaE3; cd12113 1055527003936 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 1055527003937 active site 1055527003938 PHP Thumb interface [polypeptide binding]; other site 1055527003939 metal binding site [ion binding]; metal-binding site 1055527003940 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 1055527003941 generic binding surface I; other site 1055527003942 generic binding surface II; other site 1055527003943 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 1055527003944 Heat shock protein [Posttranslational modification, protein turnover, chaperones]; Region: HslJ; COG3187 1055527003945 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 1055527003946 mce related protein; Region: MCE; pfam02470 1055527003947 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 1055527003948 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 1055527003949 Walker A/P-loop; other site 1055527003950 ATP binding site [chemical binding]; other site 1055527003951 Q-loop/lid; other site 1055527003952 ABC transporter signature motif; other site 1055527003953 Walker B; other site 1055527003954 D-loop; other site 1055527003955 H-loop/switch region; other site 1055527003956 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 1055527003957 conserved hypothetical integral membrane protein; Region: TIGR00056 1055527003958 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527003959 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 1055527003960 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 1055527003961 homodimer interface [polypeptide binding]; other site 1055527003962 substrate-cofactor binding pocket; other site 1055527003963 catalytic residue [active] 1055527003964 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527003965 DNA polymerase I; Region: pola; TIGR00593 1055527003966 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 1055527003967 active site 1055527003968 metal binding site 1 [ion binding]; metal-binding site 1055527003969 putative 5' ssDNA interaction site; other site 1055527003970 metal binding site 3; metal-binding site 1055527003971 metal binding site 2 [ion binding]; metal-binding site 1055527003972 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 1055527003973 putative DNA binding site [nucleotide binding]; other site 1055527003974 putative metal binding site [ion binding]; other site 1055527003975 3'-5' exonuclease; Region: 35EXOc; smart00474 1055527003976 active site 1055527003977 substrate binding site [chemical binding]; other site 1055527003978 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 1055527003979 active site 1055527003980 DNA binding site [nucleotide binding] 1055527003981 catalytic site [active] 1055527003982 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1055527003983 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1055527003984 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 1055527003985 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 1055527003986 thymidylate kinase; Validated; Region: tmk; PRK00698 1055527003987 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 1055527003988 TMP-binding site; other site 1055527003989 ATP-binding site [chemical binding]; other site 1055527003990 Phosphopantetheine adenylyltransferase [Coenzyme metabolism]; Region: CoaD; COG0669 1055527003991 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 1055527003992 active site 1055527003993 (T/H)XGH motif; other site 1055527003994 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 1055527003995 Flavoprotein; Region: Flavoprotein; pfam02441 1055527003996 flagellar basal body P-ring biosynthesis protein FlgA; Reviewed; Region: flgA; PRK08515 1055527003997 flagella basal body P-ring formation protein FlgA; Region: flgA_cterm; TIGR03170 1055527003998 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 1055527003999 Part of AAA domain; Region: AAA_19; pfam13245 1055527004000 Family description; Region: UvrD_C_2; pfam13538 1055527004001 Tetratricopeptide repeat; Region: TPR_9; pfam13371 1055527004002 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 1055527004003 binding surface 1055527004004 TPR motif; other site 1055527004005 seryl-tRNA synthetase; Provisional; Region: PRK05431 1055527004006 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 1055527004007 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 1055527004008 dimer interface [polypeptide binding]; other site 1055527004009 active site 1055527004010 motif 1; other site 1055527004011 motif 2; other site 1055527004012 motif 3; other site 1055527004013 Predicted amidohydrolase [General function prediction only]; Region: COG0388 1055527004014 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 1055527004015 active site 1055527004016 catalytic triad [active] 1055527004017 dimer interface [polypeptide binding]; other site 1055527004018 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK14065 1055527004019 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 1055527004020 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 1055527004021 S-adenosylmethionine binding site [chemical binding]; other site 1055527004022 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 1055527004023 uncharacterized protein, YigZ family; Region: IMPACT_YIGZ; TIGR00257 1055527004024 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 1055527004025 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 1055527004026 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 1055527004027 ABC-2 type transporter; Region: ABC2_membrane; cl17235 1055527004028 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 1055527004029 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1055527004030 HlyD family secretion protein; Region: HlyD_3; pfam13437 1055527004031 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1055527004032 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 1055527004033 Domain of unknown function DUF21; Region: DUF21; pfam01595 1055527004034 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 1055527004035 Transporter associated domain; Region: CorC_HlyC; smart01091 1055527004036 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 1055527004037 Phosphate transporter family; Region: PHO4; pfam01384 1055527004038 NifU-like domain; Region: NifU; pfam01106 1055527004039 UDP-N-acetylmuramyl-tripeptide synthetase; Region: murE; TIGR01085 1055527004040 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1055527004041 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1055527004042 Transaldolase-like proteins from plants and bacteria; Region: Transaldolase_like; cd00955 1055527004043 putative active site [active] 1055527004044 transaldolase; Provisional; Region: PRK03903 1055527004045 catalytic residue [active] 1055527004046 ribosomal protein L25, Ctc-form; Region: ctc_TL5; TIGR00731 1055527004047 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 1055527004048 5S rRNA interface [nucleotide binding]; other site 1055527004049 CTC domain interface [polypeptide binding]; other site 1055527004050 L16 interface [polypeptide binding]; other site 1055527004051 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 1055527004052 putative active site [active] 1055527004053 catalytic residue [active] 1055527004054 Predicted permeases [General function prediction only]; Region: COG0795 1055527004055 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1055527004056 Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized proteins with a DEAD domain; Region: PLDc_Bfil_DEXD_like; cd09117 1055527004057 PLD-like domain; Region: PLDc_2; pfam13091 1055527004058 homodimer interface [polypeptide binding]; other site 1055527004059 putative active site [active] 1055527004060 catalytic site [active] 1055527004061 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527004062 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3399 1055527004063 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 1055527004064 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 1055527004065 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 1055527004066 metal-binding site [ion binding] 1055527004067 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1055527004068 Soluble P-type ATPase [General function prediction only]; Region: COG4087 1055527004069 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 1055527004070 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 1055527004071 S-adenosylmethionine binding site [chemical binding]; other site 1055527004072 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 1055527004073 catalytic motif [active] 1055527004074 Zn binding site [ion binding]; other site 1055527004075 Pyrimidine reductase, riboflavin biosynthesis [Coenzyme metabolism]; Region: RibD; COG1985 1055527004076 RibD C-terminal domain; Region: RibD_C; cl17279 1055527004077 sodium--glutamate symport carrier (gltS); Region: gltS; TIGR00210 1055527004078 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 1055527004079 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 1055527004080 4Fe-4S binding domain; Region: Fer4_5; pfam12801 1055527004081 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 1055527004082 acyl-phosphate glycerol 3-phosphate acyltransferase; Region: TIGR00023 1055527004083 FolB domain; Region: folB_dom; TIGR00526 1055527004084 active site 1055527004085 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 1055527004086 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 1055527004087 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 1055527004088 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 1055527004089 Selenocysteine synthase [seryl-tRNASer selenium transferase] [Amino acid transport and metabolism]; Region: SelA; COG1921 1055527004090 L-seryl-tRNA selenium transferase; Region: SelA; pfam03841 1055527004091 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1055527004092 catalytic residue [active] 1055527004093 transcription elongation factor NusA; Provisional; Region: nusA; PRK12328 1055527004094 NusA N-terminal domain; Region: NusA_N; pfam08529 1055527004095 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 1055527004096 RNA binding site [nucleotide binding]; other site 1055527004097 homodimer interface [polypeptide binding]; other site 1055527004098 NusA-like KH domain; Region: KH_5; pfam13184 1055527004099 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 1055527004100 G-X-X-G motif; other site 1055527004101 potential frameshift: common BLAST hit: gi|308185290|ref|YP_003929423.1| type IIS restriction-modification protein 1055527004102 Restriction endonuclease [Defense mechanisms]; Region: COG3587 1055527004103 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 1055527004104 ATP binding site [chemical binding]; other site 1055527004105 putative Mg++ binding site [ion binding]; other site 1055527004106 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 1055527004107 DNA methylase; Region: N6_N4_Mtase; pfam01555 1055527004108 DNA methylase; Region: N6_N4_Mtase; pfam01555 1055527004109 ATP-dependent DNA helicase RecG; Region: recG; TIGR00643 1055527004110 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 1055527004111 ssDNA binding site; other site 1055527004112 generic binding surface II; other site 1055527004113 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 1055527004114 ATP binding site [chemical binding]; other site 1055527004115 putative Mg++ binding site [ion binding]; other site 1055527004116 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 1055527004117 nucleotide binding region [chemical binding]; other site 1055527004118 ATP-binding site [chemical binding]; other site 1055527004119 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527004120 Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Ape1-like_AP-endo; cd09087 1055527004121 active site 1055527004122 putative catalytic site [active] 1055527004123 DNA binding site [nucleotide binding] 1055527004124 putative phosphate binding site [ion binding]; other site 1055527004125 metal binding site A [ion binding]; metal-binding site 1055527004126 AP binding site [nucleotide binding]; other site 1055527004127 metal binding site B [ion binding]; metal-binding site 1055527004128 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 1055527004129 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 1055527004130 Walker A motif; other site 1055527004131 ATP binding site [chemical binding]; other site 1055527004132 Walker B motif; other site 1055527004133 arginine finger; other site 1055527004134 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 1055527004135 DnaA box-binding interface [nucleotide binding]; other site 1055527004136 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 1055527004137 Protein of unknown function (DUF2443); Region: DUF2443; pfam10398 1055527004138 glucosamine--fructose-6-phosphate aminotransferase (isomerizing); Region: glmS; TIGR01135 1055527004139 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 1055527004140 glutaminase active site [active] 1055527004141 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 1055527004142 dimer interface [polypeptide binding]; other site 1055527004143 active site 1055527004144 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 1055527004145 dimer interface [polypeptide binding]; other site 1055527004146 active site 1055527004147 Predicted alternative thymidylate synthase [Nucleotide transport and metabolism]; Region: THY1; COG1351 1055527004148 HsdM N-terminal domain; Region: HsdM_N; pfam12161 1055527004149 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 1055527004150 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 1055527004151 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1055527004152 potential frameshift: common BLAST hit: gi|308185305|ref|YP_003929438.1| typeI restriction enzyme R protein 1055527004153 Protein of unknown function DUF45; Region: DUF45; pfam01863 1055527004154 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 1055527004155 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 1055527004156 N-terminal plug; other site 1055527004157 ligand-binding site [chemical binding]; other site 1055527004158 Arginase family; Region: Arginase; cd09989 1055527004159 active site 1055527004160 Mn binding site [ion binding]; other site 1055527004161 oligomer interface [polypeptide binding]; other site 1055527004162 S-methylmethionine transporter; Provisional; Region: PRK11387 1055527004163 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 1055527004164 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 1055527004165 hexamer interface [polypeptide binding]; other site 1055527004166 ligand binding site [chemical binding]; other site 1055527004167 putative active site [active] 1055527004168 NAD(P) binding site [chemical binding]; other site 1055527004169 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 1055527004170 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 1055527004171 putative NAD(P) binding site [chemical binding]; other site 1055527004172 putative substrate binding site [chemical binding]; other site 1055527004173 catalytic Zn binding site [ion binding]; other site 1055527004174 structural Zn binding site [ion binding]; other site 1055527004175 dimer interface [polypeptide binding]; other site 1055527004176 Uncharacterized conserved protein [Function unknown]; Region: COG1479 1055527004177 Protein of unknown function DUF262; Region: DUF262; pfam03235 1055527004178 Protein of unknown function DUF262; Region: DUF262; pfam03235 1055527004179 Uncharacterized conserved protein [Function unknown]; Region: COG1479 1055527004180 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 1055527004181 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1055527004182 NAD kinase [Coenzyme metabolism]; Region: nadF; COG0061 1055527004183 ATP-NAD kinase; Region: NAD_kinase; pfam01513 1055527004184 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 1055527004185 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1055527004186 Walker A/P-loop; other site 1055527004187 ATP binding site [chemical binding]; other site 1055527004188 Q-loop/lid; other site 1055527004189 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 1055527004190 ABC transporter signature motif; other site 1055527004191 Walker B; other site 1055527004192 D-loop; other site 1055527004193 H-loop/switch region; other site 1055527004194 Domain of unknown function (DUF814); Region: DUF814; pfam05670 1055527004195 potential frameshift: common BLAST hit: gi|254780063|ref|YP_003058170.1| Cysteine-rich protein G 1055527004196 DNA polymerase III subunit epsilon; Provisional; Region: PRK08517 1055527004197 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 1055527004198 active site 1055527004199 catalytic site [active] 1055527004200 substrate binding site [chemical binding]; other site 1055527004201 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 1055527004202 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 1055527004203 substrate binding site [chemical binding]; other site 1055527004204 hexamer interface [polypeptide binding]; other site 1055527004205 metal binding site [ion binding]; metal-binding site 1055527004206 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 1055527004207 active site 1055527004208 Methyltransferase domain; Region: Methyltransf_26; pfam13659 1055527004209 elongation factor Ts; Provisional; Region: tsf; PRK09377 1055527004210 UBA/TS-N domain; Region: UBA; pfam00627 1055527004211 Elongation factor TS; Region: EF_TS; pfam00889 1055527004212 Elongation factor TS; Region: EF_TS; pfam00889 1055527004213 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 1055527004214 rRNA interaction site [nucleotide binding]; other site 1055527004215 S8 interaction site; other site 1055527004216 putative laminin-1 binding site; other site 1055527004217 putative recombination protein RecB; Provisional; Region: PRK13909 1055527004218 Family description; Region: UvrD_C_2; pfam13538 1055527004219 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 1055527004220 pH-dependent sodium/proton antiporter; Provisional; Region: nhaA; PRK14856 1055527004221 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 1055527004222 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 1055527004223 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 1055527004224 protein-export membrane protein SecF; Region: 3a0501s07; TIGR00966 1055527004225 Protein export membrane protein; Region: SecD_SecF; pfam02355 1055527004226 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 1055527004227 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 1055527004228 HIGH motif; other site 1055527004229 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1055527004230 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 1055527004231 active site 1055527004232 KMSKS motif; other site 1055527004233 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1055527004234 tRNA binding surface [nucleotide binding]; other site 1055527004235 anticodon binding site; other site 1055527004236 Lipopolysaccharide-assembly; Region: LptE; pfam04390 1055527004237 folylpolyglutamate synthase/dihydrofolate synthase; Region: folC; TIGR01499 1055527004238 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1055527004239 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1055527004240 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1055527004241 Peptidase family M23; Region: Peptidase_M23; pfam01551 1055527004242 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1055527004243 Peptidase family M23; Region: Peptidase_M23; pfam01551 1055527004244 Integral membrane protein CcmA involved in cell shape determination [Cell envelope biogenesis, outer membrane]; Region: CcmA; COG1664 1055527004245 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 1055527004246 transcription-repair coupling factor (mfd); Region: mfd; TIGR00580 1055527004247 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 1055527004248 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 1055527004249 ATP binding site [chemical binding]; other site 1055527004250 putative Mg++ binding site [ion binding]; other site 1055527004251 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 1055527004252 nucleotide binding region [chemical binding]; other site 1055527004253 ATP-binding site [chemical binding]; other site 1055527004254 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 1055527004255 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 1055527004256 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 1055527004257 [2Fe-2S] cluster binding site [ion binding]; other site 1055527004258 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 1055527004259 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 1055527004260 intrachain domain interface; other site 1055527004261 interchain domain interface [polypeptide binding]; other site 1055527004262 heme bH binding site [chemical binding]; other site 1055527004263 Qi binding site; other site 1055527004264 heme bL binding site [chemical binding]; other site 1055527004265 Qo binding site; other site 1055527004266 interchain domain interface [polypeptide binding]; other site 1055527004267 intrachain domain interface; other site 1055527004268 Qi binding site; other site 1055527004269 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 1055527004270 Qo binding site; other site 1055527004271 Cytochrome c1 [Energy production and conversion]; Region: CYT1; COG2857 1055527004272 Cytochrome c; Region: Cytochrom_C; pfam00034 1055527004273 Cytochrome c; Region: Cytochrom_C; cl11414 1055527004274 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 1055527004275 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 1055527004276 Probable transposase; Region: OrfB_IS605; pfam01385 1055527004277 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 1055527004278 potential frameshift: common BLAST hit: gi|315454048|ref|YP_004074318.1| sulfatase 1055527004279 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 1055527004280 Sulfatase; Region: Sulfatase; cl17466 1055527004281 Sulfatase; Region: Sulfatase; cl17466 1055527004282 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 1055527004283 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1055527004284 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1055527004285 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK03907 1055527004286 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 1055527004287 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1055527004288 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 1055527004289 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 1055527004290 Cell cycle protein; Region: FTSW_RODA_SPOVE; pfam01098 1055527004291 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 1055527004292 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 1055527004293 intersubunit interface [polypeptide binding]; other site 1055527004294 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 1055527004295 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 1055527004296 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 1055527004297 intersubunit interface [polypeptide binding]; other site 1055527004298 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 1055527004299 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1055527004300 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 1055527004301 dimer interface [polypeptide binding]; other site 1055527004302 decamer (pentamer of dimers) interface [polypeptide binding]; other site 1055527004303 catalytic triad [active] 1055527004304 peroxidatic and resolving cysteines [active] 1055527004305 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 1055527004306 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 1055527004307 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 1055527004308 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1055527004309 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1055527004310 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 1055527004311 G1 box; other site 1055527004312 GTP/Mg2+ binding site [chemical binding]; other site 1055527004313 Switch I region; other site 1055527004314 G2 box; other site 1055527004315 G3 box; other site 1055527004316 Switch II region; other site 1055527004317 G4 box; other site 1055527004318 G5 box; other site 1055527004319 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1934 1055527004320 OstA-like protein; Region: OstA; pfam03968 1055527004321 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 1055527004322 motif II; other site 1055527004323 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 1055527004324 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 1055527004325 Sporulation related domain; Region: SPOR; pfam05036 1055527004326 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 1055527004327 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1055527004328 catalytic residue [active] 1055527004329 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1055527004330 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 1055527004331 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 1055527004332 active site 1055527004333 riboflavin synthase, alpha subunit; Region: ribE; TIGR00187 1055527004334 Lumazine binding domain; Region: Lum_binding; pfam00677 1055527004335 Lumazine binding domain; Region: Lum_binding; pfam00677 1055527004336 flhB C-terminus-related protein; Region: flhB_rel; TIGR00789 1055527004337 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 1055527004338 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 1055527004339 Walker A/P-loop; other site 1055527004340 ATP binding site [chemical binding]; other site 1055527004341 Q-loop/lid; other site 1055527004342 ABC transporter signature motif; other site 1055527004343 Walker B; other site 1055527004344 D-loop; other site 1055527004345 H-loop/switch region; other site 1055527004346 NIL domain; Region: NIL; pfam09383 1055527004347 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; cl00427 1055527004348 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 1055527004349 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 1055527004350 active site 1055527004351 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 1055527004352 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 1055527004353 Mg++ binding site [ion binding]; other site 1055527004354 putative catalytic motif [active] 1055527004355 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 1055527004356 active site 1055527004357 hydrophilic channel; other site 1055527004358 dimerization interface [polypeptide binding]; other site 1055527004359 catalytic residues [active] 1055527004360 active site lid [active] 1055527004361 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 1055527004362 4-hydroxythreonine-4-phosphate dehydrogenase; Provisional; Region: pdxA; PRK03946 1055527004363 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 1055527004364 metallohydrolase, glycoprotease/Kae1 family; Region: gcp_kae1; TIGR00329 1055527004365 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 1055527004366 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 1055527004367 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1055527004368 hypothetical protein; Provisional; Region: PRK10236 1055527004369 Domain of unknown function (DUF3944); Region: DUF3944; pfam13099 1055527004370 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4735 1055527004371 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 1055527004372 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 1055527004373 Probable transposase; Region: OrfB_IS605; pfam01385 1055527004374 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 1055527004375 Fic family protein [Function unknown]; Region: COG3177 1055527004376 Fic/DOC family; Region: Fic; pfam02661 1055527004377 Initiator Replication protein; Region: Rep_3; pfam01051 1055527004378 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943