-- dump date 20140619_113233 -- class Genbank::misc_feature -- table misc_feature_note -- id note 102608000001 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 102608000002 putative RNA binding site [nucleotide binding]; other site 102608000003 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 102608000004 homopentamer interface [polypeptide binding]; other site 102608000005 active site 102608000006 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 102608000007 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 102608000008 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA; cl00391 102608000009 active site clefts [active] 102608000010 zinc binding site [ion binding]; other site 102608000011 dimer interface [polypeptide binding]; other site 102608000012 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 102608000013 active site 102608000014 dimer interface [polypeptide binding]; other site 102608000015 pantoate--beta-alanine ligase; Region: panC; TIGR00018 102608000016 Pantoate-beta-alanine ligase; Region: PanC; cd00560 102608000017 active site 102608000018 ATP-binding site [chemical binding]; other site 102608000019 pantoate-binding site; other site 102608000020 HXXH motif; other site 102608000021 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608000022 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 102608000023 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 102608000024 ring oligomerisation interface [polypeptide binding]; other site 102608000025 ATP/Mg binding site [chemical binding]; other site 102608000026 stacking interactions; other site 102608000027 hinge regions; other site 102608000028 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 102608000029 oligomerisation interface [polypeptide binding]; other site 102608000030 mobile loop; other site 102608000031 roof hairpin; other site 102608000032 DNA primase, catalytic core; Region: dnaG; TIGR01391 102608000033 CHC2 zinc finger; Region: zf-CHC2; pfam01807 102608000034 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 102608000035 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 102608000036 active site 102608000037 metal binding site [ion binding]; metal-binding site 102608000038 interdomain interaction site; other site 102608000039 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 102608000040 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 102608000041 Ligand Binding Site [chemical binding]; other site 102608000042 TrbC/VIRB2 family; Region: TrbC; cl01583 102608000043 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 102608000044 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 102608000045 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 102608000046 Walker A motif; other site 102608000047 ATP binding site [chemical binding]; other site 102608000048 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 102608000049 Walker B motif; other site 102608000050 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 102608000051 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 102608000052 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 102608000053 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 102608000054 active site 102608000055 phosphorylation site [posttranslational modification] 102608000056 intermolecular recognition site; other site 102608000057 dimerization interface [polypeptide binding]; other site 102608000058 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 102608000059 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 102608000060 dimer interface [polypeptide binding]; other site 102608000061 active site 102608000062 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 102608000063 catalytic residues [active] 102608000064 substrate binding site [chemical binding]; other site 102608000065 lipid A 1-phosphatase; Reviewed; Region: PRK09597 102608000066 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 102608000067 active site 102608000068 lipid A phosphoethanolamine transferase; Reviewed; Region: PRK09598 102608000069 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 102608000070 Sulfatase; Region: Sulfatase; pfam00884 102608000071 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608000072 DNA/RNA endonuclease G, NUC1 [Nucleotide transport and metabolism]; Region: NUC1; COG1864 102608000073 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 102608000074 prephenate dehydrogenase; Validated; Region: PRK08507 102608000075 Prephenate dehydrogenase; Region: PDH; pfam02153 102608000076 ATP-dependent protease La; Region: lon; TIGR00763 102608000077 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 102608000078 Walker A motif; other site 102608000079 ATP binding site [chemical binding]; other site 102608000080 Walker B motif; other site 102608000081 arginine finger; other site 102608000082 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 102608000083 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 102608000084 flagellar assembly protein FliW; Provisional; Region: PRK13282 102608000085 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 102608000086 Acyl-[acyl carrier protein]; Region: LpxA; COG1043 102608000087 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 102608000088 active site 102608000089 endopeptidase Clp ATP-binding regulatory subunit (clpX); Region: clpX; TIGR00382 102608000090 ClpX C4-type zinc finger; Region: zf-C4_ClpX; smart00994 102608000091 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 102608000092 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 102608000093 Walker A motif; other site 102608000094 ATP binding site [chemical binding]; other site 102608000095 Walker B motif; other site 102608000096 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 102608000097 rod shape-determining protein MreB; Provisional; Region: PRK13927 102608000098 MreB and similar proteins; Region: MreB_like; cd10225 102608000099 nucleotide binding site [chemical binding]; other site 102608000100 Mg binding site [ion binding]; other site 102608000101 putative protofilament interaction site [polypeptide binding]; other site 102608000102 RodZ interaction site [polypeptide binding]; other site 102608000103 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 102608000104 rod shape-determining protein MreC; Region: MreC; pfam04085 102608000105 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 102608000106 DNA methylase; Region: N6_N4_Mtase; pfam01555 102608000107 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 102608000108 DNA methylase; Region: N6_N4_Mtase; pfam01555 102608000109 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 102608000110 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 102608000111 active site 102608000112 phosphorylation site [posttranslational modification] 102608000113 intermolecular recognition site; other site 102608000114 dimerization interface [polypeptide binding]; other site 102608000115 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 102608000116 DNA binding site [nucleotide binding] 102608000117 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 102608000118 His Kinase A (phospho-acceptor) domain; Region: HisKA; pfam00512 102608000119 dimer interface [polypeptide binding]; other site 102608000120 phosphorylation site [posttranslational modification] 102608000121 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 102608000122 ATP binding site [chemical binding]; other site 102608000123 Mg2+ binding site [ion binding]; other site 102608000124 G-X-G motif; other site 102608000125 yjeF N-terminal region; Region: yjeF_nterm; TIGR00197 102608000126 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 102608000127 putative substrate binding site [chemical binding]; other site 102608000128 putative ATP binding site [chemical binding]; other site 102608000129 replicative DNA helicase; Provisional; Region: PRK08506 102608000130 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 102608000131 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 102608000132 Walker A motif; other site 102608000133 ATP binding site [chemical binding]; other site 102608000134 Walker B motif; other site 102608000135 DNA binding loops [nucleotide binding] 102608000136 Predicted membrane metal-binding protein [General function prediction only]; Region: ComEC; COG0658 102608000137 Competence protein; Region: Competence; pfam03772 102608000138 prenyltransferase; Reviewed; Region: ubiA; PRK12874 102608000139 UbiA prenyltransferase family; Region: UbiA; pfam01040 102608000140 phosphatidylserine decarboxylase; Provisional; Region: PRK03934 102608000141 Quinolinate synthetase A protein; Region: NadA; cl00420 102608000142 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK05848 102608000143 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 102608000144 dimerization interface [polypeptide binding]; other site 102608000145 active site 102608000146 Predicted helicase [General function prediction only]; Region: COG4889 102608000147 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 102608000148 DNA methylase; Region: N6_N4_Mtase; pfam01555 102608000149 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 102608000150 C-terminal peptidase (prc); Region: prc; TIGR00225 102608000151 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 102608000152 protein binding site [polypeptide binding]; other site 102608000153 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 102608000154 Catalytic dyad [active] 102608000155 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 102608000156 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 102608000157 putative acyl-acceptor binding pocket; other site 102608000158 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 102608000159 ligand binding site [chemical binding]; other site 102608000160 active site 102608000161 UGI interface [polypeptide binding]; other site 102608000162 catalytic site [active] 102608000163 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 102608000164 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 102608000165 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 102608000166 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 102608000167 Phosphoglycerate kinase; Region: PGK; pfam00162 102608000168 substrate binding site [chemical binding]; other site 102608000169 hinge regions; other site 102608000170 ADP binding site [chemical binding]; other site 102608000171 catalytic site [active] 102608000172 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 102608000173 Mg2+ transporter Helicobacter pylori CorA-like subgroup; Region: HpCorA-like; cd12836 102608000174 Cl binding site [ion binding]; other site 102608000175 oligomer interface [polypeptide binding]; other site 102608000176 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 102608000177 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 102608000178 DNA methylase; Region: N6_N4_Mtase; pfam01555 102608000179 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 102608000180 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 102608000181 DNA binding site [nucleotide binding] 102608000182 substrate interaction site [chemical binding]; other site 102608000183 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 102608000184 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 102608000185 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 102608000186 Na binding site [ion binding]; other site 102608000187 Proline dehydrogenase; Region: Pro_dh; pfam01619 102608000188 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 102608000189 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 102608000190 Glutamate binding site [chemical binding]; other site 102608000191 NAD binding site [chemical binding]; other site 102608000192 catalytic residues [active] 102608000193 Phosphoenolpyruvate carboxylase; Region: PEPcase; cl17418 102608000194 A nuclease of the HNH/ENDO VII superfamily with conserved WHH; Region: WHH; pfam14414 102608000195 SMI1 / KNR4 family; Region: SMI1_KNR4; smart00860 102608000196 potential frameshift: common BLAST hit: gi|15644696|ref|NP_206866.1| ATP-binding protein 102608000197 potential frameshift: common BLAST hit: gi|15644696|ref|NP_206866.1| ATP-binding protein 102608000198 potential frameshift: common BLAST hit: gi|108562492|ref|YP_626808.1| ATP-binding protein 102608000199 potential frameshift: common BLAST hit: gi|108562492|ref|YP_626808.1| ATP-binding protein 102608000200 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 102608000201 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 102608000202 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 102608000203 Urease accessory protein UreH [Posttranslational modification, protein turnover, chaperones]; Region: UreH; COG0829 102608000204 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 102608000205 G1 box; other site 102608000206 GTP/Mg2+ binding site [chemical binding]; other site 102608000207 G2 box; other site 102608000208 Switch I region; other site 102608000209 G3 box; other site 102608000210 Switch II region; other site 102608000211 G4 box; other site 102608000212 G5 box; other site 102608000213 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 102608000214 UreF; Region: UreF; pfam01730 102608000215 urease accessory protein UreE; Provisional; Region: ureE; PRK13261 102608000216 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 102608000217 dimer interface [polypeptide binding]; other site 102608000218 catalytic residues [active] 102608000219 AmiS/UreI family transporter; Region: AmiS_UreI; pfam02293 102608000220 urease subunit beta; Provisional; Region: ureB; PRK13985 102608000221 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 102608000222 subunit interactions [polypeptide binding]; other site 102608000223 active site 102608000224 flap region; other site 102608000225 urease subunit alpha; Provisional; Region: PRK13986 102608000226 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 102608000227 alpha-gamma subunit interface [polypeptide binding]; other site 102608000228 beta-gamma subunit interface [polypeptide binding]; other site 102608000229 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 102608000230 gamma-beta subunit interface [polypeptide binding]; other site 102608000231 alpha-beta subunit interface [polypeptide binding]; other site 102608000232 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 102608000233 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14324 102608000234 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 102608000235 active site 102608000236 substrate binding site [chemical binding]; other site 102608000237 metal binding site [ion binding]; metal-binding site 102608000238 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 102608000239 peptide chain release factor 1; Validated; Region: prfA; PRK00591 102608000240 This domain is found in peptide chain release factors; Region: PCRF; smart00937 102608000241 RF-1 domain; Region: RF-1; pfam00472 102608000242 potential frameshift: common BLAST hit: gi|308183877|ref|YP_003928010.1| outer membrane protein HorA 102608000243 potential frameshift: common BLAST hit: gi|210134284|ref|YP_002300723.1| outer membrane protein HorA 102608000244 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608000245 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608000246 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 102608000247 dimer interface [polypeptide binding]; other site 102608000248 putative CheW interface [polypeptide binding]; other site 102608000249 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 102608000250 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 102608000251 23S rRNA interface [nucleotide binding]; other site 102608000252 L3 interface [polypeptide binding]; other site 102608000253 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl17341 102608000254 Predicted dehydrogenase [General function prediction only]; Region: COG0579 102608000255 NLPC_P60 stabilising domain, N term; Region: N_NLPC_P60; pfam12912 102608000256 SH3 domain of the SH3b1 type; Region: SH3_6; pfam12913 102608000257 SH3 domain of SH3b2 type; Region: SH3_7; pfam12914 102608000258 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 102608000259 NlpC/P60 family; Region: NLPC_P60; pfam00877 102608000260 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 102608000261 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 102608000262 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 102608000263 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 102608000264 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 102608000265 DNA binding residues [nucleotide binding] 102608000266 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 102608000267 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 102608000268 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 102608000269 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 102608000270 potential frameshift: common BLAST hit: gi|15644721|ref|NP_206891.1| type II restriction enzyme R protein (hsdR) 102608000271 DpnII restriction endonuclease; Region: DpnII; pfam04556 102608000272 DpnII restriction endonuclease; Region: DpnII; pfam04556 102608000273 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 102608000274 Methyltransferase domain; Region: Methyltransf_26; pfam13659 102608000275 DNA methylase; Region: N6_N4_Mtase; pfam01555 102608000276 potential frameshift: common BLAST hit: gi|108562519|ref|YP_626835.1| alpha-1,2-fucosyltransferase 102608000277 Alpha-1,2-fucosyltransferase; Region: Fut1_Fut2_like; cd11301 102608000278 GDP-Fucose binding site [chemical binding]; other site 102608000279 GDP-fucose protein O-fucosyltransferase and related proteins; Region: O-FucT_like; cl16914 102608000280 2-hydroxyacid dehydrogenase; Provisional; Region: PRK08410 102608000281 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_4; cd12162 102608000282 putative ligand binding site [chemical binding]; other site 102608000283 putative NAD binding site [chemical binding]; other site 102608000284 catalytic site [active] 102608000285 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 102608000286 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 102608000287 pyridoxal 5'-phosphate binding site [chemical binding]; other site 102608000288 catalytic residue [active] 102608000289 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 102608000290 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 102608000291 dimer interface [polypeptide binding]; other site 102608000292 putative CheW interface [polypeptide binding]; other site 102608000293 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 102608000294 Ligand Binding Site [chemical binding]; other site 102608000295 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608000296 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 102608000297 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 102608000298 metal-binding site 102608000299 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 102608000300 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 102608000301 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 102608000302 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 102608000303 dimer interface [polypeptide binding]; other site 102608000304 putative CheW interface [polypeptide binding]; other site 102608000305 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 102608000306 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 102608000307 active site 102608000308 metal binding site [ion binding]; metal-binding site 102608000309 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 102608000310 S-ribosylhomocysteinase; Provisional; Region: PRK02260 102608000311 cystathionine gamma-synthase/cystathionine beta-lyase; Validated; Region: PRK06176 102608000312 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 102608000313 homodimer interface [polypeptide binding]; other site 102608000314 substrate-cofactor binding pocket; other site 102608000315 pyridoxal 5'-phosphate binding site [chemical binding]; other site 102608000316 catalytic residue [active] 102608000317 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 102608000318 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 102608000319 dimer interface [polypeptide binding]; other site 102608000320 pyridoxal 5'-phosphate binding site [chemical binding]; other site 102608000321 catalytic residue [active] 102608000322 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 102608000323 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 102608000324 nucleotide binding site [chemical binding]; other site 102608000325 NEF interaction site [polypeptide binding]; other site 102608000326 SBD interface [polypeptide binding]; other site 102608000327 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 102608000328 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 102608000329 dimer interface [polypeptide binding]; other site 102608000330 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 102608000331 heat-inducible transcription repressor; Provisional; Region: PRK03911 102608000332 hypothetical protein; Provisional; Region: PRK05834 102608000333 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 102608000334 flagellin B; Provisional; Region: PRK13588 102608000335 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 102608000336 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 102608000337 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 102608000338 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 102608000339 DNA topoisomerase I; Validated; Region: PRK05582 102608000340 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 102608000341 active site 102608000342 interdomain interaction site; other site 102608000343 putative metal-binding site [ion binding]; other site 102608000344 nucleotide binding site [chemical binding]; other site 102608000345 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 102608000346 domain I; other site 102608000347 DNA binding groove [nucleotide binding] 102608000348 phosphate binding site [ion binding]; other site 102608000349 domain II; other site 102608000350 domain III; other site 102608000351 nucleotide binding site [chemical binding]; other site 102608000352 catalytic site [active] 102608000353 domain IV; other site 102608000354 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 102608000355 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 102608000356 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 102608000357 Fe-S oxidoreductases [Energy production and conversion]; Region: COG0731 102608000358 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 102608000359 FeS/SAM binding site; other site 102608000360 Helicobacter pylori protein of unknown function (DUF874); Region: DUF874; pfam05917 102608000361 phosphoenolpyruvate synthase; Validated; Region: PRK06464 102608000362 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 102608000363 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 102608000364 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 102608000365 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK12305 102608000366 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 102608000367 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 102608000368 active site 102608000369 dimer interface [polypeptide binding]; other site 102608000370 motif 1; other site 102608000371 motif 2; other site 102608000372 motif 3; other site 102608000373 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 102608000374 anticodon binding site; other site 102608000375 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 102608000376 translation initiation factor IF-3; Region: infC; TIGR00168 102608000377 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 102608000378 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 102608000379 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 102608000380 23S rRNA binding site [nucleotide binding]; other site 102608000381 L21 binding site [polypeptide binding]; other site 102608000382 L13 binding site [polypeptide binding]; other site 102608000383 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608000384 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 102608000385 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 102608000386 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 102608000387 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 102608000388 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 102608000389 threonine/serine transporter TdcC; Provisional; Region: PRK13629; cl17672 102608000390 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]; Region: AroG; COG3200 102608000391 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 102608000392 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 102608000393 catalytic triad [active] 102608000394 Uncharacterized conserved protein [Function unknown]; Region: COG1556 102608000395 iron-sulfur cluster-binding protein; Region: TIGR00273 102608000396 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 102608000397 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 102608000398 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 102608000399 Cysteine-rich domain; Region: CCG; pfam02754 102608000400 Cysteine-rich domain; Region: CCG; pfam02754 102608000401 L-lactate transport; Region: lctP; TIGR00795 102608000402 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 102608000403 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 102608000404 L-lactate transport; Region: lctP; TIGR00795 102608000405 DNA glycosylase MutY; Provisional; Region: PRK13910 102608000406 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 102608000407 minor groove reading motif; other site 102608000408 helix-hairpin-helix signature motif; other site 102608000409 substrate binding pocket [chemical binding]; other site 102608000410 active site 102608000411 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 102608000412 DNA binding and oxoG recognition site [nucleotide binding] 102608000413 potential frameshift: common BLAST hit: gi|188526947|ref|YP_001909634.1| C(4)-dicarboxylates and tricarboxylates/succinate antiporter 102608000414 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 102608000415 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 102608000416 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 102608000417 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 102608000418 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 102608000419 Low-spin heme binding site [chemical binding]; other site 102608000420 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 102608000421 D-pathway; other site 102608000422 Putative water exit pathway; other site 102608000423 Binuclear center (active site) [active] 102608000424 K-pathway; other site 102608000425 Putative proton exit pathway; other site 102608000426 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 102608000427 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 102608000428 cytochrome c oxidase, cbb3-type, CcoQ subunit, epsilon-Proteobacterial; Region: cbb3_Q_epsi; TIGR02736 102608000429 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 102608000430 Cytochrome c; Region: Cytochrom_C; pfam00034 102608000431 Cytochrome c; Region: Cytochrom_C; pfam00034 102608000432 Family of unknown function (DUF4006); Region: DUF4006; pfam13179 102608000433 Predicted periplasmic solute-binding protein [General function prediction only]; Region: COG2107 102608000434 recombinase A; Provisional; Region: recA; PRK09354 102608000435 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 102608000436 hexamer interface [polypeptide binding]; other site 102608000437 Walker A motif; other site 102608000438 ATP binding site [chemical binding]; other site 102608000439 Walker B motif; other site 102608000440 enolase; Provisional; Region: eno; PRK00077 102608000441 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 102608000442 dimer interface [polypeptide binding]; other site 102608000443 metal binding site [ion binding]; metal-binding site 102608000444 substrate binding pocket [chemical binding]; other site 102608000445 AMIN domain; Region: AMIN; pfam11741 102608000446 Shikimate kinase [Amino acid transport and metabolism]; Region: AroK; COG0703 102608000447 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 102608000448 ADP binding site [chemical binding]; other site 102608000449 magnesium binding site [ion binding]; other site 102608000450 putative shikimate binding site; other site 102608000451 Cache domain; Region: Cache_1; pfam02743 102608000452 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 102608000453 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 102608000454 Ligand binding site; other site 102608000455 metal-binding site 102608000456 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 102608000457 Sel1-like repeats; Region: SEL1; smart00671 102608000458 Sel1-like repeats; Region: SEL1; smart00671 102608000459 Sel1-like repeats; Region: SEL1; smart00671 102608000460 Sel1-like repeats; Region: SEL1; smart00671 102608000461 Sel1-like repeats; Region: SEL1; smart00671 102608000462 Sel1-like repeats; Region: SEL1; smart00671 102608000463 hypothetical protein; Provisional; Region: PRK12378 102608000464 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 102608000465 dimer interface [polypeptide binding]; other site 102608000466 active site 102608000467 Schiff base residues; other site 102608000468 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 102608000469 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 102608000470 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 102608000471 dimer interface [polypeptide binding]; other site 102608000472 phosphorylation site [posttranslational modification] 102608000473 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 102608000474 ATP binding site [chemical binding]; other site 102608000475 Mg2+ binding site [ion binding]; other site 102608000476 G-X-G motif; other site 102608000477 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 102608000478 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 102608000479 active site 102608000480 phosphorylation site [posttranslational modification] 102608000481 intermolecular recognition site; other site 102608000482 dimerization interface [polypeptide binding]; other site 102608000483 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 102608000484 DNA binding site [nucleotide binding] 102608000485 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 102608000486 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 102608000487 Peptidase family U32; Region: Peptidase_U32; pfam01136 102608000488 peptide chain release factor 2; Region: prfB; TIGR00020 102608000489 This domain is found in peptide chain release factors; Region: PCRF; smart00937 102608000490 RF-1 domain; Region: RF-1; pfam00472 102608000491 potential frameshift: common BLAST hit: gi|308182346|ref|YP_003926473.1| molybdopterin biosynthesis protein 102608000492 MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin; Region: MoCF_BD; cl00451 102608000493 MoeA N-terminal region (domain I and II); Region: MoeA_N; pfam03453 102608000494 Flagellar biosynthesis pathway, component FliR [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FliR; COG1684 102608000495 Etoposide-induced protein 2.4 (EI24); Region: EI24; pfam07264 102608000496 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 102608000497 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 102608000498 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 102608000499 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 102608000500 intersubunit interface [polypeptide binding]; other site 102608000501 active site 102608000502 zinc binding site [ion binding]; other site 102608000503 Na+ binding site [ion binding]; other site 102608000504 elongation factor P; Validated; Region: PRK00529 102608000505 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 102608000506 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 102608000507 RNA binding site [nucleotide binding]; other site 102608000508 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 102608000509 RNA binding site [nucleotide binding]; other site 102608000510 GTPase subunit of restriction endonuclease [Defense mechanisms]; Region: McrB; COG1401 102608000511 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 102608000512 Walker A motif; other site 102608000513 ATP binding site [chemical binding]; other site 102608000514 Walker B motif; other site 102608000515 LlaJI restriction endonuclease; Region: RE_LlaJI; pfam09563 102608000516 pseudaminic acid synthase; Region: PseI; TIGR03586 102608000517 NeuB family; Region: NeuB; pfam03102 102608000518 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 102608000519 NeuB binding interface [polypeptide binding]; other site 102608000520 putative substrate binding site [chemical binding]; other site 102608000521 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 102608000522 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 102608000523 Walker A/P-loop; other site 102608000524 ATP binding site [chemical binding]; other site 102608000525 Q-loop/lid; other site 102608000526 ABC transporter signature motif; other site 102608000527 Walker B; other site 102608000528 D-loop; other site 102608000529 H-loop/switch region; other site 102608000530 apolipoprotein N-acyltransferase; Reviewed; Region: PRK12291 102608000531 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 102608000532 active site 102608000533 catalytic triad [active] 102608000534 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 102608000535 Colicin V production protein; Region: Colicin_V; pfam02674 102608000536 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 102608000537 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 102608000538 dimer interface [polypeptide binding]; other site 102608000539 putative anticodon binding site; other site 102608000540 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 102608000541 motif 1; other site 102608000542 active site 102608000543 motif 2; other site 102608000544 motif 3; other site 102608000545 serine hydroxymethyltransferase; Reviewed; Region: PRK13034 102608000546 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 102608000547 dimer interface [polypeptide binding]; other site 102608000548 active site 102608000549 glycine-pyridoxal phosphate binding site [chemical binding]; other site 102608000550 folate binding site [chemical binding]; other site 102608000551 Domain of unknown function (DUF1882); Region: DUF1882; pfam08966 102608000552 AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis...; Region: AE_Prim_S_like; cl01287 102608000553 Protein of unknown function DUF262; Region: DUF262; pfam03235 102608000554 Uncharacterized conserved protein [Function unknown]; Region: COG1479 102608000555 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 102608000556 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 102608000557 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 102608000558 PLD-like domain; Region: PLDc_2; pfam13091 102608000559 putative active site [active] 102608000560 catalytic site [active] 102608000561 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 102608000562 PLD-like domain; Region: PLDc_2; pfam13091 102608000563 putative active site [active] 102608000564 catalytic site [active] 102608000565 fumarate reductase iron-sulfur subunit; Provisional; Region: frdB; PRK13552 102608000566 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 102608000567 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 102608000568 fumarate reductase flavoprotein subunit; Provisional; Region: PRK08626 102608000569 L-aspartate oxidase; Provisional; Region: PRK06175 102608000570 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 102608000571 fumarate reductase cytochrome b-556 subunit; Provisional; Region: PRK13553 102608000572 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 102608000573 Iron-sulfur protein interface; other site 102608000574 proximal heme binding site [chemical binding]; other site 102608000575 distal heme binding site [chemical binding]; other site 102608000576 dimer interface [polypeptide binding]; other site 102608000577 triosephosphate isomerase; Provisional; Region: PRK14567 102608000578 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 102608000579 substrate binding site [chemical binding]; other site 102608000580 dimer interface [polypeptide binding]; other site 102608000581 catalytic triad [active] 102608000582 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08415 102608000583 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 102608000584 NAD binding site [chemical binding]; other site 102608000585 homotetramer interface [polypeptide binding]; other site 102608000586 homodimer interface [polypeptide binding]; other site 102608000587 substrate binding site [chemical binding]; other site 102608000588 active site 102608000589 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Region: lipid_A_lpxD; TIGR01853 102608000590 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 102608000591 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 102608000592 trimer interface [polypeptide binding]; other site 102608000593 active site 102608000594 UDP-GlcNAc binding site [chemical binding]; other site 102608000595 lipid binding site [chemical binding]; lipid-binding site 102608000596 S-adenosylmethionine synthetase; Validated; Region: PRK05250 102608000597 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 102608000598 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 102608000599 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 102608000600 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 102608000601 active site 102608000602 multimer interface [polypeptide binding]; other site 102608000603 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 102608000604 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 102608000605 fatty acid/phospholipid synthesis protein PlsX; Region: plsX; TIGR00182 102608000606 3-oxoacyl-(acyl-carrier-protein) synthase III; Region: fabH; TIGR00747 102608000607 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 102608000608 dimer interface [polypeptide binding]; other site 102608000609 active site 102608000610 CoA binding pocket [chemical binding]; other site 102608000611 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 102608000612 Walker A/P-loop; other site 102608000613 ATP binding site [chemical binding]; other site 102608000614 AAA ATPase domain; Region: AAA_15; pfam13175 102608000615 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cd00267 102608000616 Walker B; other site 102608000617 D-loop; other site 102608000618 H-loop/switch region; other site 102608000619 antiporter inner membrane protein; Provisional; Region: PRK11670 102608000620 Domain of unknown function DUF59; Region: DUF59; pfam01883 102608000621 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 102608000622 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 102608000623 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 102608000624 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 102608000625 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 102608000626 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 102608000627 heat shock protein 90; Provisional; Region: PRK05218 102608000628 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 102608000629 ATP binding site [chemical binding]; other site 102608000630 Mg2+ binding site [ion binding]; other site 102608000631 G-X-G motif; other site 102608000632 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 102608000633 Sel1-like repeats; Region: SEL1; smart00671 102608000634 Sel1-like repeats; Region: SEL1; smart00671 102608000635 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 102608000636 TPR motif; other site 102608000637 binding surface 102608000638 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 102608000639 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 102608000640 metal binding site [ion binding]; metal-binding site 102608000641 dimer interface [polypeptide binding]; other site 102608000642 glucose-inhibited division protein A; Region: gidA; TIGR00136 102608000643 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 102608000644 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 102608000645 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 102608000646 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 102608000647 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 102608000648 transmembrane helices; other site 102608000649 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 102608000650 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 102608000651 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: Dxr; TIGR00243 102608000652 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 102608000653 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 102608000654 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 102608000655 Beta-1,4-N-acetylgalactosaminyltransferase (CgtA); Region: CgtA; pfam06306 102608000656 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 102608000657 substrate binding site [chemical binding]; other site 102608000658 Helix-turn-helix domain; Region: HTH_28; pfam13518 102608000659 cysteine desulfurase, NifS family, epsilon proteobacteria type; Region: nifS_epsilon; TIGR03403 102608000660 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 102608000661 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 102608000662 catalytic residue [active] 102608000663 Fe-S cluster assembly protein NifU; Region: NifU_proper; TIGR02000 102608000664 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 102608000665 trimerization site [polypeptide binding]; other site 102608000666 active site 102608000667 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 102608000668 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 102608000669 DNA repair protein RadA; Region: sms; TIGR00416 102608000670 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 102608000671 Walker A motif/ATP binding site; other site 102608000672 ATP binding site [chemical binding]; other site 102608000673 Walker B motif; other site 102608000674 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 102608000675 Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: MsrA; COG0225 102608000676 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229 102608000677 SelR domain; Region: SelR; pfam01641 102608000678 Predicted permeases [General function prediction only]; Region: COG0730 102608000679 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608000680 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 102608000681 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 102608000682 Sulfate transporter family; Region: Sulfate_transp; pfam00916 102608000683 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608000684 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 102608000685 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 102608000686 Ligand binding site; other site 102608000687 oligomer interface; other site 102608000688 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 102608000689 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 102608000690 hypothetical protein; Provisional; Region: PRK04081 102608000691 Glutathionylspermidine synthase [Amino acid transport and metabolism]; Region: Gsp; COG0754 102608000692 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 102608000693 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 102608000694 binding surface 102608000695 TPR motif; other site 102608000696 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 102608000697 binding surface 102608000698 TPR motif; other site 102608000699 Sel1-like repeats; Region: SEL1; smart00671 102608000700 Sel1-like repeats; Region: SEL1; smart00671 102608000701 Cytochrome c; Region: Cytochrom_C; cl11414 102608000702 Porphobilinogen deaminase [Coenzyme metabolism]; Region: HemC; COG0181 102608000703 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 102608000704 domain interfaces; other site 102608000705 active site 102608000706 prolyl-tRNA synthetase, family II; Region: proS_fam_II; TIGR00409 102608000707 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 102608000708 dimer interface [polypeptide binding]; other site 102608000709 motif 1; other site 102608000710 active site 102608000711 motif 2; other site 102608000712 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 102608000713 putative deacylase active site [active] 102608000714 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 102608000715 active site 102608000716 motif 3; other site 102608000717 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 102608000718 anticodon binding site; other site 102608000719 glutamyl-tRNA reductase; Region: hemA; TIGR01035 102608000720 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 102608000721 tRNA; other site 102608000722 putative tRNA binding site [nucleotide binding]; other site 102608000723 putative NADP binding site [chemical binding]; other site 102608000724 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 102608000725 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 102608000726 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 102608000727 substrate binding pocket [chemical binding]; other site 102608000728 chain length determination region; other site 102608000729 substrate-Mg2+ binding site; other site 102608000730 catalytic residues [active] 102608000731 aspartate-rich region 1; other site 102608000732 active site lid residues [active] 102608000733 aspartate-rich region 2; other site 102608000734 Domain of unknown function (DUF2018); Region: DUF2018; pfam09442 102608000735 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 102608000736 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 102608000737 dimerization interface [polypeptide binding]; other site 102608000738 DPS ferroxidase diiron center [ion binding]; other site 102608000739 ion pore; other site 102608000740 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 102608000741 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 102608000742 dimer interface [polypeptide binding]; other site 102608000743 phosphorylation site [posttranslational modification] 102608000744 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 102608000745 ATP binding site [chemical binding]; other site 102608000746 Mg2+ binding site [ion binding]; other site 102608000747 G-X-G motif; other site 102608000748 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 102608000749 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 102608000750 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 102608000751 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 102608000752 ATP binding site [chemical binding]; other site 102608000753 Mg++ binding site [ion binding]; other site 102608000754 motif III; other site 102608000755 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 102608000756 nucleotide binding region [chemical binding]; other site 102608000757 ATP-binding site [chemical binding]; other site 102608000758 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 102608000759 SPFH domain / Band 7 family; Region: Band_7; pfam01145 102608000760 Protein of unknown function (DUF2393); Region: DUF2393; pfam09624 102608000761 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 102608000762 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 102608000763 Walker A/P-loop; other site 102608000764 ATP binding site [chemical binding]; other site 102608000765 Q-loop/lid; other site 102608000766 ABC transporter signature motif; other site 102608000767 Walker B; other site 102608000768 D-loop; other site 102608000769 H-loop/switch region; other site 102608000770 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 102608000771 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 102608000772 Walker A/P-loop; other site 102608000773 ATP binding site [chemical binding]; other site 102608000774 Q-loop/lid; other site 102608000775 ABC transporter signature motif; other site 102608000776 Walker B; other site 102608000777 D-loop; other site 102608000778 H-loop/switch region; other site 102608000779 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 102608000780 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 102608000781 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 102608000782 dimer interface [polypeptide binding]; other site 102608000783 conserved gate region; other site 102608000784 putative PBP binding loops; other site 102608000785 ABC-ATPase subunit interface; other site 102608000786 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608000787 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608000788 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 102608000789 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 102608000790 GDP-binding site [chemical binding]; other site 102608000791 ACT binding site; other site 102608000792 IMP binding site; other site 102608000793 Flagellar FliJ protein; Region: FliJ; pfam02050 102608000794 Uncharacterized conserved protein [Function unknown]; Region: COG3334 102608000795 RIP metalloprotease RseP; Region: TIGR00054 102608000796 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 102608000797 active site 102608000798 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 102608000799 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 102608000800 putative substrate binding region [chemical binding]; other site 102608000801 exodeoxyribonuclease VII, large subunit; Region: xseA; TIGR00237 102608000802 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 102608000803 generic binding surface II; other site 102608000804 generic binding surface I; other site 102608000805 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 102608000806 DNA methylase; Region: N6_N4_Mtase; pfam01555 102608000807 DNA methylase; Region: N6_N4_Mtase; pfam01555 102608000808 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 102608000809 DNA methylase; Region: N6_N4_Mtase; pfam01555 102608000810 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 102608000811 Clp amino terminal domain; Region: Clp_N; pfam02861 102608000812 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 102608000813 Walker A motif; other site 102608000814 ATP binding site [chemical binding]; other site 102608000815 Walker B motif; other site 102608000816 arginine finger; other site 102608000817 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 102608000818 Walker A motif; other site 102608000819 ATP binding site [chemical binding]; other site 102608000820 Walker B motif; other site 102608000821 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 102608000822 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 102608000823 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; pfam02683 102608000824 Dihydroorotase and related cyclic amidohydrolases [Nucleotide transport and metabolism]; Region: PyrC; COG0044 102608000825 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 102608000826 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 102608000827 active site 102608000828 chlorohydrolase; Provisional; Region: PRK08418 102608000829 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 102608000830 active site 102608000831 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 102608000832 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14339 102608000833 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 102608000834 FeS/SAM binding site; other site 102608000835 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 102608000836 putative acyl-acceptor binding pocket; other site 102608000837 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 102608000838 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 102608000839 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 102608000840 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 102608000841 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 102608000842 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 102608000843 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 102608000844 putative active site [active] 102608000845 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 102608000846 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 102608000847 putative acyl-acceptor binding pocket; other site 102608000848 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 102608000849 tRNA-guanine family transglycosylase; Region: tgt_general; TIGR00449 102608000850 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3400 102608000851 TrkA-C domain; Region: TrkA_C; pfam02080 102608000852 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 102608000853 active site 102608000854 dimer interface [polypeptide binding]; other site 102608000855 metal binding site [ion binding]; metal-binding site 102608000856 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 102608000857 Mechanosensitive ion channel; Region: MS_channel; pfam00924 102608000858 radical SAM methylthiotransferase, MiaB/RimO family; Region: TIGR00089 102608000859 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 102608000860 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 102608000861 FeS/SAM binding site; other site 102608000862 ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]; Region: HflB; COG0465 102608000863 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 102608000864 Walker A motif; other site 102608000865 ATP binding site [chemical binding]; other site 102608000866 Walker B motif; other site 102608000867 arginine finger; other site 102608000868 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 102608000869 Vacuolating cyotoxin; Region: VacA; pfam02691 102608000870 Autotransporter beta-domain; Region: Autotransporter; pfam03797 102608000871 diaminopimelate decarboxylase; Region: lysA; TIGR01048 102608000872 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 102608000873 active site 102608000874 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 102608000875 substrate binding site [chemical binding]; other site 102608000876 catalytic residues [active] 102608000877 dimer interface [polypeptide binding]; other site 102608000878 Chorismate mutase [Amino acid transport and metabolism]; Region: PheA; COG1605 102608000879 Uncharacterized conserved protein [Function unknown]; Region: COG4866 102608000880 aminodeoxychorismate synthase; Provisional; Region: PRK07508 102608000881 chorismate binding enzyme; Region: Chorismate_bind; cl10555 102608000882 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 102608000883 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 102608000884 substrate-cofactor binding pocket; other site 102608000885 pyridoxal 5'-phosphate binding site [chemical binding]; other site 102608000886 catalytic residue [active] 102608000887 acylamide amidohydrolase; Provisional; Region: amiE; PRK13286 102608000888 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 102608000889 multimer interface [polypeptide binding]; other site 102608000890 active site 102608000891 catalytic triad [active] 102608000892 dimer interface [polypeptide binding]; other site 102608000893 flagellar hook-associated protein FlgL; Validated; Region: flgL; PRK08412 102608000894 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 102608000895 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 102608000896 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 102608000897 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 102608000898 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 102608000899 peptide binding site [polypeptide binding]; other site 102608000900 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 102608000901 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 102608000902 dimer interface [polypeptide binding]; other site 102608000903 conserved gate region; other site 102608000904 putative PBP binding loops; other site 102608000905 ABC-ATPase subunit interface; other site 102608000906 dipeptide transporter; Provisional; Region: PRK10913 102608000907 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 102608000908 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 102608000909 dimer interface [polypeptide binding]; other site 102608000910 conserved gate region; other site 102608000911 putative PBP binding loops; other site 102608000912 ABC-ATPase subunit interface; other site 102608000913 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 102608000914 nickel import ATP-binding protein NikD; Region: nickel_nikD; TIGR02770 102608000915 Walker A/P-loop; other site 102608000916 ATP binding site [chemical binding]; other site 102608000917 Q-loop/lid; other site 102608000918 ABC transporter signature motif; other site 102608000919 Walker B; other site 102608000920 D-loop; other site 102608000921 H-loop/switch region; other site 102608000922 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 102608000923 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 102608000924 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 102608000925 Walker A/P-loop; other site 102608000926 ATP binding site [chemical binding]; other site 102608000927 Q-loop/lid; other site 102608000928 ABC transporter signature motif; other site 102608000929 Walker B; other site 102608000930 D-loop; other site 102608000931 H-loop/switch region; other site 102608000932 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 102608000933 GTPase CgtA; Reviewed; Region: obgE; PRK12299 102608000934 GTP1/OBG; Region: GTP1_OBG; pfam01018 102608000935 Obg GTPase; Region: Obg; cd01898 102608000936 G1 box; other site 102608000937 GTP/Mg2+ binding site [chemical binding]; other site 102608000938 Switch I region; other site 102608000939 G2 box; other site 102608000940 G3 box; other site 102608000941 Switch II region; other site 102608000942 G4 box; other site 102608000943 G5 box; other site 102608000944 Alginate lyase; Region: Alginate_lyase; pfam05426 102608000945 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 102608000946 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 102608000947 inhibitor-cofactor binding pocket; inhibition site 102608000948 pyridoxal 5'-phosphate binding site [chemical binding]; other site 102608000949 catalytic residue [active] 102608000950 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 102608000951 Predicted amidohydrolase [General function prediction only]; Region: COG0388 102608000952 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 102608000953 active site 102608000954 catalytic triad [active] 102608000955 dimer interface [polypeptide binding]; other site 102608000956 Catalytic domain of Helicobacter pylori peptidoglycan deacetylase (HpPgdA) and similar proteins; Region: CE4_HpPgdA_like; cd10938 102608000957 active site 102608000958 catalytic site [active] 102608000959 Zn binding site [ion binding]; other site 102608000960 tetramer interface [polypeptide binding]; other site 102608000961 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 102608000962 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 102608000963 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 102608000964 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 102608000965 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 102608000966 Major Facilitator Superfamily; Region: MFS_1; pfam07690 102608000967 putative substrate translocation pore; other site 102608000968 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 102608000969 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 102608000970 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 102608000971 Probable transposase; Region: OrfB_IS605; pfam01385 102608000972 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 102608000973 Transposase IS200 like; Region: Y1_Tnp; pfam01797 102608000974 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 102608000975 catalytic residues [active] 102608000976 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 102608000977 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 102608000978 Glycosyltransferase family 10 (fucosyltransferase); Region: Glyco_transf_10; pfam00852 102608000979 glutamate dehydrogenase; Provisional; Region: PRK09414 102608000980 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 102608000981 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 102608000982 NAD(P) binding site [chemical binding]; other site 102608000983 HemK family putative methylases; Region: hemK_fam; TIGR00536 102608000984 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 102608000985 Peptidase family M48; Region: Peptidase_M48; pfam01435 102608000986 Sporulation related domain; Region: SPOR; pfam05036 102608000987 primosome assembly protein PriA; Validated; Region: PRK05580 102608000988 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 102608000989 ATP binding site [chemical binding]; other site 102608000990 putative Mg++ binding site [ion binding]; other site 102608000991 helicase superfamily c-terminal domain; Region: HELICc; smart00490 102608000992 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 102608000993 S-adenosylmethionine binding site [chemical binding]; other site 102608000994 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 102608000995 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 102608000996 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 102608000997 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 102608000998 dimer interface [polypeptide binding]; other site 102608000999 catalytic triad [active] 102608001000 peroxidatic and resolving cysteines [active] 102608001001 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 102608001002 putative CheA interaction surface; other site 102608001003 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 102608001004 putative binding surface; other site 102608001005 active site 102608001006 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 102608001007 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 102608001008 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 102608001009 ATP binding site [chemical binding]; other site 102608001010 Mg2+ binding site [ion binding]; other site 102608001011 G-X-G motif; other site 102608001012 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 102608001013 Response regulator receiver domain; Region: Response_reg; pfam00072 102608001014 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 102608001015 active site 102608001016 phosphorylation site [posttranslational modification] 102608001017 intermolecular recognition site; other site 102608001018 dimerization interface [polypeptide binding]; other site 102608001019 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 102608001020 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 102608001021 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 102608001022 active site 102608001023 phosphorylation site [posttranslational modification] 102608001024 intermolecular recognition site; other site 102608001025 dimerization interface [polypeptide binding]; other site 102608001026 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 102608001027 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 102608001028 putative active site [active] 102608001029 putative metal binding site [ion binding]; other site 102608001030 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 102608001031 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 102608001032 catalytic residue [active] 102608001033 menaquinone biosynthesis decarboxylase, SCO4490 family; Region: mena_SCO4490; TIGR03701 102608001034 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 102608001035 D-3-phosphoglycerate dehydrogenase; Region: PGDH; TIGR01327 102608001036 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 102608001037 ligand binding site [chemical binding]; other site 102608001038 NAD binding site [chemical binding]; other site 102608001039 dimerization interface [polypeptide binding]; other site 102608001040 catalytic site [active] 102608001041 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 102608001042 putative L-serine binding site [chemical binding]; other site 102608001043 ribosomal protein S1; Region: rpsA; TIGR00717 102608001044 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 102608001045 RNA binding site [nucleotide binding]; other site 102608001046 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 102608001047 RNA binding site [nucleotide binding]; other site 102608001048 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 102608001049 RNA binding site [nucleotide binding]; other site 102608001050 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 102608001051 RNA binding site [nucleotide binding]; other site 102608001052 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 102608001053 RNA binding site [nucleotide binding]; other site 102608001054 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 102608001055 LytB protein; Region: LYTB; pfam02401 102608001056 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 102608001057 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 102608001058 hinge; other site 102608001059 active site 102608001060 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 102608001061 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 102608001062 putative tRNA-binding site [nucleotide binding]; other site 102608001063 tRNA synthetase B5 domain; Region: B5; pfam03484 102608001064 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 102608001065 dimer interface [polypeptide binding]; other site 102608001066 motif 1; other site 102608001067 motif 3; other site 102608001068 motif 2; other site 102608001069 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 102608001070 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 102608001071 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 102608001072 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 102608001073 dimer interface [polypeptide binding]; other site 102608001074 motif 1; other site 102608001075 active site 102608001076 motif 2; other site 102608001077 motif 3; other site 102608001078 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 102608001079 nucleotide binding site/active site [active] 102608001080 HIT family signature motif; other site 102608001081 catalytic residue [active] 102608001082 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 102608001083 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 102608001084 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 102608001085 catalytic residue [active] 102608001086 Protein of unknown function (DUF3972); Region: DUF3972; pfam13118 102608001087 potential frameshift: common BLAST hit: gi|188527828|ref|YP_001910515.1| biotin sulfoxide reductase BisC 102608001088 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 102608001089 potential frameshift: common BLAST hit: gi|308183150|ref|YP_003927277.1| biotin sulfoxide reductase (bisC) 102608001090 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 102608001091 potential frameshift: common BLAST hit: gi|308183150|ref|YP_003927277.1| biotin sulfoxide reductase (bisC) 102608001092 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 102608001093 potential frameshift: common BLAST hit: gi|188527828|ref|YP_001910515.1| biotin sulfoxide reductase BisC 102608001094 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 102608001095 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 102608001096 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_CT_DMSOR-BSOR-TMAOR; cd02793 102608001097 molybdopterin cofactor binding site; other site 102608001098 GMP synthase; Reviewed; Region: guaA; PRK00074 102608001099 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 102608001100 AMP/PPi binding site [chemical binding]; other site 102608001101 candidate oxyanion hole; other site 102608001102 catalytic triad [active] 102608001103 potential glutamine specificity residues [chemical binding]; other site 102608001104 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 102608001105 ATP Binding subdomain [chemical binding]; other site 102608001106 Ligand Binding sites [chemical binding]; other site 102608001107 Dimerization subdomain; other site 102608001108 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 102608001109 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 102608001110 Mechanosensitive ion channel; Region: MS_channel; pfam00924 102608001111 Mycolic acid cyclopropane synthetase; Region: CMAS; pfam02353 102608001112 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 102608001113 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 102608001114 S-adenosylmethionine binding site [chemical binding]; other site 102608001115 methionyl-tRNA synthetase; Reviewed; Region: PRK12267 102608001116 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 102608001117 active site 102608001118 HIGH motif; other site 102608001119 KMSKS motif; other site 102608001120 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 102608001121 anticodon binding site; other site 102608001122 tRNA binding surface [nucleotide binding]; other site 102608001123 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 102608001124 dimer interface [polypeptide binding]; other site 102608001125 putative tRNA-binding site [nucleotide binding]; other site 102608001126 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 102608001127 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 102608001128 Methyltransferase domain; Region: Methyltransf_23; pfam13489 102608001129 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 102608001130 S-adenosylmethionine binding site [chemical binding]; other site 102608001131 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 102608001132 active site 2 [active] 102608001133 active site 1 [active] 102608001134 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 102608001135 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 102608001136 putative ADP-binding pocket [chemical binding]; other site 102608001137 Arginine decarboxylase (spermidine biosynthesis) [Amino acid transport and metabolism]; Region: SpeA; COG1166 102608001138 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 102608001139 active site 102608001140 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 102608001141 catalytic residues [active] 102608001142 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 102608001143 Protein of unknown function (DUF3529); Region: DUF3529; pfam12046 102608001144 Single-stranded DNA-specific exonuclease [DNA replication, recombination, and repair]; Region: RecJ; COG0608 102608001145 DHH family; Region: DHH; pfam01368 102608001146 Uncharacterized conserved protein [Function unknown]; Region: COG1479 102608001147 Protein of unknown function DUF262; Region: DUF262; pfam03235 102608001148 Protein of unknown function DUF262; Region: DUF262; pfam03235 102608001149 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 102608001150 Mechanosensitive ion channel; Region: MS_channel; pfam00924 102608001151 cell division protein FtsZ; Validated; Region: PRK09330 102608001152 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 102608001153 nucleotide binding site [chemical binding]; other site 102608001154 SulA interaction site; other site 102608001155 cell division protein FtsA; Region: ftsA; TIGR01174 102608001156 Cell division protein FtsA; Region: FtsA; smart00842 102608001157 Cell division protein FtsA; Region: FtsA; pfam14450 102608001158 SurA N-terminal domain; Region: SurA_N_3; cl07813 102608001159 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 102608001160 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 102608001161 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK05964 102608001162 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 102608001163 inhibitor-cofactor binding pocket; inhibition site 102608001164 pyridoxal 5'-phosphate binding site [chemical binding]; other site 102608001165 catalytic residue [active] 102608001166 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C subunit; Region: gatC; TIGR00135 102608001167 phosphoglyceromutase; Provisional; Region: PRK05434 102608001168 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; Region: pgm_bpd_ind; TIGR01307 102608001169 glycyl-tRNA synthetase, tetrameric type, beta subunit; Region: glyS; TIGR00211 102608001170 Outer membrane efflux protein; Region: OEP; pfam02321 102608001171 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 102608001172 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 102608001173 Protein of unknown function (DUF3240); Region: DUF3240; pfam11582 102608001174 Uncharacterized virulence-associated protein D [Function unknown]; Region: VapD; COG3309 102608001175 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 102608001176 G1 box; other site 102608001177 GTP/Mg2+ binding site [chemical binding]; other site 102608001178 G2 box; other site 102608001179 Switch I region; other site 102608001180 G3 box; other site 102608001181 Switch II region; other site 102608001182 G4 box; other site 102608001183 potential frameshift: common BLAST hit: gi|254779561|ref|YP_003057667.1| ATPase 102608001184 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 102608001185 Dynamin family; Region: Dynamin_N; pfam00350 102608001186 G1 box; other site 102608001187 GTP/Mg2+ binding site [chemical binding]; other site 102608001188 G2 box; other site 102608001189 Switch I region; other site 102608001190 G3 box; other site 102608001191 Switch II region; other site 102608001192 G4 box; other site 102608001193 G5 box; other site 102608001194 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 102608001195 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 102608001196 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 102608001197 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 102608001198 dimer interface [polypeptide binding]; other site 102608001199 motif 1; other site 102608001200 active site 102608001201 motif 2; other site 102608001202 motif 3; other site 102608001203 dinuclear metal center protein, YbgI/SA1388 family; Region: YbgI_SA1388; TIGR00486 102608001204 Uncharacterized conserved protein [Function unknown]; Region: COG0327 102608001205 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 102608001206 Putative zinc ribbon domain; Region: DUF164; pfam02591 102608001207 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 102608001208 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 102608001209 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 102608001210 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 102608001211 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 102608001212 active site 102608001213 prolipoprotein diacylglyceryl transferase; Region: lgt; TIGR00544 102608001214 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 102608001215 dimer interface [polypeptide binding]; other site 102608001216 FMN binding site [chemical binding]; other site 102608001217 competence/damage-inducible protein CinA C-terminal domain; Region: cinA_cterm; TIGR00199 102608001218 putative recombination protein RecO; Provisional; Region: PRK13908 102608001219 acetyl-CoA carboxylase, carboxyl transferase, beta subunit; Region: accD; TIGR00515 102608001220 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 102608001221 Uncharacterized conserved protein [Function unknown]; Region: COG1576 102608001222 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 102608001223 TRL-like protein family; Region: TRL; pfam13146 102608001224 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 102608001225 homotrimer interaction site [polypeptide binding]; other site 102608001226 putative active site [active] 102608001227 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 102608001228 Streptococcal 67 kDa myosin-cross-reactive antigen like family; Region: Strep_67kDa_ant; cl17487 102608001229 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 102608001230 amino acid carrier protein; Region: agcS; TIGR00835 102608001231 alanine racemase; Region: alr; TIGR00492 102608001232 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 102608001233 active site 102608001234 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 102608001235 dimer interface [polypeptide binding]; other site 102608001236 substrate binding site [chemical binding]; other site 102608001237 catalytic residues [active] 102608001238 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 102608001239 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 102608001240 substrate binding pocket [chemical binding]; other site 102608001241 membrane-bound complex binding site; other site 102608001242 hinge residues; other site 102608001243 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 102608001244 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 102608001245 dimer interface [polypeptide binding]; other site 102608001246 conserved gate region; other site 102608001247 putative PBP binding loops; other site 102608001248 ABC-ATPase subunit interface; other site 102608001249 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608001250 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 102608001251 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 102608001252 Coenzyme A binding pocket [chemical binding]; other site 102608001253 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 102608001254 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Region: rSAM_QueE_Ecoli; TIGR04322 102608001255 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism]; Region: COG0720 102608001256 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 102608001257 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 102608001258 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 102608001259 substrate binding pocket [chemical binding]; other site 102608001260 chain length determination region; other site 102608001261 substrate-Mg2+ binding site; other site 102608001262 catalytic residues [active] 102608001263 aspartate-rich region 1; other site 102608001264 active site lid residues [active] 102608001265 aspartate-rich region 2; other site 102608001266 GTP cyclohydrolase I; Region: folE; TIGR00063 102608001267 GTP cyclohydrolase I; Provisional; Region: PLN03044 102608001268 active site 102608001269 heat shock protein HtpX; Provisional; Region: PRK02870 102608001270 tRNA pseudouridine synthase, TruD family; Region: tRNA_TruD_broad; TIGR00094 102608001271 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 102608001272 Permutation of conserved domain; other site 102608001273 active site 102608001274 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 102608001275 recombination protein RecR; Region: recR; TIGR00615 102608001276 RecR protein; Region: RecR; pfam02132 102608001277 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 102608001278 putative active site [active] 102608001279 putative metal-binding site [ion binding]; other site 102608001280 tetramer interface [polypeptide binding]; other site 102608001281 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 102608001282 active site 1 [active] 102608001283 dimer interface [polypeptide binding]; other site 102608001284 hexamer interface [polypeptide binding]; other site 102608001285 active site 2 [active] 102608001286 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608001287 Mechanosensitive ion channel porin domain; Region: MscS_porin; pfam12795 102608001288 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 102608001289 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 102608001290 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 102608001291 Autotransporter beta-domain; Region: Autotransporter; pfam03797 102608001292 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 102608001293 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 102608001294 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 102608001295 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 102608001296 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 102608001297 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 102608001298 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 102608001299 ATP-grasp domain; Region: ATP-grasp_4; cl17255 102608001300 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 102608001301 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 102608001302 ATP-grasp domain; Region: ATP-grasp_4; cl17255 102608001303 Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways...; Region: MGS_CPS_II; cd01424 102608001304 IMP binding site; other site 102608001305 dimer interface [polypeptide binding]; other site 102608001306 interdomain contacts; other site 102608001307 partial ornithine binding site; other site 102608001308 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 102608001309 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 102608001310 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 102608001311 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 102608001312 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 102608001313 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608001314 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608001315 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 102608001316 Part of AAA domain; Region: AAA_19; pfam13245 102608001317 Family description; Region: UvrD_C_2; pfam13538 102608001318 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 102608001319 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 102608001320 S-adenosylmethionine binding site [chemical binding]; other site 102608001321 flagellar hook protein FlgE; Validated; Region: flgE; PRK05841 102608001322 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 102608001323 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK05842 102608001324 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 102608001325 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 102608001326 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 102608001327 BioD-like N-terminal domain of phosphotransacetylase [General function prediction only]; Region: Pta; COG0857 102608001328 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl17212 102608001329 Acetokinase family; Region: Acetate_kinase; cl17229 102608001330 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 102608001331 hydrogenase accessory protein HypB; Region: hypB; TIGR00073 102608001332 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 102608001333 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypC; COG0298 102608001334 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 102608001335 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 102608001336 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608001337 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041 102608001338 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 102608001339 short chain dehydrogenase; Validated; Region: PRK06182 102608001340 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 102608001341 NADP binding site [chemical binding]; other site 102608001342 active site 102608001343 steroid binding site; other site 102608001344 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 102608001345 ABC-ATPase subunit interface; other site 102608001346 dimer interface [polypeptide binding]; other site 102608001347 putative PBP binding regions; other site 102608001348 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 102608001349 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 102608001350 Walker A/P-loop; other site 102608001351 ATP binding site [chemical binding]; other site 102608001352 Q-loop/lid; other site 102608001353 ABC transporter signature motif; other site 102608001354 Walker B; other site 102608001355 D-loop; other site 102608001356 H-loop/switch region; other site 102608001357 Vacuolating cyotoxin; Region: VacA; pfam02691 102608001358 Autotransporter beta-domain; Region: Autotransporter; pfam03797 102608001359 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 102608001360 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 102608001361 active site 102608001362 HIGH motif; other site 102608001363 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 102608001364 KMSKS motif; other site 102608001365 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 102608001366 tRNA binding surface [nucleotide binding]; other site 102608001367 anticodon binding site; other site 102608001368 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 102608001369 MviN-like protein; Region: MVIN; pfam03023 102608001370 Holliday junction DNA helicase, RuvA subunit; Region: ruvA; TIGR00084 102608001371 RuvA N terminal domain; Region: RuvA_N; pfam01330 102608001372 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 102608001373 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 102608001374 Cation transport protein; Region: TrkH; cl17365 102608001375 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 102608001376 TrkA-N domain; Region: TrkA_N; pfam02254 102608001377 TrkA-C domain; Region: TrkA_C; pfam02080 102608001378 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 102608001379 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 102608001380 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 102608001381 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 102608001382 Mg++ binding site [ion binding]; other site 102608001383 putative catalytic motif [active] 102608001384 putative substrate binding site [chemical binding]; other site 102608001385 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03815 102608001386 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 102608001387 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 102608001388 Protein of unknown function (DUF493); Region: DUF493; pfam04359 102608001389 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 102608001390 active site 102608001391 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 102608001392 Na2 binding site [ion binding]; other site 102608001393 putative substrate binding site 1 [chemical binding]; other site 102608001394 Na binding site 1 [ion binding]; other site 102608001395 putative substrate binding site 2 [chemical binding]; other site 102608001396 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 102608001397 Na2 binding site [ion binding]; other site 102608001398 putative substrate binding site 1 [chemical binding]; other site 102608001399 Na binding site 1 [ion binding]; other site 102608001400 putative substrate binding site 2 [chemical binding]; other site 102608001401 potential frameshift: common BLAST hit: gi|108562900|ref|YP_627216.1| phospholipase A1 102608001402 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; cl00248 102608001403 dimerization interface [polypeptide binding]; other site 102608001404 substrate binding site [chemical binding]; other site 102608001405 active site 102608001406 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; cl00248 102608001407 DNA polymerase III, beta subunit; Region: dnan; TIGR00663 102608001408 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 102608001409 putative DNA binding surface [nucleotide binding]; other site 102608001410 dimer interface [polypeptide binding]; other site 102608001411 beta-clamp/clamp loader binding surface; other site 102608001412 beta-clamp/translesion DNA polymerase binding surface; other site 102608001413 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 102608001414 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 102608001415 Mg2+ binding site [ion binding]; other site 102608001416 G-X-G motif; other site 102608001417 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 102608001418 anchoring element; other site 102608001419 dimer interface [polypeptide binding]; other site 102608001420 ATP binding site [chemical binding]; other site 102608001421 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 102608001422 active site 102608001423 putative metal-binding site [ion binding]; other site 102608001424 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 102608001425 R.Pab1 restriction endonuclease; Region: RE_R_Pab1; pfam09522 102608001426 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 102608001427 Peptidase family M23; Region: Peptidase_M23; pfam01551 102608001428 nudix-type nucleoside diphosphatase, YffH/AdpP family; Region: TIGR00052 102608001429 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 102608001430 dimer interface [polypeptide binding]; other site 102608001431 ADP-ribose binding site [chemical binding]; other site 102608001432 active site 102608001433 nudix motif; other site 102608001434 metal binding site [ion binding]; metal-binding site 102608001435 FAD binding domain; Region: FAD_binding_4; pfam01565 102608001436 glycolate oxidase, subunit GlcD; Region: glcD; TIGR00387 102608001437 Protein-interacting Bro1-like domain of mammalian Alix and related domains; Region: BRO1_Alix_like; cl14649 102608001438 dihydrodipicolinate reductase; Region: dapB; TIGR00036 102608001439 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 102608001440 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 102608001441 glutamine synthetase, type I; Region: GlnA; TIGR00653 102608001442 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 102608001443 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 102608001444 Uncharacterized conserved protein [Function unknown]; Region: COG1479 102608001445 Protein of unknown function DUF262; Region: DUF262; pfam03235 102608001446 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 102608001447 Uncharacterized conserved protein [Function unknown]; Region: COG3586 102608001448 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 102608001449 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 102608001450 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 102608001451 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 102608001452 active site 102608001453 HslU subunit interaction site [polypeptide binding]; other site 102608001454 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 102608001455 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 102608001456 Walker A motif; other site 102608001457 ATP binding site [chemical binding]; other site 102608001458 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 102608001459 Walker B motif; other site 102608001460 arginine finger; other site 102608001461 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 102608001462 GTPase [General function prediction only]; Region: Era; COG1159 102608001463 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 102608001464 G1 box; other site 102608001465 GTP/Mg2+ binding site [chemical binding]; other site 102608001466 Switch I region; other site 102608001467 G2 box; other site 102608001468 Switch II region; other site 102608001469 G3 box; other site 102608001470 G4 box; other site 102608001471 G5 box; other site 102608001472 KH domain; Region: KH_2; pfam07650 102608001473 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 102608001474 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 102608001475 Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion]; Region: VirD4; COG3505 102608001476 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 102608001477 Walker A motif; other site 102608001478 ATP binding site [chemical binding]; other site 102608001479 Walker B motif; other site 102608001480 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 102608001481 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 102608001482 ATP binding site [chemical binding]; other site 102608001483 Walker A motif; other site 102608001484 hexamer interface [polypeptide binding]; other site 102608001485 Walker B motif; other site 102608001486 CagZ; Region: CagZ; pfam09053 102608001487 DC-EC Repeat; Region: CagY_M; pfam07337 102608001488 DC-EC Repeat; Region: CagY_M; pfam07337 102608001489 DC-EC Repeat; Region: CagY_M; pfam07337 102608001490 DC-EC Repeat; Region: CagY_M; pfam07337 102608001491 DC-EC Repeat; Region: CagY_M; pfam07337 102608001492 DC-EC Repeat; Region: CagY_M; pfam07337 102608001493 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 102608001494 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 102608001495 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 102608001496 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 102608001497 VirB7 interaction site; other site 102608001498 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 102608001499 Cag pathogenicity island protein Cag12; Region: Cag12; pfam13117 102608001500 prolyl-tRNA synthetase; Provisional; Region: PRK08661 102608001501 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 102608001502 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 102608001503 CagA exotoxin; Region: CagA; pfam03507 102608001504 CagA exotoxin; Region: CagA; pfam03507 102608001505 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 102608001506 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 102608001507 transcription termination factor Rho; Provisional; Region: rho; PRK09376 102608001508 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 102608001509 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 102608001510 RNA binding site [nucleotide binding]; other site 102608001511 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 102608001512 multimer interface [polypeptide binding]; other site 102608001513 Walker A motif; other site 102608001514 ATP binding site [chemical binding]; other site 102608001515 Walker B motif; other site 102608001516 Ribosomal protein L31; Region: Ribosomal_L31; pfam01197 102608001517 Predicted methyltransferases [General function prediction only]; Region: COG0313 102608001518 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 102608001519 putative SAM binding site [chemical binding]; other site 102608001520 putative homodimer interface [polypeptide binding]; other site 102608001521 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 102608001522 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 102608001523 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 102608001524 acetyl-CoA carboxylase, carboxyl transferase, alpha subunit; Region: accA; TIGR00513 102608001525 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 102608001526 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK08439 102608001527 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 102608001528 dimer interface [polypeptide binding]; other site 102608001529 active site 102608001530 acyl carrier protein; Provisional; Region: acpP; PRK00982 102608001531 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 102608001532 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 102608001533 NAD(P) binding site [chemical binding]; other site 102608001534 active site 102608001535 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 102608001536 Predicted membrane protein [Function unknown]; Region: COG3059 102608001537 diaminopimelate epimerase; Region: DapF; TIGR00652 102608001538 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 102608001539 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 102608001540 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 102608001541 Domain of unknown function DUF20; Region: UPF0118; pfam01594 102608001542 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 102608001543 FeS/SAM binding site; other site 102608001544 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 102608001545 GTP-binding protein YchF; Reviewed; Region: PRK09601 102608001546 YchF GTPase; Region: YchF; cd01900 102608001547 G1 box; other site 102608001548 GTP/Mg2+ binding site [chemical binding]; other site 102608001549 Switch I region; other site 102608001550 G2 box; other site 102608001551 Switch II region; other site 102608001552 G3 box; other site 102608001553 G4 box; other site 102608001554 G5 box; other site 102608001555 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 102608001556 multifunctional aminopeptidase A; Provisional; Region: PRK00913 102608001557 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 102608001558 interface (dimer of trimers) [polypeptide binding]; other site 102608001559 Substrate-binding/catalytic site; other site 102608001560 Zn-binding sites [ion binding]; other site 102608001561 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 102608001562 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 102608001563 active site 102608001564 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 102608001565 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 102608001566 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 102608001567 Peptidase family M50; Region: Peptidase_M50; pfam02163 102608001568 active site 102608001569 putative substrate binding region [chemical binding]; other site 102608001570 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 102608001571 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 102608001572 Catalytic site [active] 102608001573 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 102608001574 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14191 102608001575 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 102608001576 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 102608001577 homodimer interface [polypeptide binding]; other site 102608001578 NADP binding site [chemical binding]; other site 102608001579 substrate binding site [chemical binding]; other site 102608001580 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 102608001581 Sulfatase; Region: Sulfatase; pfam00884 102608001582 Predicted neuraminidase (sialidase) [Carbohydrate transport and metabolism]; Region: COG4692 102608001583 BNR repeat-like domain; Region: BNR_2; pfam13088 102608001584 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 102608001585 active site 102608001586 substrate binding pocket [chemical binding]; other site 102608001587 dimer interface [polypeptide binding]; other site 102608001588 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 102608001589 TonB family C-terminal domain; Region: tonB_Cterm; TIGR01352 102608001590 flagellar motor switch protein; Validated; Region: PRK08433 102608001591 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 102608001592 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 102608001593 minor groove reading motif; other site 102608001594 helix-hairpin-helix signature motif; other site 102608001595 substrate binding pocket [chemical binding]; other site 102608001596 active site 102608001597 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 102608001598 Fe2+ transport system protein A [Inorganic ion transport and metabolism]; Region: FeoA; COG1918 102608001599 Protein of unknown function; Region: DUF3971; pfam13116 102608001600 AsmA-like C-terminal region; Region: AsmA_1; pfam13109 102608001601 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 102608001602 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 102608001603 dimerization interface [polypeptide binding]; other site 102608001604 2-oxoglutarate-acceptor oxidoreductase subunit OorD; Reviewed; Region: oorD; PRK09626 102608001605 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 102608001606 2-oxoglutarate-acceptor oxidoreductase subunit OorA; Reviewed; Region: oorA; PRK09627 102608001607 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 102608001608 dimer interface [polypeptide binding]; other site 102608001609 PYR/PP interface [polypeptide binding]; other site 102608001610 TPP binding site [chemical binding]; other site 102608001611 substrate binding site [chemical binding]; other site 102608001612 2-oxoglutarate-acceptor oxidoreductase subunit OorB; Reviewed; Region: oorB; PRK09628 102608001613 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 102608001614 TPP-binding site [chemical binding]; other site 102608001615 2-oxoglutarate-acceptor oxidoreductase subunit OorC; Reviewed; Region: oorC; PRK08441 102608001616 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 102608001617 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG5610 102608001618 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 102608001619 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 102608001620 tumor necrosis factor alpha-inducing protein; Reviewed; Region: PRK12303 102608001621 Transglycosylase; Region: Transgly; pfam00912 102608001622 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 102608001623 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 102608001624 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 102608001625 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 102608001626 catalytic residue [active] 102608001627 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 102608001628 dimer interface [polypeptide binding]; other site 102608001629 putative CheW interface [polypeptide binding]; other site 102608001630 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 102608001631 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 102608001632 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 102608001633 Walker A/P-loop; other site 102608001634 ATP binding site [chemical binding]; other site 102608001635 Q-loop/lid; other site 102608001636 ABC transporter signature motif; other site 102608001637 Walker B; other site 102608001638 D-loop; other site 102608001639 H-loop/switch region; other site 102608001640 flagellin A; Reviewed; Region: PRK12584 102608001641 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 102608001642 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 102608001643 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 102608001644 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 102608001645 3-methyladenine DNA glycosylase; Provisional; Region: PRK13913 102608001646 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 102608001647 minor groove reading motif; other site 102608001648 helix-hairpin-helix signature motif; other site 102608001649 active site 102608001650 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 102608001651 substrate binding site [chemical binding]; other site 102608001652 active site 102608001653 Outer membrane efflux protein; Region: OEP; pfam02321 102608001654 Outer membrane efflux protein; Region: OEP; pfam02321 102608001655 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 102608001656 HlyD family secretion protein; Region: HlyD_3; pfam13437 102608001657 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 102608001658 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608001659 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 102608001660 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 102608001661 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 102608001662 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 102608001663 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 102608001664 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 102608001665 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 102608001666 Autotransporter beta-domain; Region: Autotransporter; pfam03797 102608001667 potential frameshift: common BLAST hit: gi|15611369|ref|NP_223020.1| ABC transporter ATP-binding protein 102608001668 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 102608001669 Q-loop/lid; other site 102608001670 ABC transporter signature motif; other site 102608001671 Walker B; other site 102608001672 D-loop; other site 102608001673 H-loop/switch region; other site 102608001674 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 102608001675 Walker A/P-loop; other site 102608001676 ATP binding site [chemical binding]; other site 102608001677 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 102608001678 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 102608001679 nucleotide binding pocket [chemical binding]; other site 102608001680 K-X-D-G motif; other site 102608001681 catalytic site [active] 102608001682 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 102608001683 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 102608001684 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 102608001685 Dimer interface [polypeptide binding]; other site 102608001686 BRCT sequence motif; other site 102608001687 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 102608001688 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 102608001689 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 102608001690 active site 102608001691 phosphorylation site [posttranslational modification] 102608001692 intermolecular recognition site; other site 102608001693 dimerization interface [polypeptide binding]; other site 102608001694 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 102608001695 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 102608001696 dimer interface [polypeptide binding]; other site 102608001697 anticodon binding site; other site 102608001698 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 102608001699 homodimer interface [polypeptide binding]; other site 102608001700 motif 1; other site 102608001701 active site 102608001702 motif 2; other site 102608001703 GAD domain; Region: GAD; pfam02938 102608001704 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 102608001705 active site 102608001706 motif 3; other site 102608001707 adenylate kinase; Reviewed; Region: adk; PRK00279 102608001708 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 102608001709 AMP-binding site [chemical binding]; other site 102608001710 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 102608001711 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 102608001712 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 102608001713 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 102608001714 Glycosyltransferase involved in LPS biosynthesis [Cell envelope biogenesis, outer membrane]; Region: COG3306 102608001715 potential protein location (hypothetical protein) that overlaps protein (putative lipopolysaccharide biosynthesis protein) 102608001716 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 102608001717 dimer interface [polypeptide binding]; other site 102608001718 substrate binding site [chemical binding]; other site 102608001719 metal binding sites [ion binding]; metal-binding site 102608001720 MutS2 family protein; Region: mutS2; TIGR01069 102608001721 ATPase domain of DNA mismatch repair MUTS family; Region: MUTSac; smart00534 102608001722 Walker A/P-loop; other site 102608001723 ATP binding site [chemical binding]; other site 102608001724 Q-loop/lid; other site 102608001725 ABC transporter signature motif; other site 102608001726 Walker B; other site 102608001727 D-loop; other site 102608001728 H-loop/switch region; other site 102608001729 Smr domain; Region: Smr; pfam01713 102608001730 UDP-N-acetylmuramate--alanine ligase; Region: murC; TIGR01082 102608001731 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 102608001732 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 102608001733 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 102608001734 hypothetical protein; Provisional; Region: PRK05839 102608001735 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 102608001736 pyridoxal 5'-phosphate binding site [chemical binding]; other site 102608001737 homodimer interface [polypeptide binding]; other site 102608001738 catalytic residue [active] 102608001739 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 102608001740 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 102608001741 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 102608001742 Tetrahydrodipicolinate N-succinyltransferase [Amino acid transport and metabolism]; Region: DapD; COG2171 102608001743 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 102608001744 putative trimer interface [polypeptide binding]; other site 102608001745 putative CoA binding site [chemical binding]; other site 102608001746 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 102608001747 Sel1-like repeats; Region: SEL1; smart00671 102608001748 Sel1-like repeats; Region: SEL1; smart00671 102608001749 Sel1 repeat; Region: Sel1; cl02723 102608001750 Sel1-like repeats; Region: SEL1; smart00671 102608001751 Uncharacterized conserved protein [Function unknown]; Region: COG1479 102608001752 Protein of unknown function DUF262; Region: DUF262; pfam03235 102608001753 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 102608001754 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 102608001755 hydrogenase (NiFe) small subunit (hydA); Region: hydA; TIGR00391 102608001756 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 102608001757 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 102608001758 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 102608001759 Ni,Fe-hydrogenase I cytochrome b subunit [Energy production and conversion]; Region: HyaC; COG1969 102608001760 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 102608001761 nickel binding site [ion binding]; other site 102608001762 putative substrate-binding site; other site 102608001763 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608001764 Competence protein ComGF [Intracellular trafficking and secretion]; Region: ComGF; COG4940 102608001765 Predicted hydrolases of HD superfamily [General function prediction only]; Region: COG1896 102608001766 Uncharacterized conserved protein [Function unknown]; Region: COG1912 102608001767 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 102608001768 16S rRNA (cytosine(1402)-N(4))-methyltransferase; Region: TIGR00006 102608001769 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608001770 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 102608001771 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 102608001772 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 102608001773 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 102608001774 Response regulator receiver domain; Region: Response_reg; pfam00072 102608001775 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 102608001776 active site 102608001777 phosphorylation site [posttranslational modification] 102608001778 intermolecular recognition site; other site 102608001779 dimerization interface [polypeptide binding]; other site 102608001780 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 102608001781 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 102608001782 Walker A motif; other site 102608001783 ATP binding site [chemical binding]; other site 102608001784 Walker B motif; other site 102608001785 arginine finger; other site 102608001786 DNA gyrase subunit A; Validated; Region: PRK05560 102608001787 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 102608001788 CAP-like domain; other site 102608001789 active site 102608001790 primary dimer interface [polypeptide binding]; other site 102608001791 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 102608001792 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 102608001793 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 102608001794 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 102608001795 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 102608001796 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 102608001797 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 102608001798 Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcxC; COG4647 102608001799 Acetone carboxylase gamma subunit; Region: Acetone_carb_G; pfam08882 102608001800 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 102608001801 Hydantoinase B/oxoprolinase; Region: Hydantoinase_B; pfam02538 102608001802 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 102608001803 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 102608001804 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 102608001805 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3528 102608001806 Short chain fatty acid transporter; Region: SCFA_trans; pfam02667 102608001807 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 102608001808 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 102608001809 putative acyltransferase; Provisional; Region: PRK05790 102608001810 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 102608001811 dimer interface [polypeptide binding]; other site 102608001812 active site 102608001813 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 102608001814 active site 102608001815 catalytic site [active] 102608001816 substrate binding site [chemical binding]; other site 102608001817 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 102608001818 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 102608001819 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 102608001820 G1 box; other site 102608001821 GTP/Mg2+ binding site [chemical binding]; other site 102608001822 Switch I region; other site 102608001823 G2 box; other site 102608001824 G3 box; other site 102608001825 Switch II region; other site 102608001826 G4 box; other site 102608001827 G5 box; other site 102608001828 Nucleoside recognition; Region: Gate; pfam07670 102608001829 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 102608001830 Nucleoside recognition; Region: Gate; pfam07670 102608001831 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 102608001832 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 102608001833 N-terminal plug; other site 102608001834 ligand-binding site [chemical binding]; other site 102608001835 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 102608001836 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14359 102608001837 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 102608001838 Substrate binding site; other site 102608001839 Mg++ binding site; other site 102608001840 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 102608001841 active site 102608001842 substrate binding site [chemical binding]; other site 102608001843 CoA binding site [chemical binding]; other site 102608001844 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK08447 102608001845 ATP cone domain; Region: ATP-cone; pfam03477 102608001846 Class I ribonucleotide reductase; Region: RNR_I; cd01679 102608001847 active site 102608001848 dimer interface [polypeptide binding]; other site 102608001849 catalytic residues [active] 102608001850 effector binding site; other site 102608001851 R2 peptide binding site; other site 102608001852 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 102608001853 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 102608001854 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 102608001855 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 102608001856 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 102608001857 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 102608001858 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 102608001859 DNA binding site [nucleotide binding] 102608001860 active site 102608001861 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 102608001862 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 102608001863 active site 102608001864 DNA binding site [nucleotide binding] 102608001865 Int/Topo IB signature motif; other site 102608001866 aspartate aminotransferase; Provisional; Region: PRK05764 102608001867 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 102608001868 pyridoxal 5'-phosphate binding site [chemical binding]; other site 102608001869 homodimer interface [polypeptide binding]; other site 102608001870 catalytic residue [active] 102608001871 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608001872 Predicted helicase [General function prediction only]; Region: COG4889 102608001873 Predicted helicase [General function prediction only]; Region: COG4889 102608001874 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 102608001875 nucleotide binding region [chemical binding]; other site 102608001876 ATP-binding site [chemical binding]; other site 102608001877 Restriction endonuclease; Region: Mrr_cat_2; pfam13156 102608001878 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 102608001879 ATP binding site [chemical binding]; other site 102608001880 putative Mg++ binding site [ion binding]; other site 102608001881 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 102608001882 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 102608001883 Cysteine-rich domain; Region: CCG; pfam02754 102608001884 Cysteine-rich domain; Region: CCG; pfam02754 102608001885 oxygen-independent coproporphyrinogen III oxidase; Region: hemN; TIGR00538 102608001886 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 102608001887 FeS/SAM binding site; other site 102608001888 HemN C-terminal domain; Region: HemN_C; pfam06969 102608001889 Protein of unknown function (DUF2603); Region: DUF2603; pfam10788 102608001890 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 102608001891 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 102608001892 Tetramer interface [polypeptide binding]; other site 102608001893 active site 102608001894 FMN-binding site [chemical binding]; other site 102608001895 ribonuclease III; Reviewed; Region: rnc; PRK00102 102608001896 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 102608001897 dimerization interface [polypeptide binding]; other site 102608001898 active site 102608001899 metal binding site [ion binding]; metal-binding site 102608001900 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 102608001901 dsRNA binding site [nucleotide binding]; other site 102608001902 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 102608001903 RNA/DNA hybrid binding site [nucleotide binding]; other site 102608001904 active site 102608001905 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]; Region: COG2956 102608001906 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]; Region: COG1439 102608001907 SurA N-terminal domain; Region: SurA_N; pfam09312 102608001908 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 102608001909 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 102608001910 GatB domain; Region: GatB_Yqey; smart00845 102608001911 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 102608001912 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 102608001913 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 102608001914 hypothetical protein; Provisional; Region: PRK08445 102608001915 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 102608001916 FeS/SAM binding site; other site 102608001917 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 102608001918 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 102608001919 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 102608001920 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 102608001921 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 102608001922 Surface antigen; Region: Bac_surface_Ag; pfam01103 102608001923 hypothetical protein; Provisional; Region: PRK08444 102608001924 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 102608001925 FeS/SAM binding site; other site 102608001926 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 102608001927 Ferritin-like domain; Region: Ferritin; pfam00210 102608001928 ferroxidase diiron center [ion binding]; other site 102608001929 phosphoserine phosphatase SerB; Region: serB; TIGR00338 102608001930 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 102608001931 motif II; other site 102608001932 Glycosyltransferase family 10 (fucosyltransferase); Region: Glyco_transf_10; pfam00852 102608001933 Uracil-DNA glycosylases (UDG) and related enzymes; Region: UDG_like; cl00483 102608001934 ligand binding site [chemical binding]; other site 102608001935 active site 102608001936 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 102608001937 Aspartase; Region: Aspartase; cd01357 102608001938 active sites [active] 102608001939 tetramer interface [polypeptide binding]; other site 102608001940 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 102608001941 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 102608001942 hinge; other site 102608001943 active site 102608001944 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 102608001945 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 102608001946 active site 102608001947 tetramer interface; other site 102608001948 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 102608001949 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 102608001950 N-acetyl-D-glucosamine binding site [chemical binding]; other site 102608001951 catalytic residue [active] 102608001952 YGGT family; Region: YGGT; pfam02325 102608001953 glutamylglutaminyl-tRNA synthetase; Provisional; Region: PRK12410 102608001954 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 102608001955 active site 102608001956 HIGH motif; other site 102608001957 nucleotide binding site [chemical binding]; other site 102608001958 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 102608001959 active site 102608001960 KMSKS motif; other site 102608001961 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 102608001962 dimer interface [polypeptide binding]; other site 102608001963 FMN binding site [chemical binding]; other site 102608001964 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 102608001965 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 102608001966 active site 102608001967 NTP binding site [chemical binding]; other site 102608001968 metal binding triad [ion binding]; metal-binding site 102608001969 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 102608001970 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 102608001971 Ligand Binding Site [chemical binding]; other site 102608001972 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608001973 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 102608001974 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 102608001975 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 102608001976 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 102608001977 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 102608001978 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 102608001979 Walker A/P-loop; other site 102608001980 ATP binding site [chemical binding]; other site 102608001981 Q-loop/lid; other site 102608001982 ABC transporter signature motif; other site 102608001983 Walker B; other site 102608001984 D-loop; other site 102608001985 H-loop/switch region; other site 102608001986 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 102608001987 DNA polymerase III subunits gamma and tau; Validated; Region: PRK08451 102608001988 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 102608001989 Walker A motif; other site 102608001990 ATP binding site [chemical binding]; other site 102608001991 Walker B motif; other site 102608001992 arginine finger; other site 102608001993 Lysine efflux permease [General function prediction only]; Region: COG1279 102608001994 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 102608001995 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 102608001996 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 102608001997 active site 102608001998 homodimer interface [polypeptide binding]; other site 102608001999 homotetramer interface [polypeptide binding]; other site 102608002000 anaerobic c4-dicarboxylate membrane transporter family protein; Region: Dcu; TIGR00770 102608002001 Anaerobic C4-dicarboxylate transporter [General function prediction only]; Region: DcuB; COG2704 102608002002 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608002003 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 102608002004 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 102608002005 FMN binding site [chemical binding]; other site 102608002006 active site 102608002007 catalytic residues [active] 102608002008 substrate binding site [chemical binding]; other site 102608002009 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 102608002010 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 102608002011 Ligand Binding Site [chemical binding]; other site 102608002012 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 102608002013 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 102608002014 G1 box; other site 102608002015 GTP/Mg2+ binding site [chemical binding]; other site 102608002016 G2 box; other site 102608002017 Switch I region; other site 102608002018 G3 box; other site 102608002019 Switch II region; other site 102608002020 G4 box; other site 102608002021 G5 box; other site 102608002022 cyclic beta-1,2-glucan ABC transporter; Provisional; Region: PRK13657 102608002023 V-type ATP synthase subunit I; Validated; Region: PRK05771 102608002024 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 102608002025 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 102608002026 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cl15377 102608002027 FeS/SAM binding site; other site 102608002028 Predicted phosphoribosyltransferases [General function prediction only]; Region: COG2236 102608002029 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 102608002030 active site 102608002031 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 102608002032 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 102608002033 catalytic residue [active] 102608002034 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 102608002035 tetramer interfaces [polypeptide binding]; other site 102608002036 binuclear metal-binding site [ion binding]; other site 102608002037 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 102608002038 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 102608002039 ATP-grasp domain; Region: ATP-grasp_4; cl17255 102608002040 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 102608002041 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 102608002042 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 102608002043 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 102608002044 nucleotide binding site/active site [active] 102608002045 HIT family signature motif; other site 102608002046 catalytic residue [active] 102608002047 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 102608002048 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 102608002049 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 102608002050 active site 102608002051 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 102608002052 Uncharacterized protein/domain associated with GTPases [Function unknown]; Region: COG3597 102608002053 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 102608002054 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 102608002055 G1 box; other site 102608002056 Walker A/P-loop; other site 102608002057 GTP/Mg2+ binding site [chemical binding]; other site 102608002058 ATP binding site [chemical binding]; other site 102608002059 G2 box; other site 102608002060 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 102608002061 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 102608002062 active site 102608002063 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 102608002064 Interdomain contacts; other site 102608002065 Fibronectin type 3 domain-containing protein [General function prediction only]; Region: COG3401 102608002066 Cytokine receptor motif; other site 102608002067 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 102608002068 Interdomain contacts; other site 102608002069 Cytokine receptor motif; other site 102608002070 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 102608002071 Interdomain contacts; other site 102608002072 Cytokine receptor motif; other site 102608002073 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 102608002074 S-adenosylmethionine binding site [chemical binding]; other site 102608002075 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 102608002076 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 102608002077 Walker A/P-loop; other site 102608002078 ATP binding site [chemical binding]; other site 102608002079 Q-loop/lid; other site 102608002080 ABC transporter signature motif; other site 102608002081 Walker B; other site 102608002082 D-loop; other site 102608002083 H-loop/switch region; other site 102608002084 putative protein insertion permease FtsX; Region: ftsX; TIGR00439 102608002085 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 102608002086 Peptidase family M23; Region: Peptidase_M23; pfam01551 102608002087 flagellar protein FlaG; Provisional; Region: PRK08452 102608002088 flagellar capping protein; Validated; Region: fliD; PRK08453 102608002089 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 102608002090 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 102608002091 flagellar biosynthetic protein FliS; Region: fliS; TIGR00208 102608002092 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 102608002093 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 102608002094 putative ATP binding site [chemical binding]; other site 102608002095 putative substrate interface [chemical binding]; other site 102608002096 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 102608002097 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 102608002098 putative active site; other site 102608002099 catalytic triad [active] 102608002100 putative dimer interface [polypeptide binding]; other site 102608002101 Predicted permease [General function prediction only]; Region: COG2056 102608002102 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 102608002103 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Thermotoga marina NorM; Region: MATE_NorM_like; cd13137 102608002104 putative efflux protein, MATE family; Region: matE; TIGR00797 102608002105 phosphodiesterase; Provisional; Region: PRK12704 102608002106 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 102608002107 nucleic acid binding region [nucleotide binding]; other site 102608002108 G-X-X-G motif; other site 102608002109 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 102608002110 Zn2+ binding site [ion binding]; other site 102608002111 Mg2+ binding site [ion binding]; other site 102608002112 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 102608002113 signal recognition particle-docking protein FtsY; Region: ftsY; TIGR00064 102608002114 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 102608002115 Mu-like prophage protein [General function prediction only]; Region: COG3941 102608002116 potential frameshift: common BLAST hit: gi|308182926|ref|YP_003927053.1| molybdenum cofactor biosynthesis protein A 102608002117 Molybdenum cofactor biosynthesis enzyme [Coenzyme metabolism]; Region: MoaA; COG2896 102608002118 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 102608002119 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cl15377 102608002120 FeS/SAM binding site; other site 102608002121 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 102608002122 GTP binding site; other site 102608002123 flagellar biosynthetic protein FlhB; Region: flhB; TIGR00328 102608002124 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 102608002125 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 102608002126 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 102608002127 active site 102608002128 metal binding site [ion binding]; metal-binding site 102608002129 Nitronate monooxygenase; Region: NMO; pfam03060 102608002130 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 102608002131 FMN binding site [chemical binding]; other site 102608002132 substrate binding site [chemical binding]; other site 102608002133 putative catalytic residue [active] 102608002134 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 102608002135 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 102608002136 active site 102608002137 HIGH motif; other site 102608002138 dimer interface [polypeptide binding]; other site 102608002139 KMSKS motif; other site 102608002140 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 102608002141 RNA binding surface [nucleotide binding]; other site 102608002142 (p)ppGpp synthetase, RelA/SpoT family; Region: spoT_relA; TIGR00691 102608002143 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 102608002144 Zn2+ binding site [ion binding]; other site 102608002145 Mg2+ binding site [ion binding]; other site 102608002146 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 102608002147 synthetase active site [active] 102608002148 NTP binding site [chemical binding]; other site 102608002149 metal binding site [ion binding]; metal-binding site 102608002150 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 102608002151 DNA-directed RNA polymerase, subunit K/omega [Transcription]; Region: RpoZ; COG1758 102608002152 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 102608002153 putative nucleotide binding site [chemical binding]; other site 102608002154 uridine monophosphate binding site [chemical binding]; other site 102608002155 homohexameric interface [polypeptide binding]; other site 102608002156 Predicted periplasmic solute-binding protein [General function prediction only]; Region: COG1427 102608002157 aconitate hydratase 2; Region: acnB; TIGR00117 102608002158 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 102608002159 substrate binding site [chemical binding]; other site 102608002160 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 102608002161 substrate binding site [chemical binding]; other site 102608002162 ligand binding site [chemical binding]; other site 102608002163 FOG: Transposase [DNA replication, recombination, and repair]; Region: COG5659 102608002164 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 102608002165 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 102608002166 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 102608002167 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 102608002168 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 102608002169 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 102608002170 nucleotide binding region [chemical binding]; other site 102608002171 ATP-binding site [chemical binding]; other site 102608002172 SEC-C motif; Region: SEC-C; pfam02810 102608002173 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 102608002174 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 102608002175 FtsX-like permease family; Region: FtsX; pfam02687 102608002176 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 102608002177 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 102608002178 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 102608002179 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 102608002180 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 102608002181 metal-binding site [ion binding] 102608002182 heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase; Region: ATPase-IB2_Cd; TIGR01512 102608002183 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 102608002184 Soluble P-type ATPase [General function prediction only]; Region: COG4087 102608002185 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 102608002186 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 102608002187 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 102608002188 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 102608002189 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 102608002190 active site 102608002191 catalytic residues [active] 102608002192 metal binding site [ion binding]; metal-binding site 102608002193 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 102608002194 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 102608002195 oligomer interface [polypeptide binding]; other site 102608002196 active site residues [active] 102608002197 trigger factor; Provisional; Region: tig; PRK01490 102608002198 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 102608002199 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 102608002200 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608002201 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 102608002202 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 102608002203 trimer interface [polypeptide binding]; other site 102608002204 dimer interface [polypeptide binding]; other site 102608002205 putative active site [active] 102608002206 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 102608002207 MPT binding site; other site 102608002208 trimer interface [polypeptide binding]; other site 102608002209 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 102608002210 MoaE homodimer interface [polypeptide binding]; other site 102608002211 MoaD interaction [polypeptide binding]; other site 102608002212 active site residues [active] 102608002213 Ubiquitin-like proteins; Region: UBQ; cl00155 102608002214 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 102608002215 dimerization interface [polypeptide binding]; other site 102608002216 active site 102608002217 Domain of unknown function (DUF3943); Region: DUF3943; pfam13084 102608002218 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09314 102608002219 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: ribB; TIGR00506 102608002220 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cl00522 102608002221 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 102608002222 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 102608002223 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 102608002224 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 102608002225 N-terminal plug; other site 102608002226 ligand-binding site [chemical binding]; other site 102608002227 holo-[acyl-carrier-protein] synthase; Region: acpS; TIGR00516 102608002228 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK08455 102608002229 RNA methyltransferase, RsmD family; Region: TIGR00095 102608002230 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 102608002231 Uncharacterized conserved protein [Function unknown]; Region: COG1565 102608002232 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 102608002233 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism]; Region: ThiF; COG0476 102608002234 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 102608002235 ATP binding site [chemical binding]; other site 102608002236 substrate interface [chemical binding]; other site 102608002237 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 102608002238 flagellar motor protein MotA; Validated; Region: PRK08456 102608002239 flagellar motor protein MotB; Reviewed; Region: motB; PRK08457 102608002240 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 102608002241 ligand binding site [chemical binding]; other site 102608002242 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 102608002243 dimer interface [polypeptide binding]; other site 102608002244 conserved gate region; other site 102608002245 ABC-ATPase subunit interface; other site 102608002246 Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane]; Region: OpuBC; COG1732 102608002247 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 102608002248 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 102608002249 Walker A/P-loop; other site 102608002250 ATP binding site [chemical binding]; other site 102608002251 Q-loop/lid; other site 102608002252 ABC transporter signature motif; other site 102608002253 Walker B; other site 102608002254 D-loop; other site 102608002255 H-loop/switch region; other site 102608002256 excinuclease ABC, C subunit; Region: uvrC; TIGR00194 102608002257 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 102608002258 GIY-YIG motif/motif A; other site 102608002259 active site 102608002260 catalytic site [active] 102608002261 putative DNA binding site [nucleotide binding]; other site 102608002262 metal binding site [ion binding]; metal-binding site 102608002263 UvrB/uvrC motif; Region: UVR; pfam02151 102608002264 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 102608002265 homoserine dehydrogenase; Provisional; Region: PRK06349 102608002266 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 102608002267 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 102608002268 Uncharacterized protein family UPF0102; Region: UPF0102; pfam02021 102608002269 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 102608002270 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 102608002271 catalytic residues [active] 102608002272 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 102608002273 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 102608002274 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 102608002275 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 102608002276 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 102608002277 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 102608002278 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 102608002279 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 102608002280 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 102608002281 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 102608002282 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 102608002283 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 102608002284 active site 102608002285 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit; Region: gatA; TIGR00132 102608002286 indole acetimide hydrolase; Validated; Region: PRK07488 102608002287 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 102608002288 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 102608002289 CoA-binding site [chemical binding]; other site 102608002290 spermidine synthase; Provisional; Region: speE; PRK00536 102608002291 spermidine synthase; Provisional; Region: PRK00811 102608002292 GTP-binding protein Der; Reviewed; Region: PRK00093 102608002293 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 102608002294 G1 box; other site 102608002295 GTP/Mg2+ binding site [chemical binding]; other site 102608002296 Switch I region; other site 102608002297 G2 box; other site 102608002298 Switch II region; other site 102608002299 G3 box; other site 102608002300 G4 box; other site 102608002301 G5 box; other site 102608002302 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 102608002303 G1 box; other site 102608002304 GTP/Mg2+ binding site [chemical binding]; other site 102608002305 Switch I region; other site 102608002306 G2 box; other site 102608002307 G3 box; other site 102608002308 Switch II region; other site 102608002309 G4 box; other site 102608002310 G5 box; other site 102608002311 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 102608002312 IHF dimer interface [polypeptide binding]; other site 102608002313 IHF - DNA interface [nucleotide binding]; other site 102608002314 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3018 102608002315 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3018 102608002316 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 102608002317 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 102608002318 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 102608002319 NAD(P) binding site [chemical binding]; other site 102608002320 homodimer interface [polypeptide binding]; other site 102608002321 substrate binding site [chemical binding]; other site 102608002322 active site 102608002323 phosphopantothenoylcysteine decarboxylase / phosphopantothenate--cysteine ligase; Region: coaBC_dfp; TIGR00521 102608002324 Flavoprotein; Region: Flavoprotein; pfam02441 102608002325 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 102608002326 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 102608002327 thiamine phosphate binding site [chemical binding]; other site 102608002328 active site 102608002329 pyrophosphate binding site [ion binding]; other site 102608002330 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 102608002331 dimer interface [polypeptide binding]; other site 102608002332 substrate binding site [chemical binding]; other site 102608002333 ATP binding site [chemical binding]; other site 102608002334 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 102608002335 substrate binding site [chemical binding]; other site 102608002336 multimerization interface [polypeptide binding]; other site 102608002337 ATP binding site [chemical binding]; other site 102608002338 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 102608002339 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 102608002340 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 102608002341 ATP binding site [chemical binding]; other site 102608002342 putative Mg++ binding site [ion binding]; other site 102608002343 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 102608002344 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 102608002345 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 102608002346 type I restriction system adenine methylase (hsdM); Region: hsdM; TIGR00497 102608002347 HsdM N-terminal domain; Region: HsdM_N; pfam12161 102608002348 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 102608002349 S-adenosylmethionine binding site [chemical binding]; other site 102608002350 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 102608002351 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 102608002352 cofactor binding site; other site 102608002353 DNA binding site [nucleotide binding] 102608002354 substrate interaction site [chemical binding]; other site 102608002355 HaeIII restriction endonuclease; Region: RE_HaeIII; pfam09556 102608002356 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 102608002357 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 102608002358 active site 102608002359 Protein of unknown function (DUF511); Region: DUF511; cl01114 102608002360 Protein of unknown function (DUF511); Region: DUF511; cl01114 102608002361 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 102608002362 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 102608002363 Walker A/P-loop; other site 102608002364 ATP binding site [chemical binding]; other site 102608002365 Q-loop/lid; other site 102608002366 ABC transporter signature motif; other site 102608002367 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 102608002368 ABC transporter; Region: ABC_tran_2; pfam12848 102608002369 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 102608002370 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05458 102608002371 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 102608002372 active site 102608002373 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 102608002374 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 102608002375 dimer interface [polypeptide binding]; other site 102608002376 active site 102608002377 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 102608002378 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 102608002379 putative ribose interaction site [chemical binding]; other site 102608002380 putative ADP binding site [chemical binding]; other site 102608002381 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 102608002382 active site 102608002383 nucleotide binding site [chemical binding]; other site 102608002384 HIGH motif; other site 102608002385 KMSKS motif; other site 102608002386 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 102608002387 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 102608002388 NAD(P) binding site [chemical binding]; other site 102608002389 active site 102608002390 D,D-heptose 1,7-bisphosphate phosphatase; Region: GmhB_yaeD; TIGR00213 102608002391 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 102608002392 active site 102608002393 motif I; other site 102608002394 motif II; other site 102608002395 Uncharacterized conserved protein [Function unknown]; Region: COG2836 102608002396 pantothenate kinase; Reviewed; Region: PRK13333 102608002397 PQQ-like domain; Region: PQQ_2; pfam13360 102608002398 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 102608002399 trimer interface [polypeptide binding]; other site 102608002400 active site 102608002401 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 102608002402 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 102608002403 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 102608002404 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 102608002405 lipid-A-disaccharide synthase; Region: lpxB; TIGR00215 102608002406 hydrogenase nickel incorporation protein; Provisional; Region: hypA; PRK00564 102608002407 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 102608002408 flagellar hook protein FlgE; Validated; Region: flgE; PRK08425 102608002409 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 102608002410 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 102608002411 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 102608002412 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 102608002413 CDP-diacylglycerol pyrophosphatase, bacterial type; Region: cdh; TIGR00672 102608002414 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 102608002415 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 102608002416 PhnA protein; Region: PhnA; pfam03831 102608002417 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 102608002418 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 102608002419 tetramer interface [polypeptide binding]; other site 102608002420 heme binding pocket [chemical binding]; other site 102608002421 NADPH binding site [chemical binding]; other site 102608002422 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 102608002423 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 102608002424 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 102608002425 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 102608002426 active site 102608002427 putative DNA-binding cleft [nucleotide binding]; other site 102608002428 dimer interface [polypeptide binding]; other site 102608002429 Uncharacterized conserved protein [Function unknown]; Region: COG1432 102608002430 LabA_like proteins; Region: LabA_like; cd06167 102608002431 putative metal binding site [ion binding]; other site 102608002432 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 102608002433 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 102608002434 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 102608002435 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 102608002436 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 102608002437 putative heme binding pocket [chemical binding]; other site 102608002438 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 102608002439 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 102608002440 cofactor binding site; other site 102608002441 DNA binding site [nucleotide binding] 102608002442 substrate interaction site [chemical binding]; other site 102608002443 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 102608002444 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 102608002445 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 102608002446 G1 box; other site 102608002447 putative GEF interaction site [polypeptide binding]; other site 102608002448 GTP/Mg2+ binding site [chemical binding]; other site 102608002449 Switch I region; other site 102608002450 G2 box; other site 102608002451 G3 box; other site 102608002452 Switch II region; other site 102608002453 G4 box; other site 102608002454 G5 box; other site 102608002455 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 102608002456 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 102608002457 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 102608002458 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 102608002459 ADP-heptose:LPS heptosyl transferase I; Provisional; Region: PRK10964; cl15782 102608002460 Helix-turn-helix domain; Region: HTH_17; pfam12728 102608002461 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 102608002462 Methyltransferase domain; Region: Methyltransf_26; pfam13659 102608002463 TaqI-like C-terminal specificity domain; Region: TaqI_C; pfam12950 102608002464 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608002465 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 102608002466 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 102608002467 active site 102608002468 HIGH motif; other site 102608002469 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 102608002470 active site 102608002471 KMSKS motif; other site 102608002472 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 102608002473 putative bacteriocin export ABC transporter, lactococcin 972 group; Region: L_ocin_972_ABC; TIGR03608 102608002474 Walker A/P-loop; other site 102608002475 ATP binding site [chemical binding]; other site 102608002476 Q-loop/lid; other site 102608002477 ABC transporter signature motif; other site 102608002478 Walker B; other site 102608002479 D-loop; other site 102608002480 H-loop/switch region; other site 102608002481 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 102608002482 dimer interface [polypeptide binding]; other site 102608002483 conserved gate region; other site 102608002484 putative PBP binding loops; other site 102608002485 ABC-ATPase subunit interface; other site 102608002486 potential frameshift: common BLAST hit: gi|208434395|ref|YP_002266061.1| molybdenum ABC transporter 102608002487 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 102608002488 ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ModA; COG0725 102608002489 ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ModA; COG0725 102608002490 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608002491 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 102608002492 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 102608002493 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 102608002494 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_5; cd09610 102608002495 active site 102608002496 Zn binding site [ion binding]; other site 102608002497 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 102608002498 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 102608002499 putative metal binding site [ion binding]; other site 102608002500 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 102608002501 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 102608002502 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 102608002503 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 102608002504 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 102608002505 ATP binding site [chemical binding]; other site 102608002506 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 102608002507 putative Mg++ binding site [ion binding]; other site 102608002508 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 102608002509 Methyltransferase domain; Region: Methyltransf_26; pfam13659 102608002510 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 102608002511 Polyphosphate kinase [Inorganic ion transport and metabolism]; Region: Ppk; COG0855 102608002512 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 102608002513 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 102608002514 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 102608002515 putative domain interface [polypeptide binding]; other site 102608002516 putative active site [active] 102608002517 catalytic site [active] 102608002518 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 102608002519 putative active site [active] 102608002520 putative domain interface [polypeptide binding]; other site 102608002521 catalytic site [active] 102608002522 dihydroorotate dehydrogenase, subfamily 2; Region: pyrD_sub2; TIGR01036 102608002523 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 102608002524 quinone interaction residues [chemical binding]; other site 102608002525 active site 102608002526 catalytic residues [active] 102608002527 FMN binding site [chemical binding]; other site 102608002528 substrate binding site [chemical binding]; other site 102608002529 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 102608002530 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 102608002531 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 102608002532 dihydrodipicolinate synthase; Region: dapA; TIGR00674 102608002533 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 102608002534 dimer interface [polypeptide binding]; other site 102608002535 active site 102608002536 catalytic residue [active] 102608002537 7-alpha-hydroxysteroid dehydrogenase; Provisional; Region: PRK08416 102608002538 1-cyclohexenylcarbonyl_coenzyme A_reductase (ChcA)_like, classical (c) SDRs; Region: ChcA_like_SDR_c; cd05359 102608002539 putative NAD(P) binding site [chemical binding]; other site 102608002540 active site 102608002541 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase; Region: pgsA; TIGR00560 102608002542 S-methylmethionine transporter; Provisional; Region: PRK11387 102608002543 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 102608002544 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 102608002545 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 102608002546 protein binding site [polypeptide binding]; other site 102608002547 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 102608002548 protein binding site [polypeptide binding]; other site 102608002549 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 102608002550 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 102608002551 substrate binding site; other site 102608002552 dimer interface; other site 102608002553 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 102608002554 homotrimer interaction site [polypeptide binding]; other site 102608002555 zinc binding site [ion binding]; other site 102608002556 CDP-binding sites; other site 102608002557 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 102608002558 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 102608002559 active site 102608002560 dimerization interface [polypeptide binding]; other site 102608002561 5'-3' exonuclease; Provisional; Region: PRK14976 102608002562 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 102608002563 putative active site [active] 102608002564 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 102608002565 putative DNA binding site [nucleotide binding]; other site 102608002566 putative metal binding site [ion binding]; other site 102608002567 chaperone protein DnaJ; Provisional; Region: PRK14299 102608002568 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 102608002569 HSP70 interaction site [polypeptide binding]; other site 102608002570 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 102608002571 substrate binding site [polypeptide binding]; other site 102608002572 dimer interface [polypeptide binding]; other site 102608002573 Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Region: HTH_HspR; cd04766 102608002574 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 102608002575 DNA binding residues [nucleotide binding] 102608002576 putative dimer interface [polypeptide binding]; other site 102608002577 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]; Region: MGS1; COG2256 102608002578 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 102608002579 Walker A motif; other site 102608002580 ATP binding site [chemical binding]; other site 102608002581 Walker B motif; other site 102608002582 arginine finger; other site 102608002583 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 102608002584 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 102608002585 metal binding site 2 [ion binding]; metal-binding site 102608002586 putative DNA binding helix; other site 102608002587 metal binding site 1 [ion binding]; metal-binding site 102608002588 dimer interface [polypeptide binding]; other site 102608002589 structural Zn2+ binding site [ion binding]; other site 102608002590 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4731 102608002591 Beta-galactosidase, beta subunit [Carbohydrate transport and metabolism]; Region: EbgC; COG2731 102608002592 flagellar motor switch protein FliY; Validated; Region: PRK08432 102608002593 flagellar motor switch protein FliN; Region: fliN; TIGR02480 102608002594 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 102608002595 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 102608002596 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 102608002597 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 102608002598 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 102608002599 DNA binding residues [nucleotide binding] 102608002600 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 102608002601 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 102608002602 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 102608002603 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 102608002604 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 102608002605 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 102608002606 catalytic center binding site [active] 102608002607 ATP binding site [chemical binding]; other site 102608002608 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 102608002609 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 102608002610 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 102608002611 active site 102608002612 Dehydroquinase class II; Region: DHquinase_II; pfam01220 102608002613 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 102608002614 trimer interface [polypeptide binding]; other site 102608002615 active site 102608002616 dimer interface [polypeptide binding]; other site 102608002617 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 102608002618 O-Antigen ligase; Region: Wzy_C; pfam04932 102608002619 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 102608002620 16S/18S rRNA binding site [nucleotide binding]; other site 102608002621 S13e-L30e interaction site [polypeptide binding]; other site 102608002622 25S rRNA binding site [nucleotide binding]; other site 102608002623 flagellar biosynthesis protein FlhA; Region: FlhA; TIGR01398 102608002624 FHIPEP family; Region: FHIPEP; pfam00771 102608002625 Predicted phosphohydrolase (DHH superfamily) [General function prediction only]; Region: COG2404 102608002626 DHH family; Region: DHH; pfam01368 102608002627 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 102608002628 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 102608002629 active site 102608002630 intermolecular recognition site; other site 102608002631 dimerization interface [polypeptide binding]; other site 102608002632 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 102608002633 DNA binding site [nucleotide binding] 102608002634 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 102608002635 putative active site [active] 102608002636 putative metal binding site [ion binding]; other site 102608002637 acetyl-CoA synthetase; Provisional; Region: PRK00174 102608002638 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 102608002639 active site 102608002640 CoA binding site [chemical binding]; other site 102608002641 acyl-activating enzyme (AAE) consensus motif; other site 102608002642 AMP binding site [chemical binding]; other site 102608002643 acetate binding site [chemical binding]; other site 102608002644 Uncharacterized BCR, YhbC family COG0779; Region: DUF150; pfam02576 102608002645 Sm and related proteins; Region: Sm_like; cl00259 102608002646 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 102608002647 putative oligomer interface [polypeptide binding]; other site 102608002648 putative RNA binding site [nucleotide binding]; other site 102608002649 Ribosome-binding factor A; Region: RBFA; cl00542 102608002650 translation initiation factor IF-2; Region: IF-2; TIGR00487 102608002651 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 102608002652 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 102608002653 G1 box; other site 102608002654 putative GEF interaction site [polypeptide binding]; other site 102608002655 GTP/Mg2+ binding site [chemical binding]; other site 102608002656 Switch I region; other site 102608002657 G2 box; other site 102608002658 G3 box; other site 102608002659 Switch II region; other site 102608002660 G4 box; other site 102608002661 G5 box; other site 102608002662 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 102608002663 Translation-initiation factor 2; Region: IF-2; pfam11987 102608002664 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 102608002665 Predicted nucleic-acid-binding protein implicated in transcription termination [Transcription]; Region: COG2740 102608002666 putative RNA binding cleft [nucleotide binding]; other site 102608002667 homoserine kinase; Region: thrB; TIGR00191 102608002668 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 102608002669 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 102608002670 UDP-3-0-acyl N-acetylglucosamine deacetylase; Region: lpxC; TIGR00325 102608002671 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 102608002672 septum formation inhibitor; Reviewed; Region: minC; PRK00556 102608002673 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 102608002674 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 102608002675 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608002676 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608002677 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 102608002678 oligomerization interface [polypeptide binding]; other site 102608002679 active site 102608002680 metal binding site [ion binding]; metal-binding site 102608002681 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 102608002682 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 102608002683 Walker A motif; other site 102608002684 ATP binding site [chemical binding]; other site 102608002685 Walker B motif; other site 102608002686 arginine finger; other site 102608002687 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 102608002688 sec-independent translocase; Provisional; Region: PRK04098 102608002689 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 102608002690 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 102608002691 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 102608002692 rRNA small subunit methyltransferase G; Region: GidB; pfam02527 102608002693 16S rRNA (guanine(527)-N(7))-methyltransferase GidB; Region: gidB; TIGR00138 102608002694 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608002695 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 102608002696 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 102608002697 active site 102608002698 phosphorylation site [posttranslational modification] 102608002699 intermolecular recognition site; other site 102608002700 dimerization interface [polypeptide binding]; other site 102608002701 ribosomal protein L11 methyltransferase; Region: prmA; TIGR00406 102608002702 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 102608002703 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 102608002704 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 102608002705 Walker A motif; other site 102608002706 ATP binding site [chemical binding]; other site 102608002707 Walker B motif; other site 102608002708 arginine finger; other site 102608002709 Peptidase family M41; Region: Peptidase_M41; pfam01434 102608002710 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 102608002711 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 102608002712 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 102608002713 metal-binding site [ion binding] 102608002714 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 102608002715 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 102608002716 Soluble P-type ATPase [General function prediction only]; Region: COG4087 102608002717 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 102608002718 metal-binding site [ion binding] 102608002719 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cd00596 102608002720 active site 102608002721 Zn binding site [ion binding]; other site 102608002722 High-affinity nickel permease [Inorganic ion transport and metabolism]; Region: HoxN; COG3376 102608002723 Predicted endonuclease distantly related to archaeal Holliday junction resolvase and Mrr-like restriction enzymes [Defense mechanisms]; Region: COG1787 102608002724 Restriction endonuclease; Region: Mrr_cat; pfam04471 102608002725 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 102608002726 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 102608002727 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 102608002728 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 102608002729 Walker A/P-loop; other site 102608002730 ATP binding site [chemical binding]; other site 102608002731 Q-loop/lid; other site 102608002732 ABC transporter signature motif; other site 102608002733 Walker B; other site 102608002734 D-loop; other site 102608002735 H-loop/switch region; other site 102608002736 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 102608002737 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 102608002738 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 102608002739 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 102608002740 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 102608002741 hemolysin TlyA family protein; Region: tly; TIGR00478 102608002742 RNA binding surface [nucleotide binding]; other site 102608002743 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 102608002744 S-adenosylmethionine binding site [chemical binding]; other site 102608002745 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 102608002746 riboflavin kinase/FMN adenylyltransferase; Region: ribF; TIGR00083 102608002747 active site 102608002748 Riboflavin kinase; Region: Flavokinase; smart00904 102608002749 transketolase, bacterial and yeast; Region: tktlase_bact; TIGR00232 102608002750 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 102608002751 TPP-binding site [chemical binding]; other site 102608002752 dimer interface [polypeptide binding]; other site 102608002753 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 102608002754 PYR/PP interface [polypeptide binding]; other site 102608002755 dimer interface [polypeptide binding]; other site 102608002756 TPP binding site [chemical binding]; other site 102608002757 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 102608002758 Inactivated superfamily I helicase [DNA replication, recombination, and repair]; Region: COG3893 102608002759 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 102608002760 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 102608002761 TspO/MBR family; Region: TspO_MBR; cl01379 102608002762 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 102608002763 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 102608002764 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 102608002765 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 102608002766 putative substrate translocation pore; other site 102608002767 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgG; COG4786 102608002768 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 102608002769 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 102608002770 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 102608002771 cofactor binding site; other site 102608002772 DNA binding site [nucleotide binding] 102608002773 substrate interaction site [chemical binding]; other site 102608002774 GTP-binding protein LepA; Provisional; Region: PRK05433 102608002775 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 102608002776 G1 box; other site 102608002777 putative GEF interaction site [polypeptide binding]; other site 102608002778 GTP/Mg2+ binding site [chemical binding]; other site 102608002779 Switch I region; other site 102608002780 G2 box; other site 102608002781 G3 box; other site 102608002782 Switch II region; other site 102608002783 G4 box; other site 102608002784 G5 box; other site 102608002785 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 102608002786 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 102608002787 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 102608002788 1-deoxy-D-xylulose-5-phosphate synthase; Region: dxs; TIGR00204 102608002789 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 102608002790 TPP-binding site; other site 102608002791 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 102608002792 PYR/PP interface [polypeptide binding]; other site 102608002793 dimer interface [polypeptide binding]; other site 102608002794 TPP binding site [chemical binding]; other site 102608002795 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 102608002796 flagellar assembly protein H; Validated; Region: fliH; PRK06669 102608002797 Flagellar assembly protein FliH; Region: FliH; pfam02108 102608002798 flagellar motor switch protein FliG; Region: fliG; TIGR00207 102608002799 FliG C-terminal domain; Region: FliG_C; pfam01706 102608002800 flagellar basal-body M-ring protein/flagellar hook-basal body protein (fliF); Region: fliF; TIGR00206 102608002801 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 102608002802 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 102608002803 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 102608002804 active site 102608002805 CTP synthetase; Validated; Region: pyrG; PRK05380 102608002806 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 102608002807 Catalytic site [active] 102608002808 active site 102608002809 UTP binding site [chemical binding]; other site 102608002810 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 102608002811 active site 102608002812 putative oxyanion hole; other site 102608002813 catalytic triad [active] 102608002814 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 102608002815 DHH family; Region: DHH; pfam01368 102608002816 DHHA1 domain; Region: DHHA1; pfam02272 102608002817 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 102608002818 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 102608002819 active site 102608002820 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 102608002821 chlorohydrolase; Provisional; Region: PRK07213 102608002822 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 102608002823 Tetratricopeptide repeat; Region: TPR_2; pfam07719 102608002824 Sel1-like repeats; Region: SEL1; smart00671 102608002825 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 102608002826 DNA protecting protein DprA; Region: dprA; TIGR00732 102608002827 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 102608002828 cell division topological specificity factor MinE; Region: minE; TIGR01215 102608002829 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 102608002830 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 102608002831 Switch I; other site 102608002832 Switch II; other site 102608002833 ketol-acid reductoisomerase; Provisional; Region: PRK05479 102608002834 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 102608002835 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 102608002836 NAD synthetase; Provisional; Region: PRK13980 102608002837 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 102608002838 homodimer interface [polypeptide binding]; other site 102608002839 NAD binding pocket [chemical binding]; other site 102608002840 ATP binding pocket [chemical binding]; other site 102608002841 Mg binding site [ion binding]; other site 102608002842 active-site loop [active] 102608002843 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 102608002844 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 102608002845 pseudaminic acid biosynthesis N-acetyl transferase; Region: PseH; TIGR03585 102608002846 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 102608002847 Spore coat polysaccharide biosynthesis protein, predicted glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: spsG; COG3980 102608002848 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 102608002849 ligand binding site; other site 102608002850 tetramer interface; other site 102608002851 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 102608002852 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK00249 102608002853 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608002854 nuclease NucT; Provisional; Region: PRK13912 102608002855 Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar proteins; Region: PLDc_Nuc_like; cd09116 102608002856 putative active site [active] 102608002857 catalytic site [active] 102608002858 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 102608002859 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 102608002860 catalytic site [active] 102608002861 G-X2-G-X-G-K; other site 102608002862 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 102608002863 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 102608002864 arginyl-tRNA synthetase; Region: argS; TIGR00456 102608002865 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 102608002866 active site 102608002867 HIGH motif; other site 102608002868 KMSK motif region; other site 102608002869 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 102608002870 tRNA binding surface [nucleotide binding]; other site 102608002871 anticodon binding site; other site 102608002872 heme oxygenase, HugZ family; Region: heme_ox_HugZ; TIGR04109 102608002873 Protein of unknown function (DUF2470); Region: DUF2470; pfam10615 102608002874 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 102608002875 TrbC/VIRB2 family; Region: TrbC; pfam04956 102608002876 potential frameshift: common BLAST hit: gi|210135518|ref|YP_002301957.1| VirB4 type IV secretion ATPase 102608002877 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 102608002878 AAA-like domain; Region: AAA_10; pfam12846 102608002879 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 102608002880 Walker A motif; other site 102608002881 ATP binding site [chemical binding]; other site 102608002882 Walker B motif; other site 102608002883 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 102608002884 DEAD-like helicases superfamily; Region: DEXDc; smart00487 102608002885 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 102608002886 ATP binding site [chemical binding]; other site 102608002887 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 102608002888 helicase superfamily c-terminal domain; Region: HELICc; smart00490 102608002889 nucleotide binding region [chemical binding]; other site 102608002890 ATP-binding site [chemical binding]; other site 102608002891 Topoisomerase IA [DNA replication, recombination, and repair]; Region: TopA; COG0550 102608002892 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 102608002893 active site 102608002894 metal binding site [ion binding]; metal-binding site 102608002895 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 102608002896 domain I; other site 102608002897 DNA binding groove [nucleotide binding] 102608002898 phosphate binding site [ion binding]; other site 102608002899 domain II; other site 102608002900 domain III; other site 102608002901 nucleotide binding site [chemical binding]; other site 102608002902 catalytic site [active] 102608002903 domain IV; other site 102608002904 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 102608002905 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 102608002906 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 102608002907 P-loop; other site 102608002908 Magnesium ion binding site [ion binding]; other site 102608002909 preprotein translocase subunit SecA; Reviewed; Region: secA; PRK12903 102608002910 Toprim-like; Region: Toprim_2; pfam13155 102608002911 Type IV secretory pathway, TrbL components [Intracellular trafficking and secretion]; Region: TrbL; COG3846 102608002912 HipA-like C-terminal domain; Region: HipA_C; pfam07804 102608002913 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 102608002914 ferrochelatase; Region: hemH; TIGR00109 102608002915 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 102608002916 C-terminal domain interface [polypeptide binding]; other site 102608002917 active site 102608002918 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 102608002919 active site 102608002920 N-terminal domain interface [polypeptide binding]; other site 102608002921 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 102608002922 RNA methyltransferase, RsmE family; Region: TIGR00046 102608002923 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608002924 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 102608002925 trimer interface [polypeptide binding]; other site 102608002926 active site 102608002927 acetyl-CoA carboxylase, biotin carboxyl carrier protein; Region: BCCP; TIGR00531 102608002928 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 102608002929 carboxyltransferase (CT) interaction site; other site 102608002930 biotinylation site [posttranslational modification]; other site 102608002931 biotin carboxylase; Validated; Region: PRK08462 102608002932 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 102608002933 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 102608002934 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 102608002935 Methyltransferase domain; Region: Methyltransf_26; pfam13659 102608002936 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 102608002937 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 102608002938 inhibitor-cofactor binding pocket; inhibition site 102608002939 pyridoxal 5'-phosphate binding site [chemical binding]; other site 102608002940 catalytic residue [active] 102608002941 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 102608002942 dimer interface [polypeptide binding]; other site 102608002943 putative radical transfer pathway; other site 102608002944 diiron center [ion binding]; other site 102608002945 tyrosyl radical; other site 102608002946 protein-L-isoaspartate(D-aspartate) O-methyltransferase; Region: pimt; TIGR00080 102608002947 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 102608002948 S-adenosylmethionine binding site [chemical binding]; other site 102608002949 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 102608002950 Predicted permeases [General function prediction only]; Region: COG0795 102608002951 tRNA pseudouridine(38-40) synthase; Region: hisT_truA; TIGR00071 102608002952 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 102608002953 dimerization interface 3.5A [polypeptide binding]; other site 102608002954 active site 102608002955 UDP-glucose-4-epimerase GalE; Region: galE; TIGR01179 102608002956 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 102608002957 NAD binding site [chemical binding]; other site 102608002958 homodimer interface [polypeptide binding]; other site 102608002959 active site 102608002960 substrate binding site [chemical binding]; other site 102608002961 classical (c) SDR, subgroup 5; Region: SDR_c5; cd05346 102608002962 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 102608002963 putative NAD(P) binding site [chemical binding]; other site 102608002964 homodimer interface [polypeptide binding]; other site 102608002965 homotetramer interface [polypeptide binding]; other site 102608002966 active site 102608002967 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 102608002968 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 102608002969 binding surface 102608002970 TPR motif; other site 102608002971 Sel1-like repeats; Region: SEL1; smart00671 102608002972 Sel1-like repeats; Region: SEL1; smart00671 102608002973 Sel1-like repeats; Region: SEL1; smart00671 102608002974 Entner-Doudoroff aldolase; Region: eda; TIGR01182 102608002975 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 102608002976 active site 102608002977 intersubunit interface [polypeptide binding]; other site 102608002978 catalytic residue [active] 102608002979 phosphogluconate dehydratase; Validated; Region: PRK09054 102608002980 6-phosphogluconate dehydratase; Region: edd; TIGR01196 102608002981 Glucose-6-phosphate 1-dehydrogenase [Carbohydrate transport and metabolism]; Region: Zwf; COG0364 102608002982 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 102608002983 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 102608002984 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 102608002985 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 102608002986 putative active site [active] 102608002987 glucokinase; Provisional; Region: glk; PRK00292 102608002988 glucokinase, proteobacterial type; Region: glk; TIGR00749 102608002989 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 102608002990 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 102608002991 putative NAD(P) binding site [chemical binding]; other site 102608002992 putative substrate binding site [chemical binding]; other site 102608002993 catalytic Zn binding site [ion binding]; other site 102608002994 structural Zn binding site [ion binding]; other site 102608002995 dimer interface [polypeptide binding]; other site 102608002996 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 102608002997 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 102608002998 active site 102608002999 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 102608003000 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 102608003001 active site 102608003002 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608003003 pyruvate flavodoxin oxidoreductase subunit gamma; Validated; Region: PRK05844 102608003004 pyruvate/ketoisovalerate ferredoxin oxidoreductase subunit gamma; Provisional; Region: PRK14029 102608003005 pyruvate flavodoxin oxidoreductase subunit delta; Reviewed; Region: porD; PRK09625 102608003006 4Fe-4S binding domain; Region: Fer4; pfam00037 102608003007 pyruvate flavodoxin oxidoreductase subunit alpha; Reviewed; Region: porA; PRK09622 102608003008 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 102608003009 dimer interface [polypeptide binding]; other site 102608003010 PYR/PP interface [polypeptide binding]; other site 102608003011 TPP binding site [chemical binding]; other site 102608003012 substrate binding site [chemical binding]; other site 102608003013 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 102608003014 pyruvate ferredoxin oxidoreductase subunit beta; Provisional; Region: PRK11865 102608003015 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 102608003016 TPP-binding site [chemical binding]; other site 102608003017 putative dimer interface [polypeptide binding]; other site 102608003018 adenylosuccinate lyase; Provisional; Region: PRK08470 102608003019 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 102608003020 tetramer interface [polypeptide binding]; other site 102608003021 active site 102608003022 Adenylosuccinate lyase C-terminus; Region: ADSL_C; smart00998 102608003023 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608003024 excinuclease ABC subunit B; Provisional; Region: PRK05298 102608003025 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 102608003026 ATP binding site [chemical binding]; other site 102608003027 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 102608003028 putative Mg++ binding site [ion binding]; other site 102608003029 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 102608003030 nucleotide binding region [chemical binding]; other site 102608003031 ATP-binding site [chemical binding]; other site 102608003032 Ultra-violet resistance protein B; Region: UvrB; pfam12344 102608003033 UvrB/uvrC motif; Region: UVR; pfam02151 102608003034 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 102608003035 binding surface 102608003036 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 102608003037 TPR motif; other site 102608003038 Sel1-like repeats; Region: SEL1; smart00671 102608003039 Sel1-like repeats; Region: SEL1; smart00671 102608003040 Sel1-like repeats; Region: SEL1; smart00671 102608003041 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 102608003042 gamma-glutamyltranspeptidase; Region: g_glut_trans; TIGR00066 102608003043 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK08471 102608003044 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 102608003045 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 102608003046 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 102608003047 cofactor binding site; other site 102608003048 DNA binding site [nucleotide binding] 102608003049 substrate interaction site [chemical binding]; other site 102608003050 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 102608003051 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 102608003052 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 102608003053 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 102608003054 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 102608003055 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 102608003056 ligand binding site [chemical binding]; other site 102608003057 translocation protein TolB; Provisional; Region: tolB; PRK04043 102608003058 TolB amino-terminal domain; Region: TolB_N; pfam04052 102608003059 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 102608003060 TonB C terminal; Region: TonB_2; pfam13103 102608003061 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 102608003062 TolR protein; Region: tolR; TIGR02801 102608003063 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 102608003064 ATP synthase, F1 epsilon subunit (delta in mitochondria); Region: ATP_synt_epsi; TIGR01216 102608003065 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 102608003066 gamma subunit interface [polypeptide binding]; other site 102608003067 epsilon subunit interface [polypeptide binding]; other site 102608003068 LBP interface [polypeptide binding]; other site 102608003069 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 102608003070 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 102608003071 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 102608003072 alpha subunit interaction interface [polypeptide binding]; other site 102608003073 Walker A motif; other site 102608003074 ATP binding site [chemical binding]; other site 102608003075 Walker B motif; other site 102608003076 inhibitor binding site; inhibition site 102608003077 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 102608003078 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 102608003079 core domain interface [polypeptide binding]; other site 102608003080 delta subunit interface [polypeptide binding]; other site 102608003081 epsilon subunit interface [polypeptide binding]; other site 102608003082 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 102608003083 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 102608003084 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 102608003085 beta subunit interaction interface [polypeptide binding]; other site 102608003086 Walker A motif; other site 102608003087 ATP binding site [chemical binding]; other site 102608003088 Walker B motif; other site 102608003089 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 102608003090 F0F1 ATP synthase subunit delta; Provisional; Region: PRK13431 102608003091 F0F1 ATP synthase subunit B; Validated; Region: PRK08475 102608003092 F0F1 ATP synthase subunit B'; Validated; Region: PRK08476 102608003093 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 102608003094 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 102608003095 ParB-like nuclease domain; Region: ParB; smart00470 102608003096 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 102608003097 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 102608003098 P-loop; other site 102608003099 Magnesium ion binding site [ion binding]; other site 102608003100 biotin--protein ligase; Provisional; Region: PRK08477 102608003101 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 102608003102 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 102608003103 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 102608003104 putative active site [active] 102608003105 substrate binding site [chemical binding]; other site 102608003106 putative cosubstrate binding site; other site 102608003107 catalytic site [active] 102608003108 Formyl transferase, C-terminal domain; Region: Formyl_trans_C; pfam02911 102608003109 potential frameshift: common BLAST hit: gi|210135301|ref|YP_002301740.1| ATPase 102608003110 AAA domain; Region: AAA_21; pfam13304 102608003111 PHP-associated; Region: PHP_C; pfam13263 102608003112 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 102608003113 AAA domain; Region: AAA_23; pfam13476 102608003114 Walker A/P-loop; other site 102608003115 ATP binding site [chemical binding]; other site 102608003116 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4487 102608003117 Uncharacterized protein conserved in bacteria (DUF2130); Region: DUF2130; pfam09903 102608003118 Uncharacterized conserved protein [Function unknown]; Region: COG1432 102608003119 LabA_like proteins; Region: LabA_like; cd06167 102608003120 putative metal binding site [ion binding]; other site 102608003121 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 102608003122 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 102608003123 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK14593 102608003124 RimM N-terminal domain; Region: RimM; pfam01782 102608003125 PRC-barrel domain; Region: PRC; pfam05239 102608003126 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837 102608003127 KH domain; Region: KH_4; pfam13083 102608003128 G-X-X-G motif; other site 102608003129 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 102608003130 signal recognition particle protein; Provisional; Region: PRK10867 102608003131 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 102608003132 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 102608003133 P loop; other site 102608003134 GTP binding site [chemical binding]; other site 102608003135 Signal peptide binding domain; Region: SRP_SPB; pfam02978 102608003136 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 102608003137 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 102608003138 active site 102608003139 HIGH motif; other site 102608003140 nucleotide binding site [chemical binding]; other site 102608003141 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 102608003142 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 102608003143 active site 102608003144 KMSKS motif; other site 102608003145 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 102608003146 anticodon binding site; other site 102608003147 flagellar assembly protein FliW; Provisional; Region: PRK13283 102608003148 undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase; Region: murG; TIGR01133 102608003149 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 102608003150 active site 102608003151 homodimer interface [polypeptide binding]; other site 102608003152 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608003153 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608003154 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 102608003155 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 102608003156 Protein involved in cell division [Cell division and chromosome partitioning]; Region: Fic; COG2184 102608003157 Fic/DOC family; Region: Fic; cl00960 102608003158 metal-binding heat shock protein; Provisional; Region: PRK00016 102608003159 flavodoxin FldA; Validated; Region: PRK09267 102608003160 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 102608003161 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 102608003162 Uncharacterized protein, possibly involved in nitrogen fixation [Inorganic ion transport and metabolism]; Region: FixS; COG3197 102608003163 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 102608003164 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 102608003165 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 102608003166 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 102608003167 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 102608003168 active site 102608003169 dimer interface [polypeptide binding]; other site 102608003170 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 102608003171 dimer interface [polypeptide binding]; other site 102608003172 active site 102608003173 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 102608003174 carbon starvation protein A; Provisional; Region: PRK15015 102608003175 Carbon starvation protein CstA; Region: CstA; pfam02554 102608003176 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 102608003177 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 102608003178 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 102608003179 dimer interface [polypeptide binding]; other site 102608003180 conserved gate region; other site 102608003181 putative PBP binding loops; other site 102608003182 ABC-ATPase subunit interface; other site 102608003183 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 102608003184 dimer interface [polypeptide binding]; other site 102608003185 conserved gate region; other site 102608003186 putative PBP binding loops; other site 102608003187 ABC-ATPase subunit interface; other site 102608003188 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 102608003189 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 102608003190 Walker A/P-loop; other site 102608003191 ATP binding site [chemical binding]; other site 102608003192 Q-loop/lid; other site 102608003193 ABC transporter signature motif; other site 102608003194 Walker B; other site 102608003195 D-loop; other site 102608003196 H-loop/switch region; other site 102608003197 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 102608003198 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 102608003199 substrate binding pocket [chemical binding]; other site 102608003200 membrane-bound complex binding site; other site 102608003201 hinge residues; other site 102608003202 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 102608003203 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 102608003204 putative substrate translocation pore; other site 102608003205 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 102608003206 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608003207 purine-nucleoside phosphorylase, family 1 (deoD); Region: deoD; TIGR00107 102608003208 phosphopentomutase; Provisional; Region: PRK05362 102608003209 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 102608003210 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 102608003211 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 102608003212 Nucleoside recognition; Region: Gate; pfam07670 102608003213 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 102608003214 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 102608003215 Major Facilitator Superfamily; Region: MFS_1; pfam07690 102608003216 putative substrate translocation pore; other site 102608003217 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 102608003218 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 102608003219 Ligand Binding Site [chemical binding]; other site 102608003220 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 102608003221 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 102608003222 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 102608003223 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 102608003224 putative arabinose transporter; Provisional; Region: PRK03545 102608003225 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 102608003226 putative substrate translocation pore; other site 102608003227 Carbonic anhydrase [Inorganic ion transport and metabolism]; Region: Cah; COG3338 102608003228 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 102608003229 active site 102608003230 zinc binding site [ion binding]; other site 102608003231 Helicobacter pylori protein of unknown function (DUF874); Region: DUF874; pfam05917 102608003232 aspartate-semialdehyde dehydrogenase (peptidoglycan organisms); Region: asd_B; TIGR01296 102608003233 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 102608003234 Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: HisS; COG0124 102608003235 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 102608003236 dimer interface [polypeptide binding]; other site 102608003237 motif 1; other site 102608003238 active site 102608003239 motif 2; other site 102608003240 motif 3; other site 102608003241 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 102608003242 anticodon binding site; other site 102608003243 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 102608003244 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 102608003245 putative active site [active] 102608003246 elongation factor G; Reviewed; Region: PRK00007 102608003247 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 102608003248 G1 box; other site 102608003249 putative GEF interaction site [polypeptide binding]; other site 102608003250 GTP/Mg2+ binding site [chemical binding]; other site 102608003251 Switch I region; other site 102608003252 G2 box; other site 102608003253 G3 box; other site 102608003254 Switch II region; other site 102608003255 G4 box; other site 102608003256 G5 box; other site 102608003257 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 102608003258 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 102608003259 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 102608003260 30S ribosomal protein S7; Validated; Region: PRK05302 102608003261 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 102608003262 S17 interaction site [polypeptide binding]; other site 102608003263 S8 interaction site; other site 102608003264 16S rRNA interaction site [nucleotide binding]; other site 102608003265 streptomycin interaction site [chemical binding]; other site 102608003266 23S rRNA interaction site [nucleotide binding]; other site 102608003267 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 102608003268 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 102608003269 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 102608003270 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 102608003271 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 102608003272 RPB11 interaction site [polypeptide binding]; other site 102608003273 RPB12 interaction site [polypeptide binding]; other site 102608003274 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 102608003275 RPB3 interaction site [polypeptide binding]; other site 102608003276 RPB1 interaction site [polypeptide binding]; other site 102608003277 RPB11 interaction site [polypeptide binding]; other site 102608003278 RPB10 interaction site [polypeptide binding]; other site 102608003279 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 102608003280 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 102608003281 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 102608003282 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 102608003283 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 102608003284 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 102608003285 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 102608003286 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 102608003287 DNA binding site [nucleotide binding] 102608003288 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 102608003289 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 102608003290 core dimer interface [polypeptide binding]; other site 102608003291 peripheral dimer interface [polypeptide binding]; other site 102608003292 L10 interface [polypeptide binding]; other site 102608003293 L11 interface [polypeptide binding]; other site 102608003294 putative EF-Tu interaction site [polypeptide binding]; other site 102608003295 putative EF-G interaction site [polypeptide binding]; other site 102608003296 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 102608003297 23S rRNA interface [nucleotide binding]; other site 102608003298 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 102608003299 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 102608003300 mRNA/rRNA interface [nucleotide binding]; other site 102608003301 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 102608003302 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 102608003303 23S rRNA interface [nucleotide binding]; other site 102608003304 L7/L12 interface [polypeptide binding]; other site 102608003305 putative thiostrepton binding site; other site 102608003306 L25 interface [polypeptide binding]; other site 102608003307 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 102608003308 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 102608003309 putative homodimer interface [polypeptide binding]; other site 102608003310 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 102608003311 heterodimer interface [polypeptide binding]; other site 102608003312 homodimer interface [polypeptide binding]; other site 102608003313 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 102608003314 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 102608003315 elongation factor Tu; Reviewed; Region: PRK00049 102608003316 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 102608003317 G1 box; other site 102608003318 GEF interaction site [polypeptide binding]; other site 102608003319 GTP/Mg2+ binding site [chemical binding]; other site 102608003320 Switch I region; other site 102608003321 G2 box; other site 102608003322 G3 box; other site 102608003323 Switch II region; other site 102608003324 G4 box; other site 102608003325 G5 box; other site 102608003326 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 102608003327 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 102608003328 Antibiotic Binding Site [chemical binding]; other site 102608003329 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 102608003330 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 102608003331 Walker A/P-loop; other site 102608003332 ATP binding site [chemical binding]; other site 102608003333 Q-loop/lid; other site 102608003334 ABC transporter signature motif; other site 102608003335 Walker B; other site 102608003336 D-loop; other site 102608003337 H-loop/switch region; other site 102608003338 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 102608003339 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 102608003340 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG3392 102608003341 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; pfam02086 102608003342 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 102608003343 active site 102608003344 serine O-acetyltransferase; Region: cysE; TIGR01172 102608003345 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 102608003346 trimer interface [polypeptide binding]; other site 102608003347 active site 102608003348 substrate binding site [chemical binding]; other site 102608003349 CoA binding site [chemical binding]; other site 102608003350 F0F1 ATP synthase subunit C; Validated; Region: PRK08482 102608003351 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 102608003352 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 102608003353 oligomer interface [polypeptide binding]; other site 102608003354 RNA binding site [nucleotide binding]; other site 102608003355 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 102608003356 oligomer interface [polypeptide binding]; other site 102608003357 RNA binding site [nucleotide binding]; other site 102608003358 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 102608003359 putative nucleic acid binding region [nucleotide binding]; other site 102608003360 G-X-X-G motif; other site 102608003361 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 102608003362 RNA binding site [nucleotide binding]; other site 102608003363 Predicted phosphoribosyltransferases [General function prediction only]; Region: COG1926 102608003364 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 102608003365 Organic solvent tolerance protein; Region: OstA_C; pfam04453 102608003366 Predicted membrane protein/domain [Function unknown]; Region: COG1714 102608003367 phosphoribosylamine--glycine ligase; Region: purD; TIGR00877 102608003368 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 102608003369 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 102608003370 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 102608003371 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 102608003372 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 102608003373 Walker A/P-loop; other site 102608003374 ATP binding site [chemical binding]; other site 102608003375 Q-loop/lid; other site 102608003376 ABC transporter signature motif; other site 102608003377 Walker B; other site 102608003378 D-loop; other site 102608003379 H-loop/switch region; other site 102608003380 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 102608003381 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 102608003382 catalytic residue [active] 102608003383 putative FPP diphosphate binding site; other site 102608003384 putative FPP binding hydrophobic cleft; other site 102608003385 dimer interface [polypeptide binding]; other site 102608003386 putative IPP diphosphate binding site; other site 102608003387 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 102608003388 FAD binding domain; Region: FAD_binding_4; pfam01565 102608003389 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 102608003390 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 102608003391 active site residue [active] 102608003392 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 102608003393 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 102608003394 active site 102608003395 camphor resistance protein CrcB; Provisional; Region: PRK14204 102608003396 coproporphyrinogen III oxidase; Provisional; Region: PRK08446 102608003397 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 102608003398 FeS/SAM binding site; other site 102608003399 HemN C-terminal domain; Region: HemN_C; pfam06969 102608003400 Cytochrome c553 [Energy production and conversion]; Region: COG2863 102608003401 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 102608003402 putative active site [active] 102608003403 Ap4A binding site [chemical binding]; other site 102608003404 nudix motif; other site 102608003405 putative metal binding site [ion binding]; other site 102608003406 aspartate kinase; Reviewed; Region: PRK06635 102608003407 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 102608003408 putative nucleotide binding site [chemical binding]; other site 102608003409 putative catalytic residues [active] 102608003410 putative Mg ion binding site [ion binding]; other site 102608003411 putative aspartate binding site [chemical binding]; other site 102608003412 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 102608003413 putative allosteric regulatory site; other site 102608003414 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 102608003415 putative allosteric regulatory residue; other site 102608003416 DNA replication regulator; Region: HobA; pfam12163 102608003417 DNA polymerase III subunit delta'; Validated; Region: PRK08485 102608003418 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 102608003419 dihydropteroate synthase; Region: DHPS; TIGR01496 102608003420 substrate binding pocket [chemical binding]; other site 102608003421 dimer interface [polypeptide binding]; other site 102608003422 inhibitor binding site; inhibition site 102608003423 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 102608003424 EamA-like transporter family; Region: EamA; pfam00892 102608003425 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2952 102608003426 Carbamoylphosphate synthase small subunit [Amino acid transport and metabolism / Nucleotide transport and metabolism]; Region: CarA; COG0505 102608003427 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; pfam00988 102608003428 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 102608003429 catalytic site [active] 102608003430 subunit interface [polypeptide binding]; other site 102608003431 formamidase; Provisional; Region: amiF; PRK13287 102608003432 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 102608003433 multimer interface [polypeptide binding]; other site 102608003434 active site 102608003435 catalytic triad [active] 102608003436 dimer interface [polypeptide binding]; other site 102608003437 Maf-like protein; Region: Maf; pfam02545 102608003438 Maf-like protein; Reviewed; Region: PRK04056 102608003439 putative active site [active] 102608003440 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 102608003441 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 102608003442 motif 1; other site 102608003443 active site 102608003444 motif 2; other site 102608003445 motif 3; other site 102608003446 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 102608003447 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2841 102608003448 potential frameshift: common BLAST hit: gi|188528033|ref|YP_001910720.1| outer membrane protein 102608003449 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608003450 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 102608003451 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 102608003452 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 102608003453 dimer interface [polypeptide binding]; other site 102608003454 ssDNA binding site [nucleotide binding]; other site 102608003455 tetramer (dimer of dimers) interface [polypeptide binding]; other site 102608003456 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 102608003457 DNA polymerase III subunit delta; Validated; Region: PRK08487 102608003458 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 102608003459 Exoribonuclease R [Transcription]; Region: VacB; COG0557 102608003460 RNB domain; Region: RNB; pfam00773 102608003461 shikimate 5-dehydrogenase; Region: aroE; TIGR00507 102608003462 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 102608003463 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 102608003464 shikimate binding site; other site 102608003465 NAD(P) binding site [chemical binding]; other site 102608003466 Bacterial SH3 domain; Region: SH3_3; pfam08239 102608003467 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 102608003468 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 102608003469 dimer interface [polypeptide binding]; other site 102608003470 conserved gate region; other site 102608003471 putative PBP binding loops; other site 102608003472 ABC-ATPase subunit interface; other site 102608003473 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 102608003474 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 102608003475 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 102608003476 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 102608003477 active site 102608003478 HIGH motif; other site 102608003479 dimer interface [polypeptide binding]; other site 102608003480 KMSKS motif; other site 102608003481 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 102608003482 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 102608003483 S-adenosylmethionine binding site [chemical binding]; other site 102608003484 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 102608003485 ribosome recycling factor; Reviewed; Region: frr; PRK00083 102608003486 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 102608003487 hinge region; other site 102608003488 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 102608003489 active site 102608003490 RDD family; Region: RDD; pfam06271 102608003491 NAD-dependent deacetylase; Provisional; Region: PRK00481 102608003492 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 102608003493 NAD+ binding site [chemical binding]; other site 102608003494 substrate binding site [chemical binding]; other site 102608003495 Zn binding site [ion binding]; other site 102608003496 NADH dehydrogenase subunit A; Validated; Region: PRK08489 102608003497 NADH dehydrogenase subunit B; Validated; Region: PRK06411 102608003498 NADH dehydrogenase subunit C; Provisional; Region: PRK08491 102608003499 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 102608003500 NADH dehydrogenase subunit D; Validated; Region: PRK06075 102608003501 NADH dehydrogenase I, D subunit; Region: NuoD; TIGR01962 102608003502 NADH dehydrogenase subunit G; Validated; Region: PRK08493 102608003503 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 102608003504 catalytic loop [active] 102608003505 iron binding site [ion binding]; other site 102608003506 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 102608003507 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 102608003508 molybdopterin cofactor binding site; other site 102608003509 Domain of unknown function (DUF4350); Region: DUF4350; pfam14258 102608003510 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 102608003511 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 102608003512 NADH-quinone oxidoreductase, chain I; Region: NuoI; TIGR01971 102608003513 4Fe-4S binding domain; Region: Fer4; cl02805 102608003514 4Fe-4S binding domain; Region: Fer4; pfam00037 102608003515 NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion]; Region: NuoJ; COG0839 102608003516 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 102608003517 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 102608003518 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 102608003519 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 102608003520 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 102608003521 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 102608003522 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 102608003523 proton-translocating NADH-quinone oxidoreductase, chain N; Region: NDH_I_N; TIGR01770 102608003524 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 102608003525 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 102608003526 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 102608003527 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 102608003528 active site 102608003529 substrate binding site [chemical binding]; other site 102608003530 metal binding site [ion binding]; metal-binding site 102608003531 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 102608003532 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 102608003533 substrate binding site [chemical binding]; other site 102608003534 active site 102608003535 catalytic residues [active] 102608003536 heterodimer interface [polypeptide binding]; other site 102608003537 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 102608003538 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 102608003539 pyridoxal 5'-phosphate binding site [chemical binding]; other site 102608003540 catalytic residue [active] 102608003541 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional; Region: PRK09427 102608003542 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 102608003543 active site 102608003544 ribulose/triose binding site [chemical binding]; other site 102608003545 phosphate binding site [ion binding]; other site 102608003546 substrate (anthranilate) binding pocket [chemical binding]; other site 102608003547 product (indole) binding pocket [chemical binding]; other site 102608003548 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 102608003549 active site 102608003550 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 102608003551 anthranilate phosphoribosyltransferase; Region: trpD; TIGR01245 102608003552 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 102608003553 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 102608003554 Glutamine amidotransferase class-I; Region: GATase; pfam00117 102608003555 glutamine binding [chemical binding]; other site 102608003556 catalytic triad [active] 102608003557 anthranilate synthase component I, proteobacterial subset; Region: trpE_proteo; TIGR00565 102608003558 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 102608003559 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 102608003560 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 102608003561 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 102608003562 putative active site [active] 102608003563 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 102608003564 active site 102608003565 motif I; other site 102608003566 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 102608003567 motif II; other site 102608003568 Uncharacterized conserved protein [Function unknown]; Region: COG2353 102608003569 TENA/THI-4/PQQC family; Region: TENA_THI-4; cl15243 102608003570 Nicotinamide mononucleotide transporter [Coenzyme metabolism]; Region: PnuC; COG3201 102608003571 Thiamine pyrophosphokinase [Coenzyme metabolism]; Region: THI80; COG1564 102608003572 Thiamine pyrophosphokinase; Region: TPK; cd07995 102608003573 active site 102608003574 dimerization interface [polypeptide binding]; other site 102608003575 thiamine binding site [chemical binding]; other site 102608003576 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 102608003577 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 102608003578 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 102608003579 alphaNTD homodimer interface [polypeptide binding]; other site 102608003580 alphaNTD - beta interaction site [polypeptide binding]; other site 102608003581 alphaNTD - beta' interaction site [polypeptide binding]; other site 102608003582 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 102608003583 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 102608003584 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 102608003585 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 102608003586 RNA binding surface [nucleotide binding]; other site 102608003587 30S ribosomal protein S11; Validated; Region: PRK05309 102608003588 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 102608003589 30S ribosomal protein S13; Region: bact_S13; TIGR03631 102608003590 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 102608003591 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 102608003592 rRNA binding site [nucleotide binding]; other site 102608003593 predicted 30S ribosome binding site; other site 102608003594 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 102608003595 active site 102608003596 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 102608003597 SecY translocase; Region: SecY; pfam00344 102608003598 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 102608003599 ribosomal protein S5, bacterial/organelle type; Region: rpsE_bact; TIGR01021 102608003600 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 102608003601 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 102608003602 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 102608003603 23S rRNA interface [nucleotide binding]; other site 102608003604 5S rRNA interface [nucleotide binding]; other site 102608003605 L27 interface [polypeptide binding]; other site 102608003606 L5 interface [polypeptide binding]; other site 102608003607 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 102608003608 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 102608003609 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 102608003610 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08061 102608003611 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 102608003612 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 102608003613 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 102608003614 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 102608003615 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 102608003616 RNA binding site [nucleotide binding]; other site 102608003617 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 102608003618 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 102608003619 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 102608003620 putative translocon interaction site; other site 102608003621 23S rRNA interface [nucleotide binding]; other site 102608003622 signal recognition particle (SRP54) interaction site; other site 102608003623 L23 interface [polypeptide binding]; other site 102608003624 trigger factor interaction site; other site 102608003625 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 102608003626 23S rRNA interface [nucleotide binding]; other site 102608003627 5S rRNA interface [nucleotide binding]; other site 102608003628 putative antibiotic binding site [chemical binding]; other site 102608003629 L25 interface [polypeptide binding]; other site 102608003630 L27 interface [polypeptide binding]; other site 102608003631 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 102608003632 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 102608003633 G-X-X-G motif; other site 102608003634 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 102608003635 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 102608003636 putative translocon binding site; other site 102608003637 protein-rRNA interface [nucleotide binding]; other site 102608003638 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 102608003639 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 102608003640 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 102608003641 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 102608003642 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 102608003643 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 102608003644 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 102608003645 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 102608003646 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 102608003647 AAA domain; Region: AAA_14; pfam13173 102608003648 Helix-turn-helix domain; Region: HTH_36; pfam13730 102608003649 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 102608003650 RNA/DNA hybrid binding site [nucleotide binding]; other site 102608003651 active site 102608003652 fumarate hydratase; Reviewed; Region: fumC; PRK00485 102608003653 Class II fumarases; Region: Fumarase_classII; cd01362 102608003654 active site 102608003655 tetramer interface [polypeptide binding]; other site 102608003656 YtkA-like; Region: YtkA; pfam13115 102608003657 Outer membrane efflux protein; Region: OEP; pfam02321 102608003658 HlyD family secretion protein; Region: HlyD_2; pfam12700 102608003659 HlyD family secretion protein; Region: HlyD_3; pfam13437 102608003660 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 102608003661 Predicted branched-chain amino acid permeases (azaleucine resistance) [Amino acid transport and metabolism]; Region: AzlD; COG1687 102608003662 AzlC protein; Region: AzlC; cl00570 102608003663 chaperone protein DnaJ; Provisional; Region: PRK14288 102608003664 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 102608003665 HSP70 interaction site [polypeptide binding]; other site 102608003666 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 102608003667 substrate binding site [polypeptide binding]; other site 102608003668 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 102608003669 Zn binding sites [ion binding]; other site 102608003670 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 102608003671 substrate binding site [polypeptide binding]; other site 102608003672 dimer interface [polypeptide binding]; other site 102608003673 Uncharacterized conserved protein [Function unknown]; Region: COG1432 102608003674 LabA_like proteins; Region: LabA_like; cd06167 102608003675 putative metal binding site [ion binding]; other site 102608003676 tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase; Region: trmU; TIGR00420 102608003677 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 102608003678 Ligand Binding Site [chemical binding]; other site 102608003679 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 102608003680 HSP70 interaction site [polypeptide binding]; other site 102608003681 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 102608003682 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 102608003683 active site 102608003684 (T/H)XGH motif; other site 102608003685 nickel responsive regulator; Provisional; Region: PRK00630 102608003686 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 102608003687 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 102608003688 tonB-system energizer ExbB, group 2; Region: exbB2; TIGR02805 102608003689 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 102608003690 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 102608003691 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 102608003692 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 102608003693 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 102608003694 DNA methylase; Region: N6_N4_Mtase; pfam01555 102608003695 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957 102608003696 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 102608003697 Acylphosphatase; Region: Acylphosphatase; pfam00708 102608003698 [NiFe] hydrogenase maturation protein HypF; Region: hypF; TIGR00143 102608003699 HypF finger; Region: zf-HYPF; pfam07503 102608003700 HypF finger; Region: zf-HYPF; pfam07503 102608003701 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 102608003702 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 102608003703 dimerization interface [polypeptide binding]; other site 102608003704 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 102608003705 ATP binding site [chemical binding]; other site 102608003706 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 102608003707 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 102608003708 NADP binding site [chemical binding]; other site 102608003709 active site 102608003710 putative substrate binding site [chemical binding]; other site 102608003711 GDP-mannose 4,6-dehydratase; Region: gmd; TIGR01472 102608003712 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 102608003713 NADP-binding site; other site 102608003714 homotetramer interface [polypeptide binding]; other site 102608003715 substrate binding site [chemical binding]; other site 102608003716 homodimer interface [polypeptide binding]; other site 102608003717 active site 102608003718 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 102608003719 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 102608003720 Substrate binding site; other site 102608003721 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 102608003722 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 102608003723 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 102608003724 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 102608003725 VirB7 interaction site; other site 102608003726 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 102608003727 Type IV secretory pathway, TrbL components [Intracellular trafficking and secretion]; Region: TrbL; COG3846 102608003728 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 102608003729 PDZ domain; Region: PDZ_2; pfam13180 102608003730 protein binding site [polypeptide binding]; other site 102608003731 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 102608003732 hypothetical protein; Provisional; Region: PRK03762 102608003733 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 102608003734 tetramerization interface [polypeptide binding]; other site 102608003735 active site 102608003736 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 102608003737 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 102608003738 Walker A motif; other site 102608003739 ATP binding site [chemical binding]; other site 102608003740 Walker B motif; other site 102608003741 arginine finger; other site 102608003742 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 102608003743 Walker A motif; other site 102608003744 ATP binding site [chemical binding]; other site 102608003745 Walker B motif; other site 102608003746 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 102608003747 Uncharacterized conserved protein [Function unknown]; Region: COG2127 102608003748 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 102608003749 Ligand Binding Site [chemical binding]; other site 102608003750 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 102608003751 AAA domain; Region: AAA_26; pfam13500 102608003752 Protein of unknown function (DUF1523); Region: DUF1523; pfam07509 102608003753 isocitrate dehydrogenase; Validated; Region: PRK07362 102608003754 isocitrate dehydrogenase; Reviewed; Region: PRK07006 102608003755 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 102608003756 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 102608003757 dimer interface [polypeptide binding]; other site 102608003758 active site 102608003759 citrylCoA binding site [chemical binding]; other site 102608003760 NADH binding [chemical binding]; other site 102608003761 cationic pore residues; other site 102608003762 oxalacetate/citrate binding site [chemical binding]; other site 102608003763 coenzyme A binding site [chemical binding]; other site 102608003764 catalytic triad [active] 102608003765 DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases. They exists as monomers and homodimers; Region: NUC; cl00089 102608003766 Type III restriction/modification enzyme methylation subunit; Region: TypeIII_RM_meth; pfam12564 102608003767 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 102608003768 DNA methylase; Region: N6_N4_Mtase; pfam01555 102608003769 DNA methylase; Region: N6_N4_Mtase; pfam01555 102608003770 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3421 102608003771 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 102608003772 ATP binding site [chemical binding]; other site 102608003773 putative Mg++ binding site [ion binding]; other site 102608003774 biotin synthase; Provisional; Region: PRK08508 102608003775 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 102608003776 FeS/SAM binding site; other site 102608003777 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 102608003778 YihY family inner membrane protein; Region: yihY_not_rbn; TIGR00765 102608003779 Uncharacterized conserved protein [Function unknown]; Region: COG1479 102608003780 Protein of unknown function DUF262; Region: DUF262; pfam03235 102608003781 Protein of unknown function DUF262; Region: DUF262; pfam03235 102608003782 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 102608003783 7-cyano-7-deazaguanine reductase; Region: QueF-II; TIGR03139 102608003784 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 102608003785 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 102608003786 tRNA dimethylallyltransferase; Region: miaA; TIGR00174 102608003787 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 102608003788 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 102608003789 active site 102608003790 Sulfatase; Region: Sulfatase; cl17466 102608003791 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 102608003792 Sulfatase; Region: Sulfatase; pfam00884 102608003793 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13904 102608003794 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 102608003795 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 102608003796 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08472 102608003797 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 102608003798 Walker A motif/ATP binding site; other site 102608003799 Walker B motif; other site 102608003800 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 102608003801 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 102608003802 ATP binding site [chemical binding]; other site 102608003803 Walker A motif; other site 102608003804 hexamer interface [polypeptide binding]; other site 102608003805 Walker B motif; other site 102608003806 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 102608003807 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 102608003808 active site 102608003809 HIGH motif; other site 102608003810 nucleotide binding site [chemical binding]; other site 102608003811 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 102608003812 active site 102608003813 KMSKS motif; other site 102608003814 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 102608003815 tRNA binding surface [nucleotide binding]; other site 102608003816 anticodon binding site; other site 102608003817 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 102608003818 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 102608003819 RNA binding surface [nucleotide binding]; other site 102608003820 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14462 102608003821 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 102608003822 FeS/SAM binding site; other site 102608003823 KpsF/GutQ family protein; Region: kpsF; TIGR00393 102608003824 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 102608003825 putative active site [active] 102608003826 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 102608003827 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 102608003828 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 102608003829 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 102608003830 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 102608003831 dimethyladenosine transferase; Region: ksgA; TIGR00755 102608003832 formyltetrahydrofolate deformylase; Region: PurU; TIGR00655 102608003833 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 102608003834 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 102608003835 putative active site [active] 102608003836 putative substrate binding site [chemical binding]; other site 102608003837 putative cosubstrate binding site; other site 102608003838 catalytic site [active] 102608003839 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 102608003840 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 102608003841 tandem repeat interface [polypeptide binding]; other site 102608003842 oligomer interface [polypeptide binding]; other site 102608003843 active site residues [active] 102608003844 enterobactin exporter EntS; Provisional; Region: PRK10489 102608003845 rod shape-determining protein MreC; Provisional; Region: PRK13922 102608003846 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 102608003847 active site 102608003848 carbon storage regulator; Provisional; Region: PRK00568 102608003849 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK04181 102608003850 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 102608003851 SmpB-tmRNA interface; other site 102608003852 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 102608003853 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 102608003854 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 102608003855 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 102608003856 ribonuclease P protein component, eubacterial; Region: rnpA; TIGR00188 102608003857 hypothetical protein; Provisional; Region: PRK14374 102608003858 membrane protein insertase; Provisional; Region: PRK01318 102608003859 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 102608003860 Predicted RNA-binding protein [General function prediction only]; Region: Jag; COG1847 102608003861 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 102608003862 tRNA modification GTPase TrmE; Region: mnmE_trmE_thdF; TIGR00450 102608003863 Circularly permuted YlqF-related GTPases; Region: YlqF_related_GTPase; cl17249 102608003864 GTP/Mg2+ binding site [chemical binding]; other site 102608003865 G4 box; other site 102608003866 G5 box; other site 102608003867 trmE is a tRNA modification GTPase; Region: trmE; cd04164 102608003868 G1 box; other site 102608003869 G1 box; other site 102608003870 GTP/Mg2+ binding site [chemical binding]; other site 102608003871 Switch I region; other site 102608003872 Switch I region; other site 102608003873 G2 box; other site 102608003874 G2 box; other site 102608003875 Switch II region; other site 102608003876 G3 box; other site 102608003877 G3 box; other site 102608003878 Switch II region; other site 102608003879 G4 box; other site 102608003880 G5 box; other site 102608003881 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 102608003882 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608003883 LPP20 lipoprotein; Region: LPP20; pfam02169 102608003884 Collagen-binding surface adhesin SpaP (antigen I/II family) [General function prediction only]; Region: FlgN; COG3417 102608003885 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 102608003886 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 102608003887 catalytic residues [active] 102608003888 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 102608003889 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 102608003890 RNA binding surface [nucleotide binding]; other site 102608003891 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 102608003892 active site 102608003893 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; Region: PHP_PolIIIA_DnaE3; cd12113 102608003894 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 102608003895 active site 102608003896 PHP Thumb interface [polypeptide binding]; other site 102608003897 metal binding site [ion binding]; metal-binding site 102608003898 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 102608003899 generic binding surface I; other site 102608003900 generic binding surface II; other site 102608003901 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 102608003902 Heat shock protein [Posttranslational modification, protein turnover, chaperones]; Region: HslJ; COG3187 102608003903 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 102608003904 mce related protein; Region: MCE; pfam02470 102608003905 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 102608003906 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 102608003907 Walker A/P-loop; other site 102608003908 ATP binding site [chemical binding]; other site 102608003909 Q-loop/lid; other site 102608003910 ABC transporter signature motif; other site 102608003911 Walker B; other site 102608003912 D-loop; other site 102608003913 H-loop/switch region; other site 102608003914 conserved hypothetical integral membrane protein; Region: TIGR00056 102608003915 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 102608003916 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608003917 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 102608003918 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 102608003919 homodimer interface [polypeptide binding]; other site 102608003920 substrate-cofactor binding pocket; other site 102608003921 catalytic residue [active] 102608003922 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608003923 DNA polymerase I; Region: pola; TIGR00593 102608003924 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 102608003925 active site 102608003926 metal binding site 1 [ion binding]; metal-binding site 102608003927 putative 5' ssDNA interaction site; other site 102608003928 metal binding site 3; metal-binding site 102608003929 metal binding site 2 [ion binding]; metal-binding site 102608003930 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 102608003931 putative DNA binding site [nucleotide binding]; other site 102608003932 putative metal binding site [ion binding]; other site 102608003933 3'-5' exonuclease; Region: 35EXOc; smart00474 102608003934 active site 102608003935 substrate binding site [chemical binding]; other site 102608003936 catalytic site [active] 102608003937 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 102608003938 active site 102608003939 DNA binding site [nucleotide binding] 102608003940 catalytic site [active] 102608003941 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 102608003942 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 102608003943 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 102608003944 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 102608003945 thymidylate kinase; Validated; Region: tmk; PRK00698 102608003946 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 102608003947 TMP-binding site; other site 102608003948 ATP-binding site [chemical binding]; other site 102608003949 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 102608003950 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 102608003951 active site 102608003952 (T/H)XGH motif; other site 102608003953 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 102608003954 Flavoprotein; Region: Flavoprotein; pfam02441 102608003955 flagellar basal body P-ring biosynthesis protein FlgA; Reviewed; Region: flgA; PRK08515 102608003956 flagella basal body P-ring formation protein FlgA; Region: flgA_cterm; TIGR03170 102608003957 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 102608003958 Part of AAA domain; Region: AAA_19; pfam13245 102608003959 Family description; Region: UvrD_C_2; pfam13538 102608003960 TPR repeat; Region: TPR_11; pfam13414 102608003961 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 102608003962 TPR motif; other site 102608003963 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 102608003964 binding surface 102608003965 TPR motif; other site 102608003966 seryl-tRNA synthetase; Provisional; Region: PRK05431 102608003967 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 102608003968 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 102608003969 dimer interface [polypeptide binding]; other site 102608003970 active site 102608003971 motif 1; other site 102608003972 motif 2; other site 102608003973 motif 3; other site 102608003974 Predicted amidohydrolase [General function prediction only]; Region: COG0388 102608003975 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 102608003976 active site 102608003977 catalytic triad [active] 102608003978 dimer interface [polypeptide binding]; other site 102608003979 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK14065 102608003980 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 102608003981 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 102608003982 S-adenosylmethionine binding site [chemical binding]; other site 102608003983 TIGR00701 family protein; Region: TIGR00701 102608003984 uncharacterized protein, YigZ family; Region: IMPACT_YIGZ; TIGR00257 102608003985 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 102608003986 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 102608003987 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 102608003988 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 102608003989 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 102608003990 HlyD family secretion protein; Region: HlyD_3; pfam13437 102608003991 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 102608003992 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 102608003993 Domain of unknown function DUF21; Region: DUF21; pfam01595 102608003994 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 102608003995 Transporter associated domain; Region: CorC_HlyC; smart01091 102608003996 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 102608003997 Phosphate transporter family; Region: PHO4; pfam01384 102608003998 NifU-like domain; Region: NifU; pfam01106 102608003999 UDP-N-acetylmuramyl-tripeptide synthetase; Region: murE; TIGR01085 102608004000 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 102608004001 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 102608004002 Transaldolase-like proteins from plants and bacteria; Region: Transaldolase_like; cd00955 102608004003 putative active site [active] 102608004004 transaldolase; Provisional; Region: PRK03903 102608004005 catalytic residue [active] 102608004006 ribosomal protein L25, Ctc-form; Region: ctc_TL5; TIGR00731 102608004007 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 102608004008 5S rRNA interface [nucleotide binding]; other site 102608004009 CTC domain interface [polypeptide binding]; other site 102608004010 L16 interface [polypeptide binding]; other site 102608004011 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 102608004012 putative active site [active] 102608004013 catalytic residue [active] 102608004014 Predicted permeases [General function prediction only]; Region: COG0795 102608004015 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 102608004016 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG3392 102608004017 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 102608004018 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 102608004019 potential frameshift: common BLAST hit: gi|308185271|ref|YP_003929404.1| restriction endonuclease 102608004020 AlwI restriction endonuclease; Region: RE_AlwI; pfam09491 102608004021 AlwI restriction endonuclease; Region: RE_AlwI; pfam09491 102608004022 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608004023 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3399 102608004024 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 102608004025 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 102608004026 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 102608004027 metal-binding site [ion binding] 102608004028 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 102608004029 Soluble P-type ATPase [General function prediction only]; Region: COG4087 102608004030 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 102608004031 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 102608004032 S-adenosylmethionine binding site [chemical binding]; other site 102608004033 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 102608004034 catalytic motif [active] 102608004035 Zn binding site [ion binding]; other site 102608004036 Pyrimidine reductase, riboflavin biosynthesis [Coenzyme metabolism]; Region: RibD; COG1985 102608004037 RibD C-terminal domain; Region: RibD_C; cl17279 102608004038 sodium--glutamate symport carrier (gltS); Region: gltS; TIGR00210 102608004039 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 102608004040 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 102608004041 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 102608004042 4Fe-4S binding domain; Region: Fer4_5; pfam12801 102608004043 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 102608004044 acyl-phosphate glycerol 3-phosphate acyltransferase; Region: TIGR00023 102608004045 FolB domain; Region: folB_dom; TIGR00526 102608004046 active site 102608004047 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 102608004048 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 102608004049 Selenocysteine synthase [seryl-tRNASer selenium transferase] [Amino acid transport and metabolism]; Region: SelA; COG1921 102608004050 L-seryl-tRNA selenium transferase; Region: SelA; pfam03841 102608004051 transcription elongation factor NusA; Provisional; Region: nusA; PRK12328 102608004052 NusA N-terminal domain; Region: NusA_N; pfam08529 102608004053 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 102608004054 RNA binding site [nucleotide binding]; other site 102608004055 homodimer interface [polypeptide binding]; other site 102608004056 NusA-like KH domain; Region: KH_5; pfam13184 102608004057 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 102608004058 G-X-X-G motif; other site 102608004059 Type II restriction enzyme, methylase subunits [Defense mechanisms]; Region: COG1002 102608004060 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 102608004061 TaqI-like C-terminal specificity domain; Region: TaqI_C; pfam12950 102608004062 potential frameshift: common BLAST hit: gi|15612475|ref|NP_224128.1| type III restriction enzyme 102608004063 Restriction endonuclease [Defense mechanisms]; Region: COG3587 102608004064 Restriction endonuclease [Defense mechanisms]; Region: COG3587 102608004065 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 102608004066 ATP binding site [chemical binding]; other site 102608004067 putative Mg++ binding site [ion binding]; other site 102608004068 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 102608004069 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 102608004070 DNA methylase; Region: N6_N4_Mtase; cl17433 102608004071 DNA methylase; Region: N6_N4_Mtase; pfam01555 102608004072 DNA methylase; Region: N6_N4_Mtase; cl17433 102608004073 ATP-dependent DNA helicase RecG; Region: recG; TIGR00643 102608004074 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 102608004075 ssDNA binding site; other site 102608004076 generic binding surface II; other site 102608004077 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 102608004078 ATP binding site [chemical binding]; other site 102608004079 putative Mg++ binding site [ion binding]; other site 102608004080 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 102608004081 nucleotide binding region [chemical binding]; other site 102608004082 ATP-binding site [chemical binding]; other site 102608004083 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608004084 Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Ape1-like_AP-endo; cd09087 102608004085 active site 102608004086 putative catalytic site [active] 102608004087 DNA binding site [nucleotide binding] 102608004088 putative phosphate binding site [ion binding]; other site 102608004089 metal binding site A [ion binding]; metal-binding site 102608004090 AP binding site [nucleotide binding]; other site 102608004091 metal binding site B [ion binding]; metal-binding site 102608004092 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 102608004093 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 102608004094 Walker A motif; other site 102608004095 ATP binding site [chemical binding]; other site 102608004096 Walker B motif; other site 102608004097 arginine finger; other site 102608004098 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 102608004099 DnaA box-binding interface [nucleotide binding]; other site 102608004100 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 102608004101 Protein of unknown function (DUF2443); Region: DUF2443; pfam10398 102608004102 glucosamine--fructose-6-phosphate aminotransferase (isomerizing); Region: glmS; TIGR01135 102608004103 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 102608004104 glutaminase active site [active] 102608004105 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 102608004106 dimer interface [polypeptide binding]; other site 102608004107 active site 102608004108 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 102608004109 dimer interface [polypeptide binding]; other site 102608004110 active site 102608004111 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 102608004112 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 102608004113 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 102608004114 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 102608004115 HsdM N-terminal domain; Region: HsdM_N; pfam12161 102608004116 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 102608004117 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 102608004118 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 102608004119 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 102608004120 ATP binding site [chemical binding]; other site 102608004121 putative Mg++ binding site [ion binding]; other site 102608004122 Protein of unknown function DUF45; Region: DUF45; pfam01863 102608004123 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 102608004124 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 102608004125 N-terminal plug; other site 102608004126 ligand-binding site [chemical binding]; other site 102608004127 Arginase family; Region: Arginase; cd09989 102608004128 active site 102608004129 Mn binding site [ion binding]; other site 102608004130 oligomer interface [polypeptide binding]; other site 102608004131 S-methylmethionine transporter; Provisional; Region: PRK11387 102608004132 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 102608004133 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 102608004134 hexamer interface [polypeptide binding]; other site 102608004135 ligand binding site [chemical binding]; other site 102608004136 putative active site [active] 102608004137 NAD(P) binding site [chemical binding]; other site 102608004138 Uncharacterized conserved protein [Function unknown]; Region: COG1479 102608004139 Protein of unknown function DUF262; Region: DUF262; pfam03235 102608004140 Uncharacterized conserved protein [Function unknown]; Region: COG1479 102608004141 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 102608004142 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 102608004143 NAD kinase [Coenzyme metabolism]; Region: nadF; COG0061 102608004144 ATP-NAD kinase; Region: NAD_kinase; pfam01513 102608004145 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 102608004146 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 102608004147 Walker A/P-loop; other site 102608004148 ATP binding site [chemical binding]; other site 102608004149 Q-loop/lid; other site 102608004150 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 102608004151 ABC transporter signature motif; other site 102608004152 Walker B; other site 102608004153 D-loop; other site 102608004154 H-loop/switch region; other site 102608004155 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]; Region: COG1293 102608004156 Domain of unknown function (DUF814); Region: DUF814; pfam05670 102608004157 DNA polymerase III subunit epsilon; Provisional; Region: PRK08517 102608004158 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 102608004159 active site 102608004160 catalytic site [active] 102608004161 substrate binding site [chemical binding]; other site 102608004162 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 102608004163 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 102608004164 substrate binding site [chemical binding]; other site 102608004165 hexamer interface [polypeptide binding]; other site 102608004166 metal binding site [ion binding]; metal-binding site 102608004167 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 102608004168 active site 102608004169 Methyltransferase domain; Region: Methyltransf_26; pfam13659 102608004170 elongation factor Ts; Provisional; Region: tsf; PRK09377 102608004171 UBA/TS-N domain; Region: UBA; pfam00627 102608004172 Elongation factor TS; Region: EF_TS; pfam00889 102608004173 Elongation factor TS; Region: EF_TS; pfam00889 102608004174 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 102608004175 rRNA interaction site [nucleotide binding]; other site 102608004176 S8 interaction site; other site 102608004177 putative laminin-1 binding site; other site 102608004178 putative recombination protein RecB; Provisional; Region: PRK13909 102608004179 Family description; Region: UvrD_C_2; pfam13538 102608004180 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 102608004181 pH-dependent sodium/proton antiporter; Provisional; Region: nhaA; PRK14856 102608004182 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 102608004183 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 102608004184 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 102608004185 protein-export membrane protein SecF; Region: 3a0501s07; TIGR00966 102608004186 Protein export membrane protein; Region: SecD_SecF; pfam02355 102608004187 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 102608004188 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 102608004189 HIGH motif; other site 102608004190 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 102608004191 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 102608004192 active site 102608004193 KMSKS motif; other site 102608004194 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 102608004195 tRNA binding surface [nucleotide binding]; other site 102608004196 anticodon binding site; other site 102608004197 Lipopolysaccharide-assembly; Region: LptE; pfam04390 102608004198 folylpolyglutamate synthase/dihydrofolate synthase; Region: folC; TIGR01499 102608004199 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 102608004200 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 102608004201 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 102608004202 Peptidase family M23; Region: Peptidase_M23; pfam01551 102608004203 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 102608004204 Peptidase family M23; Region: Peptidase_M23; pfam01551 102608004205 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 102608004206 Integral membrane protein CcmA involved in cell shape determination [Cell envelope biogenesis, outer membrane]; Region: CcmA; COG1664 102608004207 transcription-repair coupling factor (mfd); Region: mfd; TIGR00580 102608004208 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; pfam02559 102608004209 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 102608004210 ATP binding site [chemical binding]; other site 102608004211 putative Mg++ binding site [ion binding]; other site 102608004212 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 102608004213 nucleotide binding region [chemical binding]; other site 102608004214 ATP-binding site [chemical binding]; other site 102608004215 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 102608004216 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 102608004217 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 102608004218 [2Fe-2S] cluster binding site [ion binding]; other site 102608004219 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 102608004220 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 102608004221 intrachain domain interface; other site 102608004222 interchain domain interface [polypeptide binding]; other site 102608004223 heme bH binding site [chemical binding]; other site 102608004224 Qi binding site; other site 102608004225 heme bL binding site [chemical binding]; other site 102608004226 Qo binding site; other site 102608004227 interchain domain interface [polypeptide binding]; other site 102608004228 intrachain domain interface; other site 102608004229 Qi binding site; other site 102608004230 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 102608004231 Qo binding site; other site 102608004232 Cytochrome c1 [Energy production and conversion]; Region: CYT1; COG2857 102608004233 Cytochrome c; Region: Cytochrom_C; pfam00034 102608004234 Cytochrome c; Region: Cytochrom_C; cl11414 102608004235 potential frameshift: common BLAST hit: gi|315454048|ref|YP_004074318.1| sulfatase 102608004236 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 102608004237 Sulfatase; Region: Sulfatase; cl17466 102608004238 Sulfatase; Region: Sulfatase; cl17466 102608004239 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 102608004240 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 102608004241 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 102608004242 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK03907 102608004243 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 102608004244 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 102608004245 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 102608004246 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 102608004247 Cell cycle protein; Region: FTSW_RODA_SPOVE; pfam01098 102608004248 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 102608004249 Periplasmic binding protein TroA_d. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a...; Region: TroA_d; cd01141 102608004250 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 102608004251 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 102608004252 dimer interface [polypeptide binding]; other site 102608004253 decamer (pentamer of dimers) interface [polypeptide binding]; other site 102608004254 catalytic triad [active] 102608004255 peroxidatic and resolving cysteines [active] 102608004256 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 102608004257 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 102608004258 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 102608004259 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 102608004260 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 102608004261 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 102608004262 G1 box; other site 102608004263 GTP/Mg2+ binding site [chemical binding]; other site 102608004264 Switch I region; other site 102608004265 G2 box; other site 102608004266 G3 box; other site 102608004267 Switch II region; other site 102608004268 G4 box; other site 102608004269 G5 box; other site 102608004270 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1934 102608004271 OstA-like protein; Region: OstA; pfam03968 102608004272 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 102608004273 motif II; other site 102608004274 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 102608004275 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 102608004276 Sporulation related domain; Region: SPOR; pfam05036 102608004277 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 102608004278 N-acetyl-D-glucosamine binding site [chemical binding]; other site 102608004279 catalytic residue [active] 102608004280 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 102608004281 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 102608004282 active site 102608004283 riboflavin synthase, alpha subunit; Region: ribE; TIGR00187 102608004284 Lumazine binding domain; Region: Lum_binding; pfam00677 102608004285 Lumazine binding domain; Region: Lum_binding; pfam00677 102608004286 flhB C-terminus-related protein; Region: flhB_rel; TIGR00789 102608004287 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 102608004288 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 102608004289 Walker A/P-loop; other site 102608004290 ATP binding site [chemical binding]; other site 102608004291 Q-loop/lid; other site 102608004292 ABC transporter signature motif; other site 102608004293 Walker B; other site 102608004294 D-loop; other site 102608004295 H-loop/switch region; other site 102608004296 NIL domain; Region: NIL; pfam09383 102608004297 ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]; Region: AbcD; COG2011 102608004298 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 102608004299 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 102608004300 active site 102608004301 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 102608004302 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 102608004303 Mg++ binding site [ion binding]; other site 102608004304 putative catalytic motif [active] 102608004305 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 102608004306 active site 102608004307 hydrophilic channel; other site 102608004308 dimerization interface [polypeptide binding]; other site 102608004309 catalytic residues [active] 102608004310 active site lid [active] 102608004311 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 102608004312 4-hydroxythreonine-4-phosphate dehydrogenase; Provisional; Region: pdxA; PRK03946 102608004313 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 102608004314 metallohydrolase, glycoprotease/Kae1 family; Region: gcp_kae1; TIGR00329 102608004315 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 102608004316 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 102608004317 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 102608004318 hypothetical protein; Provisional; Region: PRK10236 102608004319 Domain of unknown function (DUF3944); Region: DUF3944; pfam13099 102608004320 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4735 102608004321 Initiator Replication protein; Region: Rep_3; pfam01051