-- dump date 20140620_033952 -- class Genbank::misc_feature -- table misc_feature_note -- id note 1105108000001 TIGR00701 family protein; Region: TIGR00701 1105108000002 ferrochelatase; Reviewed; Region: hemH; PRK00035 1105108000003 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 1105108000004 C-terminal domain interface [polypeptide binding]; other site 1105108000005 active site 1105108000006 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 1105108000007 active site 1105108000008 N-terminal domain interface [polypeptide binding]; other site 1105108000009 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 1105108000010 substrate binding site [chemical binding]; other site 1105108000011 active site 1105108000012 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1806 1105108000013 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 1105108000014 catalytic residues [active] 1105108000015 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 1105108000016 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 1105108000017 Walker A/P-loop; other site 1105108000018 ATP binding site [chemical binding]; other site 1105108000019 Q-loop/lid; other site 1105108000020 ABC transporter signature motif; other site 1105108000021 Walker B; other site 1105108000022 D-loop; other site 1105108000023 H-loop/switch region; other site 1105108000024 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 1105108000025 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 1105108000026 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 1105108000027 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1105108000028 FAD/NAD binding domain (electron transfer subunit) of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate...; Region: DHOD_e_trans_like; cd06192 1105108000029 FAD binding pocket [chemical binding]; other site 1105108000030 FAD binding motif [chemical binding]; other site 1105108000031 phosphate binding motif [ion binding]; other site 1105108000032 beta-alpha-beta structure motif; other site 1105108000033 NAD binding pocket [chemical binding]; other site 1105108000034 Iron coordination center [ion binding]; other site 1105108000035 Growth inhibitor [Signal transduction mechanisms]; Region: MazF; COG2337 1105108000036 Predicted transcriptional regulator [Transcription]; Region: COG3905 1105108000037 Acyl-[acyl carrier protein]; Region: LpxA; COG1043 1105108000038 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 1105108000039 active site 1105108000040 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 1105108000041 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 1105108000042 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 1105108000043 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 1105108000044 trimer interface [polypeptide binding]; other site 1105108000045 active site 1105108000046 UDP-GlcNAc binding site [chemical binding]; other site 1105108000047 lipid binding site [chemical binding]; lipid-binding site 1105108000048 potential frameshift: common BLAST hit: gi|374318780|ref|YP_005065278.1| Putative dihydrouridine synthase Dus 1105108000049 potential frameshift: common BLAST hit: gi|229586241|ref|YP_002844742.1| Putative dihydrouridine synthase Dus 1105108000050 potential frameshift: common BLAST hit: gi|229586241|ref|YP_002844742.1| Putative dihydrouridine synthase Dus 1105108000051 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 1105108000052 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 1105108000053 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 1105108000054 intersubunit interface [polypeptide binding]; other site 1105108000055 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 1105108000056 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 1105108000057 active site 1105108000058 NTP binding site [chemical binding]; other site 1105108000059 metal binding triad [ion binding]; metal-binding site 1105108000060 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 1105108000061 Competence protein; Region: Competence; pfam03772 1105108000062 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105108000063 AAA domain; Region: AAA_22; pfam13401 1105108000064 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1105108000065 F0F1 ATP synthase subunit B; Validated; Region: PRK06568 1105108000066 F0F1 ATP synthase subunit B'; Validated; Region: PRK06569 1105108000067 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1105108000068 F0F1 ATP synthase subunit C; Validated; Region: PRK07558 1105108000069 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108000070 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 1105108000071 ATP synthase subunit 6 (eukaryotes),also subunit A (prokaryotes); Region: ATP_synt_6_or_A; TIGR01131 1105108000072 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5336 1105108000073 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 1105108000074 DsbA family; consists of DsbA and DsbA-like proteins, including DsbC, DsbG, glutathione (GSH) S-transferase kappa (GSTK), 2-hydroxychromene-2-carboxylate (HCCA) isomerase, an oxidoreductase (FrnE) presumed to be involved in frenolicin biosynthesis, a...; Region: DsbA_family; cd02972 1105108000075 catalytic residues [active] 1105108000076 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 1105108000077 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105108000078 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105108000079 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 1105108000080 S-adenosylmethionine binding site [chemical binding]; other site 1105108000081 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 1105108000082 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 1105108000083 Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair]; Region: RecF; COG1195 1105108000084 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105108000085 Walker A/P-loop; other site 1105108000086 ATP binding site [chemical binding]; other site 1105108000087 Q-loop/lid; other site 1105108000088 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105108000089 ABC transporter signature motif; other site 1105108000090 Walker B; other site 1105108000091 D-loop; other site 1105108000092 H-loop/switch region; other site 1105108000093 TENA/THI-4/PQQC family; Region: TENA_THI-4; cl15243 1105108000094 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 1105108000095 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cd00209 1105108000096 folate binding site [chemical binding]; other site 1105108000097 NADP+ binding site [chemical binding]; other site 1105108000098 Dihydropteroate synthase and related enzymes [Coenzyme metabolism]; Region: FolP; COG0294 1105108000099 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 1105108000100 dimer interface [polypeptide binding]; other site 1105108000101 inhibitor binding site; inhibition site 1105108000102 Dihydropteroate synthase and related enzymes [Coenzyme metabolism]; Region: FolP; COG0294 1105108000103 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 1105108000104 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; cl00233 1105108000105 catalytic center binding site [active] 1105108000106 ATP binding site [chemical binding]; other site 1105108000107 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 1105108000108 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase [Coenzyme metabolism]; Region: FolK; COG0801 1105108000109 tetratricopeptide repeat protein; Provisional; Region: PRK11788 1105108000110 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 1105108000111 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 1105108000112 Cu(I) binding site [ion binding]; other site 1105108000113 Putative transcriptional regulator [Transcription]; Region: COG1678 1105108000114 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 1105108000115 Colicin V production protein; Region: Colicin_V; pfam02674 1105108000116 Autotransporter beta-domain; Region: Autotransporter; smart00869 1105108000117 Protein of unknown function (DUF2748); Region: DUF2748; pfam10871 1105108000118 acetoacetyl-CoA reductase; Provisional; Region: PRK12824 1105108000119 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 1105108000120 NAD(P) binding site [chemical binding]; other site 1105108000121 homotetramer interface [polypeptide binding]; other site 1105108000122 homodimer interface [polypeptide binding]; other site 1105108000123 active site 1105108000124 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 1105108000125 Clp amino terminal domain; Region: Clp_N; pfam02861 1105108000126 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 1105108000127 Walker A motif; other site 1105108000128 ATP binding site [chemical binding]; other site 1105108000129 Walker B motif; other site 1105108000130 arginine finger; other site 1105108000131 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 1105108000132 Walker A motif; other site 1105108000133 ATP binding site [chemical binding]; other site 1105108000134 Walker B motif; other site 1105108000135 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 1105108000136 UGMP family protein; Validated; Region: PRK09604 1105108000137 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 1105108000138 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 1105108000139 Fatty acid desaturase; Region: FA_desaturase; pfam00487 1105108000140 Di-iron ligands [ion binding]; other site 1105108000141 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 1105108000142 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105108000143 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; cl17355 1105108000144 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 1105108000145 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 1105108000146 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 1105108000147 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 1105108000148 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 1105108000149 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 1105108000150 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 1105108000151 Ligand Binding Site [chemical binding]; other site 1105108000152 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108000153 FtsH Extracellular; Region: FtsH_ext; pfam06480 1105108000154 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 1105108000155 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 1105108000156 Walker A motif; other site 1105108000157 ATP binding site [chemical binding]; other site 1105108000158 Walker B motif; other site 1105108000159 arginine finger; other site 1105108000160 Peptidase family M41; Region: Peptidase_M41; pfam01434 1105108000161 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 1105108000162 cofactor binding site; other site 1105108000163 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 1105108000164 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 1105108000165 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 1105108000166 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3755 1105108000167 Uncharacterized conserved protein [Function unknown]; Region: COG1565 1105108000168 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108000169 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 1105108000170 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1105108000171 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1105108000172 membrane protein insertase; Provisional; Region: PRK01318 1105108000173 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 1105108000174 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 1105108000175 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 1105108000176 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 1105108000177 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 1105108000178 active site 1105108000179 catalytic residues [active] 1105108000180 metal binding site [ion binding]; metal-binding site 1105108000181 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105108000182 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 1105108000183 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 1105108000184 putative substrate translocation pore; other site 1105108000185 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 1105108000186 active site 1105108000187 multimer interface [polypeptide binding]; other site 1105108000188 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 1105108000189 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 1105108000190 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 1105108000191 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 1105108000192 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 1105108000193 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 1105108000194 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 1105108000195 P loop; other site 1105108000196 Nucleotide binding site [chemical binding]; other site 1105108000197 DTAP/Switch II; other site 1105108000198 Switch I; other site 1105108000199 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 1105108000200 Magnesium ion binding site [ion binding]; other site 1105108000201 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 1105108000202 ParB-like nuclease domain; Region: ParB; smart00470 1105108000203 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 1105108000204 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105108000205 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105108000206 ABC transporter; Region: ABC_tran_2; pfam12848 1105108000207 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105108000208 Protein of unknown function (DUF2672); Region: DUF2672; pfam10878 1105108000209 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; COG2877 1105108000210 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 1105108000211 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 1105108000212 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 1105108000213 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1105108000214 Zn2+ binding site [ion binding]; other site 1105108000215 Mg2+ binding site [ion binding]; other site 1105108000216 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 1105108000217 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 1105108000218 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 1105108000219 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 1105108000220 active site 1105108000221 HIGH motif; other site 1105108000222 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105108000223 KMSK motif region; other site 1105108000224 tRNA binding surface [nucleotide binding]; other site 1105108000225 DALR anticodon binding domain; Region: DALR_1; smart00836 1105108000226 anticodon binding site; other site 1105108000227 Sporulation related domain; Region: SPOR; pfam05036 1105108000228 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 1105108000229 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 1105108000230 CAP-like domain; other site 1105108000231 active site 1105108000232 primary dimer interface [polypeptide binding]; other site 1105108000233 Gram-negative porin; Region: Porin_4; pfam13609 1105108000234 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1105108000235 trimer interface [polypeptide binding]; other site 1105108000236 active site 1105108000237 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cd00557 1105108000238 SecA binding site; other site 1105108000239 Preprotein binding site; other site 1105108000240 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105108000241 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 1105108000242 active site 1105108000243 phosphorylation site [posttranslational modification] 1105108000244 intermolecular recognition site; other site 1105108000245 dimerization interface [polypeptide binding]; other site 1105108000246 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 1105108000247 DNA binding site [nucleotide binding] 1105108000248 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 1105108000249 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 1105108000250 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 1105108000251 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3820 1105108000252 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 1105108000253 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 1105108000254 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 1105108000255 EamA-like transporter family; Region: EamA; pfam00892 1105108000256 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 1105108000257 EamA-like transporter family; Region: EamA; pfam00892 1105108000258 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 1105108000259 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105108000260 putative substrate translocation pore; other site 1105108000261 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 1105108000262 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105108000263 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 1105108000264 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1105108000265 active site 1105108000266 HIGH motif; other site 1105108000267 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1105108000268 KMSKS motif; other site 1105108000269 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1105108000270 tRNA binding surface [nucleotide binding]; other site 1105108000271 anticodon binding site; other site 1105108000272 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 1105108000273 rRNA interaction site [nucleotide binding]; other site 1105108000274 S8 interaction site; other site 1105108000275 putative laminin-1 binding site; other site 1105108000276 elongation factor Ts; Provisional; Region: tsf; PRK09377 1105108000277 UBA/TS-N domain; Region: UBA; pfam00627 1105108000278 Elongation factor TS; Region: EF_TS; pfam00889 1105108000279 Elongation factor TS; Region: EF_TS; pfam00889 1105108000280 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 1105108000281 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108000282 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 1105108000283 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 1105108000284 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 1105108000285 putative acyl-acceptor binding pocket; other site 1105108000286 aspartate aminotransferase; Provisional; Region: PRK05764 1105108000287 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 1105108000288 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105108000289 homodimer interface [polypeptide binding]; other site 1105108000290 catalytic residue [active] 1105108000291 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1105108000292 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 1105108000293 binding surface 1105108000294 TPR motif; other site 1105108000295 Methyltransferase domain; Region: Methyltransf_23; pfam13489 1105108000296 Methyltransferase domain; Region: Methyltransf_18; pfam12847 1105108000297 Surface lipoprotein [Cell envelope biogenesis, outer membrane]; Region: VacJ; COG2853 1105108000298 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; COG2854 1105108000299 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 1105108000300 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 1105108000301 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1105108000302 active site 1105108000303 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108000304 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 1105108000305 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 1105108000306 active site 1105108000307 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1105108000308 dimer interface [polypeptide binding]; other site 1105108000309 substrate binding site [chemical binding]; other site 1105108000310 catalytic residues [active] 1105108000311 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 1105108000312 Permease; Region: Permease; pfam02405 1105108000313 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 1105108000314 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105108000315 Walker A/P-loop; other site 1105108000316 ATP binding site [chemical binding]; other site 1105108000317 Q-loop/lid; other site 1105108000318 ABC transporter signature motif; other site 1105108000319 Walker B; other site 1105108000320 D-loop; other site 1105108000321 H-loop/switch region; other site 1105108000322 Ribosomal protein L28 [Translation, ribosomal structure and biogenesis]; Region: RpmB; COG0227 1105108000323 50S ribosomal protein L31; Provisional; Region: PRK01397 1105108000324 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 1105108000325 G1 box; other site 1105108000326 GTP/Mg2+ binding site [chemical binding]; other site 1105108000327 Switch I region; other site 1105108000328 G2 box; other site 1105108000329 G3 box; other site 1105108000330 Switch II region; other site 1105108000331 G4 box; other site 1105108000332 G5 box; other site 1105108000333 Acetylglutamate kinase [Amino acid transport and metabolism]; Region: ArgB; COG0548 1105108000334 nucleotide binding site [chemical binding]; other site 1105108000335 substrate binding site [chemical binding]; other site 1105108000336 type IV secretion system protein VirB3; Provisional; Region: PRK13899 1105108000337 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 1105108000338 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1105108000339 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105108000340 Walker A/P-loop; other site 1105108000341 ATP binding site [chemical binding]; other site 1105108000342 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105108000343 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105108000344 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105108000345 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105108000346 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105108000347 potential frameshift: common BLAST hit: gi|67458488|ref|YP_246112.1| phosphate acetyltransferase 1105108000348 potential frameshift: common BLAST hit: gi|67458489|ref|YP_246113.1| acetate kinase 1105108000349 tRNA-(guanine-N1)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmD; COG0336 1105108000350 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 1105108000351 hypothetical protein; Provisional; Region: PRK13694 1105108000352 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 1105108000353 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 1105108000354 Protein export membrane protein; Region: SecD_SecF; pfam02355 1105108000355 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 1105108000356 SLBB domain; Region: SLBB; pfam10531 1105108000357 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 1105108000358 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 1105108000359 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 1105108000360 Catalytic site [active] 1105108000361 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 1105108000362 ribonuclease III; Reviewed; Region: rnc; PRK00102 1105108000363 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 1105108000364 dimerization interface [polypeptide binding]; other site 1105108000365 active site 1105108000366 metal binding site [ion binding]; metal-binding site 1105108000367 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 1105108000368 dsRNA binding site [nucleotide binding]; other site 1105108000369 GTPase Era; Provisional; Region: era; PRK15494 1105108000370 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108000371 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 1105108000372 G1 box; other site 1105108000373 GTP/Mg2+ binding site [chemical binding]; other site 1105108000374 Switch I region; other site 1105108000375 G2 box; other site 1105108000376 Switch II region; other site 1105108000377 G3 box; other site 1105108000378 G4 box; other site 1105108000379 G5 box; other site 1105108000380 KH domain; Region: KH_2; pfam07650 1105108000381 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 1105108000382 active site 1105108000383 putative DNA-binding cleft [nucleotide binding]; other site 1105108000384 dimer interface [polypeptide binding]; other site 1105108000385 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 1105108000386 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 1105108000387 nucleotidyltransferase substrate binding protein, HI0074 family; Region: HI0074; TIGR01987 1105108000388 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 1105108000389 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 1105108000390 AAA domain; Region: AAA_31; pfam13614 1105108000391 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 1105108000392 Walker A motif; other site 1105108000393 Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflK; cd03404 1105108000394 HflK protein; Region: hflK; TIGR01933 1105108000395 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1105108000396 Band_7_HflC: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfC (High frequency of lysogenization C). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflC; cd03405 1105108000397 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 1105108000398 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1105108000399 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 1105108000400 protein binding site [polypeptide binding]; other site 1105108000401 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 1105108000402 protein binding site [polypeptide binding]; other site 1105108000403 hypothetical protein; Validated; Region: PRK01415 1105108000404 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 1105108000405 active site residue [active] 1105108000406 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the...; Region: SQR_TypeC_SdhC; cd03499 1105108000407 Iron-sulfur protein interface; other site 1105108000408 proximal quinone binding site [chemical binding]; other site 1105108000409 SdhD (CybS) interface [polypeptide binding]; other site 1105108000410 proximal heme binding site [chemical binding]; other site 1105108000411 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory...; Region: SQR_TypeC_SdhD_like; cd03495 1105108000412 putative SdhC subunit interface [polypeptide binding]; other site 1105108000413 putative proximal heme binding site [chemical binding]; other site 1105108000414 putative Iron-sulfur protein interface [polypeptide binding]; other site 1105108000415 putative proximal quinone binding site; other site 1105108000416 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 1105108000417 L-aspartate oxidase; Provisional; Region: PRK06175 1105108000418 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 1105108000419 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1105108000420 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 1105108000421 dimer interface [polypeptide binding]; other site 1105108000422 conserved gate region; other site 1105108000423 putative PBP binding loops; other site 1105108000424 ABC-ATPase subunit interface; other site 1105108000425 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 1105108000426 S17 interaction site [polypeptide binding]; other site 1105108000427 S8 interaction site; other site 1105108000428 16S rRNA interaction site [nucleotide binding]; other site 1105108000429 streptomycin interaction site [chemical binding]; other site 1105108000430 23S rRNA interaction site [nucleotide binding]; other site 1105108000431 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 1105108000432 30S ribosomal protein S7; Validated; Region: PRK05302 1105108000433 elongation factor G; Reviewed; Region: PRK00007 1105108000434 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 1105108000435 G1 box; other site 1105108000436 putative GEF interaction site [polypeptide binding]; other site 1105108000437 GTP/Mg2+ binding site [chemical binding]; other site 1105108000438 Switch I region; other site 1105108000439 G2 box; other site 1105108000440 G3 box; other site 1105108000441 Switch II region; other site 1105108000442 G4 box; other site 1105108000443 G5 box; other site 1105108000444 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 1105108000445 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 1105108000446 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 1105108000447 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 1105108000448 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 1105108000449 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 1105108000450 putative homodimer interface [polypeptide binding]; other site 1105108000451 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 1105108000452 heterodimer interface [polypeptide binding]; other site 1105108000453 homodimer interface [polypeptide binding]; other site 1105108000454 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 1105108000455 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 1105108000456 23S rRNA interface [nucleotide binding]; other site 1105108000457 putative thiostrepton binding site; other site 1105108000458 L7/L12 interface [polypeptide binding]; other site 1105108000459 L25 interface [polypeptide binding]; other site 1105108000460 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 1105108000461 mRNA/rRNA interface [nucleotide binding]; other site 1105108000462 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 1105108000463 23S rRNA interface [nucleotide binding]; other site 1105108000464 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 1105108000465 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 1105108000466 core dimer interface [polypeptide binding]; other site 1105108000467 peripheral dimer interface [polypeptide binding]; other site 1105108000468 L10 interface [polypeptide binding]; other site 1105108000469 L11 interface [polypeptide binding]; other site 1105108000470 putative EF-Tu interaction site [polypeptide binding]; other site 1105108000471 putative EF-G interaction site [polypeptide binding]; other site 1105108000472 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 1105108000473 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 1105108000474 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 1105108000475 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 1105108000476 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 1105108000477 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 1105108000478 RPB3 interaction site [polypeptide binding]; other site 1105108000479 RPB1 interaction site [polypeptide binding]; other site 1105108000480 RPB11 interaction site [polypeptide binding]; other site 1105108000481 RPB10 interaction site [polypeptide binding]; other site 1105108000482 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 1105108000483 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 1105108000484 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 1105108000485 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 1105108000486 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 1105108000487 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 1105108000488 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 1105108000489 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 1105108000490 DNA binding site [nucleotide binding] 1105108000491 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 1105108000492 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108000493 multifunctional aminopeptidase A; Provisional; Region: PRK00913 1105108000494 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 1105108000495 interface (dimer of trimers) [polypeptide binding]; other site 1105108000496 Substrate-binding/catalytic site; other site 1105108000497 Zn-binding sites [ion binding]; other site 1105108000498 ATPase MipZ; Region: MipZ; pfam09140 1105108000499 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 1105108000500 P-loop; other site 1105108000501 Magnesium ion binding site [ion binding]; other site 1105108000502 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 1105108000503 Magnesium ion binding site [ion binding]; other site 1105108000504 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 1105108000505 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 1105108000506 dimer interface [polypeptide binding]; other site 1105108000507 anticodon binding site; other site 1105108000508 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 1105108000509 homodimer interface [polypeptide binding]; other site 1105108000510 motif 1; other site 1105108000511 active site 1105108000512 motif 2; other site 1105108000513 GAD domain; Region: GAD; pfam02938 1105108000514 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 1105108000515 active site 1105108000516 motif 3; other site 1105108000517 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 1105108000518 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 1105108000519 dihydrodipicolinate reductase; Provisional; Region: PRK00048 1105108000520 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 1105108000521 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 1105108000522 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 1105108000523 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1105108000524 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 1105108000525 substrate binding pocket [chemical binding]; other site 1105108000526 membrane-bound complex binding site; other site 1105108000527 hinge residues; other site 1105108000528 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 1105108000529 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 1105108000530 GatB domain; Region: GatB_Yqey; smart00845 1105108000531 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 1105108000532 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 1105108000533 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 1105108000534 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in a group of uncharacterized proteins from archaea and bacteria; Region: NTP-PPase_COG4997; cd11532 1105108000535 ribosome recycling factor; Reviewed; Region: frr; PRK00083 1105108000536 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 1105108000537 hinge region; other site 1105108000538 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 1105108000539 putative nucleotide binding site [chemical binding]; other site 1105108000540 uridine monophosphate binding site [chemical binding]; other site 1105108000541 homohexameric interface [polypeptide binding]; other site 1105108000542 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK06580 1105108000543 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1105108000544 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 1105108000545 putative substrate translocation pore; other site 1105108000546 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 1105108000547 Protein of unknown function (DUF2674); Region: DUF2674; pfam10879 1105108000548 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 1105108000549 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105108000550 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105108000551 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105108000552 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105108000553 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105108000554 Surface antigen; Region: Bac_surface_Ag; pfam01103 1105108000555 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 1105108000556 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 1105108000557 active site 1105108000558 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 1105108000559 protein binding site [polypeptide binding]; other site 1105108000560 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 1105108000561 putative substrate binding region [chemical binding]; other site 1105108000562 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 1105108000563 putative RNA binding site [nucleotide binding]; other site 1105108000564 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 1105108000565 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 1105108000566 S-adenosylmethionine binding site [chemical binding]; other site 1105108000567 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 1105108000568 putative coenzyme Q binding site [chemical binding]; other site 1105108000569 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108000570 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 1105108000571 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 1105108000572 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 1105108000573 RNA methyltransferase, RsmE family; Region: TIGR00046 1105108000574 Uncharacterized conserved protein [Function unknown]; Region: COG2155 1105108000575 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105108000576 Protein export membrane protein; Region: SecD_SecF; cl14618 1105108000577 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 1105108000578 IHF dimer interface [polypeptide binding]; other site 1105108000579 IHF - DNA interface [nucleotide binding]; other site 1105108000580 DNA polymerase III subunit delta'; Validated; Region: PRK06581 1105108000581 signal recognition particle protein; Provisional; Region: PRK10867 1105108000582 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 1105108000583 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 1105108000584 P loop; other site 1105108000585 GTP binding site [chemical binding]; other site 1105108000586 Signal peptide binding domain; Region: SRP_SPB; pfam02978 1105108000587 potential frameshift: common BLAST hit: gi|51473374|ref|YP_067131.1| post-proline cleaving enzyme 1105108000588 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105108000589 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105108000590 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105108000591 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105108000592 coproporphyrinogen III oxidase; Provisional; Region: PRK06582 1105108000593 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 1105108000594 FeS/SAM binding site; other site 1105108000595 HemN C-terminal domain; Region: HemN_C; pfam06969 1105108000596 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 1105108000597 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105108000598 potential frameshift: common BLAST hit: gi|229586418|ref|YP_002844919.1| cephalosporin hydroxylase 1105108000599 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 1105108000600 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1105108000601 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 1105108000602 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 1105108000603 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism]; Region: COG0720 1105108000604 active site 1105108000605 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 1105108000606 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 1105108000607 E3 interaction surface; other site 1105108000608 lipoyl attachment site [posttranslational modification]; other site 1105108000609 e3 binding domain; Region: E3_binding; pfam02817 1105108000610 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 1105108000611 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 1105108000612 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 1105108000613 TPP-binding site [chemical binding]; other site 1105108000614 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 1105108000615 dimer interface [polypeptide binding]; other site 1105108000616 PYR/PP interface [polypeptide binding]; other site 1105108000617 TPP binding site [chemical binding]; other site 1105108000618 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 1105108000619 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 1105108000620 active site 1105108000621 Zn binding site [ion binding]; other site 1105108000622 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 1105108000623 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 1105108000624 Walker A/P-loop; other site 1105108000625 ATP binding site [chemical binding]; other site 1105108000626 Q-loop/lid; other site 1105108000627 Allexivirus 40kDa protein; Region: Allexi_40kDa; pfam05549 1105108000628 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 1105108000629 ABC transporter signature motif; other site 1105108000630 Walker B; other site 1105108000631 D-loop; other site 1105108000632 H-loop/switch region; other site 1105108000633 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 1105108000634 Tetratricopeptide repeat; Region: TPR_6; pfam13174 1105108000635 ChaB; Region: ChaB; cl01887 1105108000636 ChaB; Region: ChaB; cl01887 1105108000637 chaperone protein DnaJ; Provisional; Region: PRK14300 1105108000638 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 1105108000639 HSP70 interaction site [polypeptide binding]; other site 1105108000640 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 1105108000641 substrate binding site [polypeptide binding]; other site 1105108000642 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 1105108000643 Zn binding sites [ion binding]; other site 1105108000644 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 1105108000645 dimer interface [polypeptide binding]; other site 1105108000646 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 1105108000647 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 1105108000648 nucleotide binding site [chemical binding]; other site 1105108000649 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 1105108000650 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1105108000651 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 1105108000652 Lipopolysaccharide-assembly; Region: LptE; cl01125 1105108000653 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 1105108000654 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 1105108000655 diiron binding motif [ion binding]; other site 1105108000656 Cytochrome c oxidase subunit III. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_III; cd01665 1105108000657 Subunit III/VIIa interface [polypeptide binding]; other site 1105108000658 Phospholipid binding site [chemical binding]; other site 1105108000659 Subunit I/III interface [polypeptide binding]; other site 1105108000660 Subunit III/VIb interface [polypeptide binding]; other site 1105108000661 Subunit III/VIa interface; other site 1105108000662 Subunit III/Vb interface [polypeptide binding]; other site 1105108000663 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 1105108000664 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 1105108000665 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 1105108000666 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA; Region: LbH_THP_succinylT; cd03350 1105108000667 trimer interface [polypeptide binding]; other site 1105108000668 active site 1105108000669 substrate binding site [chemical binding]; other site 1105108000670 CoA binding site [chemical binding]; other site 1105108000671 potential frameshift: common BLAST hit: gi|374318979|ref|YP_005065477.1| Bifunctional penicillin-binding protein 1C 1105108000672 potential frameshift: common BLAST hit: gi|157828132|ref|YP_001494374.1| cell surface antigen-like protein Sca8 1105108000673 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105108000674 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 1105108000675 Ligand Binding Site [chemical binding]; other site 1105108000676 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 1105108000677 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 1105108000678 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 1105108000679 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 1105108000680 catalytic loop [active] 1105108000681 iron binding site [ion binding]; other site 1105108000682 chaperone protein HscA; Provisional; Region: hscA; PRK01433 1105108000683 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 1105108000684 nucleotide binding site [chemical binding]; other site 1105108000685 co-chaperone HscB; Provisional; Region: hscB; PRK01356 1105108000686 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 1105108000687 HSP70 interaction site [polypeptide binding]; other site 1105108000688 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 1105108000689 RNA/DNA hybrid binding site [nucleotide binding]; other site 1105108000690 active site 1105108000691 excinuclease ABC subunit B; Provisional; Region: PRK05298 1105108000692 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 1105108000693 ATP binding site [chemical binding]; other site 1105108000694 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 1105108000695 nucleotide binding region [chemical binding]; other site 1105108000696 ATP-binding site [chemical binding]; other site 1105108000697 Ultra-violet resistance protein B; Region: UvrB; pfam12344 1105108000698 UvrB/uvrC motif; Region: UVR; pfam02151 1105108000699 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 1105108000700 GSH binding site [chemical binding]; other site 1105108000701 catalytic residues [active] 1105108000702 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 1105108000703 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105108000704 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105108000705 Walker A/P-loop; other site 1105108000706 ATP binding site [chemical binding]; other site 1105108000707 Q-loop/lid; other site 1105108000708 DNA gyrase subunit A; Validated; Region: PRK05560 1105108000709 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 1105108000710 CAP-like domain; other site 1105108000711 active site 1105108000712 primary dimer interface [polypeptide binding]; other site 1105108000713 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105108000714 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105108000715 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105108000716 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105108000717 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105108000718 potential frameshift: common BLAST hit: gi|341583500|ref|YP_004763991.1| transporter 1105108000719 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1105108000720 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 1105108000721 Iron-sulphur cluster assembly; Region: Fe-S_assembly; cl01123 1105108000722 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 1105108000723 active site 1105108000724 catalytic residues [active] 1105108000725 metal binding site [ion binding]; metal-binding site 1105108000726 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 1105108000727 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 1105108000728 putative active site [active] 1105108000729 substrate binding site [chemical binding]; other site 1105108000730 putative cosubstrate binding site; other site 1105108000731 catalytic site [active] 1105108000732 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 1105108000733 substrate binding site [chemical binding]; other site 1105108000734 potential frameshift: common BLAST hit: gi|374319001|ref|YP_005065499.1| capsular polysaccharide biosynthesis protein 1105108000735 Predicted ATPase [General function prediction only]; Region: COG1485 1105108000736 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 1105108000737 Walker A motif; other site 1105108000738 ATP binding site [chemical binding]; other site 1105108000739 Walker B motif; other site 1105108000740 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: PRK01424 1105108000741 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 1105108000742 potential frameshift: common BLAST hit: gi|350273268|ref|YP_004884581.1| ankyrin 1105108000743 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1105108000744 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105108000745 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105108000746 Walker A/P-loop; other site 1105108000747 ATP binding site [chemical binding]; other site 1105108000748 Q-loop/lid; other site 1105108000749 ABC transporter signature motif; other site 1105108000750 Walker B; other site 1105108000751 D-loop; other site 1105108000752 H-loop/switch region; other site 1105108000753 Protein of unknown function (DUF2671); Region: DUF2671; pfam10877 1105108000754 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 1105108000755 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 1105108000756 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 1105108000757 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 1105108000758 Plasmid encoded toxin Txe; Region: Plasmid_Txe; cl17389 1105108000759 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105108000760 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 1105108000761 putative metal binding site; other site 1105108000762 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1105108000763 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1105108000764 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1105108000765 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 1105108000766 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 1105108000767 ATP binding site [chemical binding]; other site 1105108000768 active site 1105108000769 substrate binding site [chemical binding]; other site 1105108000770 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 1105108000771 TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and...; Region: TGS_ThrRS_N; cd01667 1105108000772 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 1105108000773 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 1105108000774 active site 1105108000775 dimer interface [polypeptide binding]; other site 1105108000776 motif 1; other site 1105108000777 motif 2; other site 1105108000778 motif 3; other site 1105108000779 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 1105108000780 anticodon binding site; other site 1105108000781 potential frameshift: common BLAST hit: gi|67459373|ref|YP_246997.1| multidrug ABC transporter ATPase and permease 1105108000782 potential frameshift: common BLAST hit: gi|67459373|ref|YP_246997.1| multidrug ABC transporter ATPase and permease 1105108000783 potential frameshift: common BLAST hit: gi|67459373|ref|YP_246997.1| multidrug ABC transporter ATPase and permease 1105108000784 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); Region: DUF2310; cl02380 1105108000785 Protein of unknown function (DUF2660); Region: DUF2660; pfam10859 1105108000786 putative pectinesterase/pectinesterase inhibitor; Region: PLN02468 1105108000787 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1105108000788 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3827 1105108000789 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 1105108000790 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105108000791 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 1105108000792 DNA topoisomerase IV, B subunit, proteobacterial; Region: parE_Gneg; TIGR01055 1105108000793 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 1105108000794 ATP binding site [chemical binding]; other site 1105108000795 Mg2+ binding site [ion binding]; other site 1105108000796 G-X-G motif; other site 1105108000797 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 1105108000798 anchoring element; other site 1105108000799 dimer interface [polypeptide binding]; other site 1105108000800 ATP binding site [chemical binding]; other site 1105108000801 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 1105108000802 active site 1105108000803 metal binding site [ion binding]; metal-binding site 1105108000804 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1105108000805 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 1105108000806 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 1105108000807 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 1105108000808 protein binding site [polypeptide binding]; other site 1105108000809 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 1105108000810 Catalytic dyad [active] 1105108000811 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1105108000812 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 1105108000813 dimer interface [polypeptide binding]; other site 1105108000814 phosphorylation site [posttranslational modification] 1105108000815 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 1105108000816 ATP binding site [chemical binding]; other site 1105108000817 Mg2+ binding site [ion binding]; other site 1105108000818 G-X-G motif; other site 1105108000819 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 1105108000820 Protein of unknown function (DUF2659); Region: DUF2659; pfam10858 1105108000821 FOG: WD40-like repeat [Function unknown]; Region: COG1520 1105108000822 Beta-barrel assembly machinery (Bam) complex component B and related proteins; Region: BamB_YfgL; cd10276 1105108000823 Trp docking motif [polypeptide binding]; other site 1105108000824 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 1105108000825 23S rRNA interface [nucleotide binding]; other site 1105108000826 L3 interface [polypeptide binding]; other site 1105108000827 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 1105108000828 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 1105108000829 putative active site [active] 1105108000830 Ap4A binding site [chemical binding]; other site 1105108000831 nudix motif; other site 1105108000832 putative metal binding site [ion binding]; other site 1105108000833 response regulator PleD; Reviewed; Region: pleD; PRK09581 1105108000834 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 1105108000835 active site 1105108000836 phosphorylation site [posttranslational modification] 1105108000837 intermolecular recognition site; other site 1105108000838 dimerization interface [polypeptide binding]; other site 1105108000839 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 1105108000840 active site 1105108000841 phosphorylation site [posttranslational modification] 1105108000842 intermolecular recognition site; other site 1105108000843 dimerization interface [polypeptide binding]; other site 1105108000844 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1105108000845 metal binding site [ion binding]; metal-binding site 1105108000846 active site 1105108000847 I-site; other site 1105108000848 elongation factor P; Validated; Region: PRK00529 1105108000849 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 1105108000850 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 1105108000851 RNA binding site [nucleotide binding]; other site 1105108000852 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 1105108000853 RNA binding site [nucleotide binding]; other site 1105108000854 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 1105108000855 Inositol-monophosphatase-like domains. This family of phosphatases is dependent on bivalent metal ions such as Mg++, and many members are inhibited by Li+ (which is thought to displace a bivalent ion in the active site). Substrates include fructose-1; Region: IMPase_like; cd01637 1105108000856 active site 1105108000857 Domain of unknown function (DUF2610); Region: DUF2610; pfam11020 1105108000858 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 1105108000859 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 1105108000860 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 1105108000861 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 1105108000862 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1105108000863 HlyD family secretion protein; Region: HlyD_3; pfam13437 1105108000864 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 1105108000865 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 1105108000866 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 1105108000867 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105108000868 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105108000869 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105108000870 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 1105108000871 FAD binding domain; Region: FAD_binding_4; pfam01565 1105108000872 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 1105108000873 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 1105108000874 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 1105108000875 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1105108000876 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 1105108000877 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 1105108000878 Cell division protein FtsQ; Region: FtsQ; pfam03799 1105108000879 cell division protein FtsA; Region: ftsA; TIGR01174 1105108000880 Cell division protein FtsA; Region: FtsA; smart00842 1105108000881 Cell division protein FtsA; Region: FtsA; pfam14450 1105108000882 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 1105108000883 Cytochrome c2 [Energy production and conversion]; Region: COG3474 1105108000884 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 1105108000885 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 1105108000886 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 1105108000887 RNA binding site [nucleotide binding]; other site 1105108000888 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 1105108000889 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 1105108000890 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 1105108000891 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 1105108000892 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1105108000893 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 1105108000894 RNA binding surface [nucleotide binding]; other site 1105108000895 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1105108000896 active site 1105108000897 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 1105108000898 Beta-lactamase; Region: Beta-lactamase; pfam00144 1105108000899 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 1105108000900 putative catalytic site [active] 1105108000901 putative phosphate binding site [ion binding]; other site 1105108000902 active site 1105108000903 metal binding site A [ion binding]; metal-binding site 1105108000904 DNA binding site [nucleotide binding] 1105108000905 putative AP binding site [nucleotide binding]; other site 1105108000906 putative metal binding site B [ion binding]; other site 1105108000907 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 1105108000908 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 1105108000909 tetramer interface [polypeptide binding]; other site 1105108000910 TPP-binding site [chemical binding]; other site 1105108000911 heterodimer interface [polypeptide binding]; other site 1105108000912 phosphorylation loop region [posttranslational modification] 1105108000913 pyruvate dehydrogenase subunit beta; Validated; Region: PRK09212 1105108000914 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 1105108000915 alpha subunit interface [polypeptide binding]; other site 1105108000916 TPP binding site [chemical binding]; other site 1105108000917 heterodimer interface [polypeptide binding]; other site 1105108000918 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1105108000919 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 1105108000920 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 1105108000921 G1 box; other site 1105108000922 putative GEF interaction site [polypeptide binding]; other site 1105108000923 GTP/Mg2+ binding site [chemical binding]; other site 1105108000924 Switch I region; other site 1105108000925 G2 box; other site 1105108000926 G3 box; other site 1105108000927 Switch II region; other site 1105108000928 G4 box; other site 1105108000929 G5 box; other site 1105108000930 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 1105108000931 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 1105108000932 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: HlpA; COG2825 1105108000933 isocitrate dehydrogenase; Validated; Region: PRK09222 1105108000934 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 1105108000935 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 1105108000936 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12507 1105108000937 Predicted subunit of the Multisubunit Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: COG1563 1105108000938 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 1105108000939 Protein of unknown function (DUF2670); Region: DUF2670; pfam10875 1105108000940 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 1105108000941 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 1105108000942 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 1105108000943 [2Fe-2S] cluster binding site [ion binding]; other site 1105108000944 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 1105108000945 Qi binding site; other site 1105108000946 cytochrome b; Provisional; Region: CYTB; MTH00191 1105108000947 intrachain domain interface; other site 1105108000948 interchain domain interface [polypeptide binding]; other site 1105108000949 heme bH binding site [chemical binding]; other site 1105108000950 heme bL binding site [chemical binding]; other site 1105108000951 Qo binding site; other site 1105108000952 Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: cytochrome_b_C; cd00290 1105108000953 interchain domain interface [polypeptide binding]; other site 1105108000954 intrachain domain interface; other site 1105108000955 Qi binding site; other site 1105108000956 Qo binding site; other site 1105108000957 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 1105108000958 catalytic site [active] 1105108000959 metal binding site [ion binding]; metal-binding site 1105108000960 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 1105108000961 Cytochrome c; Region: Cytochrom_C; cl11414 1105108000962 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 1105108000963 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 1105108000964 putative dimer interface [polypeptide binding]; other site 1105108000965 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105108000966 This domain is found in peptide chain release factors; Region: PCRF; smart00937 1105108000967 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 1105108000968 RF-1 domain; Region: RF-1; pfam00472 1105108000969 GTP-binding protein LepA; Provisional; Region: PRK05433 1105108000970 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 1105108000971 G1 box; other site 1105108000972 putative GEF interaction site [polypeptide binding]; other site 1105108000973 GTP/Mg2+ binding site [chemical binding]; other site 1105108000974 Switch I region; other site 1105108000975 G2 box; other site 1105108000976 G3 box; other site 1105108000977 Switch II region; other site 1105108000978 G4 box; other site 1105108000979 G5 box; other site 1105108000980 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu...; Region: lepA_II; cd03699 1105108000981 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 1105108000982 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 1105108000983 Phage capsid family; Region: Phage_capsid; pfam05065 1105108000984 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 1105108000985 potential frameshift: common BLAST hit: gi|67458839|ref|YP_246463.1| NACHT domain-containing protein 1105108000986 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105108000987 HD domain; Region: HD_4; pfam13328 1105108000988 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105108000989 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 1105108000990 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 1105108000991 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105108000992 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105108000993 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06588 1105108000994 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105108000995 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 1105108000996 oligomeric interface; other site 1105108000997 putative active site [active] 1105108000998 homodimer interface [polypeptide binding]; other site 1105108000999 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06589 1105108001000 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105108001001 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06591 1105108001002 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105108001003 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK07375 1105108001004 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 1105108001005 VirB7 interaction site; other site 1105108001006 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 1105108001007 Protein of unknown function (DUF2706); Region: DUF2706; pfam10913 1105108001008 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 1105108001009 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 1105108001010 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 1105108001011 type IV secretion system ATPase VirB11; Provisional; Region: PRK13900 1105108001012 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 1105108001013 Walker A motif; other site 1105108001014 hexamer interface [polypeptide binding]; other site 1105108001015 ATP binding site [chemical binding]; other site 1105108001016 Walker B motif; other site 1105108001017 type IV secretion system component VirD4; Provisional; Region: PRK13897 1105108001018 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer...; Region: TraG_VirD4; cd01126 1105108001019 Walker A motif; other site 1105108001020 ATP binding site [chemical binding]; other site 1105108001021 Walker B motif; other site 1105108001022 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 1105108001023 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 1105108001024 Phage portal protein; Region: Phage_portal; pfam04860 1105108001025 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105108001026 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105108001027 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 1105108001028 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 1105108001029 active site 1105108001030 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 1105108001031 MutS domain I; Region: MutS_I; pfam01624 1105108001032 MutS domain II; Region: MutS_II; pfam05188 1105108001033 MutS domain III; Region: MutS_III; pfam05192 1105108001034 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 1105108001035 Walker A/P-loop; other site 1105108001036 ATP binding site [chemical binding]; other site 1105108001037 Q-loop/lid; other site 1105108001038 ABC transporter signature motif; other site 1105108001039 Walker B; other site 1105108001040 D-loop; other site 1105108001041 H-loop/switch region; other site 1105108001042 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 1105108001043 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105108001044 Protein of unknown function DUF45; Region: DUF45; pfam01863 1105108001045 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 1105108001046 translocation protein TolB; Provisional; Region: tolB; PRK05137 1105108001047 TolB amino-terminal domain; Region: TolB_N; pfam04052 1105108001048 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105108001049 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105108001050 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105108001051 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 1105108001052 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1105108001053 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1105108001054 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 1105108001055 DNA binding residues [nucleotide binding] 1105108001056 Cytochrome oxidase assembly factor [Posttranslational modification, protein turnover, chaperones]; Region: COX11; COG3175 1105108001057 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 1105108001058 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 1105108001059 Ligand Binding Site [chemical binding]; other site 1105108001060 amino acid transporter; Region: 2A0306; TIGR00909 1105108001061 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 1105108001062 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 1105108001063 dimer interface [polypeptide binding]; other site 1105108001064 motif 1; other site 1105108001065 active site 1105108001066 motif 2; other site 1105108001067 motif 3; other site 1105108001068 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 1105108001069 anticodon binding site; other site 1105108001070 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1105108001071 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105108001072 Walker A/P-loop; other site 1105108001073 ATP binding site [chemical binding]; other site 1105108001074 Q-loop/lid; other site 1105108001075 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1105108001076 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105108001077 TolQ protein; Region: tolQ; TIGR02796 1105108001078 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 1105108001079 TolR protein; Region: tolR; TIGR02801 1105108001080 Gram-negative bacterial tonB protein; Region: TonB; cl10048 1105108001081 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105108001082 HD domain; Region: HD_4; pfam13328 1105108001083 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 1105108001084 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105108001085 putative substrate translocation pore; other site 1105108001086 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 1105108001087 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 1105108001088 HlyD family secretion protein; Region: HlyD_3; pfam13437 1105108001089 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 1105108001090 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 1105108001091 Walker A/P-loop; other site 1105108001092 ATP binding site [chemical binding]; other site 1105108001093 Q-loop/lid; other site 1105108001094 ABC transporter signature motif; other site 1105108001095 Walker B; other site 1105108001096 D-loop; other site 1105108001097 H-loop/switch region; other site 1105108001098 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 1105108001099 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 1105108001100 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis...; Region: HIT_like; cl00228 1105108001101 nucleotide binding site/active site [active] 1105108001102 HIT family signature motif; other site 1105108001103 catalytic residue [active] 1105108001104 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 1105108001105 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105108001106 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 1105108001107 active site 1105108001108 HslU subunit interaction site [polypeptide binding]; other site 1105108001109 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 1105108001110 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 1105108001111 Walker A motif; other site 1105108001112 ATP binding site [chemical binding]; other site 1105108001113 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 1105108001114 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1105108001115 potential frameshift: common BLAST hit: gi|91205630|ref|YP_537985.1| Mg chelatase-like protein 1105108001116 potential frameshift: common BLAST hit: gi|157827341|ref|YP_001496405.1| Mg chelatase-like protein 1105108001117 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105108001118 Uncharacterized conserved protein [Function unknown]; Region: COG5464 1105108001119 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 1105108001120 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 1105108001121 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105108001122 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 1105108001123 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 1105108001124 dimerization interface [polypeptide binding]; other site 1105108001125 Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate...; Region: Frataxin; cd00503 1105108001126 putative iron binding site [ion binding]; other site 1105108001127 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105108001128 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 1105108001129 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105108001130 HIGH motif; other site 1105108001131 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105108001132 active site 1105108001133 KMSKS motif; other site 1105108001134 DNA topoisomerase I; Validated; Region: PRK06599 1105108001135 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 1105108001136 active site 1105108001137 interdomain interaction site; other site 1105108001138 putative metal-binding site [ion binding]; other site 1105108001139 nucleotide binding site [chemical binding]; other site 1105108001140 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 1105108001141 domain I; other site 1105108001142 DNA binding groove [nucleotide binding] 1105108001143 phosphate binding site [ion binding]; other site 1105108001144 domain II; other site 1105108001145 domain III; other site 1105108001146 nucleotide binding site [chemical binding]; other site 1105108001147 catalytic site [active] 1105108001148 domain IV; other site 1105108001149 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1105108001150 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 1105108001151 DNA protecting protein DprA; Region: dprA; TIGR00732 1105108001152 DNA protecting protein DprA; Region: dprA; TIGR00732 1105108001153 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1105108001154 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 1105108001155 dimer interface [polypeptide binding]; other site 1105108001156 decamer (pentamer of dimers) interface [polypeptide binding]; other site 1105108001157 catalytic triad [active] 1105108001158 peroxidatic and resolving cysteines [active] 1105108001159 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1105108001160 Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form...; Region: Band_7_stomatin_like; cd03403 1105108001161 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 1105108001162 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 1105108001163 Sulfatase; Region: Sulfatase; pfam00884 1105108001164 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair]; Region: COG0816 1105108001165 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1105108001166 sequence-specific DNA binding site [nucleotide binding]; other site 1105108001167 salt bridge; other site 1105108001168 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 1105108001169 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 1105108001170 NADP binding site [chemical binding]; other site 1105108001171 active site 1105108001172 putative substrate binding site [chemical binding]; other site 1105108001173 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 1105108001174 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 1105108001175 NAD(P) binding site [chemical binding]; other site 1105108001176 homodimer interface [polypeptide binding]; other site 1105108001177 substrate binding site [chemical binding]; other site 1105108001178 active site 1105108001179 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 1105108001180 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 1105108001181 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 1105108001182 active site 1105108001183 homodimer interface [polypeptide binding]; other site 1105108001184 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105108001185 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 1105108001186 S-adenosylmethionine binding site [chemical binding]; other site 1105108001187 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105108001188 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 1105108001189 active site 1105108001190 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105108001191 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 1105108001192 active site 1105108001193 Membrane-fusion protein [Cell envelope biogenesis, outer membrane]; Region: AcrA; COG0845 1105108001194 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1105108001195 HlyD family secretion protein; Region: HlyD_3; pfam13437 1105108001196 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105108001197 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1105108001198 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 1105108001199 catalytic site [active] 1105108001200 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1105108001201 This family is most closely related to the GT1 family of glycosyltransferases. WavL in Vibrio cholerae has been shown to be involved in the biosynthesis of the lipopolysaccharide core; Region: GT1_WavL_like; cd03819 1105108001202 putative ADP-binding pocket [chemical binding]; other site 1105108001203 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 1105108001204 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 1105108001205 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 1105108001206 RNA binding surface [nucleotide binding]; other site 1105108001207 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 1105108001208 UbiA prenyltransferase family; Region: UbiA; pfam01040 1105108001209 spore photoproduct lyase; Region: photo_TT_lyase; cl15393 1105108001210 Domain of unknown function (DUF4385); Region: DUF4385; pfam14328 1105108001211 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 1105108001212 TPR motif; other site 1105108001213 binding surface 1105108001214 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 1105108001215 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1105108001216 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 1105108001217 RimM N-terminal domain; Region: RimM; pfam01782 1105108001218 PRC-barrel domain; Region: PRC; pfam05239 1105108001219 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1105108001220 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 1105108001221 Protein of unknown function (DUF4239); Region: DUF4239; pfam14023 1105108001222 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 1105108001223 active site 1105108001224 DNA binding site [nucleotide binding] 1105108001225 hypothetical protein; Provisional; Region: PRK14388 1105108001226 NADH dehydrogenase subunit E; Validated; Region: PRK07539 1105108001227 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 1105108001228 putative dimer interface [polypeptide binding]; other site 1105108001229 [2Fe-2S] cluster binding site [ion binding]; other site 1105108001230 COG2827 Predicted endonuclease containing a URI domain 1105108001231 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 1105108001232 NADH dehydrogenase subunit D; Validated; Region: PRK06075 1105108001233 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 1105108001234 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 1105108001235 NADH dehydrogenase subunit B; Validated; Region: PRK06411 1105108001236 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 1105108001237 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 1105108001238 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4765 1105108001239 potential frameshift: common BLAST hit: gi|67458962|ref|YP_246586.1| phage protein 1105108001240 potential frameshift: common BLAST hit: gi|67458962|ref|YP_246586.1| phage protein 1105108001241 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 1105108001242 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 1105108001243 active site 1105108001244 DNA binding site [nucleotide binding] 1105108001245 Int/Topo IB signature motif; other site 1105108001246 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06603 1105108001247 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 1105108001248 NAD binding site [chemical binding]; other site 1105108001249 homotetramer interface [polypeptide binding]; other site 1105108001250 homodimer interface [polypeptide binding]; other site 1105108001251 substrate binding site [chemical binding]; other site 1105108001252 active site 1105108001253 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 1105108001254 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 1105108001255 putative active site [active] 1105108001256 catalytic triad [active] 1105108001257 putative dimer interface [polypeptide binding]; other site 1105108001258 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1105108001259 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 1105108001260 amidase catalytic site [active] 1105108001261 Zn binding residues [ion binding]; other site 1105108001262 substrate binding site [chemical binding]; other site 1105108001263 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1105108001264 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG2984 1105108001265 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cd06574 1105108001266 TM-ABC transporter signature motif; other site 1105108001267 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 1105108001268 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 1105108001269 Walker A/P-loop; other site 1105108001270 ATP binding site [chemical binding]; other site 1105108001271 Q-loop/lid; other site 1105108001272 ABC transporter signature motif; other site 1105108001273 Walker B; other site 1105108001274 D-loop; other site 1105108001275 H-loop/switch region; other site 1105108001276 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 1105108001277 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cl02529 1105108001278 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 1105108001279 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 1105108001280 catalytic core domain of class I lysyl tRNA synthetase; Region: LysRS_core_class_I; cd00674 1105108001281 active site 1105108001282 HIGH motif; other site 1105108001283 KMSKS motif; other site 1105108001284 Predicted permeases [General function prediction only]; Region: COG0679 1105108001285 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 1105108001286 Malic enzyme, N-terminal domain; Region: malic; pfam00390 1105108001287 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 1105108001288 putative NAD(P) binding site [chemical binding]; other site 1105108001289 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 1105108001290 PIN domain of ribonucleases (toxins), VapC, FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs; Region: PIN_VapC-like; cd09861 1105108001291 putative active site [active] 1105108001292 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 1105108001293 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105108001294 malate dehydrogenase; Reviewed; Region: PRK06223 1105108001295 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 1105108001296 NAD(P) binding site [chemical binding]; other site 1105108001297 dimer interface [polypeptide binding]; other site 1105108001298 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1105108001299 substrate binding site [chemical binding]; other site 1105108001300 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 1105108001301 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105108001302 CTP synthetase; Validated; Region: pyrG; PRK05380 1105108001303 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 1105108001304 Catalytic site [active] 1105108001305 active site 1105108001306 UTP binding site [chemical binding]; other site 1105108001307 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 1105108001308 active site 1105108001309 putative oxyanion hole; other site 1105108001310 catalytic triad [active] 1105108001311 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 1105108001312 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 1105108001313 Ligand binding site; other site 1105108001314 oligomer interface; other site 1105108001315 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 1105108001316 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 1105108001317 nudix motif; other site 1105108001318 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 1105108001319 GTP cyclohydrolase I; Provisional; Region: PLN03044 1105108001320 active site 1105108001321 prolyl-tRNA synthetase; Provisional; Region: PRK12325 1105108001322 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 1105108001323 dimer interface [polypeptide binding]; other site 1105108001324 motif 1; other site 1105108001325 active site 1105108001326 motif 2; other site 1105108001327 motif 3; other site 1105108001328 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 1105108001329 anticodon binding site; other site 1105108001330 Fic family protein [Function unknown]; Region: COG3177 1105108001331 Fic/DOC family; Region: Fic; pfam02661 1105108001332 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 1105108001333 RuvA N terminal domain; Region: RuvA_N; pfam01330 1105108001334 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 1105108001335 Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]; Region: RuvB; COG2255 1105108001336 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 1105108001337 Walker A motif; other site 1105108001338 ATP binding site [chemical binding]; other site 1105108001339 Walker B motif; other site 1105108001340 arginine finger; other site 1105108001341 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 1105108001342 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1105108001343 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105108001344 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105108001345 Walker A/P-loop; other site 1105108001346 ATP binding site [chemical binding]; other site 1105108001347 Q-loop/lid; other site 1105108001348 ABC transporter signature motif; other site 1105108001349 Walker B; other site 1105108001350 D-loop; other site 1105108001351 H-loop/switch region; other site 1105108001352 muropeptide transporter; Reviewed; Region: ampG; PRK11902 1105108001353 muropeptide transporter; Validated; Region: ampG; cl17669 1105108001354 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 1105108001355 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 1105108001356 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108001357 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105108001358 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 1105108001359 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 1105108001360 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 1105108001361 BON domain; Region: BON; pfam04972 1105108001362 BON domain; Region: BON; pfam04972 1105108001363 Intracellular septation protein A [Cell division and chromosome partitioning]; Region: COG2917 1105108001364 Iron permease FTR1 family; Region: FTR1; cl00475 1105108001365 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 1105108001366 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1105108001367 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 1105108001368 Protocatechuate 3,4-dioxygenase (3,4-PCD) catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis,cis-muconate. 3,4-PCDs are large aggregates of 12 protomers, each composed of an alpha- and beta-subunit and an Fe3+ ion...; Region: 3,4-PCD; cd03459 1105108001369 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 1105108001370 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 1105108001371 catalytic residues [active] 1105108001372 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 1105108001373 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1105108001374 tandem repeat interface [polypeptide binding]; other site 1105108001375 oligomer interface [polypeptide binding]; other site 1105108001376 active site residues [active] 1105108001377 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1105108001378 trimer interface [polypeptide binding]; other site 1105108001379 active site 1105108001380 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1105108001381 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 1105108001382 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1105108001383 catalytic residue [active] 1105108001384 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 1105108001385 dimer interface [polypeptide binding]; other site 1105108001386 catalytic triad [active] 1105108001387 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 1105108001388 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 1105108001389 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 1105108001390 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 1105108001391 catalytic triad [active] 1105108001392 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 1105108001393 Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_I; cd01663 1105108001394 Subunit I/III interface [polypeptide binding]; other site 1105108001395 D-pathway; other site 1105108001396 Subunit I/VIIc interface [polypeptide binding]; other site 1105108001397 Subunit I/IV interface [polypeptide binding]; other site 1105108001398 Subunit I/II interface [polypeptide binding]; other site 1105108001399 Low-spin heme (heme a) binding site [chemical binding]; other site 1105108001400 Subunit I/VIIa interface [polypeptide binding]; other site 1105108001401 Subunit I/VIa interface [polypeptide binding]; other site 1105108001402 Dimer interface; other site 1105108001403 Putative water exit pathway; other site 1105108001404 Binuclear center (heme a3/CuB) [ion binding]; other site 1105108001405 K-pathway; other site 1105108001406 Subunit I/Vb interface [polypeptide binding]; other site 1105108001407 Putative proton exit pathway; other site 1105108001408 Subunit I/VIb interface; other site 1105108001409 Subunit I/VIc interface [polypeptide binding]; other site 1105108001410 Electron transfer pathway; other site 1105108001411 Subunit I/VIIIb interface [polypeptide binding]; other site 1105108001412 Subunit I/VIIb interface [polypeptide binding]; other site 1105108001413 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 1105108001414 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 1105108001415 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 1105108001416 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108001417 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 1105108001418 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 1105108001419 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 1105108001420 Cytidylyltransferase [Cell envelope biogenesis, outer membrane / Lipid metabolism]; Region: TagD; COG0615 1105108001421 active site 1105108001422 HIGH motif; other site 1105108001423 nucleotide binding site [chemical binding]; other site 1105108001424 putative peptidase; Provisional; Region: PRK11649 1105108001425 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105108001426 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 1105108001427 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 1105108001428 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 1105108001429 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01368 1105108001430 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105108001431 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105108001432 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105108001433 cell division protein FtsW; Region: ftsW; TIGR02614 1105108001434 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 1105108001435 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 1105108001436 active site 1105108001437 homodimer interface [polypeptide binding]; other site 1105108001438 potential frameshift: common BLAST hit: gi|157828444|ref|YP_001494686.1| RND family efflux transporter 1105108001439 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 1105108001440 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105108001441 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105108001442 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105108001443 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 1105108001444 potential frameshift: common BLAST hit: gi|67459034|ref|YP_246658.1| RND family transporter membrane-fusion protein 1105108001445 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 1105108001446 potential frameshift: common BLAST hit: gi|67459035|ref|YP_246659.1| RND efflux system, outer membrane protein 1105108001447 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 1105108001448 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1105108001449 potential frameshift: common BLAST hit: gi|374319263|ref|YP_005065762.1| Transposase-like protein 1105108001450 potential frameshift: common BLAST hit: gi|374319263|ref|YP_005065762.1| Transposase-like protein 1105108001451 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105108001452 diaminopimelate epimerase; Region: DapF; TIGR00652 1105108001453 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1105108001454 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1105108001455 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 1105108001456 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1105108001457 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 1105108001458 FeS/SAM binding site; other site 1105108001459 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 1105108001460 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 1105108001461 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 1105108001462 dimer interface [polypeptide binding]; other site 1105108001463 motif 1; other site 1105108001464 active site 1105108001465 motif 2; other site 1105108001466 motif 3; other site 1105108001467 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 1105108001468 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 1105108001469 putative tRNA-binding site [nucleotide binding]; other site 1105108001470 B3/4 domain; Region: B3_4; pfam03483 1105108001471 tRNA synthetase B5 domain; Region: B5; smart00874 1105108001472 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 1105108001473 dimer interface [polypeptide binding]; other site 1105108001474 motif 1; other site 1105108001475 motif 3; other site 1105108001476 motif 2; other site 1105108001477 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 1105108001478 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 1105108001479 DNA polymerase III subunit beta; Validated; Region: PRK05643 1105108001480 putative DNA binding surface [nucleotide binding]; other site 1105108001481 dimer interface [polypeptide binding]; other site 1105108001482 beta-clamp/clamp loader binding surface; other site 1105108001483 beta-clamp/translesion DNA polymerase binding surface; other site 1105108001484 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 1105108001485 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 1105108001486 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 1105108001487 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 1105108001488 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 1105108001489 HIGH motif; other site 1105108001490 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1105108001491 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105108001492 active site 1105108001493 KMSKS motif; other site 1105108001494 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 1105108001495 tRNA binding surface [nucleotide binding]; other site 1105108001496 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108001497 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 1105108001498 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 1105108001499 catalytic site [active] 1105108001500 putative active site [active] 1105108001501 putative substrate binding site [chemical binding]; other site 1105108001502 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 1105108001503 Septum formation initiator; Region: DivIC; pfam04977 1105108001504 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 1105108001505 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 1105108001506 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cl00230 1105108001507 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 1105108001508 catalytic residue [active] 1105108001509 putative FPP diphosphate binding site; other site 1105108001510 putative FPP binding hydrophobic cleft; other site 1105108001511 dimer interface [polypeptide binding]; other site 1105108001512 putative IPP diphosphate binding site; other site 1105108001513 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105108001514 HAMP domain; Region: HAMP; pfam00672 1105108001515 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 1105108001516 dimer interface [polypeptide binding]; other site 1105108001517 phosphorylation site [posttranslational modification] 1105108001518 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 1105108001519 ATP binding site [chemical binding]; other site 1105108001520 Mg2+ binding site [ion binding]; other site 1105108001521 G-X-G motif; other site 1105108001522 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105108001523 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 1105108001524 active site 1105108001525 phosphorylation site [posttranslational modification] 1105108001526 intermolecular recognition site; other site 1105108001527 dimerization interface [polypeptide binding]; other site 1105108001528 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 1105108001529 DNA binding site [nucleotide binding] 1105108001530 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 1105108001531 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 1105108001532 homodimer interface [polypeptide binding]; other site 1105108001533 substrate-cofactor binding pocket; other site 1105108001534 catalytic residue [active] 1105108001535 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 1105108001536 dihydrodipicolinate synthase; Region: dapA; TIGR00674 1105108001537 dimer interface [polypeptide binding]; other site 1105108001538 active site 1105108001539 catalytic residue [active] 1105108001540 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 1105108001541 SmpB-tmRNA interface; other site 1105108001542 DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC...; Region: DsbA_Com1_like; cd03023 1105108001543 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 1105108001544 catalytic residues [active] 1105108001545 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 1105108001546 CoA binding domain; Region: CoA_binding; pfam02629 1105108001547 CoA-ligase; Region: Ligase_CoA; pfam00549 1105108001548 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 1105108001549 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 1105108001550 CoA-ligase; Region: Ligase_CoA; pfam00549 1105108001551 PIN domain of ribonucleases (toxins), VapC, FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs; Region: PIN_VapC-like; cd09861 1105108001552 putative active site [active] 1105108001553 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 1105108001554 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 1105108001555 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 1105108001556 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 1105108001557 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105108001558 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4395 1105108001559 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 1105108001560 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 1105108001561 Predicted membrane protein [Function unknown]; Region: COG1238 1105108001562 Predicted membrane protein/domain [Function unknown]; Region: COG1714 1105108001563 Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]; Region: RecR; COG0353 1105108001564 RecR protein; Region: RecR; pfam02132 1105108001565 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 1105108001566 putative active site [active] 1105108001567 putative metal-binding site [ion binding]; other site 1105108001568 tetramer interface [polypeptide binding]; other site 1105108001569 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 1105108001570 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 1105108001571 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1105108001572 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 1105108001573 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 1105108001574 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 1105108001575 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 1105108001576 Predicted permeases [General function prediction only]; Region: COG0679 1105108001577 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1105108001578 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 1105108001579 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1105108001580 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105108001581 potential frameshift: common BLAST hit: gi|229586729|ref|YP_002845230.1| succinate semialdehyde dehydrogenase 1105108001582 potential frameshift: common BLAST hit: gi|15892544|ref|NP_360258.1| succinate semialdehyde dehydrogenase 1105108001583 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105108001584 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 1105108001585 active site 1105108001586 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 1105108001587 Part of AAA domain; Region: AAA_19; pfam13245 1105108001588 Family description; Region: UvrD_C_2; pfam13538 1105108001589 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 1105108001590 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 1105108001591 tetramer interface [polypeptide binding]; other site 1105108001592 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105108001593 catalytic residue [active] 1105108001594 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 1105108001595 Found in ATP-dependent protease La (LON); Region: LON; smart00464 1105108001596 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 1105108001597 Walker A motif; other site 1105108001598 ATP binding site [chemical binding]; other site 1105108001599 Walker B motif; other site 1105108001600 arginine finger; other site 1105108001601 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 1105108001602 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cd00552 1105108001603 30S subunit binding site; other site 1105108001604 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 1105108001605 Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon...; Region: LbH_gamma_CA_like; cd04645 1105108001606 trimer interface [polypeptide binding]; other site 1105108001607 putative metal binding site [ion binding]; other site 1105108001608 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14171 1105108001609 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 1105108001610 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 1105108001611 homodimer interface [polypeptide binding]; other site 1105108001612 NADP binding site [chemical binding]; other site 1105108001613 substrate binding site [chemical binding]; other site 1105108001614 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 1105108001615 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1105108001616 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105108001617 potential frameshift: common BLAST hit: gi|157827080|ref|YP_001496144.1| P pilus assembly, fimbrial usher protein 1105108001618 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 1105108001619 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 1105108001620 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 1105108001621 Spore Coat Protein U domain; Region: SCPU; smart00972 1105108001622 Chitin binding domain; Region: Chitin_bind_3; cl03871 1105108001623 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 1105108001624 Class I ribonucleotide reductase; Region: RNR_I; cd01679 1105108001625 active site 1105108001626 dimer interface [polypeptide binding]; other site 1105108001627 catalytic residues [active] 1105108001628 effector binding site; other site 1105108001629 R2 peptide binding site; other site 1105108001630 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 1105108001631 dimer interface [polypeptide binding]; other site 1105108001632 putative radical transfer pathway; other site 1105108001633 diiron center [ion binding]; other site 1105108001634 tyrosyl radical; other site 1105108001635 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 1105108001636 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 1105108001637 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 1105108001638 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 1105108001639 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 1105108001640 active site 1105108001641 substrate binding site [chemical binding]; other site 1105108001642 metal binding site [ion binding]; metal-binding site 1105108001643 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 1105108001644 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105108001645 Walker A/P-loop; other site 1105108001646 ATP binding site [chemical binding]; other site 1105108001647 Q-loop/lid; other site 1105108001648 ABC transporter signature motif; other site 1105108001649 Walker B; other site 1105108001650 D-loop; other site 1105108001651 H-loop/switch region; other site 1105108001652 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108001653 OstA-like protein; Region: OstA; pfam03968 1105108001654 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 1105108001655 KpsF/GutQ family protein; Region: kpsF; TIGR00393 1105108001656 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 1105108001657 putative active site [active] 1105108001658 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 1105108001659 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 1105108001660 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 1105108001661 RNase E interface [polypeptide binding]; other site 1105108001662 trimer interface [polypeptide binding]; other site 1105108001663 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 1105108001664 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 1105108001665 RNase E interface [polypeptide binding]; other site 1105108001666 trimer interface [polypeptide binding]; other site 1105108001667 active site 1105108001668 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 1105108001669 putative nucleic acid binding region [nucleotide binding]; other site 1105108001670 G-X-X-G motif; other site 1105108001671 S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA; Region: S1_PNPase; cd04472 1105108001672 RNA binding site [nucleotide binding]; other site 1105108001673 domain interface; other site 1105108001674 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 1105108001675 16S/18S rRNA binding site [nucleotide binding]; other site 1105108001676 S13e-L30e interaction site [polypeptide binding]; other site 1105108001677 25S rRNA binding site [nucleotide binding]; other site 1105108001678 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK14846 1105108001679 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 1105108001680 RNA binding site [nucleotide binding]; other site 1105108001681 active site 1105108001682 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108001683 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105108001684 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 1105108001685 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1105108001686 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1105108001687 non-specific DNA binding site [nucleotide binding]; other site 1105108001688 salt bridge; other site 1105108001689 sequence-specific DNA binding site [nucleotide binding]; other site 1105108001690 Ribonuclease BN family enzyme [Replication, recombination, and repair]; Region: Rbn; COG1295 1105108001691 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 1105108001692 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1105108001693 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 1105108001694 uncharacterized protein, YfiH family; Region: TIGR00726 1105108001695 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 1105108001696 active site 1105108001697 catalytic residues [active] 1105108001698 metal binding site [ion binding]; metal-binding site 1105108001699 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 1105108001700 putative active site [active] 1105108001701 homotetrameric interface [polypeptide binding]; other site 1105108001702 metal binding site [ion binding]; metal-binding site 1105108001703 hypothetical protein; Provisional; Region: PRK06661 1105108001704 intersubunit interface [polypeptide binding]; other site 1105108001705 active site 1105108001706 Zn2+ binding site [ion binding]; other site 1105108001707 pyruvate phosphate dikinase; Provisional; Region: PRK09279 1105108001708 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 1105108001709 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 1105108001710 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 1105108001711 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 1105108001712 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 1105108001713 GSH binding site (G-site) [chemical binding]; other site 1105108001714 C-terminal domain interface [polypeptide binding]; other site 1105108001715 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 1105108001716 N-terminal domain interface [polypeptide binding]; other site 1105108001717 dimer interface [polypeptide binding]; other site 1105108001718 substrate binding pocket (H-site) [chemical binding]; other site 1105108001719 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP); Region: GATase1_ScBLP_like; cd03144 1105108001720 conserved cys residue [active] 1105108001721 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 1105108001722 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 1105108001723 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 1105108001724 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 1105108001725 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 1105108001726 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105108001727 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105108001728 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105108001729 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105108001730 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 1105108001731 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 1105108001732 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 1105108001733 Uncharacterized conserved protein [Function unknown]; Region: COG5448 1105108001734 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 1105108001735 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 1105108001736 Predicted membrane protein [Function unknown]; Region: COG5346 1105108001737 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 1105108001738 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 1105108001739 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 1105108001740 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 1105108001741 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 1105108001742 E3 interaction surface; other site 1105108001743 lipoyl attachment site [posttranslational modification]; other site 1105108001744 e3 binding domain; Region: E3_binding; pfam02817 1105108001745 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 1105108001746 peptide chain release factor 1; Validated; Region: prfA; PRK00591 1105108001747 This domain is found in peptide chain release factors; Region: PCRF; smart00937 1105108001748 RF-1 domain; Region: RF-1; pfam00472 1105108001749 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 1105108001750 DHH family; Region: DHH; pfam01368 1105108001751 DHHA1 domain; Region: DHHA1; pfam02272 1105108001752 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 1105108001753 S-adenosylmethionine binding site [chemical binding]; other site 1105108001754 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105108001755 transcription termination factor Rho; Provisional; Region: rho; PRK09376 1105108001756 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 1105108001757 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 1105108001758 RNA binding site [nucleotide binding]; other site 1105108001759 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 1105108001760 multimer interface [polypeptide binding]; other site 1105108001761 Walker A motif; other site 1105108001762 ATP binding site [chemical binding]; other site 1105108001763 Walker B motif; other site 1105108001764 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 1105108001765 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1105108001766 tandem repeat interface [polypeptide binding]; other site 1105108001767 oligomer interface [polypeptide binding]; other site 1105108001768 active site residues [active] 1105108001769 Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]; Region: HimA; COG0776 1105108001770 IHF - DNA interface [nucleotide binding]; other site 1105108001771 IHF dimer interface [polypeptide binding]; other site 1105108001772 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3022 1105108001773 Cytidylate kinase [Nucleotide transport and metabolism]; Region: Cmk; COG0283 1105108001774 Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor; Region: CMPK; cd02020 1105108001775 CMP-binding site; other site 1105108001776 The sites determining sugar specificity; other site 1105108001777 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 1105108001778 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 1105108001779 RNA binding site [nucleotide binding]; other site 1105108001780 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 1105108001781 RNA binding site [nucleotide binding]; other site 1105108001782 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec3; cd05688 1105108001783 RNA binding site [nucleotide binding]; other site 1105108001784 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 1105108001785 RNA binding site [nucleotide binding]; other site 1105108001786 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 1105108001787 RNA binding site [nucleotide binding]; other site 1105108001788 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 1105108001789 RNA binding site [nucleotide binding]; other site 1105108001790 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 1105108001791 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 1105108001792 oligomer interface [polypeptide binding]; other site 1105108001793 active site residues [active] 1105108001794 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 1105108001795 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1105108001796 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 1105108001797 ATP binding site [chemical binding]; other site 1105108001798 Mg2+ binding site [ion binding]; other site 1105108001799 G-X-G motif; other site 1105108001800 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105108001801 HD domain; Region: HD_4; pfam13328 1105108001802 SecA DEAD-like domain; Region: SecA_DEAD; pfam07517 1105108001803 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 1105108001804 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; cl17351 1105108001805 nucleotide binding region [chemical binding]; other site 1105108001806 ATP-binding site [chemical binding]; other site 1105108001807 Conjugal transfer protein TraD; Region: TraD; pfam06412 1105108001808 Transposase, Mutator family; Region: Transposase_mut; pfam00872 1105108001809 MULE transposase domain; Region: MULE; pfam10551 1105108001810 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 1105108001811 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 1105108001812 Retron-type reverse transcriptase [DNA replication, recombination, and repair]; Region: COG3344 1105108001813 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 1105108001814 Ti-type conjugative transfer relaxase TraA; Region: TraA_Ti; TIGR02768 1105108001815 MobA/MobL family; Region: MobA_MobL; pfam03389 1105108001816 AAA domain; Region: AAA_30; pfam13604 1105108001817 Family description; Region: UvrD_C_2; pfam13538 1105108001818 DNA primase, catalytic core; Region: dnaG; TIGR01391 1105108001819 Toprim domain; Region: Toprim_3; pfam13362 1105108001820 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 1105108001821 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 1105108001822 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 1105108001823 Walker B motif; other site 1105108001824 hypothetical protein; Provisional; Region: PRK09956 1105108001825 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 1105108001826 F sex factor protein N terminal; Region: TraD_N; pfam12615 1105108001827 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 1105108001828 Type IV secretion-system coupling protein DNA-binding domain; Region: TrwB_AAD_bind; pfam10412 1105108001829 Walker A motif; other site 1105108001830 ATP binding site [chemical binding]; other site 1105108001831 Walker B motif; other site 1105108001832 potential frameshift: common BLAST hit: gi|189184392|ref|YP_001938177.1| TPR repeat-containing protein 01_09 1105108001833 Conjugative relaxosome accessory transposon protein; Region: TraH; cl05580 1105108001834 conjugal transfer protein TrbB; Provisional; Region: PRK13728; cl17283 1105108001835 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 1105108001836 Isopentenyl-diphosphate:dimethylallyl diphosphate isomerase type 2 (IDI-2) FMN-binding domain. Two types of IDIs have been characterized at present. The long known IDI-1 is only dependent on divalent metals for activity, whereas IDI-2 requires a metal; Region: IDI-2_FMN; cd02811 1105108001837 homotetramer interface [polypeptide binding]; other site 1105108001838 FMN binding site [chemical binding]; other site 1105108001839 homodimer contacts [polypeptide binding]; other site 1105108001840 putative active site [active] 1105108001841 putative substrate binding site [chemical binding]; other site 1105108001842 Predicted acetyltransferase [General function prediction only]; Region: COG5628 1105108001843 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105108001844 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 1105108001845 Predicted transcriptional regulator [Transcription]; Region: COG1959 1105108001846 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 1105108001847 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 1105108001848 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 1105108001849 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1105108001850 catalytic residue [active] 1105108001851 cysteine desulfurase; Provisional; Region: PRK14012 1105108001852 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 1105108001853 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1105108001854 catalytic residue [active] 1105108001855 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 1105108001856 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 1105108001857 trimerization site [polypeptide binding]; other site 1105108001858 active site 1105108001859 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 1105108001860 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1105108001861 arginine:agmatin antiporter; Provisional; Region: PRK10644 1105108001862 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 1105108001863 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 1105108001864 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP; cd01085 1105108001865 active site 1105108001866 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 1105108001867 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 1105108001868 substrate binding pocket [chemical binding]; other site 1105108001869 chain length determination region; other site 1105108001870 substrate-Mg2+ binding site; other site 1105108001871 catalytic residues [active] 1105108001872 aspartate-rich region 1; other site 1105108001873 active site lid residues [active] 1105108001874 aspartate-rich region 2; other site 1105108001875 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105108001876 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 1105108001877 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 1105108001878 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 1105108001879 muropeptide transporter; Reviewed; Region: ampG; PRK11902 1105108001880 AmpG-like permease; Region: 2A0125; TIGR00901 1105108001881 Lysine efflux permease [General function prediction only]; Region: COG1279 1105108001882 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 1105108001883 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 1105108001884 active site 1105108001885 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 1105108001886 HemY protein N-terminus; Region: HemY_N; pfam07219 1105108001887 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 1105108001888 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105108001889 RelB antitoxin; Region: RelB; cl01171 1105108001890 Protein required for attachment to host cells [Cell motility and secretion]; Region: COG5622 1105108001891 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1105108001892 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1105108001893 putative acyl-acceptor binding pocket; other site 1105108001894 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 1105108001895 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 1105108001896 active site 1105108001897 HIGH motif; other site 1105108001898 dimer interface [polypeptide binding]; other site 1105108001899 KMSKS motif; other site 1105108001900 Domain of unknown function (DUF4415); Region: DUF4415; cl01401 1105108001901 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 1105108001902 AAA domain; Region: AAA_14; pfam13173 1105108001903 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 1105108001904 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 1105108001905 domain interfaces; other site 1105108001906 active site 1105108001907 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cl00700 1105108001908 dimer interface [polypeptide binding]; other site 1105108001909 catalytic triad [active] 1105108001910 Na+/proline symporter [Amino acid transport and metabolism / General function prediction only]; Region: PutP; COG0591 1105108001911 Na binding site [ion binding]; other site 1105108001912 potential frameshift: common BLAST hit: gi|157964645|ref|YP_001499469.1| ankyrin repeat-containing protein 1105108001913 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 1105108001914 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 1105108001915 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 1105108001916 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 1105108001917 Uncharacterized conserved protein [Function unknown]; Region: COG1723 1105108001918 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 1105108001919 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 1105108001920 catalytic site [active] 1105108001921 putative active site [active] 1105108001922 putative substrate binding site [chemical binding]; other site 1105108001923 Helicase and RNase D C-terminal; Region: HRDC; smart00341 1105108001924 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 1105108001925 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 1105108001926 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 1105108001927 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 1105108001928 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105108001929 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1105108001930 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 1105108001931 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 1105108001932 S-adenosylmethionine binding site [chemical binding]; other site 1105108001933 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 1105108001934 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; pfam12762 1105108001935 Protein of unknown function (DUF2532); Region: DUF2532; pfam10811 1105108001936 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1105108001937 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 1105108001938 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1105108001939 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 1105108001940 hypothetical protein; Validated; Region: PRK00110 1105108001941 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 1105108001942 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 1105108001943 Substrate binding site; other site 1105108001944 Mg++ binding site; other site 1105108001945 potential frameshift: common BLAST hit: gi|374319434|ref|YP_005065933.1| MazG-like protein 1105108001946 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 1105108001947 NADH dehydrogenase subunit 2; Provisional; Region: ND2; MTH00196 1105108001948 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105108001949 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS_aspartate_rich; cd04823 1105108001950 dimer interface [polypeptide binding]; other site 1105108001951 allosteric magnesium binding site [ion binding]; other site 1105108001952 active site 1105108001953 aspartate-rich active site metal binding site; other site 1105108001954 Schiff base residues; other site 1105108001955 primosome assembly protein PriA; Validated; Region: PRK05580 1105108001956 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 1105108001957 ATP binding site [chemical binding]; other site 1105108001958 putative Mg++ binding site [ion binding]; other site 1105108001959 helicase superfamily c-terminal domain; Region: HELICc; smart00490 1105108001960 polyprenyl P-hydroxybenzoate and phenylacrylic acid decarboxylases; Region: ubiX_pad; TIGR00421 1105108001961 Flavoprotein; Region: Flavoprotein; pfam02441 1105108001962 SacI restriction endonuclease; Region: RE_SacI; pfam09566 1105108001963 replicative DNA helicase; Provisional; Region: PRK09165 1105108001964 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 1105108001965 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 1105108001966 Walker A motif; other site 1105108001967 ATP binding site [chemical binding]; other site 1105108001968 Walker B motif; other site 1105108001969 DNA binding loops [nucleotide binding] 1105108001970 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 1105108001971 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 1105108001972 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 1105108001973 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 1105108001974 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 1105108001975 RNA binding surface [nucleotide binding]; other site 1105108001976 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 1105108001977 active site 1105108001978 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105108001979 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105108001980 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 1105108001981 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105108001982 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105108001983 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 1105108001984 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 1105108001985 S-adenosylmethionine binding site [chemical binding]; other site 1105108001986 DNA repair protein RadA; Provisional; Region: PRK11823 1105108001987 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 1105108001988 Walker A motif/ATP binding site; other site 1105108001989 ATP binding site [chemical binding]; other site 1105108001990 Walker B motif; other site 1105108001991 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 1105108001992 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 1105108001993 Recombination protein O N terminal; Region: RecO_N; pfam11967 1105108001994 Recombination protein O C terminal; Region: RecO_C; pfam02565 1105108001995 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214 1105108001996 Glycoprotease family; Region: Peptidase_M22; pfam00814 1105108001997 translation initiation factor IF-2; Validated; Region: infB; PRK05306 1105108001998 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 1105108001999 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 1105108002000 G1 box; other site 1105108002001 putative GEF interaction site [polypeptide binding]; other site 1105108002002 GTP/Mg2+ binding site [chemical binding]; other site 1105108002003 Switch I region; other site 1105108002004 G2 box; other site 1105108002005 G3 box; other site 1105108002006 Switch II region; other site 1105108002007 G4 box; other site 1105108002008 G5 box; other site 1105108002009 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 1105108002010 Translation-initiation factor 2; Region: IF-2; pfam11987 1105108002011 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 1105108002012 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 1105108002013 NusA N-terminal domain; Region: NusA_N; pfam08529 1105108002014 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 1105108002015 RNA binding site [nucleotide binding]; other site 1105108002016 homodimer interface [polypeptide binding]; other site 1105108002017 NusA-like KH domain; Region: KH_5; pfam13184 1105108002018 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 1105108002019 G-X-X-G motif; other site 1105108002020 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 1105108002021 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG0779 1105108002022 Sm and related proteins; Region: Sm_like; cl00259 1105108002023 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 1105108002024 putative oligomer interface [polypeptide binding]; other site 1105108002025 putative RNA binding site [nucleotide binding]; other site 1105108002026 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cl06868 1105108002027 NAD binding pocket [chemical binding]; other site 1105108002028 Predicted transcriptional regulator [Transcription]; Region: COG1959 1105108002029 Transcriptional regulator; Region: Rrf2; cl17282 1105108002030 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 1105108002031 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 1105108002032 RNA binding surface [nucleotide binding]; other site 1105108002033 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 1105108002034 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 1105108002035 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 1105108002036 active site 1105108002037 HIGH motif; other site 1105108002038 dimer interface [polypeptide binding]; other site 1105108002039 KMSKS motif; other site 1105108002040 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 1105108002041 RNA binding surface [nucleotide binding]; other site 1105108002042 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 1105108002043 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 1105108002044 Substrate binding site [chemical binding]; other site 1105108002045 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105108002046 potential frameshift: common BLAST hit: gi|350273648|ref|YP_004884961.1| large extracellular alpha-helical protein 1105108002047 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 1105108002048 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 1105108002049 potential frameshift: common BLAST hit: gi|15892759|ref|NP_360473.1| 3-hydroxyacyl-CoA dehydrogenase (FadB) 1105108002050 potential frameshift: common BLAST hit: gi|341584024|ref|YP_004764515.1| putative 3-hydroxyacyl-CoA dehydrogenase (FadB) 1105108002051 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 1105108002052 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 1105108002053 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 1105108002054 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 1105108002055 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108002056 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK06617 1105108002057 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 1105108002058 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK12612 1105108002059 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1105108002060 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 1105108002061 active site 1105108002062 phosphorylation site [posttranslational modification] 1105108002063 intermolecular recognition site; other site 1105108002064 dimerization interface [polypeptide binding]; other site 1105108002065 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 1105108002066 Walker A motif; other site 1105108002067 ATP binding site [chemical binding]; other site 1105108002068 Walker B motif; other site 1105108002069 arginine finger; other site 1105108002070 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1105108002071 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105108002072 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 1105108002073 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105108002074 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 1105108002075 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 1105108002076 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1105108002077 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1105108002078 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 1105108002079 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1105108002080 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1105108002081 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 1105108002082 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 1105108002083 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 1105108002084 S-adenosylmethionine binding site [chemical binding]; other site 1105108002085 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 1105108002086 MraZ protein; Region: MraZ; pfam02381 1105108002087 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 1105108002088 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 1105108002089 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 1105108002090 Na binding site [ion binding]; other site 1105108002091 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 1105108002092 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 1105108002093 GIY-YIG motif/motif A; other site 1105108002094 active site 1105108002095 catalytic site [active] 1105108002096 putative DNA binding site [nucleotide binding]; other site 1105108002097 metal binding site [ion binding]; metal-binding site 1105108002098 UvrB/uvrC motif; Region: UVR; pfam02151 1105108002099 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 1105108002100 Copper(I)-binding protein [Inorganic ion transport and metabolism]; Region: COG2847 1105108002101 DNA alkylation repair enzyme; Region: DNA_alkylation; pfam08713 1105108002102 A new structural DNA glycosylase; Region: AlkD_like; cd06561 1105108002103 active site 1105108002104 Helix-turn-helix domain; Region: HTH_18; pfam12833 1105108002105 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 1105108002106 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 1105108002107 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 1105108002108 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 1105108002109 DNA binding site [nucleotide binding] 1105108002110 active site 1105108002111 potential frameshift: common BLAST hit: gi|91205217|ref|YP_537572.1| Type I site-specific restriction-modification system, R 1105108002112 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 1105108002113 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cl02529 1105108002114 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 1105108002115 DEAD/DEAH box helicase; Region: DEAD; pfam00270 1105108002116 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 1105108002117 SEC-C motif; Region: SEC-C; pfam02810 1105108002118 peptidylprolyl isomerase; Reviewed; Region: prsA; PRK03002 1105108002119 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 1105108002120 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 1105108002121 DNA-directed RNA polymerase, omega subunit; Region: rpoZ; TIGR00690 1105108002122 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 1105108002123 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 1105108002124 hinge; other site 1105108002125 active site 1105108002126 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 1105108002127 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 1105108002128 ATP binding site [chemical binding]; other site 1105108002129 Mg2+ binding site [ion binding]; other site 1105108002130 G-X-G motif; other site 1105108002131 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 1105108002132 anchoring element; other site 1105108002133 dimer interface [polypeptide binding]; other site 1105108002134 ATP binding site [chemical binding]; other site 1105108002135 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 1105108002136 active site 1105108002137 putative metal-binding site [ion binding]; other site 1105108002138 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1105108002139 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 1105108002140 Haloacid dehalogenase-like hydrolase; Region: Hydrolase_6; pfam13344 1105108002141 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 1105108002142 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 1105108002143 MgtE intracellular N domain; Region: MgtE_N; pfam03448 1105108002144 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 1105108002145 Divalent cation transporter; Region: MgtE; pfam01769 1105108002146 S-adenosyl-l-methionine hydroxide adenosyltransferase; Region: SAM_adeno_trans; cl17774 1105108002147 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105108002148 HD domain; Region: HD_4; pfam13328 1105108002149 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105108002150 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105108002151 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 1105108002152 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 1105108002153 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 1105108002154 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 1105108002155 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 1105108002156 Cu(I) binding site [ion binding]; other site 1105108002157 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 1105108002158 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 1105108002159 dimer interface [polypeptide binding]; other site 1105108002160 substrate binding site [chemical binding]; other site 1105108002161 metal binding sites [ion binding]; metal-binding site 1105108002162 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108002163 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 1105108002164 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 1105108002165 TraX protein; Region: TraX; pfam05857 1105108002166 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 1105108002167 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 1105108002168 ssDNA binding site; other site 1105108002169 generic binding surface II; other site 1105108002170 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 1105108002171 ATP binding site [chemical binding]; other site 1105108002172 putative Mg++ binding site [ion binding]; other site 1105108002173 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 1105108002174 nucleotide binding region [chemical binding]; other site 1105108002175 ATP-binding site [chemical binding]; other site 1105108002176 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 1105108002177 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 1105108002178 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 1105108002179 V-type ATP synthase subunit I; Validated; Region: PRK05771 1105108002180 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 1105108002181 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 1105108002182 Mg++ binding site [ion binding]; other site 1105108002183 putative catalytic motif [active] 1105108002184 putative substrate binding site [chemical binding]; other site 1105108002185 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 1105108002186 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105108002187 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105108002188 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105108002189 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 1105108002190 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105108002191 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105108002192 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105108002193 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 1105108002194 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 1105108002195 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 1105108002196 ATP binding site [chemical binding]; other site 1105108002197 putative Mg++ binding site [ion binding]; other site 1105108002198 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 1105108002199 nucleotide binding region [chemical binding]; other site 1105108002200 ATP-binding site [chemical binding]; other site 1105108002201 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 1105108002202 Uncharacterized conserved protein [Function unknown]; Region: COG2938 1105108002203 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins; Region: RHOD_1; cd01522 1105108002204 active site residue [active] 1105108002205 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 1105108002206 DnaA N-terminal domain; Region: DnaA_N; pfam11638 1105108002207 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 1105108002208 Walker A motif; other site 1105108002209 ATP binding site [chemical binding]; other site 1105108002210 Walker B motif; other site 1105108002211 arginine finger; other site 1105108002212 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 1105108002213 DnaA box-binding interface [nucleotide binding]; other site 1105108002214 Patatin [General function prediction only]; Region: COG3621 1105108002215 Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17; Region: Pat17_PNPLA8_PNPLA9_like; cd07199 1105108002216 active site 1105108002217 nucleophile elbow; other site 1105108002218 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105108002219 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105108002220 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105108002221 potential frameshift: common BLAST hit: gi|341584111|ref|YP_004764602.1| nucleotidyltransferase 1105108002222 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 1105108002223 active site 1105108002224 NTP binding site [chemical binding]; other site 1105108002225 metal binding triad [ion binding]; metal-binding site 1105108002226 GTP-binding protein YchF; Reviewed; Region: PRK09601 1105108002227 YchF GTPase; Region: YchF; cd01900 1105108002228 G1 box; other site 1105108002229 GTP/Mg2+ binding site [chemical binding]; other site 1105108002230 Switch I region; other site 1105108002231 G2 box; other site 1105108002232 Switch II region; other site 1105108002233 G3 box; other site 1105108002234 G4 box; other site 1105108002235 G5 box; other site 1105108002236 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 1105108002237 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1105108002238 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 1105108002239 putative active site [active] 1105108002240 catalytic residue [active] 1105108002241 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 1105108002242 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 1105108002243 5S rRNA interface [nucleotide binding]; other site 1105108002244 CTC domain interface [polypeptide binding]; other site 1105108002245 L16 interface [polypeptide binding]; other site 1105108002246 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 1105108002247 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 1105108002248 FeS/SAM binding site; other site 1105108002249 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 1105108002250 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 1105108002251 23S rRNA binding site [nucleotide binding]; other site 1105108002252 L21 binding site [polypeptide binding]; other site 1105108002253 L13 binding site [polypeptide binding]; other site 1105108002254 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 1105108002255 ribonuclease P; Reviewed; Region: rnpA; PRK01492 1105108002256 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 1105108002257 uncharacterized subgroup of the Escherichia coli Mg2+ transporter CorA_like subfamily; Region: EcCorA-like_u1; cd12837 1105108002258 Cl binding site [ion binding]; other site 1105108002259 oligomer interface [polypeptide binding]; other site 1105108002260 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cl17270 1105108002261 Phosphotransferase enzyme family; Region: APH; pfam01636 1105108002262 substrate binding site [chemical binding]; other site 1105108002263 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cl17270 1105108002264 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 1105108002265 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1105108002266 dimerization interface [polypeptide binding]; other site 1105108002267 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 1105108002268 dimer interface [polypeptide binding]; other site 1105108002269 phosphorylation site [posttranslational modification] 1105108002270 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 1105108002271 ATP binding site [chemical binding]; other site 1105108002272 Mg2+ binding site [ion binding]; other site 1105108002273 G-X-G motif; other site 1105108002274 Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]; Region: RpsU; COG0828 1105108002275 Uncharacterized conserved protein [Function unknown]; Region: COG5590 1105108002276 COQ9; Region: COQ9; pfam08511 1105108002277 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 1105108002278 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1105108002279 HIGH motif; other site 1105108002280 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1105108002281 active site 1105108002282 KMSKS motif; other site 1105108002283 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 1105108002284 tRNA binding surface [nucleotide binding]; other site 1105108002285 anticodon binding site; other site 1105108002286 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105108002287 Ankyrin repeat; Region: Ank; pfam00023 1105108002288 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 1105108002289 TPR motif; other site 1105108002290 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 1105108002291 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1105108002292 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 1105108002293 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 1105108002294 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 1105108002295 carboxyltransferase (CT) interaction site; other site 1105108002296 biotinylation site [posttranslational modification]; other site 1105108002297 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 1105108002298 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 1105108002299 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 1105108002300 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 1105108002301 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 1105108002302 putative substrate translocation pore; other site 1105108002303 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1105108002304 putative acyl-acceptor binding pocket; other site 1105108002305 C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas); Region: AAS_C; cd05909 1105108002306 acyl-activating enzyme (AAE) consensus motif; other site 1105108002307 putative AMP binding site [chemical binding]; other site 1105108002308 TfoX N-terminal domain; Region: TfoX_N; pfam04993 1105108002309 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 1105108002310 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cl00462 1105108002311 ABC-ATPase subunit interface; other site 1105108002312 dimer interface [polypeptide binding]; other site 1105108002313 putative PBP binding regions; other site 1105108002314 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 1105108002315 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108002316 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 1105108002317 S-adenosylmethionine binding site [chemical binding]; other site 1105108002318 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 1105108002319 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105108002320 HIGH motif; other site 1105108002321 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105108002322 active site 1105108002323 KMSKS motif; other site 1105108002324 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108002325 Invasion protein B, involved in pathogenesis [General function prediction only]; Region: COG5342 1105108002326 potential frameshift: common BLAST hit: gi|350273705|ref|YP_004885018.1| chaperonin groEL 1105108002327 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 1105108002328 oligomerisation interface [polypeptide binding]; other site 1105108002329 mobile loop; other site 1105108002330 roof hairpin; other site 1105108002331 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 1105108002332 potential frameshift: common BLAST hit: gi|67458799|ref|YP_246423.1| glycosyltransferase 1105108002333 ribonuclease PH; Reviewed; Region: rph; PRK00173 1105108002334 Ribonuclease PH; Region: RNase_PH_bact; cd11362 1105108002335 hexamer interface [polypeptide binding]; other site 1105108002336 active site 1105108002337 GrpE; Region: GrpE; pfam01025 1105108002338 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 1105108002339 dimer interface [polypeptide binding]; other site 1105108002340 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 1105108002341 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 1105108002342 Domain of unknown function DUF20; Region: UPF0118; pfam01594 1105108002343 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 1105108002344 hypothetical protein; Validated; Region: PRK06620 1105108002345 proline/glycine betaine transporter; Provisional; Region: PRK10642 1105108002346 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105108002347 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 1105108002348 Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]; Region: RplQ; COG0203 1105108002349 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 1105108002350 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 1105108002351 alphaNTD - beta interaction site [polypeptide binding]; other site 1105108002352 alphaNTD homodimer interface [polypeptide binding]; other site 1105108002353 alphaNTD - beta' interaction site [polypeptide binding]; other site 1105108002354 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 1105108002355 30S ribosomal protein S11; Validated; Region: PRK05309 1105108002356 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 1105108002357 30S ribosomal protein S13; Region: bact_S13; TIGR03631 1105108002358 adenylate kinase; Reviewed; Region: adk; PRK00279 1105108002359 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 1105108002360 AMP-binding site [chemical binding]; other site 1105108002361 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 1105108002362 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 1105108002363 SecY translocase; Region: SecY; pfam00344 1105108002364 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 1105108002365 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that...; Region: Ribosomal_L30; cd01658 1105108002366 23S rRNA binding site [nucleotide binding]; other site 1105108002367 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 1105108002368 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 1105108002369 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 1105108002370 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 1105108002371 5S rRNA interface [nucleotide binding]; other site 1105108002372 23S rRNA interface [nucleotide binding]; other site 1105108002373 L5 interface [polypeptide binding]; other site 1105108002374 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 1105108002375 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1105108002376 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1105108002377 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 1105108002378 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 1105108002379 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 1105108002380 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 1105108002381 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 1105108002382 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 1105108002383 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 1105108002384 RNA binding site [nucleotide binding]; other site 1105108002385 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 1105108002386 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 1105108002387 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 1105108002388 L23 interface [polypeptide binding]; other site 1105108002389 trigger factor interaction site; other site 1105108002390 23S rRNA interface [nucleotide binding]; other site 1105108002391 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 1105108002392 23S rRNA interface [nucleotide binding]; other site 1105108002393 5S rRNA interface [nucleotide binding]; other site 1105108002394 putative antibiotic binding site [chemical binding]; other site 1105108002395 L25 interface [polypeptide binding]; other site 1105108002396 L27 interface [polypeptide binding]; other site 1105108002397 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 1105108002398 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 1105108002399 G-X-X-G motif; other site 1105108002400 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 1105108002401 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 1105108002402 putative translocon binding site; other site 1105108002403 protein-rRNA interface [nucleotide binding]; other site 1105108002404 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 1105108002405 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 1105108002406 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 1105108002407 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 1105108002408 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 1105108002409 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 1105108002410 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 1105108002411 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 1105108002412 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108002413 elongation factor Tu; Reviewed; Region: PRK00049 1105108002414 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 1105108002415 G1 box; other site 1105108002416 GEF interaction site [polypeptide binding]; other site 1105108002417 GTP/Mg2+ binding site [chemical binding]; other site 1105108002418 Switch I region; other site 1105108002419 G2 box; other site 1105108002420 G3 box; other site 1105108002421 Switch II region; other site 1105108002422 G4 box; other site 1105108002423 G5 box; other site 1105108002424 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 1105108002425 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 1105108002426 Antibiotic Binding Site [chemical binding]; other site 1105108002427 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 1105108002428 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 1105108002429 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 1105108002430 fumarate hydratase; Reviewed; Region: fumC; PRK00485 1105108002431 Class II fumarases; Region: Fumarase_classII; cd01362 1105108002432 active site 1105108002433 tetramer interface [polypeptide binding]; other site 1105108002434 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 1105108002435 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 1105108002436 putative active site [active] 1105108002437 homotetrameric interface [polypeptide binding]; other site 1105108002438 cell division protein FtsZ; Validated; Region: PRK09330 1105108002439 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 1105108002440 nucleotide binding site [chemical binding]; other site 1105108002441 SulA interaction site; other site 1105108002442 Serine protease inhibitor ecotin [General function prediction only]; Region: Eco; COG4574 1105108002443 primary substrate binding site; other site 1105108002444 inhibition loop; other site 1105108002445 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; smart00932 1105108002446 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 1105108002447 muropeptide transporter; Validated; Region: ampG; cl17669 1105108002448 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 1105108002449 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 1105108002450 ATP binding site [chemical binding]; other site 1105108002451 Mg++ binding site [ion binding]; other site 1105108002452 motif III; other site 1105108002453 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 1105108002454 nucleotide binding region [chemical binding]; other site 1105108002455 ATP-binding site [chemical binding]; other site 1105108002456 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 1105108002457 DNA-binding site [nucleotide binding]; DNA binding site 1105108002458 RNA-binding motif; other site 1105108002459 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 1105108002460 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 1105108002461 S-adenosylmethionine binding site [chemical binding]; other site 1105108002462 SurA N-terminal domain; Region: SurA_N_3; cl07813 1105108002463 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 1105108002464 Organic solvent tolerance protein; Region: OstA_C; pfam04453 1105108002465 Exonuclease VII, large subunit [DNA replication, recombination, and repair]; Region: XseA; COG1570 1105108002466 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 1105108002467 generic binding surface II; other site 1105108002468 generic binding surface I; other site 1105108002469 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1105108002470 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 1105108002471 putative catalytic site [active] 1105108002472 putative phosphate binding site [ion binding]; other site 1105108002473 active site 1105108002474 metal binding site A [ion binding]; metal-binding site 1105108002475 DNA binding site [nucleotide binding] 1105108002476 putative AP binding site [nucleotide binding]; other site 1105108002477 putative metal binding site B [ion binding]; other site 1105108002478 Uncharacterized conserved protein [Function unknown]; Region: COG4095 1105108002479 GTP-binding protein Der; Reviewed; Region: PRK00093 1105108002480 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 1105108002481 G1 box; other site 1105108002482 GTP/Mg2+ binding site [chemical binding]; other site 1105108002483 Switch I region; other site 1105108002484 G2 box; other site 1105108002485 Switch II region; other site 1105108002486 G3 box; other site 1105108002487 G4 box; other site 1105108002488 G5 box; other site 1105108002489 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 1105108002490 G1 box; other site 1105108002491 GTP/Mg2+ binding site [chemical binding]; other site 1105108002492 Switch I region; other site 1105108002493 G2 box; other site 1105108002494 G3 box; other site 1105108002495 Switch II region; other site 1105108002496 G4 box; other site 1105108002497 G5 box; other site 1105108002498 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 1105108002499 AAA domain; Region: AAA_14; pfam13173 1105108002500 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 1105108002501 ABC1 family; Region: ABC1; cl17513 1105108002502 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 1105108002503 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 1105108002504 S-adenosylmethionine binding site [chemical binding]; other site 1105108002505 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 1105108002506 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 1105108002507 DNA binding site [nucleotide binding] 1105108002508 catalytic residue [active] 1105108002509 H2TH interface [polypeptide binding]; other site 1105108002510 putative catalytic residues [active] 1105108002511 turnover-facilitating residue; other site 1105108002512 intercalation triad [nucleotide binding]; other site 1105108002513 8OG recognition residue [nucleotide binding]; other site 1105108002514 putative reading head residues; other site 1105108002515 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 1105108002516 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 1105108002517 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108002518 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105108002519 Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]; Region: {ManC}; COG0836 1105108002520 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 1105108002521 active site 1105108002522 potential frameshift: common BLAST hit: gi|15892963|ref|NP_360677.1| mannose-1-phosphate guanylyltransferase 1105108002523 potential frameshift: common BLAST hit: gi|67458630|ref|YP_246254.1| Poly-beta-hydroxyalkanoate depolymerase 1105108002524 potential frameshift: common BLAST hit: gi|67458630|ref|YP_246254.1| Poly-beta-hydroxyalkanoate depolymerase 1105108002525 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105108002526 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105108002527 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105108002528 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105108002529 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 1105108002530 active site 1105108002531 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 1105108002532 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 1105108002533 HIGH motif; other site 1105108002534 active site 1105108002535 KMSKS motif; other site 1105108002536 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 1105108002537 tRNA binding surface [nucleotide binding]; other site 1105108002538 anticodon binding site; other site 1105108002539 thymidylate kinase; Validated; Region: tmk; PRK00698 1105108002540 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 1105108002541 TMP-binding site; other site 1105108002542 ATP-binding site [chemical binding]; other site 1105108002543 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105108002544 4-hydroxybenzoate polyprenyltransferase; Reviewed; Region: ubiA; PRK12847 1105108002545 UbiA prenyltransferase family; Region: UbiA; pfam01040 1105108002546 potential frameshift: common BLAST hit: gi|350273815|ref|YP_004885128.1| transposase 1105108002547 valyl-tRNA synthetase; Reviewed; Region: valS; PRK13208 1105108002548 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105108002549 active site 1105108002550 HIGH motif; other site 1105108002551 nucleotide binding site [chemical binding]; other site 1105108002552 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1105108002553 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105108002554 active site 1105108002555 KMSKS motif; other site 1105108002556 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 1105108002557 tRNA binding surface [nucleotide binding]; other site 1105108002558 anticodon binding site; other site 1105108002559 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 1105108002560 potential frameshift: common BLAST hit: gi|157804076|ref|YP_001492625.1| ATPase 1105108002561 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 1105108002562 RmuC family; Region: RmuC; pfam02646 1105108002563 Glycosyltransferase family 10 (fucosyltransferase); Region: Glyco_transf_10; pfam00852 1105108002564 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 1105108002565 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 1105108002566 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105108002567 DoxX-like family; Region: DoxX_3; pfam13781 1105108002568 Predicted integral membrane protein (DUF2269); Region: DUF2269; pfam10027 1105108002569 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 1105108002570 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 1105108002571 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 1105108002572 Walker A motif; other site 1105108002573 ATP binding site [chemical binding]; other site 1105108002574 Walker B motif; other site 1105108002575 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1105108002576 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 1105108002577 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1105108002578 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 1105108002579 Ligand Binding Site [chemical binding]; other site 1105108002580 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 1105108002581 HicB family; Region: HicB; pfam05534 1105108002582 YcfA-like protein; Region: YcfA; cl00752 1105108002583 potential protein location (hypothetical protein MC1_05995 [Rickettsia parkeri str. Portsmouth]) that overlaps RNA (tRNA-H) 1105108002584 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 1105108002585 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105108002586 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105108002587 Walker A/P-loop; other site 1105108002588 ATP binding site [chemical binding]; other site 1105108002589 Q-loop/lid; other site 1105108002590 ABC transporter signature motif; other site 1105108002591 Walker B; other site 1105108002592 D-loop; other site 1105108002593 H-loop/switch region; other site 1105108002594 Protein of unknown function (DUF2673); Region: DUF2673; pfam10880 1105108002595 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 1105108002596 putative substrate translocation pore; other site 1105108002597 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 1105108002598 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1105108002599 FtsX-like permease family; Region: FtsX; pfam02687 1105108002600 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1105108002601 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1105108002602 Walker A/P-loop; other site 1105108002603 ATP binding site [chemical binding]; other site 1105108002604 Q-loop/lid; other site 1105108002605 ABC transporter signature motif; other site 1105108002606 Walker B; other site 1105108002607 D-loop; other site 1105108002608 H-loop/switch region; other site 1105108002609 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 1105108002610 Domain of unknown function DUF21; Region: DUF21; pfam01595 1105108002611 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 1105108002612 Transporter associated domain; Region: CorC_HlyC; smart01091 1105108002613 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 1105108002614 AAA domain; Region: AAA_22; pfam13401 1105108002615 Rickettsia outer membrane protein B; Region: rOmpB; pfam12334 1105108002616 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 1105108002617 Autotransporter beta-domain; Region: Autotransporter; smart00869 1105108002618 potential frameshift: common BLAST hit: gi|229587064|ref|YP_002845565.1| Guanosine polyphosphate pyrophosphohydrolase/synthetase 1105108002619 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 1105108002620 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 1105108002621 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 1105108002622 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 1105108002623 DNA binding residues [nucleotide binding] 1105108002624 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 1105108002625 IHF dimer interface [polypeptide binding]; other site 1105108002626 IHF - DNA interface [nucleotide binding]; other site 1105108002627 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1105108002628 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 1105108002629 catalytic triad [active] 1105108002630 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 1105108002631 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 1105108002632 putative acyl-acceptor binding pocket; other site 1105108002633 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 1105108002634 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 1105108002635 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1105108002636 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105108002637 Protein of unknown function (DUF519); Region: DUF519; pfam04378 1105108002638 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 1105108002639 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 1105108002640 nucleotide binding pocket [chemical binding]; other site 1105108002641 K-X-D-G motif; other site 1105108002642 catalytic site [active] 1105108002643 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 1105108002644 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 1105108002645 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 1105108002646 Dimer interface [polypeptide binding]; other site 1105108002647 BRCT sequence motif; other site 1105108002648 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 1105108002649 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 1105108002650 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 1105108002651 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105108002652 HD domain; Region: HD_4; pfam13328 1105108002653 potential frameshift: common BLAST hit: gi|67458578|ref|YP_246202.1| proline/betaine transporter 1105108002654 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 1105108002655 mce related protein; Region: MCE; pfam02470 1105108002656 hypothetical protein; Provisional; Region: PRK06630 1105108002657 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 1105108002658 RNA/DNA hybrid binding site [nucleotide binding]; other site 1105108002659 active site 1105108002660 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3814 1105108002661 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3494 1105108002662 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 1105108002663 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 1105108002664 CoA-binding site [chemical binding]; other site 1105108002665 ATP-binding [chemical binding]; other site 1105108002666 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 1105108002667 DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; Region: DNA_pol_III_epsilon_Ecoli_like; cd06131 1105108002668 active site 1105108002669 catalytic site [active] 1105108002670 substrate binding site [chemical binding]; other site 1105108002671 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cd06662 1105108002672 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 1105108002673 Part of AAA domain; Region: AAA_19; pfam13245 1105108002674 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 1105108002675 UvrD-like helicase C-terminal domain; Region: UvrD_C; pfam13361 1105108002676 Family description; Region: UvrD_C_2; pfam13538 1105108002677 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 1105108002678 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 1105108002679 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 1105108002680 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cl02529 1105108002681 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105108002682 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105108002683 acetyl-CoA acetyltransferase; Provisional; Region: PRK06633 1105108002684 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 1105108002685 dimer interface [polypeptide binding]; other site 1105108002686 active site 1105108002687 Uncharacterized conserved protein (DUF2048); Region: DUF2048; pfam09752 1105108002688 potential frameshift: common BLAST hit: gi|165933696|ref|YP_001650485.1| poly-beta-hydroxybutyrate polymerase 1105108002689 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105108002690 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity. They also contain a...; Region: Nudix_Hydrolase_1; cd03674 1105108002691 nudix motif; other site 1105108002692 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 1105108002693 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 1105108002694 Transporter associated domain; Region: CorC_HlyC; smart01091 1105108002695 metal-binding heat shock protein; Provisional; Region: PRK00016 1105108002696 PemK-like protein; Region: PemK; cl00995 1105108002697 lipoyl synthase; Provisional; Region: PRK05481 1105108002698 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 1105108002699 FeS/SAM binding site; other site 1105108002700 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 1105108002701 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 1105108002702 dimer interface [polypeptide binding]; other site 1105108002703 active site 1105108002704 glycine-pyridoxal phosphate binding site [chemical binding]; other site 1105108002705 folate binding site [chemical binding]; other site 1105108002706 Predicted esterase [General function prediction only]; Region: COG0400 1105108002707 putative hydrolase; Provisional; Region: PRK11460 1105108002708 Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain...; Region: GRX_PICOT_like; cd03028 1105108002709 putative GSH binding site [chemical binding]; other site 1105108002710 catalytic residues [active] 1105108002711 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 1105108002712 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1105108002713 minor groove reading motif; other site 1105108002714 helix-hairpin-helix signature motif; other site 1105108002715 substrate binding pocket [chemical binding]; other site 1105108002716 active site 1105108002717 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 1105108002718 Ycf1; Provisional; Region: ycf1; CHL00204 1105108002719 Entericidin EcnA/B family; Region: Entericidin; cl02322 1105108002720 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105108002721 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105108002722 Predicted methyltransferases [General function prediction only]; Region: COG0313 1105108002723 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 1105108002724 putative SAM binding site [chemical binding]; other site 1105108002725 putative homodimer interface [polypeptide binding]; other site 1105108002726 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 1105108002727 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 1105108002728 putative ligand binding site [chemical binding]; other site 1105108002729 twin arginine translocase protein A; Provisional; Region: tatA; PRK01470 1105108002730 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 1105108002731 tetramer interfaces [polypeptide binding]; other site 1105108002732 binuclear metal-binding site [ion binding]; other site 1105108002733 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 1105108002734 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 1105108002735 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 1105108002736 aspartate kinase; Reviewed; Region: PRK06635 1105108002737 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 1105108002738 putative nucleotide binding site [chemical binding]; other site 1105108002739 putative catalytic residues [active] 1105108002740 putative Mg ion binding site [ion binding]; other site 1105108002741 putative aspartate binding site [chemical binding]; other site 1105108002742 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 1105108002743 putative allosteric regulatory residue; other site 1105108002744 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 1105108002745 Peptidase M55, D-aminopeptidase dipeptide-binding protein family; Region: DAP_dppA; cl01007 1105108002746 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 1105108002747 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 1105108002748 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 1105108002749 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105108002750 putative substrate translocation pore; other site 1105108002751 Cell division protein ZapA (stimulator of FtsZ polymerization and Z-ring component) [Cell cycle control, cell division, chromosome partitioning]; Region: zapA; COG3027 1105108002752 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108002753 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 1105108002754 Helix-turn-helix domain; Region: HTH_25; pfam13413 1105108002755 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]; Region: COG2902 1105108002756 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 1105108002757 Predicted GTPase [General function prediction only]; Region: ThdF; COG0486 1105108002758 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 1105108002759 trmE is a tRNA modification GTPase; Region: trmE; cd04164 1105108002760 G1 box; other site 1105108002761 GTP/Mg2+ binding site [chemical binding]; other site 1105108002762 Switch I region; other site 1105108002763 G2 box; other site 1105108002764 Switch II region; other site 1105108002765 G3 box; other site 1105108002766 G4 box; other site 1105108002767 G5 box; other site 1105108002768 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 1105108002769 methyl viologen resistance protein SmvA; Provisional; Region: PRK14995 1105108002770 methyl viologen resistance protein SmvA; Provisional; Region: PRK14995 1105108002771 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 1105108002772 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 1105108002773 RecA/RadA recombinase [DNA replication, recombination, and repair]; Region: RecA; COG0468 1105108002774 hexamer interface [polypeptide binding]; other site 1105108002775 Walker A motif; other site 1105108002776 ATP binding site [chemical binding]; other site 1105108002777 Walker B motif; other site 1105108002778 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 1105108002779 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105108002780 NAD(P) binding site [chemical binding]; other site 1105108002781 active site 1105108002782 acyl carrier protein; Provisional; Region: acpP; PRK00982 1105108002783 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 1105108002784 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 1105108002785 dimer interface [polypeptide binding]; other site 1105108002786 active site 1105108002787 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1105108002788 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105108002789 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105108002790 potential frameshift: common BLAST hit: gi|374319737|ref|YP_005066236.1| Putative AAA+ superfamily ATPase 1105108002791 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108002792 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 1105108002793 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 1105108002794 catalytic site [active] 1105108002795 G-X2-G-X-G-K; other site 1105108002796 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1105108002797 sequence-specific DNA binding site [nucleotide binding]; other site 1105108002798 salt bridge; other site 1105108002799 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 1105108002800 rod shape-determining protein MreC; Region: MreC; pfam04085 1105108002801 rod shape-determining protein MreB; Provisional; Region: PRK13927 1105108002802 MreB and similar proteins; Region: MreB_like; cd10225 1105108002803 nucleotide binding site [chemical binding]; other site 1105108002804 Mg binding site [ion binding]; other site 1105108002805 putative protofilament interaction site [polypeptide binding]; other site 1105108002806 RodZ interaction site [polypeptide binding]; other site 1105108002807 Predicted permeases [General function prediction only]; Region: COG0795 1105108002808 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1105108002809 putative outer membrane lipoprotein; Provisional; Region: PRK09967 1105108002810 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1105108002811 ligand binding site [chemical binding]; other site 1105108002812 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108002813 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 1105108002814 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 1105108002815 dimer interface [polypeptide binding]; other site 1105108002816 active site 1105108002817 CoA binding pocket [chemical binding]; other site 1105108002818 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 1105108002819 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 1105108002820 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 1105108002821 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 1105108002822 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 1105108002823 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 1105108002824 P loop; other site 1105108002825 GTP binding site [chemical binding]; other site 1105108002826 DNA polymerase I; Provisional; Region: PRK05755 1105108002827 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 1105108002828 active site 1105108002829 metal binding site 1 [ion binding]; metal-binding site 1105108002830 putative 5' ssDNA interaction site; other site 1105108002831 metal binding site 3; metal-binding site 1105108002832 metal binding site 2 [ion binding]; metal-binding site 1105108002833 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 1105108002834 putative DNA binding site [nucleotide binding]; other site 1105108002835 putative metal binding site [ion binding]; other site 1105108002836 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 1105108002837 active site 1105108002838 substrate binding site [chemical binding]; other site 1105108002839 catalytic site [active] 1105108002840 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 1105108002841 active site 1105108002842 DNA binding site [nucleotide binding] 1105108002843 catalytic site [active] 1105108002844 potential frameshift: common BLAST hit: gi|157826229|ref|YP_001493949.1| S-adenosylmethionine synthetase 1105108002845 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 1105108002846 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 1105108002847 putative active site [active] 1105108002848 putative PHP Thumb interface [polypeptide binding]; other site 1105108002849 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 1105108002850 generic binding surface I; other site 1105108002851 generic binding surface II; other site 1105108002852 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 1105108002853 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 1105108002854 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 1105108002855 Protein of unknown function; Region: DUF3971; pfam13116 1105108002856 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1105108002857 Acetyl-coenzyme A transporter 1; Region: Acatn; pfam13000 1105108002858 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 1105108002859 putative substrate translocation pore; other site 1105108002860 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 1105108002861 seryl-tRNA synthetase; Provisional; Region: PRK05431 1105108002862 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 1105108002863 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 1105108002864 dimer interface [polypeptide binding]; other site 1105108002865 active site 1105108002866 motif 1; other site 1105108002867 motif 2; other site 1105108002868 motif 3; other site 1105108002869 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105108002870 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 1105108002871 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1105108002872 Integral membrane protein TerC family; Region: TerC; cl10468 1105108002873 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 1105108002874 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105108002875 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 1105108002876 S-adenosylmethionine binding site [chemical binding]; other site 1105108002877 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 1105108002878 Predicted transcriptional regulator [Transcription]; Region: COG2944 1105108002879 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1105108002880 salt bridge; other site 1105108002881 non-specific DNA binding site [nucleotide binding]; other site 1105108002882 sequence-specific DNA binding site [nucleotide binding]; other site 1105108002883 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 1105108002884 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 1105108002885 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 1105108002886 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 1105108002887 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 1105108002888 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 1105108002889 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105108002890 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 1105108002891 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105108002892 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13541 1105108002893 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105108002894 Walker A/P-loop; other site 1105108002895 ATP binding site [chemical binding]; other site 1105108002896 Q-loop/lid; other site 1105108002897 ABC transporter signature motif; other site 1105108002898 Walker B; other site 1105108002899 D-loop; other site 1105108002900 H-loop/switch region; other site 1105108002901 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 1105108002902 4Fe-4S binding domain; Region: Fer4; cl02805 1105108002903 4Fe-4S binding domain; Region: Fer4; pfam00037 1105108002904 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 1105108002905 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 1105108002906 NADH dehydrogenase subunit G; Validated; Region: PRK09130 1105108002907 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 1105108002908 catalytic loop [active] 1105108002909 iron binding site [ion binding]; other site 1105108002910 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 1105108002911 MopB_Res_Cmplx1_Nad11: The second domain of the Nad11/75-kDa subunit of the NADH-quinone oxidoreductase/respiratory complex I/NADH dehydrogenase-1(NDH-1) of eukaryotes and the Nqo3/G subunit of alphaproteobacteria NDH-1. The NADH-quinone oxidoreductase...; Region: MopB_Res-Cmplx1_Nad11; cd02773 1105108002912 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 1105108002913 Predicted membrane protein [Function unknown]; Region: COG3671 1105108002914 aconitate hydratase; Validated; Region: PRK09277 1105108002915 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 1105108002916 substrate binding site [chemical binding]; other site 1105108002917 ligand binding site [chemical binding]; other site 1105108002918 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 1105108002919 substrate binding site [chemical binding]; other site 1105108002920 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK01474 1105108002921 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 1105108002922 gamma subunit interface [polypeptide binding]; other site 1105108002923 epsilon subunit interface [polypeptide binding]; other site 1105108002924 LBP interface [polypeptide binding]; other site 1105108002925 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 1105108002926 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1105108002927 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 1105108002928 alpha subunit interaction interface [polypeptide binding]; other site 1105108002929 Walker A motif; other site 1105108002930 ATP binding site [chemical binding]; other site 1105108002931 Walker B motif; other site 1105108002932 inhibitor binding site; inhibition site 1105108002933 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1105108002934 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 1105108002935 core domain interface [polypeptide binding]; other site 1105108002936 delta subunit interface [polypeptide binding]; other site 1105108002937 epsilon subunit interface [polypeptide binding]; other site 1105108002938 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 1105108002939 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1105108002940 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 1105108002941 beta subunit interaction interface [polypeptide binding]; other site 1105108002942 Walker A motif; other site 1105108002943 ATP binding site [chemical binding]; other site 1105108002944 Walker B motif; other site 1105108002945 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1105108002946 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 1105108002947 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 1105108002948 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 1105108002949 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1105108002950 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105108002951 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1105108002952 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 1105108002953 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 1105108002954 dinuclear metal binding motif [ion binding]; other site 1105108002955 Beta-lactamase class D [Defense mechanisms]; Region: COG2602 1105108002956 Beta-lactamase class D [Defense mechanisms]; Region: COG2602 1105108002957 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 1105108002958 Transglycosylase; Region: Transgly; pfam00912 1105108002959 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1105108002960 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 1105108002961 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1105108002962 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 1105108002963 FeS/SAM binding site; other site 1105108002964 TRAM domain; Region: TRAM; pfam01938 1105108002965 HEPN domain; Region: HEPN; cl00824 1105108002966 potential frameshift: common BLAST hit: gi|67459332|ref|YP_246956.1| nucleotidyltransferase/HEPN domain-containing protein 1105108002967 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 1105108002968 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105108002969 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105108002970 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105108002971 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 1105108002972 Bacterial SH3 domain; Region: SH3_4; pfam06347 1105108002973 Bacterial SH3 domain; Region: SH3_4; pfam06347 1105108002974 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 1105108002975 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 1105108002976 TrkA-N domain; Region: TrkA_N; pfam02254 1105108002977 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 1105108002978 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 1105108002979 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105108002980 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105108002981 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105108002982 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105108002983 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 1105108002984 rRNA binding site [nucleotide binding]; other site 1105108002985 predicted 30S ribosome binding site; other site 1105108002986 Maf-like protein; Region: Maf; pfam02545 1105108002987 Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or...; Region: Maf; cd00555 1105108002988 active site 1105108002989 dimer interface [polypeptide binding]; other site 1105108002990 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 1105108002991 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 1105108002992 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 1105108002993 active site 1105108002994 DNA binding site [nucleotide binding] 1105108002995 Int/Topo IB signature motif; other site 1105108002996 Phasin protein; Region: Phasin_2; pfam09361 1105108002997 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 1105108002998 PLD-like domain; Region: PLDc_2; pfam13091 1105108002999 putative active site [active] 1105108003000 catalytic site [active] 1105108003001 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 1105108003002 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism]; Region: UbiD; COG0043 1105108003003 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 1105108003004 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 1105108003005 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 1105108003006 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105108003007 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 1105108003008 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 1105108003009 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 1105108003010 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 1105108003011 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 1105108003012 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 1105108003013 active site 1105108003014 DNA repair proteins [DNA replication, recombination, and repair]; Region: RadC; COG2003 1105108003015 DNA repair proteins [DNA replication, recombination, and repair]; Region: RadC; COG2003 1105108003016 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 1105108003017 MPN+ (JAMM) motif; other site 1105108003018 Zinc-binding site [ion binding]; other site 1105108003019 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 1105108003020 The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine precursor; Region: GT_WbpL_WbcO_like; cd06854 1105108003021 Mg++ binding site [ion binding]; other site 1105108003022 putative catalytic motif [active] 1105108003023 putative substrate binding site [chemical binding]; other site 1105108003024 Protein of unknown function (DUF721); Region: DUF721; pfam05258 1105108003025 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 1105108003026 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 1105108003027 Ferredoxin [Energy production and conversion]; Region: COG1146 1105108003028 4Fe-4S binding domain; Region: Fer4; cl02805 1105108003029 heme exporter protein CcmC; Region: ccmC; TIGR01191 1105108003030 Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a...; Region: nucleoside_deaminase; cd01285 1105108003031 nucleoside/Zn binding site; other site 1105108003032 dimer interface [polypeptide binding]; other site 1105108003033 catalytic motif [active] 1105108003034 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 1105108003035 Cation efflux family; Region: Cation_efflux; cl00316 1105108003036 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 1105108003037 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 1105108003038 substrate binding site [chemical binding]; other site 1105108003039 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 1105108003040 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 1105108003041 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 1105108003042 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1105108003043 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1105108003044 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 1105108003045 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 1105108003046 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 1105108003047 dimer interface [polypeptide binding]; other site 1105108003048 ssDNA binding site [nucleotide binding]; other site 1105108003049 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1105108003050 Phage-related lysozyme (muraminidase) [General function prediction only]; Region: COG3772 1105108003051 hypothetical protein; Reviewed; Region: PRK01530 1105108003052 heat shock protein 90; Provisional; Region: PRK05218 1105108003053 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 1105108003054 ATP binding site [chemical binding]; other site 1105108003055 Mg2+ binding site [ion binding]; other site 1105108003056 G-X-G motif; other site 1105108003057 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 1105108003058 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS); Region: KBL_like; cd06454 1105108003059 substrate-cofactor binding pocket; other site 1105108003060 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105108003061 catalytic residue [active] 1105108003062 trigger factor; Provisional; Region: tig; PRK01490 1105108003063 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1105108003064 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 1105108003065 GTPase CgtA; Reviewed; Region: obgE; PRK12299 1105108003066 GTP1/OBG; Region: GTP1_OBG; pfam01018 1105108003067 Obg GTPase; Region: Obg; cd01898 1105108003068 G1 box; other site 1105108003069 GTP/Mg2+ binding site [chemical binding]; other site 1105108003070 Switch I region; other site 1105108003071 G2 box; other site 1105108003072 G3 box; other site 1105108003073 Switch II region; other site 1105108003074 G4 box; other site 1105108003075 G5 box; other site 1105108003076 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 1105108003077 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 1105108003078 dimer interface [polypeptide binding]; other site 1105108003079 active site 1105108003080 citrylCoA binding site [chemical binding]; other site 1105108003081 NADH binding [chemical binding]; other site 1105108003082 cationic pore residues; other site 1105108003083 oxalacetate/citrate binding site [chemical binding]; other site 1105108003084 coenzyme A binding site [chemical binding]; other site 1105108003085 catalytic triad [active] 1105108003086 ATP10 protein; Region: ATP-synt_10; pfam05176 1105108003087 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 1105108003088 Fe-S cluster binding site [ion binding]; other site 1105108003089 active site 1105108003090 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1105108003091 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 1105108003092 RNA binding surface [nucleotide binding]; other site 1105108003093 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1105108003094 active site 1105108003095 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed; Region: PRK01544 1105108003096 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 1105108003097 S-adenosylmethionine binding site [chemical binding]; other site 1105108003098 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]; Region: COG0220 1105108003099 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 1105108003100 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 1105108003101 Glycyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]; Region: GlyS; COG0751 1105108003102 DALR anticodon binding domain; Region: DALR_1; pfam05746 1105108003103 glycyl-tRNA synthetase subunit alpha; Validated; Region: glyQ; PRK09348 1105108003104 motif 1; other site 1105108003105 dimer interface [polypeptide binding]; other site 1105108003106 active site 1105108003107 motif 2; other site 1105108003108 motif 3; other site 1105108003109 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 1105108003110 oligomeric interface; other site 1105108003111 putative active site [active] 1105108003112 homodimer interface [polypeptide binding]; other site 1105108003113 prevent-host-death family protein; Region: phd_fam; TIGR01552 1105108003114 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 1105108003115 potential frameshift: common BLAST hit: gi|374319835|ref|YP_005066334.1| Proline/betaine transporter 1105108003116 potential frameshift: common BLAST hit: gi|374319835|ref|YP_005066334.1| Proline/betaine transporter 1105108003117 potential frameshift: common BLAST hit: gi|374319835|ref|YP_005066334.1| Proline/betaine transporter 1105108003118 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 1105108003119 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 1105108003120 motif 1; other site 1105108003121 active site 1105108003122 motif 2; other site 1105108003123 motif 3; other site 1105108003124 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 1105108003125 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 1105108003126 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 1105108003127 dimerization interface 3.5A [polypeptide binding]; other site 1105108003128 active site 1105108003129 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 1105108003130 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 1105108003131 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1105108003132 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1105108003133 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1105108003134 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 1105108003135 DNA binding residues [nucleotide binding] 1105108003136 DNA primase, catalytic core; Region: dnaG; TIGR01391 1105108003137 CHC2 zinc finger; Region: zf-CHC2; pfam01807 1105108003138 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 1105108003139 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 1105108003140 active site 1105108003141 metal binding site [ion binding]; metal-binding site 1105108003142 interdomain interaction site; other site 1105108003143 Dolichol kinase [Lipid metabolism]; Region: SEC59; COG0170 1105108003144 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 1105108003145 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 1105108003146 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1105108003147 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 1105108003148 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 1105108003149 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 1105108003150 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 1105108003151 ligand binding site [chemical binding]; other site 1105108003152 homodimer interface [polypeptide binding]; other site 1105108003153 NAD(P) binding site [chemical binding]; other site 1105108003154 trimer interface B [polypeptide binding]; other site 1105108003155 trimer interface A [polypeptide binding]; other site 1105108003156 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 1105108003157 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 1105108003158 DNA polymerase III subunits gamma and tau; Validated; Region: PRK06645 1105108003159 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 1105108003160 Walker A motif; other site 1105108003161 ATP binding site [chemical binding]; other site 1105108003162 Walker B motif; other site 1105108003163 arginine finger; other site 1105108003164 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 1105108003165 hypothetical protein; Validated; Region: PRK00153 1105108003166 Predicted aspartyl protease [General function prediction only]; Region: COG3577 1105108003167 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 1105108003168 catalytic motif [active] 1105108003169 Catalytic residue [active] 1105108003170 Beta-lactamase; Region: Beta-lactamase; cl17358 1105108003171 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 1105108003172 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 1105108003173 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105108003174 Walker A/P-loop; other site 1105108003175 ATP binding site [chemical binding]; other site 1105108003176 Q-loop/lid; other site 1105108003177 ABC transporter signature motif; other site 1105108003178 Walker B; other site 1105108003179 D-loop; other site 1105108003180 H-loop/switch region; other site 1105108003181 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 1105108003182 putative hydrolase; Provisional; Region: PRK02113 1105108003183 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cd01610 1105108003184 active site 1105108003185 DNA-damage-inducible protein J [DNA replication, recombination, and repair]; Region: RelB; COG3077 1105108003186 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 1105108003187 Predicted permeases [General function prediction only]; Region: COG0795 1105108003188 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1105108003189 DNA polymerase III subunit chi; Provisional; Region: PRK06646 1105108003190 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 1105108003191 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 1105108003192 metal binding site [ion binding]; metal-binding site 1105108003193 dimer interface [polypeptide binding]; other site 1105108003194 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 1105108003195 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1105108003196 potential frameshift: common BLAST hit: gi|67459769|ref|YP_247393.1| Type I restriction-modification system methyltransferase subunit 1105108003197 potential frameshift: common BLAST hit: gi|157827849|ref|YP_001496913.1| Type I restriction-modification system methyltransferase subunit 1105108003198 potential frameshift: common BLAST hit: gi|157827849|ref|YP_001496913.1| Type I restriction-modification system methyltransferase subunit 1105108003199 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 1105108003200 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 1105108003201 potential frameshift: common BLAST hit: gi|229587248|ref|YP_002845749.1| Na+/H+ antiporter NhaA 1105108003202 Uncharacterized conserved protein [Function unknown]; Region: COG1434 1105108003203 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cl00630 1105108003204 putative active site [active] 1105108003205 lipoate-protein ligase B; Provisional; Region: PRK14347 1105108003206 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1105108003207 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 1105108003208 amidase catalytic site [active] 1105108003209 Zn binding residues [ion binding]; other site 1105108003210 substrate binding site [chemical binding]; other site 1105108003211 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1105108003212 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 1105108003213 ribosomal protein L33, bacterial type; Region: rpmG_bact; TIGR01023 1105108003214 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 1105108003215 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 1105108003216 ATP binding site [chemical binding]; other site 1105108003217 Mg2+ binding site [ion binding]; other site 1105108003218 G-X-G motif; other site 1105108003219 MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is...; Region: MutL_Trans; cd00782 1105108003220 ATP binding site [chemical binding]; other site 1105108003221 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 1105108003222 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4391 1105108003223 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105108003224 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105108003225 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105108003226 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 1105108003227 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105108003228 putative substrate translocation pore; other site 1105108003229 Coproporphyrinogen III oxidase [Coenzyme metabolism]; Region: HemF; COG0408 1105108003230 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 1105108003231 potential frameshift: common BLAST hit: gi|67459789|ref|YP_247413.1| prophage antirepressor