-- dump date 20140620_034037 -- class Genbank::misc_feature -- table misc_feature_note -- id note 481009000001 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1806 481009000002 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 481009000003 catalytic residues [active] 481009000004 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 481009000005 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 481009000006 Walker A/P-loop; other site 481009000007 ATP binding site [chemical binding]; other site 481009000008 Q-loop/lid; other site 481009000009 ABC transporter signature motif; other site 481009000010 Walker B; other site 481009000011 D-loop; other site 481009000012 H-loop/switch region; other site 481009000013 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 481009000014 ABC-2 type transporter; Region: ABC2_membrane; cl17235 481009000015 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 481009000016 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 481009000017 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 481009000018 FAD binding pocket [chemical binding]; other site 481009000019 FAD binding motif [chemical binding]; other site 481009000020 phosphate binding motif [ion binding]; other site 481009000021 beta-alpha-beta structure motif; other site 481009000022 NAD binding pocket [chemical binding]; other site 481009000023 Iron coordination center [ion binding]; other site 481009000024 Growth inhibitor [Signal transduction mechanisms]; Region: MazF; COG2337 481009000025 Acyl-[acyl carrier protein]; Region: LpxA; COG1043 481009000026 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 481009000027 active site 481009000028 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 481009000029 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 481009000030 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 481009000031 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 481009000032 trimer interface [polypeptide binding]; other site 481009000033 active site 481009000034 UDP-GlcNAc binding site [chemical binding]; other site 481009000035 lipid binding site [chemical binding]; lipid-binding site 481009000036 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 481009000037 active site 481009000038 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 481009000039 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 481009000040 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 481009000041 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 481009000042 FMN binding site [chemical binding]; other site 481009000043 active site 481009000044 catalytic residues [active] 481009000045 substrate binding site [chemical binding]; other site 481009000046 Putative catalytic NodB homology domain of uncharacterized protein RC0012 from Rickettsia conorii and its bacterial homologs; Region: CE4_RC0012_like; cd10963 481009000047 NodB motif; other site 481009000048 putative active site [active] 481009000049 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 481009000050 ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: LraI; COG0803 481009000051 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 481009000052 intersubunit interface [polypeptide binding]; other site 481009000053 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 481009000054 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 481009000055 active site 481009000056 NTP binding site [chemical binding]; other site 481009000057 metal binding triad [ion binding]; metal-binding site 481009000058 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 481009000059 Autotransporter beta-domain; Region: Autotransporter; pfam03797 481009000060 AAA domain; Region: AAA_22; pfam13401 481009000061 Tetratricopeptide repeat; Region: TPR_12; pfam13424 481009000062 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 481009000063 F0F1 ATP synthase subunit B; Validated; Region: PRK06568 481009000064 F0F1 ATP synthase subunit B'; Validated; Region: PRK06569 481009000065 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 481009000066 F0F1 ATP synthase subunit C; Validated; Region: PRK07558 481009000067 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 481009000068 ATP synthase subunit 6 (eukaryotes),also subunit A (prokaryotes); Region: ATP_synt_6_or_A; TIGR01131 481009000069 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5336 481009000070 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 481009000071 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 481009000072 catalytic residues [active] 481009000073 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 481009000074 Methyltransferase domain; Region: Methyltransf_31; pfam13847 481009000075 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 481009000076 S-adenosylmethionine binding site [chemical binding]; other site 481009000077 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 481009000078 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 481009000079 Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair]; Region: RecF; COG1195 481009000080 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 481009000081 Walker A/P-loop; other site 481009000082 ATP binding site [chemical binding]; other site 481009000083 Q-loop/lid; other site 481009000084 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 481009000085 ABC transporter signature motif; other site 481009000086 Walker B; other site 481009000087 D-loop; other site 481009000088 H-loop/switch region; other site 481009000089 TENA/THI-4/PQQC family; Region: TENA_THI-4; cl15243 481009000090 TENA/THI-4/PQQC family; Region: TENA_THI-4; cl15243 481009000091 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 481009000092 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 481009000093 folate binding site [chemical binding]; other site 481009000094 NADP+ binding site [chemical binding]; other site 481009000095 potential frameshift: common BLAST hit: gi|157827907|ref|YP_001494149.1| folate synthesis bifunctional protein 481009000096 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 481009000097 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 481009000098 Cu(I) binding site [ion binding]; other site 481009000099 Putative transcriptional regulator [Transcription]; Region: COG1678 481009000100 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 481009000101 Colicin V production protein; Region: Colicin_V; pfam02674 481009000102 Autotransporter beta-domain; Region: Autotransporter; smart00869 481009000103 Protein of unknown function (DUF2748); Region: DUF2748; pfam10871 481009000104 potential frameshift: common BLAST hit: gi|229586268|ref|YP_002844769.1| acetoacetyl-CoA reductase 481009000105 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 481009000106 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 481009000107 Clp amino terminal domain; Region: Clp_N; pfam02861 481009000108 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 481009000109 Walker A motif; other site 481009000110 ATP binding site [chemical binding]; other site 481009000111 Walker B motif; other site 481009000112 arginine finger; other site 481009000113 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 481009000114 Walker A motif; other site 481009000115 ATP binding site [chemical binding]; other site 481009000116 Walker B motif; other site 481009000117 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 481009000118 UGMP family protein; Validated; Region: PRK09604 481009000119 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 481009000120 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 481009000121 Fatty acid desaturase; Region: FA_desaturase; pfam00487 481009000122 Di-iron ligands [ion binding]; other site 481009000123 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 481009000124 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 481009000125 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 481009000126 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 481009000127 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 481009000128 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 481009000129 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 481009000130 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 481009000131 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 481009000132 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 481009000133 Ligand Binding Site [chemical binding]; other site 481009000134 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 481009000135 FtsH Extracellular; Region: FtsH_ext; pfam06480 481009000136 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 481009000137 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 481009000138 Walker A motif; other site 481009000139 ATP binding site [chemical binding]; other site 481009000140 Walker B motif; other site 481009000141 arginine finger; other site 481009000142 Peptidase family M41; Region: Peptidase_M41; pfam01434 481009000143 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 481009000144 cofactor binding site; other site 481009000145 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 481009000146 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 481009000147 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 481009000148 Uncharacterized conserved protein [Function unknown]; Region: COG1565 481009000149 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 481009000150 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 481009000151 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 481009000152 Mechanosensitive ion channel; Region: MS_channel; pfam00924 481009000153 membrane protein insertase; Provisional; Region: PRK01318 481009000154 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 481009000155 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 481009000156 Methyltransferase domain; Region: Methyltransf_23; pfam13489 481009000157 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 481009000158 S-adenosylmethionine binding site [chemical binding]; other site 481009000159 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 481009000160 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 481009000161 active site 481009000162 catalytic residues [active] 481009000163 metal binding site [ion binding]; metal-binding site 481009000164 TLC ATP/ADP transporter; Region: TLC; pfam03219 481009000165 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 481009000166 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 481009000167 putative substrate translocation pore; other site 481009000168 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 481009000169 active site 481009000170 multimer interface [polypeptide binding]; other site 481009000171 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 481009000172 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 481009000173 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 481009000174 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 481009000175 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 481009000176 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 481009000177 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 481009000178 P-loop; other site 481009000179 Magnesium ion binding site [ion binding]; other site 481009000180 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 481009000181 Magnesium ion binding site [ion binding]; other site 481009000182 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 481009000183 ParB-like nuclease domain; Region: ParB; smart00470 481009000184 KorB domain; Region: KorB; pfam08535 481009000185 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 481009000186 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 481009000187 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 481009000188 ABC transporter; Region: ABC_tran_2; pfam12848 481009000189 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 481009000190 Protein of unknown function (DUF2672); Region: DUF2672; pfam10878 481009000191 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; COG2877 481009000192 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 481009000193 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 481009000194 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 481009000195 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 481009000196 Zn2+ binding site [ion binding]; other site 481009000197 Mg2+ binding site [ion binding]; other site 481009000198 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 481009000199 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 481009000200 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 481009000201 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 481009000202 active site 481009000203 HIGH motif; other site 481009000204 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 481009000205 KMSK motif region; other site 481009000206 tRNA binding surface [nucleotide binding]; other site 481009000207 DALR anticodon binding domain; Region: DALR_1; smart00836 481009000208 anticodon binding site; other site 481009000209 Sporulation related domain; Region: SPOR; pfam05036 481009000210 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 481009000211 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 481009000212 CAP-like domain; other site 481009000213 active site 481009000214 primary dimer interface [polypeptide binding]; other site 481009000215 Gram-negative porin; Region: Porin_4; pfam13609 481009000216 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 481009000217 trimer interface [polypeptide binding]; other site 481009000218 active site 481009000219 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 481009000220 SecA binding site; other site 481009000221 Preprotein binding site; other site 481009000222 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 481009000223 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 481009000224 active site 481009000225 phosphorylation site [posttranslational modification] 481009000226 intermolecular recognition site; other site 481009000227 dimerization interface [polypeptide binding]; other site 481009000228 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 481009000229 DNA binding site [nucleotide binding] 481009000230 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 481009000231 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 481009000232 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 481009000233 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 481009000234 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 481009000235 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 481009000236 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 481009000237 EamA-like transporter family; Region: EamA; pfam00892 481009000238 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 481009000239 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 481009000240 metabolite-proton symporter; Region: 2A0106; TIGR00883 481009000241 putative substrate translocation pore; other site 481009000242 Protein of unknown function (DUF1258); Region: DUF1258; pfam06869 481009000243 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 481009000244 Cobalamin biosynthesis protein CobT; Region: CobT; pfam06213 481009000245 Autotransporter beta-domain; Region: Autotransporter; pfam03797 481009000246 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 481009000247 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 481009000248 active site 481009000249 HIGH motif; other site 481009000250 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 481009000251 KMSKS motif; other site 481009000252 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 481009000253 tRNA binding surface [nucleotide binding]; other site 481009000254 anticodon binding site; other site 481009000255 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 481009000256 rRNA interaction site [nucleotide binding]; other site 481009000257 S8 interaction site; other site 481009000258 putative laminin-1 binding site; other site 481009000259 elongation factor Ts; Provisional; Region: tsf; PRK09377 481009000260 UBA/TS-N domain; Region: UBA; pfam00627 481009000261 Elongation factor TS; Region: EF_TS; pfam00889 481009000262 Elongation factor TS; Region: EF_TS; pfam00889 481009000263 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 481009000264 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 481009000265 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 481009000266 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 481009000267 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 481009000268 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 481009000269 putative acyl-acceptor binding pocket; other site 481009000270 aspartate aminotransferase; Provisional; Region: PRK05764 481009000271 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 481009000272 pyridoxal 5'-phosphate binding site [chemical binding]; other site 481009000273 homodimer interface [polypeptide binding]; other site 481009000274 catalytic residue [active] 481009000275 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 481009000276 Tetratricopeptide repeat; Region: TPR_12; pfam13424 481009000277 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 481009000278 binding surface 481009000279 TPR motif; other site 481009000280 Methyltransferase domain; Region: Methyltransf_23; pfam13489 481009000281 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 481009000282 S-adenosylmethionine binding site [chemical binding]; other site 481009000283 Surface lipoprotein [Cell envelope biogenesis, outer membrane]; Region: VacJ; COG2853 481009000284 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; COG2854 481009000285 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 481009000286 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 481009000287 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 481009000288 active site 481009000289 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 481009000290 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 481009000291 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 481009000292 active site 481009000293 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 481009000294 dimer interface [polypeptide binding]; other site 481009000295 substrate binding site [chemical binding]; other site 481009000296 catalytic residues [active] 481009000297 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 481009000298 Permease; Region: Permease; pfam02405 481009000299 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 481009000300 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 481009000301 Walker A/P-loop; other site 481009000302 ATP binding site [chemical binding]; other site 481009000303 Q-loop/lid; other site 481009000304 ABC transporter signature motif; other site 481009000305 Walker B; other site 481009000306 D-loop; other site 481009000307 H-loop/switch region; other site 481009000308 CheD chemotactic sensory transduction; Region: CheD; cl00810 481009000309 Ribosomal protein L28 [Translation, ribosomal structure and biogenesis]; Region: RpmB; COG0227 481009000310 50S ribosomal protein L31; Provisional; Region: PRK01397 481009000311 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 481009000312 G1 box; other site 481009000313 GTP/Mg2+ binding site [chemical binding]; other site 481009000314 Switch I region; other site 481009000315 G2 box; other site 481009000316 G3 box; other site 481009000317 Switch II region; other site 481009000318 G4 box; other site 481009000319 G5 box; other site 481009000320 Acetylglutamate kinase [Amino acid transport and metabolism]; Region: ArgB; COG0548 481009000321 nucleotide binding site [chemical binding]; other site 481009000322 substrate binding site [chemical binding]; other site 481009000323 type IV secretion system protein VirB3; Provisional; Region: PRK13899 481009000324 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 481009000325 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 481009000326 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 481009000327 Walker A/P-loop; other site 481009000328 ATP binding site [chemical binding]; other site 481009000329 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 481009000330 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 481009000331 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 481009000332 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 481009000333 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 481009000334 potential frameshift: common BLAST hit: gi|67458488|ref|YP_246112.1| phosphate acetyltransferase 481009000335 Acetate kinase [Energy production and conversion]; Region: ackA; COG0282 481009000336 propionate/acetate kinase; Provisional; Region: PRK12379 481009000337 tRNA-(guanine-N1)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmD; COG0336 481009000338 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 481009000339 hypothetical protein; Provisional; Region: PRK13694 481009000340 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 481009000341 Protein export membrane protein; Region: SecD_SecF; pfam02355 481009000342 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 481009000343 SLBB domain; Region: SLBB; pfam10531 481009000344 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 481009000345 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 481009000346 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 481009000347 Catalytic site [active] 481009000348 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 481009000349 ribonuclease III; Reviewed; Region: rnc; PRK00102 481009000350 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 481009000351 dimerization interface [polypeptide binding]; other site 481009000352 active site 481009000353 metal binding site [ion binding]; metal-binding site 481009000354 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 481009000355 dsRNA binding site [nucleotide binding]; other site 481009000356 GTPase Era; Provisional; Region: era; PRK15494 481009000357 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 481009000358 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 481009000359 G1 box; other site 481009000360 GTP/Mg2+ binding site [chemical binding]; other site 481009000361 Switch I region; other site 481009000362 G2 box; other site 481009000363 Switch II region; other site 481009000364 G3 box; other site 481009000365 G4 box; other site 481009000366 G5 box; other site 481009000367 KH domain; Region: KH_2; pfam07650 481009000368 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 481009000369 active site 481009000370 putative DNA-binding cleft [nucleotide binding]; other site 481009000371 dimer interface [polypeptide binding]; other site 481009000372 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 481009000373 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 481009000374 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl17552 481009000375 potential frameshift: common BLAST hit: gi|165932732|ref|YP_001649521.1| nucleotidyltransferase 481009000376 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 481009000377 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 481009000378 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 481009000379 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 481009000380 Walker A motif; other site 481009000381 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 481009000382 HflK protein; Region: hflK; TIGR01933 481009000383 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 481009000384 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 481009000385 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 481009000386 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 481009000387 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 481009000388 protein binding site [polypeptide binding]; other site 481009000389 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 481009000390 protein binding site [polypeptide binding]; other site 481009000391 hypothetical protein; Validated; Region: PRK01415 481009000392 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 481009000393 active site residue [active] 481009000394 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 481009000395 Iron-sulfur protein interface; other site 481009000396 proximal quinone binding site [chemical binding]; other site 481009000397 SdhD (CybS) interface [polypeptide binding]; other site 481009000398 proximal heme binding site [chemical binding]; other site 481009000399 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 481009000400 putative SdhC subunit interface [polypeptide binding]; other site 481009000401 putative proximal heme binding site [chemical binding]; other site 481009000402 putative Iron-sulfur protein interface [polypeptide binding]; other site 481009000403 putative proximal quinone binding site; other site 481009000404 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 481009000405 L-aspartate oxidase; Provisional; Region: PRK06175 481009000406 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 481009000407 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 481009000408 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 481009000409 dimer interface [polypeptide binding]; other site 481009000410 conserved gate region; other site 481009000411 putative PBP binding loops; other site 481009000412 ABC-ATPase subunit interface; other site 481009000413 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 481009000414 S17 interaction site [polypeptide binding]; other site 481009000415 S8 interaction site; other site 481009000416 16S rRNA interaction site [nucleotide binding]; other site 481009000417 streptomycin interaction site [chemical binding]; other site 481009000418 23S rRNA interaction site [nucleotide binding]; other site 481009000419 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 481009000420 30S ribosomal protein S7; Validated; Region: PRK05302 481009000421 elongation factor G; Reviewed; Region: PRK00007 481009000422 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 481009000423 G1 box; other site 481009000424 putative GEF interaction site [polypeptide binding]; other site 481009000425 GTP/Mg2+ binding site [chemical binding]; other site 481009000426 Switch I region; other site 481009000427 G2 box; other site 481009000428 G3 box; other site 481009000429 Switch II region; other site 481009000430 G4 box; other site 481009000431 G5 box; other site 481009000432 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 481009000433 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 481009000434 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 481009000435 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 481009000436 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 481009000437 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 481009000438 putative homodimer interface [polypeptide binding]; other site 481009000439 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 481009000440 heterodimer interface [polypeptide binding]; other site 481009000441 homodimer interface [polypeptide binding]; other site 481009000442 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 481009000443 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 481009000444 23S rRNA interface [nucleotide binding]; other site 481009000445 putative thiostrepton binding site; other site 481009000446 L7/L12 interface [polypeptide binding]; other site 481009000447 L25 interface [polypeptide binding]; other site 481009000448 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 481009000449 mRNA/rRNA interface [nucleotide binding]; other site 481009000450 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 481009000451 23S rRNA interface [nucleotide binding]; other site 481009000452 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 481009000453 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 481009000454 core dimer interface [polypeptide binding]; other site 481009000455 peripheral dimer interface [polypeptide binding]; other site 481009000456 L10 interface [polypeptide binding]; other site 481009000457 L11 interface [polypeptide binding]; other site 481009000458 putative EF-Tu interaction site [polypeptide binding]; other site 481009000459 putative EF-G interaction site [polypeptide binding]; other site 481009000460 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 481009000461 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 481009000462 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 481009000463 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 481009000464 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 481009000465 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 481009000466 RPB3 interaction site [polypeptide binding]; other site 481009000467 RPB1 interaction site [polypeptide binding]; other site 481009000468 RPB11 interaction site [polypeptide binding]; other site 481009000469 RPB10 interaction site [polypeptide binding]; other site 481009000470 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 481009000471 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 481009000472 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 481009000473 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 481009000474 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 481009000475 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 481009000476 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 481009000477 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 481009000478 DNA binding site [nucleotide binding] 481009000479 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 481009000480 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 481009000481 multifunctional aminopeptidase A; Provisional; Region: PRK00913 481009000482 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 481009000483 interface (dimer of trimers) [polypeptide binding]; other site 481009000484 Substrate-binding/catalytic site; other site 481009000485 Zn-binding sites [ion binding]; other site 481009000486 ATPase MipZ; Region: MipZ; pfam09140 481009000487 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 481009000488 P-loop; other site 481009000489 Magnesium ion binding site [ion binding]; other site 481009000490 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 481009000491 Magnesium ion binding site [ion binding]; other site 481009000492 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 481009000493 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 481009000494 dimer interface [polypeptide binding]; other site 481009000495 anticodon binding site; other site 481009000496 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 481009000497 homodimer interface [polypeptide binding]; other site 481009000498 motif 1; other site 481009000499 active site 481009000500 motif 2; other site 481009000501 GAD domain; Region: GAD; pfam02938 481009000502 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 481009000503 active site 481009000504 motif 3; other site 481009000505 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 481009000506 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 481009000507 dihydrodipicolinate reductase; Provisional; Region: PRK00048 481009000508 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 481009000509 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 481009000510 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 481009000511 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 481009000512 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 481009000513 substrate binding pocket [chemical binding]; other site 481009000514 membrane-bound complex binding site; other site 481009000515 hinge residues; other site 481009000516 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 481009000517 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 481009000518 GatB domain; Region: GatB_Yqey; smart00845 481009000519 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 481009000520 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 481009000521 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 481009000522 Uncharacterized conserved protein [Function unknown]; Region: COG4997 481009000523 ribosome recycling factor; Reviewed; Region: frr; PRK00083 481009000524 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 481009000525 hinge region; other site 481009000526 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 481009000527 putative nucleotide binding site [chemical binding]; other site 481009000528 uridine monophosphate binding site [chemical binding]; other site 481009000529 homohexameric interface [polypeptide binding]; other site 481009000530 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK06580 481009000531 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 481009000532 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 481009000533 putative substrate translocation pore; other site 481009000534 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 481009000535 Protein of unknown function (DUF2674); Region: DUF2674; pfam10879 481009000536 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 481009000537 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 481009000538 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 481009000539 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 481009000540 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 481009000541 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 481009000542 Surface antigen; Region: Bac_surface_Ag; pfam01103 481009000543 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 481009000544 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 481009000545 active site 481009000546 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 481009000547 protein binding site [polypeptide binding]; other site 481009000548 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 481009000549 putative substrate binding region [chemical binding]; other site 481009000550 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 481009000551 putative RNA binding site [nucleotide binding]; other site 481009000552 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 481009000553 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 481009000554 S-adenosylmethionine binding site [chemical binding]; other site 481009000555 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 481009000556 putative coenzyme Q binding site [chemical binding]; other site 481009000557 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 481009000558 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 481009000559 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 481009000560 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 481009000561 RNA methyltransferase, RsmE family; Region: TIGR00046 481009000562 Uncharacterized conserved protein [Function unknown]; Region: COG2155 481009000563 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 481009000564 Protein export membrane protein; Region: SecD_SecF; cl14618 481009000565 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 481009000566 IHF dimer interface [polypeptide binding]; other site 481009000567 IHF - DNA interface [nucleotide binding]; other site 481009000568 DNA polymerase III subunit delta'; Validated; Region: PRK06581 481009000569 signal recognition particle protein; Provisional; Region: PRK10867 481009000570 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 481009000571 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 481009000572 P loop; other site 481009000573 GTP binding site [chemical binding]; other site 481009000574 Signal peptide binding domain; Region: SRP_SPB; pfam02978 481009000575 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 481009000576 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 481009000577 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 481009000578 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 481009000579 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 481009000580 coproporphyrinogen III oxidase; Provisional; Region: PRK06582 481009000581 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 481009000582 FeS/SAM binding site; other site 481009000583 HemN C-terminal domain; Region: HemN_C; pfam06969 481009000584 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 481009000585 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 481009000586 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 481009000587 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 481009000588 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 481009000589 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 481009000590 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism]; Region: COG0720 481009000591 active site 481009000592 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 481009000593 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 481009000594 E3 interaction surface; other site 481009000595 lipoyl attachment site [posttranslational modification]; other site 481009000596 e3 binding domain; Region: E3_binding; pfam02817 481009000597 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 481009000598 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 481009000599 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 481009000600 TPP-binding site [chemical binding]; other site 481009000601 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 481009000602 dimer interface [polypeptide binding]; other site 481009000603 PYR/PP interface [polypeptide binding]; other site 481009000604 TPP binding site [chemical binding]; other site 481009000605 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 481009000606 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 481009000607 active site 481009000608 Zn binding site [ion binding]; other site 481009000609 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 481009000610 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 481009000611 Walker A/P-loop; other site 481009000612 ATP binding site [chemical binding]; other site 481009000613 Q-loop/lid; other site 481009000614 Allexivirus 40kDa protein; Region: Allexi_40kDa; pfam05549 481009000615 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 481009000616 ABC transporter signature motif; other site 481009000617 Walker B; other site 481009000618 D-loop; other site 481009000619 H-loop/switch region; other site 481009000620 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 481009000621 Tetratricopeptide repeat; Region: TPR_6; pfam13174 481009000622 ChaB; Region: ChaB; cl01887 481009000623 ChaB; Region: ChaB; cl01887 481009000624 chaperone protein DnaJ; Provisional; Region: PRK14300 481009000625 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 481009000626 HSP70 interaction site [polypeptide binding]; other site 481009000627 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 481009000628 substrate binding site [polypeptide binding]; other site 481009000629 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 481009000630 Zn binding sites [ion binding]; other site 481009000631 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 481009000632 dimer interface [polypeptide binding]; other site 481009000633 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 481009000634 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 481009000635 nucleotide binding site [chemical binding]; other site 481009000636 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 481009000637 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 481009000638 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 481009000639 Lipopolysaccharide-assembly; Region: LptE; cl01125 481009000640 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 481009000641 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 481009000642 diiron binding motif [ion binding]; other site 481009000643 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 481009000644 Subunit III/VIIa interface [polypeptide binding]; other site 481009000645 Phospholipid binding site [chemical binding]; other site 481009000646 Subunit I/III interface [polypeptide binding]; other site 481009000647 Subunit III/VIb interface [polypeptide binding]; other site 481009000648 Subunit III/VIa interface; other site 481009000649 Subunit III/Vb interface [polypeptide binding]; other site 481009000650 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 481009000651 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 481009000652 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 481009000653 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 481009000654 trimer interface [polypeptide binding]; other site 481009000655 active site 481009000656 substrate binding site [chemical binding]; other site 481009000657 CoA binding site [chemical binding]; other site 481009000658 potential frameshift: common BLAST hit: gi|350273249|ref|YP_004884562.1| bifunctional penicillin-binding protein 1C 481009000659 Autotransporter beta-domain; Region: Autotransporter; pfam03797 481009000660 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 481009000661 Ligand Binding Site [chemical binding]; other site 481009000662 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 481009000663 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 481009000664 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 481009000665 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 481009000666 catalytic loop [active] 481009000667 iron binding site [ion binding]; other site 481009000668 chaperone protein HscA; Provisional; Region: hscA; PRK01433 481009000669 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 481009000670 nucleotide binding site [chemical binding]; other site 481009000671 co-chaperone HscB; Provisional; Region: hscB; PRK01356 481009000672 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 481009000673 HSP70 interaction site [polypeptide binding]; other site 481009000674 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 481009000675 RNA/DNA hybrid binding site [nucleotide binding]; other site 481009000676 active site 481009000677 excinuclease ABC subunit B; Provisional; Region: PRK05298 481009000678 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 481009000679 ATP binding site [chemical binding]; other site 481009000680 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 481009000681 nucleotide binding region [chemical binding]; other site 481009000682 ATP-binding site [chemical binding]; other site 481009000683 Ultra-violet resistance protein B; Region: UvrB; pfam12344 481009000684 UvrB/uvrC motif; Region: UVR; pfam02151 481009000685 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 481009000686 GSH binding site [chemical binding]; other site 481009000687 catalytic residues [active] 481009000688 potential frameshift: common BLAST hit: gi|341583496|ref|YP_004763987.1| multidrug resistance protein Atm1 481009000689 Pleckstrin homology-like domain; Region: PH-like; cl17171 481009000690 DNA gyrase subunit A; Validated; Region: PRK05560 481009000691 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 481009000692 CAP-like domain; other site 481009000693 active site 481009000694 primary dimer interface [polypeptide binding]; other site 481009000695 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 481009000696 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 481009000697 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 481009000698 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 481009000699 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 481009000700 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 481009000701 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 481009000702 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 481009000703 Iron-sulphur cluster assembly; Region: Fe-S_assembly; cl01123 481009000704 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 481009000705 active site 481009000706 catalytic residues [active] 481009000707 metal binding site [ion binding]; metal-binding site 481009000708 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 481009000709 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 481009000710 putative active site [active] 481009000711 substrate binding site [chemical binding]; other site 481009000712 putative cosubstrate binding site; other site 481009000713 catalytic site [active] 481009000714 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 481009000715 substrate binding site [chemical binding]; other site 481009000716 potential RNA of insufficient length (23S ribosomal RNA) 481009000717 Protein of unknown function (DUF563); Region: DUF563; cl15705 481009000718 Predicted ATPase [General function prediction only]; Region: COG1485 481009000719 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 481009000720 Walker A motif; other site 481009000721 ATP binding site [chemical binding]; other site 481009000722 Walker B motif; other site 481009000723 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: PRK01424 481009000724 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 481009000725 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 481009000726 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 481009000727 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 481009000728 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 481009000729 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 481009000730 Walker A/P-loop; other site 481009000731 ATP binding site [chemical binding]; other site 481009000732 Q-loop/lid; other site 481009000733 ABC transporter signature motif; other site 481009000734 Walker B; other site 481009000735 D-loop; other site 481009000736 H-loop/switch region; other site 481009000737 Protein of unknown function (DUF2671); Region: DUF2671; pfam10877 481009000738 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 481009000739 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 481009000740 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 481009000741 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 481009000742 toxin-antitoxin system, toxin component, Txe/YoeB family; Region: toxin_Txe_YoeB; TIGR02116 481009000743 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 481009000744 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 481009000745 putative metal binding site; other site 481009000746 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 481009000747 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 481009000748 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 481009000749 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 481009000750 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 481009000751 ATP binding site [chemical binding]; other site 481009000752 active site 481009000753 substrate binding site [chemical binding]; other site 481009000754 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 481009000755 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 481009000756 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 481009000757 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 481009000758 active site 481009000759 dimer interface [polypeptide binding]; other site 481009000760 motif 1; other site 481009000761 motif 2; other site 481009000762 motif 3; other site 481009000763 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 481009000764 anticodon binding site; other site 481009000765 potential frameshift: common BLAST hit: gi|67459373|ref|YP_246997.1| multidrug ABC transporter ATPase and permease 481009000766 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 481009000767 Walker A/P-loop; other site 481009000768 ATP binding site [chemical binding]; other site 481009000769 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 481009000770 ABC transporter signature motif; other site 481009000771 Walker B; other site 481009000772 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 481009000773 H-loop/switch region; other site 481009000774 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); Region: DUF2310; cl02380 481009000775 Protein of unknown function (DUF2660); Region: DUF2660; pfam10859 481009000776 V-type ATP synthase subunit I; Validated; Region: PRK05771 481009000777 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 481009000778 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3827 481009000779 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 481009000780 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 481009000781 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 481009000782 DNA topoisomerase IV, B subunit, proteobacterial; Region: parE_Gneg; TIGR01055 481009000783 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 481009000784 ATP binding site [chemical binding]; other site 481009000785 Mg2+ binding site [ion binding]; other site 481009000786 G-X-G motif; other site 481009000787 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 481009000788 anchoring element; other site 481009000789 dimer interface [polypeptide binding]; other site 481009000790 ATP binding site [chemical binding]; other site 481009000791 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 481009000792 active site 481009000793 metal binding site [ion binding]; metal-binding site 481009000794 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 481009000795 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 481009000796 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 481009000797 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 481009000798 protein binding site [polypeptide binding]; other site 481009000799 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 481009000800 Catalytic dyad [active] 481009000801 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 481009000802 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 481009000803 dimer interface [polypeptide binding]; other site 481009000804 phosphorylation site [posttranslational modification] 481009000805 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 481009000806 ATP binding site [chemical binding]; other site 481009000807 Mg2+ binding site [ion binding]; other site 481009000808 G-X-G motif; other site 481009000809 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 481009000810 Protein of unknown function (DUF2659); Region: DUF2659; pfam10858 481009000811 FOG: WD40-like repeat [Function unknown]; Region: COG1520 481009000812 Beta-barrel assembly machinery (Bam) complex component B and related proteins; Region: BamB_YfgL; cd10276 481009000813 Trp docking motif [polypeptide binding]; other site 481009000814 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 481009000815 23S rRNA interface [nucleotide binding]; other site 481009000816 L3 interface [polypeptide binding]; other site 481009000817 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 481009000818 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 481009000819 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_a; cd00913 481009000820 aromatic arch; other site 481009000821 DCoH dimer interaction site [polypeptide binding]; other site 481009000822 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 481009000823 DCoH tetramer interaction site [polypeptide binding]; other site 481009000824 substrate binding site [chemical binding]; other site 481009000825 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 481009000826 putative active site [active] 481009000827 Ap4A binding site [chemical binding]; other site 481009000828 nudix motif; other site 481009000829 putative metal binding site [ion binding]; other site 481009000830 response regulator PleD; Reviewed; Region: pleD; PRK09581 481009000831 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 481009000832 active site 481009000833 phosphorylation site [posttranslational modification] 481009000834 intermolecular recognition site; other site 481009000835 dimerization interface [polypeptide binding]; other site 481009000836 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 481009000837 active site 481009000838 phosphorylation site [posttranslational modification] 481009000839 intermolecular recognition site; other site 481009000840 dimerization interface [polypeptide binding]; other site 481009000841 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 481009000842 metal binding site [ion binding]; metal-binding site 481009000843 active site 481009000844 I-site; other site 481009000845 elongation factor P; Validated; Region: PRK00529 481009000846 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 481009000847 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 481009000848 RNA binding site [nucleotide binding]; other site 481009000849 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 481009000850 RNA binding site [nucleotide binding]; other site 481009000851 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 481009000852 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 481009000853 active site 481009000854 Domain of unknown function (DUF2610); Region: DUF2610; pfam11020 481009000855 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 481009000856 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 481009000857 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 481009000858 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 481009000859 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 481009000860 HlyD family secretion protein; Region: HlyD_3; pfam13437 481009000861 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 481009000862 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 481009000863 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 481009000864 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 481009000865 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 481009000866 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 481009000867 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 481009000868 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 481009000869 FAD binding domain; Region: FAD_binding_4; pfam01565 481009000870 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 481009000871 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 481009000872 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 481009000873 ATP-grasp domain; Region: ATP-grasp_4; cl17255 481009000874 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 481009000875 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 481009000876 Cell division protein FtsQ; Region: FtsQ; pfam03799 481009000877 cell division protein FtsA; Region: ftsA; TIGR01174 481009000878 Cell division protein FtsA; Region: FtsA; smart00842 481009000879 Cell division protein FtsA; Region: FtsA; pfam14450 481009000880 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 481009000881 Cytochrome c2 [Energy production and conversion]; Region: COG3474 481009000882 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 481009000883 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 481009000884 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 481009000885 RNA binding site [nucleotide binding]; other site 481009000886 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 481009000887 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 481009000888 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 481009000889 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 481009000890 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 481009000891 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 481009000892 RNA binding surface [nucleotide binding]; other site 481009000893 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 481009000894 active site 481009000895 potential frameshift: common BLAST hit: gi|238650484|ref|YP_002916336.1| penicillin-binding protein 4* 481009000896 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 481009000897 putative catalytic site [active] 481009000898 putative phosphate binding site [ion binding]; other site 481009000899 active site 481009000900 metal binding site A [ion binding]; metal-binding site 481009000901 DNA binding site [nucleotide binding] 481009000902 putative AP binding site [nucleotide binding]; other site 481009000903 putative metal binding site B [ion binding]; other site 481009000904 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 481009000905 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 481009000906 tetramer interface [polypeptide binding]; other site 481009000907 TPP-binding site [chemical binding]; other site 481009000908 heterodimer interface [polypeptide binding]; other site 481009000909 phosphorylation loop region [posttranslational modification] 481009000910 pyruvate dehydrogenase subunit beta; Validated; Region: PRK09212 481009000911 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 481009000912 alpha subunit interface [polypeptide binding]; other site 481009000913 TPP binding site [chemical binding]; other site 481009000914 heterodimer interface [polypeptide binding]; other site 481009000915 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 481009000916 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 481009000917 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 481009000918 G1 box; other site 481009000919 putative GEF interaction site [polypeptide binding]; other site 481009000920 GTP/Mg2+ binding site [chemical binding]; other site 481009000921 Switch I region; other site 481009000922 G2 box; other site 481009000923 G3 box; other site 481009000924 Switch II region; other site 481009000925 G4 box; other site 481009000926 G5 box; other site 481009000927 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 481009000928 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 481009000929 haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; Region: HAD-SF-IA-v3; TIGR01509 481009000930 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: HlpA; COG2825 481009000931 isocitrate dehydrogenase; Validated; Region: PRK09222 481009000932 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 481009000933 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 481009000934 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12507 481009000935 Predicted subunit of the Multisubunit Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: COG1563 481009000936 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 481009000937 Protein of unknown function (DUF2670); Region: DUF2670; pfam10875 481009000938 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 481009000939 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 481009000940 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 481009000941 [2Fe-2S] cluster binding site [ion binding]; other site 481009000942 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 481009000943 Qi binding site; other site 481009000944 cytochrome b; Provisional; Region: CYTB; MTH00191 481009000945 intrachain domain interface; other site 481009000946 interchain domain interface [polypeptide binding]; other site 481009000947 heme bH binding site [chemical binding]; other site 481009000948 heme bL binding site [chemical binding]; other site 481009000949 Qo binding site; other site 481009000950 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 481009000951 interchain domain interface [polypeptide binding]; other site 481009000952 intrachain domain interface; other site 481009000953 Qi binding site; other site 481009000954 Qo binding site; other site 481009000955 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 481009000956 catalytic site [active] 481009000957 metal binding site [ion binding]; metal-binding site 481009000958 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 481009000959 Cytochrome c; Region: Cytochrom_C; cl11414 481009000960 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 481009000961 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 481009000962 putative dimer interface [polypeptide binding]; other site 481009000963 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 481009000964 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 481009000965 PCRF domain; Region: PCRF; pfam03462 481009000966 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 481009000967 RF-1 domain; Region: RF-1; pfam00472 481009000968 GTP-binding protein LepA; Provisional; Region: PRK05433 481009000969 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 481009000970 G1 box; other site 481009000971 putative GEF interaction site [polypeptide binding]; other site 481009000972 GTP/Mg2+ binding site [chemical binding]; other site 481009000973 Switch I region; other site 481009000974 G2 box; other site 481009000975 G3 box; other site 481009000976 Switch II region; other site 481009000977 G4 box; other site 481009000978 G5 box; other site 481009000979 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 481009000980 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 481009000981 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 481009000982 methylamine dehydrogenase (amicyanin) heavy chain; Region: TTQ_MADH_Hv; TIGR02658 481009000983 potential frameshift: common BLAST hit: gi|15892293|ref|NP_360007.1| ATP-dependent protease subunit C (ClpC) 481009000984 potential frameshift: common BLAST hit: gi|67458839|ref|YP_246463.1| NACHT domain-containing protein 481009000985 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 481009000986 HD domain; Region: HD_4; pfam13328 481009000987 proline/glycine betaine transporter; Provisional; Region: PRK10642 481009000988 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 481009000989 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 481009000990 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 481009000991 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 481009000992 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06588 481009000993 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 481009000994 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 481009000995 oligomeric interface; other site 481009000996 putative active site [active] 481009000997 homodimer interface [polypeptide binding]; other site 481009000998 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06589 481009000999 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 481009001000 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06591 481009001001 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 481009001002 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK07375 481009001003 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 481009001004 VirB7 interaction site; other site 481009001005 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 481009001006 Protein of unknown function (DUF2706); Region: DUF2706; pfam10913 481009001007 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 481009001008 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 481009001009 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 481009001010 type IV secretion system ATPase VirB11; Provisional; Region: PRK13900 481009001011 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 481009001012 Walker A motif; other site 481009001013 hexamer interface [polypeptide binding]; other site 481009001014 ATP binding site [chemical binding]; other site 481009001015 Walker B motif; other site 481009001016 type IV secretion system component VirD4; Provisional; Region: PRK13897 481009001017 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 481009001018 Walker A motif; other site 481009001019 ATP binding site [chemical binding]; other site 481009001020 Walker B motif; other site 481009001021 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 481009001022 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 481009001023 Phage-related protein [Function unknown]; Region: COG4695; cl01923 481009001024 Phage portal protein; Region: Phage_portal; pfam04860 481009001025 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 481009001026 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 481009001027 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 481009001028 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 481009001029 active site 481009001030 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 481009001031 MutS domain I; Region: MutS_I; pfam01624 481009001032 MutS domain II; Region: MutS_II; pfam05188 481009001033 MutS domain III; Region: MutS_III; pfam05192 481009001034 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 481009001035 Walker A/P-loop; other site 481009001036 ATP binding site [chemical binding]; other site 481009001037 Q-loop/lid; other site 481009001038 ABC transporter signature motif; other site 481009001039 Walker B; other site 481009001040 D-loop; other site 481009001041 H-loop/switch region; other site 481009001042 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 481009001043 Peptidase family M23; Region: Peptidase_M23; pfam01551 481009001044 Protein of unknown function DUF45; Region: DUF45; pfam01863 481009001045 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 481009001046 translocation protein TolB; Provisional; Region: tolB; PRK05137 481009001047 TolB amino-terminal domain; Region: TolB_N; pfam04052 481009001048 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 481009001049 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 481009001050 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 481009001051 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 481009001052 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 481009001053 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 481009001054 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 481009001055 DNA binding residues [nucleotide binding] 481009001056 Cytochrome oxidase assembly factor [Posttranslational modification, protein turnover, chaperones]; Region: COX11; COG3175 481009001057 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 481009001058 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 481009001059 Ligand Binding Site [chemical binding]; other site 481009001060 amino acid transporter; Region: 2A0306; TIGR00909 481009001061 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 481009001062 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 481009001063 dimer interface [polypeptide binding]; other site 481009001064 motif 1; other site 481009001065 active site 481009001066 motif 2; other site 481009001067 motif 3; other site 481009001068 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 481009001069 anticodon binding site; other site 481009001070 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 481009001071 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 481009001072 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 481009001073 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 481009001074 TolQ protein; Region: tolQ; TIGR02796 481009001075 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 481009001076 TolR protein; Region: tolR; TIGR02801 481009001077 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 481009001078 HD domain; Region: HD_4; pfam13328 481009001079 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 481009001080 metabolite-proton symporter; Region: 2A0106; TIGR00883 481009001081 putative substrate translocation pore; other site 481009001082 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 481009001083 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 481009001084 HlyD family secretion protein; Region: HlyD_3; pfam13437 481009001085 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 481009001086 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 481009001087 Walker A/P-loop; other site 481009001088 ATP binding site [chemical binding]; other site 481009001089 Q-loop/lid; other site 481009001090 ABC transporter signature motif; other site 481009001091 Walker B; other site 481009001092 D-loop; other site 481009001093 H-loop/switch region; other site 481009001094 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 481009001095 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 481009001096 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 481009001097 nucleotide binding site/active site [active] 481009001098 HIT family signature motif; other site 481009001099 catalytic residue [active] 481009001100 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 481009001101 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 481009001102 active site 481009001103 HslU subunit interaction site [polypeptide binding]; other site 481009001104 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 481009001105 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 481009001106 Walker A motif; other site 481009001107 ATP binding site [chemical binding]; other site 481009001108 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 481009001109 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 481009001110 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 481009001111 potential frameshift: common BLAST hit: gi|157827341|ref|YP_001496405.1| Mg chelatase-like protein 481009001112 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 481009001113 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 481009001114 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 481009001115 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 481009001116 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 481009001117 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 481009001118 dimerization interface [polypeptide binding]; other site 481009001119 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 481009001120 putative iron binding site [ion binding]; other site 481009001121 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 481009001122 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 481009001123 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 481009001124 HIGH motif; other site 481009001125 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 481009001126 active site 481009001127 KMSKS motif; other site 481009001128 DNA topoisomerase I; Validated; Region: PRK06599 481009001129 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 481009001130 active site 481009001131 interdomain interaction site; other site 481009001132 putative metal-binding site [ion binding]; other site 481009001133 nucleotide binding site [chemical binding]; other site 481009001134 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 481009001135 domain I; other site 481009001136 DNA binding groove [nucleotide binding] 481009001137 phosphate binding site [ion binding]; other site 481009001138 domain II; other site 481009001139 domain III; other site 481009001140 nucleotide binding site [chemical binding]; other site 481009001141 catalytic site [active] 481009001142 domain IV; other site 481009001143 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 481009001144 DNA protecting protein DprA; Region: dprA; TIGR00732 481009001145 DNA protecting protein DprA; Region: dprA; TIGR00732 481009001146 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 481009001147 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 481009001148 dimer interface [polypeptide binding]; other site 481009001149 decamer (pentamer of dimers) interface [polypeptide binding]; other site 481009001150 catalytic triad [active] 481009001151 peroxidatic and resolving cysteines [active] 481009001152 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 481009001153 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 481009001154 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 481009001155 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 481009001156 Sulfatase; Region: Sulfatase; pfam00884 481009001157 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair]; Region: COG0816 481009001158 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 481009001159 sequence-specific DNA binding site [nucleotide binding]; other site 481009001160 salt bridge; other site 481009001161 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 481009001162 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 481009001163 NADP binding site [chemical binding]; other site 481009001164 active site 481009001165 putative substrate binding site [chemical binding]; other site 481009001166 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 481009001167 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 481009001168 NAD(P) binding site [chemical binding]; other site 481009001169 homodimer interface [polypeptide binding]; other site 481009001170 substrate binding site [chemical binding]; other site 481009001171 active site 481009001172 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 481009001173 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 481009001174 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 481009001175 active site 481009001176 homodimer interface [polypeptide binding]; other site 481009001177 Methyltransferase domain; Region: Methyltransf_31; pfam13847 481009001178 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 481009001179 S-adenosylmethionine binding site [chemical binding]; other site 481009001180 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 481009001181 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 481009001182 active site 481009001183 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 481009001184 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 481009001185 active site 481009001186 Membrane-fusion protein [Cell envelope biogenesis, outer membrane]; Region: AcrA; COG0845 481009001187 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 481009001188 HlyD family secretion protein; Region: HlyD_3; pfam13437 481009001189 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 481009001190 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 481009001191 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 481009001192 catalytic site [active] 481009001193 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 481009001194 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 481009001195 putative ADP-binding pocket [chemical binding]; other site 481009001196 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 481009001197 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 481009001198 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 481009001199 RNA binding surface [nucleotide binding]; other site 481009001200 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 481009001201 UbiA prenyltransferase family; Region: UbiA; pfam01040 481009001202 spore photoproduct lyase; Region: photo_TT_lyase; cl15393 481009001203 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 481009001204 Domain of unknown function (DUF4385); Region: DUF4385; pfam14328 481009001205 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 481009001206 TPR repeat; Region: TPR_11; pfam13414 481009001207 TPR motif; other site 481009001208 binding surface 481009001209 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 481009001210 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 481009001211 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 481009001212 RimM N-terminal domain; Region: RimM; pfam01782 481009001213 PRC-barrel domain; Region: PRC; pfam05239 481009001214 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 481009001215 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 481009001216 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 481009001217 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 481009001218 active site 481009001219 DNA binding site [nucleotide binding] 481009001220 YCII-related domain; Region: YCII; cl00999 481009001221 hypothetical protein; Provisional; Region: PRK14388 481009001222 NADH dehydrogenase subunit E; Validated; Region: PRK07539 481009001223 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 481009001224 putative dimer interface [polypeptide binding]; other site 481009001225 [2Fe-2S] cluster binding site [ion binding]; other site 481009001226 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 481009001227 NADH dehydrogenase subunit D; Validated; Region: PRK06075 481009001228 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 481009001229 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 481009001230 NADH dehydrogenase subunit B; Validated; Region: PRK06411 481009001231 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 481009001232 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 481009001233 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4765 481009001234 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5410 481009001235 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 481009001236 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 481009001237 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 481009001238 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 481009001239 active site 481009001240 DNA binding site [nucleotide binding] 481009001241 Int/Topo IB signature motif; other site 481009001242 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06603 481009001243 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 481009001244 NAD binding site [chemical binding]; other site 481009001245 homotetramer interface [polypeptide binding]; other site 481009001246 homodimer interface [polypeptide binding]; other site 481009001247 substrate binding site [chemical binding]; other site 481009001248 active site 481009001249 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 481009001250 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 481009001251 putative active site [active] 481009001252 catalytic triad [active] 481009001253 putative dimer interface [polypeptide binding]; other site 481009001254 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 481009001255 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 481009001256 amidase catalytic site [active] 481009001257 Zn binding residues [ion binding]; other site 481009001258 substrate binding site [chemical binding]; other site 481009001259 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 481009001260 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG2984 481009001261 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 481009001262 TM-ABC transporter signature motif; other site 481009001263 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 481009001264 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 481009001265 Walker A/P-loop; other site 481009001266 ATP binding site [chemical binding]; other site 481009001267 Q-loop/lid; other site 481009001268 ABC transporter signature motif; other site 481009001269 Walker B; other site 481009001270 D-loop; other site 481009001271 H-loop/switch region; other site 481009001272 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 481009001273 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 481009001274 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 481009001275 catalytic core domain of class I lysyl tRNA synthetase; Region: LysRS_core_class_I; cd00674 481009001276 active site 481009001277 HIGH motif; other site 481009001278 KMSKS motif; other site 481009001279 Predicted permeases [General function prediction only]; Region: COG0679 481009001280 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 481009001281 Malic enzyme, N-terminal domain; Region: malic; pfam00390 481009001282 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 481009001283 putative NAD(P) binding site [chemical binding]; other site 481009001284 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 481009001285 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 481009001286 putative active site [active] 481009001287 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 481009001288 metabolite-proton symporter; Region: 2A0106; TIGR00883 481009001289 malate dehydrogenase; Reviewed; Region: PRK06223 481009001290 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 481009001291 NAD(P) binding site [chemical binding]; other site 481009001292 dimer interface [polypeptide binding]; other site 481009001293 tetramer (dimer of dimers) interface [polypeptide binding]; other site 481009001294 substrate binding site [chemical binding]; other site 481009001295 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 481009001296 TLC ATP/ADP transporter; Region: TLC; pfam03219 481009001297 CTP synthetase; Validated; Region: pyrG; PRK05380 481009001298 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 481009001299 Catalytic site [active] 481009001300 active site 481009001301 UTP binding site [chemical binding]; other site 481009001302 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 481009001303 active site 481009001304 putative oxyanion hole; other site 481009001305 catalytic triad [active] 481009001306 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 481009001307 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 481009001308 Ligand binding site; other site 481009001309 oligomer interface; other site 481009001310 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 481009001311 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 481009001312 GTP cyclohydrolase I; Provisional; Region: PLN03044 481009001313 active site 481009001314 prolyl-tRNA synthetase; Provisional; Region: PRK12325 481009001315 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 481009001316 dimer interface [polypeptide binding]; other site 481009001317 motif 1; other site 481009001318 active site 481009001319 motif 2; other site 481009001320 motif 3; other site 481009001321 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 481009001322 anticodon binding site; other site 481009001323 Fic family protein [Function unknown]; Region: COG3177 481009001324 Fic/DOC family; Region: Fic; pfam02661 481009001325 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 481009001326 RuvA N terminal domain; Region: RuvA_N; pfam01330 481009001327 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 481009001328 Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]; Region: RuvB; COG2255 481009001329 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 481009001330 Walker A motif; other site 481009001331 ATP binding site [chemical binding]; other site 481009001332 Walker B motif; other site 481009001333 arginine finger; other site 481009001334 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 481009001335 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 481009001336 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 481009001337 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 481009001338 Walker A/P-loop; other site 481009001339 ATP binding site [chemical binding]; other site 481009001340 Q-loop/lid; other site 481009001341 ABC transporter signature motif; other site 481009001342 Walker B; other site 481009001343 D-loop; other site 481009001344 H-loop/switch region; other site 481009001345 muropeptide transporter; Reviewed; Region: ampG; PRK11902 481009001346 muropeptide transporter; Validated; Region: ampG; cl17669 481009001347 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 481009001348 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 481009001349 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 481009001350 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 481009001351 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 481009001352 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 481009001353 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 481009001354 BON domain; Region: BON; pfam04972 481009001355 BON domain; Region: BON; pfam04972 481009001356 Intracellular septation protein A [Cell division and chromosome partitioning]; Region: COG2917 481009001357 Iron permease FTR1 family; Region: FTR1; cl00475 481009001358 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 481009001359 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 481009001360 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 481009001361 Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. This family contains catechol 1,2-dioxygenases and protocatechuate 3,4-dioxygenases which are mononuclear...; Region: intradiol_dioxygenase; cl17208 481009001362 active site 481009001363 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 481009001364 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 481009001365 catalytic residues [active] 481009001366 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 481009001367 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 481009001368 tandem repeat interface [polypeptide binding]; other site 481009001369 oligomer interface [polypeptide binding]; other site 481009001370 active site residues [active] 481009001371 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 481009001372 trimer interface [polypeptide binding]; other site 481009001373 active site 481009001374 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 481009001375 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 481009001376 N-acetyl-D-glucosamine binding site [chemical binding]; other site 481009001377 catalytic residue [active] 481009001378 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 481009001379 dimer interface [polypeptide binding]; other site 481009001380 catalytic triad [active] 481009001381 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 481009001382 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 481009001383 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 481009001384 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 481009001385 catalytic triad [active] 481009001386 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 481009001387 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 481009001388 Subunit I/III interface [polypeptide binding]; other site 481009001389 D-pathway; other site 481009001390 Subunit I/VIIc interface [polypeptide binding]; other site 481009001391 Subunit I/IV interface [polypeptide binding]; other site 481009001392 Subunit I/II interface [polypeptide binding]; other site 481009001393 Low-spin heme (heme a) binding site [chemical binding]; other site 481009001394 Subunit I/VIIa interface [polypeptide binding]; other site 481009001395 Subunit I/VIa interface [polypeptide binding]; other site 481009001396 Dimer interface; other site 481009001397 Putative water exit pathway; other site 481009001398 Binuclear center (heme a3/CuB) [ion binding]; other site 481009001399 K-pathway; other site 481009001400 Subunit I/Vb interface [polypeptide binding]; other site 481009001401 Putative proton exit pathway; other site 481009001402 Subunit I/VIb interface; other site 481009001403 Subunit I/VIc interface [polypeptide binding]; other site 481009001404 Electron transfer pathway; other site 481009001405 Subunit I/VIIIb interface [polypeptide binding]; other site 481009001406 Subunit I/VIIb interface [polypeptide binding]; other site 481009001407 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 481009001408 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 481009001409 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 481009001410 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 481009001411 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 481009001412 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 481009001413 putative peptidase; Provisional; Region: PRK11649 481009001414 Peptidase family M23; Region: Peptidase_M23; pfam01551 481009001415 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 481009001416 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 481009001417 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 481009001418 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01368 481009001419 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 481009001420 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 481009001421 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 481009001422 cell division protein FtsW; Region: ftsW; TIGR02614 481009001423 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 481009001424 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 481009001425 active site 481009001426 homodimer interface [polypeptide binding]; other site 481009001427 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 481009001428 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 481009001429 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 481009001430 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 481009001431 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 481009001432 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 481009001433 potential frameshift: common BLAST hit: gi|67459034|ref|YP_246658.1| RND family transporter membrane-fusion protein 481009001434 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 481009001435 potential frameshift: common BLAST hit: gi|67459035|ref|YP_246659.1| RND efflux system, outer membrane protein 481009001436 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 481009001437 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 481009001438 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 481009001439 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 481009001440 diaminopimelate epimerase; Region: DapF; TIGR00652 481009001441 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 481009001442 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 481009001443 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 481009001444 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 481009001445 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 481009001446 FeS/SAM binding site; other site 481009001447 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 481009001448 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 481009001449 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 481009001450 dimer interface [polypeptide binding]; other site 481009001451 motif 1; other site 481009001452 active site 481009001453 motif 2; other site 481009001454 motif 3; other site 481009001455 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 481009001456 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 481009001457 putative tRNA-binding site [nucleotide binding]; other site 481009001458 B3/4 domain; Region: B3_4; pfam03483 481009001459 tRNA synthetase B5 domain; Region: B5; smart00874 481009001460 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 481009001461 dimer interface [polypeptide binding]; other site 481009001462 motif 1; other site 481009001463 motif 3; other site 481009001464 motif 2; other site 481009001465 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 481009001466 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 481009001467 DNA polymerase III subunit beta; Validated; Region: PRK05643 481009001468 putative DNA binding surface [nucleotide binding]; other site 481009001469 dimer interface [polypeptide binding]; other site 481009001470 beta-clamp/clamp loader binding surface; other site 481009001471 beta-clamp/translesion DNA polymerase binding surface; other site 481009001472 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 481009001473 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 481009001474 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 481009001475 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 481009001476 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 481009001477 HIGH motif; other site 481009001478 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 481009001479 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 481009001480 active site 481009001481 KMSKS motif; other site 481009001482 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 481009001483 tRNA binding surface [nucleotide binding]; other site 481009001484 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 481009001485 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 481009001486 catalytic site [active] 481009001487 putative active site [active] 481009001488 putative substrate binding site [chemical binding]; other site 481009001489 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 481009001490 Septum formation initiator; Region: DivIC; pfam04977 481009001491 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 481009001492 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 481009001493 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 481009001494 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 481009001495 catalytic residue [active] 481009001496 putative FPP diphosphate binding site; other site 481009001497 putative FPP binding hydrophobic cleft; other site 481009001498 dimer interface [polypeptide binding]; other site 481009001499 putative IPP diphosphate binding site; other site 481009001500 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 481009001501 HAMP domain; Region: HAMP; pfam00672 481009001502 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 481009001503 dimer interface [polypeptide binding]; other site 481009001504 phosphorylation site [posttranslational modification] 481009001505 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 481009001506 ATP binding site [chemical binding]; other site 481009001507 Mg2+ binding site [ion binding]; other site 481009001508 G-X-G motif; other site 481009001509 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 481009001510 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 481009001511 active site 481009001512 phosphorylation site [posttranslational modification] 481009001513 intermolecular recognition site; other site 481009001514 dimerization interface [polypeptide binding]; other site 481009001515 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 481009001516 DNA binding site [nucleotide binding] 481009001517 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 481009001518 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 481009001519 homodimer interface [polypeptide binding]; other site 481009001520 substrate-cofactor binding pocket; other site 481009001521 catalytic residue [active] 481009001522 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 481009001523 dihydrodipicolinate synthase; Region: dapA; TIGR00674 481009001524 dimer interface [polypeptide binding]; other site 481009001525 active site 481009001526 catalytic residue [active] 481009001527 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 481009001528 SmpB-tmRNA interface; other site 481009001529 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 481009001530 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 481009001531 catalytic residues [active] 481009001532 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 481009001533 CoA binding domain; Region: CoA_binding; pfam02629 481009001534 CoA-ligase; Region: Ligase_CoA; pfam00549 481009001535 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 481009001536 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 481009001537 CoA-ligase; Region: Ligase_CoA; pfam00549 481009001538 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 481009001539 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 481009001540 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 481009001541 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 481009001542 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 481009001543 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4395 481009001544 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 481009001545 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 481009001546 Predicted membrane protein [Function unknown]; Region: COG1238 481009001547 Predicted membrane protein/domain [Function unknown]; Region: COG1714 481009001548 Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]; Region: RecR; COG0353 481009001549 RecR protein; Region: RecR; pfam02132 481009001550 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 481009001551 putative active site [active] 481009001552 putative metal-binding site [ion binding]; other site 481009001553 tetramer interface [polypeptide binding]; other site 481009001554 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 481009001555 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 481009001556 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 481009001557 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 481009001558 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 481009001559 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 481009001560 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 481009001561 Predicted permeases [General function prediction only]; Region: COG0679 481009001562 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 481009001563 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 481009001564 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 481009001565 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 481009001566 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 481009001567 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 481009001568 tetramerization interface [polypeptide binding]; other site 481009001569 NAD(P) binding site [chemical binding]; other site 481009001570 catalytic residues [active] 481009001571 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 481009001572 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 481009001573 active site 481009001574 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 481009001575 Part of AAA domain; Region: AAA_19; pfam13245 481009001576 Family description; Region: UvrD_C_2; pfam13538 481009001577 Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: AlaS; COG0013 481009001578 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 481009001579 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 481009001580 tetramer interface [polypeptide binding]; other site 481009001581 pyridoxal 5'-phosphate binding site [chemical binding]; other site 481009001582 catalytic residue [active] 481009001583 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 481009001584 Found in ATP-dependent protease La (LON); Region: LON; smart00464 481009001585 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 481009001586 Walker A motif; other site 481009001587 ATP binding site [chemical binding]; other site 481009001588 Walker B motif; other site 481009001589 arginine finger; other site 481009001590 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 481009001591 potential frameshift: common BLAST hit: gi|67459085|ref|YP_246709.1| cell surface antigen Sca3 481009001592 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 481009001593 30S subunit binding site; other site 481009001594 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 481009001595 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 481009001596 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14171 481009001597 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 481009001598 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 481009001599 homodimer interface [polypeptide binding]; other site 481009001600 NADP binding site [chemical binding]; other site 481009001601 substrate binding site [chemical binding]; other site 481009001602 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 481009001603 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 481009001604 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 481009001605 Uncharacterized secreted protein [Function unknown]; Region: COG5430 481009001606 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 481009001607 potential frameshift: common BLAST hit: gi|157827080|ref|YP_001496144.1| P pilus assembly, fimbrial usher protein 481009001608 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 481009001609 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 481009001610 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 481009001611 Spore Coat Protein U domain; Region: SCPU; pfam05229 481009001612 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 481009001613 Class I ribonucleotide reductase; Region: RNR_I; cd01679 481009001614 active site 481009001615 dimer interface [polypeptide binding]; other site 481009001616 catalytic residues [active] 481009001617 effector binding site; other site 481009001618 R2 peptide binding site; other site 481009001619 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 481009001620 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 481009001621 dimer interface [polypeptide binding]; other site 481009001622 putative radical transfer pathway; other site 481009001623 diiron center [ion binding]; other site 481009001624 tyrosyl radical; other site 481009001625 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 481009001626 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 481009001627 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 481009001628 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 481009001629 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 481009001630 active site 481009001631 substrate binding site [chemical binding]; other site 481009001632 metal binding site [ion binding]; metal-binding site 481009001633 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 481009001634 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 481009001635 Walker A/P-loop; other site 481009001636 ATP binding site [chemical binding]; other site 481009001637 Q-loop/lid; other site 481009001638 ABC transporter signature motif; other site 481009001639 Walker B; other site 481009001640 D-loop; other site 481009001641 H-loop/switch region; other site 481009001642 OstA-like protein; Region: OstA; pfam03968 481009001643 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 481009001644 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 481009001645 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 481009001646 putative active site [active] 481009001647 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 481009001648 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 481009001649 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 481009001650 RNase E interface [polypeptide binding]; other site 481009001651 trimer interface [polypeptide binding]; other site 481009001652 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 481009001653 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 481009001654 RNase E interface [polypeptide binding]; other site 481009001655 trimer interface [polypeptide binding]; other site 481009001656 active site 481009001657 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 481009001658 putative nucleic acid binding region [nucleotide binding]; other site 481009001659 G-X-X-G motif; other site 481009001660 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 481009001661 RNA binding site [nucleotide binding]; other site 481009001662 domain interface; other site 481009001663 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 481009001664 16S/18S rRNA binding site [nucleotide binding]; other site 481009001665 S13e-L30e interaction site [polypeptide binding]; other site 481009001666 25S rRNA binding site [nucleotide binding]; other site 481009001667 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK14846 481009001668 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 481009001669 RNA binding site [nucleotide binding]; other site 481009001670 active site 481009001671 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 481009001672 TLC ATP/ADP transporter; Region: TLC; pfam03219 481009001673 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 481009001674 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 481009001675 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 481009001676 non-specific DNA binding site [nucleotide binding]; other site 481009001677 salt bridge; other site 481009001678 sequence-specific DNA binding site [nucleotide binding]; other site 481009001679 Ribonuclease BN family enzyme [Replication, recombination, and repair]; Region: Rbn; COG1295 481009001680 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 481009001681 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 481009001682 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 481009001683 uncharacterized protein, YfiH family; Region: TIGR00726 481009001684 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 481009001685 active site 481009001686 catalytic residues [active] 481009001687 metal binding site [ion binding]; metal-binding site 481009001688 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 481009001689 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 481009001690 putative active site [active] 481009001691 homotetrameric interface [polypeptide binding]; other site 481009001692 metal binding site [ion binding]; metal-binding site 481009001693 hypothetical protein; Provisional; Region: PRK06661 481009001694 intersubunit interface [polypeptide binding]; other site 481009001695 active site 481009001696 Zn2+ binding site [ion binding]; other site 481009001697 pyruvate phosphate dikinase; Provisional; Region: PRK09279 481009001698 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 481009001699 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 481009001700 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 481009001701 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 481009001702 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 481009001703 GSH binding site (G-site) [chemical binding]; other site 481009001704 C-terminal domain interface [polypeptide binding]; other site 481009001705 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 481009001706 N-terminal domain interface [polypeptide binding]; other site 481009001707 dimer interface [polypeptide binding]; other site 481009001708 substrate binding pocket (H-site) [chemical binding]; other site 481009001709 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP); Region: GATase1_ScBLP_like; cd03144 481009001710 conserved cys residue [active] 481009001711 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 481009001712 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 481009001713 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 481009001714 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 481009001715 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 481009001716 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 481009001717 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 481009001718 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 481009001719 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 481009001720 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 481009001721 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 481009001722 Uncharacterized conserved protein [Function unknown]; Region: COG5448 481009001723 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 481009001724 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 481009001725 Predicted membrane protein [Function unknown]; Region: COG5346 481009001726 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 481009001727 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 481009001728 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 481009001729 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 481009001730 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 481009001731 E3 interaction surface; other site 481009001732 lipoyl attachment site [posttranslational modification]; other site 481009001733 e3 binding domain; Region: E3_binding; pfam02817 481009001734 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 481009001735 peptide chain release factor 1; Validated; Region: prfA; PRK00591 481009001736 This domain is found in peptide chain release factors; Region: PCRF; smart00937 481009001737 RF-1 domain; Region: RF-1; pfam00472 481009001738 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 481009001739 DHH family; Region: DHH; pfam01368 481009001740 DHHA1 domain; Region: DHHA1; pfam02272 481009001741 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1, 4-benzoquinol methylase [Coenzyme metabolism]; Region: UbiG; COG2227 481009001742 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 481009001743 S-adenosylmethionine binding site [chemical binding]; other site 481009001744 transcription termination factor Rho; Provisional; Region: rho; PRK09376 481009001745 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 481009001746 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 481009001747 RNA binding site [nucleotide binding]; other site 481009001748 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 481009001749 multimer interface [polypeptide binding]; other site 481009001750 Walker A motif; other site 481009001751 ATP binding site [chemical binding]; other site 481009001752 Walker B motif; other site 481009001753 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 481009001754 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 481009001755 tandem repeat interface [polypeptide binding]; other site 481009001756 oligomer interface [polypeptide binding]; other site 481009001757 active site residues [active] 481009001758 Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]; Region: HimA; COG0776 481009001759 IHF - DNA interface [nucleotide binding]; other site 481009001760 IHF dimer interface [polypeptide binding]; other site 481009001761 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3022 481009001762 hypothetical protein; Region: PHA00670 481009001763 Conjugative relaxosome accessory transposon protein; Region: TraH; pfam06122 481009001764 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 481009001765 TPR repeat; Region: TPR_11; pfam13414 481009001766 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 481009001767 binding surface 481009001768 TPR motif; other site 481009001769 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 481009001770 binding surface 481009001771 TPR repeat; Region: TPR_11; pfam13414 481009001772 TPR motif; other site 481009001773 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 481009001774 binding surface 481009001775 TPR repeat; Region: TPR_11; pfam13414 481009001776 TPR motif; other site 481009001777 TPR repeat; Region: TPR_11; pfam13414 481009001778 F sex factor protein N terminal; Region: TraD_N; pfam12615 481009001779 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 481009001780 Type IV secretion-system coupling protein DNA-binding domain; Region: TrwB_AAD_bind; pfam10412 481009001781 Walker A motif; other site 481009001782 ATP binding site [chemical binding]; other site 481009001783 Walker B motif; other site 481009001784 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 481009001785 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 481009001786 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 481009001787 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 481009001788 synthetase active site [active] 481009001789 NTP binding site [chemical binding]; other site 481009001790 metal binding site [ion binding]; metal-binding site 481009001791 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 481009001792 active site 481009001793 metal binding site [ion binding]; metal-binding site 481009001794 interdomain interaction site; other site 481009001795 helix_turn_helix, Lux Regulon; Region: HTH_LUXR; smart00421 481009001796 DNA binding residues [nucleotide binding] 481009001797 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 481009001798 HD domain; Region: HD_4; pfam13328 481009001799 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 481009001800 His Kinase A (phospho-acceptor) domain; Region: HisKA; pfam00512 481009001801 dimer interface [polypeptide binding]; other site 481009001802 phosphorylation site [posttranslational modification] 481009001803 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 481009001804 ATP binding site [chemical binding]; other site 481009001805 Mg2+ binding site [ion binding]; other site 481009001806 G-X-G motif; other site 481009001807 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 481009001808 DnaA N-terminal domain; Region: DnaA_N; pfam11638 481009001809 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 481009001810 non-specific DNA binding site [nucleotide binding]; other site 481009001811 salt bridge; other site 481009001812 sequence-specific DNA binding site [nucleotide binding]; other site 481009001813 Cytidylate kinase [Nucleotide transport and metabolism]; Region: Cmk; COG0283 481009001814 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 481009001815 CMP-binding site; other site 481009001816 The sites determining sugar specificity; other site 481009001817 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 481009001818 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 481009001819 RNA binding site [nucleotide binding]; other site 481009001820 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 481009001821 RNA binding site [nucleotide binding]; other site 481009001822 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 481009001823 RNA binding site [nucleotide binding]; other site 481009001824 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 481009001825 RNA binding site [nucleotide binding]; other site 481009001826 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 481009001827 RNA binding site [nucleotide binding]; other site 481009001828 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 481009001829 RNA binding site [nucleotide binding]; other site 481009001830 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 481009001831 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 481009001832 oligomer interface [polypeptide binding]; other site 481009001833 active site residues [active] 481009001834 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 481009001835 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 481009001836 homotetramer interface [polypeptide binding]; other site 481009001837 FMN binding site [chemical binding]; other site 481009001838 homodimer contacts [polypeptide binding]; other site 481009001839 putative active site [active] 481009001840 putative substrate binding site [chemical binding]; other site 481009001841 Predicted acetyltransferase [General function prediction only]; Region: COG5628 481009001842 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 481009001843 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 481009001844 Coenzyme A binding pocket [chemical binding]; other site 481009001845 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 481009001846 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 481009001847 Predicted transcriptional regulator [Transcription]; Region: COG1959 481009001848 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 481009001849 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 481009001850 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 481009001851 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 481009001852 catalytic residue [active] 481009001853 cysteine desulfurase; Provisional; Region: PRK14012 481009001854 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 481009001855 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 481009001856 catalytic residue [active] 481009001857 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 481009001858 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 481009001859 trimerization site [polypeptide binding]; other site 481009001860 active site 481009001861 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 481009001862 arginine:agmatin antiporter; Provisional; Region: PRK10644 481009001863 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 481009001864 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 481009001865 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 481009001866 active site 481009001867 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 481009001868 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 481009001869 substrate binding pocket [chemical binding]; other site 481009001870 chain length determination region; other site 481009001871 substrate-Mg2+ binding site; other site 481009001872 catalytic residues [active] 481009001873 aspartate-rich region 1; other site 481009001874 active site lid residues [active] 481009001875 aspartate-rich region 2; other site 481009001876 TLC ATP/ADP transporter; Region: TLC; pfam03219 481009001877 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 481009001878 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 481009001879 muropeptide transporter; Reviewed; Region: ampG; PRK11902 481009001880 AmpG-like permease; Region: 2A0125; TIGR00901 481009001881 Lysine efflux permease [General function prediction only]; Region: COG1279 481009001882 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 481009001883 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 481009001884 active site 481009001885 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 481009001886 HemY protein N-terminus; Region: HemY_N; pfam07219 481009001887 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 481009001888 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 481009001889 RelB antitoxin; Region: RelB; cl01171 481009001890 RelB antitoxin; Region: RelB; cl01171 481009001891 Protein required for attachment to host cells [Cell motility and secretion]; Region: COG5622 481009001892 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 481009001893 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 481009001894 putative acyl-acceptor binding pocket; other site 481009001895 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 481009001896 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 481009001897 active site 481009001898 HIGH motif; other site 481009001899 dimer interface [polypeptide binding]; other site 481009001900 KMSKS motif; other site 481009001901 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 481009001902 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 481009001903 AAA domain; Region: AAA_14; pfam13173 481009001904 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 481009001905 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 481009001906 domain interfaces; other site 481009001907 active site 481009001908 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 481009001909 dimer interface [polypeptide binding]; other site 481009001910 catalytic triad [active] 481009001911 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 481009001912 dimer interface [polypeptide binding]; other site 481009001913 phosphorylation site [posttranslational modification] 481009001914 potential frameshift: common BLAST hit: gi|15892625|ref|NP_360339.1| sodium/pantothenate symporter 481009001915 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 481009001916 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 481009001917 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 481009001918 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 481009001919 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 481009001920 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 481009001921 Uncharacterized conserved protein [Function unknown]; Region: COG1723 481009001922 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 481009001923 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 481009001924 catalytic site [active] 481009001925 putative active site [active] 481009001926 putative substrate binding site [chemical binding]; other site 481009001927 Helicase and RNase D C-terminal; Region: HRDC; smart00341 481009001928 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 481009001929 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 481009001930 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 481009001931 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 481009001932 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 481009001933 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 481009001934 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 481009001935 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 481009001936 S-adenosylmethionine binding site [chemical binding]; other site 481009001937 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 481009001938 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; pfam12762 481009001939 Protein of unknown function (DUF2532); Region: DUF2532; pfam10811 481009001940 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 481009001941 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 481009001942 N-acetyl-D-glucosamine binding site [chemical binding]; other site 481009001943 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 481009001944 hypothetical protein; Validated; Region: PRK00110 481009001945 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 481009001946 Substrate binding site; other site 481009001947 Mg++ binding site; other site 481009001948 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs' Region: NTP-PPase_MazG_Cterm; cd11529 481009001949 active site 481009001950 homodimer interface [polypeptide binding]; other site 481009001951 putative chemical substrate binding site [chemical binding]; other site 481009001952 metal binding site [ion binding]; metal-binding site 481009001953 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 481009001954 AAA domain; Region: AAA_17; pfam13207 481009001955 NADH dehydrogenase subunit 2; Provisional; Region: ND2; MTH00196 481009001956 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 481009001957 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 481009001958 dimer interface [polypeptide binding]; other site 481009001959 allosteric magnesium binding site [ion binding]; other site 481009001960 active site 481009001961 aspartate-rich active site metal binding site; other site 481009001962 Schiff base residues; other site 481009001963 primosome assembly protein PriA; Validated; Region: PRK05580 481009001964 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 481009001965 ATP binding site [chemical binding]; other site 481009001966 putative Mg++ binding site [ion binding]; other site 481009001967 helicase superfamily c-terminal domain; Region: HELICc; smart00490 481009001968 3-polyprenyl-4-hydroxybenzoate decarboxylase [Coenzyme metabolism]; Region: UbiX; COG0163 481009001969 Flavoprotein; Region: Flavoprotein; pfam02441 481009001970 replicative DNA helicase; Provisional; Region: PRK09165 481009001971 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 481009001972 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 481009001973 Walker A motif; other site 481009001974 ATP binding site [chemical binding]; other site 481009001975 Walker B motif; other site 481009001976 DNA binding loops [nucleotide binding] 481009001977 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 481009001978 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 481009001979 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 481009001980 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 481009001981 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 481009001982 RNA binding surface [nucleotide binding]; other site 481009001983 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 481009001984 active site 481009001985 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 481009001986 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 481009001987 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 481009001988 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 481009001989 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 481009001990 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 481009001991 S-adenosylmethionine binding site [chemical binding]; other site 481009001992 DNA repair protein RadA; Provisional; Region: PRK11823 481009001993 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 481009001994 Walker A motif/ATP binding site; other site 481009001995 ATP binding site [chemical binding]; other site 481009001996 Walker B motif; other site 481009001997 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 481009001998 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 481009001999 Recombination protein O N terminal; Region: RecO_N; pfam11967 481009002000 Recombination protein O C terminal; Region: RecO_C; pfam02565 481009002001 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214 481009002002 Glycoprotease family; Region: Peptidase_M22; pfam00814 481009002003 translation initiation factor IF-2; Validated; Region: infB; PRK05306 481009002004 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 481009002005 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 481009002006 G1 box; other site 481009002007 putative GEF interaction site [polypeptide binding]; other site 481009002008 GTP/Mg2+ binding site [chemical binding]; other site 481009002009 Switch I region; other site 481009002010 G2 box; other site 481009002011 G3 box; other site 481009002012 Switch II region; other site 481009002013 G4 box; other site 481009002014 G5 box; other site 481009002015 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 481009002016 Translation-initiation factor 2; Region: IF-2; pfam11987 481009002017 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 481009002018 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 481009002019 NusA N-terminal domain; Region: NusA_N; pfam08529 481009002020 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 481009002021 RNA binding site [nucleotide binding]; other site 481009002022 homodimer interface [polypeptide binding]; other site 481009002023 NusA-like KH domain; Region: KH_5; pfam13184 481009002024 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 481009002025 G-X-X-G motif; other site 481009002026 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 481009002027 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG0779 481009002028 Sm and related proteins; Region: Sm_like; cl00259 481009002029 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 481009002030 putative oligomer interface [polypeptide binding]; other site 481009002031 putative RNA binding site [nucleotide binding]; other site 481009002032 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 481009002033 NAD binding pocket [chemical binding]; other site 481009002034 Predicted transcriptional regulator [Transcription]; Region: COG1959 481009002035 Transcriptional regulator; Region: Rrf2; cl17282 481009002036 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 481009002037 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 481009002038 RNA binding surface [nucleotide binding]; other site 481009002039 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 481009002040 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 481009002041 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 481009002042 active site 481009002043 HIGH motif; other site 481009002044 dimer interface [polypeptide binding]; other site 481009002045 KMSKS motif; other site 481009002046 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 481009002047 RNA binding surface [nucleotide binding]; other site 481009002048 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 481009002049 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 481009002050 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 481009002051 Substrate binding site [chemical binding]; other site 481009002052 proline/glycine betaine transporter; Provisional; Region: PRK10642 481009002053 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 481009002054 active site 481009002055 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 481009002056 potential frameshift: common BLAST hit: gi|350273648|ref|YP_004884961.1| large extracellular alpha-helical protein 481009002057 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 481009002058 potential frameshift: common BLAST hit: gi|157964695|ref|YP_001499519.1| large extracellular alpha-helical protein 481009002059 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 481009002060 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 481009002061 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 481009002062 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 481009002063 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 481009002064 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 481009002065 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 481009002066 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 481009002067 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 481009002068 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK06617 481009002069 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 481009002070 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK12612 481009002071 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 481009002072 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 481009002073 active site 481009002074 phosphorylation site [posttranslational modification] 481009002075 intermolecular recognition site; other site 481009002076 dimerization interface [polypeptide binding]; other site 481009002077 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 481009002078 Walker A motif; other site 481009002079 ATP binding site [chemical binding]; other site 481009002080 Walker B motif; other site 481009002081 arginine finger; other site 481009002082 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 481009002083 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 481009002084 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 481009002085 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 481009002086 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 481009002087 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 481009002088 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 481009002089 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 481009002090 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 481009002091 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 481009002092 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 481009002093 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 481009002094 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 481009002095 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 481009002096 S-adenosylmethionine binding site [chemical binding]; other site 481009002097 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 481009002098 MraZ protein; Region: MraZ; pfam02381 481009002099 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 481009002100 Na binding site [ion binding]; other site 481009002101 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 481009002102 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 481009002103 GIY-YIG motif/motif A; other site 481009002104 active site 481009002105 catalytic site [active] 481009002106 putative DNA binding site [nucleotide binding]; other site 481009002107 metal binding site [ion binding]; metal-binding site 481009002108 UvrB/uvrC motif; Region: UVR; pfam02151 481009002109 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 481009002110 Copper(I)-binding protein [Inorganic ion transport and metabolism]; Region: COG2847 481009002111 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 481009002112 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 481009002113 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 481009002114 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 481009002115 DNA binding site [nucleotide binding] 481009002116 active site 481009002117 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 481009002118 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 481009002119 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 481009002120 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 481009002121 DEAD/DEAH box helicase; Region: DEAD; pfam00270 481009002122 ATP binding site [chemical binding]; other site 481009002123 putative Mg++ binding site [ion binding]; other site 481009002124 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 481009002125 SEC-C motif; Region: SEC-C; pfam02810 481009002126 peptidylprolyl isomerase; Provisional; Region: prsA; PRK04405 481009002127 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 481009002128 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 481009002129 DNA-directed RNA polymerase, omega subunit; Region: rpoZ; TIGR00690 481009002130 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 481009002131 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 481009002132 hinge; other site 481009002133 active site 481009002134 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 481009002135 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 481009002136 ATP binding site [chemical binding]; other site 481009002137 Mg2+ binding site [ion binding]; other site 481009002138 G-X-G motif; other site 481009002139 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 481009002140 anchoring element; other site 481009002141 dimer interface [polypeptide binding]; other site 481009002142 ATP binding site [chemical binding]; other site 481009002143 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 481009002144 active site 481009002145 putative metal-binding site [ion binding]; other site 481009002146 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 481009002147 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 481009002148 Haloacid dehalogenase-like hydrolase; Region: Hydrolase_6; pfam13344 481009002149 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 481009002150 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 481009002151 MgtE intracellular N domain; Region: MgtE_N; pfam03448 481009002152 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 481009002153 Divalent cation transporter; Region: MgtE; pfam01769 481009002154 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 481009002155 HD domain; Region: HD_4; pfam13328 481009002156 potential frameshift: common BLAST hit: gi|67459346|ref|YP_246970.1| proline/betaine transporter 481009002157 Predicted DNA-binding protein with an HTH domain [General function prediction only]; Region: COG4710 481009002158 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 481009002159 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 481009002160 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 481009002161 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 481009002162 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 481009002163 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 481009002164 Cu(I) binding site [ion binding]; other site 481009002165 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 481009002166 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 481009002167 dimer interface [polypeptide binding]; other site 481009002168 substrate binding site [chemical binding]; other site 481009002169 metal binding sites [ion binding]; metal-binding site 481009002170 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 481009002171 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 481009002172 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 481009002173 TraX protein; Region: TraX; pfam05857 481009002174 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 481009002175 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 481009002176 ssDNA binding site; other site 481009002177 generic binding surface II; other site 481009002178 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 481009002179 ATP binding site [chemical binding]; other site 481009002180 putative Mg++ binding site [ion binding]; other site 481009002181 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 481009002182 nucleotide binding region [chemical binding]; other site 481009002183 ATP-binding site [chemical binding]; other site 481009002184 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 481009002185 potential frameshift: common BLAST hit: gi|165933489|ref|YP_001650278.1| succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B 481009002186 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 481009002187 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]; Region: MutS; COG0249 481009002188 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 481009002189 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 481009002190 Mg++ binding site [ion binding]; other site 481009002191 putative catalytic motif [active] 481009002192 putative substrate binding site [chemical binding]; other site 481009002193 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 481009002194 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 481009002195 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 481009002196 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 481009002197 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 481009002198 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 481009002199 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 481009002200 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 481009002201 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 481009002202 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 481009002203 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 481009002204 ATP binding site [chemical binding]; other site 481009002205 putative Mg++ binding site [ion binding]; other site 481009002206 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 481009002207 nucleotide binding region [chemical binding]; other site 481009002208 ATP-binding site [chemical binding]; other site 481009002209 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 481009002210 Uncharacterized conserved protein [Function unknown]; Region: COG2938 481009002211 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 481009002212 active site residue [active] 481009002213 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 481009002214 DnaA N-terminal domain; Region: DnaA_N; pfam11638 481009002215 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 481009002216 Walker A motif; other site 481009002217 ATP binding site [chemical binding]; other site 481009002218 Walker B motif; other site 481009002219 arginine finger; other site 481009002220 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 481009002221 DnaA box-binding interface [nucleotide binding]; other site 481009002222 Patatin [General function prediction only]; Region: COG3621 481009002223 Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17; Region: Pat17_PNPLA8_PNPLA9_like; cd07199 481009002224 active site 481009002225 nucleophile elbow; other site 481009002226 potential frameshift: common BLAST hit: gi|341584110|ref|YP_004764601.1| bicyclomycin resistance protein 481009002227 potential frameshift: common BLAST hit: gi|341584111|ref|YP_004764602.1| nucleotidyltransferase 481009002228 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 481009002229 active site 481009002230 NTP binding site [chemical binding]; other site 481009002231 metal binding triad [ion binding]; metal-binding site 481009002232 GTP-binding protein YchF; Reviewed; Region: PRK09601 481009002233 YchF GTPase; Region: YchF; cd01900 481009002234 G1 box; other site 481009002235 GTP/Mg2+ binding site [chemical binding]; other site 481009002236 Switch I region; other site 481009002237 G2 box; other site 481009002238 Switch II region; other site 481009002239 G3 box; other site 481009002240 G4 box; other site 481009002241 G5 box; other site 481009002242 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 481009002243 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 481009002244 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 481009002245 putative active site [active] 481009002246 catalytic residue [active] 481009002247 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 481009002248 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 481009002249 5S rRNA interface [nucleotide binding]; other site 481009002250 CTC domain interface [polypeptide binding]; other site 481009002251 L16 interface [polypeptide binding]; other site 481009002252 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 481009002253 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 481009002254 FeS/SAM binding site; other site 481009002255 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 481009002256 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 481009002257 23S rRNA binding site [nucleotide binding]; other site 481009002258 L21 binding site [polypeptide binding]; other site 481009002259 L13 binding site [polypeptide binding]; other site 481009002260 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 481009002261 ribonuclease P; Reviewed; Region: rnpA; PRK01492 481009002262 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 481009002263 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 481009002264 uncharacterized subgroup of the Escherichia coli Mg2+ transporter CorA_like subfamily; Region: EcCorA-like_u1; cd12837 481009002265 Cl binding site [ion binding]; other site 481009002266 oligomer interface [polypeptide binding]; other site 481009002267 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 481009002268 Phosphotransferase enzyme family; Region: APH; pfam01636 481009002269 substrate binding site [chemical binding]; other site 481009002270 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 481009002271 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 481009002272 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 481009002273 dimerization interface [polypeptide binding]; other site 481009002274 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 481009002275 dimer interface [polypeptide binding]; other site 481009002276 phosphorylation site [posttranslational modification] 481009002277 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 481009002278 ATP binding site [chemical binding]; other site 481009002279 Mg2+ binding site [ion binding]; other site 481009002280 G-X-G motif; other site 481009002281 Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]; Region: RpsU; COG0828 481009002282 Uncharacterized conserved protein [Function unknown]; Region: COG5590 481009002283 COQ9; Region: COQ9; pfam08511 481009002284 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 481009002285 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 481009002286 HIGH motif; other site 481009002287 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 481009002288 active site 481009002289 KMSKS motif; other site 481009002290 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 481009002291 tRNA binding surface [nucleotide binding]; other site 481009002292 anticodon binding site; other site 481009002293 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 481009002294 TPR motif; other site 481009002295 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 481009002296 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 481009002297 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 481009002298 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 481009002299 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 481009002300 carboxyltransferase (CT) interaction site; other site 481009002301 biotinylation site [posttranslational modification]; other site 481009002302 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 481009002303 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 481009002304 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 481009002305 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 481009002306 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 481009002307 putative substrate translocation pore; other site 481009002308 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 481009002309 putative acyl-acceptor binding pocket; other site 481009002310 C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas); Region: AAS_C; cd05909 481009002311 acyl-activating enzyme (AAE) consensus motif; other site 481009002312 putative AMP binding site [chemical binding]; other site 481009002313 TfoX N-terminal domain; Region: TfoX_N; pfam04993 481009002314 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 481009002315 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 481009002316 ABC-ATPase subunit interface; other site 481009002317 dimer interface [polypeptide binding]; other site 481009002318 putative PBP binding regions; other site 481009002319 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 481009002320 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 481009002321 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 481009002322 S-adenosylmethionine binding site [chemical binding]; other site 481009002323 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 481009002324 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 481009002325 HIGH motif; other site 481009002326 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 481009002327 active site 481009002328 KMSKS motif; other site 481009002329 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 481009002330 Invasion protein B, involved in pathogenesis [General function prediction only]; Region: COG5342 481009002331 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 481009002332 GroEL_like type I chaperonin. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. The symmetry of type I is seven-fold and they are found...; Region: GroEL; cd03344 481009002333 ring oligomerisation interface [polypeptide binding]; other site 481009002334 ATP/Mg binding site [chemical binding]; other site 481009002335 stacking interactions; other site 481009002336 hinge regions; other site 481009002337 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 481009002338 oligomerisation interface [polypeptide binding]; other site 481009002339 mobile loop; other site 481009002340 roof hairpin; other site 481009002341 potential frameshift: common BLAST hit: gi|67458799|ref|YP_246423.1| glycosyltransferase 481009002342 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 481009002343 potential frameshift: common BLAST hit: gi|67458799|ref|YP_246423.1| glycosyltransferase 481009002344 ribonuclease PH; Reviewed; Region: rph; PRK00173 481009002345 Ribonuclease PH; Region: RNase_PH_bact; cd11362 481009002346 hexamer interface [polypeptide binding]; other site 481009002347 active site 481009002348 GrpE; Region: GrpE; pfam01025 481009002349 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 481009002350 dimer interface [polypeptide binding]; other site 481009002351 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 481009002352 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 481009002353 Domain of unknown function DUF20; Region: UPF0118; pfam01594 481009002354 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 481009002355 hypothetical protein; Validated; Region: PRK06620 481009002356 potential frameshift: common BLAST hit: gi|67458789|ref|YP_246413.1| MFS type sugar transporter 481009002357 HD domain; Region: HD_4; pfam13328 481009002358 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 481009002359 Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]; Region: RplQ; COG0203 481009002360 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 481009002361 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 481009002362 alphaNTD - beta interaction site [polypeptide binding]; other site 481009002363 alphaNTD homodimer interface [polypeptide binding]; other site 481009002364 alphaNTD - beta' interaction site [polypeptide binding]; other site 481009002365 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 481009002366 30S ribosomal protein S11; Validated; Region: PRK05309 481009002367 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 481009002368 30S ribosomal protein S13; Region: bact_S13; TIGR03631 481009002369 adenylate kinase; Reviewed; Region: adk; PRK00279 481009002370 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 481009002371 AMP-binding site [chemical binding]; other site 481009002372 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 481009002373 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 481009002374 SecY translocase; Region: SecY; pfam00344 481009002375 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 481009002376 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 481009002377 23S rRNA binding site [nucleotide binding]; other site 481009002378 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 481009002379 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 481009002380 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 481009002381 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 481009002382 5S rRNA interface [nucleotide binding]; other site 481009002383 23S rRNA interface [nucleotide binding]; other site 481009002384 L5 interface [polypeptide binding]; other site 481009002385 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 481009002386 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 481009002387 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 481009002388 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 481009002389 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 481009002390 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 481009002391 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 481009002392 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 481009002393 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 481009002394 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 481009002395 RNA binding site [nucleotide binding]; other site 481009002396 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 481009002397 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 481009002398 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 481009002399 L23 interface [polypeptide binding]; other site 481009002400 trigger factor interaction site; other site 481009002401 23S rRNA interface [nucleotide binding]; other site 481009002402 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 481009002403 23S rRNA interface [nucleotide binding]; other site 481009002404 5S rRNA interface [nucleotide binding]; other site 481009002405 putative antibiotic binding site [chemical binding]; other site 481009002406 L25 interface [polypeptide binding]; other site 481009002407 L27 interface [polypeptide binding]; other site 481009002408 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 481009002409 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 481009002410 G-X-X-G motif; other site 481009002411 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 481009002412 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 481009002413 putative translocon binding site; other site 481009002414 protein-rRNA interface [nucleotide binding]; other site 481009002415 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 481009002416 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 481009002417 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 481009002418 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 481009002419 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 481009002420 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 481009002421 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 481009002422 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 481009002423 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 481009002424 elongation factor Tu; Reviewed; Region: PRK00049 481009002425 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 481009002426 G1 box; other site 481009002427 GEF interaction site [polypeptide binding]; other site 481009002428 GTP/Mg2+ binding site [chemical binding]; other site 481009002429 Switch I region; other site 481009002430 G2 box; other site 481009002431 G3 box; other site 481009002432 Switch II region; other site 481009002433 G4 box; other site 481009002434 G5 box; other site 481009002435 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 481009002436 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 481009002437 Antibiotic Binding Site [chemical binding]; other site 481009002438 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 481009002439 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 481009002440 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 481009002441 fumarate hydratase; Reviewed; Region: fumC; PRK00485 481009002442 Class II fumarases; Region: Fumarase_classII; cd01362 481009002443 active site 481009002444 tetramer interface [polypeptide binding]; other site 481009002445 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 481009002446 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 481009002447 putative active site [active] 481009002448 homotetrameric interface [polypeptide binding]; other site 481009002449 cell division protein FtsZ; Validated; Region: PRK09330 481009002450 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 481009002451 nucleotide binding site [chemical binding]; other site 481009002452 SulA interaction site; other site 481009002453 Serine protease inhibitor ecotin [General function prediction only]; Region: Eco; COG4574 481009002454 secondary substrate binding site; other site 481009002455 primary substrate binding site; other site 481009002456 inhibition loop; other site 481009002457 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; smart00932 481009002458 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 481009002459 muropeptide transporter; Validated; Region: ampG; cl17669 481009002460 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 481009002461 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 481009002462 ATP binding site [chemical binding]; other site 481009002463 Mg++ binding site [ion binding]; other site 481009002464 motif III; other site 481009002465 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 481009002466 nucleotide binding region [chemical binding]; other site 481009002467 ATP-binding site [chemical binding]; other site 481009002468 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 481009002469 DNA-binding site [nucleotide binding]; DNA binding site 481009002470 RNA-binding motif; other site 481009002471 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 481009002472 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 481009002473 S-adenosylmethionine binding site [chemical binding]; other site 481009002474 SurA N-terminal domain; Region: SurA_N_3; cl07813 481009002475 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 481009002476 Organic solvent tolerance protein; Region: OstA_C; pfam04453 481009002477 Exonuclease VII, large subunit [DNA replication, recombination, and repair]; Region: XseA; COG1570 481009002478 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 481009002479 generic binding surface II; other site 481009002480 generic binding surface I; other site 481009002481 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 481009002482 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 481009002483 putative catalytic site [active] 481009002484 putative phosphate binding site [ion binding]; other site 481009002485 active site 481009002486 metal binding site A [ion binding]; metal-binding site 481009002487 DNA binding site [nucleotide binding] 481009002488 putative AP binding site [nucleotide binding]; other site 481009002489 putative metal binding site B [ion binding]; other site 481009002490 Uncharacterized conserved protein [Function unknown]; Region: COG4095 481009002491 GTP-binding protein Der; Reviewed; Region: PRK00093 481009002492 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 481009002493 G1 box; other site 481009002494 GTP/Mg2+ binding site [chemical binding]; other site 481009002495 Switch I region; other site 481009002496 G2 box; other site 481009002497 Switch II region; other site 481009002498 G3 box; other site 481009002499 G4 box; other site 481009002500 G5 box; other site 481009002501 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 481009002502 G1 box; other site 481009002503 GTP/Mg2+ binding site [chemical binding]; other site 481009002504 Switch I region; other site 481009002505 G2 box; other site 481009002506 G3 box; other site 481009002507 Switch II region; other site 481009002508 G4 box; other site 481009002509 G5 box; other site 481009002510 potential frameshift: common BLAST hit: gi|67458639|ref|YP_246263.1| ATPase 481009002511 potential frameshift: common BLAST hit: gi|229587034|ref|YP_002845535.1| Putative AAA+ superfamily ATPase 481009002512 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 481009002513 ABC1 family; Region: ABC1; pfam03109 481009002514 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cd05120 481009002515 active site 481009002516 ATP binding site [chemical binding]; other site 481009002517 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 481009002518 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 481009002519 S-adenosylmethionine binding site [chemical binding]; other site 481009002520 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 481009002521 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 481009002522 DNA binding site [nucleotide binding] 481009002523 catalytic residue [active] 481009002524 H2TH interface [polypeptide binding]; other site 481009002525 putative catalytic residues [active] 481009002526 turnover-facilitating residue; other site 481009002527 intercalation triad [nucleotide binding]; other site 481009002528 8OG recognition residue [nucleotide binding]; other site 481009002529 putative reading head residues; other site 481009002530 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 481009002531 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 481009002532 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 481009002533 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 481009002534 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 481009002535 active site 481009002536 potential frameshift: common BLAST hit: gi|15892963|ref|NP_360677.1| mannose-1-phosphate guanylyltransferase 481009002537 potential frameshift: common BLAST hit: gi|67458630|ref|YP_246254.1| Poly-beta-hydroxyalkanoate depolymerase 481009002538 Protein of unknown function (DUF511); Region: DUF511; cl01114 481009002539 Protein of unknown function (DUF511); Region: DUF511; cl01114 481009002540 Protein of unknown function (DUF511); Region: DUF511; cl01114 481009002541 Protein of unknown function (DUF511); Region: DUF511; cl01114 481009002542 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 481009002543 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 481009002544 active site 481009002545 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 481009002546 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 481009002547 HIGH motif; other site 481009002548 active site 481009002549 KMSKS motif; other site 481009002550 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 481009002551 tRNA binding surface [nucleotide binding]; other site 481009002552 anticodon binding site; other site 481009002553 thymidylate kinase; Validated; Region: tmk; PRK00698 481009002554 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 481009002555 TMP-binding site; other site 481009002556 ATP-binding site [chemical binding]; other site 481009002557 metabolite-proton symporter; Region: 2A0106; TIGR00883 481009002558 4-hydroxybenzoate polyprenyltransferase; Reviewed; Region: ubiA; PRK12847 481009002559 UbiA prenyltransferase family; Region: UbiA; pfam01040 481009002560 potential frameshift: common BLAST hit: gi|350273815|ref|YP_004885128.1| transposase 481009002561 potential frameshift: common BLAST hit: gi|350273815|ref|YP_004885128.1| transposase 481009002562 valyl-tRNA synthetase; Reviewed; Region: valS; PRK13208 481009002563 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 481009002564 active site 481009002565 HIGH motif; other site 481009002566 nucleotide binding site [chemical binding]; other site 481009002567 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 481009002568 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 481009002569 active site 481009002570 KMSKS motif; other site 481009002571 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 481009002572 tRNA binding surface [nucleotide binding]; other site 481009002573 anticodon binding site; other site 481009002574 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 481009002575 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 481009002576 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 481009002577 potential frameshift: common BLAST hit: gi|157804076|ref|YP_001492625.1| ATPase 481009002578 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 481009002579 RmuC family; Region: RmuC; pfam02646 481009002580 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 481009002581 DoxX-like family; Region: DoxX_3; pfam13781 481009002582 Predicted integral membrane protein (DUF2269); Region: DUF2269; cl02335 481009002583 Predicted integral membrane protein (DUF2269); Region: DUF2269; pfam10027 481009002584 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 481009002585 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 481009002586 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 481009002587 Walker A motif; other site 481009002588 ATP binding site [chemical binding]; other site 481009002589 Walker B motif; other site 481009002590 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 481009002591 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 481009002592 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 481009002593 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 481009002594 Ligand Binding Site [chemical binding]; other site 481009002595 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 481009002596 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 481009002597 HicB family; Region: HicB; pfam05534 481009002598 YcfA-like protein; Region: YcfA; cl00752 481009002599 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 481009002600 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 481009002601 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 481009002602 Walker A/P-loop; other site 481009002603 ATP binding site [chemical binding]; other site 481009002604 Q-loop/lid; other site 481009002605 ABC transporter signature motif; other site 481009002606 Walker B; other site 481009002607 D-loop; other site 481009002608 H-loop/switch region; other site 481009002609 Protein of unknown function (DUF2673); Region: DUF2673; pfam10880 481009002610 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 481009002611 putative substrate translocation pore; other site 481009002612 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 481009002613 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 481009002614 FtsX-like permease family; Region: FtsX; pfam02687 481009002615 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 481009002616 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 481009002617 Walker A/P-loop; other site 481009002618 ATP binding site [chemical binding]; other site 481009002619 Q-loop/lid; other site 481009002620 ABC transporter signature motif; other site 481009002621 Walker B; other site 481009002622 D-loop; other site 481009002623 H-loop/switch region; other site 481009002624 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 481009002625 Domain of unknown function DUF21; Region: DUF21; pfam01595 481009002626 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 481009002627 Transporter associated domain; Region: CorC_HlyC; smart01091 481009002628 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 481009002629 Rickettsia outer membrane protein B; Region: rOmpB; pfam12334 481009002630 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 481009002631 Autotransporter beta-domain; Region: Autotransporter; smart00869 481009002632 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 481009002633 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 481009002634 synthetase active site [active] 481009002635 NTP binding site [chemical binding]; other site 481009002636 metal binding site [ion binding]; metal-binding site 481009002637 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 481009002638 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 481009002639 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 481009002640 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 481009002641 DNA binding residues [nucleotide binding] 481009002642 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 481009002643 IHF dimer interface [polypeptide binding]; other site 481009002644 IHF - DNA interface [nucleotide binding]; other site 481009002645 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 481009002646 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 481009002647 catalytic triad [active] 481009002648 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 481009002649 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 481009002650 putative acyl-acceptor binding pocket; other site 481009002651 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 481009002652 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 481009002653 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 481009002654 Peptidase family M23; Region: Peptidase_M23; pfam01551 481009002655 Protein of unknown function (DUF519); Region: DUF519; pfam04378 481009002656 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 481009002657 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 481009002658 nucleotide binding pocket [chemical binding]; other site 481009002659 K-X-D-G motif; other site 481009002660 catalytic site [active] 481009002661 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 481009002662 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 481009002663 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 481009002664 Dimer interface [polypeptide binding]; other site 481009002665 BRCT sequence motif; other site 481009002666 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 481009002667 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 481009002668 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 481009002669 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 481009002670 HD domain; Region: HD_4; pfam13328 481009002671 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 481009002672 mce related protein; Region: MCE; pfam02470 481009002673 hypothetical protein; Provisional; Region: PRK06630 481009002674 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 481009002675 RNA/DNA hybrid binding site [nucleotide binding]; other site 481009002676 active site 481009002677 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3814 481009002678 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3494 481009002679 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 481009002680 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 481009002681 CoA-binding site [chemical binding]; other site 481009002682 ATP-binding [chemical binding]; other site 481009002683 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 481009002684 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 481009002685 active site 481009002686 catalytic site [active] 481009002687 substrate binding site [chemical binding]; other site 481009002688 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 481009002689 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 481009002690 Part of AAA domain; Region: AAA_19; pfam13245 481009002691 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 481009002692 UvrD-like helicase C-terminal domain; Region: UvrD_C; pfam13361 481009002693 Family description; Region: UvrD_C_2; pfam13538 481009002694 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 481009002695 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 481009002696 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 481009002697 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 481009002698 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 481009002699 potential frameshift: common BLAST hit: gi|341584292|ref|YP_004764783.1| superfamily I DNA/RNA helicase 481009002700 Uncharacterized conserved protein (DUF2048); Region: DUF2048; pfam09752 481009002701 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 481009002702 TLC ATP/ADP transporter; Region: TLC; pfam03219 481009002703 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 481009002704 nudix motif; other site 481009002705 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 481009002706 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 481009002707 Transporter associated domain; Region: CorC_HlyC; smart01091 481009002708 metal-binding heat shock protein; Provisional; Region: PRK00016 481009002709 PemK-like protein; Region: PemK; cl00995 481009002710 lipoyl synthase; Provisional; Region: PRK05481 481009002711 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 481009002712 FeS/SAM binding site; other site 481009002713 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 481009002714 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 481009002715 dimer interface [polypeptide binding]; other site 481009002716 active site 481009002717 glycine-pyridoxal phosphate binding site [chemical binding]; other site 481009002718 folate binding site [chemical binding]; other site 481009002719 Predicted esterase [General function prediction only]; Region: COG0400 481009002720 putative hydrolase; Provisional; Region: PRK11460 481009002721 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 481009002722 putative GSH binding site [chemical binding]; other site 481009002723 catalytic residues [active] 481009002724 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 481009002725 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 481009002726 minor groove reading motif; other site 481009002727 helix-hairpin-helix signature motif; other site 481009002728 substrate binding pocket [chemical binding]; other site 481009002729 active site 481009002730 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 481009002731 Predicted small secreted protein [Function unknown]; Region: COG5510 481009002732 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 481009002733 Predicted methyltransferases [General function prediction only]; Region: COG0313 481009002734 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 481009002735 putative SAM binding site [chemical binding]; other site 481009002736 putative homodimer interface [polypeptide binding]; other site 481009002737 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 481009002738 putative ligand binding site [chemical binding]; other site 481009002739 twin arginine translocase protein A; Provisional; Region: tatA; PRK01470 481009002740 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 481009002741 tetramer interfaces [polypeptide binding]; other site 481009002742 binuclear metal-binding site [ion binding]; other site 481009002743 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 481009002744 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 481009002745 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 481009002746 aspartate kinase; Reviewed; Region: PRK06635 481009002747 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 481009002748 putative nucleotide binding site [chemical binding]; other site 481009002749 putative catalytic residues [active] 481009002750 putative Mg ion binding site [ion binding]; other site 481009002751 putative aspartate binding site [chemical binding]; other site 481009002752 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 481009002753 putative allosteric regulatory residue; other site 481009002754 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 481009002755 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 481009002756 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 481009002757 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 481009002758 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 481009002759 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 481009002760 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 481009002761 metabolite-proton symporter; Region: 2A0106; TIGR00883 481009002762 putative substrate translocation pore; other site 481009002763 Cell division protein ZapA (stimulator of FtsZ polymerization and Z-ring component) [Cell cycle control, cell division, chromosome partitioning]; Region: zapA; COG3027 481009002764 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 481009002765 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 481009002766 Helix-turn-helix domain; Region: HTH_25; pfam13413 481009002767 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]; Region: COG2902 481009002768 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 481009002769 Predicted GTPase [General function prediction only]; Region: ThdF; COG0486 481009002770 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 481009002771 trmE is a tRNA modification GTPase; Region: trmE; cd04164 481009002772 G1 box; other site 481009002773 GTP/Mg2+ binding site [chemical binding]; other site 481009002774 Switch I region; other site 481009002775 G2 box; other site 481009002776 Switch II region; other site 481009002777 G3 box; other site 481009002778 G4 box; other site 481009002779 G5 box; other site 481009002780 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 481009002781 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 481009002782 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 481009002783 RecA/RadA recombinase [DNA replication, recombination, and repair]; Region: RecA; COG0468 481009002784 hexamer interface [polypeptide binding]; other site 481009002785 Walker A motif; other site 481009002786 ATP binding site [chemical binding]; other site 481009002787 Walker B motif; other site 481009002788 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 481009002789 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 481009002790 NAD(P) binding site [chemical binding]; other site 481009002791 active site 481009002792 acyl carrier protein; Provisional; Region: acpP; PRK00982 481009002793 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 481009002794 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 481009002795 dimer interface [polypeptide binding]; other site 481009002796 active site 481009002797 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 481009002798 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 481009002799 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 481009002800 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 481009002801 AAA domain; Region: AAA_14; pfam13173 481009002802 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 481009002803 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 481009002804 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 481009002805 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 481009002806 catalytic site [active] 481009002807 G-X2-G-X-G-K; other site 481009002808 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 481009002809 sequence-specific DNA binding site [nucleotide binding]; other site 481009002810 salt bridge; other site 481009002811 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 481009002812 rod shape-determining protein MreC; Region: MreC; pfam04085 481009002813 rod shape-determining protein MreB; Provisional; Region: PRK13927 481009002814 MreB and similar proteins; Region: MreB_like; cd10225 481009002815 nucleotide binding site [chemical binding]; other site 481009002816 Mg binding site [ion binding]; other site 481009002817 putative protofilament interaction site [polypeptide binding]; other site 481009002818 RodZ interaction site [polypeptide binding]; other site 481009002819 Predicted permeases [General function prediction only]; Region: COG0795 481009002820 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 481009002821 putative outer membrane lipoprotein; Provisional; Region: PRK09967 481009002822 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 481009002823 ligand binding site [chemical binding]; other site 481009002824 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 481009002825 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 481009002826 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 481009002827 dimer interface [polypeptide binding]; other site 481009002828 active site 481009002829 CoA binding pocket [chemical binding]; other site 481009002830 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 481009002831 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 481009002832 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 481009002833 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 481009002834 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 481009002835 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 481009002836 P loop; other site 481009002837 GTP binding site [chemical binding]; other site 481009002838 DNA polymerase I; Provisional; Region: PRK05755 481009002839 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 481009002840 active site 481009002841 metal binding site 1 [ion binding]; metal-binding site 481009002842 putative 5' ssDNA interaction site; other site 481009002843 metal binding site 3; metal-binding site 481009002844 metal binding site 2 [ion binding]; metal-binding site 481009002845 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 481009002846 putative DNA binding site [nucleotide binding]; other site 481009002847 putative metal binding site [ion binding]; other site 481009002848 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 481009002849 active site 481009002850 substrate binding site [chemical binding]; other site 481009002851 catalytic site [active] 481009002852 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 481009002853 active site 481009002854 DNA binding site [nucleotide binding] 481009002855 catalytic site [active] 481009002856 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 481009002857 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 481009002858 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 481009002859 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 481009002860 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 481009002861 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 481009002862 putative active site [active] 481009002863 putative PHP Thumb interface [polypeptide binding]; other site 481009002864 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 481009002865 generic binding surface I; other site 481009002866 generic binding surface II; other site 481009002867 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 481009002868 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 481009002869 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 481009002870 Protein of unknown function; Region: DUF3971; pfam13116 481009002871 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 481009002872 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 481009002873 putative substrate translocation pore; other site 481009002874 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 481009002875 seryl-tRNA synthetase; Provisional; Region: PRK05431 481009002876 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 481009002877 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 481009002878 dimer interface [polypeptide binding]; other site 481009002879 active site 481009002880 motif 1; other site 481009002881 motif 2; other site 481009002882 motif 3; other site 481009002883 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 481009002884 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 481009002885 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 481009002886 Integral membrane protein TerC family; Region: TerC; cl10468 481009002887 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 481009002888 Methyltransferase domain; Region: Methyltransf_31; pfam13847 481009002889 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 481009002890 S-adenosylmethionine binding site [chemical binding]; other site 481009002891 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 481009002892 Predicted transcriptional regulator [Transcription]; Region: COG2944 481009002893 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 481009002894 salt bridge; other site 481009002895 non-specific DNA binding site [nucleotide binding]; other site 481009002896 sequence-specific DNA binding site [nucleotide binding]; other site 481009002897 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 481009002898 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 481009002899 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 481009002900 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 481009002901 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 481009002902 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 481009002903 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 481009002904 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 481009002905 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13541 481009002906 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 481009002907 Walker A/P-loop; other site 481009002908 ATP binding site [chemical binding]; other site 481009002909 Q-loop/lid; other site 481009002910 ABC transporter signature motif; other site 481009002911 Walker B; other site 481009002912 D-loop; other site 481009002913 H-loop/switch region; other site 481009002914 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 481009002915 4Fe-4S binding domain; Region: Fer4; cl02805 481009002916 4Fe-4S binding domain; Region: Fer4; pfam00037 481009002917 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 481009002918 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 481009002919 NADH dehydrogenase subunit G; Validated; Region: PRK09130 481009002920 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 481009002921 catalytic loop [active] 481009002922 iron binding site [ion binding]; other site 481009002923 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 481009002924 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 481009002925 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 481009002926 Predicted membrane protein [Function unknown]; Region: COG3671 481009002927 aconitate hydratase; Validated; Region: PRK09277 481009002928 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 481009002929 substrate binding site [chemical binding]; other site 481009002930 ligand binding site [chemical binding]; other site 481009002931 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 481009002932 substrate binding site [chemical binding]; other site 481009002933 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK01474 481009002934 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 481009002935 gamma subunit interface [polypeptide binding]; other site 481009002936 epsilon subunit interface [polypeptide binding]; other site 481009002937 LBP interface [polypeptide binding]; other site 481009002938 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 481009002939 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 481009002940 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 481009002941 alpha subunit interaction interface [polypeptide binding]; other site 481009002942 Walker A motif; other site 481009002943 ATP binding site [chemical binding]; other site 481009002944 Walker B motif; other site 481009002945 inhibitor binding site; inhibition site 481009002946 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 481009002947 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 481009002948 core domain interface [polypeptide binding]; other site 481009002949 delta subunit interface [polypeptide binding]; other site 481009002950 epsilon subunit interface [polypeptide binding]; other site 481009002951 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 481009002952 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 481009002953 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 481009002954 beta subunit interaction interface [polypeptide binding]; other site 481009002955 Walker A motif; other site 481009002956 ATP binding site [chemical binding]; other site 481009002957 Walker B motif; other site 481009002958 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 481009002959 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 481009002960 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 481009002961 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 481009002962 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 481009002963 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 481009002964 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 481009002965 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 481009002966 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 481009002967 dimerization interface [polypeptide binding]; other site 481009002968 DPS ferroxidase diiron center [ion binding]; other site 481009002969 ion pore; other site 481009002970 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 481009002971 Beta-lactamase class D [Defense mechanisms]; Region: COG2602 481009002972 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 481009002973 Transglycosylase; Region: Transgly; pfam00912 481009002974 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 481009002975 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 481009002976 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 481009002977 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 481009002978 FeS/SAM binding site; other site 481009002979 TRAM domain; Region: TRAM; pfam01938 481009002980 HEPN domain; Region: HEPN; cl00824 481009002981 potential frameshift: common BLAST hit: gi|67459332|ref|YP_246956.1| nucleotidyltransferase/HEPN domain-containing protein 481009002982 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 481009002983 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 481009002984 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 481009002985 Bacterial SH3 domain; Region: SH3_4; pfam06347 481009002986 Bacterial SH3 domain; Region: SH3_4; pfam06347 481009002987 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 481009002988 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 481009002989 TrkA-N domain; Region: TrkA_N; pfam02254 481009002990 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 481009002991 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 481009002992 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 481009002993 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 481009002994 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 481009002995 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 481009002996 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 481009002997 rRNA binding site [nucleotide binding]; other site 481009002998 predicted 30S ribosome binding site; other site 481009002999 Maf-like protein; Region: Maf; pfam02545 481009003000 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 481009003001 active site 481009003002 dimer interface [polypeptide binding]; other site 481009003003 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 481009003004 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 481009003005 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 481009003006 active site 481009003007 DNA binding site [nucleotide binding] 481009003008 Int/Topo IB signature motif; other site 481009003009 Phasin protein; Region: Phasin_2; pfam09361 481009003010 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 481009003011 PLD-like domain; Region: PLDc_2; pfam13091 481009003012 putative active site [active] 481009003013 catalytic site [active] 481009003014 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 481009003015 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 481009003016 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism]; Region: UbiD; COG0043 481009003017 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 481009003018 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 481009003019 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 481009003020 Autotransporter beta-domain; Region: Autotransporter; pfam03797 481009003021 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 481009003022 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 481009003023 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 481009003024 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 481009003025 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 481009003026 active site 481009003027 DNA repair proteins [DNA replication, recombination, and repair]; Region: RadC; COG2003 481009003028 DNA repair proteins [DNA replication, recombination, and repair]; Region: RadC; COG2003 481009003029 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 481009003030 MPN+ (JAMM) motif; other site 481009003031 Zinc-binding site [ion binding]; other site 481009003032 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 481009003033 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 481009003034 Mg++ binding site [ion binding]; other site 481009003035 putative catalytic motif [active] 481009003036 putative substrate binding site [chemical binding]; other site 481009003037 Protein of unknown function (DUF721); Region: DUF721; pfam05258 481009003038 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 481009003039 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 481009003040 Ferredoxin [Energy production and conversion]; Region: COG1146 481009003041 4Fe-4S binding domain; Region: Fer4; cl02805 481009003042 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 481009003043 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 481009003044 nucleoside/Zn binding site; other site 481009003045 dimer interface [polypeptide binding]; other site 481009003046 catalytic motif [active] 481009003047 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 481009003048 Cation efflux family; Region: Cation_efflux; cl00316 481009003049 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 481009003050 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 481009003051 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 481009003052 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 481009003053 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 481009003054 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 481009003055 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 481009003056 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 481009003057 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 481009003058 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 481009003059 dimer interface [polypeptide binding]; other site 481009003060 ssDNA binding site [nucleotide binding]; other site 481009003061 tetramer (dimer of dimers) interface [polypeptide binding]; other site 481009003062 hypothetical protein; Reviewed; Region: PRK01530 481009003063 heat shock protein 90; Provisional; Region: PRK05218 481009003064 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 481009003065 ATP binding site [chemical binding]; other site 481009003066 Mg2+ binding site [ion binding]; other site 481009003067 G-X-G motif; other site 481009003068 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 481009003069 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 481009003070 substrate-cofactor binding pocket; other site 481009003071 pyridoxal 5'-phosphate binding site [chemical binding]; other site 481009003072 catalytic residue [active] 481009003073 trigger factor; Provisional; Region: tig; PRK01490 481009003074 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 481009003075 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 481009003076 GTPase CgtA; Reviewed; Region: obgE; PRK12299 481009003077 GTP1/OBG; Region: GTP1_OBG; pfam01018 481009003078 Obg GTPase; Region: Obg; cd01898 481009003079 G1 box; other site 481009003080 GTP/Mg2+ binding site [chemical binding]; other site 481009003081 Switch I region; other site 481009003082 G2 box; other site 481009003083 G3 box; other site 481009003084 Switch II region; other site 481009003085 G4 box; other site 481009003086 G5 box; other site 481009003087 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 481009003088 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 481009003089 dimer interface [polypeptide binding]; other site 481009003090 active site 481009003091 citrylCoA binding site [chemical binding]; other site 481009003092 NADH binding [chemical binding]; other site 481009003093 cationic pore residues; other site 481009003094 oxalacetate/citrate binding site [chemical binding]; other site 481009003095 coenzyme A binding site [chemical binding]; other site 481009003096 catalytic triad [active] 481009003097 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 481009003098 Fe-S cluster binding site [ion binding]; other site 481009003099 active site 481009003100 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 481009003101 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 481009003102 RNA binding surface [nucleotide binding]; other site 481009003103 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 481009003104 active site 481009003105 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed; Region: PRK01544 481009003106 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 481009003107 S-adenosylmethionine binding site [chemical binding]; other site 481009003108 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]; Region: COG0220 481009003109 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 481009003110 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 481009003111 Glycyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]; Region: GlyS; COG0751 481009003112 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 481009003113 glycyl-tRNA synthetase subunit alpha; Validated; Region: glyQ; PRK09348 481009003114 motif 1; other site 481009003115 dimer interface [polypeptide binding]; other site 481009003116 active site 481009003117 motif 2; other site 481009003118 motif 3; other site 481009003119 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 481009003120 oligomeric interface; other site 481009003121 putative active site [active] 481009003122 homodimer interface [polypeptide binding]; other site 481009003123 prevent-host-death family protein; Region: phd_fam; TIGR01552 481009003124 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 481009003125 potential frameshift: common BLAST hit: gi|350273988|ref|YP_004885301.1| proline/betaine transporter 481009003126 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 481009003127 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 481009003128 motif 1; other site 481009003129 active site 481009003130 motif 2; other site 481009003131 motif 3; other site 481009003132 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 481009003133 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 481009003134 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 481009003135 dimerization interface 3.5A [polypeptide binding]; other site 481009003136 active site 481009003137 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 481009003138 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 481009003139 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 481009003140 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 481009003141 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 481009003142 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 481009003143 DNA binding residues [nucleotide binding] 481009003144 DNA primase, catalytic core; Region: dnaG; TIGR01391 481009003145 CHC2 zinc finger; Region: zf-CHC2; pfam01807 481009003146 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 481009003147 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 481009003148 active site 481009003149 metal binding site [ion binding]; metal-binding site 481009003150 interdomain interaction site; other site 481009003151 Dolichol kinase [Lipid metabolism]; Region: SEC59; COG0170 481009003152 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 481009003153 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 481009003154 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 481009003155 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 481009003156 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 481009003157 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 481009003158 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 481009003159 ligand binding site [chemical binding]; other site 481009003160 homodimer interface [polypeptide binding]; other site 481009003161 NAD(P) binding site [chemical binding]; other site 481009003162 trimer interface B [polypeptide binding]; other site 481009003163 trimer interface A [polypeptide binding]; other site 481009003164 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 481009003165 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 481009003166 DNA polymerase III subunits gamma and tau; Validated; Region: PRK06645 481009003167 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 481009003168 Walker A motif; other site 481009003169 ATP binding site [chemical binding]; other site 481009003170 Walker B motif; other site 481009003171 arginine finger; other site 481009003172 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 481009003173 hypothetical protein; Validated; Region: PRK00153 481009003174 Predicted aspartyl protease [General function prediction only]; Region: COG3577 481009003175 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 481009003176 catalytic motif [active] 481009003177 Catalytic residue [active] 481009003178 Beta-lactamase; Region: Beta-lactamase; cl17358 481009003179 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 481009003180 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 481009003181 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 481009003182 Walker A/P-loop; other site 481009003183 ATP binding site [chemical binding]; other site 481009003184 Q-loop/lid; other site 481009003185 ABC transporter signature motif; other site 481009003186 Walker B; other site 481009003187 D-loop; other site 481009003188 H-loop/switch region; other site 481009003189 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 481009003190 putative hydrolase; Provisional; Region: PRK02113 481009003191 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 481009003192 active site 481009003193 DNA-damage-inducible protein J [DNA replication, recombination, and repair]; Region: RelB; COG3077 481009003194 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 481009003195 Predicted permeases [General function prediction only]; Region: COG0795 481009003196 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 481009003197 DNA polymerase III subunit chi; Provisional; Region: PRK06646 481009003198 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 481009003199 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 481009003200 metal binding site [ion binding]; metal-binding site 481009003201 dimer interface [polypeptide binding]; other site 481009003202 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 481009003203 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 481009003204 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 481009003205 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 481009003206 Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: NhaA; COG3004 481009003207 Uncharacterized conserved protein [Function unknown]; Region: COG1434 481009003208 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 481009003209 putative active site [active] 481009003210 lipoate-protein ligase B; Provisional; Region: PRK14347 481009003211 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 481009003212 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 481009003213 amidase catalytic site [active] 481009003214 Zn binding residues [ion binding]; other site 481009003215 substrate binding site [chemical binding]; other site 481009003216 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 481009003217 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 481009003218 ribosomal protein L33, bacterial type; Region: rpmG_bact; TIGR01023 481009003219 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 481009003220 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 481009003221 ATP binding site [chemical binding]; other site 481009003222 Mg2+ binding site [ion binding]; other site 481009003223 G-X-G motif; other site 481009003224 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 481009003225 ATP binding site [chemical binding]; other site 481009003226 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 481009003227 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4391 481009003228 Tetratricopeptide repeat; Region: TPR_12; pfam13424 481009003229 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 481009003230 TPR motif; other site 481009003231 TPR repeat; Region: TPR_11; pfam13414 481009003232 binding surface 481009003233 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 481009003234 metabolite-proton symporter; Region: 2A0106; TIGR00883 481009003235 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 481009003236 Coproporphyrinogen III oxidase [Coenzyme metabolism]; Region: HemF; COG0408 481009003237 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 481009003238 potential frameshift: common BLAST hit: gi|67459789|ref|YP_247413.1| prophage antirepressor 481009003239 TIGR00701 family protein; Region: TIGR00701 481009003240 ferrochelatase; Reviewed; Region: hemH; PRK00035 481009003241 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 481009003242 C-terminal domain interface [polypeptide binding]; other site 481009003243 active site 481009003244 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 481009003245 active site 481009003246 N-terminal domain interface [polypeptide binding]; other site 481009003247 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 481009003248 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 481009003249 substrate binding site [chemical binding]; other site 481009003250 active site