-- dump date 20140620_034015 -- class Genbank::misc_feature -- table misc_feature_note -- id note 562019000001 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1806 562019000002 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 562019000003 catalytic residues [active] 562019000004 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 562019000005 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 562019000006 Walker A/P-loop; other site 562019000007 ATP binding site [chemical binding]; other site 562019000008 Q-loop/lid; other site 562019000009 ABC transporter signature motif; other site 562019000010 Walker B; other site 562019000011 D-loop; other site 562019000012 H-loop/switch region; other site 562019000013 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 562019000014 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 562019000015 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 562019000016 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 562019000017 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 562019000018 FAD binding pocket [chemical binding]; other site 562019000019 FAD binding motif [chemical binding]; other site 562019000020 phosphate binding motif [ion binding]; other site 562019000021 beta-alpha-beta structure motif; other site 562019000022 NAD binding pocket [chemical binding]; other site 562019000023 Iron coordination center [ion binding]; other site 562019000024 Growth inhibitor [Signal transduction mechanisms]; Region: MazF; COG2337 562019000025 Acyl-[acyl carrier protein]; Region: LpxA; COG1043 562019000026 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 562019000027 active site 562019000028 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 562019000029 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 562019000030 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 562019000031 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 562019000032 trimer interface [polypeptide binding]; other site 562019000033 active site 562019000034 UDP-GlcNAc binding site [chemical binding]; other site 562019000035 lipid binding site [chemical binding]; lipid-binding site 562019000036 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 562019000037 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3022 562019000038 Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]; Region: HimA; COG0776 562019000039 IHF - DNA interface [nucleotide binding]; other site 562019000040 IHF dimer interface [polypeptide binding]; other site 562019000041 authentic frameshifts: common BLAST hit: gi|15892681|ref|NP_360395.1| protease IV 562019000042 transcription termination factor Rho; Provisional; Region: rho; PRK09376 562019000043 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 562019000044 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 562019000045 RNA binding site [nucleotide binding]; other site 562019000046 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 562019000047 multimer interface [polypeptide binding]; other site 562019000048 Walker A motif; other site 562019000049 ATP binding site [chemical binding]; other site 562019000050 Walker B motif; other site 562019000051 authentic internal stop codon: common BLAST hit: gi|157964582|ref|YP_001499406.1| methyltransferase class I 562019000052 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 562019000053 DHH family; Region: DHH; pfam01368 562019000054 DHHA1 domain; Region: DHHA1; pfam02272 562019000055 peptide chain release factor 1; Validated; Region: prfA; PRK00591 562019000056 This domain is found in peptide chain release factors; Region: PCRF; smart00937 562019000057 RF-1 domain; Region: RF-1; pfam00472 562019000058 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 562019000059 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 562019000060 E3 interaction surface; other site 562019000061 lipoyl attachment site [posttranslational modification]; other site 562019000062 e3 binding domain; Region: E3_binding; pfam02817 562019000063 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 562019000064 translation initiation factor IF-3; Region: infC; TIGR00168 562019000065 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 562019000066 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 562019000067 Predicted membrane protein [Function unknown]; Region: COG5346 562019000068 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 562019000069 Conserved hypothetical protein 2217 (DUF2460); Region: DUF2460; cl02268 562019000070 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 562019000071 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 562019000072 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 562019000073 authentic frameshifts: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 562019000074 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 562019000075 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 562019000076 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 562019000077 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 562019000078 authentic frameshifts: common BLAST hit: gi|157964568|ref|YP_001499392.1| BioY family protein 562019000079 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP); Region: GATase1_ScBLP_like; cd03144 562019000080 conserved cys residue [active] 562019000081 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 562019000082 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 562019000083 GSH binding site (G-site) [chemical binding]; other site 562019000084 C-terminal domain interface [polypeptide binding]; other site 562019000085 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 562019000086 N-terminal domain interface [polypeptide binding]; other site 562019000087 dimer interface [polypeptide binding]; other site 562019000088 substrate binding pocket (H-site) [chemical binding]; other site 562019000089 pyruvate phosphate dikinase; Provisional; Region: PRK09279 562019000090 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 562019000091 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 562019000092 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 562019000093 hypothetical protein; Provisional; Region: PRK06661 562019000094 intersubunit interface [polypeptide binding]; other site 562019000095 active site 562019000096 Zn2+ binding site [ion binding]; other site 562019000097 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 562019000098 putative active site [active] 562019000099 homotetrameric interface [polypeptide binding]; other site 562019000100 metal binding site [ion binding]; metal-binding site 562019000101 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 562019000102 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 562019000103 active site 562019000104 catalytic residues [active] 562019000105 metal binding site [ion binding]; metal-binding site 562019000106 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 562019000107 uncharacterized protein, YfiH family; Region: TIGR00726 562019000108 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 562019000109 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 562019000110 Ribonuclease BN family enzyme [Replication, recombination, and repair]; Region: Rbn; COG1295 562019000111 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 562019000112 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 562019000113 non-specific DNA binding site [nucleotide binding]; other site 562019000114 salt bridge; other site 562019000115 sequence-specific DNA binding site [nucleotide binding]; other site 562019000116 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 562019000117 TLC ATP/ADP transporter; Region: TLC; pfam03219 562019000118 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK14846 562019000119 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 562019000120 RNA binding site [nucleotide binding]; other site 562019000121 active site 562019000122 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 562019000123 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 562019000124 16S/18S rRNA binding site [nucleotide binding]; other site 562019000125 S13e-L30e interaction site [polypeptide binding]; other site 562019000126 25S rRNA binding site [nucleotide binding]; other site 562019000127 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 562019000128 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 562019000129 oligomer interface [polypeptide binding]; other site 562019000130 RNA binding site [nucleotide binding]; other site 562019000131 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 562019000132 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 562019000133 RNase E interface [polypeptide binding]; other site 562019000134 trimer interface [polypeptide binding]; other site 562019000135 active site 562019000136 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 562019000137 putative nucleic acid binding region [nucleotide binding]; other site 562019000138 G-X-X-G motif; other site 562019000139 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 562019000140 RNA binding site [nucleotide binding]; other site 562019000141 domain interface; other site 562019000142 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 562019000143 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 562019000144 putative active site [active] 562019000145 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 562019000146 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 562019000147 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 562019000148 OstA-like protein; Region: OstA; pfam03968 562019000149 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 562019000150 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 562019000151 Walker A/P-loop; other site 562019000152 ATP binding site [chemical binding]; other site 562019000153 Q-loop/lid; other site 562019000154 ABC transporter signature motif; other site 562019000155 Walker B; other site 562019000156 D-loop; other site 562019000157 H-loop/switch region; other site 562019000158 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 562019000159 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 562019000160 active site 562019000161 substrate binding site [chemical binding]; other site 562019000162 metal binding site [ion binding]; metal-binding site 562019000163 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 562019000164 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 562019000165 more fragments homologous to RrIowa_0780 562019000166 authentic internal stop codon in hypothetical rickettsial gene, homolog of RrIowa_0780 562019000167 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 562019000168 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 562019000169 dimer interface [polypeptide binding]; other site 562019000170 putative radical transfer pathway; other site 562019000171 diiron center [ion binding]; other site 562019000172 tyrosyl radical; other site 562019000173 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 562019000174 Class I ribonucleotide reductase; Region: RNR_I; cd01679 562019000175 active site 562019000176 dimer interface [polypeptide binding]; other site 562019000177 catalytic residues [active] 562019000178 effector binding site; other site 562019000179 R2 peptide binding site; other site 562019000180 Chitin binding domain; Region: Chitin_bind_3; cl03871 562019000181 Spore Coat Protein U domain; Region: SCPU; smart00972 562019000182 authentic frameshifts: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 562019000183 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 562019000184 Spore Coat Protein U domain; Region: SCPU; cl02253 562019000185 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 562019000186 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 562019000187 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 562019000188 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019000189 Winged helix-turn helix; Region: HTH_29; pfam13551 562019000190 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019000191 Integrase core domain; Region: rve; pfam00665 562019000192 Integrase core domain; Region: rve_3; pfam13683 562019000193 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14171 562019000194 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 562019000195 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 562019000196 homodimer interface [polypeptide binding]; other site 562019000197 NADP binding site [chemical binding]; other site 562019000198 substrate binding site [chemical binding]; other site 562019000199 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 562019000200 Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon...; Region: LbH_gamma_CA_like; cd04645 562019000201 trimer interface [polypeptide binding]; other site 562019000202 putative metal binding site [ion binding]; other site 562019000203 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 562019000204 30S subunit binding site; other site 562019000205 authentic frameshifts in rickettsial Sca3 gene fragment 562019000206 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 562019000207 Found in ATP-dependent protease La (LON); Region: LON; smart00464 562019000208 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 562019000209 Walker A motif; other site 562019000210 ATP binding site [chemical binding]; other site 562019000211 Walker B motif; other site 562019000212 arginine finger; other site 562019000213 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 562019000214 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 562019000215 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 562019000216 tetramer interface [polypeptide binding]; other site 562019000217 pyridoxal 5'-phosphate binding site [chemical binding]; other site 562019000218 catalytic residue [active] 562019000219 hypothetical rickettsial gene (AIG_03530 homolog) disrupted by transposon insertion, COG0419: ATPase involved in DNA repair 562019000220 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019000221 Winged helix-turn helix; Region: HTH_29; pfam13551 562019000222 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019000223 Integrase core domain; Region: rve; pfam00665 562019000224 Integrase core domain; Region: rve_3; pfam13683 562019000225 hypothetical rickettsial gene (AIG_03530 homolog) disrupted by transposon insertion, COG0419: ATPase involved in DNA repair 562019000226 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 562019000227 Part of AAA domain; Region: AAA_19; pfam13245 562019000228 Family description; Region: UvrD_C_2; pfam13538 562019000229 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 562019000230 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 562019000231 active site 562019000232 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 562019000233 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 562019000234 tetramerization interface [polypeptide binding]; other site 562019000235 NAD(P) binding site [chemical binding]; other site 562019000236 catalytic residues [active] 562019000237 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 562019000238 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 562019000239 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 562019000240 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 562019000241 Predicted permeases [General function prediction only]; Region: COG0679 562019000242 authentic frameshift: common BLAST hit: gi|165933209|ref|YP_001649998.1| NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 562019000243 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 562019000244 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 562019000245 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 562019000246 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 562019000247 authentic frameshifts in hypothetical rickettsial gene 562019000248 Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]; Region: RecR; COG0353 562019000249 RecR protein; Region: RecR; pfam02132 562019000250 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 562019000251 putative active site [active] 562019000252 putative metal-binding site [ion binding]; other site 562019000253 tetramer interface [polypeptide binding]; other site 562019000254 Predicted membrane protein/domain [Function unknown]; Region: COG1714 562019000255 Predicted membrane protein [Function unknown]; Region: COG1238 562019000256 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 562019000257 authentic internal stop codon in acyltransferase 3 family member 562019000258 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4395 562019000259 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 562019000260 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 562019000261 authentic frameshifts in cytochrome b561 family gene 562019000262 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 562019000263 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 562019000264 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 562019000265 putative active site [active] 562019000266 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 562019000267 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 562019000268 CoA-ligase; Region: Ligase_CoA; pfam00549 562019000269 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 562019000270 CoA binding domain; Region: CoA_binding; pfam02629 562019000271 CoA-ligase; Region: Ligase_CoA; pfam00549 562019000272 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019000273 Winged helix-turn helix; Region: HTH_29; pfam13551 562019000274 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019000275 Integrase core domain; Region: rve; pfam00665 562019000276 Integrase core domain; Region: rve_3; pfam13683 562019000277 NADH dehydrogenase subunit 2; Provisional; Region: ND2; MTH00196 562019000278 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 562019000279 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 562019000280 dimer interface [polypeptide binding]; other site 562019000281 allosteric magnesium binding site [ion binding]; other site 562019000282 active site 562019000283 aspartate-rich active site metal binding site; other site 562019000284 Schiff base residues; other site 562019000285 primosome assembly protein PriA; Validated; Region: PRK05580 562019000286 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 562019000287 ATP binding site [chemical binding]; other site 562019000288 putative Mg++ binding site [ion binding]; other site 562019000289 helicase superfamily c-terminal domain; Region: HELICc; smart00490 562019000290 polyprenyl P-hydroxybenzoate and phenylacrylic acid decarboxylases; Region: ubiX_pad; TIGR00421 562019000291 Flavoprotein; Region: Flavoprotein; pfam02441 562019000292 replicative DNA helicase; Provisional; Region: PRK09165 562019000293 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 562019000294 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 562019000295 Walker A motif; other site 562019000296 ATP binding site [chemical binding]; other site 562019000297 Walker B motif; other site 562019000298 DNA binding loops [nucleotide binding] 562019000299 authentic frameshifts in COG0814 amino acid permease gene 562019000300 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 562019000301 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 562019000302 RNA binding surface [nucleotide binding]; other site 562019000303 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 562019000304 active site 562019000305 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 562019000306 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 562019000307 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 562019000308 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 562019000309 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 562019000310 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 562019000311 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 562019000312 DNA repair protein RadA; Provisional; Region: PRK11823 562019000313 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 562019000314 Walker A motif/ATP binding site; other site 562019000315 ATP binding site [chemical binding]; other site 562019000316 Walker B motif; other site 562019000317 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 562019000318 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 562019000319 Recombination protein O N terminal; Region: RecO_N; pfam11967 562019000320 Recombination protein O C terminal; Region: RecO_C; pfam02565 562019000321 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214 562019000322 Glycoprotease family; Region: Peptidase_M22; pfam00814 562019000323 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 562019000324 Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]; Region: InfB; COG0532 562019000325 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 562019000326 G1 box; other site 562019000327 putative GEF interaction site [polypeptide binding]; other site 562019000328 GTP/Mg2+ binding site [chemical binding]; other site 562019000329 Switch I region; other site 562019000330 G2 box; other site 562019000331 G3 box; other site 562019000332 Switch II region; other site 562019000333 G4 box; other site 562019000334 G5 box; other site 562019000335 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 562019000336 Translation-initiation factor 2; Region: IF-2; pfam11987 562019000337 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 562019000338 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 562019000339 NusA N-terminal domain; Region: NusA_N; pfam08529 562019000340 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 562019000341 RNA binding site [nucleotide binding]; other site 562019000342 homodimer interface [polypeptide binding]; other site 562019000343 NusA-like KH domain; Region: KH_5; pfam13184 562019000344 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 562019000345 G-X-X-G motif; other site 562019000346 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 562019000347 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019000348 Winged helix-turn helix; Region: HTH_29; pfam13551 562019000349 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019000350 Integrase core domain; Region: rve; pfam00665 562019000351 Integrase core domain; Region: rve_3; pfam13683 562019000352 conjugative transfer protein TraV, partial, truncated by transposon 562019000353 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 562019000354 TraE protein; Region: TraE; cl05060 562019000355 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 562019000356 Leucine-rich repeats; other site 562019000357 Substrate binding site [chemical binding]; other site 562019000358 authentic frameshifts: common BLAST hit: gi|91205255|ref|YP_537610.1| integrase 562019000359 authentic frameshifts in hypothetical rickettsial gene fragment 562019000360 glucose-6-phosphate isomerase; Provisional; Region: PTZ00430 562019000361 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 562019000362 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 562019000363 FMN binding site [chemical binding]; other site 562019000364 active site 562019000365 catalytic residues [active] 562019000366 substrate binding site [chemical binding]; other site 562019000367 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 562019000368 authentic frameshift: common BLAST hit: gi|157964614|ref|YP_001499438.1| transposase ISRpe1 562019000369 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 562019000370 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 562019000371 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 562019000372 intersubunit interface [polypeptide binding]; other site 562019000373 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 562019000374 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 562019000375 active site 562019000376 NTP binding site [chemical binding]; other site 562019000377 metal binding triad [ion binding]; metal-binding site 562019000378 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 562019000379 Competence protein; Region: Competence; pfam03772 562019000380 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019000381 Winged helix-turn helix; Region: HTH_29; pfam13551 562019000382 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019000383 Integrase core domain; Region: rve; pfam00665 562019000384 Integrase core domain; Region: rve_3; pfam13683 562019000385 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 562019000386 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 562019000387 RNA binding surface [nucleotide binding]; other site 562019000388 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 562019000389 S-adenosylmethionine binding site [chemical binding]; other site 562019000390 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 562019000391 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 562019000392 active site 562019000393 HIGH motif; other site 562019000394 dimer interface [polypeptide binding]; other site 562019000395 KMSKS motif; other site 562019000396 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 562019000397 RNA binding surface [nucleotide binding]; other site 562019000398 authentic frameshift: common BLAST hit: gi|157964614|ref|YP_001499438.1| transposase ISRpe1 562019000399 3' end of ScaI CDS 562019000400 authentic frameshifts in homolog of R. bellii A1I_04380 562019000401 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 562019000402 F0F1 ATP synthase subunit B; Validated; Region: PRK06568 562019000403 F0F1 ATP synthase subunit B'; Validated; Region: PRK06569 562019000404 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 562019000405 F0F1 ATP synthase subunit C; Validated; Region: PRK07558 562019000406 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 562019000407 ATP synthase subunit 6 (eukaryotes),also subunit A (prokaryotes); Region: ATP_synt_6_or_A; TIGR01131 562019000408 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5336 562019000409 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 562019000410 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 562019000411 catalytic residues [active] 562019000412 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 562019000413 Methyltransferase domain; Region: Methyltransf_31; pfam13847 562019000414 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 562019000415 S-adenosylmethionine binding site [chemical binding]; other site 562019000416 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 562019000417 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 562019000418 Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair]; Region: RecF; COG1195 562019000419 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 562019000420 Walker A/P-loop; other site 562019000421 ATP binding site [chemical binding]; other site 562019000422 Q-loop/lid; other site 562019000423 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 562019000424 ABC transporter signature motif; other site 562019000425 Walker B; other site 562019000426 D-loop; other site 562019000427 H-loop/switch region; other site 562019000428 authentic frameshifts in COG5424 Pyrroloquinoline quinone (Coenzyme PQQ) biosynthesis protein C 562019000429 dihydrofolate reductase FolA gene fragment 562019000430 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019000431 Winged helix-turn helix; Region: HTH_29; pfam13551 562019000432 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019000433 Integrase core domain; Region: rve; pfam00665 562019000434 Integrase core domain; Region: rve_3; pfam13683 562019000435 dihydrofolate reductase FolA gene fragment 562019000436 authentic frameshift: common BLAST hit: gi|67458431|ref|YP_246055.1| folate synthesis bifunctional protein 562019000437 authentic frameshifts in hypothetical rickettsial gene similar to RF_0041 562019000438 authentic frameshift: Cytochrome oxidase biogenesis protein Sco1/SenC/PrrC, putative copper metallochaperone 562019000439 Putative transcriptional regulator [Transcription]; Region: COG1678 562019000440 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 562019000441 Colicin V production protein; Region: Colicin_V; pfam02674 562019000442 Gene fragment of homolog of A1G_01175 562019000443 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 562019000444 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 562019000445 S-adenosylmethionine binding site [chemical binding]; other site 562019000446 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 562019000447 putative RNA binding site [nucleotide binding]; other site 562019000448 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 562019000449 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 562019000450 active site 562019000451 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 562019000452 protein binding site [polypeptide binding]; other site 562019000453 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 562019000454 putative substrate binding region [chemical binding]; other site 562019000455 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 562019000456 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 562019000457 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 562019000458 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 562019000459 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 562019000460 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 562019000461 Surface antigen; Region: Bac_surface_Ag; pfam01103 562019000462 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 562019000463 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 562019000464 putative substrate translocation pore; other site 562019000465 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 562019000466 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK06580 562019000467 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 562019000468 putative nucleotide binding site [chemical binding]; other site 562019000469 uridine monophosphate binding site [chemical binding]; other site 562019000470 homohexameric interface [polypeptide binding]; other site 562019000471 ribosome recycling factor; Reviewed; Region: frr; PRK00083 562019000472 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 562019000473 hinge region; other site 562019000474 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 562019000475 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 562019000476 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 562019000477 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 562019000478 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 562019000479 GatB domain; Region: GatB_Yqey; smart00845 562019000480 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 562019000481 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 562019000482 substrate binding pocket [chemical binding]; other site 562019000483 membrane-bound complex binding site; other site 562019000484 hinge residues; other site 562019000485 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 562019000486 dihydrodipicolinate reductase; Provisional; Region: PRK00048 562019000487 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 562019000488 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 562019000489 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 562019000490 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 562019000491 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019000492 Winged helix-turn helix; Region: HTH_29; pfam13551 562019000493 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019000494 Integrase core domain; Region: rve; pfam00665 562019000495 Integrase core domain; Region: rve_3; pfam13683 562019000496 authentic frameshifts in homolog of RF_0206 562019000497 Rickettsia outer membrane protein B; Region: rOmpB; pfam12334 562019000498 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 562019000499 Autotransporter beta-domain; Region: Autotransporter; smart00869 562019000500 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 562019000501 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 562019000502 synthetase active site [active] 562019000503 NTP binding site [chemical binding]; other site 562019000504 metal binding site [ion binding]; metal-binding site 562019000505 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 562019000506 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 562019000507 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 562019000508 IHF dimer interface [polypeptide binding]; other site 562019000509 IHF - DNA interface [nucleotide binding]; other site 562019000510 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 562019000511 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 562019000512 catalytic triad [active] 562019000513 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 562019000514 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 562019000515 putative acyl-acceptor binding pocket; other site 562019000516 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 562019000517 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 562019000518 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 562019000519 Peptidase family M23; Region: Peptidase_M23; pfam01551 562019000520 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 562019000521 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 562019000522 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 562019000523 nucleotide binding pocket [chemical binding]; other site 562019000524 K-X-D-G motif; other site 562019000525 catalytic site [active] 562019000526 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 562019000527 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 562019000528 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 562019000529 Dimer interface [polypeptide binding]; other site 562019000530 BRCT sequence motif; other site 562019000531 authentic frameshift in COG2161 Antitoxin of toxin-antitoxin stability system 562019000532 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 562019000533 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 562019000534 authentic frameshifts in COG0317 Guanosine polyphosphate pyrophosphohydrolases/synthetases 562019000535 authentic frameshift: common BLAST hit: gi|67458578|ref|YP_246202.1| proline/betaine transporter 562019000536 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 562019000537 mce related protein; Region: MCE; pfam02470 562019000538 hypothetical protein; Provisional; Region: PRK06630 562019000539 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 562019000540 RNA/DNA hybrid binding site [nucleotide binding]; other site 562019000541 active site 562019000542 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3814 562019000543 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3494 562019000544 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 562019000545 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 562019000546 CoA-binding site [chemical binding]; other site 562019000547 ATP-binding [chemical binding]; other site 562019000548 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 562019000549 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 562019000550 active site 562019000551 catalytic site [active] 562019000552 substrate binding site [chemical binding]; other site 562019000553 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 562019000554 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 562019000555 Part of AAA domain; Region: AAA_19; pfam13245 562019000556 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 562019000557 UvrD-like helicase C-terminal domain; Region: UvrD_C; pfam13361 562019000558 Family description; Region: UvrD_C_2; pfam13538 562019000559 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 562019000560 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 562019000561 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019000562 Winged helix-turn helix; Region: HTH_29; pfam13551 562019000563 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019000564 Integrase core domain; Region: rve; pfam00665 562019000565 Integrase core domain; Region: rve_3; pfam13683 562019000566 authentic frameshifts in homolog of RF_0170 562019000567 authentic frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 562019000568 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019000569 Winged helix-turn helix; Region: HTH_29; pfam13551 562019000570 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019000571 Integrase core domain; Region: rve; pfam00665 562019000572 Integrase core domain; Region: rve_3; pfam13683 562019000573 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 562019000574 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 562019000575 HlyD family secretion protein; Region: HlyD_3; pfam13437 562019000576 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 562019000577 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 562019000578 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 562019000579 Domain of unknown function (DUF2610); Region: DUF2610; pfam11020 562019000580 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 562019000581 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 562019000582 active site 562019000583 elongation factor P; Validated; Region: PRK00529 562019000584 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 562019000585 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 562019000586 RNA binding site [nucleotide binding]; other site 562019000587 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 562019000588 RNA binding site [nucleotide binding]; other site 562019000589 response regulator PleD; Reviewed; Region: pleD; PRK09581 562019000590 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 562019000591 active site 562019000592 phosphorylation site [posttranslational modification] 562019000593 intermolecular recognition site; other site 562019000594 dimerization interface [polypeptide binding]; other site 562019000595 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 562019000596 active site 562019000597 phosphorylation site [posttranslational modification] 562019000598 intermolecular recognition site; other site 562019000599 dimerization interface [polypeptide binding]; other site 562019000600 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 562019000601 metal binding site [ion binding]; metal-binding site 562019000602 active site 562019000603 I-site; other site 562019000604 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 562019000605 putative active site [active] 562019000606 Ap4A binding site [chemical binding]; other site 562019000607 nudix motif; other site 562019000608 putative metal binding site [ion binding]; other site 562019000609 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 562019000610 aromatic arch; other site 562019000611 DCoH dimer interaction site [polypeptide binding]; other site 562019000612 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 562019000613 DCoH tetramer interaction site [polypeptide binding]; other site 562019000614 substrate binding site [chemical binding]; other site 562019000615 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 562019000616 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 562019000617 23S rRNA interface [nucleotide binding]; other site 562019000618 L3 interface [polypeptide binding]; other site 562019000619 FOG: WD40-like repeat [Function unknown]; Region: COG1520 562019000620 Beta-barrel assembly machinery (Bam) complex component B and related proteins; Region: BamB_YfgL; cd10276 562019000621 Trp docking motif [polypeptide binding]; other site 562019000622 Protein of unknown function (DUF2659); Region: DUF2659; pfam10858 562019000623 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 562019000624 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 562019000625 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 562019000626 dimer interface [polypeptide binding]; other site 562019000627 phosphorylation site [posttranslational modification] 562019000628 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 562019000629 ATP binding site [chemical binding]; other site 562019000630 Mg2+ binding site [ion binding]; other site 562019000631 G-X-G motif; other site 562019000632 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 562019000633 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 562019000634 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 562019000635 protein binding site [polypeptide binding]; other site 562019000636 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 562019000637 Catalytic dyad [active] 562019000638 DNA topoisomerase IV, B subunit, proteobacterial; Region: parE_Gneg; TIGR01055 562019000639 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 562019000640 ATP binding site [chemical binding]; other site 562019000641 Mg2+ binding site [ion binding]; other site 562019000642 G-X-G motif; other site 562019000643 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 562019000644 anchoring element; other site 562019000645 dimer interface [polypeptide binding]; other site 562019000646 ATP binding site [chemical binding]; other site 562019000647 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 562019000648 active site 562019000649 metal binding site [ion binding]; metal-binding site 562019000650 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 562019000651 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 562019000652 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 562019000653 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3827 562019000654 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 562019000655 V-type ATP synthase subunit I; Validated; Region: PRK05771 562019000656 Protein of unknown function (DUF2660); Region: DUF2660; pfam10859 562019000657 authentic frameshifts in hypothetical rickettsial gene 562019000658 authentic frameshifts in ABC-type multidrug transport system, ATPase and permease components 562019000659 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 562019000660 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 562019000661 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 562019000662 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 562019000663 active site 562019000664 dimer interface [polypeptide binding]; other site 562019000665 motif 1; other site 562019000666 motif 2; other site 562019000667 motif 3; other site 562019000668 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 562019000669 anticodon binding site; other site 562019000670 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 562019000671 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 562019000672 ATP binding site [chemical binding]; other site 562019000673 active site 562019000674 substrate binding site [chemical binding]; other site 562019000675 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 562019000676 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 562019000677 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 562019000678 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 562019000679 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 562019000680 putative metal binding site; other site 562019000681 Plasmid encoded toxin Txe; Region: Plasmid_Txe; cl17389 562019000682 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 562019000683 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 562019000684 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 562019000685 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 562019000686 Protein of unknown function (DUF2671); Region: DUF2671; pfam10877 562019000687 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 562019000688 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 562019000689 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 562019000690 Walker A/P-loop; other site 562019000691 ATP binding site [chemical binding]; other site 562019000692 Q-loop/lid; other site 562019000693 ABC transporter signature motif; other site 562019000694 Walker B; other site 562019000695 D-loop; other site 562019000696 H-loop/switch region; other site 562019000697 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: PRK01424 562019000698 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 562019000699 authentic internal stop codon: pfam03969 AFG1-like ATPase 562019000700 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019000701 Winged helix-turn helix; Region: HTH_29; pfam13551 562019000702 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019000703 Integrase core domain; Region: rve; pfam00665 562019000704 Integrase core domain; Region: rve_3; pfam13683 562019000705 Protein of unknown function (DUF563); Region: DUF563; cl15705 562019000706 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 562019000707 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 562019000708 putative active site [active] 562019000709 substrate binding site [chemical binding]; other site 562019000710 putative cosubstrate binding site; other site 562019000711 catalytic site [active] 562019000712 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 562019000713 substrate binding site [chemical binding]; other site 562019000714 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 562019000715 active site 562019000716 catalytic residues [active] 562019000717 metal binding site [ion binding]; metal-binding site 562019000718 authentic frameshift: common BLAST hit: gi|67458714|ref|YP_246338.1| transporter 562019000719 DNA gyrase subunit A; Validated; Region: PRK05560 562019000720 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 562019000721 CAP-like domain; other site 562019000722 active site 562019000723 primary dimer interface [polypeptide binding]; other site 562019000724 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 562019000725 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 562019000726 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 562019000727 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 562019000728 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 562019000729 authentic frameshift: common BLAST hit: gi|157964270|ref|YP_001499094.1| multidrug resistance protein Atm1 562019000730 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 562019000731 GSH binding site [chemical binding]; other site 562019000732 catalytic residues [active] 562019000733 excinuclease ABC subunit B; Provisional; Region: PRK05298 562019000734 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 562019000735 ATP binding site [chemical binding]; other site 562019000736 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 562019000737 nucleotide binding region [chemical binding]; other site 562019000738 ATP-binding site [chemical binding]; other site 562019000739 Ultra-violet resistance protein B; Region: UvrB; pfam12344 562019000740 UvrB/uvrC motif; Region: UVR; pfam02151 562019000741 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 562019000742 RNA/DNA hybrid binding site [nucleotide binding]; other site 562019000743 active site 562019000744 co-chaperone HscB; Provisional; Region: hscB; PRK01356 562019000745 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 562019000746 HSP70 interaction site [polypeptide binding]; other site 562019000747 chaperone protein HscA; Provisional; Region: hscA; PRK01433 562019000748 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 562019000749 nucleotide binding site [chemical binding]; other site 562019000750 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 562019000751 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 562019000752 catalytic loop [active] 562019000753 iron binding site [ion binding]; other site 562019000754 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 562019000755 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 562019000756 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 562019000757 Ligand Binding Site [chemical binding]; other site 562019000758 authentic internal stop codon: common BLAST hit: gi|157964614|ref|YP_001499438.1| transposase ISRpe1 562019000759 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 562019000760 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 562019000761 trimer interface [polypeptide binding]; other site 562019000762 active site 562019000763 substrate binding site [chemical binding]; other site 562019000764 CoA binding site [chemical binding]; other site 562019000765 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 562019000766 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 562019000767 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 562019000768 Subunit III/VIIa interface [polypeptide binding]; other site 562019000769 Phospholipid binding site [chemical binding]; other site 562019000770 Subunit I/III interface [polypeptide binding]; other site 562019000771 Subunit III/VIb interface [polypeptide binding]; other site 562019000772 Subunit III/VIa interface; other site 562019000773 Subunit III/Vb interface [polypeptide binding]; other site 562019000774 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 562019000775 diiron binding motif [ion binding]; other site 562019000776 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 562019000777 Lipopolysaccharide-assembly; Region: LptE; cl01125 562019000778 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 562019000779 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 562019000780 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 562019000781 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 562019000782 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 562019000783 nucleotide binding site [chemical binding]; other site 562019000784 chaperone protein DnaJ; Provisional; Region: PRK14300 562019000785 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 562019000786 HSP70 interaction site [polypeptide binding]; other site 562019000787 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 562019000788 substrate binding site [polypeptide binding]; other site 562019000789 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 562019000790 Zn binding sites [ion binding]; other site 562019000791 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 562019000792 dimer interface [polypeptide binding]; other site 562019000793 authentic internal stop codon in COG4572 Putative cation transport regulator, cation transport regulator ChaB 562019000794 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 562019000795 Tetratricopeptide repeat; Region: TPR_6; pfam13174 562019000796 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 562019000797 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 562019000798 Walker A/P-loop; other site 562019000799 ATP binding site [chemical binding]; other site 562019000800 Q-loop/lid; other site 562019000801 Allexivirus 40kDa protein; Region: Allexi_40kDa; pfam05549 562019000802 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 562019000803 ABC transporter signature motif; other site 562019000804 Walker B; other site 562019000805 D-loop; other site 562019000806 H-loop/switch region; other site 562019000807 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 562019000808 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 562019000809 active site 562019000810 Zn binding site [ion binding]; other site 562019000811 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 562019000812 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 562019000813 TPP-binding site [chemical binding]; other site 562019000814 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 562019000815 dimer interface [polypeptide binding]; other site 562019000816 PYR/PP interface [polypeptide binding]; other site 562019000817 TPP binding site [chemical binding]; other site 562019000818 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 562019000819 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 562019000820 E3 interaction surface; other site 562019000821 lipoyl attachment site [posttranslational modification]; other site 562019000822 e3 binding domain; Region: E3_binding; pfam02817 562019000823 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 562019000824 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism]; Region: COG0720 562019000825 active site 562019000826 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 562019000827 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 562019000828 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 562019000829 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019000830 Winged helix-turn helix; Region: HTH_29; pfam13551 562019000831 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019000832 Integrase core domain; Region: rve; pfam00665 562019000833 Integrase core domain; Region: rve_3; pfam13683 562019000834 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 562019000835 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 562019000836 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 562019000837 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 562019000838 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 562019000839 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 562019000840 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 562019000841 FAD binding domain; Region: FAD_binding_4; pfam01565 562019000842 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 562019000843 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 562019000844 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 562019000845 ATP-grasp domain; Region: ATP-grasp_4; cl17255 562019000846 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 562019000847 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 562019000848 Cell division protein FtsQ; Region: FtsQ; pfam03799 562019000849 cell division protein FtsA; Region: ftsA; TIGR01174 562019000850 Cell division protein FtsA; Region: FtsA; smart00842 562019000851 Cell division protein FtsA; Region: FtsA; pfam14450 562019000852 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 562019000853 Cytochrome c2 [Energy production and conversion]; Region: COG3474 562019000854 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 562019000855 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 562019000856 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 562019000857 RNA binding site [nucleotide binding]; other site 562019000858 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 562019000859 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 562019000860 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 562019000861 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 562019000862 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 562019000863 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 562019000864 RNA binding surface [nucleotide binding]; other site 562019000865 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 562019000866 active site 562019000867 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 562019000868 Beta-lactamase; Region: Beta-lactamase; pfam00144 562019000869 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 562019000870 putative catalytic site [active] 562019000871 putative phosphate binding site [ion binding]; other site 562019000872 active site 562019000873 metal binding site A [ion binding]; metal-binding site 562019000874 DNA binding site [nucleotide binding] 562019000875 putative AP binding site [nucleotide binding]; other site 562019000876 putative metal binding site B [ion binding]; other site 562019000877 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 562019000878 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 562019000879 tetramer interface [polypeptide binding]; other site 562019000880 TPP-binding site [chemical binding]; other site 562019000881 heterodimer interface [polypeptide binding]; other site 562019000882 phosphorylation loop region [posttranslational modification] 562019000883 pyruvate dehydrogenase subunit beta; Validated; Region: PRK09212 562019000884 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 562019000885 alpha subunit interface [polypeptide binding]; other site 562019000886 TPP binding site [chemical binding]; other site 562019000887 heterodimer interface [polypeptide binding]; other site 562019000888 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 562019000889 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 562019000890 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 562019000891 G1 box; other site 562019000892 putative GEF interaction site [polypeptide binding]; other site 562019000893 GTP/Mg2+ binding site [chemical binding]; other site 562019000894 Switch I region; other site 562019000895 G2 box; other site 562019000896 G3 box; other site 562019000897 Switch II region; other site 562019000898 G4 box; other site 562019000899 G5 box; other site 562019000900 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 562019000901 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 562019000902 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 562019000903 isocitrate dehydrogenase; Validated; Region: PRK09222 562019000904 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 562019000905 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 562019000906 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12507 562019000907 Predicted subunit of the Multisubunit Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: COG1563 562019000908 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 562019000909 Protein of unknown function (DUF2670); Region: DUF2670; pfam10875 562019000910 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 562019000911 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 562019000912 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 562019000913 [2Fe-2S] cluster binding site [ion binding]; other site 562019000914 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 562019000915 Qi binding site; other site 562019000916 cytochrome b; Provisional; Region: CYTB; MTH00191 562019000917 intrachain domain interface; other site 562019000918 interchain domain interface [polypeptide binding]; other site 562019000919 heme bH binding site [chemical binding]; other site 562019000920 heme bL binding site [chemical binding]; other site 562019000921 Qo binding site; other site 562019000922 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 562019000923 interchain domain interface [polypeptide binding]; other site 562019000924 intrachain domain interface; other site 562019000925 Qi binding site; other site 562019000926 Qo binding site; other site 562019000927 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 562019000928 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 562019000929 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 562019000930 putative dimer interface [polypeptide binding]; other site 562019000931 authentic frameshifts in hypothetical rickettsial gene 562019000932 authentic frameshift in gene for COG4804 Uncharacterized conserved protein, Predicted nuclease of restriction endonuclease-like fold [General function prediction only] and DUF 1016 superfamily member 562019000933 PCRF domain; Region: PCRF; pfam03462 562019000934 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 562019000935 RF-1 domain; Region: RF-1; pfam00472 562019000936 GTP-binding protein LepA; Provisional; Region: PRK05433 562019000937 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 562019000938 G1 box; other site 562019000939 putative GEF interaction site [polypeptide binding]; other site 562019000940 GTP/Mg2+ binding site [chemical binding]; other site 562019000941 Switch I region; other site 562019000942 G2 box; other site 562019000943 G3 box; other site 562019000944 Switch II region; other site 562019000945 G4 box; other site 562019000946 G5 box; other site 562019000947 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 562019000948 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 562019000949 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 562019000950 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019000951 Winged helix-turn helix; Region: HTH_29; pfam13551 562019000952 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019000953 Integrase core domain; Region: rve; pfam00665 562019000954 Integrase core domain; Region: rve_3; pfam13683 562019000955 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 562019000956 Clp amino terminal domain; Region: Clp_N; pfam02861 562019000957 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 562019000958 Walker A motif; other site 562019000959 ATP binding site [chemical binding]; other site 562019000960 Walker B motif; other site 562019000961 arginine finger; other site 562019000962 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 562019000963 Walker A motif; other site 562019000964 ATP binding site [chemical binding]; other site 562019000965 Walker B motif; other site 562019000966 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 562019000967 UGMP family protein; Validated; Region: PRK09604 562019000968 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 562019000969 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 562019000970 Fatty acid desaturase; Region: FA_desaturase; pfam00487 562019000971 Di-iron ligands [ion binding]; other site 562019000972 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 562019000973 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 562019000974 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 562019000975 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 562019000976 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 562019000977 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 562019000978 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 562019000979 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 562019000980 Ligand Binding Site [chemical binding]; other site 562019000981 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 562019000982 FtsH Extracellular; Region: FtsH_ext; pfam06480 562019000983 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 562019000984 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 562019000985 Walker A motif; other site 562019000986 ATP binding site [chemical binding]; other site 562019000987 Walker B motif; other site 562019000988 arginine finger; other site 562019000989 Peptidase family M41; Region: Peptidase_M41; pfam01434 562019000990 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 562019000991 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 562019000992 Uncharacterized conserved protein [Function unknown]; Region: COG1565 562019000993 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 562019000994 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 562019000995 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 562019000996 Mechanosensitive ion channel; Region: MS_channel; pfam00924 562019000997 membrane protein insertase; Provisional; Region: PRK01318 562019000998 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 562019000999 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 562019001000 authentic internal stop codon and frameshift in tellurite resistance protein-related gene 562019001001 authentic internal frame shifts and internal stop codon in hypothetical rickettsial gene 562019001002 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 562019001003 active site 562019001004 catalytic residues [active] 562019001005 metal binding site [ion binding]; metal-binding site 562019001006 TLC ATP/ADP transporter; Region: TLC; pfam03219 562019001007 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 562019001008 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 562019001009 putative substrate translocation pore; other site 562019001010 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 562019001011 active site 562019001012 multimer interface [polypeptide binding]; other site 562019001013 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 562019001014 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 562019001015 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 562019001016 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 562019001017 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; cl17726 562019001018 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 562019001019 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 562019001020 P-loop; other site 562019001021 Magnesium ion binding site [ion binding]; other site 562019001022 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 562019001023 Magnesium ion binding site [ion binding]; other site 562019001024 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 562019001025 ParB-like nuclease domain; Region: ParB; smart00470 562019001026 KorB domain; Region: KorB; pfam08535 562019001027 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 562019001028 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 562019001029 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 562019001030 ABC transporter; Region: ABC_tran_2; pfam12848 562019001031 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 562019001032 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; COG2877 562019001033 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 562019001034 authentic frameshifts in gene fragment homologous to RF_0112 562019001035 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 562019001036 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 562019001037 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 562019001038 Zn2+ binding site [ion binding]; other site 562019001039 Mg2+ binding site [ion binding]; other site 562019001040 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 562019001041 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 562019001042 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 562019001043 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 562019001044 active site 562019001045 HIGH motif; other site 562019001046 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 562019001047 KMSK motif region; other site 562019001048 tRNA binding surface [nucleotide binding]; other site 562019001049 DALR anticodon binding domain; Region: DALR_1; smart00836 562019001050 anticodon binding site; other site 562019001051 Sporulation related domain; Region: SPOR; pfam05036 562019001052 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 562019001053 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 562019001054 CAP-like domain; other site 562019001055 active site 562019001056 primary dimer interface [polypeptide binding]; other site 562019001057 Gram-negative porin; Region: Porin_4; pfam13609 562019001058 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 562019001059 trimer interface [polypeptide binding]; other site 562019001060 active site 562019001061 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 562019001062 SecA binding site; other site 562019001063 Preprotein binding site; other site 562019001064 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 562019001065 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 562019001066 active site 562019001067 phosphorylation site [posttranslational modification] 562019001068 intermolecular recognition site; other site 562019001069 dimerization interface [polypeptide binding]; other site 562019001070 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 562019001071 DNA binding site [nucleotide binding] 562019001072 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 562019001073 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 562019001074 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 562019001075 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 562019001076 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 562019001077 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 562019001078 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 562019001079 EamA-like transporter family; Region: EamA; pfam00892 562019001080 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 562019001081 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 562019001082 metabolite-proton symporter; Region: 2A0106; TIGR00883 562019001083 putative substrate translocation pore; other site 562019001084 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 562019001085 Autotransporter beta-domain; Region: Autotransporter; pfam03797 562019001086 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 562019001087 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 562019001088 active site 562019001089 HIGH motif; other site 562019001090 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 562019001091 KMSKS motif; other site 562019001092 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 562019001093 tRNA binding surface [nucleotide binding]; other site 562019001094 anticodon binding site; other site 562019001095 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 562019001096 rRNA interaction site [nucleotide binding]; other site 562019001097 S8 interaction site; other site 562019001098 putative laminin-1 binding site; other site 562019001099 elongation factor Ts; Provisional; Region: tsf; PRK09377 562019001100 UBA/TS-N domain; Region: UBA; pfam00627 562019001101 Elongation factor TS; Region: EF_TS; pfam00889 562019001102 Elongation factor TS; Region: EF_TS; pfam00889 562019001103 authentic frame shifts in hypothetical rickettsial gene 562019001104 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 562019001105 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 562019001106 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 562019001107 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 562019001108 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 562019001109 putative acyl-acceptor binding pocket; other site 562019001110 aspartate aminotransferase; Provisional; Region: PRK05764 562019001111 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 562019001112 pyridoxal 5'-phosphate binding site [chemical binding]; other site 562019001113 homodimer interface [polypeptide binding]; other site 562019001114 catalytic residue [active] 562019001115 Plasmid encoded toxin Txe; Region: Plasmid_Txe; cl17389 562019001116 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 562019001117 authentic frameshifts result in RPR_02715 lacking the TPR domain of it's homologs like AIG_00720 562019001118 Methyltransferase domain; Region: Methyltransf_23; pfam13489 562019001119 Methyltransferase domain; Region: Methyltransf_18; pfam12847 562019001120 Surface lipoprotein [Cell envelope biogenesis, outer membrane]; Region: VacJ; COG2853 562019001121 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; COG2854 562019001122 authentic frameshifts: common BLAST hit: gi|157964158|ref|YP_001498982.1| ribose-phosphate pyrophosphokinase 562019001123 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 562019001124 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 562019001125 active site 562019001126 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 562019001127 dimer interface [polypeptide binding]; other site 562019001128 substrate binding site [chemical binding]; other site 562019001129 catalytic residues [active] 562019001130 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 562019001131 Permease; Region: Permease; pfam02405 562019001132 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 562019001133 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 562019001134 Walker A/P-loop; other site 562019001135 ATP binding site [chemical binding]; other site 562019001136 Q-loop/lid; other site 562019001137 ABC transporter signature motif; other site 562019001138 Walker B; other site 562019001139 D-loop; other site 562019001140 H-loop/switch region; other site 562019001141 CheD chemotactic sensory transduction; Region: CheD; cl00810 562019001142 Ribosomal protein L28 [Translation, ribosomal structure and biogenesis]; Region: RpmB; COG0227 562019001143 50S ribosomal protein L31; Provisional; Region: PRK01397 562019001144 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 562019001145 G1 box; other site 562019001146 GTP/Mg2+ binding site [chemical binding]; other site 562019001147 Switch I region; other site 562019001148 G2 box; other site 562019001149 G3 box; other site 562019001150 Switch II region; other site 562019001151 G4 box; other site 562019001152 G5 box; other site 562019001153 Acetylglutamate kinase [Amino acid transport and metabolism]; Region: ArgB; COG0548 562019001154 nucleotide binding site [chemical binding]; other site 562019001155 substrate binding site [chemical binding]; other site 562019001156 type IV secretion system protein VirB3; Provisional; Region: PRK13899 562019001157 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 562019001158 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 562019001159 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 562019001160 Walker A/P-loop; other site 562019001161 ATP binding site [chemical binding]; other site 562019001162 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 562019001163 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 562019001164 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 562019001165 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 562019001166 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 562019001167 authentic frameshift: common BLAST hit: gi|67458488|ref|YP_246112.1| phosphate acetyltransferase 562019001168 authentic frameshifts: common BLAST hit: gi|67458489|ref|YP_246113.1| acetate kinase 562019001169 tRNA-(guanine-N1)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmD; COG0336 562019001170 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 562019001171 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019001172 Winged helix-turn helix; Region: HTH_29; pfam13551 562019001173 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019001174 Integrase core domain; Region: rve; pfam00665 562019001175 Integrase core domain; Region: rve_3; pfam13683 562019001176 COG0338 Site-specific DNA methylase C-terminal fragment, truncated by transposon 562019001177 authentic frameshifts in hypothetical rickettsial gene 562019001178 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 562019001179 non-specific DNA binding site [nucleotide binding]; other site 562019001180 salt bridge; other site 562019001181 sequence-specific DNA binding site [nucleotide binding]; other site 562019001182 Cytidylate kinase [Nucleotide transport and metabolism]; Region: Cmk; COG0283 562019001183 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 562019001184 CMP-binding site; other site 562019001185 The sites determining sugar specificity; other site 562019001186 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 562019001187 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 562019001188 RNA binding site [nucleotide binding]; other site 562019001189 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 562019001190 RNA binding site [nucleotide binding]; other site 562019001191 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 562019001192 RNA binding site [nucleotide binding]; other site 562019001193 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 562019001194 RNA binding site [nucleotide binding]; other site 562019001195 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 562019001196 RNA binding site [nucleotide binding]; other site 562019001197 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 562019001198 RNA binding site [nucleotide binding]; other site 562019001199 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 562019001200 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 562019001201 oligomer interface [polypeptide binding]; other site 562019001202 active site residues [active] 562019001203 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 562019001204 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 562019001205 homotetramer interface [polypeptide binding]; other site 562019001206 FMN binding site [chemical binding]; other site 562019001207 homodimer contacts [polypeptide binding]; other site 562019001208 putative active site [active] 562019001209 putative substrate binding site [chemical binding]; other site 562019001210 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019001211 Winged helix-turn helix; Region: HTH_29; pfam13551 562019001212 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019001213 Integrase core domain; Region: rve; pfam00665 562019001214 Integrase core domain; Region: rve_3; pfam13683 562019001215 authentic frameshifts: common BLAST hit: gi|157826229|ref|YP_001493949.1| S-adenosylmethionine synthetase 562019001216 DNA polymerase I; Provisional; Region: PRK05755 562019001217 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 562019001218 active site 562019001219 metal binding site 1 [ion binding]; metal-binding site 562019001220 putative 5' ssDNA interaction site; other site 562019001221 metal binding site 3; metal-binding site 562019001222 metal binding site 2 [ion binding]; metal-binding site 562019001223 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 562019001224 putative DNA binding site [nucleotide binding]; other site 562019001225 putative metal binding site [ion binding]; other site 562019001226 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 562019001227 active site 562019001228 substrate binding site [chemical binding]; other site 562019001229 catalytic site [active] 562019001230 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 562019001231 active site 562019001232 DNA binding site [nucleotide binding] 562019001233 catalytic site [active] 562019001234 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 562019001235 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 562019001236 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 562019001237 P loop; other site 562019001238 GTP binding site [chemical binding]; other site 562019001239 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 562019001240 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 562019001241 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 562019001242 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 562019001243 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 562019001244 dimer interface [polypeptide binding]; other site 562019001245 active site 562019001246 CoA binding pocket [chemical binding]; other site 562019001247 putative outer membrane lipoprotein; Provisional; Region: PRK09967 562019001248 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 562019001249 ligand binding site [chemical binding]; other site 562019001250 Predicted permeases [General function prediction only]; Region: COG0795 562019001251 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 562019001252 rod shape-determining protein MreB; Provisional; Region: PRK13927 562019001253 MreB and similar proteins; Region: MreB_like; cd10225 562019001254 nucleotide binding site [chemical binding]; other site 562019001255 Mg binding site [ion binding]; other site 562019001256 putative protofilament interaction site [polypeptide binding]; other site 562019001257 RodZ interaction site [polypeptide binding]; other site 562019001258 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 562019001259 rod shape-determining protein MreC; Region: MreC; pfam04085 562019001260 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 562019001261 sequence-specific DNA binding site [nucleotide binding]; other site 562019001262 salt bridge; other site 562019001263 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 562019001264 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 562019001265 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 562019001266 catalytic site [active] 562019001267 G-X2-G-X-G-K; other site 562019001268 AAA domain; Region: AAA_14; pfam13173 562019001269 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 562019001270 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 562019001271 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 562019001272 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 562019001273 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 562019001274 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 562019001275 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 562019001276 dimer interface [polypeptide binding]; other site 562019001277 active site 562019001278 acyl carrier protein; Provisional; Region: acpP; PRK00982 562019001279 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 562019001280 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 562019001281 NAD(P) binding site [chemical binding]; other site 562019001282 active site 562019001283 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 562019001284 RecA/RadA recombinase [DNA replication, recombination, and repair]; Region: RecA; COG0468 562019001285 hexamer interface [polypeptide binding]; other site 562019001286 Walker A motif; other site 562019001287 ATP binding site [chemical binding]; other site 562019001288 Walker B motif; other site 562019001289 Predicted GTPase [General function prediction only]; Region: ThdF; COG0486 562019001290 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 562019001291 trmE is a tRNA modification GTPase; Region: trmE; cd04164 562019001292 G1 box; other site 562019001293 GTP/Mg2+ binding site [chemical binding]; other site 562019001294 Switch I region; other site 562019001295 G2 box; other site 562019001296 Switch II region; other site 562019001297 G3 box; other site 562019001298 G4 box; other site 562019001299 G5 box; other site 562019001300 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 562019001301 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]; Region: COG2902 562019001302 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 562019001303 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 562019001304 Helix-turn-helix domain; Region: HTH_25; pfam13413 562019001305 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 562019001306 Cell division protein ZapA (stimulator of FtsZ polymerization and Z-ring component) [Cell cycle control, cell division, chromosome partitioning]; Region: zapA; COG3027 562019001307 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 562019001308 metabolite-proton symporter; Region: 2A0106; TIGR00883 562019001309 putative substrate translocation pore; other site 562019001310 Peptidase M55, D-aminopeptidase dipeptide-binding protein family; Region: DAP_dppA; cl01007 562019001311 aspartate kinase; Reviewed; Region: PRK06635 562019001312 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 562019001313 putative nucleotide binding site [chemical binding]; other site 562019001314 putative catalytic residues [active] 562019001315 putative Mg ion binding site [ion binding]; other site 562019001316 putative aspartate binding site [chemical binding]; other site 562019001317 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 562019001318 putative allosteric regulatory residue; other site 562019001319 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 562019001320 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 562019001321 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 562019001322 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 562019001323 tetramer interfaces [polypeptide binding]; other site 562019001324 binuclear metal-binding site [ion binding]; other site 562019001325 twin arginine translocase protein A; Provisional; Region: tatA; PRK01470 562019001326 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 562019001327 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 562019001328 putative ligand binding site [chemical binding]; other site 562019001329 Predicted methyltransferases [General function prediction only]; Region: COG0313 562019001330 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 562019001331 putative SAM binding site [chemical binding]; other site 562019001332 putative homodimer interface [polypeptide binding]; other site 562019001333 authentic frameshifts in hypothetical rickettsial gene 562019001334 Predicted small secreted protein [Function unknown]; Region: COG5510 562019001335 Ycf1; Provisional; Region: ycf1; CHL00204 562019001336 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 562019001337 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 562019001338 minor groove reading motif; other site 562019001339 helix-hairpin-helix signature motif; other site 562019001340 substrate binding pocket [chemical binding]; other site 562019001341 active site 562019001342 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 562019001343 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 562019001344 putative GSH binding site [chemical binding]; other site 562019001345 catalytic residues [active] 562019001346 Predicted esterase [General function prediction only]; Region: COG0400 562019001347 putative hydrolase; Provisional; Region: PRK11460 562019001348 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 562019001349 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 562019001350 dimer interface [polypeptide binding]; other site 562019001351 active site 562019001352 glycine-pyridoxal phosphate binding site [chemical binding]; other site 562019001353 folate binding site [chemical binding]; other site 562019001354 lipoyl synthase; Provisional; Region: PRK05481 562019001355 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 562019001356 FeS/SAM binding site; other site 562019001357 metal-binding heat shock protein; Provisional; Region: PRK00016 562019001358 FOG: CBS domain [General function prediction only]; Region: COG0517 562019001359 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 562019001360 Transporter associated domain; Region: CorC_HlyC; smart01091 562019001361 authentic frameshift and internal stop codon: common BLAST hit: gi|67459575|ref|YP_247199.1| (di)nucleoside polyphosphate hydrolase 562019001362 TLC ATP/ADP transporter; Region: TLC; pfam03219 562019001363 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 562019001364 authentic frameshift: common BLAST hit: gi|67458555|ref|YP_246179.1| acetyl-CoA acetyltransferase 562019001365 authentic frameshifts etc. in hypothetical rickettsial protein 562019001366 authentic frameshifts: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 562019001367 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019001368 Winged helix-turn helix; Region: HTH_29; pfam13551 562019001369 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019001370 Integrase core domain; Region: rve; pfam00665 562019001371 Integrase core domain; Region: rve_3; pfam13683 562019001372 authentic frameshifts in homolog of RF_1099, COG0666 FOG: Ankyrin repeat 562019001373 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 562019001374 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 562019001375 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019001376 Winged helix-turn helix; Region: HTH_29; pfam13551 562019001377 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019001378 Integrase core domain; Region: rve; pfam00665 562019001379 Integrase core domain; Region: rve_3; pfam13683 562019001380 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 562019001381 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 562019001382 GIY-YIG motif/motif A; other site 562019001383 active site 562019001384 catalytic site [active] 562019001385 putative DNA binding site [nucleotide binding]; other site 562019001386 metal binding site [ion binding]; metal-binding site 562019001387 UvrB/uvrC motif; Region: UVR; pfam02151 562019001388 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 562019001389 Copper(I)-binding protein [Inorganic ion transport and metabolism]; Region: COG2847 562019001390 authentic frameshift: common BLAST hit: gi|91205507|ref|YP_537862.1| putative DNA alkylation repair protein 562019001391 authentic frameshifts in COG0350 Methylated DNA-protein cysteine methyltransferase 562019001392 COG0350 Methylated DNA-protein cysteine methyltransferase gene fragment 562019001393 authentic frameshifts: common BLAST hit: gi|91205217|ref|YP_537572.1| Type I site-specific restriction-modification system, R 562019001394 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 562019001395 DEAD/DEAH box helicase; Region: DEAD; pfam00270 562019001396 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 562019001397 SEC-C motif; Region: SEC-C; pfam02810 562019001398 peptidylprolyl isomerase; Provisional; Region: prsA; PRK04405 562019001399 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 562019001400 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 562019001401 DNA-directed RNA polymerase, omega subunit; Region: rpoZ; TIGR00690 562019001402 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 562019001403 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 562019001404 hinge; other site 562019001405 active site 562019001406 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 562019001407 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 562019001408 ATP binding site [chemical binding]; other site 562019001409 Mg2+ binding site [ion binding]; other site 562019001410 G-X-G motif; other site 562019001411 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 562019001412 anchoring element; other site 562019001413 dimer interface [polypeptide binding]; other site 562019001414 ATP binding site [chemical binding]; other site 562019001415 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 562019001416 active site 562019001417 putative metal-binding site [ion binding]; other site 562019001418 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 562019001419 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 562019001420 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 562019001421 active site 562019001422 motif I; other site 562019001423 motif II; other site 562019001424 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 562019001425 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 562019001426 MgtE intracellular N domain; Region: MgtE_N; pfam03448 562019001427 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 562019001428 Divalent cation transporter; Region: MgtE; pfam01769 562019001429 Predicted DNA-binding protein with an HTH domain [General function prediction only]; Region: COG4710 562019001430 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 562019001431 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 562019001432 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 562019001433 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 562019001434 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 562019001435 Cu(I) binding site [ion binding]; other site 562019001436 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 562019001437 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 562019001438 dimer interface [polypeptide binding]; other site 562019001439 substrate binding site [chemical binding]; other site 562019001440 metal binding sites [ion binding]; metal-binding site 562019001441 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 562019001442 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 562019001443 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 562019001444 TraX protein; Region: TraX; pfam05857 562019001445 gene fragment homologous to AIG_04970 truncated by transposon 562019001446 authentic internal stop codon: common BLAST hit: gi|157964614|ref|YP_001499438.1| transposase ISRpe1 562019001447 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 562019001448 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 562019001449 ssDNA binding site; other site 562019001450 generic binding surface II; other site 562019001451 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 562019001452 ATP binding site [chemical binding]; other site 562019001453 putative Mg++ binding site [ion binding]; other site 562019001454 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 562019001455 nucleotide binding region [chemical binding]; other site 562019001456 ATP-binding site [chemical binding]; other site 562019001457 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019001458 Winged helix-turn helix; Region: HTH_29; pfam13551 562019001459 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019001460 Integrase core domain; Region: rve; pfam00665 562019001461 Integrase core domain; Region: rve_3; pfam13683 562019001462 ribonuclease P; Reviewed; Region: rnpA; PRK01492 562019001463 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 562019001464 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 562019001465 23S rRNA binding site [nucleotide binding]; other site 562019001466 L21 binding site [polypeptide binding]; other site 562019001467 L13 binding site [polypeptide binding]; other site 562019001468 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 562019001469 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 562019001470 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 562019001471 FeS/SAM binding site; other site 562019001472 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 562019001473 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 562019001474 5S rRNA interface [nucleotide binding]; other site 562019001475 CTC domain interface [polypeptide binding]; other site 562019001476 L16 interface [polypeptide binding]; other site 562019001477 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 562019001478 putative active site [active] 562019001479 catalytic residue [active] 562019001480 authentic frameshift: common BLAST hit: gi|67458746|ref|YP_246370.1| acetyltransferase 562019001481 GTP-binding protein YchF; Reviewed; Region: PRK09601 562019001482 YchF GTPase; Region: YchF; cd01900 562019001483 G1 box; other site 562019001484 GTP/Mg2+ binding site [chemical binding]; other site 562019001485 Switch I region; other site 562019001486 G2 box; other site 562019001487 Switch II region; other site 562019001488 G3 box; other site 562019001489 G4 box; other site 562019001490 G5 box; other site 562019001491 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 562019001492 authentic frameshift: common BLAST hit: gi|91205030|ref|YP_537385.1| nucleotidyltransferase 562019001493 COG0477 Permeases of the major facilitator superfamily, bicyclomycin resistance protein 562019001494 authentic frameshift: common BLAST hit: gi|15892845|ref|NP_360559.1| patatin b1 precursor 562019001495 Patatin [General function prediction only]; Region: COG3621 562019001496 Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17; Region: Pat17_PNPLA8_PNPLA9_like; cd07199 562019001497 active site 562019001498 nucleophile elbow; other site 562019001499 authentic internal stop codon: common BLAST hit: gi|157964614|ref|YP_001499438.1| transposase ISRpe1 562019001500 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 562019001501 Na binding site [ion binding]; other site 562019001502 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 562019001503 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 562019001504 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 562019001505 MraZ protein; Region: MraZ; pfam02381 562019001506 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 562019001507 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 562019001508 S-adenosylmethionine binding site [chemical binding]; other site 562019001509 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 562019001510 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 562019001511 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 562019001512 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 562019001513 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 562019001514 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 562019001515 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 562019001516 authentic frameshift in conserved rickettsial hypothetical gene 562019001517 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 562019001518 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 562019001519 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 562019001520 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 562019001521 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 562019001522 active site 562019001523 phosphorylation site [posttranslational modification] 562019001524 intermolecular recognition site; other site 562019001525 dimerization interface [polypeptide binding]; other site 562019001526 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 562019001527 Walker A motif; other site 562019001528 ATP binding site [chemical binding]; other site 562019001529 Walker B motif; other site 562019001530 arginine finger; other site 562019001531 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 562019001532 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK12612 562019001533 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 562019001534 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK06617 562019001535 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 562019001536 authentic frameshift in COG1040 Predicted amidophosphoribosyltransferase, competence protein F 562019001537 authentic frameshifts: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase FadB 562019001538 authentic frameshift: common BLAST hit: gi|157964695|ref|YP_001499519.1| large extracellular alpha-helical protein 562019001539 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 562019001540 active site 562019001541 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 562019001542 Substrate binding site [chemical binding]; other site 562019001543 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019001544 Winged helix-turn helix; Region: HTH_29; pfam13551 562019001545 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019001546 Integrase core domain; Region: rve; pfam00665 562019001547 Integrase core domain; Region: rve_3; pfam13683 562019001548 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 562019001549 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 562019001550 dimer interface [polypeptide binding]; other site 562019001551 anticodon binding site; other site 562019001552 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 562019001553 homodimer interface [polypeptide binding]; other site 562019001554 motif 1; other site 562019001555 active site 562019001556 motif 2; other site 562019001557 GAD domain; Region: GAD; pfam02938 562019001558 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 562019001559 active site 562019001560 motif 3; other site 562019001561 ATPase MipZ; Region: MipZ; pfam09140 562019001562 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 562019001563 P-loop; other site 562019001564 Magnesium ion binding site [ion binding]; other site 562019001565 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 562019001566 Magnesium ion binding site [ion binding]; other site 562019001567 multifunctional aminopeptidase A; Provisional; Region: PRK00913 562019001568 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 562019001569 interface (dimer of trimers) [polypeptide binding]; other site 562019001570 Substrate-binding/catalytic site; other site 562019001571 Zn-binding sites [ion binding]; other site 562019001572 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 562019001573 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 562019001574 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 562019001575 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 562019001576 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 562019001577 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 562019001578 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 562019001579 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 562019001580 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 562019001581 DNA binding site [nucleotide binding] 562019001582 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 562019001583 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 562019001584 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 562019001585 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 562019001586 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 562019001587 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 562019001588 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 562019001589 RPB3 interaction site [polypeptide binding]; other site 562019001590 RPB1 interaction site [polypeptide binding]; other site 562019001591 RPB11 interaction site [polypeptide binding]; other site 562019001592 RPB10 interaction site [polypeptide binding]; other site 562019001593 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 562019001594 core dimer interface [polypeptide binding]; other site 562019001595 peripheral dimer interface [polypeptide binding]; other site 562019001596 L10 interface [polypeptide binding]; other site 562019001597 L11 interface [polypeptide binding]; other site 562019001598 putative EF-Tu interaction site [polypeptide binding]; other site 562019001599 putative EF-G interaction site [polypeptide binding]; other site 562019001600 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 562019001601 23S rRNA interface [nucleotide binding]; other site 562019001602 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 562019001603 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 562019001604 mRNA/rRNA interface [nucleotide binding]; other site 562019001605 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 562019001606 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 562019001607 23S rRNA interface [nucleotide binding]; other site 562019001608 putative thiostrepton binding site; other site 562019001609 L7/L12 interface [polypeptide binding]; other site 562019001610 L25 interface [polypeptide binding]; other site 562019001611 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 562019001612 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 562019001613 putative homodimer interface [polypeptide binding]; other site 562019001614 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 562019001615 heterodimer interface [polypeptide binding]; other site 562019001616 homodimer interface [polypeptide binding]; other site 562019001617 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 562019001618 elongation factor G; Reviewed; Region: PRK00007 562019001619 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 562019001620 G1 box; other site 562019001621 putative GEF interaction site [polypeptide binding]; other site 562019001622 GTP/Mg2+ binding site [chemical binding]; other site 562019001623 Switch I region; other site 562019001624 G2 box; other site 562019001625 G3 box; other site 562019001626 Switch II region; other site 562019001627 G4 box; other site 562019001628 G5 box; other site 562019001629 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 562019001630 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 562019001631 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 562019001632 30S ribosomal protein S7; Validated; Region: PRK05302 562019001633 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 562019001634 S17 interaction site [polypeptide binding]; other site 562019001635 S8 interaction site; other site 562019001636 16S rRNA interaction site [nucleotide binding]; other site 562019001637 streptomycin interaction site [chemical binding]; other site 562019001638 23S rRNA interaction site [nucleotide binding]; other site 562019001639 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 562019001640 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 562019001641 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 562019001642 dimer interface [polypeptide binding]; other site 562019001643 conserved gate region; other site 562019001644 putative PBP binding loops; other site 562019001645 ABC-ATPase subunit interface; other site 562019001646 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 562019001647 L-aspartate oxidase; Provisional; Region: PRK06175 562019001648 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 562019001649 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 562019001650 putative SdhC subunit interface [polypeptide binding]; other site 562019001651 putative proximal heme binding site [chemical binding]; other site 562019001652 putative Iron-sulfur protein interface [polypeptide binding]; other site 562019001653 putative proximal quinone binding site; other site 562019001654 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 562019001655 Iron-sulfur protein interface; other site 562019001656 proximal quinone binding site [chemical binding]; other site 562019001657 SdhD (CybS) interface [polypeptide binding]; other site 562019001658 proximal heme binding site [chemical binding]; other site 562019001659 hypothetical protein; Validated; Region: PRK01415 562019001660 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 562019001661 active site residue [active] 562019001662 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 562019001663 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 562019001664 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 562019001665 protein binding site [polypeptide binding]; other site 562019001666 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 562019001667 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 562019001668 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 562019001669 HflK protein; Region: hflK; TIGR01933 562019001670 AAA domain; Region: AAA_31; pfam13614 562019001671 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 562019001672 Walker A motif; other site 562019001673 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 562019001674 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 562019001675 nucleotidyltransferase substrate binding protein, HI0074 family; Region: HI0074; TIGR01987 562019001676 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 562019001677 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 562019001678 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 562019001679 active site 562019001680 putative DNA-binding cleft [nucleotide binding]; other site 562019001681 dimer interface [polypeptide binding]; other site 562019001682 GTPase Era; Provisional; Region: era; PRK15494 562019001683 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 562019001684 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 562019001685 G1 box; other site 562019001686 GTP/Mg2+ binding site [chemical binding]; other site 562019001687 Switch I region; other site 562019001688 G2 box; other site 562019001689 Switch II region; other site 562019001690 G3 box; other site 562019001691 G4 box; other site 562019001692 G5 box; other site 562019001693 KH domain; Region: KH_2; pfam07650 562019001694 ribonuclease III; Reviewed; Region: rnc; PRK00102 562019001695 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 562019001696 dimerization interface [polypeptide binding]; other site 562019001697 active site 562019001698 metal binding site [ion binding]; metal-binding site 562019001699 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 562019001700 dsRNA binding site [nucleotide binding]; other site 562019001701 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 562019001702 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 562019001703 Catalytic site [active] 562019001704 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 562019001705 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 562019001706 SLBB domain; Region: SLBB; pfam10531 562019001707 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 562019001708 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 562019001709 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 562019001710 Protein export membrane protein; Region: SecD_SecF; pfam02355 562019001711 hypothetical protein; Provisional; Region: PRK13694 562019001712 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019001713 Winged helix-turn helix; Region: HTH_29; pfam13551 562019001714 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019001715 Integrase core domain; Region: rve; pfam00665 562019001716 Integrase core domain; Region: rve_3; pfam13683 562019001717 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 562019001718 DnaA N-terminal domain; Region: DnaA_N; pfam11638 562019001719 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 562019001720 Walker A motif; other site 562019001721 ATP binding site [chemical binding]; other site 562019001722 Walker B motif; other site 562019001723 arginine finger; other site 562019001724 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 562019001725 DnaA box-binding interface [nucleotide binding]; other site 562019001726 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 562019001727 active site residue [active] 562019001728 Uncharacterized conserved protein [Function unknown]; Region: COG2938 562019001729 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 562019001730 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 562019001731 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 562019001732 ATP binding site [chemical binding]; other site 562019001733 putative Mg++ binding site [ion binding]; other site 562019001734 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 562019001735 nucleotide binding region [chemical binding]; other site 562019001736 ATP-binding site [chemical binding]; other site 562019001737 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 562019001738 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 562019001739 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 562019001740 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 562019001741 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 562019001742 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 562019001743 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 562019001744 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 562019001745 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 562019001746 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 562019001747 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 562019001748 Mg++ binding site [ion binding]; other site 562019001749 putative catalytic motif [active] 562019001750 putative substrate binding site [chemical binding]; other site 562019001751 putative WASP, N-WASP, MENA proteins, rickA gene fragment due to transposon insertion 562019001752 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019001753 Winged helix-turn helix; Region: HTH_29; pfam13551 562019001754 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019001755 Integrase core domain; Region: rve; pfam00665 562019001756 Integrase core domain; Region: rve_3; pfam13683 562019001757 authentic frameshifts in hypothetical rickettsial gene 562019001758 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 562019001759 HD domain; Region: HD_4; pfam13328 562019001760 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 562019001761 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019001762 Winged helix-turn helix; Region: HTH_29; pfam13551 562019001763 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019001764 Integrase core domain; Region: rve; pfam00665 562019001765 Integrase core domain; Region: rve_3; pfam13683 562019001766 authentic frameshift: common BLAST hit: gi|15892300|ref|NP_360014.1| protease II 562019001767 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06588 562019001768 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 562019001769 oligomeric interface; other site 562019001770 putative active site [active] 562019001771 homodimer interface [polypeptide binding]; other site 562019001772 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06589 562019001773 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 562019001774 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06591 562019001775 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 562019001776 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK07375 562019001777 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 562019001778 VirB7 interaction site; other site 562019001779 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 562019001780 Protein of unknown function (DUF2706); Region: DUF2706; pfam10913 562019001781 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 562019001782 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 562019001783 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 562019001784 type IV secretion system ATPase VirB11; Provisional; Region: PRK13900 562019001785 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 562019001786 Walker A motif; other site 562019001787 hexamer interface [polypeptide binding]; other site 562019001788 ATP binding site [chemical binding]; other site 562019001789 Walker B motif; other site 562019001790 type IV secretion system component VirD4; Provisional; Region: PRK13897 562019001791 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 562019001792 Walker A motif; other site 562019001793 ATP binding site [chemical binding]; other site 562019001794 Walker B motif; other site 562019001795 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 562019001796 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 562019001797 authentic frameshift: common BLAST hit: gi|67458863|ref|YP_246487.1| Phage portal protein 562019001798 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 562019001799 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 562019001800 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 562019001801 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 562019001802 active site 562019001803 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 562019001804 MutS domain I; Region: MutS_I; pfam01624 562019001805 MutS domain II; Region: MutS_II; pfam05188 562019001806 MutS domain III; Region: MutS_III; pfam05192 562019001807 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 562019001808 Walker A/P-loop; other site 562019001809 ATP binding site [chemical binding]; other site 562019001810 Q-loop/lid; other site 562019001811 ABC transporter signature motif; other site 562019001812 Walker B; other site 562019001813 D-loop; other site 562019001814 H-loop/switch region; other site 562019001815 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 562019001816 Peptidase family M23; Region: Peptidase_M23; pfam01551 562019001817 Protein of unknown function DUF45; Region: DUF45; pfam01863 562019001818 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 562019001819 translocation protein TolB; Provisional; Region: tolB; PRK05137 562019001820 TolB amino-terminal domain; Region: TolB_N; pfam04052 562019001821 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 562019001822 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 562019001823 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 562019001824 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 562019001825 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 562019001826 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 562019001827 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 562019001828 DNA binding residues [nucleotide binding] 562019001829 Cytochrome oxidase assembly factor [Posttranslational modification, protein turnover, chaperones]; Region: COX11; COG3175 562019001830 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 562019001831 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 562019001832 Ligand Binding Site [chemical binding]; other site 562019001833 amino acid transporter; Region: 2A0306; TIGR00909 562019001834 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 562019001835 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 562019001836 dimer interface [polypeptide binding]; other site 562019001837 motif 1; other site 562019001838 active site 562019001839 motif 2; other site 562019001840 motif 3; other site 562019001841 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 562019001842 anticodon binding site; other site 562019001843 authentic frameshifts in partial COG0488 ATPase components of ABC transporters with duplicated ATPase domains 562019001844 TolQ protein; Region: tolQ; TIGR02796 562019001845 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 562019001846 TolR protein; Region: tolR; TIGR02801 562019001847 Gram-negative bacterial tonB protein; Region: TonB; cl10048 562019001848 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 562019001849 HD domain; Region: HD_4; pfam13328 562019001850 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 562019001851 metabolite-proton symporter; Region: 2A0106; TIGR00883 562019001852 putative substrate translocation pore; other site 562019001853 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 562019001854 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 562019001855 HlyD family secretion protein; Region: HlyD_3; pfam13437 562019001856 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 562019001857 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 562019001858 Walker A/P-loop; other site 562019001859 ATP binding site [chemical binding]; other site 562019001860 Q-loop/lid; other site 562019001861 ABC transporter signature motif; other site 562019001862 Walker B; other site 562019001863 D-loop; other site 562019001864 H-loop/switch region; other site 562019001865 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 562019001866 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 562019001867 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 562019001868 nucleotide binding site/active site [active] 562019001869 HIT family signature motif; other site 562019001870 catalytic residue [active] 562019001871 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 562019001872 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 562019001873 active site 562019001874 HslU subunit interaction site [polypeptide binding]; other site 562019001875 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 562019001876 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 562019001877 Walker A motif; other site 562019001878 ATP binding site [chemical binding]; other site 562019001879 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 562019001880 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 562019001881 authentic frameshift: common BLAST hit: gi|67458910|ref|YP_246534.1| Mg chelatase-related protein 562019001882 Uncharacterized conserved protein [Function unknown]; Region: COG5464 562019001883 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 562019001884 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 562019001885 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 562019001886 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 562019001887 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 562019001888 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 562019001889 dimerization interface [polypeptide binding]; other site 562019001890 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 562019001891 putative iron binding site [ion binding]; other site 562019001892 authentic internal stop codon: common BLAST hit:gi|157964614|ref|YP_001499438.1| transposase ISRpe1 562019001893 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 562019001894 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 562019001895 active site 562019001896 HIGH motif; other site 562019001897 dimer interface [polypeptide binding]; other site 562019001898 KMSKS motif; other site 562019001899 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 562019001900 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 562019001901 putative acyl-acceptor binding pocket; other site 562019001902 Protein required for attachment to host cells [Cell motility and secretion]; Region: COG5622 562019001903 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 562019001904 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 562019001905 HemY protein N-terminus; Region: HemY_N; pfam07219 562019001906 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 562019001907 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 562019001908 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 562019001909 active site 562019001910 Lysine efflux permease [General function prediction only]; Region: COG1279 562019001911 muropeptide transporter; Reviewed; Region: ampG; PRK11902 562019001912 AmpG-like permease; Region: 2A0125; TIGR00901 562019001913 TLC ATP/ADP transporter; Region: TLC; pfam03219 562019001914 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 562019001915 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 562019001916 substrate binding pocket [chemical binding]; other site 562019001917 chain length determination region; other site 562019001918 substrate-Mg2+ binding site; other site 562019001919 catalytic residues [active] 562019001920 aspartate-rich region 1; other site 562019001921 active site lid residues [active] 562019001922 aspartate-rich region 2; other site 562019001923 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 562019001924 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 562019001925 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 562019001926 active site 562019001927 arginine:agmatin antiporter; Provisional; Region: PRK10644 562019001928 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 562019001929 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 562019001930 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 562019001931 trimerization site [polypeptide binding]; other site 562019001932 active site 562019001933 cysteine desulfurase; Provisional; Region: PRK14012 562019001934 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 562019001935 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 562019001936 catalytic residue [active] 562019001937 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 562019001938 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 562019001939 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 562019001940 catalytic residue [active] 562019001941 Predicted transcriptional regulator [Transcription]; Region: COG1959 562019001942 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 562019001943 authentic frameshifts in hypothetical rickettsial gene 562019001944 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 562019001945 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 562019001946 Coenzyme A binding pocket [chemical binding]; other site 562019001947 authentic internal stop codon: common BLAST hit: gi|157827377|ref|YP_001496441.1| acetyltransferase 562019001948 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019001949 Winged helix-turn helix; Region: HTH_29; pfam13551 562019001950 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019001951 Integrase core domain; Region: rve; pfam00665 562019001952 Integrase core domain; Region: rve_3; pfam13683 562019001953 TraD gene fragment, result of transposon insertion: common BLAST hit: gi|91205235|ref|YP_537590.1| conjugal transfer protein TraD 562019001954 authentic frameshift: common BLAST hit: gi|157827424|ref|YP_001496488.1| transposase 562019001955 authentic frameshifts: common BLAST hit: gi|157827425|ref|YP_001496489.1| conjugal transfer protein TraA 562019001956 authentic frameshift in TraD gene fragment: common BLAST hit: gi|91205235|ref|YP_537590.1| conjugal transfer protein TraD 562019001957 authentic frameshift in COG0477 Permeases of the major facilitator superfamily 562019001958 authentic internal stop codon: common BLAST hit: gi|157964614|ref|YP_001499438.1| transposase ISRpe1 562019001959 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 562019001960 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 562019001961 putative active site [active] 562019001962 putative PHP Thumb interface [polypeptide binding]; other site 562019001963 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 562019001964 generic binding surface I; other site 562019001965 generic binding surface II; other site 562019001966 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 562019001967 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 562019001968 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 562019001969 Protein of unknown function; Region: DUF3971; pfam13116 562019001970 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 562019001971 Acetyl-coenzyme A transporter 1; Region: Acatn; pfam13000 562019001972 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 562019001973 putative substrate translocation pore; other site 562019001974 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 562019001975 seryl-tRNA synthetase; Provisional; Region: PRK05431 562019001976 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 562019001977 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 562019001978 dimer interface [polypeptide binding]; other site 562019001979 active site 562019001980 motif 1; other site 562019001981 motif 2; other site 562019001982 motif 3; other site 562019001983 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 562019001984 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 562019001985 Integral membrane protein TerC family; Region: TerC; cl10468 562019001986 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 562019001987 Methyltransferase domain; Region: Methyltransf_31; pfam13847 562019001988 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 562019001989 S-adenosylmethionine binding site [chemical binding]; other site 562019001990 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 562019001991 Predicted transcriptional regulator [Transcription]; Region: COG2944 562019001992 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 562019001993 salt bridge; other site 562019001994 non-specific DNA binding site [nucleotide binding]; other site 562019001995 sequence-specific DNA binding site [nucleotide binding]; other site 562019001996 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 562019001997 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 562019001998 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 562019001999 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 562019002000 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 562019002001 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 562019002002 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 562019002003 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 562019002004 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 562019002005 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13541 562019002006 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 562019002007 Walker A/P-loop; other site 562019002008 ATP binding site [chemical binding]; other site 562019002009 Q-loop/lid; other site 562019002010 ABC transporter signature motif; other site 562019002011 Walker B; other site 562019002012 D-loop; other site 562019002013 H-loop/switch region; other site 562019002014 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 562019002015 4Fe-4S binding domain; Region: Fer4; cl02805 562019002016 4Fe-4S binding domain; Region: Fer4; pfam00037 562019002017 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 562019002018 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 562019002019 NADH dehydrogenase subunit G; Validated; Region: PRK09130 562019002020 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 562019002021 catalytic loop [active] 562019002022 iron binding site [ion binding]; other site 562019002023 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 562019002024 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 562019002025 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 562019002026 Predicted membrane protein [Function unknown]; Region: COG3671 562019002027 aconitate hydratase; Validated; Region: PRK09277 562019002028 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 562019002029 substrate binding site [chemical binding]; other site 562019002030 ligand binding site [chemical binding]; other site 562019002031 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 562019002032 substrate binding site [chemical binding]; other site 562019002033 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK01474 562019002034 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 562019002035 gamma subunit interface [polypeptide binding]; other site 562019002036 epsilon subunit interface [polypeptide binding]; other site 562019002037 LBP interface [polypeptide binding]; other site 562019002038 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 562019002039 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 562019002040 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 562019002041 alpha subunit interaction interface [polypeptide binding]; other site 562019002042 Walker A motif; other site 562019002043 ATP binding site [chemical binding]; other site 562019002044 Walker B motif; other site 562019002045 inhibitor binding site; inhibition site 562019002046 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 562019002047 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 562019002048 core domain interface [polypeptide binding]; other site 562019002049 delta subunit interface [polypeptide binding]; other site 562019002050 epsilon subunit interface [polypeptide binding]; other site 562019002051 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 562019002052 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 562019002053 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 562019002054 beta subunit interaction interface [polypeptide binding]; other site 562019002055 Walker A motif; other site 562019002056 ATP binding site [chemical binding]; other site 562019002057 Walker B motif; other site 562019002058 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 562019002059 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 562019002060 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 562019002061 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 562019002062 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 562019002063 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 562019002064 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 562019002065 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 562019002066 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 562019002067 dimerization interface [polypeptide binding]; other site 562019002068 DPS ferroxidase diiron center [ion binding]; other site 562019002069 ion pore; other site 562019002070 authentic internal stop codon: common BLAST hit: gi|157964614|ref|YP_001499438.1| transposase ISRpe1 562019002071 trigger factor; Provisional; Region: tig; PRK01490 562019002072 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 562019002073 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 562019002074 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 562019002075 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 562019002076 substrate-cofactor binding pocket; other site 562019002077 pyridoxal 5'-phosphate binding site [chemical binding]; other site 562019002078 catalytic residue [active] 562019002079 heat shock protein 90; Provisional; Region: PRK05218 562019002080 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 562019002081 ATP binding site [chemical binding]; other site 562019002082 Mg2+ binding site [ion binding]; other site 562019002083 G-X-G motif; other site 562019002084 hypothetical protein; Reviewed; Region: PRK01530 562019002085 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 562019002086 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 562019002087 dimer interface [polypeptide binding]; other site 562019002088 ssDNA binding site [nucleotide binding]; other site 562019002089 tetramer (dimer of dimers) interface [polypeptide binding]; other site 562019002090 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 562019002091 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 562019002092 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 562019002093 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 562019002094 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 562019002095 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 562019002096 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 562019002097 substrate binding site [chemical binding]; other site 562019002098 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 562019002099 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 562019002100 Cation efflux family; Region: Cation_efflux; cl00316 562019002101 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 562019002102 nucleoside/Zn binding site; other site 562019002103 dimer interface [polypeptide binding]; other site 562019002104 catalytic motif [active] 562019002105 heme exporter protein CcmC; Region: ccmC; TIGR01191 562019002106 Ferredoxin [Energy production and conversion]; Region: COG1146 562019002107 4Fe-4S binding domain; Region: Fer4; cl02805 562019002108 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 562019002109 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 562019002110 Protein of unknown function (DUF721); Region: DUF721; pfam05258 562019002111 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 562019002112 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 562019002113 Mg++ binding site [ion binding]; other site 562019002114 putative catalytic motif [active] 562019002115 putative substrate binding site [chemical binding]; other site 562019002116 authentic frameshifts: common BLAST hit: gi|165933837|ref|YP_001650626.1| DNA repair protein 562019002117 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 562019002118 active site 562019002119 authentic frameshift in COG1835 Predicted acyltransferases 562019002120 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 562019002121 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 562019002122 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 562019002123 authentic frameshifts: common BLAST hit: gi|15893196|ref|NP_360910.1| 190-kDa cell surface antigen, mutant ompA gene 562019002124 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 562019002125 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 562019002126 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism]; Region: UbiD; COG0043 562019002127 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 562019002128 PLD-like domain; Region: PLDc_2; pfam13091 562019002129 putative active site [active] 562019002130 catalytic site [active] 562019002131 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 562019002132 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 562019002133 active site 562019002134 DNA binding site [nucleotide binding] 562019002135 Int/Topo IB signature motif; other site 562019002136 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 562019002137 Maf-like protein; Region: Maf; pfam02545 562019002138 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 562019002139 active site 562019002140 dimer interface [polypeptide binding]; other site 562019002141 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 562019002142 rRNA binding site [nucleotide binding]; other site 562019002143 predicted 30S ribosome binding site; other site 562019002144 authentic frameshifts: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 562019002145 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 562019002146 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 562019002147 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 562019002148 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 562019002149 TrkA-N domain; Region: TrkA_N; pfam02254 562019002150 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 562019002151 Bacterial SH3 domain; Region: SH3_4; pfam06347 562019002152 Bacterial SH3 domain; Region: SH3_4; pfam06347 562019002153 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019002154 Winged helix-turn helix; Region: HTH_29; pfam13551 562019002155 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019002156 Integrase core domain; Region: rve; pfam00665 562019002157 Integrase core domain; Region: rve_3; pfam13683 562019002158 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 562019002159 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 562019002160 domain interfaces; other site 562019002161 active site 562019002162 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 562019002163 dimer interface [polypeptide binding]; other site 562019002164 catalytic triad [active] 562019002165 authentic frameshift: common BLAST hit: gi|91205157|ref|YP_537512.1| Na+/proline symporter and signal transduction histidine kinase 562019002166 authentic frameshift: common BLAST hit: gi|157964645|ref|YP_001499469.1| ankyrin repeat-containing protein 562019002167 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 562019002168 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 562019002169 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 562019002170 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 562019002171 Uncharacterized conserved protein [Function unknown]; Region: COG1723 562019002172 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 562019002173 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 562019002174 catalytic site [active] 562019002175 putative active site [active] 562019002176 putative substrate binding site [chemical binding]; other site 562019002177 Helicase and RNase D C-terminal; Region: HRDC; smart00341 562019002178 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 562019002179 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 562019002180 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 562019002181 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 562019002182 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 562019002183 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 562019002184 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 562019002185 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 562019002186 S-adenosylmethionine binding site [chemical binding]; other site 562019002187 partial transposable insertion element 562019002188 authentic internal stop codon: common BLAST hit: gi|157964614|ref|YP_001499438.1| transposase ISRpe1 562019002189 authentic frameshifts: common BLAST hit: gi|15892293|ref|NP_360007.1| putative ATP-dependent protease subunit C (ClpC) 562019002190 authentic gene fragment: common BLAST hit: gi|157964614|ref|YP_001499438.1| partial transposase ISRpe1 562019002191 authentic frameshifts in gene for nucleotidyltransferase/HEPN domain-containing protein, truncated by transposon 562019002192 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 562019002193 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 562019002194 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 562019002195 FeS/SAM binding site; other site 562019002196 TRAM domain; Region: TRAM; pfam01938 562019002197 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 562019002198 Transglycosylase; Region: Transgly; pfam00912 562019002199 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 562019002200 partial COG2602 Beta-lactamase class D, truncated by transposon 562019002201 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019002202 Winged helix-turn helix; Region: HTH_29; pfam13551 562019002203 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019002204 Integrase core domain; Region: rve; pfam00665 562019002205 Integrase core domain; Region: rve_3; pfam13683 562019002206 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 562019002207 Substrate binding site; other site 562019002208 Mg++ binding site; other site 562019002209 hypothetical protein; Validated; Region: PRK00110 562019002210 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 562019002211 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 562019002212 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 562019002213 N-acetyl-D-glucosamine binding site [chemical binding]; other site 562019002214 Protein of unknown function (DUF2532); Region: DUF2532; pfam10811 562019002215 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019002216 Winged helix-turn helix; Region: HTH_29; pfam13551 562019002217 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019002218 Integrase core domain; Region: rve; pfam00665 562019002219 Integrase core domain; Region: rve_3; pfam13683 562019002220 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 562019002221 SmpB-tmRNA interface; other site 562019002222 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 562019002223 dihydrodipicolinate synthase; Region: dapA; TIGR00674 562019002224 dimer interface [polypeptide binding]; other site 562019002225 active site 562019002226 catalytic residue [active] 562019002227 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 562019002228 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 562019002229 homodimer interface [polypeptide binding]; other site 562019002230 substrate-cofactor binding pocket; other site 562019002231 catalytic residue [active] 562019002232 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 562019002233 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 562019002234 active site 562019002235 phosphorylation site [posttranslational modification] 562019002236 intermolecular recognition site; other site 562019002237 dimerization interface [polypeptide binding]; other site 562019002238 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 562019002239 DNA binding site [nucleotide binding] 562019002240 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 562019002241 HAMP domain; Region: HAMP; pfam00672 562019002242 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 562019002243 dimer interface [polypeptide binding]; other site 562019002244 phosphorylation site [posttranslational modification] 562019002245 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 562019002246 ATP binding site [chemical binding]; other site 562019002247 Mg2+ binding site [ion binding]; other site 562019002248 G-X-G motif; other site 562019002249 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 562019002250 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 562019002251 catalytic residue [active] 562019002252 putative FPP diphosphate binding site; other site 562019002253 putative FPP binding hydrophobic cleft; other site 562019002254 dimer interface [polypeptide binding]; other site 562019002255 putative IPP diphosphate binding site; other site 562019002256 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 562019002257 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 562019002258 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 562019002259 Septum formation initiator; Region: DivIC; pfam04977 562019002260 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 562019002261 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 562019002262 catalytic site [active] 562019002263 putative active site [active] 562019002264 putative substrate binding site [chemical binding]; other site 562019002265 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 562019002266 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 562019002267 HIGH motif; other site 562019002268 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 562019002269 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 562019002270 active site 562019002271 KMSKS motif; other site 562019002272 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 562019002273 tRNA binding surface [nucleotide binding]; other site 562019002274 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 562019002275 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 562019002276 DNA polymerase III subunit beta; Validated; Region: PRK05643 562019002277 putative DNA binding surface [nucleotide binding]; other site 562019002278 dimer interface [polypeptide binding]; other site 562019002279 beta-clamp/clamp loader binding surface; other site 562019002280 beta-clamp/translesion DNA polymerase binding surface; other site 562019002281 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 562019002282 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 562019002283 putative tRNA-binding site [nucleotide binding]; other site 562019002284 B3/4 domain; Region: B3_4; pfam03483 562019002285 tRNA synthetase B5 domain; Region: B5; smart00874 562019002286 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 562019002287 dimer interface [polypeptide binding]; other site 562019002288 motif 1; other site 562019002289 motif 3; other site 562019002290 motif 2; other site 562019002291 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 562019002292 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 562019002293 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 562019002294 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 562019002295 dimer interface [polypeptide binding]; other site 562019002296 motif 1; other site 562019002297 active site 562019002298 motif 2; other site 562019002299 motif 3; other site 562019002300 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 562019002301 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 562019002302 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 562019002303 FeS/SAM binding site; other site 562019002304 diaminopimelate epimerase; Region: DapF; TIGR00652 562019002305 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 562019002306 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 562019002307 authentic frameshifts in transposase 562019002308 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 562019002309 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 562019002310 authentic frameshifts: common BLAST hit: gi|67459035|ref|YP_246659.1| RND efflux system, outer membrane protein 562019002311 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 562019002312 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 562019002313 active site 562019002314 homodimer interface [polypeptide binding]; other site 562019002315 cell division protein FtsW; Region: ftsW; TIGR02614 562019002316 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01368 562019002317 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 562019002318 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 562019002319 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 562019002320 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 562019002321 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 562019002322 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 562019002323 putative peptidase; Provisional; Region: PRK11649 562019002324 Peptidase family M23; Region: Peptidase_M23; pfam01551 562019002325 Cytidylyltransferase [Cell envelope biogenesis, outer membrane / Lipid metabolism]; Region: TagD; COG0615 562019002326 active site 562019002327 HIGH motif; other site 562019002328 nucleotide binding site [chemical binding]; other site 562019002329 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 562019002330 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 562019002331 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 562019002332 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 562019002333 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 562019002334 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 562019002335 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 562019002336 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 562019002337 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 562019002338 Subunit I/III interface [polypeptide binding]; other site 562019002339 D-pathway; other site 562019002340 Subunit I/VIIc interface [polypeptide binding]; other site 562019002341 Subunit I/IV interface [polypeptide binding]; other site 562019002342 Subunit I/II interface [polypeptide binding]; other site 562019002343 Low-spin heme (heme a) binding site [chemical binding]; other site 562019002344 Subunit I/VIIa interface [polypeptide binding]; other site 562019002345 Subunit I/VIa interface [polypeptide binding]; other site 562019002346 Dimer interface; other site 562019002347 Putative water exit pathway; other site 562019002348 Binuclear center (heme a3/CuB) [ion binding]; other site 562019002349 K-pathway; other site 562019002350 Subunit I/Vb interface [polypeptide binding]; other site 562019002351 Putative proton exit pathway; other site 562019002352 Subunit I/VIb interface; other site 562019002353 Subunit I/VIc interface [polypeptide binding]; other site 562019002354 Electron transfer pathway; other site 562019002355 Subunit I/VIIIb interface [polypeptide binding]; other site 562019002356 Subunit I/VIIb interface [polypeptide binding]; other site 562019002357 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 562019002358 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 562019002359 catalytic triad [active] 562019002360 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 562019002361 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 562019002362 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 562019002363 dimer interface [polypeptide binding]; other site 562019002364 catalytic triad [active] 562019002365 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 562019002366 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 562019002367 N-acetyl-D-glucosamine binding site [chemical binding]; other site 562019002368 catalytic residue [active] 562019002369 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 562019002370 trimer interface [polypeptide binding]; other site 562019002371 active site 562019002372 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 562019002373 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 562019002374 tandem repeat interface [polypeptide binding]; other site 562019002375 oligomer interface [polypeptide binding]; other site 562019002376 active site residues [active] 562019002377 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 562019002378 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 562019002379 catalytic residues [active] 562019002380 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 562019002381 Protocatechuate 3,4-dioxygenase (3,4-PCD) catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis,cis-muconate. 3,4-PCDs are large aggregates of 12 protomers, each composed of an alpha- and beta-subunit and an Fe3+ ion...; Region: 3,4-PCD; cd03459 562019002382 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 562019002383 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 562019002384 Iron permease FTR1 family; Region: FTR1; cl00475 562019002385 Intracellular septation protein A [Cell division and chromosome partitioning]; Region: COG2917 562019002386 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 562019002387 BON domain; Region: BON; pfam04972 562019002388 BON domain; Region: BON; pfam04972 562019002389 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 562019002390 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 562019002391 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 562019002392 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 562019002393 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 562019002394 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 562019002395 authentic frameshift: common BLAST hit: gi|165933121|ref|YP_001649910.1| AmpG 562019002396 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 562019002397 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 562019002398 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 562019002399 Walker A/P-loop; other site 562019002400 ATP binding site [chemical binding]; other site 562019002401 Q-loop/lid; other site 562019002402 ABC transporter signature motif; other site 562019002403 Walker B; other site 562019002404 D-loop; other site 562019002405 H-loop/switch region; other site 562019002406 Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]; Region: RuvB; COG2255 562019002407 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 562019002408 Walker A motif; other site 562019002409 ATP binding site [chemical binding]; other site 562019002410 Walker B motif; other site 562019002411 arginine finger; other site 562019002412 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 562019002413 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 562019002414 RuvA N terminal domain; Region: RuvA_N; pfam01330 562019002415 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 562019002416 authentic internal stop codon in hypothetical rickettsial gene 562019002417 Fic family protein [Function unknown]; Region: COG3177 562019002418 Fic/DOC family; Region: Fic; pfam02661 562019002419 prolyl-tRNA synthetase; Provisional; Region: PRK12325 562019002420 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 562019002421 dimer interface [polypeptide binding]; other site 562019002422 motif 1; other site 562019002423 active site 562019002424 motif 2; other site 562019002425 motif 3; other site 562019002426 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 562019002427 anticodon binding site; other site 562019002428 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 562019002429 GTP cyclohydrolase I; Provisional; Region: PLN03044 562019002430 active site 562019002431 authentic frameshifts in hypothetical rickettsial gene, AIG_02985 (IPR000883 Cytochrome c oxidase subunit I) 562019002432 authentic frameshift in MutT gene 562019002433 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 562019002434 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 562019002435 Ligand binding site; other site 562019002436 oligomer interface; other site 562019002437 CTP synthetase; Validated; Region: pyrG; PRK05380 562019002438 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 562019002439 Catalytic site [active] 562019002440 active site 562019002441 UTP binding site [chemical binding]; other site 562019002442 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 562019002443 active site 562019002444 putative oxyanion hole; other site 562019002445 catalytic triad [active] 562019002446 TLC ATP/ADP transporter; Region: TLC; pfam03219 562019002447 malate dehydrogenase; Reviewed; Region: PRK06223 562019002448 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 562019002449 NAD(P) binding site [chemical binding]; other site 562019002450 dimer interface [polypeptide binding]; other site 562019002451 tetramer (dimer of dimers) interface [polypeptide binding]; other site 562019002452 substrate binding site [chemical binding]; other site 562019002453 authentic frameshifts in hypothetical rickettsial gene similar to RF_0589 562019002454 authentic internal stop codon: common BLAST hit: gi|157964614|ref|YP_001499438.1| transposase ISRpe1 562019002455 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 562019002456 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 562019002457 catalytic core domain of class I lysyl tRNA synthetase; Region: LysRS_core_class_I; cd00674 562019002458 active site 562019002459 HIGH motif; other site 562019002460 KMSKS motif; other site 562019002461 Predicted permeases [General function prediction only]; Region: COG0679 562019002462 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 562019002463 Malic enzyme, N-terminal domain; Region: malic; pfam00390 562019002464 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 562019002465 putative NAD(P) binding site [chemical binding]; other site 562019002466 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 562019002467 Protein of unknown function (DUF2748); Region: DUF2748; pfam10871 562019002468 Gene fragment of homolog of A1G_01175 562019002469 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019002470 Winged helix-turn helix; Region: HTH_29; pfam13551 562019002471 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019002472 Integrase core domain; Region: rve; pfam00665 562019002473 Integrase core domain; Region: rve_3; pfam13683 562019002474 metabolite-proton symporter; Region: 2A0106; TIGR00883 562019002475 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 562019002476 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 562019002477 putative active site [active] 562019002478 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019002479 Winged helix-turn helix; Region: HTH_29; pfam13551 562019002480 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019002481 Integrase core domain; Region: rve; pfam00665 562019002482 Integrase core domain; Region: rve_3; pfam13683 562019002483 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 562019002484 Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]; Region: RplQ; COG0203 562019002485 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 562019002486 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 562019002487 alphaNTD - beta interaction site [polypeptide binding]; other site 562019002488 alphaNTD homodimer interface [polypeptide binding]; other site 562019002489 alphaNTD - beta' interaction site [polypeptide binding]; other site 562019002490 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 562019002491 30S ribosomal protein S11; Validated; Region: PRK05309 562019002492 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 562019002493 30S ribosomal protein S13; Region: bact_S13; TIGR03631 562019002494 adenylate kinase; Reviewed; Region: adk; PRK00279 562019002495 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 562019002496 AMP-binding site [chemical binding]; other site 562019002497 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 562019002498 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 562019002499 SecY translocase; Region: SecY; pfam00344 562019002500 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 562019002501 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 562019002502 23S rRNA binding site [nucleotide binding]; other site 562019002503 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 562019002504 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 562019002505 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 562019002506 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 562019002507 5S rRNA interface [nucleotide binding]; other site 562019002508 23S rRNA interface [nucleotide binding]; other site 562019002509 L5 interface [polypeptide binding]; other site 562019002510 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 562019002511 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 562019002512 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 562019002513 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 562019002514 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 562019002515 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 562019002516 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 562019002517 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 562019002518 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 562019002519 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 562019002520 RNA binding site [nucleotide binding]; other site 562019002521 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 562019002522 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 562019002523 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 562019002524 L23 interface [polypeptide binding]; other site 562019002525 trigger factor interaction site; other site 562019002526 23S rRNA interface [nucleotide binding]; other site 562019002527 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 562019002528 23S rRNA interface [nucleotide binding]; other site 562019002529 5S rRNA interface [nucleotide binding]; other site 562019002530 putative antibiotic binding site [chemical binding]; other site 562019002531 L25 interface [polypeptide binding]; other site 562019002532 L27 interface [polypeptide binding]; other site 562019002533 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 562019002534 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 562019002535 G-X-X-G motif; other site 562019002536 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 562019002537 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 562019002538 putative translocon binding site; other site 562019002539 protein-rRNA interface [nucleotide binding]; other site 562019002540 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 562019002541 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 562019002542 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 562019002543 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 562019002544 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 562019002545 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 562019002546 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 562019002547 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 562019002548 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 562019002549 elongation factor Tu; Reviewed; Region: PRK00049 562019002550 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 562019002551 G1 box; other site 562019002552 GEF interaction site [polypeptide binding]; other site 562019002553 GTP/Mg2+ binding site [chemical binding]; other site 562019002554 Switch I region; other site 562019002555 G2 box; other site 562019002556 G3 box; other site 562019002557 Switch II region; other site 562019002558 G4 box; other site 562019002559 G5 box; other site 562019002560 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 562019002561 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 562019002562 Antibiotic Binding Site [chemical binding]; other site 562019002563 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 562019002564 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 562019002565 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 562019002566 fumarate hydratase; Reviewed; Region: fumC; PRK00485 562019002567 Class II fumarases; Region: Fumarase_classII; cd01362 562019002568 active site 562019002569 tetramer interface [polypeptide binding]; other site 562019002570 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 562019002571 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 562019002572 putative active site [active] 562019002573 homotetrameric interface [polypeptide binding]; other site 562019002574 cell division protein FtsZ; Validated; Region: PRK09330 562019002575 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 562019002576 nucleotide binding site [chemical binding]; other site 562019002577 SulA interaction site; other site 562019002578 Serine protease inhibitor ecotin [General function prediction only]; Region: Eco; COG4574 562019002579 secondary substrate binding site; other site 562019002580 primary substrate binding site; other site 562019002581 inhibition loop; other site 562019002582 dimerization interface [polypeptide binding]; other site 562019002583 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; smart00932 562019002584 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 562019002585 muropeptide transporter; Validated; Region: ampG; cl17669 562019002586 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 562019002587 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 562019002588 ATP binding site [chemical binding]; other site 562019002589 Mg++ binding site [ion binding]; other site 562019002590 motif III; other site 562019002591 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 562019002592 nucleotide binding region [chemical binding]; other site 562019002593 ATP-binding site [chemical binding]; other site 562019002594 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 562019002595 DNA-binding site [nucleotide binding]; DNA binding site 562019002596 RNA-binding motif; other site 562019002597 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 562019002598 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 562019002599 S-adenosylmethionine binding site [chemical binding]; other site 562019002600 SurA N-terminal domain; Region: SurA_N_3; cl07813 562019002601 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 562019002602 Organic solvent tolerance protein; Region: OstA_C; pfam04453 562019002603 Exonuclease VII, large subunit [DNA replication, recombination, and repair]; Region: XseA; COG1570 562019002604 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 562019002605 generic binding surface II; other site 562019002606 generic binding surface I; other site 562019002607 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 562019002608 putative catalytic site [active] 562019002609 putative phosphate binding site [ion binding]; other site 562019002610 active site 562019002611 metal binding site A [ion binding]; metal-binding site 562019002612 DNA binding site [nucleotide binding] 562019002613 putative AP binding site [nucleotide binding]; other site 562019002614 putative metal binding site B [ion binding]; other site 562019002615 Uncharacterized conserved protein [Function unknown]; Region: COG4095 562019002616 GTP-binding protein Der; Reviewed; Region: PRK00093 562019002617 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 562019002618 G1 box; other site 562019002619 GTP/Mg2+ binding site [chemical binding]; other site 562019002620 Switch I region; other site 562019002621 G2 box; other site 562019002622 Switch II region; other site 562019002623 G3 box; other site 562019002624 G4 box; other site 562019002625 G5 box; other site 562019002626 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 562019002627 G1 box; other site 562019002628 GTP/Mg2+ binding site [chemical binding]; other site 562019002629 Switch I region; other site 562019002630 G2 box; other site 562019002631 G3 box; other site 562019002632 Switch II region; other site 562019002633 G4 box; other site 562019002634 G5 box; other site 562019002635 authentic frameshifts: common BLAST hit: gi|67458639|ref|YP_246263.1| ATPase 562019002636 authentic frameshifts in hypothetical rickettsial gene 562019002637 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 562019002638 ABC1 family; Region: ABC1; cl17513 562019002639 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 562019002640 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 562019002641 S-adenosylmethionine binding site [chemical binding]; other site 562019002642 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 562019002643 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 562019002644 DNA binding site [nucleotide binding] 562019002645 catalytic residue [active] 562019002646 H2TH interface [polypeptide binding]; other site 562019002647 putative catalytic residues [active] 562019002648 turnover-facilitating residue; other site 562019002649 intercalation triad [nucleotide binding]; other site 562019002650 8OG recognition residue [nucleotide binding]; other site 562019002651 putative reading head residues; other site 562019002652 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 562019002653 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 562019002654 authentic frameshifts: common BLAST hit: gi|15892962|ref|NP_360676.1| putative mannose-1-phosphate guanylyltransferase 562019002655 authentic frameshift: common BLAST hit: gi|67458630|ref|YP_246254.1| Poly-beta-hydroxyalkanoate depolymerase 562019002656 authentic frameshifts in COG2958 Uncharacterized protein conserved in bacteria 562019002657 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 562019002658 active site 562019002659 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 562019002660 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 562019002661 HIGH motif; other site 562019002662 active site 562019002663 KMSKS motif; other site 562019002664 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 562019002665 tRNA binding surface [nucleotide binding]; other site 562019002666 anticodon binding site; other site 562019002667 thymidylate kinase; Validated; Region: tmk; PRK00698 562019002668 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 562019002669 TMP-binding site; other site 562019002670 ATP-binding site [chemical binding]; other site 562019002671 metabolite-proton symporter; Region: 2A0106; TIGR00883 562019002672 4-hydroxybenzoate polyprenyltransferase; Reviewed; Region: ubiA; PRK12847 562019002673 UbiA prenyltransferase family; Region: UbiA; pfam01040 562019002674 authentic frameshifts: common BLAST hit: gi|67458622|ref|YP_246246.1| transposase 562019002675 valyl-tRNA synthetase; Reviewed; Region: valS; PRK13208 562019002676 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 562019002677 active site 562019002678 HIGH motif; other site 562019002679 nucleotide binding site [chemical binding]; other site 562019002680 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 562019002681 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 562019002682 active site 562019002683 KMSKS motif; other site 562019002684 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 562019002685 tRNA binding surface [nucleotide binding]; other site 562019002686 anticodon binding site; other site 562019002687 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 562019002688 authentic internal stop codon in COG1373 Predicted ATPase (AAA+ superfamily) 562019002689 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 562019002690 RmuC family; Region: RmuC; pfam02646 562019002691 authentic frameshifts in putative alpha-(1,3)-fucosyltransferase gene 562019002692 authentic frameshifts in hypothetical rickettsial gene 562019002693 authentic frameshifts in putative oxidoreductase gene 562019002694 Predicted integral membrane protein (DUF2269); Region: DUF2269; pfam10027 562019002695 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 562019002696 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 562019002697 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 562019002698 Walker A motif; other site 562019002699 ATP binding site [chemical binding]; other site 562019002700 Walker B motif; other site 562019002701 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 562019002702 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 562019002703 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 562019002704 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 562019002705 Ligand Binding Site [chemical binding]; other site 562019002706 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 562019002707 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 562019002708 HicB family; Region: HicB; pfam05534 562019002709 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 562019002710 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 562019002711 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 562019002712 Walker A/P-loop; other site 562019002713 ATP binding site [chemical binding]; other site 562019002714 Q-loop/lid; other site 562019002715 ABC transporter signature motif; other site 562019002716 Walker B; other site 562019002717 D-loop; other site 562019002718 H-loop/switch region; other site 562019002719 Protein of unknown function (DUF2673); Region: DUF2673; pfam10880 562019002720 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 562019002721 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 562019002722 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 562019002723 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 562019002724 FtsX-like permease family; Region: FtsX; pfam02687 562019002725 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 562019002726 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 562019002727 Walker A/P-loop; other site 562019002728 ATP binding site [chemical binding]; other site 562019002729 Q-loop/lid; other site 562019002730 ABC transporter signature motif; other site 562019002731 Walker B; other site 562019002732 D-loop; other site 562019002733 H-loop/switch region; other site 562019002734 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 562019002735 Domain of unknown function DUF21; Region: DUF21; pfam01595 562019002736 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 562019002737 Transporter associated domain; Region: CorC_HlyC; smart01091 562019002738 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 562019002739 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019002740 Winged helix-turn helix; Region: HTH_29; pfam13551 562019002741 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019002742 Integrase core domain; Region: rve; pfam00665 562019002743 Integrase core domain; Region: rve_3; pfam13683 562019002744 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 562019002745 putative coenzyme Q binding site [chemical binding]; other site 562019002746 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 562019002747 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 562019002748 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 562019002749 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 562019002750 RNA methyltransferase, RsmE family; Region: TIGR00046 562019002751 Uncharacterized conserved protein [Function unknown]; Region: COG2155 562019002752 authentic frameshift: common BLAST hit: gi|15892134|ref|NP_359848.1| acriflavin resistance protein D 562019002753 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 562019002754 Protein export membrane protein; Region: SecD_SecF; cl14618 562019002755 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 562019002756 IHF dimer interface [polypeptide binding]; other site 562019002757 IHF - DNA interface [nucleotide binding]; other site 562019002758 DNA polymerase III subunit delta'; Validated; Region: PRK06581 562019002759 signal recognition particle protein; Provisional; Region: PRK10867 562019002760 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 562019002761 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 562019002762 P loop; other site 562019002763 GTP binding site [chemical binding]; other site 562019002764 Signal peptide binding domain; Region: SRP_SPB; pfam02978 562019002765 authentic frameshifts: common BLAST hit: gi|51473374|ref|YP_067131.1| post-proline cleaving enzyme 562019002766 authentic frameshift in Radical SAM family enzyme, similar to coproporphyrinogen III oxidase, oxygen-independent, clustered with nucleoside-triphosphatase RdgB 562019002767 partial COG3023 Negative regulator of beta-lactamase expression, ampD 562019002768 authentic frameshift in hypothetical rickettsial gene 562019002769 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 562019002770 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 562019002771 putative active site [active] 562019002772 catalytic triad [active] 562019002773 putative dimer interface [polypeptide binding]; other site 562019002774 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06603 562019002775 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 562019002776 NAD binding site [chemical binding]; other site 562019002777 homotetramer interface [polypeptide binding]; other site 562019002778 homodimer interface [polypeptide binding]; other site 562019002779 substrate binding site [chemical binding]; other site 562019002780 active site 562019002781 authentic frameshifts in hypothetical rickettsial gene AIG_02790 562019002782 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 562019002783 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 562019002784 active site 562019002785 DNA binding site [nucleotide binding] 562019002786 Int/Topo IB signature motif; other site 562019002787 authentic frameshift: common BLAST hit: gi|67458962|ref|YP_246586.1| Phage uncharacterized protein 562019002788 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4765 562019002789 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 562019002790 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 562019002791 NADH dehydrogenase subunit B; Validated; Region: PRK06411 562019002792 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 562019002793 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 562019002794 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 562019002795 NADH dehydrogenase subunit D; Validated; Region: PRK06075 562019002796 NADH dehydrogenase subunit E; Validated; Region: PRK07539 562019002797 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 562019002798 putative dimer interface [polypeptide binding]; other site 562019002799 [2Fe-2S] cluster binding site [ion binding]; other site 562019002800 hypothetical protein; Provisional; Region: PRK14388 562019002801 YCII-related domain; Region: YCII; cl00999 562019002802 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 562019002803 active site 562019002804 DNA binding site [nucleotide binding] 562019002805 Protein of unknown function (DUF4239); Region: DUF4239; pfam14023 562019002806 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 562019002807 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 562019002808 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 562019002809 RimM N-terminal domain; Region: RimM; pfam01782 562019002810 PRC-barrel domain; Region: PRC; pfam05239 562019002811 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 562019002812 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 562019002813 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 562019002814 TPR repeat; Region: TPR_11; pfam13414 562019002815 TPR motif; other site 562019002816 binding surface 562019002817 Domain of unknown function (DUF4385); Region: DUF4385; pfam14328 562019002818 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 562019002819 spore photoproduct lyase; Region: photo_TT_lyase; cl15393 562019002820 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 562019002821 UbiA prenyltransferase family; Region: UbiA; pfam01040 562019002822 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 562019002823 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 562019002824 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 562019002825 RNA binding surface [nucleotide binding]; other site 562019002826 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 562019002827 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 562019002828 putative ADP-binding pocket [chemical binding]; other site 562019002829 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 562019002830 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 562019002831 catalytic site [active] 562019002832 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 562019002833 authentic frameshifts: common BLAST hit: gi|157964419|ref|YP_001499243.1| RND family efflux transporter MFP subunit 562019002834 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 562019002835 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 562019002836 active site 562019002837 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 562019002838 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 562019002839 active site 562019002840 Methyltransferase domain; Region: Methyltransf_31; pfam13847 562019002841 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 562019002842 S-adenosylmethionine binding site [chemical binding]; other site 562019002843 authentic frameshifts in conserved hypothetical rickettsial gene AIG_02605 562019002844 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 562019002845 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 562019002846 active site 562019002847 homodimer interface [polypeptide binding]; other site 562019002848 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 562019002849 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 562019002850 NAD(P) binding site [chemical binding]; other site 562019002851 homodimer interface [polypeptide binding]; other site 562019002852 substrate binding site [chemical binding]; other site 562019002853 active site 562019002854 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 562019002855 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 562019002856 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 562019002857 NADP binding site [chemical binding]; other site 562019002858 active site 562019002859 putative substrate binding site [chemical binding]; other site 562019002860 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 562019002861 sequence-specific DNA binding site [nucleotide binding]; other site 562019002862 salt bridge; other site 562019002863 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair]; Region: COG0816 562019002864 authentic frameshifts in COG2194 Predicted membrane-associated, metal-dependent hydrolase; putative phosphoethanolamine transferase 562019002865 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 562019002866 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 562019002867 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 562019002868 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 562019002869 dimer interface [polypeptide binding]; other site 562019002870 decamer (pentamer of dimers) interface [polypeptide binding]; other site 562019002871 catalytic triad [active] 562019002872 peroxidatic and resolving cysteines [active] 562019002873 authentic frameshifts in gene for putative DNA processing protein DprA 562019002874 DNA topoisomerase I; Validated; Region: PRK06599 562019002875 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 562019002876 active site 562019002877 interdomain interaction site; other site 562019002878 putative metal-binding site [ion binding]; other site 562019002879 nucleotide binding site [chemical binding]; other site 562019002880 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 562019002881 domain I; other site 562019002882 DNA binding groove [nucleotide binding] 562019002883 phosphate binding site [ion binding]; other site 562019002884 domain II; other site 562019002885 domain III; other site 562019002886 nucleotide binding site [chemical binding]; other site 562019002887 catalytic site [active] 562019002888 domain IV; other site 562019002889 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 562019002890 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 562019002891 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 562019002892 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 562019002893 HIGH motif; other site 562019002894 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 562019002895 active site 562019002896 KMSKS motif; other site 562019002897 authentic frameshift: common BLAST hit: gi|157964614|ref|YP_001499438.1| transposase ISRpe1 562019002898 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 562019002899 uncharacterized subgroup of the Escherichia coli Mg2+ transporter CorA_like subfamily; Region: EcCorA-like_u1; cd12837 562019002900 Cl binding site [ion binding]; other site 562019002901 oligomer interface [polypeptide binding]; other site 562019002902 authentic frameshifts in aminoglycoside 3'-phosphotransferase gene 562019002903 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 562019002904 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 562019002905 dimerization interface [polypeptide binding]; other site 562019002906 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 562019002907 dimer interface [polypeptide binding]; other site 562019002908 phosphorylation site [posttranslational modification] 562019002909 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 562019002910 ATP binding site [chemical binding]; other site 562019002911 Mg2+ binding site [ion binding]; other site 562019002912 G-X-G motif; other site 562019002913 Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]; Region: RpsU; COG0828 562019002914 Uncharacterized conserved protein [Function unknown]; Region: COG5590 562019002915 COQ9; Region: COQ9; pfam08511 562019002916 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 562019002917 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 562019002918 HIGH motif; other site 562019002919 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 562019002920 active site 562019002921 KMSKS motif; other site 562019002922 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 562019002923 tRNA binding surface [nucleotide binding]; other site 562019002924 anticodon binding site; other site 562019002925 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 562019002926 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 562019002927 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 562019002928 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 562019002929 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 562019002930 carboxyltransferase (CT) interaction site; other site 562019002931 biotinylation site [posttranslational modification]; other site 562019002932 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 562019002933 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 562019002934 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 562019002935 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 562019002936 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 562019002937 putative substrate translocation pore; other site 562019002938 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 562019002939 putative acyl-acceptor binding pocket; other site 562019002940 C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas); Region: AAS_C; cd05909 562019002941 acyl-activating enzyme (AAE) consensus motif; other site 562019002942 putative AMP binding site [chemical binding]; other site 562019002943 Regulator of competence-specific genes [Transcription]; Region: TfoX; COG3070 562019002944 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 562019002945 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 562019002946 ABC-ATPase subunit interface; other site 562019002947 dimer interface [polypeptide binding]; other site 562019002948 putative PBP binding regions; other site 562019002949 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 562019002950 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 562019002951 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 562019002952 S-adenosylmethionine binding site [chemical binding]; other site 562019002953 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 562019002954 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 562019002955 HIGH motif; other site 562019002956 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 562019002957 active site 562019002958 KMSKS motif; other site 562019002959 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 562019002960 Invasion protein B, involved in pathogenesis [General function prediction only]; Region: COG5342 562019002961 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 562019002962 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 562019002963 ring oligomerisation interface [polypeptide binding]; other site 562019002964 ATP/Mg binding site [chemical binding]; other site 562019002965 stacking interactions; other site 562019002966 hinge regions; other site 562019002967 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 562019002968 oligomerisation interface [polypeptide binding]; other site 562019002969 mobile loop; other site 562019002970 roof hairpin; other site 562019002971 authentic frameshifts: common BLAST hit: gi|67458799|ref|YP_246423.1| glycosyltransferase 562019002972 ribonuclease PH; Reviewed; Region: rph; PRK00173 562019002973 Ribonuclease PH; Region: RNase_PH_bact; cd11362 562019002974 hexamer interface [polypeptide binding]; other site 562019002975 active site 562019002976 GrpE; Region: GrpE; pfam01025 562019002977 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 562019002978 dimer interface [polypeptide binding]; other site 562019002979 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 562019002980 Domain of unknown function DUF20; Region: UPF0118; pfam01594 562019002981 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 562019002982 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 562019002983 hypothetical protein; Validated; Region: PRK06620 562019002984 authentic frameshifts: common BLAST hit: gi|67458789|ref|YP_246413.1| MFS type sugar transporter 562019002985 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019002986 Winged helix-turn helix; Region: HTH_29; pfam13551 562019002987 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019002988 Integrase core domain; Region: rve; pfam00665 562019002989 Integrase core domain; Region: rve_3; pfam13683 562019002990 authentic gene fragment: common BLAST hit: gi|157964614|ref|YP_001499438.1| transposase ISRpe1 562019002991 GTPase CgtA; Reviewed; Region: obgE; PRK12299 562019002992 GTP1/OBG; Region: GTP1_OBG; pfam01018 562019002993 Obg GTPase; Region: Obg; cd01898 562019002994 G1 box; other site 562019002995 GTP/Mg2+ binding site [chemical binding]; other site 562019002996 Switch I region; other site 562019002997 G2 box; other site 562019002998 G3 box; other site 562019002999 Switch II region; other site 562019003000 G4 box; other site 562019003001 G5 box; other site 562019003002 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 562019003003 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 562019003004 dimer interface [polypeptide binding]; other site 562019003005 active site 562019003006 citrylCoA binding site [chemical binding]; other site 562019003007 NADH binding [chemical binding]; other site 562019003008 cationic pore residues; other site 562019003009 oxalacetate/citrate binding site [chemical binding]; other site 562019003010 coenzyme A binding site [chemical binding]; other site 562019003011 catalytic triad [active] 562019003012 authentic frameshift in transcriptional regulator gene 562019003013 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 562019003014 Fe-S cluster binding site [ion binding]; other site 562019003015 active site 562019003016 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 562019003017 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 562019003018 RNA binding surface [nucleotide binding]; other site 562019003019 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 562019003020 active site 562019003021 authentic frameshifts and internal stop codon in area of hypothetical rickettsial genes 562019003022 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed; Region: PRK01544 562019003023 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 562019003024 S-adenosylmethionine binding site [chemical binding]; other site 562019003025 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]; Region: COG0220 562019003026 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 562019003027 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 562019003028 Glycyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]; Region: GlyS; COG0751 562019003029 DALR anticodon binding domain; Region: DALR_1; pfam05746 562019003030 glycyl-tRNA synthetase subunit alpha; Validated; Region: glyQ; PRK09348 562019003031 motif 1; other site 562019003032 dimer interface [polypeptide binding]; other site 562019003033 active site 562019003034 motif 2; other site 562019003035 motif 3; other site 562019003036 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 562019003037 oligomeric interface; other site 562019003038 putative active site [active] 562019003039 homodimer interface [polypeptide binding]; other site 562019003040 prevent-host-death family protein; Region: phd_fam; TIGR01552 562019003041 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 562019003042 authentic frameshift: common BLAST hit: gi|67459741|ref|YP_247365.1| proline/betaine transporter 562019003043 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 562019003044 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 562019003045 motif 1; other site 562019003046 active site 562019003047 motif 2; other site 562019003048 motif 3; other site 562019003049 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 562019003050 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 562019003051 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 562019003052 dimerization interface 3.5A [polypeptide binding]; other site 562019003053 active site 562019003054 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 562019003055 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 562019003056 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 562019003057 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 562019003058 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 562019003059 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 562019003060 DNA binding residues [nucleotide binding] 562019003061 DNA primase, catalytic core; Region: dnaG; TIGR01391 562019003062 CHC2 zinc finger; Region: zf-CHC2; pfam01807 562019003063 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 562019003064 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 562019003065 active site 562019003066 metal binding site [ion binding]; metal-binding site 562019003067 interdomain interaction site; other site 562019003068 Dolichol kinase [Lipid metabolism]; Region: SEC59; COG0170 562019003069 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 562019003070 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 562019003071 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 562019003072 authentic frameshifts in COG3288 NAD/NADP transhydrogenase subunit alpha 562019003073 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 562019003074 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 562019003075 DNA polymerase III subunits gamma and tau; Validated; Region: PRK06645 562019003076 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 562019003077 Walker A motif; other site 562019003078 ATP binding site [chemical binding]; other site 562019003079 Walker B motif; other site 562019003080 arginine finger; other site 562019003081 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 562019003082 hypothetical protein; Validated; Region: PRK00153 562019003083 Predicted aspartyl protease [General function prediction only]; Region: COG3577 562019003084 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 562019003085 catalytic motif [active] 562019003086 Catalytic residue [active] 562019003087 authentic frameshifts and internal stop codons in COG1680 beta-lactamase AmpC 562019003088 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 562019003089 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 562019003090 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 562019003091 Walker A/P-loop; other site 562019003092 ATP binding site [chemical binding]; other site 562019003093 Q-loop/lid; other site 562019003094 ABC transporter signature motif; other site 562019003095 Walker B; other site 562019003096 D-loop; other site 562019003097 H-loop/switch region; other site 562019003098 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 562019003099 putative hydrolase; Provisional; Region: PRK02113 562019003100 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 562019003101 active site 562019003102 DNA-damage-inducible protein J [DNA replication, recombination, and repair]; Region: RelB; COG3077 562019003103 Predicted permeases [General function prediction only]; Region: COG0795 562019003104 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 562019003105 DNA polymerase III subunit chi; Provisional; Region: PRK06646 562019003106 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 562019003107 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 562019003108 metal binding site [ion binding]; metal-binding site 562019003109 dimer interface [polypeptide binding]; other site 562019003110 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 562019003111 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 562019003112 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 562019003113 authentic frameshifts: common BLAST hit: gi|157827849|ref|YP_001496913.1| Type I restriction-modification system methyltransferase subunit 562019003114 authentic frameshifts in COG3004 Na+/H+ antiporter 562019003115 Uncharacterized conserved protein [Function unknown]; Region: COG1434 562019003116 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 562019003117 putative active site [active] 562019003118 lipoate-protein ligase B; Provisional; Region: PRK14347 562019003119 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 562019003120 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 562019003121 amidase catalytic site [active] 562019003122 Zn binding residues [ion binding]; other site 562019003123 substrate binding site [chemical binding]; other site 562019003124 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 562019003125 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 562019003126 ribosomal protein L33, bacterial type; Region: rpmG_bact; TIGR01023 562019003127 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 562019003128 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 562019003129 ATP binding site [chemical binding]; other site 562019003130 Mg2+ binding site [ion binding]; other site 562019003131 G-X-G motif; other site 562019003132 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 562019003133 ATP binding site [chemical binding]; other site 562019003134 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 562019003135 Tetratricopeptide repeat; Region: TPR_12; pfam13424 562019003136 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 562019003137 TPR motif; other site 562019003138 TPR repeat; Region: TPR_11; pfam13414 562019003139 binding surface 562019003140 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 562019003141 binding surface 562019003142 TPR motif; other site 562019003143 Tetratricopeptide repeat; Region: TPR_12; pfam13424 562019003144 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 562019003145 metabolite-proton symporter; Region: 2A0106; TIGR00883 562019003146 putative substrate translocation pore; other site 562019003147 Coproporphyrinogen III oxidase [Coenzyme metabolism]; Region: HemF; COG0408 562019003148 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 562019003149 authentic frameshift: common BLAST hit: gi|67459789|ref|YP_247413.1| prophage antirepressor 562019003150 TIGR00701 family protein; Region: TIGR00701 562019003151 ferrochelatase; Reviewed; Region: hemH; PRK00035 562019003152 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 562019003153 C-terminal domain interface [polypeptide binding]; other site 562019003154 active site 562019003155 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 562019003156 active site 562019003157 N-terminal domain interface [polypeptide binding]; other site 562019003158 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 562019003159 substrate binding site [chemical binding]; other site 562019003160 active site 562019003161 ParA-like protein; Provisional; Region: PHA02518 562019003162 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 562019003163 P-loop; other site 562019003164 Magnesium ion binding site [ion binding]; other site 562019003165 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 562019003166 DnaA N-terminal domain; Region: DnaA_N; pfam11638 562019003167 authentic frameshift: common BLAST hit: gi|91204872|ref|YP_537227.1| Type I restriction-modification system methyltransferase subunit 562019003168 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019003169 Winged helix-turn helix; Region: HTH_29; pfam13551 562019003170 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019003171 Integrase core domain; Region: rve; pfam00665 562019003172 Integrase core domain; Region: rve_3; pfam13683 562019003173 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 562019003174 putative trimer interface [polypeptide binding]; other site 562019003175 putative CoA binding site [chemical binding]; other site 562019003176 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 562019003177 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 562019003178 [2Fe-2S] cluster binding site [ion binding]; other site 562019003179 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 562019003180 alpha subunit interface [polypeptide binding]; other site 562019003181 active site 562019003182 substrate binding site [chemical binding]; other site 562019003183 Fe binding site [ion binding]; other site 562019003184 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 562019003185 classical (c) SDRs; Region: SDR_c; cd05233 562019003186 NAD(P) binding site [chemical binding]; other site 562019003187 active site 562019003188 3-oxoacyl-[acyl-carrier-protein]; Region: FabH; COG0332 562019003189 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 562019003190 dimer interface [polypeptide binding]; other site 562019003191 active site 562019003192 CoA binding pocket [chemical binding]; other site 562019003193 Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcpP; COG0236 562019003194 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 562019003195 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 562019003196 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 562019003197 Walker A/P-loop; other site 562019003198 ATP binding site [chemical binding]; other site 562019003199 Q-loop/lid; other site 562019003200 ABC transporter signature motif; other site 562019003201 Walker B; other site 562019003202 D-loop; other site 562019003203 H-loop/switch region; other site 562019003204 authentic frameshifts: common BLAST hit: gi|157964612|ref|YP_001499436.1| transposase 562019003205 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 562019003206 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 562019003207 putative dimer interface [polypeptide binding]; other site 562019003208 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 562019003209 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 562019003210 putative dimer interface [polypeptide binding]; other site 562019003211 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 562019003212 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 562019003213 Helix-turn-helix domain; Region: HTH_28; pfam13518 562019003214 Winged helix-turn helix; Region: HTH_29; pfam13551 562019003215 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 562019003216 Integrase core domain; Region: rve; pfam00665 562019003217 Integrase core domain; Region: rve_3; pfam13683 562019003218 COG3385 FOG: partial transposase 562019003219 COG3328 Transposase and inactivated derivatives, IS256 family transposase fragment 562019003220 authentic frameshift: common BLAST hit: gi|67459879|ref|YP_247501.1| transposase 562019003221 Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism]; Region: EmrE; COG2076 562019003222 TPR repeat; Region: TPR_11; pfam13414 562019003223 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 562019003224 binding surface 562019003225 TPR motif; other site 562019003226 TPR repeat; Region: TPR_11; pfam13414 562019003227 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 562019003228 Flagellar capping protein [Cell motility and secretion]; Region: FliD; COG1345