-- dump date 20140620_033843 -- class Genbank::misc_feature -- table misc_feature_note -- id note 1105112000001 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1806 1105112000002 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 1105112000003 catalytic residues [active] 1105112000004 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 1105112000005 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 1105112000006 Walker A/P-loop; other site 1105112000007 ATP binding site [chemical binding]; other site 1105112000008 Q-loop/lid; other site 1105112000009 ABC transporter signature motif; other site 1105112000010 Walker B; other site 1105112000011 D-loop; other site 1105112000012 H-loop/switch region; other site 1105112000013 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 1105112000014 ABC-2 type transporter; Region: ABC2_membrane; cl17235 1105112000015 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 1105112000016 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 1105112000017 FAD binding pocket [chemical binding]; other site 1105112000018 FAD binding motif [chemical binding]; other site 1105112000019 phosphate binding motif [ion binding]; other site 1105112000020 beta-alpha-beta structure motif; other site 1105112000021 NAD binding pocket [chemical binding]; other site 1105112000022 Iron coordination center [ion binding]; other site 1105112000023 PemK-like protein; Region: PemK; pfam02452 1105112000024 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 1105112000025 potential frameshift: common BLAST hit: gi|67458519|ref|YP_246143.1| tellurite resistance protein-like protein 1105112000026 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 1105112000027 membrane protein insertase; Provisional; Region: PRK01318 1105112000028 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 1105112000029 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1105112000030 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1105112000031 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 1105112000032 Uncharacterized conserved protein [Function unknown]; Region: COG1565 1105112000033 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112000034 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3755 1105112000035 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 1105112000036 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 1105112000037 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 1105112000038 cofactor binding site; other site 1105112000039 FtsH Extracellular; Region: FtsH_ext; pfam06480 1105112000040 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 1105112000041 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 1105112000042 Walker A motif; other site 1105112000043 ATP binding site [chemical binding]; other site 1105112000044 Walker B motif; other site 1105112000045 arginine finger; other site 1105112000046 Peptidase family M41; Region: Peptidase_M41; pfam01434 1105112000047 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 1105112000048 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 1105112000049 Ligand Binding Site [chemical binding]; other site 1105112000050 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112000051 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 1105112000052 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 1105112000053 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 1105112000054 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 1105112000055 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 1105112000056 potential frameshift: common BLAST hit: gi|157827734|ref|YP_001496798.1| response regulator 1105112000057 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cl17355 1105112000058 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 1105112000059 Fatty acid desaturase; Region: FA_desaturase; pfam00487 1105112000060 Di-iron ligands [ion binding]; other site 1105112000061 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 1105112000062 UGMP family protein; Validated; Region: PRK09604 1105112000063 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 1105112000064 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 1105112000065 Clp amino terminal domain; Region: Clp_N; pfam02861 1105112000066 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 1105112000067 Walker A motif; other site 1105112000068 ATP binding site [chemical binding]; other site 1105112000069 Walker B motif; other site 1105112000070 arginine finger; other site 1105112000071 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 1105112000072 Walker A motif; other site 1105112000073 ATP binding site [chemical binding]; other site 1105112000074 Walker B motif; other site 1105112000075 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 1105112000076 potential frameshift: common BLAST hit: gi|67458545|ref|YP_246169.1| acetoacetyl-CoA reductase 1105112000077 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 1105112000078 Protein of unknown function (DUF2748); Region: DUF2748; pfam10871 1105112000079 potential frameshift: common BLAST hit: gi|341583274|ref|YP_004763765.1| cell surface antigen-like protein Sca10 1105112000080 potential frameshift: common BLAST hit: gi|229586241|ref|YP_002844742.1| Putative dihydrouridine synthase Dus 1105112000081 potential frameshift: common BLAST hit: gi|165932567|ref|YP_001649356.1| tRNA-dihydrouridine synthase 1105112000082 potential frameshift: common BLAST hit: gi|238650328|ref|YP_002916180.1| nifR3-like protein 1105112000083 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 1105112000084 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 1105112000085 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 1105112000086 intersubunit interface [polypeptide binding]; other site 1105112000087 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 1105112000088 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 1105112000089 active site 1105112000090 NTP binding site [chemical binding]; other site 1105112000091 metal binding triad [ion binding]; metal-binding site 1105112000092 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 1105112000093 potential frameshift: common BLAST hit: gi|341583241|ref|YP_004763732.1| ComEC/Rec2-like protein 1105112000094 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105112000095 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1105112000096 F0F1 ATP synthase subunit B; Validated; Region: PRK06568 1105112000097 F0F1 ATP synthase subunit B'; Validated; Region: PRK06569 1105112000098 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1105112000099 F0F1 ATP synthase subunit C; Validated; Region: PRK07558 1105112000100 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 1105112000101 ATP synthase subunit 6 (eukaryotes),also subunit A (prokaryotes); Region: ATP_synt_6_or_A; TIGR01131 1105112000102 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5336 1105112000103 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 1105112000104 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 1105112000105 catalytic residues [active] 1105112000106 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 1105112000107 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105112000108 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 1105112000109 S-adenosylmethionine binding site [chemical binding]; other site 1105112000110 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 1105112000111 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 1105112000112 Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair]; Region: RecF; COG1195 1105112000113 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105112000114 Walker A/P-loop; other site 1105112000115 ATP binding site [chemical binding]; other site 1105112000116 Q-loop/lid; other site 1105112000117 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105112000118 ABC transporter signature motif; other site 1105112000119 Walker B; other site 1105112000120 D-loop; other site 1105112000121 H-loop/switch region; other site 1105112000122 potential frameshift: common BLAST hit: gi|341583262|ref|YP_004763753.1| folate synthesis bifunctional protein 1105112000123 potential frameshift: common BLAST hit: gi|67458431|ref|YP_246055.1| folate synthesis bifunctional protein 1105112000124 potential frameshift: common BLAST hit: gi|67458431|ref|YP_246055.1| folate synthesis bifunctional protein 1105112000125 Dihydroneopterin aldolase; Region: FolB; smart00905 1105112000126 active site 1105112000127 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 1105112000128 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 1105112000129 Cu(I) binding site [ion binding]; other site 1105112000130 Putative transcriptional regulator [Transcription]; Region: COG1678 1105112000131 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 1105112000132 Colicin V production protein; Region: Colicin_V; pfam02674 1105112000133 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 1105112000134 potential frameshift: common BLAST hit: gi|67458439|ref|YP_246063.1| cell surface antigen-like protein Sca10 1105112000135 potential frameshift: common BLAST hit: gi|341583274|ref|YP_004763765.1| cell surface antigen-like protein Sca10 1105112000136 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 1105112000137 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105112000138 Walker A/P-loop; other site 1105112000139 ATP binding site [chemical binding]; other site 1105112000140 Q-loop/lid; other site 1105112000141 ABC transporter signature motif; other site 1105112000142 Walker B; other site 1105112000143 D-loop; other site 1105112000144 H-loop/switch region; other site 1105112000145 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 1105112000146 Permease; Region: Permease; pfam02405 1105112000147 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 1105112000148 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 1105112000149 active site 1105112000150 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1105112000151 dimer interface [polypeptide binding]; other site 1105112000152 substrate binding site [chemical binding]; other site 1105112000153 catalytic residues [active] 1105112000154 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 1105112000155 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 1105112000156 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1105112000157 active site 1105112000158 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112000159 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; COG2854 1105112000160 Surface lipoprotein [Cell envelope biogenesis, outer membrane]; Region: VacJ; COG2853 1105112000161 TPR repeat; Region: TPR_11; pfam13414 1105112000162 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 1105112000163 binding surface 1105112000164 TPR motif; other site 1105112000165 Methyltransferase domain; Region: Methyltransf_23; pfam13489 1105112000166 Methyltransferase domain; Region: Methyltransf_18; pfam12847 1105112000167 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 1105112000168 Plasmid encoded toxin Txe; Region: Plasmid_Txe; cl17389 1105112000169 aspartate aminotransferase; Provisional; Region: PRK05764 1105112000170 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 1105112000171 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105112000172 homodimer interface [polypeptide binding]; other site 1105112000173 catalytic residue [active] 1105112000174 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 1105112000175 putative acyl-acceptor binding pocket; other site 1105112000176 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 1105112000177 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112000178 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 1105112000179 elongation factor Ts; Provisional; Region: tsf; PRK09377 1105112000180 UBA/TS-N domain; Region: UBA; pfam00627 1105112000181 Elongation factor TS; Region: EF_TS; pfam00889 1105112000182 Elongation factor TS; Region: EF_TS; pfam00889 1105112000183 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 1105112000184 rRNA interaction site [nucleotide binding]; other site 1105112000185 S8 interaction site; other site 1105112000186 putative laminin-1 binding site; other site 1105112000187 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 1105112000188 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1105112000189 active site 1105112000190 HIGH motif; other site 1105112000191 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1105112000192 KMSKS motif; other site 1105112000193 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1105112000194 tRNA binding surface [nucleotide binding]; other site 1105112000195 anticodon binding site; other site 1105112000196 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105112000197 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 1105112000198 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 1105112000199 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105112000200 putative substrate translocation pore; other site 1105112000201 EamA-like transporter family; Region: EamA; pfam00892 1105112000202 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 1105112000203 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 1105112000204 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 1105112000205 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 1105112000206 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 1105112000207 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 1105112000208 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 1105112000209 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 1105112000210 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105112000211 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 1105112000212 active site 1105112000213 phosphorylation site [posttranslational modification] 1105112000214 intermolecular recognition site; other site 1105112000215 dimerization interface [polypeptide binding]; other site 1105112000216 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 1105112000217 DNA binding site [nucleotide binding] 1105112000218 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 1105112000219 SecA binding site; other site 1105112000220 Preprotein binding site; other site 1105112000221 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1105112000222 trimer interface [polypeptide binding]; other site 1105112000223 active site 1105112000224 Gram-negative porin; Region: Porin_4; pfam13609 1105112000225 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 1105112000226 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 1105112000227 CAP-like domain; other site 1105112000228 active site 1105112000229 primary dimer interface [polypeptide binding]; other site 1105112000230 Sporulation related domain; Region: SPOR; pfam05036 1105112000231 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 1105112000232 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 1105112000233 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 1105112000234 active site 1105112000235 HIGH motif; other site 1105112000236 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105112000237 KMSK motif region; other site 1105112000238 tRNA binding surface [nucleotide binding]; other site 1105112000239 DALR anticodon binding domain; Region: DALR_1; smart00836 1105112000240 anticodon binding site; other site 1105112000241 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 1105112000242 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1105112000243 Zn2+ binding site [ion binding]; other site 1105112000244 Mg2+ binding site [ion binding]; other site 1105112000245 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 1105112000246 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 1105112000247 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; COG2877 1105112000248 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 1105112000249 Protein of unknown function (DUF2672); Region: DUF2672; pfam10878 1105112000250 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 1105112000251 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105112000252 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105112000253 Walker A/P-loop; other site 1105112000254 ATP binding site [chemical binding]; other site 1105112000255 Q-loop/lid; other site 1105112000256 ABC transporter signature motif; other site 1105112000257 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105112000258 ABC transporter; Region: ABC_tran_2; pfam12848 1105112000259 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105112000260 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 1105112000261 ParB-like nuclease domain; Region: ParB; smart00470 1105112000262 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 1105112000263 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 1105112000264 P-loop; other site 1105112000265 Magnesium ion binding site [ion binding]; other site 1105112000266 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 1105112000267 Magnesium ion binding site [ion binding]; other site 1105112000268 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 1105112000269 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 1105112000270 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 1105112000271 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 1105112000272 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 1105112000273 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 1105112000274 active site 1105112000275 multimer interface [polypeptide binding]; other site 1105112000276 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 1105112000277 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 1105112000278 putative substrate translocation pore; other site 1105112000279 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105112000280 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 1105112000281 active site 1105112000282 catalytic residues [active] 1105112000283 metal binding site [ion binding]; metal-binding site 1105112000284 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 1105112000285 Acyl-[acyl carrier protein]; Region: LpxA; COG1043 1105112000286 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 1105112000287 active site 1105112000288 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 1105112000289 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 1105112000290 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 1105112000291 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 1105112000292 trimer interface [polypeptide binding]; other site 1105112000293 active site 1105112000294 UDP-GlcNAc binding site [chemical binding]; other site 1105112000295 lipid binding site [chemical binding]; lipid-binding site 1105112000296 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 1105112000297 active site 1105112000298 potential frameshift: common BLAST hit: gi|67458401|ref|YP_246025.1| alpha-beta hydrolase family esterase 1105112000299 Ribosomal protein L28 [Translation, ribosomal structure and biogenesis]; Region: RpmB; COG0227 1105112000300 50S ribosomal protein L31; Provisional; Region: PRK01397 1105112000301 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 1105112000302 G1 box; other site 1105112000303 GTP/Mg2+ binding site [chemical binding]; other site 1105112000304 Switch I region; other site 1105112000305 G2 box; other site 1105112000306 G3 box; other site 1105112000307 Switch II region; other site 1105112000308 G4 box; other site 1105112000309 G5 box; other site 1105112000310 Acetylglutamate kinase [Amino acid transport and metabolism]; Region: ArgB; COG0548 1105112000311 substrate binding site [chemical binding]; other site 1105112000312 nucleotide binding site [chemical binding]; other site 1105112000313 type IV secretion system protein VirB3; Provisional; Region: PRK13899 1105112000314 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 1105112000315 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1105112000316 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105112000317 Walker A/P-loop; other site 1105112000318 ATP binding site [chemical binding]; other site 1105112000319 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105112000320 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105112000321 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105112000322 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105112000323 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105112000324 potential frameshift: common BLAST hit: gi|67458488|ref|YP_246112.1| phosphate acetyltransferase 1105112000325 potential frameshift: common BLAST hit: gi|157825283|ref|YP_001493003.1| phosphate acetyltransferase 1105112000326 potential frameshift: common BLAST hit: gi|67458489|ref|YP_246113.1| acetate kinase 1105112000327 tRNA-(guanine-N1)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmD; COG0336 1105112000328 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 1105112000329 hypothetical protein; Provisional; Region: PRK13694 1105112000330 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 1105112000331 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 1105112000332 Protein export membrane protein; Region: SecD_SecF; pfam02355 1105112000333 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 1105112000334 SLBB domain; Region: SLBB; pfam10531 1105112000335 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 1105112000336 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 1105112000337 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 1105112000338 Catalytic site [active] 1105112000339 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 1105112000340 ribonuclease III; Reviewed; Region: rnc; PRK00102 1105112000341 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 1105112000342 dimerization interface [polypeptide binding]; other site 1105112000343 active site 1105112000344 metal binding site [ion binding]; metal-binding site 1105112000345 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 1105112000346 dsRNA binding site [nucleotide binding]; other site 1105112000347 GTPase Era; Provisional; Region: era; PRK15494 1105112000348 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112000349 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 1105112000350 G1 box; other site 1105112000351 GTP/Mg2+ binding site [chemical binding]; other site 1105112000352 Switch I region; other site 1105112000353 G2 box; other site 1105112000354 Switch II region; other site 1105112000355 G3 box; other site 1105112000356 G4 box; other site 1105112000357 G5 box; other site 1105112000358 KH domain; Region: KH_2; pfam07650 1105112000359 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 1105112000360 active site 1105112000361 putative DNA-binding cleft [nucleotide binding]; other site 1105112000362 dimer interface [polypeptide binding]; other site 1105112000363 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 1105112000364 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 1105112000365 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 1105112000366 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 1105112000367 AAA domain; Region: AAA_31; pfam13614 1105112000368 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 1105112000369 Walker A motif; other site 1105112000370 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 1105112000371 HflK protein; Region: hflK; TIGR01933 1105112000372 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1105112000373 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 1105112000374 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 1105112000375 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1105112000376 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 1105112000377 protein binding site [polypeptide binding]; other site 1105112000378 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 1105112000379 protein binding site [polypeptide binding]; other site 1105112000380 hypothetical protein; Validated; Region: PRK01415 1105112000381 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 1105112000382 active site residue [active] 1105112000383 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 1105112000384 Iron-sulfur protein interface; other site 1105112000385 proximal quinone binding site [chemical binding]; other site 1105112000386 SdhD (CybS) interface [polypeptide binding]; other site 1105112000387 proximal heme binding site [chemical binding]; other site 1105112000388 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 1105112000389 putative SdhC subunit interface [polypeptide binding]; other site 1105112000390 putative proximal heme binding site [chemical binding]; other site 1105112000391 putative Iron-sulfur protein interface [polypeptide binding]; other site 1105112000392 putative proximal quinone binding site; other site 1105112000393 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 1105112000394 L-aspartate oxidase; Provisional; Region: PRK06175 1105112000395 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 1105112000396 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1105112000397 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 1105112000398 dimer interface [polypeptide binding]; other site 1105112000399 conserved gate region; other site 1105112000400 putative PBP binding loops; other site 1105112000401 ABC-ATPase subunit interface; other site 1105112000402 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 1105112000403 S17 interaction site [polypeptide binding]; other site 1105112000404 S8 interaction site; other site 1105112000405 16S rRNA interaction site [nucleotide binding]; other site 1105112000406 streptomycin interaction site [chemical binding]; other site 1105112000407 23S rRNA interaction site [nucleotide binding]; other site 1105112000408 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 1105112000409 30S ribosomal protein S7; Validated; Region: PRK05302 1105112000410 elongation factor G; Reviewed; Region: PRK00007 1105112000411 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 1105112000412 G1 box; other site 1105112000413 putative GEF interaction site [polypeptide binding]; other site 1105112000414 GTP/Mg2+ binding site [chemical binding]; other site 1105112000415 Switch I region; other site 1105112000416 G2 box; other site 1105112000417 G3 box; other site 1105112000418 Switch II region; other site 1105112000419 G4 box; other site 1105112000420 G5 box; other site 1105112000421 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 1105112000422 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 1105112000423 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 1105112000424 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 1105112000425 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 1105112000426 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 1105112000427 putative homodimer interface [polypeptide binding]; other site 1105112000428 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 1105112000429 heterodimer interface [polypeptide binding]; other site 1105112000430 homodimer interface [polypeptide binding]; other site 1105112000431 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 1105112000432 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 1105112000433 23S rRNA interface [nucleotide binding]; other site 1105112000434 putative thiostrepton binding site; other site 1105112000435 L7/L12 interface [polypeptide binding]; other site 1105112000436 L25 interface [polypeptide binding]; other site 1105112000437 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 1105112000438 mRNA/rRNA interface [nucleotide binding]; other site 1105112000439 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 1105112000440 23S rRNA interface [nucleotide binding]; other site 1105112000441 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 1105112000442 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 1105112000443 core dimer interface [polypeptide binding]; other site 1105112000444 peripheral dimer interface [polypeptide binding]; other site 1105112000445 L10 interface [polypeptide binding]; other site 1105112000446 L11 interface [polypeptide binding]; other site 1105112000447 putative EF-Tu interaction site [polypeptide binding]; other site 1105112000448 putative EF-G interaction site [polypeptide binding]; other site 1105112000449 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 1105112000450 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 1105112000451 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 1105112000452 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 1105112000453 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 1105112000454 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 1105112000455 RPB3 interaction site [polypeptide binding]; other site 1105112000456 RPB1 interaction site [polypeptide binding]; other site 1105112000457 RPB11 interaction site [polypeptide binding]; other site 1105112000458 RPB10 interaction site [polypeptide binding]; other site 1105112000459 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 1105112000460 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 1105112000461 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 1105112000462 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 1105112000463 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 1105112000464 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 1105112000465 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 1105112000466 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 1105112000467 DNA binding site [nucleotide binding] 1105112000468 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 1105112000469 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112000470 multifunctional aminopeptidase A; Provisional; Region: PRK00913 1105112000471 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 1105112000472 interface (dimer of trimers) [polypeptide binding]; other site 1105112000473 Substrate-binding/catalytic site; other site 1105112000474 Zn-binding sites [ion binding]; other site 1105112000475 ATPase MipZ; Region: MipZ; pfam09140 1105112000476 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 1105112000477 P-loop; other site 1105112000478 Magnesium ion binding site [ion binding]; other site 1105112000479 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 1105112000480 Magnesium ion binding site [ion binding]; other site 1105112000481 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 1105112000482 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 1105112000483 dimer interface [polypeptide binding]; other site 1105112000484 anticodon binding site; other site 1105112000485 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 1105112000486 homodimer interface [polypeptide binding]; other site 1105112000487 motif 1; other site 1105112000488 active site 1105112000489 motif 2; other site 1105112000490 GAD domain; Region: GAD; pfam02938 1105112000491 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 1105112000492 active site 1105112000493 motif 3; other site 1105112000494 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 1105112000495 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 1105112000496 dihydrodipicolinate reductase; Provisional; Region: PRK00048 1105112000497 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 1105112000498 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 1105112000499 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 1105112000500 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1105112000501 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 1105112000502 substrate binding pocket [chemical binding]; other site 1105112000503 membrane-bound complex binding site; other site 1105112000504 hinge residues; other site 1105112000505 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 1105112000506 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 1105112000507 GatB domain; Region: GatB_Yqey; smart00845 1105112000508 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 1105112000509 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 1105112000510 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 1105112000511 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain superfamily; Region: NTP-PPase; cl16941 1105112000512 ribosome recycling factor; Reviewed; Region: frr; PRK00083 1105112000513 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 1105112000514 hinge region; other site 1105112000515 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 1105112000516 putative nucleotide binding site [chemical binding]; other site 1105112000517 uridine monophosphate binding site [chemical binding]; other site 1105112000518 homohexameric interface [polypeptide binding]; other site 1105112000519 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK06580 1105112000520 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1105112000521 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 1105112000522 putative substrate translocation pore; other site 1105112000523 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 1105112000524 Protein of unknown function (DUF2674); Region: DUF2674; pfam10879 1105112000525 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 1105112000526 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105112000527 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105112000528 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105112000529 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105112000530 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105112000531 Surface antigen; Region: Bac_surface_Ag; pfam01103 1105112000532 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 1105112000533 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 1105112000534 active site 1105112000535 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 1105112000536 protein binding site [polypeptide binding]; other site 1105112000537 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 1105112000538 putative substrate binding region [chemical binding]; other site 1105112000539 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 1105112000540 putative RNA binding site [nucleotide binding]; other site 1105112000541 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 1105112000542 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 1105112000543 S-adenosylmethionine binding site [chemical binding]; other site 1105112000544 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 1105112000545 putative coenzyme Q binding site [chemical binding]; other site 1105112000546 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112000547 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 1105112000548 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 1105112000549 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 1105112000550 RNA methyltransferase, RsmE family; Region: TIGR00046 1105112000551 Uncharacterized conserved protein [Function unknown]; Region: COG2155 1105112000552 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105112000553 Protein export membrane protein; Region: SecD_SecF; cl14618 1105112000554 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 1105112000555 IHF dimer interface [polypeptide binding]; other site 1105112000556 IHF - DNA interface [nucleotide binding]; other site 1105112000557 DNA polymerase III subunit delta'; Validated; Region: PRK06581 1105112000558 signal recognition particle protein; Provisional; Region: PRK10867 1105112000559 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 1105112000560 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 1105112000561 P loop; other site 1105112000562 GTP binding site [chemical binding]; other site 1105112000563 Signal peptide binding domain; Region: SRP_SPB; pfam02978 1105112000564 potential frameshift: common BLAST hit: gi|51473374|ref|YP_067131.1| post-proline cleaving enzyme 1105112000565 potential frameshift: common BLAST hit: gi|15604049|ref|NP_220564.1| peptidase 1105112000566 potential frameshift: common BLAST hit: gi|67459496|ref|YP_247120.1| prolyl endopeptidase 1105112000567 coproporphyrinogen III oxidase; Provisional; Region: PRK06582 1105112000568 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 1105112000569 FeS/SAM binding site; other site 1105112000570 HemN C-terminal domain; Region: HemN_C; pfam06969 1105112000571 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cl02529 1105112000572 potential frameshift: common BLAST hit: gi|157826898|ref|YP_001495962.1| cephalosporin hydroxylase 1105112000573 potential frameshift: common BLAST hit: gi|157826898|ref|YP_001495962.1| cephalosporin hydroxylase 1105112000574 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1105112000575 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 1105112000576 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 1105112000577 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism]; Region: COG0720 1105112000578 active site 1105112000579 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 1105112000580 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 1105112000581 E3 interaction surface; other site 1105112000582 lipoyl attachment site [posttranslational modification]; other site 1105112000583 e3 binding domain; Region: E3_binding; pfam02817 1105112000584 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 1105112000585 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 1105112000586 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 1105112000587 TPP-binding site [chemical binding]; other site 1105112000588 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 1105112000589 dimer interface [polypeptide binding]; other site 1105112000590 PYR/PP interface [polypeptide binding]; other site 1105112000591 TPP binding site [chemical binding]; other site 1105112000592 potential frameshift: common BLAST hit: gi|350273234|ref|YP_004884547.1| thermostable carboxypeptidase 1105112000593 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 1105112000594 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 1105112000595 Walker A/P-loop; other site 1105112000596 ATP binding site [chemical binding]; other site 1105112000597 Q-loop/lid; other site 1105112000598 Allexivirus 40kDa protein; Region: Allexi_40kDa; pfam05549 1105112000599 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 1105112000600 ABC transporter signature motif; other site 1105112000601 Walker B; other site 1105112000602 D-loop; other site 1105112000603 H-loop/switch region; other site 1105112000604 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 1105112000605 Tetratricopeptide repeat; Region: TPR_6; pfam13174 1105112000606 ChaB; Region: ChaB; cl01887 1105112000607 chaperone protein DnaJ; Provisional; Region: PRK14300 1105112000608 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 1105112000609 HSP70 interaction site [polypeptide binding]; other site 1105112000610 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 1105112000611 substrate binding site [polypeptide binding]; other site 1105112000612 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 1105112000613 Zn binding sites [ion binding]; other site 1105112000614 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 1105112000615 dimer interface [polypeptide binding]; other site 1105112000616 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 1105112000617 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 1105112000618 nucleotide binding site [chemical binding]; other site 1105112000619 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 1105112000620 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1105112000621 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 1105112000622 Lipopolysaccharide-assembly; Region: LptE; pfam04390 1105112000623 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 1105112000624 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 1105112000625 diiron binding motif [ion binding]; other site 1105112000626 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 1105112000627 Subunit III/VIIa interface [polypeptide binding]; other site 1105112000628 Phospholipid binding site [chemical binding]; other site 1105112000629 Subunit I/III interface [polypeptide binding]; other site 1105112000630 Subunit III/VIb interface [polypeptide binding]; other site 1105112000631 Subunit III/VIa interface; other site 1105112000632 Subunit III/Vb interface [polypeptide binding]; other site 1105112000633 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 1105112000634 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 1105112000635 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 1105112000636 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 1105112000637 trimer interface [polypeptide binding]; other site 1105112000638 active site 1105112000639 substrate binding site [chemical binding]; other site 1105112000640 CoA binding site [chemical binding]; other site 1105112000641 Autotransporter beta-domain; Region: Autotransporter; smart00869 1105112000642 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 1105112000643 Ligand Binding Site [chemical binding]; other site 1105112000644 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 1105112000645 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 1105112000646 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 1105112000647 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 1105112000648 catalytic loop [active] 1105112000649 iron binding site [ion binding]; other site 1105112000650 chaperone protein HscA; Provisional; Region: hscA; PRK01433 1105112000651 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 1105112000652 nucleotide binding site [chemical binding]; other site 1105112000653 co-chaperone HscB; Provisional; Region: hscB; PRK01356 1105112000654 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 1105112000655 HSP70 interaction site [polypeptide binding]; other site 1105112000656 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 1105112000657 RNA/DNA hybrid binding site [nucleotide binding]; other site 1105112000658 active site 1105112000659 excinuclease ABC subunit B; Provisional; Region: PRK05298 1105112000660 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 1105112000661 ATP binding site [chemical binding]; other site 1105112000662 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 1105112000663 nucleotide binding region [chemical binding]; other site 1105112000664 ATP-binding site [chemical binding]; other site 1105112000665 Ultra-violet resistance protein B; Region: UvrB; pfam12344 1105112000666 UvrB/uvrC motif; Region: UVR; pfam02151 1105112000667 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 1105112000668 GSH binding site [chemical binding]; other site 1105112000669 catalytic residues [active] 1105112000670 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105112000671 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 1105112000672 ATP-binding cassette domain of iron-sulfur clusters transporter, subfamily C; Region: ABCC_ATM1_transporter; cd03253 1105112000673 Walker A/P-loop; other site 1105112000674 ATP binding site [chemical binding]; other site 1105112000675 Q-loop/lid; other site 1105112000676 ABC transporter signature motif; other site 1105112000677 Walker B; other site 1105112000678 D-loop; other site 1105112000679 H-loop/switch region; other site 1105112000680 DNA gyrase subunit A; Validated; Region: PRK05560 1105112000681 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 1105112000682 CAP-like domain; other site 1105112000683 active site 1105112000684 primary dimer interface [polypeptide binding]; other site 1105112000685 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105112000686 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105112000687 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105112000688 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105112000689 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105112000690 Iron-sulphur cluster assembly; Region: Fe-S_assembly; cl01123 1105112000691 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 1105112000692 active site 1105112000693 catalytic residues [active] 1105112000694 metal binding site [ion binding]; metal-binding site 1105112000695 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 1105112000696 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 1105112000697 putative active site [active] 1105112000698 substrate binding site [chemical binding]; other site 1105112000699 putative cosubstrate binding site; other site 1105112000700 catalytic site [active] 1105112000701 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 1105112000702 substrate binding site [chemical binding]; other site 1105112000703 potential frameshift: common BLAST hit: gi|157826977|ref|YP_001496041.1| capsular polysaccharide biosynthesis protein 1105112000704 Predicted ATPase [General function prediction only]; Region: COG1485 1105112000705 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 1105112000706 Walker A motif; other site 1105112000707 ATP binding site [chemical binding]; other site 1105112000708 Walker B motif; other site 1105112000709 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: PRK01424 1105112000710 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 1105112000711 potential frameshift: common BLAST hit: gi|350273268|ref|YP_004884581.1| ankyrin 1105112000712 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1105112000713 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105112000714 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105112000715 Walker A/P-loop; other site 1105112000716 ATP binding site [chemical binding]; other site 1105112000717 Q-loop/lid; other site 1105112000718 ABC transporter signature motif; other site 1105112000719 Walker B; other site 1105112000720 D-loop; other site 1105112000721 H-loop/switch region; other site 1105112000722 Protein of unknown function (DUF2671); Region: DUF2671; pfam10877 1105112000723 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 1105112000724 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 1105112000725 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 1105112000726 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 1105112000727 toxin-antitoxin system, toxin component, Txe/YoeB family; Region: toxin_Txe_YoeB; TIGR02116 1105112000728 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105112000729 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 1105112000730 putative metal binding site; other site 1105112000731 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1105112000732 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1105112000733 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1105112000734 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 1105112000735 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 1105112000736 ATP binding site [chemical binding]; other site 1105112000737 active site 1105112000738 substrate binding site [chemical binding]; other site 1105112000739 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 1105112000740 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 1105112000741 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 1105112000742 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 1105112000743 active site 1105112000744 dimer interface [polypeptide binding]; other site 1105112000745 motif 1; other site 1105112000746 motif 2; other site 1105112000747 motif 3; other site 1105112000748 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 1105112000749 anticodon binding site; other site 1105112000750 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 1105112000751 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 1105112000752 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 1105112000753 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 1105112000754 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 1105112000755 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 1105112000756 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 1105112000757 TrkA-N domain; Region: TrkA_N; pfam02254 1105112000758 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 1105112000759 Bacterial SH3 domain; Region: SH3_4; pfam06347 1105112000760 Bacterial SH3 domain; Region: SH3_4; pfam06347 1105112000761 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112000762 potential frameshift: common BLAST hit: gi|67459672|ref|YP_247296.1| nucleotidyltransferase/HEPN domain-containing protein 1105112000763 potential frameshift: common BLAST hit: gi|91204878|ref|YP_537233.1| nucleotidyltransferase 1105112000764 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 1105112000765 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1105112000766 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 1105112000767 FeS/SAM binding site; other site 1105112000768 TRAM domain; Region: TRAM; pfam01938 1105112000769 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 1105112000770 Transglycosylase; Region: Transgly; pfam00912 1105112000771 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1105112000772 potential frameshift: common BLAST hit: gi|67459667|ref|YP_247291.1| Beta-lactamase class D 1105112000773 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 1105112000774 dinuclear metal binding motif [ion binding]; other site 1105112000775 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 1105112000776 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1105112000777 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105112000778 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1105112000779 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 1105112000780 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 1105112000781 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 1105112000782 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1105112000783 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 1105112000784 beta subunit interaction interface [polypeptide binding]; other site 1105112000785 Walker A motif; other site 1105112000786 ATP binding site [chemical binding]; other site 1105112000787 Walker B motif; other site 1105112000788 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1105112000789 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 1105112000790 core domain interface [polypeptide binding]; other site 1105112000791 delta subunit interface [polypeptide binding]; other site 1105112000792 epsilon subunit interface [polypeptide binding]; other site 1105112000793 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 1105112000794 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1105112000795 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 1105112000796 alpha subunit interaction interface [polypeptide binding]; other site 1105112000797 Walker A motif; other site 1105112000798 ATP binding site [chemical binding]; other site 1105112000799 Walker B motif; other site 1105112000800 inhibitor binding site; inhibition site 1105112000801 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1105112000802 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK01474 1105112000803 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 1105112000804 gamma subunit interface [polypeptide binding]; other site 1105112000805 epsilon subunit interface [polypeptide binding]; other site 1105112000806 LBP interface [polypeptide binding]; other site 1105112000807 aconitate hydratase; Validated; Region: PRK09277 1105112000808 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 1105112000809 substrate binding site [chemical binding]; other site 1105112000810 ligand binding site [chemical binding]; other site 1105112000811 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 1105112000812 substrate binding site [chemical binding]; other site 1105112000813 Predicted membrane protein [Function unknown]; Region: COG3671 1105112000814 NADH dehydrogenase subunit G; Validated; Region: PRK09130 1105112000815 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 1105112000816 catalytic loop [active] 1105112000817 iron binding site [ion binding]; other site 1105112000818 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 1105112000819 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 1105112000820 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 1105112000821 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 1105112000822 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 1105112000823 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 1105112000824 4Fe-4S binding domain; Region: Fer4; cl02805 1105112000825 4Fe-4S binding domain; Region: Fer4; pfam00037 1105112000826 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13541 1105112000827 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105112000828 Walker A/P-loop; other site 1105112000829 ATP binding site [chemical binding]; other site 1105112000830 Q-loop/lid; other site 1105112000831 ABC transporter signature motif; other site 1105112000832 Walker B; other site 1105112000833 D-loop; other site 1105112000834 H-loop/switch region; other site 1105112000835 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 1105112000836 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105112000837 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 1105112000838 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 1105112000839 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105112000840 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 1105112000841 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 1105112000842 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 1105112000843 Predicted transcriptional regulator [Transcription]; Region: COG2944 1105112000844 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 1105112000845 salt bridge; other site 1105112000846 non-specific DNA binding site [nucleotide binding]; other site 1105112000847 sequence-specific DNA binding site [nucleotide binding]; other site 1105112000848 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105112000849 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 1105112000850 S-adenosylmethionine binding site [chemical binding]; other site 1105112000851 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 1105112000852 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 1105112000853 Integral membrane protein TerC family; Region: TerC; cl10468 1105112000854 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 1105112000855 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1105112000856 seryl-tRNA synthetase; Provisional; Region: PRK05431 1105112000857 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 1105112000858 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 1105112000859 dimer interface [polypeptide binding]; other site 1105112000860 active site 1105112000861 motif 1; other site 1105112000862 motif 2; other site 1105112000863 motif 3; other site 1105112000864 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 1105112000865 muropeptide transporter; Validated; Region: ampG; cl17669 1105112000866 Protein of unknown function; Region: DUF3971; pfam13116 1105112000867 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1105112000868 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 1105112000869 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 1105112000870 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 1105112000871 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 1105112000872 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 1105112000873 putative active site [active] 1105112000874 putative PHP Thumb interface [polypeptide binding]; other site 1105112000875 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 1105112000876 generic binding surface I; other site 1105112000877 generic binding surface II; other site 1105112000878 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 1105112000879 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 1105112000880 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 1105112000881 DNA polymerase I; Provisional; Region: PRK05755 1105112000882 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 1105112000883 active site 1105112000884 metal binding site 1 [ion binding]; metal-binding site 1105112000885 putative 5' ssDNA interaction site; other site 1105112000886 metal binding site 3; metal-binding site 1105112000887 metal binding site 2 [ion binding]; metal-binding site 1105112000888 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 1105112000889 putative DNA binding site [nucleotide binding]; other site 1105112000890 putative metal binding site [ion binding]; other site 1105112000891 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 1105112000892 active site 1105112000893 substrate binding site [chemical binding]; other site 1105112000894 catalytic site [active] 1105112000895 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 1105112000896 active site 1105112000897 DNA binding site [nucleotide binding] 1105112000898 catalytic site [active] 1105112000899 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 1105112000900 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 1105112000901 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 1105112000902 P loop; other site 1105112000903 GTP binding site [chemical binding]; other site 1105112000904 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 1105112000905 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 1105112000906 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 1105112000907 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 1105112000908 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 1105112000909 dimer interface [polypeptide binding]; other site 1105112000910 active site 1105112000911 CoA binding pocket [chemical binding]; other site 1105112000912 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 1105112000913 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1105112000914 ligand binding site [chemical binding]; other site 1105112000915 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1105112000916 Predicted permeases [General function prediction only]; Region: COG0795 1105112000917 rod shape-determining protein MreB; Provisional; Region: PRK13927 1105112000918 MreB and similar proteins; Region: MreB_like; cd10225 1105112000919 nucleotide binding site [chemical binding]; other site 1105112000920 Mg binding site [ion binding]; other site 1105112000921 putative protofilament interaction site [polypeptide binding]; other site 1105112000922 RodZ interaction site [polypeptide binding]; other site 1105112000923 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 1105112000924 rod shape-determining protein MreC; Region: MreC; pfam04085 1105112000925 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 1105112000926 sequence-specific DNA binding site [nucleotide binding]; other site 1105112000927 salt bridge; other site 1105112000928 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112000929 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 1105112000930 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 1105112000931 catalytic site [active] 1105112000932 G-X2-G-X-G-K; other site 1105112000933 potential frameshift: common BLAST hit: gi|238650596|ref|YP_002916448.1| ATPase 1105112000934 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1105112000935 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105112000936 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105112000937 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 1105112000938 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 1105112000939 dimer interface [polypeptide binding]; other site 1105112000940 active site 1105112000941 acyl carrier protein; Provisional; Region: acpP; PRK00982 1105112000942 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 1105112000943 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 1105112000944 NAD(P) binding site [chemical binding]; other site 1105112000945 homotetramer interface [polypeptide binding]; other site 1105112000946 homodimer interface [polypeptide binding]; other site 1105112000947 active site 1105112000948 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 1105112000949 RecA/RadA recombinase [DNA replication, recombination, and repair]; Region: RecA; COG0468 1105112000950 hexamer interface [polypeptide binding]; other site 1105112000951 Walker A motif; other site 1105112000952 ATP binding site [chemical binding]; other site 1105112000953 Walker B motif; other site 1105112000954 potential frameshift: common BLAST hit: gi|341584339|ref|YP_004764830.1| putative multidrug resistance protein 1105112000955 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1105112000956 methyl viologen resistance protein SmvA; Provisional; Region: PRK14995 1105112000957 Predicted GTPase [General function prediction only]; Region: ThdF; COG0486 1105112000958 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 1105112000959 trmE is a tRNA modification GTPase; Region: trmE; cd04164 1105112000960 G1 box; other site 1105112000961 GTP/Mg2+ binding site [chemical binding]; other site 1105112000962 Switch I region; other site 1105112000963 G2 box; other site 1105112000964 Switch II region; other site 1105112000965 G3 box; other site 1105112000966 G4 box; other site 1105112000967 G5 box; other site 1105112000968 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 1105112000969 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]; Region: COG2902 1105112000970 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 1105112000971 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 1105112000972 Helix-turn-helix domain; Region: HTH_25; pfam13413 1105112000973 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112000974 Cell division protein ZapA (stimulator of FtsZ polymerization and Z-ring component) [Cell cycle control, cell division, chromosome partitioning]; Region: zapA; COG3027 1105112000975 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 1105112000976 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105112000977 putative substrate translocation pore; other site 1105112000978 Peptidase M55, D-aminopeptidase dipeptide-binding protein family; Region: DAP_dppA; cl01007 1105112000979 aspartate kinase; Reviewed; Region: PRK06635 1105112000980 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 1105112000981 putative nucleotide binding site [chemical binding]; other site 1105112000982 putative catalytic residues [active] 1105112000983 putative Mg ion binding site [ion binding]; other site 1105112000984 putative aspartate binding site [chemical binding]; other site 1105112000985 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 1105112000986 putative allosteric regulatory residue; other site 1105112000987 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 1105112000988 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 1105112000989 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 1105112000990 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 1105112000991 tetramer interfaces [polypeptide binding]; other site 1105112000992 binuclear metal-binding site [ion binding]; other site 1105112000993 twin arginine translocase protein A; Provisional; Region: tatA; PRK01470 1105112000994 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 1105112000995 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 1105112000996 putative ligand binding site [chemical binding]; other site 1105112000997 Predicted methyltransferases [General function prediction only]; Region: COG0313 1105112000998 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 1105112000999 putative SAM binding site [chemical binding]; other site 1105112001000 putative homodimer interface [polypeptide binding]; other site 1105112001001 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105112001002 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 1105112001003 Predicted small secreted protein [Function unknown]; Region: COG5510 1105112001004 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 1105112001005 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1105112001006 minor groove reading motif; other site 1105112001007 helix-hairpin-helix signature motif; other site 1105112001008 substrate binding pocket [chemical binding]; other site 1105112001009 active site 1105112001010 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 1105112001011 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 1105112001012 putative GSH binding site [chemical binding]; other site 1105112001013 catalytic residues [active] 1105112001014 Predicted esterase [General function prediction only]; Region: COG0400 1105112001015 putative hydrolase; Provisional; Region: PRK11460 1105112001016 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 1105112001017 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 1105112001018 dimer interface [polypeptide binding]; other site 1105112001019 active site 1105112001020 glycine-pyridoxal phosphate binding site [chemical binding]; other site 1105112001021 folate binding site [chemical binding]; other site 1105112001022 lipoyl synthase; Provisional; Region: PRK05481 1105112001023 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 1105112001024 FeS/SAM binding site; other site 1105112001025 PemK-like protein; Region: PemK; cl00995 1105112001026 metal-binding heat shock protein; Provisional; Region: PRK00016 1105112001027 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 1105112001028 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 1105112001029 Transporter associated domain; Region: CorC_HlyC; smart01091 1105112001030 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity. They also contain a...; Region: Nudix_Hydrolase_1; cd03674 1105112001031 nudix motif; other site 1105112001032 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105112001033 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 1105112001034 Uncharacterized conserved protein (DUF2048); Region: DUF2048; pfam09752 1105112001035 potential frameshift: common BLAST hit: gi|350273857|ref|YP_004885170.1| acetyl-CoA acetyltransferase 1105112001036 potential frameshift: common BLAST hit: gi|350273857|ref|YP_004885170.1| acetyl-CoA acetyltransferase 1105112001037 potential frameshift: common BLAST hit: gi|350273857|ref|YP_004885170.1| acetyl-CoA acetyltransferase 1105112001038 potential frameshift: common BLAST hit: gi|341584292|ref|YP_004764783.1| superfamily I DNA/RNA helicase 1105112001039 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105112001040 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105112001041 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105112001042 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105112001043 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 1105112001044 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 1105112001045 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 1105112001046 Part of AAA domain; Region: AAA_19; pfam13245 1105112001047 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 1105112001048 UvrD-like helicase C-terminal domain; Region: UvrD_C; pfam13361 1105112001049 Family description; Region: UvrD_C_2; pfam13538 1105112001050 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 1105112001051 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 1105112001052 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 1105112001053 active site 1105112001054 catalytic site [active] 1105112001055 substrate binding site [chemical binding]; other site 1105112001056 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 1105112001057 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 1105112001058 CoA-binding site [chemical binding]; other site 1105112001059 ATP-binding [chemical binding]; other site 1105112001060 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3494 1105112001061 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3814 1105112001062 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 1105112001063 RNA/DNA hybrid binding site [nucleotide binding]; other site 1105112001064 active site 1105112001065 hypothetical protein; Provisional; Region: PRK06630 1105112001066 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 1105112001067 mce related protein; Region: MCE; pfam02470 1105112001068 potential frameshift: common BLAST hit: gi|67458578|ref|YP_246202.1| proline/betaine transporter 1105112001069 potential frameshift: common BLAST hit: gi|67458578|ref|YP_246202.1| proline/betaine transporter 1105112001070 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105112001071 HD domain; Region: HD_4; pfam13328 1105112001072 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105112001073 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 1105112001074 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 1105112001075 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 1105112001076 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 1105112001077 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 1105112001078 nucleotide binding pocket [chemical binding]; other site 1105112001079 K-X-D-G motif; other site 1105112001080 catalytic site [active] 1105112001081 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 1105112001082 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 1105112001083 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 1105112001084 Dimer interface [polypeptide binding]; other site 1105112001085 BRCT sequence motif; other site 1105112001086 potential frameshift: common BLAST hit: gi|238650377|ref|YP_002916229.1| protein involved in external DNA uptake 1105112001087 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1105112001088 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105112001089 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 1105112001090 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 1105112001091 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 1105112001092 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 1105112001093 putative acyl-acceptor binding pocket; other site 1105112001094 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1105112001095 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 1105112001096 catalytic triad [active] 1105112001097 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 1105112001098 IHF dimer interface [polypeptide binding]; other site 1105112001099 IHF - DNA interface [nucleotide binding]; other site 1105112001100 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 1105112001101 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 1105112001102 DNA binding residues [nucleotide binding] 1105112001103 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 1105112001104 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 1105112001105 potential frameshift: common BLAST hit: gi|157964855|ref|YP_001499679.1| guanosine polyphosphate pyrophosphohydrolase/synthetase 1105112001106 potential frameshift: common BLAST hit: gi|157964854|ref|YP_001499678.1| outer membrane protein OmpB 1105112001107 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 1105112001108 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 1105112001109 Domain of unknown function DUF21; Region: DUF21; pfam01595 1105112001110 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 1105112001111 Transporter associated domain; Region: CorC_HlyC; smart01091 1105112001112 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1105112001113 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1105112001114 Walker A/P-loop; other site 1105112001115 ATP binding site [chemical binding]; other site 1105112001116 Q-loop/lid; other site 1105112001117 ABC transporter signature motif; other site 1105112001118 Walker B; other site 1105112001119 D-loop; other site 1105112001120 H-loop/switch region; other site 1105112001121 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 1105112001122 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1105112001123 FtsX-like permease family; Region: FtsX; pfam02687 1105112001124 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 1105112001125 putative substrate translocation pore; other site 1105112001126 Protein of unknown function (DUF2673); Region: DUF2673; pfam10880 1105112001127 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 1105112001128 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105112001129 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105112001130 Walker A/P-loop; other site 1105112001131 ATP binding site [chemical binding]; other site 1105112001132 Q-loop/lid; other site 1105112001133 ABC transporter signature motif; other site 1105112001134 Walker B; other site 1105112001135 D-loop; other site 1105112001136 H-loop/switch region; other site 1105112001137 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 1105112001138 HicB family; Region: HicB; pfam05534 1105112001139 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 1105112001140 Ligand Binding Site [chemical binding]; other site 1105112001141 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 1105112001142 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1105112001143 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 1105112001144 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 1105112001145 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 1105112001146 Walker A motif; other site 1105112001147 ATP binding site [chemical binding]; other site 1105112001148 Walker B motif; other site 1105112001149 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1105112001150 Predicted integral membrane protein (DUF2269); Region: DUF2269; pfam10027 1105112001151 potential frameshift: common BLAST hit: gi|157826924|ref|YP_001495988.1| glycosyltransferase 1105112001152 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 1105112001153 RmuC family; Region: RmuC; pfam02646 1105112001154 potential frameshift: common BLAST hit: gi|67458618|ref|YP_246242.1| ATPase 1105112001155 potential frameshift: common BLAST hit: gi|67458618|ref|YP_246242.1| ATPase 1105112001156 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 1105112001157 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 1105112001158 valyl-tRNA synthetase; Reviewed; Region: valS; PRK13208 1105112001159 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105112001160 active site 1105112001161 HIGH motif; other site 1105112001162 nucleotide binding site [chemical binding]; other site 1105112001163 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1105112001164 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105112001165 active site 1105112001166 KMSKS motif; other site 1105112001167 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 1105112001168 tRNA binding surface [nucleotide binding]; other site 1105112001169 anticodon binding site; other site 1105112001170 potential frameshift: common BLAST hit: gi|350273815|ref|YP_004885128.1| transposase 1105112001171 4-hydroxybenzoate polyprenyltransferase; Reviewed; Region: ubiA; PRK12847 1105112001172 UbiA prenyltransferase family; Region: UbiA; pfam01040 1105112001173 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105112001174 thymidylate kinase; Validated; Region: tmk; PRK00698 1105112001175 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 1105112001176 TMP-binding site; other site 1105112001177 ATP-binding site [chemical binding]; other site 1105112001178 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 1105112001179 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 1105112001180 HIGH motif; other site 1105112001181 active site 1105112001182 KMSKS motif; other site 1105112001183 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 1105112001184 tRNA binding surface [nucleotide binding]; other site 1105112001185 anticodon binding site; other site 1105112001186 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 1105112001187 active site 1105112001188 potential frameshift: common BLAST hit: gi|157964831|ref|YP_001499655.1| Poly-beta-hydroxyalkanoate depolymerase 1105112001189 potential frameshift: common BLAST hit: gi|157964831|ref|YP_001499655.1| Poly-beta-hydroxyalkanoate depolymerase 1105112001190 potential frameshift: common BLAST hit: gi|67458633|ref|YP_246257.1| mannose-1-phosphate guanylyltransferase 1105112001191 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112001192 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105112001193 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 1105112001194 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 1105112001195 DNA binding site [nucleotide binding] 1105112001196 catalytic residue [active] 1105112001197 H2TH interface [polypeptide binding]; other site 1105112001198 putative catalytic residues [active] 1105112001199 turnover-facilitating residue; other site 1105112001200 intercalation triad [nucleotide binding]; other site 1105112001201 8OG recognition residue [nucleotide binding]; other site 1105112001202 putative reading head residues; other site 1105112001203 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 1105112001204 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 1105112001205 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 1105112001206 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 1105112001207 S-adenosylmethionine binding site [chemical binding]; other site 1105112001208 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 1105112001209 ABC1 family; Region: ABC1; pfam03109 1105112001210 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cd05120 1105112001211 active site 1105112001212 ATP binding site [chemical binding]; other site 1105112001213 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 1105112001214 GTP-binding protein Der; Reviewed; Region: PRK00093 1105112001215 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 1105112001216 G1 box; other site 1105112001217 GTP/Mg2+ binding site [chemical binding]; other site 1105112001218 Switch I region; other site 1105112001219 G2 box; other site 1105112001220 Switch II region; other site 1105112001221 G3 box; other site 1105112001222 G4 box; other site 1105112001223 G5 box; other site 1105112001224 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 1105112001225 G1 box; other site 1105112001226 GTP/Mg2+ binding site [chemical binding]; other site 1105112001227 Switch I region; other site 1105112001228 G2 box; other site 1105112001229 G3 box; other site 1105112001230 Switch II region; other site 1105112001231 G4 box; other site 1105112001232 G5 box; other site 1105112001233 Uncharacterized conserved protein [Function unknown]; Region: COG4095 1105112001234 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 1105112001235 putative catalytic site [active] 1105112001236 putative phosphate binding site [ion binding]; other site 1105112001237 active site 1105112001238 metal binding site A [ion binding]; metal-binding site 1105112001239 DNA binding site [nucleotide binding] 1105112001240 putative AP binding site [nucleotide binding]; other site 1105112001241 putative metal binding site B [ion binding]; other site 1105112001242 Exonuclease VII, large subunit [DNA replication, recombination, and repair]; Region: XseA; COG1570 1105112001243 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 1105112001244 generic binding surface II; other site 1105112001245 generic binding surface I; other site 1105112001246 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 1105112001247 Organic solvent tolerance protein; Region: OstA_C; pfam04453 1105112001248 SurA N-terminal domain; Region: SurA_N_3; cl07813 1105112001249 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 1105112001250 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 1105112001251 S-adenosylmethionine binding site [chemical binding]; other site 1105112001252 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 1105112001253 DNA-binding site [nucleotide binding]; DNA binding site 1105112001254 RNA-binding motif; other site 1105112001255 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 1105112001256 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 1105112001257 ATP binding site [chemical binding]; other site 1105112001258 Mg++ binding site [ion binding]; other site 1105112001259 motif III; other site 1105112001260 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 1105112001261 nucleotide binding region [chemical binding]; other site 1105112001262 ATP-binding site [chemical binding]; other site 1105112001263 muropeptide transporter; Reviewed; Region: ampG; PRK11902 1105112001264 muropeptide transporter; Validated; Region: ampG; cl17669 1105112001265 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; smart00932 1105112001266 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 1105112001267 Protease Inhibitor Ecotin; homodimeric protease inhibitor; Region: Ecotin; cl00178 1105112001268 primary substrate binding site; other site 1105112001269 inhibition loop; other site 1105112001270 cell division protein FtsZ; Validated; Region: PRK09330 1105112001271 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 1105112001272 nucleotide binding site [chemical binding]; other site 1105112001273 SulA interaction site; other site 1105112001274 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 1105112001275 putative active site [active] 1105112001276 homotetrameric interface [polypeptide binding]; other site 1105112001277 metal binding site [ion binding]; metal-binding site 1105112001278 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 1105112001279 fumarate hydratase; Reviewed; Region: fumC; PRK00485 1105112001280 Class II fumarases; Region: Fumarase_classII; cd01362 1105112001281 active site 1105112001282 tetramer interface [polypeptide binding]; other site 1105112001283 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 1105112001284 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 1105112001285 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 1105112001286 elongation factor Tu; Reviewed; Region: PRK00049 1105112001287 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 1105112001288 G1 box; other site 1105112001289 GEF interaction site [polypeptide binding]; other site 1105112001290 GTP/Mg2+ binding site [chemical binding]; other site 1105112001291 Switch I region; other site 1105112001292 G2 box; other site 1105112001293 G3 box; other site 1105112001294 Switch II region; other site 1105112001295 G4 box; other site 1105112001296 G5 box; other site 1105112001297 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 1105112001298 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 1105112001299 Antibiotic Binding Site [chemical binding]; other site 1105112001300 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 1105112001301 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 1105112001302 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 1105112001303 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 1105112001304 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 1105112001305 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 1105112001306 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 1105112001307 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 1105112001308 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 1105112001309 putative translocon binding site; other site 1105112001310 protein-rRNA interface [nucleotide binding]; other site 1105112001311 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 1105112001312 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 1105112001313 G-X-X-G motif; other site 1105112001314 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 1105112001315 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 1105112001316 23S rRNA interface [nucleotide binding]; other site 1105112001317 5S rRNA interface [nucleotide binding]; other site 1105112001318 putative antibiotic binding site [chemical binding]; other site 1105112001319 L25 interface [polypeptide binding]; other site 1105112001320 L27 interface [polypeptide binding]; other site 1105112001321 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 1105112001322 L23 interface [polypeptide binding]; other site 1105112001323 trigger factor interaction site; other site 1105112001324 23S rRNA interface [nucleotide binding]; other site 1105112001325 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 1105112001326 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 1105112001327 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 1105112001328 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 1105112001329 RNA binding site [nucleotide binding]; other site 1105112001330 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 1105112001331 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 1105112001332 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 1105112001333 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 1105112001334 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 1105112001335 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 1105112001336 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1105112001337 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1105112001338 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 1105112001339 5S rRNA interface [nucleotide binding]; other site 1105112001340 23S rRNA interface [nucleotide binding]; other site 1105112001341 L5 interface [polypeptide binding]; other site 1105112001342 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 1105112001343 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 1105112001344 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 1105112001345 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 1105112001346 23S rRNA binding site [nucleotide binding]; other site 1105112001347 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 1105112001348 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 1105112001349 SecY translocase; Region: SecY; pfam00344 1105112001350 adenylate kinase; Reviewed; Region: adk; PRK00279 1105112001351 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 1105112001352 AMP-binding site [chemical binding]; other site 1105112001353 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 1105112001354 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 1105112001355 30S ribosomal protein S13; Region: bact_S13; TIGR03631 1105112001356 30S ribosomal protein S11; Validated; Region: PRK05309 1105112001357 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 1105112001358 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 1105112001359 alphaNTD - beta interaction site [polypeptide binding]; other site 1105112001360 alphaNTD homodimer interface [polypeptide binding]; other site 1105112001361 alphaNTD - beta' interaction site [polypeptide binding]; other site 1105112001362 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 1105112001363 Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]; Region: RplQ; COG0203 1105112001364 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 1105112001365 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105112001366 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105112001367 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 1105112001368 hypothetical protein; Validated; Region: PRK06620 1105112001369 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 1105112001370 Domain of unknown function DUF20; Region: UPF0118; pfam01594 1105112001371 GrpE; Region: GrpE; pfam01025 1105112001372 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 1105112001373 dimer interface [polypeptide binding]; other site 1105112001374 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 1105112001375 ribonuclease PH; Reviewed; Region: rph; PRK00173 1105112001376 Ribonuclease PH; Region: RNase_PH_bact; cd11362 1105112001377 hexamer interface [polypeptide binding]; other site 1105112001378 active site 1105112001379 potential frameshift: common BLAST hit: gi|67458799|ref|YP_246423.1| glycosyltransferase 1105112001380 potential frameshift: common BLAST hit: gi|67458799|ref|YP_246423.1| glycosyltransferase 1105112001381 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 1105112001382 oligomerisation interface [polypeptide binding]; other site 1105112001383 mobile loop; other site 1105112001384 roof hairpin; other site 1105112001385 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 1105112001386 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 1105112001387 ring oligomerisation interface [polypeptide binding]; other site 1105112001388 ATP/Mg binding site [chemical binding]; other site 1105112001389 stacking interactions; other site 1105112001390 hinge regions; other site 1105112001391 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105112001392 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 1105112001393 synthetase active site [active] 1105112001394 NTP binding site [chemical binding]; other site 1105112001395 metal binding site [ion binding]; metal-binding site 1105112001396 potential frameshift: common BLAST hit: gi|157964772|ref|YP_001499596.1| guanosine polyphosphate pyrophosphohydrolase/synthetase 1105112001397 potential frameshift: common BLAST hit: gi|157828820|ref|YP_001495062.1| chaperonin GroEL 1105112001398 Invasion protein B, involved in pathogenesis [General function prediction only]; Region: COG5342 1105112001399 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 1105112001400 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105112001401 HIGH motif; other site 1105112001402 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105112001403 active site 1105112001404 KMSKS motif; other site 1105112001405 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112001406 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 1105112001407 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112001408 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 1105112001409 S-adenosylmethionine binding site [chemical binding]; other site 1105112001410 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 1105112001411 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 1105112001412 dimer interface [polypeptide binding]; other site 1105112001413 putative PBP binding regions; other site 1105112001414 ABC-ATPase subunit interface; other site 1105112001415 TfoX N-terminal domain; Region: TfoX_N; cl17592 1105112001416 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 1105112001417 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 1105112001418 putative substrate translocation pore; other site 1105112001419 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1105112001420 putative acyl-acceptor binding pocket; other site 1105112001421 C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas); Region: AAS_C; cd05909 1105112001422 acyl-activating enzyme (AAE) consensus motif; other site 1105112001423 putative AMP binding site [chemical binding]; other site 1105112001424 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 1105112001425 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 1105112001426 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 1105112001427 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 1105112001428 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1105112001429 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 1105112001430 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 1105112001431 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 1105112001432 carboxyltransferase (CT) interaction site; other site 1105112001433 biotinylation site [posttranslational modification]; other site 1105112001434 TPR repeat; Region: TPR_11; pfam13414 1105112001435 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 1105112001436 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1105112001437 HIGH motif; other site 1105112001438 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1105112001439 active site 1105112001440 KMSKS motif; other site 1105112001441 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 1105112001442 tRNA binding surface [nucleotide binding]; other site 1105112001443 anticodon binding site; other site 1105112001444 Uncharacterized conserved protein [Function unknown]; Region: COG5590 1105112001445 COQ9; Region: COQ9; pfam08511 1105112001446 Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]; Region: RpsU; COG0828 1105112001447 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 1105112001448 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 1105112001449 dimerization interface [polypeptide binding]; other site 1105112001450 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 1105112001451 dimer interface [polypeptide binding]; other site 1105112001452 phosphorylation site [posttranslational modification] 1105112001453 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 1105112001454 ATP binding site [chemical binding]; other site 1105112001455 Mg2+ binding site [ion binding]; other site 1105112001456 G-X-G motif; other site 1105112001457 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cl17270 1105112001458 potential frameshift: common BLAST hit: gi|15892870|ref|NP_360584.1| aminoglycoside 3-N-acetyltransferase 1105112001459 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 1105112001460 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 1105112001461 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 1105112001462 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 1105112001463 uncharacterized subgroup of the Escherichia coli Mg2+ transporter CorA_like subfamily; Region: EcCorA-like_u1; cd12837 1105112001464 Cl binding site [ion binding]; other site 1105112001465 oligomer interface [polypeptide binding]; other site 1105112001466 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105112001467 ribonuclease P; Reviewed; Region: rnpA; PRK01492 1105112001468 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 1105112001469 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 1105112001470 23S rRNA binding site [nucleotide binding]; other site 1105112001471 L21 binding site [polypeptide binding]; other site 1105112001472 L13 binding site [polypeptide binding]; other site 1105112001473 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 1105112001474 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 1105112001475 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 1105112001476 FeS/SAM binding site; other site 1105112001477 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 1105112001478 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 1105112001479 5S rRNA interface [nucleotide binding]; other site 1105112001480 CTC domain interface [polypeptide binding]; other site 1105112001481 L16 interface [polypeptide binding]; other site 1105112001482 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 1105112001483 putative active site [active] 1105112001484 catalytic residue [active] 1105112001485 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1105112001486 GTP-binding protein YchF; Reviewed; Region: PRK09601 1105112001487 YchF GTPase; Region: YchF; cd01900 1105112001488 G1 box; other site 1105112001489 GTP/Mg2+ binding site [chemical binding]; other site 1105112001490 Switch I region; other site 1105112001491 G2 box; other site 1105112001492 Switch II region; other site 1105112001493 G3 box; other site 1105112001494 G4 box; other site 1105112001495 G5 box; other site 1105112001496 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 1105112001497 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 1105112001498 metal binding triad [ion binding]; metal-binding site 1105112001499 HEPN domain; Region: HEPN; cl00824 1105112001500 potential frameshift: common BLAST hit: gi|350273736|ref|YP_004885049.1| bicyclomycin resistance protein 1105112001501 potential frameshift: common BLAST hit: gi|350273736|ref|YP_004885049.1| bicyclomycin resistance protein 1105112001502 Patatin [General function prediction only]; Region: COG3621 1105112001503 Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17; Region: Pat17_PNPLA8_PNPLA9_like; cd07199 1105112001504 active site 1105112001505 nucleophile elbow; other site 1105112001506 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 1105112001507 DnaA N-terminal domain; Region: DnaA_N; pfam11638 1105112001508 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 1105112001509 Walker A motif; other site 1105112001510 ATP binding site [chemical binding]; other site 1105112001511 Walker B motif; other site 1105112001512 arginine finger; other site 1105112001513 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 1105112001514 DnaA box-binding interface [nucleotide binding]; other site 1105112001515 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 1105112001516 active site residue [active] 1105112001517 Uncharacterized conserved protein [Function unknown]; Region: COG2938 1105112001518 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 1105112001519 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 1105112001520 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 1105112001521 ATP binding site [chemical binding]; other site 1105112001522 putative Mg++ binding site [ion binding]; other site 1105112001523 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 1105112001524 nucleotide binding region [chemical binding]; other site 1105112001525 ATP-binding site [chemical binding]; other site 1105112001526 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 1105112001527 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 1105112001528 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105112001529 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105112001530 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105112001531 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105112001532 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 1105112001533 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105112001534 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105112001535 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 1105112001536 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 1105112001537 Mg++ binding site [ion binding]; other site 1105112001538 putative catalytic motif [active] 1105112001539 putative substrate binding site [chemical binding]; other site 1105112001540 V-type ATP synthase subunit I; Validated; Region: PRK05771 1105112001541 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 1105112001542 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 1105112001543 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 1105112001544 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 1105112001545 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 1105112001546 ssDNA binding site; other site 1105112001547 generic binding surface II; other site 1105112001548 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 1105112001549 ATP binding site [chemical binding]; other site 1105112001550 putative Mg++ binding site [ion binding]; other site 1105112001551 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 1105112001552 nucleotide binding region [chemical binding]; other site 1105112001553 ATP-binding site [chemical binding]; other site 1105112001554 TraX protein; Region: TraX; pfam05857 1105112001555 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112001556 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 1105112001557 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 1105112001558 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 1105112001559 dimer interface [polypeptide binding]; other site 1105112001560 substrate binding site [chemical binding]; other site 1105112001561 metal binding sites [ion binding]; metal-binding site 1105112001562 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 1105112001563 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 1105112001564 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 1105112001565 Cu(I) binding site [ion binding]; other site 1105112001566 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 1105112001567 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 1105112001568 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 1105112001569 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105112001570 Predicted DNA-binding protein with an HTH domain [General function prediction only]; Region: COG4710 1105112001571 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105112001572 HD domain; Region: HD_4; pfam13328 1105112001573 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 1105112001574 MgtE intracellular N domain; Region: MgtE_N; pfam03448 1105112001575 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 1105112001576 Divalent cation transporter; Region: MgtE; pfam01769 1105112001577 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 1105112001578 Haloacid dehalogenase-like hydrolase; Region: Hydrolase_6; pfam13344 1105112001579 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 1105112001580 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 1105112001581 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 1105112001582 ATP binding site [chemical binding]; other site 1105112001583 Mg2+ binding site [ion binding]; other site 1105112001584 G-X-G motif; other site 1105112001585 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 1105112001586 anchoring element; other site 1105112001587 dimer interface [polypeptide binding]; other site 1105112001588 ATP binding site [chemical binding]; other site 1105112001589 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 1105112001590 active site 1105112001591 putative metal-binding site [ion binding]; other site 1105112001592 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1105112001593 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 1105112001594 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 1105112001595 hinge; other site 1105112001596 active site 1105112001597 DNA-directed RNA polymerase, omega subunit; Region: rpoZ; TIGR00690 1105112001598 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 1105112001599 peptidylprolyl isomerase; Reviewed; Region: prsA; PRK03095 1105112001600 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 1105112001601 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 1105112001602 DEAD/DEAH box helicase; Region: DEAD; pfam00270 1105112001603 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 1105112001604 SEC-C motif; Region: SEC-C; pfam02810 1105112001605 potential frameshift: common BLAST hit: gi|67459332|ref|YP_246956.1| nucleotidyltransferase/HEPN domain-containing protein 1105112001606 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cl02529 1105112001607 potential frameshift: common BLAST hit: gi|91205221|ref|YP_537576.1| Type I restriction-modification system, M subunit 1105112001608 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 1105112001609 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 1105112001610 DNA binding site [nucleotide binding] 1105112001611 active site 1105112001612 A new structural DNA glycosylase; Region: AlkD_like; cd06561 1105112001613 DNA alkylation repair enzyme; Region: DNA_alkylation; pfam08713 1105112001614 active site 1105112001615 Copper(I)-binding protein [Inorganic ion transport and metabolism]; Region: COG2847 1105112001616 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 1105112001617 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 1105112001618 GIY-YIG motif/motif A; other site 1105112001619 active site 1105112001620 catalytic site [active] 1105112001621 putative DNA binding site [nucleotide binding]; other site 1105112001622 metal binding site [ion binding]; metal-binding site 1105112001623 UvrB/uvrC motif; Region: UVR; pfam02151 1105112001624 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 1105112001625 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 1105112001626 Na binding site [ion binding]; other site 1105112001627 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 1105112001628 MraZ protein; Region: MraZ; pfam02381 1105112001629 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 1105112001630 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 1105112001631 S-adenosylmethionine binding site [chemical binding]; other site 1105112001632 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 1105112001633 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 1105112001634 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1105112001635 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1105112001636 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 1105112001637 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1105112001638 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1105112001639 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 1105112001640 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 1105112001641 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105112001642 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1105112001643 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 1105112001644 active site 1105112001645 phosphorylation site [posttranslational modification] 1105112001646 intermolecular recognition site; other site 1105112001647 dimerization interface [polypeptide binding]; other site 1105112001648 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 1105112001649 Walker A motif; other site 1105112001650 ATP binding site [chemical binding]; other site 1105112001651 Walker B motif; other site 1105112001652 arginine finger; other site 1105112001653 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1105112001654 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK12612 1105112001655 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112001656 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK06617 1105112001657 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 1105112001658 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105112001659 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105112001660 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105112001661 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105112001662 Alpha-2-macroglobulin family N-terminal region; Region: A2M_N_2; pfam07703 1105112001663 Alpha-2-macroglobulin family; Region: A2M; pfam00207 1105112001664 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 1105112001665 surface patch; other site 1105112001666 thioester region; other site 1105112001667 specificity defining residues; other site 1105112001668 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 1105112001669 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 1105112001670 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 1105112001671 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 1105112001672 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 1105112001673 active site 1105112001674 HIGH motif; other site 1105112001675 dimer interface [polypeptide binding]; other site 1105112001676 KMSKS motif; other site 1105112001677 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 1105112001678 RNA binding surface [nucleotide binding]; other site 1105112001679 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 1105112001680 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 1105112001681 RNA binding surface [nucleotide binding]; other site 1105112001682 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 1105112001683 Transcriptional regulator; Region: Rrf2; cl17282 1105112001684 Rrf2 family protein; Region: rrf2_super; TIGR00738 1105112001685 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG0779 1105112001686 Sm and related proteins; Region: Sm_like; cl00259 1105112001687 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 1105112001688 putative oligomer interface [polypeptide binding]; other site 1105112001689 putative RNA binding site [nucleotide binding]; other site 1105112001690 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 1105112001691 NusA N-terminal domain; Region: NusA_N; pfam08529 1105112001692 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 1105112001693 RNA binding site [nucleotide binding]; other site 1105112001694 homodimer interface [polypeptide binding]; other site 1105112001695 NusA-like KH domain; Region: KH_5; pfam13184 1105112001696 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 1105112001697 G-X-X-G motif; other site 1105112001698 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 1105112001699 translation initiation factor IF-2; Validated; Region: infB; PRK05306 1105112001700 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 1105112001701 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 1105112001702 G1 box; other site 1105112001703 putative GEF interaction site [polypeptide binding]; other site 1105112001704 GTP/Mg2+ binding site [chemical binding]; other site 1105112001705 Switch I region; other site 1105112001706 G2 box; other site 1105112001707 G3 box; other site 1105112001708 Switch II region; other site 1105112001709 G4 box; other site 1105112001710 G5 box; other site 1105112001711 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 1105112001712 Translation-initiation factor 2; Region: IF-2; pfam11987 1105112001713 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 1105112001714 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214 1105112001715 Glycoprotease family; Region: Peptidase_M22; pfam00814 1105112001716 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 1105112001717 Recombination protein O N terminal; Region: RecO_N; pfam11967 1105112001718 Recombination protein O C terminal; Region: RecO_C; pfam02565 1105112001719 DNA repair protein RadA; Provisional; Region: PRK11823 1105112001720 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 1105112001721 Walker A motif/ATP binding site; other site 1105112001722 ATP binding site [chemical binding]; other site 1105112001723 Walker B motif; other site 1105112001724 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 1105112001725 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 1105112001726 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 1105112001727 S-adenosylmethionine binding site [chemical binding]; other site 1105112001728 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105112001729 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105112001730 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 1105112001731 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105112001732 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 1105112001733 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 1105112001734 RNA binding surface [nucleotide binding]; other site 1105112001735 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 1105112001736 active site 1105112001737 potential frameshift: common BLAST hit: gi|67459254|ref|YP_246878.1| to amino acid permeases 1105112001738 replicative DNA helicase; Provisional; Region: PRK09165 1105112001739 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 1105112001740 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 1105112001741 Walker A motif; other site 1105112001742 ATP binding site [chemical binding]; other site 1105112001743 Walker B motif; other site 1105112001744 DNA binding loops [nucleotide binding] 1105112001745 polyprenyl P-hydroxybenzoate and phenylacrylic acid decarboxylases; Region: ubiX_pad; TIGR00421 1105112001746 Flavoprotein; Region: Flavoprotein; pfam02441 1105112001747 primosome assembly protein PriA; Validated; Region: PRK05580 1105112001748 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 1105112001749 ATP binding site [chemical binding]; other site 1105112001750 putative Mg++ binding site [ion binding]; other site 1105112001751 helicase superfamily c-terminal domain; Region: HELICc; smart00490 1105112001752 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 1105112001753 dimer interface [polypeptide binding]; other site 1105112001754 allosteric magnesium binding site [ion binding]; other site 1105112001755 active site 1105112001756 aspartate-rich active site metal binding site; other site 1105112001757 Schiff base residues; other site 1105112001758 NADH dehydrogenase subunit 2; Provisional; Region: ND2; MTH00196 1105112001759 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105112001760 potential frameshift: common BLAST hit: gi|67458839|ref|YP_246463.1| NACHT domain-containing protein 1105112001761 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 1105112001762 Predicted transcriptional regulator [Transcription]; Region: COG1959 1105112001763 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 1105112001764 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 1105112001765 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 1105112001766 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1105112001767 catalytic residue [active] 1105112001768 cysteine desulfurase; Provisional; Region: PRK14012 1105112001769 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 1105112001770 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1105112001771 catalytic residue [active] 1105112001772 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 1105112001773 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 1105112001774 trimerization site [polypeptide binding]; other site 1105112001775 active site 1105112001776 Iron-sulfur cluster assembly accessory protein; Region: TIGR00049 1105112001777 arginine:agmatin antiporter; Provisional; Region: PRK10644 1105112001778 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 1105112001779 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 1105112001780 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112001781 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 1105112001782 active site 1105112001783 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 1105112001784 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 1105112001785 substrate binding pocket [chemical binding]; other site 1105112001786 chain length determination region; other site 1105112001787 substrate-Mg2+ binding site; other site 1105112001788 catalytic residues [active] 1105112001789 aspartate-rich region 1; other site 1105112001790 active site lid residues [active] 1105112001791 aspartate-rich region 2; other site 1105112001792 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105112001793 potential frameshift: common BLAST hit: gi|67459228|ref|YP_246852.1| lipopolysaccharide 1,2-glucosyltransferase RfaJ 1105112001794 AmpG-like permease; Region: 2A0125; TIGR00901 1105112001795 Lysine efflux permease [General function prediction only]; Region: COG1279 1105112001796 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 1105112001797 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 1105112001798 active site 1105112001799 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 1105112001800 HemY protein N-terminus; Region: HemY_N; pfam07219 1105112001801 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 1105112001802 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105112001803 RelB antitoxin; Region: RelB; cl01171 1105112001804 Protein required for attachment to host cells [Cell motility and secretion]; Region: COG5622 1105112001805 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1105112001806 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1105112001807 putative acyl-acceptor binding pocket; other site 1105112001808 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 1105112001809 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 1105112001810 active site 1105112001811 HIGH motif; other site 1105112001812 dimer interface [polypeptide binding]; other site 1105112001813 KMSKS motif; other site 1105112001814 Protein of unknown function (DUF497); Region: DUF497; pfam04365 1105112001815 potential frameshift: common BLAST hit: gi|91205198|ref|YP_537553.1| ATPase AAA 1105112001816 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 1105112001817 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 1105112001818 domain interfaces; other site 1105112001819 active site 1105112001820 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 1105112001821 dimer interface [polypeptide binding]; other site 1105112001822 catalytic triad [active] 1105112001823 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 1105112001824 ATP binding site [chemical binding]; other site 1105112001825 G-X-G motif; other site 1105112001826 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 1105112001827 dimer interface [polypeptide binding]; other site 1105112001828 phosphorylation site [posttranslational modification] 1105112001829 potential frameshift: common BLAST hit: gi|15604329|ref|NP_220845.1| alkaline phosphatase synthesis sensor protein PhoR 1105112001830 potential frameshift: common BLAST hit: gi|157964645|ref|YP_001499469.1| ankyrin repeat-containing protein 1105112001831 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 1105112001832 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 1105112001833 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 1105112001834 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 1105112001835 Uncharacterized conserved protein [Function unknown]; Region: COG1723 1105112001836 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 1105112001837 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 1105112001838 catalytic site [active] 1105112001839 putative active site [active] 1105112001840 putative substrate binding site [chemical binding]; other site 1105112001841 Helicase and RNase D C-terminal; Region: HRDC; smart00341 1105112001842 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 1105112001843 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 1105112001844 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 1105112001845 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 1105112001846 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105112001847 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1105112001848 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 1105112001849 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 1105112001850 S-adenosylmethionine binding site [chemical binding]; other site 1105112001851 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 1105112001852 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; pfam12762 1105112001853 Protein of unknown function (DUF2532); Region: DUF2532; pfam10811 1105112001854 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1105112001855 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 1105112001856 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1105112001857 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 1105112001858 hypothetical protein; Validated; Region: PRK00110 1105112001859 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 1105112001860 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 1105112001861 Substrate binding site; other site 1105112001862 Mg++ binding site; other site 1105112001863 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 1105112001864 putative CoA binding site [chemical binding]; other site 1105112001865 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 1105112001866 putative CoA binding site [chemical binding]; other site 1105112001867 TPR repeat; Region: TPR_11; pfam13414 1105112001868 Tetratricopeptide repeat; Region: TPR_1; pfam00515 1105112001869 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105112001870 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105112001871 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105112001872 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 1105112001873 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1105112001874 Coenzyme A binding pocket [chemical binding]; other site 1105112001875 Predicted acetyltransferase [General function prediction only]; Region: COG5628 1105112001876 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 1105112001877 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 1105112001878 homotetramer interface [polypeptide binding]; other site 1105112001879 FMN binding site [chemical binding]; other site 1105112001880 homodimer contacts [polypeptide binding]; other site 1105112001881 putative active site [active] 1105112001882 putative substrate binding site [chemical binding]; other site 1105112001883 Acetyltransferase (GNAT) domain; Region: Acetyltransf_8; pfam13523 1105112001884 Phosphotransferase enzyme family; Region: APH; pfam01636 1105112001885 Aminoglycoside/hydroxyurea antibiotic resistance kinase; Region: APH_6_hur; cl17810 1105112001886 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 1105112001887 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 1105112001888 oligomer interface [polypeptide binding]; other site 1105112001889 active site residues [active] 1105112001890 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 1105112001891 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 1105112001892 RNA binding site [nucleotide binding]; other site 1105112001893 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 1105112001894 RNA binding site [nucleotide binding]; other site 1105112001895 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 1105112001896 RNA binding site [nucleotide binding]; other site 1105112001897 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 1105112001898 RNA binding site [nucleotide binding]; other site 1105112001899 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 1105112001900 RNA binding site [nucleotide binding]; other site 1105112001901 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 1105112001902 RNA binding site [nucleotide binding]; other site 1105112001903 Cytidylate kinase [Nucleotide transport and metabolism]; Region: Cmk; COG0283 1105112001904 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 1105112001905 CMP-binding site; other site 1105112001906 The sites determining sugar specificity; other site 1105112001907 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 1105112001908 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1105112001909 sequence-specific DNA binding site [nucleotide binding]; other site 1105112001910 salt bridge; other site 1105112001911 Protein of unknown function (DUF328); Region: DUF328; cl01143 1105112001912 Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]; Region: HimA; COG0776 1105112001913 IHF - DNA interface [nucleotide binding]; other site 1105112001914 IHF dimer interface [polypeptide binding]; other site 1105112001915 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 1105112001916 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1105112001917 tandem repeat interface [polypeptide binding]; other site 1105112001918 oligomer interface [polypeptide binding]; other site 1105112001919 active site residues [active] 1105112001920 transcription termination factor Rho; Provisional; Region: rho; PRK09376 1105112001921 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 1105112001922 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 1105112001923 RNA binding site [nucleotide binding]; other site 1105112001924 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 1105112001925 multimer interface [polypeptide binding]; other site 1105112001926 Walker A motif; other site 1105112001927 ATP binding site [chemical binding]; other site 1105112001928 Walker B motif; other site 1105112001929 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 1105112001930 S-adenosylmethionine binding site [chemical binding]; other site 1105112001931 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105112001932 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 1105112001933 DHH family; Region: DHH; pfam01368 1105112001934 DHHA1 domain; Region: DHHA1; pfam02272 1105112001935 peptide chain release factor 1; Validated; Region: prfA; PRK00591 1105112001936 This domain is found in peptide chain release factors; Region: PCRF; smart00937 1105112001937 RF-1 domain; Region: RF-1; pfam00472 1105112001938 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 1105112001939 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 1105112001940 E3 interaction surface; other site 1105112001941 lipoyl attachment site [posttranslational modification]; other site 1105112001942 e3 binding domain; Region: E3_binding; pfam02817 1105112001943 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 1105112001944 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 1105112001945 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 1105112001946 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 1105112001947 Predicted membrane protein [Function unknown]; Region: COG5346 1105112001948 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 1105112001949 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; pfam08780 1105112001950 potential frameshift: common BLAST hit: gi|67459142|ref|YP_246766.1| HK97 family phage prohead protease/phage major capsid protein 1105112001951 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 1105112001952 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 1105112001953 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 1105112001954 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 1105112001955 ExoU and VipD-like proteins; homologus to patatin, cPLA2, and iPLA2; Region: Pat_ExoU_VipD_like; cd07207 1105112001956 active site 1105112001957 nucleophile elbow; other site 1105112001958 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 1105112001959 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 1105112001960 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 1105112001961 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 1105112001962 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 1105112001963 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP); Region: GATase1_ScBLP_like; cd03144 1105112001964 conserved cys residue [active] 1105112001965 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 1105112001966 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 1105112001967 GSH binding site (G-site) [chemical binding]; other site 1105112001968 C-terminal domain interface [polypeptide binding]; other site 1105112001969 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 1105112001970 N-terminal domain interface [polypeptide binding]; other site 1105112001971 dimer interface [polypeptide binding]; other site 1105112001972 substrate binding pocket (H-site) [chemical binding]; other site 1105112001973 pyruvate phosphate dikinase; Provisional; Region: PRK09279 1105112001974 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 1105112001975 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 1105112001976 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 1105112001977 hypothetical protein; Provisional; Region: PRK06661 1105112001978 intersubunit interface [polypeptide binding]; other site 1105112001979 active site 1105112001980 Zn2+ binding site [ion binding]; other site 1105112001981 potential frameshift: common BLAST hit: gi|67459124|ref|YP_246748.1| toxin of toxin-antitoxin system 1105112001982 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 1105112001983 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112001984 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 1105112001985 active site 1105112001986 catalytic residues [active] 1105112001987 metal binding site [ion binding]; metal-binding site 1105112001988 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 1105112001989 uncharacterized protein, YfiH family; Region: TIGR00726 1105112001990 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 1105112001991 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1105112001992 Ribonuclease BN family enzyme [Replication, recombination, and repair]; Region: Rbn; COG1295 1105112001993 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1105112001994 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 1105112001995 non-specific DNA binding site [nucleotide binding]; other site 1105112001996 salt bridge; other site 1105112001997 sequence-specific DNA binding site [nucleotide binding]; other site 1105112001998 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 1105112001999 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105112002000 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK14846 1105112002001 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 1105112002002 RNA binding site [nucleotide binding]; other site 1105112002003 active site 1105112002004 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112002005 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 1105112002006 16S/18S rRNA binding site [nucleotide binding]; other site 1105112002007 S13e-L30e interaction site [polypeptide binding]; other site 1105112002008 25S rRNA binding site [nucleotide binding]; other site 1105112002009 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 1105112002010 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 1105112002011 RNase E interface [polypeptide binding]; other site 1105112002012 trimer interface [polypeptide binding]; other site 1105112002013 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 1105112002014 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 1105112002015 RNase E interface [polypeptide binding]; other site 1105112002016 trimer interface [polypeptide binding]; other site 1105112002017 active site 1105112002018 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 1105112002019 putative nucleic acid binding region [nucleotide binding]; other site 1105112002020 G-X-X-G motif; other site 1105112002021 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 1105112002022 RNA binding site [nucleotide binding]; other site 1105112002023 domain interface; other site 1105112002024 KpsF/GutQ family protein; Region: kpsF; TIGR00393 1105112002025 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 1105112002026 putative active site [active] 1105112002027 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 1105112002028 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 1105112002029 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112002030 OstA-like protein; Region: OstA; cl00844 1105112002031 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 1105112002032 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 1105112002033 Walker A/P-loop; other site 1105112002034 ATP binding site [chemical binding]; other site 1105112002035 Q-loop/lid; other site 1105112002036 ABC transporter signature motif; other site 1105112002037 Walker B; other site 1105112002038 D-loop; other site 1105112002039 H-loop/switch region; other site 1105112002040 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 1105112002041 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 1105112002042 active site 1105112002043 substrate binding site [chemical binding]; other site 1105112002044 metal binding site [ion binding]; metal-binding site 1105112002045 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 1105112002046 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 1105112002047 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 1105112002048 dimer interface [polypeptide binding]; other site 1105112002049 diiron center [ion binding]; other site 1105112002050 putative radical transfer pathway; other site 1105112002051 tyrosyl radical; other site 1105112002052 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 1105112002053 Class I ribonucleotide reductase; Region: RNR_I; cd01679 1105112002054 active site 1105112002055 dimer interface [polypeptide binding]; other site 1105112002056 catalytic residues [active] 1105112002057 effector binding site; other site 1105112002058 R2 peptide binding site; other site 1105112002059 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 1105112002060 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 1105112002061 Chitin binding domain; Region: Chitin_bind_3; cl03871 1105112002062 Spore Coat Protein U domain; Region: SCPU; cl02253 1105112002063 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 1105112002064 potential frameshift: common BLAST hit: gi|157827080|ref|YP_001496144.1| P pilus assembly, fimbrial usher protein 1105112002065 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 1105112002066 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 1105112002067 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 1105112002068 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1105112002069 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105112002070 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14171 1105112002071 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 1105112002072 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 1105112002073 homodimer interface [polypeptide binding]; other site 1105112002074 NADP binding site [chemical binding]; other site 1105112002075 substrate binding site [chemical binding]; other site 1105112002076 potential frameshift: common BLAST hit: gi|229586740|ref|YP_002845241.1| Carbonic anhydrases/acetyltransferase, isoleucine patch superfamily 1105112002077 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 1105112002078 30S subunit binding site; other site 1105112002079 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 1105112002080 Found in ATP-dependent protease La (LON); Region: LON; smart00464 1105112002081 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 1105112002082 Walker A motif; other site 1105112002083 ATP binding site [chemical binding]; other site 1105112002084 Walker B motif; other site 1105112002085 arginine finger; other site 1105112002086 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 1105112002087 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 1105112002088 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 1105112002089 tetramer interface [polypeptide binding]; other site 1105112002090 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105112002091 catalytic residue [active] 1105112002092 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 1105112002093 Part of AAA domain; Region: AAA_19; pfam13245 1105112002094 Family description; Region: UvrD_C_2; pfam13538 1105112002095 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105112002096 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 1105112002097 active site 1105112002098 potential frameshift: common BLAST hit: gi|165933216|ref|YP_001650005.1| succinate-semialdehyde dehydrogenase (NADP+) 1105112002099 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 1105112002100 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1105112002101 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105112002102 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1105112002103 Predicted permeases [General function prediction only]; Region: COG0679 1105112002104 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 1105112002105 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 1105112002106 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 1105112002107 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 1105112002108 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1105112002109 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 1105112002110 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 1105112002111 Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]; Region: RecR; COG0353 1105112002112 RecR protein; Region: RecR; pfam02132 1105112002113 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 1105112002114 putative active site [active] 1105112002115 putative metal-binding site [ion binding]; other site 1105112002116 tetramer interface [polypeptide binding]; other site 1105112002117 Predicted membrane protein/domain [Function unknown]; Region: COG1714 1105112002118 Predicted membrane protein [Function unknown]; Region: COG1238 1105112002119 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 1105112002120 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4395 1105112002121 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 1105112002122 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105112002123 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 1105112002124 potential frameshift: common BLAST hit: gi|229586712|ref|YP_002845213.1| Putative nucleic-acid-binding protein, containing PIN domain 1105112002125 potential frameshift: common BLAST hit: gi|229586712|ref|YP_002845213.1| Putative nucleic-acid-binding protein, containing PIN domain 1105112002126 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 1105112002127 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 1105112002128 CoA-ligase; Region: Ligase_CoA; pfam00549 1105112002129 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 1105112002130 CoA binding domain; Region: CoA_binding; pfam02629 1105112002131 CoA-ligase; Region: Ligase_CoA; pfam00549 1105112002132 DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC...; Region: DsbA_Com1_like; cd03023 1105112002133 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 1105112002134 catalytic residues [active] 1105112002135 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 1105112002136 SmpB-tmRNA interface; other site 1105112002137 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 1105112002138 dihydrodipicolinate synthase; Region: dapA; TIGR00674 1105112002139 dimer interface [polypeptide binding]; other site 1105112002140 active site 1105112002141 catalytic residue [active] 1105112002142 branched-chain amino acid aminotransferase; Validated; Region: PRK06606 1105112002143 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 1105112002144 homodimer interface [polypeptide binding]; other site 1105112002145 substrate-cofactor binding pocket; other site 1105112002146 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105112002147 catalytic residue [active] 1105112002148 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105112002149 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 1105112002150 active site 1105112002151 phosphorylation site [posttranslational modification] 1105112002152 intermolecular recognition site; other site 1105112002153 dimerization interface [polypeptide binding]; other site 1105112002154 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 1105112002155 DNA binding site [nucleotide binding] 1105112002156 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105112002157 HAMP domain; Region: HAMP; pfam00672 1105112002158 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 1105112002159 dimer interface [polypeptide binding]; other site 1105112002160 phosphorylation site [posttranslational modification] 1105112002161 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 1105112002162 ATP binding site [chemical binding]; other site 1105112002163 Mg2+ binding site [ion binding]; other site 1105112002164 G-X-G motif; other site 1105112002165 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 1105112002166 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 1105112002167 catalytic residue [active] 1105112002168 putative FPP diphosphate binding site; other site 1105112002169 putative FPP binding hydrophobic cleft; other site 1105112002170 dimer interface [polypeptide binding]; other site 1105112002171 putative IPP diphosphate binding site; other site 1105112002172 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 1105112002173 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 1105112002174 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 1105112002175 Septum formation initiator; Region: DivIC; pfam04977 1105112002176 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 1105112002177 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 1105112002178 catalytic site [active] 1105112002179 putative active site [active] 1105112002180 putative substrate binding site [chemical binding]; other site 1105112002181 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 1105112002182 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 1105112002183 HIGH motif; other site 1105112002184 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1105112002185 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105112002186 active site 1105112002187 KMSKS motif; other site 1105112002188 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 1105112002189 tRNA binding surface [nucleotide binding]; other site 1105112002190 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 1105112002191 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 1105112002192 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 1105112002193 DNA polymerase III subunit beta; Validated; Region: PRK05643 1105112002194 putative DNA binding surface [nucleotide binding]; other site 1105112002195 dimer interface [polypeptide binding]; other site 1105112002196 beta-clamp/clamp loader binding surface; other site 1105112002197 beta-clamp/translesion DNA polymerase binding surface; other site 1105112002198 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 1105112002199 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 1105112002200 putative tRNA-binding site [nucleotide binding]; other site 1105112002201 B3/4 domain; Region: B3_4; pfam03483 1105112002202 tRNA synthetase B5 domain; Region: B5; smart00874 1105112002203 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 1105112002204 dimer interface [polypeptide binding]; other site 1105112002205 motif 1; other site 1105112002206 motif 3; other site 1105112002207 motif 2; other site 1105112002208 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 1105112002209 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 1105112002210 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 1105112002211 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 1105112002212 dimer interface [polypeptide binding]; other site 1105112002213 motif 1; other site 1105112002214 active site 1105112002215 motif 2; other site 1105112002216 motif 3; other site 1105112002217 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 1105112002218 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1105112002219 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 1105112002220 FeS/SAM binding site; other site 1105112002221 diaminopimelate epimerase; Region: DapF; TIGR00652 1105112002222 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1105112002223 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1105112002224 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105112002225 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105112002226 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 1105112002227 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1105112002228 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1105112002229 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 1105112002230 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 1105112002231 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 1105112002232 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 1105112002233 potential frameshift: common BLAST hit: gi|157827177|ref|YP_001496241.1| RND family efflux transporter 1105112002234 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 1105112002235 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 1105112002236 active site 1105112002237 homodimer interface [polypeptide binding]; other site 1105112002238 cell division protein FtsW; Region: ftsW; TIGR02614 1105112002239 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01368 1105112002240 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105112002241 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105112002242 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105112002243 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 1105112002244 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 1105112002245 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 1105112002246 putative peptidase; Provisional; Region: PRK11649 1105112002247 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105112002248 Cytidylyltransferase [Cell envelope biogenesis, outer membrane / Lipid metabolism]; Region: TagD; COG0615 1105112002249 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 1105112002250 active site 1105112002251 HIGH motif; other site 1105112002252 nucleotide binding site [chemical binding]; other site 1105112002253 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112002254 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 1105112002255 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 1105112002256 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 1105112002257 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 1105112002258 CoA binding site [chemical binding]; other site 1105112002259 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 1105112002260 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 1105112002261 Subunit I/III interface [polypeptide binding]; other site 1105112002262 D-pathway; other site 1105112002263 Subunit I/VIIc interface [polypeptide binding]; other site 1105112002264 Subunit I/IV interface [polypeptide binding]; other site 1105112002265 Subunit I/II interface [polypeptide binding]; other site 1105112002266 Low-spin heme (heme a) binding site [chemical binding]; other site 1105112002267 Subunit I/VIIa interface [polypeptide binding]; other site 1105112002268 Subunit I/VIa interface [polypeptide binding]; other site 1105112002269 Dimer interface; other site 1105112002270 Putative water exit pathway; other site 1105112002271 Binuclear center (heme a3/CuB) [ion binding]; other site 1105112002272 K-pathway; other site 1105112002273 Subunit I/Vb interface [polypeptide binding]; other site 1105112002274 Putative proton exit pathway; other site 1105112002275 Subunit I/VIb interface; other site 1105112002276 Subunit I/VIc interface [polypeptide binding]; other site 1105112002277 Electron transfer pathway; other site 1105112002278 Subunit I/VIIIb interface [polypeptide binding]; other site 1105112002279 Subunit I/VIIb interface [polypeptide binding]; other site 1105112002280 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 1105112002281 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 1105112002282 catalytic triad [active] 1105112002283 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 1105112002284 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 1105112002285 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 1105112002286 dimer interface [polypeptide binding]; other site 1105112002287 catalytic triad [active] 1105112002288 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 1105112002289 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1105112002290 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 1105112002291 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1105112002292 catalytic residue [active] 1105112002293 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1105112002294 trimer interface [polypeptide binding]; other site 1105112002295 active site 1105112002296 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 1105112002297 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1105112002298 tandem repeat interface [polypeptide binding]; other site 1105112002299 oligomer interface [polypeptide binding]; other site 1105112002300 active site residues [active] 1105112002301 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 1105112002302 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 1105112002303 catalytic residues [active] 1105112002304 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 1105112002305 Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. This family contains catechol 1,2-dioxygenases and protocatechuate 3,4-dioxygenases which are mononuclear...; Region: intradiol_dioxygenase; cl17208 1105112002306 active site 1105112002307 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1105112002308 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 1105112002309 Iron permease FTR1 family; Region: FTR1; cl00475 1105112002310 Intracellular septation protein A [Cell division and chromosome partitioning]; Region: COG2917 1105112002311 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 1105112002312 BON domain; Region: BON; pfam04972 1105112002313 BON domain; Region: BON; pfam04972 1105112002314 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105112002315 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105112002316 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 1105112002317 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 1105112002318 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 1105112002319 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 1105112002320 muropeptide transporter; Reviewed; Region: ampG; PRK11902 1105112002321 muropeptide transporter; Validated; Region: ampG; cl17669 1105112002322 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1105112002323 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105112002324 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105112002325 Walker A/P-loop; other site 1105112002326 ATP binding site [chemical binding]; other site 1105112002327 Q-loop/lid; other site 1105112002328 ABC transporter signature motif; other site 1105112002329 Walker B; other site 1105112002330 D-loop; other site 1105112002331 H-loop/switch region; other site 1105112002332 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 1105112002333 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 1105112002334 Walker A motif; other site 1105112002335 ATP binding site [chemical binding]; other site 1105112002336 Walker B motif; other site 1105112002337 arginine finger; other site 1105112002338 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 1105112002339 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 1105112002340 RuvA N terminal domain; Region: RuvA_N; pfam01330 1105112002341 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 1105112002342 Fic family protein [Function unknown]; Region: COG3177 1105112002343 Fic/DOC family; Region: Fic; pfam02661 1105112002344 prolyl-tRNA synthetase; Provisional; Region: PRK12325 1105112002345 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 1105112002346 dimer interface [polypeptide binding]; other site 1105112002347 motif 1; other site 1105112002348 active site 1105112002349 motif 2; other site 1105112002350 motif 3; other site 1105112002351 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 1105112002352 anticodon binding site; other site 1105112002353 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 1105112002354 GTP cyclohydrolase I; Provisional; Region: PLN03044 1105112002355 active site 1105112002356 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_19; cd04678 1105112002357 nudix motif; other site 1105112002358 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 1105112002359 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 1105112002360 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 1105112002361 Ligand binding site; other site 1105112002362 oligomer interface; other site 1105112002363 CTP synthetase; Validated; Region: pyrG; PRK05380 1105112002364 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 1105112002365 Catalytic site [active] 1105112002366 active site 1105112002367 UTP binding site [chemical binding]; other site 1105112002368 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 1105112002369 active site 1105112002370 putative oxyanion hole; other site 1105112002371 catalytic triad [active] 1105112002372 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105112002373 malate dehydrogenase; Reviewed; Region: PRK06223 1105112002374 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 1105112002375 NAD(P) binding site [chemical binding]; other site 1105112002376 dimer interface [polypeptide binding]; other site 1105112002377 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1105112002378 substrate binding site [chemical binding]; other site 1105112002379 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105112002380 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 1105112002381 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 1105112002382 putative active site [active] 1105112002383 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 1105112002384 Malic enzyme, N-terminal domain; Region: malic; pfam00390 1105112002385 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 1105112002386 putative NAD(P) binding site [chemical binding]; other site 1105112002387 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 1105112002388 Predicted permeases [General function prediction only]; Region: COG0679 1105112002389 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 1105112002390 catalytic core domain of class I lysyl tRNA synthetase; Region: LysRS_core_class_I; cd00674 1105112002391 active site 1105112002392 HIGH motif; other site 1105112002393 KMSKS motif; other site 1105112002394 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 1105112002395 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 1105112002396 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 1105112002397 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 1105112002398 potential frameshift: common BLAST hit: gi|15892423|ref|NP_360137.1| ABC transporter ATP-binding protein 1105112002399 potential frameshift: common BLAST hit: gi|229586633|ref|YP_002845134.1| ABC transporter substrate-binding protein 1105112002400 potential frameshift: common BLAST hit: gi|165933077|ref|YP_001649866.1| ABC transporter substrate-binding protein 1105112002401 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1105112002402 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 1105112002403 amidase catalytic site [active] 1105112002404 Zn binding residues [ion binding]; other site 1105112002405 substrate binding site [chemical binding]; other site 1105112002406 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1105112002407 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 1105112002408 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 1105112002409 putative active site [active] 1105112002410 catalytic triad [active] 1105112002411 putative dimer interface [polypeptide binding]; other site 1105112002412 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06603 1105112002413 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 1105112002414 NAD binding site [chemical binding]; other site 1105112002415 homotetramer interface [polypeptide binding]; other site 1105112002416 homodimer interface [polypeptide binding]; other site 1105112002417 substrate binding site [chemical binding]; other site 1105112002418 active site 1105112002419 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 1105112002420 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 1105112002421 active site 1105112002422 DNA binding site [nucleotide binding] 1105112002423 Int/Topo IB signature motif; other site 1105112002424 potential frameshift: common BLAST hit: gi|67458962|ref|YP_246586.1| phage protein 1105112002425 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4765 1105112002426 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 1105112002427 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 1105112002428 NADH dehydrogenase subunit B; Validated; Region: PRK06411 1105112002429 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 1105112002430 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 1105112002431 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 1105112002432 NADH dehydrogenase subunit D; Validated; Region: PRK06075 1105112002433 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 1105112002434 catalytic site [active] 1105112002435 metal binding site [ion binding]; metal-binding site 1105112002436 NADH dehydrogenase subunit E; Validated; Region: PRK07539 1105112002437 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 1105112002438 putative dimer interface [polypeptide binding]; other site 1105112002439 [2Fe-2S] cluster binding site [ion binding]; other site 1105112002440 hypothetical protein; Provisional; Region: PRK14388 1105112002441 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 1105112002442 active site 1105112002443 DNA binding site [nucleotide binding] 1105112002444 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 1105112002445 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 1105112002446 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1105112002447 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 1105112002448 RimM N-terminal domain; Region: RimM; pfam01782 1105112002449 PRC-barrel domain; Region: PRC; pfam05239 1105112002450 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 1105112002451 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1105112002452 Domain of unknown function (DUF4385); Region: DUF4385; pfam14328 1105112002453 spore photoproduct lyase; Region: photo_TT_lyase; cl15393 1105112002454 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 1105112002455 UbiA prenyltransferase family; Region: UbiA; pfam01040 1105112002456 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 1105112002457 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 1105112002458 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 1105112002459 RNA binding surface [nucleotide binding]; other site 1105112002460 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1105112002461 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 1105112002462 putative ADP-binding pocket [chemical binding]; other site 1105112002463 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1105112002464 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105112002465 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105112002466 Membrane-fusion protein [Cell envelope biogenesis, outer membrane]; Region: AcrA; COG0845 1105112002467 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1105112002468 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105112002469 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 1105112002470 active site 1105112002471 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105112002472 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 1105112002473 active site 1105112002474 potential frameshift: common BLAST hit: gi|238651057|ref|YP_002916914.1| methyltransferase 1105112002475 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 1105112002476 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 1105112002477 active site 1105112002478 homodimer interface [polypeptide binding]; other site 1105112002479 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 1105112002480 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 1105112002481 NAD(P) binding site [chemical binding]; other site 1105112002482 homodimer interface [polypeptide binding]; other site 1105112002483 substrate binding site [chemical binding]; other site 1105112002484 active site 1105112002485 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 1105112002486 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 1105112002487 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 1105112002488 NADP binding site [chemical binding]; other site 1105112002489 active site 1105112002490 putative substrate binding site [chemical binding]; other site 1105112002491 potential frameshift: common BLAST hit: gi|157964412|ref|YP_001499236.1| plasmid maintenance system antidote protein 1105112002492 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair]; Region: COG0816 1105112002493 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 1105112002494 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 1105112002495 Sulfatase; Region: Sulfatase; pfam00884 1105112002496 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1105112002497 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 1105112002498 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1105112002499 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 1105112002500 dimer interface [polypeptide binding]; other site 1105112002501 decamer (pentamer of dimers) interface [polypeptide binding]; other site 1105112002502 catalytic triad [active] 1105112002503 peroxidatic and resolving cysteines [active] 1105112002504 DNA protecting protein DprA; Region: dprA; TIGR00732 1105112002505 DNA topoisomerase I; Validated; Region: PRK06599 1105112002506 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 1105112002507 active site 1105112002508 interdomain interaction site; other site 1105112002509 putative metal-binding site [ion binding]; other site 1105112002510 nucleotide binding site [chemical binding]; other site 1105112002511 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 1105112002512 domain I; other site 1105112002513 DNA binding groove [nucleotide binding] 1105112002514 phosphate binding site [ion binding]; other site 1105112002515 domain II; other site 1105112002516 domain III; other site 1105112002517 nucleotide binding site [chemical binding]; other site 1105112002518 catalytic site [active] 1105112002519 domain IV; other site 1105112002520 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1105112002521 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 1105112002522 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105112002523 HIGH motif; other site 1105112002524 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105112002525 active site 1105112002526 KMSKS motif; other site 1105112002527 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 1105112002528 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 1105112002529 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105112002530 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 1105112002531 putative iron binding site [ion binding]; other site 1105112002532 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 1105112002533 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 1105112002534 dimerization interface [polypeptide binding]; other site 1105112002535 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 1105112002536 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 1105112002537 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105112002538 potential frameshift: common BLAST hit: gi|67458910|ref|YP_246534.1| Mg chelatase-like protein 1105112002539 potential frameshift: common BLAST hit: gi|67458910|ref|YP_246534.1| Mg chelatase-like protein 1105112002540 potential frameshift: common BLAST hit: gi|157827341|ref|YP_001496405.1| Mg chelatase-like protein 1105112002541 potential frameshift: common BLAST hit: gi|91205630|ref|YP_537985.1| Mg chelatase-like protein 1105112002542 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 1105112002543 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 1105112002544 Walker A motif; other site 1105112002545 ATP binding site [chemical binding]; other site 1105112002546 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 1105112002547 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1105112002548 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 1105112002549 active site 1105112002550 HslU subunit interaction site [polypeptide binding]; other site 1105112002551 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105112002552 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 1105112002553 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 1105112002554 nucleotide binding site/active site [active] 1105112002555 HIT family signature motif; other site 1105112002556 catalytic residue [active] 1105112002557 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 1105112002558 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 1105112002559 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 1105112002560 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105112002561 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 1105112002562 Walker A/P-loop; other site 1105112002563 ATP binding site [chemical binding]; other site 1105112002564 Q-loop/lid; other site 1105112002565 ABC transporter signature motif; other site 1105112002566 Walker B; other site 1105112002567 D-loop; other site 1105112002568 H-loop/switch region; other site 1105112002569 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 1105112002570 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 1105112002571 HlyD family secretion protein; Region: HlyD_3; pfam13437 1105112002572 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 1105112002573 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105112002574 putative substrate translocation pore; other site 1105112002575 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105112002576 HD domain; Region: HD_4; pfam13328 1105112002577 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 1105112002578 TolR protein; Region: tolR; TIGR02801 1105112002579 TolQ protein; Region: tolQ; TIGR02796 1105112002580 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1105112002581 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105112002582 Walker A/P-loop; other site 1105112002583 ATP binding site [chemical binding]; other site 1105112002584 Q-loop/lid; other site 1105112002585 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 1105112002586 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 1105112002587 dimer interface [polypeptide binding]; other site 1105112002588 motif 1; other site 1105112002589 active site 1105112002590 motif 2; other site 1105112002591 motif 3; other site 1105112002592 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 1105112002593 anticodon binding site; other site 1105112002594 amino acid transporter; Region: 2A0306; TIGR00909 1105112002595 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 1105112002596 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 1105112002597 Ligand Binding Site [chemical binding]; other site 1105112002598 Cytochrome oxidase assembly factor [Posttranslational modification, protein turnover, chaperones]; Region: COX11; COG3175 1105112002599 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 1105112002600 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1105112002601 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1105112002602 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 1105112002603 DNA binding residues [nucleotide binding] 1105112002604 translocation protein TolB; Provisional; Region: tolB; PRK05137 1105112002605 TolB amino-terminal domain; Region: TolB_N; pfam04052 1105112002606 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105112002607 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105112002608 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 1105112002609 potential frameshift: common BLAST hit: gi|229586557|ref|YP_002845058.1| Putative metal-dependent hydrolase 1105112002610 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105112002611 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 1105112002612 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 1105112002613 MutS domain I; Region: MutS_I; pfam01624 1105112002614 MutS domain II; Region: MutS_II; pfam05188 1105112002615 MutS domain III; Region: MutS_III; pfam05192 1105112002616 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 1105112002617 Walker A/P-loop; other site 1105112002618 ATP binding site [chemical binding]; other site 1105112002619 Q-loop/lid; other site 1105112002620 ABC transporter signature motif; other site 1105112002621 Walker B; other site 1105112002622 D-loop; other site 1105112002623 H-loop/switch region; other site 1105112002624 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 1105112002625 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 1105112002626 active site 1105112002627 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105112002628 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105112002629 Phage-related protein [Function unknown]; Region: COG4695; cl01923 1105112002630 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 1105112002631 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 1105112002632 type IV secretion system component VirD4; Provisional; Region: PRK13897 1105112002633 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 1105112002634 Walker A motif; other site 1105112002635 ATP binding site [chemical binding]; other site 1105112002636 Walker B motif; other site 1105112002637 type IV secretion system ATPase VirB11; Provisional; Region: PRK13900 1105112002638 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 1105112002639 Walker A motif; other site 1105112002640 hexamer interface [polypeptide binding]; other site 1105112002641 ATP binding site [chemical binding]; other site 1105112002642 Walker B motif; other site 1105112002643 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 1105112002644 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 1105112002645 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 1105112002646 Protein of unknown function (DUF2706); Region: DUF2706; pfam10913 1105112002647 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 1105112002648 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 1105112002649 VirB7 interaction site; other site 1105112002650 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK07375 1105112002651 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06591 1105112002652 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105112002653 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06589 1105112002654 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105112002655 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 1105112002656 oligomeric interface; other site 1105112002657 putative active site [active] 1105112002658 homodimer interface [polypeptide binding]; other site 1105112002659 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06588 1105112002660 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105112002661 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 1105112002662 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105112002663 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105112002664 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 1105112002665 potential frameshift: common BLAST hit: gi|67458844|ref|YP_246468.1| MFS type sugar transporter 1105112002666 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105112002667 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105112002668 HD domain; Region: HD_4; pfam13328 1105112002669 HEAT repeats; Region: HEAT_2; pfam13646 1105112002670 potential frameshift: common BLAST hit: gi|67459245|ref|YP_246869.1| NTPase 1105112002671 potential frameshift: common BLAST hit: gi|15892293|ref|NP_360007.1| ATP-dependent protease subunit C (ClpC) 1105112002672 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 1105112002673 hydrophobic ligand binding site; other site 1105112002674 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 1105112002675 bifunctional preprotein translocase subunit SecD/SecF; Reviewed; Region: PRK13024 1105112002676 potential frameshift: common BLAST hit: gi|165933830|ref|YP_001650619.1| outer membrane protein A 1105112002677 potential frameshift: common BLAST hit: gi|341584421|ref|YP_004764912.1| 190-kDa cell surface antigen 1105112002678 Phage capsid family; Region: Phage_capsid; pfam05065 1105112002679 GTP-binding protein LepA; Provisional; Region: PRK05433 1105112002680 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 1105112002681 G1 box; other site 1105112002682 putative GEF interaction site [polypeptide binding]; other site 1105112002683 GTP/Mg2+ binding site [chemical binding]; other site 1105112002684 Switch I region; other site 1105112002685 G2 box; other site 1105112002686 G3 box; other site 1105112002687 Switch II region; other site 1105112002688 G4 box; other site 1105112002689 G5 box; other site 1105112002690 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 1105112002691 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 1105112002692 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 1105112002693 PCRF domain; Region: PCRF; pfam03462 1105112002694 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 1105112002695 RF-1 domain; Region: RF-1; pfam00472 1105112002696 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105112002697 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 1105112002698 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 1105112002699 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 1105112002700 putative dimer interface [polypeptide binding]; other site 1105112002701 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 1105112002702 Cytochrome c; Region: Cytochrom_C; cl11414 1105112002703 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 1105112002704 catalytic site [active] 1105112002705 metal binding site [ion binding]; metal-binding site 1105112002706 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 1105112002707 Qi binding site; other site 1105112002708 cytochrome b; Provisional; Region: CYTB; MTH00191 1105112002709 intrachain domain interface; other site 1105112002710 interchain domain interface [polypeptide binding]; other site 1105112002711 heme bH binding site [chemical binding]; other site 1105112002712 heme bL binding site [chemical binding]; other site 1105112002713 Qo binding site; other site 1105112002714 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 1105112002715 interchain domain interface [polypeptide binding]; other site 1105112002716 intrachain domain interface; other site 1105112002717 Qi binding site; other site 1105112002718 Qo binding site; other site 1105112002719 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 1105112002720 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 1105112002721 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 1105112002722 [2Fe-2S] cluster binding site [ion binding]; other site 1105112002723 Protein of unknown function (DUF2670); Region: DUF2670; pfam10875 1105112002724 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12507 1105112002725 Predicted subunit of the Multisubunit Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: COG1563 1105112002726 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 1105112002727 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 1105112002728 isocitrate dehydrogenase; Validated; Region: PRK09222 1105112002729 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 1105112002730 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: HlpA; COG2825 1105112002731 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 1105112002732 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 1105112002733 G1 box; other site 1105112002734 putative GEF interaction site [polypeptide binding]; other site 1105112002735 GTP/Mg2+ binding site [chemical binding]; other site 1105112002736 Switch I region; other site 1105112002737 G2 box; other site 1105112002738 G3 box; other site 1105112002739 Switch II region; other site 1105112002740 G4 box; other site 1105112002741 G5 box; other site 1105112002742 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 1105112002743 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 1105112002744 pyruvate dehydrogenase subunit beta; Validated; Region: PRK09212 1105112002745 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 1105112002746 alpha subunit interface [polypeptide binding]; other site 1105112002747 TPP binding site [chemical binding]; other site 1105112002748 heterodimer interface [polypeptide binding]; other site 1105112002749 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1105112002750 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 1105112002751 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 1105112002752 tetramer interface [polypeptide binding]; other site 1105112002753 TPP-binding site [chemical binding]; other site 1105112002754 heterodimer interface [polypeptide binding]; other site 1105112002755 phosphorylation loop region [posttranslational modification] 1105112002756 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 1105112002757 putative catalytic site [active] 1105112002758 putative phosphate binding site [ion binding]; other site 1105112002759 active site 1105112002760 metal binding site A [ion binding]; metal-binding site 1105112002761 DNA binding site [nucleotide binding] 1105112002762 putative AP binding site [nucleotide binding]; other site 1105112002763 putative metal binding site B [ion binding]; other site 1105112002764 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 1105112002765 Beta-lactamase; Region: Beta-lactamase; pfam00144 1105112002766 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1105112002767 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 1105112002768 RNA binding surface [nucleotide binding]; other site 1105112002769 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1105112002770 active site 1105112002771 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 1105112002772 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 1105112002773 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 1105112002774 RNA binding site [nucleotide binding]; other site 1105112002775 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 1105112002776 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 1105112002777 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 1105112002778 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 1105112002779 Cytochrome c2 [Energy production and conversion]; Region: COG3474 1105112002780 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 1105112002781 cell division protein FtsA; Region: ftsA; TIGR01174 1105112002782 Cell division protein FtsA; Region: FtsA; smart00842 1105112002783 Cell division protein FtsA; Region: FtsA; pfam14450 1105112002784 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 1105112002785 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 1105112002786 Cell division protein FtsQ; Region: FtsQ; pfam03799 1105112002787 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 1105112002788 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 1105112002789 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1105112002790 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 1105112002791 FAD binding domain; Region: FAD_binding_4; pfam01565 1105112002792 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 1105112002793 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 1105112002794 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105112002795 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105112002796 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105112002797 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 1105112002798 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 1105112002799 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105112002800 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105112002801 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 1105112002802 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1105112002803 HlyD family secretion protein; Region: HlyD_3; pfam13437 1105112002804 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 1105112002805 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 1105112002806 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 1105112002807 Domain of unknown function (DUF2610); Region: DUF2610; pfam11020 1105112002808 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 1105112002809 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 1105112002810 active site 1105112002811 elongation factor P; Validated; Region: PRK00529 1105112002812 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 1105112002813 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 1105112002814 RNA binding site [nucleotide binding]; other site 1105112002815 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 1105112002816 RNA binding site [nucleotide binding]; other site 1105112002817 response regulator PleD; Reviewed; Region: pleD; PRK09581 1105112002818 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 1105112002819 active site 1105112002820 phosphorylation site [posttranslational modification] 1105112002821 intermolecular recognition site; other site 1105112002822 dimerization interface [polypeptide binding]; other site 1105112002823 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 1105112002824 active site 1105112002825 phosphorylation site [posttranslational modification] 1105112002826 intermolecular recognition site; other site 1105112002827 dimerization interface [polypeptide binding]; other site 1105112002828 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1105112002829 metal binding site [ion binding]; metal-binding site 1105112002830 active site 1105112002831 I-site; other site 1105112002832 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 1105112002833 putative active site [active] 1105112002834 Ap4A binding site [chemical binding]; other site 1105112002835 nudix motif; other site 1105112002836 putative metal binding site [ion binding]; other site 1105112002837 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 1105112002838 aromatic arch; other site 1105112002839 DCoH dimer interaction site [polypeptide binding]; other site 1105112002840 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 1105112002841 DCoH tetramer interaction site [polypeptide binding]; other site 1105112002842 substrate binding site [chemical binding]; other site 1105112002843 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 1105112002844 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 1105112002845 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 1105112002846 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 1105112002847 23S rRNA interface [nucleotide binding]; other site 1105112002848 L3 interface [polypeptide binding]; other site 1105112002849 FOG: WD40-like repeat [Function unknown]; Region: COG1520 1105112002850 Beta-barrel assembly machinery (Bam) complex component B and related proteins; Region: BamB_YfgL; cd10276 1105112002851 Trp docking motif [polypeptide binding]; other site 1105112002852 Protein of unknown function (DUF2659); Region: DUF2659; pfam10858 1105112002853 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 1105112002854 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1105112002855 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 1105112002856 dimer interface [polypeptide binding]; other site 1105112002857 phosphorylation site [posttranslational modification] 1105112002858 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 1105112002859 ATP binding site [chemical binding]; other site 1105112002860 Mg2+ binding site [ion binding]; other site 1105112002861 G-X-G motif; other site 1105112002862 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 1105112002863 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 1105112002864 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 1105112002865 protein binding site [polypeptide binding]; other site 1105112002866 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 1105112002867 Catalytic dyad [active] 1105112002868 DNA topoisomerase IV, B subunit, proteobacterial; Region: parE_Gneg; TIGR01055 1105112002869 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 1105112002870 ATP binding site [chemical binding]; other site 1105112002871 Mg2+ binding site [ion binding]; other site 1105112002872 G-X-G motif; other site 1105112002873 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 1105112002874 anchoring element; other site 1105112002875 dimer interface [polypeptide binding]; other site 1105112002876 ATP binding site [chemical binding]; other site 1105112002877 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 1105112002878 active site 1105112002879 metal binding site [ion binding]; metal-binding site 1105112002880 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1105112002881 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 1105112002882 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 1105112002883 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3827 1105112002884 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1105112002885 Protein of unknown function (DUF2660); Region: DUF2660; pfam10859 1105112002886 potential frameshift: common BLAST hit: gi|67459373|ref|YP_246997.1| multidrug ABC transporter ATPase and permease 1105112002887 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 1105112002888 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 1105112002889 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 1105112002890 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105112002891 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105112002892 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105112002893 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 1105112002894 rRNA binding site [nucleotide binding]; other site 1105112002895 predicted 30S ribosome binding site; other site 1105112002896 Maf-like protein; Region: Maf; pfam02545 1105112002897 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 1105112002898 active site 1105112002899 dimer interface [polypeptide binding]; other site 1105112002900 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 1105112002901 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 1105112002902 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 1105112002903 active site 1105112002904 DNA binding site [nucleotide binding] 1105112002905 Int/Topo IB signature motif; other site 1105112002906 potential frameshift: common BLAST hit: gi|67459688|ref|YP_247312.1| phasin family protein 1105112002907 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 1105112002908 PLD-like domain; Region: PLDc_2; pfam13091 1105112002909 putative active site [active] 1105112002910 catalytic site [active] 1105112002911 potential frameshift: common BLAST hit: gi|67459690|ref|YP_247314.1| Poly(3-hydroxyalkanoate) synthetase 1105112002912 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism]; Region: UbiD; COG0043 1105112002913 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 1105112002914 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 1105112002915 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 1105112002916 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105112002917 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 1105112002918 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105112002919 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cl02529 1105112002920 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 1105112002921 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 1105112002922 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 1105112002923 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 1105112002924 potential frameshift: common BLAST hit: gi|229587187|ref|YP_002845688.1| Putative acyltransferase 1105112002925 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 1105112002926 active site 1105112002927 DNA repair proteins [DNA replication, recombination, and repair]; Region: RadC; COG2003 1105112002928 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 1105112002929 MPN+ (JAMM) motif; other site 1105112002930 Zinc-binding site [ion binding]; other site 1105112002931 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 1105112002932 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 1105112002933 Mg++ binding site [ion binding]; other site 1105112002934 putative catalytic motif [active] 1105112002935 putative substrate binding site [chemical binding]; other site 1105112002936 Protein of unknown function (DUF721); Region: DUF721; pfam05258 1105112002937 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 1105112002938 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 1105112002939 Ferredoxin [Energy production and conversion]; Region: COG1146 1105112002940 4Fe-4S binding domain; Region: Fer4; cl02805 1105112002941 heme exporter protein CcmC; Region: ccmC; TIGR01191 1105112002942 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 1105112002943 nucleoside/Zn binding site; other site 1105112002944 dimer interface [polypeptide binding]; other site 1105112002945 catalytic motif [active] 1105112002946 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 1105112002947 Cation efflux family; Region: Cation_efflux; cl00316 1105112002948 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 1105112002949 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 1105112002950 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 1105112002951 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 1105112002952 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 1105112002953 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1105112002954 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1105112002955 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 1105112002956 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 1105112002957 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 1105112002958 dimer interface [polypeptide binding]; other site 1105112002959 ssDNA binding site [nucleotide binding]; other site 1105112002960 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1105112002961 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 1105112002962 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 1105112002963 hypothetical protein; Reviewed; Region: PRK01530 1105112002964 heat shock protein 90; Provisional; Region: PRK05218 1105112002965 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 1105112002966 ATP binding site [chemical binding]; other site 1105112002967 Mg2+ binding site [ion binding]; other site 1105112002968 G-X-G motif; other site 1105112002969 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 1105112002970 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 1105112002971 substrate-cofactor binding pocket; other site 1105112002972 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105112002973 catalytic residue [active] 1105112002974 falcipain-2; Provisional; Region: PTZ00021 1105112002975 trigger factor; Provisional; Region: tig; PRK01490 1105112002976 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1105112002977 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 1105112002978 GTPase CgtA; Reviewed; Region: obgE; PRK12299 1105112002979 GTP1/OBG; Region: GTP1_OBG; pfam01018 1105112002980 Obg GTPase; Region: Obg; cd01898 1105112002981 G1 box; other site 1105112002982 GTP/Mg2+ binding site [chemical binding]; other site 1105112002983 Switch I region; other site 1105112002984 G2 box; other site 1105112002985 G3 box; other site 1105112002986 Switch II region; other site 1105112002987 G4 box; other site 1105112002988 G5 box; other site 1105112002989 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 1105112002990 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 1105112002991 dimer interface [polypeptide binding]; other site 1105112002992 active site 1105112002993 citrylCoA binding site [chemical binding]; other site 1105112002994 NADH binding [chemical binding]; other site 1105112002995 cationic pore residues; other site 1105112002996 oxalacetate/citrate binding site [chemical binding]; other site 1105112002997 coenzyme A binding site [chemical binding]; other site 1105112002998 catalytic triad [active] 1105112002999 Predicted transcriptional regulator [Transcription]; Region: COG3636; cl17681 1105112003000 ATP10 protein; Region: ATP-synt_10; pfam05176 1105112003001 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 1105112003002 Fe-S cluster binding site [ion binding]; other site 1105112003003 active site 1105112003004 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1105112003005 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 1105112003006 RNA binding surface [nucleotide binding]; other site 1105112003007 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1105112003008 active site 1105112003009 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed; Region: PRK01544 1105112003010 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 1105112003011 S-adenosylmethionine binding site [chemical binding]; other site 1105112003012 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]; Region: COG0220 1105112003013 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 1105112003014 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 1105112003015 Glycyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]; Region: GlyS; COG0751 1105112003016 DALR anticodon binding domain; Region: DALR_1; pfam05746 1105112003017 glycyl-tRNA synthetase subunit alpha; Validated; Region: glyQ; PRK09348 1105112003018 motif 1; other site 1105112003019 dimer interface [polypeptide binding]; other site 1105112003020 active site 1105112003021 motif 2; other site 1105112003022 motif 3; other site 1105112003023 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 1105112003024 oligomeric interface; other site 1105112003025 putative active site [active] 1105112003026 homodimer interface [polypeptide binding]; other site 1105112003027 prevent-host-death family protein; Region: phd_fam; TIGR01552 1105112003028 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 1105112003029 potential frameshift: common BLAST hit: gi|67459741|ref|YP_247365.1| proline/betaine transporter 1105112003030 potential frameshift: common BLAST hit: gi|67459741|ref|YP_247365.1| proline/betaine transporter 1105112003031 potential frameshift: common BLAST hit: gi|157827810|ref|YP_001496874.1| oxidoreductase 1105112003032 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4391 1105112003033 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 1105112003034 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 1105112003035 ATP binding site [chemical binding]; other site 1105112003036 Mg2+ binding site [ion binding]; other site 1105112003037 G-X-G motif; other site 1105112003038 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 1105112003039 ATP binding site [chemical binding]; other site 1105112003040 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 1105112003041 ribosomal protein L33, bacterial type; Region: rpmG_bact; TIGR01023 1105112003042 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 1105112003043 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1105112003044 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 1105112003045 amidase catalytic site [active] 1105112003046 Zn binding residues [ion binding]; other site 1105112003047 substrate binding site [chemical binding]; other site 1105112003048 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1105112003049 lipoate-protein ligase B; Provisional; Region: PRK14347 1105112003050 Uncharacterized conserved protein [Function unknown]; Region: COG1434 1105112003051 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 1105112003052 putative active site [active] 1105112003053 Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: NhaA; COG3004 1105112003054 potential frameshift: common BLAST hit: gi|157827849|ref|YP_001496913.1| Type I restriction-modification system methyltransferase subunit 1105112003055 potential frameshift: common BLAST hit: gi|157827849|ref|YP_001496913.1| Type I restriction-modification system methyltransferase subunit 1105112003056 potential frameshift: common BLAST hit: gi|157827849|ref|YP_001496913.1| Type I restriction-modification system methyltransferase subunit 1105112003057 potential frameshift: common BLAST hit: gi|238651120|ref|YP_002916978.1| putative type I restriction enzyme S subunit 1105112003058 potential frameshift: common BLAST hit: gi|15893271|ref|NP_360985.1| type I restriction enzyme S subunit 1105112003059 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 1105112003060 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 1105112003061 metal binding site [ion binding]; metal-binding site 1105112003062 dimer interface [polypeptide binding]; other site 1105112003063 DNA polymerase III subunit chi; Provisional; Region: PRK06646 1105112003064 Predicted permeases [General function prediction only]; Region: COG0795 1105112003065 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1105112003066 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 1105112003067 DNA-damage-inducible protein J [DNA replication, recombination, and repair]; Region: RelB; COG3077 1105112003068 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 1105112003069 active site 1105112003070 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 1105112003071 putative hydrolase; Provisional; Region: PRK02113 1105112003072 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 1105112003073 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105112003074 Walker A/P-loop; other site 1105112003075 ATP binding site [chemical binding]; other site 1105112003076 Q-loop/lid; other site 1105112003077 ABC transporter signature motif; other site 1105112003078 Walker B; other site 1105112003079 D-loop; other site 1105112003080 H-loop/switch region; other site 1105112003081 Beta-lactamase; Region: Beta-lactamase; pfam00144 1105112003082 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 1105112003083 Predicted aspartyl protease [General function prediction only]; Region: COG3577 1105112003084 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 1105112003085 catalytic motif [active] 1105112003086 Catalytic residue [active] 1105112003087 hypothetical protein; Validated; Region: PRK00153 1105112003088 potential frameshift: common BLAST hit: gi|157965023|ref|YP_001499847.1| DNA polymerase III subunits gamma and tau 1105112003089 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 1105112003090 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl17548 1105112003091 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 1105112003092 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 1105112003093 ligand binding site [chemical binding]; other site 1105112003094 homodimer interface [polypeptide binding]; other site 1105112003095 NAD(P) binding site [chemical binding]; other site 1105112003096 trimer interface B [polypeptide binding]; other site 1105112003097 trimer interface A [polypeptide binding]; other site 1105112003098 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 1105112003099 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 1105112003100 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 1105112003101 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 1105112003102 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1105112003103 Dolichol kinase [Lipid metabolism]; Region: SEC59; COG0170 1105112003104 DNA primase, catalytic core; Region: dnaG; TIGR01391 1105112003105 CHC2 zinc finger; Region: zf-CHC2; pfam01807 1105112003106 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 1105112003107 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 1105112003108 active site 1105112003109 metal binding site [ion binding]; metal-binding site 1105112003110 interdomain interaction site; other site 1105112003111 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 1105112003112 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 1105112003113 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1105112003114 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1105112003115 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1105112003116 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 1105112003117 DNA binding residues [nucleotide binding] 1105112003118 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 1105112003119 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 1105112003120 dimerization interface 3.5A [polypeptide binding]; other site 1105112003121 active site 1105112003122 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 1105112003123 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 1105112003124 motif 1; other site 1105112003125 active site 1105112003126 motif 2; other site 1105112003127 motif 3; other site 1105112003128 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 1105112003129 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105112003130 TPR repeat; Region: TPR_11; pfam13414 1105112003131 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 1105112003132 TPR motif; other site 1105112003133 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 1105112003134 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105112003135 putative substrate translocation pore; other site 1105112003136 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 1105112003137 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 1105112003138 potential frameshift: common BLAST hit: gi|67459789|ref|YP_247413.1| prophage antirepressor 1105112003139 TIGR00701 family protein; Region: TIGR00701 1105112003140 ferrochelatase; Reviewed; Region: hemH; PRK00035 1105112003141 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 1105112003142 C-terminal domain interface [polypeptide binding]; other site 1105112003143 active site 1105112003144 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 1105112003145 active site 1105112003146 N-terminal domain interface [polypeptide binding]; other site 1105112003147 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 1105112003148 substrate binding site [chemical binding]; other site 1105112003149 active site 1105112003150 ParA-like protein; Provisional; Region: PHA02518 1105112003151 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 1105112003152 P-loop; other site 1105112003153 Magnesium ion binding site [ion binding]; other site 1105112003154 HicB family; Region: HicB; pfam05534 1105112003155 putative transposase; Provisional; Region: PRK09857 1105112003156 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 1105112003157 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 1105112003158 catalytic residues [active] 1105112003159 catalytic nucleophile [active] 1105112003160 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 1105112003161 Presynaptic Site I dimer interface [polypeptide binding]; other site 1105112003162 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 1105112003163 Synaptic Flat tetramer interface [polypeptide binding]; other site 1105112003164 Synaptic Site I dimer interface [polypeptide binding]; other site 1105112003165 DNA binding site [nucleotide binding] 1105112003166 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 1105112003167 DNA-binding interface [nucleotide binding]; DNA binding site 1105112003168 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105112003169 HD domain; Region: HD_4; pfam13328 1105112003170 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 1105112003171 synthetase active site [active] 1105112003172 NTP binding site [chemical binding]; other site 1105112003173 metal binding site [ion binding]; metal-binding site 1105112003174 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 1105112003175 Leucine-rich repeats; other site 1105112003176 Substrate binding site [chemical binding]; other site 1105112003177 DnaA N-terminal domain; Region: DnaA_N; pfam11638