-- dump date 20140620_033654 -- class Genbank::misc_feature -- table misc_feature_note -- id note 293613000001 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1806 293613000002 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 293613000003 catalytic residues [active] 293613000004 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 293613000005 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 293613000006 Walker A/P-loop; other site 293613000007 ATP binding site [chemical binding]; other site 293613000008 Q-loop/lid; other site 293613000009 ABC transporter signature motif; other site 293613000010 Walker B; other site 293613000011 D-loop; other site 293613000012 H-loop/switch region; other site 293613000013 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 293613000014 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 293613000015 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 293613000016 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 293613000017 FAD binding pocket [chemical binding]; other site 293613000018 FAD binding motif [chemical binding]; other site 293613000019 phosphate binding motif [ion binding]; other site 293613000020 beta-alpha-beta structure motif; other site 293613000021 NAD binding pocket [chemical binding]; other site 293613000022 Iron coordination center [ion binding]; other site 293613000023 Acyl-[acyl carrier protein]; Region: LpxA; COG1043 293613000024 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 293613000025 active site 293613000026 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 293613000027 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 293613000028 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 293613000029 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 293613000030 trimer interface [polypeptide binding]; other site 293613000031 active site 293613000032 UDP-GlcNAc binding site [chemical binding]; other site 293613000033 lipid binding site [chemical binding]; lipid-binding site 293613000034 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 293613000035 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 293613000036 FMN binding site [chemical binding]; other site 293613000037 active site 293613000038 catalytic residues [active] 293613000039 substrate binding site [chemical binding]; other site 293613000040 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 293613000041 ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: LraI; COG0803 293613000042 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 293613000043 intersubunit interface [polypeptide binding]; other site 293613000044 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 293613000045 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 293613000046 active site 293613000047 NTP binding site [chemical binding]; other site 293613000048 metal binding triad [ion binding]; metal-binding site 293613000049 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 293613000050 Autotransporter beta-domain; Region: Autotransporter; pfam03797 293613000051 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 293613000052 F0F1 ATP synthase subunit B; Validated; Region: PRK06568 293613000053 F0F1 ATP synthase subunit B'; Validated; Region: PRK06569 293613000054 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 293613000055 F0F1 ATP synthase subunit C; Validated; Region: PRK07558 293613000056 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 293613000057 ATP synthase subunit 6 (eukaryotes),also subunit A (prokaryotes); Region: ATP_synt_6_or_A; TIGR01131 293613000058 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5336 293613000059 Thioredoxin; Region: Thioredoxin_4; pfam13462 293613000060 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 293613000061 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 293613000062 Methyltransferase domain; Region: Methyltransf_31; pfam13847 293613000063 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 293613000064 S-adenosylmethionine binding site [chemical binding]; other site 293613000065 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 293613000066 recombination protein F; Reviewed; Region: recF; PRK00064 293613000067 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 293613000068 Walker A/P-loop; other site 293613000069 ATP binding site [chemical binding]; other site 293613000070 Q-loop/lid; other site 293613000071 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 293613000072 ABC transporter signature motif; other site 293613000073 Walker B; other site 293613000074 D-loop; other site 293613000075 H-loop/switch region; other site 293613000076 Putative transcriptional regulator [Transcription]; Region: COG1678 293613000077 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 293613000078 Colicin V production protein; Region: Colicin_V; pfam02674 293613000079 Protein of unknown function (DUF2748); Region: DUF2748; pfam10871 293613000080 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 293613000081 Clp amino terminal domain; Region: Clp_N; pfam02861 293613000082 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 293613000083 Walker A motif; other site 293613000084 ATP binding site [chemical binding]; other site 293613000085 Walker B motif; other site 293613000086 arginine finger; other site 293613000087 Protein of unknown function (DUF1640); Region: DUF1640; pfam07798 293613000088 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 293613000089 Walker A motif; other site 293613000090 ATP binding site [chemical binding]; other site 293613000091 Walker B motif; other site 293613000092 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 293613000093 UGMP family protein; Validated; Region: PRK09604 293613000094 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 293613000095 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 293613000096 Fatty acid desaturase; Region: FA_desaturase; pfam00487 293613000097 Di-iron ligands [ion binding]; other site 293613000098 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 293613000099 Protein of unknown function (DUF713); Region: DUF713; pfam05218 293613000100 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 293613000101 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 293613000102 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 293613000103 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 293613000104 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 293613000105 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 293613000106 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 293613000107 Ligand Binding Site [chemical binding]; other site 293613000108 FtsH Extracellular; Region: FtsH_ext; pfam06480 293613000109 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 293613000110 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 293613000111 Walker A motif; other site 293613000112 ATP binding site [chemical binding]; other site 293613000113 Walker B motif; other site 293613000114 arginine finger; other site 293613000115 Peptidase family M41; Region: Peptidase_M41; pfam01434 293613000116 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 293613000117 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 293613000118 Uncharacterized conserved protein [Function unknown]; Region: COG1565 293613000119 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 293613000120 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 293613000121 Mechanosensitive ion channel; Region: MS_channel; pfam00924 293613000122 membrane protein insertase; Provisional; Region: PRK01318 293613000123 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 293613000124 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 293613000125 TLC ATP/ADP transporter; Region: TLC; pfam03219 293613000126 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 293613000127 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 293613000128 putative substrate translocation pore; other site 293613000129 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 293613000130 active site 293613000131 multimer interface [polypeptide binding]; other site 293613000132 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 293613000133 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 293613000134 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 293613000135 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 293613000136 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 293613000137 P-loop; other site 293613000138 Magnesium ion binding site [ion binding]; other site 293613000139 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 293613000140 Magnesium ion binding site [ion binding]; other site 293613000141 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 293613000142 ParB-like nuclease domain; Region: ParB; smart00470 293613000143 KorB domain; Region: KorB; pfam08535 293613000144 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 293613000145 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 293613000146 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 293613000147 ABC transporter; Region: ABC_tran_2; pfam12848 293613000148 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 293613000149 Protein of unknown function (DUF2672); Region: DUF2672; pfam10878 293613000150 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 293613000151 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 293613000152 Iron-sulfur cluster assembly accessory protein; Region: TIGR00049 293613000153 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 293613000154 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 293613000155 Zn2+ binding site [ion binding]; other site 293613000156 Mg2+ binding site [ion binding]; other site 293613000157 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 293613000158 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 293613000159 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 293613000160 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 293613000161 active site 293613000162 HIGH motif; other site 293613000163 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 293613000164 KMSK motif region; other site 293613000165 tRNA binding surface [nucleotide binding]; other site 293613000166 DALR anticodon binding domain; Region: DALR_1; smart00836 293613000167 anticodon binding site; other site 293613000168 Sporulation related domain; Region: SPOR; pfam05036 293613000169 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 293613000170 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 293613000171 CAP-like domain; other site 293613000172 active site 293613000173 primary dimer interface [polypeptide binding]; other site 293613000174 Gram-negative porin; Region: Porin_4; pfam13609 293613000175 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 293613000176 trimer interface [polypeptide binding]; other site 293613000177 active site 293613000178 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 293613000179 SecA binding site; other site 293613000180 Preprotein binding site; other site 293613000181 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 293613000182 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 293613000183 active site 293613000184 phosphorylation site [posttranslational modification] 293613000185 intermolecular recognition site; other site 293613000186 dimerization interface [polypeptide binding]; other site 293613000187 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 293613000188 DNA binding site [nucleotide binding] 293613000189 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 293613000190 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 293613000191 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 293613000192 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3820 293613000193 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 293613000194 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 293613000195 EamA-like transporter family; Region: EamA; pfam00892 293613000196 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 293613000197 EamA-like transporter family; Region: EamA; cl17759 293613000198 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 293613000199 metabolite-proton symporter; Region: 2A0106; TIGR00883 293613000200 putative substrate translocation pore; other site 293613000201 Preprotein translocase SecG subunit; Region: SecG; cl09123 293613000202 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 293613000203 Autotransporter beta-domain; Region: Autotransporter; pfam03797 293613000204 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 293613000205 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 293613000206 active site 293613000207 HIGH motif; other site 293613000208 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 293613000209 KMSKS motif; other site 293613000210 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 293613000211 tRNA binding surface [nucleotide binding]; other site 293613000212 anticodon binding site; other site 293613000213 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 293613000214 rRNA interaction site [nucleotide binding]; other site 293613000215 S8 interaction site; other site 293613000216 putative laminin-1 binding site; other site 293613000217 elongation factor Ts; Provisional; Region: tsf; PRK09377 293613000218 UBA/TS-N domain; Region: UBA; pfam00627 293613000219 Elongation factor TS; Region: EF_TS; pfam00889 293613000220 Elongation factor TS; Region: EF_TS; pfam00889 293613000221 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 293613000222 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 293613000223 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 293613000224 putative acyl-acceptor binding pocket; other site 293613000225 aspartate aminotransferase; Provisional; Region: PRK05764 293613000226 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 293613000227 pyridoxal 5'-phosphate binding site [chemical binding]; other site 293613000228 homodimer interface [polypeptide binding]; other site 293613000229 catalytic residue [active] 293613000230 Tetratricopeptide repeat; Region: TPR_12; pfam13424 293613000231 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 293613000232 binding surface 293613000233 TPR motif; other site 293613000234 Methyltransferase domain; Region: Methyltransf_23; pfam13489 293613000235 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 293613000236 S-adenosylmethionine binding site [chemical binding]; other site 293613000237 Surface lipoprotein [Cell envelope biogenesis, outer membrane]; Region: VacJ; COG2853 293613000238 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; COG2854 293613000239 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 293613000240 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 293613000241 active site 293613000242 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 293613000243 dimer interface [polypeptide binding]; other site 293613000244 substrate binding site [chemical binding]; other site 293613000245 catalytic residues [active] 293613000246 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 293613000247 Permease; Region: Permease; pfam02405 293613000248 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 293613000249 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 293613000250 Walker A/P-loop; other site 293613000251 ATP binding site [chemical binding]; other site 293613000252 Q-loop/lid; other site 293613000253 ABC transporter signature motif; other site 293613000254 Walker B; other site 293613000255 D-loop; other site 293613000256 H-loop/switch region; other site 293613000257 Ribosomal protein L28 [Translation, ribosomal structure and biogenesis]; Region: RpmB; COG0227 293613000258 50S ribosomal protein L31; Provisional; Region: PRK01397 293613000259 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 293613000260 G1 box; other site 293613000261 GTP/Mg2+ binding site [chemical binding]; other site 293613000262 Switch I region; other site 293613000263 G2 box; other site 293613000264 G3 box; other site 293613000265 Switch II region; other site 293613000266 G4 box; other site 293613000267 G5 box; other site 293613000268 type IV secretion system protein VirB3; Provisional; Region: PRK13899 293613000269 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 293613000270 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 293613000271 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 293613000272 Walker A/P-loop; other site 293613000273 ATP binding site [chemical binding]; other site 293613000274 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 293613000275 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 293613000276 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 293613000277 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 293613000278 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 293613000279 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl17212 293613000280 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl17212 293613000281 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 293613000282 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 293613000283 hypothetical protein; Provisional; Region: PRK13694 293613000284 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 293613000285 Protein export membrane protein; Region: SecD_SecF; pfam02355 293613000286 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 293613000287 SLBB domain; Region: SLBB; pfam10531 293613000288 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 293613000289 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 293613000290 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 293613000291 Catalytic site [active] 293613000292 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 293613000293 ribonuclease III; Reviewed; Region: rnc; PRK00102 293613000294 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 293613000295 dimerization interface [polypeptide binding]; other site 293613000296 active site 293613000297 metal binding site [ion binding]; metal-binding site 293613000298 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 293613000299 dsRNA binding site [nucleotide binding]; other site 293613000300 GTPase Era; Reviewed; Region: era; PRK00089 293613000301 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 293613000302 G1 box; other site 293613000303 GTP/Mg2+ binding site [chemical binding]; other site 293613000304 Switch I region; other site 293613000305 G2 box; other site 293613000306 Switch II region; other site 293613000307 G3 box; other site 293613000308 G4 box; other site 293613000309 G5 box; other site 293613000310 KH domain; Region: KH_2; pfam07650 293613000311 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 293613000312 active site 293613000313 putative DNA-binding cleft [nucleotide binding]; other site 293613000314 dimer interface [polypeptide binding]; other site 293613000315 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 293613000316 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 293613000317 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 293613000318 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 293613000319 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 293613000320 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 293613000321 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 293613000322 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 293613000323 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 293613000324 HflK protein; Region: hflK; TIGR01933 293613000325 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 293613000326 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 293613000327 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 293613000328 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 293613000329 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 293613000330 protein binding site [polypeptide binding]; other site 293613000331 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 293613000332 protein binding site [polypeptide binding]; other site 293613000333 hypothetical protein; Validated; Region: PRK01415 293613000334 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 293613000335 active site residue [active] 293613000336 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 293613000337 Iron-sulfur protein interface; other site 293613000338 proximal quinone binding site [chemical binding]; other site 293613000339 SdhD (CybS) interface [polypeptide binding]; other site 293613000340 proximal heme binding site [chemical binding]; other site 293613000341 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 293613000342 putative SdhC subunit interface [polypeptide binding]; other site 293613000343 putative proximal heme binding site [chemical binding]; other site 293613000344 putative Iron-sulfur protein interface [polypeptide binding]; other site 293613000345 putative proximal quinone binding site; other site 293613000346 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 293613000347 L-aspartate oxidase; Provisional; Region: PRK06175 293613000348 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 293613000349 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 293613000350 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 293613000351 dimer interface [polypeptide binding]; other site 293613000352 conserved gate region; other site 293613000353 putative PBP binding loops; other site 293613000354 ABC-ATPase subunit interface; other site 293613000355 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 293613000356 S17 interaction site [polypeptide binding]; other site 293613000357 S8 interaction site; other site 293613000358 16S rRNA interaction site [nucleotide binding]; other site 293613000359 streptomycin interaction site [chemical binding]; other site 293613000360 23S rRNA interaction site [nucleotide binding]; other site 293613000361 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 293613000362 30S ribosomal protein S7; Validated; Region: PRK05302 293613000363 elongation factor G; Reviewed; Region: PRK00007 293613000364 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 293613000365 G1 box; other site 293613000366 putative GEF interaction site [polypeptide binding]; other site 293613000367 GTP/Mg2+ binding site [chemical binding]; other site 293613000368 Switch I region; other site 293613000369 G2 box; other site 293613000370 G3 box; other site 293613000371 Switch II region; other site 293613000372 G4 box; other site 293613000373 G5 box; other site 293613000374 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 293613000375 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 293613000376 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 293613000377 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 293613000378 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 293613000379 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 293613000380 putative homodimer interface [polypeptide binding]; other site 293613000381 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 293613000382 heterodimer interface [polypeptide binding]; other site 293613000383 homodimer interface [polypeptide binding]; other site 293613000384 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 293613000385 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 293613000386 23S rRNA interface [nucleotide binding]; other site 293613000387 putative thiostrepton binding site; other site 293613000388 L7/L12 interface [polypeptide binding]; other site 293613000389 L25 interface [polypeptide binding]; other site 293613000390 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 293613000391 mRNA/rRNA interface [nucleotide binding]; other site 293613000392 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 293613000393 23S rRNA interface [nucleotide binding]; other site 293613000394 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 293613000395 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 293613000396 core dimer interface [polypeptide binding]; other site 293613000397 peripheral dimer interface [polypeptide binding]; other site 293613000398 L10 interface [polypeptide binding]; other site 293613000399 L11 interface [polypeptide binding]; other site 293613000400 putative EF-Tu interaction site [polypeptide binding]; other site 293613000401 putative EF-G interaction site [polypeptide binding]; other site 293613000402 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 293613000403 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 293613000404 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 293613000405 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 293613000406 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 293613000407 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 293613000408 RPB3 interaction site [polypeptide binding]; other site 293613000409 RPB1 interaction site [polypeptide binding]; other site 293613000410 RPB11 interaction site [polypeptide binding]; other site 293613000411 RPB10 interaction site [polypeptide binding]; other site 293613000412 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 293613000413 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 293613000414 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 293613000415 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 293613000416 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 293613000417 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 293613000418 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 293613000419 PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_glc; cl00162 293613000420 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 293613000421 DNA binding site [nucleotide binding] 293613000422 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 293613000423 multifunctional aminopeptidase A; Provisional; Region: PRK00913 293613000424 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 293613000425 interface (dimer of trimers) [polypeptide binding]; other site 293613000426 Substrate-binding/catalytic site; other site 293613000427 Zn-binding sites [ion binding]; other site 293613000428 ATPase MipZ; Region: MipZ; pfam09140 293613000429 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 293613000430 P-loop; other site 293613000431 Magnesium ion binding site [ion binding]; other site 293613000432 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 293613000433 Magnesium ion binding site [ion binding]; other site 293613000434 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 293613000435 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 293613000436 dimer interface [polypeptide binding]; other site 293613000437 anticodon binding site; other site 293613000438 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 293613000439 homodimer interface [polypeptide binding]; other site 293613000440 motif 1; other site 293613000441 active site 293613000442 motif 2; other site 293613000443 GAD domain; Region: GAD; pfam02938 293613000444 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 293613000445 active site 293613000446 motif 3; other site 293613000447 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 293613000448 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 293613000449 dihydrodipicolinate reductase; Provisional; Region: PRK00048 293613000450 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 293613000451 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 293613000452 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 293613000453 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 293613000454 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 293613000455 substrate binding pocket [chemical binding]; other site 293613000456 membrane-bound complex binding site; other site 293613000457 hinge residues; other site 293613000458 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 293613000459 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 293613000460 GatB domain; Region: GatB_Yqey; smart00845 293613000461 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 293613000462 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 293613000463 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 293613000464 ribosome recycling factor; Reviewed; Region: frr; PRK00083 293613000465 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 293613000466 hinge region; other site 293613000467 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 293613000468 putative nucleotide binding site [chemical binding]; other site 293613000469 uridine monophosphate binding site [chemical binding]; other site 293613000470 homohexameric interface [polypeptide binding]; other site 293613000471 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK06580 293613000472 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 293613000473 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 293613000474 putative substrate translocation pore; other site 293613000475 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 293613000476 Protein of unknown function (DUF2674); Region: DUF2674; pfam10879 293613000477 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 293613000478 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 293613000479 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 293613000480 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 293613000481 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 293613000482 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 293613000483 Surface antigen; Region: Bac_surface_Ag; pfam01103 293613000484 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 293613000485 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 293613000486 active site 293613000487 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 293613000488 protein binding site [polypeptide binding]; other site 293613000489 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 293613000490 putative substrate binding region [chemical binding]; other site 293613000491 Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus...; Region: Terminator_NusB; cd00619 293613000492 putative RNA binding site [nucleotide binding]; other site 293613000493 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 293613000494 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 293613000495 S-adenosylmethionine binding site [chemical binding]; other site 293613000496 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 293613000497 putative coenzyme Q binding site [chemical binding]; other site 293613000498 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 293613000499 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 293613000500 trimer interface [polypeptide binding]; other site 293613000501 active site 293613000502 substrate binding site [chemical binding]; other site 293613000503 CoA binding site [chemical binding]; other site 293613000504 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 293613000505 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 293613000506 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 293613000507 Subunit III/VIIa interface [polypeptide binding]; other site 293613000508 Phospholipid binding site [chemical binding]; other site 293613000509 Subunit I/III interface [polypeptide binding]; other site 293613000510 Subunit III/VIb interface [polypeptide binding]; other site 293613000511 Subunit III/VIa interface; other site 293613000512 Subunit III/Vb interface [polypeptide binding]; other site 293613000513 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 293613000514 diiron binding motif [ion binding]; other site 293613000515 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 293613000516 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 293613000517 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 293613000518 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 293613000519 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 293613000520 Nucleotide-binding domain of human HSPA9, Escherichia coli DnaK, and similar proteins; Region: HSPA9-like_NBD; cd11733 293613000521 nucleotide binding site [chemical binding]; other site 293613000522 NEF interaction site [polypeptide binding]; other site 293613000523 SBD interface [polypeptide binding]; other site 293613000524 chaperone protein DnaJ; Provisional; Region: PRK14300 293613000525 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 293613000526 HSP70 interaction site [polypeptide binding]; other site 293613000527 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 293613000528 substrate binding site [polypeptide binding]; other site 293613000529 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 293613000530 Zn binding sites [ion binding]; other site 293613000531 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 293613000532 dimer interface [polypeptide binding]; other site 293613000533 ChaB; Region: ChaB; cl01887 293613000534 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 293613000535 Tetratricopeptide repeat; Region: TPR_6; pfam13174 293613000536 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 293613000537 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 293613000538 Walker A/P-loop; other site 293613000539 ATP binding site [chemical binding]; other site 293613000540 Q-loop/lid; other site 293613000541 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 293613000542 ABC transporter signature motif; other site 293613000543 Walker B; other site 293613000544 D-loop; other site 293613000545 H-loop/switch region; other site 293613000546 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 293613000547 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 293613000548 active site 293613000549 Zn binding site [ion binding]; other site 293613000550 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 293613000551 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 293613000552 TPP-binding site [chemical binding]; other site 293613000553 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 293613000554 dimer interface [polypeptide binding]; other site 293613000555 PYR/PP interface [polypeptide binding]; other site 293613000556 TPP binding site [chemical binding]; other site 293613000557 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 293613000558 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 293613000559 E3 interaction surface; other site 293613000560 lipoyl attachment site [posttranslational modification]; other site 293613000561 e3 binding domain; Region: E3_binding; pfam02817 293613000562 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 293613000563 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism]; Region: COG0720 293613000564 active site 293613000565 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 293613000566 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 293613000567 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 293613000568 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 293613000569 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 293613000570 coproporphyrinogen III oxidase; Provisional; Region: PRK06582 293613000571 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 293613000572 FeS/SAM binding site; other site 293613000573 HemN C-terminal domain; Region: HemN_C; pfam06969 293613000574 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 293613000575 signal recognition particle protein; Provisional; Region: PRK10867 293613000576 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 293613000577 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 293613000578 P loop; other site 293613000579 GTP binding site [chemical binding]; other site 293613000580 Signal peptide binding domain; Region: SRP_SPB; pfam02978 293613000581 DNA polymerase III subunit delta'; Validated; Region: PRK06581 293613000582 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 293613000583 IHF dimer interface [polypeptide binding]; other site 293613000584 IHF - DNA interface [nucleotide binding]; other site 293613000585 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 293613000586 Uncharacterized conserved protein [Function unknown]; Region: COG2155 293613000587 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 293613000588 RNA methyltransferase, RsmE family; Region: TIGR00046 293613000589 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 293613000590 Ligand Binding Site [chemical binding]; other site 293613000591 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 293613000592 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 293613000593 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 293613000594 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 293613000595 catalytic loop [active] 293613000596 iron binding site [ion binding]; other site 293613000597 chaperone protein HscA; Provisional; Region: hscA; PRK01433 293613000598 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 293613000599 nucleotide binding site [chemical binding]; other site 293613000600 co-chaperone HscB; Provisional; Region: hscB; PRK01356 293613000601 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 293613000602 HSP70 interaction site [polypeptide binding]; other site 293613000603 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 293613000604 RNA/DNA hybrid binding site [nucleotide binding]; other site 293613000605 active site 293613000606 excinuclease ABC subunit B; Provisional; Region: PRK05298 293613000607 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 293613000608 ATP binding site [chemical binding]; other site 293613000609 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 293613000610 nucleotide binding region [chemical binding]; other site 293613000611 ATP-binding site [chemical binding]; other site 293613000612 Ultra-violet resistance protein B; Region: UvrB; pfam12344 293613000613 UvrB/uvrC motif; Region: UVR; pfam02151 293613000614 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 293613000615 GSH binding site [chemical binding]; other site 293613000616 catalytic residues [active] 293613000617 secreted effector protein PipB; Provisional; Region: PRK15197 293613000618 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 293613000619 Part of AAA domain; Region: AAA_19; pfam13245 293613000620 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 293613000621 Family description; Region: UvrD_C_2; pfam13538 293613000622 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 293613000623 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 293613000624 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 293613000625 active site 293613000626 catalytic site [active] 293613000627 substrate binding site [chemical binding]; other site 293613000628 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 293613000629 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 293613000630 CoA-binding site [chemical binding]; other site 293613000631 ATP-binding [chemical binding]; other site 293613000632 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3494 293613000633 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3814 293613000634 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 293613000635 RNA/DNA hybrid binding site [nucleotide binding]; other site 293613000636 active site 293613000637 hypothetical protein; Provisional; Region: PRK06630 293613000638 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 293613000639 mce related protein; Region: MCE; pfam02470 293613000640 similar to hypothetical protein 293613000641 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 293613000642 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 293613000643 DNA gyrase subunit A; Validated; Region: PRK05560 293613000644 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 293613000645 CAP-like domain; other site 293613000646 active site 293613000647 primary dimer interface [polypeptide binding]; other site 293613000648 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 293613000649 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 293613000650 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 293613000651 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 293613000652 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 293613000653 active site 293613000654 catalytic residues [active] 293613000655 metal binding site [ion binding]; metal-binding site 293613000656 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 293613000657 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 293613000658 putative active site [active] 293613000659 substrate binding site [chemical binding]; other site 293613000660 putative cosubstrate binding site; other site 293613000661 catalytic site [active] 293613000662 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 293613000663 substrate binding site [chemical binding]; other site 293613000664 Predicted ATPase [General function prediction only]; Region: COG1485 293613000665 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 293613000666 Walker A motif; other site 293613000667 ATP binding site [chemical binding]; other site 293613000668 Walker B motif; other site 293613000669 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 293613000670 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: PRK01424 293613000671 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 293613000672 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 293613000673 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 293613000674 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 293613000675 Walker A/P-loop; other site 293613000676 ATP binding site [chemical binding]; other site 293613000677 Q-loop/lid; other site 293613000678 ABC transporter signature motif; other site 293613000679 Walker B; other site 293613000680 D-loop; other site 293613000681 H-loop/switch region; other site 293613000682 Protein of unknown function (DUF2671); Region: DUF2671; pfam10877 293613000683 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 293613000684 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 293613000685 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 293613000686 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 293613000687 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 293613000688 putative metal binding site; other site 293613000689 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 293613000690 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 293613000691 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 293613000692 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 293613000693 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 293613000694 ATP binding site [chemical binding]; other site 293613000695 active site 293613000696 substrate binding site [chemical binding]; other site 293613000697 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 293613000698 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 293613000699 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 293613000700 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 293613000701 active site 293613000702 dimer interface [polypeptide binding]; other site 293613000703 motif 1; other site 293613000704 motif 2; other site 293613000705 motif 3; other site 293613000706 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 293613000707 anticodon binding site; other site 293613000708 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); Region: DUF2310; cl02380 293613000709 Protein of unknown function (DUF2660); Region: DUF2660; pfam10859 293613000710 Transposase IS200 like; Region: Y1_Tnp; pfam01797 293613000711 Transposase IS200 like; Region: Y1_Tnp; cl00848 293613000712 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 293613000713 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3827 293613000714 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 293613000715 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 293613000716 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 293613000717 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 293613000718 ATP binding site [chemical binding]; other site 293613000719 Mg2+ binding site [ion binding]; other site 293613000720 G-X-G motif; other site 293613000721 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 293613000722 anchoring element; other site 293613000723 dimer interface [polypeptide binding]; other site 293613000724 ATP binding site [chemical binding]; other site 293613000725 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 293613000726 active site 293613000727 metal binding site [ion binding]; metal-binding site 293613000728 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 293613000729 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 293613000730 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 293613000731 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 293613000732 protein binding site [polypeptide binding]; other site 293613000733 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 293613000734 Catalytic dyad [active] 293613000735 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 293613000736 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 293613000737 dimer interface [polypeptide binding]; other site 293613000738 phosphorylation site [posttranslational modification] 293613000739 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 293613000740 ATP binding site [chemical binding]; other site 293613000741 Mg2+ binding site [ion binding]; other site 293613000742 G-X-G motif; other site 293613000743 Tetratricopeptide repeat; Region: TPR_16; pfam13432 293613000744 Protein of unknown function (DUF2659); Region: DUF2659; pfam10858 293613000745 FOG: WD40-like repeat [Function unknown]; Region: COG1520 293613000746 Beta-barrel assembly machinery (Bam) complex component B and related proteins; Region: BamB_YfgL; cd10276 293613000747 Trp docking motif [polypeptide binding]; other site 293613000748 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 293613000749 23S rRNA interface [nucleotide binding]; other site 293613000750 L3 interface [polypeptide binding]; other site 293613000751 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 293613000752 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 293613000753 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 293613000754 aromatic arch; other site 293613000755 DCoH dimer interaction site [polypeptide binding]; other site 293613000756 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 293613000757 DCoH tetramer interaction site [polypeptide binding]; other site 293613000758 substrate binding site [chemical binding]; other site 293613000759 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 293613000760 putative active site [active] 293613000761 Ap4A binding site [chemical binding]; other site 293613000762 nudix motif; other site 293613000763 putative metal binding site [ion binding]; other site 293613000764 response regulator PleD; Reviewed; Region: pleD; PRK09581 293613000765 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 293613000766 active site 293613000767 phosphorylation site [posttranslational modification] 293613000768 intermolecular recognition site; other site 293613000769 dimerization interface [polypeptide binding]; other site 293613000770 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 293613000771 active site 293613000772 phosphorylation site [posttranslational modification] 293613000773 intermolecular recognition site; other site 293613000774 dimerization interface [polypeptide binding]; other site 293613000775 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 293613000776 metal binding site [ion binding]; metal-binding site 293613000777 active site 293613000778 I-site; other site 293613000779 elongation factor P; Validated; Region: PRK00529 293613000780 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 293613000781 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 293613000782 RNA binding site [nucleotide binding]; other site 293613000783 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 293613000784 RNA binding site [nucleotide binding]; other site 293613000785 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 293613000786 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 293613000787 active site 293613000788 Domain of unknown function (DUF2610); Region: DUF2610; pfam11020 293613000789 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 293613000790 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 293613000791 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 293613000792 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 293613000793 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 293613000794 HlyD family secretion protein; Region: HlyD_3; pfam13437 293613000795 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 293613000796 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 293613000797 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 293613000798 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 293613000799 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 293613000800 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 293613000801 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 293613000802 FAD binding domain; Region: FAD_binding_4; pfam01565 293613000803 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 293613000804 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 293613000805 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 293613000806 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 293613000807 ATP-grasp domain; Region: ATP-grasp_4; cl17255 293613000808 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 293613000809 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 293613000810 Cell division protein FtsQ; Region: FtsQ; pfam03799 293613000811 cell division protein FtsA; Region: ftsA; TIGR01174 293613000812 Cell division protein FtsA; Region: FtsA; smart00842 293613000813 Cell division protein FtsA; Region: FtsA; pfam14450 293613000814 Cytochrome c2 [Energy production and conversion]; Region: COG3474 293613000815 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 293613000816 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 293613000817 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 293613000818 RNA binding site [nucleotide binding]; other site 293613000819 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 293613000820 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 293613000821 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 293613000822 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 293613000823 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 293613000824 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 293613000825 RNA binding surface [nucleotide binding]; other site 293613000826 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 293613000827 active site 293613000828 Beta-lactamase; Region: Beta-lactamase; pfam00144 293613000829 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 293613000830 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 293613000831 putative catalytic site [active] 293613000832 putative phosphate binding site [ion binding]; other site 293613000833 active site 293613000834 metal binding site A [ion binding]; metal-binding site 293613000835 DNA binding site [nucleotide binding] 293613000836 putative AP binding site [nucleotide binding]; other site 293613000837 putative metal binding site B [ion binding]; other site 293613000838 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 293613000839 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 293613000840 tetramer interface [polypeptide binding]; other site 293613000841 TPP-binding site [chemical binding]; other site 293613000842 heterodimer interface [polypeptide binding]; other site 293613000843 phosphorylation loop region [posttranslational modification] 293613000844 pyruvate dehydrogenase subunit beta; Validated; Region: PRK09212 293613000845 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 293613000846 alpha subunit interface [polypeptide binding]; other site 293613000847 TPP binding site [chemical binding]; other site 293613000848 heterodimer interface [polypeptide binding]; other site 293613000849 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 293613000850 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 293613000851 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 293613000852 G1 box; other site 293613000853 putative GEF interaction site [polypeptide binding]; other site 293613000854 GTP/Mg2+ binding site [chemical binding]; other site 293613000855 Switch I region; other site 293613000856 G2 box; other site 293613000857 G3 box; other site 293613000858 Switch II region; other site 293613000859 G4 box; other site 293613000860 G5 box; other site 293613000861 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 293613000862 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 293613000863 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 293613000864 isocitrate dehydrogenase; Validated; Region: PRK09222 293613000865 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 293613000866 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 293613000867 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12507 293613000868 Predicted subunit of the Multisubunit Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: COG1563 293613000869 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 293613000870 Protein of unknown function (DUF2670); Region: DUF2670; pfam10875 293613000871 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 293613000872 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 293613000873 [2Fe-2S] cluster binding site [ion binding]; other site 293613000874 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 293613000875 cytochrome b; Provisional; Region: CYTB; MTH00191 293613000876 Qi binding site; other site 293613000877 intrachain domain interface; other site 293613000878 interchain domain interface [polypeptide binding]; other site 293613000879 heme bH binding site [chemical binding]; other site 293613000880 heme bL binding site [chemical binding]; other site 293613000881 Qo binding site; other site 293613000882 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 293613000883 interchain domain interface [polypeptide binding]; other site 293613000884 intrachain domain interface; other site 293613000885 Qi binding site; other site 293613000886 Qo binding site; other site 293613000887 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 293613000888 Cytochrome c; Region: Cytochrom_C; cl11414 293613000889 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 293613000890 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 293613000891 putative dimer interface [polypeptide binding]; other site 293613000892 peptide chain release factor 2; Validated; Region: prfB; PRK00578 293613000893 PCRF domain; Region: PCRF; pfam03462 293613000894 RF-1 domain; Region: RF-1; pfam00472 293613000895 GTP-binding protein LepA; Provisional; Region: PRK05433 293613000896 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 293613000897 G1 box; other site 293613000898 putative GEF interaction site [polypeptide binding]; other site 293613000899 GTP/Mg2+ binding site [chemical binding]; other site 293613000900 Switch I region; other site 293613000901 G2 box; other site 293613000902 G3 box; other site 293613000903 Switch II region; other site 293613000904 G4 box; other site 293613000905 G5 box; other site 293613000906 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 293613000907 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 293613000908 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 293613000909 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 293613000910 hypothetical protein; Validated; Region: PRK06620 293613000911 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 293613000912 Domain of unknown function DUF20; Region: UPF0118; pfam01594 293613000913 GrpE; Region: GrpE; pfam01025 293613000914 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 293613000915 dimer interface [polypeptide binding]; other site 293613000916 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 293613000917 ribonuclease PH; Reviewed; Region: rph; PRK00173 293613000918 Ribonuclease PH; Region: RNase_PH_bact; cd11362 293613000919 hexamer interface [polypeptide binding]; other site 293613000920 active site 293613000921 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 293613000922 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 293613000923 oligomerisation interface [polypeptide binding]; other site 293613000924 mobile loop; other site 293613000925 roof hairpin; other site 293613000926 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 293613000927 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 293613000928 ring oligomerisation interface [polypeptide binding]; other site 293613000929 ATP/Mg binding site [chemical binding]; other site 293613000930 stacking interactions; other site 293613000931 hinge regions; other site 293613000932 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 293613000933 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 293613000934 synthetase active site [active] 293613000935 NTP binding site [chemical binding]; other site 293613000936 metal binding site [ion binding]; metal-binding site 293613000937 Invasion associated locus B (IalB) protein; Region: IalB; cl02207 293613000938 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 293613000939 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 293613000940 HIGH motif; other site 293613000941 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 293613000942 active site 293613000943 KMSKS motif; other site 293613000944 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 293613000945 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 293613000946 S-adenosylmethionine binding site [chemical binding]; other site 293613000947 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 293613000948 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 293613000949 dimer interface [polypeptide binding]; other site 293613000950 putative PBP binding regions; other site 293613000951 ABC-ATPase subunit interface; other site 293613000952 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 293613000953 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 293613000954 putative substrate translocation pore; other site 293613000955 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 293613000956 putative acyl-acceptor binding pocket; other site 293613000957 C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas); Region: AAS_C; cd05909 293613000958 acyl-activating enzyme (AAE) consensus motif; other site 293613000959 putative AMP binding site [chemical binding]; other site 293613000960 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 293613000961 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 293613000962 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 293613000963 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 293613000964 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 293613000965 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 293613000966 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 293613000967 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 293613000968 carboxyltransferase (CT) interaction site; other site 293613000969 biotinylation site [posttranslational modification]; other site 293613000970 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 293613000971 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 293613000972 HIGH motif; other site 293613000973 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 293613000974 active site 293613000975 KMSKS motif; other site 293613000976 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 293613000977 tRNA binding surface [nucleotide binding]; other site 293613000978 anticodon binding site; other site 293613000979 Uncharacterized conserved protein [Function unknown]; Region: COG5590 293613000980 COQ9; Region: COQ9; pfam08511 293613000981 Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]; Region: RpsU; COG0828 293613000982 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 293613000983 Serpentine type 7TM GPCR chemoreceptor Srh; Region: 7TM_GPCR_Srh; cl11665 293613000984 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 293613000985 dimerization interface [polypeptide binding]; other site 293613000986 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 293613000987 dimer interface [polypeptide binding]; other site 293613000988 phosphorylation site [posttranslational modification] 293613000989 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 293613000990 ATP binding site [chemical binding]; other site 293613000991 Mg2+ binding site [ion binding]; other site 293613000992 G-X-G motif; other site 293613000993 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 293613000994 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 293613000995 metal ion transporter CorA-like divalent cation transporter superfamily; Region: MIT_CorA-like; cl00459 293613000996 ribonuclease P; Reviewed; Region: rnpA; PRK01492 293613000997 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 293613000998 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 293613000999 23S rRNA binding site [nucleotide binding]; other site 293613001000 L21 binding site [polypeptide binding]; other site 293613001001 L13 binding site [polypeptide binding]; other site 293613001002 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 293613001003 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 293613001004 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 293613001005 FeS/SAM binding site; other site 293613001006 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 293613001007 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 293613001008 5S rRNA interface [nucleotide binding]; other site 293613001009 CTC domain interface [polypeptide binding]; other site 293613001010 L16 interface [polypeptide binding]; other site 293613001011 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 293613001012 putative active site [active] 293613001013 catalytic residue [active] 293613001014 GTP-binding protein YchF; Reviewed; Region: PRK09601 293613001015 YchF GTPase; Region: YchF; cd01900 293613001016 G1 box; other site 293613001017 GTP/Mg2+ binding site [chemical binding]; other site 293613001018 Switch I region; other site 293613001019 G2 box; other site 293613001020 Switch II region; other site 293613001021 G3 box; other site 293613001022 G4 box; other site 293613001023 G5 box; other site 293613001024 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 293613001025 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 293613001026 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 293613001027 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 293613001028 putative substrate translocation pore; other site 293613001029 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 293613001030 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 293613001031 active site 293613001032 nucleophile elbow; other site 293613001033 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 293613001034 DnaA N-terminal domain; Region: DnaA_N; pfam11638 293613001035 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 293613001036 Walker A motif; other site 293613001037 ATP binding site [chemical binding]; other site 293613001038 Walker B motif; other site 293613001039 arginine finger; other site 293613001040 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 293613001041 DnaA box-binding interface [nucleotide binding]; other site 293613001042 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 293613001043 active site residue [active] 293613001044 Uncharacterized conserved protein [Function unknown]; Region: COG2938 293613001045 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 293613001046 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 293613001047 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 293613001048 ATP binding site [chemical binding]; other site 293613001049 putative Mg++ binding site [ion binding]; other site 293613001050 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 293613001051 nucleotide binding region [chemical binding]; other site 293613001052 ATP-binding site [chemical binding]; other site 293613001053 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 293613001054 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 293613001055 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 293613001056 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 293613001057 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 293613001058 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 293613001059 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 293613001060 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 293613001061 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 293613001062 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 293613001063 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 293613001064 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 293613001065 Mg++ binding site [ion binding]; other site 293613001066 putative catalytic motif [active] 293613001067 putative substrate binding site [chemical binding]; other site 293613001068 Coenzyme A transferase; Region: CoA_trans; cl17247 293613001069 Coenzyme A transferase; Region: CoA_trans; cl17247 293613001070 Coenzyme A transferase; Region: CoA_trans; cl17247 293613001071 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 293613001072 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 293613001073 ssDNA binding site; other site 293613001074 generic binding surface II; other site 293613001075 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 293613001076 ATP binding site [chemical binding]; other site 293613001077 putative Mg++ binding site [ion binding]; other site 293613001078 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 293613001079 nucleotide binding region [chemical binding]; other site 293613001080 ATP-binding site [chemical binding]; other site 293613001081 TraX protein; Region: TraX; pfam05857 293613001082 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 293613001083 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 293613001084 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 293613001085 dimer interface [polypeptide binding]; other site 293613001086 substrate binding site [chemical binding]; other site 293613001087 metal binding sites [ion binding]; metal-binding site 293613001088 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 293613001089 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 293613001090 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 293613001091 Cu(I) binding site [ion binding]; other site 293613001092 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 293613001093 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 293613001094 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 293613001095 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 293613001096 MgtE intracellular N domain; Region: MgtE_N; pfam03448 293613001097 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 293613001098 Divalent cation transporter; Region: MgtE; pfam01769 293613001099 Transposase IS200 like; Region: Y1_Tnp; cl00848 293613001100 Transposase IS200 like; Region: Y1_Tnp; cl00848 293613001101 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 293613001102 Haloacid dehalogenase-like hydrolase; Region: Hydrolase_6; pfam13344 293613001103 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 293613001104 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 293613001105 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 293613001106 Mg2+ binding site [ion binding]; other site 293613001107 G-X-G motif; other site 293613001108 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 293613001109 anchoring element; other site 293613001110 dimer interface [polypeptide binding]; other site 293613001111 ATP binding site [chemical binding]; other site 293613001112 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 293613001113 active site 293613001114 putative metal-binding site [ion binding]; other site 293613001115 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 293613001116 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 293613001117 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 293613001118 hinge; other site 293613001119 active site 293613001120 DNA-directed RNA polymerase, omega subunit; Region: rpoZ; TIGR00690 293613001121 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 293613001122 peptidylprolyl isomerase; Reviewed; Region: prsA; PRK02998 293613001123 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 293613001124 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 293613001125 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 293613001126 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 293613001127 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cl17351 293613001128 nucleotide binding region [chemical binding]; other site 293613001129 SEC-C motif; Region: SEC-C; pfam02810 293613001130 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 293613001131 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 293613001132 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 293613001133 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 293613001134 Na binding site [ion binding]; other site 293613001135 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 293613001136 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 293613001137 GIY-YIG motif/motif A; other site 293613001138 active site 293613001139 catalytic site [active] 293613001140 putative DNA binding site [nucleotide binding]; other site 293613001141 metal binding site [ion binding]; metal-binding site 293613001142 UvrB/uvrC motif; Region: UVR; pfam02151 293613001143 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 293613001144 Copper(I)-binding protein [Inorganic ion transport and metabolism]; Region: COG2847 293613001145 A new structural DNA glycosylase; Region: AlkD_like; cl11434 293613001146 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 293613001147 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 293613001148 DNA binding site [nucleotide binding] 293613001149 active site 293613001150 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 293613001151 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 293613001152 MraZ protein; Region: MraZ; pfam02381 293613001153 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 293613001154 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 293613001155 S-adenosylmethionine binding site [chemical binding]; other site 293613001156 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 293613001157 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 293613001158 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 293613001159 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 293613001160 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 293613001161 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 293613001162 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 293613001163 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 293613001164 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 293613001165 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 293613001166 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 293613001167 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 293613001168 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 293613001169 active site 293613001170 phosphorylation site [posttranslational modification] 293613001171 intermolecular recognition site; other site 293613001172 dimerization interface [polypeptide binding]; other site 293613001173 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 293613001174 Walker A motif; other site 293613001175 ATP binding site [chemical binding]; other site 293613001176 Walker B motif; other site 293613001177 arginine finger; other site 293613001178 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 293613001179 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK12612 293613001180 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK06617 293613001181 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 293613001182 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 293613001183 metabolite-proton symporter; Region: 2A0106; TIGR00883 293613001184 putative substrate translocation pore; other site 293613001185 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 293613001186 HD domain; Region: HD_4; pfam13328 293613001187 similar to hypothetical protein 293613001188 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 293613001189 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 293613001190 active site 293613001191 HIGH motif; other site 293613001192 dimer interface [polypeptide binding]; other site 293613001193 KMSKS motif; other site 293613001194 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 293613001195 RNA binding surface [nucleotide binding]; other site 293613001196 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 293613001197 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 293613001198 RNA binding surface [nucleotide binding]; other site 293613001199 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 293613001200 S-adenosylmethionine binding site [chemical binding]; other site 293613001201 ribosome maturation protein RimP; Reviewed; Region: PRK00092 293613001202 Sm and related proteins; Region: Sm_like; cl00259 293613001203 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 293613001204 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 293613001205 NusA N-terminal domain; Region: NusA_N; pfam08529 293613001206 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 293613001207 RNA binding site [nucleotide binding]; other site 293613001208 homodimer interface [polypeptide binding]; other site 293613001209 NusA-like KH domain; Region: KH_5; pfam13184 293613001210 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 293613001211 G-X-X-G motif; other site 293613001212 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 293613001213 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 293613001214 Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]; Region: InfB; COG0532 293613001215 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 293613001216 G1 box; other site 293613001217 putative GEF interaction site [polypeptide binding]; other site 293613001218 GTP/Mg2+ binding site [chemical binding]; other site 293613001219 Switch I region; other site 293613001220 G2 box; other site 293613001221 G3 box; other site 293613001222 Switch II region; other site 293613001223 G4 box; other site 293613001224 G5 box; other site 293613001225 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 293613001226 Translation-initiation factor 2; Region: IF-2; pfam11987 293613001227 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 293613001228 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214 293613001229 Glycoprotease family; Region: Peptidase_M22; pfam00814 293613001230 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 293613001231 Recombination protein O C terminal; Region: RecO_C; pfam02565 293613001232 DNA repair protein RadA; Provisional; Region: PRK11823 293613001233 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 293613001234 Walker A motif/ATP binding site; other site 293613001235 ATP binding site [chemical binding]; other site 293613001236 Walker B motif; other site 293613001237 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 293613001238 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 293613001239 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 293613001240 S-adenosylmethionine binding site [chemical binding]; other site 293613001241 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 293613001242 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 293613001243 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 293613001244 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 293613001245 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 293613001246 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 293613001247 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 293613001248 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 293613001249 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 293613001250 RNA binding surface [nucleotide binding]; other site 293613001251 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 293613001252 active site 293613001253 replicative DNA helicase; Provisional; Region: PRK09165 293613001254 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 293613001255 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 293613001256 Walker A motif; other site 293613001257 ATP binding site [chemical binding]; other site 293613001258 Walker B motif; other site 293613001259 DNA binding loops [nucleotide binding] 293613001260 polyprenyl P-hydroxybenzoate and phenylacrylic acid decarboxylases; Region: ubiX_pad; TIGR00421 293613001261 Flavoprotein; Region: Flavoprotein; pfam02441 293613001262 primosome assembly protein PriA; Validated; Region: PRK05580 293613001263 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 293613001264 ATP binding site [chemical binding]; other site 293613001265 putative Mg++ binding site [ion binding]; other site 293613001266 helicase superfamily c-terminal domain; Region: HELICc; smart00490 293613001267 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 293613001268 dimer interface [polypeptide binding]; other site 293613001269 allosteric magnesium binding site [ion binding]; other site 293613001270 active site 293613001271 aspartate-rich active site metal binding site; other site 293613001272 Schiff base residues; other site 293613001273 NADH dehydrogenase subunit 2; Provisional; Region: ND2; MTH00144 293613001274 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 293613001275 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 293613001276 Transposase IS200 like; Region: Y1_Tnp; cl00848 293613001277 Transposase IS200 like; Region: Y1_Tnp; cl00848 293613001278 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 293613001279 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 293613001280 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 293613001281 catalytic residue [active] 293613001282 cysteine desulfurase; Provisional; Region: PRK14012 293613001283 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 293613001284 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 293613001285 catalytic residue [active] 293613001286 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 293613001287 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 293613001288 trimerization site [polypeptide binding]; other site 293613001289 active site 293613001290 Iron-sulfur cluster assembly accessory protein; Region: TIGR00049 293613001291 arginine:agmatin antiporter; Provisional; Region: PRK10644 293613001292 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 293613001293 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 293613001294 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 293613001295 active site 293613001296 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 293613001297 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 293613001298 substrate binding pocket [chemical binding]; other site 293613001299 chain length determination region; other site 293613001300 substrate-Mg2+ binding site; other site 293613001301 catalytic residues [active] 293613001302 aspartate-rich region 1; other site 293613001303 active site lid residues [active] 293613001304 aspartate-rich region 2; other site 293613001305 TLC ATP/ADP transporter; Region: TLC; pfam03219 293613001306 Transposase IS200 like; Region: Y1_Tnp; pfam01797 293613001307 muropeptide transporter; Reviewed; Region: ampG; PRK11902 293613001308 AmpG-like permease; Region: 2A0125; TIGR00901 293613001309 Lysine efflux permease [General function prediction only]; Region: COG1279 293613001310 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 293613001311 active site 293613001312 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 293613001313 HemY protein N-terminus; Region: HemY_N; pfam07219 293613001314 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 293613001315 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 293613001316 Protein required for attachment to host cells; Region: Host_attach; cl02398 293613001317 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 293613001318 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 293613001319 putative acyl-acceptor binding pocket; other site 293613001320 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 293613001321 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 293613001322 active site 293613001323 HIGH motif; other site 293613001324 dimer interface [polypeptide binding]; other site 293613001325 KMSKS motif; other site 293613001326 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 293613001327 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 293613001328 domain interfaces; other site 293613001329 active site 293613001330 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cl00700 293613001331 Kinase/pyrophosphorylase; Region: Kinase-PPPase; cl00780 293613001332 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; cl00080 293613001333 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 293613001334 dimer interface [polypeptide binding]; other site 293613001335 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 293613001336 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 293613001337 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 293613001338 Uncharacterized ACR, YagE family COG1723; Region: DUF155; cl00751 293613001339 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 293613001340 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 293613001341 catalytic site [active] 293613001342 putative active site [active] 293613001343 putative substrate binding site [chemical binding]; other site 293613001344 HRDC domain; Region: HRDC; cl02578 293613001345 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 293613001346 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 293613001347 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 293613001348 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 293613001349 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 293613001350 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 293613001351 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 293613001352 Methyltransferase domain; Region: Methyltransf_11; pfam08241 293613001353 Protein of unknown function (DUF2532); Region: DUF2532; pfam10811 293613001354 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 293613001355 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 293613001356 N-acetyl-D-glucosamine binding site [chemical binding]; other site 293613001357 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 293613001358 hypothetical protein; Validated; Region: PRK00110 293613001359 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 293613001360 Substrate binding site; other site 293613001361 Mg++ binding site; other site 293613001362 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain superfamily; Region: NTP-PPase; cl16941 293613001363 metal binding site [ion binding]; metal-binding site 293613001364 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 293613001365 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 293613001366 homotetramer interface [polypeptide binding]; other site 293613001367 FMN binding site [chemical binding]; other site 293613001368 homodimer contacts [polypeptide binding]; other site 293613001369 putative active site [active] 293613001370 putative substrate binding site [chemical binding]; other site 293613001371 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 293613001372 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 293613001373 oligomer interface [polypeptide binding]; other site 293613001374 active site residues [active] 293613001375 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 293613001376 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 293613001377 RNA binding site [nucleotide binding]; other site 293613001378 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 293613001379 RNA binding site [nucleotide binding]; other site 293613001380 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 293613001381 RNA binding site [nucleotide binding]; other site 293613001382 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 293613001383 RNA binding site [nucleotide binding]; other site 293613001384 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 293613001385 RNA binding site [nucleotide binding]; other site 293613001386 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 293613001387 RNA binding site [nucleotide binding]; other site 293613001388 Cytidylate kinase [Nucleotide transport and metabolism]; Region: Cmk; COG0283 293613001389 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 293613001390 CMP-binding site; other site 293613001391 The sites determining sugar specificity; other site 293613001392 Integrase core domain; Region: rve_3; pfam13683 293613001393 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 293613001394 HD domain; Region: HD_4; pfam13328 293613001395 Predicted neuraminidase (sialidase) [Carbohydrate transport and metabolism]; Region: COG4692 293613001396 BNR repeat-like domain; Region: BNR_2; pfam13088 293613001397 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 293613001398 metabolite-proton symporter; Region: 2A0106; TIGR00883 293613001399 putative substrate translocation pore; other site 293613001400 Conjugal transfer protein TraD; Region: TraD; pfam06412 293613001401 MobA/MobL family; Region: MobA_MobL; pfam03389 293613001402 MobA/MobL family; Region: MobA_MobL; pfam03389 293613001403 AAA domain; Region: AAA_30; pfam13604 293613001404 Ti-type conjugative transfer relaxase TraA; Region: TraA_Ti; TIGR02768 293613001405 CHC2 zinc finger; Region: zf-CHC2; cl17510 293613001406 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 293613001407 active site 293613001408 metal binding site [ion binding]; metal-binding site 293613001409 interdomain interaction site; other site 293613001410 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 293613001411 Walker A motif; other site 293613001412 F sex factor protein N terminal; Region: TraD_N; pfam12615 293613001413 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 293613001414 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 293613001415 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 293613001416 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 293613001417 tandem repeat interface [polypeptide binding]; other site 293613001418 oligomer interface [polypeptide binding]; other site 293613001419 active site residues [active] 293613001420 transcription termination factor Rho; Provisional; Region: rho; PRK09376 293613001421 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 293613001422 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 293613001423 RNA binding site [nucleotide binding]; other site 293613001424 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 293613001425 multimer interface [polypeptide binding]; other site 293613001426 Walker A motif; other site 293613001427 ATP binding site [chemical binding]; other site 293613001428 Walker B motif; other site 293613001429 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 293613001430 S-adenosylmethionine binding site [chemical binding]; other site 293613001431 Methyltransferase domain; Region: Methyltransf_31; pfam13847 293613001432 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 293613001433 DHH family; Region: DHH; pfam01368 293613001434 DHHA1 domain; Region: DHHA1; pfam02272 293613001435 peptide chain release factor 1; Validated; Region: prfA; PRK00591 293613001436 This domain is found in peptide chain release factors; Region: PCRF; smart00937 293613001437 RF-1 domain; Region: RF-1; pfam00472 293613001438 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 293613001439 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 293613001440 E3 interaction surface; other site 293613001441 lipoyl attachment site [posttranslational modification]; other site 293613001442 e3 binding domain; Region: E3_binding; pfam02817 293613001443 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 293613001444 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 293613001445 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 293613001446 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 293613001447 Predicted membrane protein [Function unknown]; Region: COG5346 293613001448 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 293613001449 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 293613001450 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 293613001451 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 293613001452 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 293613001453 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 293613001454 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 293613001455 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 293613001456 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 293613001457 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 293613001458 conserved cys residue [active] 293613001459 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 293613001460 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 293613001461 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 293613001462 GSH binding site (G-site) [chemical binding]; other site 293613001463 C-terminal domain interface [polypeptide binding]; other site 293613001464 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 293613001465 N-terminal domain interface [polypeptide binding]; other site 293613001466 dimer interface [polypeptide binding]; other site 293613001467 substrate binding pocket (H-site) [chemical binding]; other site 293613001468 pyruvate phosphate dikinase; Provisional; Region: PRK09279 293613001469 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 293613001470 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 293613001471 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 293613001472 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 293613001473 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; cl00234 293613001474 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 293613001475 uncharacterized protein, YfiH family; Region: TIGR00726 293613001476 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 293613001477 Ribonuclease BN family enzyme [Replication, recombination, and repair]; Region: Rbn; COG1295 293613001478 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 293613001479 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 293613001480 non-specific DNA binding site [nucleotide binding]; other site 293613001481 salt bridge; other site 293613001482 sequence-specific DNA binding site [nucleotide binding]; other site 293613001483 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 293613001484 TLC ATP/ADP transporter; Region: TLC; pfam03219 293613001485 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK01528 293613001486 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 293613001487 RNA binding site [nucleotide binding]; other site 293613001488 active site 293613001489 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 293613001490 16S/18S rRNA binding site [nucleotide binding]; other site 293613001491 S13e-L30e interaction site [polypeptide binding]; other site 293613001492 25S rRNA binding site [nucleotide binding]; other site 293613001493 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 293613001494 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 293613001495 RNase E interface [polypeptide binding]; other site 293613001496 trimer interface [polypeptide binding]; other site 293613001497 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 293613001498 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 293613001499 RNase E interface [polypeptide binding]; other site 293613001500 trimer interface [polypeptide binding]; other site 293613001501 active site 293613001502 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl17245 293613001503 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 293613001504 RNA binding site [nucleotide binding]; other site 293613001505 domain interface; other site 293613001506 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 293613001507 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 293613001508 putative active site [active] 293613001509 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 293613001510 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 293613001511 OstA-like protein; Region: OstA; pfam03968 293613001512 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 293613001513 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 293613001514 Walker A/P-loop; other site 293613001515 ATP binding site [chemical binding]; other site 293613001516 Q-loop/lid; other site 293613001517 ABC transporter signature motif; other site 293613001518 Walker B; other site 293613001519 D-loop; other site 293613001520 H-loop/switch region; other site 293613001521 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 293613001522 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 293613001523 active site 293613001524 substrate binding site [chemical binding]; other site 293613001525 metal binding site [ion binding]; metal-binding site 293613001526 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 293613001527 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 293613001528 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 293613001529 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 293613001530 dimer interface [polypeptide binding]; other site 293613001531 putative radical transfer pathway; other site 293613001532 diiron center [ion binding]; other site 293613001533 tyrosyl radical; other site 293613001534 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 293613001535 Class I ribonucleotide reductase; Region: RNR_I; cd01679 293613001536 active site 293613001537 dimer interface [polypeptide binding]; other site 293613001538 catalytic residues [active] 293613001539 effector binding site; other site 293613001540 R2 peptide binding site; other site 293613001541 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 293613001542 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 293613001543 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 293613001544 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 293613001545 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14171 293613001546 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 293613001547 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 293613001548 homodimer interface [polypeptide binding]; other site 293613001549 NADP binding site [chemical binding]; other site 293613001550 substrate binding site [chemical binding]; other site 293613001551 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 293613001552 30S subunit binding site; other site 293613001553 Phage terminase large subunit (GpA); Region: Terminase_GpA; pfam05876 293613001554 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 293613001555 Found in ATP-dependent protease La (LON); Region: LON; smart00464 293613001556 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 293613001557 Walker A motif; other site 293613001558 ATP binding site [chemical binding]; other site 293613001559 Walker B motif; other site 293613001560 arginine finger; other site 293613001561 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 293613001562 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 293613001563 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 293613001564 tetramer interface [polypeptide binding]; other site 293613001565 pyridoxal 5'-phosphate binding site [chemical binding]; other site 293613001566 catalytic residue [active] 293613001567 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 293613001568 Part of AAA domain; Region: AAA_19; pfam13245 293613001569 Family description; Region: UvrD_C_2; pfam13538 293613001570 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 293613001571 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 293613001572 active site 293613001573 Transposase IS200 like; Region: Y1_Tnp; cl00848 293613001574 Transposase IS200 like; Region: Y1_Tnp; pfam01797 293613001575 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 293613001576 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 293613001577 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 293613001578 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 293613001579 Predicted permeases [General function prediction only]; Region: COG0679 293613001580 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 293613001581 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 293613001582 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 293613001583 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 293613001584 ATP-NAD kinase; Region: NAD_kinase; pfam01513 293613001585 recombination protein RecR; Reviewed; Region: recR; PRK00076 293613001586 RecR protein; Region: RecR; pfam02132 293613001587 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 293613001588 putative active site [active] 293613001589 putative metal-binding site [ion binding]; other site 293613001590 tetramer interface [polypeptide binding]; other site 293613001591 Predicted membrane protein/domain [Function unknown]; Region: COG1714 293613001592 Predicted membrane protein [Function unknown]; Region: COG1238 293613001593 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 293613001594 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4395 293613001595 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 293613001596 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 293613001597 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 293613001598 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 293613001599 CoA-ligase; Region: Ligase_CoA; pfam00549 293613001600 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 293613001601 CoA binding domain; Region: CoA_binding; pfam02629 293613001602 CoA-ligase; Region: Ligase_CoA; pfam00549 293613001603 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 293613001604 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 293613001605 catalytic residues [active] 293613001606 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 293613001607 SmpB-tmRNA interface; other site 293613001608 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 293613001609 dihydrodipicolinate synthase; Region: dapA; TIGR00674 293613001610 dimer interface [polypeptide binding]; other site 293613001611 active site 293613001612 catalytic residue [active] 293613001613 branched-chain amino acid aminotransferase; Validated; Region: PRK06606 293613001614 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 293613001615 homodimer interface [polypeptide binding]; other site 293613001616 substrate-cofactor binding pocket; other site 293613001617 pyridoxal 5'-phosphate binding site [chemical binding]; other site 293613001618 catalytic residue [active] 293613001619 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 293613001620 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 293613001621 active site 293613001622 phosphorylation site [posttranslational modification] 293613001623 intermolecular recognition site; other site 293613001624 dimerization interface [polypeptide binding]; other site 293613001625 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 293613001626 DNA binding site [nucleotide binding] 293613001627 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 293613001628 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 293613001629 dimer interface [polypeptide binding]; other site 293613001630 phosphorylation site [posttranslational modification] 293613001631 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 293613001632 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 293613001633 ATP binding site [chemical binding]; other site 293613001634 Mg2+ binding site [ion binding]; other site 293613001635 G-X-G motif; other site 293613001636 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 293613001637 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 293613001638 catalytic residue [active] 293613001639 putative FPP diphosphate binding site; other site 293613001640 putative FPP binding hydrophobic cleft; other site 293613001641 dimer interface [polypeptide binding]; other site 293613001642 putative IPP diphosphate binding site; other site 293613001643 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 293613001644 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 293613001645 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 293613001646 Septum formation initiator; Region: DivIC; pfam04977 293613001647 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 293613001648 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 293613001649 catalytic site [active] 293613001650 putative active site [active] 293613001651 putative substrate binding site [chemical binding]; other site 293613001652 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 293613001653 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 293613001654 HIGH motif; other site 293613001655 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 293613001656 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 293613001657 active site 293613001658 KMSKS motif; other site 293613001659 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 293613001660 tRNA binding surface [nucleotide binding]; other site 293613001661 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 293613001662 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 293613001663 DNA polymerase III subunit beta; Validated; Region: PRK05643 293613001664 putative DNA binding surface [nucleotide binding]; other site 293613001665 dimer interface [polypeptide binding]; other site 293613001666 beta-clamp/clamp loader binding surface; other site 293613001667 beta-clamp/translesion DNA polymerase binding surface; other site 293613001668 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 293613001669 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 293613001670 putative tRNA-binding site [nucleotide binding]; other site 293613001671 B3/4 domain; Region: B3_4; pfam03483 293613001672 tRNA synthetase B5 domain; Region: B5; smart00874 293613001673 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 293613001674 dimer interface [polypeptide binding]; other site 293613001675 motif 1; other site 293613001676 motif 3; other site 293613001677 motif 2; other site 293613001678 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 293613001679 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 293613001680 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 293613001681 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 293613001682 dimer interface [polypeptide binding]; other site 293613001683 motif 1; other site 293613001684 active site 293613001685 motif 2; other site 293613001686 motif 3; other site 293613001687 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 293613001688 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 293613001689 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 293613001690 FeS/SAM binding site; other site 293613001691 diaminopimelate epimerase; Region: DapF; TIGR00652 293613001692 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 293613001693 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 293613001694 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 293613001695 similar to hypothetical protein; COG0253 Diaminopimelate epimerase 293613001696 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 293613001697 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 293613001698 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 293613001699 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 293613001700 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 293613001701 active site 293613001702 homodimer interface [polypeptide binding]; other site 293613001703 cell division protein FtsW; Region: ftsW; TIGR02614 293613001704 Domain of unknown function (DUF4166); Region: DUF4166; pfam13761 293613001705 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01368 293613001706 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 293613001707 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 293613001708 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 293613001709 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 293613001710 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 293613001711 putative peptidase; Provisional; Region: PRK11649 293613001712 Peptidase family M23; Region: Peptidase_M23; pfam01551 293613001713 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 293613001714 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 293613001715 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 293613001716 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 293613001717 active site 293613001718 substrate binding site [chemical binding]; other site 293613001719 trimer interface [polypeptide binding]; other site 293613001720 CoA binding site [chemical binding]; other site 293613001721 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 293613001722 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 293613001723 Subunit I/III interface [polypeptide binding]; other site 293613001724 D-pathway; other site 293613001725 Subunit I/VIIc interface [polypeptide binding]; other site 293613001726 Subunit I/IV interface [polypeptide binding]; other site 293613001727 Subunit I/II interface [polypeptide binding]; other site 293613001728 Low-spin heme (heme a) binding site [chemical binding]; other site 293613001729 Subunit I/VIIa interface [polypeptide binding]; other site 293613001730 Subunit I/VIa interface [polypeptide binding]; other site 293613001731 Dimer interface; other site 293613001732 Putative water exit pathway; other site 293613001733 Binuclear center (heme a3/CuB) [ion binding]; other site 293613001734 K-pathway; other site 293613001735 Subunit I/Vb interface [polypeptide binding]; other site 293613001736 Putative proton exit pathway; other site 293613001737 Subunit I/VIb interface; other site 293613001738 Subunit I/VIc interface [polypeptide binding]; other site 293613001739 Electron transfer pathway; other site 293613001740 Subunit I/VIIIb interface [polypeptide binding]; other site 293613001741 Subunit I/VIIb interface [polypeptide binding]; other site 293613001742 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 293613001743 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 293613001744 catalytic triad [active] 293613001745 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 293613001746 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 293613001747 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 293613001748 dimer interface [polypeptide binding]; other site 293613001749 catalytic triad [active] 293613001750 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 293613001751 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 293613001752 N-acetyl-D-glucosamine binding site [chemical binding]; other site 293613001753 catalytic residue [active] 293613001754 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 293613001755 trimer interface [polypeptide binding]; other site 293613001756 active site 293613001757 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 293613001758 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 293613001759 tandem repeat interface [polypeptide binding]; other site 293613001760 oligomer interface [polypeptide binding]; other site 293613001761 active site residues [active] 293613001762 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 293613001763 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 293613001764 catalytic residues [active] 293613001765 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 293613001766 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 293613001767 active site 293613001768 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 293613001769 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 293613001770 Iron permease FTR1 family; Region: FTR1; cl00475 293613001771 Intracellular septation protein A; Region: IspA; cl01098 293613001772 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 293613001773 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 293613001774 BON domain; Region: BON; pfam04972 293613001775 BON domain; Region: BON; pfam04972 293613001776 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 293613001777 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 293613001778 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 293613001779 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 293613001780 muropeptide transporter; Reviewed; Region: ampG; PRK11902 293613001781 AmpG-like permease; Region: 2A0125; TIGR00901 293613001782 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 293613001783 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 293613001784 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 293613001785 Walker A/P-loop; other site 293613001786 ATP binding site [chemical binding]; other site 293613001787 Q-loop/lid; other site 293613001788 ABC transporter signature motif; other site 293613001789 Walker B; other site 293613001790 D-loop; other site 293613001791 H-loop/switch region; other site 293613001792 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 293613001793 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 293613001794 Walker A motif; other site 293613001795 ATP binding site [chemical binding]; other site 293613001796 Walker B motif; other site 293613001797 arginine finger; other site 293613001798 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 293613001799 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 293613001800 RuvA N terminal domain; Region: RuvA_N; pfam01330 293613001801 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 293613001802 Fic family protein [Function unknown]; Region: COG3177 293613001803 prolyl-tRNA synthetase; Provisional; Region: PRK12325 293613001804 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 293613001805 dimer interface [polypeptide binding]; other site 293613001806 motif 1; other site 293613001807 active site 293613001808 motif 2; other site 293613001809 motif 3; other site 293613001810 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 293613001811 anticodon binding site; other site 293613001812 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 293613001813 GTP cyclohydrolase I; Provisional; Region: PLN03044 293613001814 active site 293613001815 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 293613001816 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 293613001817 active site 293613001818 TLC ATP/ADP transporter; Region: TLC; pfam03219 293613001819 malate dehydrogenase; Reviewed; Region: PRK06223 293613001820 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 293613001821 NAD(P) binding site [chemical binding]; other site 293613001822 dimer interface [polypeptide binding]; other site 293613001823 tetramer (dimer of dimers) interface [polypeptide binding]; other site 293613001824 substrate binding site [chemical binding]; other site 293613001825 metabolite-proton symporter; Region: 2A0106; TIGR00883 293613001826 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 293613001827 Malic enzyme, N-terminal domain; Region: malic; pfam00390 293613001828 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 293613001829 putative NAD(P) binding site [chemical binding]; other site 293613001830 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 293613001831 Predicted permeases [General function prediction only]; Region: COG0679 293613001832 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 293613001833 catalytic core domain of class I lysyl tRNA synthetase; Region: LysRS_core_class_I; cd00674 293613001834 active site 293613001835 HIGH motif; other site 293613001836 KMSKS motif; other site 293613001837 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 293613001838 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cl00454 293613001839 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 293613001840 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 293613001841 amidase catalytic site [active] 293613001842 Zn binding residues [ion binding]; other site 293613001843 substrate binding site [chemical binding]; other site 293613001844 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 293613001845 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 293613001846 putative active site [active] 293613001847 catalytic triad [active] 293613001848 putative dimer interface [polypeptide binding]; other site 293613001849 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06603 293613001850 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 293613001851 NAD binding site [chemical binding]; other site 293613001852 homotetramer interface [polypeptide binding]; other site 293613001853 homodimer interface [polypeptide binding]; other site 293613001854 substrate binding site [chemical binding]; other site 293613001855 active site 293613001856 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 293613001857 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 293613001858 active site 293613001859 DNA binding site [nucleotide binding] 293613001860 Int/Topo IB signature motif; other site 293613001861 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4765 293613001862 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 293613001863 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 293613001864 NADH dehydrogenase subunit B; Validated; Region: PRK06411 293613001865 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 293613001866 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 293613001867 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 293613001868 catalytic site [active] 293613001869 metal binding site [ion binding]; metal-binding site 293613001870 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 293613001871 NADH dehydrogenase subunit D; Validated; Region: PRK06075 293613001872 NADH dehydrogenase subunit E; Validated; Region: PRK07539 293613001873 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 293613001874 putative dimer interface [polypeptide binding]; other site 293613001875 [2Fe-2S] cluster binding site [ion binding]; other site 293613001876 Haemolytic domain; Region: Haemolytic; cl00506 293613001877 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 293613001878 active site 293613001879 DNA binding site [nucleotide binding] 293613001880 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 293613001881 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 293613001882 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 293613001883 RimM N-terminal domain; Region: RimM; pfam01782 293613001884 PRC-barrel domain; Region: PRC; pfam05239 293613001885 Domain of unknown function (DUF4385); Region: DUF4385; pfam14328 293613001886 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 293613001887 UbiA prenyltransferase family; Region: UbiA; pfam01040 293613001888 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 293613001889 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 293613001890 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 293613001891 RNA binding surface [nucleotide binding]; other site 293613001892 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 293613001893 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 293613001894 putative ADP-binding pocket [chemical binding]; other site 293613001895 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 293613001896 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 293613001897 catalytic site [active] 293613001898 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 293613001899 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 293613001900 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 293613001901 HlyD family secretion protein; Region: HlyD_3; pfam13437 293613001902 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 293613001903 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 293613001904 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 293613001905 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 293613001906 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 293613001907 active site 293613001908 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 293613001909 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 293613001910 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 293613001911 This family is most closely related to the GT1 family of glycosyltransferases. wcfI in Bacteroides fragilis has been shown to be involved in the capsular polysaccharide biosynthesis; Region: GT1_wcfI_like; cd03825 293613001912 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 293613001913 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 293613001914 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 293613001915 active site 293613001916 homodimer interface [polypeptide binding]; other site 293613001917 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 293613001918 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 293613001919 NAD(P) binding site [chemical binding]; other site 293613001920 homodimer interface [polypeptide binding]; other site 293613001921 substrate binding site [chemical binding]; other site 293613001922 active site 293613001923 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 293613001924 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 293613001925 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 293613001926 NADP binding site [chemical binding]; other site 293613001927 active site 293613001928 putative substrate binding site [chemical binding]; other site 293613001929 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair]; Region: COG0816 293613001930 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 293613001931 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 293613001932 Sulfatase; Region: Sulfatase; pfam00884 293613001933 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 293613001934 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 293613001935 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 293613001936 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 293613001937 dimer interface [polypeptide binding]; other site 293613001938 decamer (pentamer of dimers) interface [polypeptide binding]; other site 293613001939 catalytic triad [active] 293613001940 peroxidatic and resolving cysteines [active] 293613001941 DNA topoisomerase I; Validated; Region: PRK06599 293613001942 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 293613001943 active site 293613001944 interdomain interaction site; other site 293613001945 putative metal-binding site [ion binding]; other site 293613001946 nucleotide binding site [chemical binding]; other site 293613001947 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 293613001948 domain I; other site 293613001949 DNA binding groove [nucleotide binding] 293613001950 phosphate binding site [ion binding]; other site 293613001951 domain II; other site 293613001952 domain III; other site 293613001953 nucleotide binding site [chemical binding]; other site 293613001954 catalytic site [active] 293613001955 domain IV; other site 293613001956 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 293613001957 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 293613001958 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 293613001959 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 293613001960 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 293613001961 active site 293613001962 HIGH motif; other site 293613001963 nucleotide binding site [chemical binding]; other site 293613001964 active site 293613001965 KMSKS motif; other site 293613001966 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 293613001967 frataxin-like protein; Provisional; Region: cyaY; PRK01379 293613001968 putative iron binding site [ion binding]; other site 293613001969 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 293613001970 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 293613001971 dimerization interface [polypeptide binding]; other site 293613001972 flagellar hook-associated protein FlgK; Region: flgK_ends; TIGR02492 293613001973 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 293613001974 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 293613001975 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 293613001976 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 293613001977 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 293613001978 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 293613001979 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 293613001980 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 293613001981 Walker A motif; other site 293613001982 ATP binding site [chemical binding]; other site 293613001983 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 293613001984 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 293613001985 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 293613001986 active site 293613001987 HslU subunit interaction site [polypeptide binding]; other site 293613001988 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 293613001989 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 293613001990 nucleotide binding site/active site [active] 293613001991 HIT family signature motif; other site 293613001992 catalytic residue [active] 293613001993 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 293613001994 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 293613001995 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 293613001996 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 293613001997 Walker A/P-loop; other site 293613001998 ATP binding site [chemical binding]; other site 293613001999 Q-loop/lid; other site 293613002000 ABC transporter signature motif; other site 293613002001 Walker B; other site 293613002002 D-loop; other site 293613002003 H-loop/switch region; other site 293613002004 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 293613002005 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 293613002006 HlyD family secretion protein; Region: HlyD_3; pfam13437 293613002007 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 293613002008 metabolite-proton symporter; Region: 2A0106; TIGR00883 293613002009 putative substrate translocation pore; other site 293613002010 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 293613002011 HD domain; Region: HD_4; pfam13328 293613002012 Gram-negative bacterial tonB protein; Region: TonB; cl10048 293613002013 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 293613002014 TolR protein; Region: tolR; TIGR02801 293613002015 TolQ protein; Region: tolQ; TIGR02796 293613002016 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 293613002017 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 293613002018 dimer interface [polypeptide binding]; other site 293613002019 motif 1; other site 293613002020 active site 293613002021 motif 2; other site 293613002022 motif 3; other site 293613002023 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 293613002024 anticodon binding site; other site 293613002025 amino acid transporter; Region: 2A0306; TIGR00909 293613002026 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 293613002027 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 293613002028 Ligand Binding Site [chemical binding]; other site 293613002029 galactosyl transferase GMA12/MNN10 family; Region: Glyco_transf_34; cl05288 293613002030 Cytochrome oxidase assembly factor [Posttranslational modification, protein turnover, chaperones]; Region: COX11; COG3175 293613002031 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 293613002032 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 293613002033 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 293613002034 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 293613002035 DNA binding residues [nucleotide binding] 293613002036 translocation protein TolB; Provisional; Region: tolB; PRK05137 293613002037 TolB amino-terminal domain; Region: TolB_N; pfam04052 293613002038 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 293613002039 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 293613002040 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 293613002041 Peptidase family M23; Region: Peptidase_M23; pfam01551 293613002042 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 293613002043 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 293613002044 SpoVT / AbrB like domain; Region: SpoVT_AbrB; smart00966 293613002045 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 293613002046 MutS domain I; Region: MutS_I; pfam01624 293613002047 MutS domain II; Region: MutS_II; pfam05188 293613002048 MutS domain III; Region: MutS_III; pfam05192 293613002049 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 293613002050 Walker A/P-loop; other site 293613002051 ATP binding site [chemical binding]; other site 293613002052 Q-loop/lid; other site 293613002053 ABC transporter signature motif; other site 293613002054 Walker B; other site 293613002055 D-loop; other site 293613002056 H-loop/switch region; other site 293613002057 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 293613002058 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 293613002059 active site 293613002060 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 293613002061 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 293613002062 Phage-related protein [Function unknown]; Region: COG4695; cl01923 293613002063 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 293613002064 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 293613002065 type IV secretion system component VirD4; Provisional; Region: PRK13897 293613002066 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 293613002067 Walker A motif; other site 293613002068 ATP binding site [chemical binding]; other site 293613002069 Walker B motif; other site 293613002070 type IV secretion system ATPase VirB11; Provisional; Region: PRK13900 293613002071 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 293613002072 Walker A motif; other site 293613002073 hexamer interface [polypeptide binding]; other site 293613002074 ATP binding site [chemical binding]; other site 293613002075 Walker B motif; other site 293613002076 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 293613002077 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 293613002078 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 293613002079 VirB8 protein; Region: VirB8; cl01500 293613002080 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 293613002081 VirB7 interaction site; other site 293613002082 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK07375 293613002083 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06591 293613002084 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 293613002085 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06589 293613002086 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 293613002087 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; Region: VapC; COG1487 293613002088 putative active site [active] 293613002089 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06588 293613002090 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 293613002091 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 293613002092 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 293613002093 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 293613002094 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 293613002095 Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]; Region: RplQ; COG0203 293613002096 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 293613002097 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 293613002098 alphaNTD - beta interaction site [polypeptide binding]; other site 293613002099 alphaNTD homodimer interface [polypeptide binding]; other site 293613002100 alphaNTD - beta' interaction site [polypeptide binding]; other site 293613002101 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 293613002102 30S ribosomal protein S11; Validated; Region: PRK05309 293613002103 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 293613002104 30S ribosomal protein S13; Region: bact_S13; TIGR03631 293613002105 adenylate kinase; Reviewed; Region: adk; PRK00279 293613002106 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 293613002107 AMP-binding site [chemical binding]; other site 293613002108 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 293613002109 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 293613002110 SecY translocase; Region: SecY; pfam00344 293613002111 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 293613002112 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 293613002113 23S rRNA binding site [nucleotide binding]; other site 293613002114 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 293613002115 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 293613002116 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 293613002117 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 293613002118 23S rRNA interface [nucleotide binding]; other site 293613002119 L21e interface [polypeptide binding]; other site 293613002120 5S rRNA interface [nucleotide binding]; other site 293613002121 L27 interface [polypeptide binding]; other site 293613002122 L5 interface [polypeptide binding]; other site 293613002123 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 293613002124 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 293613002125 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 293613002126 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 293613002127 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 293613002128 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 293613002129 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 293613002130 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 293613002131 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 293613002132 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 293613002133 RNA binding site [nucleotide binding]; other site 293613002134 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 293613002135 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 293613002136 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 293613002137 L23 interface [polypeptide binding]; other site 293613002138 trigger factor interaction site; other site 293613002139 23S rRNA interface [nucleotide binding]; other site 293613002140 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 293613002141 23S rRNA interface [nucleotide binding]; other site 293613002142 5S rRNA interface [nucleotide binding]; other site 293613002143 putative antibiotic binding site [chemical binding]; other site 293613002144 L25 interface [polypeptide binding]; other site 293613002145 L27 interface [polypeptide binding]; other site 293613002146 ribosomal protein S3, bacterial type; Region: rpsC_bact; TIGR01009 293613002147 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 293613002148 G-X-X-G motif; other site 293613002149 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 293613002150 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 293613002151 putative translocon binding site; other site 293613002152 protein-rRNA interface [nucleotide binding]; other site 293613002153 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 293613002154 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 293613002155 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 293613002156 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 293613002157 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 293613002158 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 293613002159 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 293613002160 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 293613002161 elongation factor Tu; Reviewed; Region: PRK00049 293613002162 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 293613002163 G1 box; other site 293613002164 GEF interaction site [polypeptide binding]; other site 293613002165 GTP/Mg2+ binding site [chemical binding]; other site 293613002166 Switch I region; other site 293613002167 G2 box; other site 293613002168 G3 box; other site 293613002169 Switch II region; other site 293613002170 G4 box; other site 293613002171 G5 box; other site 293613002172 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 293613002173 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 293613002174 Antibiotic Binding Site [chemical binding]; other site 293613002175 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 293613002176 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 293613002177 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 293613002178 fumarate hydratase; Reviewed; Region: fumC; PRK00485 293613002179 Class II fumarases; Region: Fumarase_classII; cd01362 293613002180 active site 293613002181 tetramer interface [polypeptide binding]; other site 293613002182 cell division protein FtsZ; Validated; Region: PRK09330 293613002183 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 293613002184 nucleotide binding site [chemical binding]; other site 293613002185 SulA interaction site; other site 293613002186 Protease Inhibitor Ecotin; homodimeric protease inhibitor; Region: Ecotin; cl00178 293613002187 secondary substrate binding site; other site 293613002188 primary substrate binding site; other site 293613002189 inhibition loop; other site 293613002190 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; smart00932 293613002191 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 293613002192 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 293613002193 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 293613002194 ATP binding site [chemical binding]; other site 293613002195 Mg++ binding site [ion binding]; other site 293613002196 motif III; other site 293613002197 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 293613002198 nucleotide binding region [chemical binding]; other site 293613002199 ATP-binding site [chemical binding]; other site 293613002200 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 293613002201 DNA-binding site [nucleotide binding]; DNA binding site 293613002202 RNA-binding motif; other site 293613002203 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 293613002204 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 293613002205 S-adenosylmethionine binding site [chemical binding]; other site 293613002206 SurA N-terminal domain; Region: SurA_N_3; cl07813 293613002207 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 293613002208 Organic solvent tolerance protein; Region: OstA_C; pfam04453 293613002209 Exonuclease VII, large subunit [DNA replication, recombination, and repair]; Region: XseA; COG1570 293613002210 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 293613002211 generic binding surface II; other site 293613002212 generic binding surface I; other site 293613002213 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 293613002214 putative catalytic site [active] 293613002215 putative phosphate binding site [ion binding]; other site 293613002216 active site 293613002217 metal binding site A [ion binding]; metal-binding site 293613002218 DNA binding site [nucleotide binding] 293613002219 putative AP binding site [nucleotide binding]; other site 293613002220 putative metal binding site B [ion binding]; other site 293613002221 GTP-binding protein Der; Reviewed; Region: PRK00093 293613002222 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 293613002223 G1 box; other site 293613002224 GTP/Mg2+ binding site [chemical binding]; other site 293613002225 Switch I region; other site 293613002226 G2 box; other site 293613002227 Switch II region; other site 293613002228 G3 box; other site 293613002229 G4 box; other site 293613002230 G5 box; other site 293613002231 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 293613002232 G1 box; other site 293613002233 GTP/Mg2+ binding site [chemical binding]; other site 293613002234 Switch I region; other site 293613002235 G2 box; other site 293613002236 G3 box; other site 293613002237 Switch II region; other site 293613002238 G4 box; other site 293613002239 G5 box; other site 293613002240 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 293613002241 ABC1 family; Region: ABC1; pfam03109 293613002242 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 293613002243 active site 293613002244 ATP binding site [chemical binding]; other site 293613002245 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 293613002246 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 293613002247 S-adenosylmethionine binding site [chemical binding]; other site 293613002248 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 293613002249 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 293613002250 DNA binding site [nucleotide binding] 293613002251 catalytic residue [active] 293613002252 H2TH interface [polypeptide binding]; other site 293613002253 putative catalytic residues [active] 293613002254 turnover-facilitating residue; other site 293613002255 intercalation triad [nucleotide binding]; other site 293613002256 8OG recognition residue [nucleotide binding]; other site 293613002257 putative reading head residues; other site 293613002258 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 293613002259 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 293613002260 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 293613002261 PHB de-polymerase C-terminus; Region: PHB_depo_C; pfam06850 293613002262 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 293613002263 active site 293613002264 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 293613002265 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 293613002266 active site 293613002267 HIGH motif; other site 293613002268 KMSKS motif; other site 293613002269 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 293613002270 tRNA binding surface [nucleotide binding]; other site 293613002271 anticodon binding site; other site 293613002272 thymidylate kinase; Validated; Region: tmk; PRK00698 293613002273 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 293613002274 TMP-binding site; other site 293613002275 ATP-binding site [chemical binding]; other site 293613002276 metabolite-proton symporter; Region: 2A0106; TIGR00883 293613002277 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 293613002278 4-hydroxybenzoate polyprenyltransferase; Reviewed; Region: ubiA; PRK12847 293613002279 UbiA prenyltransferase family; Region: UbiA; pfam01040 293613002280 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 293613002281 valyl-tRNA synthetase; Reviewed; Region: valS; PRK13208 293613002282 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 293613002283 active site 293613002284 HIGH motif; other site 293613002285 nucleotide binding site [chemical binding]; other site 293613002286 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 293613002287 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 293613002288 active site 293613002289 KMSKS motif; other site 293613002290 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 293613002291 tRNA binding surface [nucleotide binding]; other site 293613002292 anticodon binding site; other site 293613002293 AAA domain; Region: AAA_14; pfam13173 293613002294 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 293613002295 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 293613002296 RmuC family; Region: RmuC; pfam02646 293613002297 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cl01298 293613002298 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 293613002299 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 293613002300 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 293613002301 Walker A motif; other site 293613002302 ATP binding site [chemical binding]; other site 293613002303 Walker B motif; other site 293613002304 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 293613002305 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 293613002306 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 293613002307 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 293613002308 Ligand Binding Site [chemical binding]; other site 293613002309 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 293613002310 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 293613002311 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 293613002312 Walker A/P-loop; other site 293613002313 ATP binding site [chemical binding]; other site 293613002314 Q-loop/lid; other site 293613002315 ABC transporter signature motif; other site 293613002316 Walker B; other site 293613002317 D-loop; other site 293613002318 H-loop/switch region; other site 293613002319 Protein of unknown function (DUF2673); Region: DUF2673; pfam10880 293613002320 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 293613002321 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 293613002322 FtsX-like permease family; Region: FtsX; pfam02687 293613002323 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 293613002324 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 293613002325 Walker A/P-loop; other site 293613002326 ATP binding site [chemical binding]; other site 293613002327 Q-loop/lid; other site 293613002328 ABC transporter signature motif; other site 293613002329 Walker B; other site 293613002330 D-loop; other site 293613002331 H-loop/switch region; other site 293613002332 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 293613002333 Ulp1 protease family, C-terminal catalytic domain; Region: Peptidase_C48; cl17784 293613002334 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 293613002335 Domain of unknown function DUF21; Region: DUF21; pfam01595 293613002336 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 293613002337 Transporter associated domain; Region: CorC_HlyC; smart01091 293613002338 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 293613002339 Rickettsia outer membrane protein B; Region: rOmpB; pfam12334 293613002340 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 293613002341 Autotransporter beta-domain; Region: Autotransporter; smart00869 293613002342 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 293613002343 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 293613002344 synthetase active site [active] 293613002345 NTP binding site [chemical binding]; other site 293613002346 metal binding site [ion binding]; metal-binding site 293613002347 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 293613002348 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 293613002349 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 293613002350 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 293613002351 putative acyl-acceptor binding pocket; other site 293613002352 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 293613002353 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 293613002354 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 293613002355 Peptidase family M23; Region: Peptidase_M23; pfam01551 293613002356 Protein of unknown function (DUF519); Region: DUF519; pfam04378 293613002357 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 293613002358 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 293613002359 nucleotide binding pocket [chemical binding]; other site 293613002360 K-X-D-G motif; other site 293613002361 catalytic site [active] 293613002362 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 293613002363 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 293613002364 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 293613002365 Dimer interface [polypeptide binding]; other site 293613002366 BRCT sequence motif; other site 293613002367 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 293613002368 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 293613002369 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 293613002370 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 293613002371 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 293613002372 TLC ATP/ADP transporter; Region: TLC; pfam03219 293613002373 magnesium/cobalt efflux protein CorC; Provisional; Region: PRK15094 293613002374 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 293613002375 Transporter associated domain; Region: CorC_HlyC; smart01091 293613002376 metal-binding heat shock protein; Provisional; Region: PRK00016 293613002377 lipoyl synthase; Provisional; Region: PRK05481 293613002378 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 293613002379 FeS/SAM binding site; other site 293613002380 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 293613002381 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 293613002382 dimer interface [polypeptide binding]; other site 293613002383 active site 293613002384 glycine-pyridoxal phosphate binding site [chemical binding]; other site 293613002385 folate binding site [chemical binding]; other site 293613002386 putative hydrolase; Provisional; Region: PRK11460 293613002387 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 293613002388 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 293613002389 putative GSH binding site [chemical binding]; other site 293613002390 catalytic residues [active] 293613002391 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 293613002392 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 293613002393 minor groove reading motif; other site 293613002394 helix-hairpin-helix signature motif; other site 293613002395 substrate binding pocket [chemical binding]; other site 293613002396 active site 293613002397 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 293613002398 Predicted methyltransferases [General function prediction only]; Region: COG0313 293613002399 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 293613002400 putative SAM binding site [chemical binding]; other site 293613002401 putative homodimer interface [polypeptide binding]; other site 293613002402 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 293613002403 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 293613002404 putative ligand binding site [chemical binding]; other site 293613002405 twin arginine translocase protein A; Provisional; Region: tatA; PRK01470 293613002406 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 293613002407 tetramer interfaces [polypeptide binding]; other site 293613002408 binuclear metal-binding site [ion binding]; other site 293613002409 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 293613002410 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 293613002411 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 293613002412 aspartate kinase; Reviewed; Region: PRK06635 293613002413 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 293613002414 putative nucleotide binding site [chemical binding]; other site 293613002415 putative catalytic residues [active] 293613002416 putative Mg ion binding site [ion binding]; other site 293613002417 putative aspartate binding site [chemical binding]; other site 293613002418 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 293613002419 putative allosteric regulatory residue; other site 293613002420 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 293613002421 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 293613002422 metabolite-proton symporter; Region: 2A0106; TIGR00883 293613002423 putative substrate translocation pore; other site 293613002424 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 293613002425 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 293613002426 Helix-turn-helix domain; Region: HTH_25; pfam13413 293613002427 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]; Region: COG2902 293613002428 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 293613002429 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 293613002430 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 293613002431 trmE is a tRNA modification GTPase; Region: trmE; cd04164 293613002432 G1 box; other site 293613002433 GTP/Mg2+ binding site [chemical binding]; other site 293613002434 Switch I region; other site 293613002435 G2 box; other site 293613002436 Switch II region; other site 293613002437 G3 box; other site 293613002438 G4 box; other site 293613002439 G5 box; other site 293613002440 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 293613002441 recombinase A; Provisional; Region: recA; PRK09354 293613002442 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 293613002443 hexamer interface [polypeptide binding]; other site 293613002444 Walker A motif; other site 293613002445 ATP binding site [chemical binding]; other site 293613002446 Walker B motif; other site 293613002447 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 293613002448 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 293613002449 NAD(P) binding site [chemical binding]; other site 293613002450 active site 293613002451 acyl carrier protein; Provisional; Region: acpP; PRK00982 293613002452 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 293613002453 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 293613002454 dimer interface [polypeptide binding]; other site 293613002455 active site 293613002456 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 293613002457 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 293613002458 catalytic site [active] 293613002459 G-X2-G-X-G-K; other site 293613002460 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 293613002461 sequence-specific DNA binding site [nucleotide binding]; other site 293613002462 salt bridge; other site 293613002463 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 293613002464 rod shape-determining protein MreC; Region: MreC; pfam04085 293613002465 rod shape-determining protein MreB; Provisional; Region: PRK13927 293613002466 MreB and similar proteins; Region: MreB_like; cd10225 293613002467 nucleotide binding site [chemical binding]; other site 293613002468 Mg binding site [ion binding]; other site 293613002469 putative protofilament interaction site [polypeptide binding]; other site 293613002470 RodZ interaction site [polypeptide binding]; other site 293613002471 Predicted permeases [General function prediction only]; Region: COG0795 293613002472 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 293613002473 peptidoglycan-associated outer membrane lipoprotein; Provisional; Region: PRK10802 293613002474 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 293613002475 ligand binding site [chemical binding]; other site 293613002476 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 293613002477 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 293613002478 dimer interface [polypeptide binding]; other site 293613002479 active site 293613002480 CoA binding pocket [chemical binding]; other site 293613002481 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 293613002482 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 293613002483 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 293613002484 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 293613002485 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 293613002486 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 293613002487 P loop; other site 293613002488 GTP binding site [chemical binding]; other site 293613002489 DNA polymerase I; Provisional; Region: PRK05755 293613002490 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 293613002491 active site 293613002492 metal binding site 1 [ion binding]; metal-binding site 293613002493 putative 5' ssDNA interaction site; other site 293613002494 metal binding site 3; metal-binding site 293613002495 metal binding site 2 [ion binding]; metal-binding site 293613002496 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 293613002497 putative DNA binding site [nucleotide binding]; other site 293613002498 putative metal binding site [ion binding]; other site 293613002499 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 293613002500 active site 293613002501 DNA binding site [nucleotide binding] 293613002502 catalytic site [active] 293613002503 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 293613002504 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 293613002505 putative active site [active] 293613002506 putative PHP Thumb interface [polypeptide binding]; other site 293613002507 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 293613002508 generic binding surface I; other site 293613002509 generic binding surface II; other site 293613002510 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 293613002511 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 293613002512 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 293613002513 Protein of unknown function; Region: DUF3971; pfam13116 293613002514 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 293613002515 muropeptide transporter; Validated; Region: ampG; cl17669 293613002516 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 293613002517 seryl-tRNA synthetase; Provisional; Region: PRK05431 293613002518 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 293613002519 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 293613002520 dimer interface [polypeptide binding]; other site 293613002521 active site 293613002522 motif 1; other site 293613002523 motif 2; other site 293613002524 motif 3; other site 293613002525 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 293613002526 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 293613002527 Integral membrane protein TerC family; Region: TerC; cl10468 293613002528 Methyltransferase domain; Region: Methyltransf_31; pfam13847 293613002529 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 293613002530 S-adenosylmethionine binding site [chemical binding]; other site 293613002531 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 293613002532 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 293613002533 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 293613002534 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 293613002535 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 293613002536 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 293613002537 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 293613002538 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 293613002539 proton-translocating NADH-quinone oxidoreductase, chain M; Region: NDH_I_M; TIGR01972 293613002540 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 293613002541 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13541 293613002542 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 293613002543 Walker A/P-loop; other site 293613002544 ATP binding site [chemical binding]; other site 293613002545 Q-loop/lid; other site 293613002546 ABC transporter signature motif; other site 293613002547 Walker B; other site 293613002548 D-loop; other site 293613002549 H-loop/switch region; other site 293613002550 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 293613002551 4Fe-4S binding domain; Region: Fer4; cl02805 293613002552 4Fe-4S binding domain; Region: Fer4; pfam00037 293613002553 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 293613002554 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 293613002555 NADH dehydrogenase subunit G; Validated; Region: PRK09130 293613002556 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 293613002557 catalytic loop [active] 293613002558 iron binding site [ion binding]; other site 293613002559 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 293613002560 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 293613002561 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 293613002562 Predicted membrane protein [Function unknown]; Region: COG3671 293613002563 aconitate hydratase; Validated; Region: PRK09277 293613002564 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 293613002565 substrate binding site [chemical binding]; other site 293613002566 ligand binding site [chemical binding]; other site 293613002567 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 293613002568 substrate binding site [chemical binding]; other site 293613002569 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK01474 293613002570 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 293613002571 gamma subunit interface [polypeptide binding]; other site 293613002572 epsilon subunit interface [polypeptide binding]; other site 293613002573 LBP interface [polypeptide binding]; other site 293613002574 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 293613002575 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 293613002576 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 293613002577 alpha subunit interaction interface [polypeptide binding]; other site 293613002578 Walker A motif; other site 293613002579 ATP binding site [chemical binding]; other site 293613002580 Walker B motif; other site 293613002581 inhibitor binding site; inhibition site 293613002582 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 293613002583 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 293613002584 core domain interface [polypeptide binding]; other site 293613002585 delta subunit interface [polypeptide binding]; other site 293613002586 epsilon subunit interface [polypeptide binding]; other site 293613002587 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 293613002588 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 293613002589 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 293613002590 beta subunit interaction interface [polypeptide binding]; other site 293613002591 Walker A motif; other site 293613002592 ATP binding site [chemical binding]; other site 293613002593 Walker B motif; other site 293613002594 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 293613002595 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 293613002596 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 293613002597 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 293613002598 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 293613002599 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 293613002600 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 293613002601 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 293613002602 Transglycosylase; Region: Transgly; pfam00912 293613002603 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 293613002604 RNA binding site [nucleotide binding]; other site 293613002605 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 293613002606 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 293613002607 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 293613002608 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 293613002609 FeS/SAM binding site; other site 293613002610 TRAM domain; Region: TRAM; pfam01938 293613002611 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 293613002612 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 293613002613 Bacterial SH3 domain; Region: SH3_4; pfam06347 293613002614 Bacterial SH3 domain; Region: SH3_4; pfam06347 293613002615 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 293613002616 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 293613002617 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 293613002618 TrkA-N domain; Region: TrkA_N; pfam02254 293613002619 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 293613002620 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 293613002621 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 293613002622 rRNA binding site [nucleotide binding]; other site 293613002623 predicted 30S ribosome binding site; other site 293613002624 Maf-like protein; Region: Maf; pfam02545 293613002625 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 293613002626 active site 293613002627 dimer interface [polypeptide binding]; other site 293613002628 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 293613002629 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 293613002630 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 293613002631 active site 293613002632 DNA binding site [nucleotide binding] 293613002633 Int/Topo IB signature motif; other site 293613002634 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 293613002635 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 293613002636 putative active site [active] 293613002637 catalytic site [active] 293613002638 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism]; Region: UbiD; COG0043 293613002639 periplasmic folding chaperone; Provisional; Region: PRK10788 293613002640 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 293613002641 Autotransporter beta-domain; Region: Autotransporter; pfam03797 293613002642 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 293613002643 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 293613002644 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 293613002645 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 293613002646 active site 293613002647 Mpr1p, Pad1p N-terminal (MPN) domains; Region: MPN; cl13996 293613002648 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 293613002649 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 293613002650 Mg++ binding site [ion binding]; other site 293613002651 putative catalytic motif [active] 293613002652 putative substrate binding site [chemical binding]; other site 293613002653 Protein of unknown function (DUF721); Region: DUF721; pfam05258 293613002654 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 293613002655 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 293613002656 Ferredoxin [Energy production and conversion]; Region: COG1146 293613002657 4Fe-4S binding domain; Region: Fer4; cl02805 293613002658 heme exporter protein CcmC; Region: ccmC; TIGR01191 293613002659 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 293613002660 nucleoside/Zn binding site; other site 293613002661 dimer interface [polypeptide binding]; other site 293613002662 catalytic motif [active] 293613002663 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 293613002664 Cation efflux family; Region: Cation_efflux; cl00316 293613002665 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 293613002666 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 293613002667 substrate binding site [chemical binding]; other site 293613002668 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 293613002669 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 293613002670 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 293613002671 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 293613002672 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 293613002673 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 293613002674 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 293613002675 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 293613002676 dimer interface [polypeptide binding]; other site 293613002677 ssDNA binding site [nucleotide binding]; other site 293613002678 tetramer (dimer of dimers) interface [polypeptide binding]; other site 293613002679 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 293613002680 hypothetical protein; Reviewed; Region: PRK01530 293613002681 heat shock protein 90; Provisional; Region: PRK05218 293613002682 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 293613002683 ATP binding site [chemical binding]; other site 293613002684 Mg2+ binding site [ion binding]; other site 293613002685 G-X-G motif; other site 293613002686 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 293613002687 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 293613002688 substrate-cofactor binding pocket; other site 293613002689 pyridoxal 5'-phosphate binding site [chemical binding]; other site 293613002690 catalytic residue [active] 293613002691 trigger factor; Provisional; Region: tig; PRK01490 293613002692 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 293613002693 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 293613002694 GTPase CgtA; Reviewed; Region: obgE; PRK12299 293613002695 GTP1/OBG; Region: GTP1_OBG; pfam01018 293613002696 Obg GTPase; Region: Obg; cd01898 293613002697 G1 box; other site 293613002698 GTP/Mg2+ binding site [chemical binding]; other site 293613002699 Switch I region; other site 293613002700 G2 box; other site 293613002701 G3 box; other site 293613002702 Switch II region; other site 293613002703 G4 box; other site 293613002704 G5 box; other site 293613002705 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 293613002706 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 293613002707 dimer interface [polypeptide binding]; other site 293613002708 active site 293613002709 citrylCoA binding site [chemical binding]; other site 293613002710 NADH binding [chemical binding]; other site 293613002711 cationic pore residues; other site 293613002712 oxalacetate/citrate binding site [chemical binding]; other site 293613002713 coenzyme A binding site [chemical binding]; other site 293613002714 catalytic triad [active] 293613002715 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 293613002716 Fe-S cluster binding site [ion binding]; other site 293613002717 active site 293613002718 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 293613002719 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 293613002720 RNA binding surface [nucleotide binding]; other site 293613002721 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 293613002722 active site 293613002723 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 293613002724 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 293613002725 S-adenosylmethionine binding site [chemical binding]; other site 293613002726 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 293613002727 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 293613002728 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 293613002729 DALR anticodon binding domain; Region: DALR_1; pfam05746 293613002730 glycyl-tRNA synthetase subunit alpha; Validated; Region: glyQ; PRK09348 293613002731 motif 1; other site 293613002732 dimer interface [polypeptide binding]; other site 293613002733 active site 293613002734 motif 2; other site 293613002735 motif 3; other site 293613002736 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 293613002737 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 293613002738 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 293613002739 motif 1; other site 293613002740 active site 293613002741 motif 2; other site 293613002742 motif 3; other site 293613002743 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 293613002744 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 293613002745 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 293613002746 dimerization interface 3.5A [polypeptide binding]; other site 293613002747 active site 293613002748 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 293613002749 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 293613002750 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 293613002751 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 293613002752 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 293613002753 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 293613002754 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 293613002755 DNA binding residues [nucleotide binding] 293613002756 DNA primase, catalytic core; Region: dnaG; TIGR01391 293613002757 CHC2 zinc finger; Region: zf-CHC2; pfam01807 293613002758 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 293613002759 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 293613002760 active site 293613002761 metal binding site [ion binding]; metal-binding site 293613002762 interdomain interaction site; other site 293613002763 Dolichol kinase [Lipid metabolism]; Region: SEC59; COG0170 293613002764 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 293613002765 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 293613002766 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 293613002767 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 293613002768 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 293613002769 Outer membrane lipoprotein-sorting protein [Cell envelope biogenesis, outer membrane]; Region: LolA; COG2834 293613002770 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 293613002771 DNA polymerase III subunits gamma and tau; Validated; Region: PRK06645 293613002772 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 293613002773 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 293613002774 Walker B motif; other site 293613002775 arginine finger; other site 293613002776 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 293613002777 hypothetical protein; Validated; Region: PRK00153 293613002778 Predicted aspartyl protease [General function prediction only]; Region: COG3577 293613002779 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 293613002780 catalytic motif [active] 293613002781 Catalytic residue [active] 293613002782 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 293613002783 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 293613002784 Walker A/P-loop; other site 293613002785 ATP binding site [chemical binding]; other site 293613002786 Q-loop/lid; other site 293613002787 ABC transporter signature motif; other site 293613002788 Walker B; other site 293613002789 D-loop; other site 293613002790 H-loop/switch region; other site 293613002791 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 293613002792 putative hydrolase; Provisional; Region: PRK02113 293613002793 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 293613002794 active site 293613002795 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 293613002796 Predicted permeases [General function prediction only]; Region: COG0795 293613002797 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 293613002798 DNA polymerase III subunit chi; Provisional; Region: PRK06646 293613002799 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 293613002800 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 293613002801 metal binding site [ion binding]; metal-binding site 293613002802 dimer interface [polypeptide binding]; other site 293613002803 lipoate-protein ligase B; Provisional; Region: PRK14347 293613002804 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 293613002805 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 293613002806 amidase catalytic site [active] 293613002807 Zn binding residues [ion binding]; other site 293613002808 substrate binding site [chemical binding]; other site 293613002809 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 293613002810 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 293613002811 ribosomal protein L33, bacterial type; Region: rpmG_bact; TIGR01023 293613002812 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 293613002813 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 293613002814 ATP binding site [chemical binding]; other site 293613002815 Mg2+ binding site [ion binding]; other site 293613002816 G-X-G motif; other site 293613002817 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 293613002818 ATP binding site [chemical binding]; other site 293613002819 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 293613002820 Zinc-finger domain; Region: zf-CHCC; cl01821 293613002821 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 293613002822 NAD(P) binding site [chemical binding]; other site 293613002823 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 293613002824 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 293613002825 active site 293613002826 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 293613002827 metabolite-proton symporter; Region: 2A0106; TIGR00883 293613002828 putative substrate translocation pore; other site 293613002829 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 293613002830 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 293613002831 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 293613002832 ferrochelatase; Reviewed; Region: hemH; PRK00035 293613002833 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 293613002834 C-terminal domain interface [polypeptide binding]; other site 293613002835 active site 293613002836 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 293613002837 active site 293613002838 N-terminal domain interface [polypeptide binding]; other site 293613002839 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 293613002840 substrate binding site [chemical binding]; other site 293613002841 active site