-- dump date 20111121_015355 -- class Genbank::misc_feature -- table misc_feature_note -- id note 391009000001 chromosomal replication initiation protein; Provisional; Region: dnaA; PRK14088 391009000002 hypothetical protein; Validated; Region: PRK06672 391009000003 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...; Region: AAA; cd00009 391009000004 Walker A motif; other site 391009000005 ATP binding site [chemical binding]; other site 391009000006 Walker B motif; other site 391009000007 arginine finger; other site 391009000008 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 391009000009 DnaA box-binding interface [nucleotide binding]; other site 391009000010 Ferredoxin [Energy production and conversion]; Region: Fer; COG1141 391009000011 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 391009000012 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009000013 Walker A/P-loop; other site 391009000014 ATP binding site [chemical binding]; other site 391009000015 Q-loop/lid; other site 391009000016 ABC transporter signature motif; other site 391009000017 Walker B; other site 391009000018 D-loop; other site 391009000019 H-loop/switch region; other site 391009000020 mycofactocin system FadH/OYE family oxidoreductase 2; Region: mycofact_OYE_2; TIGR03997 391009000021 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as...; Region: OYE_like_FMN_family; cd02803 391009000022 active site 391009000023 FMN binding site [chemical binding]; other site 391009000024 substrate binding site [chemical binding]; other site 391009000025 putative catalytic residue [active] 391009000026 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 391009000027 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 391009000028 Ferredoxin [Energy production and conversion]; Region: COG1146 391009000029 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 391009000030 This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme; Region: NifX_NifB; cd00562 391009000031 This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of...; Region: MTH1175; cd00851 391009000032 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]; Region: COG1149 391009000033 This protein family's function is unkown. It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion; Region: Fer4_NifH_child; cd03110 391009000034 P loop nucleotide binding; other site 391009000035 switch II; other site 391009000036 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]; Region: COG1149 391009000037 This protein family's function is unkown. It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion; Region: Fer4_NifH_child; cd03110 391009000038 P loop nucleotide binding; other site 391009000039 switch II; other site 391009000040 1-pyrroline-5-carboxylate dehydrogenase; Provisional; Region: PRK03137 391009000041 Delta(1)-pyrroline-5-carboxylate dehydrogenase, RocA; Region: ALDH_PutA-P5CDH-RocA; cd07124 391009000042 Glutamate binding site [chemical binding]; other site 391009000043 homodimer interface [polypeptide binding]; other site 391009000044 NAD binding site [chemical binding]; other site 391009000045 catalytic residues [active] 391009000046 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 391009000047 Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea; Region: PBP1_BmpA_PnrA_like; cd06354 391009000048 ligand binding site [chemical binding]; other site 391009000049 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 391009000050 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and...; Region: ABC_Carb_Monos_I; cd03216 391009000051 Walker A/P-loop; other site 391009000052 ATP binding site [chemical binding]; other site 391009000053 Q-loop/lid; other site 391009000054 ABC transporter signature motif; other site 391009000055 Walker B; other site 391009000056 D-loop; other site 391009000057 H-loop/switch region; other site 391009000058 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (; Region: ABC_Carb_Monos_II; cd03215 391009000059 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (; Region: TM_PBP1_transp_TpRbsC_like; cd06580 391009000060 TM-ABC transporter signature motif; other site 391009000061 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (; Region: TM_PBP1_transp_TpRbsC_like; cd06580 391009000062 TM-ABC transporter signature motif; other site 391009000063 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 391009000064 Uncharacterised protein, DegV family COG1307; Region: DegV; cl00577 391009000065 DNA repair protein RadA; Provisional; Region: PRK11823 391009000066 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009000067 Walker A motif; other site 391009000068 ATP binding site [chemical binding]; other site 391009000069 Walker B motif; other site 391009000070 Clp protease ATP binding subunit; Region: clpC; CHL00095 391009000071 Clp amino terminal domain; Region: Clp_N; pfam02861 391009000072 Clp amino terminal domain; Region: Clp_N; pfam02861 391009000073 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...; Region: AAA; cd00009 391009000074 Walker A motif; other site 391009000075 ATP binding site [chemical binding]; other site 391009000076 Walker B motif; other site 391009000077 arginine finger; other site 391009000078 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...; Region: AAA; cd00009 391009000079 Walker A motif; other site 391009000080 ATP binding site [chemical binding]; other site 391009000081 Walker B motif; other site 391009000082 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 391009000083 Protein of unknown function (DUF3604); Region: DUF3604; pfam12228 391009000084 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 391009000085 ABC-type uncharacterized transport system; Region: ABC_transp_aux; pfam09822 391009000086 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 391009000087 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 391009000088 active site 391009000089 metal binding site [ion binding]; metal-binding site 391009000090 homotetramer interface [polypeptide binding]; other site 391009000091 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 391009000092 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 391009000093 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; cl14056 391009000094 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 391009000095 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 391009000096 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 391009000097 Isochorismatase family; Region: Isochorismatase; pfam00857 391009000098 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 391009000099 catalytic triad [active] 391009000100 conserved cis-peptide bond; other site 391009000101 Biotin synthase-related enzyme [General function prediction only]; Region: COG2516 391009000102 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 391009000103 FeS/SAM binding site; other site 391009000104 Y-family of DNA polymerases; Region: PolY; cl12025 391009000105 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 391009000106 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 four-...; Region: RecG_wedge_OBF; cd04488 391009000107 ssDNA binding site; other site 391009000108 generic binding surface II; other site 391009000109 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 391009000110 ATP binding site [chemical binding]; other site 391009000111 putative Mg++ binding site [ion binding]; other site 391009000112 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 391009000113 nucleotide binding region [chemical binding]; other site 391009000114 ATP-binding site [chemical binding]; other site 391009000115 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 391009000116 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 391009000117 Walker A/P-loop; other site 391009000118 ATP binding site [chemical binding]; other site 391009000119 Q-loop/lid; other site 391009000120 ABC transporter signature motif; other site 391009000121 Walker B; other site 391009000122 D-loop; other site 391009000123 H-loop/switch region; other site 391009000124 Thiamine pyrophosphokinase; Region: TPK; cd07995 391009000125 thiamine pyrophosphokinase; Region: thi_PPkinase; TIGR01378 391009000126 active site 391009000127 dimerization interface [polypeptide binding]; other site 391009000128 thiamine binding site [chemical binding]; other site 391009000129 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 391009000130 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 391009000131 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 391009000132 Cobalamin binding protein BtuF. These proteins have been shown to function as initial receptors in ABC transport of vitamin B12 (cobalamin) in eubacterial and some archaeal species. They belong to the TroA superfamily of helical backbone metal...; Region: BtuF; cd01144 391009000133 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 391009000134 cobalamin binding residues [chemical binding]; other site 391009000135 putative BtuC binding residues; other site 391009000136 dimer interface [polypeptide binding]; other site 391009000137 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...; Region: TM_ABC_iron-siderophores_like; cd06550 391009000138 ABC-ATPase subunit interface; other site 391009000139 dimer interface [polypeptide binding]; other site 391009000140 putative PBP binding regions; other site 391009000141 Predicted sugar phosphatases of the HAD superfamily [Carbohydrate transport and metabolism]; Region: NagD; COG0647 391009000142 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 391009000143 RNA polymerase factor sigma-70; Validated; Region: PRK08295 391009000144 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391009000145 lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-I; Region: Lumazine_synthase-I; cd09209 391009000146 homopentamer interface [polypeptide binding]; other site 391009000147 active site 391009000148 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09318 391009000149 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 391009000150 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cd00641 391009000151 dimerization interface [polypeptide binding]; other site 391009000152 active site 391009000153 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 391009000154 Lumazine binding domain; Region: Lum_binding; pfam00677 391009000155 Lumazine binding domain; Region: Lum_binding; pfam00677 391009000156 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 391009000157 Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the...; Region: Riboflavin_deaminase-reductase; cd01284 391009000158 catalytic motif [active] 391009000159 Zn binding site [ion binding]; other site 391009000160 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5,10-...; Region: DHFR; cl00161 391009000161 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 connected by an extended linker. The...; Region: HAMP; cd06225 391009000162 dimerization interface [polypeptide binding]; other site 391009000163 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 391009000164 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 391009000165 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 391009000166 trimerization site [polypeptide binding]; other site 391009000167 active site 391009000168 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 391009000169 Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS...; Region: SufS_like; cd06453 391009000170 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 391009000171 catalytic residue [active] 391009000172 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 391009000173 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 391009000174 FeS assembly protein SufB; Region: sufB; TIGR01980 391009000175 Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]; Region: sufC; COG0396 391009000176 ABC-type transport system involved in Fe-S cluster assembly, ATPase component. Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under...; Region: ABC_FeS_Assembly; cd03217 391009000177 Walker A/P-loop; other site 391009000178 ATP binding site [chemical binding]; other site 391009000179 Q-loop/lid; other site 391009000180 ABC transporter signature motif; other site 391009000181 Walker B; other site 391009000182 D-loop; other site 391009000183 H-loop/switch region; other site 391009000184 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 391009000185 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 391009000186 ring oligomerisation interface [polypeptide binding]; other site 391009000187 ATP/Mg binding site [chemical binding]; other site 391009000188 stacking interactions; other site 391009000189 hinge regions; other site 391009000190 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...; Region: cpn10; cd00320 391009000191 oligomerisation interface [polypeptide binding]; other site 391009000192 mobile loop; other site 391009000193 roof hairpin; other site 391009000194 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 post-...; Region: RIBOc; cl00258 391009000195 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_HprK; cl00270 391009000196 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 391009000197 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 391009000198 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 391009000199 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 391009000200 Predicted amino acid racemase [Amino acid transport and metabolism]; Region: COG3457 391009000201 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1; Region: PLPDE_III_AR_like_1; cd06815 391009000202 dimer interface [polypeptide binding]; other site 391009000203 active site 391009000204 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 391009000205 substrate binding site [chemical binding]; other site 391009000206 catalytic residue [active] 391009000207 site-specific tyrosine recombinase XerD-like protein; Reviewed; Region: xerD; PRK02436 391009000208 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 391009000209 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 391009000210 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...; Region: Ribosomal_S15p_S13e; cd00353 391009000211 16S/18S rRNA binding site [nucleotide binding]; other site 391009000212 S13e-L30e interaction site [polypeptide binding]; other site 391009000213 25S rRNA binding site [nucleotide binding]; other site 391009000214 prolyl-tRNA synthetase; Provisional; Region: PRK09194 391009000215 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 formation...; Region: ProRS_core_prok; cd00779 391009000216 dimer interface [polypeptide binding]; other site 391009000217 motif 1; other site 391009000218 active site 391009000219 motif 2; other site 391009000220 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and single-...; Region: ProRS-INS; cd04334 391009000221 putative deacylase active site [active] 391009000222 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 391009000223 active site 391009000224 motif 3; other site 391009000225 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-...; Region: ProRS_anticodon_short; cd00861 391009000226 anticodon binding site; other site 391009000227 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 391009000228 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 391009000229 active site 391009000230 HIGH motif; other site 391009000231 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 391009000232 KMSKS motif; other site 391009000233 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 391009000234 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 391009000235 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 391009000236 active site 391009000237 HIGH motif; other site 391009000238 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 391009000239 active site 391009000240 KMSKS motif; other site 391009000241 Permease family; Region: Xan_ur_permease; pfam00860 391009000242 Sulfate transporter family; Region: Sulfate_transp; cl00967 391009000243 Predicted O-acyltransferase [General function prediction only]; Region: COG3274; cl00792 391009000244 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14330 391009000245 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 391009000246 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 391009000247 FeS/SAM binding site; other site 391009000248 Uncharacterized conserved protein [Function unknown]; Region: COG1284 391009000249 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 391009000250 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; cl10498 391009000251 Isochorismatase family; Region: Isochorismatase; pfam00857 391009000252 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 391009000253 catalytic triad [active] 391009000254 conserved cis-peptide bond; other site 391009000255 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 391009000256 Cation efflux family; Region: Cation_efflux; cl00316 391009000257 ADP-glucose phosphorylase; Region: PLN02643 391009000258 Galactose-1-phosphate uridyl transferase (GalT): This enzyme plays a key role in galactose metabolism by catalysing the transfer of a uridine 5'-phosphoryl group from UDP-galactose 1-phosphate. The structure of E.coli GalT reveals that the enzyme...; Region: GalT; cd00608 391009000259 dimer interface [polypeptide binding]; other site 391009000260 active site 391009000261 glycogen synthase; Provisional; Region: glgA; PRK00654 391009000262 This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family...; Region: GT1_Glycogen_synthase_DULL1_like; cd03791 391009000263 ADP-binding pocket [chemical binding]; other site 391009000264 homodimer interface [polypeptide binding]; other site 391009000265 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 391009000266 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 391009000267 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 391009000268 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 391009000269 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...; Region: AAA; cd00009 391009000270 Walker A motif; other site 391009000271 ATP binding site [chemical binding]; other site 391009000272 Walker B motif; other site 391009000273 arginine finger; other site 391009000274 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 391009000275 Uncharacterised protein family UPF0047; Region: UPF0047; cl00439 391009000276 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 391009000277 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase...; Region: B12-binding_like; cl00293 391009000278 Coenzyme B12-dependent glutamate mutase epsilon subunit-like family; contains proteins similar to Clostridium cochlearium glutamate mutase (Glm) and Streptomyces tendae Tu901 NikV. Glm catalyzes a carbon-skeleton rearrangement of L-glutamate to L-threo-; Region: Glm_e; cl02025 391009000279 substrate binding site [chemical binding]; other site 391009000280 B12 cofactor binding site [chemical binding]; other site 391009000281 heterodimer (sigma-epsilon) interface [polypeptide binding]; other site 391009000282 homodimer (epsilon-epsilon) interface [polypeptide binding]; other site 391009000283 NAD binding domain of 6-phosphogluconate dehydrogenase; Region: NAD_binding_2; pfam03446 391009000284 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009000285 NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain; Region: Octopine_DH; pfam02317 391009000286 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 391009000287 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009000288 MOFRL family; Region: MOFRL; cl01013 391009000289 NAD synthase; Region: NAD_synthase; pfam02540 391009000290 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to...; Region: NAD_synthase; cd00553 391009000291 homodimer interface [polypeptide binding]; other site 391009000292 NAD binding pocket [chemical binding]; other site 391009000293 ATP binding pocket [chemical binding]; other site 391009000294 Mg binding site [ion binding]; other site 391009000295 active-site loop [active] 391009000296 chaperone protein DnaJ; Provisional; Region: PRK14282 391009000297 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...; Region: DnaJ; cd06257 391009000298 HSP70 interaction site [polypeptide binding]; other site 391009000299 DnaJ central domain; Region: DnaJ_CXXCXGXG; cl14908 391009000300 DnaJ C terminal domain; Region: DnaJ_C; pfam01556 391009000301 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 391009000302 dimer interface [polypeptide binding]; other site 391009000303 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 391009000304 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 391009000305 heat shock gene repressor HrcA; Region: hrcA; TIGR00331 391009000306 HrcA protein C terminal domain; Region: HrcA; pfam01628 391009000307 benzoate transport; Region: 2A0115; TIGR00895 391009000308 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 391009000309 putative substrate translocation pore; other site 391009000310 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 391009000311 Predicted small molecule binding protein (contains 3H domain) [General function prediction only]; Region: COG1827 391009000312 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 391009000313 3H domain; Region: 3H; pfam02829 391009000314 Haemolysin-III related; Region: HlyIII; cl03831 391009000315 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 391009000316 putative heme d1 biosynthesis radical SAM protein NirJ2; Region: rSAM_NirJ2; TIGR04055 391009000317 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 391009000318 FeS/SAM binding site; other site 391009000319 radical SAM additional 4Fe4S-binding domain; Region: rSAM_more_4Fe4S; TIGR04085 391009000320 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 391009000321 M42 Peptidase, Endoglucanases; Region: M42_Frv; cd05656 391009000322 oligomer interface [polypeptide binding]; other site 391009000323 active site 391009000324 metal binding site [ion binding]; metal-binding site 391009000325 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 391009000326 M42 Peptidase, Endoglucanases; Region: M42_Frv; cd05656 391009000327 oligomer interface [polypeptide binding]; other site 391009000328 active site 391009000329 metal binding site [ion binding]; metal-binding site 391009000330 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 391009000331 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...; Region: GMPK; cd00071 391009000332 catalytic site [active] 391009000333 G-X2-G-X-G-K; other site 391009000334 Domain of unknown function (DUF370); Region: DUF370; cl00898 391009000335 hypothetical protein; Provisional; Region: PRK11820 391009000336 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 391009000337 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 391009000338 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 391009000339 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 391009000340 Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR...; Region: TPP_OGFOR; cd03375 391009000341 TPP-binding site [chemical binding]; other site 391009000342 2-ketoisovalerate ferredoxin reductase; Validated; Region: PRK07119 391009000343 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 391009000344 dimer interface [polypeptide binding]; other site 391009000345 PYR/PP interface [polypeptide binding]; other site 391009000346 TPP binding site [chemical binding]; other site 391009000347 substrate binding site [chemical binding]; other site 391009000348 Ferredoxin [Energy production and conversion]; Region: COG1146 391009000349 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-; Region: HCP_like; cl14655 391009000350 antiporter inner membrane protein; Provisional; Region: PRK11670 391009000351 Acetokinase family; Region: Acetate_kinase; cl01029 391009000352 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 391009000353 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 391009000354 Acetokinase family; Region: Acetate_kinase; cl01029 391009000355 aspartate aminotransferase; Provisional; Region: PRK08361 391009000356 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 391009000357 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391009000358 homodimer interface [polypeptide binding]; other site 391009000359 catalytic residue [active] 391009000360 Alanine-glyoxylate aminotransferase (AGAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to alanine-glyoxylate aminotransferase (AGAT), serine-...; Region: AGAT_like; cd06451 391009000361 homodimer interface [polypeptide binding]; other site 391009000362 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391009000363 catalytic residue [active] 391009000364 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 391009000365 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009000366 Carbon starvation protein CstA; Region: CstA; cl00856 391009000367 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 391009000368 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 391009000369 active site 391009000370 phosphorylation site [posttranslational modification] 391009000371 intermolecular recognition site; other site 391009000372 dimerization interface [polypeptide binding]; other site 391009000373 LytTr DNA-binding domain; Region: LytTR; cl04498 391009000374 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 391009000375 Protein of unknown function (DUF1393); Region: DUF1393; cl01942 391009000376 Histidine kinase; Region: His_kinase; pfam06580 391009000377 peptidase; Reviewed; Region: PRK13004 391009000378 M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases; Region: M20_ArgE_DapE_like4; cd05649 391009000379 putative metal binding site [ion binding]; other site 391009000380 putative dimer interface [polypeptide binding]; other site 391009000381 probable carbamoyltransferase YgeW; Region: ygeW; TIGR03316 391009000382 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 391009000383 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 391009000384 phenylhydantoinase; Validated; Region: PRK08323 391009000385 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have...; Region: metallo-dependent_hydrolases; cl00281 391009000386 active site 391009000387 putative chlorohydrolase/aminohydrolase; Validated; Region: PRK07203 391009000388 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have...; Region: metallo-dependent_hydrolases; cl00281 391009000389 active site 391009000390 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 391009000391 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 391009000392 phosphate binding site [ion binding]; other site 391009000393 4Fe-4S binding domain; Region: Fer4; cl02805 391009000394 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 391009000395 Stage V sporulation protein S (SpoVS); Region: SpoVS; cl01005 391009000396 bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor; Reviewed; Region: ushA; PRK09558 391009000397 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 391009000398 active site 391009000399 metal binding site [ion binding]; metal-binding site 391009000400 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 391009000401 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 391009000402 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 391009000403 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009000404 Walker A/P-loop; other site 391009000405 ATP binding site [chemical binding]; other site 391009000406 Q-loop/lid; other site 391009000407 ABC transporter signature motif; other site 391009000408 Walker B; other site 391009000409 D-loop; other site 391009000410 H-loop/switch region; other site 391009000411 Uncharacterised ACR, COG1259; Region: DUF151; cl00553 391009000412 1-acyl-sn-glycerol-3-phosphate acyltransferase; Provisional; Region: PRK15018 391009000413 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 391009000414 putative acyl-acceptor binding pocket; other site 391009000415 thiamine biosynthesis protein ThiI; Provisional; Region: PRK01565 391009000416 THUMP domain; Region: THUMP; cl12076 391009000417 ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide; Region: ThiI; cd01712 391009000418 Ligand Binding Site [chemical binding]; other site 391009000419 Uncharacterized family 2; belongs to a superfamily containing transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this family was previously known as part of DUF156; Region: CsoR-like_DUF156_2; cd10159 391009000420 putative homotetramer interface [polypeptide binding]; other site 391009000421 putative homodimer interface [polypeptide binding]; other site 391009000422 putative allosteric switch controlling residues; other site 391009000423 putative metal binding site [ion binding]; other site 391009000424 putative homodimer-homodimer interface [polypeptide binding]; other site 391009000425 NlpC/P60 family; Region: NLPC_P60; cl11438 391009000426 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 391009000427 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 391009000428 Glucan exporter ATP-binding protein. In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide...; Region: ABCC_Glucan_exporter_like; cd03254 391009000429 Walker A/P-loop; other site 391009000430 ATP binding site [chemical binding]; other site 391009000431 Q-loop/lid; other site 391009000432 ABC transporter signature motif; other site 391009000433 Walker B; other site 391009000434 D-loop; other site 391009000435 H-loop/switch region; other site 391009000436 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 391009000437 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 391009000438 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009000439 Walker A/P-loop; other site 391009000440 ATP binding site [chemical binding]; other site 391009000441 Q-loop/lid; other site 391009000442 ABC transporter signature motif; other site 391009000443 Walker B; other site 391009000444 D-loop; other site 391009000445 H-loop/switch region; other site 391009000446 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 391009000447 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 391009000448 MG2 domain; Region: A2M_N; pfam01835 391009000449 Bacterial Ig-like domain (group 1); Region: Big_1; cl10510 391009000450 Alpha-2-macroglobulin family N-terminal region; Region: A2M_N_2; pfam07703 391009000451 Alpha-2-macroglobulin family; Region: A2M; pfam00207 391009000452 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 391009000453 surface patch; other site 391009000454 thioester region; other site 391009000455 specificity defining residues; other site 391009000456 Protein of unknown function (DUF1175); Region: DUF1175; cl14898 391009000457 Iron-containing alcohol dehydrogenase; Region: Fe-ADH8; cd08186 391009000458 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 391009000459 putative active site [active] 391009000460 metal binding site [ion binding]; metal-binding site 391009000461 coenzyme A disulfide reductase; Reviewed; Region: PRK09564 391009000462 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 391009000463 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 391009000464 CAAX amino terminal protease self- immunity; Region: Abi; cl00558 391009000465 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 connected by an extended linker. The...; Region: HAMP; cl01054 391009000466 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM)-like family; contains proteins similar to MCM, and the large subunit of Streptomyces coenzyme B12-dependent isobutyryl-CoA mutase (ICM). MCM catalyzes the isomerization of methylmalonyl-; Region: MM_CoA_mutase; cl00817 391009000467 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 391009000468 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 391009000469 oligoendopeptidase, M3 family; Region: M3_not_pepF; TIGR02289 391009000470 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_1; cd09606 391009000471 active site 391009000472 Zn binding site [ion binding]; other site 391009000473 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 391009000474 MatE; Region: MatE; pfam01554 391009000475 MatE; Region: MatE; pfam01554 391009000476 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 391009000477 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and...; Region: Aldo_ket_red; cd06660 391009000478 active site 391009000479 catalytic tetrad [active] 391009000480 Thermophilic metalloprotease (M29); Region: Peptidase_M29; pfam02073 391009000481 ABC-2 type transporter; Region: ABC2_membrane; cl11417 391009000482 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 391009000483 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009000484 Walker A/P-loop; other site 391009000485 ATP binding site [chemical binding]; other site 391009000486 Q-loop/lid; other site 391009000487 ABC transporter signature motif; other site 391009000488 Walker B; other site 391009000489 D-loop; other site 391009000490 H-loop/switch region; other site 391009000491 ABC-2 type transporter; Region: ABC2_membrane; cl11417 391009000492 Macro domain, Af1521- and BAL-like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-...; Region: Macro_Af1521_BAL_like; cd02907 391009000493 ADP-ribose binding site [chemical binding]; other site 391009000494 recombination factor protein RarA; Reviewed; Region: PRK13342 391009000495 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...; Region: AAA; cd00009 391009000496 Walker A motif; other site 391009000497 ATP binding site [chemical binding]; other site 391009000498 Walker B motif; other site 391009000499 arginine finger; other site 391009000500 MgsA AAA+ ATPase C terminal; Region: MgsA_C; cl13440 391009000501 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 391009000502 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009000503 NAD(P) binding site [chemical binding]; other site 391009000504 active site 391009000505 Mn-dependent transcriptional regulator [Transcription]; Region: TroR; COG1321 391009000506 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 391009000507 Uracil DNA glycosylase superfamily; Region: UDG; cl00483 391009000508 pyruvate phosphate dikinase; Provisional; Region: PRK09279 391009000509 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 391009000510 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 391009000511 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 391009000512 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14357 391009000513 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 391009000514 Substrate binding site [chemical binding]; other site 391009000515 Mg++ binding site [ion binding]; other site 391009000516 N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU), C-terminal left-handed beta-helix (LbH) acetyltransferase domain: GlmU is also known as UDP-N-acetylglucosamine pyrophosphorylase. It is a bifunctional bacterial enzyme that catalyzes two...; Region: LbH_GlmU_C; cd03353 391009000517 active site 391009000518 substrate binding site [chemical binding]; other site 391009000519 CoA binding site [chemical binding]; other site 391009000520 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 391009000521 ribose-phosphate pyrophosphokinase; Region: ribP_PPkin; TIGR01251 391009000522 Ribosomal_L25_TL5_CTC: Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain. L25 is a single-domain protein, homologous to the N-terminal domain of TL5 and CTC, which each contain two domains. CTC is a known stress protein, and proteins of this...; Region: Ribosomal_L25_TL5_CTC; cd00495 391009000523 5S rRNA interface [nucleotide binding]; other site 391009000524 CTC domain interface; other site 391009000525 L16 interface [polypeptide binding]; other site 391009000526 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 391009000527 putative active site [active] 391009000528 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...; Region: TM_PBP2; cl00427 391009000529 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...; Region: TM_PBP2; cl00427 391009000530 Maltose-binding periplasmic proteins/domains [Carbohydrate transport and metabolism]; Region: MalE; COG2182 391009000531 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009000532 Active site [active] 391009000533 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 391009000534 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 391009000535 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 391009000536 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 391009000537 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 391009000538 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 391009000539 DNA binding site [nucleotide binding] 391009000540 Int/Topo IB signature motif; other site 391009000541 active site 391009000542 enolase; Provisional; Region: eno; PRK00077 391009000543 Enolase: Enolases are homodimeric enzymes that catalyse the reversible dehydration of 2-phospho-D-glycerate to phosphoenolpyruvate as part of the glycolytic and gluconeogenesis pathways. The reaction is facilitated by the presence of metal ions; Region: enolase; cd03313 391009000544 dimer interface [polypeptide binding]; other site 391009000545 metal binding site [ion binding]; metal-binding site 391009000546 substrate binding pocket [chemical binding]; other site 391009000547 S-layer homology domain; Region: SLH; pfam00395 391009000548 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 391009000549 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 391009000550 active site 391009000551 HIGH motif; other site 391009000552 dimer interface [polypeptide binding]; other site 391009000553 KMSKS motif; other site 391009000554 Preprotein translocase SecG subunit; Region: SecG; cl09123 391009000555 radical SAM family uncharacterized protein; Region: rSAM_fuse_unch; TIGR03960 391009000556 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase...; Region: B12-binding_like; cl00293 391009000557 B12 binding site [chemical binding]; other site 391009000558 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 391009000559 FeS/SAM binding site; other site 391009000560 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 391009000561 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; cl12011 391009000562 Uncharacterized ACR, COG1993; Region: DUF190; cl00872 391009000563 CrcB-like protein; Region: CRCB; cl09114 391009000564 NTPase/HAM1. This family consists of the HAM1 protein and pyrophosphate-releasing xanthosine/ inosine triphosphatase. HAM1 protects the cell against mutagenesis by the base analog 6-N-hydroxylaminopurine (HAP) in E. Coli and S. cerevisiae. A Ham1-...; Region: HAM1; cd00515 391009000565 active site 391009000566 dimerization interface [polypeptide binding]; other site 391009000567 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; cl00679 391009000568 Protein of unknown function (DUF501); Region: DUF501; cl00652 391009000569 ribosomal protein L11 methyltransferase; Reviewed; Region: prmA; PRK00517 391009000570 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 391009000571 S-adenosylmethionine binding site [chemical binding]; other site 391009000572 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 391009000573 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 391009000574 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 391009000575 putative peptidoglycan binding site; other site 391009000576 Peptidase family M23; Region: Peptidase_M23; pfam01551 391009000577 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 391009000578 Prokaryotic protein of unknown function (DUF849); Region: DUF849; cl01276 391009000579 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cd05188 391009000580 NAD(P) binding site [chemical binding]; other site 391009000581 lysine-2,3-aminomutase; Region: lys_2_3_AblA; TIGR03820 391009000582 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 391009000583 FeS/SAM binding site; other site 391009000584 Lysine-2,3-aminomutase; Region: LAM_C; pfam12544 391009000585 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of...; Region: R_hydratase; cd03449 391009000586 dimer interaction site [polypeptide binding]; other site 391009000587 substrate-binding tunnel; other site 391009000588 active site 391009000589 catalytic site [active] 391009000590 substrate binding site [chemical binding]; other site 391009000591 MutS domain III; Region: MutS_III; pfam05192 391009000592 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009000593 Walker A/P-loop; other site 391009000594 ATP binding site [chemical binding]; other site 391009000595 Q-loop/lid; other site 391009000596 ABC transporter signature motif; other site 391009000597 Walker B; other site 391009000598 D-loop; other site 391009000599 H-loop/switch region; other site 391009000600 D-Lysine 5,6-aminomutase alpha subunit; Region: Lys-AminoMut_A; pfam09043 391009000601 Predicted cobalamin binding protein [General function prediction only]; Region: COG5012 391009000602 B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine...; Region: B12-binding; cd02067 391009000603 B12 binding site [chemical binding]; other site 391009000604 cobalt ligand [ion binding]; other site 391009000605 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 391009000606 Major Facilitator Superfamily; Region: MFS_1; pfam07690 391009000607 putative substrate translocation pore; other site 391009000608 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 391009000609 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 391009000610 radical SAM family uncharacterized protein; Region: rSAM_fuse_unch; TIGR03960 391009000611 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; cl14056 391009000612 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 391009000613 FtsH Extracellular; Region: FtsH_ext; pfam06480 391009000614 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 391009000615 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...; Region: AAA; cd00009 391009000616 Walker A motif; other site 391009000617 ATP binding site [chemical binding]; other site 391009000618 Walker B motif; other site 391009000619 arginine finger; other site 391009000620 Peptidase family M41; Region: Peptidase_M41; pfam01434 391009000621 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 391009000622 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 391009000623 Ligand Binding Site [chemical binding]; other site 391009000624 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 391009000625 M42 Peptidase, Endoglucanases; Region: M42_Frv; cd05656 391009000626 oligomer interface [polypeptide binding]; other site 391009000627 active site 391009000628 metal binding site [ion binding]; metal-binding site 391009000629 Bacitracin resistance protein BacA; Region: BacA; cl00858 391009000630 Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria...; Region: Imidazolone-5PH; cd01296 391009000631 active site 391009000632 N-Utilization Substance G (NusG) N terminal (NGN) insert and Lin0431 are part of DUF1312; Region: DUF1312; cd09846 391009000633 Heptaprenyl diphosphate synthase component I; Region: Hpre_diP_synt_I; cl01973 391009000634 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 391009000635 active site 391009000636 dimer interface [polypeptide binding]; other site 391009000637 hypothetical protein; Reviewed; Region: PRK00024 391009000638 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 391009000639 MPN+ (JAMM) motif; other site 391009000640 Zinc-binding site [ion binding]; other site 391009000641 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 391009000642 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 391009000643 DXD motif; other site 391009000644 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 391009000645 active site 391009000646 Uncharacterised protein family (UPF0104); Region: UPF0104; cl04219 391009000647 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 391009000648 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 391009000649 protein binding site [polypeptide binding]; other site 391009000650 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 391009000651 Catalytic dyad [active] 391009000652 tRNA(1-methyladenosine) methyltransferase and related methyltransferases [Translation, ribosomal structure and biogenesis]; Region: GCD14; COG2519 391009000653 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; cl12011 391009000654 Predicted HD superfamily hydrolase involved in NAD metabolism [Coenzyme metabolism]; Region: COG1713 391009000655 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 391009000656 Protein of unknown function (DUF503); Region: DUF503; cl00669 391009000657 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 391009000658 active site 391009000659 HslU subunit interaction site [polypeptide binding]; other site 391009000660 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 391009000661 SUA5 domain; Region: SUA5; pfam03481 391009000662 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 391009000663 putative active site [active] 391009000664 catalytic site [active] 391009000665 Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar proteins; Region: PLDc_Nuc_like; cd09116 391009000666 putative active site [active] 391009000667 catalytic site [active] 391009000668 GTP-binding protein LepA; Provisional; Region: PRK05433 391009000669 LepA subfamily. LepA belongs to the GTPase family of and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and...; Region: LepA; cd01890 391009000670 G1 box; other site 391009000671 putative GEF interaction site [polypeptide binding]; other site 391009000672 GTP/Mg2+ binding site [chemical binding]; other site 391009000673 Switch I region; other site 391009000674 G2 box; other site 391009000675 G3 box; other site 391009000676 Switch II region; other site 391009000677 G4 box; other site 391009000678 G5 box; other site 391009000679 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-...; Region: lepA_II; cd03699 391009000680 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 391009000681 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 391009000682 UDP-N-acetylmuramoylalanine--D-glutamate ligase; Region: murD; TIGR01087 391009000683 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 391009000684 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 391009000685 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; cl11520 391009000686 Glucose inhibited division protein A; Region: GIDA; pfam01134 391009000687 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 391009000688 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 391009000689 putative active site [active] 391009000690 substrate binding site [chemical binding]; other site 391009000691 putative cosubstrate binding site; other site 391009000692 catalytic site [active] 391009000693 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 391009000694 substrate binding site [chemical binding]; other site 391009000695 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; cl12011 391009000696 MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid...; Region: MECDP_synthase; cd00554 391009000697 homotrimer interaction site [polypeptide binding]; other site 391009000698 zinc binding site [ion binding]; other site 391009000699 CDP-binding sites; other site 391009000700 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK05293 391009000701 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 391009000702 ligand binding site [chemical binding]; other site 391009000703 oligomer interface [polypeptide binding]; other site 391009000704 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and rate-...; Region: LbH_G1P_AT_C; cd04651 391009000705 dimer interface [polypeptide binding]; other site 391009000706 N-terminal domain interface [polypeptide binding]; other site 391009000707 sulfate 1 binding site; other site 391009000708 ADP-glucose pyrophosphorylase [Carbohydrate transport and metabolism]; Region: GlgC; COG0448 391009000709 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 391009000710 ligand binding site [chemical binding]; other site 391009000711 oligomer interface [polypeptide binding]; other site 391009000712 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and rate-...; Region: LbH_G1P_AT_C; cd04651 391009000713 dimer interface [polypeptide binding]; other site 391009000714 N-terminal domain interface [polypeptide binding]; other site 391009000715 sulfate 1 binding site; other site 391009000716 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 391009000717 intersubunit interface [polypeptide binding]; other site 391009000718 active site 391009000719 catalytic residue [active] 391009000720 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 391009000721 SmpB-tmRNA interface; other site 391009000722 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 391009000723 Global regulator protein family; Region: CsrA; cl00670 391009000724 FliW protein; Region: FliW; cl00740 391009000725 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 391009000726 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 391009000727 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 391009000728 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; cl01178 391009000729 DAK2 domain fusion protein YloV; Region: YloV; TIGR03599 391009000730 DAK2 domain; Region: Dak2; cl03685 391009000731 Protein of unknown function (DUF322); Region: DUF322; cl00574 391009000732 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 391009000733 TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products with important pharmaceutical activity. DXS...; Region: TPP_DXS; cd02007 391009000734 TPP-binding site; other site 391009000735 Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins; Region: TPP_PYR_DXS_TK_like; cd07033 391009000736 PYR/PP interface [polypeptide binding]; other site 391009000737 dimer interface [polypeptide binding]; other site 391009000738 TPP binding site [chemical binding]; other site 391009000739 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 391009000740 seryl-tRNA synthetase; Provisional; Region: PRK05431 391009000741 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 391009000742 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 391009000743 dimer interface [polypeptide binding]; other site 391009000744 active site 391009000745 motif 1; other site 391009000746 motif 2; other site 391009000747 motif 3; other site 391009000748 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Region: COG0182; cl00348 391009000749 Initiation factor 2 subunit family; Region: IF-2B; pfam01008 391009000750 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 391009000751 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 391009000752 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 391009000753 HIGH motif; other site 391009000754 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 391009000755 active site 391009000756 KMSKS motif; other site 391009000757 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 391009000758 tRNA binding surface [nucleotide binding]; other site 391009000759 RNA methyltransferase; Region: Methyltrans_RNA; cl00611 391009000760 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 391009000761 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 391009000762 active site 391009000763 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...; Region: PDZ_metalloprotease; cd00989 391009000764 protein binding site [polypeptide binding]; other site 391009000765 RIP metalloprotease RseP; Region: TIGR00054 391009000766 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 391009000767 putative substrate binding region [chemical binding]; other site 391009000768 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 391009000769 active site 391009000770 Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]; Region: PleD; COG3706 391009000771 phosphorylation site [posttranslational modification] 391009000772 intermolecular recognition site; other site 391009000773 dimerization interface [polypeptide binding]; other site 391009000774 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391009000775 metal binding site [ion binding]; metal-binding site 391009000776 active site 391009000777 I-site; other site 391009000778 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 391009000779 Zn2+ binding site [ion binding]; other site 391009000780 Mg2+ binding site [ion binding]; other site 391009000781 GcpE protein; Region: GcpE; pfam04551 391009000782 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; Region: ispG_gcpE; TIGR00612 391009000783 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...; Region: beta_clamp; cl02940 391009000784 putative DNA binding surface [nucleotide binding]; other site 391009000785 dimer interface [polypeptide binding]; other site 391009000786 beta-clamp/clamp loader binding surface; other site 391009000787 beta-clamp/translesion DNA polymerase binding surface; other site 391009000788 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have...; Region: metallo-dependent_hydrolases; cl00281 391009000789 active site 391009000790 dihydroorotate dehydrogenase electron transfer subunit; Reviewed; Region: PRK00054 391009000791 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)-...; Region: DHOD_e_trans_like; cd06192 391009000792 FAD binding pocket [chemical binding]; other site 391009000793 FAD binding motif [chemical binding]; other site 391009000794 phosphate binding motif [ion binding]; other site 391009000795 beta-alpha-beta structure motif; other site 391009000796 NAD binding pocket [chemical binding]; other site 391009000797 Iron coordination center [ion binding]; other site 391009000798 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 391009000799 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 391009000800 phosphate binding site [ion binding]; other site 391009000801 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase contains two...; Region: OMP_decarboxylase_like; cd04725 391009000802 active site 391009000803 dimer interface [polypeptide binding]; other site 391009000804 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 391009000805 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 391009000806 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 391009000807 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 391009000808 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 391009000809 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 391009000810 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 391009000811 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 391009000812 Uncharacterised protein family (UPF0081); Region: UPF0081; cl00525 391009000813 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 391009000814 RNA binding site [nucleotide binding]; other site 391009000815 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 391009000816 Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]; Region: PriA; COG1198 391009000817 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 391009000818 ATP binding site [chemical binding]; other site 391009000819 putative Mg++ binding site [ion binding]; other site 391009000820 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; cl14882 391009000821 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 391009000822 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 protein...; Region: CSP_CDS; cd04458 391009000823 DNA-binding site [nucleotide binding]; DNA binding site 391009000824 RNA-binding motif; other site 391009000825 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 391009000826 Lipoate-protein ligase A [Coenzyme metabolism]; Region: LplA; COG0095 391009000827 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 391009000828 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 391009000829 tetramerization interface [polypeptide binding]; other site 391009000830 active site 391009000831 GAF domain; Region: GAF; cl00853 391009000832 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 391009000833 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 391009000834 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 trans-...; Region: HisKA; cd00082 391009000835 dimer interface [polypeptide binding]; other site 391009000836 phosphorylation site [posttranslational modification] 391009000837 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 391009000838 ATP binding site [chemical binding]; other site 391009000839 Mg2+ binding site [ion binding]; other site 391009000840 G-X-G motif; other site 391009000841 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 A site...; Region: RaiA; cd00552 391009000842 30S subunit binding site; other site 391009000843 Uncharacterised protein, DegV family COG1307; Region: DegV; cl00577 391009000844 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 391009000845 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 391009000846 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 391009000847 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 391009000848 alpha subunit interaction interface [polypeptide binding]; other site 391009000849 Walker A motif; other site 391009000850 ATP binding site [chemical binding]; other site 391009000851 Walker B motif; other site 391009000852 inhibitor binding site; inhibition site 391009000853 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 391009000854 ATP synthase; Region: ATP-synt; cl00365 391009000855 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 391009000856 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 391009000857 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 391009000858 beta subunit interaction interface [polypeptide binding]; other site 391009000859 Walker A motif; other site 391009000860 ATP binding site [chemical binding]; other site 391009000861 Walker B motif; other site 391009000862 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 391009000863 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 391009000864 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 391009000865 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 391009000866 ATP synthase subunit C; Region: ATP-synt_C; cl00466 391009000867 ATP synthase A chain; Region: ATP-synt_A; cl00413 391009000868 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; cl09754 391009000869 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 391009000870 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 391009000871 Similar to Prolidase and Aminopeptidase P. The members of this subfamily presumably catalyse hydrolysis of Xaa-Pro dipeptides and/or release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP-like; cd01092 391009000872 active site 391009000873 Uncharacterised protein family (UPF0081); Region: UPF0081; cl00525 391009000874 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 391009000875 DHH family; Region: DHH; pfam01368 391009000876 DHHA1 domain; Region: DHHA1; pfam02272 391009000877 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat...; Region: Hsp33; cd00498 391009000878 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 391009000879 dimerization interface [polypeptide binding]; other site 391009000880 domain crossover interface; other site 391009000881 redox-dependent activation switch; other site 391009000882 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 391009000883 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 connected by an extended linker. The...; Region: HAMP; cl01054 391009000884 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 trans-...; Region: HisKA; cd00082 391009000885 dimer interface [polypeptide binding]; other site 391009000886 phosphorylation site [posttranslational modification] 391009000887 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 391009000888 ATP binding site [chemical binding]; other site 391009000889 Mg2+ binding site [ion binding]; other site 391009000890 G-X-G motif; other site 391009000891 formate--tetrahydrofolate ligase; Provisional; Region: PRK13505 391009000892 Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2...; Region: FTHFS; cd00477 391009000893 Potassium binding sites [ion binding]; other site 391009000894 Cesium cation binding sites [ion binding]; other site 391009000895 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 391009000896 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 391009000897 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 391009000898 NAD(P) binding site [chemical binding]; other site 391009000899 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; cl12011 391009000900 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; cl12011 391009000901 DpnII restriction endonuclease; Region: DpnII; pfam04556 391009000902 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl00408 391009000903 Phosphopantetheine attachment site; Region: PP-binding; cl09936 391009000904 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 391009000905 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 391009000906 TPR motif; other site 391009000907 binding surface 391009000908 Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a...; Region: PKCI_related; cd01276 391009000909 nucleotide binding site/active site [active] 391009000910 HIT family signature motif; other site 391009000911 catalytic residue [active] 391009000912 adenylosuccinate synthetase; Provisional; Region: PRK01117 391009000913 Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosynthesis of AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the r-...; Region: AdSS; cd03108 391009000914 GDP-binding site [chemical binding]; other site 391009000915 ACT binding site; other site 391009000916 IMP binding site; other site 391009000917 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 391009000918 conserved hypothetical protein; Region: glmL_fam; TIGR01319 391009000919 Predicted phosphoesterase (MutT family) [General function prediction only]; Region: COG4112 391009000920 4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate synthase [Lipid metabolism]; Region: IspE; COG1947 391009000921 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 391009000922 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 391009000923 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 391009000924 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 391009000925 active site 391009000926 HIGH motif; other site 391009000927 dimer interface [polypeptide binding]; other site 391009000928 KMSKS motif; other site 391009000929 Mechanosensitive ion channel; Region: MS_channel; pfam00924 391009000930 Cache domain; Region: Cache_1; pfam02743 391009000931 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 connected by an extended linker. The...; Region: HAMP; cd06225 391009000932 dimerization interface [polypeptide binding]; other site 391009000933 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 391009000934 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 391009000935 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 391009000936 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 391009000937 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK07739 391009000938 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK07739 391009000939 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 391009000940 flagellar hook-associated protein FlgL; Validated; Region: flgL; PRK07701 391009000941 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 391009000942 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 391009000943 S-adenosylmethionine binding site [chemical binding]; other site 391009000944 CHASE2 domain; Region: CHASE2; cl01732 391009000945 cyclase homology domain; Region: CHD; cd07302 391009000946 nucleotidyl binding site; other site 391009000947 metal binding site [ion binding]; metal-binding site 391009000948 dimer interface [polypeptide binding]; other site 391009000949 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 391009000950 Protein of unknown function (DUF3307); Region: DUF3307; pfam11750 391009000951 FecR protein; Region: FecR; pfam04773 391009000952 GAF domain; Region: GAF; cl00853 391009000953 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 391009000954 Zn2+ binding site [ion binding]; other site 391009000955 Mg2+ binding site [ion binding]; other site 391009000956 L-serine dehydratase, iron-sulfur-dependent, beta subunit; Region: sda_beta; TIGR00719 391009000957 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 391009000958 ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-like; cd04879 391009000959 L-serine binding site [chemical binding]; other site 391009000960 L-serine deaminase [Amino acid transport and metabolism]; Region: SdaA; COG1760 391009000961 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 391009000962 transcription termination factor Rho; Provisional; Region: rho; PRK09376 391009000963 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3330 391009000964 Uncharacterized conserved protein [Function unknown]; Region: COG1543 391009000965 Domain of unknown function (DUF1957); Region: DUF1957; pfam09210 391009000966 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 391009000967 pyruvate/ketoisovalerate ferredoxin oxidoreductase subunit gamma; Provisional; Region: PRK14029 391009000968 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate family; Region: PorD_KorD; TIGR02179 391009000969 pyruvate flavodoxin oxidoreductase subunit alpha; Reviewed; Region: porA; PRK09622 391009000970 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 391009000971 dimer interface [polypeptide binding]; other site 391009000972 PYR/PP interface [polypeptide binding]; other site 391009000973 TPP binding site [chemical binding]; other site 391009000974 substrate binding site [chemical binding]; other site 391009000975 TPP-binding module; composed of proteins similar to the beta subunit (porB) of the Helicobacter pylori four-subunit pyruvate ferredoxin oxidoreductase (PFOR), which are also found in archaea and some hyperthermophilic bacteria. PFOR catalyzes the...; Region: TPP_PFOR_porB_like; cd03376 391009000976 pyruvate ferredoxin oxidoreductase subunit beta; Provisional; Region: PRK11865 391009000977 TPP-binding site [chemical binding]; other site 391009000978 putative dimer interface [polypeptide binding]; other site 391009000979 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 391009000980 This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins. WecA is an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate (Und-P) GlcNAc-1-phosphate transferase that catalyzes the formation of a phosphodiester bond...; Region: GT_WecA_like; cd06853 391009000981 Mg++ binding site [ion binding]; other site 391009000982 putative catalytic motif [active] 391009000983 substrate binding site [chemical binding]; other site 391009000984 VanZ like family; Region: VanZ; cl01971 391009000985 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 connected by an extended linker. The...; Region: HAMP; cl01054 391009000986 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 391009000987 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 391009000988 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cd09725 391009000989 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-B; cd09722 391009000990 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 391009000991 CRISPR/Cas system-associated protein Cas3''; Region: Cas3''_I; cd09641 391009000992 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; cl14882 391009000993 CRISPR/Cas system-associated RAMP superfamily protein Cas5; Region: Cas5_I; cl12040 391009000994 CRISPR/Cas system-associated RAMP superfamily protein Cas7; Region: Cas7_I-C; cl01465 391009000995 CRISPR/Cas system-associated protein Cas8b; Region: Cas8b_I-B; cl09718 391009000996 CRISPR/Cas system-associated protein Cas8b; Region: Cas8b_I-B; cl09718 391009000997 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cl11443 391009000998 Peptidase family M48; Region: Peptidase_M48; cl12018 391009000999 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 391009001000 Polysaccharide biosynthesis protein; Region: Polysacc_synt; cl10513 391009001001 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 391009001002 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 391009001003 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 391009001004 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 391009001005 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 391009001006 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 391009001007 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 391009001008 active site 391009001009 UDP-N-acetylglucosamine 2-epimerase; Region: Epimerase_2; pfam02350 391009001010 homodimer interface [polypeptide binding]; other site 391009001011 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 391009001012 DEAD-like helicases superfamily; Region: DEXDc; smart00487 391009001013 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 391009001014 ATP binding site [chemical binding]; other site 391009001015 putative Mg++ binding site [ion binding]; other site 391009001016 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 391009001017 nucleotide binding region [chemical binding]; other site 391009001018 ATP-binding site [chemical binding]; other site 391009001019 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 391009001020 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 391009001021 H+ Antiporter protein; Region: 2A0121; TIGR00900 391009001022 putative substrate translocation pore; other site 391009001023 Protein of unknown function(DUF2089); Region: DUF2089; pfam09862 391009001024 GTPase CgtA; Reviewed; Region: obgE; PRK12297 391009001025 GTP1/OBG; Region: GTP1_OBG; pfam01018 391009001026 Obg subfamily. The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins...; Region: Obg; cd01898 391009001027 G1 box; other site 391009001028 GTP/Mg2+ binding site [chemical binding]; other site 391009001029 Switch I region; other site 391009001030 G2 box; other site 391009001031 G3 box; other site 391009001032 Switch II region; other site 391009001033 G4 box; other site 391009001034 G5 box; other site 391009001035 Domain of unknown function (DUF1967); Region: DUF1967; cl07779 391009001036 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 391009001037 Nicotinic acid mononucleotide adenylyltransferase [Coenzyme metabolism]; Region: NadD; COG1057 391009001038 active site 391009001039 (T/H)XGH motif; other site 391009001040 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 391009001041 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...; Region: DUS_like_FMN; cd02801 391009001042 FMN binding site [chemical binding]; other site 391009001043 active site 391009001044 catalytic residues [active] 391009001045 substrate binding site [chemical binding]; other site 391009001046 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 391009001047 aspartate aminotransferase; Provisional; Region: PRK08361 391009001048 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 391009001049 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391009001050 homodimer interface [polypeptide binding]; other site 391009001051 catalytic residue [active] 391009001052 2-phosphosulpholactate phosphatase; Region: 2-ph_phosp; cl00895 391009001053 Phosphosulfolactate phosphohydrolase and related enzymes [Coenzyme metabolism / General function prediction only]; Region: COG2045 391009001054 FecR protein; Region: FecR; pfam04773 391009001055 Transglycosylase; Region: Transgly; cl07896 391009001056 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 391009001057 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 391009001058 Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion...; Region: enolase_like; cl14814 391009001059 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 391009001060 active site 391009001061 multimer interface [polypeptide binding]; other site 391009001062 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 391009001063 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 391009001064 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 391009001065 AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal...; Region: PurM-like; cl10019 391009001066 dimerization interface [polypeptide binding]; other site 391009001067 ATP binding site [chemical binding]; other site 391009001068 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 391009001069 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 391009001070 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 391009001071 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 391009001072 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 391009001073 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 391009001074 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 391009001075 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 391009001076 active site 391009001077 substrate binding site [chemical binding]; other site 391009001078 cosubstrate binding site; other site 391009001079 catalytic site [active] 391009001080 amidophosphoribosyltransferase; Region: purF; TIGR01134 391009001081 Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to...; Region: Gn_AT_II; cl00319 391009001082 active site 391009001083 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 391009001084 FOG: WD40-like repeat [Function unknown]; Region: COG1520 391009001085 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 391009001086 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 391009001087 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 391009001088 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cl02788 391009001089 Recombinase; Region: Recombinase; pfam07508 391009001090 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 391009001091 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...; Region: ParA; cd02042 391009001092 P-loop; other site 391009001093 Magnesium ion binding site [ion binding]; other site 391009001094 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...; Region: ParA; cd02042 391009001095 Magnesium ion binding site [ion binding]; other site 391009001096 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 391009001097 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 391009001098 catalytic residues [active] 391009001099 catalytic nucleophile [active] 391009001100 Recombinase; Region: Recombinase; pfam07508 391009001101 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 391009001102 non-specific DNA binding site [nucleotide binding]; other site 391009001103 salt bridge; other site 391009001104 sequence-specific DNA binding site [nucleotide binding]; other site 391009001105 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (...; Region: S24_LexA-like; cd06529 391009001106 Catalytic site [active] 391009001107 Protein of unknown function DUF45; Region: DUF45; cl00636 391009001108 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 391009001109 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 391009001110 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 391009001111 ATP binding site [chemical binding]; other site 391009001112 putative Mg++ binding site [ion binding]; other site 391009001113 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 391009001114 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 391009001115 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 391009001116 HsdM N-terminal domain; Region: HsdM_N; pfam12161 391009001117 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 391009001118 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; cl12011 391009001119 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 391009001120 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009001121 Walker A/P-loop; other site 391009001122 ATP binding site [chemical binding]; other site 391009001123 Q-loop/lid; other site 391009001124 ABC transporter signature motif; other site 391009001125 Walker B; other site 391009001126 D-loop; other site 391009001127 H-loop/switch region; other site 391009001128 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 391009001129 ABC-2 type transporter; Region: ABC2_membrane; cl11417 391009001130 C-terminal processing peptidase family S41; Region: Peptidase_S41; cd06567 391009001131 Active site serine [active] 391009001132 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 391009001133 Active site serine [active] 391009001134 Arylsulfatase regulator (Fe-S oxidoreductase) [General function prediction only]; Region: AslB; COG0641 391009001135 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 391009001136 FeS/SAM binding site; other site 391009001137 radical SAM additional 4Fe4S-binding domain; Region: rSAM_more_4Fe4S; TIGR04085 391009001138 Bacterial transcriptional regulator; Region: IclR; pfam01614 391009001139 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 391009001140 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 391009001141 Clp amino terminal domain; Region: Clp_N; pfam02861 391009001142 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...; Region: AAA; cd00009 391009001143 Walker A motif; other site 391009001144 ATP binding site [chemical binding]; other site 391009001145 Walker B motif; other site 391009001146 arginine finger; other site 391009001147 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...; Region: AAA; cd00009 391009001148 Walker A motif; other site 391009001149 ATP binding site [chemical binding]; other site 391009001150 Walker B motif; other site 391009001151 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 391009001152 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They...; Region: rubredoxin; cd00730 391009001153 Rubredoxin; Region: Rubredoxin; pfam00301 391009001154 iron binding site [ion binding]; other site 391009001155 putative iron-only hydrogenase system regulator; Region: hyd_TM1266; TIGR03959 391009001156 Heme NO binding; Region: HNOB; pfam07700 391009001157 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 391009001158 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 391009001159 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 391009001160 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; cl09940 391009001161 Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this...; Region: PseudoU_synth_RsuA_like; cd02870 391009001162 active site 391009001163 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 391009001164 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 391009001165 NAD binding site [chemical binding]; other site 391009001166 homodimer interface [polypeptide binding]; other site 391009001167 active site 391009001168 substrate binding site [chemical binding]; other site 391009001169 UvrD/REP helicase; Region: UvrD-helicase; cl14126 391009001170 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 391009001171 putative recombination protein RecB; Provisional; Region: PRK13909 391009001172 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 391009001173 ATP-dependent nuclease, subunit B [DNA replication, recombination, and repair]; Region: AddB; COG3857 391009001174 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 391009001175 Alpha-galactosidase [Carbohydrate transport and metabolism]; Region: GalA; COG3345 391009001176 The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-...; Region: GH31; cl11402 391009001177 Galactose-1-phosphate uridylyltransferase [Energy production and conversion]; Region: GalT; COG1085 391009001178 Galactose-1-phosphate uridyl transferase (GalT): This enzyme plays a key role in galactose metabolism by catalysing the transfer of a uridine 5'-phosphoryl group from UDP-galactose 1-phosphate. The structure of E.coli GalT reveals that the enzyme...; Region: GalT; cd00608 391009001179 dimer interface [polypeptide binding]; other site 391009001180 active site 391009001181 galactokinase; Provisional; Region: PRK03817 391009001182 Galactokinase galactose-binding signature; Region: GalKase_gal_bdg; pfam10509 391009001183 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 391009001184 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 higher-...; Region: HU_IHF; cd00591 391009001185 IHF dimer interface [polypeptide binding]; other site 391009001186 IHF - DNA interface [nucleotide binding]; other site 391009001187 shikimate kinase; Reviewed; Region: aroK; PRK00131 391009001188 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009001189 Active site [active] 391009001190 Uncharacterised protein family UPF0047; Region: UPF0047; cl00439 391009001191 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 391009001192 metal binding site 2 [ion binding]; metal-binding site 391009001193 putative DNA binding helix; other site 391009001194 metal binding site 1 [ion binding]; metal-binding site 391009001195 dimer interface [polypeptide binding]; other site 391009001196 structural Zn2+ binding site [ion binding]; other site 391009001197 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...; Region: TroA-like; cl00262 391009001198 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 391009001199 intersubunit interface [polypeptide binding]; other site 391009001200 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 391009001201 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-...; Region: ABC_Metallic_Cations; cd03235 391009001202 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...; Region: TM_ABC_iron-siderophores_like; cl00462 391009001203 dimer interface [polypeptide binding]; other site 391009001204 ABC-ATPase subunit interface; other site 391009001205 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 391009001206 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 391009001207 active site 391009001208 Riboflavin kinase; Region: Flavokinase; pfam01687 391009001209 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 391009001210 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 391009001211 minor groove reading motif; other site 391009001212 helix-hairpin-helix signature motif; other site 391009001213 substrate binding pocket [chemical binding]; other site 391009001214 active site 391009001215 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 391009001216 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 391009001217 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 391009001218 inhibitor-cofactor binding pocket; inhibition site 391009001219 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391009001220 catalytic residue [active] 391009001221 Sulfate transporter family; Region: Sulfate_transp; cl00967 391009001222 Permease family; Region: Xan_ur_permease; pfam00860 391009001223 hypothetical protein; Validated; Region: PRK07668 391009001224 O-Antigen ligase; Region: Wzy_C; cl04850 391009001225 reticulocyte binding protein 2-like protein; Provisional; Region: PTZ00440 391009001226 ribonucleotide-diphosphate reductase subunit alpha; Provisional; Region: PRK12364 391009001227 Curli production assembly/transport component CsgG; Region: CsgG; cl00639 391009001228 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 391009001229 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 391009001230 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 391009001231 Walker A/P-loop; other site 391009001232 ATP binding site [chemical binding]; other site 391009001233 Q-loop/lid; other site 391009001234 ABC transporter signature motif; other site 391009001235 Walker B; other site 391009001236 D-loop; other site 391009001237 H-loop/switch region; other site 391009001238 ABC-2 type transporter; Region: ABC2_membrane; cl11417 391009001239 ABC-2 type transporter; Region: ABC2_membrane; cl11417 391009001240 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 391009001241 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391009001242 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 391009001243 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 391009001244 Bacterial pullanase-associated domain; Region: PUD; pfam03714 391009001245 pullulanase, type I; Region: pulA_typeI; TIGR02104 391009001246 Pullulanase domain N-terminus. Pullulanase (AKA dextrinase; alpha-dextrin endo-1,6-alpha glucosidase) is an enzyme with action similar to that of isoamylase; it cleaves 1,6-alpha-glucosidic linkages in pullulan, amylopectin, and glycogen, and in alpha-...; Region: Pullulanase_N_term; cd02860 391009001247 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 391009001248 Response regulator receiver domain; Region: Response_reg; pfam00072 391009001249 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 391009001250 active site 391009001251 phosphorylation site [posttranslational modification] 391009001252 intermolecular recognition site; other site 391009001253 dimerization interface [polypeptide binding]; other site 391009001254 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 391009001255 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 391009001256 HIGH motif; other site 391009001257 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 391009001258 active site 391009001259 KMSKS motif; other site 391009001260 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 391009001261 tRNA binding surface [nucleotide binding]; other site 391009001262 anticodon binding site; other site 391009001263 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 391009001264 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 391009001265 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 391009001266 EamA-like transporter family; Region: EamA; cl01037 391009001267 rod shape-determining protein MreB; Provisional; Region: PRK13930 391009001268 Cell division protein FtsA; Region: FtsA; cl11496 391009001269 flagellar basal body rod protein FlgG; Reviewed; Region: flgG; PRK12818 391009001270 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 391009001271 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 391009001272 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 391009001273 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 391009001274 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 391009001275 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 391009001276 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 391009001277 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 391009001278 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP; Region: ABC_HisP_GlnQ_permeases; cd03262 391009001279 Walker A/P-loop; other site 391009001280 ATP binding site [chemical binding]; other site 391009001281 Q-loop/lid; other site 391009001282 ABC transporter signature motif; other site 391009001283 Walker B; other site 391009001284 D-loop; other site 391009001285 H-loop/switch region; other site 391009001286 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 391009001287 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...; Region: TM_PBP2; cd06261 391009001288 dimer interface [polypeptide binding]; other site 391009001289 conserved gate region; other site 391009001290 putative PBP binding loops; other site 391009001291 ABC-ATPase subunit interface; other site 391009001292 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...; Region: PBPb; cd00134 391009001293 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 391009001294 substrate binding pocket [chemical binding]; other site 391009001295 membrane-bound complex binding site; other site 391009001296 hinge residues; other site 391009001297 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 391009001298 Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate...; Region: GFAT; cd00714 391009001299 glutaminase active site [active] 391009001300 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_1; cd05008 391009001301 dimer interface [polypeptide binding]; other site 391009001302 active site 391009001303 SIS (Sugar ISomerase) domain repeat 2 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_2; cd05009 391009001304 dimer interface [polypeptide binding]; other site 391009001305 active site 391009001306 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 391009001307 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 391009001308 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 391009001309 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 catalyze...; Region: LT_GEWL; cd00254 391009001310 N-acetyl-D-glucosamine binding site [chemical binding]; other site 391009001311 catalytic residue [active] 391009001312 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 391009001313 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 391009001314 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 391009001315 V-type ATP synthase subunit H; Validated; Region: PRK08404 391009001316 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 391009001317 FliG C-terminal domain; Region: FliG_C; pfam01706 391009001318 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 391009001319 active site 391009001320 substrate binding site [chemical binding]; other site 391009001321 catalytic site [active] 391009001322 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 391009001323 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 391009001324 putative active site [active] 391009001325 PhoH-like protein; Region: PhoH; cl12134 391009001326 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]; Region: COG3593 391009001327 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009001328 Uncharacterized conserved protein [Function unknown]; Region: COG4717 391009001329 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...; Region: AAK_UMPK-PyrH-Ec; cd04254 391009001330 putative nucleotide binding site [chemical binding]; other site 391009001331 uridine monophosphate binding site [chemical binding]; other site 391009001332 homohexameric interface [polypeptide binding]; other site 391009001333 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 391009001334 YlqF. Proteins of the YlqF family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases...; Region: YlqF; cd01856 391009001335 GTP/Mg2+ binding site [chemical binding]; other site 391009001336 G4 box; other site 391009001337 G5 box; other site 391009001338 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 391009001339 G1 box; other site 391009001340 G1 box; other site 391009001341 GTP/Mg2+ binding site [chemical binding]; other site 391009001342 Switch I region; other site 391009001343 G2 box; other site 391009001344 G2 box; other site 391009001345 G3 box; other site 391009001346 G3 box; other site 391009001347 Switch II region; other site 391009001348 Switch II region; other site 391009001349 Predicted inhibitor of MCP methylation, homolog of CheC [Cell motility and secretion]; Region: COG1406 391009001350 CheC-like family; Region: CheC; pfam04509 391009001351 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 391009001352 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 391009001353 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 391009001354 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 391009001355 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 391009001356 Serine carboxypeptidase S28; Region: Peptidase_S28; pfam05577 391009001357 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 391009001358 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 391009001359 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 391009001360 redox-sensing transcriptional repressor Rex; Provisional; Region: PRK05472 391009001361 Putative DNA-binding protein N-terminus; Region: Put_DNA-bind_N; pfam06971 391009001362 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009001363 NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75 kD subunit (chain G) [Energy production and conversion]; Region: NuoG; COG1034 391009001364 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; cl00159 391009001365 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 391009001366 hydrogenase, Fe-only; Region: Fe_only_hydrog; TIGR02512 391009001367 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 391009001368 Iron hydrogenase small subunit; Region: Fe_hyd_SSU; pfam02256 391009001369 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...; Region: TRX_Fd_NuoE; cd03064 391009001370 putative dimer interface [polypeptide binding]; other site 391009001371 [2Fe-2S] cluster binding site [ion binding]; other site 391009001372 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:; Region: TRX_Fd_family; cd02980 391009001373 dimer interface [polypeptide binding]; other site 391009001374 [2Fe-2S] cluster binding site [ion binding]; other site 391009001375 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 391009001376 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 391009001377 SLBB domain; Region: SLBB; pfam10531 391009001378 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 391009001379 4Fe-4S binding domain; Region: Fer4; cl02805 391009001380 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 391009001381 4Fe-4S binding domain; Region: Fer4; cl02805 391009001382 NADH-quinone oxidoreductase, E subunit; Region: nuoE_fam; TIGR01958 391009001383 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...; Region: TRX_Fd_NuoE; cd03064 391009001384 putative dimer interface [polypeptide binding]; other site 391009001385 [2Fe-2S] cluster binding site [ion binding]; other site 391009001386 hydrogenase, Fe-only; Region: Fe_only_hydrog; TIGR02512 391009001387 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 391009001388 Predicted Fe-S protein [General function prediction only]; Region: COG2000 391009001389 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:; Region: TRX_Fd_family; cd02980 391009001390 dimer interface [polypeptide binding]; other site 391009001391 [2Fe-2S] cluster binding site [ion binding]; other site 391009001392 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 391009001393 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; cl09944 391009001394 active site 391009001395 phosphorylation site [posttranslational modification] 391009001396 intermolecular recognition site; other site 391009001397 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 391009001398 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 391009001399 Zn2+ binding site [ion binding]; other site 391009001400 Mg2+ binding site [ion binding]; other site 391009001401 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 trans-...; Region: HisKA; cd00082 391009001402 dimer interface [polypeptide binding]; other site 391009001403 phosphorylation site [posttranslational modification] 391009001404 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 391009001405 ATP binding site [chemical binding]; other site 391009001406 Mg2+ binding site [ion binding]; other site 391009001407 G-X-G motif; other site 391009001408 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...; Region: PBPb; cd00134 391009001409 substrate binding pocket [chemical binding]; other site 391009001410 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 391009001411 membrane-bound complex binding site; other site 391009001412 hinge residues; other site 391009001413 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...; Region: PBPb; cd00134 391009001414 substrate binding pocket [chemical binding]; other site 391009001415 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 391009001416 membrane-bound complex binding site; other site 391009001417 hinge residues; other site 391009001418 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have...; Region: metallo-dependent_hydrolases; cl00281 391009001419 Metallo-dependent hydrolases, subgroup C is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_C; cd01309 391009001420 active site 391009001421 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 391009001422 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 391009001423 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 391009001424 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 391009001425 DNA-directed RNA polymerase subunit beta'; Provisional; Region: rpoC2; PRK02597 391009001426 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 391009001427 DNA-directed RNA polymerase, beta' subunit, predominant form; Region: rpoC_TIGR; TIGR02386 391009001428 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 391009001429 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 391009001430 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 391009001431 Rpb1 - Rpb5 interaction site [polypeptide binding]; other site 391009001432 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 391009001433 DNA binding site [nucleotide binding] 391009001434 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 391009001435 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 391009001436 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; cl04593 391009001437 RNA polymerase beta subunit; Region: RNA_pol_Rpb2_1; cl04591 391009001438 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 391009001439 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 391009001440 RPB10 interaction site [polypeptide binding]; other site 391009001441 RPB1 interaction site [polypeptide binding]; other site 391009001442 RPB11 interaction site [polypeptide binding]; other site 391009001443 RPB3 interaction site [polypeptide binding]; other site 391009001444 RPB12 interaction site [polypeptide binding]; other site 391009001445 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 391009001446 core dimer interface [polypeptide binding]; other site 391009001447 peripheral dimer interface [polypeptide binding]; other site 391009001448 L10 interface [polypeptide binding]; other site 391009001449 L11 interface [polypeptide binding]; other site 391009001450 putative EF-Tu interaction site [polypeptide binding]; other site 391009001451 putative EF-G interaction site [polypeptide binding]; other site 391009001452 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...; Region: Ribosomal_L10; cd05797 391009001453 23S rRNA interface [nucleotide binding]; other site 391009001454 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 391009001455 WbqC-like protein family; Region: WbqC; pfam08889 391009001456 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 391009001457 FeS/SAM binding site; other site 391009001458 Predicted Fe-S oxidoreductases [General function prediction only]; Region: COG0535 391009001459 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 391009001460 FeS/SAM binding site; other site 391009001461 exosortase 1 system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 391009001462 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 391009001463 active site 391009001464 dimer interface [polypeptide binding]; other site 391009001465 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes...; Region: Asn_Synthase_B_C; cd01991 391009001466 Ligand Binding Site [chemical binding]; other site 391009001467 Molecular Tunnel; other site 391009001468 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 391009001469 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 391009001470 inhibitor-cofactor binding pocket; inhibition site 391009001471 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391009001472 catalytic residue [active] 391009001473 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 391009001474 active site 391009001475 substrate binding site [chemical binding]; other site 391009001476 cosubstrate binding site; other site 391009001477 catalytic site [active] 391009001478 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 391009001479 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 391009001480 substrate binding site [chemical binding]; other site 391009001481 tetramer interface [polypeptide binding]; other site 391009001482 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 391009001483 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 391009001484 NAD binding site [chemical binding]; other site 391009001485 substrate binding site [chemical binding]; other site 391009001486 homodimer interface [polypeptide binding]; other site 391009001487 active site 391009001488 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 391009001489 Glycosyl transferases group 1; Region: Glycos_transf_1; cl12012 391009001490 flagellin; Reviewed; Region: PRK08869 391009001491 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 391009001492 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 391009001493 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 391009001494 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 391009001495 putative metal binding site [ion binding]; other site 391009001496 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 391009001497 active site 391009001498 (T/H)XGH motif; other site 391009001499 replicative DNA helicase; Region: DnaB; TIGR00665 391009001500 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 391009001501 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 391009001502 Walker A motif; other site 391009001503 ATP binding site [chemical binding]; other site 391009001504 Walker B motif; other site 391009001505 DNA binding loops [nucleotide binding] 391009001506 TM0106 family; Region: TIGR03491 391009001507 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 391009001508 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 391009001509 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 391009001510 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 391009001511 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 391009001512 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 391009001513 homotrimer interaction site [polypeptide binding]; other site 391009001514 putative active site [active] 391009001515 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]; Region: COG2231 391009001516 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 391009001517 minor groove reading motif; other site 391009001518 helix-hairpin-helix signature motif; other site 391009001519 substrate binding pocket [chemical binding]; other site 391009001520 active site 391009001521 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 391009001522 putative substrate translocation pore; other site 391009001523 Major Facilitator Superfamily; Region: MFS_1; pfam07690 391009001524 Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to...; Region: MGS; cd01422 391009001525 active site 391009001526 dimer interfaces [polypeptide binding]; other site 391009001527 catalytic residues [active] 391009001528 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 391009001529 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 391009001530 active site 391009001531 motif I; other site 391009001532 motif II; other site 391009001533 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; cl11391 391009001534 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 391009001535 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 391009001536 Dimer interface [polypeptide binding]; other site 391009001537 anticodon binding site; other site 391009001538 Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well...; Region: AsxRS_core; cd00776 391009001539 homodimer interface [polypeptide binding]; other site 391009001540 motif 1; other site 391009001541 motif 2; other site 391009001542 active site 391009001543 motif 3; other site 391009001544 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 391009001545 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 391009001546 active site 391009001547 Zn binding site [ion binding]; other site 391009001548 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 391009001549 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; Region: Ribosomal_L7Ae; cl00600 391009001550 Uncharacterized ACR, COG1469; Region: DUF198; cl00642 391009001551 sucrose-phosphate synthase, putative, glycosyltransferase domain; Region: sucr_P_syn_N; TIGR02472 391009001552 This family is most closely related to the GT1 family of glycosyltransferases. The sucrose-phosphate synthases in this family may be unique to plants and photosynthetic bacteria. This enzyme catalyzes the synthesis of sucrose 6-phosphate from fructose...; Region: GT1_Sucrose_synthase; cd03800 391009001553 putative ADP-binding pocket [chemical binding]; other site 391009001554 Fructokinases (FRKs) mainly from bacteria and plants are enzymes with high specificity for fructose, as are all FRKs, but they catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into...; Region: bac_FRK; cd01167 391009001555 putative substrate binding site [chemical binding]; other site 391009001556 putative ATP binding site [chemical binding]; other site 391009001557 DNA polymerase III subunit beta; Validated; Region: PRK05643 391009001558 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...; Region: beta_clamp; cd00140 391009001559 putative DNA binding surface [nucleotide binding]; other site 391009001560 dimer interface [polypeptide binding]; other site 391009001561 beta-clamp/clamp loader binding surface; other site 391009001562 beta-clamp/translesion DNA polymerase binding surface; other site 391009001563 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 391009001564 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009001565 Walker A/P-loop; other site 391009001566 ATP binding site [chemical binding]; other site 391009001567 Q-loop/lid; other site 391009001568 ABC transporter signature motif; other site 391009001569 Walker B; other site 391009001570 D-loop; other site 391009001571 H-loop/switch region; other site 391009001572 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 391009001573 flagellin; Reviewed; Region: PRK08869 391009001574 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 391009001575 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 391009001576 Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones]; Region: PflA; COG1180 391009001577 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 391009001578 FeS/SAM binding site; other site 391009001579 ApbE family; Region: ApbE; cl00643 391009001580 Uncharacterised BCR, YbaB family COG0718; Region: DUF149; cl00494 391009001581 Rhomboid family; Region: Rhomboid; cl11446 391009001582 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 391009001583 putative peptidoglycan binding site; other site 391009001584 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 391009001585 carbonyl reductase sniffer-like, classical (c) SDRs; Region: carb_red_sniffer_like_SDR_c; cd05325 391009001586 short chain dehydrogenase; Provisional; Region: PRK06123 391009001587 NADP binding site [chemical binding]; other site 391009001588 homodimer interface [polypeptide binding]; other site 391009001589 active site 391009001590 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 391009001591 Isoamylase N-terminus domain. Isoamylase (aka glycogen 6-glucanohydrolase) is one of the starch-debranching enzymes that catalyzes the hydrolysis of alpha-1,6-glucosidic linkages specific in alpha-glucans such as amylopectin or glycogen. Isoamylase...; Region: Isoamylase_N_term; cd02852 391009001592 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 391009001593 OsmC-like protein; Region: OsmC; cl00767 391009001594 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 391009001595 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 391009001596 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide...; Region: NrdH; cd02976 391009001597 catalytic residues [active] 391009001598 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 391009001599 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 391009001600 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 391009001601 Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO)-like family, N-terminal TRX-fold subdomain; composed of proteins with similarity to PfPDO, a redox active thermostable protein believed to be the archaeal counterpart of bacterial DsbA and...; Region: PfPDO_like_N; cd02975 391009001602 Glutaredoxin-like domain protein; Region: GlrX_arch; TIGR02187 391009001603 catalytic residues [active] 391009001604 Thioredoxin (TRX)-Glutaredoxin (GRX)-like family; composed of archaeal and bacterial proteins that show similarity to both TRX and GRX, including the C-terminal TRX-fold subdomain of Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). All...; Region: TRX_GRX_like; cd02973 391009001605 catalytic residues [active] 391009001606 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as...; Region: ADPRase_NUDT5; cd03424 391009001607 dimer interface [polypeptide binding]; other site 391009001608 ADP-ribose binding site [chemical binding]; other site 391009001609 active site 391009001610 nudix motif; other site 391009001611 metal binding site [ion binding]; metal-binding site 391009001612 Flagellar protein FliS; Region: FliS; cl00654 391009001613 Protein of unknown function (DUF1015); Region: DUF1015; cl01715 391009001614 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 391009001615 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 391009001616 Walker A/P-loop; other site 391009001617 ATP binding site [chemical binding]; other site 391009001618 Q-loop/lid; other site 391009001619 ABC transporter signature motif; other site 391009001620 Walker B; other site 391009001621 D-loop; other site 391009001622 H-loop/switch region; other site 391009001623 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 391009001624 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 391009001625 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 391009001626 Walker A/P-loop; other site 391009001627 ATP binding site [chemical binding]; other site 391009001628 Q-loop/lid; other site 391009001629 ABC transporter signature motif; other site 391009001630 Walker B; other site 391009001631 D-loop; other site 391009001632 H-loop/switch region; other site 391009001633 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 391009001634 Autophagy protein Apg17; Region: APG17; pfam04108 391009001635 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...; Region: TM_PBP2; cd06261 391009001636 dimer interface [polypeptide binding]; other site 391009001637 conserved gate region; other site 391009001638 putative PBP binding loops; other site 391009001639 ABC-ATPase subunit interface; other site 391009001640 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 391009001641 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...; Region: TM_PBP2; cl00427 391009001642 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cd00995 391009001643 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 391009001644 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 391009001645 S-adenosylmethionine binding site [chemical binding]; other site 391009001646 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...; Region: TM_PBP2; cd06261 391009001647 putative PBP binding loops; other site 391009001648 dimer interface [polypeptide binding]; other site 391009001649 ABC-ATPase subunit interface; other site 391009001650 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...; Region: TM_PBP2; cd06261 391009001651 dimer interface [polypeptide binding]; other site 391009001652 conserved gate region; other site 391009001653 putative PBP binding loops; other site 391009001654 ABC-ATPase subunit interface; other site 391009001655 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 391009001656 PotA is an ABC-type transporter and the ATPase component of the spermidine/putrescine-preferential uptake system consisting of PotA, -B, -C, and -D. PotA has two domains with the N-terminal domain containing the ATPase activity and the residues...; Region: ABC_PotA_N; cd03300 391009001657 Walker A/P-loop; other site 391009001658 ATP binding site [chemical binding]; other site 391009001659 Q-loop/lid; other site 391009001660 ABC transporter signature motif; other site 391009001661 Walker B; other site 391009001662 D-loop; other site 391009001663 H-loop/switch region; other site 391009001664 TOBE domain; Region: TOBE_2; cl01440 391009001665 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 391009001666 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 391009001667 spermidine synthase; Provisional; Region: PRK00811 391009001668 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 391009001669 S-adenosylmethionine binding site [chemical binding]; other site 391009001670 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; cl00687 391009001671 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 391009001672 non-specific DNA binding site [nucleotide binding]; other site 391009001673 salt bridge; other site 391009001674 sequence-specific DNA binding site [nucleotide binding]; other site 391009001675 Cupin domain; Region: Cupin_2; cl09118 391009001676 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 391009001677 This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and deoxyribose-1-...; Region: PGM2; cd05799 391009001678 active site 391009001679 substrate binding site [chemical binding]; other site 391009001680 metal binding site [ion binding]; metal-binding site 391009001681 Uncharacterized conserved protein [Function unknown]; Region: COG5495 391009001682 Domain of unknown function (DUF2520); Region: DUF2520; pfam10728 391009001683 Protein of unknown function (DUF554); Region: DUF554; cl00784 391009001684 EamA-like transporter family; Region: EamA; cl01037 391009001685 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 391009001686 7TM receptor with intracellular HD hydrolase; Region: 7TM-7TMR_HD; pfam07698 391009001687 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 391009001688 Zn2+ binding site [ion binding]; other site 391009001689 Mg2+ binding site [ion binding]; other site 391009001690 Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two...; Region: Prefoldin; cl09111 391009001691 PhoH-like protein; Region: PhoH; cl12134 391009001692 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi...; Region: TPR; cl02429 391009001693 binding surface 391009001694 TPR motif; other site 391009001695 Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]; Region: ArgK; COG1703 391009001696 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 391009001697 Walker A; other site 391009001698 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen...; Region: MM_CoA_mut_B12_BD; cd02071 391009001699 B12 binding site [chemical binding]; other site 391009001700 cobalt ligand [ion binding]; other site 391009001701 Biotin carboxyl carrier protein [Lipid metabolism]; Region: AccB; COG0511 391009001702 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 391009001703 carboxyltransferase (CT) interaction site; other site 391009001704 biotinylation site [posttranslational modification]; other site 391009001705 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 391009001706 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 391009001707 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 391009001708 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 391009001709 dimer interface [polypeptide binding]; other site 391009001710 substrate binding site [chemical binding]; other site 391009001711 metal binding site [ion binding]; metal-binding site 391009001712 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 391009001713 ligand binding site [chemical binding]; other site 391009001714 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 391009001715 SecA preprotein cross-linking domain; Region: SecA_PP_bind; pfam01043 391009001716 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 391009001717 nucleotide binding region [chemical binding]; other site 391009001718 ATP-binding site [chemical binding]; other site 391009001719 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 391009001720 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB; cd01045 391009001721 diiron binding motif [ion binding]; other site 391009001722 Sulfatase; Region: Sulfatase; cl10460 391009001723 chromosome segregation protein; Provisional; Region: PRK03918 391009001724 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...; Region: TM_PBP2; cd06261 391009001725 dimer interface [polypeptide binding]; other site 391009001726 conserved gate region; other site 391009001727 putative PBP binding loops; other site 391009001728 ABC-ATPase subunit interface; other site 391009001729 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...; Region: TM_PBP2; cd06261 391009001730 dimer interface [polypeptide binding]; other site 391009001731 conserved gate region; other site 391009001732 putative PBP binding loops; other site 391009001733 ABC-ATPase subunit interface; other site 391009001734 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 391009001735 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 391009001736 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 391009001737 Clp amino terminal domain; Region: Clp_N; pfam02861 391009001738 Clp amino terminal domain; Region: Clp_N; pfam02861 391009001739 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...; Region: AAA; cd00009 391009001740 Walker A motif; other site 391009001741 ATP binding site [chemical binding]; other site 391009001742 Walker B motif; other site 391009001743 arginine finger; other site 391009001744 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...; Region: AAA; cd00009 391009001745 Walker A motif; other site 391009001746 ATP binding site [chemical binding]; other site 391009001747 Walker B motif; other site 391009001748 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 391009001749 isoaspartyl dipeptidase; Provisional; Region: PRK10657 391009001750 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have...; Region: metallo-dependent_hydrolases; cl00281 391009001751 active site 391009001752 CAAX amino terminal protease self- immunity; Region: Abi; cl00558 391009001753 This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of...; Region: MTH1175; cd00851 391009001754 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 391009001755 Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]; Region: sufC; COG0396 391009001756 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009001757 Walker A/P-loop; other site 391009001758 ATP binding site [chemical binding]; other site 391009001759 Q-loop/lid; other site 391009001760 ABC transporter signature motif; other site 391009001761 Walker B; other site 391009001762 D-loop; other site 391009001763 H-loop/switch region; other site 391009001764 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 391009001765 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 391009001766 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 391009001767 NAD(P) binding site [chemical binding]; other site 391009001768 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK08271 391009001769 Class III ribonucleotide reductase; Region: RNR_III; cd01675 391009001770 effector binding site; other site 391009001771 active site 391009001772 Zn binding site [ion binding]; other site 391009001773 glycine loop; other site 391009001774 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; cl14056 391009001775 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK08665 391009001776 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 391009001777 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 391009001778 active site 391009001779 dimer interface [polypeptide binding]; other site 391009001780 effector binding site; other site 391009001781 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 391009001782 TSCPD domain; Region: TSCPD; cl14834 391009001783 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 391009001784 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 391009001785 YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate...; Region: YhcR_OBF_like; cd04486 391009001786 generic binding surface II; other site 391009001787 generic binding surface I; other site 391009001788 Glycerol-3-phosphate responsive antiterminator; Region: G3P_antiterm; cl00852 391009001789 glycerol kinase; Provisional; Region: glpK; PRK00047 391009001790 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 391009001791 FGGY family of carbohydrate kinases, C-terminal domain; Region: FGGY_C; pfam02782 391009001792 Protein of unknown function (DUF1667); Region: DUF1667; cl01591 391009001793 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 391009001794 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009001795 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 391009001796 Predicted dehydrogenase [General function prediction only]; Region: COG0579 391009001797 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 391009001798 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 391009001799 Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain [Signal transduction mechanisms]; Region: COG5001 391009001800 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391009001801 metal binding site [ion binding]; metal-binding site 391009001802 active site 391009001803 I-site; other site 391009001804 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 391009001805 flagellin; Provisional; Region: PRK12802 391009001806 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or...; Region: Nudix_Hydrolase; cl00447 391009001807 nudix motif; other site 391009001808 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 391009001809 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 391009001810 Domain of unknown function DUF123; Region: DUF123; cl00790 391009001811 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 391009001812 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 391009001813 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...; Region: AAA; cd00009 391009001814 Walker A motif; other site 391009001815 ATP binding site [chemical binding]; other site 391009001816 Walker B motif; other site 391009001817 UGMP family protein; Validated; Region: PRK09604 391009001818 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 391009001819 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 391009001820 FOG: CBS domain [General function prediction only]; Region: COG0517 391009001821 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-...; Region: CBS_pair; cd02205 391009001822 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; cl00075 391009001823 FtsH protease regulator HflC; Provisional; Region: PRK11029 391009001824 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 391009001825 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 391009001826 HflK protein; Region: hflK; TIGR01933 391009001827 Rubrerythrin [Energy production and conversion]; Region: COG1592 391009001828 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 391009001829 binuclear metal center [ion binding]; other site 391009001830 Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-...; Region: rubredoxin_SM; cd00729 391009001831 iron binding site [ion binding]; other site 391009001832 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 391009001833 Glycyl-tRNA synthetase beta subunit; Region: tRNA_synt_2f; pfam02092 391009001834 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 391009001835 glycyl-tRNA synthetase, tetrameric type, alpha subunit; Region: glyQ; TIGR00388 391009001836 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 391009001837 motif 1; other site 391009001838 dimer interface [polypeptide binding]; other site 391009001839 active site 391009001840 motif 2; other site 391009001841 motif 3; other site 391009001842 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 391009001843 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 391009001844 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 391009001845 dimer interface [polypeptide binding]; other site 391009001846 ssDNA binding site [nucleotide binding]; other site 391009001847 tetramer (dimer of dimers) interface [polypeptide binding]; other site 391009001848 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 391009001849 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 391009001850 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 391009001851 N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; Region: NGN; cl02766 391009001852 pyruvate carboxylase; Reviewed; Region: PRK12999 391009001853 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 391009001854 putative homodimer interface [polypeptide binding]; other site 391009001855 KOW (Kyprides, Ouzounis, Woese) motif; Region: KOW; smart00739 391009001856 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 391009001857 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 391009001858 23S rRNA interface [nucleotide binding]; other site 391009001859 L7/L12 interface [polypeptide binding]; other site 391009001860 putative thiostrepton binding site; other site 391009001861 L25 interface [polypeptide binding]; other site 391009001862 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...; Region: Ribosomal_L1; cd00403 391009001863 mRNA/rRNA interface [nucleotide binding]; other site 391009001864 Domain of unknown function (DUF368); Region: DUF368; cl00893 391009001865 GAF domain; Region: GAF; cl00853 391009001866 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391009001867 metal binding site [ion binding]; metal-binding site 391009001868 active site 391009001869 I-site; other site 391009001870 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5,10-...; Region: DHFR; cd00209 391009001871 folate binding site [chemical binding]; other site 391009001872 NADP+ binding site [chemical binding]; other site 391009001873 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 391009001874 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 391009001875 catalytic loop [active] 391009001876 iron binding site [ion binding]; other site 391009001877 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron...; Region: FNR_like; cl06868 391009001878 FAD binding pocket [chemical binding]; other site 391009001879 conserved FAD binding motif [chemical binding]; other site 391009001880 phosphate binding motif [ion binding]; other site 391009001881 beta-alpha-beta structure motif; other site 391009001882 NAD binding pocket [chemical binding]; other site 391009001883 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 391009001884 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 391009001885 FMN-binding domain; Region: FMN_bind; cl01081 391009001886 RnfE family; Region: NQR2_RnfD_RnfE; cl00779 391009001887 Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]; Region: {ManC}; COG0836 391009001888 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 391009001889 Substrate binding site [chemical binding]; other site 391009001890 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 391009001891 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 391009001892 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 391009001893 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 391009001894 Ligand binding site [chemical binding]; other site 391009001895 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 391009001896 Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases; Region: SCAD_SBCAD; cd01158 391009001897 FAD binding site [chemical binding]; other site 391009001898 homotetramer interface [polypeptide binding]; other site 391009001899 substrate binding pocket [chemical binding]; other site 391009001900 catalytic base [active] 391009001901 Protein of unknown function (DUF342); Region: DUF342; pfam03961 391009001902 DNA polymerase III PolC; Validated; Region: polC; PRK00448 391009001903 Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane]; Region: GumC; COG3206 391009001904 Chain length determinant protein; Region: Wzz; cl01623 391009001905 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 391009001906 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 391009001907 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 391009001908 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 391009001909 SLBB domain; Region: SLBB; pfam10531 391009001910 DHH family; Region: DHH; pfam01368 391009001911 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 391009001912 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 391009001913 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 391009001914 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 391009001915 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 391009001916 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 391009001917 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK14654 391009001918 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 undecaprenyl-pyrophosphoryl-N-...; Region: GT_MraY; cd06852 391009001919 Mg++ binding site [ion binding]; other site 391009001920 putative catalytic motif [active] 391009001921 putative substrate binding site [chemical binding]; other site 391009001922 This subfamily is composed of uncharacterized bacterial glycosyltransferases in the MraY-like family. This family contains both eukaryotic and prokaryotic UDP-D-N-acetylhexosamine:polyprenol phosphate D-N-acetylhexosamine-1-phosphate transferases...; Region: GT_MraY_like; cd06912 391009001923 Mg++ binding site [ion binding]; other site 391009001924 putative catalytic motif [active] 391009001925 Rod binding protein; Region: Rod-binding; cl01626 391009001926 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 391009001927 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 391009001928 Flagellar L-ring protein; Region: FlgH; cl00905 391009001929 SAF domain; Region: SAF; cl00555 391009001930 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 391009001931 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 391009001932 ATP binding site [chemical binding]; other site 391009001933 Mg2+ binding site [ion binding]; other site 391009001934 G-X-G motif; other site 391009001935 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 391009001936 anchoring element; other site 391009001937 dimer interface [polypeptide binding]; other site 391009001938 ATP binding site [chemical binding]; other site 391009001939 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...; Region: TOPRIM_TopoIIA_GyrB; cd03366 391009001940 active site 391009001941 putative metal-binding site [ion binding]; other site 391009001942 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 391009001943 Protein of unknown function (DUF721); Region: DUF721; cl02324 391009001944 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and 4-amino-4-deoxychorismate...; Region: PLPDE_IV; cd00449 391009001945 homodimer interface [polypeptide binding]; other site 391009001946 substrate-cofactor binding pocket; other site 391009001947 Aminotransferase class IV; Region: Aminotran_4; pfam01063 391009001948 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391009001949 catalytic residue [active] 391009001950 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 391009001951 MiaB-like tRNA modifying enzyme; Region: MiaB-like-C; TIGR01579 391009001952 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 391009001953 FeS/SAM binding site; other site 391009001954 FOG: CBS domain [General function prediction only]; Region: COG0517 391009001955 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-...; Region: CBS_pair; cl10010 391009001956 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 391009001957 1-phosphofructokinase (FruK), minor 6-phosphofructokinase (pfkB) and related sugar kinases. FruK plays an important role in the predominant pathway for fructose utilisation.This group also contains tagatose-6-phophate kinase, an enzyme of the tagatose...; Region: FruK_PfkB_like; cd01164 391009001958 putative substrate binding site [chemical binding]; other site 391009001959 putative ATP binding site [chemical binding]; other site 391009001960 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009001961 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 391009001962 Walker A/P-loop; other site 391009001963 ATP binding site [chemical binding]; other site 391009001964 Q-loop/lid; other site 391009001965 ABC transporter signature motif; other site 391009001966 Walker B; other site 391009001967 D-loop; other site 391009001968 H-loop/switch region; other site 391009001969 putative DNA modification/repair radical SAM protein; Region: rSAM_link_UDG; TIGR03916 391009001970 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 391009001971 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 391009001972 metal-binding site [ion binding] 391009001973 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 391009001974 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; cl11391 391009001975 Predicted membrane protein (DUF2078); Region: DUF2078; cl01373 391009001976 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cl00207 391009001977 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...; Region: SHMT; cd00378 391009001978 dimer interface [polypeptide binding]; other site 391009001979 glycine-pyridoxal phosphate binding site [chemical binding]; other site 391009001980 active site 391009001981 folate binding site [chemical binding]; other site 391009001982 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 391009001983 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 391009001984 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 391009001985 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 391009001986 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 391009001987 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 391009001988 sulfate transport protein; Provisional; Region: cysT; CHL00187 391009001989 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...; Region: TM_PBP2; cd06261 391009001990 dimer interface [polypeptide binding]; other site 391009001991 conserved gate region; other site 391009001992 putative PBP binding loops; other site 391009001993 ABC-ATPase subunit interface; other site 391009001994 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...; Region: TM_PBP2; cd06261 391009001995 dimer interface [polypeptide binding]; other site 391009001996 conserved gate region; other site 391009001997 putative PBP binding loops; other site 391009001998 ABC-ATPase subunit interface; other site 391009001999 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_1; cd05008 391009002000 dimer interface [polypeptide binding]; other site 391009002001 active site 391009002002 SIS (Sugar ISomerase) domain repeat 2 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_2; cd05009 391009002003 dimer interface [polypeptide binding]; other site 391009002004 active site 391009002005 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate. This is the first committed step in the biosynthetic pathway to...; Region: NagA; cd00854 391009002006 active site 391009002007 dimer interface [polypeptide binding]; other site 391009002008 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 391009002009 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 391009002010 putative dimer interface [polypeptide binding]; other site 391009002011 active site pocket [active] 391009002012 putative cataytic base [active] 391009002013 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a...; Region: CbiX_SirB_N; cd03416 391009002014 putative active site [active] 391009002015 Precorrin isomerase [Coenzyme metabolism]; Region: CobH; cl00913 391009002016 Precorrin-8X methylmutase; Region: CbiC; pfam02570 391009002017 CbiD; Region: CbiD; cl00828 391009002018 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 391009002019 Precorrin-6B methylase 2 [Coenzyme metabolism]; Region: CobL; COG2242 391009002020 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 391009002021 S-adenosylmethionine binding site [chemical binding]; other site 391009002022 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 391009002023 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 391009002024 cobalamin biosynthesis protein CbiG; Validated; Region: PRK05788 391009002025 Cobalamin synthesis G N-terminal; Region: CbiG_N; pfam11760 391009002026 Cobalamin biosynthesis central region; Region: CbiG_mid; pfam11761 391009002027 Cobalamin synthesis G C-terminus; Region: CbiG_C; cl12133 391009002028 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 391009002029 Precorrin-6x reductase CbiJ/CobK; Region: CbiJ; cl00922 391009002030 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 391009002031 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 391009002032 tRNA; other site 391009002033 putative tRNA binding site [nucleotide binding]; other site 391009002034 putative NADP binding site [chemical binding]; other site 391009002035 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 391009002036 porphobilinogen deaminase; Region: hemC; TIGR00212 391009002037 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; cl03189 391009002038 domain interfaces; other site 391009002039 active site 391009002040 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 391009002041 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...; Region: HemD; cd06578 391009002042 active site 391009002043 Uroporphyrinogen-III synthase HemD; Region: HEM4; pfam02602 391009002044 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; cd00384 391009002045 dimer interface [polypeptide binding]; other site 391009002046 active site 391009002047 Schiff base residues; other site 391009002048 precorrin-2 dehydrogenase; Validated; Region: PRK06719 391009002049 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 391009002050 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase...; Region: OAT_like; cd00610 391009002051 inhibitor-cofactor binding pocket; inhibition site 391009002052 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391009002053 catalytic residue [active] 391009002054 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; cl00397 391009002055 Cobalt transport protein component CbiN; Region: CbiN; cl00842 391009002056 Cobalt transport protein; Region: CbiQ; cl00463 391009002057 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 391009002058 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This...; Region: ABC_cobalt_CbiO_domain1; cd03225 391009002059 Walker A/P-loop; other site 391009002060 ATP binding site [chemical binding]; other site 391009002061 Q-loop/lid; other site 391009002062 ABC transporter signature motif; other site 391009002063 Walker B; other site 391009002064 D-loop; other site 391009002065 H-loop/switch region; other site 391009002066 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This...; Region: Alpha_ANH_like_IV; cd01994 391009002067 Ligand Binding Site [chemical binding]; other site 391009002068 Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus; Region: RNase_HI_bacteria_HBD; cd09277 391009002069 RNA/DNA hybrid binding site [nucleotide binding]; other site 391009002070 active site 391009002071 GMP synthase; Reviewed; Region: guaA; PRK00074 391009002072 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 391009002073 AMP/PPi binding site [chemical binding]; other site 391009002074 candidate oxyanion hole; other site 391009002075 catalytic triad [active] 391009002076 potential glutamine specificity residues [chemical binding]; other site 391009002077 The C-terminal domain of GMP synthetase. It contains two subdomains; the ATP pyrophosphatase domain which closes to the N-termial and the dimerization domain at C-terminal end. The ATP-PPase is a twisted, five-stranded parallel beta-sheet sandwiched...; Region: GMP_synthase_C; cd01997 391009002078 ATP Binding subdomain [chemical binding]; other site 391009002079 Ligand Binding sites [chemical binding]; other site 391009002080 Dimerization subdomain; other site 391009002081 LemA family; Region: LemA; cl00742 391009002082 Predicted membrane protein (DUF2207); Region: DUF2207; pfam09972 391009002083 Predicted membrane protein [Function unknown]; Region: COG4907 391009002084 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 391009002085 Tryptophan synthase-beta: Trptophan synthase is a bifunctional enzyme that catalyses the last two steps in the biosynthesis of L-tryptophan via its alpha and beta reactions. In the alpha reaction, indole 3-glycerol phosphate is cleaved reversibly to...; Region: Trp-synth_B; cd06446 391009002086 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391009002087 catalytic residue [active] 391009002088 Phosphate transporter family; Region: PHO4; cl00396 391009002089 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cl00514 391009002090 FMN binding site [chemical binding]; other site 391009002091 dimer interface [polypeptide binding]; other site 391009002092 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 391009002093 Homocysteine/selenocysteine methylase (S-methylmethionine-dependent) [Amino acid transport and metabolism]; Region: MHT1; cl14105 391009002094 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 391009002095 Pterin binding enzyme; Region: Pterin_bind; pfam00809 391009002096 substrate binding pocket [chemical binding]; other site 391009002097 dimer interface [polypeptide binding]; other site 391009002098 inhibitor binding site; inhibition site 391009002099 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase...; Region: B12-binding_like; cl00293 391009002100 B12 binding site [chemical binding]; other site 391009002101 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 391009002102 Methylenetetrahydrofolate reductase; Region: MTHFR; pfam02219 391009002103 Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine...; Region: MTHFR; cd00537 391009002104 FAD binding site [chemical binding]; other site 391009002105 ApbE family; Region: ApbE; cl00643 391009002106 Domain of unknown function DUF39; Region: DUF39; cl14897 391009002107 hypothetical protein; Provisional; Region: PRK13795 391009002108 Pyrococcus aspartate kinase subunit, putative; Region: AspKin_pair; TIGR02078 391009002109 AAK_AK: Amino Acid Kinase Superfamily (AAK), Aspartokinase (AK); this CD includes the N-terminal catalytic domain of aspartokinase (4-L-aspartate-4-phosphotransferase;). AK is the first enzyme in the biosynthetic pathway of the aspartate family of...; Region: AAK_AK; cd04234 391009002110 putative catalytic residues [active] 391009002111 putative nucleotide binding site [chemical binding]; other site 391009002112 aspartate binding site [chemical binding]; other site 391009002113 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 391009002114 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 391009002115 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by...; Region: PRX_BCP; cd03017 391009002116 catalytic triad [active] 391009002117 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 391009002118 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 391009002119 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009002120 Walker A/P-loop; other site 391009002121 ATP binding site [chemical binding]; other site 391009002122 Q-loop/lid; other site 391009002123 ABC transporter signature motif; other site 391009002124 Walker B; other site 391009002125 D-loop; other site 391009002126 H-loop/switch region; other site 391009002127 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 391009002128 Predicted transcriptional regulator [Transcription]; Region: COG2345 391009002129 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 391009002130 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 ATP-dependent...; Region: HisRS-like_core; cd00773 391009002131 dimer interface [polypeptide binding]; other site 391009002132 motif 1; other site 391009002133 active site 391009002134 motif 2; other site 391009002135 motif 3; other site 391009002136 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 391009002137 anticodon binding site; other site 391009002138 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 391009002139 TPR motif; other site 391009002140 binding surface 391009002141 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 391009002142 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 391009002143 active site 391009002144 motif I; other site 391009002145 motif II; other site 391009002146 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; cl11391 391009002147 G1P_TT_long represents the long form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_long; cd04189 391009002148 glucose-1-phosphate thymidylylransferase, long form; Region: rmlA_long; TIGR01208 391009002149 substrate binding site [chemical binding]; other site 391009002150 metal binding site [ion binding]; metal-binding site 391009002151 Oligomer interface [polypeptide binding]; other site 391009002152 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 391009002153 Cache domain; Region: Cache_1; pfam02743 391009002154 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 connected by an extended linker. The...; Region: HAMP; cl01054 391009002155 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 391009002156 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 391009002157 PAS domain S-box; Region: sensory_box; TIGR00229 391009002158 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 391009002159 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391009002160 metal binding site [ion binding]; metal-binding site 391009002161 active site 391009002162 I-site; other site 391009002163 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 391009002164 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 391009002165 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...; Region: TM_PBP2; cd06261 391009002166 dimer interface [polypeptide binding]; other site 391009002167 conserved gate region; other site 391009002168 putative PBP binding loops; other site 391009002169 ABC-ATPase subunit interface; other site 391009002170 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 391009002171 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...; Region: TM_PBP2; cd06261 391009002172 dimer interface [polypeptide binding]; other site 391009002173 conserved gate region; other site 391009002174 putative PBP binding loops; other site 391009002175 ABC-ATPase subunit interface; other site 391009002176 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 391009002177 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 391009002178 hybrid cluster protein; Provisional; Region: PRK05290 391009002179 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-; Region: HCP_like; cl14655 391009002180 ACS interaction site; other site 391009002181 CODH interaction site; other site 391009002182 Hybrid cluster protein (HCP), formerly known as prismane, is thought to play a role in nitrogen metabolism but its specific function is unknown. HCP has three structural domains, an N-terminal alpha-helical domain, and two similar domains comprising a...; Region: HCP; cd01914 391009002183 hybrid metal cluster; other site 391009002184 Uncharacterized conserved protein [Function unknown]; Region: COG2461 391009002185 Family of unknown function (DUF438); Region: DUF438; pfam04282 391009002186 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cl00047 391009002187 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 391009002188 phosphoglucomutase-2-like protein; Provisional; Region: PTZ00150 391009002189 This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and deoxyribose-1-...; Region: PGM2; cd05799 391009002190 active site 391009002191 substrate binding site [chemical binding]; other site 391009002192 metal binding site [ion binding]; metal-binding site 391009002193 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009002194 Peroxiredoxin (PRX) family, AhpE-like subfamily; composed of proteins similar to Mycobacterium tuberculosis AhpE. AhpE is described as a 1-cys PRX because of the absence of a resolving cysteine. The structure and sequence of AhpE, however, show greater...; Region: PRX_AhpE_like; cd03018 391009002195 dimer interface [polypeptide binding]; other site 391009002196 catalytic triad [active] 391009002197 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 391009002198 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 391009002199 L-Ala-D/L-Glu epimerase; Provisional; Region: PRK15129 391009002200 L-Ala-D/L-Glu epimerase catalyzes the epimerization of L-Ala-D/L-Glu and other dipeptides. The genomic context and the substrate specificity of characterized members of this family from E.coli and B.subtilis indicates a possible role in the metabolism...; Region: L-Ala-DL-Glu_epimerase; cd03319 391009002201 active site 391009002202 Pyroglutamyl peptidase (PGP) type I, also known as pyrrolidone carboxyl peptidase (pcp) type I: Enzymes responsible for cleaving pyroglutamate (pGlu) from the N-terminal end of specialized proteins. The N-terminal pGlu protects these proteins from...; Region: Peptidase_C15; cd00501 391009002203 putative substrate binding pocket [chemical binding]; other site 391009002204 AC domain interface; other site 391009002205 catalytic triad [active] 391009002206 AB domain interface; other site 391009002207 interchain disulfide; other site 391009002208 Transcriptional regulators [Transcription]; Region: PurR; COG1609 391009002209 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 391009002210 DNA binding site [nucleotide binding] 391009002211 domain linker motif; other site 391009002212 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; Region: PBP1_LacI_like_1; cd06277 391009002213 putative dimerization interface [polypeptide binding]; other site 391009002214 putative ligand binding site [chemical binding]; other site 391009002215 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 391009002216 active site 391009002217 Alpha-galactosidases/6-phospho-beta-glucosidases, family 4 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: CelF; COG1486 391009002218 Glycoside Hydrolases Family 4; Alpha-glucosidases and alpha-galactosidases; Region: GH4_alpha_glucosidase_galactosidase; cd05297 391009002219 NAD binding site [chemical binding]; other site 391009002220 sugar binding site [chemical binding]; other site 391009002221 divalent metal binding site [ion binding]; other site 391009002222 putative tetramer (dimer of dimers) interface [polypeptide binding]; other site 391009002223 dimer interface [polypeptide binding]; other site 391009002224 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 391009002225 dimerization interface [polypeptide binding]; other site 391009002226 putative DNA binding site [nucleotide binding]; other site 391009002227 putative Zn2+ binding site [ion binding]; other site 391009002228 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 391009002229 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 391009002230 active site 391009002231 metal binding site [ion binding]; metal-binding site 391009002232 homotetramer interface [polypeptide binding]; other site 391009002233 DNA mismatch repair protein MutL; Region: mutl; TIGR00585 391009002234 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 391009002235 ATP binding site [chemical binding]; other site 391009002236 Mg2+ binding site [ion binding]; other site 391009002237 G-X-G motif; other site 391009002238 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 391009002239 ATP binding site [chemical binding]; other site 391009002240 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 391009002241 trehalose synthase; Region: treS_nterm; TIGR02456 391009002242 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 391009002243 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 391009002244 active site 391009002245 metal binding site [ion binding]; metal-binding site 391009002246 homotetramer interface [polypeptide binding]; other site 391009002247 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 391009002248 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 391009002249 Zn2+ binding site [ion binding]; other site 391009002250 Mg2+ binding site [ion binding]; other site 391009002251 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391009002252 metal binding site [ion binding]; metal-binding site 391009002253 active site 391009002254 I-site; other site 391009002255 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]; Region: COG1031 391009002256 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; cl14056 391009002257 RNA polymerase sigma factor RpoE; Provisional; Region: PRK09652 391009002258 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391009002259 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...; Region: Sigma70_r4; cd06171 391009002260 DNA binding residues [nucleotide binding] 391009002261 Protein of unknown function DUF72; Region: DUF72; cl00777 391009002262 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 391009002263 UvrD/REP helicase; Region: UvrD-helicase; cl14126 391009002264 UvrD/REP helicase; Region: UvrD-helicase; cl14126 391009002265 Putative hydrophobic ligand-binding SRPBCC domain of Micromonospora echinospora CalC, human Aha1, and related proteins; Region: SRPBCC_CalC_Aha1-like; cd07814 391009002266 putative hydrophobic ligand binding site [chemical binding]; other site 391009002267 Transcriptional regulators [Transcription]; Region: PurR; COG1609 391009002268 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 391009002269 DNA binding site [nucleotide binding] 391009002270 domain linker motif; other site 391009002271 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 391009002272 competence damage-inducible protein A; Provisional; Region: PRK00549 391009002273 Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of...; Region: cinA; cd00885 391009002274 putative MPT binding site; other site 391009002275 Competence-damaged protein; Region: CinA; cl00666 391009002276 CTP synthetase; Validated; Region: pyrG; PRK05380 391009002277 CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer...; Region: CTGs; cd03113 391009002278 Catalytic site [active] 391009002279 Active site [active] 391009002280 UTP binding site [chemical binding]; other site 391009002281 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 391009002282 active site 391009002283 putative oxyanion hole; other site 391009002284 catalytic triad [active] 391009002285 histidinol-phosphatase; Provisional; Region: PRK05588 391009002286 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 391009002287 elongation factor Ts; Reviewed; Region: tsf; PRK12332 391009002288 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 391009002289 Elongation factor TS; Region: EF_TS; pfam00889 391009002290 PAS fold; Region: PAS_4; pfam08448 391009002291 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 391009002292 Sigma factor PP2C-like phosphatases; Region: PP2C_SIG; smart00331 391009002293 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 391009002294 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 391009002295 Phosphate transporter family; Region: PHO4; cl00396 391009002296 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...; Region: PBPb; cd00134 391009002297 substrate binding pocket [chemical binding]; other site 391009002298 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 391009002299 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391009002300 metal binding site [ion binding]; metal-binding site 391009002301 active site 391009002302 I-site; other site 391009002303 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 391009002304 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 391009002305 indolepyruvate ferredoxin oxidoreductase, alpha subunit; Region: IOR_alpha; TIGR03336 391009002306 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 391009002307 dimer interface [polypeptide binding]; other site 391009002308 PYR/PP interface [polypeptide binding]; other site 391009002309 TPP binding site [chemical binding]; other site 391009002310 substrate binding site [chemical binding]; other site 391009002311 TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as indolepyruvate or phenylpyruvate, which are generated by the...; Region: TPP_IOR_alpha; cd02008 391009002312 TPP-binding site; other site 391009002313 4Fe-4S binding domain; Region: Fer4; cl02805 391009002314 Permease P (pink-eyed dilution). Mutations in the human melanosomal P gene were responsible for classic phenotype of oculocutaneous albinism type 2 (OCA2). Although the precise function of the P protein is unknown, it was predicted to regulate the...; Region: P_permease; cd01116 391009002315 transmembrane helices; other site 391009002316 ribosome biogenesis GTPase YqeH; Region: GTPase_YqeH; TIGR03597 391009002317 YqeH. YqeH is an essential GTP-binding protein. Depletion of YqeH induces an excess initiation of DNA replication, suggesting that it negatively controls initiation of chromosome replication. The YqeH subfamily is common in eukaryotes and sporadically...; Region: YqeH; cd01855 391009002318 GTP/Mg2+ binding site [chemical binding]; other site 391009002319 G4 box; other site 391009002320 G5 box; other site 391009002321 G1 box; other site 391009002322 Switch I region; other site 391009002323 G2 box; other site 391009002324 G3 box; other site 391009002325 Switch II region; other site 391009002326 propanediol utilization phosphotransacylase; Provisional; Region: PRK15070 391009002327 Propanediol utilisation protein PduL; Region: PduL; pfam06130 391009002328 Propanediol utilisation protein PduL; Region: PduL; pfam06130 391009002329 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009002330 H-loop/switch region; other site 391009002331 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 391009002332 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 391009002333 E or 'early' set-like proteins. These alpha amylase-like sugar utilizing enzymes which may be related to the immunoglobulin and/or fibronectin type III superfamilies are associated with different types of catalytic domains at either the N-terminal or...; Region: E_set_proteins_like; cd02861 391009002334 E or 'early' set-like proteins. These alpha amylase-like sugar utilizing enzymes which may be related to the immunoglobulin and/or fibronectin type III superfamilies are associated with different types of catalytic domains at either the N-terminal or...; Region: E_set_proteins_like; cd02861 391009002335 Alpha-amylase/alpha-mannosidase [Carbohydrate transport and metabolism]; Region: COG1449 391009002336 DOMON-like domain of various glycoside hydrolases; Region: DOMON_glucodextranase_like; cd09626 391009002337 putative ligand binding site [chemical binding]; other site 391009002338 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 391009002339 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK07234 391009002340 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 391009002341 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to PFK family that includes ATP- and pyrophosphate (PPi)- dependent phosphofructokinases...; Region: PFK; cl00204 391009002342 active site 391009002343 ADP/pyrophosphate binding site [chemical binding]; other site 391009002344 dimerization interface [polypeptide binding]; other site 391009002345 allosteric effector site; other site 391009002346 fructose-1,6-bisphosphate binding site; other site 391009002347 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 391009002348 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 391009002349 dimer interface [polypeptide binding]; other site 391009002350 active site 391009002351 metal binding site [ion binding]; metal-binding site 391009002352 GTPase Era; Reviewed; Region: era; PRK00089 391009002353 Era subfamily. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit...; Region: Era; cd04163 391009002354 G1 box; other site 391009002355 GTP/Mg2+ binding site [chemical binding]; other site 391009002356 Switch I region; other site 391009002357 G2 box; other site 391009002358 Switch II region; other site 391009002359 G3 box; other site 391009002360 G4 box; other site 391009002361 G5 box; other site 391009002362 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...; Region: KH-I; cl00098 391009002363 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 391009002364 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 391009002365 putative tRNA-binding site [nucleotide binding]; other site 391009002366 B3/4 domain; Region: B3_4; cl11458 391009002367 tRNA synthetase B5 domain; Region: B5; cl08394 391009002368 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 391009002369 dimer interface [polypeptide binding]; other site 391009002370 motif 1; other site 391009002371 motif 3; other site 391009002372 motif 2; other site 391009002373 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 391009002374 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 391009002375 binding surface 391009002376 TPR motif; other site 391009002377 Domain of unknown function (DUF205); Region: DUF205; cl00410 391009002378 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 391009002379 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 391009002380 active site 391009002381 UDP-N-acetylglucosamine 2-epimerase; Region: Epimerase_2; pfam02350 391009002382 homodimer interface [polypeptide binding]; other site 391009002383 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 391009002384 dinuclear metal binding motif [ion binding]; other site 391009002385 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 391009002386 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 391009002387 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...; Region: TM_PBP2; cd06261 391009002388 dimer interface [polypeptide binding]; other site 391009002389 conserved gate region; other site 391009002390 putative PBP binding loops; other site 391009002391 ABC-ATPase subunit interface; other site 391009002392 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...; Region: TM_PBP2; cd06261 391009002393 dimer interface [polypeptide binding]; other site 391009002394 conserved gate region; other site 391009002395 putative PBP binding loops; other site 391009002396 ABC-ATPase subunit interface; other site 391009002397 Cache domain; Region: Cache_1; pfam02743 391009002398 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391009002399 I-site; other site 391009002400 active site 391009002401 metal binding site [ion binding]; metal-binding site 391009002402 Protein of unknown function (DUF445); Region: DUF445; pfam04286 391009002403 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; cl11520 391009002404 Flavin-dependent tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA [Cell cycle control, cell division, chromosome partitioning]; Region: GidA; COG0445 391009002405 dihydrolipoamide dehydrogenase; Region: lipoamide_DH; TIGR01350 391009002406 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 391009002407 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 391009002408 Sugar fermentation stimulation protein; Region: SfsA; cl00647 391009002409 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 391009002410 Predicted permease; Region: DUF318; cl00487 391009002411 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 391009002412 dimerization interface [polypeptide binding]; other site 391009002413 putative DNA binding site [nucleotide binding]; other site 391009002414 putative Zn2+ binding site [ion binding]; other site 391009002415 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 391009002416 MatE; Region: MatE; pfam01554 391009002417 MatE; Region: MatE; pfam01554 391009002418 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 391009002419 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 391009002420 ABC transporter; Region: ABC_tran_2; pfam12848 391009002421 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 391009002422 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 391009002423 Walker A motif; other site 391009002424 Protein of unknown function (DUF327); Region: DUF327; cl00753 391009002425 Survival protein SurE; Region: SurE; cl00448 391009002426 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(...; Region: Pep_deformylase; cd00487 391009002427 active site 391009002428 catalytic residues [active] 391009002429 metal binding site [ion binding]; metal-binding site 391009002430 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 391009002431 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 391009002432 ATP binding site [chemical binding]; other site 391009002433 Mg++ binding site [ion binding]; other site 391009002434 motif III; other site 391009002435 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 391009002436 nucleotide binding region [chemical binding]; other site 391009002437 ATP-binding site [chemical binding]; other site 391009002438 DbpA RNA binding domain; Region: DbpA; pfam03880 391009002439 Outer membrane protein (OmpH-like); Region: OmpH; cl08146 391009002440 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 391009002441 The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in...; Region: ABC_YhbG; cd03218 391009002442 Walker A/P-loop; other site 391009002443 ATP binding site [chemical binding]; other site 391009002444 Q-loop/lid; other site 391009002445 ABC transporter signature motif; other site 391009002446 Walker B; other site 391009002447 D-loop; other site 391009002448 H-loop/switch region; other site 391009002449 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 391009002450 Uncharacterized protein conserved in bacteria (DUF2344); Region: DUF2344; cl02090 391009002451 Response regulator receiver domain; Region: Response_reg; pfam00072 391009002452 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 391009002453 active site 391009002454 phosphorylation site [posttranslational modification] 391009002455 intermolecular recognition site; other site 391009002456 dimerization interface [polypeptide binding]; other site 391009002457 Sigma factor PP2C-like phosphatases; Region: PP2C_SIG; smart00331 391009002458 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 391009002459 elongation factor P; Validated; Region: PRK00529 391009002460 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 391009002461 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 N-formylmethionyl-...; Region: S1_EF-P_repeat_1; cd04470 391009002462 RNA binding site [nucleotide binding]; other site 391009002463 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 N-formylmethionyl-...; Region: S1_EF-P_repeat_2; cd05794 391009002464 RNA binding site [nucleotide binding]; other site 391009002465 Protein of unknown function (DUF322); Region: DUF322; cl00574 391009002466 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 391009002467 putative RNA binding site [nucleotide binding]; other site 391009002468 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 391009002469 Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhB; cl12017 391009002470 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 391009002471 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 391009002472 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 391009002473 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391009002474 metal binding site [ion binding]; metal-binding site 391009002475 active site 391009002476 I-site; other site 391009002477 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 391009002478 putative dimer interface [polypeptide binding]; other site 391009002479 active site pocket [active] 391009002480 putative cataytic base [active] 391009002481 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is...; Region: CobU; cd00544 391009002482 homotrimer interface [polypeptide binding]; other site 391009002483 Walker A motif; other site 391009002484 GTP binding site [chemical binding]; other site 391009002485 Walker B motif; other site 391009002486 Cobalamin-5-phosphate synthase; Region: CobS; cl00415 391009002487 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 391009002488 cobyric acid synthase; Provisional; Region: PRK00784 391009002489 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 391009002490 catalytic triad [active] 391009002491 CobD/Cbib protein; Region: CobD_Cbib; cl00561 391009002492 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 391009002493 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 391009002494 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391009002495 homodimer interface [polypeptide binding]; other site 391009002496 catalytic residue [active] 391009002497 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a...; Region: CobA_CobO_BtuR; cd00561 391009002498 Walker A motif; other site 391009002499 homodimer interface [polypeptide binding]; other site 391009002500 ATP binding site [chemical binding]; other site 391009002501 hydroxycobalamin binding site [chemical binding]; other site 391009002502 Walker B motif; other site 391009002503 Peptidase S8 family domain in Thermitase-like proteins; Region: Peptidases_S8_Thermitase_like; cd07484 391009002504 active site 391009002505 catalytic triad [active] 391009002506 DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]; Region: DnrI; COG3629 391009002507 Fructose-1,6-bisphosphatase/sedoheptulose 1,7-bisphosphatase and related proteins [Carbohydrate transport and metabolism]; Region: GlpX; COG1494 391009002508 Bacterial fructose-1,6-bisphosphatase, glpX-encoded. A dimeric enzyme dependent on Mg(2+). glpX-encoded FPBase (FBPase class II) differs from other members of the inositol-phosphatase superfamily by permutation of secondary structure elements. The core...; Region: FBPase_glpX; cd01516 391009002509 putative active site [active] 391009002510 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 391009002511 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 391009002512 RNA binding surface [nucleotide binding]; other site 391009002513 PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PseudoU_synth_RsuA; cd02553 391009002514 active site 391009002515 uracil binding [chemical binding]; other site 391009002516 DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and...; Region: DHPS; cd00739 391009002517 dihydropteroate synthase; Region: DHPS; TIGR01496 391009002518 substrate binding pocket [chemical binding]; other site 391009002519 dimer interface [polypeptide binding]; other site 391009002520 inhibitor binding site; inhibition site 391009002521 Esterase/lipase [General function prediction only]; Region: COG1647 391009002522 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 391009002523 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 391009002524 catalytic residue [active] 391009002525 Phosphocholine cytidylyltransferases catalyze the synthesis of CDP-choline; Region: PC_cytidylyltransferase; cd02523 391009002526 active site 391009002527 metal binding site [ion binding]; metal-binding site 391009002528 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 391009002529 Uncharacterised protein family (UPF0104); Region: UPF0104; cl04219 391009002530 Major Facilitator Superfamily; Region: MFS_1; pfam07690 391009002531 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a...; Region: Hint; cl12032 391009002532 hypothetical protein; Reviewed; Region: PRK09588 391009002533 sulfate ABC transporter, ATP-binding protein; Region: 3a0106s01; TIGR00968 391009002534 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 391009002535 Walker A/P-loop; other site 391009002536 ATP binding site [chemical binding]; other site 391009002537 Q-loop/lid; other site 391009002538 ABC transporter signature motif; other site 391009002539 Walker B; other site 391009002540 D-loop; other site 391009002541 H-loop/switch region; other site 391009002542 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 391009002543 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...; Region: TM_PBP2; cl00427 391009002544 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 391009002545 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 391009002546 Domain of unknown function DUF20; Region: UPF0118; cl00465 391009002547 Asparaginase (amidohydrolase): Asparaginases are tetrameric enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases, one highly specific for asparagine and localised to the...; Region: Asparaginase; cl00216 391009002548 active site/substrate binding site [active] 391009002549 tetramer interface [polypeptide binding]; other site 391009002550 Rhomboid family; Region: Rhomboid; cl11446 391009002551 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 391009002552 putative active site [active] 391009002553 Flagellar FliJ protein; Region: FliJ; cl09161 391009002554 flagellar export protein FliJ; Region: flagell_FliJ; TIGR02473 391009002555 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 391009002556 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 391009002557 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (...; Region: ABC_SMC_barmotin; cd03278 391009002558 Walker A/P-loop; other site 391009002559 ATP binding site [chemical binding]; other site 391009002560 ABC transporter signature motif; other site 391009002561 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 in...; Region: TOP4c; cl00148 391009002562 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; pfam06470 391009002563 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009002564 Q-loop/lid; other site 391009002565 ABC transporter signature motif; other site 391009002566 Walker B; other site 391009002567 D-loop; other site 391009002568 H-loop/switch region; other site 391009002569 UDP-N-acetylmuramate--alanine ligase; Region: murC; TIGR01082 391009002570 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 391009002571 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 391009002572 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 391009002573 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 391009002574 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...; Region: GT1_MurG; cd03785 391009002575 active site 391009002576 homodimer interface [polypeptide binding]; other site 391009002577 glyoxylate reductase; Reviewed; Region: PRK13243 391009002578 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009002579 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the...; Region: mcbC-like_oxidoreductase; cd02142 391009002580 putative FMN binding site [chemical binding]; other site 391009002581 NADPH bind site [chemical binding]; other site 391009002582 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 391009002583 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 391009002584 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; cl11391 391009002585 DNA helicase, putative; Region: TIGR00376 391009002586 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; cl14882 391009002587 Predicted membrane protein (DUF2078); Region: DUF2078; cl01373 391009002588 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 391009002589 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 391009002590 Uncharacterized conserved protein related to dihydrodipicolinate reductase [Function unknown]; Region: COG3804 391009002591 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009002592 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 391009002593 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD)...; Region: Trp-synth-beta_II; cd00640 391009002594 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 391009002595 catalytic residue [active] 391009002596 D-Lysine 5,6-aminomutase alpha subunit; Region: Lys-AminoMut_A; pfam09043 391009002597 B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine...; Region: B12-binding; cd02067 391009002598 B12 binding site [chemical binding]; other site 391009002599 cobalt ligand [ion binding]; other site 391009002600 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 391009002601 putative deoxyribonuclease YjjV; Provisional; Region: PRK11449 391009002602 active site 391009002603 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 391009002604 RuvA N terminal domain; Region: RuvA_N; pfam01330 391009002605 DRTGG domain; Region: DRTGG; cl12147 391009002606 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 391009002607 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 391009002608 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 391009002609 ATP binding site [chemical binding]; other site 391009002610 Mg2+ binding site [ion binding]; other site 391009002611 G-X-G motif; other site 391009002612 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 391009002613 Surface antigen; Region: Bac_surface_Ag; cl03097 391009002614 Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]; Region: COG2872 391009002615 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 391009002616 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 391009002617 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 391009002618 RNA binding surface [nucleotide binding]; other site 391009002619 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 391009002620 active site 391009002621 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 391009002622 pyruvate kinase; Provisional; Region: PRK05826 391009002623 domain interfaces; other site 391009002624 active site 391009002625 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 391009002626 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 391009002627 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 391009002628 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 391009002629 23S rRNA binding site [nucleotide binding]; other site 391009002630 L21 binding site [polypeptide binding]; other site 391009002631 L13 binding site [polypeptide binding]; other site 391009002632 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 391009002633 rRNA interaction site [nucleotide binding]; other site 391009002634 S8 interaction site; other site 391009002635 putative laminin-1 binding site; other site 391009002636 thymidylate kinase; Validated; Region: tmk; PRK00698 391009002637 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...; Region: TMPK; cd01672 391009002638 TMP-binding site; other site 391009002639 ATP-binding site [chemical binding]; other site 391009002640 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 391009002641 FliP family; Region: FliP; cl00593 391009002642 Response regulator receiver domain; Region: Response_reg; pfam00072 391009002643 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 391009002644 active site 391009002645 phosphorylation site [posttranslational modification] 391009002646 intermolecular recognition site; other site 391009002647 dimerization interface [polypeptide binding]; other site 391009002648 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 391009002649 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 391009002650 putative binding surface; other site 391009002651 active site 391009002652 P2 response regulator binding domain; Region: P2; pfam07194 391009002653 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 391009002654 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 391009002655 ATP binding site [chemical binding]; other site 391009002656 Mg2+ binding site [ion binding]; other site 391009002657 G-X-G motif; other site 391009002658 CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling...; Region: CheA_reg; cd00731 391009002659 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 391009002660 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 391009002661 RNA binding surface [nucleotide binding]; other site 391009002662 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; cl12011 391009002663 tRNA pseudouridine synthase ACD; Provisional; Region: PRK14586 391009002664 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1)...; Region: PseudoU_synth_EcTruA; cd02570 391009002665 dimerization interface 3.5A [polypeptide binding]; other site 391009002666 active site 391009002667 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391009002668 metal binding site [ion binding]; metal-binding site 391009002669 active site 391009002670 I-site; other site 391009002671 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 391009002672 Protein of unknown function DUF58; Region: DUF58; pfam01882 391009002673 MoxR-like ATPases [General function prediction only]; Region: COG0714 391009002674 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...; Region: AAA; cd00009 391009002675 Walker A motif; other site 391009002676 ATP binding site [chemical binding]; other site 391009002677 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009002678 Walker B motif; other site 391009002679 arginine finger; other site 391009002680 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 391009002681 Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]; Region: HemN; COG0635 391009002682 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 391009002683 FeS/SAM binding site; other site 391009002684 HemN C-terminal region; Region: HemN_C; pfam06969 391009002685 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 391009002686 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 391009002687 GatB domain; Region: GatB_Yqey; cl11497 391009002688 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 391009002689 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 391009002690 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 391009002691 S17 interaction site [polypeptide binding]; other site 391009002692 S8 interaction site; other site 391009002693 16S rRNA interaction site [nucleotide binding]; other site 391009002694 streptomycin interaction site [chemical binding]; other site 391009002695 23S rRNA interaction site [nucleotide binding]; other site 391009002696 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 391009002697 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 391009002698 elongation factor G; Reviewed; Region: PRK00007 391009002699 Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved...; Region: EF-G; cd01886 391009002700 G1 box; other site 391009002701 putative GEF interaction site [polypeptide binding]; other site 391009002702 GTP/Mg2+ binding site [chemical binding]; other site 391009002703 Switch I region; other site 391009002704 G2 box; other site 391009002705 G3 box; other site 391009002706 Switch II region; other site 391009002707 G4 box; other site 391009002708 G5 box; other site 391009002709 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...; Region: EFG_mtEFG_II; cd04088 391009002710 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...; Region: EFG_mtEFG1_IV; cd01434 391009002711 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...; Region: EFG_mtEFG_C; cd03713 391009002712 elongation factor Tu; Reviewed; Region: PRK00049 391009002713 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 391009002714 G1 box; other site 391009002715 GEF interaction site [polypeptide binding]; other site 391009002716 GTP/Mg2+ binding site [chemical binding]; other site 391009002717 Switch I region; other site 391009002718 G2 box; other site 391009002719 G3 box; other site 391009002720 Switch II region; other site 391009002721 G4 box; other site 391009002722 G5 box; other site 391009002723 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 391009002724 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 391009002725 Antibiotic Binding Site [chemical binding]; other site 391009002726 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 391009002727 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 391009002728 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 391009002729 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 391009002730 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 391009002731 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 391009002732 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 391009002733 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 391009002734 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 391009002735 putative translocon binding site; other site 391009002736 protein-rRNA interface [nucleotide binding]; other site 391009002737 ribosomal protein S3, bacterial type; Region: rpsC_bact; TIGR01009 391009002738 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...; Region: 30S_S3_KH; cd02412 391009002739 G-X-X-G motif; other site 391009002740 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 391009002741 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 391009002742 23S rRNA interface [nucleotide binding]; other site 391009002743 5S rRNA interface [nucleotide binding]; other site 391009002744 putative antibiotic binding site [chemical binding]; other site 391009002745 L25 interface [polypeptide binding]; other site 391009002746 L27 interface [polypeptide binding]; other site 391009002747 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...; Region: Ribosomal_L29_HIP; cl09943 391009002748 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 391009002749 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 391009002750 KOW motif; Region: KOW; cl00354 391009002751 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 391009002752 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 391009002753 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 391009002754 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 391009002755 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 391009002756 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 391009002757 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 391009002758 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 391009002759 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 391009002760 23S rRNA interface [nucleotide binding]; other site 391009002761 L21e interface [polypeptide binding]; other site 391009002762 5S rRNA interface [nucleotide binding]; other site 391009002763 L27 interface [polypeptide binding]; other site 391009002764 L5 interface [polypeptide binding]; other site 391009002765 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 391009002766 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 391009002767 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 391009002768 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...; Region: Ribosomal_L30; cd01658 391009002769 23S rRNA binding site [nucleotide binding]; other site 391009002770 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 391009002771 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 391009002772 SecY translocase; Region: SecY; pfam00344 391009002773 adenylate kinase; Reviewed; Region: adk; PRK00279 391009002774 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 391009002775 AMP-binding site [chemical binding]; other site 391009002776 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 391009002777 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 391009002778 active site 391009002779 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 391009002780 rRNA binding site [nucleotide binding]; other site 391009002781 predicted 30S ribosome binding site; other site 391009002782 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 391009002783 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 391009002784 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 391009002785 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 391009002786 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 391009002787 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 391009002788 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 391009002789 RNA binding surface [nucleotide binding]; other site 391009002790 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 391009002791 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 391009002792 alphaNTD - beta interaction site [polypeptide binding]; other site 391009002793 alphaNTD homodimer interface [polypeptide binding]; other site 391009002794 alphaNTD - beta' interaction site [polypeptide binding]; other site 391009002795 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 391009002796 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 391009002797 trigger factor; Region: tig; TIGR00115 391009002798 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 391009002799 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 391009002800 oligomer interface [polypeptide binding]; other site 391009002801 active site residues [active] 391009002802 Domain of unknown function DUF28; Region: DUF28; cl00361 391009002803 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 391009002804 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 391009002805 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; cl12011 391009002806 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 391009002807 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 391009002808 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 391009002809 RNA binding surface [nucleotide binding]; other site 391009002810 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 391009002811 active site 391009002812 glutamine synthetase, type I; Region: GlnA; TIGR00653 391009002813 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 391009002814 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 391009002815 TM1410 hypothetical-related protein; Region: DUF297; cl00997 391009002816 Uncharacterized protein conserved in bacteria (DUF2194); Region: DUF2194; pfam09960 391009002817 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4878 391009002818 Predicted membrane protein [Function unknown]; Region: COG4267 391009002819 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule...; Region: GT1_like_3; cd03813 391009002820 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 391009002821 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 391009002822 Zn2+ binding site [ion binding]; other site 391009002823 Mg2+ binding site [ion binding]; other site 391009002824 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 391009002825 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 391009002826 MutS domain I; Region: MutS_I; pfam01624 391009002827 MutS domain II; Region: MutS_II; pfam05188 391009002828 MutS family domain IV; Region: MutS_IV; pfam05190 391009002829 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal...; Region: ABC_MutS1; cd03284 391009002830 Walker A/P-loop; other site 391009002831 ATP binding site [chemical binding]; other site 391009002832 Q-loop/lid; other site 391009002833 ABC transporter signature motif; other site 391009002834 Walker B; other site 391009002835 D-loop; other site 391009002836 H-loop/switch region; other site 391009002837 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 391009002838 Zn2+ binding site [ion binding]; other site 391009002839 Mg2+ binding site [ion binding]; other site 391009002840 AMMECR1; Region: AMMECR1; cl00911 391009002841 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 391009002842 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This...; Region: Alpha_ANH_like_II; cd01993 391009002843 TIGR00269 family protein; Region: TIGR00269 391009002844 L-cysteine desulfidase [Amino acid transport and metabolism]; Region: COG3681 391009002845 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 391009002846 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 391009002847 ABC-type uncharacterized transport system; Region: ABC_transp_aux; pfam09822 391009002848 Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]; Region: XylB; COG1070 391009002849 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 391009002850 FGGY family of carbohydrate kinases, C-terminal domain; Region: FGGY_C; pfam02782 391009002851 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; cl14056 391009002852 Radical SAM; Region: Elp3; smart00729 391009002853 Alpha-mannosidase [Carbohydrate transport and metabolism]; Region: AMS1; COG0383 391009002854 Glycosyl hydrolases family 38 N-terminal domain; Region: Glyco_hydro_38; pfam01074 391009002855 Alpha mannosidase, middle domain; Region: Alpha-mann_mid; cl08536 391009002856 Glycosyl hydrolases family 38 C-terminal domain; Region: Glyco_hydro_38C; pfam07748 391009002857 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 391009002858 DNA-binding site [nucleotide binding]; DNA binding site 391009002859 Transcriptional regulators [Transcription]; Region: PurR; COG1609 391009002860 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 391009002861 dimerization interface [polypeptide binding]; other site 391009002862 ligand binding site [chemical binding]; other site 391009002863 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 391009002864 active site 391009002865 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 391009002866 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...; Region: TM_PBP2; cd06261 391009002867 dimer interface [polypeptide binding]; other site 391009002868 conserved gate region; other site 391009002869 putative PBP binding loops; other site 391009002870 ABC-ATPase subunit interface; other site 391009002871 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...; Region: TM_PBP2; cd06261 391009002872 dimer interface [polypeptide binding]; other site 391009002873 conserved gate region; other site 391009002874 putative PBP binding loops; other site 391009002875 ABC-ATPase subunit interface; other site 391009002876 Endo-beta-N-acetylglucosaminidase (ENGase) hydrolyzes the N-N'-diacetylchitobiosyl core of N-glycosylproteins. The beta-1,4-glycosyl bond located between two N-acetylglucosamine residues is hydrolyzed such that N-acetylglucosamine 1 remains with the...; Region: GH85_ENGase; cd06547 391009002877 putative active site [active] 391009002878 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cl14635 391009002879 Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes; Region: FA58C; cl12042 391009002880 sugar binding site [chemical binding]; other site 391009002881 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 391009002882 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 391009002883 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 391009002884 The (Largely Archaeal Putative) Hydrophobe/Amphiphile Efflux-3 (HAE3) Family; Region: 2A067; TIGR00921 391009002885 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 391009002886 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 391009002887 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 391009002888 putative trimer interface [polypeptide binding]; other site 391009002889 putative CoA binding site [chemical binding]; other site 391009002890 WcxM-like, Left-handed parallel beta-Helix (LbH) N-terminal domain: This group is composed of Xanthomonas campestris WcxM and proteins with similarity to the WcxM N-terminal domain. WcxM is thought to be bifunctional, catalyzing both the isomerization...; Region: LbH_WxcM_N_like; cd03358 391009002891 putative trimer interface [polypeptide binding]; other site 391009002892 putative active site [active] 391009002893 putative substrate binding site [chemical binding]; other site 391009002894 putative CoA binding site [chemical binding]; other site 391009002895 Chromate transporter; Region: Chromate_transp; pfam02417 391009002896 DNA topoisomerase I; Validated; Region: PRK05582 391009002897 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 391009002898 active site 391009002899 metal binding site [ion binding]; metal-binding site 391009002900 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...; Region: TOP1Ac; cd00186 391009002901 domain I; other site 391009002902 DNA binding groove [nucleotide binding] 391009002903 phosphate binding site [ion binding]; other site 391009002904 domain II; other site 391009002905 domain III; other site 391009002906 nucleotide binding site [chemical binding]; other site 391009002907 catalytic site [active] 391009002908 domain IV; other site 391009002909 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 391009002910 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 391009002911 Predicted HD-superfamily hydrolase [General function prediction only]; Region: COG3481 391009002912 YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in...; Region: YhaM_OBF_like; cd04492 391009002913 generic binding surface II; other site 391009002914 generic binding surface I; other site 391009002915 CRISPR/Cas system-associated protein Cas3''; Region: Cas3''_I; cd09641 391009002916 alanine racemase; Reviewed; Region: alr; PRK00053 391009002917 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 391009002918 active site 391009002919 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 391009002920 dimer interface [polypeptide binding]; other site 391009002921 substrate binding site [chemical binding]; other site 391009002922 catalytic residues [active] 391009002923 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 391009002924 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 391009002925 FtsX-like permease family; Region: FtsX; pfam02687 391009002926 FtsX-like permease family; Region: FtsX; pfam02687 391009002927 RNA polymerase sigma factor RpoD; Validated; Region: PRK09210 391009002928 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 391009002929 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 391009002930 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391009002931 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 391009002932 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...; Region: Sigma70_r4; cd06171 391009002933 DNA binding residues [nucleotide binding] 391009002934 DNA primase, catalytic core; Region: dnaG; TIGR01391 391009002935 CHC2 zinc finger; Region: zf-CHC2; cl02597 391009002936 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 391009002937 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 391009002938 active site 391009002939 metal binding site [ion binding]; metal-binding site 391009002940 interdomain interaction site; other site 391009002941 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 391009002942 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 391009002943 23S rRNA interface [nucleotide binding]; other site 391009002944 L3 interface [polypeptide binding]; other site 391009002945 Protein of unknown function (DUF1393); Region: DUF1393; cl01942 391009002946 Protein of unknown function (DUF3816); Region: DUF3816; pfam12822 391009002947 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 391009002948 Protein of unknown function (DUF464); Region: DUF464; cl01080 391009002949 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 391009002950 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 391009002951 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 includes...; Region: RuvC_resolvase; cd00529 391009002952 active site 391009002953 putative DNA-binding cleft [nucleotide binding]; other site 391009002954 dimer interface [polypeptide binding]; other site 391009002955 DNA polymerase III PolC; Validated; Region: polC; PRK00448 391009002956 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 391009002957 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 391009002958 active site 391009002959 substrate binding site [chemical binding]; other site 391009002960 catalytic site [active] 391009002961 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 391009002962 Protein of unknown function, DUF655; Region: DUF655; cl00648 391009002963 Stage V sporulation protein S (SpoVS); Region: SpoVS; cl01005 391009002964 Protein of unknown function (DUF1385); Region: DUF1385; cl01595 391009002965 diaminopimelate decarboxylase; Region: lysA; TIGR01048 391009002966 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 391009002967 active site 391009002968 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 391009002969 substrate binding site [chemical binding]; other site 391009002970 catalytic residues [active] 391009002971 dimer interface [polypeptide binding]; other site 391009002972 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 391009002973 M20 Peptidase Aminoacylase 1 family; Region: M20_Acy1; cd03886 391009002974 metal binding site [ion binding]; metal-binding site 391009002975 dimer interface [polypeptide binding]; other site 391009002976 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 391009002977 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 391009002978 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 391009002979 dimer interface [polypeptide binding]; other site 391009002980 motif 1; other site 391009002981 active site 391009002982 motif 2; other site 391009002983 motif 3; other site 391009002984 tRNA pseudouridine synthase B; Provisional; Region: PRK14124 391009002985 PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of...; Region: PseudoU_synth_EcTruB; cd02573 391009002986 RNA binding site [nucleotide binding]; other site 391009002987 active site 391009002988 GTP-binding protein YchF; Reviewed; Region: PRK09601 391009002989 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 391009002990 G1 box; other site 391009002991 GTP/Mg2+ binding site [chemical binding]; other site 391009002992 G2 box; other site 391009002993 Switch I region; other site 391009002994 G3 box; other site 391009002995 Switch II region; other site 391009002996 G4 box; other site 391009002997 G5 box; other site 391009002998 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 391009002999 Domain of unknown function (DUF370); Region: DUF370; cl00898 391009003000 B12-binding domain/radical SAM domain protein, MJ_1487 family; Region: B12_SAM_MJ_1487; TIGR04013 391009003001 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase...; Region: B12-binding_like; cl00293 391009003002 B12 binding site [chemical binding]; other site 391009003003 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 391009003004 FeS/SAM binding site; other site 391009003005 Predicted amidohydrolase [General function prediction only]; Region: COG0388 391009003006 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 391009003007 active site 391009003008 catalytic triad [active] 391009003009 dimer interface [polypeptide binding]; other site 391009003010 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 391009003011 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 391009003012 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009003013 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 391009003014 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 391009003015 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 391009003016 motif II; other site 391009003017 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 391009003018 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin...; Region: NPD_like; cd04730 391009003019 FMN binding site [chemical binding]; other site 391009003020 substrate binding site [chemical binding]; other site 391009003021 putative catalytic residue [active] 391009003022 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 391009003023 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 391009003024 Protein of unknown function (DUF2922); Region: DUF2922; pfam11148 391009003025 exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase; Region: EPS_sugtrans; TIGR03025 391009003026 Bacterial sugar transferase; Region: Bac_transf; cl00939 391009003027 This family is most closely related to the GT1 family of glycosyltransferases. cap1E in Streptococcus pneumoniae is required for the synthesis of type 1 capsular polysaccharides; Region: GT1_cap1E_like; cd03808 391009003028 putative ADP-binding pocket [chemical binding]; other site 391009003029 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 391009003030 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 391009003031 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009003032 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 391009003033 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 391009003034 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 391009003035 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 391009003036 active site 391009003037 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 391009003038 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 391009003039 substrate binding site [chemical binding]; other site 391009003040 tetramer interface [polypeptide binding]; other site 391009003041 Cupin domain; Region: Cupin_2; cl09118 391009003042 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 391009003043 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 391009003044 NADP binding site [chemical binding]; other site 391009003045 active site 391009003046 putative substrate binding site [chemical binding]; other site 391009003047 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 391009003048 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 391009003049 NAD binding site [chemical binding]; other site 391009003050 substrate binding site [chemical binding]; other site 391009003051 homodimer interface [polypeptide binding]; other site 391009003052 active site 391009003053 Putative glycosyl/glycerophosphate transferases involved in teichoic acid biosynthesis TagF/TagB/EpsJ/RodC [Cell envelope biogenesis, outer membrane]; Region: TagB; COG1887 391009003054 CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase; Region: Glyphos_transf; pfam04464 391009003055 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 391009003056 Polysaccharide biosynthesis protein; Region: Polysacc_synt; cl10513 391009003057 glycerol-3-phosphate cytidylyltransferase; Region: G3P_Cytidylyltransferase; cd02171 391009003058 active site 391009003059 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 391009003060 putative active site [active] 391009003061 Protein of unknown function (DUF2922); Region: DUF2922; pfam11148 391009003062 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 391009003063 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 391009003064 NAD binding site [chemical binding]; other site 391009003065 homodimer interface [polypeptide binding]; other site 391009003066 active site 391009003067 substrate binding site [chemical binding]; other site 391009003068 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 391009003069 putative active site [active] 391009003070 putative metal binding site [ion binding]; other site 391009003071 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 391009003072 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 391009003073 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009003074 ABC transporter signature motif; other site 391009003075 Walker B; other site 391009003076 D-loop; other site 391009003077 H-loop/switch region; other site 391009003078 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009003079 Divergent AAA domain; Region: AAA_4; pfam04326 391009003080 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 391009003081 Archaeal ATPase; Region: Arch_ATPase; pfam01637 391009003082 Archaea bacterial proteins of unknown function; Region: DUF234; pfam03008 391009003083 nif11-class bacteriocin maturation radical SAM enzyme; Region: rSAM_nif11; TIGR04064 391009003084 radical SAM additional 4Fe4S-binding domain; Region: rSAM_more_4Fe4S; TIGR04085 391009003085 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 391009003086 C-terminal processing peptidase family S41; Region: Peptidase_S41; cd06567 391009003087 Active site serine [active] 391009003088 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; cl00973 391009003089 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 391009003090 ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The...; Region: ABC_ATPase; cd00267 391009003091 Q-loop/lid; other site 391009003092 ABC transporter signature motif; other site 391009003093 Walker B; other site 391009003094 D-loop; other site 391009003095 H-loop/switch region; other site 391009003096 Protein of unknown function, DUF488; Region: DUF488; cl01246 391009003097 Predicted nucleotidyltransferase [General function prediction only]; Region: COG1665 391009003098 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 391009003099 S-adenosylmethionine binding site [chemical binding]; other site 391009003100 EamA-like transporter family; Region: EamA; cl01037 391009003101 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 391009003102 EamA-like transporter family; Region: EamA; cl01037 391009003103 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 391009003104 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 391009003105 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 391009003106 phosphoprotein phosphatases of the metallophosphatase superfamily, metallophosphatase domain; Region: MPP_PPP_family; cd00144 391009003107 active site 391009003108 metal binding site [ion binding]; metal-binding site 391009003109 septum formation inhibitor; Provisional; Region: minC; PRK13992 391009003110 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 391009003111 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 391009003112 EamA-like transporter family; Region: EamA; cl01037 391009003113 flagellar basal-body rod protein FlgB; Region: FlgB; TIGR01396 391009003114 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 391009003115 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 391009003116 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 391009003117 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 391009003118 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 391009003119 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 391009003120 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...; Region: ACD_sHsps-like; cd06464 391009003121 putative dimer interface [polypeptide binding]; other site 391009003122 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 391009003123 Domain of unknown function (DUF74); Region: DUF74; cl00426 391009003124 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is 'interfacial activation', the process of becoming...; Region: Lipase; cl14883 391009003125 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 391009003126 nucleophilic elbow; other site 391009003127 catalytic triad; other site 391009003128 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 391009003129 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 391009003130 Walker A/P-loop; other site 391009003131 ATP binding site [chemical binding]; other site 391009003132 Q-loop/lid; other site 391009003133 ABC transporter signature motif; other site 391009003134 Walker B; other site 391009003135 D-loop; other site 391009003136 H-loop/switch region; other site 391009003137 Predicted transcriptional regulators [Transcription]; Region: COG1725 391009003138 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 391009003139 DNA-binding site [nucleotide binding]; DNA binding site 391009003140 putative acyltransferase; Provisional; Region: PRK05790 391009003141 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 391009003142 dimer interface [polypeptide binding]; other site 391009003143 active site 391009003144 Coenzyme A transferase; Region: CoA_trans; cl00773 391009003145 Coenzyme A transferase; Region: CoA_trans; cl00773 391009003146 Alkaline phosphatase homologues; Region: alkPPc; smart00098 391009003147 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH...; Region: alkPPc; cd00016 391009003148 active site 391009003149 dimer interface [polypeptide binding]; other site 391009003150 putative oxidoreductase; Provisional; Region: PRK12831 391009003151 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-; Region: HCP_like; cl14655 391009003152 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 391009003153 ferredoxin-NADP(+) reductase subunit alpha; Reviewed; Region: PRK06222 391009003154 FAD/NAD binding domain in the 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)-...; Region: DHOD_e_trans_like1; cd06219 391009003155 FAD binding pocket [chemical binding]; other site 391009003156 FAD binding motif [chemical binding]; other site 391009003157 phosphate binding motif [ion binding]; other site 391009003158 beta-alpha-beta structure motif; other site 391009003159 NAD binding pocket [chemical binding]; other site 391009003160 Iron coordination center [ion binding]; other site 391009003161 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-...; Region: ribokinase_pfkB_like; cl00192 391009003162 substrate binding site [chemical binding]; other site 391009003163 ATP binding site [chemical binding]; other site 391009003164 ROK family protein (putative glucokinase); Region: ROK_glcA_fam; TIGR00744 391009003165 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 391009003166 Uncharacterized homolog of biotin synthetase [Function unknown]; Region: COG1856 391009003167 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 391009003168 FeS/SAM binding site; other site 391009003169 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 391009003170 Response regulator receiver domain; Region: Response_reg; pfam00072 391009003171 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 391009003172 active site 391009003173 phosphorylation site [posttranslational modification] 391009003174 intermolecular recognition site; other site 391009003175 dimerization interface [polypeptide binding]; other site 391009003176 CheB methylesterase; Region: CheB_methylest; pfam01339 391009003177 Response regulator receiver domain; Region: Response_reg; pfam00072 391009003178 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 391009003179 active site 391009003180 phosphorylation site [posttranslational modification] 391009003181 intermolecular recognition site; other site 391009003182 dimerization interface [polypeptide binding]; other site 391009003183 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 391009003184 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 391009003185 ATP binding site [chemical binding]; other site 391009003186 Mg2+ binding site [ion binding]; other site 391009003187 G-X-G motif; other site 391009003188 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; cl12011 391009003189 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 391009003190 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 391009003191 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 391009003192 ribosomal protein S12 methylthiotransferase RimO; Region: TIGR01125 391009003193 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 391009003194 FeS/SAM binding site; other site 391009003195 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 391009003196 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 391009003197 2',5' RNA ligase family; Region: 2_5_RNA_ligase; pfam02834 391009003198 recombinase A; Provisional; Region: recA; PRK09354 391009003199 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 391009003200 hexamer interface [polypeptide binding]; other site 391009003201 Walker A motif; other site 391009003202 ATP binding site [chemical binding]; other site 391009003203 Walker B motif; other site 391009003204 RecX family; Region: RecX; cl00936 391009003205 phosphodiesterase; Provisional; Region: PRK12704 391009003206 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...; Region: KH-I; cl00098 391009003207 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 391009003208 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 391009003209 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 391009003210 Walker A/P-loop; other site 391009003211 ATP binding site [chemical binding]; other site 391009003212 Q-loop/lid; other site 391009003213 ABC transporter signature motif; other site 391009003214 Walker B; other site 391009003215 D-loop; other site 391009003216 H-loop/switch region; other site 391009003217 TOBE domain; Region: TOBE_2; cl01440 391009003218 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 391009003219 FeS/SAM binding site; other site 391009003220 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 391009003221 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 391009003222 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 391009003223 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 391009003224 RNA binding site [nucleotide binding]; other site 391009003225 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:; Region: TRX_Fd_family; cd02980 391009003226 dimer interface [polypeptide binding]; other site 391009003227 [2Fe-2S] cluster binding site [ion binding]; other site 391009003228 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 391009003229 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 391009003230 SLBB domain; Region: SLBB; pfam10531 391009003231 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 391009003232 NADH-quinone oxidoreductase, E subunit; Region: nuoE_fam; TIGR01958 391009003233 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...; Region: TRX_Fd_NuoE; cd03064 391009003234 putative dimer interface [polypeptide binding]; other site 391009003235 [2Fe-2S] cluster binding site [ion binding]; other site 391009003236 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:; Region: TRX_Fd_family; cd02980 391009003237 dimer interface [polypeptide binding]; other site 391009003238 [2Fe-2S] cluster binding site [ion binding]; other site 391009003239 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 391009003240 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 391009003241 SLBB domain; Region: SLBB; pfam10531 391009003242 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 391009003243 Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits [Energy production and conversion]; Region: COG4231 391009003244 4Fe-4S binding domain; Region: Fer4; cl02805 391009003245 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:; Region: TRX_Fd_family; cd02980 391009003246 dimer interface [polypeptide binding]; other site 391009003247 [2Fe-2S] cluster binding site [ion binding]; other site 391009003248 NADH-quinone oxidoreductase, E subunit; Region: nuoE_fam; TIGR01958 391009003249 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...; Region: TRX_Fd_NuoE; cd03064 391009003250 putative dimer interface [polypeptide binding]; other site 391009003251 [2Fe-2S] cluster binding site [ion binding]; other site 391009003252 glutamate formiminotransferase; Region: FtcD; TIGR02024 391009003253 Formiminotransferase domain, N-terminal subdomain; Region: FTCD_N; pfam07837 391009003254 Formiminotransferase domain; Region: FTCD; pfam02971 391009003255 IMPase, inositol monophosphatase and related domains. A family of Mg++ dependent phosphatases, inhibited by lithium, many of which may act on inositol monophosphate substrate. They dephosphorylate inositol phosphate to generate inositol, which may be...; Region: IMPase; cd01639 391009003256 active site 391009003257 dimerization interface [polypeptide binding]; other site 391009003258 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 391009003259 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 391009003260 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 391009003261 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 391009003262 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 391009003263 HIGH motif; other site 391009003264 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 391009003265 active site 391009003266 KMSKS motif; other site 391009003267 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Region: COG0182; cl00348 391009003268 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 391009003269 Radical SAM; Region: Elp3; smart00729 391009003270 FeS/SAM binding site; other site 391009003271 GatB domain; Region: GatB_Yqey; cl11497 391009003272 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 391009003273 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 391009003274 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 391009003275 anti sigma factor interaction site; other site 391009003276 regulatory phosphorylation site [posttranslational modification]; other site 391009003277 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 391009003278 LexA repressor; Validated; Region: PRK00215 391009003279 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (...; Region: S24_LexA-like; cd06529 391009003280 Catalytic site [active] 391009003281 Archease protein family (DUF101/UPF0211); Region: Archease; cl00606 391009003282 DNA gyrase subunit A; Validated; Region: PRK05560 391009003283 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 in...; Region: TOP4c; cd00187 391009003284 CAP-like domain; other site 391009003285 Active site [active] 391009003286 primary dimer interface [polypeptide binding]; other site 391009003287 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 391009003288 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 391009003289 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 391009003290 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 391009003291 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 391009003292 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 391009003293 methionyl-tRNA synthetase; Reviewed; Region: PRK12267 391009003294 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 391009003295 active site 391009003296 HIGH motif; other site 391009003297 KMSKS motif; other site 391009003298 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 391009003299 tRNA binding surface [nucleotide binding]; other site 391009003300 anticodon binding site; other site 391009003301 tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine...; Region: tRNA_bind_EcMetRS_like; cd02800 391009003302 dimer interface [polypeptide binding]; other site 391009003303 putative tRNA-binding site [nucleotide binding]; other site 391009003304 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cl01709 391009003305 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 391009003306 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 391009003307 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...; Region: TM_PBP2; cd06261 391009003308 dimer interface [polypeptide binding]; other site 391009003309 conserved gate region; other site 391009003310 putative PBP binding loops; other site 391009003311 ABC-ATPase subunit interface; other site 391009003312 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 391009003313 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...; Region: TM_PBP2; cd06261 391009003314 dimer interface [polypeptide binding]; other site 391009003315 conserved gate region; other site 391009003316 putative PBP binding loops; other site 391009003317 ABC-ATPase subunit interface; other site 391009003318 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 391009003319 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 391009003320 Walker A/P-loop; other site 391009003321 ATP binding site [chemical binding]; other site 391009003322 Q-loop/lid; other site 391009003323 ABC transporter signature motif; other site 391009003324 Walker B; other site 391009003325 D-loop; other site 391009003326 H-loop/switch region; other site 391009003327 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 391009003328 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 391009003329 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 391009003330 Walker A/P-loop; other site 391009003331 ATP binding site [chemical binding]; other site 391009003332 Q-loop/lid; other site 391009003333 ABC transporter signature motif; other site 391009003334 Walker B; other site 391009003335 D-loop; other site 391009003336 H-loop/switch region; other site 391009003337 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 391009003338 bifunctional aspartate carbamoyltransferase catalytic subunit/aspartate carbamoyltransferase regulatory subunit; Provisional; Region: pyrB; PRK13376 391009003339 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 391009003340 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 391009003341 Aspartate carbamoyltransferase regulatory chain, allosteric domain; Region: PyrI; pfam01948 391009003342 Aspartate carbamoyltransferase regulatory chain, metal binding domain; Region: PyrI_C; pfam02748 391009003343 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 391009003344 Zn2+ binding site [ion binding]; other site 391009003345 Mg2+ binding site [ion binding]; other site 391009003346 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 391009003347 metal binding site 2 [ion binding]; metal-binding site 391009003348 putative DNA binding helix; other site 391009003349 metal binding site 1 [ion binding]; metal-binding site 391009003350 dimer interface [polypeptide binding]; other site 391009003351 structural Zn2+ binding site [ion binding]; other site 391009003352 peroxiredoxin; Provisional; Region: PRK13189 391009003353 Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by...; Region: PRX_1cys; cd03016 391009003354 dimer interface [polypeptide binding]; other site 391009003355 decamer (pentamer of dimers) interface [polypeptide binding]; other site 391009003356 catalytic triad [active] 391009003357 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They...; Region: rubredoxin; cd00730 391009003358 Rubredoxin; Region: Rubredoxin; pfam00301 391009003359 iron binding site [ion binding]; other site 391009003360 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 391009003361 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 391009003362 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 391009003363 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 391009003364 Ferritin-like domain; Region: Ferritin; pfam00210 391009003365 ferroxidase diiron center [ion binding]; other site 391009003366 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 391009003367 non-specific DNA interactions [nucleotide binding]; other site 391009003368 DNA binding site [nucleotide binding] 391009003369 sequence specific DNA binding site [nucleotide binding]; other site 391009003370 putative cAMP binding site [chemical binding]; other site 391009003371 desulfoferrodoxin; Region: dfx_rbo; TIGR00320 391009003372 Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small...; Region: DSRD; cd00974 391009003373 non-heme iron binding site [ion binding]; other site 391009003374 dimer interface [polypeptide binding]; other site 391009003375 Superoxide reductase-like (SORL) domain; present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin. Superoxide reductase-like proteins scavenge superoxide anion radicals as a defense mechanism...; Region: SORL; cl00014 391009003376 non-heme iron binding site [ion binding]; other site 391009003377 Cache domain; Region: Cache_1; pfam02743 391009003378 septation ring formation regulator EzrA; Provisional; Region: PRK04778 391009003379 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 391009003380 Zn2+ binding site [ion binding]; other site 391009003381 Mg2+ binding site [ion binding]; other site 391009003382 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 391009003383 Thymidine kinase; Region: TK; cl00631 391009003384 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 391009003385 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 391009003386 active site 391009003387 metal binding site [ion binding]; metal-binding site 391009003388 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 391009003389 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 391009003390 putative peptidoglycan binding site; other site 391009003391 Uncharacterised ACR, YkgG family COG1556; Region: DUF162; cl00674 391009003392 redox-sensing transcriptional repressor Rex; Provisional; Region: PRK05472 391009003393 Putative DNA-binding protein N-terminus; Region: Put_DNA-bind_N; pfam06971 391009003394 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009003395 Na+/H+ ion antiporter subunit; Region: MNHE; cl00807 391009003396 Multiple resistance and pH regulation protein F (MrpF / PhaF); Region: MrpF_PhaF; cl09154 391009003397 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; cl00583 391009003398 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12507 391009003399 Domain related to MnhB subunit of Na+/H+ antiporter; Region: MnhB; cl00676 391009003400 Domain related to MnhB subunit of Na+/H+ antiporter; Region: MnhB; cl00676 391009003401 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 391009003402 NADH dehydrogenase subunit N; Validated; Region: PRK08377 391009003403 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 391009003404 NADH dehydrogenase subunit M; Validated; Region: PRK08668 391009003405 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 391009003406 NADH dehydrogenase; Region: NADHdh; cl00469 391009003407 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 391009003408 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl00539 391009003409 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; cl00417 391009003410 putative oxidoreductase; Provisional; Region: PRK13984 391009003411 4Fe-4S binding domain; Region: Fer4; cl02805 391009003412 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-; Region: HCP_like; cl14655 391009003413 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 391009003414 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB; cd01045 391009003415 diiron binding motif [ion binding]; other site 391009003416 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 391009003417 Ligand binding site [chemical binding]; other site 391009003418 metal binding site [ion binding]; metal-binding site 391009003419 Glycosyl hydrolase family 20 (GH20) catalytic domain of N-acetyl-beta-D-glucosaminidase (GcnA, also known as BhsA) and related proteins. GcnA is an exoglucosidase which cleaves N-acetyl-beta-D-galactosamine (NAG) and N-acetyl-beta-D-galactosamine...; Region: GH20_GcnA-like; cd06565 391009003420 putative active site [active] 391009003421 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 391009003422 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 391009003423 CoA-disulfide reductase; Region: CoA_CoA_reduc; TIGR03385 391009003424 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 391009003425 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 391009003426 serine O-acetyltransferase; Region: cysE; TIGR01172 391009003427 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of L-...; Region: LbH_SAT; cd03354 391009003428 trimer interface [polypeptide binding]; other site 391009003429 active site 391009003430 substrate binding site [chemical binding]; other site 391009003431 CoA binding site [chemical binding]; other site 391009003432 cysteine synthases; Region: cysKM; TIGR01136 391009003433 CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine...; Region: CBS_like; cd01561 391009003434 dimer interface [polypeptide binding]; other site 391009003435 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391009003436 catalytic residue [active] 391009003437 AIR carboxylase; Region: AIRC; cl00310 391009003438 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 391009003439 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 391009003440 active site 391009003441 ATP binding site [chemical binding]; other site 391009003442 substrate binding site [chemical binding]; other site 391009003443 Phosphoribosylformylglycinamidine (FGAM) synthase; Region: PurS; cl00789 391009003444 Glutamine amidotransferase [Amino acid transport and metabolism]; Region: HisH; COG0118 391009003445 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 391009003446 putative active site [active] 391009003447 catalytic triad [active] 391009003448 phosphoribosylformylglycinamidine synthase II; Provisional; Region: PRK14090 391009003449 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), first repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP...; Region: PurL_repeat1; cd02203 391009003450 dimerization interface [polypeptide binding]; other site 391009003451 ATP binding site [chemical binding]; other site 391009003452 AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal...; Region: PurM-like; cl10019 391009003453 dimerization interface [polypeptide binding]; other site 391009003454 ATP binding site [chemical binding]; other site 391009003455 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_HprK; cl00270 391009003456 active site 391009003457 metal-binding site [ion binding] 391009003458 nucleotide-binding site [chemical binding]; other site 391009003459 Indigoidine synthase A like protein; Region: Indigoidine_A; cl00983 391009003460 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 391009003461 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 391009003462 active site 391009003463 metal binding site [ion binding]; metal-binding site 391009003464 homotetramer interface [polypeptide binding]; other site 391009003465 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 391009003466 aspartate aminotransferase; Provisional; Region: PRK06836 391009003467 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 391009003468 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391009003469 homodimer interface [polypeptide binding]; other site 391009003470 catalytic residue [active] 391009003471 adenylosuccinate lyase; Provisional; Region: PRK07492 391009003472 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 391009003473 tetramer interface [polypeptide binding]; other site 391009003474 active site 391009003475 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 391009003476 dimerization interface [polypeptide binding]; other site 391009003477 putative DNA binding site [nucleotide binding]; other site 391009003478 putative Zn2+ binding site [ion binding]; other site 391009003479 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 391009003480 Cation efflux family; Region: Cation_efflux; cl00316 391009003481 Type II secretory pathway, component HofQ [Intracellular trafficking and secretion]; Region: HofQ; COG4796 391009003482 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 391009003483 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 391009003484 active site 391009003485 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 391009003486 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391009003487 homodimer interface [polypeptide binding]; other site 391009003488 catalytic residue [active] 391009003489 Cation transport protein; Region: TrkH; cl10514 391009003490 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 391009003491 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 391009003492 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009003493 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 391009003494 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009003495 Response regulator receiver domain; Region: Response_reg; pfam00072 391009003496 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 391009003497 active site 391009003498 phosphorylation site [posttranslational modification] 391009003499 intermolecular recognition site; other site 391009003500 dimerization interface [polypeptide binding]; other site 391009003501 Triosephosphate isomerase (TIM) is a glycolytic enzyme that catalyzes the interconversion of dihydroxyacetone phosphate and D-glyceraldehyde-3-phosphate. The reaction is very efficient and requires neither cofactors nor metal ions. TIM, usually...; Region: TIM; cd00311 391009003502 dimer interface [polypeptide binding]; other site 391009003503 substrate binding site [chemical binding]; other site 391009003504 catalytic triad [active] 391009003505 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cd00318 391009003506 substrate binding site [chemical binding]; other site 391009003507 hinge regions; other site 391009003508 ADP binding site [chemical binding]; other site 391009003509 catalytic site [active] 391009003510 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009003511 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 391009003512 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 391009003513 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 391009003514 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 391009003515 Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they...; Region: ATPase_flagellum-secretory_path_III; cd01136 391009003516 Walker A motif/ATP binding site; other site 391009003517 Walker B motif; other site 391009003518 type III secretion apparatus protein, HrpE/YscL family; Region: HrpE_YscL_not; TIGR02499 391009003519 Flagellar assembly protein FliH; Region: FliH; pfam02108 391009003520 Acetokinase family; Region: Acetate_kinase; cl01029 391009003521 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose...; Region: TBP_aldolase_IIB; cd00947 391009003522 hypothetical protein; Provisional; Region: PRK08185 391009003523 intersubunit interface [polypeptide binding]; other site 391009003524 active site 391009003525 zinc binding site [ion binding]; other site 391009003526 Na+ binding site [ion binding]; other site 391009003527 Cell division ATPase FtsA [Cell division and chromosome partitioning]; Region: ftsA; COG0849 391009003528 Cell division protein FtsA; Region: FtsA; cl11496 391009003529 Cell division protein FtsA; Region: FtsA; cl11496 391009003530 cell division protein FtsZ; Validated; Region: PRK09330 391009003531 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...; Region: FtsZ_type1; cd02201 391009003532 nucleotide binding site [chemical binding]; other site 391009003533 SulA interaction site; other site 391009003534 chain length determinant protein tyrosine kinase EpsG; Region: EpsG; TIGR03029 391009003535 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 391009003536 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 391009003537 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 391009003538 Walker A motif; other site 391009003539 ATP binding site [chemical binding]; other site 391009003540 Walker B motif; other site 391009003541 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 round of...; Region: RRF; cd00520 391009003542 hinge region; other site 391009003543 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 391009003544 catalytic residue [active] 391009003545 putative FPP diphosphate binding site; other site 391009003546 putative FPP binding hydrophobic cleft; other site 391009003547 dimer interface [polypeptide binding]; other site 391009003548 putative IPP diphosphate binding site; other site 391009003549 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 391009003550 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 391009003551 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 formation...; Region: AlaRS_core; cd00673 391009003552 motif 1; other site 391009003553 active site 391009003554 motif 2; other site 391009003555 motif 3; other site 391009003556 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 391009003557 DHHA1 domain; Region: DHHA1; pfam02272 391009003558 rod shape-determining protein MreB; Provisional; Region: PRK13930 391009003559 Cell division protein FtsA; Region: FtsA; cl11496 391009003560 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391009003561 active site 391009003562 I-site; other site 391009003563 metal binding site [ion binding]; metal-binding site 391009003564 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Validated; Region: PRK09369 391009003565 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 391009003566 hinge; other site 391009003567 active site 391009003568 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 391009003569 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 391009003570 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 391009003571 NAD(P) binding site [chemical binding]; other site 391009003572 homodimer interface [polypeptide binding]; other site 391009003573 substrate binding site [chemical binding]; other site 391009003574 active site 391009003575 Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved...; Region: EF-G_bact; cd04170 391009003576 elongation factor G; Reviewed; Region: PRK12740 391009003577 G1 box; other site 391009003578 putative GEF interaction site [polypeptide binding]; other site 391009003579 GTP/Mg2+ binding site [chemical binding]; other site 391009003580 Switch I region; other site 391009003581 G2 box; other site 391009003582 G3 box; other site 391009003583 Switch II region; other site 391009003584 G4 box; other site 391009003585 G5 box; other site 391009003586 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...; Region: EFG_mtEFG_II; cd04088 391009003587 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...; Region: EFG_mtEFG1_IV; cd01434 391009003588 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...; Region: EFG_mtEFG_C; cd03713 391009003589 MgtE intracellular N domain; Region: MgtE_N; cl15244 391009003590 Flagellar hook-length control protein FliK; Region: Flg_hook; cl14669 391009003591 Flagellar hook capping protein; Region: FlgD; cl04347 391009003592 flagellar hook protein FlgE; Validated; Region: flgE; PRK08425 391009003593 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 391009003594 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 391009003595 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 391009003596 Flagellar protein (FlbD); Region: FlbD; cl00683 391009003597 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 391009003598 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 391009003599 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 391009003600 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 391009003601 ligand binding site [chemical binding]; other site 391009003602 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 391009003603 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 391009003604 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 391009003605 flagellar motor switch protein; Validated; Region: PRK08119 391009003606 CheC-like family; Region: CheC; pfam04509 391009003607 CheC-like family; Region: CheC; pfam04509 391009003608 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 391009003609 Sodium:neurotransmitter symporter family; Region: SNF; cl11976 391009003610 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...; Region: AAA; cd00009 391009003611 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 391009003612 Walker A motif; other site 391009003613 ATP binding site [chemical binding]; other site 391009003614 Walker B motif; other site 391009003615 arginine finger; other site 391009003616 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-...; Region: ribokinase_pfkB_like; cl00192 391009003617 Putative transcriptional regulators (Ypuh-like); Region: DUF387; cl00612 391009003618 ScpA/B protein; Region: ScpA_ScpB; cl00598 391009003619 FOG: CBS domain [General function prediction only]; Region: COG0517 391009003620 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-...; Region: CBS_pair; cd02205 391009003621 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 391009003622 Flavoprotein; Region: Flavoprotein; cl08021 391009003623 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 391009003624 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 391009003625 Ketopantoate hydroxymethyltransferase (KPHMT) is the first enzyme in the pantothenate biosynthesis pathway. Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate (vitamin B5), which is a...; Region: KPHMT-like; cd06557 391009003626 oligomerization interface [polypeptide binding]; other site 391009003627 active site 391009003628 metal binding site [ion binding]; metal-binding site 391009003629 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 391009003630 Polysaccharide pyruvyl transferase family protein [Cell wall/membrane/envelope biogenesis]; Region: WcaK; cl09156 391009003631 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; pfam04230 391009003632 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 391009003633 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 391009003634 Walker A/P-loop; other site 391009003635 ATP binding site [chemical binding]; other site 391009003636 Q-loop/lid; other site 391009003637 ABC transporter signature motif; other site 391009003638 Walker B; other site 391009003639 D-loop; other site 391009003640 H-loop/switch region; other site 391009003641 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 catalyze...; Region: LT_GEWL; cd00254 391009003642 N-acetyl-D-glucosamine binding site [chemical binding]; other site 391009003643 catalytic residue [active] 391009003644 Divergent PAP2 family; Region: DUF212; cl00855 391009003645 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; cl00075 391009003646 Uncharacterized BCR, COG1636; Region: DUF208; pfam02677 391009003647 D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but...; Region: Dtyr_deacylase; cd00563 391009003648 putative active site [active] 391009003649 dimerization interface [polypeptide binding]; other site 391009003650 putative tRNAtyr binding site [nucleotide binding]; other site 391009003651 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 391009003652 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 391009003653 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 391009003654 synthetase active site [active] 391009003655 NTP binding site [chemical binding]; other site 391009003656 metal binding site [ion binding]; metal-binding site 391009003657 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named...; Region: TGS_RelA_SpoT; cd01668 391009003658 Domains similar to the eukaryotic reeler domain and bacterial cohesins; Region: Reeler_cohesin_like; cl14606 391009003659 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some...; Region: Peptidase_C1; cl00298 391009003660 active site 391009003661 xanthine dehydrogenase subunit XdhA; Provisional; Region: PRK09970 391009003662 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; pfam01315 391009003663 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 391009003664 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 391009003665 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 391009003666 catalytic loop [active] 391009003667 iron binding site [ion binding]; other site 391009003668 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 391009003669 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 391009003670 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; pfam03450 391009003671 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 391009003672 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; pfam03450 391009003673 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 391009003674 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 391009003675 threonine synthase; Validated; Region: PRK06260 391009003676 Threonine synthase is a pyridoxal phosphate (PLP) dependent enzyme that catalyses the last reaction in the synthesis of threonine from aspartate. It proceeds by converting O-phospho-L-homoserine (OPH) into threonine and inorganic phosphate. In plants...; Region: Thr-synth_1; cd01563 391009003677 homodimer interface [polypeptide binding]; other site 391009003678 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391009003679 catalytic residue [active] 391009003680 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 391009003681 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 391009003682 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...; Region: TGS_ThrRS_N; cd01667 391009003683 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 391009003684 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 391009003685 active site 391009003686 dimer interface [polypeptide binding]; other site 391009003687 motif 1; other site 391009003688 motif 2; other site 391009003689 motif 3; other site 391009003690 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 391009003691 anticodon binding site; other site 391009003692 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 391009003693 Zn2+ binding site [ion binding]; other site 391009003694 Mg2+ binding site [ion binding]; other site 391009003695 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 391009003696 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 391009003697 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 391009003698 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 391009003699 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 391009003700 dimer interface [polypeptide binding]; other site 391009003701 active site 391009003702 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 391009003703 catalytic residues [active] 391009003704 substrate binding site [chemical binding]; other site 391009003705 The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common...; Region: Glyco_transf_WecG_TagA; cd06533 391009003706 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 391009003707 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; cl12011 391009003708 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 391009003709 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 391009003710 TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase...; Region: trmE; cd04164 391009003711 G1 box; other site 391009003712 GTP/Mg2+ binding site [chemical binding]; other site 391009003713 Switch I region; other site 391009003714 G2 box; other site 391009003715 Switch II region; other site 391009003716 G3 box; other site 391009003717 G4 box; other site 391009003718 G5 box; other site 391009003719 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 391009003720 Protein of unknown function DUF124; Region: DUF124; cl00884 391009003721 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; cl00743 391009003722 UDP-N-acetyl-D-mannosaminuronate dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: WecC; COG0677 391009003723 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009003724 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 391009003725 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 391009003726 PAP2_like_5 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_5; cd03394 391009003727 active site 391009003728 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 391009003729 Major Facilitator Superfamily; Region: MFS_1; pfam07690 391009003730 putative substrate translocation pore; other site 391009003731 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 391009003732 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 391009003733 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391009003734 metal binding site [ion binding]; metal-binding site 391009003735 active site 391009003736 I-site; other site 391009003737 Glycerophosphodiester phosphodiesterase domain of Thermotoga maritime and similar proteins; Region: GDPD_TmGDE_like; cd08568 391009003738 Glycerophosphoryl diester phosphodiesterase family; Region: GDPD; pfam03009 391009003739 putative active site [active] 391009003740 catalytic site [active] 391009003741 putative metal binding site [ion binding]; other site 391009003742 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 391009003743 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), 8-amino-7-...; Region: KBL_like; cd06454 391009003744 substrate-cofactor binding pocket; other site 391009003745 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391009003746 catalytic residue [active] 391009003747 Threonine dehydrogenase; Region: TDH; cd05281 391009003748 L-threonine 3-dehydrogenase; Validated; Region: tdh; PRK05396 391009003749 structural Zn binding site [ion binding]; other site 391009003750 catalytic Zn binding site [ion binding]; other site 391009003751 tetramer interface [polypeptide binding]; other site 391009003752 NADP binding site [chemical binding]; other site 391009003753 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 391009003754 MatE; Region: MatE; pfam01554 391009003755 MatE; Region: MatE; pfam01554 391009003756 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 391009003757 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 391009003758 Walker A/P-loop; other site 391009003759 ATP binding site [chemical binding]; other site 391009003760 Q-loop/lid; other site 391009003761 ABC transporter signature motif; other site 391009003762 Walker B; other site 391009003763 D-loop; other site 391009003764 H-loop/switch region; other site 391009003765 Predicted transcriptional regulators [Transcription]; Region: COG1725 391009003766 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 391009003767 DNA-binding site [nucleotide binding]; DNA binding site 391009003768 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 391009003769 Lyase class I_like superfamily: contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase, which catalyze similar beta-elimination reactions; Region: Lyase_I_like; cl00013 391009003770 tetramer interface [polypeptide binding]; other site 391009003771 hydrogenase maturation GTPase HydF; Region: GTP_HydF; TIGR03918 391009003772 Era (E. coli Ras-like protein)-like. This family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngG), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs)...; Region: Era_like; cd00880 391009003773 G1 box; other site 391009003774 GTP/Mg2+ binding site [chemical binding]; other site 391009003775 Switch I region; other site 391009003776 G2 box; other site 391009003777 Switch II region; other site 391009003778 G3 box; other site 391009003779 G4 box; other site 391009003780 G5 box; other site 391009003781 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 391009003782 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 391009003783 substrate binding pocket [chemical binding]; other site 391009003784 chain length determination region; other site 391009003785 substrate-Mg2+ binding site; other site 391009003786 catalytic residues [active] 391009003787 aspartate-rich region 1; other site 391009003788 active site lid residues [active] 391009003789 aspartate-rich region 2; other site 391009003790 Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage...; Region: UMPK; cd02023 391009003791 Sugar specificity; other site 391009003792 Pyrimidine base specificity; other site 391009003793 ATP-binding site [chemical binding]; other site 391009003794 HD superfamily phosphohydrolases [General function prediction only]; Region: COG1078 391009003795 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 391009003796 Zn2+ binding site [ion binding]; other site 391009003797 Mg2+ binding site [ion binding]; other site 391009003798 Bordetella pertussis Bvg accessory factor family; Region: Bvg_acc_factor; cl09130 391009003799 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase...; Region: B12-binding_like; cl00293 391009003800 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; cl14056 391009003801 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the...; Region: S2P-M50_like_1; cd06158 391009003802 active site 391009003803 putative substrate binding region [chemical binding]; other site 391009003804 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 391009003805 P-loop ATPase protein family; Region: ATP_bind_2; cl10035 391009003806 shikimate kinase; Reviewed; Region: aroK; PRK00131 391009003807 family of mostly uncharacterized proteins similar to B.subtilis YvcK; Region: YvcK_like; cd07187 391009003808 Uncharacterised protein family UPF0052; Region: UPF0052; pfam01933 391009003809 phosphate binding site [ion binding]; other site 391009003810 putative substrate binding pocket [chemical binding]; other site 391009003811 dimer interface [polypeptide binding]; other site 391009003812 Sporulation Regulator WhiA N terminal; Region: WhiA_N; pfam10298 391009003813 Sporulation Regulator WhiA C terminal domain; Region: HTH_WhiA; pfam02650 391009003814 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 391009003815 ATP cone domain; Region: ATP-cone; pfam03477 391009003816 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 391009003817 domain; Region: GreA_GreB_N; pfam03449 391009003818 C-term; Region: GreA_GreB; pfam01272 391009003819 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 391009003820 LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-...; Region: LysRS_N; cd04322 391009003821 dimer interface [polypeptide binding]; other site 391009003822 putative anticodon binding site; other site 391009003823 Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three...; Region: LysRS_core; cd00775 391009003824 motif 1; other site 391009003825 active site 391009003826 motif 2; other site 391009003827 motif 3; other site 391009003828 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 391009003829 M28, and M42; Region: Zinc_peptidase_like; cl14876 391009003830 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; cl09940 391009003831 GAF domain; Region: GAF; cl00853 391009003832 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 391009003833 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 391009003834 Glucan exporter ATP-binding protein. In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide...; Region: ABCC_Glucan_exporter_like; cd03254 391009003835 Walker A/P-loop; other site 391009003836 ATP binding site [chemical binding]; other site 391009003837 Q-loop/lid; other site 391009003838 ABC transporter signature motif; other site 391009003839 Walker B; other site 391009003840 D-loop; other site 391009003841 H-loop/switch region; other site 391009003842 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 391009003843 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 391009003844 Walker A/P-loop; other site 391009003845 ATP binding site [chemical binding]; other site 391009003846 Q-loop/lid; other site 391009003847 ABC transporter signature motif; other site 391009003848 Walker B; other site 391009003849 D-loop; other site 391009003850 H-loop/switch region; other site 391009003851 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 391009003852 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 391009003853 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 391009003854 Walker A/P-loop; other site 391009003855 ATP binding site [chemical binding]; other site 391009003856 Q-loop/lid; other site 391009003857 ABC transporter signature motif; other site 391009003858 Walker B; other site 391009003859 D-loop; other site 391009003860 H-loop/switch region; other site 391009003861 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 391009003862 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_4; cd08500 391009003863 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 391009003864 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 391009003865 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...; Region: TM_PBP2; cd06261 391009003866 dimer interface [polypeptide binding]; other site 391009003867 conserved gate region; other site 391009003868 putative PBP binding loops; other site 391009003869 ABC-ATPase subunit interface; other site 391009003870 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 391009003871 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...; Region: TM_PBP2; cd06261 391009003872 dimer interface [polypeptide binding]; other site 391009003873 conserved gate region; other site 391009003874 putative PBP binding loops; other site 391009003875 ABC-ATPase subunit interface; other site 391009003876 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; cl11391 391009003877 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi...; Region: TPR; cl02429 391009003878 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 391009003879 transcription termination factor Rho; Provisional; Region: rho; PRK09376 391009003880 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 391009003881 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...; Region: Rho_CSD; cd04459 391009003882 RNA binding site [nucleotide binding]; other site 391009003883 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...; Region: rho_factor; cd01128 391009003884 multimer interface [polypeptide binding]; other site 391009003885 Walker A motif; other site 391009003886 ATP binding site [chemical binding]; other site 391009003887 Walker B motif; other site 391009003888 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 391009003889 RF-1 domain; Region: RF-1; cl02875 391009003890 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 391009003891 RF-1 domain; Region: RF-1; cl02875 391009003892 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 391009003893 Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism...; Region: PilT; cd01131 391009003894 Walker A motif; other site 391009003895 ATP binding site [chemical binding]; other site 391009003896 Walker B motif; other site 391009003897 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14962 391009003898 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...; Region: AAA; cd00009 391009003899 Walker A motif; other site 391009003900 ATP binding site [chemical binding]; other site 391009003901 Walker B motif; other site 391009003902 arginine finger; other site 391009003903 IPP transferase; Region: IPPT; cl00403 391009003904 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 391009003905 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 391009003906 active site 391009003907 nucleophile elbow; other site 391009003908 endonuclease IV; Provisional; Region: PRK01060 391009003909 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of D-arabino-6-...; Region: AP2Ec; cd00019 391009003910 AP (apurinic/apyrimidinic) site pocket; other site 391009003911 DNA interaction; other site 391009003912 Metal-binding active site; metal-binding site 391009003913 Protein of unknown function (DUF1622); Region: DUF1622; cl01991 391009003914 NAD synthetase; Provisional; Region: PRK13981 391009003915 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 391009003916 multimer interface [polypeptide binding]; other site 391009003917 active site 391009003918 catalytic triad [active] 391009003919 protein interface 1 [polypeptide binding]; other site 391009003920 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to...; Region: NAD_synthase; cd00553 391009003921 homodimer interface [polypeptide binding]; other site 391009003922 NAD binding pocket [chemical binding]; other site 391009003923 ATP binding pocket [chemical binding]; other site 391009003924 Mg binding site [ion binding]; other site 391009003925 active-site loop [active] 391009003926 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 391009003927 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 391009003928 Domain related to MnhB subunit of Na+/H+ antiporter; Region: MnhB; cl00676 391009003929 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 391009003930 Sulfatase; Region: Sulfatase; cl10460 391009003931 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, archaeal form; Region: apgM; TIGR00306 391009003932 Competence protein; Region: Competence; cl00471 391009003933 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 391009003934 metal binding site 2 [ion binding]; metal-binding site 391009003935 putative DNA binding helix; other site 391009003936 metal binding site 1 [ion binding]; metal-binding site 391009003937 dimer interface [polypeptide binding]; other site 391009003938 structural Zn2+ binding site [ion binding]; other site 391009003939 transcription elongation factor NusA; Provisional; Region: nusA; PRK12327 391009003940 NusA N-terminal domain; Region: NusA_N; pfam08529 391009003941 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...; Region: S1_NusA; cd04455 391009003942 RNA binding site [nucleotide binding]; other site 391009003943 homodimer interface [polypeptide binding]; other site 391009003944 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 391009003945 G-X-X-G motif; other site 391009003946 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG0779 391009003947 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members...; Region: Sm_like; cl00259 391009003948 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members...; Region: Sm_like; cl00259 391009003949 Sm1 motif; other site 391009003950 RNA binding pocket [nucleotide binding]; other site 391009003951 Cupin domain; Region: Cupin_2; cl09118 391009003952 Formiminotransferase-cyclodeaminase; Region: FTCD_C; cl01350 391009003953 Queuine tRNA-ribosyltransferase; Region: TGT; cl00409 391009003954 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 391009003955 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14319 391009003956 GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of UDP-N-...; Region: GlmM; cd05802 391009003957 active site 391009003958 substrate binding site [chemical binding]; other site 391009003959 metal binding site [ion binding]; metal-binding site 391009003960 Domain of unknown function DUF59; Region: DUF59; cl00941 391009003961 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 391009003962 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; cl12011 391009003963 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 391009003964 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 391009003965 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 391009003966 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 391009003967 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 391009003968 putative active site [active] 391009003969 putative metal binding site [ion binding]; other site 391009003970 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 391009003971 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 391009003972 DHH family; Region: DHH; pfam01368 391009003973 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-...; Region: CBS_pair; cl10010 391009003974 FOG: CBS domain [General function prediction only]; Region: COG0517 391009003975 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with an upstream DHH domain which performs a phosphoesterase function and a downstream polyA polymerase domain. CBS is a small domain originally...; Region: CBS_pair_DHH_polyA_Pol_assoc; cd04595 391009003976 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 391009003977 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 391009003978 active site 391009003979 NTP binding site [chemical binding]; other site 391009003980 metal binding triad [ion binding]; metal-binding site 391009003981 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 391009003982 translocation protein TolB; Provisional; Region: tolB; PRK05137 391009003983 tol-pal system beta propeller repeat protein TolB; Region: propeller_TolB; TIGR02800 391009003984 Zc3h12a-like Ribonuclease NYN domain; Region: RNase_Zc3h12a; pfam11977 391009003985 RNA polymerase sigma factor, FliA/WhiG family; Region: FliA_WhiG; TIGR02479 391009003986 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391009003987 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...; Region: Sigma70_r4; cl01055 391009003988 CheD chemotactic sensory transduction; Region: CheD; cl00810 391009003989 Chemotaxis protein CheC, inhibitor of MCP methylation [Cell motility and secretion / Signal transduction mechanisms]; Region: CheC; COG1776 391009003990 CheC-like family; Region: CheC; pfam04509 391009003991 CheC-like family; Region: CheC; pfam04509 391009003992 c-di-GMP-binding protein [Signal transduction mechanisms]; Region: COG5581 391009003993 Flagellar protein YcgR; Region: YcgR_2; pfam12945 391009003994 PilZ domain; Region: PilZ; cl01260 391009003995 PilZ domain; Region: PilZ; cl01260 391009003996 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 391009003997 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 391009003998 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 391009003999 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 391009004000 Flagellar biosynthesis pathway, component FlhA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhA; cl07980 391009004001 FHIPEP family; Region: FHIPEP; pfam00771 391009004002 spore cortex-lytic enzyme; Region: spore_SleB; TIGR02869 391009004003 proteasome-activating nucleotidase; Provisional; Region: PRK03992 391009004004 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cl00065 391009004005 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 391009004006 Interdomain contacts; other site 391009004007 Cytokine receptor motif; other site 391009004008 Phage-related minor tail protein; Region: PhageMin_Tail; pfam10145 391009004009 Phage-related protein [Function unknown]; Region: COG5412 391009004010 membrane protein P6; Region: PHA01399 391009004011 Bacteriophage protein of unknown function (DUF646); Region: DUF646; cl12124 391009004012 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 391009004013 Phage portal protein, SPP1 Gp6-like; Region: Phage_prot_Gp6; pfam05133 391009004014 large terminase protein; Provisional; Region: 17; PHA02533 391009004015 Terminase-like family; Region: Terminase_6; pfam03237 391009004016 LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback...; Region: LabA_like; cd06167 391009004017 putative metal binding site [ion binding]; other site 391009004018 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 391009004019 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 391009004020 RecT family; Region: RecT; cl04285 391009004021 Phage-related protein, predicted endonuclease [DNA replication, recombination, and repair]; Region: COG5377 391009004022 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 391009004023 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 391009004024 non-specific DNA binding site [nucleotide binding]; other site 391009004025 salt bridge; other site 391009004026 sequence-specific DNA binding site [nucleotide binding]; other site 391009004027 Predicted transcriptional regulator [Transcription]; Region: COG2932 391009004028 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 391009004029 non-specific DNA binding site [nucleotide binding]; other site 391009004030 salt bridge; other site 391009004031 sequence-specific DNA binding site [nucleotide binding]; other site 391009004032 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (...; Region: S24_LexA-like; cd06529 391009004033 Catalytic site [active] 391009004034 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; cl12011 391009004035 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; cl12011 391009004036 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 391009004037 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 391009004038 catalytic residues [active] 391009004039 Recombinase; Region: Recombinase; pfam07508 391009004040 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 391009004041 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 391009004042 PSP1 C-terminal conserved region; Region: PSP1; cl00770 391009004043 Uncharacterised P-loop hydrolase UPF0079; Region: UPF0079; cl00520 391009004044 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 391009004045 Found in ATP-dependent protease La (LON); Region: LON; cl01056 391009004046 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...; Region: AAA; cd00009 391009004047 Walker A motif; other site 391009004048 ATP binding site [chemical binding]; other site 391009004049 Walker B motif; other site 391009004050 arginine finger; other site 391009004051 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 391009004052 The YihA (EngB) subfamily. This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and...; Region: YihA_EngB; cd01876 391009004053 Elongation factor Tu GTP binding domain; Region: GTP_EFTU; pfam00009 391009004054 G1 box; other site 391009004055 GTP/Mg2+ binding site [chemical binding]; other site 391009004056 Switch I region; other site 391009004057 G2 box; other site 391009004058 G3 box; other site 391009004059 Switch II region; other site 391009004060 G4 box; other site 391009004061 G5 box; other site 391009004062 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 391009004063 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 391009004064 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 391009004065 active site 391009004066 HIGH motif; other site 391009004067 KMSK motif region; other site 391009004068 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 391009004069 tRNA binding surface [nucleotide binding]; other site 391009004070 anticodon binding site; other site 391009004071 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 391009004072 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 trans-...; Region: HisKA; cd00082 391009004073 dimer interface [polypeptide binding]; other site 391009004074 phosphorylation site [posttranslational modification] 391009004075 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 391009004076 ATP binding site [chemical binding]; other site 391009004077 Mg2+ binding site [ion binding]; other site 391009004078 G-X-G motif; other site 391009004079 Predicted signal transduction protein [Signal transduction mechanisms]; Region: COG1639 391009004080 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 391009004081 Ribosome-binding factor A; Region: RBFA; cl00542 391009004082 FlaG protein; Region: FlaG; cl00591 391009004083 Flagellar capping protein [Cell motility and secretion]; Region: FliD; COG1345 391009004084 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 391009004085 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 391009004086 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 391009004087 metal ion-dependent adhesion site (MIDAS); other site 391009004088 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14469 391009004089 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; cl14056 391009004090 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2815 391009004091 PASTA domain. This domain is found at the C-termini of several Penicillin-binding proteins (PBPs) and bacterial serine/threonine kinases. It is a small globular fold consisting of 3 beta-sheets and an alpha-helix. The name PASTA is derived from PBP and...; Region: PASTA; cl02768 391009004092 GTPase RsgA; Reviewed; Region: PRK00098 391009004093 YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence...; Region: YjeQ_engC; cd01854 391009004094 GTPase/OB domain interface [polypeptide binding]; other site 391009004095 GTPase/Zn-binding domain interface [polypeptide binding]; other site 391009004096 GTP/Mg2+ binding site [chemical binding]; other site 391009004097 G4 box; other site 391009004098 G5 box; other site 391009004099 G1 box; other site 391009004100 Switch I region; other site 391009004101 G2 box; other site 391009004102 G3 box; other site 391009004103 Switch II region; other site 391009004104 uncharacterized radical SAM protein YgiQ; Region: SAM_YgiQ; TIGR03904 391009004105 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase...; Region: B12-binding_like; cl00293 391009004106 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; cl14056 391009004107 Domain of unknown function DUF21; Region: DUF21; pfam01595 391009004108 FOG: CBS domain [General function prediction only]; Region: COG0517 391009004109 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 391009004110 Transporter associated domain; Region: CorC_HlyC; pfam03471 391009004111 Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on...; Region: cytidine_deaminase; cd01283 391009004112 active site 391009004113 catalytic motif [active] 391009004114 Zn binding site [ion binding]; other site 391009004115 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009004116 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 391009004117 Walker A/P-loop; other site 391009004118 ATP binding site [chemical binding]; other site 391009004119 Q-loop/lid; other site 391009004120 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides...; Region: ABC_RecN; cd03241 391009004121 ABC transporter signature motif; other site 391009004122 Walker B; other site 391009004123 D-loop; other site 391009004124 H-loop/switch region; other site 391009004125 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 391009004126 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 391009004127 nucleotide binding pocket [chemical binding]; other site 391009004128 K-X-D-G motif; other site 391009004129 catalytic site [active] 391009004130 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 391009004131 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 391009004132 Helix-hairpin-helix motif; Region: HHH_2; pfam12826 391009004133 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 391009004134 Dimer interface [polypeptide binding]; other site 391009004135 BRCT sequence motif; other site 391009004136 ribonuclease R; Region: RNase_R; TIGR02063 391009004137 RNB domain; Region: RNB; pfam00773 391009004138 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an...; Region: S1_RNase_R; cd04471 391009004139 RNA binding site [nucleotide binding]; other site 391009004140 16S rRNA methyltransferase B; Provisional; Region: PRK14903 391009004141 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the rRNA-...; Region: NusB_Sun; cl00223 391009004142 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; cl12011 391009004143 Putative neutral zinc metallopeptidase; Region: Zn_peptidase_2; cl01049 391009004144 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391009004145 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 391009004146 active site 391009004147 phosphorylation site [posttranslational modification] 391009004148 intermolecular recognition site; other site 391009004149 dimerization interface [polypeptide binding]; other site 391009004150 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...; Region: trans_reg_C; cd00383 391009004151 DNA binding site [nucleotide binding] 391009004152 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 391009004153 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 391009004154 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 391009004155 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 391009004156 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 391009004157 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 391009004158 Domain of unknown function DUF20; Region: UPF0118; cl00465 391009004159 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 391009004160 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 391009004161 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 391009004162 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 391009004163 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 391009004164 Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative...; Region: RPE; cd00429 391009004165 substrate binding site [chemical binding]; other site 391009004166 hexamer interface [polypeptide binding]; other site 391009004167 metal binding site [ion binding]; metal-binding site 391009004168 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 391009004169 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 391009004170 DHH family; Region: DHH; pfam01368 391009004171 DHHA1 domain; Region: DHHA1; pfam02272 391009004172 Archaeal ATPase; Region: Arch_ATPase; pfam01637 391009004173 Predicted ATPase [General function prediction only]; Region: COG3899 391009004174 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391009004175 metal binding site [ion binding]; metal-binding site 391009004176 active site 391009004177 I-site; other site 391009004178 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: PRK14653 391009004179 FAD binding domain; Region: FAD_binding_4; pfam01565 391009004180 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 391009004181 M18 Peptidase Aminopeptidase I; Region: M18_API; cd05659 391009004182 oligomer interface [polypeptide binding]; other site 391009004183 putative active site [active] 391009004184 metal binding site [ion binding]; metal-binding site 391009004185 Transcriptional regulators [Transcription]; Region: MarR; COG1846 391009004186 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 391009004187 PEGA domain; Region: PEGA; pfam08308 391009004188 S-layer homology domain; Region: SLH; pfam00395 391009004189 chromosome segregation protein; Provisional; Region: PRK03918 391009004190 Protein of unknown function (DUF342); Region: DUF342; pfam03961 391009004191 Phosphomannose isomerase [Carbohydrate transport and metabolism]; Region: ManA; COG1482 391009004192 mannose-6-phosphate isomerase; Provisional; Region: PRK15131; cl14659 391009004193 Protein of unknown function DUF89; Region: DUF89; cl00680 391009004194 Phosphopantetheine attachment site; Region: PP-binding; cl09936 391009004195 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 391009004196 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...; Region: AAA; cd00009 391009004197 Walker A motif; other site 391009004198 ATP binding site [chemical binding]; other site 391009004199 Walker B motif; other site 391009004200 arginine finger; other site 391009004201 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 391009004202 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 391009004203 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 391009004204 catalytic residue [active] 391009004205 YGGT family; Region: YGGT; cl00508 391009004206 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 391009004207 ATP-NAD kinase; Region: NAD_kinase; pfam01513 391009004208 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 391009004209 PhoU domain; Region: PhoU; pfam01895 391009004210 PhoU domain; Region: PhoU; pfam01895 391009004211 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 391009004212 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 391009004213 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 391009004214 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 391009004215 TRAM domain; Region: TRAM; cl01282 391009004216 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 391009004217 S-adenosylmethionine binding site [chemical binding]; other site 391009004218 Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates 5-aminoimidazole-4-carboxamide-; Region: IMPCH; cd01421 391009004219 purine monophosphate binding site [chemical binding]; other site 391009004220 dimer interface [polypeptide binding]; other site 391009004221 putative catalytic residues [active] 391009004222 Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhB; cl12017 391009004223 PEGA domain; Region: PEGA; pfam08308 391009004224 peptide chain release factor 2; Validated; Region: prfB; PRK00578 391009004225 RF-1 domain; Region: RF-1; cl02875 391009004226 RF-1 domain; Region: RF-1; cl02875 391009004227 septum site-determining protein MinD; Region: minD_bact; TIGR01968 391009004228 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a...; Region: MinD; cd02036 391009004229 Switch I; other site 391009004230 Switch II; other site 391009004231 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 391009004232 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 391009004233 P loop; other site 391009004234 GTP binding site [chemical binding]; other site 391009004235 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1655 391009004236 Uncharacterized protein conserved in bacteria (DUF2225); Region: DUF2225; pfam09986 391009004237 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 391009004238 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 391009004239 putative peptidoglycan binding site; other site 391009004240 Peptidase family M23; Region: Peptidase_M23; pfam01551 391009004241 3D domain; Region: 3D; cl01439 391009004242 Predicted transcriptional regulator [Transcription]; Region: COG1959 391009004243 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 391009004244 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 391009004245 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 391009004246 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 391009004247 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 391009004248 Cell envelope-related transcriptional attenuator domain; Region: LytR_cpsA_psr; cl00581 391009004249 Endonuclease_V, a DNA repair enzyme that initiates repair of nitrosative deaminated purine bases; Region: Endonuclease_V; cd06559 391009004250 Active_site [active] 391009004251 radical SAM protein, TIGR01212 family; Region: TIGR01212 391009004252 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; cl14056 391009004253 N-ethylammeline chlorohydrolase; Provisional; Region: PRK08393 391009004254 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 391009004255 active site 391009004256 putative substrate binding pocket [chemical binding]; other site 391009004257 Domain of unknown function DUF143; Region: DUF143; cl00519 391009004258 folylpolyglutamate synthase/dihydrofolate synthase; Region: folC; TIGR01499 391009004259 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 391009004260 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 391009004261 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 391009004262 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 391009004263 active site 391009004264 HIGH motif; other site 391009004265 nucleotide binding site [chemical binding]; other site 391009004266 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 391009004267 active site 391009004268 KMSKS motif; other site 391009004269 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 391009004270 tRNA binding surface [nucleotide binding]; other site 391009004271 anticodon binding site; other site 391009004272 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 391009004273 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391009004274 metal binding site [ion binding]; metal-binding site 391009004275 active site 391009004276 I-site; other site 391009004277 C subunit; Region: rnfC; TIGR01945 391009004278 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 391009004279 SLBB domain; Region: SLBB; pfam10531 391009004280 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-; Region: HCP_like; cl14655 391009004281 RnfE family; Region: NQR2_RnfD_RnfE; cl00779 391009004282 FMN-binding domain; Region: FMN_bind; cl01081 391009004283 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 391009004284 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 391009004285 Permease P (pink-eyed dilution). Mutations in the human melanosomal P gene were responsible for classic phenotype of oculocutaneous albinism type 2 (OCA2). Although the precise function of the P protein is unknown, it was predicted to regulate the...; Region: P_permease; cd01116 391009004286 transmembrane helices; other site 391009004287 K+-dependent Na+/Ca+ exchanger related-protein; Region: TIGR00367 391009004288 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 391009004289 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 391009004290 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 391009004291 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 391009004292 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key...; Region: CBS_pair_IMPDH; cd04601 391009004293 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the...; Region: IMPDH; cd00381 391009004294 active site 391009004295 Cache domain; Region: Cache_2; pfam08269 391009004296 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 connected by an extended linker. The...; Region: HAMP; cd06225 391009004297 dimerization interface [polypeptide binding]; other site 391009004298 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 391009004299 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 391009004300 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 391009004301 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 391009004302 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 391009004303 S-adenosylmethionine binding site [chemical binding]; other site 391009004304 L-aspartate dehydrogenase; Provisional; Region: PRK13303 391009004305 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009004306 Domain of unknown function DUF108; Region: DUF108; pfam01958 391009004307 Quinolinate synthetase A protein; Region: NadA; cl00420 391009004308 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with 5-...; Region: QPRTase; cd01572 391009004309 nicotinate-nucleotide pyrophosphorylase; Region: nadC; TIGR00078 391009004310 dimerization interface [polypeptide binding]; other site 391009004311 active site 391009004312 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 391009004313 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 391009004314 dimer interface [polypeptide binding]; other site 391009004315 active site 391009004316 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 391009004317 putative enoyl-(acyl-carrier-protein) reductase II; Region: enACPred_II; TIGR03151 391009004318 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin...; Region: NPD_like; cd04730 391009004319 FMN binding site [chemical binding]; other site 391009004320 substrate binding site [chemical binding]; other site 391009004321 putative catalytic residue [active] 391009004322 BioY family; Region: BioY; cl00560 391009004323 Acyl transferase domain; Region: Acyl_transf_1; cl08282 391009004324 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 391009004325 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 391009004326 Ribulose 1,5-bisphosphate synthetase, converts PRPP to RuBP, flavoprotein [Carbohydrate transport and metabolism]; Region: THI4; COG1635 391009004327 ThiC family; Region: ThiC; cl08031 391009004328 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 391009004329 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of D-arabino-6-...; Region: AP2Ec; cl12060 391009004330 Metal-binding active site; metal-binding site 391009004331 AP (apurinic/apyrimidinic) site pocket; other site 391009004332 phosphomethylpyrimidine kinase; Provisional; Region: PRK08573 391009004333 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-...; Region: ribokinase_pfkB_like; cl00192 391009004334 substrate binding site [chemical binding]; other site 391009004335 ATP binding site [chemical binding]; other site 391009004336 Archaeal phosphomethylpyrimidine kinase; Region: MethylPyrKinase; cl00871 391009004337 6-phosphofructokinase; Provisional; Region: PRK03202 391009004338 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to PFK family that includes ATP- and pyrophosphate (PPi)- dependent phosphofructokinases...; Region: PFK; cl00204 391009004339 active site 391009004340 ADP/pyrophosphate binding site [chemical binding]; other site 391009004341 dimerization interface [polypeptide binding]; other site 391009004342 allosteric effector site; other site 391009004343 fructose-1,6-bisphosphate binding site; other site 391009004344 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 391009004345 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have...; Region: metallo-dependent_hydrolases; cl00281 391009004346 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have...; Region: metallo-dependent_hydrolases; cl00281 391009004347 active site 391009004348 biotin synthase; Provisional; Region: PRK07094 391009004349 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; cl14056 391009004350 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 391009004351 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09613 391009004352 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 391009004353 FeS/SAM binding site; other site 391009004354 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 391009004355 putative iron-only hydrogenase system regulator; Region: hyd_TM1266; TIGR03959 391009004356 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 391009004357 catalytic loop [active] 391009004358 iron binding site [ion binding]; other site 391009004359 sulfite reductase, subunit C; Region: sulfite_red_C; TIGR02912 391009004360 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 391009004361 hydrogenase, Fe-only; Region: Fe_only_hydrog; TIGR02512 391009004362 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 391009004363 Iron hydrogenase small subunit; Region: Fe_hyd_SSU; pfam02256 391009004364 Membrane transport protein; Region: Mem_trans; cl09117 391009004365 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 391009004366 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 post-...; Region: RIBOc; cd00593 391009004367 dimerization interface [polypeptide binding]; other site 391009004368 active site 391009004369 metal binding site [ion binding]; metal-binding site 391009004370 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...; Region: DSRM; cd00048 391009004371 dsRNA binding site [nucleotide binding]; other site 391009004372 ATP-utilizing enzymes of the PP-loop superfamily [General function prediction only]; Region: COG1606 391009004373 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 391009004374 Ligand Binding Site [chemical binding]; other site 391009004375 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 391009004376 integral membrane protein MviN; Region: mviN; TIGR01695 391009004377 MatE; Region: MatE; pfam01554 391009004378 ferredoxin; Validated; Region: PRK07118 391009004379 Putative Fe-S cluster; Region: FeS; pfam04060 391009004380 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 391009004381 pantoate--beta-alanine ligase; Region: panC; TIGR00018 391009004382 Pantoate-beta-alanine ligase; Region: PanC; cd00560 391009004383 active site 391009004384 ATP-binding site [chemical binding]; other site 391009004385 pantoate-binding site; other site 391009004386 HXXH motif; other site 391009004387 Alpha-glucosidase II (alpha-D-glucoside glucohydrolase) is a glycosyl hydrolase family 31 (GH31) enzyme, found in bacteria and plants, which has exo-alpha-1,4-glucosidase and oligo-1,6-glucosidase activities. Alpha-glucosidase II has been characterized...; Region: GH31_glucosidase_II_MalA; cd06604 391009004388 trimer interface [polypeptide binding]; other site 391009004389 active site 391009004390 homohexamer (dimer of homotrimer) interface [polypeptide binding]; other site 391009004391 catalytic site [active] 391009004392 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 391009004393 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 391009004394 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 391009004395 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 391009004396 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 391009004397 Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to...; Region: PNPase_KH; cd02393 391009004398 putative nucleic acid binding region [nucleotide binding]; other site 391009004399 G-X-X-G motif; other site 391009004400 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 391009004401 RNA binding site [nucleotide binding]; other site 391009004402 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 391009004403 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 391009004404 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 391009004405 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 391009004406 Zn2+ binding site [ion binding]; other site 391009004407 Mg2+ binding site [ion binding]; other site 391009004408 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 391009004409 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...; Region: AAA; cd00009 391009004410 Walker A motif; other site 391009004411 ATP binding site [chemical binding]; other site 391009004412 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009004413 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...; Region: TM_PBP2; cl00427 391009004414 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...; Region: TM_PBP2; cd06261 391009004415 dimer interface [polypeptide binding]; other site 391009004416 putative PBP binding loops; other site 391009004417 ABC-ATPase subunit interface; other site 391009004418 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 391009004419 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...; Region: TM_PBP2; cd06261 391009004420 dimer interface [polypeptide binding]; other site 391009004421 conserved gate region; other site 391009004422 putative PBP binding loops; other site 391009004423 ABC-ATPase subunit interface; other site 391009004424 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 391009004425 active site 391009004426 intersubunit interactions; other site 391009004427 catalytic residue [active] 391009004428 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 391009004429 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 391009004430 dimer interface [polypeptide binding]; other site 391009004431 anticodon binding site; other site 391009004432 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 the...; Region: AspRS_core; cd00777 391009004433 homodimer interface [polypeptide binding]; other site 391009004434 motif 1; other site 391009004435 active site 391009004436 motif 2; other site 391009004437 GAD domain; Region: GAD; pfam02938 391009004438 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 391009004439 active site 391009004440 motif 3; other site 391009004441 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 391009004442 anti sigma factor interaction site; other site 391009004443 regulatory phosphorylation site [posttranslational modification]; other site 391009004444 cytidylate kinase; Provisional; Region: cmk; PRK00023 391009004445 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 391009004446 CMP-binding site; other site 391009004447 The sites determining sugar specificity; other site 391009004448 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed; Region: PRK00087 391009004449 LytB protein; Region: LYTB; cl00507 391009004450 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 391009004451 RNA binding site [nucleotide binding]; other site 391009004452 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 391009004453 RNA binding site [nucleotide binding]; other site 391009004454 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 391009004455 RNA binding site [nucleotide binding]; other site 391009004456 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 391009004457 RNA binding site [nucleotide binding]; other site 391009004458 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 391009004459 RNA binding site [nucleotide binding]; other site 391009004460 GTP-binding protein Der; Reviewed; Region: PRK00093 391009004461 EngA1 subfamily. This CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that...; Region: EngA1; cd01894 391009004462 G1 box; other site 391009004463 GTP/Mg2+ binding site [chemical binding]; other site 391009004464 Switch I region; other site 391009004465 G2 box; other site 391009004466 Switch II region; other site 391009004467 G3 box; other site 391009004468 G4 box; other site 391009004469 G5 box; other site 391009004470 EngA2 subfamily. This CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that...; Region: EngA2; cd01895 391009004471 G1 box; other site 391009004472 GTP/Mg2+ binding site [chemical binding]; other site 391009004473 Switch I region; other site 391009004474 G2 box; other site 391009004475 G3 box; other site 391009004476 Switch II region; other site 391009004477 G4 box; other site 391009004478 G5 box; other site 391009004479 Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea; Region: PBP1_BmpA_PnrA_like; cd06354 391009004480 ligand binding site [chemical binding]; other site 391009004481 Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily; Region: PBP1_ABC_transporter_LIVBP_like; cd06268 391009004482 ligand binding site [chemical binding]; other site 391009004483 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 391009004484 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 391009004485 Zn2+ binding site [ion binding]; other site 391009004486 Mg2+ binding site [ion binding]; other site 391009004487 Ribonuclease P; Region: Ribonuclease_P; cl00457 391009004488 Domain of unknown function DUF37; Region: DUF37; cl00506 391009004489 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 391009004490 Predicted RNA-binding protein [General function prediction only]; Region: Jag; COG1847 391009004491 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...; Region: KH-I; cl00098 391009004492 G-X-X-G motif; other site 391009004493 R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine...; Region: R3H_jag; cd02644 391009004494 RxxxH motif; other site 391009004495 Cupin domain; Region: Cupin_2; cl09118 391009004496 Ion channel; Region: Ion_trans_2; cl11596 391009004497 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 391009004498 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009004499 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 391009004500 glutamine synthetase, type I; Region: GlnA; TIGR00653 391009004501 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 391009004502 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 391009004503 Response regulator receiver domain; Region: Response_reg; pfam00072 391009004504 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 391009004505 active site 391009004506 phosphorylation site [posttranslational modification] 391009004507 intermolecular recognition site; other site 391009004508 dimerization interface [polypeptide binding]; other site 391009004509 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391009004510 metal binding site [ion binding]; metal-binding site 391009004511 active site 391009004512 I-site; other site 391009004513 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 391009004514 putative catalytic site [active] 391009004515 putative metal binding site [ion binding]; other site 391009004516 putative phosphate binding site [ion binding]; other site 391009004517 Glycosyl hydrolase family 1; Region: Glyco_hydro_1; cl01046 391009004518 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 391009004519 YhhN-like protein; Region: YhhN; cl01505 391009004520 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 391009004521 phosphodiesterase; Provisional; Region: PRK12704 391009004522 RmuC family; Region: RmuC; pfam02646 391009004523 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 391009004524 catalytic residues [active] 391009004525 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 391009004526 EamA-like transporter family; Region: EamA; cl01037 391009004527 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 391009004528 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009004529 Walker A/P-loop; other site 391009004530 ATP binding site [chemical binding]; other site 391009004531 Q-loop/lid; other site 391009004532 ABC transporter signature motif; other site 391009004533 Walker B; other site 391009004534 D-loop; other site 391009004535 H-loop/switch region; other site 391009004536 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 391009004537 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cd09725 391009004538 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-II-III; cl00656 391009004539 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cd09725 391009004540 CRISPR/Cas system-associated protein Csm6; Region: Csm6_III-A; cd09742 391009004541 CRISPR/Cas system-associated RAMP superfamily protein; Region: RAMP_I_III; cl00592 391009004542 CRISPR/Cas system-associated protein Cas10; Region: Cas10_III; cd09679 391009004543 CRISPR-associated protein Cas10/Cmr2, subtype III-B; Region: cas_TM1794_Cmr2; TIGR02577 391009004544 CRISPR-associated protein (Cas_Cmr3); Region: Cas_Cmr3; pfam09700 391009004545 CRISPR/Cas system-associated RAMP superfamily protein Cmr3; Region: Cmr3_III-B; cd09748 391009004546 CRISPR/Cas system-associated RAMP superfamily protein; Region: RAMP_I_III; cl00592 391009004547 CRISPR/Cas system-associated protein Cmr5; Region: Cmr5_III-B; cd09749 391009004548 CRISPR/Cas system-associated RAMP superfamily protein; Region: RAMP_I_III; cl00592 391009004549 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 391009004550 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 391009004551 CRISPR-associated protein, MJ1666 family; Region: cas_MJ1666; TIGR01897 391009004552 CRISPR/Cas system-associated protein Csx1; Region: Csx1_III-U; cd09728 391009004553 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 391009004554 CRISPR-associated protein Cas10/Csm1, subtype III-A/MTUBE; Region: cas_TM1811_Csm1; TIGR02578 391009004555 CRISPR/Cas system-associated protein Csm2; Region: Csm2_III-A; cl00622 391009004556 CRISPR/Cas system-associated RAMP superfamily protein; Region: RAMP_I_III; cl00592 391009004557 CRISPR/Cas system-associated RAMP superfamily protein; Region: RAMP_I_III; cl00592 391009004558 CRISPR/Cas system-associated RAMP superfamily protein; Region: RAMP_I_III; cl00592 391009004559 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cd09652 391009004560 Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus; Region: RNase_HI_bacteria_HBD; cd09277 391009004561 RNA/DNA hybrid binding site [nucleotide binding]; other site 391009004562 active site 391009004563 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; cl12011 391009004564 Archaeal ATPase; Region: Arch_ATPase; pfam01637 391009004565 Archaea bacterial proteins of unknown function; Region: DUF234; pfam03008 391009004566 Protein of unknown function DUF262; Region: DUF262; cl14890 391009004567 Uncharacterized conserved protein (DUF2081); Region: DUF2081; cl09179 391009004568 N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; Region: PLDc_N_DEXD_a; cd09179 391009004569 putative active site [active] 391009004570 catalytic site [active] 391009004571 DNA phosphorothioation system restriction enzyme; Region: dnd_restrict_1; TIGR04095 391009004572 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 391009004573 ATP binding site [chemical binding]; other site 391009004574 putative Mg++ binding site [ion binding]; other site 391009004575 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 391009004576 nucleotide binding region [chemical binding]; other site 391009004577 ATP-binding site [chemical binding]; other site 391009004578 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009004579 Walker A/P-loop; other site 391009004580 ATP binding site [chemical binding]; other site 391009004581 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 391009004582 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 391009004583 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; cl12011 391009004584 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; cl12011 391009004585 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 391009004586 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; cl14882 391009004587 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 391009004588 active site 391009004589 NTP binding site [chemical binding]; other site 391009004590 metal binding triad [ion binding]; metal-binding site 391009004591 antibiotic binding site [chemical binding]; other site 391009004592 Protein of unknown function DUF86; Region: DUF86; cl01031 391009004593 Citrate transporter; Region: CitMHS; pfam03600 391009004594 Permease P (pink-eyed dilution). Mutations in the human melanosomal P gene were responsible for classic phenotype of oculocutaneous albinism type 2 (OCA2). Although the precise function of the P protein is unknown, it was predicted to regulate the...; Region: P_permease; cd01116 391009004595 transmembrane helices; other site 391009004596 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 391009004597 catalytic residues [active] 391009004598 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 391009004599 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 391009004600 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 391009004601 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 391009004602 Walker A/P-loop; other site 391009004603 ATP binding site [chemical binding]; other site 391009004604 Q-loop/lid; other site 391009004605 ABC transporter signature motif; other site 391009004606 Walker B; other site 391009004607 D-loop; other site 391009004608 H-loop/switch region; other site 391009004609 TOBE domain; Region: TOBE_2; cl01440 391009004610 Axonemal dynein light chain; Region: Ax_dynein_light; pfam10211 391009004611 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...; Region: TM_PBP2; cd06261 391009004612 dimer interface [polypeptide binding]; other site 391009004613 conserved gate region; other site 391009004614 putative PBP binding loops; other site 391009004615 ABC-ATPase subunit interface; other site 391009004616 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...; Region: TM_PBP2; cd06261 391009004617 dimer interface [polypeptide binding]; other site 391009004618 conserved gate region; other site 391009004619 putative PBP binding loops; other site 391009004620 ABC-ATPase subunit interface; other site 391009004621 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 391009004622 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 391009004623 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]; Region: LigT; COG1514 391009004624 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 391009004625 active site 391009004626 NAD binding site [chemical binding]; other site 391009004627 DsrE/DsrF-like family; Region: DrsE; cl00672 391009004628 A new structural DNA glycosylase; Region: AlkD_like; cd06561 391009004629 Active site [active] 391009004630 PAS fold; Region: PAS_4; pfam08448 391009004631 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 391009004632 putative active site [active] 391009004633 heme pocket [chemical binding]; other site 391009004634 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 391009004635 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 391009004636 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 391009004637 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...; Region: TM_PBP2; cd06261 391009004638 dimer interface [polypeptide binding]; other site 391009004639 conserved gate region; other site 391009004640 putative PBP binding loops; other site 391009004641 ABC-ATPase subunit interface; other site 391009004642 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 391009004643 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...; Region: TM_PBP2; cd06261 391009004644 dimer interface [polypeptide binding]; other site 391009004645 conserved gate region; other site 391009004646 putative PBP binding loops; other site 391009004647 ABC-ATPase subunit interface; other site 391009004648 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 391009004649 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 391009004650 Walker A/P-loop; other site 391009004651 ATP binding site [chemical binding]; other site 391009004652 Q-loop/lid; other site 391009004653 ABC transporter signature motif; other site 391009004654 Walker B; other site 391009004655 D-loop; other site 391009004656 H-loop/switch region; other site 391009004657 TOBE domain; Region: TOBE_2; cl01440 391009004658 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 391009004659 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 391009004660 Predicted P-loop ATPase [General function prediction only]; Region: COG4928 391009004661 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 391009004662 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 391009004663 dipeptidase PepV; Reviewed; Region: PRK07318 391009004664 M20 Peptidase Xaa-His dipeptidase (PepV) degrades hydrophobic dipeptides; Region: M20_PepV; cd03888 391009004665 active site 391009004666 metal binding site [ion binding]; metal-binding site 391009004667 Major Facilitator Superfamily; Region: MFS_1; pfam07690 391009004668 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB2; cd01048 391009004669 diiron binding motif [ion binding]; other site 391009004670 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 391009004671 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 391009004672 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 391009004673 PASTA domain. This domain is found at the C-termini of several Penicillin-binding proteins (PBPs) and bacterial serine/threonine kinases. It is a small globular fold consisting of 3 beta-sheets and an alpha-helix. The name PASTA is derived from PBP and...; Region: PASTA; cl02768 391009004674 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 391009004675 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; cl12011 391009004676 hydroxydechloroatrazine ethylaminohydrolase; Reviewed; Region: PRK08203 391009004677 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 391009004678 active site 391009004679 putative substrate binding pocket [chemical binding]; other site 391009004680 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 391009004681 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD)...; Region: Trp-synth-beta_II; cl00342 391009004682 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 391009004683 catalytic residue [active] 391009004684 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 391009004685 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; pfam01315 391009004686 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 391009004687 Adenine deaminase [Nucleotide transport and metabolism]; Region: AdeC; COG1001 391009004688 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have...; Region: metallo-dependent_hydrolases; cl00281 391009004689 Adenine deaminase (AdeC) directly deaminates adenine to form hypoxanthine. This reaction is part of one of the adenine salvage pathways, as well as the degradation pathway. It is important for adenine utilization as a purine, as well as a nitrogen...; Region: AdeC; cd01295 391009004690 active site 391009004691 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have...; Region: metallo-dependent_hydrolases; cl00281 391009004692 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 391009004693 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 391009004694 Walker A/P-loop; other site 391009004695 ATP binding site [chemical binding]; other site 391009004696 Q-loop/lid; other site 391009004697 ABC transporter signature motif; other site 391009004698 Walker B; other site 391009004699 D-loop; other site 391009004700 H-loop/switch region; other site 391009004701 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 391009004702 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 391009004703 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 391009004704 Walker A/P-loop; other site 391009004705 ATP binding site [chemical binding]; other site 391009004706 Q-loop/lid; other site 391009004707 ABC transporter signature motif; other site 391009004708 Walker B; other site 391009004709 D-loop; other site 391009004710 H-loop/switch region; other site 391009004711 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 391009004712 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 391009004713 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 391009004714 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...; Region: TM_PBP2; cd06261 391009004715 dimer interface [polypeptide binding]; other site 391009004716 conserved gate region; other site 391009004717 putative PBP binding loops; other site 391009004718 ABC-ATPase subunit interface; other site 391009004719 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 391009004720 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...; Region: TM_PBP2; cd06261 391009004721 dimer interface [polypeptide binding]; other site 391009004722 conserved gate region; other site 391009004723 putative PBP binding loops; other site 391009004724 ABC-ATPase subunit interface; other site 391009004725 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 391009004726 GIY-YIG catalytic domain; Region: GIY-YIG; cl01061 391009004727 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 391009004728 Helix-hairpin-helix motif; Region: HHH_2; pfam12826 391009004729 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and L-...; Region: GCS_H; cd06848 391009004730 lipoyl attachment site [posttranslational modification]; other site 391009004731 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 391009004732 Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this...; Region: FeoB; cd01879 391009004733 G1 box; other site 391009004734 GTP/Mg2+ binding site [chemical binding]; other site 391009004735 Switch I region; other site 391009004736 G2 box; other site 391009004737 G3 box; other site 391009004738 Switch II region; other site 391009004739 G4 box; other site 391009004740 G5 box; other site 391009004741 Nucleoside recognition; Region: Gate; cl00486 391009004742 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 391009004743 Nucleoside recognition; Region: Gate; cl00486 391009004744 FeoA domain; Region: FeoA; cl00838 391009004745 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 391009004746 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 391009004747 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 391009004748 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 391009004749 Memo (mediator of ErbB2-driven cell motility) is co-precipitated with the C terminus of ErbB2, a protein involved in cell motility; Region: MEMO_like; cd07361 391009004750 putative ligand binding pocket/active site [active] 391009004751 putative metal binding site [ion binding]; other site 391009004752 Type II secretory pathway, component PulD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulD; COG1450 391009004753 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 391009004754 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 391009004755 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 391009004756 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 391009004757 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 391009004758 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This...; Region: ABC_cobalt_CbiO_domain1; cd03225 391009004759 Walker A/P-loop; other site 391009004760 ATP binding site [chemical binding]; other site 391009004761 Q-loop/lid; other site 391009004762 ABC transporter signature motif; other site 391009004763 Walker B; other site 391009004764 D-loop; other site 391009004765 H-loop/switch region; other site 391009004766 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; cl12011 391009004767 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 391009004768 S-adenosylmethionine binding site [chemical binding]; other site 391009004769 Flavin Reductases; Region: FlaRed; cl00801 391009004770 transketolase; Reviewed; Region: PRK05899 391009004771 Thiamine pyrophosphate (TPP) family, Transketolase (TK) subfamily, TPP-binding module; TK catalyzes the transfer of a two-carbon unit from ketose phosphates to aldose phosphates. In heterotrophic organisms, TK provides a link between glycolysis and the...; Region: TPP_TK; cd02012 391009004772 TPP-binding site [chemical binding]; other site 391009004773 dimer interface [polypeptide binding]; other site 391009004774 Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins; Region: TPP_PYR_DXS_TK_like; cd07033 391009004775 PYR/PP interface [polypeptide binding]; other site 391009004776 dimer interface [polypeptide binding]; other site 391009004777 TPP binding site [chemical binding]; other site 391009004778 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 391009004779 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 391009004780 S-adenosylmethionine synthetase; Validated; Region: PRK05250 391009004781 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 391009004782 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 391009004783 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 391009004784 Peptidase family M23; Region: Peptidase_M23; pfam01551 391009004785 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 391009004786 HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual...; Region: HflX; cd01878 391009004787 G1 box; other site 391009004788 GTP/Mg2+ binding site [chemical binding]; other site 391009004789 Switch I region; other site 391009004790 G2 box; other site 391009004791 G3 box; other site 391009004792 Switch II region; other site 391009004793 G4 box; other site 391009004794 G5 box; other site 391009004795 Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that...; Region: Hfq; cd01716 391009004796 Sm1 motif; other site 391009004797 intra - hexamer interaction site; other site 391009004798 inter - hexamer interaction site [polypeptide binding]; other site 391009004799 nucleotide binding pocket [chemical binding]; other site 391009004800 Sm2 motif; other site 391009004801 Sporulation and spore germination; Region: Germane; pfam10646 391009004802 threonyl-tRNA synthetase; Reviewed; Region: PRK12444 391009004803 GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but...; Region: TGS; cl03735 391009004804 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 391009004805 Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK); Region: UMPK_like; cd02028 391009004806 Active site [active] 391009004807 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 391009004808 S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and...; Region: S1_RNase_E; cd04453 391009004809 homodimer interface [polypeptide binding]; other site 391009004810 oligonucleotide binding site [chemical binding]; other site 391009004811 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009004812 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 391009004813 oligomerization interface [polypeptide binding]; other site 391009004814 active site 391009004815 NAD+ binding site [chemical binding]; other site 391009004816 Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the...; Region: deoxycytidylate_deaminase; cd01286 391009004817 catalytic motif [active] 391009004818 Zn binding site [ion binding]; other site 391009004819 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Validated; Region: PRK05778 391009004820 Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR...; Region: TPP_OGFOR; cd03375 391009004821 TPP-binding site [chemical binding]; other site 391009004822 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 391009004823 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 391009004824 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 391009004825 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 391009004826 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 391009004827 active site 391009004828 phosphorylation site [posttranslational modification] 391009004829 intermolecular recognition site; other site 391009004830 dimerization interface [polypeptide binding]; other site 391009004831 CheB methylesterase; Region: CheB_methylest; pfam01339 391009004832 S-layer homology domain; Region: SLH; pfam00395 391009004833 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 391009004834 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 391009004835 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 391009004836 tyrosine 2,3-aminomutase; Region: Tyr_2_3_mutase; TIGR03832 391009004837 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 391009004838 active sites [active] 391009004839 tetramer interface [polypeptide binding]; other site 391009004840 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; cl00920 391009004841 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 391009004842 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 391009004843 Coenzyme A binding pocket [chemical binding]; other site 391009004844 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 391009004845 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cd00838 391009004846 active site 391009004847 metal binding site [ion binding]; metal-binding site 391009004848 Mn-dependent transcriptional regulator [Transcription]; Region: TroR; COG1321 391009004849 Iron dependent repressor, metal binding and dimerisation domain; Region: Fe_dep_repr_C; pfam02742 391009004850 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 391009004851 M42 Peptidase, Endoglucanase-like subfamily; Region: M42_glucanase_like; cd05657 391009004852 putative oligomer interface [polypeptide binding]; other site 391009004853 putative active site [active] 391009004854 metal binding site [ion binding]; metal-binding site 391009004855 Domain related to MnhB subunit of Na+/H+ antiporter; Region: MnhB; cl00676 391009004856 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; cl00583 391009004857 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 391009004858 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009004859 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 391009004860 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; cl12011 391009004861 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 391009004862 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 391009004863 B.subtilis YXKO protein of unknown function and related proteins. Based on the conservation of the ATP binding site, the substrate binding site and the Mg2+binding site and structural homology this group is a member of the ribokinase-like superfamily; Region: YXKO-related; cd01171 391009004864 putative substrate binding site [chemical binding]; other site 391009004865 putative ATP binding site [chemical binding]; other site 391009004866 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 catalyze...; Region: LT_GEWL; cd00254 391009004867 N-acetyl-D-glucosamine binding site [chemical binding]; other site 391009004868 catalytic residue [active] 391009004869 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 391009004870 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 391009004871 binding surface 391009004872 TPR motif; other site 391009004873 Anaphase-promoting complex, cyclosome, subunit 3; Region: Apc3; pfam12895 391009004874 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 391009004875 binding surface 391009004876 TPR motif; other site 391009004877 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 391009004878 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic...; Region: Tryp_SPc; cl00149 391009004879 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 C-...; Region: PDZ_serine_protease; cd00987 391009004880 protein binding site [polypeptide binding]; other site 391009004881 This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of...; Region: GT1_Glycogen_Phosphorylase; cd04300 391009004882 homodimer interface [polypeptide binding]; other site 391009004883 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 391009004884 active site pocket [active] 391009004885 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 391009004886 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 391009004887 Catalytic site [active] 391009004888 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 391009004889 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 391009004890 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 391009004891 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 391009004892 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 391009004893 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 391009004894 RimM N-terminal domain; Region: RimM; pfam01782 391009004895 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to...; Region: PRCH; cl09959 391009004896 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837; cl00794 391009004897 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 391009004898 signal recognition particle protein; Provisional; Region: PRK10867 391009004899 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 391009004900 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 391009004901 P loop; other site 391009004902 GTP binding site [chemical binding]; other site 391009004903 Signal peptide binding domain; Region: SRP_SPB; pfam02978 391009004904 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 391009004905 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 391009004906 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 391009004907 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...; Region: TM_PBP2; cd06261 391009004908 dimer interface [polypeptide binding]; other site 391009004909 conserved gate region; other site 391009004910 putative PBP binding loops; other site 391009004911 ABC-ATPase subunit interface; other site 391009004912 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...; Region: TM_PBP2; cl00427 391009004913 Ferritin-CCC1, N-terminal ferritin-like diiron-binding domain; Region: Ferritin_CCC1_N; cd01044 391009004914 diiron binding motif [ion binding]; other site 391009004915 CCC1-related domain of ferritin; Region: Ferritin_CCC1_C; cd02431 391009004916 Domain of unknown function (DUF364); Region: DUF364; cl00885 391009004917 N-glycosylase/DNA lyase; Provisional; Region: PRK01229 391009004918 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 391009004919 minor groove reading motif; other site 391009004920 helix-hairpin-helix signature motif; other site 391009004921 substrate binding pocket [chemical binding]; other site 391009004922 active site 391009004923 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]; Region: COG3947 391009004924 ornithine carbamoyltransferase; Validated; Region: PRK02102 391009004925 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 391009004926 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 391009004927 Predicted GTPase [General function prediction only]; Region: COG2403 391009004928 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 391009004929 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 391009004930 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 391009004931 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 391009004932 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 391009004933 Zn2+ binding site [ion binding]; other site 391009004934 Mg2+ binding site [ion binding]; other site 391009004935 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 391009004936 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...; Region: TM_PBP2; cd06261 391009004937 dimer interface [polypeptide binding]; other site 391009004938 conserved gate region; other site 391009004939 putative PBP binding loops; other site 391009004940 ABC-ATPase subunit interface; other site 391009004941 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...; Region: TM_PBP2; cd06261 391009004942 dimer interface [polypeptide binding]; other site 391009004943 conserved gate region; other site 391009004944 putative PBP binding loops; other site 391009004945 ABC-ATPase subunit interface; other site 391009004946 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 391009004947 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 391009004948 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 391009004949 Trehalose phosphorylase (TP) reversibly catalyzes trehalose synthesis and degradation from alpha-glucose-1-phosphate (alpha-Glc-1-P) and glucose. The catalyzing activity includes the phosphorolysis of trehalose, which produce alpha-Glc-1-P and glucose...; Region: GT1_Trehalose_phosphorylase; cd03792 391009004950 D-allose kinase; Provisional; Region: PRK09698 391009004951 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 391009004952 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 trans-...; Region: HisKA; cd00082 391009004953 dimer interface [polypeptide binding]; other site 391009004954 phosphorylation site [posttranslational modification] 391009004955 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 391009004956 ATP binding site [chemical binding]; other site 391009004957 Mg2+ binding site [ion binding]; other site 391009004958 G-X-G motif; other site 391009004959 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391009004960 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 391009004961 active site 391009004962 phosphorylation site [posttranslational modification] 391009004963 intermolecular recognition site; other site 391009004964 dimerization interface [polypeptide binding]; other site 391009004965 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...; Region: trans_reg_C; cd00383 391009004966 DNA binding site [nucleotide binding] 391009004967 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 391009004968 PhoU domain; Region: PhoU; pfam01895 391009004969 phosphate ABC transporter ATP-binding protein; Provisional; Region: PRK14262 391009004970 Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein...; Region: ABC_PstB_phosphate_transporter; cd03260 391009004971 Walker A/P-loop; other site 391009004972 ATP binding site [chemical binding]; other site 391009004973 Q-loop/lid; other site 391009004974 ABC transporter signature motif; other site 391009004975 Walker B; other site 391009004976 D-loop; other site 391009004977 H-loop/switch region; other site 391009004978 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...; Region: TM_PBP2; cd06261 391009004979 dimer interface [polypeptide binding]; other site 391009004980 conserved gate region; other site 391009004981 putative PBP binding loops; other site 391009004982 ABC-ATPase subunit interface; other site 391009004983 phosphate ABC transporter, permease protein PstC; Region: phosphate_pstC; TIGR02138 391009004984 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...; Region: TM_PBP2; cd06261 391009004985 dimer interface [polypeptide binding]; other site 391009004986 conserved gate region; other site 391009004987 putative PBP binding loops; other site 391009004988 ABC-ATPase subunit interface; other site 391009004989 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 391009004990 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 391009004991 NAD(P) binding site [chemical binding]; other site 391009004992 catalytic residues [active] 391009004993 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 391009004994 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 391009004995 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 391009004996 uncharacterized subgroup of aldehyde reductase and flavonoid reductase related proteins, extended (e) SDRs; Region: AR_FR_like_1_SDR_e; cd05228 391009004997 hopanoid-associated sugar epimerase; Region: HpnA; TIGR03466 391009004998 putative NADP binding site [chemical binding]; other site 391009004999 putative substrate binding site [chemical binding]; other site 391009005000 active site 391009005001 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 391009005002 1-phosphofructokinase (FruK), minor 6-phosphofructokinase (pfkB) and related sugar kinases. FruK plays an important role in the predominant pathway for fructose utilisation.This group also contains tagatose-6-phophate kinase, an enzyme of the tagatose...; Region: FruK_PfkB_like; cd01164 391009005003 putative substrate binding site [chemical binding]; other site 391009005004 putative ATP binding site [chemical binding]; other site 391009005005 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 391009005006 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 391009005007 NAD(P) binding site [chemical binding]; other site 391009005008 homotetramer interface [polypeptide binding]; other site 391009005009 homodimer interface [polypeptide binding]; other site 391009005010 active site 391009005011 Cobalt transport protein; Region: CbiQ; cl00463 391009005012 Inorganic pyrophosphatase [Energy production and conversion]; Region: OVP1; cl11452 391009005013 Inorganic H+ pyrophosphatase; Region: H_PPase; pfam03030 391009005014 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 391009005015 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 391009005016 active site 391009005017 phosphorylation site [posttranslational modification] 391009005018 intermolecular recognition site; other site 391009005019 dimerization interface [polypeptide binding]; other site 391009005020 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...; Region: trans_reg_C; cd00383 391009005021 DNA binding site [nucleotide binding] 391009005022 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 391009005023 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 trans-...; Region: HisKA; cd00082 391009005024 dimer interface [polypeptide binding]; other site 391009005025 phosphorylation site [posttranslational modification] 391009005026 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 391009005027 ATP binding site [chemical binding]; other site 391009005028 Mg2+ binding site [ion binding]; other site 391009005029 G-X-G motif; other site 391009005030 pyrimidine-nucleoside phosphorylase; Region: Y_phosphoryl; TIGR02644 391009005031 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 391009005032 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 391009005033 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; pfam07831 391009005034 Predicted periplasmic protein (DUF2233); Region: DUF2233; cl10481 391009005035 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 391009005036 glucose-6-phosphate isomerase; Provisional; Region: PRK00973 391009005037 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the first SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_1; cd05015 391009005038 active site 391009005039 dimer interface [polypeptide binding]; other site 391009005040 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the second SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_2; cd05016 391009005041 dimer interface [polypeptide binding]; other site 391009005042 active site 391009005043 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009005044 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 391009005045 metal binding site [ion binding]; metal-binding site 391009005046 active site 391009005047 I-site; other site 391009005048 excinuclease ABC subunit B; Provisional; Region: PRK05298 391009005049 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 391009005050 ATP binding site [chemical binding]; other site 391009005051 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 391009005052 nucleotide binding region [chemical binding]; other site 391009005053 ATP-binding site [chemical binding]; other site 391009005054 Ultra-violet resistance protein B; Region: UvrB; pfam12344 391009005055 UvrB/uvrC motif; Region: UVR; pfam02151 391009005056 Fibronectin-binding protein A N-terminus (FbpA); Region: FbpA; pfam05833 391009005057 Domain of unknown function (DUF814); Region: DUF814; pfam05670 391009005058 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_7; cd08512 391009005059 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 391009005060 hypothetical protein; Provisional; Region: PRK13670 391009005061 hypothetical protein; Provisional; Region: PRK13671 391009005062 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 391009005063 CarD-like/TRCF domain; Region: CarD_TRCF; cl00588 391009005064 DEAD-like helicases superfamily; Region: DEXDc; smart00487 391009005065 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 391009005066 ATP binding site [chemical binding]; other site 391009005067 putative Mg++ binding site [ion binding]; other site 391009005068 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 391009005069 nucleotide binding region [chemical binding]; other site 391009005070 ATP-binding site [chemical binding]; other site 391009005071 TRCF domain; Region: TRCF; pfam03461 391009005072 DNA integrity scanning protein DisA; Provisional; Region: PRK13482 391009005073 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 391009005074 DisA bacterial checkpoint controller linker region; Region: DisA-linker; pfam10635 391009005075 Glutamine Amidotransferase (GATase_I) involved in pyridoxine biosynthesis; Region: GATase1_PB; cd01749 391009005076 predicted active site [active] 391009005077 catalytic triad [active] 391009005078 pyridoxal biosynthesis lyase PdxS; Provisional; Region: PRK04180 391009005079 PdxS is a subunit of the pyridoxal 5'-phosphate (PLP) synthase, an important enzyme in deoxyxylulose 5-phosphate (DXP)-independent pathway for de novo biosynthesis of PLP, present in some eubacteria, in archaea, fungi, plants, plasmodia, and some...; Region: pdxS; cd04727 391009005080 active site 391009005081 multimer interface [polypeptide binding]; other site 391009005082 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, isobutyryl-CoA mutase (ICM)-like subfamily; contains archaeal and bacterial proteins similar to the large subunit of Streptomyces cinnamonensis coenzyme B12-dependent ICM. ICM...; Region: MM_CoA_mutase_ICM_like; cd03680 391009005083 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 391009005084 intersubunit interface [polypeptide binding]; other site 391009005085 active site 391009005086 Zn2+ binding site [ion binding]; other site 391009005087 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 391009005088 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cd00483 391009005089 catalytic center binding site [active] 391009005090 ATP binding site [chemical binding]; other site 391009005091 oxaloacetate decarboxylase; Provisional; Region: PRK14041 391009005092 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 391009005093 active site 391009005094 catalytic residues [active] 391009005095 metal binding site [ion binding]; metal-binding site 391009005096 homodimer binding site [polypeptide binding]; other site 391009005097 Conserved carboxylase domain; Region: PYC_OADA; pfam02436 391009005098 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 391009005099 translation initiation factor IF-2; Region: IF-2; TIGR00487 391009005100 IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily. IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases...; Region: IF2_eIF5B; cd01887 391009005101 G1 box; other site 391009005102 putative GEF interaction site [polypeptide binding]; other site 391009005103 GTP/Mg2+ binding site [chemical binding]; other site 391009005104 Switch I region; other site 391009005105 G2 box; other site 391009005106 G3 box; other site 391009005107 Switch II region; other site 391009005108 G4 box; other site 391009005109 G5 box; other site 391009005110 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...; Region: IF2_mtIF2_II; cd03702 391009005111 Translation-initiation factor 2; Region: IF-2; pfam11987 391009005112 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...; Region: mtIF2_IVc; cd03692 391009005113 Domain of unknown function (DUF3783); Region: DUF3783; pfam12646 391009005114 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 391009005115 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 391009005116 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 391009005117 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 391009005118 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 391009005119 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 391009005120 CoA-ligase; Region: Ligase_CoA; pfam00549 391009005121 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 391009005122 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009005123 Predicted permease [General function prediction only]; Region: COG2985 391009005124 Predicted Permease Membrane Region; Region: Asp-Al_Ex; cl06061 391009005125 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 391009005126 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009005127 Semialdehyde dehydrogenase, dimerisation domain; Region: Semialdhyde_dhC; pfam02774 391009005128 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 391009005129 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 391009005130 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 391009005131 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 391009005132 dihydrodipicolinate synthase; Region: dapA; TIGR00674 391009005133 dimer interface [polypeptide binding]; other site 391009005134 active site 391009005135 catalytic residue [active] 391009005136 dihydrodipicolinate reductase; Provisional; Region: PRK00048 391009005137 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 391009005138 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 391009005139 Tetrahydrodipicolinate succinyltransferase N-terminal; Region: DapD_N; pfam08503 391009005140 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase; Region: DapD_Ac; TIGR03532 391009005141 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 391009005142 trimer interface [polypeptide binding]; other site 391009005143 active site 391009005144 substrate binding site [chemical binding]; other site 391009005145 CoA binding site [chemical binding]; other site 391009005146 aspartate kinase; Reviewed; Region: PRK06635 391009005147 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 391009005148 putative nucleotide binding site [chemical binding]; other site 391009005149 putative catalytic residues [active] 391009005150 putative Mg ion binding site [ion binding]; other site 391009005151 putative aspartate binding site [chemical binding]; other site 391009005152 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins; Region: ACT_AKii-LysC-BS-like_1; cd04913 391009005153 putative allosteric regulatory site; other site 391009005154 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 391009005155 acetylornithine aminotransferase; Provisional; Region: PRK02627 391009005156 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase...; Region: OAT_like; cd00610 391009005157 inhibitor-cofactor binding pocket; inhibition site 391009005158 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391009005159 catalytic residue [active] 391009005160 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 391009005161 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 391009005162 inhibitor-cofactor binding pocket; inhibition site 391009005163 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391009005164 catalytic residue [active] 391009005165 Apolipoprotein N-acyltransferase [Cell envelope biogenesis, outer membrane]; Region: Lnt; COG0815 391009005166 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 391009005167 putative active site [active] 391009005168 catalytic triad [active] 391009005169 putative dimer interface [polypeptide binding]; other site 391009005170 nicotinate phosphoribosyltransferase; Provisional; Region: PRK07188 391009005171 Phosphoribosyltransferase (PRTase) type II; This family contains two enzymes that play an important role in NAD production by either allowing quinolinic acid (QA) , quinolinate phosphoribosyl transferase (QAPRTase), or nicotinic acid (NA), nicotinate...; Region: PRTase_typeII; cl12019 391009005172 active site 391009005173 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 391009005174 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 391009005175 Glycine cleavage system protein P (pyridoxal-binding), N-terminal domain [Amino acid transport and metabolism]; Region: GcvP; COG0403 391009005176 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2...; Region: GDC-P; cd00613 391009005177 tetramer interface [polypeptide binding]; other site 391009005178 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391009005179 catalytic residue [active] 391009005180 Glycine cleavage system protein P (pyridoxal-binding), C-terminal domain [Amino acid transport and metabolism]; Region: GcvP; COG1003 391009005181 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2...; Region: GDC-P; cd00613 391009005182 tetramer interface [polypeptide binding]; other site 391009005183 pyridoxal 5'-phosphate binding site [chemical binding]; other site 391009005184 catalytic residue [active] 391009005185 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 391009005186 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 391009005187 active site 391009005188 NAD binding site [chemical binding]; other site 391009005189 metal binding site [ion binding]; metal-binding site 391009005190 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 391009005191 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 391009005192 S-adenosylmethionine binding site [chemical binding]; other site 391009005193 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 391009005194 Coenzyme A pyrophosphatase (CoAse), a member of the Nudix hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes. The need of CoAses mainly arises under conditions of oxidative...; Region: CoAse; cd03426 391009005195 putative active site [active] 391009005196 putative CoA binding site [chemical binding]; other site 391009005197 nudix motif; other site 391009005198 metal binding site [ion binding]; metal-binding site 391009005199 diaminopimelate aminotransferase; Provisional; Region: PRK13983 391009005200 M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases; Region: M20_ArgE_DapE_like1; cd05650 391009005201 metal binding site [ion binding]; metal-binding site 391009005202 urocanate hydratase; Provisional; Region: PRK05414 391009005203 urocanate hydratase; Region: hutU; TIGR01228 391009005204 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cl01116 391009005205 2-oxoglutarate ferredoxin oxidoreductase subunit alpha; Validated; Region: PRK08659 391009005206 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 391009005207 dimer interface [polypeptide binding]; other site 391009005208 PYR/PP interface [polypeptide binding]; other site 391009005209 TPP binding site [chemical binding]; other site 391009005210 substrate binding site [chemical binding]; other site 391009005211 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-; Region: HCP_like; cl14655 391009005212 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 391009005213 subunit; Region: OAD_beta; cl00816 391009005214 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 391009005215 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 391009005216 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This...; Region: ABC_cobalt_CbiO_domain1; cd03225 391009005217 Walker A/P-loop; other site 391009005218 ATP binding site [chemical binding]; other site 391009005219 Q-loop/lid; other site 391009005220 ABC transporter signature motif; other site 391009005221 Walker B; other site 391009005222 D-loop; other site 391009005223 H-loop/switch region; other site 391009005224 Uncharacterized conserved protein [Function unknown]; Region: COG1912 391009005225 S-adenosyl-l-methionine hydroxide adenosyltransferase; Region: SAM_adeno_trans; pfam01887 391009005226 6-phosphofructokinase; Provisional; Region: PRK03202 391009005227 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to PFK family that includes ATP- and pyrophosphate (PPi)- dependent phosphofructokinases...; Region: PFK; cl00204 391009005228 active site 391009005229 ADP/pyrophosphate binding site [chemical binding]; other site 391009005230 dimerization interface [polypeptide binding]; other site 391009005231 allosteric effector site; other site 391009005232 fructose-1,6-bisphosphate binding site; other site 391009005233 Inorganic H+ pyrophosphatase; Region: H_PPase; pfam03030 391009005234 Inorganic pyrophosphatase [Energy production and conversion]; Region: OVP1; cl11452 391009005235 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 391009005236 Protein export membrane protein; Region: SecD_SecF; cl14618 391009005237 protein-export membrane protein SecD; Region: secD; TIGR01129 391009005238 Protein export membrane protein; Region: SecD_SecF; cl14618 391009005239 Preprotein translocase subunit; Region: YajC; cl00806 391009005240 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase [Coenzyme metabolism]; Region: FolD; COG0190 391009005241 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 391009005242 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 391009005243 homodimer interface [polypeptide binding]; other site 391009005244 NADP binding site [chemical binding]; other site 391009005245 substrate binding site [chemical binding]; other site 391009005246 DRTGG domain; Region: DRTGG; cl12147 391009005247 Thymidylate synthase complementing protein; Region: Thy1; cl03630 391009005248 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 391009005249 RNA/DNA hybrid binding site [nucleotide binding]; other site 391009005250 active site 391009005251 Protein of unknown function (DUF3242); Region: DUF3242; pfam11586 391009005252 Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only]; Region: LipA; COG1075 391009005253 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 391009005254 NAD-dependent deacetylase; Provisional; Region: PRK14138 391009005255 SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+...; Region: SIR2-fam; cd01407 391009005256 NAD+ binding site [chemical binding]; other site 391009005257 substrate binding site [chemical binding]; other site 391009005258 Zn binding site [ion binding]; other site 391009005259 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 391009005260 Chromate transporter; Region: Chromate_transp; pfam02417 391009005261 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 391009005262 DNA polymerase I; Provisional; Region: PRK05755 391009005263 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 391009005264 active site 391009005265 metal binding site 1 [ion binding]; metal-binding site 391009005266 putative 5' ssDNA interaction site; other site 391009005267 metal binding site 3; metal-binding site 391009005268 metal binding site 2 [ion binding]; metal-binding site 391009005269 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 391009005270 putative DNA binding site [nucleotide binding]; other site 391009005271 putative metal binding site [ion binding]; other site 391009005272 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Region: DNA_polA_I_Ecoli_like_exo; cd06139 391009005273 active site 391009005274 catalytic site [active] 391009005275 substrate binding site [chemical binding]; other site 391009005276 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 391009005277 active site 391009005278 DNA binding site [nucleotide binding] 391009005279 catalytic site [active] 391009005280 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 391009005281 cell division protein FtsA; Region: ftsA; TIGR01174 391009005282 Cell division protein FtsA; Region: FtsA; cl11496 391009005283 Cell division protein FtsA; Region: FtsA; cl11496 391009005284 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 391009005285 MutS2 homologs in bacteria and eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also...; Region: ABC_MutS2; cd03280 391009005286 Walker A/P-loop; other site 391009005287 ATP binding site [chemical binding]; other site 391009005288 Q-loop/lid; other site 391009005289 ABC transporter signature motif; other site 391009005290 Walker B; other site 391009005291 D-loop; other site 391009005292 H-loop/switch region; other site 391009005293 Outer membrane protein (OmpH-like); Region: OmpH; cl08146 391009005294 Smr domain; Region: Smr; cl02619 391009005295 Phosphate transporter family; Region: PHO4; cl00396 391009005296 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 391009005297 Uncharacterised protein family (UPF0104); Region: UPF0104; cl04219 391009005298 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 391009005299 substrate binding site [chemical binding]; other site 391009005300 dimer interface [polypeptide binding]; other site 391009005301 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 391009005302 carbamate kinase; Reviewed; Region: PRK12686 391009005303 AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an...; Region: AAK_CK; cd04235 391009005304 putative substrate binding site [chemical binding]; other site 391009005305 nucleotide binding site [chemical binding]; other site 391009005306 nucleotide binding site [chemical binding]; other site 391009005307 homodimer interface [polypeptide binding]; other site 391009005308 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 391009005309 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 391009005310 Peptidase M55, D-aminopeptidase dipeptide-binding protein family; Region: DAP_dppA; cl01007 391009005311 SxDxEG motif; other site 391009005312 active site 391009005313 metal binding site [ion binding]; metal-binding site 391009005314 homopentamer interface [polypeptide binding]; other site