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Transfer RNA Biogenesis - Dickeya dadantii 3937
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AEukaryotic type
B 5'processing factors
C Ribonucrease P
B 3'processing and CCA adding factors
C 3'processing factors
D Dda3937_01051 elaC; Ribonuclease Z K00784 rnz; ribonuclease Z [EC:3.1.26.11]
D Dda3937_00013 Ribonuclease K01166 RNASET2; ribonuclease T2 [EC:4.6.1.19]
C CCA adding factors
D Dda3937_00174 cca; multifunctional tRNA nucleotidyl transferase, 2'3'-cyclic phosphodiesterase, 2'-nucleotidase, and phosphatase K00974 cca; tRNA nucleotidyltransferase (CCA-adding enzyme) [EC:2.7.7.72 3.1.3.- 3.1.4.-]
B tRNA spricing factors
C tRNA splicing endonuclease complex
C tRNA splicing ligase complex
C Other tRNA splicing factors
B tRNA transport factors
C tRNA export factors
C tRNA import factors
B Aminoacyl-tRNA synthetases (AARSs)
C Multi-aminoacyl-tRNA synthetase complex (MSC)
D Dda3937_03502 gltX; glutamyl-tRNA synthetase K01885 EARS; glutamyl-tRNA synthetase [EC:6.1.1.17]
D Dda3937_03912 proS; prolyl-tRNA synthetase K01881 PARS; prolyl-tRNA synthetase [EC:6.1.1.15]
D Dda3937_01396 ileS; isoleucyl-tRNA synthetase K01870 IARS; isoleucyl-tRNA synthetase [EC:6.1.1.5]
D Dda3937_02477 leuS; leucyl-tRNA synthetase K01869 LARS; leucyl-tRNA synthetase [EC:6.1.1.4]
D Dda3937_03935 metG; methionyl-tRNA synthetase K01874 MARS; methionyl-tRNA synthetase [EC:6.1.1.10]
D Dda3937_01562 glnS; glutamyl-tRNA synthetase K01886 QARS; glutaminyl-tRNA synthetase [EC:6.1.1.18]
D Dda3937_01606 argS; arginyl-tRNA synthetase K01887 RARS; arginyl-tRNA synthetase [EC:6.1.1.19]
D Dda3937_02292 lysS; Lysyl-tRNA synthetase (class II) K04567 KARS; lysyl-tRNA synthetase, class II [EC:6.1.1.6]
D Dda3937_01616 aspS; aspartyl-tRNA synthetase K01876 DARS2; aspartyl-tRNA synthetase [EC:6.1.1.12]
C Other AARSs
D Dda3937_03152 alaS; alanyl-tRNA synthetase K01872 AARS; alanyl-tRNA synthetase [EC:6.1.1.7]
D Dda3937_03662 asnS; Asparaginyl-tRNA synthetase K01893 NARS; asparaginyl-tRNA synthetase [EC:6.1.1.22]
D Dda3937_03683 thrS; threonyl-tRNA synthetase K01868 TARS; threonyl-tRNA synthetase [EC:6.1.1.3]
D Dda3937_00132 serS; seryl-tRNA synthetase, also charges selenocysteinyl-tRNA with serine K01875 SARS; seryl-tRNA synthetase [EC:6.1.1.11]
D Dda3937_01678 cysS; cysteinyl-tRNA synthetase K01883 CARS; cysteinyl-tRNA synthetase [EC:6.1.1.16]
D Dda3937_01296 valS; valyl-tRNA synthetase K01873 VARS; valyl-tRNA synthetase [EC:6.1.1.9]
D Dda3937_03706 hisS; histidyl tRNA synthetase K01892 HARS; histidyl-tRNA synthetase [EC:6.1.1.21]
D Dda3937_03679 pheS; phenylalanine tRNA synthetase, alpha subunit K01889 FARSA; phenylalanyl-tRNA synthetase alpha chain [EC:6.1.1.20]
D Dda3937_03678 pheT; phenylalanine tRNA synthetase, beta subunit K01890 FARSB; phenylalanyl-tRNA synthetase beta chain [EC:6.1.1.20]
D Dda3937_00065 tyrS; tyrosyl-tRNA synthetase K01866 YARS; tyrosyl-tRNA synthetase [EC:6.1.1.1]
D Dda3937_04188 trpS; tryptophan-tRNA ligase K01867 WARS; tryptophanyl-tRNA synthetase [EC:6.1.1.2]
C Trans-editing factors
D Dda3937_01121 dtd; D-Tyr-tRNA(Tyr) deacylase K07560 dtd; D-aminoacyl-tRNA deacylase [EC:3.1.1.96]
C AARS associated factors
D Dda3937_02254 hinT; purine nucleoside phosphoramidase K02503 HINT1_2; histidine triad (HIT) family protein [EC:3.9.1.-]
B tRNA modification factors
C Deaminases
C Dihydorouridine synthases
C Methylthiotransferase
C Methyltransferases
D Dda3937_03398 yggH; tRNA (m7G46) methyltransferase, SAM-dependent K03439 trmB; tRNA (guanine-N7-)-methyltransferase [EC:2.1.1.33]
D Dda3937_03913 yaeB; conserved protein K22900 TRMO; tRNA (adenine37-N6)-methyltransferase [EC:2.1.1.-]
C Psudouridine synthases
D Dda3937_02105 truA; tRNA pseudouridine synthase A K06173 truA; tRNA pseudouridine38-40 synthase [EC:5.4.99.12]
D Dda3937_02339 truB; tRNA U55 pseudouridine synthase K03177 truB; tRNA pseudouridine55 synthase [EC:5.4.99.25]
D Dda3937_03908 truD; tRNA(Glu) U13 pseudouridine synthase K06176 truD; tRNA pseudouridine13 synthase [EC:5.4.99.27]
C Thiolation factors
D Dda3937_02172 nifS; Cysteine desulfurase K04487 iscS; cysteine desulfurase [EC:2.8.1.7]
D Dda3937_04379 iscS; Cysteine desulfurase K04487 iscS; cysteine desulfurase [EC:2.8.1.7]
C KEOPS/EKC complex
C Elongator complex
C Elongator related proteins
C Other tRNA modification factors
D Dda3937_01527 rimN; tRNA (ANN) t(6)A37 threonylcarbamoyladenosine biosynthesis protein K07566 tsaC; L-threonylcarbamoyladenylate synthase [EC:2.7.7.87]
D Dda3937_00435 miaA; delta(2)-isopentenylpyrophosphate tRNA-adenosine transferase K00791 miaA; tRNA dimethylallyltransferase [EC:2.5.1.75]
D Dda3937_01064 mnmE; 5-methylaminomethyl-2-thiouridine-synthesizing GTPase K03650 mnmE; tRNA modification GTPase [EC:3.6.-.-]
D Dda3937_00154 gidA; glucose-inhibited cell-division protein K03495 gidA; tRNA uridine 5-carboxymethylaminomethyl modification enzyme
B tRNA degradation factors
C TRAMP complex
C Rapid tRNA decay (RTD) pathway factors
D Dda3937_00161 cysQ; PAPS (adenosine 3'-phosphate 5'-phosphosulfate) 3'(2'),5'-bisphosphate nucleotidase K01082 cysQ; 3'(2'), 5'-bisphosphate nucleotidase [EC:3.1.3.7]
C Other tRNA degradation factors
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AProkaryotic type
B 5'processing factors
C Ribonucrease P
D Dda3937_01061 rnpA; protein C5 component of RNase P K03536 rnpA; ribonuclease P protein component [EC:3.1.26.5]
D Dda3937_04682 rnpB; RNase P, RNA component; M1 RNA K01978 rnpB; M1 RNA
B 3'processing and CCA adding factors
C 3'processing factors
D Dda3937_01051 elaC; Ribonuclease Z K00784 rnz; ribonuclease Z [EC:3.1.26.11]
D Dda3937_00092 rnt; ribonuclease T (RNase T) K03683 rnt; ribonuclease T [EC:3.1.13.-]
D Dda3937_03257 rph; ribonuclease PH K00989 rph; ribonuclease PH [EC:2.7.7.56]
D Dda3937_03104 rnb; ribonuclease II K01147 rnb; exoribonuclease II [EC:3.1.13.1]
D Dda3937_02918 rnd; ribonuclease D K03684 rnd; ribonuclease D [EC:3.1.13.5]
D Dda3937_00013 Ribonuclease K01166 RNASET2; ribonuclease T2 [EC:4.6.1.19]
C CCA adding factors
D Dda3937_00174 cca; multifunctional tRNA nucleotidyl transferase, 2'3'-cyclic phosphodiesterase, 2'-nucleotidase, and phosphatase K00974 cca; tRNA nucleotidyltransferase (CCA-adding enzyme) [EC:2.7.7.72 3.1.3.- 3.1.4.-]
B tRNA spricing factors
C tRNA splicing endonucleases
C tRNA splicing ligases
C Other tRNA splicing factors
D Dda3937_00508 ligT; 2'-5' RNA ligase K01975 thpR; RNA 2',3'-cyclic 3'-phosphodiesterase [EC:3.1.4.58]
B tRNA transport factors
C tRNA export factors
D Dda3937_00403 yjjK; ABC transporter ATP-binding protein yjjK K06020 ettA; energy-dependent translational throttle protein EttA
B Aminoacyl-tRNA synthetases (AARSs)
C Multi-aminoacyl-tRNA synthetase complex (MSC)
D Dda3937_02477 leuS; leucyl-tRNA synthetase K01869 LARS; leucyl-tRNA synthetase [EC:6.1.1.4]
D Dda3937_03912 proS; prolyl-tRNA synthetase K01881 PARS; prolyl-tRNA synthetase [EC:6.1.1.15]
C Other AARSs
D Dda3937_00065 tyrS; tyrosyl-tRNA synthetase K01866 YARS; tyrosyl-tRNA synthetase [EC:6.1.1.1]
D Dda3937_04188 trpS; tryptophan-tRNA ligase K01867 WARS; tryptophanyl-tRNA synthetase [EC:6.1.1.2]
D Dda3937_03683 thrS; threonyl-tRNA synthetase K01868 TARS; threonyl-tRNA synthetase [EC:6.1.1.3]
D Dda3937_01396 ileS; isoleucyl-tRNA synthetase K01870 IARS; isoleucyl-tRNA synthetase [EC:6.1.1.5]
D Dda3937_02292 lysS; Lysyl-tRNA synthetase (class II) K04567 KARS; lysyl-tRNA synthetase, class II [EC:6.1.1.6]
D Dda3937_03152 alaS; alanyl-tRNA synthetase K01872 AARS; alanyl-tRNA synthetase [EC:6.1.1.7]
D Dda3937_01296 valS; valyl-tRNA synthetase K01873 VARS; valyl-tRNA synthetase [EC:6.1.1.9]
D Dda3937_03935 metG; methionyl-tRNA synthetase K01874 MARS; methionyl-tRNA synthetase [EC:6.1.1.10]
D Dda3937_00132 serS; seryl-tRNA synthetase, also charges selenocysteinyl-tRNA with serine K01875 SARS; seryl-tRNA synthetase [EC:6.1.1.11]
D Dda3937_01616 aspS; aspartyl-tRNA synthetase K01876 DARS2; aspartyl-tRNA synthetase [EC:6.1.1.12]
D Dda3937_01011 glyQ; glycine tRNA synthetase, alpha subunit K01878 glyQ; glycyl-tRNA synthetase alpha chain [EC:6.1.1.14]
D Dda3937_01010 glyS; glycine tRNA synthetase, beta subunit K01879 glyS; glycyl-tRNA synthetase beta chain [EC:6.1.1.14]
D Dda3937_01678 cysS; cysteinyl-tRNA synthetase K01883 CARS; cysteinyl-tRNA synthetase [EC:6.1.1.16]
D Dda3937_03502 gltX; glutamyl-tRNA synthetase K01885 EARS; glutamyl-tRNA synthetase [EC:6.1.1.17]
D Dda3937_01562 glnS; glutamyl-tRNA synthetase K01886 QARS; glutaminyl-tRNA synthetase [EC:6.1.1.18]
D Dda3937_01606 argS; arginyl-tRNA synthetase K01887 RARS; arginyl-tRNA synthetase [EC:6.1.1.19]
D Dda3937_03679 pheS; phenylalanine tRNA synthetase, alpha subunit K01889 FARSA; phenylalanyl-tRNA synthetase alpha chain [EC:6.1.1.20]
D Dda3937_03678 pheT; phenylalanine tRNA synthetase, beta subunit K01890 FARSB; phenylalanyl-tRNA synthetase beta chain [EC:6.1.1.20]
D Dda3937_03706 hisS; histidyl tRNA synthetase K01892 HARS; histidyl-tRNA synthetase [EC:6.1.1.21]
D Dda3937_03662 asnS; Asparaginyl-tRNA synthetase K01893 NARS; asparaginyl-tRNA synthetase [EC:6.1.1.22]
D Dda3937_00511 yadB; glutamyl-Q tRNA(Asp) synthetase K01894 gluQ; glutamyl-Q tRNA(Asp) synthetase [EC:6.1.1.-]
C Trans-editing factors
D Dda3937_01121 dtd; D-Tyr-tRNA(Tyr) deacylase K07560 dtd; D-aminoacyl-tRNA deacylase [EC:3.1.1.96]
D Dda3937_04156 ybaK; bifunctional cys-tRNA Pro deacetylase/cys-tRNA Cys deacylase K03976 ybaK; Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase [EC:3.1.1.-]
D Dda3937_02426 Putative cytoplasmic protein K19055 prdX; Ala-tRNA(Pro) deacylase [EC:3.1.1.-]
B tRNA modification factors
C Deaminases
D Dda3937_03381 tadA; tRNA-specific adenosine-34 deaminase K11991 tadA; tRNA(adenine34) deaminase [EC:3.5.4.33]
C Dihydorouridine synthases
D Dda3937_03441 dusA; tRNA dihydrouridine synthase A K05539 dusA; tRNA-dihydrouridine synthase A [EC:1.-.-.-]
D Dda3937_01596 dusB; tRNA-dihydrouridine synthase B K05540 dusB; tRNA-dihydrouridine synthase B [EC:1.-.-.-]
D Dda3937_02904 dusC; tRNA-dihydrouridine synthase C K05541 dusC; tRNA-dihydrouridine synthase C [EC:1.-.-.-]
C Methylthiotransferases
D Dda3937_02467 miaB; isopentenyl-adenosine A37 tRNA methylthiolase K06168 miaB; tRNA-2-methylthio-N6-dimethylallyladenosine synthase [EC:2.8.4.3]
C Methyltransferases
D Dda3937_01611 cmoA; tRNA methyltransferase, S-adenosyl-L-methionine-dependent methyltransferase K15256 cmoA; tRNA (cmo5U34)-methyltransferase [EC:2.1.1.-]
D Dda3937_01610 cmoB; tRNA methyltransferase, S-adenosyl-L-methionine-dependent methyltransferase K15257 cmoB; tRNA (mo5U34)-methyltransferase [EC:2.1.1.-]
D Dda3937_03198 smtA; predicted S-adenosyl-L-methionine-dependent methyltransferase K06219 smtA; tRNA 5-carboxymethoxyuridine methyltransferase [EC:2.1.1.-]
D Dda3937_00395 RNA methyltransferase, TrmH family, group 1 K02533 lasT; tRNA/rRNA methyltransferase [EC:2.1.1.-]
D Dda3937_03896 trmA; tRNA (uracil-5-)-methyltransferase K00557 trmA; tRNA (uracil-5-)-methyltransferase [EC:2.1.1.35]
D Dda3937_03398 yggH; tRNA (m7G46) methyltransferase, SAM-dependent K03439 trmB; tRNA (guanine-N7-)-methyltransferase [EC:2.1.1.33]
D Dda3937_03947 trmD; tRNA (guanine-1-)-methyltransferase K00554 trmD; tRNA (guanine37-N1)-methyltransferase [EC:2.1.1.228]
D Dda3937_01064 mnmE; 5-methylaminomethyl-2-thiouridine-synthesizing GTPase K03650 mnmE; tRNA modification GTPase [EC:3.6.-.-]
D Dda3937_00891 yfiF; predicted methyltransferase K03214 yfiF; RNA methyltransferase, TrmH family [EC:2.1.1.-]
D Dda3937_01126 trmH; tRNA (Guanosine-2'-O-)-methyltransferase K00556 trmH; tRNA (guanosine-2'-O-)-methyltransferase [EC:2.1.1.34]
D Dda3937_02375 trmJ; tRNA:Cm32/Um32 methyltransferase K15396 trmJ; tRNA (cytidine32/uridine32-2'-O)-methyltransferase [EC:2.1.1.200]
D Dda3937_03048 yibK; predicted rRNA methylase K03216 trmL; tRNA (cytidine/uridine-2'-O-)-methyltransferase [EC:2.1.1.207]
D Dda3937_03913 yaeB; conserved protein K22900 TRMO; tRNA (adenine37-N6)-methyltransferase [EC:2.1.1.-]
D Dda3937_03842 yfiC; predicted S-adenosyl-L-methionine-dependent methyltransferase K15460 yfiC; tRNA1Val (adenine37-N6)-methyltransferase [EC:2.1.1.223]
C Psudouridine synthases
D Dda3937_02105 truA; tRNA pseudouridine synthase A K06173 truA; tRNA pseudouridine38-40 synthase [EC:5.4.99.12]
D Dda3937_02339 truB; tRNA U55 pseudouridine synthase K03177 truB; tRNA pseudouridine55 synthase [EC:5.4.99.25]
D Dda3937_00873 truC; tRNA pseudouridine synthase K06175 truC; tRNA pseudouridine65 synthase [EC:5.4.99.26]
D Dda3937_03908 truD; tRNA(Glu) U13 pseudouridine synthase K06176 truD; tRNA pseudouridine13 synthase [EC:5.4.99.27]
D Dda3937_01375 rluA; Ribosomal large subunit pseudouridine synthase A K06177 rluA; tRNA pseudouridine32 synthase / 23S rRNA pseudouridine746 synthase [EC:5.4.99.28 5.4.99.29]
C Thiolation factors
D Dda3937_02085 mnmA; tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase K00566 mnmA; tRNA-uridine 2-sulfurtransferase [EC:2.8.1.13]
D Dda3937_03138 ttcA; putative tRNA 2-thiocytidine (s(2)C32) synthase K14058 ttcA; tRNA 2-thiocytidine biosynthesis protein TtcA
D Dda3937_02007 sirA; sulfur transfer protein K04085 tusA; tRNA 2-thiouridine synthesizing protein A [EC:2.8.1.-]
D Dda3937_00521 yheL; subunit of the heterohexameric YheLMN (TusBCD) mediator of sulfur relay K07237 tusB; tRNA 2-thiouridine synthesizing protein B
D Dda3937_00522 yheM; subunit of the heterohexameric YheLMN (TusBCD) mediator of sulfur relay K07236 tusC; tRNA 2-thiouridine synthesizing protein C
D Dda3937_00523 yheN; tRNA 2-thiouridine synthesizing protein, subunit of sulfur transfer complex, TusD K07235 tusD; tRNA 2-thiouridine synthesizing protein D [EC:2.8.1.-]
D Dda3937_01699 yccK; sulfur transfer protein K11179 tusE; tRNA 2-thiouridine synthesizing protein E [EC:2.8.1.-]
D Dda3937_03691 iscA; FeS cluster assembly protein K13628 iscA; iron-sulfur cluster assembly protein
D Dda3937_02172 nifS; Cysteine desulfurase K04487 iscS; cysteine desulfurase [EC:2.8.1.7]
D Dda3937_04379 iscS; Cysteine desulfurase K04487 iscS; cysteine desulfurase [EC:2.8.1.7]
D Dda3937_02302 ygfZ; predicted folate-dependent regulatory protein K06980 ygfZ; tRNA-modifying protein YgfZ
C KEOPS/EKC complex
C Other tRNA modification factors
D Dda3937_00154 gidA; glucose-inhibited cell-division protein K03495 gidA; tRNA uridine 5-carboxymethylaminomethyl modification enzyme
D Dda3937_00435 miaA; delta(2)-isopentenylpyrophosphate tRNA-adenosine transferase K00791 miaA; tRNA dimethylallyltransferase [EC:2.5.1.75]
D Dda3937_03294 tRNA-(MS[2]IO[6]A)-hydroxylase K06169 miaE; tRNA 2-(methylsulfanyl)-N6-isopentenyladenosine37 hydroxylase [EC:1.14.99.69]
D Dda3937_02116 mnmC; bifunctional 5-carboxymethylamino-methyl-2-thiouridine oxidoreductase/5-aminomethyl-2-thiouridine methylase K15461 mnmC; tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein [EC:2.1.1.61 1.5.-.-]
D Dda3937_01947 queA; S-adenosylmethionine:tRNA ribosyltransferase-isomerase K07568 queA; S-adenosylmethionine:tRNA ribosyltransferase-isomerase [EC:2.4.99.17]
D Dda3937_03314 queC; enzyme in preQ0 biosynthesis K06920 queC; 7-cyano-7-deazaguanine synthase [EC:6.3.4.20]
D Dda3937_00205 ygcM; 6-carboxy-5,6,7,8-tetrahydropterin synthase K01737 queD; 6-pyruvoyltetrahydropterin/6-carboxytetrahydropterin synthase [EC:4.2.3.12 4.1.2.50]
D Dda3937_00204 ygcF; conserved protein K10026 queE; 7-carboxy-7-deazaguanine synthase [EC:4.3.99.3]
D Dda3937_01462 queF; NADPH dependent preQ0 reductase K06879 queF; 7-cyano-7-deazaguanine reductase [EC:1.7.1.13]
D Dda3937_00441 yjeS; predicted Fe-S electron transport protein K18979 queG; epoxyqueuosine reductase [EC:1.17.99.6]
D Dda3937_02900 hypothetical protein K09765 queH; epoxyqueuosine reductase [EC:1.17.99.6]
D Dda3937_01948 tgt; tRNA-guanine transglycosylase K00773 tgt; queuine tRNA-ribosyltransferase [EC:2.4.2.29]
D Dda3937_01963 thiI; sulfur transfer protein K03151 thiI; tRNA uracil 4-sulfurtransferase [EC:2.8.1.4]
D Dda3937_01894 tilS; tRNA(Ile)-lysidine synthetase K04075 tilS; tRNA(Ile)-lysidine synthase [EC:6.3.4.19]
D Dda3937_02503 ypfI; predicted hydrolase K06957 tmcA; tRNA(Met) cytidine acetyltransferase [EC:2.3.1.193]
D Dda3937_03715 yeaZ; predicted peptidase K14742 tsaB; tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
D Dda3937_01527 rimN; tRNA (ANN) t(6)A37 threonylcarbamoyladenosine biosynthesis protein K07566 tsaC; L-threonylcarbamoyladenylate synthase [EC:2.7.7.87]
D Dda3937_03531 ygjD; predicted peptidase K25706 tsaD; tRNA N6-adenosine threonylcarbamoyltransferase [EC:2.3.1.234]
D Dda3937_00438 yjeE; ATPase with strong ADP affinity K06925 tsaE; tRNA threonylcarbamoyladenosine biosynthesis protein TsaE
D Dda3937_00863 ygdL; conserved protein K22132 tcdA; tRNA threonylcarbamoyladenosine dehydratase
B tRNA degradation factors
C Dda3937_02609 rnr; exoribonuclease R, RNase R K12573 rnr; ribonuclease R [EC:3.1.13.1]
C Dda3937_02337 pnp; polynucleotide phosphorylase/polyadenylase K00962 pnp; polyribonucleotide nucleotidyltransferase [EC:2.7.7.8]
C Dda3937_02403 virulence associated protein C K18828 mvpA; tRNA(fMet)-specific endonuclease VapC [EC:3.1.-.-]
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#[ BRITE | KEGG2 | KEGG ]
#Last updated: February 29, 2024