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Conserved domains on  [gi|922581118|ref|NP_001300129|]
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tRNA (uracil(54)-C(5))-methyltransferase [Caenorhabditis elegans]

Protein Classification

class I SAM-dependent RNA methyltransferase( domain architecture ID 1903519)

class I SAM-dependent RNA methyltransferase catalyzes the methylation of a specific RNA substrate using S-adenosyl-L-methionine (SAM or AdoMet) as the methyl donor

CATH:  2.20.25.110
EC:  2.1.1.-
Gene Ontology:  GO:0008173|GO:1904047
PubMed:  12504684|12826405
SCOP:  3000118

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TrmA super family cl43665
tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure ...
 2-127 1.29e-24

tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family is part of the Pathway/BioSystem: tRNA modification


The actual alignment was detected with superfamily member COG2265:

Pssm-ID: 441866 [Multi-domain]  Cd Length: 377  Bit Score: 96.40  E-value: 1.29e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922581118   2 IAEAVEDAKQNAKQNKMETCcKYIAGKAEDTFRSMRYHlpNGFDlrksrVVgVLDPPRAGMHEKVilaCREMETM--RRL 79
Cdd:COG2265  264 VPEAVEDARENARLNGLKNV-EFVAGDLEEVLPELLWG--GRPD-----VV-VLDPPRAGAGPEV---LEALAALgpRRI 331

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 922581118  80 IFVSCEP-----NAAIsnivnLCrpsSRKYTgdafsVTRVQPVDMFPQTNHME 127
Cdd:COG2265  332 VYVSCNPatlarDLAL-----LV---EGGYR-----LEKVQPVDMFPHTHHVE 371
 
Name Accession Description Interval E-value
TrmA COG2265
tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure ...
 2-127 1.29e-24

tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441866 [Multi-domain]  Cd Length: 377  Bit Score: 96.40  E-value: 1.29e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922581118   2 IAEAVEDAKQNAKQNKMETCcKYIAGKAEDTFRSMRYHlpNGFDlrksrVVgVLDPPRAGMHEKVilaCREMETM--RRL 79
Cdd:COG2265  264 VPEAVEDARENARLNGLKNV-EFVAGDLEEVLPELLWG--GRPD-----VV-VLDPPRAGAGPEV---LEALAALgpRRI 331

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 922581118  80 IFVSCEP-----NAAIsnivnLCrpsSRKYTgdafsVTRVQPVDMFPQTNHME 127
Cdd:COG2265  332 VYVSCNPatlarDLAL-----LV---EGGYR-----LEKVQPVDMFPHTHHVE 371
rumA TIGR00479
23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA ...
 2-127 1.76e-18

23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 129571 [Multi-domain]  Cd Length: 431  Bit Score: 79.87  E-value: 1.76e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922581118    2 IAEAVEDAKQNAKQNKMETCcKYIAGKAEDTFRSMrYHLPNGFDlrksrvVGVLDPPRAGMHEKVILACREMETmRRLIF 81
Cdd:TIGR00479 323 VPESVEKAQQNAELNGIANV-TFYHGTLETVLPKQ-PWAGNGFD------KVLLDPPRKGCAAGVLRTIIKLKP-ERIVY 393

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 922581118   82 VSCEPNAAISNIVNLCRpssrkytgDAFSVTRVQPVDMFPQTNHME 127
Cdd:TIGR00479 394 VSCNPATLARDLEALCK--------AGYTIARVQPVDMFPHTGHVE 431
rumA PRK13168
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD;
3-127 5.99e-07

23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD;


Pssm-ID: 237291 [Multi-domain]  Cd Length: 443  Bit Score: 47.07  E-value: 5.99e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922581118   3 AEAVEDAKQNAKQNKMETCCKYIAGKAEDTFRSMRyhLPNGFDlrksRVVgvLDPPRAGMHEkvilACREMETM--RRLI 80
Cdd:PRK13168 329 EAMVERARENARRNGLDNVTFYHANLEEDFTDQPW--ALGGFD----KVL--LDPPRAGAAE----VMQALAKLgpKRIV 396

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 922581118  81 FVSCEPnaaisniVNLCRpssrkytgDA-------FSVTRVQPVDMFPQTNHME 127
Cdd:PRK13168 397 YVSCNP-------ATLAR--------DAgvlveagYRLKRAGMLDMFPHTGHVE 435
tRNA_U5-meth_tr pfam05958
tRNA (Uracil-5-)-methyltransferase; This family consists of (Uracil-5-)-methyltransferases EC: ...
 56-127 5.48e-06

tRNA (Uracil-5-)-methyltransferase; This family consists of (Uracil-5-)-methyltransferases EC:2.1.1.35 from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalyzed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity.


Pssm-ID: 428692  Cd Length: 357  Bit Score: 43.97  E-value: 5.48e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 922581118   56 DPPRAGMHEKVILACREMEtmrRLIFVSCEPNAAISNIVNLcrpssrkytGDAFSVTRVQPVDMFPQTNHME 127
Cdd:pfam05958 290 DPPRAGLDPETLKLVQAYP---RILYISCNPETLCANLEQL---------SKTHRVERFALFDQFPYTHHME 349
 
Name Accession Description Interval E-value
TrmA COG2265
tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure ...
 2-127 1.29e-24

tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441866 [Multi-domain]  Cd Length: 377  Bit Score: 96.40  E-value: 1.29e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922581118   2 IAEAVEDAKQNAKQNKMETCcKYIAGKAEDTFRSMRYHlpNGFDlrksrVVgVLDPPRAGMHEKVilaCREMETM--RRL 79
Cdd:COG2265  264 VPEAVEDARENARLNGLKNV-EFVAGDLEEVLPELLWG--GRPD-----VV-VLDPPRAGAGPEV---LEALAALgpRRI 331

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 922581118  80 IFVSCEP-----NAAIsnivnLCrpsSRKYTgdafsVTRVQPVDMFPQTNHME 127
Cdd:COG2265  332 VYVSCNPatlarDLAL-----LV---EGGYR-----LEKVQPVDMFPHTHHVE 371
rumA TIGR00479
23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA ...
 2-127 1.76e-18

23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 129571 [Multi-domain]  Cd Length: 431  Bit Score: 79.87  E-value: 1.76e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922581118    2 IAEAVEDAKQNAKQNKMETCcKYIAGKAEDTFRSMrYHLPNGFDlrksrvVGVLDPPRAGMHEKVILACREMETmRRLIF 81
Cdd:TIGR00479 323 VPESVEKAQQNAELNGIANV-TFYHGTLETVLPKQ-PWAGNGFD------KVLLDPPRKGCAAGVLRTIIKLKP-ERIVY 393

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 922581118   82 VSCEPNAAISNIVNLCRpssrkytgDAFSVTRVQPVDMFPQTNHME 127
Cdd:TIGR00479 394 VSCNPATLARDLEALCK--------AGYTIARVQPVDMFPHTGHVE 431
rumA PRK13168
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD;
3-127 5.99e-07

23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD;


Pssm-ID: 237291 [Multi-domain]  Cd Length: 443  Bit Score: 47.07  E-value: 5.99e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922581118   3 AEAVEDAKQNAKQNKMETCCKYIAGKAEDTFRSMRyhLPNGFDlrksRVVgvLDPPRAGMHEkvilACREMETM--RRLI 80
Cdd:PRK13168 329 EAMVERARENARRNGLDNVTFYHANLEEDFTDQPW--ALGGFD----KVL--LDPPRAGAAE----VMQALAKLgpKRIV 396

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 922581118  81 FVSCEPnaaisniVNLCRpssrkytgDA-------FSVTRVQPVDMFPQTNHME 127
Cdd:PRK13168 397 YVSCNP-------ATLAR--------DAgvlveagYRLKRAGMLDMFPHTGHVE 435
PRK05031 PRK05031
tRNA (uracil-5-)-methyltransferase; Validated
 5-127 2.99e-06

tRNA (uracil-5-)-methyltransferase; Validated


Pssm-ID: 235332  Cd Length: 362  Bit Score: 44.82  E-value: 2.99e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 922581118   5 AVEDAKQNAKQNKMETCcKYIAGKAED---------TFRSMRyhlpnGFDLRKSRVVGVL-DPPRAGMHEKVILACREME 74
Cdd:PRK05031 240 SVAAAQYNIAANGIDNV-QIIRMSAEEftqamngvrEFNRLK-----GIDLKSYNFSTIFvDPPRAGLDDETLKLVQAYE 313

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 922581118  75 tmrRLIFVSCEPNAAISNIVNLCrpssrkytgDAFSVTRVQPVDMFPQTNHME 127
Cdd:PRK05031 314 ---RILYISCNPETLCENLETLS---------QTHKVERFALFDQFPYTHHME 354
tRNA_U5-meth_tr pfam05958
tRNA (Uracil-5-)-methyltransferase; This family consists of (Uracil-5-)-methyltransferases EC: ...
 56-127 5.48e-06

tRNA (Uracil-5-)-methyltransferase; This family consists of (Uracil-5-)-methyltransferases EC:2.1.1.35 from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalyzed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity.


Pssm-ID: 428692  Cd Length: 357  Bit Score: 43.97  E-value: 5.48e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 922581118   56 DPPRAGMHEKVILACREMEtmrRLIFVSCEPNAAISNIVNLcrpssrkytGDAFSVTRVQPVDMFPQTNHME 127
Cdd:pfam05958 290 DPPRAGLDPETLKLVQAYP---RILYISCNPETLCANLEQL---------SKTHRVERFALFDQFPYTHHME 349
rumB PRK03522
23S rRNA (uracil(747)-C(5))-methyltransferase RlmC;
54-127 1.16e-04

23S rRNA (uracil(747)-C(5))-methyltransferase RlmC;


Pssm-ID: 235128 [Multi-domain]  Cd Length: 315  Bit Score: 40.24  E-value: 1.16e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 922581118  54 VLDPPRAGMHEKVilaCREMETM--RRLIFVSCEPNAAISNIVNLcrPSSRkytgdafsVTRVQPVDMFPQTNHME 127
Cdd:PRK03522 245 LVNPPRRGIGKEL---CDYLSQMapRFILYSSCNAQTMAKDLAHL--PGYR--------IERVQLFDMFPHTAHYE 307
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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