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Conserved domains on  [gi|6323638|ref|NP_013709|]
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tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase [Saccharomyces cerevisiae S288C]

Protein Classification

class I SAM-dependent methyltransferase family protein( domain architecture ID 1001310)

class I SAM-dependent methyltransferase family protein that catalyzes the transfer of the methyl or the alpha-amino-alpha-carboxypropyl (acp) group from S-adenosyl-L-methionine (SAM or AdoMet) to one or more specific substrates; similar to tRNA (guanine(37)-N1)-methyltransferase and tRNA wybutosine-synthesizing protein 2 homolog

CATH:  3.40.50.150|3.30.300.110
EC:  2.-.-.-
Gene Ontology:  GO:0008175|GO:0030488
PubMed:  12826405|12504684

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Trm5 super family cl34477
tRNA G37 N-methylase Trm5 [Translation, ribosomal structure and biogenesis]; tRNA G37 ...
 255-459 1.32e-13

tRNA G37 N-methylase Trm5 [Translation, ribosomal structure and biogenesis]; tRNA G37 N-methylase Trm5 is part of the Pathway/BioSystem: tRNA modification


The actual alignment was detected with superfamily member COG2520:

Pssm-ID: 442010 [Multi-domain]  Cd Length: 333  Bit Score: 71.43  E-value: 1.32e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323638  255 MFSRGNIKEKKRVLTtfpDICNND-VVDLYAGIGYFTFSYLTKGARTLFAFELNPWSVEGLKRGLKANGFNKS-----GN 328
Cdd:COG2520 162 YFSPRLATERLRIAE---LVKPGErVLDMFAGVGPFSIPIAKRSGAKVVAIDINPDAVEYLKENIRLNKVEDRvtpilGD 238

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323638  329 CHVFQESNEMCVQRlteflsqnpgfrlrirhINLGLLPSSKQGWPLAIKLiylqgasLEKVTM-HIHENVHidaiEDGSF 407
Cdd:COG2520 239 AREVAPELEGKADR-----------------IIMNLPHSADEFLDAALRA-------LKPGGViHYYEIVP----EEDPF 290

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|..
gi 6323638  408 EKnviveldAINESIALIRNRGIKLQFVRSKleRIKTFAPDIWHVCVDVDVI 459
Cdd:COG2520 291 ER-------AEERIEEAAEEAGYEVEILEKR--RVKSYSPGVYHVVVDVRVS 333
 
Name Accession Description Interval E-value
Trm5 COG2520
tRNA G37 N-methylase Trm5 [Translation, ribosomal structure and biogenesis]; tRNA G37 ...
 255-459 1.32e-13

tRNA G37 N-methylase Trm5 [Translation, ribosomal structure and biogenesis]; tRNA G37 N-methylase Trm5 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 442010 [Multi-domain]  Cd Length: 333  Bit Score: 71.43  E-value: 1.32e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323638  255 MFSRGNIKEKKRVLTtfpDICNND-VVDLYAGIGYFTFSYLTKGARTLFAFELNPWSVEGLKRGLKANGFNKS-----GN 328
Cdd:COG2520 162 YFSPRLATERLRIAE---LVKPGErVLDMFAGVGPFSIPIAKRSGAKVVAIDINPDAVEYLKENIRLNKVEDRvtpilGD 238

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323638  329 CHVFQESNEMCVQRlteflsqnpgfrlrirhINLGLLPSSKQGWPLAIKLiylqgasLEKVTM-HIHENVHidaiEDGSF 407
Cdd:COG2520 239 AREVAPELEGKADR-----------------IIMNLPHSADEFLDAALRA-------LKPGGViHYYEIVP----EEDPF 290

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|..
gi 6323638  408 EKnviveldAINESIALIRNRGIKLQFVRSKleRIKTFAPDIWHVCVDVDVI 459
Cdd:COG2520 291 ER-------AEERIEEAAEEAGYEVEILEKR--RVKSYSPGVYHVVVDVRVS 333
Met_10 pfam02475
Met-10+ like-protein; The methionine-10 mutant allele of N. crassa codes for a protein of ...
 255-321 1.46e-07

Met-10+ like-protein; The methionine-10 mutant allele of N. crassa codes for a protein of unknown function, Swiss:O27901. However, homologous proteins have been found in yeast suggesting this protein may be involved in methionine biosynthesis, transport and/or utilization.


Pssm-ID: 396850 [Multi-domain]  Cd Length: 198  Bit Score: 51.58  E-value: 1.46e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6323638    255 MFSRGNIKEKKRVLTTFPDicNNDVVDLYAGIGYFTFSYLTKG-ARTLFAFELNPWSVEGLKRGLKAN 321
Cdd:pfam02475  81 YWSPRLIAERERIAKLVEP--GEVVVDMFAGIGPFSIPIAKHSkARRVYAIELNPESYKYLKENIKLN 146
rumA TIGR00479
23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA ...
 279-345 3.26e-03

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: 39.80  E-value: 3.26e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 6323638    279 VVDLYAGIGYFTFsYLTKGARTLFAFELNPWSVEGLKRGLKANGFNksgNCHVFQESNEMCVQRLTE 345
Cdd:TIGR00479 296 VLDAYCGMGTFTL-PLAKQAKSVVGVEGVPESVEKAQQNAELNGIA---NVTFYHGTLETVLPKQPW 358
 
Name Accession Description Interval E-value
Trm5 COG2520
tRNA G37 N-methylase Trm5 [Translation, ribosomal structure and biogenesis]; tRNA G37 ...
 255-459 1.32e-13

tRNA G37 N-methylase Trm5 [Translation, ribosomal structure and biogenesis]; tRNA G37 N-methylase Trm5 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 442010 [Multi-domain]  Cd Length: 333  Bit Score: 71.43  E-value: 1.32e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323638  255 MFSRGNIKEKKRVLTtfpDICNND-VVDLYAGIGYFTFSYLTKGARTLFAFELNPWSVEGLKRGLKANGFNKS-----GN 328
Cdd:COG2520 162 YFSPRLATERLRIAE---LVKPGErVLDMFAGVGPFSIPIAKRSGAKVVAIDINPDAVEYLKENIRLNKVEDRvtpilGD 238

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323638  329 CHVFQESNEMCVQRlteflsqnpgfrlrirhINLGLLPSSKQGWPLAIKLiylqgasLEKVTM-HIHENVHidaiEDGSF 407
Cdd:COG2520 239 AREVAPELEGKADR-----------------IIMNLPHSADEFLDAALRA-------LKPGGViHYYEIVP----EEDPF 290

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|..
gi 6323638  408 EKnviveldAINESIALIRNRGIKLQFVRSKleRIKTFAPDIWHVCVDVDVI 459
Cdd:COG2520 291 ER-------AEERIEEAAEEAGYEVEILEKR--RVKSYSPGVYHVVVDVRVS 333
Met_10 pfam02475
Met-10+ like-protein; The methionine-10 mutant allele of N. crassa codes for a protein of ...
 255-321 1.46e-07

Met-10+ like-protein; The methionine-10 mutant allele of N. crassa codes for a protein of unknown function, Swiss:O27901. However, homologous proteins have been found in yeast suggesting this protein may be involved in methionine biosynthesis, transport and/or utilization.


Pssm-ID: 396850 [Multi-domain]  Cd Length: 198  Bit Score: 51.58  E-value: 1.46e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6323638    255 MFSRGNIKEKKRVLTTFPDicNNDVVDLYAGIGYFTFSYLTKG-ARTLFAFELNPWSVEGLKRGLKAN 321
Cdd:pfam02475  81 YWSPRLIAERERIAKLVEP--GEVVVDMFAGIGPFSIPIAKHSkARRVYAIELNPESYKYLKENIKLN 146
TrmA COG2265
tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure ...
 279-333 2.22e-04

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: 43.24  E-value: 2.22e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 6323638  279 VVDLYAGIGYFTFsYLTKGARTLFAFELNPWSVEGLKRGLKANGFNksgNCHVFQ 333
Cdd:COG2265 237 VLDLYCGVGTFAL-PLARRAKKVIGVEIVPEAVEDARENARLNGLK---NVEFVA 287
COG4076 COG4076
Predicted RNA methylase [General function prediction only];
279-331 7.24e-04

Predicted RNA methylase [General function prediction only];


Pssm-ID: 443253 [Multi-domain]  Cd Length: 230  Bit Score: 41.18  E-value: 7.24e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 6323638  279 VVDLYAGIGYFTFSYLTKGARTLFAFELNPWSVEGLKRGLKANGFnkSGNCHV 331
Cdd:COG4076  39 VLDIGTGSGLLSMLAARAGAKKVYAVEVNPDIAAVARRIIAANGL--SDRITV 89
rumA TIGR00479
23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA ...
 279-345 3.26e-03

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: 39.80  E-value: 3.26e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 6323638    279 VVDLYAGIGYFTFsYLTKGARTLFAFELNPWSVEGLKRGLKANGFNksgNCHVFQESNEMCVQRLTE 345
Cdd:TIGR00479 296 VLDAYCGMGTFTL-PLAKQAKSVVGVEGVPESVEKAQQNAELNGIA---NVTFYHGTLETVLPKQPW 358
 
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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