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Conserved domains on  [gi|218764490|gb|ACL06956|]
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protein of unknown function UPF0066 [Desulfatibacillum aliphaticivorans]

Protein Classification

SAM-dependent methyltransferase( domain architecture ID 10004381)

S-adenosylmethionine-dependent methyltransferase such as tRNA (adenine(37)-N6)-methyltransferase TrmO, which methylates position 37 (m(6)t(6)A37) to form N6-methyl-N6-threonylcarbamoyladenosine of the tRNA anticodon loop of tRNA(Thr)(GGU) that read codons starting with adenosine

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TrmO COG1720
tRNA (Thr-GGU) A37 N6-methylase [Translation, ribosomal structure and biogenesis]; tRNA ...
 1-150 6.56e-82

tRNA (Thr-GGU) A37 N6-methylase [Translation, ribosomal structure and biogenesis]; tRNA (Thr-GGU) A37 N6-methylase is part of the Pathway/BioSystem: tRNA modification


:

Pssm-ID: 441326  Cd Length: 152  Bit Score: 238.12  E-value: 6.56e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 218764490   1 MIQMNPIGTIHTPFKETQGMPIQPAGARGVEGALEVLPELAEGLKDVDGFSHVIILYHFHQSNGYTLRVTPFLDK-EERG 79
Cdd:COG1720    1 EITLRPIGVIRSPFKEKFGIPRQPRLAPGAEGEIELFPEYAEALRGLEGFSHLWLLYWFHRARRWRLTVRPRLGGnERRG 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 218764490  80 VFSTRAPKRPNPIGLSVVEVVKVEGNIVHVKNIDVLDGTPLLDIKPYVPKFDTPEFSRTGWLEEAQKNARK 150
Cdd:COG1720   81 VFATRSPHRPNPIGLSVVRLLGVEGNRLHVRGLDLLDGTPVLDIKPYVPYADAIPDARSGWAEEAPEELLA 151
 
Name Accession Description Interval E-value
TrmO COG1720
tRNA (Thr-GGU) A37 N6-methylase [Translation, ribosomal structure and biogenesis]; tRNA ...
 1-150 6.56e-82

tRNA (Thr-GGU) A37 N6-methylase [Translation, ribosomal structure and biogenesis]; tRNA (Thr-GGU) A37 N6-methylase is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441326  Cd Length: 152  Bit Score: 238.12  E-value: 6.56e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 218764490   1 MIQMNPIGTIHTPFKETQGMPIQPAGARGVEGALEVLPELAEGLKDVDGFSHVIILYHFHQSNGYTLRVTPFLDK-EERG 79
Cdd:COG1720    1 EITLRPIGVIRSPFKEKFGIPRQPRLAPGAEGEIELFPEYAEALRGLEGFSHLWLLYWFHRARRWRLTVRPRLGGnERRG 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 218764490  80 VFSTRAPKRPNPIGLSVVEVVKVEGNIVHVKNIDVLDGTPLLDIKPYVPKFDTPEFSRTGWLEEAQKNARK 150
Cdd:COG1720   81 VFATRSPHRPNPIGLSVVRLLGVEGNRLHVRGLDLLDGTPVLDIKPYVPYADAIPDARSGWAEEAPEELLA 151
TrmO pfam01980
tRNA-methyltransferase O; This family includes members such as TrmO (tRNA-methyltransferase O) ...
 19-131 9.88e-66

tRNA-methyltransferase O; This family includes members such as TrmO (tRNA-methyltransferase O) also known as YaeB, which contains a single-sheeted beta-barrel structure. TrmO is an AdoMet-dependent methyltransferase responsible for m6t6A formation. Its human homolog, is responsible for formation of m6t6A37 in cytoplasmic tRNASer. Lack of TrmO decreases attenuation activity of the thr operon, indicating that N6 methylation of m6t6A37 ensures efficient decoding of ACY codons. In bacteria and eukaryotes, TrmO has a C-terminal domain containing the conserved DPRxxY motif. Where the Asp194 and Arg196 in this motif of E. coli TrmO are necessary for N6-methylation. However, no archaeal YaeB has a C-terminal domain containing the DPRxxY motif that is conserved in bacterial and mammalian TrmO homologs.


Pssm-ID: 460402  Cd Length: 116  Bit Score: 195.69  E-value: 9.88e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 218764490   19 GMPIQPAGARGVEGALEVLPEL--AEGLKDVDGFSHVIILYHFHQSNGYTLRVTPFLDKEER-GVFSTRAPKRPNPIGLS 95
Cdd:pfam01980   1 GIPRQPGLAPDARGTIELFPEYnnAEALRGLEGFSHLWLLYWFHRNTGRPLVRPPRLGGNERvGVFATRSPFRPNPIGLS 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 218764490   96 VVEVVKVEGNIVHVKNIDVLDGTPLLDIKPYVPKFD 131
Cdd:pfam01980  81 VVKLLRVEGNVLHVSGVDLLDGTPVLDIKPYVPYAD 116
UPF0066 cd09281
Escherichia coli YaeB and related proteins; Uncharacterized protein family UPF0066. This ...
 6-126 1.53e-62

Escherichia coli YaeB and related proteins; Uncharacterized protein family UPF0066. This domain includes Escherichia coli YeaB, Archeoglobus fulgidus AF0241, and Agrobacterium tumefaciens VirR. Proteins with this domain are probable S-adenosylmethionine-dependent methyltransferases but they have not been functionally characterized and the substrate is unknown.


Pssm-ID: 187753  Cd Length: 124  Bit Score: 188.08  E-value: 1.53e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 218764490   6 PIGTIHTPFKETQGMPiQPAGARGVEGALEVLPELAEGLKDVDGFSHVIILYHFHQSNGYTLRVT----PFLDKEERGVF 81
Cdd:cd09281    1 PIGVVRSPFKERFGAP-QQGLVGGVESEIEIDPEYAEGLKGLEEFSHIWVLYWFHKADREELRVTvrppPRGDNPKVGVF 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 218764490  82 STRAPKRPNPIGLSVVEVVKVEGNIVHVKNIDVLDGTPLLDIKPY 126
Cdd:cd09281   80 ATRSPHRPNPIGLSVVRLLKVEGNRLHVSGLDALDGTPVLDIKPY 124
tRNA_TsaA TIGR00104
tRNA-Thr(GGU) m(6)t(6)A37 methyltransferase TsaA; This protein has been characterized by ...
 1-137 3.13e-45

tRNA-Thr(GGU) m(6)t(6)A37 methyltransferase TsaA; This protein has been characterized by crystallography in complex with S-Adenosylmethionine, making it a probable S-adenosylmethionine-dependent methyltransferase. Analysis in EcoGene links this protein to the enzyme characterization mapped to the tsaA gene in Escherichia coli. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 129210  Cd Length: 142  Bit Score: 144.92  E-value: 3.13e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 218764490    1 MIQMNPIGTIHTPFKETQGMPIQPAGARGVeGALEVLPELAEGLKDVDGFSHVIILYHFHQ--SNGYTLRVTP--FLDKE 76
Cdd:TIGR00104   2 DLQLKPIGVIRSPYKEKFDAPRQGRFSDEV-GEIEIFPEYADAVRGLEQFSHLIVLYWFDQaqRGKWQLTVVPprLGGNQ 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 218764490   77 ERGVFSTRAPKRPNPIGLSVVEVVKVEGNIVHVKNIDVLDGTPLLDIKPYVPKFDTPEFSR 137
Cdd:TIGR00104  81 RRGVFATRSPHRPNPIGLSVVELLEVECNILKVGGLDALDGTPVIDIKPYSEYIDSVPNAQ 141
 
Name Accession Description Interval E-value
TrmO COG1720
tRNA (Thr-GGU) A37 N6-methylase [Translation, ribosomal structure and biogenesis]; tRNA ...
 1-150 6.56e-82

tRNA (Thr-GGU) A37 N6-methylase [Translation, ribosomal structure and biogenesis]; tRNA (Thr-GGU) A37 N6-methylase is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441326  Cd Length: 152  Bit Score: 238.12  E-value: 6.56e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 218764490   1 MIQMNPIGTIHTPFKETQGMPIQPAGARGVEGALEVLPELAEGLKDVDGFSHVIILYHFHQSNGYTLRVTPFLDK-EERG 79
Cdd:COG1720    1 EITLRPIGVIRSPFKEKFGIPRQPRLAPGAEGEIELFPEYAEALRGLEGFSHLWLLYWFHRARRWRLTVRPRLGGnERRG 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 218764490  80 VFSTRAPKRPNPIGLSVVEVVKVEGNIVHVKNIDVLDGTPLLDIKPYVPKFDTPEFSRTGWLEEAQKNARK 150
Cdd:COG1720   81 VFATRSPHRPNPIGLSVVRLLGVEGNRLHVRGLDLLDGTPVLDIKPYVPYADAIPDARSGWAEEAPEELLA 151
TrmO pfam01980
tRNA-methyltransferase O; This family includes members such as TrmO (tRNA-methyltransferase O) ...
 19-131 9.88e-66

tRNA-methyltransferase O; This family includes members such as TrmO (tRNA-methyltransferase O) also known as YaeB, which contains a single-sheeted beta-barrel structure. TrmO is an AdoMet-dependent methyltransferase responsible for m6t6A formation. Its human homolog, is responsible for formation of m6t6A37 in cytoplasmic tRNASer. Lack of TrmO decreases attenuation activity of the thr operon, indicating that N6 methylation of m6t6A37 ensures efficient decoding of ACY codons. In bacteria and eukaryotes, TrmO has a C-terminal domain containing the conserved DPRxxY motif. Where the Asp194 and Arg196 in this motif of E. coli TrmO are necessary for N6-methylation. However, no archaeal YaeB has a C-terminal domain containing the DPRxxY motif that is conserved in bacterial and mammalian TrmO homologs.


Pssm-ID: 460402  Cd Length: 116  Bit Score: 195.69  E-value: 9.88e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 218764490   19 GMPIQPAGARGVEGALEVLPEL--AEGLKDVDGFSHVIILYHFHQSNGYTLRVTPFLDKEER-GVFSTRAPKRPNPIGLS 95
Cdd:pfam01980   1 GIPRQPGLAPDARGTIELFPEYnnAEALRGLEGFSHLWLLYWFHRNTGRPLVRPPRLGGNERvGVFATRSPFRPNPIGLS 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 218764490   96 VVEVVKVEGNIVHVKNIDVLDGTPLLDIKPYVPKFD 131
Cdd:pfam01980  81 VVKLLRVEGNVLHVSGVDLLDGTPVLDIKPYVPYAD 116
UPF0066 cd09281
Escherichia coli YaeB and related proteins; Uncharacterized protein family UPF0066. This ...
 6-126 1.53e-62

Escherichia coli YaeB and related proteins; Uncharacterized protein family UPF0066. This domain includes Escherichia coli YeaB, Archeoglobus fulgidus AF0241, and Agrobacterium tumefaciens VirR. Proteins with this domain are probable S-adenosylmethionine-dependent methyltransferases but they have not been functionally characterized and the substrate is unknown.


Pssm-ID: 187753  Cd Length: 124  Bit Score: 188.08  E-value: 1.53e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 218764490   6 PIGTIHTPFKETQGMPiQPAGARGVEGALEVLPELAEGLKDVDGFSHVIILYHFHQSNGYTLRVT----PFLDKEERGVF 81
Cdd:cd09281    1 PIGVVRSPFKERFGAP-QQGLVGGVESEIEIDPEYAEGLKGLEEFSHIWVLYWFHKADREELRVTvrppPRGDNPKVGVF 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 218764490  82 STRAPKRPNPIGLSVVEVVKVEGNIVHVKNIDVLDGTPLLDIKPY 126
Cdd:cd09281   80 ATRSPHRPNPIGLSVVRLLKVEGNRLHVSGLDALDGTPVLDIKPY 124
tRNA_TsaA TIGR00104
tRNA-Thr(GGU) m(6)t(6)A37 methyltransferase TsaA; This protein has been characterized by ...
 1-137 3.13e-45

tRNA-Thr(GGU) m(6)t(6)A37 methyltransferase TsaA; This protein has been characterized by crystallography in complex with S-Adenosylmethionine, making it a probable S-adenosylmethionine-dependent methyltransferase. Analysis in EcoGene links this protein to the enzyme characterization mapped to the tsaA gene in Escherichia coli. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 129210  Cd Length: 142  Bit Score: 144.92  E-value: 3.13e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 218764490    1 MIQMNPIGTIHTPFKETQGMPIQPAGARGVeGALEVLPELAEGLKDVDGFSHVIILYHFHQ--SNGYTLRVTP--FLDKE 76
Cdd:TIGR00104   2 DLQLKPIGVIRSPYKEKFDAPRQGRFSDEV-GEIEIFPEYADAVRGLEQFSHLIVLYWFDQaqRGKWQLTVVPprLGGNQ 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 218764490   77 ERGVFSTRAPKRPNPIGLSVVEVVKVEGNIVHVKNIDVLDGTPLLDIKPYVPKFDTPEFSR 137
Cdd:TIGR00104  81 RRGVFATRSPHRPNPIGLSVVELLEVECNILKVGGLDALDGTPVIDIKPYSEYIDSVPNAQ 141
 
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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