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Conserved domains on  [gi|1958775194|ref|XP_038965383|]
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tRNA (adenine(37)-N6)-methyltransferase isoform X2 [Rattus norvegicus]

Protein Classification

tRNA (N6-threonylcarbamoyladenosine(37)-N6)-methyltransferase TrmO( domain architecture ID 15875202)

tRNA (N6-threonylcarbamoyladenosine(37)-N6)-methyltransferase TrmO 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 pfam01980
tRNA-methyltransferase O; This family includes members such as TrmO (tRNA-methyltransferase O) ...
 2-90 3.91e-51

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: 166.03  E-value: 3.91e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958775194   2 GLEQFSHVWILFVFHKNGHlnyKAKVQPPRLNG-AKTGVFSTRSPHRPNAIGLTLAKLEKVEGGAVYLSGIDMIHGTPVL 80
Cdd:pfam01980  30 GLEGFSHLWLLYWFHRNTG---RPLVRPPRLGGnERVGVFATRSPFRPNPIGLSVVKLLRVEGNVLHVSGVDLLDGTPVL 106

                          90
                  ....*....|
gi 1958775194  81 DIKPYIADYD 90
Cdd:pfam01980 107 DIKPYVPYAD 116
TrmO_C super family cl39727
TrmO C-terminal domain; This domain is found at the C-terminus of TrmO tRNA methyltransferase ...
 251-313 1.11e-04

TrmO C-terminal domain; This domain is found at the C-terminus of TrmO tRNA methyltransferase proteins. This domain has a RelE fold.


The actual alignment was detected with superfamily member pfam18389:

Pssm-ID: 465738  Cd Length: 65  Bit Score: 39.90  E-value: 1.11e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958775194 251 ATLQVRFTPHAEMDLRKLSSGGASQTSFkyfhsaeeakcaIEAMLSADPRSVYRRKLCEDRLF 313
Cdd:pfam18389   1 APLEVEFSEEAEAQLAALQRQYPDLREL------------IEQVLAQDPRPAYQKDKPDERVY 51
 
Name Accession Description Interval E-value
TrmO pfam01980
tRNA-methyltransferase O; This family includes members such as TrmO (tRNA-methyltransferase O) ...
 2-90 3.91e-51

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: 166.03  E-value: 3.91e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958775194   2 GLEQFSHVWILFVFHKNGHlnyKAKVQPPRLNG-AKTGVFSTRSPHRPNAIGLTLAKLEKVEGGAVYLSGIDMIHGTPVL 80
Cdd:pfam01980  30 GLEGFSHLWLLYWFHRNTG---RPLVRPPRLGGnERVGVFATRSPFRPNPIGLSVVKLLRVEGNVLHVSGVDLLDGTPVL 106

                          90
                  ....*....|
gi 1958775194  81 DIKPYIADYD 90
Cdd:pfam01980 107 DIKPYVPYAD 116
TrmO COG1720
tRNA (Thr-GGU) A37 N6-methylase [Translation, ribosomal structure and biogenesis]; tRNA ...
 2-94 1.37e-44

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: 150.29  E-value: 1.37e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958775194   2 GLEQFSHVWILFVFHKNGHlnYKAKVQPpRLNG-AKTGVFSTRSPHRPNAIGLTLAKLEKVEGGAVYLSGIDMIHGTPVL 80
Cdd:COG1720    46 GLEGFSHLWLLYWFHRARR--WRLTVRP-RLGGnERRGVFATRSPHRPNPIGLSVVRLLGVEGNRLHVRGLDLLDGTPVL 122

                          90
                  ....*....|....
gi 1958775194  81 DIKPYIADYDSPQN 94
Cdd:COG1720   123 DIKPYVPYADAIPD 136
UPF0066 cd09281
Escherichia coli YaeB and related proteins; Uncharacterized protein family UPF0066. This ...
 1-85 1.12e-43

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: 146.87  E-value: 1.12e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958775194   1 MGLEQFSHVWILFVFHKNGHLNYKAKV-QPPRLNGAKTGVFSTRSPHRPNAIGLTLAKLEKVEGGAVYLSGIDMIHGTPV 79
Cdd:cd09281    39 KGLEEFSHIWVLYWFHKADREELRVTVrPPPRGDNPKVGVFATRSPHRPNPIGLSVVRLLKVEGNRLHVSGLDALDGTPV 118


                  ....*.
gi 1958775194  80 LDIKPY 85
Cdd:cd09281   119 LDIKPY 124
tRNA_TsaA TIGR00104
tRNA-Thr(GGU) m(6)t(6)A37 methyltransferase TsaA; This protein has been characterized by ...
 2-96 2.72e-33

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: 120.65  E-value: 2.72e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958775194   2 GLEQFSHVWILFVFHKNGHLNYKAKVQPPRLNG-AKTGVFSTRSPHRPNAIGLTLAKLEKVEGGAVYLSGIDMIHGTPVL 80
Cdd:TIGR00104  46 GLEQFSHLIVLYWFDQAQRGKWQLTVVPPRLGGnQRRGVFATRSPHRPNPIGLSVVELLEVECNILKVGGLDALDGTPVI 125

                          90
                  ....*....|....*.
gi 1958775194  81 DIKPYIADYDSPQNLE 96
Cdd:TIGR00104 126 DIKPYSEYIDSVPNAQ 141
TrmO_C pfam18389
TrmO C-terminal domain; This domain is found at the C-terminus of TrmO tRNA methyltransferase ...
 251-313 1.11e-04

TrmO C-terminal domain; This domain is found at the C-terminus of TrmO tRNA methyltransferase proteins. This domain has a RelE fold.


Pssm-ID: 465738  Cd Length: 65  Bit Score: 39.90  E-value: 1.11e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958775194 251 ATLQVRFTPHAEMDLRKLSSGGASQTSFkyfhsaeeakcaIEAMLSADPRSVYRRKLCEDRLF 313
Cdd:pfam18389   1 APLEVEFSEEAEAQLAALQRQYPDLREL------------IEQVLAQDPRPAYQKDKPDERVY 51
 
Name Accession Description Interval E-value
TrmO pfam01980
tRNA-methyltransferase O; This family includes members such as TrmO (tRNA-methyltransferase O) ...
 2-90 3.91e-51

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: 166.03  E-value: 3.91e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958775194   2 GLEQFSHVWILFVFHKNGHlnyKAKVQPPRLNG-AKTGVFSTRSPHRPNAIGLTLAKLEKVEGGAVYLSGIDMIHGTPVL 80
Cdd:pfam01980  30 GLEGFSHLWLLYWFHRNTG---RPLVRPPRLGGnERVGVFATRSPFRPNPIGLSVVKLLRVEGNVLHVSGVDLLDGTPVL 106

                          90
                  ....*....|
gi 1958775194  81 DIKPYIADYD 90
Cdd:pfam01980 107 DIKPYVPYAD 116
TrmO COG1720
tRNA (Thr-GGU) A37 N6-methylase [Translation, ribosomal structure and biogenesis]; tRNA ...
 2-94 1.37e-44

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: 150.29  E-value: 1.37e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958775194   2 GLEQFSHVWILFVFHKNGHlnYKAKVQPpRLNG-AKTGVFSTRSPHRPNAIGLTLAKLEKVEGGAVYLSGIDMIHGTPVL 80
Cdd:COG1720    46 GLEGFSHLWLLYWFHRARR--WRLTVRP-RLGGnERRGVFATRSPHRPNPIGLSVVRLLGVEGNRLHVRGLDLLDGTPVL 122

                          90
                  ....*....|....
gi 1958775194  81 DIKPYIADYDSPQN 94
Cdd:COG1720   123 DIKPYVPYADAIPD 136
UPF0066 cd09281
Escherichia coli YaeB and related proteins; Uncharacterized protein family UPF0066. This ...
 1-85 1.12e-43

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: 146.87  E-value: 1.12e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958775194   1 MGLEQFSHVWILFVFHKNGHLNYKAKV-QPPRLNGAKTGVFSTRSPHRPNAIGLTLAKLEKVEGGAVYLSGIDMIHGTPV 79
Cdd:cd09281    39 KGLEEFSHIWVLYWFHKADREELRVTVrPPPRGDNPKVGVFATRSPHRPNPIGLSVVRLLKVEGNRLHVSGLDALDGTPV 118


                  ....*.
gi 1958775194  80 LDIKPY 85
Cdd:cd09281   119 LDIKPY 124
tRNA_TsaA TIGR00104
tRNA-Thr(GGU) m(6)t(6)A37 methyltransferase TsaA; This protein has been characterized by ...
 2-96 2.72e-33

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: 120.65  E-value: 2.72e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958775194   2 GLEQFSHVWILFVFHKNGHLNYKAKVQPPRLNG-AKTGVFSTRSPHRPNAIGLTLAKLEKVEGGAVYLSGIDMIHGTPVL 80
Cdd:TIGR00104  46 GLEQFSHLIVLYWFDQAQRGKWQLTVVPPRLGGnQRRGVFATRSPHRPNPIGLSVVELLEVECNILKVGGLDALDGTPVI 125

                          90
                  ....*....|....*.
gi 1958775194  81 DIKPYIADYDSPQNLE 96
Cdd:TIGR00104 126 DIKPYSEYIDSVPNAQ 141
TrmO_C pfam18389
TrmO C-terminal domain; This domain is found at the C-terminus of TrmO tRNA methyltransferase ...
 251-313 1.11e-04

TrmO C-terminal domain; This domain is found at the C-terminus of TrmO tRNA methyltransferase proteins. This domain has a RelE fold.


Pssm-ID: 465738  Cd Length: 65  Bit Score: 39.90  E-value: 1.11e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958775194 251 ATLQVRFTPHAEMDLRKLSSGGASQTSFkyfhsaeeakcaIEAMLSADPRSVYRRKLCEDRLF 313
Cdd:pfam18389   1 APLEVEFSEEAEAQLAALQRQYPDLREL------------IEQVLAQDPRPAYQKDKPDERVY 51
 
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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