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Conserved domains on  [gi|1002297440|ref|XP_015612147|]
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uncharacterized protein [Oryza sativa Japonica Group]

Protein Classification

SAM-dependent methyltransferase( domain architecture ID 10487987)

SAM (S-adenosylmethionine)-dependent methyltransferase similar to 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 pfam01980
tRNA-methyltransferase O; This family includes members such as TrmO (tRNA-methyltransferase O) ...
 107-234 1.29e-64

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: 201.47  E-value: 1.29e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002297440 107 GTPRQPLVVPLARATVMLDPARVPAEALEGLADYSHCWILYVFHLNTDldkmwndparsklKAKVRVPRLKGG-KMGVLA 185
Cdd:pfam01980   1 GIPRQPGLAPDARGTIELFPEYNNAEALRGLEGFSHLWLLYWFHRNTG-------------RPLVRPPRLGGNeRVGVFA 67

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1002297440 186 TRSPHRPNPIGLSVAKVEAVDGHSILLSGVDLVDGTPVLDIKPYLPYSD 234
Cdd:pfam01980  68 TRSPFRPNPIGLSVVKLLRVEGNVLHVSGVDLLDGTPVLDIKPYVPYAD 116
 
Name Accession Description Interval E-value
TrmO pfam01980
tRNA-methyltransferase O; This family includes members such as TrmO (tRNA-methyltransferase O) ...
 107-234 1.29e-64

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: 201.47  E-value: 1.29e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002297440 107 GTPRQPLVVPLARATVMLDPARVPAEALEGLADYSHCWILYVFHLNTDldkmwndparsklKAKVRVPRLKGG-KMGVLA 185
Cdd:pfam01980   1 GIPRQPGLAPDARGTIELFPEYNNAEALRGLEGFSHLWLLYWFHRNTG-------------RPLVRPPRLGGNeRVGVFA 67

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1002297440 186 TRSPHRPNPIGLSVAKVEAVDGHSILLSGVDLVDGTPVLDIKPYLPYSD 234
Cdd:pfam01980  68 TRSPFRPNPIGLSVVKLLRVEGNVLHVSGVDLLDGTPVLDIKPYVPYAD 116
TrmO COG1720
tRNA (Thr-GGU) A37 N6-methylase [Translation, ribosomal structure and biogenesis]; tRNA ...
 89-246 5.80e-58

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: 185.73  E-value: 5.80e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002297440  89 SFPMASIGVVQSCFSTRNGTPRQPLVVPLARATVMLDPARvpAEALEGLADYSHCWILYVFHLNtdldkmwndpARSKLK 168
Cdd:COG1720     1 EITLRPIGVIRSPFKEKFGIPRQPRLAPGAEGEIELFPEY--AEALRGLEGFSHLWLLYWFHRA----------RRWRLT 68

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002297440 169 AKvrvPRLKGG-KMGVLATRSPHRPNPIGLSVAKVEAVDGHSILLSGVDLVDGTPVLDIKPYLPYSDGVKGAAIPnWLE 246
Cdd:COG1720    69 VR---PRLGGNeRRGVFATRSPHRPNPIGLSVVRLLGVEGNRLHVRGLDLLDGTPVLDIKPYVPYADAIPDARSG-WAE 143
UPF0066 cd09281
Escherichia coli YaeB and related proteins; Uncharacterized protein family UPF0066. This ...
 95-229 1.45e-53

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: 173.45  E-value: 1.45e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002297440  95 IGVVQSCFSTRNGTPRQPLVvPLARATVMLDPARvpAEALEGLADYSHCWILYVFHLNTdldkmwndpaRSKLKAKVRVP 174
Cdd:cd09281     2 IGVVRSPFKERFGAPQQGLV-GGVESEIEIDPEY--AEGLKGLEEFSHIWVLYWFHKAD----------REELRVTVRPP 68

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1002297440 175 RLKGG-KMGVLATRSPHRPNPIGLSVAKVEAVDGHSILLSGVDLVDGTPVLDIKPY 229
Cdd:cd09281    69 PRGDNpKVGVFATRSPHRPNPIGLSVVRLLKVEGNRLHVSGLDALDGTPVLDIKPY 124
tRNA_TsaA TIGR00104
tRNA-Thr(GGU) m(6)t(6)A37 methyltransferase TsaA; This protein has been characterized by ...
 95-241 1.31e-35

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: 127.58  E-value: 1.31e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002297440  95 IGVVQSCFSTRNGTPRQPLVVPLARATVMLDPArvpAEALEGLADYSHCWILYVFHLNTdldkmwndpaRSKLKAKVRVP 174
Cdd:TIGR00104   8 IGVIRSPYKEKFDAPRQGRFSDEVGEIEIFPEY---ADAVRGLEQFSHLIVLYWFDQAQ----------RGKWQLTVVPP 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002297440 175 RLKGG-KMGVLATRSPHRPNPIGLSVAKVEAVDGHSILLSGVDLVDGTPVLDIKPYLPYSDGVKGAAI 241
Cdd:TIGR00104  75 RLGGNqRRGVFATRSPHRPNPIGLSVVELLEVECNILKVGGLDALDGTPVIDIKPYSEYIDSVPNAQS 142
 
Name Accession Description Interval E-value
TrmO pfam01980
tRNA-methyltransferase O; This family includes members such as TrmO (tRNA-methyltransferase O) ...
 107-234 1.29e-64

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: 201.47  E-value: 1.29e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002297440 107 GTPRQPLVVPLARATVMLDPARVPAEALEGLADYSHCWILYVFHLNTDldkmwndparsklKAKVRVPRLKGG-KMGVLA 185
Cdd:pfam01980   1 GIPRQPGLAPDARGTIELFPEYNNAEALRGLEGFSHLWLLYWFHRNTG-------------RPLVRPPRLGGNeRVGVFA 67

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1002297440 186 TRSPHRPNPIGLSVAKVEAVDGHSILLSGVDLVDGTPVLDIKPYLPYSD 234
Cdd:pfam01980  68 TRSPFRPNPIGLSVVKLLRVEGNVLHVSGVDLLDGTPVLDIKPYVPYAD 116
TrmO COG1720
tRNA (Thr-GGU) A37 N6-methylase [Translation, ribosomal structure and biogenesis]; tRNA ...
 89-246 5.80e-58

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: 185.73  E-value: 5.80e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002297440  89 SFPMASIGVVQSCFSTRNGTPRQPLVVPLARATVMLDPARvpAEALEGLADYSHCWILYVFHLNtdldkmwndpARSKLK 168
Cdd:COG1720     1 EITLRPIGVIRSPFKEKFGIPRQPRLAPGAEGEIELFPEY--AEALRGLEGFSHLWLLYWFHRA----------RRWRLT 68

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002297440 169 AKvrvPRLKGG-KMGVLATRSPHRPNPIGLSVAKVEAVDGHSILLSGVDLVDGTPVLDIKPYLPYSDGVKGAAIPnWLE 246
Cdd:COG1720    69 VR---PRLGGNeRRGVFATRSPHRPNPIGLSVVRLLGVEGNRLHVRGLDLLDGTPVLDIKPYVPYADAIPDARSG-WAE 143
UPF0066 cd09281
Escherichia coli YaeB and related proteins; Uncharacterized protein family UPF0066. This ...
 95-229 1.45e-53

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: 173.45  E-value: 1.45e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002297440  95 IGVVQSCFSTRNGTPRQPLVvPLARATVMLDPARvpAEALEGLADYSHCWILYVFHLNTdldkmwndpaRSKLKAKVRVP 174
Cdd:cd09281     2 IGVVRSPFKERFGAPQQGLV-GGVESEIEIDPEY--AEGLKGLEEFSHIWVLYWFHKAD----------REELRVTVRPP 68

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1002297440 175 RLKGG-KMGVLATRSPHRPNPIGLSVAKVEAVDGHSILLSGVDLVDGTPVLDIKPY 229
Cdd:cd09281    69 PRGDNpKVGVFATRSPHRPNPIGLSVVRLLKVEGNRLHVSGLDALDGTPVLDIKPY 124
tRNA_TsaA TIGR00104
tRNA-Thr(GGU) m(6)t(6)A37 methyltransferase TsaA; This protein has been characterized by ...
 95-241 1.31e-35

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: 127.58  E-value: 1.31e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002297440  95 IGVVQSCFSTRNGTPRQPLVVPLARATVMLDPArvpAEALEGLADYSHCWILYVFHLNTdldkmwndpaRSKLKAKVRVP 174
Cdd:TIGR00104   8 IGVIRSPYKEKFDAPRQGRFSDEVGEIEIFPEY---ADAVRGLEQFSHLIVLYWFDQAQ----------RGKWQLTVVPP 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002297440 175 RLKGG-KMGVLATRSPHRPNPIGLSVAKVEAVDGHSILLSGVDLVDGTPVLDIKPYLPYSDGVKGAAI 241
Cdd:TIGR00104  75 RLGGNqRRGVFATRSPHRPNPIGLSVVELLEVECNILKVGGLDALDGTPVIDIKPYSEYIDSVPNAQS 142
 
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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