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Conserved domains on  [gi|74203559|dbj|BAE23052|]
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unnamed protein product [Mus musculus]

Protein Classification

UPF0004 domain-containing protein( domain architecture ID 10469078)

UPF0004 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
UPF0004 pfam00919
Uncharacterized protein family UPF0004; This family is the N terminal half of the Prosite ...
 100-181 7.96e-30

Uncharacterized protein family UPF0004; This family is the N terminal half of the Prosite family. The C-terminal half has been shown to be related to MiaB proteins. This domain is a nearly always found in conjunction with pfam04055 and pfam01938 although its function is uncertain.


:

Pssm-ID: 459997 [Multi-domain]  Cd Length: 98  Bit Score: 105.29  E-value: 7.96e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74203559   100 KVYLETYGCQMNVNDTEIAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKVLKTKRprsrvpLRIGI 179
Cdd:pfam00919   1 KVYIETLGCQMNQADSEIMAGLLEKAGYEVVEDEEEADVVVINTCTVRENAEQKSRQTIGRLKRLKKPD------AKIVV 74


                  ..
gi 74203559   180 LG 181
Cdd:pfam00919  75 TG 76
 
Name Accession Description Interval E-value
UPF0004 pfam00919
Uncharacterized protein family UPF0004; This family is the N terminal half of the Prosite ...
 100-181 7.96e-30

Uncharacterized protein family UPF0004; This family is the N terminal half of the Prosite family. The C-terminal half has been shown to be related to MiaB proteins. This domain is a nearly always found in conjunction with pfam04055 and pfam01938 although its function is uncertain.


Pssm-ID: 459997 [Multi-domain]  Cd Length: 98  Bit Score: 105.29  E-value: 7.96e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74203559   100 KVYLETYGCQMNVNDTEIAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKVLKTKRprsrvpLRIGI 179
Cdd:pfam00919   1 KVYIETLGCQMNQADSEIMAGLLEKAGYEVVEDEEEADVVVINTCTVRENAEQKSRQTIGRLKRLKKPD------AKIVV 74


                  ..
gi 74203559   180 LG 181
Cdd:pfam00919  75 TG 76
MiaB COG0621
tRNA A37 methylthiotransferase MiaB [Translation, ribosomal structure and biogenesis]; tRNA ...
 99-181 3.80e-26

tRNA A37 methylthiotransferase MiaB [Translation, ribosomal structure and biogenesis]; tRNA A37 methylthiotransferase MiaB is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440386 [Multi-domain]  Cd Length: 435  Bit Score: 103.24  E-value: 3.80e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74203559  99 RKVYLETYGCQMNVNDTEIAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKVLKTKRPRsrvpLRIG 178
Cdd:COG0621   2 KKVYIVTLGCQMNQVDSERMAGLLEAAGYELVDDPEEADVVVVNTCSVREKAEEKSRQTIGRLAELKRKNPD----AKIV 77


                ...
gi 74203559 179 ILG 181
Cdd:COG0621  78 VTG 80
PRK14328 PRK14328
(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
 98-181 5.71e-24

(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional


Pssm-ID: 237675 [Multi-domain]  Cd Length: 439  Bit Score: 97.36  E-value: 5.71e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74203559   98 QRKVYLETYGCQMNVNDTEIAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKVLKTKRPRsrvpLRI 177
Cdd:PRK14328   1 NKKYFIETYGCQMNEEDSEKLAGMLKSMGYERTENREEADIIIFNTCCVRENAENKVFGNLGELKKLKEKNPN----LII 76


                 ....
gi 74203559  178 GILG 181
Cdd:PRK14328  77 GVCG 80
TIGR00089 TIGR00089
radical SAM methylthiotransferase, MiaB/RimO family; This subfamily contains the tRNA-i(6)A37 ...
 100-168 1.71e-23

radical SAM methylthiotransferase, MiaB/RimO family; This subfamily contains the tRNA-i(6)A37 modification enzyme, MiaB (TIGR01574). The phylogenetic tree indicates 4 distinct clades, one of which corresponds to MiaB. The other three clades are modelled by hypothetical equivalogs (TIGR01125, TIGR01579 and TIGR01578). Together, the four models hit every sequence hit by the subfamily model without any overlap between them. This subfamily is aparrently a part of a larger superfamily of enzymes utilizing both a 4Fe4S cluster and S-adenosyl methionine (SAM) to initiate radical reactions. MiaB acts on a particular isoprenylated Adenine base of certain tRNAs causing thiolation at an aromatic carbon, and probably also transferring a methyl grouyp from SAM to the thiol. The particular substrate of the three other clades is unknown but may be very closely related.


Pssm-ID: 272900 [Multi-domain]  Cd Length: 429  Bit Score: 96.16  E-value: 1.71e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 74203559   100 KVYLETYGCQMNVNDTEIAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKVLKTKR 168
Cdd:TIGR00089   1 KVYIETYGCQMNEADSEIMAGLLKEGGYEVTDDPEEADVIIINTCAVREKAEQKVRSRLGELAKLKKKN 69
 
Name Accession Description Interval E-value
UPF0004 pfam00919
Uncharacterized protein family UPF0004; This family is the N terminal half of the Prosite ...
 100-181 7.96e-30

Uncharacterized protein family UPF0004; This family is the N terminal half of the Prosite family. The C-terminal half has been shown to be related to MiaB proteins. This domain is a nearly always found in conjunction with pfam04055 and pfam01938 although its function is uncertain.


Pssm-ID: 459997 [Multi-domain]  Cd Length: 98  Bit Score: 105.29  E-value: 7.96e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74203559   100 KVYLETYGCQMNVNDTEIAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKVLKTKRprsrvpLRIGI 179
Cdd:pfam00919   1 KVYIETLGCQMNQADSEIMAGLLEKAGYEVVEDEEEADVVVINTCTVRENAEQKSRQTIGRLKRLKKPD------AKIVV 74


                  ..
gi 74203559   180 LG 181
Cdd:pfam00919  75 TG 76
MiaB COG0621
tRNA A37 methylthiotransferase MiaB [Translation, ribosomal structure and biogenesis]; tRNA ...
 99-181 3.80e-26

tRNA A37 methylthiotransferase MiaB [Translation, ribosomal structure and biogenesis]; tRNA A37 methylthiotransferase MiaB is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440386 [Multi-domain]  Cd Length: 435  Bit Score: 103.24  E-value: 3.80e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74203559  99 RKVYLETYGCQMNVNDTEIAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKVLKTKRPRsrvpLRIG 178
Cdd:COG0621   2 KKVYIVTLGCQMNQVDSERMAGLLEAAGYELVDDPEEADVVVVNTCSVREKAEEKSRQTIGRLAELKRKNPD----AKIV 77


                ...
gi 74203559 179 ILG 181
Cdd:COG0621  78 VTG 80
PRK14328 PRK14328
(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
 98-181 5.71e-24

(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional


Pssm-ID: 237675 [Multi-domain]  Cd Length: 439  Bit Score: 97.36  E-value: 5.71e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74203559   98 QRKVYLETYGCQMNVNDTEIAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKVLKTKRPRsrvpLRI 177
Cdd:PRK14328   1 NKKYFIETYGCQMNEEDSEKLAGMLKSMGYERTENREEADIIIFNTCCVRENAENKVFGNLGELKKLKEKNPN----LII 76


                 ....
gi 74203559  178 GILG 181
Cdd:PRK14328  77 GVCG 80
TIGR00089 TIGR00089
radical SAM methylthiotransferase, MiaB/RimO family; This subfamily contains the tRNA-i(6)A37 ...
 100-168 1.71e-23

radical SAM methylthiotransferase, MiaB/RimO family; This subfamily contains the tRNA-i(6)A37 modification enzyme, MiaB (TIGR01574). The phylogenetic tree indicates 4 distinct clades, one of which corresponds to MiaB. The other three clades are modelled by hypothetical equivalogs (TIGR01125, TIGR01579 and TIGR01578). Together, the four models hit every sequence hit by the subfamily model without any overlap between them. This subfamily is aparrently a part of a larger superfamily of enzymes utilizing both a 4Fe4S cluster and S-adenosyl methionine (SAM) to initiate radical reactions. MiaB acts on a particular isoprenylated Adenine base of certain tRNAs causing thiolation at an aromatic carbon, and probably also transferring a methyl grouyp from SAM to the thiol. The particular substrate of the three other clades is unknown but may be very closely related.


Pssm-ID: 272900 [Multi-domain]  Cd Length: 429  Bit Score: 96.16  E-value: 1.71e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 74203559   100 KVYLETYGCQMNVNDTEIAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKVLKTKR 168
Cdd:TIGR00089   1 KVYIETYGCQMNEADSEIMAGLLKEGGYEVTDDPEEADVIIINTCAVREKAEQKVRSRLGELAKLKKKN 69
miaB-methiolase TIGR01574
tRNA-N(6)-(isopentenyl)adenosine-37 thiotransferase enzyme MiaB; This model represents ...
 100-181 4.20e-20

tRNA-N(6)-(isopentenyl)adenosine-37 thiotransferase enzyme MiaB; This model represents homologs of the MiaB enzyme responsible for the modification of the isopentenylated adenine-37 base of most bacterial and eukaryotic tRNAs that read codons beginning with uracil (all except tRNA(I,V) Ser). Adenine-37 is next to the anticodon on the 3' side in these tRNA's, and lack of modification at this site leads to an increased spontaneous mutation frequency. Isopentenylated A-37 is modified by methylthiolation at position 2, either by MiaB alone or in concert with a separate methylase yet to be discovered (MiaC?). MiaB contains a 4Fe-4S cluster which is labile under oxidizing conditions. Additionally, the sequence is homologous (via PSI-BLAST searches) to the biotin synthetase, BioB, which utilizes both an iron-sulfur cluster and S-adenosym methionine (SAM) to generate a radical which is responsible for initiating the insertion of sulfur into the substrate. It is reasonable to surmise that the methyl group of SAM becomes the methyl group of the product, but this has not been shown, and the possibility of a separate methylase exists. This equivalog is a member of a subfamily (TIGR00089) which contains several other hypothetical equivalogs which are all probably enzymes with similar function acting on different substrates. These enzymes contain a TRAM domain (pfam01938) which is believed to be responsible for binding to tRNAs. Hits to this model span all major groups of bacteria and eukaryotes, but not archaea, which are known to lack this particular tRNA modification. The enzyme from Thermotoga maritima has been cloned, expressed, spectroscopically characterized and shown to complement the E. coli MiaB enzyme. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 273700 [Multi-domain]  Cd Length: 438  Bit Score: 86.41  E-value: 4.20e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74203559   100 KVYLETYGCQMNVNDTE-IAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKVLKTKRPrsrvPLRIG 178
Cdd:TIGR01574   1 KLFIQTYGCQMNVRDSEhMAALLTAKEGYALTEDAKEADVLLINTCSVREKAEHKVFGELGGFKKLKKKNP----DLIIG 76


                  ...
gi 74203559   179 ILG 181
Cdd:TIGR01574  77 VCG 79
PRK14336 PRK14336
(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
 100-175 1.84e-13

(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional


Pssm-ID: 184632 [Multi-domain]  Cd Length: 418  Bit Score: 67.63  E-value: 1.84e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 74203559  100 KVYLETYGCQMNVNDTEIAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKVLKTKRPRSRVPL 175
Cdd:PRK14336   3 GYYLWTIGCQMNQAESERLGRLFELWGYSLADKAEDAELVLVNSCVVREHAENKVINRLHLLRKLKNKNPKLKIAL 78
 
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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