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Conserved domains on  [gi|818624376|gb|KKS72383|]
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(Dimethylallyl)adenosine tRNA methylthiotransferase MiaB, partial [candidate division WWE3 bacterium GW2011_GWD1_42_70]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MiaB super family cl33981
tRNA A37 methylthiotransferase MiaB [Translation, ribosomal structure and biogenesis]; tRNA ...
 1-54 9.36e-17

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


The actual alignment was detected with superfamily member COG0621:

Pssm-ID: 440386 [Multi-domain]  Cd Length: 435  Bit Score: 72.04  E-value: 9.36e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 818624376   1 GFPGETREQFLDTVELVKKINFSVAFIAMYSSRKGTVSEKtFDDDVPSAEKKYR 54
Cdd:COG0621  303 GFPGETEEDFEETLDFVEEVRFDRLHVFPYSPRPGTPAAK-MPDQVPEEVKKER 355
 
Name Accession Description Interval E-value
MiaB COG0621
tRNA A37 methylthiotransferase MiaB [Translation, ribosomal structure and biogenesis]; tRNA ...
 1-54 9.36e-17

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: 72.04  E-value: 9.36e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 818624376   1 GFPGETREQFLDTVELVKKINFSVAFIAMYSSRKGTVSEKtFDDDVPSAEKKYR 54
Cdd:COG0621  303 GFPGETEEDFEETLDFVEEVRFDRLHVFPYSPRPGTPAAK-MPDQVPEEVKKER 355
PRK14328 PRK14328
(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
 1-61 3.36e-15

(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional


Pssm-ID: 237675 [Multi-domain]  Cd Length: 439  Bit Score: 67.70  E-value: 3.36e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 818624376   1 GFPGETREQFLDTVELVKKINFSVAFIAMYSSRKGTVSEKtFDDDVPSAEKKYRHDFLTKA 61
Cdd:PRK14328 307 GFPGETEEDFEETLDLVKEVRYDSAFTFIYSKRKGTPAAK-MEDQVPEDVKHERFNRLVEL 366
TIGR00089 TIGR00089
radical SAM methylthiotransferase, MiaB/RimO family; This subfamily contains the tRNA-i(6)A37 ...
 1-60 8.86e-15

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: 66.50  E-value: 8.86e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624376    1 GFPGETREQFLDTVELVKKINFSVAFIAMYSSRKGTVSeKTFDDDVPSAEKKYRHDFLTK 60
Cdd:TIGR00089 299 GFPGETEEDFEETLDLVEEVKFDKLHSFIYSPRPGTPA-ADMKDQVPEEVKKERLERLIA 357
Elp3 smart00729
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
 1-57 1.25e-07

Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.


Pssm-ID: 214792 [Multi-domain]  Cd Length: 216  Bit Score: 45.86  E-value: 1.25e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 818624376     1 GFPGETREQFLDTVELVKKINFSVAFIAMYSSRKGTVSEKTFDDDVPSAEKKYRHDF 57
Cdd:smart00729 160 GLPGETEEDFEETLKLLKELGPDRVSIFPLSPRPGTPLAKMYKRLKPPTKEERAELL 216
 
Name Accession Description Interval E-value
MiaB COG0621
tRNA A37 methylthiotransferase MiaB [Translation, ribosomal structure and biogenesis]; tRNA ...
 1-54 9.36e-17

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: 72.04  E-value: 9.36e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 818624376   1 GFPGETREQFLDTVELVKKINFSVAFIAMYSSRKGTVSEKtFDDDVPSAEKKYR 54
Cdd:COG0621  303 GFPGETEEDFEETLDFVEEVRFDRLHVFPYSPRPGTPAAK-MPDQVPEEVKKER 355
PRK14328 PRK14328
(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
 1-61 3.36e-15

(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional


Pssm-ID: 237675 [Multi-domain]  Cd Length: 439  Bit Score: 67.70  E-value: 3.36e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 818624376   1 GFPGETREQFLDTVELVKKINFSVAFIAMYSSRKGTVSEKtFDDDVPSAEKKYRHDFLTKA 61
Cdd:PRK14328 307 GFPGETEEDFEETLDLVKEVRYDSAFTFIYSKRKGTPAAK-MEDQVPEDVKHERFNRLVEL 366
TIGR00089 TIGR00089
radical SAM methylthiotransferase, MiaB/RimO family; This subfamily contains the tRNA-i(6)A37 ...
 1-60 8.86e-15

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: 66.50  E-value: 8.86e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 818624376    1 GFPGETREQFLDTVELVKKINFSVAFIAMYSSRKGTVSeKTFDDDVPSAEKKYRHDFLTK 60
Cdd:TIGR00089 299 GFPGETEEDFEETLDLVEEVKFDKLHSFIYSPRPGTPA-ADMKDQVPEEVKKERLERLIA 357
PRK14336 PRK14336
(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
 1-54 2.72e-12

(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional


Pssm-ID: 184632 [Multi-domain]  Cd Length: 418  Bit Score: 59.54  E-value: 2.72e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 818624376   1 GFPGETREQFLDTVELVKKINFSVAFIAMYSSRKGTVSEKTFDDDVPSAEKKYR 54
Cdd:PRK14336 284 GFPSETEEQFNQSYKLMADIGYDAIHVAAYSPRPQTVAARDMADDVPVIEKKRR 337
Elp3 smart00729
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
 1-57 1.25e-07

Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.


Pssm-ID: 214792 [Multi-domain]  Cd Length: 216  Bit Score: 45.86  E-value: 1.25e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 818624376     1 GFPGETREQFLDTVELVKKINFSVAFIAMYSSRKGTVSEKTFDDDVPSAEKKYRHDF 57
Cdd:smart00729 160 GLPGETEEDFEETLKLLKELGPDRVSIFPLSPRPGTPLAKMYKRLKPPTKEERAELL 216
YgiQ COG1032
Radical SAM superfamily enzyme YgiQ, UPF0313 family [General function prediction only];
1-36 9.23e-05

Radical SAM superfamily enzyme YgiQ, UPF0313 family [General function prediction only];


Pssm-ID: 440655 [Multi-domain]  Cd Length: 394  Bit Score: 38.39  E-value: 9.23e-05
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 818624376   1 GFPGETREQFLDTVELVKKINFSVAFIAMYSSRKGT 36
Cdd:COG1032  325 GLPGETEEDIEETIEFIKELGPDQAQVSIFTPLPGT 360
 
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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