MiaB-like tRNA modifying enzyme, archaeal-type; This clade of sequences is closely related to ...
65-247
2.16e-66
MiaB-like tRNA modifying enzyme, archaeal-type; This clade of sequences is closely related to MiaB, a modifier of isopentenylated adenosine-37 of certain eukaryotic and bacterial tRNAs (see TIGR01574). Sequence alignments suggest that this equivalog performs the same chemical transformation as MiaB, perhaps on a different (or differently modified) tRNA base substrate. This clade is a member of a subfamily (TIGR00089) and spans the archaea and eukaryotes. The only archaeal miaB-like genes are in this clade, while eukaryotes have sequences described by this model as well as ones falling within the scope of the MiaB equivalog model. [Protein synthesis, tRNA and rRNA base modification]
The actual alignment was detected with superfamily member TIGR01578:
Pssm-ID: 273703 [Multi-domain] Cd Length: 420 Bit Score: 211.56 E-value: 2.16e-66
MiaB-like tRNA modifying enzyme, archaeal-type; This clade of sequences is closely related to ...
65-247
2.16e-66
MiaB-like tRNA modifying enzyme, archaeal-type; This clade of sequences is closely related to MiaB, a modifier of isopentenylated adenosine-37 of certain eukaryotic and bacterial tRNAs (see TIGR01574). Sequence alignments suggest that this equivalog performs the same chemical transformation as MiaB, perhaps on a different (or differently modified) tRNA base substrate. This clade is a member of a subfamily (TIGR00089) and spans the archaea and eukaryotes. The only archaeal miaB-like genes are in this clade, while eukaryotes have sequences described by this model as well as ones falling within the scope of the MiaB equivalog model. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 273703 [Multi-domain] Cd Length: 420 Bit Score: 211.56 E-value: 2.16e-66
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: 136.75 E-value: 1.15e-37
Uncharacterized protein family UPF0004; This family is the N terminal half of the Prosite ...
65-146
1.30e-27
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: 101.82 E-value: 1.30e-27
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
207-243
2.38e-03
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: 38.15 E-value: 2.38e-03
MiaB-like tRNA modifying enzyme, archaeal-type; This clade of sequences is closely related to ...
65-247
2.16e-66
MiaB-like tRNA modifying enzyme, archaeal-type; This clade of sequences is closely related to MiaB, a modifier of isopentenylated adenosine-37 of certain eukaryotic and bacterial tRNAs (see TIGR01574). Sequence alignments suggest that this equivalog performs the same chemical transformation as MiaB, perhaps on a different (or differently modified) tRNA base substrate. This clade is a member of a subfamily (TIGR00089) and spans the archaea and eukaryotes. The only archaeal miaB-like genes are in this clade, while eukaryotes have sequences described by this model as well as ones falling within the scope of the MiaB equivalog model. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 273703 [Multi-domain] Cd Length: 420 Bit Score: 211.56 E-value: 2.16e-66
radical SAM methylthiotransferase, MiaB/RimO family; This subfamily contains the tRNA-i(6)A37 ...
65-244
3.85e-38
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: 137.76 E-value: 3.85e-38
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: 136.75 E-value: 1.15e-37
Uncharacterized protein family UPF0004; This family is the N terminal half of the Prosite ...
65-146
1.30e-27
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: 101.82 E-value: 1.30e-27
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
207-243
2.38e-03
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: 38.15 E-value: 2.38e-03
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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Functional characterization of the conserved domain architecture found on the query.
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This image shows a graphical summary of conserved domains identified on the query sequence.
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if a domain or superfamily has been annotated with functional sites (conserved features),
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click on the bars or triangles to view your query sequence embedded in a multiple sequence alignment of the proteins used to develop the corresponding domain model.
The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
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To view your query sequence embedded in that multiple sequence alignment, click on the colored bars in the Graphical Summary portion of the search results page,
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Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence.
(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
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(labeled illustration) Four types of hits can be shown, as available,
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