TIGR01212 family radical SAM protein such as Bacillus subtilis protein YtqA that generates radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity; contains a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; transfer of a single electron from the iron-sulfur cluster to SAM leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical
radical SAM protein, TIGR01212 family; Members of this family are apparent radical-SAM enzymes, ...
15-315
0e+00
radical SAM protein, TIGR01212 family; Members of this family are apparent radical-SAM enzymes, related to the N-terminal region of the bifunctional ELP3, whose C-terminal region is part of the elongator complex and appears to acetylate histones and other proteins. ELP3 binds S-adenosylmethionine (SAM) and was recently shown to be involved in a DNA demethylation process in eukaryotes. Close sequence similarity of this family (with lacks the GNAT family acetyltransferase domain) to the ELP3 N-terminal region and a strong match to the pfam04055 support identification of this family as radical SAM despite the atypical spacing between first and second Cys residues in the 4Fe4S-binding motif. [Unknown function, Enzymes of unknown specificity]
Pssm-ID: 130279 [Multi-domain] Cd Length: 302 Bit Score: 542.81 E-value: 0e+00
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
42-257
2.42e-36
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: 130.21 E-value: 2.42e-36
Radical_SAM C-terminal domain; This domain is found as a C-terminal extension to a subset of ...
220-302
2.83e-36
Radical_SAM C-terminal domain; This domain is found as a C-terminal extension to a subset of Radical_SAM domains. It is found in archaeal, bacterial, fungal, plant and human proteins.
Pssm-ID: 465061 [Multi-domain] Cd Length: 83 Bit Score: 125.59 E-value: 2.83e-36
radical SAM protein, TIGR01212 family; Members of this family are apparent radical-SAM enzymes, ...
15-315
0e+00
radical SAM protein, TIGR01212 family; Members of this family are apparent radical-SAM enzymes, related to the N-terminal region of the bifunctional ELP3, whose C-terminal region is part of the elongator complex and appears to acetylate histones and other proteins. ELP3 binds S-adenosylmethionine (SAM) and was recently shown to be involved in a DNA demethylation process in eukaryotes. Close sequence similarity of this family (with lacks the GNAT family acetyltransferase domain) to the ELP3 N-terminal region and a strong match to the pfam04055 support identification of this family as radical SAM despite the atypical spacing between first and second Cys residues in the 4Fe4S-binding motif. [Unknown function, Enzymes of unknown specificity]
Pssm-ID: 130279 [Multi-domain] Cd Length: 302 Bit Score: 542.81 E-value: 0e+00
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
42-257
2.42e-36
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: 130.21 E-value: 2.42e-36
Radical_SAM C-terminal domain; This domain is found as a C-terminal extension to a subset of ...
220-302
2.83e-36
Radical_SAM C-terminal domain; This domain is found as a C-terminal extension to a subset of Radical_SAM domains. It is found in archaeal, bacterial, fungal, plant and human proteins.
Pssm-ID: 465061 [Multi-domain] Cd Length: 83 Bit Score: 125.59 E-value: 2.83e-36
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
53-211
6.71e-14
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.
Pssm-ID: 427681 [Multi-domain] Cd Length: 159 Bit Score: 68.32 E-value: 6.71e-14
Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase ...
156-252
1.32e-06
Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase [Coenzyme transport and metabolism]; Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase is part of the Pathway/BioSystem: Heme biosynthesis
Pssm-ID: 440400 [Multi-domain] Cd Length: 400 Bit Score: 49.41 E-value: 1.32e-06
Biotin synthase or related enzyme [Coenzyme transport and metabolism]; Biotin synthase or ...
182-236
2.68e-03
Biotin synthase or related enzyme [Coenzyme transport and metabolism]; Biotin synthase or related enzyme is part of the Pathway/BioSystem: Biotin biosynthesis
Pssm-ID: 440268 [Multi-domain] Cd Length: 308 Bit Score: 38.88 E-value: 2.68e-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.
(labeled illustration) Full Display shows all domain models, in each hit category below, that meet or exceed the RPS-BLAST threshold for statistical significance.
(labeled illustration) Four types of hits can be shown, as available,
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specific hits meet or exceed a domain-specific e-value threshold
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and represent a very high confidence that the query sequence belongs to the same protein family as the sequences use to create the domain model
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