flavodoxin domain-containing radical SAM protein similar to S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 that catalyzes the condensation of N-methylguanine with 2 carbon atoms from pyruvate to form the tricyclic 4-demethylwyosine, an intermediate in wybutosine biosynthesis
wyosine biosynthesis protein TYW1; Members of this protein family are the archaeal protein ...
360-656
2.19e-106
wyosine biosynthesis protein TYW1; Members of this protein family are the archaeal protein TWY1, a radical SAM protein that catalyzes the second step in creating the wye-bases, wyosine and derivatives such as wybutosine, for tRNA base modification. [Protein synthesis, tRNA and rRNA base modification]
The actual alignment was detected with superfamily member TIGR03972:
Pssm-ID: 274890 [Multi-domain] Cd Length: 297 Bit Score: 326.13 E-value: 2.19e-106
Flavoprotein (flavin reductase) subunit CysJ of sulfite and N-hydroxylaminopurine reductases ...
81-246
5.39e-30
Flavoprotein (flavin reductase) subunit CysJ of sulfite and N-hydroxylaminopurine reductases [Nucleotide transport and metabolism, Inorganic ion transport and metabolism]; Flavoprotein (flavin reductase) subunit CysJ of sulfite and N-hydroxylaminopurine reductases is part of the Pathway/BioSystem: Cysteine biosynthesis
The actual alignment was detected with superfamily member COG0369:
Pssm-ID: 440138 [Multi-domain] Cd Length: 561 Bit Score: 125.26 E-value: 5.39e-30
wyosine biosynthesis protein TYW1; Members of this protein family are the archaeal protein ...
360-656
2.19e-106
wyosine biosynthesis protein TYW1; Members of this protein family are the archaeal protein TWY1, a radical SAM protein that catalyzes the second step in creating the wye-bases, wyosine and derivatives such as wybutosine, for tRNA base modification. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 274890 [Multi-domain] Cd Length: 297 Bit Score: 326.13 E-value: 2.19e-106
Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal ...
389-645
1.18e-49
Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal structure and biogenesis]; Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 440495 [Multi-domain] Cd Length: 248 Bit Score: 174.22 E-value: 1.18e-49
Flavoprotein (flavin reductase) subunit CysJ of sulfite and N-hydroxylaminopurine reductases ...
81-246
5.39e-30
Flavoprotein (flavin reductase) subunit CysJ of sulfite and N-hydroxylaminopurine reductases [Nucleotide transport and metabolism, Inorganic ion transport and metabolism]; Flavoprotein (flavin reductase) subunit CysJ of sulfite and N-hydroxylaminopurine reductases is part of the Pathway/BioSystem: Cysteine biosynthesis
Pssm-ID: 440138 [Multi-domain] Cd Length: 561 Bit Score: 125.26 E-value: 5.39e-30
Wyosine base formation; Some proteins in this family appear to be important in wyosine base ...
594-657
1.63e-24
Wyosine base formation; Some proteins in this family appear to be important in wyosine base formation in a subset of phenylalanine specific tRNAs. It has been proposed that they participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW.
Pssm-ID: 400775 Cd Length: 63 Bit Score: 96.91 E-value: 1.63e-24
flavodoxin, short chain; Flavodoxins are small redox-active proteins with a flavin ...
79-198
1.44e-05
flavodoxin, short chain; Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They can act in nitrogen fixation by nitrogenase, in sulfite reduction, and light-dependent NADP+ reduction in during photosynthesis, among other roles. This model describes the short chain type. Many of these are involved in sulfite reduction. [Energy metabolism, Electron transport]
Pssm-ID: 273789 [Multi-domain] Cd Length: 140 Bit Score: 45.41 E-value: 1.44e-05
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
412-633
3.66e-05
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.
Pssm-ID: 100105 [Multi-domain] Cd Length: 204 Bit Score: 45.40 E-value: 3.66e-05
wyosine biosynthesis protein TYW1; Members of this protein family are the archaeal protein ...
360-656
2.19e-106
wyosine biosynthesis protein TYW1; Members of this protein family are the archaeal protein TWY1, a radical SAM protein that catalyzes the second step in creating the wye-bases, wyosine and derivatives such as wybutosine, for tRNA base modification. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 274890 [Multi-domain] Cd Length: 297 Bit Score: 326.13 E-value: 2.19e-106
Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal ...
389-645
1.18e-49
Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal structure and biogenesis]; Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 440495 [Multi-domain] Cd Length: 248 Bit Score: 174.22 E-value: 1.18e-49
Flavoprotein (flavin reductase) subunit CysJ of sulfite and N-hydroxylaminopurine reductases ...
81-246
5.39e-30
Flavoprotein (flavin reductase) subunit CysJ of sulfite and N-hydroxylaminopurine reductases [Nucleotide transport and metabolism, Inorganic ion transport and metabolism]; Flavoprotein (flavin reductase) subunit CysJ of sulfite and N-hydroxylaminopurine reductases is part of the Pathway/BioSystem: Cysteine biosynthesis
Pssm-ID: 440138 [Multi-domain] Cd Length: 561 Bit Score: 125.26 E-value: 5.39e-30
Wyosine base formation; Some proteins in this family appear to be important in wyosine base ...
594-657
1.63e-24
Wyosine base formation; Some proteins in this family appear to be important in wyosine base formation in a subset of phenylalanine specific tRNAs. It has been proposed that they participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW.
Pssm-ID: 400775 Cd Length: 63 Bit Score: 96.91 E-value: 1.63e-24
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
416-587
4.15e-07
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: 50.22 E-value: 4.15e-07
flavodoxin, short chain; Flavodoxins are small redox-active proteins with a flavin ...
79-198
1.44e-05
flavodoxin, short chain; Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They can act in nitrogen fixation by nitrogenase, in sulfite reduction, and light-dependent NADP+ reduction in during photosynthesis, among other roles. This model describes the short chain type. Many of these are involved in sulfite reduction. [Energy metabolism, Electron transport]
Pssm-ID: 273789 [Multi-domain] Cd Length: 140 Bit Score: 45.41 E-value: 1.44e-05
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
412-633
3.66e-05
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.
Pssm-ID: 100105 [Multi-domain] Cd Length: 204 Bit Score: 45.40 E-value: 3.66e-05
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
409-564
7.93e-05
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, chromosome partitioning, Coenzyme transport and metabolism];
Pssm-ID: 440301 [Multi-domain] Cd Length: 159 Bit Score: 43.74 E-value: 7.93e-05
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.
Click on the triangle to view details about the feature, including a multiple sequence alignment
of your query sequence and the protein sequences used to curate the domain model,
where hash marks (#) above the aligned sequences show the location of the conserved feature residues.
The thumbnail image, if present, provides an approximate view of the feature's location in 3 dimensions.
Click on the triangle for interactive 3D structure viewing options.
Functional characterization of the conserved domain architecture found on the query.
Click here to see more details.
This image shows a graphical summary of conserved domains identified on the query sequence.
The Show Concise/Full Display button at the top of the page can be used to select the desired level of detail: only top scoring hits
(labeled illustration) or all hits
(labeled illustration).
Domains are color coded according to superfamilies
to which they have been assigned. Hits with scores that pass a domain-specific threshold
(specific hits) are drawn in bright colors.
Others (non-specific hits) and
superfamily placeholders are drawn in pastel colors.
if a domain or superfamily has been annotated with functional sites (conserved features),
they are mapped to the query sequence and indicated through sets of triangles
with the same color and shade of the domain or superfamily that provides the annotation. Mouse over the colored bars or triangles to see descriptions of the domains and features.
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.
Click on the domain model's accession number to view the multiple sequence alignment of the proteins used to develop the corresponding domain model.
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,
or click on the triangles, if present, that represent functional sites (conserved features)
mapped to the query sequence.
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,
for each region on the query sequence:
specific hits meet or exceed a domain-specific e-value threshold
(illustrated example)
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
non-specific hits
meet or exceed the RPS-BLAST threshold for statistical significance (default E-value cutoff of 0.01, or an E-value selected by user via the
advanced search options)
the domain superfamily to which the specific and non-specific hits belong
multi-domain models that were computationally detected and are likely to contain multiple single domains
Retrieve proteins that contain one or more of the domains present in the query sequence, using the Conserved Domain Architecture Retrieval Tool
(CDART).
Modify your query to search against a different database and/or use advanced search options
