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 ...
352-647
1.27e-113
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: 344.62 E-value: 1.27e-113
Flavoprotein (flavin reductase) subunit CysJ of sulfite and N-hydroxylaminopurine reductases ...
76-237
3.27e-28
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: 119.87 E-value: 3.27e-28
wyosine biosynthesis protein TYW1; Members of this protein family are the archaeal protein ...
352-647
1.27e-113
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: 344.62 E-value: 1.27e-113
Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal ...
381-637
1.98e-54
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: 187.32 E-value: 1.98e-54
Flavoprotein (flavin reductase) subunit CysJ of sulfite and N-hydroxylaminopurine reductases ...
76-237
3.27e-28
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: 119.87 E-value: 3.27e-28
Wyosine base formation; Some proteins in this family appear to be important in wyosine base ...
586-649
1.71e-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: 1.71e-24
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
404-596
4.45e-08
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: 53.88 E-value: 4.45e-08
flavodoxin, short chain; Flavodoxins are small redox-active proteins with a flavin ...
74-179
7.34e-04
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: 40.40 E-value: 7.34e-04
wyosine biosynthesis protein TYW1; Members of this protein family are the archaeal protein ...
352-647
1.27e-113
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: 344.62 E-value: 1.27e-113
Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal ...
381-637
1.98e-54
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: 187.32 E-value: 1.98e-54
Flavoprotein (flavin reductase) subunit CysJ of sulfite and N-hydroxylaminopurine reductases ...
76-237
3.27e-28
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: 119.87 E-value: 3.27e-28
Wyosine base formation; Some proteins in this family appear to be important in wyosine base ...
586-649
1.71e-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: 1.71e-24
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
408-579
4.49e-09
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: 56.00 E-value: 4.49e-09
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
404-596
4.45e-08
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: 53.88 E-value: 4.45e-08
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
407-557
6.00e-08
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: 52.60 E-value: 6.00e-08
flavodoxin, short chain; Flavodoxins are small redox-active proteins with a flavin ...
74-179
7.34e-04
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: 40.40 E-value: 7.34e-04
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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