radical SAM family uncharacterized protein; This model describes a radical SAM protein, or ...
32-575
1.45e-149
radical SAM family uncharacterized protein; This model describes a radical SAM protein, or protein region, regularly found paired with or fused to a region described by TIGR03936. PSI-BLAST analysis of TIGR03936 suggests a relationship to the tRNA pseudouridine synthase TruA, suggesting that this system may act in RNA modification. [Unknown function, Enzymes of unknown specificity]
The actual alignment was detected with superfamily member TIGR03960:
Pssm-ID: 188475 [Multi-domain] Cd Length: 605 Bit Score: 443.26 E-value: 1.45e-149
radical SAM family uncharacterized protein; This model describes a radical SAM protein, or ...
32-575
1.45e-149
radical SAM family uncharacterized protein; This model describes a radical SAM protein, or protein region, regularly found paired with or fused to a region described by TIGR03936. PSI-BLAST analysis of TIGR03936 suggests a relationship to the tRNA pseudouridine synthase TruA, suggesting that this system may act in RNA modification. [Unknown function, Enzymes of unknown specificity]
Pssm-ID: 188475 [Multi-domain] Cd Length: 605 Bit Score: 443.26 E-value: 1.45e-149
Radical SAM proteins, N-terminal; This domain is found at the N-terminal of radical SAM ...
47-198
7.23e-72
Radical SAM proteins, N-terminal; This domain is found at the N-terminal of radical SAM proteins from bacteria and archaea. Proteins containing this domain are thought to catalyze diverse reactions, including methylations, isomerization, ring formation, anaerobic oxidation and protein radical formation. The function of this domain is unknown.
Pssm-ID: 466211 Cd Length: 151 Bit Score: 226.83 E-value: 7.23e-72
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
251-445
2.90e-29
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: 115.19 E-value: 2.90e-29
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
252-442
7.88e-09
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: 55.80 E-value: 7.88e-09
radical SAM family uncharacterized protein; This model describes a radical SAM protein, or ...
32-575
1.45e-149
radical SAM family uncharacterized protein; This model describes a radical SAM protein, or protein region, regularly found paired with or fused to a region described by TIGR03936. PSI-BLAST analysis of TIGR03936 suggests a relationship to the tRNA pseudouridine synthase TruA, suggesting that this system may act in RNA modification. [Unknown function, Enzymes of unknown specificity]
Pssm-ID: 188475 [Multi-domain] Cd Length: 605 Bit Score: 443.26 E-value: 1.45e-149
Radical SAM proteins, N-terminal; This domain is found at the N-terminal of radical SAM ...
47-198
7.23e-72
Radical SAM proteins, N-terminal; This domain is found at the N-terminal of radical SAM proteins from bacteria and archaea. Proteins containing this domain are thought to catalyze diverse reactions, including methylations, isomerization, ring formation, anaerobic oxidation and protein radical formation. The function of this domain is unknown.
Pssm-ID: 466211 Cd Length: 151 Bit Score: 226.83 E-value: 7.23e-72
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
251-445
2.90e-29
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: 115.19 E-value: 2.90e-29
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
254-407
3.77e-16
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: 76.03 E-value: 3.77e-16
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
252-442
7.88e-09
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: 55.80 E-value: 7.88e-09
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
251-386
7.32e-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: 43.35 E-value: 7.32e-05
B12 binding domain_like associated with radical SAM domain. This domain shows similarity with ...
132-176
3.33e-04
B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the signature motif Asp-X-His-X-X-Gly, which contains the histidine that acts as a cobalt ligand. The function of this domain remains unclear.
Pssm-ID: 239019 [Multi-domain] Cd Length: 127 Bit Score: 40.76 E-value: 3.33e-04
B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 ...
94-170
5.98e-03
B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins. Not all members of this family contain the conserved binding motif.
Pssm-ID: 239016 [Multi-domain] Cd Length: 125 Bit Score: 36.98 E-value: 5.98e-03
B12 binding domain; This domain binds to B12 (adenosylcobamide), it is found in several ...
94-169
6.35e-03
B12 binding domain; This domain binds to B12 (adenosylcobamide), it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, which is important for B12 binding.
Pssm-ID: 426713 [Multi-domain] Cd Length: 121 Bit Score: 36.92 E-value: 6.35e-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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