[FeFe] hydrogenase H-cluster radical SAM maturase HydE; This model describes the radical SAM ...
6-311
1.02e-126
[FeFe] hydrogenase H-cluster radical SAM maturase HydE; This model describes the radical SAM protein HydE, one of a pair of radical SAM proteins, along with GTP-binding protein HydF, for maturation of [Fe] hydrogenase in Chlamydomonas reinhardtii and numerous bacteria. [Protein fate, Protein modification and repair]
The actual alignment was detected with superfamily member TIGR03956:
Pssm-ID: 274880 [Multi-domain] Cd Length: 340 Bit Score: 366.50 E-value: 1.02e-126
[FeFe] hydrogenase H-cluster radical SAM maturase HydE; This model describes the radical SAM ...
6-311
1.02e-126
[FeFe] hydrogenase H-cluster radical SAM maturase HydE; This model describes the radical SAM protein HydE, one of a pair of radical SAM proteins, along with GTP-binding protein HydF, for maturation of [Fe] hydrogenase in Chlamydomonas reinhardtii and numerous bacteria. [Protein fate, Protein modification and repair]
Pssm-ID: 274880 [Multi-domain] Cd Length: 340 Bit Score: 366.50 E-value: 1.02e-126
Biotin synthase or related enzyme [Coenzyme transport and metabolism]; Biotin synthase or ...
14-334
1.93e-115
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: 336.64 E-value: 1.93e-115
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
53-254
2.24e-26
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: 104.41 E-value: 2.24e-26
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
59-207
5.52e-22
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: 90.66 E-value: 5.52e-22
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
57-243
9.72e-11
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: 60.42 E-value: 9.72e-11
[FeFe] hydrogenase H-cluster radical SAM maturase HydE; This model describes the radical SAM ...
6-311
1.02e-126
[FeFe] hydrogenase H-cluster radical SAM maturase HydE; This model describes the radical SAM protein HydE, one of a pair of radical SAM proteins, along with GTP-binding protein HydF, for maturation of [Fe] hydrogenase in Chlamydomonas reinhardtii and numerous bacteria. [Protein fate, Protein modification and repair]
Pssm-ID: 274880 [Multi-domain] Cd Length: 340 Bit Score: 366.50 E-value: 1.02e-126
Biotin synthase or related enzyme [Coenzyme transport and metabolism]; Biotin synthase or ...
14-334
1.93e-115
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: 336.64 E-value: 1.93e-115
2-iminoacetate synthase ThiH/Menaquinone biosynthesis enzymes MqnC and MqnE [Coenzyme ...
5-288
4.99e-36
2-iminoacetate synthase ThiH/Menaquinone biosynthesis enzymes MqnC and MqnE [Coenzyme transport and metabolism]; 2-iminoacetate synthase ThiH/Menaquinone biosynthesis enzymes MqnC and MqnE is part of the Pathway/BioSystem: Thiamine biosynthesis
Pssm-ID: 440680 [Multi-domain] Cd Length: 351 Bit Score: 133.33 E-value: 4.99e-36
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
53-254
2.24e-26
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: 104.41 E-value: 2.24e-26
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
59-207
5.52e-22
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: 90.66 E-value: 5.52e-22
7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofH subunit; This enzyme, together with ...
21-288
1.28e-19
7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofH subunit; This enzyme, together with CofG, complete the biosynthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, the chromophore of coenzyme F420. The chromophore is also used in cyanobacteria DNA photolyases. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]
Pssm-ID: 132590 [Multi-domain] Cd Length: 343 Bit Score: 88.49 E-value: 1.28e-19
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
54-195
3.75e-14
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: 69.16 E-value: 3.75e-14
radical SAM domain protein, CofH subfamily; This protein family includes the CofH protein of ...
57-288
1.39e-11
radical SAM domain protein, CofH subfamily; This protein family includes the CofH protein of coenzyme F(420) biosynthesis from Methanocaldococcus jannaschii, but appears to hit genomes more broadly than just the subset that make coenzyme F(420), so that narrower group is being built as a separate family. [Hypothetical proteins, Conserved]
Pssm-ID: 273071 [Multi-domain] Cd Length: 309 Bit Score: 64.34 E-value: 1.39e-11
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
57-243
9.72e-11
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: 60.42 E-value: 9.72e-11
Biotin and Thiamin Synthesis associated domain; Biotin synthase (BioB), , catalyses the last ...
226-292
1.19e-10
Biotin and Thiamin Synthesis associated domain; Biotin synthase (BioB), , catalyses the last step of the biotin biosynthetic pathway. The reaction consists in the introduction of a sulphur atom into dethiobiotin. BioB functions as a homodimer. Thiamin synthesis if a complex process involving at least six gene products (ThiFSGH, ThiI and ThiJ). Two of the proteins required for the biosynthesis of the thiazole moiety of thiamine (vitamin B(1)) are ThiG and ThiH (this entry) and form a heterodimer. Both of these reactions are thought of involve the binding of co-factors, and both function as dimers.. This domain therefore may be involved in co-factor binding or dimerisation.
Pssm-ID: 214877 [Multi-domain] Cd Length: 94 Bit Score: 57.49 E-value: 1.19e-10
Biotin and Thiamin Synthesis associated domain; Biotin synthase (BioB), EC:2.8.1.6, catalyzes the last step of the biotin biosynthetic pathway. The reaction consists in the introduction of a sulphur atom into dethiobiotin. BioB functions as a homodimer. Thiamin synthesis if a complex process involving at least six gene products (ThiFSGH, ThiI and ThiJ). Two of the proteins required for the biosynthesis of the thiazole moiety of thiamine (vitamin B(1)) are ThiG and ThiH (this family) and form a heterodimer. Both of these reactions are thought of involve the binding of co-factors, and both function as dimers. This domain therefore may be involved in co-factor binding or dimerization (Finn, RD personal observation).
Pssm-ID: 462054 [Multi-domain] Cd Length: 85 Bit Score: 55.54 E-value: 4.94e-10
7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofG subunit; This model represents ...
57-261
9.59e-10
7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofG subunit; This model represents either a subunit or a domain, depending on whether or not the genes are fused, of a bifunctional protein that completes the synthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin, or FO. FO is the chromophore of coenzyme F(420), involved in methanogenesis in methanogenic archaea but found in certain other lineages as well. The chromophore also occurs as a cofactor in DNA photolyases in Cyanobacteria. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]
Pssm-ID: 132589 [Multi-domain] Cd Length: 322 Bit Score: 58.84 E-value: 9.59e-10
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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