radical SAM protein 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
7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofH subunit; This enzyme, together with ...
493-836
0e+00
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: 631.62 E-value: 0e+00
2-iminoacetate synthase ThiH/Menaquinone biosynthesis enzymes MqnC and MqnE [Coenzyme ...
487-835
7.18e-161
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: 472.69 E-value: 7.18e-161
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
538-696
4.59e-17
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: 79.11 E-value: 4.59e-17
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
536-715
1.18e-10
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: 61.97 E-value: 1.18e-10
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
74-293
6.00e-09
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: 57.03 E-value: 6.00e-09
7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofH subunit; This enzyme, together with ...
493-836
0e+00
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: 631.62 E-value: 0e+00
7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofG subunit; This model represents ...
70-398
0e+00
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: 568.08 E-value: 0e+00
2-iminoacetate synthase ThiH/Menaquinone biosynthesis enzymes MqnC and MqnE [Coenzyme ...
487-835
7.18e-161
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: 472.69 E-value: 7.18e-161
radical SAM domain protein, CofH subfamily; This protein family includes the CofH protein of ...
528-835
4.42e-125
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: 378.66 E-value: 4.42e-125
dehypoxanthine futalosine cyclase; members of this protein family are involved in menaquinone ...
492-835
4.14e-105
dehypoxanthine futalosine cyclase; members of this protein family are involved in menaquinone biosynthesis by an alternate pathway via futalosine. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone]
Pssm-ID: 274731 [Multi-domain] Cd Length: 340 Bit Score: 328.06 E-value: 4.14e-105
putative menaquinone biosynthesis radical SAM enzyme, SCO4494 family; Members of this protein ...
492-838
4.06e-91
putative menaquinone biosynthesis radical SAM enzyme, SCO4494 family; Members of this protein family appear to be involved in menaquinone biosynthesis by an alternate pathway via futalosine, based on close phylogenetic correlation with known markers of the futalosine pathway, gene clustering in many organisms, and paralogy with the SCO4550 protein. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone]
Pssm-ID: 213851 [Multi-domain] Cd Length: 351 Bit Score: 291.58 E-value: 4.06e-91
2-iminoacetate synthase ThiH/Menaquinone biosynthesis enzymes MqnC and MqnE [Coenzyme ...
18-379
3.31e-61
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: 211.14 E-value: 3.31e-61
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
538-696
4.59e-17
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: 79.11 E-value: 4.59e-17
Biotin synthase or related enzyme [Coenzyme transport and metabolism]; Biotin synthase or ...
28-310
1.87e-14
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: 75.09 E-value: 1.87e-14
Biotin synthase or related enzyme [Coenzyme transport and metabolism]; Biotin synthase or ...
492-646
7.18e-14
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: 73.16 E-value: 7.18e-14
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
536-715
1.18e-10
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: 61.97 E-value: 1.18e-10
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
79-257
9.55e-10
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: 58.31 E-value: 9.55e-10
radical SAM domain protein, CofH subfamily; This protein family includes the CofH protein of ...
69-379
2.37e-09
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: 59.72 E-value: 2.37e-09
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
74-293
6.00e-09
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: 57.03 E-value: 6.00e-09
CofH/MqnC C-terminal region; This entry represents the C-terminal half of the CofH and MqnC ...
719-840
1.15e-08
CofH/MqnC C-terminal region; This entry represents the C-terminal half of the CofH and MqnC enzymes. This entry is found to the C-terminus of pfam04055.
Pssm-ID: 437120 [Multi-domain] Cd Length: 125 Bit Score: 54.01 E-value: 1.15e-08
7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofH subunit; This enzyme, together with ...
29-340
1.11e-06
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: 51.51 E-value: 1.11e-06
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
536-696
3.96e-06
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: 48.55 E-value: 3.96e-06
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
77-289
2.86e-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: 46.17 E-value: 2.86e-05
7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofG subunit; This model represents ...
529-835
6.13e-05
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: 46.13 E-value: 6.13e-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.
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Functional characterization of the conserved domain architecture found on the query.
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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,
or click on the triangles, if present, that represent functional sites (conserved features)
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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.
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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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