hopanoid C-3 methylase HpnR; Members of this are family are a B12-binding domain/radical SAM ...
1-489
0e+00
hopanoid C-3 methylase HpnR; Members of this are family are a B12-binding domain/radical SAM domain protein required for 3-methylhopanoid production. Activity was confirmed by mutant phenotype by disrupting this gene in Methylococcus capsulatus strain Bath. This protein family should only occur in genomes that encode a squalene-hopene cyclase (see TIGR01507). [Fatty acid and phospholipid metabolism, Biosynthesis]
:
Pssm-ID: 275160 [Multi-domain] Cd Length: 490 Bit Score: 966.87 E-value: 0e+00
hopanoid C-3 methylase HpnR; Members of this are family are a B12-binding domain/radical SAM ...
1-489
0e+00
hopanoid C-3 methylase HpnR; Members of this are family are a B12-binding domain/radical SAM domain protein required for 3-methylhopanoid production. Activity was confirmed by mutant phenotype by disrupting this gene in Methylococcus capsulatus strain Bath. This protein family should only occur in genomes that encode a squalene-hopene cyclase (see TIGR01507). [Fatty acid and phospholipid metabolism, Biosynthesis]
Pssm-ID: 275160 [Multi-domain] Cd Length: 490 Bit Score: 966.87 E-value: 0e+00
B12 binding domain; This domain binds to B12 (adenosylcobamide), it is found in several ...
14-131
7.83e-24
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: 96.24 E-value: 7.83e-24
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
187-375
1.04e-20
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: 90.54 E-value: 1.04e-20
B12 binding domain_like associated with radical SAM domain. This domain shows similarity with ...
21-145
1.10e-20
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: 87.76 E-value: 1.10e-20
hopanoid C-3 methylase HpnR; Members of this are family are a B12-binding domain/radical SAM ...
1-489
0e+00
hopanoid C-3 methylase HpnR; Members of this are family are a B12-binding domain/radical SAM domain protein required for 3-methylhopanoid production. Activity was confirmed by mutant phenotype by disrupting this gene in Methylococcus capsulatus strain Bath. This protein family should only occur in genomes that encode a squalene-hopene cyclase (see TIGR01507). [Fatty acid and phospholipid metabolism, Biosynthesis]
Pssm-ID: 275160 [Multi-domain] Cd Length: 490 Bit Score: 966.87 E-value: 0e+00
B12 binding domain; This domain binds to B12 (adenosylcobamide), it is found in several ...
14-131
7.83e-24
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: 96.24 E-value: 7.83e-24
B12-binding domain/radical SAM domain protein, MJ_0865 family; Members of this family have ...
28-369
4.81e-21
B12-binding domain/radical SAM domain protein, MJ_0865 family; Members of this family have both a B12 binding homology domain (pfam02310) and a radical SAM domain (pfam04055), and occur only once per genome. This protein occurs so far only in methanogenic archaea. Some species with members of this family have a related protein with similar domain architecture (see TIGR04013). [Unknown function, Enzymes of unknown specificity]
Pssm-ID: 274918 [Multi-domain] Cd Length: 434 Bit Score: 95.58 E-value: 4.81e-21
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
187-375
1.04e-20
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: 90.54 E-value: 1.04e-20
B12 binding domain_like associated with radical SAM domain. This domain shows similarity with ...
21-145
1.10e-20
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: 87.76 E-value: 1.10e-20
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
191-332
2.77e-15
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: 73.33 E-value: 2.77e-15
B12-binding domain/radical SAM domain protein, rhizo-twelve system; A variety of bacteria, ...
22-399
5.21e-14
B12-binding domain/radical SAM domain protein, rhizo-twelve system; A variety of bacteria, including multiple species of Bradyrhizobium, Mesorhizobium, and Methylobacterium, have a typically twelve-gene cassette (hence the designation rhizo-twelve) for the biosynthesis of some unknown oligosaccaride. This family is a B12-binding domain/radical SAM domain protein found in roughly have of these cassettes, but nowhere else.
Pssm-ID: 275111 [Multi-domain] Cd Length: 422 Bit Score: 74.05 E-value: 5.21e-14
lipid biosynthesis B12-binding/radical SAM protein; Members of this protein family occur in ...
22-131
1.48e-09
lipid biosynthesis B12-binding/radical SAM protein; Members of this protein family occur in conserved genomic contexts highly suggestive of lipid biosynthesis, including an island shared between Kuenenia stuttgartiensis, which produces ladderanes, and Desulfotalea psychrophila, which produces a different kind of unusual polyunsaturated hydrocarbon.
Pssm-ID: 188587 Cd Length: 151 Bit Score: 56.58 E-value: 1.48e-09
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
189-371
1.57e-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: 57.73 E-value: 1.57e-09
B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 ...
24-135
7.15e-08
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: 51.23 E-value: 7.15e-08
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
188-332
1.14e-07
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: 51.44 E-value: 1.14e-07
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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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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(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.
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