radical SAM/CxCxxxxC motif protein YfkAB contains an N-terminal radical SAM domain and a C-terminal domain with a CxCxxxxC motif that suggests binding to an additional metallocluster; may have a housekeeping function
radical SAM/CxCxxxxC motif protein YfkAB; Members of this highly conserved family in some ...
8-371
0e+00
radical SAM/CxCxxxxC motif protein YfkAB; Members of this highly conserved family in some Firmicutes have an N-terminal radical SAM domain (pfam04055) and a C-terminal pfam08756 domain with a CxCxxxxC motif that suggests binding to an additional metallocluster. It appears all correct sequences in this family are about 370 amino acids in length, containing the YfkA and YfkB regions originally reported as separate ORFs in Bacillus subtilis. Partial Phylogenetic Profiling shows occurrences almost exclusively in the Bacilli, with very few examples of either lateral transfer or gene loss. The essentially monophyletic distribution suggests a housekeeping function. Members have no well-conserved gene neighborhood. The function is unknown. [Unknown function, Enzymes of unknown specificity]
:
Pssm-ID: 275271 [Multi-domain] Cd Length: 363 Bit Score: 677.49 E-value: 0e+00
radical SAM/CxCxxxxC motif protein YfkAB; Members of this highly conserved family in some ...
8-371
0e+00
radical SAM/CxCxxxxC motif protein YfkAB; Members of this highly conserved family in some Firmicutes have an N-terminal radical SAM domain (pfam04055) and a C-terminal pfam08756 domain with a CxCxxxxC motif that suggests binding to an additional metallocluster. It appears all correct sequences in this family are about 370 amino acids in length, containing the YfkA and YfkB regions originally reported as separate ORFs in Bacillus subtilis. Partial Phylogenetic Profiling shows occurrences almost exclusively in the Bacilli, with very few examples of either lateral transfer or gene loss. The essentially monophyletic distribution suggests a housekeeping function. Members have no well-conserved gene neighborhood. The function is unknown. [Unknown function, Enzymes of unknown specificity]
Pssm-ID: 275271 [Multi-domain] Cd Length: 363 Bit Score: 677.49 E-value: 0e+00
YfkB-like domain; This protein is adjacent to YfkA in B. subtilis. In other bacterial species ...
221-370
1.48e-102
YfkB-like domain; This protein is adjacent to YfkA in B. subtilis. In other bacterial species it is fused to this protein. As YfkA contains a Radical SAM domain it suggests this domain is interacts with them.
Pssm-ID: 430194 Cd Length: 149 Bit Score: 299.55 E-value: 1.48e-102
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
34-192
1.81e-19
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: 84.57 E-value: 1.81e-19
twitch domain-containing radical SAM protein; Members of this family are unusual among radical ...
40-332
1.67e-06
twitch domain-containing radical SAM protein; Members of this family are unusual among radical SAM proteins in several ways. First, the N-terminal region consists of an iron-sulfur cluster-binding twitch domain (half of a SPASM domain), something usually found C-terminal to the radical SAM domain. Second, the radical SAM domains in many of the members of this family score poorly vs. the Pfam HMM, PF04055 (version 19), used to identify radical SAM. Lastly, the majority of members sequenced to date come from uncultured bacteria from marine or aquifer sources rather than from conventionally cultured bacterial isolates. The function is unknown.
Pssm-ID: 468123 [Multi-domain] Cd Length: 396 Bit Score: 49.57 E-value: 1.67e-06
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
38-142
3.79e-06
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: 47.33 E-value: 3.79e-06
radical SAM/CxCxxxxC motif protein YfkAB; Members of this highly conserved family in some ...
8-371
0e+00
radical SAM/CxCxxxxC motif protein YfkAB; Members of this highly conserved family in some Firmicutes have an N-terminal radical SAM domain (pfam04055) and a C-terminal pfam08756 domain with a CxCxxxxC motif that suggests binding to an additional metallocluster. It appears all correct sequences in this family are about 370 amino acids in length, containing the YfkA and YfkB regions originally reported as separate ORFs in Bacillus subtilis. Partial Phylogenetic Profiling shows occurrences almost exclusively in the Bacilli, with very few examples of either lateral transfer or gene loss. The essentially monophyletic distribution suggests a housekeeping function. Members have no well-conserved gene neighborhood. The function is unknown. [Unknown function, Enzymes of unknown specificity]
Pssm-ID: 275271 [Multi-domain] Cd Length: 363 Bit Score: 677.49 E-value: 0e+00
YfkB-like domain; This protein is adjacent to YfkA in B. subtilis. In other bacterial species ...
221-370
1.48e-102
YfkB-like domain; This protein is adjacent to YfkA in B. subtilis. In other bacterial species it is fused to this protein. As YfkA contains a Radical SAM domain it suggests this domain is interacts with them.
Pssm-ID: 430194 Cd Length: 149 Bit Score: 299.55 E-value: 1.48e-102
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
34-192
1.81e-19
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: 84.57 E-value: 1.81e-19
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
38-187
3.60e-11
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: 61.00 E-value: 3.60e-11
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
42-129
6.26e-07
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic radical activating enzyme NrdG/QueE is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 440367 [Multi-domain] Cd Length: 205 Bit Score: 49.37 E-value: 6.26e-07
twitch domain-containing radical SAM protein; Members of this family are unusual among radical ...
40-332
1.67e-06
twitch domain-containing radical SAM protein; Members of this family are unusual among radical SAM proteins in several ways. First, the N-terminal region consists of an iron-sulfur cluster-binding twitch domain (half of a SPASM domain), something usually found C-terminal to the radical SAM domain. Second, the radical SAM domains in many of the members of this family score poorly vs. the Pfam HMM, PF04055 (version 19), used to identify radical SAM. Lastly, the majority of members sequenced to date come from uncultured bacteria from marine or aquifer sources rather than from conventionally cultured bacterial isolates. The function is unknown.
Pssm-ID: 468123 [Multi-domain] Cd Length: 396 Bit Score: 49.57 E-value: 1.67e-06
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
38-142
3.79e-06
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: 47.33 E-value: 3.79e-06
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in ...
31-123
3.08e-03
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in Syntrophobacter fumaroxidans MPOB, Chlorobium limicola DSM 245, Methanocella paludicola SANAE, and delta proteobacterium NaphS2 contains two PqqE-like radical SAM/SPASM domain proteins, a PqqD homolog, and a conserved hypothetical protein. These components suggest modification of a ribosomally produced peptide precursor, but the precursor has not been identified. Of the two PqqE homologs of the cassette, this family is the more distant in sequence.
Pssm-ID: 211974 [Multi-domain] Cd Length: 353 Bit Score: 39.44 E-value: 3.08e-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.
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