radical SAM/SPASM domain protein, FxsB family; This model describes a radical SAM (pfam04055) ...
8-366
0e+00
radical SAM/SPASM domain protein, FxsB family; This model describes a radical SAM (pfam04055)/SPASM domain (TIGR04085) fusion subfamily distinct from PqqE, MftC, anaerobic sulfatase maturases, and other peptide maturases. The combined region described in this model can itself be fused to another domain, such as TIGR04267, or stand alone. Members occurring in the same cassette as a member of family TIGR04268 should be designated FxsB.
:
Pssm-ID: 275093 [Multi-domain] Cd Length: 363 Bit Score: 548.56 E-value: 0e+00
HEXXH motif domain; Some proteins with this domain toward the C-terminus have an N-terminal ...
392-589
3.18e-22
HEXXH motif domain; Some proteins with this domain toward the C-terminus have an N-terminal region with a radical SAM domain (pfam04055) and a SPASM domain (TIGR04085), a combination frequently associated with peptide modification. All seed alignment members, and all family members that are not fused to a radical SAM domain, have a motif HEXXH that suggests metalloprotease activity. A role in peptide or protein maturation is suggested.
The actual alignment was detected with superfamily member NF040587:
Pssm-ID: 473052 Cd Length: 364 Bit Score: 98.64 E-value: 3.18e-22
radical SAM/SPASM domain protein, FxsB family; This model describes a radical SAM (pfam04055) ...
8-366
0e+00
radical SAM/SPASM domain protein, FxsB family; This model describes a radical SAM (pfam04055)/SPASM domain (TIGR04085) fusion subfamily distinct from PqqE, MftC, anaerobic sulfatase maturases, and other peptide maturases. The combined region described in this model can itself be fused to another domain, such as TIGR04267, or stand alone. Members occurring in the same cassette as a member of family TIGR04268 should be designated FxsB.
Pssm-ID: 275093 [Multi-domain] Cd Length: 363 Bit Score: 548.56 E-value: 0e+00
FxsB C-terminal extension domain without HExxH motif; This HMM describes a branch of the ...
392-589
3.18e-22
FxsB C-terminal extension domain without HExxH motif; This HMM describes a branch of the TIGR04267 domain family in which the presumptive metal-binding motif, shared by many metallo-proteases, has been been lost. The domain appears as a C-terminal extension for some of the radical SAM enzyme family FxsB proteins, involved in post-translational modification of the 60-amino acid long RiPP precursor proteins, collectively named FxsA.
Pssm-ID: 468561 Cd Length: 364 Bit Score: 98.64 E-value: 3.18e-22
HEXXH motif domain; Some proteins with this domain toward the C-terminus have an N-terminal ...
380-644
1.55e-14
HEXXH motif domain; Some proteins with this domain toward the C-terminus have an N-terminal region with a radical SAM domain (pfam04055) and a SPASM domain (TIGR04085), a combination frequently associated with peptide modification. All seed alignment members, and all family members that are not fused to a radical SAM domain, have a motif HEXXH that suggests metalloprotease activity. A role in peptide or protein maturation is suggested.
Pssm-ID: 275091 Cd Length: 399 Bit Score: 75.90 E-value: 1.55e-14
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
13-153
1.14e-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: 64.28 E-value: 1.14e-11
radical SAM/SPASM peptide maturase DarW; DarW is a radical SAM/SPASM domain-containing peptide ...
7-375
1.63e-11
radical SAM/SPASM peptide maturase DarW; DarW is a radical SAM/SPASM domain-containing peptide maturase most closely related to the darobactin maturase DarE.
Pssm-ID: 469197 [Multi-domain] Cd Length: 415 Bit Score: 66.45 E-value: 1.63e-11
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
18-153
2.51e-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: 62.16 E-value: 2.51e-11
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
15-132
2.30e-07
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: 52.02 E-value: 2.30e-07
radical SAM/SPASM domain protein, FxsB family; This model describes a radical SAM (pfam04055) ...
8-366
0e+00
radical SAM/SPASM domain protein, FxsB family; This model describes a radical SAM (pfam04055)/SPASM domain (TIGR04085) fusion subfamily distinct from PqqE, MftC, anaerobic sulfatase maturases, and other peptide maturases. The combined region described in this model can itself be fused to another domain, such as TIGR04267, or stand alone. Members occurring in the same cassette as a member of family TIGR04268 should be designated FxsB.
Pssm-ID: 275093 [Multi-domain] Cd Length: 363 Bit Score: 548.56 E-value: 0e+00
FxsB C-terminal extension domain without HExxH motif; This HMM describes a branch of the ...
392-589
3.18e-22
FxsB C-terminal extension domain without HExxH motif; This HMM describes a branch of the TIGR04267 domain family in which the presumptive metal-binding motif, shared by many metallo-proteases, has been been lost. The domain appears as a C-terminal extension for some of the radical SAM enzyme family FxsB proteins, involved in post-translational modification of the 60-amino acid long RiPP precursor proteins, collectively named FxsA.
Pssm-ID: 468561 Cd Length: 364 Bit Score: 98.64 E-value: 3.18e-22
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
11-142
1.31e-15
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: 74.55 E-value: 1.31e-15
HEXXH motif domain; Some proteins with this domain toward the C-terminus have an N-terminal ...
380-644
1.55e-14
HEXXH motif domain; Some proteins with this domain toward the C-terminus have an N-terminal region with a radical SAM domain (pfam04055) and a SPASM domain (TIGR04085), a combination frequently associated with peptide modification. All seed alignment members, and all family members that are not fused to a radical SAM domain, have a motif HEXXH that suggests metalloprotease activity. A role in peptide or protein maturation is suggested.
Pssm-ID: 275091 Cd Length: 399 Bit Score: 75.90 E-value: 1.55e-14
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
13-153
1.14e-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: 64.28 E-value: 1.14e-11
radical SAM/SPASM peptide maturase DarW; DarW is a radical SAM/SPASM domain-containing peptide ...
7-375
1.63e-11
radical SAM/SPASM peptide maturase DarW; DarW is a radical SAM/SPASM domain-containing peptide maturase most closely related to the darobactin maturase DarE.
Pssm-ID: 469197 [Multi-domain] Cd Length: 415 Bit Score: 66.45 E-value: 1.63e-11
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
18-153
2.51e-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: 62.16 E-value: 2.51e-11
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
15-132
2.30e-07
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: 52.02 E-value: 2.30e-07
putative peptide-modifying radical SAM enzyme, Mhun_1560 family; Members of this family are ...
19-153
1.96e-06
putative peptide-modifying radical SAM enzyme, Mhun_1560 family; Members of this family are radical SAM enzymes, homologous to a variety of other peptide-modifying radical SAM, and found primarily in methanogenic archaea.
Pssm-ID: 274966 [Multi-domain] Cd Length: 376 Bit Score: 50.50 E-value: 1.96e-06
GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) [Coenzyme transport and ...
1-142
6.51e-05
GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) [Coenzyme transport and metabolism]; GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) is part of the Pathway/BioSystem: Molybdopterin biosynthesis
Pssm-ID: 442141 [Multi-domain] Cd Length: 329 Bit Score: 45.44 E-value: 6.51e-05
radical SAM additional 4Fe4S-binding SPASM domain; This domain contains regions binding ...
294-355
1.31e-04
radical SAM additional 4Fe4S-binding SPASM domain; This domain contains regions binding additional 4Fe4S clusters found in various radical SAM proteins C-terminal to the domain described by model pfam04055. Radical SAM enzymes with this domain tend to be involved in protein modification, including anaerobic sulfatase maturation proteins, a quinohemoprotein amine dehydrogenase biogenesis protein, the Pep1357-cyclizing radical SAM enzyme, and various bacteriocin biosynthesis proteins. The motif CxxCxxxxxCxxxC is nearly invariant for members of this family, although PqqE has a variant form. We name this domain SPASM for Subtilosin, PQQ, Anaerobic Sulfatase, and Mycofactocin.
Pssm-ID: 274968 [Multi-domain] Cd Length: 93 Bit Score: 41.41 E-value: 1.31e-04
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in ...
7-133
2.67e-04
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: 43.67 E-value: 2.67e-04
radical SAM peptide maturase, CXXX-repeat target family; Members of this radical SAM domain ...
15-152
6.06e-04
radical SAM peptide maturase, CXXX-repeat target family; Members of this radical SAM domain protein are predicted peptide maturases, similar to PqqE, AlbA, the mycofactocin radical SAM maturase, and many others that share the peptide modification radical SAM protein C-terminal additional 4Fe4S-binding domain (TIGR04085). Members co-occur with a protein of unknown function that may be a chaperone or immunity protein and with a peptide that may have twelve or more cysteines occurring regularly spaced every fourth residue. These Cys residues tend to be flanked by residues with small side chains that provide minimal steric hindrance to crosslink formation by the radical SAM enzyme as in the subtilosin A system.
Pssm-ID: 200366 [Multi-domain] Cd Length: 359 Bit Score: 42.57 E-value: 6.06e-04
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
17-109
1.00e-03
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: 40.89 E-value: 1.00e-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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