radical SAM family protein may generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity and contain a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; may belong to the SPL (spore photoproduct lyase) radical SAM family
PA0069 family radical SAM protein; PA0069 from Pseudomonas aeruginosa is the founding member a ...
8-352
0e+00
PA0069 family radical SAM protein; PA0069 from Pseudomonas aeruginosa is the founding member a family of radical SAM enzymes of unknown function. Note that inclusion of some members of this family in COG1533, along with some spore photoproduct lyase (SPL) proteins, has led to some family members being annotated as SPL.
:
Pssm-ID: 468133 Cd Length: 348 Bit Score: 560.69 E-value: 0e+00
PA0069 family radical SAM protein; PA0069 from Pseudomonas aeruginosa is the founding member a ...
8-352
0e+00
PA0069 family radical SAM protein; PA0069 from Pseudomonas aeruginosa is the founding member a family of radical SAM enzymes of unknown function. Note that inclusion of some members of this family in COG1533, along with some spore photoproduct lyase (SPL) proteins, has led to some family members being annotated as SPL.
Pssm-ID: 468133 Cd Length: 348 Bit Score: 560.69 E-value: 0e+00
Rv2578c family radical SAM protein; This radical SAM family, which includes Rv2578c from ...
43-307
3.52e-73
Rv2578c family radical SAM protein; This radical SAM family, which includes Rv2578c from Mycobacterium tuberculosis, is uncharacterized, but is notable in part because inteins are found in many members of this family. Although inteins are viewed mostly as selfish genetic elements, they occur often in important housekeeping proteins, such as RecA, in a way that suggests domestication of the element into a regulatory system in which triggering intein excision results in an irreverisible change to the host protein. Intein-containing members of this family are found by HMM NF038136. Rv2578c itself appears to be part of the SOS regulon.
Pssm-ID: 468378 Cd Length: 315 Bit Score: 229.35 E-value: 3.52e-73
radical SAM mobile pair protein B; Members of this family are the downstream member (B) of a ...
46-239
1.88e-23
radical SAM mobile pair protein B; Members of this family are the downstream member (B) of a pair of tandem-encoded radical SAM enzymes. Most of these radical SAM gene pairs have an additional upstream regulatory gene in the MarR family. Examples of high sequence identity (over 96 percent) from cassettes in several Treponema species of the oral cavity to those in multiple Firmicutes in the gut microbiome suggest recent lateral gene transfer, as might be expected for antibiotic resistance genes. The function is unknown.
Pssm-ID: 275263 [Multi-domain] Cd Length: 285 Bit Score: 98.07 E-value: 1.88e-23
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
69-243
1.58e-19
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: 84.11 E-value: 1.58e-19
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
67-269
1.95e-13
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: 68.51 E-value: 1.95e-13
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
66-275
3.27e-11
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: 62.03 E-value: 3.27e-11
intein-containing Rv2578c family radical SAM protein; This radical SAM family consists of ...
35-82
1.03e-06
intein-containing Rv2578c family radical SAM protein; This radical SAM family consists of intein-containing radical SAM proteins related to (but not including) Rv2578c from Mycobacterium tuberculosisis. Rv2578c and its homologs are uncharacterized, but presence of inteins in multiple members of the family is notable. Although inteins are viewed mostly as selfish genetic elements, they occur often in important housekeeping proteins, such as RecA, in a way that suggests domestication of the element into a regulatory system in which triggering intein excision results in an irreverisible and situationally beneficial change to the host protein.
Pssm-ID: 468379 [Multi-domain] Cd Length: 572 Bit Score: 50.20 E-value: 1.03e-06
PA0069 family radical SAM protein; PA0069 from Pseudomonas aeruginosa is the founding member a ...
8-352
0e+00
PA0069 family radical SAM protein; PA0069 from Pseudomonas aeruginosa is the founding member a family of radical SAM enzymes of unknown function. Note that inclusion of some members of this family in COG1533, along with some spore photoproduct lyase (SPL) proteins, has led to some family members being annotated as SPL.
Pssm-ID: 468133 Cd Length: 348 Bit Score: 560.69 E-value: 0e+00
Rv2578c family radical SAM protein; This radical SAM family, which includes Rv2578c from ...
43-307
3.52e-73
Rv2578c family radical SAM protein; This radical SAM family, which includes Rv2578c from Mycobacterium tuberculosis, is uncharacterized, but is notable in part because inteins are found in many members of this family. Although inteins are viewed mostly as selfish genetic elements, they occur often in important housekeeping proteins, such as RecA, in a way that suggests domestication of the element into a regulatory system in which triggering intein excision results in an irreverisible change to the host protein. Intein-containing members of this family are found by HMM NF038136. Rv2578c itself appears to be part of the SOS regulon.
Pssm-ID: 468378 Cd Length: 315 Bit Score: 229.35 E-value: 3.52e-73
radical SAM mobile pair protein B; Members of this family are the downstream member (B) of a ...
46-239
1.88e-23
radical SAM mobile pair protein B; Members of this family are the downstream member (B) of a pair of tandem-encoded radical SAM enzymes. Most of these radical SAM gene pairs have an additional upstream regulatory gene in the MarR family. Examples of high sequence identity (over 96 percent) from cassettes in several Treponema species of the oral cavity to those in multiple Firmicutes in the gut microbiome suggest recent lateral gene transfer, as might be expected for antibiotic resistance genes. The function is unknown.
Pssm-ID: 275263 [Multi-domain] Cd Length: 285 Bit Score: 98.07 E-value: 1.88e-23
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
69-243
1.58e-19
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: 84.11 E-value: 1.58e-19
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
67-269
1.95e-13
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: 68.51 E-value: 1.95e-13
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
66-275
3.27e-11
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: 62.03 E-value: 3.27e-11
intein-containing Rv2578c family radical SAM protein; This radical SAM family consists of ...
35-82
1.03e-06
intein-containing Rv2578c family radical SAM protein; This radical SAM family consists of intein-containing radical SAM proteins related to (but not including) Rv2578c from Mycobacterium tuberculosisis. Rv2578c and its homologs are uncharacterized, but presence of inteins in multiple members of the family is notable. Although inteins are viewed mostly as selfish genetic elements, they occur often in important housekeeping proteins, such as RecA, in a way that suggests domestication of the element into a regulatory system in which triggering intein excision results in an irreverisible and situationally beneficial change to the host protein.
Pssm-ID: 468379 [Multi-domain] Cd Length: 572 Bit Score: 50.20 E-value: 1.03e-06
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
66-226
1.86e-03
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: 38.35 E-value: 1.86e-03
Putative catalytic domain of lipopolysaccharide biosynthesis protein WalW and its bacterial ...
112-245
5.44e-03
Putative catalytic domain of lipopolysaccharide biosynthesis protein WalW and its bacterial homologs; This family corresponds to a group of uncharacterized lipopolysaccharide biosynthesis protein WalW found in bacteria. Although their biochemical properties remain to be determined, members of this family is composed of a seven-stranded barrel with detectable sequence similarity to the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily.
Pssm-ID: 200561 [Multi-domain] Cd Length: 295 Bit Score: 38.00 E-value: 5.44e-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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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