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 ...
37-384
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: 688.19 E-value: 0e+00
PA0069 family radical SAM protein; PA0069 from Pseudomonas aeruginosa is the founding member a ...
37-384
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: 688.19 E-value: 0e+00
Rv2578c family radical SAM protein; This radical SAM family, which includes Rv2578c from ...
93-360
2.29e-72
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: 228.58 E-value: 2.29e-72
radical SAM mobile pair protein B; Members of this family are the downstream member (B) of a ...
80-273
8.71e-29
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: 113.48 E-value: 8.71e-29
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
99-273
2.19e-18
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: 81.42 E-value: 2.19e-18
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
96-303
1.70e-14
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: 72.05 E-value: 1.70e-14
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
97-275
7.09e-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: 58.11 E-value: 7.09e-10
intein-containing Rv2578c family radical SAM protein; This radical SAM family consists of ...
90-115
1.13e-03
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: 40.95 E-value: 1.13e-03
PA0069 family radical SAM protein; PA0069 from Pseudomonas aeruginosa is the founding member a ...
37-384
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: 688.19 E-value: 0e+00
Rv2578c family radical SAM protein; This radical SAM family, which includes Rv2578c from ...
93-360
2.29e-72
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: 228.58 E-value: 2.29e-72
radical SAM mobile pair protein B; Members of this family are the downstream member (B) of a ...
80-273
8.71e-29
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: 113.48 E-value: 8.71e-29
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
99-273
2.19e-18
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: 81.42 E-value: 2.19e-18
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
96-303
1.70e-14
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: 72.05 E-value: 1.70e-14
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
97-275
7.09e-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: 58.11 E-value: 7.09e-10
intein-containing Rv2578c family radical SAM protein; This radical SAM family consists of ...
90-115
1.13e-03
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: 40.95 E-value: 1.13e-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.
Click on the triangle to view details about the feature, including a multiple sequence alignment
of your query sequence and the protein sequences used to curate the domain model,
where hash marks (#) above the aligned sequences show the location of the conserved feature residues.
The thumbnail image, if present, provides an approximate view of the feature's location in 3 dimensions.
Click on the triangle for interactive 3D structure viewing options.
Functional characterization of the conserved domain architecture found on the query.
Click here to see more details.
This image shows a graphical summary of conserved domains identified on the query sequence.
The Show Concise/Full Display button at the top of the page can be used to select the desired level of detail: only top scoring hits
(labeled illustration) or all hits
(labeled illustration).
Domains are color coded according to superfamilies
to which they have been assigned. Hits with scores that pass a domain-specific threshold
(specific hits) are drawn in bright colors.
Others (non-specific hits) and
superfamily placeholders are drawn in pastel colors.
if a domain or superfamily has been annotated with functional sites (conserved features),
they are mapped to the query sequence and indicated through sets of triangles
with the same color and shade of the domain or superfamily that provides the annotation. Mouse over the colored bars or triangles to see descriptions of the domains and features.
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.
Click on the domain model's accession number to view the multiple sequence alignment of the proteins used to develop the corresponding domain model.
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)
mapped to the query sequence.
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.
(labeled illustration) Four types of hits can be shown, as available,
for each region on the query sequence:
specific hits meet or exceed a domain-specific e-value threshold
(illustrated example)
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
non-specific hits
meet or exceed the RPS-BLAST threshold for statistical significance (default E-value cutoff of 0.01, or an E-value selected by user via the
advanced search options)
the domain superfamily to which the specific and non-specific hits belong
multi-domain models that were computationally detected and are likely to contain multiple single domains
Retrieve proteins that contain one or more of the domains present in the query sequence, using the Conserved Domain Architecture Retrieval Tool
(CDART).
Modify your query to search against a different database and/or use advanced search options
