23S rRNA (adenine(2503)-C(2))-methyltransferase RlmN is a dual-specificity RNA methyltransferase that specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs
Adenine C2-methylase RlmN of 23S rRNA A2503 and tRNA A37 [Translation, ribosomal structure and ...
10-352
0e+00
Adenine C2-methylase RlmN of 23S rRNA A2503 and tRNA A37 [Translation, ribosomal structure and biogenesis]; Adenine C2-methylase RlmN of 23S rRNA A2503 and tRNA A37 is part of the Pathway/BioSystem: 23S rRNA modification
:
Pssm-ID: 440582 Cd Length: 338 Bit Score: 600.09 E-value: 0e+00
Adenine C2-methylase RlmN of 23S rRNA A2503 and tRNA A37 [Translation, ribosomal structure and ...
10-352
0e+00
Adenine C2-methylase RlmN of 23S rRNA A2503 and tRNA A37 [Translation, ribosomal structure and biogenesis]; Adenine C2-methylase RlmN of 23S rRNA A2503 and tRNA A37 is part of the Pathway/BioSystem: 23S rRNA modification
Pssm-ID: 440582 Cd Length: 338 Bit Score: 600.09 E-value: 0e+00
23S rRNA (adenine(2503)-C(2))-methyltransferase; Members of this family are RlmN, a 23S rRNA ...
3-359
1.39e-172
23S rRNA (adenine(2503)-C(2))-methyltransferase; Members of this family are RlmN, a 23S rRNA m2A2503 methyltransferase in the radical SAM enzyme family. Closely related is Cfr, a Staphylococcus sciuri plasmid-borne homolog to this family, Cfr, has been identified as essential to transferrable resistance to chloramphenicol and florfenicol. Cfr methylates 23S RNA at a different site. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 272874 Cd Length: 355 Bit Score: 485.09 E-value: 1.39e-172
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
115-278
1.27e-14
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: 71.02 E-value: 1.27e-14
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
115-316
3.16e-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: 56.19 E-value: 3.16e-09
Adenine C2-methylase RlmN of 23S rRNA A2503 and tRNA A37 [Translation, ribosomal structure and ...
10-352
0e+00
Adenine C2-methylase RlmN of 23S rRNA A2503 and tRNA A37 [Translation, ribosomal structure and biogenesis]; Adenine C2-methylase RlmN of 23S rRNA A2503 and tRNA A37 is part of the Pathway/BioSystem: 23S rRNA modification
Pssm-ID: 440582 Cd Length: 338 Bit Score: 600.09 E-value: 0e+00
23S rRNA (adenine(2503)-C(2))-methyltransferase; Members of this family are RlmN, a 23S rRNA ...
3-359
1.39e-172
23S rRNA (adenine(2503)-C(2))-methyltransferase; Members of this family are RlmN, a 23S rRNA m2A2503 methyltransferase in the radical SAM enzyme family. Closely related is Cfr, a Staphylococcus sciuri plasmid-borne homolog to this family, Cfr, has been identified as essential to transferrable resistance to chloramphenicol and florfenicol. Cfr methylates 23S RNA at a different site. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 272874 Cd Length: 355 Bit Score: 485.09 E-value: 1.39e-172
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
115-278
1.27e-14
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: 71.02 E-value: 1.27e-14
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
115-316
3.16e-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: 56.19 E-value: 3.16e-09
Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal ...
168-331
1.60e-03
Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal structure and biogenesis]; Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 440495 [Multi-domain] Cd Length: 248 Bit Score: 39.79 E-value: 1.60e-03
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
114-218
4.48e-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: 38.19 E-value: 4.48e-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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Functional characterization of the conserved domain architecture found on the query.
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This image shows a graphical summary of conserved domains identified on the query sequence.
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if a domain or superfamily has been annotated with functional sites (conserved features),
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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)
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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
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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
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