rlmB Resolved · high auto-curated
H37Rv Rv3579c · MTBC0 mtbc0_003798 ·
322 aa · 4045102–4046070 (-) ·
RefSeq NP_218096.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB |
|---|---|
| MTBC0 PGAP re-annotation | 23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB |
| Revised (this work) | 23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB. Pfam: SpoU_sub_bind (PF08032.18), SpoU_methylase (PF00588.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFY5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized tRNA/rRNA methyltransferase Rv3579c |
| EC (curated) |
EC 2.1.1.-
|
UniProt still lists this protein as Uncharacterized tRNA/rRNA methyltransferase Rv3579c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rlmB |
| eggNOG description | Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family |
| Orthologous group | COG0566 |
| EC number |
EC 2.1.1.185
|
| KEGG orthology |
K03218
|
| Gene Ontology (57) |
GO:0000154, GO:0000451, GO:0000453, GO:0001510, GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006139 +45 more
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.335 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 5 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.13% of strains (183) · clonal |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
SpoU_sub_bind | PF08032.18 | 8.3e-15 | 70–144 | RNA 2'-O ribose methyltransferase substrate binding |
SpoU_methylase | PF00588.25 | 5.7e-38 | 161–300 | SpoU rRNA Methylase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cysS1 (cysteine--tRNA ligase), high confidence from genomic context alone (score 939 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3580c cysS1 |
cysteine--tRNA ligase | 947 | 939 ctx | neighborhood:882 coexpression:443 |
Rv0640 rplK |
50S ribosomal protein L11 | 829 | 829 ctx | fusion:435 experimental:696 |
Rv3581c ispF |
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 808 | 802 ctx | neighborhood:799 |
Rv3582c ispD |
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase | 800 | 800 ctx | neighborhood:799 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 809 | 792 ctx | neighborhood:456 cooccurence:420 |
Rv3583c carD |
RNA polymerase-binding transcription factor CarD | 789 | 790 ctx | neighborhood:788 |
Rv2420c rsfS hyp |
hypothetical protein | 783 | 773 | experimental:763 |
Rv3456c rplQ |
50S ribosomal protein L17 | 768 | 764 | experimental:739 |
Rv2442c rplU |
50S ribosomal protein L21 | 750 | 751 | experimental:739 |
Rv0723 rplO |
50S ribosomal protein L15 | 747 | 747 | experimental:732 |
Rv0701 rplC |
50S ribosomal protein L3 | 735 | 722 | experimental:664 |
Rv3443c rplM |
50S ribosomal protein L13 | 718 | 705 | experimental:687 |
Rv0715 rplX |
50S ribosomal protein L24 | 703 | 704 | experimental:676 |
Rv1540 |
RNA pseudouridine synthase | 666 | 649 | experimental:466 |
Rv2364c era |
GTPase Era | 642 | 629 ctx | cooccurence:567 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: 23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB
- MTBC0 PGAP product: 23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB
- Pfam (hmmscan --cut_ga): SpoU_sub_bind PF08032.18 (E=8e-15), SpoU_methylase PF00588.25 (E=6e-38)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_218096.1)
- Domains: Pfam-A via hmmscan --cut_ga — SpoU_sub_bind (PF08032.18), SpoU_methylase (PF00588.25)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG0566 - Curated reference: UniProt P9WFY5 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
86 functional partner(s); context anchor
cysS1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003798|Rv3579c|rlmB MPGNSRRRGAVRKSGTKKGAGVGSGGQRRRGLEGRGPTPPAHLRPHHPAAKRARAQPRRPVKRADETETVLGRNPVLECLRAGVPATALYVALGTEADERLTECVARAADSGIAIVELLRADLDRMTANHLHQGIALQVPPYNYAHPDDLLAAALDQPPALLVALDNLSDPRNLGAIVRSVAAFGGHGVLIPQRRSASVTAVAWRTSAGAAARIPVARATNLTRTLKGWADRGVRVIGLDAGGGTALDDVDGTDSLVVVVGSEGKGLSRLVRQNCDEVVSIPMAAQAESLNASVAAGVVLAEIARQRRRPREPREQTQNRMI