rsmH Resolved · high auto-curated
H37Rv Rv2165c · MTBC0 mtbc0_002301 ·
396 aa · 2455600–2456790 (-) ·
RefSeq NP_216681.4
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | rRNA small subunit methyltransferase H |
|---|---|
| MTBC0 PGAP re-annotation | 16S rRNA (cytosine(1402)-N(4))-methyltransferase RsmH |
| Revised (this work) | 16S rRNA (cytosine(1402)-N(4))-methyltransferase RsmH. Pfam: Methyltransf_5 (PF01795.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJP1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribosomal RNA small subunit methyltransferase H |
| EC (curated) |
EC 2.1.1.199
|
| Curated function | Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rsmH |
| eggNOG description | Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA |
| Orthologous group | COG0275 |
| EC number |
EC 2.1.1.199
|
| KEGG orthology |
K03438
|
| Gene Ontology (57) |
GO:0000154, GO:0001510, GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005886, GO:0006139, GO:0006364, GO:0006396 +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 | 0.383 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 7 missense, 0 nonsense, 0 frameshift |
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 |
|---|---|---|---|---|
Methyltransf_5 | PF01795.26 | 2.4e-118 | 63–379 | MraW methylase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mraZ (transcriptional regulator MraZ), high confidence from genomic context alone (score 995 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2166c mraZ |
transcriptional regulator MraZ | 999 | 995 ctx | neighborhood:817 coexpression:968 textmining:920 |
Rv2163c pbpB |
penicillin-binding membrane protein PbpB | 972 | 945 ctx | neighborhood:881 coexpression:500 textmining:520 |
Rv2164c hyp |
hypothetical protein | 969 | 910 ctx | neighborhood:882 textmining:673 |
Rv3442c rpsI |
30S ribosomal protein S9 | 834 | 820 | experimental:771 |
Rv2909c rpsP |
30S ribosomal protein S16 | 810 | 800 | experimental:771 |
Rv0053 rpsF |
30S ribosomal protein S6 | 798 | 772 | experimental:771 |
Rv1643 rplT |
50S ribosomal protein L20 | 710 | 710 ctx | cooccurence:699 |
Rv2158c murE |
UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase | 778 | 691 ctx | neighborhood:544 |
Rv2157c murF |
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | 755 | 680 ctx | neighborhood:544 |
Rv2404c lepA |
GTP-binding protein LepA | 705 | 667 ctx | cooccurence:586 |
Rv2152c murC |
UDP-N-acetylmuramate--alanine ligase | 731 | 649 ctx | neighborhood:544 |
Rv2151c ftsQ |
cell division protein FtsQ | 729 | 646 ctx | neighborhood:544 |
Rv2785c rpsO |
30S ribosomal protein S15 | 722 | 637 | experimental:519 |
Rv2367c ybeY |
endoribonuclease | 652 | 636 | experimental:474 |
Rv2155c murD |
UDP-N-acetylmuramoylalanine--D-glutamate ligase | 705 | 616 ctx | neighborhood:544 |
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: rRNA small subunit methyltransferase H
- MTBC0 PGAP product: 16S rRNA (cytosine(1402)-N(4))-methyltransferase RsmH
- Pfam (hmmscan --cut_ga): Methyltransf_5 PF01795.26 (E=2e-118)
- (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_216681.4)
- Domains: Pfam-A via hmmscan --cut_ga — Methyltransf_5 (PF01795.26)
- 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
COG0275 - Curated reference: UniProt P9WJP1 (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 —
113 functional partner(s); context anchor
mraZ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002301|Rv2165c|rsmH MQTRAPWSLPEATLAYFPNARFVSSDRDLGAGAAPGIAASRSTACQTWGGITVADPGSGPTGFGHVPVLAQRCFELLTPALTRYYPDGSQAVLLDATIGAGGHAERFLEGLPGLRLIGLDRDPTALDVARSRLVRFADRLTLVHTRYDCLGAALAESGYAAVGSVDGILFDLGVSSMQLDRAERGFAYATDAPLDMRMDPTTPLTAADIVNTYDEAALADILRRYGEERFARRIAAGIVRRRAKTPFTSTAELVALLYQAIPAPARRVGGHPAKRTFQALRIAVNDELESLRTAVPAALDALAIGGRIAVLAYQSLEDRIVKRVFAEAVASATPAGLPVELPGHEPRFRSLTHGAERASVAEIERNPRSTPVRLRALQRVEHRAQSQQWATEKGDS