rsmI Resolved · high auto-curated
H37Rv Rv1003 · MTBC0 mtbc0_001078 ·
285 aa · 1127358–1128215 (+) ·
RefSeq NP_215519.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | rRNA small subunit methyltransferase I |
|---|---|
| MTBC0 PGAP re-annotation | 16S rRNA (cytidine(1402)-2'-O)-methyltransferase |
| Revised (this work) | 16S rRNA (cytidine(1402)-2'-O)-methyltransferase. Pfam: TP_methylase (PF00590.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGW7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribosomal RNA small subunit methyltransferase I |
| EC (curated) |
EC 2.1.1.198
|
| Curated function | Catalyzes the 2'-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | rsmI |
| eggNOG description | Catalyzes the 2'-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA |
| Orthologous group | COG0313 |
| EC number |
EC 2.1.1.198
|
| KEGG orthology |
K07056
|
| Gene Ontology (41) |
GO:0000154, GO:0000451, GO:0000453, GO:0001510, GO:0005575, GO:0005623, GO:0005886, GO:0006139, GO:0006364, GO:0006396, GO:0006725, GO:0006807 +29 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 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 |
|---|---|---|---|---|
TP_methylase | PF00590.26 | 1.3e-27 | 11–208 | Tetrapyrrole (Corrin/Porphyrin) Methylases |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pmt (dolichyl-phosphate-mannose--protein mannosyltransferase), high confidence from genomic context alone (score 786 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1002c pmt |
dolichyl-phosphate-mannose--protein mannosyltransferase | 786 | 786 ctx | neighborhood:783 |
Rv3752c tadA |
cytidine/deoxycytidylate deaminase | 684 | 684 ctx | fusion:662 |
Rv3423c alr |
alanine racemase | 564 | 564 ctx | cooccurence:432 |
Rv2689c hyp |
hypothetical protein | 592 | 536 ctx | cooccurence:490 |
Rv2153c murG |
UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol-N-acetylglucosamine transferase | 434 | 435 ctx | cooccurence:414 |
Rv2150c ftsZ |
cell division protein FtsZ | 561 | 428 ctx | cooccurence:413 |
Rv2364c era |
GTPase Era | 455 | 427 ctx | cooccurence:409 |
Rv2344c dgt |
deoxyguanosine triphosphate triphosphohydrolase | 426 | 426 | coexpression:416 |
Rv2902c rnhB |
ribonuclease HII | 426 | 406 | |
Rv2165c rsmH |
rRNA small subunit methyltransferase H | 978 | 399 | textmining:965 |
Rv2455c korA |
2-oxoglutarate oxidoreductase subunit KorA | 408 | 386 | |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 483 | 319 | |
Rv0640 rplK |
50S ribosomal protein L11 | 405 | 308 | |
Rv3919c gid |
16S rRNA (guanine(527)-N(7))-methyltransferase RsmG | 720 | 286 | textmining:625 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 553 | 258 | textmining:423 |
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 I
- MTBC0 PGAP product: 16S rRNA (cytidine(1402)-2'-O)-methyltransferase
- Pfam (hmmscan --cut_ga): TP_methylase PF00590.26 (E=1e-27)
- (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_215519.1)
- Domains: Pfam-A via hmmscan --cut_ga — TP_methylase (PF00590.26)
- 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
COG0313 - Curated reference: UniProt P9WGW7 (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 —
24 functional partner(s); context anchor
pmt - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001078|Rv1003|rsmI MSSGRLLLGATPLGQPSDASPRLAAALATADVVAAEDTRRVRKLAKALDIRIGGRVVSLFDRVEALRVTALLDAINNGATVLVVSDAGTPVISDPGYRLVAACIDAGVSVTCLPGPSAVTTALVMSGLPAEKFCFEGFAPRKGAARRAWLAELAEERRTCVFFESPRRLAACLNDAVEQLGGARPAAICRELTKVHEEVVRGSLDELAIWAAGGVLGEITVVVAGAAPHAELSSLIAQVEEFVAAGIRVKDACSEVAAAHPGVRTRQLYDAVLQSRRETGGPAQP