Rv1220c Resolved · high auto-curated
H37Rv Rv1220c · MTBC0 - ·
215 aa · 1363503–1364150 (-) ·
RefSeq NP_215736.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | methyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Methyltransferase. Pfam: Methyltransf_3 (PF01596.24), Methyltransf_31 (PF13847.13), Methyltransf_25 (PF13649.13), Methyltransf_24 (PF13578.13), Methyltransf_11 (PF08241.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WJZ7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable O-methyltransferase Rv1220c |
| EC (curated) |
EC 2.1.1.-
|
| Curated function | Probably specifically methylates an O atom of its substrate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | O-Methyltransferase |
| Orthologous group | COG4122 |
| Gene Ontology (8) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.39 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
Methyltransf_3 | PF01596.24 | 2.8e-27 | 41–212 | O-methyltransferase |
Methyltransf_31 | PF13847.13 | 9.1e-08 | 58–167 | Methyltransferase domain |
Methyltransf_25 | PF13649.13 | 1.4e-08 | 62–159 | Methyltransferase domain |
Methyltransf_24 | PF13578.13 | 1.3e-13 | 64–164 | Methyltransferase domain |
Methyltransf_11 | PF08241.19 | 2.3e-06 | 64–163 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1703c (methyltransferase), medium confidence from genomic context alone (score 691 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1703c |
methyltransferase | 691 | 691 ctx | cooccurence:691 |
Rv1219c raaS |
transcriptional regulator | 912 | 576 ctx | neighborhood:574 textmining:803 |
Rv1217c |
tetronasin ABC transporter integral membrane protein | 650 | 552 ctx | neighborhood:550 |
Rv1221 sigE |
ECF RNA polymerase sigma factor SigE | 550 | 551 ctx | neighborhood:551 |
Rv1216c |
integral membrane protein | 653 | 537 ctx | neighborhood:536 |
Rv1218c |
tetronasin ABC transporter ATP-binding protein | 605 | 522 ctx | neighborhood:516 |
Rv1215c hyp |
hypothetical protein | 863 | 463 ctx | neighborhood:457 textmining:756 |
Rv1222 rseA |
anti-sigma E factor RseA | 435 | 435 ctx | neighborhood:433 |
Rv2372c rsmE |
rRNA small subunit methyltransferase E | 410 | 411 | coexpression:411 |
Rv2928 tesA |
thioesterase TesA | 404 | 405 | |
Rv1710 scpB |
segregation and condensation protein ScpB | 400 | 401 | |
Rv1224 tatB |
Sec-independent protein translocase protein TatB | 405 | 397 | |
Rv3330 dacB1 |
penicillin-binding protein DacB | 854 | 267 | textmining:810 |
Rv2779c |
Lrp/AsnC family transcriptional regulator | 634 | 52 | textmining:630 |
Rv3489 hyp |
hypothetical protein | 758 | 50 | textmining:756 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): methyltransferase
- Pfam (hmmscan --cut_ga): Methyltransf_3 PF01596.24 (E=3e-27), Methyltransf_31 PF13847.13 (E=9e-08), Methyltransf_25 PF13649.13 (E=1e-08), Methyltransf_24 PF13578.13 (E=1e-13), Methyltransf_11 PF08241.19 (E=2e-06)
- (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_215736.1)
- Domains: Pfam-A via hmmscan --cut_ga — Methyltransf_3 (PF01596.24), Methyltransf_31 (PF13847.13), Methyltransf_25 (PF13649.13), Methyltransf_24 (PF13578.13), Methyltransf_11 (PF08241.19)
- 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
COG4122 - Curated reference: UniProt P9WJZ7 (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 —
16 functional partner(s); context anchor
Rv1703c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1220c| MPGQPAPSRGESLWAHAEGSISEDVILAGARERATDIGAGAVTPAVGALLCLLAKLSGGKAVAEVGTGAGVSGLWLLSGMRDDGVLTTIDIEPEHLRLARQAFAEAGIGPSRTRLISGRAQEVLTRLADASYDLVFIDADPIDQPDYVAEGVRLLRSGGVIVVHRAALGGRAGDPGARDAEVIAVREAARLIAEDERLTPALVPLGDGVLAAVRD