Rv3322c Resolved · high auto-curated
H37Rv Rv3322c · MTBC0 - ·
204 aa · 3708438–3709052 (-) ·
RefSeq YP_177958.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | methyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Methyltransferase. Pfam: Methyltransf_25 (PF13649.13). |
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 |
L7N687
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible methyltransferase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| eggNOG description | methyltransferase |
| Orthologous group | COG2890 |
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 | 0.297 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.14% of strains (209) · 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 |
|---|---|---|---|---|
Methyltransf_25 | PF13649.13 | 9.5e-08 | 51–140 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: moaX (MoaD-MoaE fusion protein MoaX), high confidence from genomic context alone (score 884 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3323c moaX |
MoaD-MoaE fusion protein MoaX | 885 | 884 ctx | neighborhood:882 |
Rv3324A |
Rv3324A, len: 44 aa. Probable pseudogene moaB3,fragment of pterin-4-alpha-carbinolamine dehydratase,equivalent to C-terminus of MT3426|Q8VJ3 | 843 | 843 ctx | neighborhood:801 |
Rv3324c moaC3 |
cyclic pyranopterin monophosphate synthase accessory protein | 808 | 807 ctx | neighborhood:801 |
Rv3320c vapC44 |
ribonuclease VapC44 | 566 | 567 ctx | neighborhood:564 |
Rv3321c vapB44 |
antitoxin VapB44 | 565 | 565 ctx | neighborhood:564 |
Rv3325 |
Rv3325, (MTV016.25), len: 108 aa. Putative Transposase for IS6110 (fragment). Identical to many other M. tuberculosis IS6110 transposase sub | 559 | 559 ctx | neighborhood:559 |
Rv3326 |
Probable transposase; Rv3326, (MTV016.26), len: 328 aa. Probable transposase for insertion element IS6110. Identical to many other M. tuberc | 559 | 559 ctx | neighborhood:559 |
Rv3327 |
transposase fusion protein | 460 | 457 ctx | neighborhood:449 |
Rv0341 iniB |
isoniazid inducible protein IniB | 427 | 428 | |
Rv2209 |
integral membrane protein | 427 | 427 ctx | cooccurence:422 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 406 | 406 ctx | cooccurence:406 |
Rv1523 |
methyltransferase | 887 | 166 | textmining:871 |
Rv3448 eccD4 |
ESX-4 secretion system protein EccD4 | 481 | 156 | textmining:411 |
Rv1895 |
zinc-binding alcohol dehydrogenase | 765 | 139 | textmining:739 |
Rv1522c mmpL12 |
transmembrane transport protein MmpL12 | 804 | 47 | textmining:803 |
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_25 PF13649.13 (E=1e-07)
- (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 YP_177958.1)
- Domains: Pfam-A via hmmscan --cut_ga — Methyltransf_25 (PF13649.13)
- 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
COG2890 - Curated reference: UniProt L7N687 (TrEMBL, unreviewed; 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 —
15 functional partner(s); context anchor
moaX - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3322c| MSVQTDPALREHPNRVDWNARYERAGSAHAPFAPVPWLADVLRAGVPDGPVLELASGRSGTALALAAHGRQVTAIDVSDVALLQLDSEAVRRGVADRLNLVQADLGCWEPGETRFALVLSRLFWDAAIFHRACEAVMPGGVLAWESLALSGAEAGTASAKRRVKPGEPACLLPADFTVVHEGQGNCDSAPSRIMIARRSPLPGA