Rv1254 Resolved · high auto-curated
H37Rv Rv1254 · MTBC0 mtbc0_001343 ·
383 aa · 1410102–1411253 (+) ·
RefSeq NP_215770.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | acyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | acyltransferase |
| Revised (this work) | Acyltransferase. Pfam: Acyl_transf_3 (PF01757.29). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
Q11064
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable acyltransferase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| eggNOG description | Acyltransferase |
| Orthologous group | COG1835 |
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 | 0.214 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 3 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 |
|---|---|---|---|---|
Acyl_transf_3 | PF01757.29 | 3.3e-28 | 23–371 | Acyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: deaD (ATP-dependent RNA helicase DeaD), high confidence from genomic context alone (score 884 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1253 deaD |
ATP-dependent RNA helicase DeaD | 884 | 884 ctx | neighborhood:881 |
Rv3635 |
transmembrane protein | 655 | 640 ctx | cooccurence:627 |
Rv0227c |
membrane protein | 686 | 615 ctx | cooccurence:601 |
Rv3906c hyp |
hypothetical protein | 588 | 589 ctx | cooccurence:582 |
Rv3035 hyp |
hypothetical protein | 588 | 589 ctx | cooccurence:582 |
Rv1252c lprE |
lipoprotein LprE | 583 | 584 ctx | neighborhood:581 |
Rv1251c hyp |
hypothetical protein | 550 | 550 ctx | neighborhood:513 |
Rv0756c hyp |
hypothetical protein | 548 | 549 ctx | cooccurence:545 |
Rv3810 pirG |
cell surface protein | 538 | 538 ctx | cooccurence:537 |
Rv3444c esxT |
ESAT-6 like protein EsxT | 507 | 508 ctx | cooccurence:505 |
Rv1836c hyp |
hypothetical protein | 505 | 505 ctx | cooccurence:502 |
Rv0111 |
acyltransferase | 491 | 492 ctx | cooccurence:487 |
Rv2719c chiZ |
membrane protein | 489 | 489 ctx | cooccurence:481 |
Rv2743c hyp |
hypothetical protein | 469 | 469 ctx | cooccurence:456 |
Rv1489A hyp |
hypothetical protein | 543 | 462 ctx | cooccurence:459 |
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: acyltransferase
- MTBC0 PGAP product: acyltransferase
- Pfam (hmmscan --cut_ga): Acyl_transf_3 PF01757.29 (E=3e-28)
- (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_215770.1)
- Domains: Pfam-A via hmmscan --cut_ga — Acyl_transf_3 (PF01757.29)
- 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
COG1835 - Curated reference: UniProt Q11064 (TrEMBL, unreviewed; Predicted)
- 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 —
43 functional partner(s); context anchor
deaD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001343|Rv1254| MTLPKERAAQGGLERIAHVDRVASLTGIRAVAALLVVGTHAAYTTGKYTHGYWGLMSSRMEIGVPIFFVLSGFLLFRPWVKSAATGGPPPSLSRYAWHRVRRIMPAYTVTVLLAYLVYHFRTAGPNPGHTWVGLFRNLTLTQIYTDGYLGAFLHQGLTQMWSLAVEVAFYLALPALAYLLLVLVCRRRWQPRLLLATMAGLTMISPAWLILVHNTHWMPDGARLWLPTYLAWFVGGMMLAVLAAMGVRCYAFVAIPLAVICYFIVSTPIAGAPTTSPTALAEALVKTAFYAVIAVLAVAPLALGDQGWYAQLLASRPMVFLGEISYEIFLIHLVTMEIAMVDVLGYRVYTSSMVNLCLVTLVLTIPLAWLLHRFTRVQGDRPS