Rv1575 Resolved · medium auto-curated
H37Rv Rv1575 · MTBC0 - ·
166 aa · 1780199–1780699 (+) ·
RefSeq NP_216091.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phage protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Phage protein. |
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 |
L0T9U5
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable PhiRv1 phage protein |
Conservation & selection (intra-MTBC, 145 209 strains) pseudogene candidate
| pN/pS | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 40.58% of strains (58924) · 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1574 (phage protein), high confidence from genomic context alone (score 807 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1574 |
phage protein | 807 | 807 ctx | neighborhood:773 |
Rv1573 |
phage protein | 467 | 467 ctx | neighborhood:441 |
Rv3869 eccB1 |
ESX-1 secretion system protein EccB | 523 | 68 | textmining:510 |
Rv0823c dusB |
tRNA-dihydrouridine synthase | 655 | 55 | textmining:650 |
Rv2790c ltp1 |
lipid-transfer protein | 807 | 54 | textmining:805 |
Rv0458 |
aldehyde dehydrogenase | 629 | 54 | textmining:624 |
Rv3170 aofH |
flavin-containing monoamine oxidase | 805 | 47 | textmining:804 |
Rv0724 sppA |
protease IV SppA | 804 | 47 | textmining:803 |
Rv1758 cut1 |
cutinase | 440 | 47 | textmining:437 |
Rv0176 |
Mce associated transmembrane protein | 652 | 46 | textmining:651 |
Rv0120c fusA2 |
elongation factor G | 654 | 44 | textmining:653 |
Rv1132 hyp |
hypothetical protein | 808 | 41 | textmining:808 |
Rv2561 |
Rv2561, (MTCY9C4.07c), len: 97 aa. Conserved hypothetical protein, highly similar in part (and longer 33 aa) to upstream ORF AAK46951|RV2562 | 807 | 41 | textmining:807 |
Rv2542 hyp |
hypothetical protein | 806 | 41 | textmining:806 |
Rv2216 |
epimerase family protein | 549 | 41 | textmining:549 |
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): phage protein
- (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_216091.2)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt L0T9U5 (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 —
15 functional partner(s); context anchor
Rv1574 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1575| MEPKPSQRHTDKEVGAALGISAGTYKRLKRIDNATRSDDKEIRLFAEKQMAPLAAGSPSWNGRKPSSGNRKAATMAARLDILAWGPWAPSQNRSVVRRKQTLLSAQPSASPPAPTGGSNESTTQPAASWRVGGPAPLSRGRPRLALSYLRGSLHLQNSKRVAHQHI