Rv3091 Family assigned · medium auto-curated
H37Rv Rv3091 · MTBC0 mtbc0_003285 ·
563 aa · 3480480–3482171 (+) ·
RefSeq NP_217607.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | patatin-like phospholipase family protein |
| Revised (this work) | Patatin-like phospholipase family protein. Pfam: Patatin (PF01734.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YB49
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Patatin-like phospholipase |
| Orthologous group | COG1752 |
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 | 0.529 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 9 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.22% of strains (316) · 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 |
|---|---|---|---|---|
Patatin | PF01734.28 | 9.2e-23 | 182–420 | Patatin-like phospholipase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PE_PGRS42 (PE-PGRS family protein PE_PGRS42), high confidence from genomic context alone (score 749 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2487c PE_PGRS42 |
PE-PGRS family protein PE_PGRS42 | 749 | 749 ctx | cooccurence:749 |
Rv3090 hyp |
hypothetical protein | 732 | 732 ctx | neighborhood:732 |
Rv2098c PE_PGRS36 |
PE-PGRS family protein PE_PGRS36; Rv2098c, (MTCY49.38c), len: 434 aa. PE_PGRS36,Member of the Mycobacterium tuberculosis PE family, PGRS sub | 704 | 705 ctx | cooccurence:701 |
Rv1157c hyp |
hypothetical protein | 702 | 702 ctx | cooccurence:697 |
Rv0977 PE_PGRS16 |
PE-PGRS family protein PE_PGRS16 | 598 | 599 ctx | cooccurence:598 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 583 | 583 ctx | cooccurence:583 |
Rv0872c PE_PGRS15 |
PE-PGRS family protein PE_PGRS15 | 582 | 582 ctx | cooccurence:582 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 567 | 567 ctx | cooccurence:567 |
Rv2853 PE_PGRS48 |
PE-PGRS family protein PE_PGRS48 | 551 | 551 ctx | cooccurence:551 |
Rv3067 hyp |
hypothetical protein | 544 | 544 ctx | neighborhood:544 |
Rv2305 hyp |
hypothetical protein | 520 | 520 ctx | cooccurence:517 |
Rv2044c hyp |
hypothetical protein | 511 | 511 ctx | cooccurence:511 |
Rv0124 PE_PGRS2 |
PE-PGRS family protein PE_PGRS2 | 495 | 495 ctx | cooccurence:495 |
Rv3080c pknK |
serine/threonine-protein kinase PknK | 477 | 477 ctx | cooccurence:457 |
Rv2100 hyp |
hypothetical protein | 456 | 456 ctx | cooccurence:456 |
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: hypothetical protein
- MTBC0 PGAP product: patatin-like phospholipase family protein
- Pfam (hmmscan --cut_ga): Patatin PF01734.28 (E=9e-23)
- (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_217607.1)
- Domains: Pfam-A via hmmscan --cut_ga — Patatin (PF01734.28)
- 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
COG1752 - Curated reference: UniProt I6YB49 (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 —
20 functional partner(s); context anchor
PE_PGRS42 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003285|Rv3091| MPIPFADGMLSRLGRRGAALDLIEEFEDESGEPPASLSPADLLAAEPALLLQKMENRLVRHHLANPDVLSGEQLRKLRYILNFARLADFEPGAAGPGGSRGRGDISVGGQVAPWRSRVVDALYAPLREEPDPVTALEGAKDVLATLVDDQDDQRRVLIERHGSDFSATELDAEVGYKKLVTVLGGGGGAGFVYIGGMQRLLAAGQVPDYMIGSSFGSIIGSLVARELPVPIDEYAEWAKTVSYRAILGPERRRSRHGLAGMFTLRFDQFAHTLLSRADGERMRMSDLAIPFDVVVAGVRRQPYAALPSRFRHRERSTLTLRSLPFLPIGIGPWVAARMWQVAAFIDLRVVKPIVISADGATRDVNVVDAASFSSAIPGVLHHETSDPRMLPILDELCADQDVAAMVDGGAASNVPVELAWERVRDGRLGTRNACYLAFDCFHPHWDPRHLWLVPITQAVQLQMVRNLPYADHLVRFEPTLSPVNLAPSAAAIDRACRWGRDSVEPAIAVTSALLEPTWWEGDRPPAAEPKERTKSAASSMSAVMAAIQAPTGRFRRWRSRHLT