Rv2565 Family assigned · medium auto-curated
H37Rv Rv2565 · MTBC0 mtbc0_002732 ·
583 aa · 2908155–2909906 (+) ·
RefSeq NP_217081.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | NTE family protein |
|---|---|
| MTBC0 PGAP re-annotation | patatin-like phospholipase family protein |
| Revised (this work) | Patatin-like phospholipase family protein. Pfam: cNMP_binding (PF00027.36), 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 |
P9WIY7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized NTE family protein Rv2565 |
UniProt still lists this protein as Uncharacterized NTE family protein Rv2565; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| eggNOG description | Patatin-like phospholipase |
| Orthologous group | COG0664 |
| KEGG orthology |
K07001
|
| Gene Ontology (11) |
GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0016787, GO:0044424, GO:0044444, GO:0044464
|
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 | 0.925 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.26% of strains (376) · 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 |
|---|---|---|---|---|
cNMP_binding | PF00027.36 | 6.8e-17 | 42–124 | Cyclic nucleotide-binding domain |
Patatin | PF01734.28 | 4.4e-27 | 309–466 | Patatin-like phospholipase |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2566 hyp |
hypothetical protein | 773 | 773 ctx | neighborhood:770 |
Rv2567 hyp |
hypothetical protein | 763 | 763 ctx | neighborhood:763 |
Rv2435c |
cyclase | 602 | 579 | experimental:408 |
Rv2488c |
LuxR family transcriptional regulator | 626 | 578 | experimental:440 |
Rv1358 |
transcriptional regulator | 625 | 577 | experimental:440 |
Rv0386 |
transcriptional regulator | 624 | 575 | experimental:440 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 670 | 570 | database:431 |
Rv2048c pks12 |
polyketide synthase | 670 | 570 | database:431 |
Rv1527c pks5 |
polyketide synthase | 669 | 569 | database:431 |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 667 | 566 | database:431 |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 667 | 565 | database:431 |
Rv2562 |
Rv2562, (MTCY9C4.06c), len: 129 aa. Conserved hypothetical protein, highly similar, but shorter 83 aa, to downstream ORF AAK46951|RV2561|MT2 | 581 | 564 | |
Rv0148 |
short-chain type dehydrogenase/reductase | 578 | 561 | database:431 |
Rv2561 |
Rv2561, (MTCY9C4.07c), len: 97 aa. Conserved hypothetical protein, highly similar in part (and longer 33 aa) to upstream ORF AAK46951|RV2562 | 553 | 536 | |
Rv1663 pks17 |
polyketide synthase | 569 | 526 | database:431 |
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: NTE family protein
- MTBC0 PGAP product: patatin-like phospholipase family protein
- Pfam (hmmscan --cut_ga): cNMP_binding PF00027.36 (E=7e-17), Patatin PF01734.28 (E=4e-27)
- (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_217081.1)
- Domains: Pfam-A via hmmscan --cut_ga — cNMP_binding (PF00027.36), 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
COG0664 - Curated reference: UniProt P9WIY7 (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 — 73 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002732|Rv2565| MTTARRRPKRRGTDARTALRNVPILADIDDEQLERLATTVERRHVPANQWLFHAGEPADSIYIVDSGRFVAVAPEGHVFAEMASGDSIGDLGVIAGAARSAGVRALRDGVVWRIAAETFTDMLEATPLLQSAMLRAMARMLRQSRPAKTARRPRVIGVVSNGDTAAAPMVDAIATSLDSHGRTAVIAPPVETTSAVQEYDELVEAFSETLDRAERSNDWVLVVADRGAGDLWRHYVSAQSDRLVVLVDQRYPPDAVDSLATQRPVHLITCLAEPDPSWWDRLAPVSHHPANSDGFGALARRIAGRSLGLVMAGGGARGLAHFGVYQELTEAGVVIDRFGGTSSGAIASAAFALGMDAGDAIAAAREFIAGSDPLGDYTIPISALTRGGRVDRLVQGFFGNTLIEHLPRGFFSVSADMITGDQIIHRRGSVSGAVRASISIPGLIPPVHNGEQLLVDGGLLNNLPANVMCADTDGEVICVDLRRTFVPSKGFGLLPPIVTPPGLLRRLLTGTDNALPPLQETLLRAFDLAASTANLRELPRVAAIIEPDVSKIGVLNFKQIDAALEAGRMAARAALQAQPDLVR