Rv2574 Family assigned · medium auto-curated
H37Rv Rv2574 · MTBC0 mtbc0_002741 ·
167 aa · 2922350–2922853 (+) ·
RefSeq NP_217090.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | SRPBCC family protein |
| Revised (this work) | SRPBCC family protein. Pfam: Polyketide_cyc2 (PF10604.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WL87
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2574 |
UniProt still lists this protein as Uncharacterized protein Rv2574; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Polyketide cyclase / dehydrase and lipid transport |
| Orthologous group | COG3427 |
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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) pseudogene candidate
| pN/pS | 0.563 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 2.81% of strains (4083) · 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 |
|---|---|---|---|---|
Polyketide_cyc2 | PF10604.16 | 1.0e-23 | 19–156 | Polyketide cyclase / dehydrase and lipid transport |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2573 (2-dehydropantoate 2-reductase), high confidence from genomic context alone (score 742 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) |
|---|---|---|---|---|
Rv2573 |
2-dehydropantoate 2-reductase | 742 | 742 ctx | neighborhood:703 |
Rv2575 |
membrane protein | 697 | 697 ctx | neighborhood:682 |
Rv1057 hyp |
hypothetical protein | 663 | 664 ctx | cooccurence:660 |
Rv0955 |
integral membrane protein | 646 | 647 ctx | cooccurence:645 |
Rv2633c hyp |
hypothetical protein | 613 | 613 ctx | cooccurence:598 |
Rv2378c mbtG |
L-lysine N6-monooxygenase | 611 | 611 ctx | cooccurence:611 |
Rv1132 hyp |
hypothetical protein | 572 | 573 ctx | cooccurence:570 |
Rv1157c hyp |
hypothetical protein | 564 | 564 ctx | cooccurence:559 |
Rv3604c |
transmembrane protein | 545 | 546 ctx | cooccurence:543 |
Rv3169 hyp |
hypothetical protein | 523 | 523 ctx | cooccurence:521 |
Rv3577 hyp |
hypothetical protein | 513 | 513 ctx | cooccurence:510 |
Rv0236c aftD |
alpha-(1->3)-arabinofuranosyltransferase | 512 | 513 ctx | cooccurence:510 |
Rv0256c PPE2 |
PPE family protein PPE2 | 496 | 497 ctx | cooccurence:494 |
Rv2557 hyp |
hypothetical protein | 468 | 469 ctx | cooccurence:468 |
Rv1159 pimE |
polyprenol-phosphate-mannose-dependent alpha-(1-2)-phosphatidylinositol pentamannoside mannosyltransferase | 458 | 459 ctx | cooccurence:440 |
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: SRPBCC family protein
- Pfam (hmmscan --cut_ga): Polyketide_cyc2 PF10604.16 (E=1e-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_217090.1)
- Domains: Pfam-A via hmmscan --cut_ga — Polyketide_cyc2 (PF10604.16)
- 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
COG3427 - Curated reference: UniProt P9WL87 (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 —
20 functional partner(s); context anchor
Rv2573 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002741|Rv2574| MYPCERVGLSFTETAPYLFRNTVDLAITPEQLFEVLADPQAWPRWATVITKVTWTSPEPFGAGTTRIVEMRGGIVGDEEFISWEPFTRMAFRFNECSTRAVGAFAEDYRVQAIPGGCRLTWTMAQKLAGPARPALFVFRPLLNLALRRFLRNLRRYTDARFAAAQQS