Rv1060 Family assigned · medium auto-curated
H37Rv Rv1060 · MTBC0 mtbc0_001140 ·
157 aa · 1190847–1191320 (+) ·
RefSeq NP_215576.1
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 |
O53408
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | SRPBCC family protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Polyketide cyclase / dehydrase and lipid transport |
| Orthologous group | 2FAVW |
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 | 0.471 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 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 |
|---|---|---|---|---|
Polyketide_cyc2 | PF10604.16 | 5.7e-17 | 7–155 | Polyketide cyclase / dehydrase and lipid transport |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadD14 (fatty-acid--CoA ligase FadD14), high confidence from genomic context alone (score 774 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) |
|---|---|---|---|---|
Rv1061 hyp |
hypothetical protein | 853 | 853 ctx | neighborhood:832 |
Rv1062 hyp |
hypothetical protein | 831 | 832 ctx | neighborhood:832 |
Rv1059 hyp |
hypothetical protein | 809 | 809 ctx | neighborhood:808 |
Rv1058 fadD14 |
fatty-acid--CoA ligase FadD14 | 775 | 774 ctx | neighborhood:738 |
Rv2487c PE_PGRS42 |
PE-PGRS family protein PE_PGRS42 | 718 | 718 ctx | cooccurence:718 |
Rv3899c hyp |
hypothetical protein | 686 | 686 ctx | cooccurence:686 |
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 | 685 | 686 ctx | cooccurence:684 |
Rv1057 hyp |
hypothetical protein | 575 | 576 ctx | neighborhood:404 |
Rv3768 hyp |
hypothetical protein | 560 | 560 ctx | cooccurence:560 |
Rv0048c |
membrane protein | 548 | 549 ctx | cooccurence:546 |
Rv0977 PE_PGRS16 |
PE-PGRS family protein PE_PGRS16 | 540 | 540 ctx | cooccurence:540 |
Rv3435c |
transmembrane protein | 534 | 535 ctx | cooccurence:532 |
Rv3894c eccC2 |
ESX-2 type VII secretion system protein EccC | 525 | 525 ctx | cooccurence:525 |
Rv2423 hyp |
hypothetical protein | 524 | 524 ctx | cooccurence:522 |
Rv2248 hyp |
hypothetical protein | 512 | 512 ctx | cooccurence:512 |
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=6e-17)
- (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_215576.1)
- 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
2FAVW - Curated reference: UniProt O53408 (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 —
23 functional partner(s); context anchor
fadD14 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001140|Rv1060| MAKSVVVEQSRAIPVQSEDAFGGTLAAALPVICSHWYGLIPPIKEVRDQTGAWDSVGQARVITMVGGGRVREELTSVDPPRSFGYTLTDIKGPLAPLVALVEGKWSFAPADTGTTVTWQWTIHPRSALAAPVLPVFARMWRGYARGVLEKLSALLVG