Rv1883c Family assigned · medium auto-curated
H37Rv Rv1883c · MTBC0 mtbc0_001997 ·
158 aa · 2151270–2151746 (-) ·
RefSeq NP_216399.1
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), Polyketide_cyc (PF03364.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07748
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Coenzyme Q-binding protein COQ10 START domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | polyketide cyclase dehydrase |
| Orthologous group | COG3832 |
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 3 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 | 4.1e-17 | 10–156 | Polyketide cyclase / dehydrase and lipid transport |
Polyketide_cyc | PF03364.26 | 6.6e-14 | 15–144 | Polyketide cyclase / dehydrase and lipid transport |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpfC (resuscitation-promoting factor RpfC), high confidence from genomic context alone (score 950 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) |
|---|---|---|---|---|
Rv1884c rpfC |
resuscitation-promoting factor RpfC | 950 | 950 ctx | neighborhood:692 coexpression:845 |
Rv1882c |
short-chain type dehydrogenase/reductase | 866 | 866 ctx | neighborhood:844 |
Rv1815 hyp |
hypothetical protein | 798 | 798 | coexpression:798 |
Rv1881c lppE |
lipoprotein LppE | 762 | 762 ctx | neighborhood:751 |
Rv0385 |
monooxygenase | 760 | 732 | coexpression:713 |
Rv1880c cyp140 |
cytochrome P450 Cyp140 | 699 | 698 ctx | neighborhood:694 |
Rv1885c |
chorismate mutase | 647 | 647 ctx | neighborhood:642 |
Rv1886c fbpB |
diacylglycerol acyltransferase/mycolyltransferase Ag85B | 636 | 636 ctx | neighborhood:618 |
Rv3776 hyp |
hypothetical protein | 523 | 523 ctx | cooccurence:520 |
Rv0171 mce1C |
Mce family protein Mce1C | 507 | 507 ctx | cooccurence:485 |
Rv0515 hyp |
hypothetical protein | 491 | 492 ctx | cooccurence:484 |
Rv0336 hyp |
hypothetical protein | 491 | 491 ctx | cooccurence:484 |
Rv0172 mce1D |
Mce family protein Mce1D | 490 | 490 ctx | cooccurence:464 |
Rv0591 mce2C |
Mce family protein Mce2C | 485 | 485 ctx | cooccurence:482 |
Rv0174 mce1F |
Mce family protein Mce1F | 461 | 462 |
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=4e-17), Polyketide_cyc PF03364.26 (E=7e-14)
- (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_216399.1)
- Domains: Pfam-A via hmmscan --cut_ga — Polyketide_cyc2 (PF10604.16), Polyketide_cyc (PF03364.26)
- 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
COG3832 - Curated reference: UniProt O07748 (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 —
26 functional partner(s); context anchor
rpfC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001997|Rv1883c| MCLDQVMEGSATVHMAAPPDKIWTLIADVRNTGRFSPETFEAEWLDGATGPALGARFRGHVRRNGIGPVYWTVCEVTACEPGREFGFAVLLGDRPVNNWHYRLTPTADGTEVTESFRLPPSVLTTVYYRVFGGWLRQRRNIRDMTKTLQRIKDLVEAG