Rv1249c Still unknown · low auto-curated
H37Rv Rv1249c · MTBC0 mtbc0_001338 ·
262 aa · 1401638–1402426 (-) ·
RefSeq NP_215765.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O50464
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | 5-oxoprolinase (ATP-hydrolyzing) activity |
| Orthologous group | COG1540 |
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 | 0.521 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 8 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: kgd (multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase), high confidence from genomic context alone (score 749 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0264c hyp |
hypothetical protein | 814 | 778 | coexpression:760 |
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase | 749 | 749 ctx | neighborhood:747 |
Rv0263c hyp |
hypothetical protein | 791 | 746 | coexpression:725 |
Rv1245c |
short-chain type dehydrogenase/reductase | 684 | 684 ctx | neighborhood:602 |
Rv1188 |
proline dehydrogenase | 612 | 612 | coexpression:612 |
Rv1171 hyp |
hypothetical protein | 609 | 609 ctx | cooccurence:605 |
Rv0048c |
membrane protein | 582 | 583 ctx | cooccurence:579 |
Rv3667 acs |
acetyl-CoAsynthetase | 560 | 561 | coexpression:561 |
Rv1250 |
MFS-type drug transporter | 518 | 518 ctx | neighborhood:513 |
Rv2923c hyp |
hypothetical protein | 491 | 491 ctx | cooccurence:414 |
Rv2852c mqo |
malate:quinone oxidoreductase | 484 | 484 | coexpression:418 |
Rv2560 hyp |
hypothetical protein | 471 | 471 ctx | cooccurence:466 |
Rv3063 cstA |
carbon starvation protein A | 469 | 470 | coexpression:460 |
Rv0889c citA |
citrate synthase 2 | 464 | 464 | coexpression:462 |
Rv0896 gltA2 |
citrate synthase 1 | 463 | 464 | coexpression: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: membrane protein
- MTBC0 PGAP product: hypothetical protein
- (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_215765.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG1540 - Curated reference: UniProt O50464 (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 —
38 functional partner(s); context anchor
kgd - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001338|Rv1249c| MSARRIRSWKRFDNRSANAAEPDPQLAGTGGRPKVSTRALAQVIERSSRIQGPAAQAYVARLRRAHPGASPAKIVAKLEKRFLSVVTASGAAVGAAATLPGIGTLAAWFAAAGEVVVFLEATALFVLALASVHAIPLDHRERRRALVLAVLVGDNTTAVADLLGPGRTSGGWVSETMASLPLPAISSLNSRMLKYVVKRFALKRGALMFGKLVPMGIGAIIGAIGNRLVGKKLVRNARSAFGTPPARWPVTLHVLPTVRDAS