Rv0760c Family assigned · medium auto-curated
H37Rv Rv0760c · MTBC0 mtbc0_000809 ·
139 aa · 858691–859110 (-) ·
RefSeq NP_215274.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | ketosteroid isomerase family protein |
| Revised (this work) | Ketosteroid isomerase family protein. Pfam: NTF2 (PF02136.27), SnoaL_2 (PF12680.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6WZD7
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | nuclear transport factor 2 |
| Orthologous group | COG3631 |
| EC number |
EC 5.3.3.1
|
| KEGG orthology |
K01822
|
| KEGG pathways |
map00140, map00984, map01100, map01120
|
| KEGG modules |
M00107, M00110
|
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 | 0.442 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 4.45% of strains (6460) · 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 |
|---|---|---|---|---|
NTF2 | PF02136.27 | 1.5e-14 | 12–135 | Nuclear transport factor 2 (NTF2) domain |
SnoaL_2 | PF12680.14 | 1.7e-10 | 18–123 | SnoaL-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: adhB (alcohol dehydrogenase B), high confidence from genomic context alone (score 973 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) |
|---|---|---|---|---|
Rv0761c adhB |
alcohol dehydrogenase B | 973 | 973 ctx | neighborhood:874 coexpression:797 |
Rv1817 |
flavoprotein | 947 | 946 ctx | cooccurence:476 database:900 |
Rv3537 kstD |
3-oxosteroid 1-dehydrogenase | 940 | 938 ctx | cooccurence:404 database:900 |
Rv0763c |
ferredoxin | 832 | 832 ctx | neighborhood:769 |
Rv2299c htpG |
chaperone protein HtpG | 785 | 785 | coexpression:785 |
Rv0310c hyp |
hypothetical protein | 740 | 741 ctx | cooccurence:720 |
Rv3526 kshA |
3-ketosteroid-9-alpha-monooxygenase oxygenase subunit | 736 | 736 ctx | cooccurence:728 |
Rv3541c chsH1 hyp |
hypothetical protein | 727 | 728 ctx | cooccurence:727 |
Rv3521 hyp |
hypothetical protein | 722 | 722 ctx | cooccurence:721 |
Rv0762c hyp |
hypothetical protein | 720 | 720 ctx | neighborhood:578 |
Rv3568c hsaC |
extradiol dioxygenase | 712 | 713 ctx | cooccurence:703 |
Rv3527 hyp |
hypothetical protein | 703 | 703 ctx | cooccurence:702 |
Rv3522 ltp4 |
lipid transfer protein | 690 | 691 ctx | cooccurence:690 |
Rv3542c chsH2 hyp |
hypothetical protein | 682 | 682 ctx | cooccurence:681 |
Rv3552 |
CoA-transferase subunit beta | 682 | 682 ctx | cooccurence:682 |
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: ketosteroid isomerase family protein
- Pfam (hmmscan --cut_ga): NTF2 PF02136.27 (E=1e-14), SnoaL_2 PF12680.14 (E=2e-10)
- (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_215274.1)
- Domains: Pfam-A via hmmscan --cut_ga — NTF2 (PF02136.27), SnoaL_2 (PF12680.14)
- 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
COG3631 - Curated reference: UniProt I6WZD7 (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 —
51 functional partner(s); context anchor
adhB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000809|Rv0760c| MTQTTQSPALIASQSSWRCVQAHDREGWLALMADDVVIEDPIGKSVTNPDGSGIKGKEAVGAFFDTHIAANRLTVTCEETFPSSSPDEIAHILVLHSEFDGGFTSEVRGVFTYRVNKAGLITNMRGYWNLDMMTFGNQE