Rv1718 Resolved · high auto-curated
H37Rv Rv1718 · MTBC0 mtbc0_001828 ·
272 aa · 1956824–1957642 (+) ·
RefSeq NP_216234.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | 3-keto-5-aminohexanoate cleavage protein |
| Revised (this work) | 3-keto-5-aminohexanoate cleavage protein. Pfam: BKACE (PF05853.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71976
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | 3-keto-5-aminohexanoate cleavage protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | beta-keto acid cleavage enzyme |
| Orthologous group | COG3246 |
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 | 0.532 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 missense, 0 nonsense, 4 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 10.18% of strains (14783) · convergent |
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 |
|---|---|---|---|---|
BKACE | PF05853.19 | 4.8e-91 | 3–268 | beta-keto acid cleavage enzyme |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadB3 (3-hydroxybutyryl-CoA dehydrogenase FadB), high confidence from genomic context alone (score 972 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) |
|---|---|---|---|---|
Rv1716 hyp |
hypothetical protein | 977 | 978 ctx | neighborhood:808 coexpression:860 |
Rv1715 fadB3 |
3-hydroxybutyryl-CoA dehydrogenase FadB | 973 | 972 ctx | neighborhood:808 coexpression:860 |
Rv1717 hyp |
hypothetical protein | 969 | 970 ctx | neighborhood:717 coexpression:845 |
Rv1714 |
oxidoreductase | 966 | 966 ctx | neighborhood:808 coexpression:831 |
Rv1719 |
transcriptional regulator | 935 | 935 ctx | neighborhood:867 coexpression:449 |
Rv3728 |
membrane protein | 730 | 730 | coexpression:730 |
Rv1713 engA |
GTPase Der | 482 | 482 ctx | neighborhood:455 |
Rv1712 cmk |
cytidylate kinase | 471 | 472 ctx | neighborhood:454 |
Rv1711 |
RNA pseudouridine synthase | 468 | 468 ctx | neighborhood:451 |
Rv1710 scpB |
segregation and condensation protein ScpB | 459 | 459 ctx | neighborhood:451 |
Rv1709 scpA |
segregation and condensation protein ScpA | 456 | 456 ctx | neighborhood:449 |
Rv1708 |
initiation inhibitor protein | 454 | 454 ctx | neighborhood:451 |
Rv1707 |
transmembrane protein | 433 | 433 |
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: 3-keto-5-aminohexanoate cleavage protein
- Pfam (hmmscan --cut_ga): BKACE PF05853.19 (E=5e-91)
- (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_216234.1)
- Domains: Pfam-A via hmmscan --cut_ga — BKACE (PF05853.19)
- 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
COG3246 - Curated reference: UniProt P71976 (TrEMBL, unreviewed; Predicted)
- 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 —
13 functional partner(s); context anchor
fadB3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001828|Rv1718| MSIVITVAPTGPIATKADNPALPTSPEEIATAVEQAYHAGAAVAHIHLRDENERPTADPNIARRAMDLIGERCPILIQLSTGVGLTVPFEQREQLVELRPRMATLNPCSMSFGAGEFRNPPQAVRRLAARMRELDIKPELEIYDTGHLEACLRLWAEDLLAEPLQFSIVLGVRGGMAATADNLLTMVRRLPPGAIWQVIAIGKANMELTAMGLALGGNARVGLEDTLYLRKGELAPSNLALVSRTIRLAEALDLPIASVEEAEAALQLPGTS