Rv0487 Family assigned · medium auto-curated
H37Rv Rv0487 · MTBC0 mtbc0_000512 ·
183 aa · 580152–580703 (+) ·
RefSeq NP_215001.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | YbjN domain-containing protein |
| Revised (this work) | YbjN domain-containing protein. Pfam: YbjN (PF10722.15). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKU9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0487 |
UniProt still lists this protein as Uncharacterized protein Rv0487; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Putative bacterial sensory transduction regulator |
| Orthologous group | 2AZ39 |
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 | 0.99 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
YbjN | PF10722.15 | 6.9e-22 | 11–136 | Putative bacterial sensory transduction regulator |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mshA (D-inositol 3-phosphate glycosyltransferase), high confidence from genomic context alone (score 898 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) |
|---|---|---|---|---|
Rv0486 mshA |
D-inositol 3-phosphate glycosyltransferase | 898 | 898 ctx | neighborhood:882 |
Rv3679 |
anion transporter ATPase | 759 | 759 ctx | cooccurence:758 |
Rv0244c fadE5 |
acyl-CoA dehydrogenase FadE5 | 746 | 747 ctx | cooccurence:745 |
Rv3662c hyp |
hypothetical protein | 743 | 743 ctx | cooccurence:741 |
Rv1467c fadE15 |
acyl-CoA dehydrogenase | 722 | 722 ctx | cooccurence:722 |
Rv2185c TB16.3 hyp |
hypothetical protein | 717 | 717 ctx | cooccurence:717 |
Rv3680 |
anion transporter ATPase | 712 | 713 ctx | cooccurence:709 |
Rv0857 hyp |
hypothetical protein | 709 | 709 ctx | cooccurence:696 |
Rv0485 |
transcriptional regulator | 700 | 699 ctx | neighborhood:695 |
Rv0854 hyp |
hypothetical protein | 691 | 691 ctx | cooccurence:691 |
Rv0474 |
HTH-type transcriptional regulator | 687 | 688 ctx | cooccurence:682 |
Rv0489 gpm1 |
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase | 656 | 656 ctx | neighborhood:654 |
Rv0490 senX3 |
two component sensor histidine kinase SenX3 | 633 | 634 ctx | neighborhood:622 |
Rv0491 regX3 |
two component sensory transduction protein RegX | 609 | 610 ctx | neighborhood:604 |
Rv3197A whiB7 |
transcriptional regulator WhiB7 | 596 | 596 ctx | cooccurence:595 |
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: YbjN domain-containing protein
- Pfam (hmmscan --cut_ga): YbjN PF10722.15 (E=7e-22)
- (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_215001.1)
- Domains: Pfam-A via hmmscan --cut_ga — YbjN (PF10722.15)
- 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
2AZ39 - Curated reference: UniProt P9WKU9 (SwissProt, reviewed; 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 —
28 functional partner(s); context anchor
mshA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000512|Rv0487| MTSSLPTVQRVIQNALEVSQLKYSQHPRPGGAPPALIVELPGERKLKINTILSVGEHSVRVEAFVCRKPDENREDVYRFLLRRNRRLYGVAYTLDNVGDIYLVGQMALSAVDADEVDRVLGQVLEVVDSDFNALLELGFRSSIQREWQWRLSRGESLQNLQAFAHLRPTTMQSAQRDEKELGG