Rv0789c Family assigned · low
H37Rv Rv0789c · MTBC0 - ·
199 aa · 883451–884050 (-) ·
RefSeq NP_215304.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | YbjN-like fold (putative sensor / regulatory protein). RefSeq leaves it 'hypothetical protein'. The AlphaFold model superposes on YbjN, a putative transcription regulator (PDB 6vu7; Foldseek prob 1.0, E 1e-5, TM 0.80). Fold-level assignment; the regulatory role and partners are not established. |
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
I6Y4U0
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | YbjN domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2A1AM |
|---|
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 | 0.699 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 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: Rv0792c (transcriptional regulator), high confidence from genomic context alone (score 734 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) |
|---|---|---|---|---|
Rv0790c hyp |
hypothetical protein | 966 | 753 ctx | neighborhood:750 textmining:870 |
Rv0791c hyp |
hypothetical protein | 966 | 752 ctx | neighborhood:750 textmining:870 |
Rv0792c |
transcriptional regulator | 903 | 734 ctx | neighborhood:730 textmining:654 |
Rv0793 |
monooxygenase | 935 | 527 ctx | neighborhood:524 textmining:870 |
Rv2478c hyp |
hypothetical protein | 552 | 47 | textmining:550 |
Rv0023 |
transcriptional regulator | 431 | 41 | textmining:431 |
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
- Foldseek -> YbjN putative regulator (6vu7), prob 1.0, E 1e-5, TM 0.80
- Structural homology: AlphaFold DB model + Foldseek vs PDB (project 'Still unknown gene function', phase5-7, 2026-06-10). A fold-level family assignment, not a demonstrated activity.
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_215304.1)
- 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
2A1AM - Curated reference: UniProt I6Y4U0 (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 —
6 functional partner(s); context anchor
Rv0792c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0789c| MSRRAIHSGRAAPRRSGNSHLVLRNRVPSSKDSPRRRPHHEFMTESIGEPLSTNLIERYLRARGRRYFRGHHDAEFFFVANAHLRLHVHLEISPAYRDVFTIRVSPAYFFPATDHTRLAEIVNAWNLQNHEVTAIVHGSSDPHRIGVAAERSLIRDRIRFDDFATFVDNAVSAATELFGQLTAAGLPPTATPPLLRDAG