Rv3192 Family assigned · medium auto-curated
H37Rv Rv3192 · MTBC0 - ·
153 aa · 3559563–3560024 (+) ·
RefSeq NP_217708.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Bac_luciferase (PF00296.27) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
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 |
O53338
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Conserved hypothetical alanine and proline-rich protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| eggNOG description | COG2141 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases |
| Orthologous group | COG2141 |
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 | 0.356 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.31% of strains (453) · 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 |
|---|---|---|---|---|
Bac_luciferase | PF00296.27 | 1.5e-14 | 31–142 | Luciferase-like monooxygenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2765 (hydrolase), medium confidence from genomic context alone (score 582 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) |
|---|---|---|---|---|
Rv2765 |
hydrolase | 582 | 582 ctx | neighborhood:512 |
Rv3368c |
oxidoreductase | 494 | 476 ctx | cooccurence:437 |
Rv1907c hyp |
hypothetical protein | 423 | 423 ctx | cooccurence:422 |
Rv0245 |
oxidoreductase | 425 | 402 | |
Rv1939 |
oxidoreductase | 417 | 395 | |
Rv3567c hsaB |
flavin-dependent monooxygenase reductase subunit HsaB | 401 | 377 | |
Rv3005c hyp |
hypothetical protein | 472 | 197 | |
Rv1510 hyp |
hypothetical protein | 449 | 163 | |
Rv2704 hyp |
hypothetical protein | 652 | 102 | textmining:629 |
Rv1085c |
hemolysin-like protein | 407 | 94 | |
Rv0052 hyp |
hypothetical protein | 871 | 51 | textmining:870 |
Rv3630 |
integral membrane protein | 442 | 50 | textmining:437 |
Rv0024 |
NLP/P60 family protein | 440 | 50 | textmining:435 |
Rv2706c hyp |
hypothetical protein | 630 | 47 | textmining:628 |
Rv2705c hyp |
hypothetical protein | 629 | 47 | textmining:627 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): Bac_luciferase PF00296.27 (E=1e-14)
- (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_217708.1)
- Domains: Pfam-A via hmmscan --cut_ga — Bac_luciferase (PF00296.27)
- 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
COG2141 - Curated reference: UniProt O53338 (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 —
20 functional partner(s); context anchor
Rv2765 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3192| MIPQPLSQLGDLARRPGRRVLCSPKTAAPSISNATVASPAAPGLELSTGIALAFPRGPFVPAAAAWELQEATSGKFQLGLGTQVRKNVVHRYGMAFHRPGPRLRYLLAVKACFAVFQTGTPDHHGEFDNPDFITAQWSPARIDPPGPSPAGPR