Rv3072c Family assigned · medium auto-curated
H37Rv Rv3072c · MTBC0 - ·
174 aa · 3435798–3436322 (-) ·
RefSeq NP_217588.1
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 |
P95086
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Luciferase-like domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| eggNOG description | F420-dependent oxidoreductase, Rv2161c |
| 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 | 0.921 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 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 |
|---|---|---|---|---|
Bac_luciferase | PF00296.27 | 1.7e-17 | 15–133 | Luciferase-like monooxygenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2893 (oxidoreductase), high confidence from genomic context alone (score 730 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) |
|---|---|---|---|---|
Rv3073c hyp |
hypothetical protein | 818 | 818 ctx | neighborhood:817 |
Rv0791c hyp |
hypothetical protein | 756 | 743 ctx | cooccurence:743 |
Rv2893 |
oxidoreductase | 743 | 730 ctx | cooccurence:728 |
Rv0940c |
oxidoreductase | 722 | 722 ctx | cooccurence:722 |
Rv3093c |
oxidoreductase | 705 | 705 ctx | cooccurence:703 |
Rv2951c |
phthiodiolone/phenolphthiodiolone dimycocerosates ketoreductase | 706 | 691 ctx | cooccurence:690 |
Rv1855c |
oxidoreductase | 690 | 690 ctx | cooccurence:690 |
Rv0132c fgd2 |
F420-dependent glucose-6-phosphate dehydrogenase | 688 | 689 ctx | cooccurence:688 |
Rv3178 |
nitroreductase | 659 | 638 ctx | cooccurence:638 |
Rv3520c |
coenzyme F420-dependent oxidoreductase | 622 | 623 ctx | cooccurence:609 |
Rv3547 ddn |
deazaflavin-dependent nitroreductase | 636 | 613 ctx | cooccurence:613 |
Rv1261c hyp |
hypothetical protein | 599 | 599 ctx | cooccurence:598 |
Rv3262 fbiB |
coenzyme F420:L-glutamate ligase | 631 | 593 ctx | cooccurence:541 |
Rv3074 hyp |
hypothetical protein | 584 | 584 ctx | neighborhood:580 |
Rv0044c |
oxidoreductase | 570 | 570 ctx | cooccurence:570 |
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=2e-17)
- (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_217588.1)
- 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 P95086 (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 —
24 functional partner(s); context anchor
Rv2893 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3072c| MACVRRSCDVTGTARAGIGAGADPAVVDAVAVAADDCGFATLWVGEHVVMVDRPASRYPYSRDGVIAVPAQADWLDPMIALSFAAAASSRVDVATGVLLLPEHNPVIVAKEAASLDRLSGRRLTLGVASDGPRRSSTRSECHSSGAQSAPPNTSLQCAHYGATTSHRSTATVGS