Rv3079c Resolved · high auto-curated
H37Rv Rv3079c · MTBC0 mtbc0_003273 ·
275 aa · 3463134–3463961 (-) ·
RefSeq NP_217595.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | LLM class F420-dependent oxidoreductase |
| Revised (this work) | LLM class F420-dependent oxidoreductase. Pfam: Bac_luciferase (PF00296.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6XG43
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
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) pseudogene candidate
| pN/pS | 2.476 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 5 missense, 2 nonsense, 0 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 17.66% of strains (25651) · 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 | 2.3e-38 | 18–218 | Luciferase-like monooxygenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pknK (serine/threonine-protein kinase PknK), high confidence from genomic context alone (score 902 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) |
|---|---|---|---|---|
Rv3080c pknK |
serine/threonine-protein kinase PknK | 902 | 902 ctx | neighborhood:647 coexpression:735 |
Rv2893 |
oxidoreductase | 738 | 739 ctx | cooccurence:737 |
Rv2951c |
phthiodiolone/phenolphthiodiolone dimycocerosates ketoreductase | 679 | 679 ctx | cooccurence:679 |
Rv3262 fbiB |
coenzyme F420:L-glutamate ligase | 685 | 666 ctx | cooccurence:621 |
Rv0044c |
oxidoreductase | 651 | 652 ctx | cooccurence:648 |
Rv3520c |
coenzyme F420-dependent oxidoreductase | 633 | 633 ctx | cooccurence:632 |
Rv3093c |
oxidoreductase | 617 | 617 ctx | cooccurence:617 |
Rv3261 fbiA |
2-phospho-L-lactate transferase | 629 | 607 ctx | cooccurence:593 |
Rv0121c hyp |
hypothetical protein | 612 | 597 ctx | cooccurence:591 |
Rv0407 fgd1 |
F420-dependent glucose-6-phosphate dehydrogenase | 594 | 595 ctx | cooccurence:585 |
Rv3178 |
nitroreductase | 594 | 569 ctx | cooccurence:567 |
Rv3547 ddn |
deazaflavin-dependent nitroreductase | 568 | 541 ctx | cooccurence:539 |
Rv1261c hyp |
hypothetical protein | 539 | 540 ctx | cooccurence:537 |
Rv2983 cofC |
2-phospho-L-lactate guanylyltransferase | 529 | 479 ctx | cooccurence:459 |
Rv3081 hyp |
hypothetical protein | 476 | 476 ctx | neighborhood:473 |
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: LLM class F420-dependent oxidoreductase
- Pfam (hmmscan --cut_ga): Bac_luciferase PF00296.27 (E=2e-38)
- (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_217595.1)
- 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 I6XG43 (TrEMBL, unreviewed; 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 —
18 functional partner(s); context anchor
pknK - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003273|Rv3079c| MQFGVLTFVTDEGIGPAELGAALEHRGFESLFLAEHTHIPVNTQSPYPGGGPIPEKYYRTLDPFVALAAAAATTQSLVLGTGIALIPERDPIVTAKEVASLDLVSQGRFRFGVGVGWLREEVANHGVDPAVRGRVIDERLRAIIEIWTQEQAEFHGTYVDFDPIYCWPKPVTKPYPPLYVGGGPANFPRIARLNAGWIAISPSPQRLSGPLQRLRAMAGGDVPVTVCQWGEAAAKDLEGYRHLGVERVLLELPTEPRDPTLRYLDKLQAELARLA