Rv3093c Resolved · high auto-curated
H37Rv Rv3093c · MTBC0 mtbc0_003287 ·
334 aa · 3483124–3484128 (-) ·
RefSeq NP_217609.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase |
|---|---|
| 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 |
O05772
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Hypothetical oxidoreductase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| eggNOG description | Luciferase-like monooxygenase |
| 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 | 0.588 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 missense, 0 nonsense, 4 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 9.55% of strains (13866) · convergent |
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 | 2.2e-40 | 17–297 | Luciferase-like monooxygenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3095 (HTH-type transcriptional regulator), high confidence from genomic context alone (score 899 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3094c hyp |
hypothetical protein | 983 | 983 ctx | neighborhood:881 coexpression:865 |
Rv3095 |
HTH-type transcriptional regulator | 898 | 899 ctx | neighborhood:636 coexpression:733 |
Rv3262 fbiB |
coenzyme F420:L-glutamate ligase | 781 | 767 ctx | cooccurence:737 |
Rv3261 fbiA |
2-phospho-L-lactate transferase | 760 | 747 ctx | cooccurence:739 |
Rv2951c |
phthiodiolone/phenolphthiodiolone dimycocerosates ketoreductase | 742 | 743 ctx | cooccurence:742 |
Rv2893 |
oxidoreductase | 735 | 735 ctx | cooccurence:735 |
Rv2161c hyp |
hypothetical protein | 730 | 730 ctx | cooccurence:730 |
Rv3092c |
integral membrane protein | 723 | 723 ctx | neighborhood:707 |
Rv1261c hyp |
hypothetical protein | 718 | 719 ctx | cooccurence:718 |
Rv3547 ddn |
deazaflavin-dependent nitroreductase | 730 | 713 ctx | cooccurence:713 |
Rv3072c hyp |
hypothetical protein | 705 | 705 ctx | cooccurence:703 |
Rv0132c fgd2 |
F420-dependent glucose-6-phosphate dehydrogenase | 705 | 705 ctx | cooccurence:705 |
Rv1855c |
oxidoreductase | 700 | 701 ctx | cooccurence:700 |
Rv3178 |
nitroreductase | 702 | 684 ctx | cooccurence:684 |
Rv1360 |
oxidoreductase | 662 | 662 ctx | cooccurence:660 |
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: oxidoreductase
- MTBC0 PGAP product: LLM class F420-dependent oxidoreductase
- Pfam (hmmscan --cut_ga): Bac_luciferase PF00296.27 (E=2e-40)
- (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_217609.1)
- 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 O05772 (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 —
24 functional partner(s); context anchor
Rv3095 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003287|Rv3093c| MTDIEVALPFWLDRPDHEATDVALAAADTGFAALWIGEMATYDAFALATSIGLRTPNMTLKVGPLAVGVRGPVGLALGVSSVASLTGCRVDLALGASSPAIVAGWHGRPWAHHVPVMRETIECLRSIFTGARVEYSGRHVNSRGFRLRGAAPDTRIALGAFGPGMIRLAAQHADEVVLNLASPFRVGRVRAAIDSAAAAAGRAAPRLTVWVPVAVNPGAAAHSQLAAQLAVYLAPPGYGEMFSALGFDGLVRSARSRATRRELAVAVPSELLDRVCALGSPDRVAARLRAYADAGADCVAVVPATAEDPGGRVALRALRPGGLYGTAGDNDGRR