Rv1936 Resolved · high auto-curated
H37Rv Rv1936 · MTBC0 mtbc0_002050 ·
369 aa · 2206500–2207609 (+) ·
RefSeq NP_216452.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | monooxygenase |
|---|---|
| MTBC0 PGAP re-annotation | LLM class flavin-dependent oxidoreductase |
| Revised (this work) | LLM class flavin-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 |
P95278
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible monooxygenase |
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 | 0.415 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.24% of strains (355) · 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-41 | 1–322 | Luciferase-like monooxygenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1937 (oxygenase), high confidence from genomic context alone (score 979 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1937 |
oxygenase | 981 | 979 ctx | neighborhood:792 cooccurence:468 coexpression:829 |
Rv1938 ephB |
epoxide hydrolase EphB | 977 | 962 ctx | neighborhood:769 coexpression:799 textmining:434 |
Rv1935c echA13 |
enoyl-CoA hydratase EchA13 | 908 | 882 ctx | neighborhood:492 coexpression:731 |
Rv1939 |
oxidoreductase | 877 | 873 ctx | neighborhood:757 coexpression:423 |
Rv1940 ribA1 |
riboflavin biosynthesis protein RibA | 854 | 849 ctx | neighborhood:760 |
Rv1941 |
short-chain type dehydrogenase/reductase | 817 | 757 ctx | neighborhood:757 |
Rv2161c hyp |
hypothetical protein | 676 | 677 ctx | cooccurence:673 |
Rv1934c fadE17 |
acyl-CoA dehydrogenase FadE17 | 648 | 648 ctx | neighborhood:472 |
Rv0132c fgd2 |
F420-dependent glucose-6-phosphate dehydrogenase | 623 | 624 ctx | cooccurence:620 |
Rv1933c fadE18 |
acyl-CoA dehydrogenase FadE18 | 631 | 553 ctx | neighborhood:463 |
Rv3072c hyp |
hypothetical protein | 513 | 513 ctx | cooccurence:513 |
Rv1965 yrbE3B |
integral membrane protein | 457 | 458 | coexpression:458 |
Rv3007c |
oxidoreductase | 403 | 381 | |
Rv1963c mce3R |
transcriptional repressor Mce3R | 670 | 309 | textmining:543 |
Rv2740 ephG |
epoxide hydrolase | 495 | 44 | textmining:494 |
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: monooxygenase
- MTBC0 PGAP product: LLM class flavin-dependent oxidoreductase
- Pfam (hmmscan --cut_ga): Bac_luciferase PF00296.27 (E=1e-41)
- (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_216452.1)
- 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 P95278 (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 —
17 functional partner(s); context anchor
Rv1937 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002050|Rv1936| MEIGIFLMPAHPPERTLYDATRWDLDVIELADQLGYVEAWVGEHFTVPWEPICAPDLLLAQALLRTQQIKLAPGAHLLPYHHPVELAHRVAYFDHLAQGRFMLGVGASGIPGDWALYDVDGKNGEHREMTREALEIMLRIWTEDEPWEHRGKYWNANGIAPMFEGLMRRHIKPYQKPHPPIGVTGFSAGSETLKLAGERGYIPMSLDLNTEYVATHWDAVEEGALRSGRTPDRRDWRLVREVLVAETDEQAFRYAVDGTMGRAMREYVLPTFRMFGMTKFYKHNPSVPDDEVTPEYLAENTFVVGSVQTVVDKLEATYDQVGGFGHLLILGFDYSDNPGPWKESLRLLAHEVMPRLNARLATKPATAVV