Rv1939 Family assigned · medium auto-curated
H37Rv Rv1939 · MTBC0 mtbc0_002053 ·
171 aa · 2211210–2211725 (+) ·
RefSeq NP_216455.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | flavin reductase family protein |
| Revised (this work) | Flavin reductase family protein. Pfam: Flavin_Reduct (PF01613.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95275
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable oxidoreductase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Flavin reductase like domain |
| Orthologous group | COG1853 |
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 | 2.014 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 6 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.13% of strains (196) · 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 |
|---|---|---|---|---|
Flavin_Reduct | PF01613.25 | 1.6e-34 | 25–168 | Flavin reductase like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ribA1 (riboflavin biosynthesis protein RibA), high confidence from genomic context alone (score 970 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1940 ribA1 |
riboflavin biosynthesis protein RibA | 971 | 970 ctx | neighborhood:807 coexpression:852 |
Rv1938 ephB |
epoxide hydrolase EphB | 968 | 968 ctx | neighborhood:786 coexpression:858 |
Rv1937 |
oxygenase | 958 | 955 ctx | neighborhood:779 coexpression:805 |
Rv1936 |
monooxygenase | 877 | 873 ctx | neighborhood:757 coexpression:423 |
Rv1941 |
short-chain type dehydrogenase/reductase | 803 | 802 ctx | neighborhood:801 |
Rv3007c |
oxidoreductase | 722 | 723 ctx | cooccurence:720 |
Rv1935c echA13 |
enoyl-CoA hydratase EchA13 | 509 | 509 ctx | neighborhood:481 |
Rv1934c fadE17 |
acyl-CoA dehydrogenase FadE17 | 525 | 507 ctx | neighborhood:467 |
Rv1933c fadE18 |
acyl-CoA dehydrogenase FadE18 | 496 | 476 ctx | neighborhood:459 |
Rv0791c hyp |
hypothetical protein | 424 | 402 | |
Rv3192 hyp |
hypothetical protein | 417 | 395 | |
Rv1360 |
oxidoreductase | 401 | 378 | |
Rv0407 fgd1 |
F420-dependent glucose-6-phosphate dehydrogenase | 400 | 377 |
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: flavin reductase family protein
- Pfam (hmmscan --cut_ga): Flavin_Reduct PF01613.25 (E=2e-34)
- (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_216455.1)
- Domains: Pfam-A via hmmscan --cut_ga — Flavin_Reduct (PF01613.25)
- 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
COG1853 - Curated reference: UniProt P95275 (TrEMBL, unreviewed; Inferred from homology)
- 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 —
13 functional partner(s); context anchor
ribA1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002053|Rv1939| MSCTFDMVPETVDHLDEVGLRRVFGCFPCGVIAVCAMVDDQPVGMAASSFTSVSVDPPLVSICVQNCSTTWPKLRDRPRLGVSVLAEGHDAACMSLSRKEGNRFAGVFWSELSSGGVVIAGAGAWLDCRPYAEIPAGDHLIALLEICAVRADPETPPLVFHGSRFRRLESR