Rv3007c Family assigned · medium auto-curated
H37Rv Rv3007c · MTBC0 mtbc0_003196 ·
204 aa · 3387145–3387759 (-) ·
RefSeq NP_217523.1
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 |
O53254
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Possible 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) pseudogene candidate
| pN/pS | 1.241 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 17.52% of strains (25445) · 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 | 1.1e-29 | 22–162 | Flavin reductase like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1939 (oxidoreductase), high confidence from genomic context alone (score 723 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1939 |
oxidoreductase | 722 | 723 ctx | cooccurence:720 |
Rv0245 |
oxidoreductase | 686 | 687 ctx | cooccurence:684 |
Rv3009c gatB |
aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B | 552 | 552 ctx | neighborhood:538 |
Rv3008 hyp |
hypothetical protein | 532 | 532 ctx | neighborhood:514 |
Rv3079c hyp |
hypothetical protein | 430 | 409 | |
Rv0791c hyp |
hypothetical protein | 412 | 390 | |
Rv3618 |
monooxygenase | 411 | 388 | |
Rv1936 |
monooxygenase | 403 | 381 | |
Rv3554 fdxB |
electron transfer protein FdxB | 405 | 373 |
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=1e-29)
- (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_217523.1)
- 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 O53254 (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 —
9 functional partner(s); context anchor
Rv1939 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003196|Rv3007c| MSEDVARIHDGDVIDESFDELMGMLDHPVFVVTTQADGHPAGCLVSFATQTSVQPPSFMVGLPRSTGTSEVASRSEHLAVHVLSQRQHVLAELFGSQTEEEVNKFARCSWRAGPCGMPILDDAAAWFIGRTASRSDVGDYVAYLLEPVSVWAPECSEDLLYLSDLDFDVDDIDPGKEASPRFYERERGDETRRYGVVRFTLDVP