Rv0925c Family assigned · medium auto-curated
H37Rv Rv0925c · MTBC0 mtbc0_000983 ·
245 aa · 1035113–1035850 (-) ·
RefSeq NP_215440.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | flavodoxin family protein |
| Revised (this work) | Flavodoxin family protein. Pfam: FMN_red (PF03358.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y946
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 |
S Function unknown
|
|---|---|
| eggNOG description | NADPH-dependent FMN reductase |
| Orthologous group | COG0655 |
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 | 0.315 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.11% of strains (156) · 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 |
|---|---|---|---|---|
FMN_red | PF03358.21 | 2.5e-08 | 21–169 | NADPH-dependent FMN reductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mntH (divalent metal cation transporter MntH), high confidence from genomic context alone (score 722 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) |
|---|---|---|---|---|
Rv0924c mntH |
divalent metal cation transporter MntH | 722 | 722 ctx | neighborhood:708 |
Rv0923c hyp |
hypothetical protein | 710 | 710 ctx | neighborhood:708 |
Rv0007 |
membrane protein | 660 | 648 | coexpression:648 |
Rv0926c hyp |
hypothetical protein | 637 | 637 ctx | neighborhood:613 |
Rv0927c |
oxidoreductase | 537 | 534 ctx | neighborhood:511 |
Rv1884c rpfC |
resuscitation-promoting factor RpfC | 472 | 447 | coexpression:446 |
Rv3701c egtD |
histidine-specific methyltransferase EtgD | 444 | 445 ctx | cooccurence:411 |
Rv2450c rpfE |
resuscitation-promoting factor RpfE | 466 | 441 | coexpression:440 |
Rv1449c tkt |
transketolase | 457 | 436 | coexpression:426 |
Rv0867c rpfA |
resuscitation-promoting factor RpfA | 446 | 424 | coexpression:424 |
Rv2389c rpfD |
resuscitation-promoting factor RpfD | 444 | 422 | coexpression:422 |
Rv1448c tal |
transaldolase | 418 | 418 | coexpression:406 |
Rv0432 sodC |
superoxide dismutase | 442 | 415 | coexpression:409 |
Rv1954A |
Rv1954A, len: 100 aa. Hypothetical unknown protein. | 412 | 413 | coexpression:413 |
Rv3372 otsB2 |
trehalose 6-phosphate phosphatase | 411 | 412 | coexpression:412 |
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: flavodoxin family protein
- Pfam (hmmscan --cut_ga): FMN_red PF03358.21 (E=2e-08)
- (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_215440.1)
- Domains: Pfam-A via hmmscan --cut_ga — FMN_red (PF03358.21)
- 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
COG0655 - Curated reference: UniProt I6Y946 (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 —
23 functional partner(s); context anchor
mntH - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000983|Rv0925c| MTTTSDQNAAAPPRFDGLRALFINATLKRSPELSHTDGLIERSSGIMREHGVQVDTLRAVDHDIATGVWPDMTEHGWATDEWPALYRRVLDAHILVLCGPIWLGDNSSVMKRVIERLYACSSLLNEDGQYAYYGRAGGCLITGNEDGVKHCAMNVLYSLQHLGYTIPPQADAGWIGEAGPGPSYLDPGSGGPENDFTNRNTTFMTFNLMHIAQMLRVAGGIPAYGNQRTKWDAGCRPDFANPDYR