Rv3054c Resolved · high auto-curated
H37Rv Rv3054c · MTBC0 mtbc0_003246 ·
184 aa · 3436731–3437285 (-) ·
RefSeq NP_217570.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | NADPH-dependent FMN reductase |
| Revised (this work) | NADPH-dependent FMN reductase. Pfam: FMN_red (PF03358.21), Flavodoxin_2 (PF02525.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95105
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | NADPH-dependent FMN reductase-like domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | FMN reductase |
| Orthologous group | COG0431 |
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 | 0.681 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 missense, 0 nonsense, 0 frameshift |
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 | 1.9e-38 | 8–155 | NADPH-dependent FMN reductase |
Flavodoxin_2 | PF02525.23 | 1.9e-06 | 9–118 | Flavodoxin-like fold |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3055 (TetR family transcriptional regulator), high confidence from genomic context alone (score 824 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) |
|---|---|---|---|---|
Rv3055 |
TetR family transcriptional regulator | 828 | 824 ctx | neighborhood:736 |
Rv3056 dinP |
DNA polymerase IV 2 | 778 | 778 ctx | neighborhood:778 |
Rv2466c hyp |
hypothetical protein | 745 | 745 | coexpression:729 |
Rv3463 hyp |
hypothetical protein | 960 | 696 | coexpression:639 textmining:875 |
Rv1251c hyp |
hypothetical protein | 422 | 423 | coexpression:403 |
Rv2400c subI |
sulfate ABC transporter substrate-binding lipoprotein SubI | 403 | 350 | |
Rv2643 arsC |
arsenic-transport integral membrane protein ArsC | 644 | 319 | textmining:500 |
Rv1286 cysC |
adenylyl-sulfate kinase | 443 | 179 | |
Rv3223c sigH |
ECF RNA polymerase sigma factor SigH | 657 | 115 | textmining:629 |
Rv3913 trxB2 |
thioredoxin reductase | 509 | 103 | textmining:475 |
Rv3914 trxC |
thioredoxin TrxC | 489 | 78 | textmining:469 |
Rv0331 |
dehydrogenase/reductase | 881 | 73 | textmining:878 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 657 | 55 | textmining:652 |
Rv0352 dnaJ1 |
chaperone protein DnaJ | 441 | 51 | textmining:436 |
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: NADPH-dependent FMN reductase
- Pfam (hmmscan --cut_ga): FMN_red PF03358.21 (E=2e-38), Flavodoxin_2 PF02525.23 (E=2e-06)
- (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_217570.1)
- Domains: Pfam-A via hmmscan --cut_ga — FMN_red (PF03358.21), Flavodoxin_2 (PF02525.23)
- 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
COG0431 - Curated reference: UniProt P95105 (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 —
14 functional partner(s); context anchor
Rv3055 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003246|Rv3054c| MSDTKSDIKILALVGSLRAASFNRQIAELAAKVAPDGVTVTMFEGLGDLPFYNEDIDTATEVPAPVSALREAASDAHAALVVTPEYNGSIPAVIKNAIDWLSRPFGDGALKDKPLAVIGGSMGRYGGVWAHDETRKSFSIAGTRVVDAIKLSVPFQTLGKSVADDAGLAANVRDAVGNLAAEVG