Rv3368c Family assigned · medium auto-curated
H37Rv Rv3368c · MTBC0 mtbc0_003583 ·
214 aa · 3807052–3807696 (-) ·
RefSeq NP_217885.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | nitroreductase family protein |
| Revised (this work) | Nitroreductase family protein. Pfam: Nitroreductase (PF00881.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O50397
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible oxidoreductase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| eggNOG description | nitroreductase |
| Orthologous group | COG0778 |
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 | 0.17 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 3 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 |
|---|---|---|---|---|
Nitroreductase | PF00881.30 | 4.6e-24 | 13–189 | Nitroreductase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dnaE2 (error-prone DNA polymerase), medium confidence from genomic context alone (score 581 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3463 hyp |
hypothetical protein | 616 | 602 ctx | cooccurence:571 |
Rv3370c dnaE2 |
error-prone DNA polymerase | 580 | 581 ctx | neighborhood:463 |
Rv3369 hyp |
hypothetical protein | 578 | 578 ctx | neighborhood:573 |
Rv0274 hyp |
hypothetical protein | 563 | 554 | coexpression:415 |
Rv1747 |
ABC transporter ATP-binding protein/permease | 575 | 551 | coexpression:438 |
Rv1375 hyp |
hypothetical protein | 522 | 492 | coexpression:475 |
Rv1875 hyp |
hypothetical protein | 481 | 481 ctx | cooccurence:450 |
Rv3192 hyp |
hypothetical protein | 494 | 476 ctx | cooccurence:437 |
Rv1598c hyp |
hypothetical protein | 445 | 446 ctx | cooccurence:444 |
Rv1686c |
ABC transporter permease | 458 | 439 | coexpression:421 |
Rv1457c |
antibiotic ABC transporter permease | 458 | 439 | coexpression:421 |
Rv2937 drrB |
daunorubicin ABC transporter permease DrrB | 456 | 437 | coexpression:419 |
Rv2938 drrC |
daunorubicin ABC transporter permease DrrC | 456 | 437 | coexpression:419 |
Rv1322A hyp |
hypothetical protein | 438 | 426 | coexpression:416 |
Rv3568c hsaC |
extradiol dioxygenase | 436 | 424 | coexpression:414 |
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: nitroreductase family protein
- Pfam (hmmscan --cut_ga): Nitroreductase PF00881.30 (E=5e-24)
- (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_217885.1)
- Domains: Pfam-A via hmmscan --cut_ga — Nitroreductase (PF00881.30)
- 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
COG0778 - Curated reference: UniProt O50397 (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 —
31 functional partner(s); context anchor
dnaE2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003583|Rv3368c| MTLNLSVDEVLTTTRSVRKRLDFDKPVPRDVLMECLELALQAPTGSNSQGWQWVFVEDAAKKKAIADVYLANARGYLSGPAPEYPDGDTRGERMGRVRDSATYLAEHMHRAPVLLIPCLKGREDESAVGGVSFWASLFPAVWSFCLALRSRGLGSCWTTLHLLDNGEHKVADVLGIPYDEYSQGGLLPIAYTQGIDFRPAKRLPAESVTHWNGW