Rv1598c Family assigned · medium auto-curated
H37Rv Rv1598c · MTBC0 mtbc0_001704 ·
136 aa · 1811037–1811447 (-) ·
RefSeq NP_216114.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | nitroreductase family deazaflavin-dependent oxidoreductase |
| Revised (this work) | Nitroreductase family deazaflavin-dependent oxidoreductase. Pfam: F420H2_quin_red (PF04075.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06592
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 | deazaflavin-dependent nitroreductase family protein |
| Orthologous group | 2C2H7 |
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 | 1.034 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
F420H2_quin_red | PF04075.21 | 3.9e-05 | 23–95 | F420H(2)-dependent quinone reductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mmpL5 (transmembrane transport protein MmpL5), high confidence from genomic context alone (score 725 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) |
|---|---|---|---|---|
Rv0676c mmpL5 |
transmembrane transport protein MmpL5 | 724 | 725 ctx | cooccurence:724 |
Rv0290 eccD3 |
ESX-3 secretion system protein EccD | 709 | 709 ctx | cooccurence:709 |
Rv2339 mmpL9 |
transmembrane transport protein MmpL9 | 702 | 703 ctx | cooccurence:702 |
Rv0507 mmpL2 |
transmembrane transport protein MmpL2 | 700 | 701 ctx | cooccurence:699 |
Rv0450c mmpL4 |
transmembrane transport protein MmpL4 | 693 | 693 ctx | cooccurence:693 |
Rv0402c mmpL1 |
transmembrane transport protein MmpL1 | 691 | 691 ctx | cooccurence:691 |
Rv0283 eccB3 |
ESX-3 secretion system protein EccB3 | 690 | 691 ctx | cooccurence:689 |
Rv1303 hyp |
hypothetical protein | 684 | 684 ctx | cooccurence:684 |
Rv1600 hisC1 |
histidinol-phosphate aminotransferase | 673 | 673 ctx | neighborhood:670 |
Rv1601 hisB |
imidazole glycerol-phosphate dehydratase | 672 | 672 ctx | neighborhood:670 |
Rv0756c hyp |
hypothetical protein | 657 | 657 ctx | cooccurence:653 |
Rv1599 hisD |
histidinol dehydrogenase | 634 | 634 ctx | neighborhood:631 |
Rv1602 hisH |
imidazole glycerol phosphate synthase subunit HisH | 633 | 633 ctx | neighborhood:631 |
Rv2942 mmpL7 |
transmembrane transport protein MmpL7 | 606 | 606 ctx | cooccurence:604 |
Rv1275 lprC |
lipoprotein LprC | 595 | 595 ctx | cooccurence:594 |
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: nitroreductase family deazaflavin-dependent oxidoreductase
- Pfam (hmmscan --cut_ga): F420H2_quin_red PF04075.21 (E=4e-05)
- (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_216114.1)
- Domains: Pfam-A via hmmscan --cut_ga — F420H2_quin_red (PF04075.21)
- 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
2C2H7 - Curated reference: UniProt O06592 (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 —
47 functional partner(s); context anchor
mmpL5 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001704|Rv1598c| MSAKDHPNNAPGVPMVFPLWLERLQVKYINRALKPIARYLPGTATIEHRGRKSGKPYQTIVTAYRKDGVLAIALAHGKTDWVKNVLAAGEADVHFARGVVHVINPRIVPAGSDGQGLPRMARLQLRRIGVFVGDIA