Rv1871c Family assigned · medium auto-curated
H37Rv Rv1871c · MTBC0 mtbc0_001984 ·
129 aa · 2139534–2139923 (-) ·
RefSeq NP_216387.1
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 |
P95144
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 |
C Energy production and conversion
|
|---|---|
| eggNOG description | F420H(2)-dependent quinone reductase |
| Orthologous group | COG1902 |
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 | 0.683 · 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 |
|---|---|---|---|---|
F420H2_quin_red | PF04075.21 | 1.7e-39 | 8–128 | F420H(2)-dependent quinone reductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lldD2 (L-lactate dehydrogenase), high confidence from genomic context alone (score 964 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) |
|---|---|---|---|---|
Rv1872c lldD2 |
L-lactate dehydrogenase | 965 | 964 ctx | neighborhood:750 coexpression:862 |
Rv3804c fbpA |
diacylglycerol acyltransferase/mycolyltransferase Ag85A | 848 | 843 | coexpression:811 |
Rv1870c hyp |
hypothetical protein | 814 | 815 ctx | neighborhood:799 |
Rv3583c carD |
RNA polymerase-binding transcription factor CarD | 800 | 800 | coexpression:800 |
Rv0685 tuf |
elongation factor Tu | 754 | 755 | coexpression:754 |
Rv3648c cspA |
cold shock protein A | 738 | 739 | coexpression:739 |
Rv1793 esxN |
ESAT-6 like protein EsxN | 732 | 732 | coexpression:732 |
Rv1630 rpsA |
30S ribosomal protein S1 | 732 | 732 | coexpression:732 |
Rv2346c esxO |
ESAT-6 like protein EsxO | 730 | 730 | coexpression:730 |
Rv1869c |
reductase | 734 | 724 ctx | neighborhood:720 |
Rv1919c hyp |
hypothetical protein | 721 | 721 ctx | cooccurence:718 |
Rv0180c |
transmembrane protein | 609 | 610 ctx | cooccurence:597 |
Rv1873 hyp |
hypothetical protein | 556 | 556 ctx | neighborhood:556 |
Rv0703 rplW |
50S ribosomal protein L23 | 540 | 540 | coexpression:533 |
Rv1546 hyp |
hypothetical protein | 530 | 530 ctx | cooccurence:526 |
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=2e-39)
- (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_216387.1)
- 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
COG1902 - Curated reference: UniProt P95144 (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 —
37 functional partner(s); context anchor
lldD2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001984|Rv1871c| MNAAMNLKREFVHRVQRFVVNPIGRQLPMTMLETIGRKTGQPRRTAVGGRVVDNQFWMVSEHGEHSDYVYNIKANPAVRVRIGGRWRSGTAYLLPDDDPRQRLRGLPRLNSAGVRAMGTDLLTIRVDLD