Rv3127 Resolved · medium auto-curated
H37Rv Rv3127 · MTBC0 mtbc0_003323 ·
344 aa · 3513512–3514546 (+) ·
RefSeq NP_217643.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | NAD(P)H nitroreductase |
| Revised (this work) | NAD(P)H nitroreductase. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WL07
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv3127 |
UniProt still lists this protein as Uncharacterized protein Rv3127; 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 | NAD(P)H nitroreductase |
| Orthologous group | COG0778 |
| Gene Ontology (8) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0030312, GO:0044464, GO:0071944
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3134c (universal stress protein), high confidence from genomic context alone (score 911 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) |
|---|---|---|---|---|
Rv1738 hyp |
hypothetical protein | 954 | 922 ctx | cooccurence:465 coexpression:860 textmining:436 |
Rv1996 |
universal stress protein | 916 | 913 | coexpression:860 |
Rv3134c |
universal stress protein | 933 | 911 ctx | cooccurence:403 coexpression:855 |
Rv3131 |
NAD(P)H nitroreductase | 912 | 893 | coexpression:860 |
Rv3130c tgs1 |
diacyglycerol O-acyltransferase | 913 | 889 | coexpression:863 |
Rv0080 hyp |
hypothetical protein | 883 | 883 | coexpression:845 |
Rv2623 TB31.7 |
universal stress protein | 882 | 878 | coexpression:803 |
Rv2032 acg |
NAD(P)H nitroreductase | 869 | 864 | coexpression:859 |
Rv2031c hspX |
alpha-crystallin | 909 | 861 | coexpression:860 |
Rv0079 hyp |
hypothetical protein | 890 | 860 | coexpression:860 |
Rv2007c fdxA |
ferredoxin | 854 | 849 | coexpression:846 |
Rv2030c hyp |
hypothetical protein | 882 | 848 | coexpression:808 |
Rv2626c hrp1 |
hypoxic response protein | 863 | 840 | coexpression:839 |
Rv1733c |
transmembrane protein | 902 | 836 | coexpression:813 textmining:432 |
Rv2627c hyp |
hypothetical protein | 829 | 829 | coexpression:828 |
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: NAD(P)H nitroreductase
- (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_217643.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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 P9WL07 (SwissProt, reviewed; 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 —
64 functional partner(s); context anchor
Rv3134c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003323|Rv3127| MLKNAVLLACRAPSVHNSQPWRWVAESGSEHTTVHLFVNRHRTVPATDHSGRQAIISCGAVLDHLRIAMTAAHWQANITRFPQPNQPDQLATVEFSPIDHVTAGQRNRAQAILQRRTDRLPFDSPMYWHLFEPALRDAVDKDVAMLDVVSDDQRTRLVVASQLSEVLRRDDPYYHAELEWWTSPFVLAHGVPPDTLASDAERLRVDLGRDFPVRSYQNRRAELADDRSKVLVLSTPSDTRADALRCGEVLSTILLECTMAGMATCTLTHLIESSDSRDIVRGLTRQRGEPQALIRVGIAPPLAAVPAPTPRRPLDSVLQIRQTPEKGRNASDRNARETGWFSPP