Rv3424c Still unknown · low auto-curated
H37Rv Rv3424c · MTBC0 mtbc0_003639 ·
120 aa · 3867153–3867515 (-) ·
RefSeq NP_217941.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKY3
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv3424c |
UniProt still lists this protein as Uncharacterized protein Rv3424c; the revised annotation above is ahead of the current UniProt record.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.479 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.13% of strains (193) · clonal |
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: PPE57 (PPE family protein PPE57), medium confidence from genomic context alone (score 533 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) |
|---|---|---|---|---|
Rv3425 PPE57 |
PPE family protein PPE57 | 533 | 533 ctx | neighborhood:525 |
Rv3420c rimI |
ribosomal-protein-alanine acetyltransferase RimI | 416 | 416 ctx | neighborhood:408 |
Rv3423c alr |
alanine racemase | 414 | 414 ctx | neighborhood:408 |
Rv3422c tsaE |
tRNA threonylcarbamoyladenosine biosynthesis protein | 412 | 412 ctx | neighborhood:408 |
Rv3419c gcp |
O-sialoglycoprotein endopeptidase | 412 | 412 ctx | neighborhood:408 |
Rv3421c tsaB hyp |
hypothetical protein | 410 | 410 ctx | neighborhood:408 |
Rv1501 hyp |
hypothetical protein | 813 | 70 | textmining:808 |
Rv2339 mmpL9 |
transmembrane transport protein MmpL9 | 657 | 54 | textmining:653 |
Rv1507c hyp |
hypothetical protein | 661 | 50 | textmining:658 |
Rv0451c mmpS4 |
membrane protein MmpS4 | 414 | 47 | textmining:411 |
Rv3585 radA |
DNA repair protein RadA | 655 | 46 | textmining:654 |
Rv1067c PE_PGRS19 |
PE-PGRS family protein PE_PGRS19 | 801 | 41 | textmining:801 |
Rv3903c cpnT hyp |
hypothetical protein | 650 | 41 | textmining:650 |
Rv1463 sufC |
ABC transporter ATP-binding protein | 547 | 41 | textmining:547 |
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: hypothetical protein
- (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_217941.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt P9WKY3 (SwissProt, reviewed; Predicted)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Model confidence: ESMFold per-residue pLDDT (mean 31.3, very low)
- 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
PPE57 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003639|Rv3424c| MPNPVTMLYGRKADLVILPHVLAEERPHPYSTPGRKRGAQIALTTGIDALASFAPQIVNPRHGLSRVVQCLGGCENKRHAYFRSISKTPHIRARGVPSVCAVRTVGVDGAKRPPKPIPVQ