Rv2342 Still unknown · low auto-curated
H37Rv Rv2342 · MTBC0 mtbc0_002494 ·
85 aa · 2645022–2645279 (+) ·
RefSeq NP_216858.1
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 |
P95238
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein |
UniProt still lists this protein as Uncharacterized protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2DRKZ |
|---|
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 | 0.48 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 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: Rv3802c (membrane protein), high confidence from genomic context alone (score 762 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) |
|---|---|---|---|---|
Rv3802c |
membrane protein | 761 | 762 ctx | cooccurence:756 |
Rv2673 aftC |
alpha-(1->3)-arabinofuranosyltransferase | 757 | 757 ctx | cooccurence:757 |
Rv1780 hyp |
hypothetical protein | 756 | 756 ctx | cooccurence:755 |
Rv1476 |
membrane protein | 752 | 752 ctx | cooccurence:750 |
Rv3850 hyp |
hypothetical protein | 746 | 747 ctx | cooccurence:746 |
Rv3805c aftB |
terminal beta-(1->2)-arabinofuranosyltransferase | 741 | 742 ctx | cooccurence:740 |
Rv1610 |
membrane protein | 741 | 741 ctx | cooccurence:740 |
Rv1125 hyp |
hypothetical protein | 733 | 734 ctx | cooccurence:733 |
Rv0479c |
membrane protein | 732 | 733 ctx | cooccurence:729 |
Rv0383c ttfA hyp |
hypothetical protein | 730 | 730 ctx | cooccurence:730 |
Rv0466 hyp |
hypothetical protein | 720 | 720 ctx | cooccurence:720 |
Rv3244c lpqB |
lipoprotein LpqB | 715 | 715 ctx | cooccurence:712 |
Rv2876 |
transmembrane protein | 706 | 707 ctx | cooccurence:705 |
Rv0227c |
membrane protein | 693 | 694 ctx | cooccurence:693 |
Rv1890c hyp |
hypothetical protein | 690 | 691 ctx | cooccurence:690 |
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_216858.1)
- 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
2DRKZ - Curated reference: UniProt P95238 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 54.8, low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
85 functional partner(s); context anchor
Rv3802c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002494|Rv2342| MIGYVAVLGLGYVLGAKAGRRRYEQIASTYRALTGSPVARSMIEGGRRKIANRISPDAGFVTLAEIDNQTAVVQRGVERQPKTAR