Rv2293c Family assigned · medium auto-curated
H37Rv Rv2293c · MTBC0 - ·
246 aa · 2564292–2565032 (-) ·
RefSeq NP_216809.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains PNP_UDP_1 (PF01048.27) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WLE1
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Uncharacterized protein Rv2293c |
UniProt still lists this protein as Uncharacterized protein Rv2293c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| eggNOG description | nucleoside metabolic process |
| Orthologous group | COG0775 |
| EC number |
EC 3.2.2.9
|
| KEGG orthology |
K01243
|
| KEGG pathways |
map00270, map01100, map01230
|
| KEGG modules |
M00034, M00609
|
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 | 0.458 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 4 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 61.75% of strains (89666) · reference-fixed |
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 |
|---|---|---|---|---|
PNP_UDP_1 | PF01048.27 | 7.7e-12 | 40–146 | Phosphorylase superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1004c (membrane protein), high confidence from genomic context alone (score 787 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) |
|---|---|---|---|---|
Rv2292c hyp |
hypothetical protein | 869 | 869 ctx | neighborhood:662 fusion:623 |
Rv1004c |
membrane protein | 786 | 787 ctx | cooccurence:770 |
Rv1753c PPE24 |
PPE family protein PPE24 | 777 | 778 ctx | cooccurence:766 |
Rv3347c PPE55 |
PPE family protein PPE55 | 775 | 775 ctx | cooccurence:772 |
Rv0355c PPE8 |
PPE family protein PPE8 | 775 | 775 ctx | cooccurence:772 |
Rv3350c PPE56 |
PPE family protein PPE56 | 773 | 774 ctx | cooccurence:771 |
Rv0304c PPE5 |
PPE family protein PPE5 | 773 | 773 ctx | cooccurence:770 |
Rv1917c PPE34 |
PPE family protein PPE34 | 773 | 773 ctx | cooccurence:771 |
Rv3343c PPE54 |
PPE family protein PPE54 | 772 | 772 ctx | cooccurence:769 |
Rv2209 |
integral membrane protein | 771 | 771 ctx | cooccurence:770 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 770 | 770 ctx | cooccurence:770 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 770 | 770 ctx | cooccurence:770 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 768 | 768 ctx | cooccurence:768 |
Rv2819c csm5 |
CRISPR type III-associated RAMP protein Csm5 | 766 | 766 ctx | cooccurence:764 |
Rv0341 iniB |
isoniazid inducible protein IniB | 765 | 765 ctx | cooccurence:765 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): PNP_UDP_1 PF01048.27 (E=8e-12)
- (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_216809.1)
- Domains: Pfam-A via hmmscan --cut_ga — PNP_UDP_1 (PF01048.27)
- 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
COG0775 - Curated reference: UniProt P9WLE1 (SwissProt, reviewed; Inferred from homology)
- 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 —
103 functional partner(s); context anchor
Rv1004c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2293c| MGAPLRHCLLVAAALSLGCGVAAADPGYVANVIPCEQRTLVLSAFPAEADAVLAHTALDANPVVVADRRRYYLGSISGKKVIVAMTGIGLVNATNTTETAFARFTCASSIAIAAVMFSGVAGGAGRTSIGDVAIPARWTLDNGATFRGVDPGMLATAQTLSVVLDNINTLGNPVCLCRNVPVVRLNHLGRQPQLFVGGDGSSSDKNNGQAFPCIPNGGSVFAANPVVHPIAHLAIPVTFSRRRDPG