Rv2143 Family assigned · medium auto-curated
H37Rv Rv2143 · MTBC0 mtbc0_002279 ·
352 aa · 2430356–2431414 (+) ·
RefSeq NP_216659.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | phosphoribosyltransferase family protein |
| Revised (this work) | Phosphoribosyltransferase family protein. Pfam: Pribosyltran (PF00156.34). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06232
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Phosphoribosyltransferase domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | phosphoribosyl transferase |
| Orthologous group | COG1926 |
| KEGG orthology |
K07100
|
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 | 0.287 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Pribosyltran | PF00156.34 | 3.7e-12 | 152–325 | Phosphoribosyl transferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rip3 (zinc metalloprotease Rip3), medium confidence from genomic context alone (score 621 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) |
|---|---|---|---|---|
Rv0574c hyp |
hypothetical protein | 631 | 631 ctx | cooccurence:583 |
Rv2625c rip3 |
zinc metalloprotease Rip3 | 621 | 621 ctx | cooccurence:608 |
Rv2142c parE2 |
toxin ParE2 | 470 | 470 ctx | neighborhood:467 |
Rv2142A parD2 |
antitoxin ParD2 | 467 | 467 ctx | neighborhood:467 |
Rv2753c dapA |
4-hydroxy-tetrahydrodipicolinate synthase | 467 | 390 |
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: phosphoribosyltransferase family protein
- Pfam (hmmscan --cut_ga): Pribosyltran PF00156.34 (E=4e-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_216659.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pribosyltran (PF00156.34)
- 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
COG1926 - Curated reference: UniProt O06232 (TrEMBL, unreviewed; 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)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
5 functional partner(s); context anchor
rip3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002279|Rv2143| MEAPPYAGDPTFERLRRSFQPADLLPELQAAGVHYTIAVEAADDPAENESLLATARHHDWIARVIGWVPLADPDEVTESSTHGRHRPDASWRRDLRCPGLLPPGCHQPVLVVGLVGQQPEMRPMNPPSGFLRRTPTRRFRDRRDAGRVLADELASYRGRDRLLVLGLARGGVPVGWEVASALGAELDVFLVRKLGVPQWRELAMGALASGGGVVMNDDVVSSLRITDQQVRAAIDSETAELQRRELAYRGGRPVVDPRARIVILVDDGIATGASMLAAVRTIRATGPESIVVAVPVGPATACRELAAEADDVVCATMPAAFEAVGQVYNDFHQVTDDEVRELLATPTTGAAT