php Resolved · high auto-curated
H37Rv Rv0230c · MTBC0 mtbc0_000245 ·
326 aa · 275364–276344 (-) ·
RefSeq NP_214744.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphotriesterase |
|---|---|
| MTBC0 PGAP re-annotation | phosphotriesterase-related protein |
| Revised (this work) | Phosphotriesterase-related protein. Pfam: PTE (PF02126.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHN9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphotriesterase homology protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | php |
| eggNOG description | Phosphotriesterase |
| Orthologous group | COG1735 |
| KEGG orthology |
K07048
|
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 | 0.324 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 6 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 |
|---|---|---|---|---|
PTE | PF02126.26 | 2.0e-153 | 3–319 | Phosphotriesterase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0232 (transcriptional regulator), high confidence from genomic context alone (score 749 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0229c vapC51 hyp |
hypothetical protein | 902 | 799 ctx | neighborhood:799 textmining:532 |
Rv0232 |
transcriptional regulator | 749 | 749 ctx | neighborhood:697 |
Rv0231 fadE4 |
acyl-CoA dehydrogenase FadE4 | 790 | 746 ctx | neighborhood:737 |
Rv0233 nrdB |
ribonucleoside-diphosphate reductase subunit beta NrdB | 689 | 690 ctx | neighborhood:688 |
Rv2250A |
Possible flavoprotein; Rv2250A, len: 139 aa. Conserved hypothetical protein, possibly flavoprotein. Similar to N-terminus of SCF91.28c|AL132 | 440 | 441 ctx | cooccurence:433 |
Rv1635c |
mannosyltransferase | 412 | 412 ctx | cooccurence:412 |
Rv3830c |
TetR family transcriptional regulator | 410 | 373 | |
Rv2994 |
MFS-type transporter | 635 | 55 | textmining:630 |
Rv3632 |
membrane protein | 520 | 47 | textmining:517 |
Rv1619 hyp |
hypothetical protein | 443 | 45 | textmining:441 |
Rv1438 tpi |
triosephosphate isomerase | 519 | 41 | textmining:519 |
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: phosphotriesterase
- MTBC0 PGAP product: phosphotriesterase-related protein
- Pfam (hmmscan --cut_ga): PTE PF02126.26 (E=2e-153)
- (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_214744.1)
- Domains: Pfam-A via hmmscan --cut_ga — PTE (PF02126.26)
- 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
COG1735 - Curated reference: UniProt P9WHN9 (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 —
11 functional partner(s); context anchor
Rv0232 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000245|Rv0230c|php MPELNTARGPIDTADLGVTLMHEHVFIMTTEIAQNYPEAWGDEDKRVAGAIARLGELKARGVDTIVDLTVIGLGRYIPRIARVAAATELNIVVATGLYTYNDVPFYFHYLGPGAQLDGPEIMTDMFVRDIEHGIADTGIKAGILKCATDEPGLTPGVERVLRAVAQAHKRTGAPISTHTHAGLRRGLDQQRIFAEEGVDLSRVVIGHCGDSTDVGYLEELIAAGSYLGMDRFGVDVISPFQDRVNIVARMCERGHADKMVLSHDACCYFDALPEELVPVAMPNWHYLHIHNDVIPALKQHGVTDEQLHTMLVDNPRRIFERQGGYQ