phoH1 Resolved · high auto-curated
H37Rv Rv2368c · MTBC0 - ·
352 aa · 2648916–2649974 (-) ·
RefSeq YP_177874.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphate starvation-inducible protein PhoH |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Phosphate starvation-inducible protein PhoH. Pfam: PhoH (PF02562.23), AAA_30 (PF13604.13), AAA_19 (PF13245.13). |
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 |
P9WIA3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | PhoH-like protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| Preferred name | phoH |
| eggNOG description | Phosphate starvation-inducible protein PhoH |
| Orthologous group | COG1702 |
| KEGG orthology |
K06217
|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.548 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 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 |
|---|---|---|---|---|
PhoH | PF02562.23 | 1.5e-96 | 126–328 | PhoH-like protein |
AAA_30 | PF13604.13 | 2.9e-08 | 133–283 | AAA domain |
AAA_19 | PF13245.13 | 1.9e-07 | 135–282 | AAA domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ybeY (endoribonuclease), high confidence from genomic context alone (score 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2367c ybeY |
endoribonuclease | 996 | 996 ctx | neighborhood:881 coexpression:967 |
Rv2366c |
transmembrane protein | 976 | 976 ctx | neighborhood:881 coexpression:806 |
Rv2365c hyp |
hypothetical protein | 944 | 944 ctx | neighborhood:881 coexpression:548 |
Rv2364c era |
GTPase Era | 917 | 910 ctx | neighborhood:791 coexpression:519 |
Rv2362c recO |
DNA repair protein RecO | 790 | 783 | coexpression:730 |
Rv2369c hyp |
hypothetical protein | 774 | 774 ctx | neighborhood:773 |
Rv2370c hyp |
hypothetical protein | 774 | 773 ctx | neighborhood:773 |
Rv2420c rsfS hyp |
hypothetical protein | 573 | 573 ctx | cooccurence:546 |
Rv1712 cmk |
cytidylate kinase | 573 | 573 ctx | cooccurence:535 |
Rv2457c clpX |
ATP-dependent CLP protease ATP-binding subunit ClpX | 550 | 550 | coexpression:407 |
Rv1901 cinA |
competence damage-inducible protein CinA | 523 | 524 | |
Rv2372c rsmE |
rRNA small subunit methyltransferase E | 517 | 517 ctx | neighborhood:514 |
Rv2371 PE_PGRS40 |
PE-PGRS family protein PE_PGRS40 | 497 | 497 ctx | neighborhood:497 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 477 | 477 | |
Rv3752c tadA |
cytidine/deoxycytidylate deaminase | 458 | 459 ctx | cooccurence:456 |
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): phosphate starvation-inducible protein PhoH
- Pfam (hmmscan --cut_ga): PhoH PF02562.23 (E=2e-96), AAA_30 PF13604.13 (E=3e-08), AAA_19 PF13245.13 (E=2e-07)
- (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 YP_177874.1)
- Domains: Pfam-A via hmmscan --cut_ga — PhoH (PF02562.23), AAA_30 (PF13604.13), AAA_19 (PF13245.13)
- 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
COG1702 - Curated reference: UniProt P9WIA3 (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 —
25 functional partner(s); context anchor
ybeY - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2368c|phoH1 MTSRETRAADAAGARQADAQVRSSIDVPPDLVVGLLGSADENLRALERTLSADLHVRGNAVTLCGEPADVALAERVISELIAIVASGQSLTPEVVRHSVAMLVGTGNESPAEVLTLDILSRRGKTIRPKTLNQKRYVDAIDANTIVFGIGPAGTGKTYLAMAKAVHALQTKQVTRIILTRPAVEAGERLGFLPGTLSEKIDPYLRPLYDALYDMMDPELIPKLMSAGVIEVAPLAYMRGRTLNDAFIVLDEAQNTTAEQMKMFLTRLGFGSKVVVTGDVTQIDLPGGARSGLRAAVDILEDIDDIHIAELTSVDVVRHRLVSEIVDAYARYEEPGSGLNRAARRASGARGRR