phoY1 Resolved · high auto-curated
H37Rv Rv3301c · MTBC0 mtbc0_003509 ·
221 aa · 3708992–3709657 (-) ·
RefSeq NP_217818.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphate transport system transcriptional regulator PhoY |
|---|---|
| MTBC0 PGAP re-annotation | phosphate signaling complex protein PhoU |
| Revised (this work) | Phosphate signaling complex protein PhoU. Pfam: PhoU (PF01895.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WI97
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphate-specific transport system accessory protein PhoU homolog 1 |
| Curated function | Plays a role in the regulation of phosphate uptake. In this role, it may bind, possibly as a chaperone, to PhoR, PhoP or a PhoR-PhoP complex to promote dephosphorylation of phospho-PhoP, or inhibit formation of the PhoR-PhoP transitory complex (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | phoU |
| eggNOG description | Plays a role in the regulation of phosphate uptake |
| Orthologous group | COG0704 |
| KEGG orthology |
K02039
|
| Gene Ontology (49) |
GO:0003674, GO:0005488, GO:0005515, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0008150, GO:0009892, GO:0010563 +37 more
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 3 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.12% of strains (171) · clonal |
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 |
|---|---|---|---|---|
PhoU | PF01895.25 | 1.1e-16 | 17–103 | PhoU domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: phoT (phosphate ABC transporter ATP-binding protein PhoT), high confidence from genomic context alone (score 924 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0820 phoT |
phosphate ABC transporter ATP-binding protein PhoT | 944 | 924 ctx | cooccurence:768 coexpression:667 |
Rv0930 pstA1 |
phosphate ABC transporter permease PstA | 957 | 923 ctx | cooccurence:762 coexpression:671 textmining:476 |
Rv0936 pstA2 |
phosphate ABC transporter permease PstA | 941 | 921 ctx | cooccurence:757 coexpression:670 |
Rv0933 pstB |
phosphate ABC transporter ATP-binding protein PstB | 972 | 920 ctx | cooccurence:756 coexpression:669 textmining:671 |
Rv3300c hyp |
hypothetical protein | 943 | 843 ctx | neighborhood:792 textmining:656 |
Rv0178 |
Mce associated membrane protein | 812 | 812 | coexpression:812 |
Rv3692 moxR2 |
methanol dehydrogenase transcriptional regulator MoxR | 805 | 805 | coexpression:805 |
Rv1282c oppC |
oligopeptide ABC transporter permease OppC | 810 | 801 | coexpression:801 |
Rv0935 pstC1 |
phosphate ABC transporter permease PstC | 871 | 784 ctx | cooccurence:750 textmining:428 |
Rv0929 pstC2 |
phosphate ABC transporter permease PstC | 835 | 784 ctx | cooccurence:746 |
Rv3299c atsB |
arylsulfatase AtsB | 777 | 777 ctx | neighborhood:714 |
Rv0894 |
transcriptional regulator | 751 | 751 | coexpression:751 |
Rv1359 |
transcriptional regulator | 745 | 741 | coexpression:740 |
Rv0909 |
antitoxin | 733 | 733 | coexpression:733 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 741 | 732 | coexpression:732 |
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: phosphate transport system transcriptional regulator PhoY
- MTBC0 PGAP product: phosphate signaling complex protein PhoU
- Pfam (hmmscan --cut_ga): PhoU PF01895.25 (E=1e-16)
- (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_217818.1)
- Domains: Pfam-A via hmmscan --cut_ga — PhoU (PF01895.25)
- 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
COG0704 - Curated reference: UniProt P9WI97 (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 —
53 functional partner(s); context anchor
phoT - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003509|Rv3301c|phoY1 MRTVYHQRLTELAGRLGEMCSLAGIAMKRATQALLEADIGAAEQVIRDHERIVAMRAQVEKEAFALLALQHPVAGELREIFSAVQIIADTERMGALAVHIAKITRREYPNQVLPEEVRNCFADMAKVAIALGDSARQVLVNRDPQEAAQLHDRDDAMDDLHRHLLSVLIDREWRHGVRVGVETALLGRFFERFADHAVEVGRRVIFMVTGVLPTEDEISTY