pstA1 Family assigned · medium auto-curated
H37Rv Rv0930 · MTBC0 - ·
308 aa · 1036999–1037925 (+) ·
RefSeq NP_215445.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphate ABC transporter permease PstA |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Phosphate ABC transporter permease PstA. Pfam: BPD_transp_1 (PF00528.28). |
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 |
P9WG11
SwissProt · reviewed
· Evidence at transcript level
|
|---|---|
| UniProt name | Phosphate transport system permease protein PstA 1 |
| Curated function | Part of the binding-protein-dependent transport system for phosphate; probably responsible for the translocation of the substrate across the membrane. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | pstA |
| eggNOG description | Phosphate transport system permease |
| Orthologous group | COG0581 |
| KEGG orthology |
K02038
|
| KEGG pathways |
map02010
|
| KEGG modules |
M00222
|
| Gene Ontology (8) |
GO:0008150, GO:0040007, GO:0044110, GO:0044116, GO:0044117, GO:0044403, GO:0044419, GO:0051704
|
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 | 1.873 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 99.79% of strains (144901) · 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 |
|---|---|---|---|---|
BPD_transp_1 | PF00528.28 | 8.2e-19 | 103–303 | Binding-protein-dependent transport system inner membrane component |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pstC2 (phosphate ABC transporter permease PstC), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0929 pstC2 |
phosphate ABC transporter permease PstC | 999 | 999 ctx | neighborhood:881 fusion:834 coexpression:841 database:800 |
Rv0928 pstS3 |
phosphate ABC transporter substrate-binding lipoprotein PstS | 999 | 996 ctx | neighborhood:775 cooccurence:750 coexpression:667 database:800 textmining:778 |
Rv0935 pstC1 |
phosphate ABC transporter permease PstC | 994 | 992 ctx | fusion:842 coexpression:671 database:800 |
Rv0820 phoT |
phosphate ABC transporter ATP-binding protein PhoT | 994 | 986 ctx | cooccurence:774 coexpression:674 database:800 textmining:652 |
Rv0933 pstB |
phosphate ABC transporter ATP-binding protein PstB | 993 | 986 ctx | cooccurence:773 coexpression:670 database:800 textmining:579 |
Rv0932c pstS2 |
phosphate ABC transporter substrate-binding lipoprotein PstS | 990 | 983 ctx | cooccurence:745 coexpression:651 database:800 textmining:452 |
Rv0934 pstS1 |
phosphate ABC transporter substrate-binding lipoprotein PstS | 984 | 979 ctx | cooccurence:707 coexpression:648 database:800 |
Rv0936 pstA2 |
phosphate ABC transporter permease PstA | 936 | 927 | database:900 |
Rv3301c phoY1 |
phosphate transport system transcriptional regulator PhoY | 957 | 923 ctx | cooccurence:762 coexpression:671 textmining:476 |
Rv0821c phoY2 |
phosphate-transport system transcriptional regulator PhoY2 | 956 | 923 ctx | cooccurence:764 coexpression:668 textmining:466 |
Rv0927c |
oxidoreductase | 467 | 446 ctx | neighborhood:438 |
Rv3842c glpQ1 |
glycerophosphoryl diester phosphodiesterase | 434 | 400 | |
Rv2277c |
glycerolphosphodiesterase | 424 | 390 | |
Rv0317c glpQ2 |
glycerophosphoryl diester phosphodiesterase GlpQ | 418 | 383 | |
Rv3396c guaA |
GMP synthase | 499 | 291 |
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 ABC transporter permease PstA
- Pfam (hmmscan --cut_ga): BPD_transp_1 PF00528.28 (E=8e-19)
- (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_215445.2)
- Domains: Pfam-A via hmmscan --cut_ga — BPD_transp_1 (PF00528.28)
- 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
COG0581 - Curated reference: UniProt P9WG11 (SwissProt, reviewed; Evidence at transcript 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
pstC2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0930|pstA1 MSPSMSIEALDQPVKPVVFRPLTLRRRIKNSVATTFFFTSFVVALIPLVWLLWVVIARGWFAVTRSGWWTHSLRGVLPEQFAGGVYHALYGTLVQAGVAAVLAVPLGLMTAVYLVEYGTGRMSRVTTFTVDVLAGVPSIVAALFVFSLWIATLGFQQSAFAVALALVLLMLPVVVRAGEEMLRLVPDELREASYALGVPKWKTIVRIVAPIAMPGIVSGILLSIARVVGETAPVLVLVGYSHSINLDVFHGNMASLPLLIYTELTNPEHAGFLRVWGAALTLIIVVATINLAAAMIRFVATRRRRLPL