pstC2 Family assigned · medium auto-curated
H37Rv Rv0929 · MTBC0 mtbc0_000987 ·
324 aa · 1039245–1040219 (+) ·
RefSeq NP_215444.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphate ABC transporter permease PstC |
|---|---|
| MTBC0 PGAP re-annotation | phosphate ABC transporter permease subunit PstC |
| Revised (this work) | Phosphate ABC transporter permease subunit PstC. 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.
Curated reference (UniProt)
| UniProt |
P9WG05
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphate transport system permease protein PstC 2 |
| Curated function | Part of the ABC transporter complex PstSACB involved in phosphate import; 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 | pstC |
| eggNOG description | probably responsible for the translocation of the substrate across the membrane |
| Orthologous group | COG0573 |
| KEGG orthology |
K02037
|
| 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 | 0.762 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
BPD_transp_1 | PF00528.28 | 2.0e-14 | 104–317 | Binding-protein-dependent transport system inner membrane component |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pstS3 (phosphate ABC transporter substrate-binding lipoprotein PstS), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0928 pstS3 |
phosphate ABC transporter substrate-binding lipoprotein PstS | 999 | 999 ctx | neighborhood:778 cooccurence:771 coexpression:913 database:800 textmining:693 |
Rv0930 pstA1 |
phosphate ABC transporter permease PstA | 999 | 999 ctx | neighborhood:881 fusion:834 coexpression:841 database:800 |
Rv0820 phoT |
phosphate ABC transporter ATP-binding protein PhoT | 994 | 986 ctx | cooccurence:773 coexpression:672 database:800 textmining:613 |
Rv0933 pstB |
phosphate ABC transporter ATP-binding protein PstB | 992 | 985 ctx | cooccurence:769 coexpression:670 database:800 textmining:536 |
Rv0932c pstS2 |
phosphate ABC transporter substrate-binding lipoprotein PstS | 991 | 984 ctx | cooccurence:770 coexpression:648 database:800 textmining:480 |
Rv0936 pstA2 |
phosphate ABC transporter permease PstA | 987 | 984 ctx | fusion:665 coexpression:670 database:800 |
Rv0934 pstS1 |
phosphate ABC transporter substrate-binding lipoprotein PstS | 986 | 983 ctx | cooccurence:761 coexpression:648 database:800 |
Rv0935 pstC1 |
phosphate ABC transporter permease PstC | 921 | 922 | database:900 |
Rv3301c phoY1 |
phosphate transport system transcriptional regulator PhoY | 835 | 784 ctx | cooccurence:746 |
Rv0821c phoY2 |
phosphate-transport system transcriptional regulator PhoY2 | 834 | 783 ctx | cooccurence:751 |
Rv0927c |
oxidoreductase | 474 | 455 ctx | neighborhood:439 |
Rv0926c hyp |
hypothetical protein | 402 | 402 | |
Rv0819 mshD |
mycothiol acetyltransferase | 460 | 240 | |
Rv0637 hadC |
(3R)-hydroxyacyl-ACP dehydratase subunit HadC | 443 | 48 | textmining:439 |
Rv3601c panD |
aspartate 1-decarboxylase | 512 | 44 | textmining:511 |
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 ABC transporter permease PstC
- MTBC0 PGAP product: phosphate ABC transporter permease subunit PstC
- Pfam (hmmscan --cut_ga): BPD_transp_1 PF00528.28 (E=2e-14)
- (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_215444.1)
- 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
COG0573 - Curated reference: UniProt P9WG05 (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 —
15 functional partner(s); context anchor
pstS3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000987|Rv0929|pstC2 MVTEPLTKPALVAVDMRPARRGERLFKLAASAAGSTIVIAILLIAIFLLVRAVPSLRANHANFFTSTQFDTSDDEQLAFGVRDLFMVTALSSITALVLAVPVAVGIAVFLTHYAPRRLSRPFGAMVDLLAAVPSIIFGLWGIFVLAPKLEPIARFLNRNLGWLFLFKQGNVSLAGGGTIFTAGIVLSVMILPIVTSISREVFRQTPLIQIEAALALGATKWEVVRMTVLPYGRSGVVAASMLGLGRALGETVAVLVILRSAARPGTWSLFDGGYTFASKIASAASEFSEPLPTGAYISAGFALFVLTFLVNAAARAIAGGKVNG