pstS2 Family assigned · medium auto-curated
H37Rv Rv0932c · MTBC0 - ·
370 aa · 1039936–1041048 (-) ·
RefSeq YP_177769.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphate ABC transporter substrate-binding lipoprotein PstS |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Phosphate ABC transporter substrate-binding lipoprotein PstS. Pfam: PBP_like_2 (PF12849.13), SBP_bac_1 (PF01547.31). |
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 |
P9WGT9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphate-binding protein PstS 2 |
| Curated function | Functions in inorganic phosphate uptake, although probably not the main uptake protein under phosphate starvation. Part of the ABC transporter complex PstSACB involved in phosphate import (Probable). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | pstS |
| eggNOG description | Part of the ABC transporter complex PstSACB involved in phosphate import |
| Orthologous group | COG0226 |
| KEGG orthology |
K02040
|
| KEGG pathways |
map02010, map02020, map05152
|
| KEGG modules |
M00222
|
| Gene Ontology (15) |
GO:0005575, GO:0005576, GO:0005623, GO:0005886, GO:0006810, GO:0006811, GO:0006817, GO:0006820, GO:0008150, GO:0015698, GO:0016020, GO:0044464 +3 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 | 0.334 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 7 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.20% of strains (290) · 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 |
|---|---|---|---|---|
PBP_like_2 | PF12849.13 | 4.3e-43 | 47–335 | PBP superfamily domain |
SBP_bac_1 | PF01547.31 | 1.2e-15 | 53–343 | Bacterial extracellular solute-binding protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pstC1 (phosphate ABC transporter permease PstC), high confidence from genomic context alone (score 987 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0935 pstC1 |
phosphate ABC transporter permease PstC | 991 | 987 ctx | cooccurence:720 coexpression:650 database:800 |
Rv0929 pstC2 |
phosphate ABC transporter permease PstC | 991 | 984 ctx | cooccurence:770 coexpression:648 database:800 textmining:480 |
Rv0930 pstA1 |
phosphate ABC transporter permease PstA | 990 | 983 ctx | cooccurence:745 coexpression:651 database:800 textmining:452 |
Rv0936 pstA2 |
phosphate ABC transporter permease PstA | 986 | 983 ctx | cooccurence:642 coexpression:650 database:800 |
Rv0933 pstB |
phosphate ABC transporter ATP-binding protein PstB | 982 | 973 ctx | neighborhood:513 coexpression:650 database:800 |
Rv0820 phoT |
phosphate ABC transporter ATP-binding protein PhoT | 973 | 963 ctx | cooccurence:461 coexpression:660 database:800 |
Rv0934 pstS1 |
phosphate ABC transporter substrate-binding lipoprotein PstS | 975 | 961 ctx | neighborhood:478 database:900 |
Rv0928 pstS3 |
phosphate ABC transporter substrate-binding lipoprotein PstS | 905 | 903 | database:900 |
Rv0931c pknD |
serine/threonine-protein kinase PknD | 878 | 869 ctx | neighborhood:716 coexpression:557 |
Rv3301c phoY1 |
phosphate transport system transcriptional regulator PhoY | 673 | 571 | coexpression:418 |
Rv0821c phoY2 |
phosphate-transport system transcriptional regulator PhoY2 | 673 | 571 | coexpression:418 |
Rv0414c thiE |
thiamine-phosphate synthase | 454 | 455 | coexpression:455 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 480 | 454 | coexpression:423 |
Rv1238 sugC |
sugar ABC transporter ATP-binding protein SugC | 420 | 391 | |
Rv2832c ugpC |
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC | 418 | 389 |
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 substrate-binding lipoprotein PstS
- Pfam (hmmscan --cut_ga): PBP_like_2 PF12849.13 (E=4e-43), SBP_bac_1 PF01547.31 (E=1e-15)
- (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_177769.1)
- Domains: Pfam-A via hmmscan --cut_ga — PBP_like_2 (PF12849.13), SBP_bac_1 (PF01547.31)
- 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
COG0226 - Curated reference: UniProt P9WGT9 (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 —
36 functional partner(s); context anchor
pstC1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0932c|pstS2 MKFARSGAAVSLLAAGTLVLTACGGGTNSSSSGAGGTSGSVHCGGKKELHSSGSTAQENAMEQFVYAYVRSCPGYTLDYNANGSGAGVTQFLNNETDFAGSDVPLNPSTGQPDRSAERCGSPAWDLPTVFGPIAITYNIKGVSTLNLDGPTTAKIFNGTITVWNDPQIQALNSGTDLPPTPISVIFRSDKSGTSDNFQKYLDGASNGAWGKGASETFNGGVGVGASGNNGTSALLQTTDGSITYNEWSFAVGKQLNMAQIITSAGPDPVAITTESVGKTIAGAKIMGQGNDLVLDTSSFYRPTQPGSYPIVLATYEIVCSKYPDATTGTAVRAFMQAAIGPGQEGLDQYGSIPLPKSFQAKLAAAVNAIS