phoT Family assigned · medium auto-curated
H37Rv Rv0820 · MTBC0 mtbc0_000869 ·
258 aa · 915793–916569 (+) ·
RefSeq NP_215335.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phosphate ABC transporter ATP-binding protein PhoT |
|---|---|
| MTBC0 PGAP re-annotation | phosphate ABC transporter ATP-binding protein PstB |
| Revised (this work) | Phosphate ABC transporter ATP-binding protein PstB. Pfam: ABC_tran (PF00005.34). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQL1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphate import ATP-binding protein PstB 1 |
| EC (curated) |
EC 7.3.2.1
|
| Curated function | Part of the ABC transporter complex PstSACB involved in phosphate import (Probable). Responsible for energy coupling to the transport system. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | pstB |
| eggNOG description | Part of the ABC transporter complex PstSACB involved in phosphate import. Responsible for energy coupling to the transport system |
| Orthologous group | COG1117 |
| EC number |
EC 3.6.3.27
|
| KEGG orthology |
K02036
|
| 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 | 0.334 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 3 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.65% of strains (941) · 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 |
|---|---|---|---|---|
ABC_tran | PF00005.34 | 2.5e-29 | 21–176 | ABC transporter |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pstA1 (phosphate ABC transporter permease PstA), high confidence from genomic context alone (score 986 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0930 pstA1 |
phosphate ABC transporter permease PstA | 994 | 986 ctx | cooccurence:774 coexpression:674 database:800 textmining:652 |
Rv0929 pstC2 |
phosphate ABC transporter permease PstC | 994 | 986 ctx | cooccurence:773 coexpression:672 database:800 textmining:613 |
Rv0936 pstA2 |
phosphate ABC transporter permease PstA | 990 | 985 ctx | cooccurence:774 coexpression:674 database:800 textmining:412 |
Rv0935 pstC1 |
phosphate ABC transporter permease PstC | 988 | 985 ctx | cooccurence:774 coexpression:673 database:800 |
Rv0928 pstS3 |
phosphate ABC transporter substrate-binding lipoprotein PstS | 982 | 965 ctx | cooccurence:481 coexpression:648 database:800 textmining:512 |
Rv0932c pstS2 |
phosphate ABC transporter substrate-binding lipoprotein PstS | 973 | 963 ctx | cooccurence:461 coexpression:660 database:800 |
Rv0934 pstS1 |
phosphate ABC transporter substrate-binding lipoprotein PstS | 971 | 962 ctx | cooccurence:442 coexpression:647 database:800 |
Rv0821c phoY2 |
phosphate-transport system transcriptional regulator PhoY2 | 945 | 924 ctx | cooccurence:769 coexpression:668 |
Rv3301c phoY1 |
phosphate transport system transcriptional regulator PhoY | 944 | 924 ctx | cooccurence:768 coexpression:667 |
Rv0933 pstB |
phosphate ABC transporter ATP-binding protein PstB | 908 | 908 | database:900 |
Rv0819 mshD |
mycothiol acetyltransferase | 809 | 690 ctx | neighborhood:680 textmining:412 |
Rv0818 |
transcriptional regulator | 703 | 688 ctx | neighborhood:680 |
Rv0817c lmeA hyp |
hypothetical protein | 509 | 510 ctx | neighborhood:510 |
Rv0816c thiX |
thioredoxin ThiX | 509 | 509 ctx | neighborhood:509 |
Rv2438c nadE |
glutamine-dependent NAD(+) synthetase | 422 | 422 | coexpression:421 |
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 ATP-binding protein PhoT
- MTBC0 PGAP product: phosphate ABC transporter ATP-binding protein PstB
- Pfam (hmmscan --cut_ga): ABC_tran PF00005.34 (E=2e-29)
- (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_215335.1)
- Domains: Pfam-A via hmmscan --cut_ga — ABC_tran (PF00005.34)
- 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
COG1117 - Curated reference: UniProt P9WQL1 (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 —
27 functional partner(s); context anchor
pstA1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000869|Rv0820|phoT MAKRLDLTDVNIYYGSFHAVADVSLAILPRSVTAFIGPSGCGKTTVLRTLNRMHEVIPGARVEGAVLLDDQDIYAPGIDPVGVRRAIGMVFQRPNPFPAMSIRNNVVAGLKLQGVRNRKVLDDTAESSLRGANLWDEVKDRLDKPGGGLSGGQQQRLCIARAIAVQPDVLLMDEPCSSLDPISTMAIEDLISELKQQYTIVIVTHNMQQAARVSDQTAFFNLEAVGKPGRLVEIASTEKIFSNPNQKATEDYISGRFG