pitA Resolved · high auto-curated
H37Rv Rv0545c · MTBC0 mtbc0_000574 ·
417 aa · 639761–641014 (-) ·
RefSeq NP_215059.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | low-affinity inorganic phosphate transporter |
|---|---|
| MTBC0 PGAP re-annotation | anion permease |
| Revised (this work) | Anion permease. Pfam: PHO4 (PF01384.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIA7
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable low-affinity inorganic phosphate transporter |
| Curated function | Low-affinity inorganic phosphate transporter. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | pitA |
| eggNOG description | phosphate transporter |
| Orthologous group | COG0306 |
| KEGG orthology |
K03306
|
| Gene Ontology (33) |
GO:0003674, GO:0005215, GO:0005315, GO:0005575, GO:0005623, GO:0005886, GO:0005887, GO:0006810, GO:0006811, GO:0006817, GO:0006820, GO:0008150 +21 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 | 0.097 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 2 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 |
|---|---|---|---|---|
PHO4 | PF01384.26 | 5.5e-84 | 22–322 | Phosphate transporter family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0544c (transmembrane protein), high confidence from genomic context alone (score 905 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0544c |
transmembrane protein | 904 | 905 ctx | neighborhood:881 |
Rv0543c hyp |
hypothetical protein | 848 | 848 ctx | neighborhood:803 |
Rv0542c menE |
2-succinylbenzoic acid--CoA ligase | 753 | 753 ctx | neighborhood:741 |
Rv0541c |
integral membrane protein | 745 | 745 ctx | neighborhood:738 |
Rv0547c |
oxidoreductase | 715 | 716 ctx | neighborhood:714 |
Rv0546c hyp |
hypothetical protein | 526 | 526 ctx | neighborhood:519 |
Rv2847c cysG |
multifunctional uroporphyrin-III C-methyltransferase/precorrin-2 oxidase/ferrochelatase | 570 | 507 | coexpression:441 |
Rv2883c pyrH |
uridylate kinase | 492 | 493 | coexpression:492 |
Rv1640c lysX |
bifunctional lysine--tRNA ligase/phosphatidylglycerol lysyltransferase | 456 | 457 | coexpression:442 |
Rv0548c menB |
1,4-dihydroxy-2-naphthoyl-CoA synthase | 430 | 430 | |
Rv1841c hyp |
hypothetical protein | 423 | 424 | |
Rv3598c lysS |
lysine--tRNA ligase | 421 | 421 | coexpression:419 |
Rv1613 trpA |
tryptophan synthase subunit alpha | 479 | 415 | coexpression:415 |
Rv2889c tsf |
elongation factor EF-Ts | 407 | 408 | coexpression:408 |
Rv3232c ppk2 |
polyphosphate kinase | 412 | 352 |
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: low-affinity inorganic phosphate transporter
- MTBC0 PGAP product: anion permease
- Pfam (hmmscan --cut_ga): PHO4 PF01384.26 (E=6e-84)
- (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_215059.1)
- Domains: Pfam-A via hmmscan --cut_ga — PHO4 (PF01384.26)
- 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
COG0306 - Curated reference: UniProt P9WIA7 (SwissProt, reviewed; Inferred from homology)
- 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 —
30 functional partner(s); context anchor
Rv0544c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000574|Rv0545c|pitA MNLQLFLLLIVVVTALAFDFTNGFHDTGNAMATSIASGALAPRVAVALSAVLNLIGAFLSTAVAATIAKGLIDANLVTLELVFAGLVGGIVWNLLTWLLGIPSSSSHALIGGIVGATIAAVGLRGVIWSGVVSKVIVPAVVAALLATLVGAVGTWLVYRTTRGVAEKRTERGFRRGQIGSASLVSLAHGTNDAQKTMGVIFLALMSYGAVSTTASVPPLWVIVSCAVAMAAGTYLGGWRIIRTLGKGLVEIKPPQGMAAESSSAAVILLSAHFGYALSTTQVATGSVLGSGVGKPGAEVRWGVAGRMVVAWLVTLPLAGLVGAFTYGLVHFIGGYPGAILGFALLWLTATAIWLRSRRAPIDHTNVNADWEGNLTAGLEAGAQPLADQRPPVPAPPAPTPPPNHRAPQFGVTTRNAP