impA Family assigned · medium auto-curated
H37Rv Rv1604 · MTBC0 mtbc0_001710 ·
270 aa · 1816003–1816815 (+) ·
RefSeq NP_216120.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | inositol-monophosphatase ImpA |
|---|---|
| MTBC0 PGAP re-annotation | inositol monophosphatase family protein |
| Revised (this work) | Inositol monophosphatase family protein. Pfam: Inositol_P (PF00459.31). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53907
SwissProt · reviewed
· Evidence at transcript level
|
|---|---|
| UniProt name | Probable inositol 1-monophosphatase ImpA |
| EC (curated) |
EC 3.1.3.25
|
| Curated function | Catalyzes the dephosphorylation of inositol 1-phosphate (I-1-P) to yield free myo-inositol, a key metabolite in mycobacteria. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | impA |
| eggNOG description | Inositol monophosphatase |
| Orthologous group | COG0483 |
| EC number |
EC 3.1.3.25
|
| KEGG orthology |
K01092
|
| KEGG pathways |
map00521, map00562, map01100, map04070
|
| KEGG modules |
M00131
|
| Gene Ontology (61) |
GO:0003674, GO:0003824, GO:0005575, GO:0005623, GO:0005886, GO:0005975, GO:0006020, GO:0006021, GO:0006066, GO:0006793, GO:0006796, GO:0007154 +49 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 | 0.647 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 7 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 |
|---|---|---|---|---|
Inositol_P | PF00459.31 | 1.7e-57 | 18–261 | Inositol monophosphatase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hisF (imidazole glycerol phosphate synthase subunit HisF), high confidence from genomic context alone (score 983 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1605 hisF |
imidazole glycerol phosphate synthase subunit HisF | 998 | 983 ctx | neighborhood:881 coexpression:865 textmining:921 |
Rv1603 hisA |
1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase | 997 | 983 ctx | neighborhood:882 coexpression:860 textmining:879 |
Rv1606 hisI |
phosphoribosyl-AMP cyclohydrolase | 978 | 977 ctx | neighborhood:881 coexpression:817 |
Rv1602 hisH |
imidazole glycerol phosphate synthase subunit HisH | 975 | 974 ctx | neighborhood:876 coexpression:801 |
Rv1601 hisB |
imidazole glycerol-phosphate dehydratase | 973 | 970 ctx | neighborhood:876 coexpression:770 |
Rv2701c suhB |
inositol-1-monophosphatase SuhB | 939 | 929 | database:900 |
Rv0046c ino1 |
inositol-3-phosphate synthase | 983 | 908 | database:900 textmining:827 |
Rv1600 hisC1 |
histidinol-phosphate aminotransferase | 913 | 908 ctx | neighborhood:876 |
Rv1599 hisD |
histidinol dehydrogenase | 928 | 902 ctx | neighborhood:876 |
Rv2349c plcC |
phospholipase C | 900 | 901 | database:900 |
Rv1755c plcD |
Rv1755c, (MT1799, MTCY28.21c), len: 280 aa. Probable plcD, phospholipase C 4 (fragment) (see citations below),highly similar to C-terminus o | 900 | 901 | database:900 |
Rv2350c plcB |
membrane-associated phospholipase B | 900 | 900 | database:900 |
Rv2351c plcA |
membrane-associated phospholipase A | 900 | 900 | database:900 |
Rv3608c folP1 |
dihydropteroate synthase | 744 | 745 | coexpression:736 |
Rv2841c nusA |
transcription termination/antitermination protein NusA | 570 | 568 | experimental:484 |
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: inositol-monophosphatase ImpA
- MTBC0 PGAP product: inositol monophosphatase family protein
- Pfam (hmmscan --cut_ga): Inositol_P PF00459.31 (E=2e-57)
- (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_216120.1)
- Domains: Pfam-A via hmmscan --cut_ga — Inositol_P (PF00459.31)
- 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
COG0483 - Curated reference: UniProt O53907 (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 —
39 functional partner(s); context anchor
hisF - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001710|Rv1604|impA MHLDSLVAPLVEQASAILDAATALFLVGHRADSAVRKKGNDFATEVDLAIERQVVAALVAATGIEVHGEEFGGPAVDSRWVWVLDPIDGTINYAAGSPLAAILLGLLHDGVPVAGLTWMPFTDQRYTAVAGGPLIKNGVPQPPLADAELANVLVGVGTFSADSRGQFPGRYRLAVLEKLSRVSSRLRMHGSTGIDLVFVADGILGGAISFGGHVWDHAAGVALVRAAGGVVTDLAGQPWTPASRSALAGPPRVHAQILEILGSIGEPEDY