cysQ Resolved · high auto-curated
H37Rv Rv2131c · MTBC0 mtbc0_002264 ·
267 aa · 2419780–2420583 (-) ·
RefSeq NP_216647.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 3'(2'),5'-bisphosphate nucleotidase CysQ |
|---|---|
| MTBC0 PGAP re-annotation | 3'(2')%2C5'-bisphosphate nucleotidase CysQ |
| Revised (this work) | 3'(2')%2C5'-bisphosphate nucleotidase CysQ. 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 |
P9WKJ1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 3'-phosphoadenosine 5'-phosphate phosphatase |
| EC (curated) |
EC 3.1.3.11, EC 3.1.3.25, EC 3.1.3.7
|
| Curated function | Phosphatase with a broad specificity. Its primary physiological function is to dephosphorylate 3'-phosphoadenosine 5'-phosphate (PAP) and 3'-phosphoadenosine 5'-phosphosulfate (PAPS). Thus, plays a role in mycobacterial sulfur metabolism, since it can serve as a key regulator of the sulfate assimilation pathway by controlling the pools of PAP and PAPS in the cell. To a lesser extent, is also able to hydrolyze inositol 1-phosphate (I-1-P), fructose 1,6-bisphosphate (FBP) (to fructose 6-phosphate (F-6-P)) and AMP in vitro, but this might not be significant in vivo. Glucose-1-phosphate (G-1-P), p. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | cysQ |
| eggNOG description | Inositol monophosphatase |
| Orthologous group | COG1218 |
| EC number |
EC 3.1.3.7
|
| KEGG orthology |
K01082
|
| KEGG pathways |
map00920, map01100, map01120, map01130
|
| Gene Ontology (64) |
GO:0000103, GO:0000287, GO:0003674, GO:0003824, GO:0005488, GO:0005575, GO:0005623, GO:0005886, GO:0006082, GO:0006139, GO:0006163, GO:0006725 +52 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 | 0.122 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 1 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 | 1.1e-25 | 45–240 | Inositol monophosphatase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mshC (cysteine:1D-myo-inosityl 2-amino-2-deoxy--D-glucopyranoside ligase), high confidence from genomic context alone (score 814 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1286 cysC |
adenylyl-sulfate kinase | 982 | 963 | database:900 textmining:554 |
Rv1285 cysD |
sulfate adenylyltransferase subunit 2 | 940 | 930 | database:900 |
Rv2392 cysH |
phosphoadenosine phosphosulfate reductase | 968 | 911 | database:900 textmining:659 |
Rv2837c nrnA |
bifunctional oligoribonuclease/PAP phosphatase NrnA | 963 | 901 | database:900 textmining:644 |
Rv2130c mshC |
cysteine:1D-myo-inosityl 2-amino-2-deoxy--D-glucopyranoside ligase | 823 | 814 ctx | neighborhood:805 |
Rv2129c |
oxidoreductase | 609 | 609 ctx | neighborhood:555 |
Rv2132 hyp |
hypothetical protein | 572 | 572 ctx | neighborhood:572 |
Rv2764c thyA |
thymidylate synthase ThyA | 566 | 567 | coexpression:461 |
Rv2134c hyp |
hypothetical protein | 563 | 563 ctx | neighborhood:544 |
Rv0363c fba |
fructose-bisphosphate aldolase | 561 | 562 | database:500 |
Rv2136c uppP |
undecaprenyl-diphosphatase | 560 | 561 ctx | neighborhood:544 |
Rv2133c hyp |
hypothetical protein | 550 | 550 ctx | neighborhood:544 |
Rv2135c hyp |
hypothetical protein | 573 | 549 ctx | neighborhood:544 |
Rv2137c hyp |
hypothetical protein | 545 | 546 ctx | neighborhood:544 |
Rv0946c pgi |
glucose-6-phosphate isomerase | 550 | 533 | database:500 |
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: 3'(2'),5'-bisphosphate nucleotidase CysQ
- MTBC0 PGAP product: 3'(2')%2C5'-bisphosphate nucleotidase CysQ
- Pfam (hmmscan --cut_ga): Inositol_P PF00459.31 (E=1e-25)
- (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_216647.1)
- 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
COG1218 - Curated reference: UniProt P9WKJ1 (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 —
34 functional partner(s); context anchor
mshC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002264|Rv2131c|cysQ MVSPAAPDLTDDLTDAELAADLAADAGKLLLQVRAEIGFDQPWTLGEAGDRQANSLLLRRLQAERPGDAVLSEEAHDDLARLKSDRVWIIDPLDGTREFSTPGRDDWAVHIALWRRSSNGQPEITDAAVALPARGNVVYRTDTVTSGAAPAGVPGTLRIAVSATRPPAVLHRIRQTLAIQPVSIGSAGAKAMAVIDGYVDAYLHAGGQWEWDSAAPAGVMLAAGMHASRLDGSPLRYNQLDPYLPDLLMCRAEVAPILLGAIADAWR