aroD Resolved · high auto-curated
H37Rv Rv2537c · MTBC0 mtbc0_002703 ·
147 aa · 2884038–2884481 (-) ·
RefSeq NP_217053.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 3-dehydroquinate dehydratase |
|---|---|
| MTBC0 PGAP re-annotation | type II 3-dehydroquinate dehydratase |
| Revised (this work) | Type II 3-dehydroquinate dehydratase. Pfam: DHquinase_II (PF01220.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPX7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 3-dehydroquinate dehydratase |
| EC (curated) |
EC 4.2.1.10
|
| Curated function | Catalyzes a trans-dehydration via an enolate intermediate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | aroQ |
| eggNOG description | Catalyzes a trans-dehydration via an enolate intermediate |
| Orthologous group | COG0757 |
| EC number |
EC 4.2.1.10
|
| KEGG orthology |
K03786
|
| KEGG pathways |
map00400, map01100, map01110, map01130, map01230
|
| KEGG modules |
M00022
|
| Gene Ontology (34) |
GO:0003674, GO:0003824, GO:0003855, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006082, GO:0008150, GO:0008152, GO:0009058 +22 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 | 0.716 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
DHquinase_II | PF01220.25 | 3.0e-54 | 6–141 | Dehydroquinase class II |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: aroB (3-dehydroquinate synthase), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2538c aroB |
3-dehydroquinate synthase | 999 | 998 ctx | neighborhood:882 fusion:681 database:900 textmining:588 |
Rv2552c aroE |
shikimate 5-dehydrogenase | 984 | 965 ctx | neighborhood:544 database:900 textmining:589 |
Rv2539c aroK |
shikimate kinase | 952 | 919 ctx | neighborhood:882 textmining:433 |
Rv2540c aroF |
chorismate synthase | 947 | 912 ctx | neighborhood:882 textmining:420 |
Rv2386c mbtI |
salicylate synthase | 822 | 807 | database:800 |
Rv3215 entC |
isochorismate synthase | 825 | 801 | database:800 |
Rv1440 secG |
protein-export membrane protein SecG | 620 | 620 | coexpression:598 |
Rv2553c mltG |
membrane protein | 600 | 600 ctx | neighborhood:544 |
Rv2535c pepQ |
cytoplasmic peptidase PepQ | 596 | 596 ctx | fusion:513 |
Rv2554c ruvX |
Holliday junction resolvase | 581 | 581 ctx | neighborhood:544 |
Rv2462c tig |
trigger factor | 625 | 577 | coexpression:563 |
Rv2541 hyp |
hypothetical protein | 570 | 570 ctx | neighborhood:569 |
Rv2555c alaS |
alanine--tRNA ligase | 546 | 547 ctx | neighborhood:544 |
Rv2551c hyp |
hypothetical protein | 541 | 541 ctx | neighborhood:535 |
Rv3443c rplM |
50S ribosomal protein L13 | 497 | 498 | coexpression:457 |
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-dehydroquinate dehydratase
- MTBC0 PGAP product: type II 3-dehydroquinate dehydratase
- Pfam (hmmscan --cut_ga): DHquinase_II PF01220.25 (E=3e-54)
- (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_217053.1)
- Domains: Pfam-A via hmmscan --cut_ga — DHquinase_II (PF01220.25)
- 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
COG0757 - Curated reference: UniProt P9WPX7 (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 —
30 functional partner(s); context anchor
aroB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002703|Rv2537c|aroD MSELIVNVINGPNLGRLGRREPAVYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAEHVGT