aroB Resolved · high auto-curated
H37Rv Rv2538c · MTBC0 mtbc0_002704 ·
362 aa · 2884478–2885566 (-) ·
RefSeq NP_217054.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 3-dehydroquinate synthase |
|---|---|
| MTBC0 PGAP re-annotation | 3-dehydroquinate synthase |
| Revised (this work) | 3-dehydroquinate synthase. Pfam: Fe-ADH_2 (PF13685.13), DHQ_synthase (PF01761.27), DHQS_C (PF24621.3). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPX9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 3-dehydroquinate synthase |
| EC (curated) |
EC 4.2.3.4
|
| Curated function | Catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | aroB |
| eggNOG description | Catalyzes the conversion of 3-deoxy-D-arabino- heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ) |
| Orthologous group | COG0337 |
| EC number |
EC 2.7.1.71, EC 4.2.3.4
|
| KEGG orthology |
K01735, K13829
|
| KEGG pathways |
map00400, map01100, map01110, map01130, map01230
|
| KEGG modules |
M00022
|
| Gene Ontology (58) |
GO:0003674, GO:0003824, GO:0003856, GO:0005488, GO:0005507, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886 +46 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 0 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 |
|---|---|---|---|---|
Fe-ADH_2 | PF13685.13 | 2.7e-07 | 21–175 | Iron-containing alcohol dehydrogenase |
DHQ_synthase | PF01761.27 | 4.9e-42 | 69–180 | 3-dehydroquinate synthase N-terminal |
DHQS_C | PF24621.3 | 5.4e-46 | 183–325 | 3-dehydroquinate synthase C-terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: aroK (shikimate kinase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2539c aroK |
shikimate kinase | 999 | 1000 ctx | neighborhood:882 fusion:900 cooccurence:753 coexpression:942 textmining:929 |
Rv2537c aroD |
3-dehydroquinate dehydratase | 999 | 998 ctx | neighborhood:882 fusion:681 database:900 textmining:588 |
Rv2540c aroF |
chorismate synthase | 999 | 994 ctx | neighborhood:882 cooccurence:751 coexpression:813 textmining:922 |
Rv3227 aroA |
3-phosphoshikimate 1-carboxyvinyltransferase | 992 | 986 ctx | fusion:900 cooccurence:645 coexpression:580 textmining:510 |
Rv2552c aroE |
shikimate 5-dehydrogenase | 994 | 984 ctx | neighborhood:409 fusion:900 cooccurence:688 textmining:677 |
Rv2178c aroG |
phospho-2-dehydro-3-deoxyheptonate aldolase AroG | 992 | 916 | database:900 textmining:911 |
Rv3754 tyrA |
prephenate dehydrogenase TyrA | 884 | 712 | coexpression:499 textmining:614 |
Rv1026 ppx2 hyp |
hypothetical protein | 646 | 646 ctx | fusion:608 |
Rv3100c smpB |
SsrA-binding protein | 640 | 641 | coexpression:629 |
Rv3419c gcp |
O-sialoglycoprotein endopeptidase | 597 | 597 ctx | fusion:567 |
Rv2541 hyp |
hypothetical protein | 570 | 570 ctx | neighborhood:569 |
Rv3859c gltB |
glutamate synthase large subunit | 569 | 545 ctx | neighborhood:544 |
Rv2551c hyp |
hypothetical protein | 541 | 542 ctx | neighborhood:535 |
Rv3772 hisC2 |
histidinol-phosphate aminotransferase | 558 | 510 | coexpression:426 |
Rv0013 trpG |
anthranilate synthase component II | 612 | 494 |
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 synthase
- MTBC0 PGAP product: 3-dehydroquinate synthase
- Pfam (hmmscan --cut_ga): Fe-ADH_2 PF13685.13 (E=3e-07), DHQ_synthase PF01761.27 (E=5e-42), DHQS_C PF24621.3 (E=5e-46)
- (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_217054.1)
- Domains: Pfam-A via hmmscan --cut_ga — Fe-ADH_2 (PF13685.13), DHQ_synthase (PF01761.27), DHQS_C (PF24621.3)
- 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
COG0337 - Curated reference: UniProt P9WPX9 (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 —
46 functional partner(s); context anchor
aroK - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002704|Rv2538c|aroB MTDIGAPVTVQVAVDPPYPVVIGTGLLDELEDLLADRHKVAVVHQPGLAETAEEIRKRLAGKGVDAHRIEIPDAEAGKDLPVVGFIWEVLGRIGIGRKDALVSLGGGAATDVAGFAAATWLRGVSIVHLPTTLLGMVDAAVGGKTGINTDAGKNLVGAFHQPLAVLVDLATLQTLPRDEMICGMAEVVKAGFIADPVILDLIEADPQAALDPAGDVLPELIRRAITVKAEVVAADEKESELREILNYGHTLGHAIERRERYRWRHGAAVSVGLVFAAELARLAGRLDDATAQRHRTILSSLGLPVSYDPDALPQLLEIMAGDKKTRAGVLRFVVLDGLAKPGRMVGPDPGLLVTAYAGVCAP