aroE Resolved · high auto-curated
H37Rv Rv2552c · MTBC0 mtbc0_002720 ·
269 aa · 2894751–2895560 (-) ·
RefSeq NP_217068.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | shikimate 5-dehydrogenase |
|---|---|
| MTBC0 PGAP re-annotation | shikimate dehydrogenase |
| Revised (this work) | Shikimate dehydrogenase. Pfam: Shikimate_dh_N (PF08501.17), SDH_C (PF18317.7). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y120
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable shikimate 5-dehydrogenase AroE |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | aroE |
| eggNOG description | shikimate 5-dehydrogenase |
| Orthologous group | COG0169 |
| EC number |
EC 1.1.1.25
|
| KEGG orthology |
K00014
|
| KEGG pathways |
map00400, map01100, map01110, map01130, map01230
|
| KEGG modules |
M00022
|
| Gene Ontology (46) |
GO:0000166, GO:0003674, GO:0003824, GO:0004764, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006082, GO:0008150 +34 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) pseudogene candidate
| pN/pS | 0.763 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 10 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 10.19% of strains (14804) · clonal |
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 |
|---|---|---|---|---|
Shikimate_dh_N | PF08501.17 | 5.2e-17 | 10–92 | Shikimate dehydrogenase substrate binding domain |
SDH_C | PF18317.7 | 5.0e-10 | 236–262 | Shikimate 5'-dehydrogenase C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: aroA (3-phosphoshikimate 1-carboxyvinyltransferase), high confidence from genomic context alone (score 987 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3227 aroA |
3-phosphoshikimate 1-carboxyvinyltransferase | 995 | 987 ctx | fusion:898 cooccurence:637 coexpression:646 textmining:657 |
Rv2538c aroB |
3-dehydroquinate synthase | 994 | 984 ctx | neighborhood:409 fusion:900 cooccurence:688 textmining:677 |
Rv2539c aroK |
shikimate kinase | 992 | 978 ctx | neighborhood:544 cooccurence:529 database:900 textmining:668 |
Rv2553c mltG |
membrane protein | 968 | 968 ctx | neighborhood:881 coexpression:746 |
Rv2537c aroD |
3-dehydroquinate dehydratase | 984 | 965 ctx | neighborhood:544 database:900 textmining:589 |
Rv2551c hyp |
hypothetical protein | 941 | 940 ctx | neighborhood:805 coexpression:703 |
Rv2540c aroF |
chorismate synthase | 981 | 909 ctx | neighborhood:544 cooccurence:679 coexpression:427 textmining:804 |
Rv2554c ruvX |
Holliday junction resolvase | 909 | 909 ctx | neighborhood:881 |
Rv2555c alaS |
alanine--tRNA ligase | 888 | 888 ctx | neighborhood:881 |
Rv2386c mbtI |
salicylate synthase | 902 | 865 | database:800 |
Rv3215 entC |
isochorismate synthase | 880 | 862 | database:800 |
Rv2556c hyp |
hypothetical protein | 782 | 782 ctx | neighborhood:779 |
Rv0514 |
transmembrane protein | 748 | 748 | coexpression:748 |
Rv2421c nadD |
nicotinate-nucleotide adenylyltransferase | 736 | 713 | coexpression:689 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 567 | 567 | coexpression:431 |
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: shikimate 5-dehydrogenase
- MTBC0 PGAP product: shikimate dehydrogenase
- Pfam (hmmscan --cut_ga): Shikimate_dh_N PF08501.17 (E=5e-17), SDH_C PF18317.7 (E=5e-10)
- (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_217068.1)
- Domains: Pfam-A via hmmscan --cut_ga — Shikimate_dh_N (PF08501.17), SDH_C (PF18317.7)
- 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
COG0169 - Curated reference: UniProt I6Y120 (TrEMBL, unreviewed; 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 —
80 functional partner(s); context anchor
aroA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002720|Rv2552c|aroE MSEGPKKAGVLGSPIAHSRSPQLHLAAYRALGLHDWTYERIECGAAELPVVVGGFGPEWVGVSVTMPGKFAALRFADERTARADLVGSANTLVRTPHGWRADNTDIDGVAGALGAAAGHALVLGSGGTAPAAVVGLAELGVTDITVVARNSDKAARLVDLGTRVGVATRFCAFDSGGLADAVAAAEVLVSTIPAEVAAGYAGTLAAIPVLLDAIYDPWPTPLAAAVGSAGGRVISGLQMLLHQAFAQVEQFTGLPAPREAMTCALAALD