aroF Resolved · high auto-curated
H37Rv Rv2540c · MTBC0 mtbc0_002706 ·
401 aa · 2886097–2887302 (-) ·
RefSeq NP_217056.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | chorismate synthase |
|---|---|
| MTBC0 PGAP re-annotation | chorismate synthase |
| Revised (this work) | Chorismate synthase. Pfam: Chorismate_synt (PF01264.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPY1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Chorismate synthase |
| EC (curated) |
EC 4.2.3.5
|
| Curated function | Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | aroC |
| eggNOG description | Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system |
| Orthologous group | COG0082 |
| EC number |
EC 4.2.3.5
|
| KEGG orthology |
K01736
|
| KEGG pathways |
map00400, map01100, map01110, map01130, map01230
|
| KEGG modules |
M00022
|
| Gene Ontology (63) |
GO:0000166, GO:0003674, GO:0003824, GO:0004107, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006082, GO:0006520 +51 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 | 0.062 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 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 |
|---|---|---|---|---|
Chorismate_synt | PF01264.27 | 1.3e-119 | 2–367 | Chorismate synthase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: aroB (3-dehydroquinate synthase), high confidence from genomic context alone (score 994 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2538c aroB |
3-dehydroquinate synthase | 999 | 994 ctx | neighborhood:882 cooccurence:751 coexpression:813 textmining:922 |
Rv3227 aroA |
3-phosphoshikimate 1-carboxyvinyltransferase | 995 | 989 ctx | cooccurence:508 coexpression:770 database:900 textmining:561 |
Rv2539c aroK |
shikimate kinase | 997 | 980 ctx | neighborhood:882 cooccurence:756 textmining:863 |
Rv2455c korA |
2-oxoglutarate oxidoreductase subunit KorA | 968 | 967 | experimental:965 |
Rv0948c |
chorismate mutase | 975 | 965 | coexpression:644 database:900 |
Rv1885c |
chorismate mutase | 974 | 965 | coexpression:643 database:900 |
Rv1609 trpE |
anthranilate synthase component I | 968 | 948 | database:900 textmining:410 |
Rv2537c aroD |
3-dehydroquinate dehydratase | 947 | 912 ctx | neighborhood:882 textmining:420 |
Rv2386c mbtI |
salicylate synthase | 944 | 910 ctx | cooccurence:441 database:800 textmining:410 |
Rv3215 entC |
isochorismate synthase | 935 | 910 ctx | cooccurence:548 database:800 |
Rv1005c pabB |
para-aminobenzoate synthase component I | 918 | 910 ctx | cooccurence:433 database:800 |
Rv2552c aroE |
shikimate 5-dehydrogenase | 981 | 909 ctx | neighborhood:544 cooccurence:679 coexpression:427 textmining:804 |
Rv0013 trpG |
anthranilate synthase component II | 917 | 901 ctx | cooccurence:412 database:800 |
Rv3754 tyrA |
prephenate dehydrogenase TyrA | 944 | 809 | coexpression:709 textmining:719 |
Rv2949c |
chorismate pyruvate-lyase | 808 | 801 | database:800 |
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: chorismate synthase
- MTBC0 PGAP product: chorismate synthase
- Pfam (hmmscan --cut_ga): Chorismate_synt PF01264.27 (E=1e-119)
- (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_217056.1)
- Domains: Pfam-A via hmmscan --cut_ga — Chorismate_synt (PF01264.27)
- 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
COG0082 - Curated reference: UniProt P9WPY1 (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 —
63 functional partner(s); context anchor
aroB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002706|Rv2540c|aroF MLRWITAGESHGRALVAVVEGMVAGVHVTSADIADQLARRRLGYGRGARMTFERDAVTVLSGIRHGSTLGGPIAIEIGNTEWPKWETVMAADPVDPAELADVARNAPLTRPRPGHADYAGMLKYGFDDARPVLERASARETAARVAAGTVARAFLRQALGVEVLSHVISIGASAPYEGPPPRAEDLPAIDASPVRAYDKAAEADMIAQIEAAKKDGDTLGGVVEAVALGLPVGLGSFTSGDHRLDSQLAAAVMGIQAIKGVEIGDGFQTARRRGSRAHDEMYPGPDGVVRSTNRAGGLEGGMTNGQPLRVRAAMKPISTVPRALATVDLATGDEAVAIHQRSDVCAVPAAGVVVETMVALVLARAALEKFGGDSLAETQRNIAAYQRSVADREAPAARVSG