aroA Resolved · high auto-curated
H37Rv Rv3227 · MTBC0 mtbc0_003436 ·
450 aa · 3625519–3626871 (+) ·
RefSeq NP_217744.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 3-phosphoshikimate 1-carboxyvinyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | 3-phosphoshikimate 1-carboxyvinyltransferase |
| Revised (this work) | 3-phosphoshikimate 1-carboxyvinyltransferase. Pfam: EPSP_synthase (PF00275.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPY5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 3-phosphoshikimate 1-carboxyvinyltransferase |
| EC (curated) |
EC 2.5.1.19
|
| Curated function | Catalyzes the transfer of the enolpyruvyl moiety of phosphoenolpyruvate (PEP) to the 5-hydroxyl of shikimate-3-phosphate (S3P) to produce enolpyruvyl shikimate-3-phosphate and inorganic phosphate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | aroA |
| eggNOG description | Catalyzes the transfer of the enolpyruvyl moiety of phosphoenolpyruvate (PEP) to the 5-hydroxyl of shikimate-3- phosphate (S3P) to produce enolpyruvyl shikimate-3-phosphate and inorganic phosphate |
| Orthologous group | COG0128 |
| EC number |
EC 2.5.1.19
|
| KEGG orthology |
K00800
|
| KEGG pathways |
map00400, map01100, map01110, map01130, map01230
|
| KEGG modules |
M00022
|
| Gene Ontology (35) |
GO:0003674, GO:0003824, GO:0003866, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006082, GO:0008150, GO:0008152 +23 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 | 0.401 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 synonymous, 9 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 |
|---|---|---|---|---|
EPSP_synthase | PF00275.26 | 1.9e-119 | 8–417 | EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: aroF (chorismate synthase), high confidence from genomic context alone (score 989 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2540c aroF |
chorismate synthase | 995 | 989 ctx | cooccurence:508 coexpression:770 database:900 textmining:561 |
Rv2552c aroE |
shikimate 5-dehydrogenase | 995 | 987 ctx | fusion:898 cooccurence:637 coexpression:646 textmining:657 |
Rv2538c aroB |
3-dehydroquinate synthase | 992 | 986 ctx | fusion:900 cooccurence:645 coexpression:580 textmining:510 |
Rv2539c aroK |
shikimate kinase | 988 | 977 ctx | cooccurence:562 coexpression:471 database:900 textmining:529 |
Rv1712 cmk |
cytidylate kinase | 923 | 913 ctx | fusion:896 |
Rv3228 rsgA hyp |
hypothetical protein | 948 | 904 ctx | neighborhood:882 textmining:485 |
Rv3226c hyp |
hypothetical protein | 886 | 788 ctx | neighborhood:787 textmining:485 |
Rv3754 tyrA |
prephenate dehydrogenase TyrA | 763 | 691 | coexpression:648 |
Rv3859c gltB |
glutamate synthase large subunit | 686 | 687 | coexpression:647 |
Rv0948c |
chorismate mutase | 716 | 678 | coexpression:660 |
Rv1885c |
chorismate mutase | 716 | 678 | coexpression:660 |
Rv0884c serC |
phosphoserine aminotransferase | 733 | 677 | coexpression:650 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 683 | 639 | coexpression:435 |
Rv1600 hisC1 |
histidinol-phosphate aminotransferase | 598 | 542 | coexpression:404 |
Rv3772 hisC2 |
histidinol-phosphate aminotransferase | 543 | 494 | coexpression:408 |
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-phosphoshikimate 1-carboxyvinyltransferase
- MTBC0 PGAP product: 3-phosphoshikimate 1-carboxyvinyltransferase
- Pfam (hmmscan --cut_ga): EPSP_synthase PF00275.26 (E=2e-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_217744.1)
- Domains: Pfam-A via hmmscan --cut_ga — EPSP_synthase (PF00275.26)
- 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
COG0128 - Curated reference: UniProt P9WPY5 (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 —
32 functional partner(s); context anchor
aroF - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003436|Rv3227|aroA MKTWPAPTAPTPVRATVTVPGSKSQTNRALVLAALAAAQGRGASTISGALRSRDTELMLDALQTLGLRVDGVGSELTVSGRIEPGPGARVDCGLAGTVLRFVPPLAALGSVPVTFDGDQQARGRPIAPLLDALRELGVAVDGTGLPFRVRGNGSLAGGTVAIDASASSQFVSGLLLSAASFTDGLTVQHTGSSLPSAPHIAMTAAMLRQAGVDIDDSTPNRWQVRPGPVAARRWDIEPDLTNAVAFLSAAVVSGGTVRITGWPRVSVQPADHILAILRQLNAVVIHADSSLEVRGPTGYDGFDVDLRAVGELTPSVAALAALASPGSVSRLSGIAHLRGHETDRLAALSTEINRLGGTCRETPDGLVITATPLRPGIWRAYADHRMAMAGAIIGLRVAGVEVDDIAATTKTLPEFPRLWAEMVGPGQGWGYPQPRSGQRARRATGQGSGG