pheA Resolved · high auto-curated
H37Rv Rv3838c · MTBC0 mtbc0_004068 ·
321 aa · 4335815–4336780 (-) ·
RefSeq NP_218355.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | prephenate dehydratase |
|---|---|
| MTBC0 PGAP re-annotation | prephenate dehydratase |
| Revised (this work) | Prephenate dehydratase. Pfam: PDT (PF00800.24), ACT (PF01842.32). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIC3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Prephenate dehydratase |
| EC (curated) |
EC 4.2.1.51
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | pheA |
| eggNOG description | Prephenate dehydratase |
| Orthologous group | COG0077 |
| EC number |
EC 4.2.1.51
|
| KEGG orthology |
K04518
|
| KEGG pathways |
map00400, map01100, map01110, map01130, map01230
|
| KEGG modules |
M00024
|
| Gene Ontology (61) |
GO:0003674, GO:0003824, GO:0004664, GO:0005488, GO:0005515, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0006082, GO:0006520, GO:0006558 +49 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 | 0.332 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 6 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 |
|---|---|---|---|---|
PDT | PF00800.24 | 3.9e-44 | 4–190 | Prephenate dehydratase |
ACT | PF01842.32 | 1.6e-11 | 207–267 | ACT domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3837c (phosphoglycerate mutase), high confidence from genomic context alone (score 884 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3754 tyrA |
prephenate dehydrogenase TyrA | 992 | 946 | database:900 textmining:874 |
Rv0948c |
chorismate mutase | 940 | 909 | database:900 |
Rv1885c |
chorismate mutase | 937 | 909 | database:900 |
Rv2231c cobC |
aminotransferase | 916 | 908 | database:900 |
Rv3772 hisC2 |
histidinol-phosphate aminotransferase | 916 | 907 | database:900 |
Rv1600 hisC1 |
histidinol-phosphate aminotransferase | 916 | 907 | database:900 |
Rv3837c |
phosphoglycerate mutase | 884 | 884 ctx | neighborhood:882 |
Rv1908c katG |
catalase-peroxidase | 801 | 801 | database:800 |
Rv3839 hyp |
hypothetical protein | 784 | 784 ctx | neighborhood:781 |
Rv3565 aspB |
aspartate aminotransferase AspB | 779 | 768 ctx | fusion:528 database:500 |
Rv3002c ilvN |
acetolactate synthase small subunit | 731 | 709 ctx | cooccurence:502 |
Rv2386c mbtI |
salicylate synthase | 746 | 641 | database:500 |
Rv0337c aspC |
aspartate aminotransferase | 646 | 627 | database:500 |
Rv3840 |
transcriptional regulator | 609 | 594 ctx | neighborhood:591 |
Rv0884c serC |
phosphoserine aminotransferase | 660 | 557 | coexpression:520 |
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: prephenate dehydratase
- MTBC0 PGAP product: prephenate dehydratase
- Pfam (hmmscan --cut_ga): PDT PF00800.24 (E=4e-44), ACT PF01842.32 (E=2e-11)
- (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_218355.1)
- Domains: Pfam-A via hmmscan --cut_ga — PDT (PF00800.24), ACT (PF01842.32)
- 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
COG0077 - Curated reference: UniProt P9WIC3 (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 —
49 functional partner(s); context anchor
Rv3837c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004068|Rv3838c|pheA MVRIAYLGPEGTFTEAALVRMVAAGLVPETGPDALQRMPVESAPAALAAVRDGGADYACVPIENSIDGSVLPTLDSLAIGVRLQVFAETTLDVTFSIVVKPGRNAADVRTLAAFPVAAAQVRQWLAAHLPAADLRPAYSNADAARQVADGLVDAAVTSPLAAARWGLAALADGVVDESNARTRFVLVGRPGPPPARTGADRTSAVLRIDNQPGALVAALAEFGIRGIDLTRIESRPTRTELGTYLFFVDCVGHIDDEAVAEALKAVHRRCADVRYLGSWPTGPAAGAQPPLVDEASRWLARLRAGKPEQTLVRPDDQGAQA