phyA Resolved · high auto-curated
H37Rv Rv3397c · MTBC0 mtbc0_003610 ·
302 aa · 3839529–3840437 (-) ·
RefSeq NP_217914.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phytoene synthase |
|---|---|
| MTBC0 PGAP re-annotation | presqualene diphosphate synthase HpnD |
| Revised (this work) | Presqualene diphosphate synthase HpnD. Pfam: SQS_PSY (PF00494.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHP3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phytoene synthase |
| EC (curated) |
EC 2.5.1.-
|
| Curated function | Involved in the biosynthesis of carotenoids. Catalyzes the condensation of two molecules of geranylgeranyl diphosphate (GGPP) to give prephytoene diphosphate (PPPP) and the subsequent rearrangement of the cyclopropylcarbinyl intermediate to yield phytoene (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | crtB |
| eggNOG description | Phytoene synthase |
| Orthologous group | COG1562 |
| EC number |
EC 2.5.1.32, EC 2.5.1.99
|
| KEGG orthology |
K02291
|
| KEGG pathways |
map00906, map01062, map01100, map01110
|
| KEGG modules |
M00097
|
| Gene Ontology (29) |
GO:0003674, GO:0003824, GO:0004337, GO:0004659, GO:0006629, GO:0006720, GO:0006721, GO:0008150, GO:0008152, GO:0008299, GO:0008610, GO:0009058 +17 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 | 0.892 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 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 |
|---|---|---|---|---|
SQS_PSY | PF00494.25 | 6.0e-62 | 16–268 | Squalene/phytoene synthase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: idsA1 (multifunctional dimethylallyltransferase/geranyltranstransferase/farnesyltranstransferase), high confidence from genomic context alone (score 995 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3398c idsA1 |
multifunctional dimethylallyltransferase/geranyltranstransferase/farnesyltranstransferase | 995 | 995 ctx | neighborhood:741 coexpression:876 database:800 |
Rv2173 idsA2 |
geranylgeranyl pyrophosphate synthetase IdsA | 954 | 886 | database:800 textmining:620 |
Rv3399 |
S-adenosylmethionine-dependent methyltransferase | 880 | 880 ctx | neighborhood:508 coexpression:767 |
Rv0562 grcC1 |
polyprenyl-diphosphate synthase GrcC | 903 | 864 | database:800 |
Rv0989c grcC2 |
polyprenyl-diphosphate synthase GrcC | 903 | 863 | database:800 |
Rv3383c idsB |
polyprenyl synthetase IdsB | 873 | 863 | database:800 |
Rv3152 nuoH |
NADH-quinone oxidoreductase subunit H | 859 | 851 | database:844 |
Rv1814 erg3 |
membrane-bound C-5 sterol desaturase | 877 | 840 | experimental:785 |
Rv3396c guaA |
GMP synthase | 792 | 793 ctx | neighborhood:789 |
Rv2836c dinF |
DNA-damage-inducible protein DinF | 790 | 777 | coexpression:751 |
Rv1436 gap |
glyceraldehyde 3-phosphate dehydrogenase | 793 | 771 | coexpression:768 |
Rv3147 nuoC |
NADH-quinone oxidoreductase subunit C | 795 | 765 | database:727 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 766 | 754 | database:727 |
Rv3148 nuoD |
NADH-quinone oxidoreductase subunit D | 756 | 740 | database:727 |
Rv3146 nuoB |
NADH-quinone oxidoreductase subunit B | 746 | 735 | database:727 |
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: phytoene synthase
- MTBC0 PGAP product: presqualene diphosphate synthase HpnD
- Pfam (hmmscan --cut_ga): SQS_PSY PF00494.25 (E=6e-62)
- (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_217914.1)
- Domains: Pfam-A via hmmscan --cut_ga — SQS_PSY (PF00494.25)
- 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
COG1562 - Curated reference: UniProt P9WHP3 (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 —
116 functional partner(s); context anchor
idsA1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003610|Rv3397c|phyA MTEIEQAYRITESITRTAARNFYYGIRLLPREKRAALSAVYALGRRIDDVADGELAPETKITELDAIRKSLDNIDDSSDPVLVALADAARRFPVPIAMFAELIDGARMEIDWTGCRDFDELIVYCRRGAGTIGKLCLSIFGPVSTATSRYAEQLGIALQQTNILRDVREDFLNGRIYLPRDELDRLGVRLRLDDTGALDDPDGRLAALLRFSADRAADWYSLGLRLIPHLDRRSAACCAAMSGIYRRQLALIRASPAVVYDRRISLSGLKKAQVAAAALASSVTCGPAHGPLPADLGSHPSH