idsA1 Resolved · high auto-curated
H37Rv Rv3398c · MTBC0 - ·
359 aa · 3815027–3816106 (-) ·
RefSeq YP_177970.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | multifunctional dimethylallyltransferase/geranyltranstransferase/farnesyltranstransferase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Multifunctional dimethylallyltransferase/geranyltranstransferase/farnesyltranstransferase. Pfam: polyprenyl_synt (PF00348.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WKH1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | (2E,6E)-farnesyl diphosphate synthase |
| EC (curated) |
EC 2.5.1.10
|
| Curated function | Catalyzes the condensation of isopentenyl pyrophosphate (IPP) with geranyl diphosphate (GPP) to yield (2E,6E)-farnesyl diphosphate (E,E-FPP). May be used for squalene and possibly sterol biosynthesis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | idsA1 |
| eggNOG description | Belongs to the FPP GGPP synthase family |
| Orthologous group | COG0142 |
| EC number |
EC 2.5.1.1, EC 2.5.1.10, EC 2.5.1.29
|
| KEGG orthology |
K13787, K13789
|
| KEGG pathways |
map00900, map01100, map01110, map01130
|
| KEGG modules |
M00364, M00365, M00366
|
| Gene Ontology (43) |
GO:0000287, GO:0003674, GO:0003824, GO:0004161, GO:0004659, GO:0005488, GO:0005506, GO:0006629, GO:0006644, GO:0006720, GO:0006721, GO:0006793 +31 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 | 0.098 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 2 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.19% of strains (282) · 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 |
|---|---|---|---|---|
polyprenyl_synt | PF00348.23 | 7.9e-56 | 70–292 | Polyprenyl synthetase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: phyA (phytoene synthase), high confidence from genomic context alone (score 995 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3397c phyA |
phytoene synthase | 995 | 995 ctx | neighborhood:741 coexpression:876 database:800 |
Rv1086 |
(2Z,6E)-farnesyl diphosphate synthase | 980 | 966 ctx | cooccurence:644 database:900 textmining:462 |
Rv0989c grcC2 |
polyprenyl-diphosphate synthase GrcC | 948 | 926 | database:900 |
Rv0562 grcC1 |
polyprenyl-diphosphate synthase GrcC | 948 | 925 | database:900 |
Rv2173 idsA2 |
geranylgeranyl pyrophosphate synthetase IdsA | 943 | 916 | database:900 |
Rv3383c idsB |
polyprenyl synthetase IdsB | 930 | 916 | database:900 |
Rv1745c idi |
isopentenyl-diphosphate delta-isomerase | 951 | 911 | database:900 textmining:478 |
Rv3382c lytB1 |
4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 968 | 906 | database:900 textmining:675 |
Rv1110 lytB2 |
4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 964 | 906 | database:900 textmining:641 |
Rv3399 |
S-adenosylmethionine-dependent methyltransferase | 789 | 789 ctx | neighborhood:567 coexpression:458 |
Rv3396c guaA |
GMP synthase | 788 | 778 ctx | neighborhood:686 |
Rv2361c uppS |
decaprenyl diphosphate synthase | 880 | 653 ctx | cooccurence:622 textmining:669 |
Rv2752c rnj |
ribonuclease J | 527 | 528 | coexpression:512 |
Rv2337c hyp |
hypothetical protein | 518 | 510 | database:419 |
Rv0721 rpsE |
30S ribosomal protein S5 | 500 | 500 | coexpression:414 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): multifunctional dimethylallyltransferase/geranyltranstransferase/farnesyltranstransferase
- Pfam (hmmscan --cut_ga): polyprenyl_synt PF00348.23 (E=8e-56)
- (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 YP_177970.1)
- Domains: Pfam-A via hmmscan --cut_ga — polyprenyl_synt (PF00348.23)
- 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
COG0142 - Curated reference: UniProt P9WKH1 (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 —
42 functional partner(s); context anchor
phyA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3398c|idsA1 MRGTDEKYGLPPQPDSDRMTRRTLPVLGLAHELITPTLRQMADRLDPHMRPVVSYHLGWSDERGRPVNNNCGKAIRPALVFVAAEAAGADPHSAIPGAVSVELVHNFSLVHDDLMDRDEHRRHRPTVWALWGDAMALLAGDAMLSLAHEVLLDCDSPHVGAALRAISEATRELIRGQAADTAFESRTDVALDECLKMAEGKTAALMAASAEVGALLAGAPRSVREALVAYGRHIGLAFQLVDDLLGIWGRPEITGKPVYSDLRSRKKTLPVTWTVAHGGSAGRRLAAWLVDETGSQTASDDELAAVAELIECGGGRRWASAEARRHVTQGIDMVARIGIPDRPAAELQDLAHYIVDRQA