idsA2 Resolved · high auto-curated
H37Rv Rv2173 · MTBC0 mtbc0_002307 ·
352 aa · 2460854–2461912 (+) ·
RefSeq NP_216689.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | geranylgeranyl pyrophosphate synthetase IdsA |
|---|---|
| MTBC0 PGAP re-annotation | bifunctional (2E%2C6E)-farnesyl/geranyl diphosphate synthase |
| Revised (this work) | Bifunctional (2E%2C6E)-farnesyl/geranyl diphosphate synthase. 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.
Curated reference (UniProt)
| UniProt |
O53507
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | (2E,6E)-farnesyl diphosphate synthase |
| EC (curated) |
EC 2.5.1.1, EC 2.5.1.10
|
| Curated function | Catalyzes the sequential condensations of isopentenyl pyrophosphate (IPP) with dimethylallyl diphosphate (DMAPP) to yield geranyl diphosphate (GPP) and with GPP to yield (2E,6E)-farnesyl diphosphate (E,E-FPP). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | crtE |
| 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
|
| KEGG pathways |
map00900, map01100, map01110, map01130
|
| KEGG modules |
M00364, M00365
|
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 | 0.183 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
polyprenyl_synt | PF00348.23 | 2.3e-46 | 36–290 | Polyprenyl synthetase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1086 ((2Z,6E)-farnesyl diphosphate synthase), high confidence from genomic context alone (score 971 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1086 |
(2Z,6E)-farnesyl diphosphate synthase | 986 | 971 ctx | cooccurence:697 database:900 textmining:564 |
Rv1745c idi |
isopentenyl-diphosphate delta-isomerase | 982 | 950 | database:900 textmining:670 |
Rv0562 grcC1 |
polyprenyl-diphosphate synthase GrcC | 946 | 924 | database:900 |
Rv0989c grcC2 |
polyprenyl-diphosphate synthase GrcC | 943 | 918 | database:900 |
Rv3383c idsB |
polyprenyl synthetase IdsB | 941 | 918 | database:900 |
Rv3398c idsA1 |
multifunctional dimethylallyltransferase/geranyltranstransferase/farnesyltranstransferase | 943 | 916 | database:900 |
Rv2174 mptA |
alpha(1->6)-mannopyranosyltransferase A | 949 | 911 ctx | neighborhood:882 textmining:455 |
Rv3382c lytB1 |
4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 983 | 906 | database:900 textmining:828 |
Rv1110 lytB2 |
4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 970 | 906 | database:900 textmining:702 |
Rv3397c phyA |
phytoene synthase | 954 | 886 | database:800 textmining:620 |
Rv2172c hyp |
hypothetical protein | 749 | 736 ctx | neighborhood:706 |
Rv2361c uppS |
decaprenyl diphosphate synthase | 863 | 694 ctx | cooccurence:666 textmining:572 |
Rv2752c rnj |
ribonuclease J | 529 | 530 | coexpression:514 |
Rv0721 rpsE |
30S ribosomal protein S5 | 526 | 526 | coexpression:411 |
Rv1107c xseB |
exodeoxyribonuclease VII small subunit | 552 | 516 | coexpression:417 |
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: geranylgeranyl pyrophosphate synthetase IdsA
- MTBC0 PGAP product: bifunctional (2E%2C6E)-farnesyl/geranyl diphosphate synthase
- Pfam (hmmscan --cut_ga): polyprenyl_synt PF00348.23 (E=2e-46)
- (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_216689.1)
- 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 O53507 (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
Rv1086 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002307|Rv2173|idsA2 MAGAITDQLRRYLHGRRRAAAHMGSDYDGLIADLEDFVLGGGKRLRPLFAYWGWHAVASREPDPDVLLLFSALELLHAWALVHDDLIDRSATRRGRPTAQLRYAALHRDRDWRGSPDQFGMSAAILLGDLAQVWADDIVSKVCQSALAPDAQRRVHRVWADIRNEVLGGQYLDIVAEASAAESIESAMNVATLKTACYTVSRPLQLGTAAAADRSDVAAIFEHFGADLGVAFQLRDDVLGVFGDPAVTGKPSGDDLKSGKRTVLVAEAVELADRSDPLAAKLLRTSIGTRLTDAQVRELRTVIEAVGARAAAESRIAALTQRALATLASAPINATAKAGLSELAMMAANRSA