idi Resolved · high auto-curated
H37Rv Rv1745c · MTBC0 mtbc0_001858 ·
203 aa · 1983452–1984063 (-) ·
RefSeq NP_216261.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | isopentenyl-diphosphate delta-isomerase |
|---|---|
| MTBC0 PGAP re-annotation | isopentenyl-diphosphate Delta-isomerase |
| Revised (this work) | Isopentenyl-diphosphate Delta-isomerase. Pfam: NUDIX (PF00293.35). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKK5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Isopentenyl-diphosphate Delta-isomerase |
| EC (curated) |
EC 5.3.3.2
|
| Curated function | Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | idi |
| eggNOG description | Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP) |
| Orthologous group | COG1443 |
| EC number |
EC 5.3.3.2
|
| KEGG orthology |
K01823
|
| KEGG pathways |
map00900, map01100, map01110, map01130
|
| KEGG modules |
M00095, M00096, M00364, M00365, M00366, M00367
|
| Gene Ontology (34) |
GO:0003674, GO:0003824, GO:0004452, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0006629, GO:0006644, GO:0006720, GO:0006793, GO:0006796 +22 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) pseudogene candidate
| pN/pS | 0.464 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 3 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 9.98% of strains (14489) · 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 |
|---|---|---|---|---|
NUDIX | PF00293.35 | 3.1e-20 | 39–170 | NUDIX domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1744c (membrane protein), high confidence from genomic context alone (score 885 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2173 idsA2 |
geranylgeranyl pyrophosphate synthetase IdsA | 982 | 950 | database:900 textmining:670 |
Rv3383c idsB |
polyprenyl synthetase IdsB | 920 | 914 | database:900 |
Rv3398c idsA1 |
multifunctional dimethylallyltransferase/geranyltranstransferase/farnesyltranstransferase | 951 | 911 | database:900 textmining:478 |
Rv1086 |
(2Z,6E)-farnesyl diphosphate synthase | 939 | 905 | database:900 |
Rv3382c lytB1 |
4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 945 | 901 | database:900 textmining:477 |
Rv1110 lytB2 |
4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 945 | 901 | database:900 textmining:477 |
Rv1744c |
membrane protein | 885 | 885 ctx | neighborhood:882 |
Rv1746 pknF |
serine/threonine-protein kinase PknF | 730 | 546 ctx | neighborhood:541 textmining:431 |
Rv3377c |
type B diterpene cyclase | 604 | 532 | coexpression:440 |
Rv3397c phyA |
phytoene synthase | 810 | 526 | coexpression:410 textmining:617 |
Rv1814 erg3 |
membrane-bound C-5 sterol desaturase | 562 | 473 | coexpression:440 |
Rv1937 |
oxygenase | 582 | 443 | coexpression:437 |
Rv1260 |
oxidoreductase | 481 | 440 | coexpression:440 |
Rv0575c |
oxidoreductase | 480 | 439 | coexpression:439 |
Rv3254 hyp |
hypothetical protein | 480 | 439 | coexpression:439 |
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: isopentenyl-diphosphate delta-isomerase
- MTBC0 PGAP product: isopentenyl-diphosphate Delta-isomerase
- Pfam (hmmscan --cut_ga): NUDIX PF00293.35 (E=3e-20)
- (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_216261.1)
- Domains: Pfam-A via hmmscan --cut_ga — NUDIX (PF00293.35)
- 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
COG1443 - Curated reference: UniProt P9WKK5 (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 —
29 functional partner(s); context anchor
Rv1744c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001858|Rv1745c|idi MTRSYRPAPPIERVVLLNDRGDATGVADKATVHTGDTPLHLAFSSYVFDLHDQLLITRRAATKRTWPAVWTNSCCGHPLPGESLPGAIRRRLAAELGLTPDRVDLILPGFRYRAAMADGTVENEICPVYRVQVDQQPRPNSDEVDAIRWLSWEQFVRDVTAGVIAPVSPWCRSQLGYLTKLGPCPAQWPVADDCRLPKAAHGN