idsB Family assigned · medium auto-curated
H37Rv Rv3383c · MTBC0 mtbc0_003596 ·
350 aa · 3822798–3823850 (-) ·
RefSeq NP_217900.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | polyprenyl synthetase IdsB |
|---|---|
| MTBC0 PGAP re-annotation | polyprenyl synthetase family protein |
| Revised (this work) | Polyprenyl synthetase family protein. 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 |
O50410
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Geranylgeranyl diphosphate synthase |
| EC (curated) |
EC 2.5.1.29
|
| Curated function | Catalyzes the condensation of isopentenyl pyrophosphate (IPP) with (2E,6E)-farnesyl diphosphate (E,E-FPP) to yield geranylgeranyl diphosphate (GGPP). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | idsB |
| eggNOG description | Involved in biosynthesis of membrane ether-linked lipids. catalyzes the trans-addition of the three molecules of IPP onto DMAPP to form geranylgeranyl pyrophosphate which is a precursor of the ether-linked lipids. catalyzes the consecutive condensation of |
| 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 | 1.588 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 9 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 | 1.6e-60 | 66–302 | Polyprenyl synthetase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lytB1 (4-hydroxy-3-methylbut-2-enyl diphosphate reductase), high confidence from genomic context alone (score 988 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3382c lytB1 |
4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 995 | 988 ctx | neighborhood:833 database:900 textmining:673 |
Rv1086 |
(2Z,6E)-farnesyl diphosphate synthase | 978 | 966 ctx | cooccurence:646 database:900 textmining:402 |
Rv0989c grcC2 |
polyprenyl-diphosphate synthase GrcC | 944 | 928 | database:900 |
Rv0562 grcC1 |
polyprenyl-diphosphate synthase GrcC | 941 | 925 | database:900 |
Rv2173 idsA2 |
geranylgeranyl pyrophosphate synthetase IdsA | 941 | 918 | database:900 |
Rv3398c idsA1 |
multifunctional dimethylallyltransferase/geranyltranstransferase/farnesyltranstransferase | 930 | 916 | database:900 |
Rv1745c idi |
isopentenyl-diphosphate delta-isomerase | 920 | 914 | database:900 |
Rv1110 lytB2 |
4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 957 | 906 | database:900 textmining:566 |
Rv3397c phyA |
phytoene synthase | 873 | 863 | database:800 |
Rv2361c uppS |
decaprenyl diphosphate synthase | 761 | 662 ctx | cooccurence:631 |
Rv3377c |
type B diterpene cyclase | 925 | 567 | textmining:836 |
Rv3381c |
Rv3381c, (MTV004.39c), len: 108 aa. Putative Transposase for IS6110 (fragment). Identical to many other M. tuberculosis IS6110 transposase s | 548 | 548 ctx | neighborhood:547 |
Rv3380c |
Probable transposase; Rv3380c, (MTV004.38c), len: 328 aa. Probable transposase subunit for IS6110. Identical to many other M. tuberculosis I | 908 | 547 ctx | neighborhood:547 textmining:806 |
Rv2752c rnj |
ribonuclease J | 533 | 534 | coexpression:518 |
Rv0721 rpsE |
30S ribosomal protein S5 | 526 | 527 | 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: polyprenyl synthetase IdsB
- MTBC0 PGAP product: polyprenyl synthetase family protein
- Pfam (hmmscan --cut_ga): polyprenyl_synt PF00348.23 (E=2e-60)
- (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_217900.1)
- 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 O50410 (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 —
54 functional partner(s); context anchor
lytB1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003596|Rv3383c|idsB MGGVLTLDAAFLGSVPADLGKALLERARADCGPVLHRAIESMREPLATMAGYHLGWWNADRSTAAGSSGKYFRAALVYAAAAACGGDVGDATPVSAAVELVHNFTLLHDDVMDGDATRRGRPTVWSVWGVGGAILLGDALHATAVRILTGLTDECVAVRAIRRLQMSCLDLCIGQFEDCLLEGQPEVTVDDYLRMAAGKTAALTGCCCALGALVANADDATIAALERFGHELGLAFQCVDDLIGIWGDPGVTGKPVGNDLARRKATLPVVAALNSRSEAATELAALYQAPAAMTASDVERATALVKVAGGGHVAQRCADERIQAAIAALPDAVRSPDLIALSQLICRREC