Rv1086 Family assigned · medium auto-curated
H37Rv Rv1086 · MTBC0 mtbc0_001166 ·
262 aa · 1218864–1219652 (+) ·
RefSeq NP_215602.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | (2Z,6E)-farnesyl diphosphate synthase |
|---|---|
| MTBC0 PGAP re-annotation | (2Z%2C6E)-farnesyl diphosphate synthase |
| Revised (this work) | Undecaprenyl diphosphate synthase family protein. Pfam: Prenyltransf (PF01255.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFF5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | (2Z,6E)-farnesyl diphosphate synthase |
| EC (curated) |
EC 2.5.1.68
|
| Curated function | Catalyzes the condensation of only one isopentenyl pyrophosphate (IPP) unit in the cis configuration to E-geranyl diphosphate (E-GPP) generating the 15 carbon product (2Z,6E)-farnesyl diphosphate (Z-FPP or EZ-FPP). Z-FPP is the precursor of decaprenyl diphosphate, which has a central role in the biosynthesis of the mycobacterial cell wall. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | uppS1 |
| eggNOG description | Catalyzes the condensation of isopentenyl diphosphate (IPP) with allylic pyrophosphates generating different type of terpenoids |
| Orthologous group | COG0020 |
| EC number |
EC 2.5.1.31, EC 2.5.1.68
|
| KEGG orthology |
K00806, K12503
|
| KEGG pathways |
map00900, map01110
|
| Gene Ontology (47) |
GO:0000287, GO:0002094, GO:0003674, GO:0003824, GO:0004659, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886 +35 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 | 2.662 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 8 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 |
|---|---|---|---|---|
Prenyltransf | PF01255.25 | 7.8e-08 | 8–37 | Putative undecaprenyl diphosphate synthase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: idsA2 (geranylgeranyl pyrophosphate synthetase IdsA), high confidence from genomic context alone (score 971 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2173 idsA2 |
geranylgeranyl pyrophosphate synthetase IdsA | 986 | 971 ctx | cooccurence:697 database:900 textmining:564 |
Rv3398c idsA1 |
multifunctional dimethylallyltransferase/geranyltranstransferase/farnesyltranstransferase | 980 | 966 ctx | cooccurence:644 database:900 textmining:462 |
Rv3383c idsB |
polyprenyl synthetase IdsB | 978 | 966 ctx | cooccurence:646 database:900 textmining:402 |
Rv2361c uppS |
decaprenyl diphosphate synthase | 940 | 922 | database:900 |
Rv1745c idi |
isopentenyl-diphosphate delta-isomerase | 939 | 905 | database:900 |
Rv1110 lytB2 |
4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 909 | 904 | database:900 |
Rv3382c lytB1 |
4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 907 | 901 | database:900 |
Rv0562 grcC1 |
polyprenyl-diphosphate synthase GrcC | 904 | 722 ctx | cooccurence:695 textmining:672 |
Rv2881c cdsA |
phosphatidate cytidylyltransferase | 732 | 703 | coexpression:692 |
Rv2870c dxr |
1-deoxy-D-xylulose 5-phosphate reductoisomerase | 811 | 702 | coexpression:691 |
Rv2845c proS |
proline--tRNA ligase | 657 | 658 | coexpression:645 |
Rv2841c nusA |
transcription termination/antitermination protein NusA | 632 | 633 | coexpression:619 |
Rv0989c grcC2 |
polyprenyl-diphosphate synthase GrcC | 749 | 628 ctx | cooccurence:596 |
Rv2869c rip |
zinc metalloprotease | 637 | 622 | coexpression:608 |
Rv2842c rimP |
ribosome maturation factor RimP | 608 | 609 | coexpression:594 |
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: (2Z,6E)-farnesyl diphosphate synthase
- MTBC0 PGAP product: undecaprenyl diphosphate synthase family protein
- Pfam (hmmscan --cut_ga): Prenyltransf PF01255.25 (E=8e-08)
- (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_215602.1)
- Domains: Pfam-A via hmmscan --cut_ga — Prenyltransf (PF01255.25)
- 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
COG0020 - Curated reference: UniProt P9WFF5 (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 —
63 functional partner(s); context anchor
idsA2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001166|Rv1086| MEIIPPRLKEPLYRLYELRLRQGLAASKSDLPRHIAVLCDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTENLQRDPDELAALIEIITDVVEEICAPANHWSVRTVGDLGLIGEEPARRLRGAVESTPEVASFHVNVAVGYGGRREIVDAVRALLSKELANGATAEELVDAVTVEGISENLYTSGQPDPDLVIRTSGEQRLSGFLLWQSAYSEMWFTEAHWPAFRHVDFLRALRDYSARHRRYGR