Rv2361c Resolved · high auto-curated
H37Rv Rv2361c · MTBC0 mtbc0_002513 ·
296 aa · 2666771–2667661 (-) ·
RefSeq NP_216877.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | decaprenyl diphosphate synthase |
|---|---|
| MTBC0 PGAP re-annotation | decaprenyl diphosphate synthase |
| Revised (this work) | Decaprenyl diphosphate synthase. 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 |
P9WFF7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Decaprenyl diphosphate synthase |
| EC (curated) |
EC 2.5.1.86, EC 2.5.1.87
|
| Curated function | Catalyzes the sequential condensation of isopentenyl diphosphate (IPP) in the cis configuration with (2Z,6E)-farnesyl diphosphate (Z-FPP or EZ-FPP) generating the 50 carbon product trans,polycis-decaprenyl diphosphate. When (2E,6E)-farnesyl diphosphate (E-FPP or EE-FPP) is used in vitro, both primary products decaprenyl diphosphate and (2E,6E,10E)-geranylgeranyl diphosphate (EEE-GGPP) are synthesized. M.tuberculosis does not synthesize (2E,6E,10Z)-geranylgeranyl diphosphate (EEZ-GGPP) and heptaprenyl diphosphate. Can also accept many different allylic substrates, including E-geranyl diphosphat. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | uppS |
| 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 2.5.1.86, EC 2.5.1.88
|
| KEGG orthology |
K00806, K14215, K21273
|
| KEGG pathways |
map00900, map01110
|
| Gene Ontology (50) |
GO:0000287, GO:0002094, GO:0003674, GO:0003824, GO:0004659, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886 +38 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 | 0.055 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 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 |
|---|---|---|---|---|
Prenyltransf | PF01255.25 | 2.5e-76 | 74–294 | Putative undecaprenyl diphosphate synthase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: recO (DNA repair protein RecO), high confidence from genomic context alone (score 890 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1086 |
(2Z,6E)-farnesyl diphosphate synthase | 940 | 922 | database:900 |
Rv2360c hyp |
hypothetical protein | 937 | 904 ctx | neighborhood:882 |
Rv2362c recO |
DNA repair protein RecO | 932 | 890 ctx | neighborhood:882 textmining:411 |
Rv2363 amiA2 |
amidase | 794 | 794 ctx | neighborhood:786 |
Rv2870c dxr |
1-deoxy-D-xylulose 5-phosphate reductoisomerase | 919 | 732 | coexpression:687 textmining:713 |
Rv2881c cdsA |
phosphatidate cytidylyltransferase | 826 | 730 | coexpression:693 |
Rv2173 idsA2 |
geranylgeranyl pyrophosphate synthetase IdsA | 863 | 694 ctx | cooccurence:666 textmining:572 |
Rv2845c proS |
proline--tRNA ligase | 689 | 689 | coexpression:647 |
Rv0562 grcC1 |
polyprenyl-diphosphate synthase GrcC | 936 | 673 ctx | cooccurence:643 textmining:814 |
Rv3383c idsB |
polyprenyl synthetase IdsB | 761 | 662 ctx | cooccurence:631 |
Rv3398c idsA1 |
multifunctional dimethylallyltransferase/geranyltranstransferase/farnesyltranstransferase | 880 | 653 ctx | cooccurence:622 textmining:669 |
Rv2869c rip |
zinc metalloprotease | 665 | 651 | coexpression:603 |
Rv2841c nusA |
transcription termination/antitermination protein NusA | 626 | 626 | coexpression:612 |
Rv2842c rimP |
ribosome maturation factor RimP | 606 | 606 | coexpression:591 |
Rv2882c frr |
ribosome recycling factor | 641 | 603 | coexpression:548 |
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: decaprenyl diphosphate synthase
- MTBC0 PGAP product: decaprenyl diphosphate synthase
- Pfam (hmmscan --cut_ga): Prenyltransf PF01255.25 (E=2e-76)
- (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_216877.1)
- 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 P9WFF7 (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 —
68 functional partner(s); context anchor
recO - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002513|Rv2361c| MARDARKRTSSNFPQLPPAPDDYPTFPDTSTWPVVFPELPAAPYGGPCRPPQHTSKAAAPRIPADRLPNHVAIVMDGNGRWATQRGLARTEGHKMGEAVVIDIACGAIELGIKWLSLYAFSTENWKRSPEEVRFLMGFNRDVVRRRRDTLKKLGVRIRWVGSRPRLWRSVINELAVAEEMTKSNDVITINYCVNYGGRTEITEATREIAREVAAGRLNPERITESTIARHLQRPDIPDVDLFLRTSGEQRSSNFMLWQAAYAEYIFQDKLWPDYDRRDLWAACEEYASRTRRFGSA