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Prior-Knowledge Description Expectation Prediction Conclusion Leaf Statistics
Evidence_35 TIGR01240 HMM None - {{∅}} None - {{∅}} Unexplained
Component_110 1-deoxy-D-xylulose 5-phosphate reductoisomerase None - {{∅}} True - {{t}} Unconfirmed presence
Component_54406 uncharacterized syntenic membrane protein None - {{∅}} None - {{∅}} Unexplained
Component_113 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_38 TIGR01833 HMM None - {{∅}} None - {{∅}} Unexplained
Evidence_45 TIGR00154 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Component_102 phosphomevalonate kinase None - {{∅}} None - {{∅}} Unexplained
Component_101 mevalonate kinase None - {{∅}} None - {{∅}} Unexplained
Component_111 4-diphosphocytidyl-2C-methyl-D-erythritol kinase None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_43 TIGR00204 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Component_54341 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_75410 TIGR03462 HMM None - {{∅}} None - {{∅}} Unexplained
Component_105 hydroxymethylglutaryl-CoA reductase None - {{∅}} None - {{∅}} Unexplained
Component_54404 source of IPP None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_29 TIGR01217 HMM None - {{∅}} None - {{∅}} Unexplained
Evidence_75399 TIGR02734 HMM None - {{∅}} None - {{∅}} Unexplained
Evidence_75392 TIGR02731 HMM None - {{∅}} None - {{∅}} Unexplained
Evidence_32 TIGR01219 HMM None - {{∅}} None - {{∅}} Unexplained
Evidence_75394 PF00494 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Component_54405 lycopene cyclases None - {{∅}} None - {{∅}} Unexplained
Evidence_75400 TIGR02734 HMM None - {{∅}} None - {{∅}} Unexplained
Component_103 diphosphomevalonate decarboxylase None - {{∅}} None - {{∅}} Unexplained
Evidence_75401 TIGR01790 HMM None - {{∅}} None - {{∅}} Unexplained
Evidence_75397 GenProp0048 GENPROP None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_34 TIGR01223 HMM None - {{∅}} None - {{∅}} Unexplained
Component_109 deoxyxylulose-5-phosphate synthase None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_75391 TIGR02732 HMM None - {{∅}} None - {{∅}} Unexplained
Evidence_75404 TIGR03460 HMM None - {{∅}} None - {{∅}} Unexplained
Evidence_75396 TIGR02151 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_42 TIGR00533 HMM None - {{∅}} None - {{∅}} Unexplained
Component_54400 phytoene desaturase (1.14.99.-) None - {{∅}} None - {{∅}} Unexplained
Component_104 hydroxymethylglutaryl-CoA synthase None - {{∅}} None - {{∅}} Unexplained
Component_54345 4-hydroxy-3-methylbut-2-enyl diphosphate reductase None - {{∅}} True - {{t}} Unconfirmed presence
GenProp0047 IPP biosynthesis via mevalonate~Isoprenyl pyrophosphate (IPP) is synthesized in eukaryotes, archaea and certain bacteria by the mevalonate pathway (which is in contrast to the non-mevalonate pathway found more generally in prokaryotes). The bacteria containing this pathway are believed to have acquired it by lateral transfer, possible in more than one independent event [Wilding, et. al. (2000) J. Bacteriol. 182, 4319-4327]. Archaea are believed to possess a mevalonate pathway for production of IPP, but several of the steps are divergent from the known enzymes in eukaryotes and have not yet been conclusively identified [PMID: 11042147]. In eukaryotes this pathway is highly regulated to control the production of steroids which require IPP as a precursor. IPP is also required for the synthesis of menaquinone, ubiquinone, terpenoids, isoprene and prenylated proteins. The pathway begins with synthesis of (S)-3-hydroxy-3-methylglutaryl-CoA from acetyl-CoA and acetoacetyl-CoA by HMG-CoA synthase and contains 5 steps all of which are included as required elements for the assignment of the YES state for this property. Some organisms contain a pathway-specific acetoacetyl-CoA synthase which is included in the gene lists for this property but is not a required element for the determination of the property state. Other species likely obtain acetoacetyl-CoA from beta-oxidation of fatty acids or related processes. None - {{∅}} None - {{∅}} Unexplained
Component_112 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_75393 PF00348 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_75395 TIGR02150 HMM None - {{∅}} None - {{∅}} Unexplained
Evidence_75315 TIGR00612 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Component_54401 geranylgeranyl pyrophosphate synthase None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_2544 TIGR00748 HMM None - {{∅}} None - {{∅}} Unexplained
Component_54399 zeta-carotene desaturase (1.14.99.30) None - {{∅}} None - {{∅}} Unexplained
Evidence_75402 TIGR03459 HMM None - {{∅}} None - {{∅}} Unexplained
Evidence_31 TIGR00549 HMM None - {{∅}} None - {{∅}} Unexplained
Component_54403 isopentenyl-diphosphate delta-isomerase (5.3.3.2) None - {{∅}} True - {{t}} Unconfirmed presence
Component_99 acetoacetyl-CoA synthase None - {{∅}} None - {{∅}} Unexplained
Evidence_47 TIGR00453 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_39 TIGR01835 HMM None - {{∅}} None - {{∅}} Unexplained
Evidence_33 TIGR01220 HMM None - {{∅}} None - {{∅}} Unexplained
GenProp0758 lycopene biosynthesis from IPP~ None - {{∅}} None - {{∅},{t}} Unexplained
Component_54402 phytoene synthase (2.5.1.32) None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_44 TIGR00243 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_75398 GenProp0047 GENPROP None - {{∅}} None - {{∅}} Unexplained
GenProp0048 IPP biosynthesis via deoxyxylulose~The pathway for the biosynthesis of isoprenyl pyrophosphate (IPP) in most bacteria has been variously referred to as the non-mevalonate pathway (in contrast to the pathway found in eukaryotes), the glyceraldehyde-3-phosphate(GAP)-pyruvate pathway and the deoxyxylulose pathway. This pathway contains six characterized enzymes and may involve additional proteins as well. None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_46 TIGR00151 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_75319 TIGR00216 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_55132 TIGR00532 HMM None - {{∅}} None - {{∅}} Unexplained