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Prior-Knowledge Description Expectation Prediction Conclusion Leaf Statistics
Evidence_35 TIGR01240 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_110 1-deoxy-D-xylulose 5-phosphate reductoisomerase None - {{∅}} True - {{t}} Unconfirmed presence
Component_113 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_38 TIGR01833 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_54360 glutamine--fructose-6-phosphate transaminase (isomerizing) None - {{∅}} True - {{t}} Unconfirmed presence
GenProp0968 O-antigen polymerization/export system wzx/wzy/wzz~The Wzx/Wzy/Wzz system trnasports the O-antigen monomers from the cytoplasmic face of the plama membrane to the periplamic face and then polymerizes the monomers to form the mature O-antigen. The Wzx protein is the transporter (aka the flippase), Wzy is the polymerase and Wzz is the chain length determinant protein. None - {{∅}} Both - {{t},{f}} Unconfirmed contradictory
Component_63457 O-antigen polymerase None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_85632 GenProp1046 GENPROP None - {{∅}} None - {{∅}} Unexplained
Evidence_85217 GenProp0047 GENPROP None - {{∅}} False - {{f}} Unconfirmed absence
GenProp0971 biosynthesis of undecaprenyl phosphate (Und-P)~Undecaprenyl phosphate (Und-P) is synthesized de novo from farnesyl diphosphate via eight successive additions of isopentenyl diphosphate followed by a final removal of one phosphate. Und-P is used as a carrier for polysaccharide units via a pyrophosphate linkage. Removal of the polysaccharide results in Und-PP, so the phosphatase is also used in the recycling back to Und-P. None - {{∅}} Both - {{t},{f}} Unconfirmed contradictory
Component_111 4-diphosphocytidyl-2C-methyl-D-erythritol kinase None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_85413 GenProp0932 GENPROP None - {{∅}} None - {{∅}} Unexplained
Evidence_85415 GenProp0963 GENPROP None - {{∅}} None - {{∅}} Unexplained
Evidence_85631 GenProp1045 GENPROP None - {{∅}} None - {{∅}} Unexplained
Component_105 hydroxymethylglutaryl-CoA reductase None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_29 TIGR01217 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_85630 GenProp1043 GENPROP None - {{∅}} None - {{∅}} Unexplained
Component_63456 O-antigen transporter (flippase) None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_32 TIGR01219 HMM None - {{∅}} False - {{f}} Unconfirmed absence
GenProp0046 IPP biosynthesis~Isopentenyl pyrophosphate (IPP) is the common intermediate of isoprenoid metabolism which includes the biosynthesis of terpenoid natural products, sterols, bile acids, carotenoids, vitamins K and E, isoprene and other prenylated compounds. IPP may be synthesized via one of two separate pathways, the mevalonate pathway is typical of eukaryotes while the deoxyxylulose pathway is typical of prokaryotes. This property summarizes the states of the two child properties, IPP biosynthesis via mevalonate and IPP biosynthesis from deoxyxylulose. None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_85640 GenProp1047 GENPROP None - {{∅}} None - {{∅}} Unexplained
Component_103 diphosphomevalonate decarboxylase None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_34 TIGR01223 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_63451 O-antigen export system None - {{∅}} Both - {{t},{f}} Unconfirmed contradictory
Evidence_85626 GenProp1035 GENPROP None - {{∅}} None - {{∅}} Unexplained
Component_63674 any O-antigen monomer system None - {{∅}} None - {{∅}} Unexplained
Component_54345 4-hydroxy-3-methylbut-2-enyl diphosphate reductase None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_85194 GenProp0913 GENPROP None - {{∅}} None - {{∅}} Unexplained
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 - {{∅}} False - {{f}} Unconfirmed absence
Evidence_85216 TIGR00055 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Component_112 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_85219 GenProp0046 GENPROP None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_75315 TIGR00612 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_85218 GenProp0048 GENPROP None - {{∅}} True - {{t}} Unconfirmed presence
Component_63483 source of UDP-GlcNAc None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_2544 TIGR00748 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_63452 ligation to Lipid A core None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_75335 TIGR01455 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_99 acetoacetyl-CoA synthase None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_39 TIGR01835 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_63449 Initiation: Und-PP-GlcNAc formation None - {{∅}} Both - {{t},{f}} Unconfirmed contradictory
Evidence_33 TIGR01220 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_85434 GenProp1018 GENPROP None - {{∅}} None - {{∅}} Unexplained
Evidence_85212 TIGR02380 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_54362 glucosamine-1-phosphate N-acetyltransferase/UDP-N-acetylglucosamine diphosphorylase None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_55132 TIGR00532 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_85627 GenProp1036 GENPROP None - {{∅}} None - {{∅}} Unexplained
Evidence_85623 GenProp1023 GENPROP None - {{∅}} None - {{∅}} Unexplained
Component_63458 O-antigen chain length determinant protein None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_85831 TIGR04370 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_85193 GenProp0970 GENPROP None - {{∅}} Both - {{t},{f}} Unconfirmed contradictory
Evidence_85197 GenProp0968 GENPROP None - {{∅}} Both - {{t},{f}} Unconfirmed contradictory
Evidence_45 TIGR00154 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Component_102 phosphomevalonate kinase None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_85628 GenProp1038 GENPROP None - {{∅}} None - {{∅}} Unexplained
Component_101 mevalonate kinase None - {{∅}} False - {{f}} Unconfirmed absence
GenProp0970 biosynthesis of Und-PP-GlcNAc~N-acetylglucosamine-1-pyrophospho-undecaprenol (Und-PP-GlcNAc) is synthesized by the WecA enzyme in E. coli from UDP-GlcNAc and undecaprenyl phosphate. None - {{∅}} Both - {{t},{f}} Unconfirmed contradictory
Evidence_75334 TIGR01135 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_85629 GenProp1042 GENPROP None - {{∅}} None - {{∅}} Unexplained
Evidence_43 TIGR00204 HMM None - {{∅}} True - {{t}} Unconfirmed presence
GenProp0750 UDP-N-acetylglucosamine biosynthesis from fructose-6-phosphate~This pathway converts fructose-6-phosphate in four steps to activated N-acetylglucosamine. GlmS produces glucosamine-6-phosphate. GlmM isomerizes this product to glucosamine-1-phosphate. GlmU, which is bifunctional, adds an acetyl group from acetyl-CoA, then acts as N-acetylglucosamine-1-phosphate uridylyltransferase. The product, UDP-N-acetyl-D-glucosamine, is then used both for murein biosynthesis and (in species with LPS) for lipopolysaccharide biosynthesis. None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_85414 GenProp0949 GENPROP None - {{∅}} None - {{∅}} Unexplained
Component_54341 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_85667 GenProp1049 GENPROP None - {{∅}} None - {{∅}} Unexplained
Evidence_85199 PF01943 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_85214 GenProp0971 GENPROP None - {{∅}} Both - {{t},{f}} Unconfirmed contradictory
Evidence_85202 TIGR03007 HMM None - {{∅}} False - {{f}} Unconfirmed absence
GenProp0966 E. coli O-antigen biosynthesis~In E. coli biosynthesis of the O-antigen consists of initiation by ligation of (usually) N-acetyl-glucosamine to undecaprenylphosphate (Und-P) to form Und-PP-GlcNAc, followed by O-antigen specific ligation of several nucleotide triphosphate sugars onto the initiating GlcNAc residue. The completed Und-PP-O-antigen monomer is transferred to the periplasmic face of the membrane, polymerized and ligated to the lipid A outer core by one of three systems: The Wzy-dependent path consisting of Wzx, Wzy, and Wzz; the ABC-transporter-dependent pathway and the synthase-dependent pathway. The Wzy-pathway is most common in E. coli. None - {{∅}} Both - {{∅},{t},{f}} Unconfirmed contradictory
Component_63486 undecaprenyl-diphosphate synthase None - {{∅}} True - {{t}} Unconfirmed presence
Component_109 deoxyxylulose-5-phosphate synthase None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_85624 GenProp1030 GENPROP None - {{∅}} None - {{∅}} Unexplained
Evidence_75336 TIGR01173 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_63487 IPP biosynthesis None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_42 TIGR00533 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_84971 TIGR03990 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Component_104 hydroxymethylglutaryl-CoA synthase None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_85215 TIGR00753 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_85213 GenProp0750 GENPROP None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_85412 GenProp0953 GENPROP None - {{∅}} None - {{∅}} Unexplained
GenProp0913 E. coli O-antigen monomer biosynthesis clusters~blast database at /usr/local/projects/GSTEC/BLAST/ gstec01 : 1.2741 : O2/H4 : GenProp0963 gstec02 : 97.0246 : O5/H- gstec03 : 5.0588 : O8/H- gstec04 : 97.0259 : O11/H- gstec05 : H30 : O26/H11 gstec06 : 95.0941 : O45/H2 gstec07 : 1.2264 : O76/H- gstec08 : 97.0264 : O88/H25 gstec09 : 96.0497 : O91/H21 gstec10 : 99.0741 : O91/H- gstec11 : 3.2608 : O103/H2 : GenProp0953 gstec12 : 93.0624 : O103/H6 : GenProp0953 gstec13 : 4.0522 : O111/H- : GenProp0949 gstec14 : JB1-95 : O111/H- : GenProp0949 gstec15 : 96.154 : O113/H12 gstec16 : 5.0959 : O121/H19 gstec17 : 9.1649 : O2/H- : GenProp0963 gstec18 : 9.0111 : O128/H2 gstec19 : 4.0967 : O145/H2 gstec20 : 2.3916 : O147/H- gstec21 : 3.3884 : O153/H- gstec22 : 2.4168 : O157/H12 gstec23 : 3.2303 : O157/H16 gstec24 : 3003 : O157/H45 gstec25 : TW07793 : O157/H39 gstec26 : B41 : O101/NHM gstec27 : 900105 (10e) : O26/H11 None - {{∅}} None - {{∅}} Unexplained
Evidence_84972 TIGR03991 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_85622 GenProp1020 GENPROP None - {{∅}} None - {{∅}} Unexplained
Evidence_85832 PF04932 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Component_54361 phosphoglucosamine mutase None - {{∅}} True - {{t}} Unconfirmed presence
Component_63488 source of isopentenyl diphosphate (IPP) None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_31 TIGR00549 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_85417 GenProp0947 GENPROP None - {{∅}} None - {{∅}} Unexplained
Component_63484 source of undecaprenyl phosphate (Und-P) None - {{∅}} Both - {{t},{f}} Unconfirmed contradictory
Evidence_85620 GenProp1019 GENPROP None - {{∅}} None - {{∅}} Unexplained
Evidence_47 TIGR00453 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_85621 GenProp1014 GENPROP None - {{∅}} None - {{∅}} Unexplained
Evidence_85201 PF02706 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Component_63450 O-antigen monomer biosynthesis None - {{∅}} None - {{∅}} Unexplained
Evidence_44 TIGR00243 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_85625 GenProp1031 GENPROP None - {{∅}} None - {{∅}} Unexplained
Component_63485 undecaprenyl-diphosphate phosphohydrolase None - {{∅}} False - {{f}} Unconfirmed absence
Component_63482 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase None - {{∅}} False - {{f}} Unconfirmed absence
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_85416 GenProp0974 GENPROP None - {{∅}} None - {{∅}} Unexplained