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Prior-Knowledge Description Expectation Prediction Conclusion Leaf Statistics
Component_48863 putative ring-opening aldehyde dehydrogenase, PaaN None - {{∅}} True - {{t}} Unconfirmed presence
Component_50868 putative regulator (?) None - {{∅}} True - {{t}} Unconfirmed presence
Component_46823 phenylacetate-CoA oxygenase, PaaJ subunit None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_61368 TIGR02279 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Component_46822 phenylacetate-CoA oxygenase, PaaI subunit None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_59321 TIGR02160 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Component_48866 3-hydroxyacyl-CoA dehydrogenase, PaaC None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_59318 TIGR02157 HMM None - {{∅}} True - {{t}} Unconfirmed presence
GenProp0210 phenylacetic acid catabolism~The degradation of phenylacetic acid via phenylacetyl-CoA to TCA intermediates is the core of an extended catabolon [1] for the degradation of various monosubstituted phenyl compounds and polymers including styrene, tropic acid, ethylbenzene, 2-phenylethylamine, phenylacetyl amide, phenyl alkanoates, poly-hydroxyphenylalkanoates, and trans-styrylacetic acid. The pathway consists of four major stages: ligation of phenylacetic acid with CoA, hydroxylation of the phenyl ring at the 2-position, oxidative ring opening and fatty-acid beta-oxidation like steps on the acyclic compound. The precise nature of the intermediates following 2-hydroxyphenylacetyl-CoA are not known. The gene symbol nomenclature for the enzymes in this pathway has been standardized in [1] due to the heterogeneity among the various organisms studied. This new standard is different from all of the old gene symbols, and may add somewhat to the confusion. A key is reproduced below as an aid to the bewildered. The genes of this pathway are typically organized into a single divergon. Some of the genes involved in the final fatty-acid-like degradation (paaABCDE) are occasionally absent and presumably substituted with genes of similar function found elsewhere in the genome. paaA and paaB both code for genes having the same general function (enoyl-CoA hydratases), but often paaA is absent (possibly paaB in these organisms provides both activities). paaD is the most reliable marker of this part of the pathway, nearly always detectable as a distinct homolog within the gene clusters. paaN, which codes for the ring-opening enzyme, is generally related to aldehyde dehydrogenases, but at least three different homology families appear to have evolved members into the specific paaN role. Pseudomonas putida appears to include a transport system (paaLM), but as this has not been reported in any other organism it has not been included in this Genome Property at this time. Gene Name Gene-sym (E.coli/P.putida/A.evansii) ------------------------------------- Phenylacetyl-CoA ligase paaF (paaK/phaE/pacD) Ring-hydroxylating complex. Protein 1 paaG (paaA/phaF/pacE) Ring-hydroxylating complex. Protein 2 paaH (paaB/phaO/pacF) Ring-hydroxylating complex. Protein 3 paaI (paaC/phaG/pacG) Ring-hydroxylating complex. Protein 4 paaJ (paaD/phaH/pacH) Ring-hydroxylating complex. Protein 5 paaK (paaE/phaI/pacI) Ring-opening enzyme paaN (paaZ/phaL/pacL) Enoyl-CoA hydratase 1 paaA (paaF/phaA/----) Enoyl-CoA hydratase 2 paaB (paaG/phaB/pacA) 3-OH-acyl-CoA dehydrogenase paaC (paaH/phaC/pacB) Putative thioesterase paaD (paaI/----/pacC) Ketothiolase paaE (paaJ/phaD/----) Permease paaL (----/phaJ/----) Porine paaM (----/phaK/----) Repressor protein paaX (paaX/phaN/----) Putative regulator paaY (paaY/phaM/pacM) None - {{∅}} True - {{t}} Unconfirmed presence
Component_48862 negative transcriptional regulator None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_59317 TIGR02156 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_59320 TIGR02159 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Component_46819 phenylacetate-CoA ligase None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_59319 TIGR02158 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_61369 TIGR02280 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Component_48865 enoyl-CoA hydratase/isomerase, PaaB None - {{∅}} True - {{t}} Unconfirmed presence
Component_46820 phenylacetate-CoA oxygenase, PaaG subunit None - {{∅}} True - {{t}} Unconfirmed presence
Component_46824 phenylacetate-CoA oxygenase/reductase, PaaK subunit None - {{∅}} True - {{t}} Unconfirmed presence
Component_50866 putative thioesterase, PaaD None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_61365 TIGR02277 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_63374 TIGR02288 HMM None - {{∅}} None - {{∅}} Unexplained
Component_46821 phenylacetate-CoA oxygenase, PaaH subunit None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_59316 TIGR02155 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_61366 TIGR02278 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_63373 TIGR02287 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_63370 TIGR02286 HMM None - {{∅}} True - {{t}} Unconfirmed presence