Table 1 Relevant pathways for methanogenesis
From: Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes
Dataset | ReliefF | SVMAttributeEval | Wrapper (naïve Bayes) |
|---|---|---|---|
Complete (266) | Reduction of CO2 to CH4 (methane1) ↑ | Reduction of CO2 to CH4 (methane1) ↑ | Reduction of CO2 to CH4 (methane1) ↑ |
|  | Biosynthesis of cardiolipin (phospholipids1) ↓ | Biosynthesis of cardiolipin (phospholipids1) ↓ | Degradation of L-lysine to crotonyl-CoA (lysine3) ↓ |
|  | Biosynthesis of peptidoglycan I (aminosugars4) ↓ | beta-Oxidation of fatty acids (fa2) ↓ | Biosynthesis of coenzyme A (coa1) ↓ |
|  | Heme biosynthesis (pyrrole3) ↓ | Degradation of L-threonine to L-2-aminoacetate (threonine2) ↓ |  |
|  | Pentose phosphate cycle (non-oxidative branch) (ppc3) ↓ | Biosynthesis of phosphatidylserine (phospholipids3) ↑ |  |
Archaea (23) | Biosynthesis of 2'-deoxythymidine-5'-triphosphate (dtn1) ↑ | Biosynthesis of 2'-deoxythymidine-5'-triphosphate (dtn1) ↑ | Reduction of CO2 to CH4 (methane1) ↓ |
|  | Reduction of CO2 to CH4 (methane1) ↑ | Biosynthesis of L-phenylalanine from chorismate (aaa4) ↑ | Biosynthesis of 2'-deoxythymidine-5'-triphosphate (dtn1) ↑ |
|  | Biosynthesis of phosphatidylserine (phospholipids3) ↑ | Reduction of CO2 to CH4 (methane1) ↑ | Degradation of L-threonine to L-2-aminoacetate (threonine2) ↓ |
|  | Degradation of L-threonine to L-2-aminoacetate (threonine2) ↓ | Degradation of dGMP to deoxyguanosine (dgn2) ↓ | Degradation of L-lysine to crotonyl-CoA (lysine3) ↓ |
|  | Degradation of tryptophane to 6-hydroxymelatonin (trp5) ↑ | Biosynthesis of phosphatidylserine (phospholipids3) ↑ | Biosynthesis of coenzyme B12 (coba1) ↑ |
Archaea (23) (without methane1) | Biosynthesis of 2'-deoxythymidine-5'-triphosphate (dtn1) ↑ | Biosynthesis of 2'-deoxythymidine-5'-triphosphate (dtn1) ↑ | Biosynthesis of 2'-deoxythymidine-5'-triphosphate (dtn1) ↑ |
|  | Biosynthesis of phosphatidylserine (phospholipids3) ↑ | Biosynthesis of L-phenylalanine from chorismate (aaa4) ↑ | Biosynthesis of coenzyme B12 (coba1) ↑ |
|  | Degradation of L-threonine to L-2-aminoacetate (threonine2) ↓ | Degradation of L-threonine to L-2-aminoacetate (threonine2) ↓ | Degradation of L-valine (vas4) ↓ |
|  | Degradation of tryptophane to 6-hydroxymelatonin (trp5) ↑ | Biosynthesis of phosphatidylserine (phospholipids3) ↑ | Degradation of L-threonine to L-2-aminoacetate (threonine2) ↓ |
|  | Biosynthesis of coenzyme B12 (coba1) ↑ | Odd-numbered fatty acid metabolism (glf2) ↓ | Degradation of L-lysine to crotonyl-CoA (lysine3) ↓ |