FEV_KEGG.Experiments.02 module¶

Question¶

Which enzyme edges (substrate -> enzyme -> product) are present in eco00260, but not in eco01100?

Method¶

Download pathway definition as KGML.
Convert to substance-reaction graph.
Convert to substance-gene graph.
Calculate difference (eco00260 - eco01100). Do not subtract nodes, to keep all surviving edges.
Convert difference graph to substance-enzyme graph. Not necessary earlier, because each unique gene object ist mapped to the same unique enzyme object.
Print enzyme edges (substrate -> gene name, enzyme name, all associated EC numbers, enzyme long name -> product).

Result¶

18 results
C00022 -> b2366 dsdA [4.3.1.18] D-serine dehydratase -> C00740
C00037 -> b2903 gcvP [1.4.4.2] glycine dehydrogenase -> C00011
C00037 -> b3617 kbl [2.3.1.29] glycine C-acetyltransferase -> C03508
C00065 -> b2585 pssA [2.7.8.8] CDP-diacylglycerol---serine O-phosphatidyltransferase -> C02737
C00101 -> b2905 gcvT [2.1.2.10] aminomethyltransferase -> C00014
C00101 -> b2905 gcvT [2.1.2.10] aminomethyltransferase -> C02972
C00168 -> b3553 ghrB [1.1.1.215, 1.1.1.81, 1.1.1.79] glyoxylate/hydroxypyruvate/2-ketogluconate reductase -> C00258
C00188 -> b3616 tdh [1.1.1.103] threonine 3-dehydrogenase -> C03508
C00258 -> b3553 ghrB [1.1.1.215, 1.1.1.81, 1.1.1.79] glyoxylate/hydroxypyruvate/2-ketogluconate reductase -> C00168
C00740 -> b2366 dsdA [4.3.1.18] D-serine dehydratase -> C00022
C01242 -> b2905 gcvT [2.1.2.10] aminomethyltransferase -> C00014
C01242 -> b2905 gcvT [2.1.2.10] aminomethyltransferase -> C02972
C01888 -> b1386 tynA [1.4.3.21] primary-amine oxidase -> C00546
C02051 -> b2903 gcvP [1.4.4.2] glycine dehydrogenase -> C00011
C02051 -> b2903 gcvP [1.4.4.2] glycine dehydrogenase -> C01242
C02972 -> b0116 lpd [1.8.1.4] dihydrolipoamide dehydrogenase -> C02051
C03508 -> b3617 kbl [2.3.1.29] glycine C-acetyltransferase -> C00037
C05519 -> b1539 ydfG [1.1.1.-, 1.1.1.381] 3-hydroxy acid dehydrogenase / malonic semialdehyde reductase -> C03508

Conclusion¶

Global map 01100 does not necessarily contain all enzyme edges for an organism.