FEV_KEGG.Experiments.09 module

Question

Which reactions, independent of substrate and product, are present in eco01100, but not in a combination of all non-overview metabolic pathways?

Method

  • Download pathway description as KGML.
  • Convert to substance-reaction graph.
  • Get set of reactions for each graph.
  • Calculate difference of reaction sets.
  • Print reactions (reaction ID).

Result

161 results
R00107
R00149
R00160
R00173
R00185
R00206
R00209
R00229
R00243
R00257
R00287
R00305
R00320
R00346
R00352
R00369
R00396
R00400
R00414
R00431
R00432
R00502
R00530
R00531
R00550
R00616
R00618
R00648
R00688
R00689
R00692
R00703
R00709
R00710
R00717
R00726
R00727
R00729
R00746
R00841
R00859
R00861
R00866
R00883
R00895
R00907
R00943
R00951
R00978
R01022
R01039
R01063
R01067
R01088
R01122
R01128
R01151
R01156
R01171
R01176
R01217
R01218
R01225
R01278
R01287
R01290
R01324
R01326
R01415
R01434
R01447
R01523
R01555
R01667
R01730
R01741
R01769
R01788
R01829
R01867
R01869
R01911
R01967
R01986
R02014
R02020
R02022
R02073
R02089
R02107
R02124
R02189
R02197
R02239
R02282
R02296
R02415
R02474
R02494
R02537
R02596
R02727
R02821
R03222
R03295
R03354
R03438
R03776
R03856
R03919
R03989
R04007
R04027
R04230
R04413
R04432
R04753
R04859
R04985
R05000
R05053
R05081
R05198
R05705
R06613
R06740
R06975
R06985
R07064
R07147
R07276
R07279
R07376
R07407
R07410
R07818
R08211
R08379
R08557
R08558
R08574
R08714
R08768
R08769
R08773
R08774
R08775
R08781
R09084
R09085
R09127
R09254
R09281
R09944
R10161
R10178
R10305
R10343
R10404
R10699
R11308

Conclusion

The overview map eco01100 contains reactions that are not present in any of the single metabolism pathways.

Further research shows the reasons for such strange results:

  • There seems to have been some mistake in creating eco01100, because some genes are assigned reactions which actually belong to a different enzyme function. Example: R10699. Eco01100 maps this to the gene eco:b0774, which is classified as EC:2.6.1.62, which actually only performs R03231. Under this reaction, the gene occurs in pathway 00780 and 01100, the latter just adds rn:R10699, for an unknown reason. R10699 actually performs a different enzyme function: 2.6.1.105. This function does not occur in any enzyme associated with an eco gene.
  • Some single pathway files in KGML format do not contain a “reaction tag”, even though they should, according to the “entry tags” present in the same file and the pathway image. Example: R05000 only exists in eco011000, but not in eco00130, where it should, because eco00130 contains all compound and gene entries necessary for this reaction. It simply does not contain the “reaction tag”, probably due to an error in KEGG’s algorithms for creating KGML files.
  • Maybe more.

The overview map 01100 is unreliable and should, thus, not be used for exact research of reactions. However, using only the single pathways can also be unreliable, if the graph construction was to rely upon the “reaction tag”.

One solution could be to combine all single pathways plus the overview pathway 01100. But this adds reactions unknown to any single pathway. These reactions could possibly represent enzymes not present in any single pathway, but they might not. In case no additional enzymes occur in 01100, this solution would at least work on the substance-gene level and onward.

Another solution could be not to rely upon “reaction tags”, which represent pre-computed graph data. Then, however, we would have to compute the graph data ourselves, requiring a constant factor of more downloads (EC or KO files, plus reaction files) from KEGG (factor of roughly 10) and more computation time needed.