Automated generation of genome-scale metabolic draft reconstructions based on KEGG

BMC Bioinformatics

Table 1 Example output using the OrgRxnGen flag within AutoKEGGRec

KEGG ID	eco	ecj	ecd	ebw	ecok	Sum	Total	Genes
R00001						0	0	0
R00002						0	0	0
R00004	b4226	JW4185	ECDH10B_4421	BWG_3936	ECMDS42_3668	5	1	1
R00005						0	0	0
R00006	b0078, b3670, b0077, b3671, b3769	JW0077, JW3645, JW0076, JW3646, JW3742	ECDH10B_3853, ECDH10B_3958, ECDH10B_3854	BWG_0073, BWG_0074, BWG_3454, BWG_3361, BWG_3362	ECMDS42_3207, ECMDS42_0071, ECMDS42_0072, ECMDS42_3105, ECMDS42_3106	5	1	3;5
R00008						0	0	0
R00009	b1732, b3942	JW1721, JW3914	ECDH10B_1870, ECDH10B_4131	BWG_1545, BWG_3611	ECMDS42_1407, ECMDS42_3380	5	1	2
R00010	b1197, b3519	JW3487, JW1186	ECDH10B_3696, ECDH10B_1250	BWG_3208, BWG_1022	ECMDS42_2954, ECMDS42_0984	5	1	2
R00011						0	0	0
R00012						0	0	0
R00013	b0507	JW0495	ECDH10B_0463	BWG_0384	ECMDS42_0400	5	1	1
R00014	b0114, b0078, b3670, b0077, b3671, b3769	JW0110, JW0077, JW3645, JW0076, JW3646, JW3742	ECDH10B_0094, ECDH10B_3853, ECDH10B_3958, ECDH10B_3854	BWG_0073, BWG_0074, BWG_3454, BWG_3361, BWG_3362, BWG_0107	ECMDS42_3207, ECMDS42_0071, ECMDS42_0072, ECMDS42_0105, ECMDS42_3105, ECMDS42_3106	5	1	4;6
R00015						0	0	0
R00017	b3518	JW3486	ECDH10B_3695	BWG_3207	ECMDS42_2953	5	1	1

Here the Organism-Reaction-Gene matrix for the five E. coli K-12 strains is shown. The genes encoding the the first 14 reactions in KEGG, followed by the genes, if any, for the different organisms. Also provided with this output, in the three rightmost columns, is the Sum of organisms whose metabolism contains this reaction, the Total fraction of strains whose metabolism contains this reaction, and the number of Genes for the different organisms for that reaction

ISSN: 1471-2105