TABLE 3.

Critical KEGG pathways in planta (nonexhaustive)

Pathway code	KEGG pathway	No. of genes:		% of genes in pathway
		Criticala	Totalb
General and diverse pathways
xhr01110	Biosynthesis of secondary metabolites	84	301	27.9
xhr01240	Biosynthesis of cofactors	19	128	14.8
xhr00910	Nitrogen metabolism	9	14	64.3
xhr03070	Bacterial secretion system	16	70	22.9
Amino acid metabolism
xhr01230	Biosynthesis of amino acids	54	109	49.5
xhr00220	Arginine biosynthesis	12	13	92.3
xhr00290	Valine, leucine, and isoleucine biosynthesis	10	13	76.9
xhr00250	Alanine, aspartate, and glutamate metabolism	16	25	64
xhr00400	Phenylalanine, tyrosine, and tryptophan biosynthesis	11	26	42.3
xhr00260	Glycine, serine, and threonine metabolism	14	35	40
xhr00340	Histidine metabolism	6	18	33.3
xhr00270	Cysteine and methionine metabolism	11	37	29.7
Carbon compound metabolism
xhr01200	Carbon metabolism	18	92	19.6
xhr01210	2-Oxocarboxylic acid metabolism	12	21	57.1
xhr00030	Pentose phosphate pathway	9	25	36
xhr00500	Starch and sucrose metabolism	12	38	31.6
xhr00010	Glycolysis/gluconeogenesis	9	31	29
xhr00052	Galactose metabolism	5	20	25
xhr00051	Fructose and mannose metabolism	5	21	23.8
Nucleobase metabolism
xhr00240	Pyrimidine metabolism	7	25	28
xhr00230	Purine metabolism	11	54	20.4
Polysaccharide metabolism
xhr00541	O-antigen nucleotide sugar biosynthesis	9	16	56.3

^aNumber of genes identified as conditionally essential in planta (q value of ≤0.05).

^bTotal number of genes in model pathway in the X. hortorum-specific KEGG pathway database.