Experiment set3IT090 for Xanthomonas campestris pv. campestris strain 8004

Xantho_MME_glucose_dropout_LTH

Group: xantho_mme_glucose_dropout_lth
Media: Xantho_MME_glucose_dropout_LTH
Culturing: Xantho_ML2, flask, Aerobic, at 28 (C)
By: Alice on 7/9/18
Media components: 10.5 g/L Potassium phosphate dibasic, 4.5 g/L Potassium phosphate monobasic, 1 g/L Ammonium Sulfate, 1 mM Magnesium Sulfate Heptahydrate, 20 mM D-Glucose, 1.5 g/L Takara_DO_Supp_MinusHisLeuTrp

Specific Phenotypes

For 9 genes in this experiment

SEED Subsystems

Subsystem	#Specific
NAD and NADP cofactor biosynthesis global	4
Glycine Biosynthesis	2
Arginine and Ornithine Degradation	1
Glycine and Serine Utilization	1
NAD regulation	1
Quinolinic acid and its derivatives	1
Threonine degradation	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Arginine and proline metabolism
• Tryptophan metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Urea cycle and metabolism of amino groups
• Glycine, serine and threonine metabolism
• Lysine biosynthesis
• Nicotinate and nicotinamide metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-threonine degradation II	2	2	2
L-arginine degradation I (arginase pathway)	3	3	2
L-threonine degradation III (to methylglyoxal)	3	2	2
L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde	5	4	3
NAD de novo biosynthesis II (from tryptophan)	9	8	5
NAD biosynthesis from 2-amino-3-carboxymuconate semialdehyde	4	4	2
L-arginine degradation VI (arginase 2 pathway)	4	4	2
aminopropanol phosphate biosynthesis II	4	2	2
L-arginine degradation VII (arginase 3 pathway)	2	1	1
L-canavanine degradation I	2	1	1
putrescine biosynthesis III	2	1	1
3-hydroxy-4-methyl-anthranilate biosynthesis II	5	3	2
superpathway of NAD biosynthesis in eukaryotes	14	11	5
L-proline biosynthesis III (from L-ornithine)	3	3	1
L-ornithine biosynthesis II	3	3	1
L-tryptophan degradation I (via anthranilate)	3	2	1
L-Nδ-acetylornithine biosynthesis	7	5	2
L-citrulline biosynthesis	8	6	2
superpathway of putrescine biosynthesis	4	2	1
L-tryptophan degradation IX	12	5	3
L-ornithine biosynthesis I	5	5	1
urea cycle	5	3	1
L-arginine degradation XIII (reductive Stickland reaction)	5	3	1
L-tryptophan degradation III (eukaryotic)	15	7	3
L-arginine degradation II (AST pathway)	5	1	1
L-tryptophan degradation XI (mammalian, via kynurenine)	23	8	4
superpathway of L-threonine metabolism	18	12	3
superpathway of L-citrulline metabolism	12	8	2
NAD de novo biosynthesis I	6	4	1
NAD de novo biosynthesis IV (anaerobic)	6	4	1
NAD de novo biosynthesis III	6	4	1
L-tryptophan degradation XII (Geobacillus)	12	4	2
3-hydroxy-4-methyl-anthranilate biosynthesis I	6	2	1
2-nitrobenzoate degradation I	7	1	1
superpathway of polyamine biosynthesis II	8	6	1
superpathway of polyamine biosynthesis I	8	4	1
superpathway of arginine and polyamine biosynthesis	17	12	2
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	9	1
L-lysine biosynthesis I	9	9	1
L-arginine biosynthesis I (via L-ornithine)	9	8	1
nicotine biosynthesis	9	1	1
L-arginine biosynthesis II (acetyl cycle)	10	8	1
superpathway of nicotine biosynthesis	12	2	1
aspartate superpathway	25	21	2
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	4	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	13	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	8	1