Experiment set8IT027 for Xanthomonas campestris pv. campestris strain 8004

D-Glucose 16.67 mM carbon source

Group: carbon source
Media: CaMM_noCarbon + D-Glucose (17 mM)
Culturing: Xantho_ML2, tube, Aerobic, at 28 (C)
By: Alice on 5/19/22
Media components: 10.5 g/L Potassium phosphate dibasic, 4.5 g/L Potassium phosphate monobasic, 1 g/L Ammonium Sulfate, 0.1 mM Calcium chloride, 1 mM Magnesium sulfate, 0.00625 g/L Iron (II) sulfate heptahydrate, 0.0625 g/L EDTA disodium dihydrate, 0.0225 g/L Zinc sulfate heptahydrate, 0.0143 g/L Boric Acid, 0.0063 g/L Manganese (II) chloride tetrahydrate, 0.002 g/L Cobalt chloride hexahydrate, 0.0019 g/L Copper (II) sulfate pentahydrate, 0.0014 g/L Ammonium heptamolybdate tetrahydrate

Specific Phenotypes

For 29 genes in this experiment

For carbon source D-Glucose in Xanthomonas campestris pv. campestris strain 8004

For carbon source D-Glucose across organisms

SEED Subsystems

Subsystem	#Specific
Cysteine Biosynthesis	3
Methionine Biosynthesis	2
Trehalose Biosynthesis	2
ATP-dependent RNA helicases, bacterial	1
Fermentations: Mixed acid	1
Glycine and Serine Utilization	1
Glycogen metabolism	1
Maltose and Maltodextrin Utilization	1
Mannose Metabolism	1
Methionine Degradation	1
NAD and NADP cofactor biosynthesis global	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
One-carbon metabolism by tetrahydropterines	1
Peptidoglycan Biosynthesis	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Serine-glyoxylate cycle	1
Xanthan Exopolysaccharide Biosynthesis and Export	1
ZZ gjo need homes	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Methionine metabolism
• Lysine degradation
• Arginine and proline metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• Benzoate degradation via CoA ligation
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Glycine, serine and threonine metabolism
• Lysine biosynthesis
• Histidine metabolism
• Tyrosine metabolism
• Aminophosphonate metabolism
• Selenoamino acid metabolism
• Cyanoamino acid metabolism
• Starch and sucrose metabolism
• Glycosaminoglycan degradation
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Ethylbenzene degradation
• Styrene degradation
• Butanoate metabolism
• One carbon pool by folate
• Methane metabolism
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Folate biosynthesis
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
L-cysteine biosynthesis III (from L-homocysteine)	2	2	1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis I	2	2	1
hydrogen sulfide biosynthesis II (mammalian)	6	4	3
indole-3-acetate biosynthesis III (bacteria)	2	1	1
indole-3-acetate biosynthesis IV (bacteria)	2	1	1
acrylonitrile degradation I	2	1	1
L-tryptophan degradation I (via anthranilate)	3	2	1
taurine biosynthesis III	3	1	1
L-arginine degradation X (arginine monooxygenase pathway)	3	1	1
microcin B17 biosynthesis	3	1	1
superpathway of acrylonitrile degradation	3	1	1
molybdenum cofactor biosynthesis	3	1	1
homocysteine and cysteine interconversion	4	3	1
dimethylsulfoniopropanoate biosynthesis III (algae and phytoplankton)	4	1	1
L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde	5	4	1
superpathway of L-cysteine biosynthesis (mammalian)	5	4	1
3-hydroxy-4-methyl-anthranilate biosynthesis II	5	3	1
superpathway of L-cysteine biosynthesis (fungi)	6	5	1
folate transformations I	13	9	2
ethene biosynthesis III (microbes)	7	6	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
superpathway of thiamine diphosphate biosynthesis III (eukaryotes)	7	3	1
L-homomethionine biosynthesis	7	2	1
partial TCA cycle (obligate autotrophs)	8	7	1
nitrogen remobilization from senescing leaves	8	6	1
folate transformations III (E. coli)	9	9	1
NAD de novo biosynthesis II (from tryptophan)	9	8	1
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae)	10	9	1
xanthan biosynthesis	10	8	1
superpathway of thiamine diphosphate biosynthesis I	10	7	1
reductive acetyl coenzyme A pathway I (homoacetogenic bacteria)	10	3	1
folate transformations II (plants)	11	10	1
superpathway of thiamine diphosphate biosynthesis II	11	9	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	7	1
L-tryptophan degradation XI (mammalian, via kynurenine)	23	8	2
L-tryptophan degradation IX	12	5	1
L-tryptophan degradation XII (Geobacillus)	12	4	1
indole-3-acetate biosynthesis II	12	3	1
formaldehyde assimilation I (serine pathway)	13	8	1
superpathway of NAD biosynthesis in eukaryotes	14	11	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	8	1
L-tryptophan degradation III (eukaryotic)	15	7	1
mixed acid fermentation	16	11	1
superpathway of L-methionine salvage and degradation	16	8	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	8	1
ethene biosynthesis V (engineered)	25	17	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	19	2
superpathway of aromatic compound degradation via 3-oxoadipate	35	13	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	8	1