Experiment set15IT095 for Pseudomonas fluorescens FW300-N2E3

L-Citrulline

Group: carbon source
Media: RCH2_defined_noCarbon + L-Citrulline (5 mM), pH=7
Culturing: pseudo3_N2E3_ML2a, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 4-Aug-21
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 11 genes in this experiment

For carbon source L-Citrulline in Pseudomonas fluorescens FW300-N2E3

For carbon source L-Citrulline across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	2
Fermentations: Mixed acid	1
Folate Biosynthesis	1
Glycine and Serine Utilization	1
Glycine cleavage system	1
Orphan regulatory proteins	1
Pyruvate Alanine Serine Interconversions	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Rhamnose containing glycans	1
Teichoic and lipoteichoic acids biosynthesis	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
• Fatty acid biosynthesis
• Urea cycle and metabolism of amino groups
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Butanoate metabolism
• One carbon pool by folate
• Methane metabolism
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Folate biosynthesis
• Atrazine degradation
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
urea degradation I	3	2	2
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
cyanuric acid degradation II	5	3	2
cyanuric acid degradation I	5	2	2
cyanate degradation	3	3	1
tetrahydrofolate biosynthesis I	3	3	1
dTMP de novo biosynthesis (mitochondrial)	3	3	1
L-citrulline degradation	3	3	1
superpathway of allantoin degradation in yeast	6	4	2
L-arginine degradation V (arginine deiminase pathway)	4	4	1
tetrahydromonapterin biosynthesis	4	3	1
superpathway of atrazine degradation	8	3	2
L-arginine degradation II (AST pathway)	5	5	1
uracil degradation III	5	2	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
partial TCA cycle (obligate autotrophs)	8	8	1
nitrogen remobilization from senescing leaves	8	6	1
folate transformations III (E. coli)	9	9	1
Escherichia coli serotype O:8 O antigen biosynthesis	9	2	1
allantoin degradation IV (anaerobic)	9	2	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
folate transformations II (plants)	11	10	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
formaldehyde assimilation I (serine pathway)	13	6	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	1
mixed acid fermentation	16	12	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
ethene biosynthesis V (engineered)	25	19	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1
superpathway of chorismate metabolism	59	43	1