Experiment set5IT086 for Pseudomonas simiae WCS417

Adenine hydrochloride hydrate nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + Adenine hydrochloride hydrate (10 mM), pH=7
Culturing: fluoroDangl_ML3, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 3/2/2015
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 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 15 genes in this experiment

For nitrogen source Adenine hydrochloride hydrate in Pseudomonas simiae WCS417

For nitrogen source Adenine hydrochloride hydrate across organisms

SEED Subsystems

Subsystem	#Specific
Biotin biosynthesis	2
Purine conversions	2
2-Ketogluconate Utilization	1
D-gluconate and ketogluconates metabolism	1
Fermentations: Mixed acid	1
Methionine Biosynthesis	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Threonine and Homoserine Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Glycine, serine and threonine metabolism
• Biotin metabolism
• Pentose phosphate pathway
• Ubiquinone and menaquinone biosynthesis
• Cysteine metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Glutathione metabolism
• Pyruvate metabolism
• Naphthalene and anthracene degradation
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
thiosulfate disproportionation IV (rhodanese)	1	1	1
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
L-threonine biosynthesis	2	2	1
8-amino-7-oxononanoate biosynthesis III	2	1	1
L-cysteine degradation III	2	1	1
8-amino-7-oxononanoate biosynthesis II	2	1	1
purine deoxyribonucleosides degradation II	3	3	1
L-serine biosynthesis I	3	3	1
adenine and adenosine salvage V	3	2	1
purine deoxyribonucleosides degradation I	4	4	1
biotin biosynthesis from 8-amino-7-oxononanoate I	4	4	1
adenine and adenosine salvage III	4	4	1
superpathway of L-serine and glycine biosynthesis I	4	4	1
adenosine nucleotides degradation II	5	5	1
glucose degradation (oxidative)	5	5	1
8-amino-7-oxononanoate biosynthesis IV	5	4	1
sulfide oxidation IV (mitochondria)	5	2	1
superpathway of L-threonine biosynthesis	6	6	1
purine ribonucleosides degradation	6	5	1
L-methionine biosynthesis II	6	5	1
biotin biosynthesis II	6	4	1
superpathway of purine deoxyribonucleosides degradation	7	5	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
biotin biosynthesis I	15	14	2
partial TCA cycle (obligate autotrophs)	8	8	1
nitrogen remobilization from senescing leaves	8	6	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
purine nucleotides degradation II (aerobic)	11	11	1
8-amino-7-oxononanoate biosynthesis I	11	10	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	1
superpathway of L-isoleucine biosynthesis I	13	13	1
formaldehyde assimilation I (serine pathway)	13	6	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	1
mixed acid fermentation	16	12	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
aspartate superpathway	25	22	1
ethene biosynthesis V (engineered)	25	18	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1