Experiment set5IT092 for Pseudomonas simiae WCS417

Sodium nitrate nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + Sodium nitrate (20 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 16 genes in this experiment

For nitrogen source Sodium nitrate in Pseudomonas simiae WCS417

For nitrogen source Sodium nitrate across organisms

SEED Subsystems

Subsystem	#Specific
Nitrate and nitrite ammonification	6
Molybdenum cofactor biosynthesis	3
Biotin biosynthesis	2
2-Ketogluconate Utilization	1
Ammonia assimilation	1
Coenzyme B12 biosynthesis	1
Dissimilatory nitrite reductase	1
Experimental tye	1
Heme and Siroheme Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Biotin metabolism
• Porphyrin and chlorophyll metabolism
• Nitrogen metabolism
• Pentose phosphate pathway
• Ubiquinone and menaquinone biosynthesis
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Glutathione metabolism
• Naphthalene and anthracene degradation
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway
• mTOR signaling pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
bis(guanylyl molybdenum cofactor) biosynthesis	2	2	2
bis(guanylyl tungstenpterin) cofactor biosynthesis	1	1	1
guanylyl molybdenum cofactor biosynthesis	1	1	1
siroheme biosynthesis	4	4	3
alkylnitronates degradation	2	2	1
nitrate reduction V (assimilatory)	2	1	1
8-amino-7-oxononanoate biosynthesis III	2	1	1
8-amino-7-oxononanoate biosynthesis II	2	1	1
factor 430 biosynthesis	7	3	3
biotin biosynthesis from 8-amino-7-oxononanoate I	4	4	1
glucose degradation (oxidative)	5	5	1
cob(II)yrinate a,c-diamide biosynthesis I (early cobalt insertion)	15	12	3
8-amino-7-oxononanoate biosynthesis IV	5	4	1
biotin biosynthesis II	6	4	1
cob(II)yrinate a,c-diamide biosynthesis II (late cobalt incorporation)	13	13	2
biotin biosynthesis I	15	14	2
8-amino-7-oxononanoate biosynthesis I	11	10	1
adenosylcobalamin biosynthesis I (anaerobic)	36	28	3
adenosylcobalamin biosynthesis II (aerobic)	33	31	2