Experiment set17IT058 for Pseudomonas stutzeri RCH2

LB with Choline chloride 90 mM

Group: stress
Media: LB + Choline chloride (90 mM)
Culturing: psRCH2_ML7c, 48 well microplate; Tecan Infinite F200, Aerobic, at 28 (C), shaken=orbital
By: Kelly on 4/17/2014
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 885 A5,A6

Specific Phenotypes

For 29 genes in this experiment

For stress Choline chloride in Pseudomonas stutzeri RCH2

For stress Choline chloride across organisms

SEED Subsystems

Subsystem	#Specific
Choline and Betaine Uptake and Betaine Biosynthesis	3
ATP-dependent RNA helicases, bacterial	2
Biotin biosynthesis	1
Campylobacter Iron Metabolism	1
Maltose and Maltodextrin Utilization	1
Phosphate metabolism	1
Polyamine Metabolism	1
Protein degradation	1
Ribosome activity modulation	1
n-Phenylalkanoic acid degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycine, serine and threonine metabolism
• Ubiquinone and menaquinone biosynthesis
• Nucleotide sugars metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Fatty acid metabolism
• Puromycin biosynthesis
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Benzoxazinone biosynthesis
• Starch and sucrose metabolism
• Glycosaminoglycan degradation
• alpha-Linolenic acid metabolism
• Naphthalene and anthracene degradation
• Trinitrotoluene degradation
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	2
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	2
choline degradation I	2	2	2
long-chain fatty acid activation	1	1	1
choline-O-sulfate degradation	3	2	2
γ-linolenate biosynthesis II (animals)	2	1	1
linoleate biosynthesis II (animals)	2	1	1
β-alanine biosynthesis IV	2	1	1
β-alanine biosynthesis I	2	1	1
L-tryptophan biosynthesis	6	6	2
fatty acid salvage	6	6	2
fatty acid biosynthesis initiation (type II)	3	3	1
glycine betaine biosynthesis III (plants)	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
dimethylsulfoniopropanoate biosynthesis I (Wollastonia)	3	1	1
alkane biosynthesis II	3	1	1
starch degradation I	3	1	1
oleate biosynthesis I (plants)	3	1	1
phytol degradation	4	3	1
choline degradation IV	4	2	1
phosphatidylcholine acyl editing	4	1	1
wax esters biosynthesis II	4	1	1
dimethylsulfoniopropanoate biosynthesis II (Spartina)	4	1	1
long chain fatty acid ester synthesis (engineered)	4	1	1
sporopollenin precursors biosynthesis	18	4	4
superpathway of fatty acid biosynthesis initiation	5	4	1
octane oxidation	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
stearate biosynthesis II (bacteria and plants)	6	5	1
stearate biosynthesis IV	6	4	1
6-gingerol analog biosynthesis (engineered)	6	2	1
DIBOA-glucoside biosynthesis	6	1	1
stearate biosynthesis I (animals)	6	1	1
superpathway of L-tryptophan biosynthesis	13	13	2
ceramide degradation by α-oxidation	7	2	1
capsaicin biosynthesis	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
glycogen degradation I	8	7	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
2-deoxy-D-ribose degradation II	8	2	1
superpathway of fatty acid biosynthesis II (plant)	43	38	5
superpathway of aromatic amino acid biosynthesis	18	18	2
suberin monomers biosynthesis	20	2	2
superpathway of benzoxazinoid glucosides biosynthesis	13	1	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
superpathway of fatty acid biosynthesis I (E. coli)	16	15	1
cutin biosynthesis	16	1	1
superpathway of fatty acids biosynthesis (E. coli)	53	51	3
palmitate biosynthesis III	29	21	1
superpathway of chorismate metabolism	59	44	2
streptorubin B biosynthesis	34	20	1
oleate β-oxidation	35	30	1