Experiment set3IT035 for Pseudomonas simiae WCS417

LB with Tetracycline hydrochloride 0.001 mg/ml

Group: stress
Media: LB + Tetracycline hydrochloride (0.001 mg/ml)
Culturing: fluoroDangl_ML3, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Mark on 3/2/2015
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 1165 B7,B8

Specific Phenotypes

For 11 genes in this experiment

For stress Tetracycline hydrochloride in Pseudomonas simiae WCS417

For stress Tetracycline hydrochloride across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter alkylphosphonate (TC 3.A.1.9.1)	1
N-linked Glycosylation in Bacteria	1
Oxidative stress	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Tyrosine metabolism
• Nucleotide sugars metabolism
• Porphyrin and chlorophyll metabolism
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Galactose metabolism
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Histidine metabolism
• Benzoate degradation via hydroxylation
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Benzoxazinone biosynthesis
• Starch and sucrose metabolism
• Streptomycin biosynthesis
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
UDP-α-D-glucose biosynthesis	2	2	1
trehalose degradation V	3	2	1
GDP-α-D-glucose biosynthesis	3	2	1
sucrose degradation IV (sucrose phosphorylase)	4	3	1
starch degradation V	4	3	1
glycogen biosynthesis I (from ADP-D-Glucose)	4	3	1
UDP-N-acetyl-β-L-fucosamine biosynthesis	4	2	1
starch degradation III	4	2	1
UDP-N-acetyl-β-L-quinovosamine biosynthesis	4	1	1
dTDP-β-L-rhamnose biosynthesis	5	5	1
glucose and glucose-1-phosphate degradation	5	4	1
sucrose degradation II (sucrose synthase)	5	4	1
D-galactose degradation I (Leloir pathway)	5	3	1
CDP-6-deoxy-D-gulose biosynthesis	5	3	1
glucosylglycerol biosynthesis	5	2	1
glycogen degradation II	6	5	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
CMP-pseudaminate biosynthesis	6	1	1
CMP-diacetamido-8-epilegionaminic acid biosynthesis	7	1	1
sucrose biosynthesis II	8	6	1
glycogen degradation I	8	6	1
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	3	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
chitin biosynthesis	9	5	1
starch biosynthesis	10	5	1
O-antigen building blocks biosynthesis (E. coli)	11	10	1
colanic acid building blocks biosynthesis	11	8	1
streptomycin biosynthesis	18	3	1
superpathway of anaerobic sucrose degradation	19	14	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	5	1
superpathway of UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis	24	9	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	1