Experiment set4IT095 for Pseudomonas simiae WCS417

LB with Doxycycline hyclate 0.001 mg/ml

Group: stress
Media: LB + Doxycycline hyclate (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: 1164 D7,D8

Specific Phenotypes

For 24 genes in this experiment

For stress Doxycycline hyclate in Pseudomonas simiae WCS417

For stress Doxycycline hyclate across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter alkylphosphonate (TC 3.A.1.9.1)	1
Biotin biosynthesis	1
Heat shock dnaK gene cluster extended	1
N-linked Glycosylation in Bacteria	1
Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes	1
Orphan regulatory proteins	1
Oxidative stress	1
Proteasome bacterial	1
Proteolysis in bacteria, ATP-dependent	1
Rhamnose containing glycans	1
Teichoic and lipoteichoic acids biosynthesis	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:

• Nucleotide sugars metabolism
• Ubiquinone and menaquinone biosynthesis
• Tyrosine metabolism
• Porphyrin and chlorophyll metabolism
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Fatty acid metabolism
• Puromycin biosynthesis
• Histidine metabolism
• Benzoate degradation via hydroxylation
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Benzoxazinone biosynthesis
• Aminophosphonate metabolism
• Starch and sucrose metabolism
• High-mannose type N-glycan biosynthesis
• Streptomycin biosynthesis
• Glycosaminoglycan degradation
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Sphingolipid metabolism
• 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
long-chain fatty acid activation	1	1	1
UDP-α-D-glucose biosynthesis	2	2	1
linoleate biosynthesis II (animals)	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
trehalose degradation V	3	2	1
GDP-α-D-glucose biosynthesis	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
alkane biosynthesis II	3	1	1
oleate biosynthesis I (plants)	3	1	1
starch degradation V	4	3	1
sucrose degradation IV (sucrose phosphorylase)	4	3	1
phytol degradation	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
wax esters biosynthesis II	4	1	1
long chain fatty acid ester synthesis (engineered)	4	1	1
UDP-N-acetyl-β-L-quinovosamine biosynthesis	4	1	1
phosphatidylcholine acyl editing	4	1	1
sporopollenin precursors biosynthesis	18	4	4
dTDP-β-L-rhamnose biosynthesis	5	5	1
octane oxidation	5	4	1
sucrose degradation II (sucrose synthase)	5	4	1
glucose and glucose-1-phosphate degradation	5	4	1
CDP-6-deoxy-D-gulose biosynthesis	5	3	1
D-galactose degradation I (Leloir pathway)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
glucosylglycerol biosynthesis	5	2	1
Salmonella enterica serotype O:3,10 O antigen biosynthesis	5	1	1
fatty acid salvage	6	6	1
glycogen degradation II	6	5	1
stearate biosynthesis II (bacteria and plants)	6	5	1
stearate biosynthesis IV	6	4	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
6-gingerol analog biosynthesis (engineered)	6	2	1
Salmonella enterica serotype O:2 O antigen biosynthesis	6	1	1
Salmonella enterica serotype O:9 O antigen biosynthesis	6	1	1
Salmonella enterica serotype O:9,46 O antigen biosynthesis	6	1	1
stearate biosynthesis I (animals)	6	1	1
Porphyromonas gingivalis O-LPS antigen biosynthesis	6	1	1
CMP-pseudaminate biosynthesis	6	1	1
Salmonella enterica serotype O:4 O antigen biosynthesis (group B1)	6	1	1
ceramide degradation by α-oxidation	7	2	1
CMP-diacetamido-8-epilegionaminic acid biosynthesis	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
capsaicin biosynthesis	7	1	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
2-deoxy-D-ribose degradation II	8	7	1
glycogen degradation I	8	6	1
sucrose biosynthesis II	8	6	1
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
Salmonella enterica serotype O:8 O antigen biosynthesis	8	1	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
chitin biosynthesis	9	5	1
Salmonella enterica serotype O:9,46,27 O antigen biosynthesis	9	1	1
starch biosynthesis	10	5	1
suberin monomers biosynthesis	20	2	2
superpathway of fatty acid biosynthesis II (plant)	43	38	4
O-antigen building blocks biosynthesis (E. coli)	11	10	1
colanic acid building blocks biosynthesis	11	8	1
succinoglycan biosynthesis	14	1	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
cutin biosynthesis	16	1	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 fatty acids biosynthesis (E. coli)	53	49	2
palmitate biosynthesis III	29	21	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	1
oleate β-oxidation	35	30	1