Experiment set4IT016 for Dinoroseobacter shibae DFL-12

marine broth with Sodium perchlorate monohydrate 50 mM

Group: stress
Media: marine_broth_2216 + Sodium perchlorate monohydrate (50 mM)
Culturing: Dino_ML3, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Adam on 2/27/2014
Media components: 5 g/L Bacto Peptone, 1 g/L Yeast Extract, 0.1 g/L Ferric citrate, 19.45 g/L Sodium Chloride, 5.9 g/L Magnesium chloride hexahydrate, 3.24 g/L Magnesium sulfate, 1.8 g/L Calcium chloride, 0.55 g/L Potassium Chloride, 0.16 g/L Sodium bicarbonate, 0.08 g/L Potassium bromide, 34 mg/L Strontium chloride, 22 mg/L Boric Acid, 4 mg/L Sodium metasilicate, 2.4 mg/L sodium fluoride, 8 mg/L Disodium phosphate
Growth plate: 827 E1,E2

Specific Phenotypes

For 8 genes in this experiment

For stress Sodium perchlorate monohydrate in Dinoroseobacter shibae DFL-12

For stress Sodium perchlorate monohydrate across organisms

SEED Subsystems

Subsystem	#Specific
Serine-glyoxylate cycle	2
Methionine Biosynthesis	1
Photorespiration (oxidative C2 cycle)	1
Propionate-CoA to Succinate Module	1
TCA Cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Methionine metabolism
• Cysteine metabolism
• Glyoxylate and dicarboxylate metabolism
• Biosynthesis of plant hormones
• Citrate cycle (TCA cycle)
• Taurine and hypotaurine metabolism
• Selenoamino acid metabolism
• C5-Branched dibasic acid metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Sulfur metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
taurine degradation I	1	1	1
L-homocysteine biosynthesis	2	2	1
glyoxylate cycle	6	6	2
hypotaurine degradation	3	3	1
superpathway of L-cysteine biosynthesis (fungi)	6	4	2
L-methionine biosynthesis III	4	4	1
nitrogen remobilization from senescing leaves	8	6	2
partial TCA cycle (obligate autotrophs)	8	6	2
homocysteine and cysteine interconversion	4	2	1
TCA cycle II (plants and fungi)	9	8	2
TCA cycle V (2-oxoglutarate synthase)	9	8	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	8	2
TCA cycle VII (acetate-producers)	9	6	2
TCA cycle VI (Helicobacter)	9	6	2
methylaspartate cycle	19	14	4
TCA cycle III (animals)	10	9	2
TCA cycle I (prokaryotic)	10	9	2
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae)	10	8	2
L-methionine biosynthesis I	5	4	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation III	5	2	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation II	5	2	1
ethylmalonyl-CoA pathway	11	8	2
reductive TCA cycle I	11	7	2
superpathway of glyoxylate bypass and TCA	12	11	2
L-methionine biosynthesis II	6	5	1
reductive TCA cycle II	12	6	2
superpathway of taurine degradation	6	3	1
superpathway of glyoxylate cycle and fatty acid degradation	14	12	2
superpathway of L-homoserine and L-methionine biosynthesis	8	7	1
mixed acid fermentation	16	10	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	8	1
superpathway of S-adenosyl-L-methionine biosynthesis	9	8	1
superpathway of the 3-hydroxypropanoate cycle	18	12	2
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	19	2
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
ethene biosynthesis V (engineered)	25	17	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	2
3-hydroxypropanoate cycle	13	9	1
formaldehyde assimilation I (serine pathway)	13	9	1
glyoxylate assimilation	13	8	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	7	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	17	1
aspartate superpathway	25	21	1