Experiment setBH27 for Dinoroseobacter shibae DFL-12

marine broth with Cholin acetate 40 mM

Group: stress
Media: marine_broth_2216 + Cholin acetate (40 mM)
Culturing: Dino_ML3, 48 well microplate; Tecan Infinite F200, Aerobic, at 30 (C), shaken=orbital
By: Jordan on 10/23/2013
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: 767 B3,B4

Specific Phenotypes

For 33 genes in this experiment

For stress Cholin acetate in Dinoroseobacter shibae DFL-12

For stress Cholin acetate across organisms

SEED Subsystems

Subsystem	#Specific
Chlorophyll Biosynthesis	7
Carotenoids	2
Photosystem II-type photosynthetic reaction center	2
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Methionine Degradation	1
Photorespiration (oxidative C2 cycle)	1
Proline, 4-hydroxyproline uptake and utilization	1
Propionate-CoA to Succinate Module	1
Propionyl-CoA to Succinyl-CoA Module	1
Proteolysis in bacteria, ATP-dependent	1
Serine-glyoxylate cycle	1
TCA Cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones
• Porphyrin and chlorophyll metabolism
• Biosynthesis of phenylpropanoids
• Citrate cycle (TCA cycle)
• Carotenoid biosynthesis - General
• 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
• Glycolysis / Gluconeogenesis
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• Puromycin biosynthesis
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Valine, leucine and isoleucine biosynthesis
• Arginine and proline metabolism
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Benzoate degradation via hydroxylation
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Ether lipid metabolism
• alpha-Linolenic acid metabolism
• Tetrachloroethene degradation
• Naphthalene and anthracene degradation
• Trinitrotoluene degradation
• Propanoate metabolism
• Butanoate metabolism
• C5-Branched dibasic acid metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Nicotinate and nicotinamide metabolism
• Nitrogen metabolism
• Alkaloid biosynthesis I
• Insect hormone biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
nitrogen fixation I (ferredoxin)	1	1	1
pyruvate decarboxylation to acetyl CoA I	3	3	2
neurosporene biosynthesis	5	2	2
glyoxylate cycle	6	6	2
pyruvate fermentation to acetate II	3	3	1
propanoyl CoA degradation I	3	3	1
3,8-divinyl-chlorophyllide a biosynthesis III (aerobic, light independent)	9	8	3
3,8-divinyl-chlorophyllide a biosynthesis II (anaerobic)	9	8	3
pyruvate fermentation to acetate V	3	2	1
trans-lycopene biosynthesis I	6	2	2
methylaspartate cycle	19	14	6
ethylmalonyl-CoA pathway	11	8	3
partial TCA cycle (obligate autotrophs)	8	6	2
nitrogen remobilization from senescing leaves	8	6	2
creatinine degradation I	4	3	1
2-oxobutanoate degradation I	4	3	1
pyruvate fermentation to acetate and (S)-lactate I	4	3	1
trans-lycopene biosynthesis II (oxygenic phototrophs and green sulfur bacteria)	8	3	2
β-carotene biosynthesis (engineered)	8	2	2
superpathway of bacteriochlorophyll a biosynthesis	26	20	6
bacteriochlorophyll a biosynthesis	13	8	3
TCA cycle IV (2-oxoglutarate decarboxylase)	9	8	2
TCA cycle V (2-oxoglutarate synthase)	9	8	2
3,8-divinyl-chlorophyllide a biosynthesis I (aerobic, light-dependent)	9	8	2
TCA cycle II (plants and fungi)	9	8	2
superpathway of the 3-hydroxypropanoate cycle	18	12	4
TCA cycle VII (acetate-producers)	9	6	2
TCA cycle VI (Helicobacter)	9	6	2
spirilloxanthin and 2,2'-diketo-spirilloxanthin biosynthesis	9	2	2
TCA cycle III (animals)	10	9	2
TCA cycle I (prokaryotic)	10	9	2
anaerobic energy metabolism (invertebrates, mitochondrial)	10	6	2
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	19	4
reductive TCA cycle I	11	7	2
superpathway of glyoxylate bypass and TCA	12	11	2
reductive TCA cycle II	12	6	2
spheroidene and spheroidenone biosynthesis	6	1	1
3-hydroxypropanoate cycle	13	9	2
glyoxylate assimilation	13	8	2
superpathway of glyoxylate cycle and fatty acid degradation	14	12	2
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	7	2
lycopadiene biosynthesis	7	1	1
mixed acid fermentation	16	10	2
superpathway of anaerobic energy metabolism (invertebrates)	17	10	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	3
superpathway of carotenoid biosynthesis in plants	22	3	2
ethene biosynthesis V (engineered)	25	17	2
formaldehyde assimilation I (serine pathway)	13	9	1
superpathway of L-methionine salvage and degradation	16	10	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	11	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	18	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
mycolate biosynthesis	205	21	1
superpathway of mycolate biosynthesis	239	22	1