Experiment setBH30 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 E3,E4

Specific Phenotypes

For 31 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	5
Carotenoids	3
Photosystem II-type photosynthetic reaction center	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
High affinity phosphate transporter and control of PHO regulon	1
Phosphate metabolism	1
Photorespiration (oxidative C2 cycle)	1
Proline, 4-hydroxyproline uptake and utilization	1
Propionyl-CoA to Succinyl-CoA Module	1
Proteolysis in bacteria, ATP-dependent	1
Purine conversions	1
Ribonucleotide reduction	1
Serine-glyoxylate cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Biosynthesis of plant hormones
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Benzoate degradation via hydroxylation
• Pyruvate metabolism
• Biosynthesis of terpenoids and steroids
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Oxidative phosphorylation
• Puromycin biosynthesis
• Pyrimidine metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• Glutathione metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Ether lipid metabolism
• alpha-Linolenic acid metabolism
• Biphenyl degradation
• 1- and 2-Methylnaphthalene degradation
• Tetrachloroethene degradation
• Naphthalene and anthracene degradation
• Fluorene degradation
• Glyoxylate and dicarboxylate metabolism
• Trinitrotoluene degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• C5-Branched dibasic acid metabolism
• Nicotinate and nicotinamide metabolism
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
nitrogen fixation I (ferredoxin)	1	1	1
adenosine deoxyribonucleotides de novo biosynthesis I	2	2	1
polyphosphate metabolism	2	2	1
guanosine deoxyribonucleotides de novo biosynthesis I	2	2	1
guanosine deoxyribonucleotides de novo biosynthesis II	4	3	2
adenosine deoxyribonucleotides de novo biosynthesis II	4	3	2
allantoin degradation to ureidoglycolate I (urea producing)	2	1	1
neurosporene biosynthesis	5	2	2
propanoyl CoA degradation I	3	3	1
urate conversion to allantoin III	3	3	1
urate conversion to allantoin II	3	2	1
urate conversion to allantoin I	3	2	1
trans-lycopene biosynthesis I	6	2	2
allantoin degradation to glyoxylate I	3	1	1
superpathway of adenosine nucleotides de novo biosynthesis II	7	6	2
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)	14	11	4
ethylmalonyl-CoA pathway	11	8	3
superpathway of guanosine nucleotides de novo biosynthesis II	8	7	2
creatinine degradation I	4	3	1
2-oxobutanoate degradation I	4	3	1
trans-lycopene biosynthesis II (oxygenic phototrophs and green sulfur bacteria)	8	3	2
β-carotene biosynthesis (engineered)	8	2	2
allantoin degradation to ureidoglycolate II (ammonia producing)	4	1	1
bacteriochlorophyll a biosynthesis	13	8	3
pyrimidine deoxyribonucleotides de novo biosynthesis III	9	9	2
3,8-divinyl-chlorophyllide a biosynthesis II (anaerobic)	9	8	2
3,8-divinyl-chlorophyllide a biosynthesis III (aerobic, light independent)	9	8	2
pyrimidine deoxyribonucleotides de novo biosynthesis I	9	8	2
superpathway of the 3-hydroxypropanoate cycle	18	12	4
spirilloxanthin and 2,2'-diketo-spirilloxanthin biosynthesis	9	2	2
methylaspartate cycle	19	14	4
superpathway of adenosine nucleotides de novo biosynthesis I	5	5	1
allantoin degradation to glyoxylate II	5	2	1
allantoin degradation to glyoxylate III	5	1	1
superpathway of bacteriochlorophyll a biosynthesis	26	20	5
superpathway of guanosine nucleotides de novo biosynthesis I	6	6	1
superpathway of allantoin degradation in yeast	6	3	1
spheroidene and spheroidenone biosynthesis	6	1	1
superpathway of purine nucleotides de novo biosynthesis II	26	23	4
3-hydroxypropanoate cycle	13	9	2
glyoxylate assimilation	13	8	2
ureide biosynthesis	7	6	1
pyrimidine deoxyribonucleotides de novo biosynthesis IV	7	5	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	7	2
lycopadiene biosynthesis	7	1	1
pyrimidine deoxyribonucleotides biosynthesis from CTP	8	5	1
superpathway of allantoin degradation in plants	8	3	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	18	16	2
3,8-divinyl-chlorophyllide a biosynthesis I (aerobic, light-dependent)	9	8	1
superpathway of purines degradation in plants	18	13	2
allantoin degradation IV (anaerobic)	9	5	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	6	1
superpathway of purine nucleotides de novo biosynthesis I	21	21	2
superpathway of carotenoid biosynthesis in plants	22	3	2
superpathway of histidine, purine, and pyrimidine biosynthesis	46	42	4
formaldehyde assimilation I (serine pathway)	13	9	1
superpathway of purine nucleotide salvage	14	13	1
superpathway of L-methionine salvage and degradation	16	10	1
superpathway of anaerobic energy metabolism (invertebrates)	17	10	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	11	1
mycolate biosynthesis	205	21	1
superpathway of mycolate biosynthesis	239	22	1