Experiment set5IT089 for Dinoroseobacter shibae DFL-12

marine broth with Sodium nitrite 0.6 mM

Group: stress
Media: marine_broth_2216 + Sodium nitrite (0.6 mM)
Culturing: Dino_ML3, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Adam on 5/14/2014
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: 918 B5,B6

Specific Phenotypes

For 36 genes in this experiment

For stress Sodium nitrite in Dinoroseobacter shibae DFL-12

For stress Sodium nitrite across organisms

SEED Subsystems

Subsystem	#Specific
Chlorophyll Biosynthesis	5
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	2
Bacterial Cell Division	2
Biogenesis of c-type cytochromes	1
Carotenoids	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Cysteine Biosynthesis	1
DNA repair, bacterial	1
Heat shock dnaK gene cluster extended	1
High affinity phosphate transporter and control of PHO regulon	1
Methionine Biosynthesis	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Oxygen and light sensor PpaA-PpsR	1
Periplasmic disulfide interchange	1
Phosphate metabolism	1
Propionyl-CoA to Succinyl-CoA Module	1
Purine conversions	1
Ribonucleotide reduction	1
Sulfur oxidation	1
Transport of Zinc	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Porphyrin and chlorophyll metabolism
• Pyrimidine metabolism
• Glycine, serine and threonine metabolism
• Glutathione metabolism
• Oxidative phosphorylation
• Purine metabolism
• Cysteine metabolism
• Valine, leucine and isoleucine degradation
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Benzoate degradation via hydroxylation
• Benzoxazinone biosynthesis
• Selenoamino acid metabolism
• Tetrachloroethene degradation
• Naphthalene and anthracene degradation
• Propanoate metabolism
• Nicotinate and nicotinamide metabolism
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Sulfur metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
nitrogen fixation I (ferredoxin)	1	1	1
sulfide oxidation II (flavocytochrome c)	1	1	1
polyphosphate metabolism	2	2	1
L-cysteine biosynthesis I	2	2	1
guanosine deoxyribonucleotides de novo biosynthesis I	2	2	1
adenosine deoxyribonucleotides de novo biosynthesis I	2	2	1
adenosine deoxyribonucleotides de novo biosynthesis II	4	3	2
guanosine deoxyribonucleotides de novo biosynthesis II	4	3	2
glycine betaine biosynthesis II (Gram-positive bacteria)	2	1	1
glycine betaine biosynthesis I (Gram-negative bacteria)	2	1	1
choline degradation I	2	1	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)	14	11	5
pyrimidine deoxyribonucleotides de novo biosynthesis III	9	9	3
propanoyl CoA degradation I	3	3	1
3,8-divinyl-chlorophyllide a biosynthesis II (anaerobic)	9	8	3
pyrimidine deoxyribonucleotides de novo biosynthesis I	9	8	3
3,8-divinyl-chlorophyllide a biosynthesis III (aerobic, light independent)	9	8	3
choline-O-sulfate degradation	3	1	1
pyrimidine deoxyribonucleotides dephosphorylation	3	1	1
superpathway of adenosine nucleotides de novo biosynthesis II	7	6	2
superpathway of guanosine nucleotides de novo biosynthesis II	8	7	2
2-oxobutanoate degradation I	4	3	1
3,8-divinyl-chlorophyllide a biosynthesis I (aerobic, light-dependent)	9	8	2
tRNA processing	10	10	2
superpathway of adenosine nucleotides de novo biosynthesis I	5	5	1
seleno-amino acid biosynthesis (plants)	5	3	1
superpathway of guanosine nucleotides de novo biosynthesis I	6	6	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	18	16	3
superpathway of purine nucleotides de novo biosynthesis II	26	23	4
pyrimidine deoxyribonucleotides de novo biosynthesis IV	7	5	1
pyrimidine deoxyribonucleotides de novo biosynthesis II	7	4	1
pyrimidine deoxyribonucleotides biosynthesis from CTP	8	5	1
superpathway of bacteriochlorophyll a biosynthesis	26	20	3
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	6	1
superpathway of purine nucleotides de novo biosynthesis I	21	21	2
superpathway of histidine, purine, and pyrimidine biosynthesis	46	42	4
3-hydroxypropanoate cycle	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
superpathway of the 3-hydroxypropanoate cycle	18	12	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	11	1
methylaspartate cycle	19	14	1
superpathway of seleno-compound metabolism	19	6	1
mycolate biosynthesis	205	21	1
superpathway of mycolate biosynthesis	239	22	1