Experiment set1H41 for Dinoroseobacter shibae DFL-12

marine broth with Chloramphenicol 0.0002 mg/ml

Group: stress
Media: marine_broth_2216 + Chloramphenicol (2e-04 mg/ml)
Culturing: Dino_ML3, 48 well microplate; Tecan Infinite F200, Aerobic, at 30 (C), shaken=orbital
By: Jordan on 8/22/2013
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: 658 A7,A8

Specific Phenotypes

For 7 genes in this experiment

For stress Chloramphenicol in Dinoroseobacter shibae DFL-12

For stress Chloramphenicol across organisms

SEED Subsystems

Subsystem	#Specific
Isoleucine degradation	1
Leucine Degradation and HMG-CoA Metabolism	1
NAD and NADP cofactor biosynthesis global	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	1
Universal GTPases	1
Valine degradation	1
Xylose utilization	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Pentose and glucuronate interconversions
• Puromycin biosynthesis
• Valine, leucine and isoleucine degradation
• Tryptophan metabolism
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• Trinitrotoluene degradation
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• 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
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
xylitol degradation I	2	2	1
D-xylose degradation I	2	2	1
D-arabinitol degradation I	2	1	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	1
pyruvate decarboxylation to acetyl CoA I	3	3	1
L-tryptophan degradation I (via anthranilate)	3	1	1
L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde	5	1	1
3-hydroxy-4-methyl-anthranilate biosynthesis II	5	1	1
NAD de novo biosynthesis II (from tryptophan)	9	4	1
L-tryptophan degradation XI (mammalian, via kynurenine)	23	5	2
L-tryptophan degradation IX	12	2	1
L-tryptophan degradation XII (Geobacillus)	12	2	1
superpathway of NAD biosynthesis in eukaryotes	14	6	1
L-tryptophan degradation III (eukaryotic)	15	4	1
superpathway of glucose and xylose degradation	17	14	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	19	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	13	1
superpathway of pentose and pentitol degradation	42	15	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	10	1