Experiment set4IT007 for Dinoroseobacter shibae DFL-12

marine broth with Paraquat dichloride 0.015 mg/ml

Group: stress
Media: marine_broth_2216 + Paraquat dichloride (0.015 mg/ml)
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 B7,B8

Specific Phenotypes

For 20 genes in this experiment

For stress Paraquat dichloride in Dinoroseobacter shibae DFL-12

For stress Paraquat dichloride across organisms

SEED Subsystems

Subsystem	#Specific
Glycerol and Glycerol-3-phosphate Uptake and Utilization	5
Polyamine Metabolism	3
ABC transporter alkylphosphonate (TC 3.A.1.9.1)	2
Branched-Chain Amino Acid Biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Proline, 4-hydroxyproline uptake and utilization	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Valine, leucine and isoleucine biosynthesis
• Arginine and proline metabolism
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Glycerophospholipid metabolism
• Pyruvate metabolism
• Nitrogen metabolism
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamine biosynthesis I	1	1	1
ammonia assimilation cycle I	2	2	1
ammonia assimilation cycle II	2	2	1
glycerophosphodiester degradation	2	2	1
phosphatidylcholine resynthesis via glycerophosphocholine	2	1	1
ammonia assimilation cycle III	3	3	1
superpathway of ammonia assimilation (plants)	3	3	1
L-aspartate degradation III (anaerobic)	3	1	1
L-aspartate degradation II (aerobic)	3	1	1
creatinine degradation I	4	3	1
glycerol and glycerophosphodiester degradation	4	3	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
L-leucine biosynthesis	6	6	1
3-methylbutanol biosynthesis (engineered)	7	6	1
L-glutamate and L-glutamine biosynthesis	7	6	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
anandamide biosynthesis I	12	3	1
superpathway of branched chain amino acid biosynthesis	17	17	1