Experiment set1H36 for Desulfovibrio vulgaris Miyazaki F

MoYLS4 with Nalidixic acid sodium salt 0.0078125 mg/ml

Group: stress
Media: MoYLS4 + Nalidixic acid sodium salt (0.0078125 mg/ml), pH=7.2
Culturing: Miya_ML3, hungate, Anaerobic, at 30 (C), shaken=0 rpm
Growth: about 4.4 generations
By: Jen on 3/20/2014
Media components: 1 g/L Yeast Extract, 30 mM Sodium sulfate, 60 mM Sodium D,L-Lactate, 20 mM Ammonium chloride, 30 mM Tris hydrochloride, 0.12 mM EDTA, 1 mM Sodium sulfide nonahydrate, 8 mM Magnesium chloride hexahydrate, 0.6 mM Calcium chloride, 2 mM Potassium phosphate dibasic, 60 uM Iron (II) chloride tetrahydrate, 15 uM Manganese (II) chloride tetrahydrate, 7.8 uM Cobalt chloride hexahydrate, 9 uM Zinc chloride, 1.26 uM Sodium molybdate, 1.92 uM Boric Acid, 2.28 uM Nickel (II) sulfate hexahydrate, 0.06 uM copper (II) chloride dihydrate, 0.21 uM Sodium selenite pentahydrate, 0.144 uM Sodium tungstate dihydrate, Thauer's vitamin mix (0.01 mg/L Pyridoxine HCl, 0.005 mg/L 4-Aminobenzoic acid, 0.005 mg/L Lipoic acid, 0.005 mg/L Nicotinic Acid, 0.005 mg/L Riboflavin, 0.005 mg/L Thiamine HCl, 0.005 mg/L calcium pantothenate, 0.002 mg/L biotin, 0.002 mg/L Folic Acid, 0.0001 mg/L Cyanocobalamin, 0.2 mg/L Choline chloride)

Specific Phenotypes

For 25 genes in this experiment

For stress Nalidixic acid sodium salt in Desulfovibrio vulgaris Miyazaki F

For stress Nalidixic acid sodium salt across organisms

SEED Subsystems

Subsystem	#Specific
DNA repair, bacterial	3
DNA-replication	1
Folate Biosynthesis	1
Fructose utilization	1
Pentose phosphate pathway	1
Phage capsid proteins	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose phosphate pathway
• Pentose and glucuronate interconversions
• Galactose metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
UDP-α-D-glucose biosynthesis	2	2	1
pentose phosphate pathway (non-oxidative branch) I	5	5	1
sucrose degradation II (sucrose synthase)	5	3	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
stachyose degradation	7	2	1
pentose phosphate pathway	8	6	1
sucrose biosynthesis II	8	6	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	6	1
Rubisco shunt	10	8	1
colanic acid building blocks biosynthesis	11	10	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	1
Bifidobacterium shunt	15	13	1
superpathway of glucose and xylose degradation	17	12	1
type I lipoteichoic acid biosynthesis (S. aureus)	17	5	1
superpathway of anaerobic sucrose degradation	19	15	1