Experiment set1H19 for Desulfovibrio vulgaris Miyazaki F

MoYLS4 with Carbenicillin disodium salt 0.0625 mg/ml

Group: stress
Media: MoYLS4 + Carbenicillin disodium salt (0.0625 mg/ml), pH=7.2
Culturing: Miya_ML3, hungate, Anaerobic, at 30 (C), shaken=0 rpm
Growth: about 3.7 generations
By: Jen on 3/14/2014
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 21 genes in this experiment

For stress Carbenicillin disodium salt in Desulfovibrio vulgaris Miyazaki F

For stress Carbenicillin disodium salt across organisms

SEED Subsystems

Subsystem	#Specific
Bacterial Cell Division	3
Bacterial Cytoskeleton	1
Beta-lactamase	1
Capsular Polysaccharide (CPS) of Campylobacter	1
De Novo Pyrimidine Synthesis	1
Energy-conserving hydrogenase (ferredoxin)	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
LMPTP YwlE cluster	1
NiFe hydrogenase maturation	1
Oxidative stress	1
Peptidoglycan Biosynthesis	1
Transport of Zinc	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Nucleotide sugars metabolism
• Pentose and glucuronate interconversions
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Oxidative phosphorylation
• Pyrimidine metabolism
• Alanine and aspartate metabolism
• Penicillin and cephalosporin biosynthesis
• beta-Lactam resistance
• Starch and sucrose metabolism
• Glycosaminoglycan degradation
• Nitrogen metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pyrimidine nucleobases salvage I	1	1	1
UDP-α-D-glucose biosynthesis	2	2	1
L-glutamate degradation II	2	2	1
pyrimidine nucleobases salvage II	2	1	1
L-aspartate degradation II (aerobic)	3	2	1
L-aspartate degradation III (anaerobic)	3	2	1
superpathway of pyrimidine nucleobases salvage	4	4	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	2	1
sucrose degradation II (sucrose synthase)	5	3	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
L-canavanine degradation II	6	1	1
stachyose degradation	7	2	1
sucrose biosynthesis II	8	6	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
superpathway of pyrimidine ribonucleosides salvage	10	6	1
colanic acid building blocks biosynthesis	11	10	1
type I lipoteichoic acid biosynthesis (S. aureus)	17	5	1
superpathway of anaerobic sucrose degradation	19	15	1