Experiment set2IT018 for Desulfovibrio vulgaris Miyazaki F

MoYLS4 with Polymyxin B sulfate 0.1 mg/ml

Group: stress
Media: MoYLS4 + Polymyxin B sulfate (0.1 mg/ml), pH=7.2
Culturing: Miya_ML3, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Jen on 11/23/2014
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 26 genes in this experiment

For stress Polymyxin B sulfate in Desulfovibrio vulgaris Miyazaki F

For stress Polymyxin B sulfate across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter oligopeptide (TC 3.A.1.5.1)	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
ATP-dependent RNA helicases, bacterial	1
Bacterial Chemotaxis	1
DNA-replication	1
De Novo Pyrimidine Synthesis	1
Fructose and Mannose Inducible PTS	1
Fructose utilization	1
LMPTP YwlE cluster	1
Mannitol Utilization	1
Queuosine-Archaeosine Biosynthesis	1
Sex pheromones in Enterococcus faecalis and other Firmicutes	1
Transcription factors bacterial	1
Transport of Nickel and Cobalt	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Pentose and glucuronate interconversions
• Galactose metabolism
• Pyrimidine metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• Folate biosynthesis
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

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
pyrimidine nucleobases salvage II	2	1	1
superpathway of pyrimidine nucleobases salvage	4	4	1
queuosine biosynthesis I (de novo)	4	3	1
sucrose degradation II (sucrose synthase)	5	3	1
queuosine biosynthesis III (queuosine salvage)	5	2	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	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