Experiment set2IT069 for Herbaspirillum seropedicae SmR1

LB with Thallium(I) acetate 0.001 mg/ml

Group: stress
Media: LB + Thallium(I) acetate (0.001 mg/ml)
Culturing: HerbieS_ML4, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 3.7 generations
By: Mark on 3/10/2016
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: Herbie_SP2 C4

Specific Phenotypes

For 7 genes in this experiment

For stress Thallium(I) acetate in Herbaspirillum seropedicae SmR1

For stress Thallium(I) acetate across organisms

SEED Subsystems

Subsystem	#Specific
DNA repair, UvrABC system	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Heat shock dnaK gene cluster extended	1
Heme and Siroheme Biosynthesis	1
Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway	1
Lactose and Galactose Uptake and Utilization	1
N-linked Glycosylation in Bacteria	1
Phosphate metabolism	1
Queuosine-Archaeosine Biosynthesis	1
Rhamnose containing glycans	1
linker unit-arabinogalactan synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Porphyrin and chlorophyll metabolism
• Galactose metabolism
• Ubiquinone and menaquinone biosynthesis
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Nucleotide sugars metabolism
• Glycerolipid metabolism
• Glycerophospholipid metabolism
• Naphthalene and anthracene degradation
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
UDP-α-D-galactose biosynthesis	1	1	1
UDP-N-acetyl-D-galactosamine biosynthesis I	1	1	1
phospholipid remodeling (phosphatidate, yeast)	2	1	1
palmitoleate biosynthesis III (cyanobacteria)	2	1	1
UDP-N-acetyl-α-D-quinovosamine biosynthesis	2	1	1
UDP-α-D-galactofuranose biosynthesis	2	1	1
oleate biosynthesis III (cyanobacteria)	3	2	1
D-galactose detoxification	3	1	1
CDP-diacylglycerol biosynthesis II	4	4	1
CDP-diacylglycerol biosynthesis I	4	4	1
CDP-diacylglycerol biosynthesis III	5	3	1
D-galactose degradation I (Leloir pathway)	5	3	1
phosphatidate biosynthesis (yeast)	5	3	1
phosphatidylglycerol biosynthesis II	6	6	1
phosphatidylglycerol biosynthesis I	6	6	1
superpathway of phospholipid biosynthesis III (E. coli)	12	10	2
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
superpathway of stearidonate biosynthesis (cyanobacteria)	6	2	1
palmitoyl ethanolamide biosynthesis	6	2	1
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	1
stachyose degradation	7	2	1
stigma estolide biosynthesis	7	2	1
diacylglycerol and triacylglycerol biosynthesis	7	2	1
anandamide biosynthesis II	8	2	1
UDP-sugars interconversion	9	2	1
teichuronic acid biosynthesis (B. subtilis 168)	9	2	1
colanic acid building blocks biosynthesis	11	9	1
anandamide biosynthesis I	12	3	1
superpathway of cardiolipin biosynthesis (bacteria)	13	9	1
superpathway of phospholipid biosynthesis II (plants)	28	10	2
plasmalogen biosynthesis I (aerobic)	16	2	1
mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	18	1	1
superpathway of UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis	24	12	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	1