Experiment set1IT042 for Pedobacter sp. GW460-11-11-14-LB5

R2A with sodium fluoride 25 mM

Group: stress
Media: R2A + sodium fluoride (25 mM)
Culturing: Pedo557_ML3, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
Growth: about 4.6 generations
By: Adam on 17-May-17
Media components: 0.5 g/L Bacto Peptone, 0.5 g/L casamino acids, 0.5 g/L Yeast Extract, 0.5 g/L D-Glucose, 0.5 g/L Starch, 0.3 g/L Potassium phosphate dibasic, 0.05 g/L Magnesium Sulfate Heptahydrate, 0.3 g/L Sodium pyruvate
Growth plate: 1754 B5

Specific Phenotypes

For 4 genes in this experiment

For stress sodium fluoride in Pedobacter sp. GW460-11-11-14-LB5

For stress sodium fluoride across organisms

SEED Subsystems

Subsystem	#Specific
Aromatic amino acid degradation	1
Heat shock dnaK gene cluster extended	1
NAD and NADP cofactor biosynthesis global	1
Phosphate metabolism	1
YcfH	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Tryptophan metabolism
• Ubiquinone and menaquinone biosynthesis
• Oxidative phosphorylation
• Histidine metabolism
• Tyrosine metabolism
• Benzoxazinone biosynthesis
• Naphthalene and anthracene degradation
• Porphyrin and chlorophyll metabolism
• 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
L-tryptophan degradation I (via anthranilate)	3	2	1
3-hydroxy-4-methyl-anthranilate biosynthesis II	5	2	1
L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde	5	2	1
3-hydroxy-4-methyl-anthranilate biosynthesis I	6	1	1
glyphosate degradation III	7	1	1
(aminomethyl)phosphonate degradation	8	1	1
NAD de novo biosynthesis II (from tryptophan)	9	6	1
L-tryptophan degradation IX	12	2	1
L-tryptophan degradation XII (Geobacillus)	12	2	1
superpathway of NAD biosynthesis in eukaryotes	14	7	1
L-tryptophan degradation III (eukaryotic)	15	5	1
L-tryptophan degradation XI (mammalian, via kynurenine)	23	6	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	4	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	6	1