Experiment setAIT052 for Pseudomonas fluorescens FW300-N2E2

LB with Cadmium chloride hemipentahydrate 0.000015625 M

Group: stress
Media: LB + Cadmium chloride hemipentahydrate (1.5625e-05 M)
Culturing: pseudo6_N2E2_ML5, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=500 rpm
By: Hans_Hualan on 2/5/2016
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride

Specific Phenotypes

For 9 genes in this experiment

For stress Cadmium chloride hemipentahydrate in Pseudomonas fluorescens FW300-N2E2

For stress Cadmium chloride hemipentahydrate across organisms

SEED Subsystems

Subsystem	#Specific
Cysteine Biosynthesis	3
Glycine and Serine Utilization	3
Methionine Biosynthesis	3
Pyruvate Alanine Serine Interconversions	2
Carboxysome	1
Conserved gene cluster possibly involved in RNA metabolism	1
Cyanate hydrolysis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycine cleavage system	1
Photorespiration (oxidative C2 cycle)	1
Threonine anaerobic catabolism gene cluster	1
Threonine and Homoserine Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Cysteine metabolism
• Glycine, serine and threonine metabolism
• Sulfur metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Selenoamino acid metabolism
• Carbon fixation in photosynthetic organisms
• Nitrogen metabolism
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
L-cysteine biosynthesis I	2	2	2
L-aspartate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
D-serine degradation	3	3	2
L-cysteine degradation II	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
L-glutamate degradation II	2	2	1
atromentin biosynthesis	2	1	1
L-tyrosine degradation II	2	1	1
malate/L-aspartate shuttle pathway	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
glycine betaine degradation III	7	7	3
seleno-amino acid biosynthesis (plants)	5	3	2
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
glycine betaine degradation I	8	6	3
L-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
cyanate degradation	3	3	1
glycine biosynthesis II	3	3	1
glycine cleavage	3	3	1
glycine degradation	3	3	1
L-methionine biosynthesis II	6	5	2
L-phenylalanine degradation II (anaerobic)	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
(R)-cysteate degradation	3	1	1
sulfolactate degradation III	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	3
L-cysteine biosynthesis VII (from S-sulfo-L-cysteine)	4	3	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
L-mimosine degradation	8	4	2
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
glutathione-mediated detoxification I	8	3	2
L-tryptophan degradation VIII (to tryptophol)	4	1	1
N-3-oxalyl-L-2,3-diaminopropanoate biosynthesis	4	1	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	2
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	3
L-tyrosine degradation I	5	5	1
trans-4-hydroxy-L-proline degradation I	5	3	1
superpathway of plastoquinol biosynthesis	5	2	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
superpathway of L-threonine biosynthesis	6	6	1
TCA cycle VIII (Chlamydia)	6	4	1
superpathway of sulfolactate degradation	6	2	1
D-cycloserine biosynthesis	6	1	1
coenzyme M biosynthesis II	6	1	1
hydrogen sulfide biosynthesis II (mammalian)	6	1	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
L-cysteine biosynthesis VI (reverse transsulfuration)	7	3	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
purine nucleobases degradation II (anaerobic)	24	16	3
superpathway of aromatic amino acid biosynthesis	18	18	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
superpathway of seleno-compound metabolism	19	6	2
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
rosmarinic acid biosynthesis I	10	3	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
indole-3-acetate biosynthesis II	12	5	1
superpathway of L-isoleucine biosynthesis I	13	13	1
3-hydroxypropanoate cycle	13	6	1
glyoxylate assimilation	13	6	1
superpathway of rosmarinic acid biosynthesis	14	4	1
superpathway of anaerobic energy metabolism (invertebrates)	17	8	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	9	1
superpathway of the 3-hydroxypropanoate cycle	18	7	1
aspartate superpathway	25	22	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	2
superpathway of chorismate metabolism	59	43	2