Experiment set13IT082 for Pseudomonas fluorescens FW300-N2E2

LB with Cobalt chloride hexahydrate 0.6 mM

Group: stress
Media: LB + Cobalt chloride hexahydrate (0.6 mM)
Culturing: pseudo6_N2E2_ML5b, 48 well microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 25-Jul-16
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: Plate1 B7,B8

Specific Phenotypes

For 19 genes in this experiment

For stress Cobalt chloride hexahydrate in Pseudomonas fluorescens FW300-N2E2

For stress Cobalt chloride hexahydrate across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	2
Alanine biosynthesis	1
Carboxysome	1
Copper homeostasis: copper tolerance	1
Cysteine Biosynthesis	1
Fatty Acid Biosynthesis FASII	1
Folate Biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycine and Serine Utilization	1
Methionine Biosynthesis	1
Phosphate metabolism	1
Pyruvate Alanine Serine Interconversions	1
Respiratory dehydrogenases 1	1
Threonine anaerobic catabolism gene cluster	1
Threonine and Homoserine Biosynthesis	1
mycolic acid synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Cysteine metabolism
• Fatty acid biosynthesis
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Glycerophospholipid metabolism
• Sulfur metabolism
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of phenylpropanoids
• Oxidative phosphorylation
• Glutamate metabolism
• Alanine and aspartate metabolism
• Lysine degradation
• Histidine metabolism
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Selenoamino acid metabolism
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Butanoate metabolism
• One carbon pool by folate
• Methane metabolism
• Carbon fixation in photosynthetic organisms
• Thiamine metabolism
• Folate biosynthesis
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-cysteine degradation IV	1	1	1
L-alanine biosynthesis III	1	1	1
L-aspartate degradation I	1	1	1
L-aspartate biosynthesis	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-ornithine degradation I (L-proline biosynthesis)	1	1	1
L-serine degradation	3	3	2
L-cysteine degradation II	3	3	2
D-serine degradation	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
NADH to cytochrome bo oxidase electron transfer II	2	2	1
L-cysteine biosynthesis I	2	2	1
L-glutamate degradation II	2	2	1
NADH to cytochrome bo oxidase electron transfer I	2	2	1
L-tyrosine degradation II	2	1	1
NADH to nitrate electron transfer	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
malate/L-aspartate shuttle pathway	2	1	1
L-proline biosynthesis II (from arginine)	2	1	1
atromentin biosynthesis	2	1	1
cytidylyl molybdenum cofactor sulfurylation	2	1	1
NADH to cytochrome bd oxidase electron transfer II	2	1	1
NADH to cytochrome aa3 oxidase electron transfer	2	1	1
nitrate reduction VIIIb (dissimilatory)	2	1	1
L-arginine degradation VII (arginase 3 pathway)	2	1	1
NADH to cytochrome bd oxidase electron transfer I	2	1	1
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
aerobic respiration III (alternative oxidase pathway)	3	3	1
assimilatory sulfate reduction III	3	3	1
L-phenylalanine biosynthesis I	3	3	1
tetrahydrofolate biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
dTMP de novo biosynthesis (mitochondrial)	3	3	1
L-methionine biosynthesis II	6	5	2
L-phenylalanine degradation II (anaerobic)	3	2	1
oleate biosynthesis III (cyanobacteria)	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
bis(guanylyl molybdopterin) cofactor sulfurylation	3	1	1
sulfolactate degradation III	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
(R)-cysteate degradation	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
glycine betaine degradation III	7	7	2
thiazole component of thiamine diphosphate biosynthesis II	7	4	2
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	12	12	3
assimilatory sulfate reduction I	4	4	1
superpathway of L-alanine biosynthesis	4	4	1
CDP-diacylglycerol biosynthesis II	4	4	1
CDP-diacylglycerol biosynthesis I	4	4	1
gondoate biosynthesis (anaerobic)	4	4	1
glycine betaine degradation I	8	6	2
tetrahydromonapterin biosynthesis	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	3	1
aerobic respiration I (cytochrome c)	4	3	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
L-mimosine degradation	8	4	2
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
glutathione-mediated detoxification I	8	3	2
L-tryptophan degradation VIII (to tryptophol)	4	1	1
tRNA-uridine 2-thiolation (yeast mitochondria)	4	1	1
tRNA-uridine 2-thiolation (mammalian mitochondria)	4	1	1
palmitate biosynthesis III	29	28	7
tetradecanoate biosynthesis (mitochondria)	25	23	6
palmitate biosynthesis II (type II fatty acid synthase)	31	29	7
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	2
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	8	2
oleate biosynthesis IV (anaerobic)	14	13	3
superpathway of fatty acids biosynthesis (E. coli)	53	49	11
L-tyrosine degradation I	5	5	1
fatty acid elongation -- saturated	5	5	1
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	18	4
mitochondrial NADPH production (yeast)	5	4	1
8-amino-7-oxononanoate biosynthesis IV	5	4	1
cis-vaccenate biosynthesis	5	4	1
seleno-amino acid biosynthesis (plants)	5	3	1
phosphatidate biosynthesis (yeast)	5	3	1
trans-4-hydroxy-L-proline degradation I	5	3	1
[2Fe-2S] iron-sulfur cluster biosynthesis	10	4	2
superpathway of plastoquinol biosynthesis	5	2	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
tRNA-uridine 2-thiolation (thermophilic bacteria)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
superpathway of fatty acid biosynthesis II (plant)	43	38	8
8-amino-7-oxononanoate biosynthesis I	11	9	2
superpathway of thiamine diphosphate biosynthesis II	11	8	2
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	2
anteiso-branched-chain fatty acid biosynthesis	34	30	6
odd iso-branched-chain fatty acid biosynthesis	34	30	6
even iso-branched-chain fatty acid biosynthesis	34	30	6
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	2
superpathway of L-threonine biosynthesis	6	6	1
(5Z)-dodecenoate biosynthesis I	6	6	1
phosphatidylglycerol biosynthesis I	6	6	1
phosphatidylglycerol biosynthesis II	6	6	1
superpathway of phospholipid biosynthesis III (E. coli)	12	11	2
stearate biosynthesis II (bacteria and plants)	6	5	1
(5Z)-dodecenoate biosynthesis II	6	5	1
molybdopterin biosynthesis	6	4	1
stearate biosynthesis IV	6	4	1
TCA cycle VIII (Chlamydia)	6	4	1
thiazole component of thiamine diphosphate biosynthesis I	6	3	1
Fe(II) oxidation	6	3	1
NAD(P)/NADPH interconversion	6	3	1
petroselinate biosynthesis	6	2	1
superpathway of sulfolactate degradation	6	2	1
superpathway of stearidonate biosynthesis (cyanobacteria)	6	2	1
palmitoyl ethanolamide biosynthesis	6	2	1
coenzyme M biosynthesis II	6	1	1
streptorubin B biosynthesis	34	20	5
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
diacylglycerol and triacylglycerol biosynthesis	7	3	1
stigma estolide biosynthesis	7	2	1
staphyloferrin B biosynthesis	7	1	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
biotin biosynthesis I	15	13	2
superpathway of fatty acid biosynthesis I (E. coli)	16	15	2
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
anandamide biosynthesis II	8	2	1
2-allylmalonyl-CoA biosynthesis	8	2	1
tRNA-uridine 2-thiolation (cytoplasmic)	8	1	1
superpathway of aromatic amino acid biosynthesis	18	18	2
folate transformations III (E. coli)	9	9	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae)	10	8	1
superpathway of thiamine diphosphate biosynthesis I	10	7	1
rosmarinic acid biosynthesis I	10	3	1
folate transformations II (plants)	11	10	1
tRNA-uridine 2-thiolation and selenation (bacteria)	11	4	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
purine nucleobases degradation II (anaerobic)	24	16	2
indole-3-acetate biosynthesis II	12	5	1
anandamide biosynthesis I	12	3	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of cardiolipin biosynthesis (bacteria)	13	10	1
dapdiamides biosynthesis	13	2	1
zwittermicin A biosynthesis	13	1	1
superpathway of phospholipid biosynthesis II (plants)	28	10	2
superpathway of rosmarinic acid biosynthesis	14	4	1
sulfazecin biosynthesis	16	2	1
superpathway of anaerobic energy metabolism (invertebrates)	17	8	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
superpathway of seleno-compound metabolism	19	6	1
superpathway of chorismate metabolism	59	43	3
aspartate superpathway	25	22	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
mycolate biosynthesis	205	20	5
superpathway of mycolate biosynthesis	239	21	5
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1