Experiment set2IT006 for Pseudomonas fluorescens FW300-N2E2

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D-Galactose carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + D-Galactose (20 mM), pH=7
Culturing: pseudo6_N2E2_ML5, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 3/9/2015
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 74 genes in this experiment

For carbon source D-Galactose in Pseudomonas fluorescens FW300-N2E2

For carbon source D-Galactose across organisms

SEED Subsystems

Subsystem #Specific
L-Arabinose utilization 5
Alginate metabolism 4
HMG CoA Synthesis 3
Leucine Degradation and HMG-CoA Metabolism 3
Photorespiration (oxidative C2 cycle) 3
Coenzyme PQQ synthesis 2
D-galactarate, D-glucarate and D-glycerate catabolism 2
D-galactonate catabolism 2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 2
Glycine and Serine Utilization 2
Glycine cleavage system 2
Lipid A modifications 2
Pyrroloquinoline Quinone biosynthesis 2
Serine-glyoxylate cycle 2
2-phosphoglycolate salvage 1
ABC transporter alkylphosphonate (TC 3.A.1.9.1) 1
Ammonia assimilation 1
Bacterial Chemotaxis 1
Benzoate transport and degradation cluster 1
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more. 1
Chorismate Synthesis 1
Cobalt-zinc-cadmium resistance 1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) 1
D-Galacturonate and D-Glucuronate Utilization 1
Experimental tye 1
Flagellar motility 1
Flagellum 1
Glycolate, glyoxylate interconversions 1
Hfl operon 1
Mannitol Utilization 1
Mannose Metabolism 1
Polyamine Metabolism 1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization 1
Ribosome biogenesis bacterial 1
Threonine and Homoserine Biosynthesis 1
Tryptophan synthesis 1
Twin-arginine translocation system 1
Two-component regulatory systems in Campylobacter 1
Universal GTPases 1
Universal stress protein family 1
YjeE 1
tRNA processing 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
L-glutamate biosynthesis I 2 2 2
L-aspartate biosynthesis 1 1 1
L-glutamine degradation II 1 1 1
L-aspartate degradation I 1 1 1
3-(4-hydroxyphenyl)pyruvate biosynthesis 1 1 1
L-alanine biosynthesis II 1 1 1
L-glutamine degradation I 1 1 1
L-alanine degradation III 1 1 1
D-galactonate degradation 3 3 2
ammonia assimilation cycle III 3 3 2
alginate biosynthesis I (algal) 3 3 2
superpathway of L-alanine biosynthesis 4 4 2
L-glutamate degradation II 2 2 1
UDP-α-D-glucose biosynthesis 2 2 1
3-dehydroquinate biosynthesis I 2 2 1
L-alanine biosynthesis I 2 2 1
3-oxoadipate degradation 2 2 1
atromentin biosynthesis 2 1 1
L-alanine degradation V (oxidative Stickland reaction) 2 1 1
malate/L-aspartate shuttle pathway 2 1 1
L-tryptophan degradation IV (via indole-3-lactate) 2 1 1
L-tyrosine degradation II 2 1 1
C4 photosynthetic carbon assimilation cycle, NAD-ME type 11 6 4
L-alanine degradation II (to D-lactate) 3 3 1
L-phenylalanine biosynthesis I 3 3 1
glycine degradation 3 3 1
D-glucarate degradation II 3 3 1
glycine cleavage 3 3 1
L-tyrosine biosynthesis I 3 3 1
glycine biosynthesis II 3 3 1
L-leucine degradation I 6 5 2
β-1,4-D-mannosyl-N-acetyl-D-glucosamine degradation 3 2 1
L-phenylalanine degradation II (anaerobic) 3 2 1
GDP-α-D-glucose biosynthesis 3 2 1
trehalose degradation V 3 2 1
L-asparagine degradation III (mammalian) 3 2 1
5-(methoxycarbonylmethoxy)uridine biosynthesis 3 1 1
sulfolactate degradation III 3 1 1
L-tyrosine degradation IV (to 4-methylphenol) 3 1 1
pyruvate fermentation to acetate and alanine 3 1 1
indole-3-acetate biosynthesis VI (bacteria) 3 1 1
(R)-cysteate degradation 3 1 1
alginate biosynthesis II (bacterial) 7 6 2
L-glutamate and L-glutamine biosynthesis 7 6 2
C4 photosynthetic carbon assimilation cycle, PEPCK type 14 9 4
anaerobic energy metabolism (invertebrates, cytosol) 7 4 2
pyrroloquinoline quinone biosynthesis 7 4 2
GDP-mannose biosynthesis 4 4 1
L-asparagine biosynthesis III (tRNA-dependent) 4 4 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 4 1
glycogen biosynthesis I (from ADP-D-Glucose) 4 3 1
sucrose degradation IV (sucrose phosphorylase) 4 3 1
D-fructuronate degradation 4 3 1
starch degradation V 4 3 1
D-glucarate degradation I 4 3 1
superpathway of L-aspartate and L-asparagine biosynthesis 4 3 1
L-phenylalanine degradation III 4 2 1
starch degradation III 4 2 1
L-tyrosine degradation III 4 2 1
L-tryptophan degradation VIII (to tryptophol) 4 1 1
acridone alkaloid biosynthesis 4 1 1
superpathway of aromatic amino acid biosynthesis 18 18 4
photorespiration III 9 5 2
photorespiration I 9 5 2
superpathway of L-phenylalanine biosynthesis 10 10 2
tRNA processing 10 10 2
superpathway of L-tyrosine biosynthesis 10 10 2
dTDP-β-L-rhamnose biosynthesis 5 5 1
L-tyrosine degradation I 5 5 1
sucrose degradation II (sucrose synthase) 5 4 1
glucose and glucose-1-phosphate degradation 5 4 1
superpathway of D-glucarate and D-galactarate degradation 5 4 1
photorespiration II 10 6 2
D-galactose degradation I (Leloir pathway) 5 3 1
CDP-6-deoxy-D-gulose biosynthesis 5 3 1
mannitol cycle 5 3 1
ferrichrome A biosynthesis 5 3 1
trans-4-hydroxy-L-proline degradation I 5 3 1
glucosylglycerol biosynthesis 5 2 1
superpathway of plastoquinol biosynthesis 5 2 1
4-hydroxy-2(1H)-quinolone biosynthesis 5 2 1
4-hydroxybenzoate biosynthesis I (eukaryotes) 5 1 1
L-phenylalanine degradation VI (reductive Stickland reaction) 5 1 1
L-tryptophan degradation XIII (reductive Stickland reaction) 5 1 1
L-tyrosine degradation V (reductive Stickland reaction) 5 1 1
colanic acid building blocks biosynthesis 11 9 2
L-tryptophan biosynthesis 6 6 1
superpathway of L-threonine biosynthesis 6 6 1
glycogen degradation II 6 5 1
L-arabinose degradation III 6 5 1
L-arabinose degradation V 6 4 1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis 6 4 1
TCA cycle VIII (Chlamydia) 6 4 1
catechol degradation III (ortho-cleavage pathway) 6 4 1
L-alanine degradation VI (reductive Stickland reaction) 6 2 1
superpathway of sulfolactate degradation 6 2 1
coenzyme M biosynthesis II 6 1 1
superpathway of L-tryptophan biosynthesis 13 13 2
chorismate biosynthesis I 7 7 1
superpathway of salicylate degradation 7 4 1
superpathway of β-D-glucuronosides degradation 7 4 1
4-methylcatechol degradation (ortho cleavage) 7 3 1
L-glucose degradation 7 3 1
L-glutamate degradation XI (reductive Stickland reaction) 7 3 1
β-(1,4)-mannan degradation 7 2 1
sucrose biosynthesis II 8 6 1
glycogen degradation I 8 6 1
L-citrulline biosynthesis 8 6 1
L-arabinose degradation IV 8 5 1
glycogen biosynthesis III (from α-maltose 1-phosphate) 8 3 1
superpathway of anaerobic energy metabolism (invertebrates) 17 8 2
folate transformations III (E. coli) 9 9 1
sucrose biosynthesis I (from photosynthesis) 9 7 1
superpathway of L-methionine biosynthesis (transsulfuration) 9 7 1
aromatic compounds degradation via β-ketoadipate 9 7 1
chitin biosynthesis 9 6 1
reductive glycine pathway of autotrophic CO2 fixation 9 5 1
L-phenylalanine degradation IV (mammalian, via side chain) 9 5 1
superpathway of L-alanine fermentation (Stickland reaction) 9 4 1
peptidoglycan recycling II 10 8 1
L-glutamate degradation V (via hydroxyglutarate) 10 6 1
starch biosynthesis 10 5 1
superpathway of hexuronide and hexuronate degradation 10 5 1
rosmarinic acid biosynthesis I 10 3 1
superpathway of quinolone and alkylquinolone biosynthesis 10 2 1
O-antigen building blocks biosynthesis (E. coli) 11 10 1
folate transformations II (plants) 11 10 1
toluene degradation III (aerobic) (via p-cresol) 11 8 1
(S)-reticuline biosynthesis I 11 1 1
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 12 1
superpathway of L-citrulline metabolism 12 8 1
indole-3-acetate biosynthesis II 12 5 1
superpathway of L-isoleucine biosynthesis I 13 13 1
folate transformations I 13 9 1
superpathway of GDP-mannose-derived O-antigen building blocks biosynthesis 14 7 1
superpathway of rosmarinic acid biosynthesis 14 4 1
superpathway of chorismate metabolism 59 43 4
superpathway of microbial D-galacturonate and D-glucuronate degradation 31 16 2
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 16 1
mandelate degradation to acetyl-CoA 18 9 1
streptomycin biosynthesis 18 3 1
superpathway of anaerobic sucrose degradation 19 14 1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis 19 5 1
aspartate superpathway 25 22 1
anaerobic aromatic compound degradation (Thauera aromatica) 27 4 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 21 2
superpathway of aerobic toluene degradation 30 14 1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis 33 12 1
superpathway of aromatic compound degradation via 3-oxoadipate 35 15 1
superpathway of pentose and pentitol degradation 42 15 1