Experiment set12IT009 for Pseudomonas fluorescens SBW25-INTG

Sodium malate (C) and Ammonium chloride (N); with TAPS

Group: stress
Media: MME_noNitrogen_noCarbon + Sodium malate (30 mM) + Ammonium chloride (10 mM) + TAPS sodium salt (20 mM) + Sodium Chloride (400 mM), pH=8.5
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 8 (C), shaken=1300 rpm
By: Rob Egbert on 11-May-21
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 4 genes in this experiment

For stress Sodium malate in Pseudomonas fluorescens SBW25-INTG

For stress Sodium malate across organisms

SEED Subsystems

Subsystem	#Specific
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycogen metabolism	1
Maltose and Maltodextrin Utilization	1
Putative TldE-TldD proteolytic complex	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:

• Glutamate metabolism
• Alanine and aspartate metabolism
• Cysteine metabolism
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Starch and sucrose metabolism
• Carbon fixation in photosynthetic organisms
• 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
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
L-aspartate biosynthesis	1	1	1
L-glutamate degradation II	2	2	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
malate/L-aspartate shuttle pathway	2	1	1
L-tyrosine degradation II	2	1	1
atromentin biosynthesis	2	1	1
L-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
L-asparagine degradation III (mammalian)	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
sulfolactate degradation III	3	1	1
(R)-cysteate degradation	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
starch degradation V	4	3	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
L-tyrosine degradation I	5	5	1
trans-4-hydroxy-L-proline degradation I	5	3	1
superpathway of plastoquinol biosynthesis	5	2	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
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	2
superpathway of L-threonine biosynthesis	6	6	1
TCA cycle VIII (Chlamydia)	6	5	1
superpathway of sulfolactate degradation	6	2	1
coenzyme M biosynthesis II	6	1	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
glycogen degradation I	8	6	1
sucrose biosynthesis II	8	6	1
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
starch degradation II	9	1	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
rosmarinic acid biosynthesis I	10	1	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
superpathway of rosmarinic acid biosynthesis	14	1	1
superpathway of anaerobic energy metabolism (invertebrates)	17	8	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	22	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
superpathway of chorismate metabolism	59	42	2
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1