Experiment set7IT002 for Pseudomonas syringae pv. syringae B728a

Succinic Acid carbon source

Group: carbon source
Media: M9 minimal media_noCarbon + Succinic Acid (33.87247015 mM)
Culturing: SyringaeB728a_ML2, 24 well microplate, Aerobic, at 28 (C), shaken=250 rpm
By: Tyler Helmann on 10/29/18
Media components: 2 mM Magnesium sulfate, 0.1 mM Calcium chloride, 12.8 g/L Sodium phosphate dibasic heptahydrate, 3 g/L Potassium phosphate monobasic, 0.5 g/L Sodium Chloride, 1 g/L Ammonium chloride

Specific Phenotypes

For 9 genes in this experiment

For carbon source Succinic Acid in Pseudomonas syringae pv. syringae B728a

For carbon source Succinic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	3
ABC transporter oligopeptide (TC 3.A.1.5.1)	2
Copper homeostasis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	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:

• Arginine and proline metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Carbon fixation in photosynthetic organisms
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Fatty acid biosynthesis
• Cysteine metabolism
• Valine, leucine and isoleucine biosynthesis
• Lysine degradation
• Histidine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Butanoate metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-aspartate biosynthesis	1	1	1
L-alanine biosynthesis II	1	1	1
L-aspartate degradation I	1	1	1
L-alanine degradation III	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
superpathway of L-alanine biosynthesis	4	4	2
L-glutamate degradation II	2	2	1
malate/L-aspartate shuttle pathway	2	2	1
L-alanine biosynthesis I	2	2	1
atromentin biosynthesis	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
L-tyrosine degradation II	2	1	1
L-alanine degradation V (oxidative Stickland reaction)	2	1	1
L-arginine degradation II (AST pathway)	5	5	2
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	8	4
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
L-asparagine degradation III (mammalian)	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
L-alanine degradation II (to D-lactate)	3	2	1
sulfolactate degradation III	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
(R)-cysteate degradation	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
pyruvate fermentation to acetate and alanine	3	1	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	2
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	4
superpathway of L-aspartate and L-asparagine biosynthesis	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	4	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-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
TCA cycle VIII (Chlamydia)	6	6	1
superpathway of L-threonine biosynthesis	6	6	1
superpathway of sulfolactate degradation	6	3	1
coenzyme M biosynthesis II	6	2	1
L-alanine degradation VI (reductive Stickland reaction)	6	1	1
superpathway of anaerobic energy metabolism (invertebrates)	17	11	2
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	4	1
superpathway of L-alanine fermentation (Stickland reaction)	9	3	1
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	4	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of rosmarinic acid biosynthesis	14	4	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	2	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	2
superpathway of chorismate metabolism	59	42	2