Experiment set5IT088 for Pseudomonas fluorescens FW300-N2C3

D-Serine nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + D-Serine (5 mM), pH=7
Culturing: pseudo5_N2-C3_1_ML2, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 12/17/2014
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 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 34 genes in this experiment

For nitrogen source D-Serine in Pseudomonas fluorescens FW300-N2C3

For nitrogen source D-Serine across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	8
D-galactarate, D-glucarate and D-glycerate catabolism	2
Peptidoglycan Biosynthesis	2
Threonine and Homoserine Biosynthesis	2
Urea decomposition	2
Ammonia assimilation	1
Bacterial Cytoskeleton	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Cobalt-zinc-cadmium resistance	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycogen metabolism	1
Maltose and Maltodextrin Utilization	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Queuosine-Archaeosine Biosynthesis	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	1
Ribosome biogenesis bacterial	1
Type IV pilus	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Peptidoglycan biosynthesis
• Glutamate metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Carbon fixation in photosynthetic organisms
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Cysteine metabolism
• Valine, leucine and isoleucine biosynthesis
• Lysine degradation
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Starch and sucrose metabolism
• Vitamin B6 metabolism
• Nicotinate and nicotinamide metabolism
• Biotin metabolism
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of phenylpropanoids
• 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 degradation III	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
L-alanine biosynthesis II	1	1	1
superpathway of L-alanine biosynthesis	4	4	2
L-threonine biosynthesis	2	2	1
L-alanine biosynthesis I	2	2	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-alanine degradation V (oxidative Stickland reaction)	2	1	1
L-tyrosine degradation II	2	1	1
atromentin biosynthesis	2	1	1
glycogen degradation I	8	6	3
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	4
superpathway of L-threonine biosynthesis	6	6	2
L-phenylalanine biosynthesis I	3	3	1
L-alanine degradation II (to D-lactate)	3	3	1
L-tyrosine biosynthesis I	3	3	1
glycogen degradation II	6	5	2
L-asparagine degradation III (mammalian)	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	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
pyruvate fermentation to acetate and alanine	3	1	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	4
anaerobic energy metabolism (invertebrates, cytosol)	7	4	2
starch degradation V	4	3	1
NAD biosynthesis from 2-amino-3-carboxymuconate semialdehyde	4	3	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
starch degradation III	4	2	1
creatinine degradation I	4	2	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	3
L-tryptophan degradation VIII (to tryptophol)	4	1	1
L-tyrosine degradation I	5	5	1
peptidoglycan recycling II	10	8	2
NAD salvage pathway V (PNC V cycle)	5	3	1
trans-4-hydroxy-L-proline degradation I	5	3	1
NAD salvage pathway II (PNC IV cycle)	5	3	1
superpathway of plastoquinol biosynthesis	5	2	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
creatinine degradation II	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
peptidoglycan biosynthesis II (staphylococci)	17	12	3
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	3
NAD de novo biosynthesis IV (anaerobic)	6	5	1
NAD de novo biosynthesis I	6	5	1
NAD de novo biosynthesis III	6	4	1
TCA cycle VIII (Chlamydia)	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-isoleucine biosynthesis I	13	13	2
peptidoglycan recycling I	14	11	2
NAD salvage pathway I (PNC VI cycle)	7	5	1
sucrose biosynthesis II	8	6	1
glycine betaine degradation I	8	6	1
aspartate superpathway	25	22	3
peptidoglycan biosynthesis V (β-lactam resistance)	17	11	2
superpathway of anaerobic energy metabolism (invertebrates)	17	8	2
superpathway of aromatic amino acid biosynthesis	18	18	2
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
superpathway of L-alanine fermentation (Stickland reaction)	9	4	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	4	1
NAD de novo biosynthesis II (from tryptophan)	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
NAD salvage (plants)	11	6	1
(S)-reticuline biosynthesis I	11	1	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	12	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
indole-3-acetate biosynthesis II	12	5	1
superpathway of NAD biosynthesis in eukaryotes	14	6	1
superpathway of rosmarinic acid biosynthesis	14	4	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	1
peptidoglycan biosynthesis III (mycobacteria)	15	11	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	3	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	2
superpathway of chorismate metabolism	59	44	2