Experiment set5IT025 for Pseudomonas fluorescens FW300-N2E3

Gly-Glu nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + Gly-Glu (5 mM), pH=7
Culturing: pseudo3_N2E3_ML2, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 12/17/2015
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 26 genes in this experiment

For nitrogen source Gly-Glu in Pseudomonas fluorescens FW300-N2E3

For nitrogen source Gly-Glu across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter dipeptide (TC 3.A.1.5.2)	6
Arginine and Ornithine Degradation	3
D-ribose utilization	3
Bacterial Chemotaxis	2
2-Ketogluconate Utilization	1
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	1
Arginine Biosynthesis extended	1
Deoxyribose and Deoxynucleoside Catabolism	1
Glycine and Serine Utilization	1
Glycine cleavage system	1
Glycine reductase, sarcosine reductase and betaine reductase	1
Lysine degradation	1
Maltose and Maltodextrin Utilization	1
Photorespiration (oxidative C2 cycle)	1
Proline, 4-hydroxyproline uptake and utilization	1
Respiratory dehydrogenases 1	1
Ribosome biogenesis bacterial	1
Thioredoxin-disulfide reductase	1
Trehalose Biosynthesis	1
Wyeosine-MimG Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose phosphate pathway
• Arginine and proline metabolism
• Urea cycle and metabolism of amino groups
• Pyrimidine metabolism
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Tryptophan metabolism
• Glutathione metabolism
• Starch and sucrose metabolism
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-proline degradation I	3	3	2
proline to cytochrome bo oxidase electron transfer	2	2	1
ribose phosphorylation	2	1	1
thioredoxin pathway	2	1	1
glycine cleavage	3	3	1
glycine biosynthesis II	3	3	1
2-deoxy-D-ribose degradation I	3	2	1
L-arginine degradation I (arginase pathway)	3	2	1
ethene biosynthesis II (microbes)	4	4	1
glucose degradation (oxidative)	5	5	1
L-ornithine biosynthesis I	5	5	1
(5R)-carbapenem carboxylate biosynthesis	6	1	1
L-Nδ-acetylornithine biosynthesis	7	5	1
lipoprotein posttranslational modification (Gram-negative bacteria)	7	2	1
L-citrulline biosynthesis	8	7	1
ketogluconate metabolism	8	4	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
superpathway of L-citrulline metabolism	12	9	1
superpathway of arginine and polyamine biosynthesis	17	16	1