Experiment set3IT063 for Burkholderia phytofirmans PsJN

L-Proline nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + L-Proline (20 mM), pH=7
Culturing: BFirm_ML3, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 6.1 generations
By: Mark on 1/27/2016
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)
Growth plate: Plate 1 B6

Specific Phenotypes

For 8 genes in this experiment

For nitrogen source L-Proline in Burkholderia phytofirmans PsJN

For nitrogen source L-Proline across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	5
Arginine and Ornithine Degradation	1
Biotin biosynthesis	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Proline, 4-hydroxyproline uptake and utilization	1
Respiratory dehydrogenases 1	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glutamate metabolism
• Arginine and proline metabolism
• Nicotinate and nicotinamide metabolism
• Biotin metabolism
• Nitrogen metabolism

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
NAD salvage pathway II (PNC IV cycle)	5	5	2
NAD de novo biosynthesis I	6	6	2
NAD de novo biosynthesis III	6	6	2
NAD de novo biosynthesis IV (anaerobic)	6	5	2
L-arginine degradation I (arginase pathway)	3	1	1
NAD salvage pathway I (PNC VI cycle)	7	5	2
NAD biosynthesis from 2-amino-3-carboxymuconate semialdehyde	4	4	1
biotin biosynthesis from 8-amino-7-oxononanoate I	4	4	1
ethene biosynthesis II (microbes)	4	1	1
NAD salvage pathway V (PNC V cycle)	5	3	1
(5R)-carbapenem carboxylate biosynthesis	6	1	1
L-Nδ-acetylornithine biosynthesis	7	4	1
L-citrulline biosynthesis	8	6	1
NAD de novo biosynthesis II (from tryptophan)	9	8	1
NAD salvage (plants)	11	5	1
superpathway of L-citrulline metabolism	12	8	1
aspartate superpathway	25	23	2
superpathway of NAD biosynthesis in eukaryotes	14	9	1
biotin biosynthesis I	15	13	1