Experiment set2IT063 for Herbaspirillum seropedicae SmR1

L-Proline nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + L-Proline (20 mM), pH=7
Culturing: HerbieS_ML4, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 3.6 generations
By: Mark on 3/10/2016
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: Nplate1 B6

Specific Phenotypes

For 4 genes in this experiment

For nitrogen source L-Proline in Herbaspirillum seropedicae SmR1

For nitrogen source L-Proline across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	1
Branched-Chain Amino Acid Biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	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:

• Arginine and proline metabolism
• Glutamate metabolism
• Methionine metabolism
• Lysine biosynthesis
• Lysine degradation
• Aminophosphonate metabolism
• Nucleotide sugars metabolism
• Caprolactam degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-alanine degradation III	1	1	1
L-alanine biosynthesis II	1	1	1
L-proline degradation I	3	3	2
proline to cytochrome bo oxidase electron transfer	2	2	1
L-alanine degradation V (oxidative Stickland reaction)	2	1	1
L-alanine degradation II (to D-lactate)	3	3	1
L-arginine degradation I (arginase pathway)	3	2	1
pyruvate fermentation to acetate and alanine	3	1	1
superpathway of L-alanine biosynthesis	4	4	1
ethene biosynthesis II (microbes)	4	1	1
L-alanine degradation VI (reductive Stickland reaction)	6	2	1
(5R)-carbapenem carboxylate biosynthesis	6	1	1
anaerobic energy metabolism (invertebrates, cytosol)	7	7	1
L-Nδ-acetylornithine biosynthesis	7	5	1
L-citrulline biosynthesis	8	7	1
superpathway of L-alanine fermentation (Stickland reaction)	9	4	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	7	1
superpathway of L-citrulline metabolism	12	9	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	8	1
superpathway of anaerobic energy metabolism (invertebrates)	17	13	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1