Experiment set1IT027 for Sinorhizobium meliloti 1021

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L-Proline carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Proline (20 mM), pH=7
Culturing: Smeli_ML6, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 5.2 generations
By: Mark on 6/2/2015
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 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: Smeli_carbon_plate2 B2

Specific Phenotypes

For 18 genes in this experiment

For carbon source L-Proline in Sinorhizobium meliloti 1021

For carbon source L-Proline across organisms

SEED Subsystems

Subsystem #Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1) 4
Calvin-Benson cycle 4
CO2 uptake, carboxysome 3
Photorespiration (oxidative C2 cycle) 3
Carboxysome 2
Pentose phosphate pathway 2
2-phosphoglycolate salvage 1
Choline and Betaine Uptake and Betaine Biosynthesis 1
Cysteine Biosynthesis 1
Glycolate, glyoxylate interconversions 1
Glycolysis and Gluconeogenesis 1
Ketoisovalerate oxidoreductase 1
Proline, 4-hydroxyproline uptake and utilization 1
Pyruvate metabolism I: anaplerotic reactions, PEP 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
acetate and ATP formation from acetyl-CoA III 1 1 1
acetate conversion to acetyl-CoA 1 1 1
pentose phosphate pathway (partial) 3 3 2
L-cysteine biosynthesis I 2 2 1
pentose phosphate pathway (non-oxidative branch) II 6 5 3
sedoheptulose bisphosphate bypass 2 1 1
pentose phosphate pathway (non-oxidative branch) I 5 5 2
Calvin-Benson-Bassham cycle 13 12 5
pentose phosphate pathway 8 8 3
ethanol degradation II 3 3 1
ethanol degradation IV 3 3 1
superpathway of acetate utilization and formation 3 3 1
pentose phosphate pathway (oxidative branch) I 3 3 1
formaldehyde assimilation II (assimilatory RuMP Cycle) 9 7 3
L-proline degradation I 3 2 1
L-isoleucine biosynthesis V 3 2 1
ethanol degradation III 3 2 1
L-arginine degradation I (arginase pathway) 3 2 1
Rubisco shunt 10 10 3
oxygenic photosynthesis 17 13 5
C4 photosynthetic carbon assimilation cycle, NADP-ME type 7 4 2
formaldehyde assimilation III (dihydroxyacetone cycle) 12 11 3
chitin deacetylation 4 3 1
ethene biosynthesis II (microbes) 4 1 1
photorespiration III 9 8 2
photorespiration I 9 8 2
photorespiration II 10 8 2
ethene biosynthesis V (engineered) 25 19 5
seleno-amino acid biosynthesis (plants) 5 2 1
sucrose degradation V (sucrose α-glucosidase) 5 2 1
2-methylcitrate cycle I 5 1 1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 22 5
1-butanol autotrophic biosynthesis (engineered) 27 21 5
superpathway of glucose and xylose degradation 17 15 3
β-alanine biosynthesis II 6 5 1
methylgallate degradation 6 4 1
L-isoleucine biosynthesis IV 6 4 1
superpathway of bitter acids biosynthesis 18 3 3
2-methylcitrate cycle II 6 1 1
lupulone and humulone biosynthesis 6 1 1
adlupulone and adhumulone biosynthesis 6 1 1
colupulone and cohumulone biosynthesis 6 1 1
gluconeogenesis I 13 12 2
C4 photosynthetic carbon assimilation cycle, PEPCK type 14 8 2
protocatechuate degradation I (meta-cleavage pathway) 8 5 1
superpathway of sulfate assimilation and cysteine biosynthesis 9 9 1
sucrose biosynthesis I (from photosynthesis) 9 7 1
reductive glycine pathway of autotrophic CO2 fixation 9 6 1
1,3-propanediol biosynthesis (engineered) 9 5 1
cis-geranyl-CoA degradation 9 2 1
superpathway of coenzyme A biosynthesis II (plants) 10 9 1
glycolysis IV 10 8 1
glycolysis V (Pyrococcus) 10 6 1
superpathway of vanillin and vanillate degradation 10 5 1
nucleoside and nucleotide degradation (archaea) 10 4 1
glycolysis III (from glucose) 11 10 1
glycolysis II (from fructose 6-phosphate) 11 9 1
glycolysis VI (from fructose) 11 7 1
homolactic fermentation 12 10 1
gluconeogenesis III 12 9 1
syringate degradation 12 5 1
glycolysis I (from glucose 6-phosphate) 13 10 1
Bifidobacterium shunt 15 14 1
superpathway of glycolysis and the Entner-Doudoroff pathway 17 14 1
superpathway of hexitol degradation (bacteria) 18 13 1
gluconeogenesis II (Methanobacterium thermoautotrophicum) 18 7 1
superpathway of anaerobic sucrose degradation 19 14 1
hexitol fermentation to lactate, formate, ethanol and acetate 19 12 1
superpathway of seleno-compound metabolism 19 7 1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle 22 19 1
superpathway of N-acetylneuraminate degradation 22 16 1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 22 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 20 1