Experiment set29IT066 for Pseudomonas putida KT2440

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Rhamnogalacturonan - from potato carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Rhamnogalacturonan - from potato (10 mM)
Culturing: Putida_ML5_JBEI, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=200 rpm
By: Matthias Schmidt on 4/13/21
Media components: 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 9.5 mM Ammonium chloride, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate

Specific Phenotypes

For 8 genes in this experiment

For carbon source Rhamnogalacturonan - from potato in Pseudomonas putida KT2440

For carbon source Rhamnogalacturonan - from potato across organisms

SEED Subsystems

Subsystem #Specific
D-Galacturonate and D-Glucuronate Utilization 3
D-galactarate, D-glucarate and D-glycerate catabolism 3
Entner-Doudoroff Pathway 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
D-galactarate degradation II 3 3 2
D-glucuronate degradation III 2 2 1
D-galacturonate degradation III 2 1 1
D-glucuronate degradation II 5 4 2
D-galacturonate degradation II 5 3 2
D-glucarate degradation II 3 3 1
sorbitol biosynthesis II 3 2 1
D-galactarate degradation I 4 3 1
L-ascorbate biosynthesis VI (plants, myo-inositol pathway) 4 1 1
glucose degradation (oxidative) 5 5 1
superpathway of D-glucarate and D-galactarate degradation 5 4 1
glucose and glucose-1-phosphate degradation 5 4 1
L-ascorbate biosynthesis IV (animals, D-glucuronate pathway) 6 3 1
L-ascorbate biosynthesis VIII (engineered pathway) 7 5 1
superpathway of microbial D-galacturonate and D-glucuronate degradation 31 13 4
Entner-Doudoroff pathway III (semi-phosphorylative) 9 5 1
Entner-Doudoroff pathway II (non-phosphorylative) 9 5 1