Experiment set11IT022 for Agrobacterium fabrum C58

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methyl-alpha-D-xylopyranoside carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + methyl-alpha-D-xylopyranoside (5 mM), pH=7
Culturing: Agro_ML11, 24-well plate, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 1/6/22
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 7 genes in this experiment

For carbon source methyl-alpha-D-xylopyranoside in Agrobacterium fabrum C58

For carbon source methyl-alpha-D-xylopyranoside across organisms

SEED Subsystems

Subsystem #Specific
Xylose utilization 2
Chitin and N-acetylglucosamine utilization 1
Choline and Betaine Uptake and Betaine Biosynthesis 1
Inositol catabolism 1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization 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-xylose degradation I 2 2 2
glycine betaine biosynthesis II (Gram-positive bacteria) 2 2 1
glycine betaine biosynthesis I (Gram-negative bacteria) 2 2 1
xylitol degradation I 2 2 1
choline degradation I 2 2 1
D-arabinitol degradation I 2 1 1
choline-O-sulfate degradation 3 3 1
superpathway of glucose and xylose degradation 17 16 2
superpathway of pentose and pentitol degradation 42 16 2