Experiment set4S505 for Lysobacter sp. OAE881

Compare to:

Ying_sugar7 rep B; time point 2

Group: carbon source
Media: SDM_noCarbon + 1X Ying_sugar7
Culturing: Lysobacter_OAE881_ML4, tube, Aerobic, at 28 (C), shaken=180 rpm
By: Ying and Valentine on 1-Sep-23
Media components: 1.5 g/L Ammonium chloride, 0.6 g/L Potassium phosphate monobasic, 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)

Ying_sugar7 1x includes: 366 uM Sucrose, 366 uM D-Glucose, 366 uM D-Trehalose dihydrate, 366 uM m-Inositol, 366 uM D-Xylose, 366 uM D-Mannitol, 366 uM N-Acetyl-D-Glucosamine

Specific Phenotypes

For 4 genes in this experiment

For carbon source Ying_sugar7 in Lysobacter sp. OAE881

For carbon source Ying_sugar7 across organisms

SEED Subsystems

Subsystem #Specific
Arginine Biosynthesis extended 1
DNA-replication 1
DNA repair, bacterial UvrD and related helicases 1
Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway 1
Lactose and Galactose Uptake and Utilization 1
N-linked Glycosylation in Bacteria 1
Rhamnose containing glycans 1
linker unit-arabinogalactan synthesis 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
UDP-α-D-galactose biosynthesis 1 1 1
UDP-N-acetyl-D-galactosamine biosynthesis I 1 1 1
UDP-α-D-galactofuranose biosynthesis 2 1 1
D-galactose detoxification 3 1 1
L-ornithine biosynthesis I 5 5 1
D-galactose degradation I (Leloir pathway) 5 3 1
L-arginine degradation II (AST pathway) 5 1 1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis 6 4 1
UDP-N-acetyl-D-galactosamine biosynthesis II 7 5 1
stachyose degradation 7 2 1
L-arginine biosynthesis III (via N-acetyl-L-citrulline) 9 9 1
L-lysine biosynthesis I 9 8 1
L-arginine biosynthesis I (via L-ornithine) 9 8 1
UDP-sugars interconversion 9 3 1
teichuronic acid biosynthesis (B. subtilis 168) 9 2 1
L-arginine biosynthesis II (acetyl cycle) 10 8 1
colanic acid building blocks biosynthesis 11 8 1
superpathway of arginine and polyamine biosynthesis 17 12 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 14 1
mycolyl-arabinogalactan-peptidoglycan complex biosynthesis 18 1 1
aspartate superpathway 25 19 1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis 33 12 1