Experiment set5S279 for Lysobacter sp. OAE881

Ying_sugar7 rep B; time point 3

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 16 genes in this experiment

For carbon source Ying_sugar7 in Lysobacter sp. OAE881

For carbon source Ying_sugar7 across organisms

SEED Subsystems

Subsystem	#Specific
DNA-replication	3
DNA repair, bacterial	2
Flagellum	2
Arginine Biosynthesis extended	1
Chitin and N-acetylglucosamine utilization	1
DNA repair, UvrABC system	1
DNA repair, bacterial RecFOR pathway	1
DNA repair, bacterial UvrD and related helicases	1
Flagellar motility	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
Trehalose Biosynthesis	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:

• Nucleotide sugars metabolism
• Galactose metabolism
• Lysine biosynthesis
• Starch and sucrose metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Glycolysis / Gluconeogenesis
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Arginine and proline metabolism
• Streptomycin biosynthesis
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Folate biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
UDP-N-acetyl-D-galactosamine biosynthesis I	1	1	1
UDP-α-D-galactose biosynthesis	1	1	1
trehalose degradation II (cytosolic)	2	2	1
trehalose biosynthesis I	2	2	1
trehalose degradation I (low osmolarity)	2	1	1
UDP-α-D-galactofuranose biosynthesis	2	1	1
N-acetylglucosamine degradation II	3	3	1
trehalose degradation V	3	2	1
GDP-α-D-glucose biosynthesis	3	2	1
trehalose degradation IV	3	1	1
D-galactose detoxification	3	1	1
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	2
sucrose degradation III (sucrose invertase)	4	3	1
L-ornithine biosynthesis I	5	5	1
D-galactose degradation I (Leloir pathway)	5	3	1
glucose and glucose-1-phosphate degradation	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-glucosamine biosynthesis II	6	4	1
glycogen degradation II	6	3	1
stachyose degradation	7	2	1
chitin derivatives degradation	8	4	1
sucrose biosynthesis II	8	4	1
glycogen degradation I	8	3	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
chitin biosynthesis	9	6	1
1,3-propanediol biosynthesis (engineered)	9	5	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
glycolysis III (from glucose)	11	10	1
colanic acid building blocks biosynthesis	11	8	1
homolactic fermentation	12	10	1
Bifidobacterium shunt	15	12	1
superpathway of arginine and polyamine biosynthesis	17	12	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	14	1
heterolactic fermentation	18	12	1
mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	18	1	1
aspartate superpathway	25	19	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	1