Experiment set6IT053 for Sphingomonas koreensis DSMZ 15582

D-Cellobiose carbon source; no added vitamins

Group: nutrient
Media: RCH2_defined_noCarbon_noVitamins + D-Cellobiose (20 mM), pH=7
Culturing: korea_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=200 rpm
By: Adam on 15-Mar-20
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)

Specific Phenotypes

For 30 genes in this experiment

For nutrient D-Cellobiose in Sphingomonas koreensis DSMZ 15582

For nutrient D-Cellobiose across organisms

SEED Subsystems

Subsystem	#Specific
Beta-Glucoside Metabolism	1
Methionine Biosynthesis	1
N-heterocyclic aromatic compound degradation	1
Potassium homeostasis	1
Protein chaperones	1
Rhamnose containing glycans	1
Universal GTPases	1
dTDP-rhamnose synthesis	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:

• Methionine metabolism
• Selenoamino acid metabolism
• Cysteine metabolism
• Cyanoamino acid metabolism
• Starch and sucrose metabolism
• Streptomycin biosynthesis
• Polyketide sugar unit biosynthesis
• Sulfur metabolism
• Phenylpropanoid biosynthesis
• Biosynthesis of vancomycin group antibiotics
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-methionine degradation II	3	3	3
neolinustatin bioactivation	3	2	2
linustatin bioactivation	4	2	2
linamarin degradation	2	1	1
seleno-amino acid detoxification and volatilization I	2	1	1
dimethyl sulfide biosynthesis from methionine	2	1	1
lotaustralin degradation	2	1	1
L-threonine degradation I	6	5	2
seleno-amino acid detoxification and volatilization III	3	2	1
cellulose degradation II (fungi)	3	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	2
homocysteine and cysteine interconversion	4	2	1
dTDP-β-D-fucofuranose biosynthesis	4	1	1
dTDP-N-acetylviosamine biosynthesis	4	1	1
dTDP-N-acetylthomosamine biosynthesis	4	1	1
dTDP-6-deoxy-α-D-allose biosynthesis	4	1	1
L-methionine biosynthesis I	5	4	1
dTDP-β-L-rhamnose biosynthesis	5	2	1
coumarin biosynthesis (via 2-coumarate)	5	2	1
dTDP-3-acetamido-3,6-dideoxy-α-D-glucose biosynthesis	5	1	1
dTDP-4-O-demethyl-β-L-noviose biosynthesis	5	1	1
dTDP-α-D-mycaminose biosynthesis	5	1	1
dTDP-3-acetamido-α-D-fucose biosynthesis	5	1	1
L-methionine biosynthesis II	6	5	1
superpathway of L-cysteine biosynthesis (fungi)	6	4	1
dTDP-D-desosamine biosynthesis	6	1	1
dTDP-α-D-ravidosamine and dTDP-4-acetyl-α-D-ravidosamine biosynthesis	6	1	1
α-tomatine degradation	6	1	1
dTDP-sibirosamine biosynthesis	6	1	1
dTDP-L-daunosamine biosynthesis	6	1	1
superpathway of L-isoleucine biosynthesis I	13	13	2
hypoglycin biosynthesis	14	4	2
dTDP-β-L-olivose biosynthesis	7	2	1
dTDP-β-L-digitoxose biosynthesis	7	2	1
dTDP-β-L-mycarose biosynthesis	7	1	1
superpathway of L-homoserine and L-methionine biosynthesis	8	7	1
dTDP-β-L-megosamine biosynthesis	8	2	1
dTDP-β-L-4-epi-vancosamine biosynthesis	8	2	1
superpathway of branched chain amino acid biosynthesis	17	17	2
superpathway of S-adenosyl-L-methionine biosynthesis	9	8	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	8	1
superpathway of L-threonine metabolism	18	14	2
dTDP-α-D-forosamine biosynthesis	9	2	1
dTDP-α-D-olivose, dTDP-α-D-oliose and dTDP-α-D-mycarose biosynthesis	9	2	1
superpathway of seleno-compound metabolism	19	8	2
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae)	10	8	1
superpathway of enterobacterial common antigen biosynthesis	10	1	1
O-antigen building blocks biosynthesis (E. coli)	11	7	1
firefly bioluminescence	14	3	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	17	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	2	1
superpathway of novobiocin biosynthesis	19	2	1
superpathway of erythromycin biosynthesis	19	1	1
superpathway of megalomicin A biosynthesis	22	2	1
superpathway of dTDP-glucose-derived antibiotic building blocks biosynthesis	23	2	1
aspartate superpathway	25	24	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	9	1