Experiment set3IT050 for Echinicola vietnamensis KMM 6221, DSM 17526

Sodium nitrate nitrogen source

Group: nitrogen source
Media: DinoMM_noNitrogen_HighNutrient_GlucoseC + Sodium nitrate (20 mM), pH=7
Culturing: Cola_ML5, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
Growth: about 4.6 generations
By: Adam on 8-May-17
Media components: 20 g/L Sea salts, 0.1 g/L Potassium phosphate monobasic, 20 mM D-Glucose, 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)
Growth plate: 1719 D2

Specific Phenotypes

For 24 genes in this experiment

For nitrogen source Sodium nitrate in Echinicola vietnamensis KMM 6221, DSM 17526

For nitrogen source Sodium nitrate across organisms

SEED Subsystems

Subsystem	#Specific
Molybdenum cofactor biosynthesis	5
Nitrate and nitrite ammonification	3
Transport of Molybdenum	3
Lipid A-Ara4N pathway ( Polymyxin resistance )	1
Rhamnose containing glycans	1
Rubrerythrin	1
Teichoic and lipoteichoic acids biosynthesis	1
Teichuronic acid biosynthesis	1
Thiamin biosynthesis	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:

• Nucleotide sugars metabolism
• Polyketide sugar unit biosynthesis
• Nitrogen metabolism
• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Starch and sucrose metabolism
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Streptomycin biosynthesis
• Keratan sulfate biosynthesis
• Lipopolysaccharide biosynthesis
• Peptidoglycan biosynthesis
• Glycerolipid metabolism
• Inositol phosphate metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Carotenoid biosynthesis - General
• Zeatin biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Flavone and flavonol biosynthesis
• Biosynthesis of vancomycin group antibiotics

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
UDP-α-D-glucuronate biosynthesis (from UDP-glucose)	1	1	1
UDP-α-D-xylose biosynthesis	2	2	1
nitrate reduction V (assimilatory)	2	1	1
alkylnitronates degradation	2	1	1
molybdenum cofactor biosynthesis	3	1	1
dTDP-6-deoxy-α-D-allose biosynthesis	4	2	1
dTDP-N-acetylviosamine biosynthesis	4	2	1
dTDP-N-acetylthomosamine biosynthesis	4	2	1
dTDP-β-D-fucofuranose biosynthesis	4	2	1
dTDP-β-L-rhamnose biosynthesis	5	5	1
dTDP-4-O-demethyl-β-L-noviose biosynthesis	5	3	1
Salmonella enterica serotype O:54 O antigen biosynthesis	5	2	1
dTDP-3-acetamido-α-D-fucose biosynthesis	5	2	1
dTDP-3-acetamido-3,6-dideoxy-α-D-glucose biosynthesis	5	2	1
dTDP-α-D-mycaminose biosynthesis	5	2	1
thiazole component of thiamine diphosphate biosynthesis I	6	5	1
dTDP-sibirosamine biosynthesis	6	3	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	3	1
dTDP-L-daunosamine biosynthesis	6	3	1
dTDP-α-D-ravidosamine and dTDP-4-acetyl-α-D-ravidosamine biosynthesis	6	2	1
dTDP-D-desosamine biosynthesis	6	2	1
thiazole component of thiamine diphosphate biosynthesis II	7	5	1
dTDP-β-L-olivose biosynthesis	7	3	1
dTDP-β-L-digitoxose biosynthesis	7	3	1
dTDP-β-L-mycarose biosynthesis	7	2	1
dTDP-β-L-4-epi-vancosamine biosynthesis	8	3	1
dTDP-β-L-megosamine biosynthesis	8	3	1
UDP-sugars interconversion	9	3	1
dTDP-α-D-forosamine biosynthesis	9	3	1
dTDP-α-D-olivose, dTDP-α-D-oliose and dTDP-α-D-mycarose biosynthesis	9	3	1
teichuronic acid biosynthesis (B. subtilis 168)	9	3	1
superpathway of thiamine diphosphate biosynthesis I	10	9	1
superpathway of enterobacterial common antigen biosynthesis	10	3	1
poly(3-O-β-D-glucopyranosyl-N-acetylgalactosamine 1-phosphate) wall teichoic acid biosynthesis	10	2	1
colanic acid building blocks biosynthesis	11	9	1
superpathway of thiamine diphosphate biosynthesis II	11	9	1
O-antigen building blocks biosynthesis (E. coli)	11	8	1
poly(glycerol phosphate) wall teichoic acid biosynthesis	11	3	1
poly(ribitol phosphate) wall teichoic acid biosynthesis I (B. subtilis)	12	2	1
phytate degradation I	14	3	1
poly(ribitol phosphate) wall teichoic acid biosynthesis II (S. aureus)	14	2	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	5	1
superpathway of novobiocin biosynthesis	19	4	1
superpathway of erythromycin biosynthesis	19	2	1
superpathway of megalomicin A biosynthesis	22	3	1
superpathway of dTDP-glucose-derived antibiotic building blocks biosynthesis	23	3	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	10	1