Experiment set3IT042 for Echinicola vietnamensis KMM 6221, DSM 17526

L-Methionine nitrogen source

Group: nitrogen source
Media: DinoMM_noNitrogen_HighNutrient_GlucoseC + L-Methionine (20 mM), pH=7
Culturing: Cola_ML5, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
Growth: about 3.7 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: 1717 C5

Specific Phenotypes

For 32 genes in this experiment

For nitrogen source L-Methionine in Echinicola vietnamensis KMM 6221, DSM 17526

For nitrogen source L-Methionine across organisms

SEED Subsystems

Subsystem	#Specific
Rhamnose containing glycans	2
dTDP-rhamnose synthesis	2
linker unit-arabinogalactan synthesis	2
Alanine biosynthesis	1
Alginate metabolism	1
Branched-Chain Amino Acid Biosynthesis	1
Colanic acid biosynthesis	1
DNA Repair Base Excision	1
Glycine and Serine Utilization	1
Isoleucine degradation	1
Leucine Biosynthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Lipid A-Ara4N pathway ( Polymyxin resistance )	1
Multidrug Resistance Efflux Pumps	1
Propionyl-CoA to Succinyl-CoA Module	1
Pyridoxin (Vitamin B6) Biosynthesis	1
Pyruvate Alanine Serine Interconversions	1
Serine-glyoxylate cycle	1
Serine Biosynthesis	1
Teichoic and lipoteichoic acids biosynthesis	1
Teichuronic acid biosynthesis	1
Valine degradation	1
Zinc resistance	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Nucleotide sugars metabolism
• Polyketide sugar unit biosynthesis
• Lipopolysaccharide biosynthesis
• Glycosphingolipid biosynthesis - ganglio series
• Glyoxylate and dicarboxylate metabolism
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Valine, leucine and isoleucine biosynthesis
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine 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
• Peptidoglycan biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Ethylbenzene degradation
• Butanoate metabolism
• Pantothenate and CoA biosynthesis
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Zeatin biosynthesis
• Flavonoid biosynthesis
• Flavone and flavonol biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of vancomycin group antibiotics
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• T cell receptor signaling pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
UDP-α-D-xylose biosynthesis	2	2	2
UDP-α-D-glucuronate biosynthesis (from UDP-glucose)	1	1	1
L-alanine biosynthesis I	2	1	1
propanoyl CoA degradation I	3	3	1
L-serine biosynthesis I	3	3	1
L-isoleucine biosynthesis V	3	2	1
L-valine degradation II	3	2	1
L-isoleucine degradation II	3	2	1
L-leucine degradation III	3	2	1
L-cysteine biosynthesis IX (Trichomonas vaginalis)	3	2	1
conversion of succinate to propanoate	3	1	1
L-valine degradation III (oxidative Stickland reaction)	3	1	1
L-isoleucine degradation III (oxidative Stickland reaction)	3	1	1
L-leucine degradation V (oxidative Stickland reaction)	3	1	1
superpathway of L-serine and glycine biosynthesis I	4	4	1
L-valine biosynthesis	4	4	1
2-oxobutanoate degradation I	4	3	1
dTDP-N-acetylviosamine biosynthesis	4	2	1
dTDP-β-D-fucofuranose biosynthesis	4	2	1
dTDP-N-acetylthomosamine biosynthesis	4	2	1
dTDP-6-deoxy-α-D-allose biosynthesis	4	2	1
superpathway of L-alanine biosynthesis	4	2	1
L-serine biosynthesis II	4	1	1
UDP-sugars interconversion	9	3	2
dTDP-β-L-rhamnose biosynthesis	5	5	1
dTDP-4-O-demethyl-β-L-noviose biosynthesis	5	3	1
dTDP-α-D-mycaminose biosynthesis	5	2	1
dTDP-3-acetamido-3,6-dideoxy-α-D-glucose biosynthesis	5	2	1
Salmonella enterica serotype O:54 O antigen biosynthesis	5	2	1
dTDP-3-acetamido-α-D-fucose biosynthesis	5	2	1
L-leucine degradation IV (reductive Stickland reaction)	5	1	1
superpathway of branched chain amino acid biosynthesis	17	17	3
L-leucine biosynthesis	6	6	1
L-leucine degradation I	6	4	1
L-isoleucine degradation I	6	4	1
dTDP-L-daunosamine biosynthesis	6	3	1
dTDP-sibirosamine biosynthesis	6	3	1
L-isoleucine biosynthesis IV	6	3	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	3	1
dTDP-D-desosamine biosynthesis	6	2	1
dTDP-α-D-ravidosamine and dTDP-4-acetyl-α-D-ravidosamine biosynthesis	6	2	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-isoleucine biosynthesis III	7	4	1
pyruvate fermentation to propanoate I	7	4	1
dTDP-β-L-digitoxose biosynthesis	7	3	1
dTDP-β-L-olivose biosynthesis	7	3	1
dTDP-β-L-mycarose biosynthesis	7	2	1
L-isoleucine biosynthesis II	8	6	1
dTDP-β-L-megosamine biosynthesis	8	3	1
dTDP-β-L-4-epi-vancosamine biosynthesis	8	3	1
L-valine degradation I	8	3	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	7	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
anaerobic energy metabolism (invertebrates, mitochondrial)	10	6	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
O-antigen building blocks biosynthesis (E. coli)	11	8	1
L-glutamate degradation VIII (to propanoate)	11	4	1
poly(glycerol phosphate) wall teichoic acid biosynthesis	11	3	1
poly(ribitol phosphate) wall teichoic acid biosynthesis I (B. subtilis)	12	2	1
superpathway of L-isoleucine biosynthesis I	13	13	1
3-hydroxypropanoate cycle	13	7	1
formaldehyde assimilation I (serine pathway)	13	6	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	5	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	3	1
poly(ribitol phosphate) wall teichoic acid biosynthesis II (S. aureus)	14	2	1
superpathway of L-methionine salvage and degradation	16	9	1
superpathway of anaerobic energy metabolism (invertebrates)	17	10	1
superpathway of L-threonine metabolism	18	11	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	10	1
superpathway of the 3-hydroxypropanoate cycle	18	7	1
methylaspartate cycle	19	11	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
even iso-branched-chain fatty acid biosynthesis	34	24	1
odd iso-branched-chain fatty acid biosynthesis	34	24	1
anteiso-branched-chain fatty acid biosynthesis	34	24	1