Experiment set5IT015 for Azospirillum brasilense Sp245

L-Malic acid carbon source and no Nitrogen; normal Wolfe's minerals with nitroloacetic acid; 8 days

Group: nitrogen fixation
Media: RCH2_defined_noCarbon_minimalN + L-Malic acid (20 mM)
Culturing: AzoBra_ML2a, serum bottle, Anaerobic, at 30 (C), shaken=0 rpm
By: Kelly Wetmore; Jordan Baker on 26-Mar-19
Media components: 0.1 g/L Potassium Chloride, 0.49 g/L Sodium phosphate monobasic monohydrate, 0.97 g/L Potassium phosphate dibasic, 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)

Specific Phenotypes

For 18 genes in this experiment

For nitrogen fixation L-Malic acid in Azospirillum brasilense Sp245

For nitrogen fixation L-Malic acid across organisms

SEED Subsystems

Subsystem	#Specific
Nitrogen fixation	7
Acetyl-CoA fermentation to Butyrate	2
Bacterial hemoglobins	1
CBSS-343509.6.peg.2644	1
Cobalamin synthesis	1
Coenzyme B12 biosynthesis	1
Fatty Acid Biosynthesis FASII	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Polyhydroxybutyrate metabolism	1
Redox-dependent regulation of nucleus processes	1
mycolic acid synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Fatty acid biosynthesis
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Glycosaminoglycan degradation
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Tetrachloroethene degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Butanoate metabolism
• Nicotinate and nicotinamide metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
nitrogen fixation I (ferredoxin)	1	1	1
nitrogen fixation II (flavodoxin)	1	1	1
adenosylcobalamin salvage from cobalamin	5	5	4
adenosylcobinamide-GDP salvage from cobinamide I	5	5	3
adenosylcobinamide-GDP biosynthesis from cobyrinate a,c-diamide	6	6	3
adenosylcobinamide-GDP salvage from cobinamide II	6	5	3
cobalamin salvage (eukaryotic)	8	4	4
fatty acid elongation -- saturated	5	5	2
superpathway of adenosylcobalamin salvage from cobinamide I	8	8	3
superpathway of adenosylcobalamin salvage from cobinamide II	9	8	3
gondoate biosynthesis (anaerobic)	4	4	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	7
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	8	2
oleate biosynthesis IV (anaerobic)	14	13	3
superpathway of fatty acids biosynthesis (E. coli)	53	48	11
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	17	4
cis-vaccenate biosynthesis	5	4	1
8-amino-7-oxononanoate biosynthesis IV	5	4	1
NAD salvage pathway V (PNC V cycle)	5	3	1
superpathway of fatty acid biosynthesis I (E. coli)	16	14	3
superpathway of fatty acid biosynthesis II (plant)	43	38	8
8-amino-7-oxononanoate biosynthesis I	11	9	2
anteiso-branched-chain fatty acid biosynthesis	34	31	6
even iso-branched-chain fatty acid biosynthesis	34	31	6
odd iso-branched-chain fatty acid biosynthesis	34	31	6
stearate biosynthesis II (bacteria and plants)	6	5	1
(5Z)-dodecenoate biosynthesis I	6	5	1
(5Z)-dodecenoate biosynthesis II	6	4	1
streptorubin B biosynthesis	34	20	5
NAD salvage pathway I (PNC VI cycle)	7	5	1
biotin biosynthesis I	15	10	2
adenosylcobalamin biosynthesis II (aerobic)	33	27	3
NAD salvage (plants)	11	5	1
adenosylcobalamin biosynthesis I (anaerobic)	36	25	3
superpathway of NAD biosynthesis in eukaryotes	14	5	1
mycolate biosynthesis	205	23	4
superpathway of mycolate biosynthesis	239	24	4