Experiment set7IT035 for Herbaspirillum seropedicae SmR1

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: HerbieS_ML4a, serum bottle, Anaerobic, at 30 (C), shaken=0 rpm
Growth: about 3.3 generations
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 29 genes in this experiment

For nitrogen fixation L-Malic acid in Herbaspirillum seropedicae SmR1

For nitrogen fixation L-Malic acid across organisms

SEED Subsystems

Subsystem	#Specific
Nitrogen fixation	9
Acetyl-CoA fermentation to Butyrate	3
Alanine biosynthesis	1
Ammonia assimilation	1
Bacterial Chemotaxis	1
Bacterial hemoglobins	1
Heat shock dnaK gene cluster extended	1
Lipid A-Ara4N pathway ( Polymyxin resistance )	1
Orphan regulatory proteins	1
Protein chaperones	1
Proteolysis in bacteria, ATP-dependent	1
Ribosome biogenesis bacterial	1
Thiamin biosynthesis	1
Transcription factors bacterial	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Lysine biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Methionine metabolism
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Aminophosphonate metabolism
• Nucleotide sugars metabolism
• Pyruvate metabolism
• Tetrachloroethene degradation
• Naphthalene and anthracene degradation
• Thiamine metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Caprolactam degradation
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
nitrogen fixation II (flavodoxin)	1	1	1
L-cysteine degradation IV	1	1	1
L-alanine biosynthesis III	1	1	1
nitrogen fixation I (ferredoxin)	1	1	1
cytidylyl molybdenum cofactor sulfurylation	2	1	1
FeMo cofactor biosynthesis	6	2	2
bis(guanylyl molybdopterin) cofactor sulfurylation	3	1	1
thiazole component of thiamine diphosphate biosynthesis II	7	5	2
superpathway of L-alanine biosynthesis	4	4	1
tRNA-uridine 2-thiolation (mammalian mitochondria)	4	1	1
tRNA-uridine 2-thiolation (yeast mitochondria)	4	1	1
[2Fe-2S] iron-sulfur cluster biosynthesis	10	3	2
tRNA-uridine 2-thiolation (thermophilic bacteria)	5	1	1
superpathway of thiamine diphosphate biosynthesis II	11	9	2
thiazole component of thiamine diphosphate biosynthesis I	6	4	1
molybdopterin biosynthesis	6	3	1
tRNA-uridine 2-thiolation (cytoplasmic)	8	1	1
L-lysine biosynthesis IV	9	2	1
superpathway of thiamine diphosphate biosynthesis I	10	8	1
L-lysine biosynthesis V	10	2	1
tRNA-uridine 2-thiolation and selenation (bacteria)	11	2	1
coenzyme B biosynthesis	16	2	1