Experiment set7IT029 for Herbaspirillum seropedicae SmR1

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

Group: nitrogen fixation
Media: RCH2_defined_noCarbon_minimalN + D-Glucose (20 mM)
Culturing: HerbieS_ML4a, serum bottle, Anaerobic, at 30 (C), shaken=0 rpm
Growth: about 4.0 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 39 genes in this experiment

For nitrogen fixation D-Glucose in Herbaspirillum seropedicae SmR1

For nitrogen fixation D-Glucose across organisms

SEED Subsystems

Subsystem #Specific
Nitrogen fixation 10
Acetyl-CoA fermentation to Butyrate 3
Bacterial Chemotaxis 3
Alanine biosynthesis 2
Protein chaperones 2
Ammonia assimilation 1
Bacterial hemoglobins 1
Chitin and N-acetylglucosamine utilization 1
Heat shock dnaK gene cluster extended 1
Hydantoin metabolism 1
Lipid A-Ara4N pathway ( Polymyxin resistance ) 1
Molybdenum cofactor biosynthesis 1
Multidrug Resistance Efflux Pumps 1
Orphan regulatory proteins 1
Proteolysis in bacteria, ATP-dependent 1
Ribosome biogenesis bacterial 1
Sialic Acid Metabolism 1
Soluble cytochromes and functionally related electron carriers 1
Thiamin biosynthesis 1
Transport of Molybdenum 1
UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
L-cysteine degradation IV 1 1 1
nitrogen fixation I (ferredoxin) 1 1 1
L-alanine biosynthesis III 1 1 1
nitrogen fixation II (flavodoxin) 1 1 1
N-acetylglucosamine degradation I 2 2 1
cytidylyl molybdenum cofactor sulfurylation 2 1 1
N-acetylglucosamine degradation II 3 3 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
D-galactosamine and N-acetyl-D-galactosamine degradation 4 1 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
N-acetyl-D-galactosamine degradation 5 1 1
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
superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation 6 2 1
chitin derivatives degradation 8 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
peptidoglycan recycling I 14 10 1
coenzyme B biosynthesis 16 2 1
superpathway of N-acetylneuraminate degradation 22 15 1
phosphinothricin tripeptide biosynthesis 25 2 1
phosalacine biosynthesis 25 2 1