Experiment set1S323 for Acinetobacter radioresistens SK82

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L-Serine nitrogen source

Group: nitrogen source
Media: RCH2_defined_noNitrogen + L-Serine (20 mM)
Culturing: Acinetobacter_SK82_ML3, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=200 rpm
By: Kiani on 5/1/24
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM Sodium D,L-Lactate, 30 mM PIPES sesquisodium salt, 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 37 genes in this experiment

For nitrogen source L-Serine in Acinetobacter radioresistens SK82

For nitrogen source L-Serine across organisms

SEED Subsystems

Subsystem #Specific
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 2
Methionine Biosynthesis 2
Rhamnose containing glycans 2
Threonine and Homoserine Biosynthesis 2
linker unit-arabinogalactan synthesis 2
Choline and Betaine Uptake and Betaine Biosynthesis 1
Conserved gene cluster associated with Met-tRNA formyltransferase 1
De Novo Purine Biosynthesis 1
Glycine and Serine Utilization 1
Heat shock dnaK gene cluster extended 1
Isoleucine degradation 1
Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway 1
Lactose and Galactose Uptake and Utilization 1
N-linked Glycosylation in Bacteria 1
Pyruvate Alanine Serine Interconversions 1
Ribosomal protein S12p Asp methylthiotransferase 1
Rubrerythrin 1
TCA Cycle 1
Valine degradation 1
dTDP-rhamnose synthesis 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
3-(4-hydroxyphenyl)pyruvate biosynthesis 1 1 1
UDP-N-acetyl-D-galactosamine biosynthesis I 1 1 1
L-aspartate biosynthesis 1 1 1
L-asparagine degradation I 1 1 1
UDP-α-D-galactose biosynthesis 1 1 1
L-aspartate degradation I 1 1 1
L-asparagine degradation III (mammalian) 3 2 2
L-glutamate degradation II 2 2 1
malate/L-aspartate shuttle pathway 2 2 1
choline degradation I 2 2 1
glycine betaine biosynthesis II (Gram-positive bacteria) 2 2 1
tetrahydrofolate salvage from 5,10-methenyltetrahydrofolate 2 2 1
L-threonine biosynthesis 2 2 1
glycine betaine biosynthesis I (Gram-negative bacteria) 2 2 1
superpathway of L-aspartate and L-asparagine biosynthesis 4 3 2
atromentin biosynthesis 2 1 1
L-tyrosine degradation II 2 1 1
β-alanine biosynthesis I 2 1 1
β-alanine biosynthesis IV 2 1 1
UDP-α-D-galactofuranose biosynthesis 2 1 1
L-tryptophan degradation IV (via indole-3-lactate) 2 1 1
octane oxidation 5 4 2
superpathway of L-threonine biosynthesis 6 6 2
superpathway of 5-aminoimidazole ribonucleotide biosynthesis 6 6 2
choline-O-sulfate degradation 3 3 1
L-phenylalanine biosynthesis I 3 3 1
ethanol degradation II 3 3 1
L-tyrosine biosynthesis I 3 3 1
L-serine biosynthesis I 3 3 1
ethanol degradation IV 3 3 1
hypotaurine degradation 3 2 1
L-phenylalanine degradation II (anaerobic) 3 2 1
glycine betaine biosynthesis III (plants) 3 2 1
ethanol degradation III 3 2 1
indole-3-acetate biosynthesis VI (bacteria) 3 1 1
L-methionine salvage from L-homocysteine 3 1 1
sulfolactate degradation III 3 1 1
D-galactose detoxification 3 1 1
histamine degradation 3 1 1
(R)-cysteate degradation 3 1 1
L-tyrosine degradation IV (to 4-methylphenol) 3 1 1
dimethylsulfoniopropanoate biosynthesis I (Wollastonia) 3 1 1
L-methionine biosynthesis III 4 4 1
superpathway of L-serine and glycine biosynthesis I 4 4 1
phytol degradation 4 3 1
L-tyrosine degradation III 4 2 1
L-phenylalanine degradation III 4 2 1
fatty acid α-oxidation I (plants) 4 2 1
choline degradation IV 4 2 1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 8 3 2
putrescine degradation III 4 1 1
L-tryptophan degradation X (mammalian, via tryptamine) 4 1 1
dimethylsulfoniopropanoate biosynthesis II (Spartina) 4 1 1
ferulate and sinapate biosynthesis 4 1 1
L-tryptophan degradation VIII (to tryptophol) 4 1 1
superpathway of L-methionine biosynthesis (transsulfuration) 9 7 2
5-aminoimidazole ribonucleotide biosynthesis II 5 5 1
dTDP-β-L-rhamnose biosynthesis 5 5 1
5-aminoimidazole ribonucleotide biosynthesis I 5 5 1
L-tyrosine degradation I 5 4 1
L-methionine biosynthesis I 5 3 1
superpathway of plastoquinol biosynthesis 5 3 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
mitochondrial NADPH production (yeast) 5 2 1
cytosolic NADPH production (yeast) 5 2 1
N-(1-deoxy-D-fructos-1-yl)-L-asparagine degradation 5 2 1
trans-4-hydroxy-L-proline degradation I 5 2 1
D-galactose degradation I (Leloir pathway) 5 2 1
L-phenylalanine degradation VI (reductive Stickland reaction) 5 1 1
4-hydroxybenzoate biosynthesis I (eukaryotes) 5 1 1
L-tyrosine degradation V (reductive Stickland reaction) 5 1 1
L-tryptophan degradation XIII (reductive Stickland reaction) 5 1 1
dopamine degradation 5 1 1
C4 photosynthetic carbon assimilation cycle, NAD-ME type 11 8 2
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 11 2
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 16 3
TCA cycle VIII (Chlamydia) 6 5 1
L-methionine biosynthesis II 6 5 1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis 6 4 1
3-methyl-branched fatty acid α-oxidation 6 3 1
superpathway of sulfolactate degradation 6 2 1
coenzyme M biosynthesis II 6 1 1
alkane oxidation 6 1 1
superpathway of L-isoleucine biosynthesis I 13 13 2
noradrenaline and adrenaline degradation 13 4 2
anaerobic energy metabolism (invertebrates, cytosol) 7 6 1
C4 photosynthetic carbon assimilation cycle, PEPCK type 14 8 2
serotonin degradation 7 3 1
UDP-N-acetyl-D-galactosamine biosynthesis II 7 3 1
ceramide degradation by α-oxidation 7 2 1
stachyose degradation 7 2 1
limonene degradation IV (anaerobic) 7 1 1
partial TCA cycle (obligate autotrophs) 8 7 1
nitrogen remobilization from senescing leaves 8 6 1
superpathway of L-homoserine and L-methionine biosynthesis 8 6 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
aromatic biogenic amine degradation (bacteria) 8 1 1
aspartate superpathway 25 22 3
superpathway of aromatic amino acid biosynthesis 18 18 2
TCA cycle V (2-oxoglutarate synthase) 9 8 1
folate transformations III (E. coli) 9 8 1
superpathway of sulfate assimilation and cysteine biosynthesis 9 8 1
TCA cycle IV (2-oxoglutarate decarboxylase) 9 7 1
superpathway of S-adenosyl-L-methionine biosynthesis 9 7 1
TCA cycle VI (Helicobacter) 9 6 1
TCA cycle VII (acetate-producers) 9 6 1
L-phenylalanine degradation IV (mammalian, via side chain) 9 4 1
UDP-sugars interconversion 9 2 1
teichuronic acid biosynthesis (B. subtilis 168) 9 2 1
superpathway of L-phenylalanine biosynthesis 10 10 1
superpathway of L-tyrosine biosynthesis 10 10 1
TCA cycle I (prokaryotic) 10 8 1
rosmarinic acid biosynthesis I 10 1 1
O-antigen building blocks biosynthesis (E. coli) 11 10 1
folate transformations II (plants) 11 9 1
reductive TCA cycle I 11 7 1
colanic acid building blocks biosynthesis 11 7 1
(S)-reticuline biosynthesis I 11 1 1
superpathway of tetrahydrofolate biosynthesis and salvage 12 10 1
superpathway of glyoxylate bypass and TCA 12 10 1
indole-3-acetate biosynthesis II 12 3 1
folate transformations I 13 8 1
superpathway of rosmarinic acid biosynthesis 14 1 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II 15 13 1
mixed acid fermentation 16 12 1
superpathway of L-methionine salvage and degradation 16 5 1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis 33 12 2
superpathway of anaerobic energy metabolism (invertebrates) 17 11 1
mycolyl-arabinogalactan-peptidoglycan complex biosynthesis 18 1 1
methylaspartate cycle 19 10 1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis 19 5 1
superpathway of purine nucleotides de novo biosynthesis I 21 21 1
ethene biosynthesis V (engineered) 25 18 1
superpathway of purine nucleotides de novo biosynthesis II 26 24 1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 20 1
anaerobic aromatic compound degradation (Thauera aromatica) 27 3 1
superpathway of chorismate metabolism 59 36 2
superpathway of histidine, purine, and pyrimidine biosynthesis 46 43 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 20 1