Experiment set4IT045 for Escherichia coli BL21

Mixed culture, Halobacteriovorax-1

Group: balo
Media: M9 (0.1x), pH=7
Culturing: BL21_ML4, flask, Aerobic, at 30C (C), shaken=200 rpm
By: AR on 5/19/21
Media components: 0.4 g/L D-Glucose, 0.2 mM Magnesium sulfate, 0.01 mM Calcium chloride, 1.28 g/L Sodium phosphate dibasic heptahydrate, 0.3 g/L Potassium phosphate monobasic, 0.05 g/L Sodium Chloride, 0.1 g/L Ammonium chloride (final concentrations)

Specific Phenotypes

For 18 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Arginine Biosynthesis extended	8
Methionine Biosynthesis	3
Threonine and Homoserine Biosynthesis	3
Glycine and Serine Utilization	2
Lysine Biosynthesis DAP Pathway	2
Serine Biosynthesis	2
Arginine Deiminase Pathway	1
Arginine and Ornithine Degradation	1
DNA-binding regulatory proteins, strays	1
Fermentations: Mixed acid	1
One-carbon metabolism by tetrahydropterines	1
Pyridoxin (Vitamin B6) Biosynthesis	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Serine-glyoxylate cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Arginine and proline metabolism
• Urea cycle and metabolism of amino groups
• Glycine, serine and threonine metabolism
• Lysine biosynthesis
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Alanine and aspartate metabolism
• Biosynthesis of plant hormones
• Geraniol degradation
• Tryptophan metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• One carbon pool by folate
• Methane metabolism
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Vitamin B6 metabolism
• Limonene and pinene degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-ornithine biosynthesis I	5	5	5
L-threonine biosynthesis	2	2	2
L-arginine biosynthesis I (via L-ornithine)	9	9	8
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	7
L-arginine biosynthesis II (acetyl cycle)	10	9	7
superpathway of L-threonine biosynthesis	6	6	4
L-serine biosynthesis I	3	3	2
L-homoserine biosynthesis	3	3	2
nitric oxide biosynthesis II (mammals)	3	2	2
urea cycle	5	3	3
superpathway of L-serine and glycine biosynthesis I	4	4	2
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
canavanine biosynthesis	4	2	2
superpathway of arginine and polyamine biosynthesis	17	16	8
L-citrulline degradation	3	3	1
L-cysteine biosynthesis IX (Trichomonas vaginalis)	3	2	1
L-arginine biosynthesis IV (archaea)	9	4	3
superpathway of L-isoleucine biosynthesis I	13	13	4
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	18	5
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	4
superpathway of L-homoserine and L-methionine biosynthesis	8	8	2
dipicolinate biosynthesis	4	3	1
L-arginine degradation V (arginine deiminase pathway)	4	3	1
superpathway of L-citrulline metabolism	12	8	3
spermidine biosynthesis II	4	2	1
L-methionine biosynthesis IV	4	2	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	2
superpathway of S-adenosyl-L-methionine biosynthesis	9	9	2
L-lysine biosynthesis I	9	9	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	9	2
L-arginine degradation II (AST pathway)	5	5	1
aspartate superpathway	25	24	5
L-arginine degradation XIII (reductive Stickland reaction)	5	3	1
ectoine biosynthesis	5	2	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	10	2
L-methionine biosynthesis II	6	5	1
norspermidine biosynthesis	6	2	1
L-arginine degradation XIV (oxidative Stickland reaction)	6	1	1
folate transformations I	13	9	2
L-lysine biosynthesis VI	7	6	1
L-lysine biosynthesis III	7	6	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
3-dehydroquinate biosynthesis II (archaea)	7	3	1
cremeomycin biosynthesis	7	2	1
L-glutamate degradation XI (reductive Stickland reaction)	7	2	1
partial TCA cycle (obligate autotrophs)	8	7	1
L-citrulline biosynthesis	8	6	1
nitrogen remobilization from senescing leaves	8	5	1
grixazone biosynthesis	8	2	1
superpathway of polyamine biosynthesis III	8	2	1
folate transformations III (E. coli)	9	9	1
L-lysine biosynthesis II	9	6	1
L-glutamate degradation V (via hydroxyglutarate)	10	5	1
reductive acetyl coenzyme A pathway I (homoacetogenic bacteria)	10	3	1
folate transformations II (plants)	11	10	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	8	1
chorismate biosynthesis II (archaea)	12	8	1
formaldehyde assimilation I (serine pathway)	13	8	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	1
mixed acid fermentation	16	16	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
ethene biosynthesis V (engineered)	25	18	1
platensimycin biosynthesis	26	6	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	2