Experiment set2S181 for Escherichia coli ECRC101

Casamino-acids

Group: carbon source
Media: M9_plus_Casamino-acids + Casamino-acids (5 mg/mL)
Culturing: Ecoli_ECRC101_ML1, 48 well microplate, Aerobic, at 37 (C), shaken=double orbital, continuous, 205cpm
By: Lucas on 12/16/24

Specific Phenotypes

For 12 genes in this experiment

For carbon source Casamino-acids in Escherichia coli ECRC101

For carbon source Casamino-acids across organisms

SEED Subsystems

Subsystem	#Specific
NAD and NADP cofactor biosynthesis global	2
NAD regulation	2
Serine-glyoxylate cycle	2
TCA Cycle	2
Thiamin biosynthesis	2
Biotin biosynthesis	1
Coenzyme A Biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Citrate cycle (TCA cycle)
• Alanine and aspartate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Nicotinate and nicotinamide metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones
• Ubiquinone and menaquinone biosynthesis
• Methionine metabolism
• Tryptophan metabolism
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• Carbon fixation in photosynthetic organisms
• Thiamine metabolism
• Riboflavin metabolism
• Pantothenate and CoA biosynthesis
• Biotin metabolism
• Porphyrin and chlorophyll metabolism
• Terpenoid biosynthesis
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
biotin biosynthesis from 8-amino-7-oxononanoate I	4	4	2
thiamine diphosphate biosynthesis I (E. coli)	2	2	1
thiamine diphosphate biosynthesis II (Bacillus)	2	2	1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis I	2	2	1
malate/L-aspartate shuttle pathway	2	2	1
L-glutamate degradation II	2	2	1
biotin biosynthesis from 8-amino-7-oxononanoate II	4	3	2
biotin biosynthesis from 8-amino-7-oxononanoate III	5	3	2
thiamine diphosphate salvage V	3	3	1
L-aspartate degradation III (anaerobic)	3	3	1
L-aspartate degradation II (aerobic)	3	3	1
NAD de novo biosynthesis IV (anaerobic)	6	5	2
TCA cycle VIII (Chlamydia)	6	5	2
NAD de novo biosynthesis I	6	5	2
biotin biosynthesis II	6	4	2
thiamine diphosphate biosynthesis III (Staphylococcus)	3	1	1
thiamine diphosphate biosynthesis IV (eukaryotes)	3	1	1
superpathway of thiamine diphosphate biosynthesis I	10	10	3
pyruvate fermentation to propanoate I	7	5	2
incomplete reductive TCA cycle	7	5	2
superpathway of thiamine diphosphate biosynthesis III (eukaryotes)	7	3	2
superpathway of thiamine diphosphate biosynthesis II	11	9	3
phosphopantothenate biosynthesis I	4	4	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	4	1
NAD biosynthesis from 2-amino-3-carboxymuconate semialdehyde	4	3	1
phosphopantothenate biosynthesis III (archaea)	4	2	1
heme a biosynthesis	4	2	1
TCA cycle II (plants and fungi)	9	7	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	2
TCA cycle V (2-oxoglutarate synthase)	9	7	2
nicotine biosynthesis	9	3	2
thiamine diphosphate salvage II	5	5	1
TCA cycle I (prokaryotic)	10	9	2
TCA cycle III (animals)	10	8	2
reductive TCA cycle I	11	8	2
L-glutamate degradation VIII (to propanoate)	11	7	2
glyoxylate cycle	6	6	1
thiazole component of thiamine diphosphate biosynthesis I	6	6	1
superpathway of glyoxylate bypass and TCA	12	11	2
reductive TCA cycle II	12	8	2
NAD de novo biosynthesis III	6	4	1
superpathway of nicotine biosynthesis	12	4	2
L-canavanine degradation II	6	1	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	10	2
superpathway of glyoxylate cycle and fatty acid degradation	14	11	2
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
thiazole component of thiamine diphosphate biosynthesis II	7	5	1
thiamine diphosphate salvage IV (yeast)	7	4	1
biotin biosynthesis I	15	15	2
mixed acid fermentation	16	16	2
partial TCA cycle (obligate autotrophs)	8	7	1
thiamine diphosphate formation from pyrithiamine and oxythiamine (yeast)	8	4	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	2
superpathway of coenzyme A biosynthesis I (bacteria)	9	9	1
TCA cycle VI (Helicobacter)	9	7	1
TCA cycle VII (acetate-producers)	9	6	1
NAD de novo biosynthesis II (from tryptophan)	9	3	1
methylaspartate cycle	19	11	2
anaerobic energy metabolism (invertebrates, mitochondrial)	10	7	1
superpathway of coenzyme A biosynthesis II (plants)	10	5	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	2
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	8	1
gluconeogenesis III	12	9	1
aspartate superpathway	25	24	2
gluconeogenesis I	13	13	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	2
formaldehyde assimilation I (serine pathway)	13	8	1
superpathway of NAD biosynthesis in eukaryotes	14	7	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	2