Experiment set20IT014 for Escherichia coli BW25113

M9 Acetate 0.5% aerobic

Group:
Media: M9_Avi_noCarbon + Sodium acetate (61 mM)
Culturing: Keio_ML9a, tube, Aerobic, at 37 (C), shaken=250 rpm
By: Avi on 27-Apr-17

Specific Phenotypes

For 56 genes in this experiment

For Sodium acetate across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	2
Methionine Biosynthesis	2
Methionine Degradation	2
Pyruvate metabolism I: anaplerotic reactions, PEP	2
Serine-glyoxylate cycle	2
TCA Cycle	2
ATP-dependent RNA helicases, bacterial	1
Ammonia assimilation	1
Beta-Glucoside Metabolism	1
Biogenesis of cytochrome c oxidases	1
CBSS-562.2.peg.5158 SK3 including	1
Curli production	1
D-ribose utilization	1
Deoxyribose and Deoxynucleoside Catabolism	1
Flavodoxin	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
LOS core oligosaccharide biosynthesis	1
N-Acetyl-Galactosamine and Galactosamine Utilization	1
Orphan regulatory proteins	1
Staphylococcal phi-Mu50B-like prophages	1
Universal stress protein family	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
• Reductive carboxylate cycle (CO2 fixation)
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Purine metabolism
• Lipopolysaccharide biosynthesis
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Photosynthesis
• Glutamate metabolism
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Selenoamino acid metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Ethylbenzene degradation
• Butanoate metabolism
• Carbon fixation in photosynthetic organisms
• Thiamine metabolism
• Lipoic acid metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate biosynthesis I	2	2	2
L-malate degradation I	1	1	1
L-cysteine degradation IV	1	1	1
L-glutamine degradation II	1	1	1
L-glutamine degradation I	1	1	1
L-alanine biosynthesis III	1	1	1
ammonia assimilation cycle III	3	3	2
glyoxylate cycle	6	6	3
ribose phosphorylation	2	2	1
chitobiose degradation	2	2	1
polyphosphate metabolism	2	2	1
cytidylyl molybdenum cofactor sulfurylation	2	1	1
partial TCA cycle (obligate autotrophs)	8	7	3
2-deoxy-D-ribose degradation I	3	3	1
superpathway of glyoxylate bypass and TCA	12	11	4
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	3
TCA cycle VI (Helicobacter)	9	7	3
TCA cycle V (2-oxoglutarate synthase)	9	7	3
TCA cycle II (plants and fungi)	9	7	3
TCA cycle VII (acetate-producers)	9	6	3
bis(guanylyl molybdopterin) cofactor sulfurylation	3	1	1
TCA cycle I (prokaryotic)	10	9	3
TCA cycle III (animals)	10	8	3
superpathway of glyoxylate cycle and fatty acid degradation	14	11	4
L-glutamate and L-glutamine biosynthesis	7	5	2
thiazole component of thiamine diphosphate biosynthesis II	7	5	2
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	2
reductive TCA cycle I	11	8	3
superpathway of L-alanine biosynthesis	4	4	1
reductive TCA cycle II	12	8	3
nitrogen remobilization from senescing leaves	8	5	2
L-asparagine biosynthesis III (tRNA-dependent)	4	1	1
tRNA-uridine 2-thiolation (mammalian mitochondria)	4	1	1
photosynthesis light reactions	4	1	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	1	1
tRNA-uridine 2-thiolation (yeast mitochondria)	4	1	1
NADPH to cytochrome c oxidase via plastocyanin (thylakoid membrane)	4	1	1
2-methylcitrate cycle I	5	5	1
[2Fe-2S] iron-sulfur cluster biosynthesis	10	4	2
tRNA-uridine 2-thiolation (thermophilic bacteria)	5	1	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	5
mixed acid fermentation	16	16	3
superpathway of thiamine diphosphate biosynthesis II	11	9	2
thiazole component of thiamine diphosphate biosynthesis I	6	6	1
molybdopterin biosynthesis	6	6	1
ppGpp metabolism	6	6	1
TCA cycle VIII (Chlamydia)	6	5	1
2-methylcitrate cycle II	6	4	1
superpathway of photosynthetic hydrogen production	6	3	1
methylgallate degradation	6	2	1
methylaspartate cycle	19	9	3
gluconeogenesis I	13	13	2
pyruvate fermentation to propanoate I	7	5	1
incomplete reductive TCA cycle	7	5	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	3
L-citrulline biosynthesis	8	6	1
protocatechuate degradation I (meta-cleavage pathway)	8	3	1
tRNA-uridine 2-thiolation (cytoplasmic)	8	1	1
ethene biosynthesis V (engineered)	25	18	3
superpathway of thiamine diphosphate biosynthesis I	10	10	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	7	1
glycolysis V (Pyrococcus)	10	7	1
superpathway of vanillin and vanillate degradation	10	3	1
glycolysis II (from fructose 6-phosphate)	11	11	1
tRNA-uridine 2-thiolation and selenation (bacteria)	11	7	1
L-glutamate degradation VIII (to propanoate)	11	5	1
superpathway of L-citrulline metabolism	12	8	1
syringate degradation	12	3	1
glycolysis I (from glucose 6-phosphate)	13	13	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	10	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	17	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	1
oxygenic photosynthesis	17	11	1
superpathway of hexitol degradation (bacteria)	18	18	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	19	1
superpathway of anaerobic sucrose degradation	19	17	1
superpathway of N-acetylneuraminate degradation	22	22	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	2