Experiment set5S120 for Erwinia amylovora T8

Matrix:KB soft agar;Phage:PBS;Temp:28;Samp:32-3

Group:
Media:
Culturing: Erwinia_T8_ML2, at 28 (C)
By: Milo on 17-Aug-24

Specific Phenotypes

For 5 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Biogenesis of c-type cytochromes	1
Biotin biosynthesis	1
ECF class transporters	1
Entner-Doudoroff Pathway	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Periplasmic disulfide interchange	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Glycolysis / Gluconeogenesis
• Lipopolysaccharide biosynthesis
• Pyruvate metabolism
• Carbon fixation in photosynthetic organisms
• Folate biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
periplasmic disulfide bond reduction	2	2	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
Entner-Doudoroff pathway I	9	8	1
Entner-Doudoroff pathway III (semi-phosphorylative)	9	7	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	6	1
Rubisco shunt	10	9	1
glycolysis IV	10	8	1
glycolysis V (Pyrococcus)	10	7	1
glycolysis III (from glucose)	11	11	1
glycolysis II (from fructose 6-phosphate)	11	11	1
cytochrome c biogenesis (system I type)	11	9	1
glycolysis VI (from fructose)	11	8	1
homolactic fermentation	12	11	1
glycolysis I (from glucose 6-phosphate)	13	13	1
Bifidobacterium shunt	15	12	1
mixed acid fermentation	16	14	1
glycerol degradation to butanol	16	9	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	16	1
superpathway of glucose and xylose degradation	17	14	1
superpathway of anaerobic energy metabolism (invertebrates)	17	10	1
superpathway of hexitol degradation (bacteria)	18	15	1
heterolactic fermentation	18	15	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	18	1
superpathway of anaerobic sucrose degradation	19	17	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
superpathway of N-acetylneuraminate degradation	22	18	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	23	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1