Experiment set1S292 for Escherichia fergusonii Becca

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BHIS_CaCl2 no phage control

Group: no phage control
Media: BHIS_CaCl2
Culturing: E_fergusonii_Becca_ML3
By: Taylor on 1/4/24
Media components: 7.7 g/L Calf brains, 9.8 g/L Beef heart, 10 g/L Proteose Peptone, 5 g/L Sodium Chloride, 2.5 g/L Disodium phosphate, 1 g/L L-Cysteine, 2 g/L Sodium bicarbonate, 0.005 g/L Hemin, 1 mM Calcium chloride dihydrate

Specific Phenotypes

For 79 genes in this experiment

SEED Subsystems

Subsystem #Specific
Hydrogenases 4
LOS core oligosaccharide biosynthesis 4
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) 3
Membrane-bound Ni, Fe-hydrogenase 3
Chorismate Synthesis 2
Lactose and Galactose Uptake and Utilization 2
Lipid A modifications 2
Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes 2
Orphan regulatory proteins 2
Serine-glyoxylate cycle 2
Succinate dehydrogenase 2
TCA Cycle 2
Anaerobic respiratory reductases 1
Arginine and Ornithine Degradation 1
Bacterial Cell Division 1
CMP-N-acetylneuraminate Biosynthesis 1
Capsular heptose biosynthesis 1
Cluster-based Subsystem Grouping Hypotheticals - perhaps Proteosome Related 1
Cysteine Biosynthesis 1
D-Galacturonate and D-Glucuronate Utilization 1
DNA-binding regulatory proteins, strays 1
Flavodoxin 1
Formate hydrogenase 1
Glutathione: Redox cycle 1
KDO2-Lipid A biosynthesis 1
Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway 1
N-Acetyl-Galactosamine and Galactosamine Utilization 1
N-linked Glycosylation in Bacteria 1
NiFe hydrogenase maturation 1
Phenylalanine and Tyrosine Branches from Chorismate 1
Polyadenylation bacterial 1
Polyamine Metabolism 1
Proteolysis in bacteria, ATP-dependent 1
RNA processing and degradation, bacterial 1
Rhamnose containing glycans 1
Ribonuclease H 1
Ribosomal protein S5p acylation 1
Ribosome biogenesis bacterial 1
Sialic Acid Metabolism 1
Transcription factors bacterial 1
Trehalose Uptake and Utilization 1
Twin-arginine translocation system 1
Type III secretion system orphans 1
YeiH 1
linker unit-arabinogalactan 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
hydrogen production III 1 1 1
cellulose biosynthesis 1 1 1
UDP-α-D-galactose biosynthesis 1 1 1
UDP-N-acetyl-α-D-mannosamine biosynthesis 1 1 1
hydrogen production VIII 1 1 1
UDP-N-acetyl-D-galactosamine biosynthesis I 1 1 1
hydrogen oxidation I (aerobic) 1 1 1
succinate to cytochrome bd oxidase electron transfer 2 2 1
glycerol-3-phosphate to fumarate electron transfer 2 2 1
NADH to fumarate electron transfer 2 2 1
hydrogen production VI 2 1 1
superpathway of hydrogen production 2 1 1
succinate to cytochrome bo oxidase electron transfer 2 1 1
succinate to cytochrome aa3 oxidase electron transfer 2 1 1
hydrogen to fumarate electron transfer 2 1 1
UDP-α-D-galactofuranose biosynthesis 2 1 1
chorismate biosynthesis from 3-dehydroquinate 5 5 2
molybdenum cofactor biosynthesis 3 3 1
D-galactose detoxification 3 3 1
glutathione-peroxide redox reactions 3 2 1
aerobic respiration III (alternative oxidase pathway) 3 2 1
CMP-N-acetylneuraminate biosynthesis II (bacteria) 3 1 1
NiFe(CO)(CN)2 cofactor biosynthesis 10 9 3
chorismate biosynthesis I 7 7 2
aerobic respiration I (cytochrome c) 4 2 1
aerobic respiration II (cytochrome c) (yeast) 4 2 1
GDP-D-glycero-α-D-manno-heptose biosynthesis 4 1 1
superpathway of L-phenylalanine biosynthesis 10 10 2
superpathway of L-tyrosine biosynthesis 10 10 2
tRNA processing 10 10 2
ADP-L-glycero-β-D-manno-heptose biosynthesis 5 5 1
D-galactose degradation I (Leloir pathway) 5 5 1
CMP-N-acetylneuraminate biosynthesis I (eukaryotes) 5 2 1
chorismate biosynthesis II (archaea) 12 8 2
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis 6 4 1
superpathway of photosynthetic hydrogen production 6 3 1
superpathway of L-tryptophan biosynthesis 13 13 2
stachyose degradation 7 7 1
incomplete reductive TCA cycle 7 5 1
UDP-N-acetyl-D-galactosamine biosynthesis II 7 5 1
pyruvate fermentation to propanoate I 7 4 1
superpathway of aromatic amino acid biosynthesis 18 18 2
superpathway of fermentation (Chlamydomonas reinhardtii) 9 8 1
TCA cycle VI (Helicobacter) 9 7 1
UDP-sugars interconversion 9 2 1
teichuronic acid biosynthesis (B. subtilis 168) 9 2 1
TCA cycle III (animals) 10 8 1
lipid A-core biosynthesis (Salmonella) 10 8 1
lipid A-core biosynthesis (E. coli K-12) 10 7 1
colanic acid building blocks biosynthesis 11 11 1
reductive TCA cycle I 11 8 1
L-glutamate degradation VIII (to propanoate) 11 4 1
reductive TCA cycle II 12 8 1
L-glutamate degradation VII (to butanoate) 12 5 1
glycolysis I (from glucose 6-phosphate) 13 13 1
(S)-lactate fermentation to propanoate, acetate and hydrogen 13 9 1
superpathway of CMP-sialic acids biosynthesis 15 3 1
mixed acid fermentation 16 16 1
superpathway of glycolysis and the Entner-Doudoroff pathway 17 17 1
mycolyl-arabinogalactan-peptidoglycan complex biosynthesis 18 1 1
superpathway of UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis 24 9 1
superpathway of Kdo2-lipid A biosynthesis 25 22 1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 25 1
superpathway of chorismate metabolism 59 54 2
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis 33 13 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 22 1