Experiment set7IT037 for Caulobacter crescentus NA1000

PYE 0.5x 30C survival rep3 28 days

Group: survival
Media: PYE (0.5x)
Culturing: Caulo_ML2, tube, Aerobic, at 30 (C), shaken=200 rpm
By: Sneha on 8-Aug-18
Media components: 1 g/L Bacto Peptone, 0.5 g/L Yeast Extract, 0.4 mM Magnesium sulfate, 0.25 mM Calcium chloride (final concentrations)

Specific Phenotypes

For 20 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Entner-Doudoroff Pathway	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Hemin transport system	1
Methylglyoxal Metabolism	1
Proteasome bacterial	1
Purine Utilization	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Terminal cytochrome C oxidases	1
Xylose utilization	1
YbbK	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Ubiquinone and menaquinone biosynthesis
• Histidine metabolism
• Tryptophan metabolism
• Limonene and pinene degradation
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Fatty acid metabolism
• Oxidative phosphorylation
• Urea cycle and metabolism of amino groups
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Arginine and proline metabolism
• Tyrosine metabolism
• Benzoxazinone biosynthesis
• beta-Alanine metabolism
• Glycerolipid metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
putrescine degradation V	2	2	1
arsenite to oxygen electron transfer	2	1	1
putrescine degradation I	2	1	1
ethylene glycol degradation	2	1	1
ethanol degradation II	3	3	1
ethanol degradation IV	3	3	1
putrescine degradation IV	3	2	1
ethanol degradation III	3	2	1
hypotaurine degradation	3	2	1
histamine degradation	3	1	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
aerobic respiration I (cytochrome c)	4	3	1
phytol degradation	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
putrescine degradation III	4	2	1
D-arabinose degradation II	4	1	1
mitochondrial NADPH production (yeast)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
octane oxidation	5	2	1
dopamine degradation	5	2	1
3-methyl-branched fatty acid α-oxidation	6	3	1
Fe(II) oxidation	6	3	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	8	2
serotonin degradation	7	4	1
superpathway of glycol metabolism and degradation	7	3	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	6	1
superpathway of ornithine degradation	8	5	1
aromatic biogenic amine degradation (bacteria)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
Entner-Doudoroff pathway II (non-phosphorylative)	9	4	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	5	1
superpathway of L-arginine and L-ornithine degradation	13	7	1
superpathway of pentose and pentitol degradation	42	12	1