Experiment set6IT032 for Caulobacter crescentus NA1000

PYE 25C survival rep2 12 days

Group: survival
Media: PYE
Culturing: Caulo_ML2, tube, Aerobic, at 25 (C), shaken=200 rpm
By: Sneha on 8-Aug-18
Media components: 2 g/L Bacto Peptone, 1 g/L Yeast Extract, 0.8 mM Magnesium sulfate, 0.5 mM Calcium chloride

Specific Phenotypes

For 22 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Flagellum	3
Biogenesis of cytochrome c oxidases	1
Carboxysome	1
Cyanate hydrolysis	1
Entner-Doudoroff Pathway	1
Flagellar motility	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Methylglyoxal Metabolism	1
Molybdenum cofactor biosynthesis	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Transport of Molybdenum	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Ascorbate and aldarate metabolism
• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Tryptophan metabolism
• Butanoate metabolism
• Limonene and pinene degradation
• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• Glutamate metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• Glycerophospholipid metabolism
• Pyruvate metabolism
• 2,4-Dichlorobenzoate degradation
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Retinol metabolism
• Porphyrin and chlorophyll metabolism
• Nitrogen metabolism
• Alkaloid biosynthesis II

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
putrescine degradation V	2	2	1
ethylene glycol degradation	2	1	1
4-aminobutanoate degradation II	2	1	1
putrescine degradation I	2	1	1
4-aminobutanoate degradation III	2	1	1
ethanol degradation IV	3	3	1
ethanol degradation II	3	3	1
ferulate degradation	3	3	1
putrescine degradation IV	3	2	1
ethanol degradation III	3	2	1
cyanate degradation	3	2	1
hypotaurine degradation	3	2	1
superpathway of 4-aminobutanoate degradation	3	1	1
histamine degradation	3	1	1
phytol degradation	4	3	1
putrescine degradation III	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	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
L-lysine degradation IV	5	1	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	5	2
tetrapyrrole biosynthesis I (from glutamate)	6	5	1
L-lysine degradation X	6	3	1
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
L-lysine degradation III	6	1	1
noradrenaline and adrenaline degradation	13	8	2
superpathway of L-arginine and L-ornithine degradation	13	7	2
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	5	1
serotonin degradation	7	4	1
superpathway of glycol metabolism and degradation	7	3	1
L-lysine degradation I	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
4-hydroxyphenylacetate degradation	8	2	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	8	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	4	1
superpathway of heme b biosynthesis from glutamate	10	8	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	7	1
nicotine degradation II (pyrrolidine pathway)	11	2	1
3-hydroxypropanoate cycle	13	9	1
glyoxylate assimilation	13	8	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	8	1
nicotine degradation I (pyridine pathway)	17	4	1
superpathway of the 3-hydroxypropanoate cycle	18	12	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	11	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	7	1
suberin monomers biosynthesis	20	3	1
adenosylcobalamin biosynthesis II (aerobic)	33	15	1
adenosylcobalamin biosynthesis I (anaerobic)	36	14	1
superpathway of pentose and pentitol degradation	42	12	1
superpathway of L-lysine degradation	43	8	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	18	1