Experiment set6IT037 for Caulobacter crescentus NA1000

PYE_noCalcium 25C survival rep1 12 days

Group: survival
Media: PYE_noCalcium
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

Specific Phenotypes

For 37 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	2
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	2
Arginine Biosynthesis extended	1
Biogenesis of cytochrome c oxidases	1
Carboxysome	1
Cyanate hydrolysis	1
Entner-Doudoroff Pathway	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Hemin transport system	1
Ketoisovalerate oxidoreductase	1
LOS core oligosaccharide biosynthesis	1
Methylglyoxal Metabolism	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Queuosine-Archaeosine Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Arginine and proline metabolism
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Urea cycle and metabolism of amino groups
• Lysine biosynthesis
• Histidine metabolism
• Tryptophan metabolism
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• Pyruvate metabolism
• Propanoate metabolism
• Carotenoid biosynthesis - General
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Fructose and mannose metabolism
• Fatty acid metabolism
• Ubiquinone and menaquinone biosynthesis
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Tyrosine metabolism
• Benzoxazinone biosynthesis
• beta-Alanine metabolism
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Keratan sulfate biosynthesis
• Peptidoglycan biosynthesis
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Glycerophospholipid metabolism
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• 2,4-Dichlorobenzoate degradation
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Retinol metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Zeatin biosynthesis
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Flavone and flavonol biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetate conversion to acetyl-CoA	1	1	1
acetate and ATP formation from acetyl-CoA III	1	1	1
ethanol degradation IV	3	3	2
ethanol degradation II	3	3	2
ethanol degradation III	3	2	2
putrescine degradation V	2	2	1
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
ethylene glycol degradation	2	1	1
putrescine degradation I	2	1	1
L-arginine degradation II (AST pathway)	5	3	2
ferulate degradation	3	3	1
putrescine degradation IV	3	2	1
hypotaurine degradation	3	2	1
L-isoleucine biosynthesis V	3	2	1
cyanate degradation	3	2	1
histamine degradation	3	1	1
superpathway of acetate utilization and formation	3	1	1
phytol degradation	4	3	1
chitin deacetylation	4	2	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
L-ornithine biosynthesis I	5	5	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
2-methylcitrate cycle I	5	1	1
L-isoleucine biosynthesis IV	6	4	1
β-alanine biosynthesis II	6	4	1
3-methyl-branched fatty acid α-oxidation	6	3	1
superpathway of bitter acids biosynthesis	18	3	3
2-methylcitrate cycle II	6	1	1
alkane oxidation	6	1	1
adlupulone and adhumulone biosynthesis	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
lupulone and humulone biosynthesis	6	1	1
noradrenaline and adrenaline degradation	13	8	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
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
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-lysine biosynthesis I	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	4	1
reductive glycine pathway of autotrophic CO2 fixation	9	4	1
cis-geranyl-CoA degradation	9	1	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of coenzyme A biosynthesis II (plants)	10	8	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	7	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	5	1
3-hydroxypropanoate cycle	13	9	1
glyoxylate assimilation	13	8	1
superpathway of L-arginine and L-ornithine degradation	13	7	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	8	1
superpathway of arginine and polyamine biosynthesis	17	12	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	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
aspartate superpathway	25	23	1
superpathway of pentose and pentitol degradation	42	12	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	18	1