Experiment set4IT022 for Pseudomonas putida KT2440

LB with Formaldehyde 0.03125 vol%

Group: stress
Media: LB + Formaldehyde (0.03125 vol%)
Culturing: Putida_ML5, 48 well microplate; Tecan Safire, Aerobic, at 30 (C), shaken=orbital
Growth: about 7.4 generations
By: Mitch on 10/28/16
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride

Specific Phenotypes

For 7 genes in this experiment

For stress Formaldehyde in Pseudomonas putida KT2440

For stress Formaldehyde across organisms

SEED Subsystems

Subsystem	#Specific
Glutathione-dependent pathway of formaldehyde detoxification	3
DNA repair, bacterial DinG and relatives	1
Folate Biosynthesis	1
Glycine Biosynthesis	1
Glycine and Serine Utilization	1
LMPTP YwlE cluster	1
Photorespiration (oxidative C2 cycle)	1
Serine-glyoxylate cycle	1
Serine Biosynthesis	1
Transport of Zinc	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Methane metabolism
• Glycine, serine and threonine metabolism
• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• Tyrosine metabolism
• Cyanoamino acid metabolism
• 1- and 2-Methylnaphthalene degradation
• 3-Chloroacrylic acid degradation
• One carbon pool by folate
• Retinol metabolism
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
glycine biosynthesis I	1	1	1
acetaldehyde biosynthesis I	1	1	1
formaldehyde oxidation II (glutathione-dependent)	3	3	2
ethanol degradation I	2	1	1
pyruvate fermentation to ethanol II	2	1	1
ethanol degradation II	3	3	1
glycine degradation	3	3	1
dTMP de novo biosynthesis (mitochondrial)	3	3	1
methylglyoxal degradation VIII	3	2	1
L-valine degradation II	3	2	1
L-leucine degradation III	3	2	1
methylglyoxal degradation I	3	2	1
L-isoleucine degradation II	3	2	1
pyruvate fermentation to ethanol I	3	1	1
pyruvate fermentation to ethanol III	3	1	1
L-methionine degradation III	3	1	1
superpathway of L-serine and glycine biosynthesis I	4	4	1
phytol degradation	4	3	1
salidroside biosynthesis	4	3	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
glycine betaine degradation II (mammalian)	4	1	1
ethanolamine utilization	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
folate polyglutamylation	5	4	1
acetylene degradation (anaerobic)	5	3	1
phenylethanol biosynthesis	5	3	1
protein S-nitrosylation and denitrosylation	5	3	1
(S)-propane-1,2-diol degradation	5	2	1
superpathway of C1 compounds oxidation to CO2	12	5	2
noradrenaline and adrenaline degradation	13	8	2
glycine betaine degradation III	7	7	1
3-methylbutanol biosynthesis (engineered)	7	6	1
serotonin degradation	7	4	1
glycine betaine degradation I	8	6	1
superpathway of methylglyoxal degradation	8	5	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
folate transformations III (E. coli)	9	9	1
photorespiration I	9	6	1
photorespiration III	9	6	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	4	1
photorespiration II	10	7	1
folate transformations II (plants)	11	10	1
folate transformations I	13	9	1
formaldehyde assimilation I (serine pathway)	13	7	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	4	1
L-tryptophan degradation V (side chain pathway)	13	1	1
mixed acid fermentation	16	12	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	6	1
heterolactic fermentation	18	12	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of anaerobic sucrose degradation	19	13	1
superpathway of N-acetylneuraminate degradation	22	12	1
purine nucleobases degradation II (anaerobic)	24	16	1