Experiment set4IT066 for Pseudomonas fluorescens SBW25-INTG

Temperature shift 30_to_34

Group: temperature shift
Media: soilextract_PNNL_Prosser_PlotA_B_20191220 + D-Glucose (10 mM) + Ammonium chloride (10 mM)
Culturing: PseudoSBW25_INTG_ML3, tube, Aerobic, at 30_to_34 (C)
By: Joshua Elmore on 1/6/20

Specific Phenotypes

For 35 genes in this experiment

For temperature shift D-Glucose in Pseudomonas fluorescens SBW25-INTG

For temperature shift D-Glucose across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter oligopeptide (TC 3.A.1.5.1)	4
Cysteine Biosynthesis	3
ABC transporter alkylphosphonate (TC 3.A.1.9.1)	2
Arginine and Ornithine Degradation	1
Bacterial Cell Division	1
Beta-Glucoside Metabolism	1
Carboxysome	1
Conserved gene cluster possibly involved in RNA metabolism	1
Cyanate hydrolysis	1
DNA-replication	1
Fructose and Mannose Inducible PTS	1
Fructose utilization	1
Glutamate dehydrogenases	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Mannitol Utilization	1
Methionine Biosynthesis	1
Proline Synthesis	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pyrimidine metabolism
• Starch and sucrose metabolism
• Nitrogen metabolism
• Glycolysis / Gluconeogenesis
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Purine metabolism
• Glutamate metabolism
• Cysteine metabolism
• Arginine and proline metabolism
• Cyanoamino acid metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Porphyrin and chlorophyll metabolism
• Sulfur metabolism
• Phenylpropanoid biosynthesis
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate biosynthesis III	1	1	1
adenosylcobalamin salvage from cobalamin	5	5	4
neolinustatin bioactivation	3	2	2
adenosylcobinamide-GDP salvage from cobinamide I	5	5	3
adenosylcobinamide-GDP biosynthesis from cobyrinate a,c-diamide	6	6	3
L-cysteine biosynthesis I	2	2	1
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
adenosylcobinamide-GDP salvage from cobinamide II	6	5	3
cobalamin salvage (eukaryotic)	8	4	4
linustatin bioactivation	4	2	2
lotaustralin degradation	2	1	1
pseudouridine degradation	2	1	1
linamarin degradation	2	1	1
superpathway of adenosylcobalamin salvage from cobinamide I	8	8	3
superpathway of adenosylcobalamin salvage from cobinamide II	9	8	3
cyanate degradation	3	2	1
cellulose degradation II (fungi)	3	2	1
molybdenum cofactor biosynthesis	3	1	1
L-cysteine biosynthesis VII (from S-sulfo-L-cysteine)	4	3	1
N-3-oxalyl-L-2,3-diaminopropanoate biosynthesis	4	1	1
seleno-amino acid biosynthesis (plants)	5	3	1
coumarin biosynthesis (via 2-coumarate)	5	2	1
α-tomatine degradation	6	1	1
D-cycloserine biosynthesis	6	1	1
L-glutamate and L-glutamine biosynthesis	7	6	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
L-cysteine biosynthesis VI (reverse transsulfuration)	7	3	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
adenosylcobalamin biosynthesis II (aerobic)	33	30	3
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	1
adenosylcobalamin biosynthesis I (anaerobic)	36	27	3
3-hydroxypropanoate cycle	13	6	1
glyoxylate assimilation	13	4	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	1
firefly bioluminescence	14	2	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	8	1
superpathway of the 3-hydroxypropanoate cycle	18	6	1
superpathway of seleno-compound metabolism	19	8	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1