Experiment set42IT031 for Pseudomonas putida KT2440

P. put PUT 10 MOI 10

Group: phage
Media: LB_plus_SM_buffer + Kan (50 ug/ml)
Culturing: Putida_ML5, 48 well microplate; Epoch2, Aerobic, at 30 (C), shaken=double orbital, continuous, 205cpm
By: Vivek on 1/18/23
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride, 100 mM Sodium Chloride, 4 mM Magnesium sulfate, 0.005 vol% Gelatin, 25 mM Tris hydrochloride

Specific Phenotypes

For 40 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Polyamine Metabolism	3
Choline and Betaine Uptake and Betaine Biosynthesis	2
Peptidoglycan Biosynthesis	2
ABC transporter alkylphosphonate (TC 3.A.1.9.1)	1
ABC transporter dipeptide (TC 3.A.1.5.2)	1
Ammonia assimilation	1
Aromatic amino acid degradation	1
Bacterial Chemotaxis	1
Biogenesis of c-type cytochromes	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
DNA-replication	1
Entner-Doudoroff Pathway	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Heat shock dnaK gene cluster extended	1
Heme and Siroheme Biosynthesis	1
KDO2-Lipid A biosynthesis	1
Methylglyoxal Metabolism	1
Multidrug Resistance Efflux Pumps	1
Periplasmic disulfide interchange	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Queuosine-Archaeosine Biosynthesis	1
Ton and Tol transport systems	1
Transcription factors bacterial	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
• Urea cycle and metabolism of amino groups
• Tryptophan metabolism
• Lipopolysaccharide biosynthesis
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Histidine metabolism
• Naphthalene and anthracene degradation
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• Purine metabolism
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Lysine degradation
• Tyrosine metabolism
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Benzoxazinone biosynthesis
• beta-Alanine metabolism
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• Glycerolipid metabolism
• Pyruvate metabolism
• Biphenyl degradation
• Toluene and xylene degradation
• 1- and 2-Methylnaphthalene degradation
• 1,4-Dichlorobenzene degradation
• Fluorene degradation
• Carbazole degradation
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Ethylbenzene degradation
• Styrene degradation
• Butanoate metabolism
• Folate biosynthesis
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• 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
L-glutamate biosynthesis I	2	2	2
S-methyl-5'-thioadenosine degradation II	1	1	1
L-glutamine degradation I	1	1	1
L-glutamine degradation II	1	1	1
adenine and adenosine salvage III	4	4	3
ammonia assimilation cycle III	3	3	2
adenine and adenosine salvage V	3	2	2
choline degradation I	2	2	1
adenine and adenosine salvage I	2	2	1
putrescine degradation V	2	2	1
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	1
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	1
purine ribonucleosides degradation	6	5	3
putrescine degradation I	2	1	1
ethylene glycol degradation	2	1	1
adenosine nucleotides degradation II	5	5	2
choline-O-sulfate degradation	3	3	1
ethanol degradation IV	3	3	1
ethanol degradation II	3	3	1
hypotaurine degradation	3	2	1
ethanol degradation III	3	2	1
putrescine degradation IV	3	2	1
2-hydroxypenta-2,4-dienoate degradation	3	2	1
histamine degradation	3	1	1
L-glutamate and L-glutamine biosynthesis	7	6	2
L-arginine degradation IX (arginine:pyruvate transaminase pathway)	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
superpathway of ornithine degradation	8	6	2
putrescine degradation II	4	3	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	3	1
putrescine degradation III	4	3	1
L-arginine degradation VIII (arginine oxidase pathway)	4	3	1
phytol degradation	4	3	1
D-arabinose degradation II	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
CMP-3-deoxy-D-manno-octulosonate biosynthesis	5	5	1
mitochondrial NADPH production (yeast)	5	4	1
octane oxidation	5	4	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
dopamine degradation	5	2	1
catechol degradation I (meta-cleavage pathway)	5	2	1
purine nucleotides degradation II (aerobic)	11	11	2
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	2
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
superpathway of L-arginine and L-ornithine degradation	13	11	2
noradrenaline and adrenaline degradation	13	8	2
superpathway of glycol metabolism and degradation	7	6	1
serotonin degradation	7	4	1
CMP-8-amino-3,8-dideoxy-D-manno-octulosonate biosynthesis	7	4	1
catechol degradation II (meta-cleavage pathway)	7	3	1
toluene degradation V (aerobic) (via toluene-cis-diol)	7	2	1
ceramide degradation by α-oxidation	7	2	1
toluene degradation I (aerobic) (via o-cresol)	7	2	1
limonene degradation IV (anaerobic)	7	1	1
L-citrulline biosynthesis	8	7	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
aromatic biogenic amine degradation (bacteria)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
3-phenylpropanoate and 3-(3-hydroxyphenyl)propanoate degradation	8	2	1
p-cumate degradation	8	2	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
meta cleavage pathway of aromatic compounds	10	5	1
nucleoside and nucleotide degradation (archaea)	10	2	1
L-methionine salvage cycle III	11	5	1
p-cymene degradation	11	2	1
superpathway of L-citrulline metabolism	12	9	1
naphthalene degradation to acetyl-CoA	12	3	1
L-tryptophan degradation XII (Geobacillus)	12	2	1
L-tryptophan degradation IX	12	2	1
toluene degradation IV (aerobic) (via catechol)	13	6	1
superpathway of purine nucleotide salvage	14	13	1
superpathway of (Kdo)2-lipid A biosynthesis	17	14	1
mandelate degradation to acetyl-CoA	18	11	1
superpathway of Kdo2-lipid A biosynthesis	25	16	1
superpathway of aerobic toluene degradation	30	13	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	19	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	13	1
superpathway of pentose and pentitol degradation	42	10	1