Experiment set42IT027 for Pseudomonas putida KT2440

P. put South MOI 1

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 33 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Choline and Betaine Uptake and Betaine Biosynthesis	2
Conserved gene cluster associated with Met-tRNA formyltransferase	2
Peptidoglycan Biosynthesis	2
ABC transporter alkylphosphonate (TC 3.A.1.9.1)	1
ABC transporter dipeptide (TC 3.A.1.5.2)	1
Alginate metabolism	1
Aromatic amino acid degradation	1
Bacterial Chemotaxis	1
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
DNA-replication	1
Heat shock dnaK gene cluster extended	1
Heme and Siroheme Biosynthesis	1
KDO2-Lipid A biosynthesis	1
Lipid A modifications	1
Mannose Metabolism	1
Multidrug Resistance Efflux Pumps	1
Polyamine Metabolism	1
Queuosine-Archaeosine Biosynthesis	1
Ribosome biogenesis bacterial	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:

• Lipopolysaccharide biosynthesis
• Nucleotide sugars metabolism
• Ubiquinone and menaquinone biosynthesis
• Glycine, serine and threonine metabolism
• Histidine metabolism
• Tyrosine metabolism
• Benzoxazinone biosynthesis
• Porphyrin and chlorophyll metabolism
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Purine metabolism
• Lysine degradation
• Phenylalanine metabolism
• Tryptophan metabolism
• Starch and sucrose metabolism
• Streptomycin biosynthesis
• Glycosaminoglycan degradation
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Butanoate metabolism
• Folate biosynthesis
• Limonene and pinene degradation
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Alkaloid biosynthesis II
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
choline degradation I	2	2	1
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	1
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	1
UDP-α-D-glucose biosynthesis	2	2	1
choline-O-sulfate degradation	3	3	1
trehalose degradation V	3	2	1
β-1,4-D-mannosyl-N-acetyl-D-glucosamine degradation	3	2	1
GDP-α-D-glucose biosynthesis	3	2	1
GDP-mannose biosynthesis	4	4	1
glycogen biosynthesis I (from ADP-D-Glucose)	4	3	1
starch degradation V	4	3	1
sucrose degradation IV (sucrose phosphorylase)	4	2	1
starch degradation III	4	2	1
dTDP-β-L-rhamnose biosynthesis	5	5	1
CMP-3-deoxy-D-manno-octulosonate biosynthesis	5	5	1
glucose and glucose-1-phosphate degradation	5	4	1
sucrose degradation II (sucrose synthase)	5	3	1
glucosylglycerol biosynthesis	5	2	1
D-galactose degradation I (Leloir pathway)	5	2	1
CDP-6-deoxy-D-gulose biosynthesis	5	1	1
colanic acid building blocks biosynthesis	11	9	2
glycogen degradation II	6	5	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
CMP-8-amino-3,8-dideoxy-D-manno-octulosonate biosynthesis	7	4	1
β-(1,4)-mannan degradation	7	2	1
sucrose biosynthesis II	8	6	1
glycogen degradation I	8	6	1
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	3	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
chitin biosynthesis	9	5	1
starch biosynthesis	10	5	1
O-antigen building blocks biosynthesis (E. coli)	11	10	1
superpathway of GDP-mannose-derived O-antigen building blocks biosynthesis	14	7	1
superpathway of (Kdo)2-lipid A biosynthesis	17	14	1
streptomycin biosynthesis	18	1	1
superpathway of anaerobic sucrose degradation	19	13	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	5	1
superpathway of Kdo2-lipid A biosynthesis	25	16	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	1