Experiment set35IT071 for Pseudomonas putida KT2440

PUT8 MOI 0.1

Group: phage
Media: LB_plus_SM_buffer + PUT8 MOI 0.1 + Kan (50 ug/ml)
Culturing: Putida_ML5, 48 well microplate; Epoch2, Aerobic, at 30 (C), shaken=double orbital, continuous, 205cpm
By: Vivek on 10/22/21
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 19 genes in this experiment

For phage PUT8 MOI 0.1 in Pseudomonas putida KT2440

For phage PUT8 MOI 0.1 across organisms

SEED Subsystems

Subsystem	#Specific
Conserved gene cluster associated with Met-tRNA formyltransferase	2
ABC transporter alkylphosphonate (TC 3.A.1.9.1)	1
ABC transporter dipeptide (TC 3.A.1.5.2)	1
Bacterial Chemotaxis	1
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
DNA-replication	1
Experimental tye	1
Heme and Siroheme Biosynthesis	1
KDO2-Lipid A biosynthesis	1
Lipid A modifications	1
Multidrug Resistance Efflux Pumps	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
• Ubiquinone and menaquinone biosynthesis
• Histidine metabolism
• Tyrosine metabolism
• Benzoxazinone biosynthesis
• Porphyrin and chlorophyll metabolism
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Purine metabolism
• Glycine, serine and threonine metabolism
• Lysine degradation
• Phenylalanine metabolism
• Tryptophan metabolism
• Nucleotide sugars metabolism
• 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
heme b biosynthesis II (oxygen-independent)	4	3	1
CMP-3-deoxy-D-manno-octulosonate biosynthesis	5	5	1
superpathway of heme b biosynthesis from uroporphyrinogen-III	6	4	1
CMP-8-amino-3,8-dideoxy-D-manno-octulosonate biosynthesis	7	4	1
3,8-divinyl-chlorophyllide a biosynthesis II (anaerobic)	9	3	1
superpathway of (Kdo)2-lipid A biosynthesis	17	14	1
superpathway of Kdo2-lipid A biosynthesis	25	16	1
superpathway of bacteriochlorophyll a biosynthesis	26	6	1