Experiment set35IT070 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 27 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
Peptidoglycan Biosynthesis	3
ABC transporter dipeptide (TC 3.A.1.5.2)	1
Alginate metabolism	1
Bacterial Chemotaxis	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
DNA-replication	1
DNA repair, bacterial MutL-MutS system	1
Experimental tye	1
Heme and Siroheme Biosynthesis	1
KDO2-Lipid A biosynthesis	1
Mannose Metabolism	1
Multidrug Resistance Efflux Pumps	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:

• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Porphyrin and chlorophyll metabolism
• Biosynthesis of alkaloids derived from shikimate pathway
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Purine metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Benzoxazinone biosynthesis
• Starch and sucrose metabolism
• Streptomycin biosynthesis
• Glycosaminoglycan degradation
• Peptidoglycan biosynthesis
• Naphthalene and anthracene degradation
• Folate biosynthesis
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
UDP-α-D-glucose biosynthesis	2	2	1
β-1,4-D-mannosyl-N-acetyl-D-glucosamine degradation	3	2	1
GDP-α-D-glucose biosynthesis	3	2	1
trehalose degradation V	3	2	1
GDP-mannose biosynthesis	4	4	1
starch degradation V	4	3	1
heme b biosynthesis II (oxygen-independent)	4	3	1
glycogen biosynthesis I (from ADP-D-Glucose)	4	3	1
starch degradation III	4	2	1
sucrose degradation IV (sucrose phosphorylase)	4	2	1
dTDP-β-L-rhamnose biosynthesis	5	5	1
chorismate biosynthesis from 3-dehydroquinate	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 heme b biosynthesis from uroporphyrinogen-III	6	4	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	2
chorismate biosynthesis I	7	7	1
CMP-8-amino-3,8-dideoxy-D-manno-octulosonate biosynthesis	7	4	1
β-(1,4)-mannan degradation	7	2	1
glycogen degradation I	8	6	1
sucrose biosynthesis II	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
3,8-divinyl-chlorophyllide a biosynthesis II (anaerobic)	9	3	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
starch biosynthesis	10	5	1
O-antigen building blocks biosynthesis (E. coli)	11	10	1
chorismate biosynthesis II (archaea)	12	8	1
superpathway of L-tryptophan biosynthesis	13	13	1
superpathway of GDP-mannose-derived O-antigen building blocks biosynthesis	14	7	1
superpathway of (Kdo)2-lipid A biosynthesis	17	14	1
peptidoglycan biosynthesis II (staphylococci)	17	12	1
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	1
superpathway of aromatic amino acid biosynthesis	18	18	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 bacteriochlorophyll a biosynthesis	26	6	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	1
superpathway of chorismate metabolism	59	42	1