Experiment set40IT085 for Pseudomonas putida KT2440

P. putida PUT10 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 1/12/23
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	4
Peptidoglycan Biosynthesis	3
Choline and Betaine Uptake and Betaine 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
Biogenesis of c-type cytochromes	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
DNA-replication	1
Heat shock dnaK gene cluster extended	1
Heme and Siroheme Biosynthesis	1
Mannose Metabolism	1
Multidrug Resistance Efflux Pumps	1
Periplasmic disulfide interchange	1
Putative TldE-TldD proteolytic complex	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:

• Nucleotide sugars metabolism
• Ubiquinone and menaquinone biosynthesis
• Lipopolysaccharide biosynthesis
• Porphyrin and chlorophyll metabolism
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Glycine, serine and threonine metabolism
• Arginine and proline metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• 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 alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
S-methyl-5'-thioadenosine degradation II	1	1	1
adenine and adenosine salvage III	4	4	3
adenine and adenosine salvage V	3	2	2
adenine and adenosine salvage I	2	2	1
UDP-α-D-glucose biosynthesis	2	2	1
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
purine ribonucleosides degradation	6	5	3
adenosine nucleotides degradation II	5	5	2
choline-O-sulfate degradation	3	3	1
trehalose degradation V	3	2	1
GDP-α-D-glucose biosynthesis	3	2	1
β-1,4-D-mannosyl-N-acetyl-D-glucosamine degradation	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
putrescine degradation II	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
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
purine nucleotides degradation II (aerobic)	11	11	2
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
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	2
β-(1,4)-mannan degradation	7	2	1
glycogen degradation I	8	6	1
superpathway of ornithine degradation	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
starch biosynthesis	10	5	1
nucleoside and nucleotide degradation (archaea)	10	2	1
O-antigen building blocks biosynthesis (E. coli)	11	10	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	1
L-methionine salvage cycle III	11	5	1
superpathway of L-arginine and L-ornithine degradation	13	11	1
superpathway of purine nucleotide salvage	14	13	1
superpathway of GDP-mannose-derived O-antigen building blocks biosynthesis	14	7	1
peptidoglycan biosynthesis II (staphylococci)	17	12	1
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	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 mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	1