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 38 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Peptidoglycan Biosynthesis	3
Polyamine Metabolism	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
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
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:

• Ubiquinone and menaquinone biosynthesis
• Lipopolysaccharide biosynthesis
• Porphyrin and chlorophyll 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
• Nucleotide sugars metabolism
• 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
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	1
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	1
adenine and adenosine salvage I	2	2	1
choline degradation I	2	2	1
purine ribonucleosides degradation	6	5	3
adenosine nucleotides degradation II	5	5	2
choline-O-sulfate degradation	3	3	1
putrescine degradation II	4	3	1
purine nucleotides degradation II (aerobic)	11	11	2
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	2
superpathway of ornithine degradation	8	6	1
nucleoside and nucleotide degradation (archaea)	10	2	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
peptidoglycan biosynthesis II (staphylococci)	17	12	1
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	1