Experiment set5IT041 for Pseudomonas fluorescens FW300-N2E3

outer cut, LB soft agar motility assay

Group: motility
Media: LB + Agar (3 g/L)
Culturing: pseudo3_N2E3_ML2, Agar plate, Aerobic, at 30 (C), shaken=0 rpm, (Solid)
By: Mark on 12/17/2015
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride

Specific Phenotypes

For 74 genes in this experiment

For motility Agar in Pseudomonas fluorescens FW300-N2E3

For motility Agar across organisms

SEED Subsystems

Subsystem	#Specific
Flagellum	30
Flagellar motility	14
Bacterial Chemotaxis	7
Flagellum in Campylobacter	4
Proteolysis in bacteria, ATP-dependent	2
Two-component regulatory systems in Campylobacter	2
ZZ gjo need homes	2
Alginate metabolism	1
Arginine and Ornithine Degradation	1
Bacterial Cytoskeleton	1
Bacterial hemoglobins	1
Cysteine Biosynthesis	1
DNA-binding regulatory proteins, strays	1
DNA repair, bacterial RecFOR pathway	1
Folate Biosynthesis	1
Glutaredoxins	1
Glutathione: Redox cycle	1
Glycine Biosynthesis	1
Glycine and Serine Utilization	1
Iron acquisition in Vibrio	1
LMPTP YwlE cluster	1
Photorespiration (oxidative C2 cycle)	1
Plasmid replication	1
Proteasome bacterial	1
Protein chaperones	1
Serine-glyoxylate cycle	1
Serine Biosynthesis	1
SigmaB stress responce regulation	1
Transcription initiation, bacterial sigma factors	1
Two cell division clusters relating to chromosome partitioning	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Tyrosine metabolism
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Fatty acid metabolism
• Ubiquinone and menaquinone biosynthesis
• Oxidative phosphorylation
• Photosynthesis
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Phenylalanine metabolism
• beta-Alanine metabolism
• Cyanoamino acid metabolism
• Glutathione metabolism
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Ethylbenzene degradation
• Styrene degradation
• Butanoate metabolism
• One carbon pool by folate
• Methane metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
glycine biosynthesis I	1	1	1
dTMP de novo biosynthesis (mitochondrial)	3	3	1
glycine degradation	3	3	1
gentisate degradation I	3	1	1
superpathway of L-serine and glycine biosynthesis I	4	4	1
4-hydroxy-2-nonenal detoxification	4	1	1
glycine betaine degradation II (mammalian)	4	1	1
L-tyrosine degradation I	5	5	1
L-arginine degradation II (AST pathway)	5	5	1
folate polyglutamylation	5	4	1
pentachlorophenol degradation	10	4	2
L-leucine degradation I	6	5	1
5-nitroanthranilate degradation	6	2	1
glycine betaine degradation III	7	7	1
alginate degradation	7	2	1
glycine betaine degradation I	8	6	1
glutathione-mediated detoxification I	8	3	1
folate transformations III (E. coli)	9	9	1
photorespiration III	9	5	1
photorespiration I	9	5	1
gliotoxin biosynthesis	9	2	1
glutathione-mediated detoxification II	9	2	1
photorespiration II	10	6	1
3-phenylpropanoate degradation	10	4	1
folate transformations II (plants)	11	10	1
indole glucosinolate activation (intact plant cell)	12	3	1
camalexin biosynthesis	12	2	1
folate transformations I	13	9	1
formaldehyde assimilation I (serine pathway)	13	6	1
purine nucleobases degradation II (anaerobic)	24	16	1