Experiment set1IT020 for Pseudomonas simiae WCS417

LB with Neomycin trisulfate salt hydrate 0.04 mg/ml

Group: stress
Media: LB + Neomycin trisulfate salt hydrate (0.04 mg/ml)
Culturing: fluoroDangl_ML3, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Mark on 2/19/2015
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 1143 E3,E4

Specific Phenotypes

For 36 genes in this experiment

For stress Neomycin trisulfate salt hydrate in Pseudomonas simiae WCS417

For stress Neomycin trisulfate salt hydrate across organisms

SEED Subsystems

Subsystem	#Specific
Oxidative stress	3
ABC transporter alkylphosphonate (TC 3.A.1.9.1)	2
2-phosphoglycolate salvage	1
Alginate metabolism	1
Copper homeostasis	1
DNA repair, bacterial	1
Glycolate, glyoxylate interconversions	1
Lipid A modifications	1
Mannose Metabolism	1
N-linked Glycosylation in Bacteria	1
Orphan regulatory proteins	1
Peptidoglycan Biosynthesis	1
Photorespiration (oxidative C2 cycle)	1
Pterin biosynthesis	1
Rhamnose containing glycans	1
Teichoic and lipoteichoic acids biosynthesis	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
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Puromycin biosynthesis
• Glycine, serine and threonine metabolism
• Tyrosine metabolism
• Benzoate degradation via hydroxylation
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Benzoxazinone biosynthesis
• Aminophosphonate metabolism
• Starch and sucrose metabolism
• High-mannose type N-glycan biosynthesis
• Streptomycin biosynthesis
• Glycosaminoglycan degradation
• Glycerophospholipid metabolism
• Sphingolipid metabolism
• 1- and 2-Methylnaphthalene degradation
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
UDP-α-D-glucose biosynthesis	2	2	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
sucrose degradation IV (sucrose phosphorylase)	4	3	1
glycogen biosynthesis I (from ADP-D-Glucose)	4	3	1
starch degradation V	4	3	1
starch degradation III	4	2	1
UDP-N-acetyl-β-L-fucosamine biosynthesis	4	2	1
UDP-N-acetyl-β-L-quinovosamine biosynthesis	4	1	1
dTDP-β-L-rhamnose biosynthesis	5	5	1
sucrose degradation II (sucrose synthase)	5	4	1
glucose and glucose-1-phosphate degradation	5	4	1
D-galactose degradation I (Leloir pathway)	5	3	1
CDP-6-deoxy-D-gulose biosynthesis	5	3	1
glucosylglycerol biosynthesis	5	2	1
Salmonella enterica serotype O:3,10 O antigen biosynthesis	5	1	1
colanic acid building blocks biosynthesis	11	8	2
glycogen degradation II	6	5	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
Salmonella enterica serotype O:9,46 O antigen biosynthesis	6	1	1
Salmonella enterica serotype O:9 O antigen biosynthesis	6	1	1
Salmonella enterica serotype O:4 O antigen biosynthesis (group B1)	6	1	1
Salmonella enterica serotype O:2 O antigen biosynthesis	6	1	1
Porphyromonas gingivalis O-LPS antigen biosynthesis	6	1	1
CMP-pseudaminate biosynthesis	6	1	1
β-(1,4)-mannan degradation	7	2	1
CMP-diacetamido-8-epilegionaminic acid biosynthesis	7	1	1
glycogen degradation I	8	6	1
sucrose biosynthesis II	8	6	1
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	3	1
Salmonella enterica serotype O:8 O antigen biosynthesis	8	1	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
chitin biosynthesis	9	5	1
photorespiration I	9	5	1
photorespiration III	9	5	1
Salmonella enterica serotype O:9,46,27 O antigen biosynthesis	9	1	1
peptidoglycan recycling II	10	8	1
photorespiration II	10	6	1
starch biosynthesis	10	5	1
O-antigen building blocks biosynthesis (E. coli)	11	10	1
peptidoglycan recycling I	14	11	1
superpathway of GDP-mannose-derived O-antigen building blocks biosynthesis	14	6	1
succinoglycan biosynthesis	14	1	1
streptomycin biosynthesis	18	3	1
superpathway of anaerobic sucrose degradation	19	14	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	5	1
superpathway of UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis	24	9	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	1