Experiment set3IT040 for Pseudomonas simiae WCS417

LB with Gentamicin sulfate salt 0.008 mg/ml

Group: stress
Media: LB + Gentamicin sulfate salt (0.008 mg/ml)
Culturing: fluoroDangl_ML3, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Mark on 3/2/2015
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 1165 F1,F2

Specific Phenotypes

For 45 genes in this experiment

For stress Gentamicin sulfate salt in Pseudomonas simiae WCS417

For stress Gentamicin sulfate salt across organisms

SEED Subsystems

Subsystem	#Specific
Polyamine Metabolism	4
DNA-replication	2
Queuosine-Archaeosine Biosynthesis	2
ATP-dependent RNA helicases, bacterial	1
Acid resistance mechanisms	1
Arginine and Ornithine Degradation	1
Bacterial hemoglobins	1
Biogenesis of c-type cytochromes	1
Biogenesis of cytochrome c oxidases	1
DNA Repair Base Excision	1
DNA repair, bacterial MutL-MutS system	1
De Novo Pyrimidine Synthesis	1
Flavohaemoglobin	1
Glutaredoxins	1
Heat shock dnaK gene cluster extended	1
LMPTP YwlE cluster	1
Multidrug Resistance Efflux Pumps	1
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	1
N-linked Glycosylation in Bacteria	1
Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes	1
Orphan regulatory proteins	1
Periplasmic disulfide interchange	1
Potassium homeostasis	1
Proteasome bacterial	1
Proteolysis in bacteria, ATP-dependent	1
Rhamnose containing glycans	1
Teichoic and lipoteichoic acids biosynthesis	1
Transcription factors bacterial	1
ZZ gjo need homes	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Purine metabolism
• Pyrimidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• Benzoate degradation via CoA ligation
• Porphyrin and chlorophyll metabolism
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Puromycin biosynthesis
• Histidine metabolism
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Benzoxazinone biosynthesis
• Aminophosphonate metabolism
• Cyanoamino acid metabolism
• High-mannose type N-glycan biosynthesis
• Glycerophospholipid metabolism
• Sphingolipid metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Styrene degradation
• Butanoate metabolism
• Biotin metabolism
• Folate biosynthesis
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
arginine dependent acid resistance	1	1	1
pyrimidine nucleobases salvage I	1	1	1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	2
putrescine biosynthesis II	3	3	2
indole-3-acetate biosynthesis III (bacteria)	2	2	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
pyrimidine nucleobases salvage II	2	2	1
indole-3-acetate biosynthesis IV (bacteria)	2	2	1
putrescine biosynthesis I	2	2	1
acrylonitrile degradation I	2	2	1
superpathway of acrylonitrile degradation	3	2	1
L-arginine degradation X (arginine monooxygenase pathway)	3	2	1
biotin-carboxyl carrier protein assembly	4	4	1
superpathway of putrescine biosynthesis	4	4	1
superpathway of pyrimidine nucleobases salvage	4	4	1
queuosine biosynthesis I (de novo)	4	4	1
superpathway of polyamine biosynthesis II	8	6	2
UDP-N-acetyl-β-L-fucosamine biosynthesis	4	2	1
UDP-N-acetyl-β-L-quinovosamine biosynthesis	4	1	1
spermidine biosynthesis III	4	1	1
tRNA processing	10	8	2
Salmonella enterica serotype O:3,10 O antigen biosynthesis	5	1	1
Salmonella enterica serotype O:2 O antigen biosynthesis	6	1	1
CMP-pseudaminate biosynthesis	6	1	1
Porphyromonas gingivalis O-LPS antigen biosynthesis	6	1	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
CMP-diacetamido-8-epilegionaminic acid biosynthesis	7	1	1
superpathway of polyamine biosynthesis I	8	6	1
Salmonella enterica serotype O:8 O antigen biosynthesis	8	1	1
Salmonella enterica serotype O:9,46,27 O antigen biosynthesis	9	1	1
superpathway of pyrimidine ribonucleosides salvage	10	6	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	8	1
indole-3-acetate biosynthesis II	12	5	1
superpathway of L-arginine and L-ornithine degradation	13	10	1
succinoglycan biosynthesis	14	1	1
superpathway of arginine and polyamine biosynthesis	17	15	1
superpathway of UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis	24	9	1