Experiment set4H2 for Shewanella amazonensis SB2B

LB with sodium fluoride 50 mM

Group: stress
Media: LB + sodium fluoride (50 mM)
Culturing: SB2B_ML5, 48 well microplate; Tecan Infinite F200, Aerobic, at 37 (C), shaken=orbital
By: Adam on 7/26/2013
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 588 C5,C6

Specific Phenotypes

For 18 genes in this experiment

For stress sodium fluoride in Shewanella amazonensis SB2B

For stress sodium fluoride across organisms

SEED Subsystems

Subsystem	#Specific
Purine conversions	2
2-phosphoglycolate salvage	1
Bacterial Cell Division	1
Bacterial Cytoskeleton	1
DNA repair, UvrABC system	1
DNA repair, bacterial MutL-MutS system	1
Glycolate, glyoxylate interconversions	1
Hfl operon	1
High affinity phosphate transporter and control of PHO regulon	1
Phosphate metabolism	1
Photorespiration (oxidative C2 cycle)	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Universal GTPases	1
cAMP signaling in bacteria	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Nucleotide sugars metabolism
• Pentose phosphate pathway
• Oxidative phosphorylation
• Puromycin biosynthesis
• Pyrimidine metabolism
• Other glycan degradation
• Aminosugars metabolism
• Glycosaminoglycan degradation
• Lipopolysaccharide biosynthesis
• alpha-Linolenic acid metabolism
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Glyoxylate and dicarboxylate metabolism
• Trinitrotoluene degradation
• Nicotinate and nicotinamide metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Drug metabolism - other enzymes

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
guanine and guanosine salvage III	1	1	1
pyrimidine ribonucleosides salvage I	3	3	2
polyphosphate metabolism	2	2	1
superpathway of guanine and guanosine salvage	3	3	1
adenine and adenosine salvage V	3	3	1
chitin degradation II (Vibrio)	6	2	2
superpathway of pyrimidine ribonucleosides salvage	10	9	2
peptidoglycan recycling II	10	5	2
peptidoglycan recycling I	14	11	2
chitin degradation III (Serratia)	7	2	1
photorespiration I	9	7	1
photorespiration III	9	7	1
photorespiration II	10	8	1
nucleoside and nucleotide degradation (archaea)	10	4	1