Experiment setAH26 for Shewanella oneidensis MR-1

M5 outer

Group: motility
Media: LB + Agar (3 g/L)
Culturing: MR1_ML3, Agar plate, Aerobic, at 30 (C), shaken=0 rpm, (Solid)
By: Adam on 8/28/2013
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride

Specific Phenotypes

For 42 genes in this experiment

For motility Agar in Shewanella oneidensis MR-1

For motility Agar across organisms

SEED Subsystems

Subsystem	#Specific
Bacterial hemoglobins	2
Proteolysis in bacteria, ATP-dependent	2
Purine conversions	2
Bacterial Cell Division	1
Bacterial Chemotaxis	1
Bacterial Cytoskeleton	1
DNA repair, UvrABC system	1
DNA repair, bacterial	1
Menaquinone and Phylloquinone Biosynthesis	1
Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Protein chaperones	1
Twin-arginine translocation system	1
Two cell division clusters relating to chromosome partitioning	1
YcfH	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
• Purine metabolism
• Pentose phosphate pathway
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Pyrimidine metabolism
• Lysine degradation
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Phenylalanine metabolism
• gamma-Hexachlorocyclohexane degradation
• Fluorobenzoate degradation
• Tryptophan metabolism
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• Peptidoglycan biosynthesis
• Fluorene degradation
• Propanoate metabolism
• Biotin metabolism
• Isoflavonoid biosynthesis
• Biosynthesis of unsaturated fatty acids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
guanine and guanosine salvage III	1	1	1
8-methylmenaquinone biosynthesis	1	1	1
adenine and adenosine salvage V	3	3	2
ribose phosphorylation	2	1	1
purine deoxyribonucleosides degradation II	3	3	1
superpathway of guanine and guanosine salvage	3	3	1
pyrimidine deoxyribonucleotides dephosphorylation	3	1	1
adenine and adenosine salvage III	4	4	1
purine deoxyribonucleosides degradation I	4	4	1
adenosine nucleotides degradation II	5	3	1
7,8-dimethylmenaquinone biosynthesis	5	1	1
purine ribonucleosides degradation	6	6	1
2-carboxy-1,4-naphthoquinol biosynthesis	7	7	1
superpathway of purine deoxyribonucleosides degradation	7	7	1
pyrimidine deoxyribonucleotides de novo biosynthesis II	7	7	1
pyrimidine deoxyribonucleotides de novo biosynthesis I	9	9	1
superpathway of demethylmenaquinol-8 biosynthesis I	9	9	1
superpathway of demethylmenaquinol-9 biosynthesis	9	8	1
superpathway of demethylmenaquinol-6 biosynthesis I	9	8	1
pyrimidine deoxyribonucleotides de novo biosynthesis III	9	8	1
superpathway of menaquinol-8 biosynthesis I	10	10	1
superpathway of menaquinol-6 biosynthesis	10	9	1
superpathway of menaquinol-7 biosynthesis	10	9	1
superpathway of menaquinol-13 biosynthesis	10	9	1
superpathway of menaquinol-9 biosynthesis	10	9	1
superpathway of menaquinol-10 biosynthesis	10	9	1
superpathway of menaquinol-12 biosynthesis	10	9	1
superpathway of menaquinol-11 biosynthesis	10	9	1
purine nucleotides degradation II (aerobic)	11	8	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)	14	14	1
superpathway of phylloquinol biosynthesis	15	8	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	18	18	1
superpathway of chorismate metabolism	59	50	1