Experiment set5IT075 for Shewanella loihica PV-4

Anaerobic growth with fumarate as E acceptor

Group: anaerobic
Media: ShewMM + Sodium Fumarate dibasic (20 mM)
Culturing: PV4_ML1, hungate, Anaerobic, at 30 (C), shaken=200 rpm
Growth: about 3.7 generations
By: Kelly on 8/28/2013
Media components: 1.5 g/L Ammonium chloride, 1.75 g/L Sodium Chloride, 0.61 g/L Magnesium chloride hexahydrate, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM Sodium D,L-Lactate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 25 genes in this experiment

For anaerobic Sodium Fumarate dibasic in Shewanella loihica PV-4

For anaerobic Sodium Fumarate dibasic across organisms

SEED Subsystems

Subsystem	#Specific
Molybdenum cofactor biosynthesis	4
Menaquinone and Phylloquinone Biosynthesis	3
Formate hydrogenase	2
Methionine Biosynthesis	2
Butanol Biosynthesis	1
Chorismate Synthesis	1
Cobalt-zinc-cadmium resistance	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
Fermentations: Mixed acid	1
Nitrate and nitrite ammonification	1
Ribonucleotide reduction	1
Soluble cytochromes and functionally related electron carriers	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
• Biosynthesis of phenylpropanoids
• Biosynthesis of plant hormones
• Butanoate metabolism
• Citrate cycle (TCA cycle)
• Oxidative phosphorylation
• Purine metabolism
• Puromycin biosynthesis
• Pyrimidine metabolism
• Methionine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Lipopolysaccharide biosynthesis
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Methane metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Nitrogen metabolism
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
bis(guanylyl molybdenum cofactor) biosynthesis	2	2	2
guanylyl molybdenum cofactor biosynthesis	1	1	1
formate oxidation to CO2	1	1	1
bis(guanylyl tungstenpterin) cofactor biosynthesis	1	1	1
2-carboxy-1,4-naphthoquinol biosynthesis	7	7	5
superpathway of demethylmenaquinol-8 biosynthesis I	9	9	5
superpathway of demethylmenaquinol-9 biosynthesis	9	8	5
superpathway of demethylmenaquinol-6 biosynthesis I	9	8	5
superpathway of menaquinol-8 biosynthesis I	10	10	5
3-dehydroquinate biosynthesis I	2	2	1
nitrate reduction IV (dissimilatory)	2	2	1
superpathway of menaquinol-6 biosynthesis	10	9	5
superpathway of menaquinol-13 biosynthesis	10	9	5
superpathway of menaquinol-12 biosynthesis	10	9	5
superpathway of menaquinol-10 biosynthesis	10	9	5
superpathway of menaquinol-7 biosynthesis	10	9	5
superpathway of menaquinol-9 biosynthesis	10	9	5
superpathway of menaquinol-11 biosynthesis	10	9	5
salicylate biosynthesis I	2	1	1
reductive monocarboxylic acid cycle	2	1	1
pyruvate fermentation to acetate IV	3	3	1
pyruvate fermentation to ethanol I	3	3	1
molybdopterin biosynthesis	6	5	2
S-adenosyl-L-methionine salvage II	3	2	1
salicylate biosynthesis II	3	2	1
2,3-dihydroxybenzoate biosynthesis	3	2	1
superpathway of phylloquinol biosynthesis	15	7	5
formate to nitrite electron transfer	3	1	1
pyrimidine deoxyribonucleotides de novo biosynthesis II	7	7	2
adenosine deoxyribonucleotides de novo biosynthesis II	4	4	1
S-adenosyl-L-methionine salvage I	4	4	1
guanosine deoxyribonucleotides de novo biosynthesis II	4	4	1
L-methionine biosynthesis III	4	3	1
oxalate degradation VI	4	1	1
L-methionine biosynthesis I	5	5	1
seleno-amino acid biosynthesis (plants)	5	3	1
oxalate degradation III	5	1	1
L-threonine degradation I	6	6	1
L-methionine biosynthesis II	6	5	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)	14	14	2
superpathway of adenosine nucleotides de novo biosynthesis II	7	7	1
chorismate biosynthesis I	7	7	1
superpathway of guanosine nucleotides de novo biosynthesis II	8	8	1
superpathway of L-homoserine and L-methionine biosynthesis	8	8	1
superpathway of S-adenosyl-L-methionine biosynthesis	9	9	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	9	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	7	1
vibriobactin biosynthesis	9	2	1
superpathway of chorismate metabolism	59	51	6
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
enterobactin biosynthesis	11	5	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	11	1
bacillibactin biosynthesis	12	4	1
superpathway of C1 compounds oxidation to CO2	12	4	1
superpathway of L-tryptophan biosynthesis	13	13	1
superpathway of purine nucleotides de novo biosynthesis II	26	25	2
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	7	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	1
purine nucleobases degradation I (anaerobic)	15	5	1
mixed acid fermentation	16	15	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	18	1
superpathway of aromatic amino acid biosynthesis	18	18	1
superpathway of L-threonine metabolism	18	15	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of seleno-compound metabolism	19	8	1
superpathway of N-acetylneuraminate degradation	22	16	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	45	2
purine nucleobases degradation II (anaerobic)	24	11	1
aspartate superpathway	25	24	1