Experiment set2IT071 for Pseudomonas fluorescens FW300-N2C3

L-Histidine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Histidine (20 mM), pH=7.2
Culturing: pseudo5_N2-C3_1_ML2, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.3 generations
By: Jayashree on 6/12/2014
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 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 44 genes in this experiment

For carbon source L-Histidine in Pseudomonas fluorescens FW300-N2C3

For carbon source L-Histidine across organisms

SEED Subsystems

Subsystem	#Specific
Histidine Degradation	6
Molybdenum cofactor biosynthesis	3
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	2
Formate hydrogenase	2
HMG CoA Synthesis	2
ATP-dependent RNA helicases, bacterial	1
Ammonia assimilation	1
Biotin biosynthesis	1
Cobalamin synthesis	1
Coenzyme B12 biosynthesis	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
D-galactonate catabolism	1
D-gluconate and ketogluconates metabolism	1
Fructose utilization	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycine and Serine Utilization	1
Glycine cleavage system	1
Homogentisate pathway of aromatic compound degradation	1
Leucine Degradation and HMG-CoA Metabolism	1
Methionine Salvage	1
Photorespiration (oxidative C2 cycle)	1
Serine-glyoxylate cycle	1
Universal stress protein family	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Histidine metabolism
• Porphyrin and chlorophyll metabolism
• Nitrogen metabolism
• Glyoxylate and dicarboxylate metabolism
• Ubiquinone and menaquinone biosynthesis
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Methionine metabolism
• Valine, leucine and isoleucine degradation
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Naphthalene and anthracene degradation
• One carbon pool by folate
• Methane metabolism
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-histidine degradation II	5	5	5
L-histidine degradation I	4	4	4
bis(guanylyl molybdenum cofactor) biosynthesis	2	2	2
L-glutamate biosynthesis I	2	2	2
bis(guanylyl tungstenpterin) cofactor biosynthesis	1	1	1
guanylyl molybdenum cofactor biosynthesis	1	1	1
L-glutamine degradation I	1	1	1
formate oxidation to CO2	1	1	1
L-glutamine degradation II	1	1	1
ammonia assimilation cycle III	3	3	2
L-histidine degradation III	6	4	3
L-histidine degradation VI	8	7	3
glycine cleavage	3	3	1
glycine biosynthesis II	3	3	1
5'-deoxyadenosine degradation I	3	1	1
L-glutamate and L-glutamine biosynthesis	7	6	2
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	4	1
5'-deoxyadenosine degradation II	4	1	1
oxalate degradation VI	4	1	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation III	5	2	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation II	5	2	1
oxalate degradation III	5	1	1
L-leucine degradation I	6	5	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation I	7	2	1
L-citrulline biosynthesis	8	6	1
L-lysine degradation V	9	6	1
L-methionine salvage cycle III	11	5	1
L-methionine salvage cycle II (plants)	11	3	1
superpathway of L-citrulline metabolism	12	8	1
superpathway of C1 compounds oxidation to CO2	12	5	1
L-methionine salvage cycle I (bacteria and plants)	12	4	1
cob(II)yrinate a,c-diamide biosynthesis II (late cobalt incorporation)	13	13	1
cob(II)yrinate a,c-diamide biosynthesis I (early cobalt insertion)	15	13	1
purine nucleobases degradation I (anaerobic)	15	6	1
purine nucleobases degradation II (anaerobic)	24	16	1
adenosylcobalamin biosynthesis II (aerobic)	33	31	1
adenosylcobalamin biosynthesis I (anaerobic)	36	29	1
superpathway of L-lysine degradation	43	19	1