Experiment set8IT060 for Phaeobacter inhibens DSM 17395

Adenosine nitrogen source

Group: nitrogen source
Media: DinoMM_noNitrogen_HighNutrient_SucroseC + Adenosine (2.5 mM), pH=7.2
Culturing: Phaeo_ML1, tube, Aerobic, at 25 (C), shaken=200 rpm
By: Mark on 1/20/2015
Media components: 20 g/L Sea salts, 0.1 g/L Potassium phosphate monobasic, 20 mM Sucrose, 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 24 genes in this experiment

For nitrogen source Adenosine in Phaeobacter inhibens DSM 17395

For nitrogen source Adenosine across organisms

SEED Subsystems

Subsystem	#Specific
NAD and NADP cofactor biosynthesis global	3
NAD regulation	3
Heat shock dnaK gene cluster extended	2
High affinity phosphate transporter and control of PHO regulon	2
Phosphate metabolism	2
Allantoin Utilization	1
Branched-Chain Amino Acid Biosynthesis	1
Control of cell elongation - division cycle in Bacilli	1
D-ribose utilization	1
DNA Repair Base Excision	1
Deoxyribose and Deoxynucleoside Catabolism	1
Fructose utilization	1
Mannitol Utilization	1
Molybdenum cofactor biosynthesis	1
Purine conversions	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
RNA processing and degradation, bacterial	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	1
Sucrose utilization	1
Sucrose utilization Shewanella	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Valine, leucine and isoleucine biosynthesis
• Pyruvate metabolism
• Nicotinate and nicotinamide metabolism
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Ubiquinone and menaquinone biosynthesis
• Alanine and aspartate metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Naphthalene and anthracene degradation
• Carbon fixation in photosynthetic organisms
• Thiamine metabolism
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
NAD de novo biosynthesis I	6	6	3
guanine and guanosine salvage II	2	2	1
guanine and guanosine salvage I	2	2	1
xanthine and xanthosine salvage	2	2	1
ribose phosphorylation	2	1	1
tRNA processing	10	10	4
2-deoxy-D-ribose degradation I	3	3	1
D-sorbitol degradation I	3	3	1
NAD de novo biosynthesis III	6	5	2
NAD de novo biosynthesis IV (anaerobic)	6	5	2
superpathway of guanine and guanosine salvage	3	2	1
nicotine biosynthesis	9	3	3
phosphatidylcholine biosynthesis V	3	1	1
sucrose degradation I (sucrose phosphotransferase)	3	1	1
UTP and CTP dephosphorylation I	7	5	2
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	2
NAD biosynthesis from 2-amino-3-carboxymuconate semialdehyde	4	4	1
sucrose degradation IV (sucrose phosphorylase)	4	3	1
sucrose degradation III (sucrose invertase)	4	3	1
arsenic detoxification (bacteria)	4	2	1
superpathway of nicotine biosynthesis	12	4	3
sucrose degradation VII (sucrose 3-dehydrogenase)	4	1	1
sucrose degradation II (sucrose synthase)	5	4	1
mannitol cycle	5	3	1
allantoin degradation to glyoxylate II	5	1	1
L-leucine biosynthesis	6	6	1
arsenate detoxification I	6	3	1
methylgallate degradation	6	2	1
pyrimidine deoxyribonucleotides de novo biosynthesis IV	7	6	1
3-methylbutanol biosynthesis (engineered)	7	6	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	7	2
pyrimidine deoxyribonucleotides biosynthesis from CTP	8	6	1
protocatechuate degradation I (meta-cleavage pathway)	8	3	1
superpathway of allantoin degradation in plants	8	1	1
aspartate superpathway	25	23	3
pyrimidine deoxyribonucleotides de novo biosynthesis I	9	9	1
pyrimidine deoxyribonucleotides de novo biosynthesis III	9	8	1
NAD de novo biosynthesis II (from tryptophan)	9	6	1
superpathway of vanillin and vanillate degradation	10	3	1
syringate degradation	12	3	1
gluconeogenesis I	13	12	1
superpathway of purine nucleotide salvage	14	13	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)	14	12	1
superpathway of NAD biosynthesis in eukaryotes	14	8	1
superpathway of branched chain amino acid biosynthesis	17	17	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	18	17	1
heterolactic fermentation	18	13	1
superpathway of anaerobic sucrose degradation	19	14	1