Experiment set5IT071 for Sphingomonas koreensis DSMZ 15582

L-Glutamine nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + L-Glutamine (5 mM)
Culturing: korea_ML2, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 6.5 generations
By: Mark on 1/26/2015
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 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 64 genes in this experiment

For nitrogen source L-Glutamine in Sphingomonas koreensis DSMZ 15582

For nitrogen source L-Glutamine across organisms

SEED Subsystems

Subsystem	#Specific
Cobalt-zinc-cadmium resistance	2
ABC transporter oligopeptide (TC 3.A.1.5.1)	1
ABC transporter peptide (TC 3.A.1.5.5)	1
ATP-dependent RNA helicases, bacterial	1
Beta-lactamase	1
Biogenesis of c-type cytochromes	1
Catechol branch of beta-ketoadipate pathway	1
Copper homeostasis: copper tolerance	1
DNA-replication	1
Folate Biosynthesis	1
Glycine and Serine Utilization	1
Leucine Degradation and HMG-CoA Metabolism	1
Peptidoglycan Biosynthesis	1
Periplasmic disulfide interchange	1
Phosphate metabolism	1
Polyhydroxybutyrate metabolism	1
Potassium homeostasis	1
Protocatechuate branch of beta-ketoadipate pathway	1
Pyruvate Alanine Serine Interconversions	1
RNA processing and degradation, bacterial	1
Ribosomal protein S12p Asp methylthiotransferase	1
Serine-glyoxylate cycle	1
Sex pheromones in Enterococcus faecalis and other Firmicutes	1
Tn552	1
Transcription factors bacterial	1
Type IV pilus	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Synthesis and degradation of ketone bodies
• Purine metabolism
• Glycine, serine and threonine metabolism
• Benzoxazinone biosynthesis
• Lipopolysaccharide biosynthesis
• Peptidoglycan biosynthesis
• Butanoate metabolism
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Ubiquinone and menaquinone biosynthesis
• Puromycin biosynthesis
• Glutamate metabolism
• Cysteine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine degradation
• Penicillin and cephalosporin biosynthesis
• beta-Lactam resistance
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Glutathione metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Glyoxylate and dicarboxylate metabolism
• Biotin metabolism
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Drug metabolism - other enzymes
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
nostoxanthin biosynthesis	2	2	2
L-glutamine degradation I	1	1	1
long-chain fatty acid activation	1	1	1
ketolysis	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
D-serine degradation	3	2	2
L-cysteine degradation II	3	2	2
L-glutamate biosynthesis I	2	2	1
γ-linolenate biosynthesis II (animals)	2	1	1
linoleate biosynthesis II (animals)	2	1	1
glycine betaine degradation III	7	4	3
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
glycine betaine degradation I	8	4	3
dTMP de novo biosynthesis (mitochondrial)	3	3	1
glycine degradation	3	3	1
tetrahydrofolate biosynthesis I	3	3	1
ammonia assimilation cycle III	3	3	1
L-methionine biosynthesis II	6	5	2
alkane biosynthesis II	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
oleate biosynthesis I (plants)	3	1	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
phytol degradation	4	4	1
guanosine ribonucleotides de novo biosynthesis	4	4	1
L-mimosine degradation	8	4	2
wax esters biosynthesis II	4	2	1
tetrahydromonapterin biosynthesis	4	2	1
glutathione-mediated detoxification I	8	3	2
muropeptide degradation	4	1	1
phosphatidylcholine acyl editing	4	1	1
long chain fatty acid ester synthesis (engineered)	4	1	1
sporopollenin precursors biosynthesis	18	4	4
tRNA processing	10	10	2
ketogenesis	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
octane oxidation	5	2	1
superpathway of guanosine nucleotides de novo biosynthesis I	6	6	1
fatty acid salvage	6	5	1
stearate biosynthesis II (bacteria and plants)	6	4	1
stearate biosynthesis IV	6	3	1
6-gingerol analog biosynthesis (engineered)	6	3	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	2
stearate biosynthesis I (animals)	6	1	1
L-glutamate and L-glutamine biosynthesis	7	4	1
capsaicin biosynthesis	7	3	1
ceramide degradation by α-oxidation	7	2	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
superpathway of guanosine nucleotides de novo biosynthesis II	8	7	1
L-citrulline biosynthesis	8	6	1
purine nucleobases degradation II (anaerobic)	24	11	3
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
peptidoglycan biosynthesis II (staphylococci)	17	12	2
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	2
peptidoglycan biosynthesis V (β-lactam resistance)	17	11	2
folate transformations III (E. coli)	9	8	1
TCA cycle VI (Helicobacter)	9	7	1
photorespiration I	9	6	1
photorespiration III	9	6	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
photorespiration II	10	6	1
peptidoglycan recycling II	10	3	1
suberin monomers biosynthesis	20	4	2
superpathway of fatty acid biosynthesis II (plant)	43	37	4
folate transformations II (plants)	11	8	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	11	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
superpathway of L-citrulline metabolism	12	8	1
superpathway of purine nucleotide salvage	14	11	1
peptidoglycan recycling I	14	9	1
peptidoglycan biosynthesis III (mycobacteria)	15	11	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
cutin biosynthesis	16	1	1
superpathway of purine nucleotides de novo biosynthesis I	21	21	1
superpathway of purine nucleotides de novo biosynthesis II	26	24	1
superpathway of fatty acids biosynthesis (E. coli)	53	48	2
palmitate biosynthesis III	29	21	1
oleate β-oxidation	35	30	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	43	1
superpathway of chorismate metabolism	59	37	1