Experiment set6IT032 for Marinobacter adhaerens HP15

marine broth with Cisplatin 0.025 mg/ml

Group: stress
Media: marine_broth_2216 + Cisplatin (0.025 mg/ml)
Culturing: Marino_ML2, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Adam on 3/4/2014
Media components: 5 g/L Bacto Peptone, 1 g/L Yeast Extract, 0.1 g/L Ferric citrate, 19.45 g/L Sodium Chloride, 5.9 g/L Magnesium chloride hexahydrate, 3.24 g/L Magnesium sulfate, 1.8 g/L Calcium chloride, 0.55 g/L Potassium Chloride, 0.16 g/L Sodium bicarbonate, 0.08 g/L Potassium bromide, 34 mg/L Strontium chloride, 22 mg/L Boric Acid, 4 mg/L Sodium metasilicate, 2.4 mg/L sodium fluoride, 8 mg/L Disodium phosphate
Growth plate: 828 C5,C6

Specific Phenotypes

For 59 genes in this experiment

For stress Cisplatin in Marinobacter adhaerens HP15

For stress Cisplatin across organisms

SEED Subsystems

Subsystem	#Specific
DNA-replication	6
DNA repair, bacterial	3
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	2
DNA repair, UvrABC system	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
Ammonia assimilation	1
DNA Repair Base Excision	1
DNA repair, bacterial DinG and relatives	1
DNA repair, bacterial MutL-MutS system	1
DNA repair, bacterial RecFOR pathway	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Queuosine-Archaeosine Biosynthesis	1
RNA processing and degradation, bacterial	1
Transcription factors bacterial	1
Valine degradation	1
ZZ gjo need homes	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Valine, leucine and isoleucine degradation
• beta-Alanine metabolism
• Propanoate metabolism
• Nitrogen metabolism
• Biosynthesis of plant hormones
• Fatty acid elongation in mitochondria
• Fatty acid metabolism
• Pyrimidine metabolism
• Glutamate metabolism
• Methionine metabolism
• Cysteine metabolism
• Geraniol degradation
• Lysine degradation
• Tryptophan metabolism
• Selenoamino acid metabolism
• Lipopolysaccharide biosynthesis
• alpha-Linolenic acid metabolism
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Folate biosynthesis
• Limonene and pinene degradation
• Sulfur metabolism
• Caprolactam degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate biosynthesis I	2	2	2
L-glutamine degradation II	1	1	1
L-glutamine degradation I	1	1	1
ammonia assimilation cycle III	3	3	2
benzoyl-CoA biosynthesis	3	3	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
2-methyl-branched fatty acid β-oxidation	14	10	3
tRNA processing	10	10	2
adipate degradation	5	5	1
fatty acid β-oxidation IV (unsaturated, even number)	5	4	1
adipate biosynthesis	5	4	1
propanoyl-CoA degradation II	5	3	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
acrylate degradation I	5	3	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	1	1
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	2
β-alanine biosynthesis II	6	4	1
methyl ketone biosynthesis (engineered)	6	3	1
fatty acid β-oxidation I (generic)	7	5	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	4	1
benzoyl-CoA degradation I (aerobic)	7	3	1
L-citrulline biosynthesis	8	7	1
L-valine degradation I	8	7	1
phenylacetate degradation I (aerobic)	9	9	1
valproate β-oxidation	9	6	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
superpathway of coenzyme A biosynthesis II (plants)	10	8	1
3-phenylpropanoate degradation	10	3	1
superpathway of phenylethylamine degradation	11	10	1
Spodoptera littoralis pheromone biosynthesis	22	4	2
oleate β-oxidation	35	30	3
superpathway of L-citrulline metabolism	12	9	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
platensimycin biosynthesis	26	7	1