Experiment set1IT058 for Pontibacter actiniarum KMM 6156, DSM 19842

marine broth with Thallium(I) acetate 0.001 mg/ml

Group: stress
Media: marine_broth_2216 + Thallium(I) acetate (0.001 mg/ml)
Culturing: Ponti_ML7, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
Growth: about 4.7 generations
By: Adam on 29-Mar-17
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: 1732 C5

Specific Phenotypes

For 48 genes in this experiment

For stress Thallium(I) acetate in Pontibacter actiniarum KMM 6156, DSM 19842

For stress Thallium(I) acetate across organisms

SEED Subsystems

Subsystem	#Specific
Nitrate and nitrite ammonification	2
Acetyl-CoA fermentation to Butyrate	1
Anaerobic respiratory reductases	1
Butanol Biosynthesis	1
Chitin and N-acetylglucosamine utilization	1
Fermentations: Mixed acid	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glutathione: Non-redox reactions	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Isoleucine degradation	1
Maltose and Maltodextrin Utilization	1
Methylglyoxal Metabolism	1
N-Acetyl-Galactosamine and Galactosamine Utilization	1
NAD and NADP cofactor biosynthesis global	1
Oxidative stress	1
Propionyl-CoA to Succinyl-CoA Module	1
Serine-glyoxylate cycle	1
Thiamin biosynthesis	1
Ton and Tol transport systems	1
Transport of Zinc	1
Trehalose Biosynthesis	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Thiamine metabolism
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Methionine metabolism
• Valine, leucine and isoleucine degradation
• Starch and sucrose metabolism
• Nitrogen metabolism
• Glycolysis / Gluconeogenesis
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Cyanoamino acid metabolism
• Other glycan degradation
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Glycosaminoglycan degradation
• Glycerophospholipid metabolism
• alpha-Linolenic acid metabolism
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Retinol metabolism
• Limonene and pinene degradation
• Phenylpropanoid biosynthesis
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
hydroxymethylpyrimidine salvage	2	2	2
acetaldehyde biosynthesis I	1	1	1
S-methyl-5'-thioadenosine degradation IV	1	1	1
neolinustatin bioactivation	3	2	2
thiamine diphosphate salvage II	5	4	3
thiamine diphosphate biosynthesis I (E. coli)	2	2	1
L-glutamate degradation II	2	2	1
thiamine diphosphate biosynthesis II (Bacillus)	2	2	1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis I	2	2	1
linustatin bioactivation	4	2	2
pyruvate fermentation to ethanol II	2	1	1
lotaustralin degradation	2	1	1
S-methyl-5'-thioadenosine degradation I	2	1	1
ethanol degradation I	2	1	1
linamarin degradation	2	1	1
thiamine diphosphate salvage IV (yeast)	7	3	3
thiamine diphosphate formation from pyrithiamine and oxythiamine (yeast)	8	3	3
ethanol degradation II	3	3	1
propanoyl CoA degradation I	3	3	1
thiamine diphosphate salvage V	3	2	1
L-aspartate degradation III (anaerobic)	3	2	1
L-isoleucine degradation II	3	2	1
methylglyoxal degradation I	3	2	1
L-valine degradation II	3	2	1
cellulose degradation II (fungi)	3	2	1
L-aspartate degradation II (aerobic)	3	2	1
L-leucine degradation III	3	2	1
methylglyoxal degradation VIII	3	2	1
chitin degradation II (Vibrio)	6	3	2
pyruvate fermentation to ethanol III	3	1	1
phosphatidylcholine biosynthesis V	3	1	1
pyruvate fermentation to ethanol I	3	1	1
conversion of succinate to propanoate	3	1	1
thiamine diphosphate biosynthesis III (Staphylococcus)	3	1	1
L-methionine degradation III	3	1	1
thiamine diphosphate biosynthesis IV (eukaryotes)	3	1	1
superpathway of thiamine diphosphate biosynthesis III (eukaryotes)	7	3	2
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
phytol degradation	4	3	1
2-oxobutanoate degradation I	4	3	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
S-adenosyl-L-methionine salvage I	4	2	1
cytidine-5'-diphosphate-glycerol biosynthesis	4	1	1
salidroside biosynthesis	4	1	1
5'-deoxyadenosine degradation II	4	1	1
L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde	5	5	1
superpathway of thiamine diphosphate biosynthesis I	10	9	2
pyruvate fermentation to isobutanol (engineered)	5	4	1
3-hydroxy-4-methyl-anthranilate biosynthesis II	5	4	1
autoinducer AI-2 biosynthesis I	5	3	1
coumarin biosynthesis (via 2-coumarate)	5	2	1
ethanolamine utilization	5	1	1
phenylethanol biosynthesis	5	1	1
acetylene degradation (anaerobic)	5	1	1
(S)-propane-1,2-diol degradation	5	1	1
superpathway of thiamine diphosphate biosynthesis II	11	9	2
glycogen degradation II	6	5	1
pyruvate fermentation to butanol II (engineered)	6	5	1
autoinducer AI-2 biosynthesis II (Vibrio)	6	4	1
3-hydroxy-4-methyl-anthranilate biosynthesis I	6	3	1
L-canavanine degradation II	6	1	1
α-tomatine degradation	6	1	1
noradrenaline and adrenaline degradation	13	4	2
3-methylbutanol biosynthesis (engineered)	7	6	1
L-cysteine biosynthesis VI (reverse transsulfuration)	7	4	1
pyruvate fermentation to propanoate I	7	4	1
serotonin degradation	7	3	1
chitin degradation III (Serratia)	7	3	1
superpathway of methylglyoxal degradation	8	4	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis II	8	2	1
NAD de novo biosynthesis II (from tryptophan)	9	9	1
photorespiration I	9	4	1
photorespiration III	9	4	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	2	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	6	1
photorespiration II	10	5	1
peptidoglycan recycling II	10	3	1
pyruvate fermentation to hexanol (engineered)	11	7	1
L-glutamate degradation VIII (to propanoate)	11	4	1
L-methionine salvage cycle II (plants)	11	2	1
L-tryptophan degradation IX	12	7	1
L-methionine salvage cycle I (bacteria and plants)	12	4	1
3-hydroxypropanoate cycle	13	8	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	6	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	6	1
L-tryptophan degradation V (side chain pathway)	13	1	1
superpathway of NAD biosynthesis in eukaryotes	14	11	1
peptidoglycan recycling I	14	7	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	3	1
firefly bioluminescence	14	2	1
L-tryptophan degradation III (eukaryotic)	15	10	1
mixed acid fermentation	16	10	1
superpathway of L-methionine salvage and degradation	16	9	1
superpathway of anaerobic energy metabolism (invertebrates)	17	11	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	6	1
heterolactic fermentation	18	11	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	11	1
superpathway of the 3-hydroxypropanoate cycle	18	8	1
superpathway of anaerobic sucrose degradation	19	13	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	11	1
methylaspartate cycle	19	11	1
superpathway of N-acetylneuraminate degradation	22	11	1
L-tryptophan degradation XI (mammalian, via kynurenine)	23	11	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1