Experiment set2IT067 for Echinicola vietnamensis KMM 6221, DSM 17526

marine broth with Doxycycline hyclate 0.032 mg/ml

Group: stress
Media: marine_broth_2216 + Doxycycline hyclate (0.032 mg/ml)
Culturing: Cola_ML5, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
Growth: about 4.7 generations
By: Adam on 8-May-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: 1726 D2

Specific Phenotypes

For 34 genes in this experiment

For stress Doxycycline hyclate in Echinicola vietnamensis KMM 6221, DSM 17526

For stress Doxycycline hyclate across organisms

SEED Subsystems

Subsystem	#Specific
Proline, 4-hydroxyproline uptake and utilization	2
Aromatic amino acid degradation	1
Auxin biosynthesis	1
Auxin degradation	1
DNA repair, UvrABC system	1
DNA repair, bacterial MutL-MutS system	1
Fatty Acid Biosynthesis FASII	1
Iron acquisition in Vibrio	1
L-Arabinose utilization	1
Maltose and Maltodextrin Utilization	1
Multidrug Resistance Efflux Pumps	1
Oxidative stress	1
Photorespiration (oxidative C2 cycle)	1
Pyruvate Alanine Serine Interconversions	1
Respiratory dehydrogenases 1	1
Sialic Acid Metabolism	1
Ton and Tol transport systems	1
mycolic acid synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Arginine and proline metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• Nucleotide sugars metabolism
• Methane metabolism
• Alkaloid biosynthesis I
• Galactose metabolism
• Fatty acid biosynthesis
• Puromycin biosynthesis
• Lysine biosynthesis
• Histidine metabolism
• Tyrosine metabolism
• Starch and sucrose metabolism
• alpha-Linolenic acid metabolism
• Trinitrotoluene degradation
• Porphyrin and chlorophyll metabolism
• Indole and ipecac alkaloid biosynthesis
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of phenylpropanoids
• 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
betanidin degradation	1	1	1
betaxanthin biosynthesis (via dopamine)	2	2	1
isoniazid activation	2	2	1
superoxide radicals degradation	2	2	1
trans-4-hydroxy-L-proline degradation II	4	3	2
proline to cytochrome bo oxidase electron transfer	2	1	1
octopamine biosynthesis	2	1	1
baicalein degradation (hydrogen peroxide detoxification)	2	1	1
methanol oxidation to formaldehyde IV	2	1	1
L-dopa degradation II (bacterial)	2	1	1
ethanol degradation IV	3	3	1
L-proline degradation I	3	3	1
betaxanthin biosynthesis	3	2	1
starch degradation I	3	1	1
L-tryptophan degradation VI (via tryptamine)	3	1	1
gondoate biosynthesis (anaerobic)	4	4	1
reactive oxygen species degradation	4	4	1
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	12	9	3
L-tryptophan degradation X (mammalian, via tryptamine)	4	3	1
salidroside biosynthesis	4	2	1
luteolin triglucuronide degradation	4	1	1
catecholamine biosynthesis	4	1	1
serotonin and melatonin biosynthesis	4	1	1
xanthommatin biosynthesis	4	1	1
palmitate biosynthesis III	29	21	7
tetradecanoate biosynthesis (mitochondria)	25	12	6
palmitate biosynthesis II (type II fatty acid synthase)	31	29	7
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	8	2
oleate biosynthesis IV (anaerobic)	14	13	3
superpathway of fatty acids biosynthesis (E. coli)	53	48	11
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	17	4
fatty acid elongation -- saturated	5	4	1
8-amino-7-oxononanoate biosynthesis IV	5	4	1
cis-vaccenate biosynthesis	5	4	1
phenylethanol biosynthesis	5	2	1
hydroxycinnamic acid tyramine amides biosynthesis	5	1	1
superpathway of fatty acid biosynthesis II (plant)	43	38	8
8-amino-7-oxononanoate biosynthesis I	11	9	2
(S)-reticuline biosynthesis I	11	3	2
even iso-branched-chain fatty acid biosynthesis	34	24	6
odd iso-branched-chain fatty acid biosynthesis	34	24	6
anteiso-branched-chain fatty acid biosynthesis	34	24	6
(5Z)-dodecenoate biosynthesis I	6	5	1
(5Z)-dodecenoate biosynthesis II	6	4	1
stearate biosynthesis II (bacteria and plants)	6	4	1
petroselinate biosynthesis	6	3	1
stearate biosynthesis IV	6	3	1
(5R)-carbapenem carboxylate biosynthesis	6	1	1
beta-carboline biosynthesis	6	1	1
psilocybin biosynthesis	6	1	1
hydroxycinnamic acid serotonin amides biosynthesis	6	1	1
streptorubin B biosynthesis	34	20	5
L-Nδ-acetylornithine biosynthesis	7	6	1
(S)-reticuline biosynthesis II	7	1	1
biotin biosynthesis I	15	13	2
L-citrulline biosynthesis	8	8	1
superpathway of fatty acid biosynthesis I (E. coli)	16	14	2
glycogen degradation I	8	3	1
2-allylmalonyl-CoA biosynthesis	8	2	1
methanofuran biosynthesis	8	1	1
sesamin biosynthesis	8	1	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	4	1
justicidin B biosynthesis	10	1	1
matairesinol biosynthesis	10	1	1
superpathway of L-citrulline metabolism	12	10	1
indole-3-acetate biosynthesis II	12	4	1
secologanin and strictosidine biosynthesis	17	1	1
Amaryllidacea alkaloids biosynthesis	26	1	1
superpathway of betalain biosynthesis	27	13	1
mycolate biosynthesis	205	23	5
superpathway of mycolate biosynthesis	239	24	5