Experiment set7IT079 for Marinobacter adhaerens HP15

marine broth with Benzalkonium Chloride 0.004 mg/ml

Group: stress
Media: marine_broth_2216 + Benzalkonium Chloride (0.004 mg/ml)
Culturing: Marino_ML2, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Jake on 5/20/2014
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: 930 C7,C8

Specific Phenotypes

For 32 genes in this experiment

For stress Benzalkonium Chloride in Marinobacter adhaerens HP15

For stress Benzalkonium Chloride across organisms

SEED Subsystems

Subsystem	#Specific
Coenzyme PQQ synthesis	3
Pyrroloquinoline Quinone biosynthesis	3
Branched-Chain Amino Acid Biosynthesis	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
DNA-replication	1
Entner-Doudoroff Pathway	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway	1
Lactose and Galactose Uptake and Utilization	1
Leucine Degradation and HMG-CoA Metabolism	1
Lipid A-Ara4N pathway ( Polymyxin resistance )	1
Methylglyoxal Metabolism	1
N-linked Glycosylation in Bacteria	1
Orphan regulatory proteins	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Rhamnose containing glycans	1
Soluble cytochromes and functionally related electron carriers	1
Teichuronic acid biosynthesis	1
Transcription factors bacterial	1
linker unit-arabinogalactan synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Tyrosine metabolism
• Nucleotide sugars metabolism
• Pyruvate metabolism
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Limonene and pinene degradation
• Pentose and glucuronate interconversions
• Galactose metabolism
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Glycine, serine and threonine metabolism
• Geraniol degradation
• Valine, leucine and isoleucine biosynthesis
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Starch and sucrose metabolism
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• 1,2-Dichloroethane degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Folate biosynthesis
• Retinol metabolism
• Caprolactam degradation
• Alkaloid biosynthesis II
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
ethanol degradation I	2	2	2
UDP-α-D-galactose biosynthesis	1	1	1
UDP-N-acetyl-D-galactosamine biosynthesis I	1	1	1
UDP-α-D-glucuronate biosynthesis (from UDP-glucose)	1	1	1
acetaldehyde biosynthesis I	1	1	1
ethanol degradation II	3	3	2
pyruvate fermentation to ethanol III	3	3	2
pyruvate fermentation to ethanol I	3	2	2
UDP-α-D-xylose biosynthesis	2	2	1
L-threonine degradation IV	2	2	1
phytol degradation	4	3	2
pyruvate fermentation to ethanol II	2	1	1
phenylethanol degradation	2	1	1
putrescine degradation I	2	1	1
putrescine degradation V	2	1	1
phenylethylamine degradation I	2	1	1
ethylene glycol degradation	2	1	1
phenylethylamine degradation II	2	1	1
UDP-α-D-galactofuranose biosynthesis	2	1	1
ethanolamine utilization	5	5	2
acetylene degradation (anaerobic)	5	4	2
ethanol degradation IV	3	3	1
2-hydroxypenta-2,4-dienoate degradation	3	3	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	2
L-leucine degradation III	3	2	1
ethanol degradation III	3	2	1
L-valine degradation II	3	2	1
hypotaurine degradation	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
putrescine degradation IV	3	2	1
L-isoleucine degradation II	3	2	1
histamine degradation	3	1	1
2-deoxy-α-D-ribose 1-phosphate degradation	3	1	1
styrene degradation	3	1	1
2-deoxy-D-ribose degradation I	3	1	1
2-aminoethylphosphonate degradation I	3	1	1
D-galactose detoxification	3	1	1
sulfoacetaldehyde degradation IV	3	1	1
L-methionine degradation III	3	1	1
noradrenaline and adrenaline degradation	13	4	4
serotonin degradation	7	3	2
L-tyrosine degradation III	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
L-phenylalanine degradation III	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	1	1
salidroside biosynthesis	4	1	1
putrescine degradation III	4	1	1
D-arabinose degradation II	4	1	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	5	2
4-oxopentanoate degradation	9	4	2
UDP-sugars interconversion	9	3	2
teichuronic acid biosynthesis (B. subtilis 168)	9	2	2
catechol degradation I (meta-cleavage pathway)	5	5	1
octane oxidation	5	5	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
(S)-propane-1,2-diol degradation	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
mitochondrial NADPH production (yeast)	5	2	1
D-galactose degradation I (Leloir pathway)	5	2	1
dopamine degradation	5	1	1
phenylethanol biosynthesis	5	1	1
colanic acid building blocks biosynthesis	11	8	2
3-methyl-branched fatty acid α-oxidation	6	3	1
superpathway of pyrimidine deoxyribonucleosides degradation	6	2	1
alkane oxidation	6	1	1
triethylamine degradation	6	1	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	6	2
catechol degradation II (meta-cleavage pathway)	7	6	1
3-methylbutanol biosynthesis (engineered)	7	6	1
toluene degradation I (aerobic) (via o-cresol)	7	5	1
toluene degradation V (aerobic) (via toluene-cis-diol)	7	5	1
superpathway of glycol metabolism and degradation	7	4	1
UDP-N-acetyl-D-galactosamine biosynthesis II	7	4	1
pyrroloquinoline quinone biosynthesis	7	4	1
stachyose degradation	7	2	1
ceramide degradation by α-oxidation	7	2	1
superpathway of purine deoxyribonucleosides degradation	7	1	1
limonene degradation IV (anaerobic)	7	1	1
mixed acid fermentation	16	11	2
superpathway of ornithine degradation	8	5	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	4	1
p-cumate degradation	8	3	1
3-phenylpropanoate and 3-(3-hydroxyphenyl)propanoate degradation	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
butanol and isobutanol biosynthesis (engineered)	8	2	1
aromatic biogenic amine degradation (bacteria)	8	1	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	8	2
heterolactic fermentation	18	14	2
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	3	1
tunicamycin biosynthesis	9	3	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	15	2
meta cleavage pathway of aromatic compounds	10	9	1
superpathway of phenylethylamine degradation	11	10	1
superpathway of N-acetylneuraminate degradation	22	13	2
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	5	1
p-cymene degradation	11	3	1
L-tryptophan degradation IX	12	6	1
L-tryptophan degradation XII (Geobacillus)	12	6	1
naphthalene degradation to acetyl-CoA	12	5	1
toluene degradation IV (aerobic) (via catechol)	13	9	1
superpathway of L-arginine and L-ornithine degradation	13	7	1
cannabinoid biosynthesis	13	6	1
L-tryptophan degradation V (side chain pathway)	13	1	1
superpathway of L-threonine metabolism	18	12	1
mandelate degradation to acetyl-CoA	18	9	1
mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	18	1	1
superpathway of anaerobic sucrose degradation	19	14	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
superpathway of aerobic toluene degradation	30	13	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	10	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	13	1
superpathway of pentose and pentitol degradation	42	4	1