Experiment set1IT052 for Rhodanobacter denitrificans FW104-10B01

R2A with Nickel (II) chloride hexahydrate 0.3125 mM

Group: stress
Media: R2A + Nickel (II) chloride hexahydrate (0.3125 mM)
Culturing: rhodanobacter_10B01_ML12, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Trenton on 1/24/21
Media components: 0.5 g/L Bacto Peptone, 0.5 g/L casamino acids, 0.5 g/L Yeast Extract, 0.5 g/L D-Glucose, 0.5 g/L Starch, 0.3 g/L Potassium phosphate dibasic, 0.05 g/L Magnesium Sulfate Heptahydrate, 0.3 g/L Sodium pyruvate

Specific Phenotypes

For 31 genes in this experiment

For stress Nickel (II) chloride hexahydrate in Rhodanobacter denitrificans FW104-10B01

For stress Nickel (II) chloride hexahydrate across organisms

SEED Subsystems

Subsystem	#Specific
Cobalt-zinc-cadmium resistance	2
Ammonia assimilation	1
Biotin biosynthesis	1
Branched-Chain Amino Acid Biosynthesis	1
D-ribose utilization	1
Deoxyribose and Deoxynucleoside Catabolism	1
Entner-Doudoroff Pathway	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Multidrug Resistance Efflux Pumps	1
Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Orphan regulatory proteins	1
Pentose phosphate pathway	1
Protein chaperones	1
Proteolysis in bacteria, ATP-dependent	1
Ribosomal protein S12p Asp methylthiotransferase	1
Terminal cytochrome C oxidases	1
Threonine and Homoserine Biosynthesis	1
n-Phenylalkanoic acid degradation	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose phosphate pathway
• Puromycin biosynthesis
• Lipopolysaccharide biosynthesis
• Alkaloid biosynthesis I
• Biosynthesis of plant hormones
• Fatty acid metabolism
• Oxidative phosphorylation
• Purine metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Cysteine metabolism
• Valine, leucine and isoleucine degradation
• Valine, leucine and isoleucine biosynthesis
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Glutathione metabolism
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• Trinitrotoluene degradation
• Carbon fixation in photosynthetic organisms
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis II
• Insect hormone biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-aspartate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
long-chain fatty acid activation	1	1	1
malate/L-aspartate shuttle pathway	2	2	1
ribose phosphorylation	2	1	1
linoleate biosynthesis II (animals)	2	1	1
atromentin biosynthesis	2	1	1
arsenite to oxygen electron transfer	2	1	1
L-glutamate degradation II	2	1	1
L-tyrosine degradation II	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
L-asparagine degradation III (mammalian)	3	3	1
L-phenylalanine biosynthesis I	3	3	1
pentose phosphate pathway (oxidative branch) I	3	3	1
L-tyrosine biosynthesis I	3	3	1
2-deoxy-D-ribose degradation I	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
(R)-cysteate degradation	3	1	1
alkane biosynthesis II	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
oleate biosynthesis I (plants)	3	1	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
sulfolactate degradation III	3	1	1
L-phenylalanine degradation II (anaerobic)	3	1	1
phytol degradation	4	3	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
aerobic respiration I (cytochrome c)	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	2	1
phosphatidylcholine acyl editing	4	2	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
long chain fatty acid ester synthesis (engineered)	4	1	1
wax esters biosynthesis II	4	1	1
sporopollenin precursors biosynthesis	18	4	4
L-tyrosine degradation I	5	4	1
cytosolic NADPH production (yeast)	5	3	1
trans-4-hydroxy-L-proline degradation I	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
octane oxidation	5	2	1
superpathway of plastoquinol biosynthesis	5	2	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	7	2
superpathway of L-threonine biosynthesis	6	6	1
stearate biosynthesis II (bacteria and plants)	6	5	1
TCA cycle VIII (Chlamydia)	6	5	1
fatty acid salvage	6	5	1
stearate biosynthesis IV	6	4	1
formaldehyde oxidation I	6	3	1
Fe(II) oxidation	6	2	1
6-gingerol analog biosynthesis (engineered)	6	2	1
superpathway of sulfolactate degradation	6	2	1
stearate biosynthesis I (animals)	6	1	1
coenzyme M biosynthesis II	6	1	1
anaerobic energy metabolism (invertebrates, cytosol)	7	7	1
L-lysine biosynthesis VI	7	6	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	8	2
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
capsaicin biosynthesis	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
pentose phosphate pathway	8	8	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	4	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
2-deoxy-D-ribose degradation II	8	2	1
superpathway of aromatic amino acid biosynthesis	18	18	2
Entner-Doudoroff pathway I	9	9	1
L-lysine biosynthesis I	9	9	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
L-lysine biosynthesis II	9	7	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	2	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
suberin monomers biosynthesis	20	2	2
rosmarinic acid biosynthesis I	10	1	1
superpathway of fatty acid biosynthesis II (plant)	43	38	4
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	11	1
indole-3-acetate biosynthesis II	12	3	1
aspartate superpathway	25	23	2
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of rosmarinic acid biosynthesis	14	1	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
cutin biosynthesis	16	1	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	16	1
superpathway of glucose and xylose degradation	17	14	1
superpathway of anaerobic energy metabolism (invertebrates)	17	13	1
heterolactic fermentation	18	15	1
superpathway of fatty acids biosynthesis (E. coli)	53	49	2
anaerobic aromatic compound degradation (Thauera aromatica)	27	1	1
palmitate biosynthesis III	29	21	1
superpathway of chorismate metabolism	59	40	2
oleate β-oxidation	35	32	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	25	1