Experiment set11IT046 for Ralstonia solanacearum IBSBF1503

water survival rep C; Treatment=watercosm; Collection=outgrowth_in_CPG; Time=180_days

Group: survival
Media: Water + Treatment=watercosm; Collection=outgrowth_in_CPG; Time=180_days
Culturing: RalstoniaBSBF1503_ML2, flask, Aerobic, at 28 (C)
By: Brian Ingel on 6-Nov-21

Specific Phenotypes

For 36 genes in this experiment

For survival Treatment=watercosm; Collection=outgrowth_in_CPG; Time=180_days in Ralstonia solanacearum IBSBF1503

For survival Treatment=watercosm; Collection=outgrowth_in_CPG; Time=180_days across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	2
Purine Utilization	2
Allantoin Utilization	1
Ammonia assimilation	1
D-ribose utilization	1
Glutamate dehydrogenases	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glutathione: Non-redox reactions	1
Heat shock dnaK gene cluster extended	1
Iron acquisition in Vibrio	1
Methylglyoxal Metabolism	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Photorespiration (oxidative C2 cycle)	1
Proline Synthesis	1
Redox-dependent regulation of nucleus processes	1
Ribosome biogenesis bacterial	1
Terminal cytochrome C oxidases	1
Transport of Iron	1
Type IV pilus	1
YbbK	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Nicotinate and nicotinamide metabolism
• Ascorbate and aldarate metabolism
• Arginine and proline metabolism
• Lipopolysaccharide biosynthesis
• Pyruvate metabolism
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Fatty acid biosynthesis
• Oxidative phosphorylation
• Urea cycle and metabolism of amino groups
• Pyrimidine metabolism
• Glutamate metabolism
• Methionine metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Selenoamino acid metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Glycosaminoglycan degradation
• Ether lipid metabolism
• alpha-Linolenic acid metabolism
• Sphingolipid metabolism
• Naphthalene and anthracene degradation
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Thiamine metabolism
• Riboflavin metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Aminoacyl-tRNA biosynthesis
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate degradation I	1	1	1
acyl-CoA hydrolysis	1	1	1
glycolate and glyoxylate degradation II	2	2	1
palmitoleate biosynthesis IV (fungi and animals)	2	2	1
allantoin degradation to ureidoglycolate I (urea producing)	2	1	1
arsenite to oxygen electron transfer	2	1	1
adenosine nucleotides degradation II	5	4	2
methylglyoxal degradation VIII	3	3	1
L-alanine degradation II (to D-lactate)	3	3	1
L-ornithine biosynthesis II	3	3	1
allantoin degradation to glyoxylate I	3	2	1
ethene biosynthesis IV (engineered)	3	2	1
methylglyoxal degradation I	3	2	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
guanosine nucleotides degradation II	4	4	1
L-proline biosynthesis I (from L-glutamate)	4	4	1
adenosine nucleotides degradation I	8	7	2
inosine 5'-phosphate degradation	4	3	1
aerobic respiration I (cytochrome c)	4	3	1
guanosine nucleotides degradation III	4	3	1
guanosine nucleotides degradation I	4	3	1
chitin deacetylation	4	2	1
aerobic respiration II (cytochrome c) (yeast)	4	2	1
adipate degradation	5	5	1
NAD salvage pathway V (PNC V cycle)	5	4	1
purine nucleotides degradation II (aerobic)	11	8	2
fatty acid salvage	6	6	1
glyoxylate cycle	6	6	1
purine nucleotides degradation I (plants)	12	10	2
superpathway of guanosine nucleotides degradation (plants)	6	5	1
superpathway of purines degradation in plants	18	14	3
purine nucleobases degradation II (anaerobic)	24	16	4
superpathway of allantoin degradation in yeast	6	4	1
Fe(II) oxidation	6	2	1
NAD salvage pathway I (PNC VI cycle)	7	6	1
L-Nδ-acetylornithine biosynthesis	7	6	1
superpathway of glycol metabolism and degradation	7	5	1
ureide biosynthesis	7	5	1
D-xylose degradation IV	7	3	1
4-aminobutanoate degradation V	7	3	1
L-glutamate degradation XI (reductive Stickland reaction)	7	2	1
caffeine degradation III (bacteria, via demethylation)	7	1	1
coenzyme M biosynthesis I	7	1	1
L-citrulline biosynthesis	8	8	1
superpathway of methylglyoxal degradation	8	5	1
superpathway of allantoin degradation in plants	8	4	1
L-arabinose degradation IV	8	4	1
theophylline degradation	9	1	1
L-glutamate degradation V (via hydroxyglutarate)	10	5	1
caffeine degradation IV (bacteria, via demethylation and oxidation)	10	1	1
tRNA charging	21	20	2
NAD salvage (plants)	11	6	1
oleate β-oxidation	35	31	3
superpathway of glyoxylate bypass and TCA	12	11	1
superpathway of L-citrulline metabolism	12	10	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
superpathway of NAD biosynthesis in eukaryotes	14	10	1
2-methyl-branched fatty acid β-oxidation	14	9	1
firefly bioluminescence	14	3	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	2	1
methylaspartate cycle	19	11	1
jasmonic acid biosynthesis	19	5	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	23	1
superpathway of pentose and pentitol degradation	42	9	1