Experiment set1S74 for Castellaniella sp019104865 MT123

Anaerobic, pH5.5

Group: ph; anaerobic
Media: CRBTM_UGA_Anaerobic_MES, pH=5.5
Culturing: Castellaniella_MT123_ML3, tube, Anaerobic, at 30 (C)
By: Mike Adams lab on 6/19/23
Media components: 3.74 mM Ammonium chloride, 1.34 mM Potassium Chloride, 2 mM Magnesium Sulfate Heptahydrate, 0.1 mM Calcium chloride dihydrate, 0.17 mM Sodium Chloride, 20 mM Sodium D,L-Lactate, 40 mM MES sodium salt, 10 mM Sodium nitrate, ATCC Wolfe's mineral mix (5 mg/L EDTA, 3 mg/L Magnesium Sulfate Heptahydrate, 5 mg/L Manganese (II) sulfate monohydrate, 10 mg/L Sodium Chloride, 1 mg/L Iron (II) sulfate heptahydrate, 1 mg/L Cobalt(II) nitrate hexahydrate, 1 mg/L Calcium chloride dihydrate, 1 mg/L Zinc sulfate heptahydrate, 0.1 mg/L Copper (II) sulfate pentahydrate, 0.1 mg/L Aluminum potassium sulfate dodecahydrate, 0.1 mg/L Boric Acid, 0.1 mg/L Sodium Molybdate Dihydrate, 0.01 mg/L Sodium selenite pentahydrate, 0.1 mg/L Sodium tungstate dihydrate, 0.2 mg/L Nickel (II) chloride hexahydrate), ATCC Wolfe's vitamin mix (20 ug/L Folic Acid, 100 ug/L Pyridoxine HCl, 50 ug/L Riboflavin, 20 ug/L biotin, 50 ug/L Thiamine HCl, 50 ug/L Nicotinic Acid, 50 ug/L calcium pantothenate, 1 ug/L Cyanocobalamin, 50 ug/L 4-Aminobenzoic acid, 50 ug/L Lipoic acid)

Specific Phenotypes

For 32 genes in this experiment

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	2
Branched-Chain Amino Acid Biosynthesis	2
Leucine Degradation and HMG-CoA Metabolism	2
Purine conversions	2
Serine-glyoxylate cycle	2
Catechol branch of beta-ketoadipate pathway	1
Cysteine Biosynthesis	1
D-gluconate and ketogluconates metabolism	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycine and Serine Utilization	1
Glycine cleavage system	1
High affinity phosphate transporter and control of PHO regulon	1
Isoleucine degradation	1
Phosphate metabolism	1
Photorespiration (oxidative C2 cycle)	1
Propionate-CoA to Succinate Module	1
Protocatechuate branch of beta-ketoadipate pathway	1
Pyruvate Alanine Serine Interconversions	1
Respiratory dehydrogenases 1	1
Soluble cytochromes and functionally related electron carriers	1
TCA Cycle	1
Terminal cytochrome d ubiquinol oxidases	1
Terminal cytochrome oxidases	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Biosynthesis of alkaloids derived from histidine and purine
• Citrate cycle (TCA cycle)
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Nitrogen metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Synthesis and degradation of ketone bodies
• Oxidative phosphorylation
• Purine metabolism
• Geraniol degradation
• Valine, leucine and isoleucine biosynthesis
• Phenylalanine metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Glyoxylate and dicarboxylate metabolism
• Butanoate metabolism
• One carbon pool by folate
• Reductive carboxylate cycle (CO2 fixation)
• Pantothenate and CoA biosynthesis
• Drug metabolism - other enzymes

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
cis-cyclopropane fatty acid (CFA) biosynthesis	1	1	1
glycine cleavage	3	3	2
glycine biosynthesis II	3	3	2
polyphosphate metabolism	2	2	1
L-alanine degradation I	2	2	1
sterculate biosynthesis	2	1	1
glyoxylate cycle	6	6	2
2-oxoglutarate decarboxylation to succinyl-CoA	3	3	1
pyruvate decarboxylation to acetyl CoA I	3	3	1
ketolysis	3	3	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	1
TCA cycle VI (Helicobacter)	9	6	3
guanosine ribonucleotides de novo biosynthesis	4	4	1
L-valine biosynthesis	4	4	1
partial TCA cycle (obligate autotrophs)	8	7	2
inosine 5'-phosphate degradation	4	3	1
nitrogen remobilization from senescing leaves	8	5	2
TCA cycle V (2-oxoglutarate synthase)	9	8	2
TCA cycle VII (acetate-producers)	9	7	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	2
TCA cycle II (plants and fungi)	9	7	2
TCA cycle I (prokaryotic)	10	8	2
pyruvate fermentation to isobutanol (engineered)	5	4	1
TCA cycle III (animals)	10	7	2
reductive TCA cycle I	11	6	2
superpathway of guanosine nucleotides de novo biosynthesis I	6	6	1
superpathway of glyoxylate bypass and TCA	12	10	2
5-oxo-L-proline metabolism	6	4	1
L-isoleucine biosynthesis IV	6	4	1
γ-glutamyl cycle	6	4	1
reductive TCA cycle II	12	6	2
L-isoleucine biosynthesis I (from threonine)	7	7	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	2
ureide biosynthesis	7	5	1
L-isoleucine biosynthesis III	7	4	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	17	3
superpathway of guanosine nucleotides de novo biosynthesis II	8	7	1
mixed acid fermentation	16	12	2
adenosine nucleotides degradation I	8	5	1
L-isoleucine biosynthesis II	8	4	1
superpathway of branched chain amino acid biosynthesis	17	17	2
methylaspartate cycle	19	10	2
purine nucleotides degradation II (aerobic)	11	8	1
purine nucleotides degradation I (plants)	12	7	1
ethene biosynthesis V (engineered)	25	17	2
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	2
superpathway of purine nucleotide salvage	14	12	1
superpathway of L-threonine metabolism	18	13	1
superpathway of purines degradation in plants	18	11	1
superpathway of purine nucleotides de novo biosynthesis I	21	21	1
superpathway of purine nucleotides de novo biosynthesis II	26	23	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	43	1
mycolate biosynthesis	205	20	3
superpathway of mycolate biosynthesis	239	21	3