Experiment set4S619 for Rhodanobacter sp. FW510-T8

R2A_HOMOPIPES; pH5

Group: pH
Media: R2A_HOMOPIPES, pH=5
Culturing: rhodanobacter_T8_ML1, 96 well deep well block, Aerobic, at 23 (C), shaken=700 rpm
By: Hira on 10/21/2025
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, 30 mM HOMOPIPES

Specific Phenotypes

For 16 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Biogenesis of cytochrome c oxidases	2
Terminal cytochrome C oxidases	2
Bacterial Cell Division	1
Cobalt-zinc-cadmium resistance	1
DNA repair, bacterial	1
Heat shock dnaK gene cluster extended	1
Methionine Salvage	1
Soluble cytochromes and functionally related electron carriers	1
Ubiquinone Biosynthesis	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
• Oxidative phosphorylation
• Methionine metabolism
• Histidine metabolism
• Phenylalanine metabolism
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• Tryptophan metabolism
• Cyanoamino acid metabolism
• Toluene and xylene degradation
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• 1,4-Dichlorobenzene degradation
• Benzoate degradation via CoA ligation
• Styrene degradation
• Methane metabolism
• Limonene and pinene degradation
• Brassinosteroid biosynthesis
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Isoflavonoid biosynthesis
• Alkaloid biosynthesis I
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
arsenite to oxygen electron transfer	2	1	1
5'-deoxyadenosine degradation I	3	2	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
aerobic respiration I (cytochrome c)	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	2	1
5'-deoxyadenosine degradation II	4	1	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation III	5	1	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation II	5	1	1
Fe(II) oxidation	6	2	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation I	7	6	1
L-methionine salvage cycle III	11	10	1
L-methionine salvage cycle II (plants)	11	7	1
L-methionine salvage cycle I (bacteria and plants)	12	9	1