Experiment set4S618 for Rhodanobacter sp. FW510-T8

R2A_MES; pH5

Group: pH
Media: R2A_MES, pH=5
Culturing: rhodanobacter_T8_ML1, 96 well deep well block, Aerobic, at 23 (C), shaken=700 rpm
By: Hira on 10/21/2025

Specific Phenotypes

For 19 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Biogenesis of cytochrome c oxidases	2
Oxidative stress	2
Terminal cytochrome C oxidases	2
Entner-Doudoroff Pathway	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Lipoic acid metabolism	1
Phosphate metabolism	1
PnuC-like transporters	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Soluble cytochromes and functionally related electron carriers	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Glycolysis / Gluconeogenesis
• Oxidative phosphorylation
• Pyruvate metabolism
• Carbon fixation in photosynthetic organisms
• Lipoic acid 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 histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
lipoate biosynthesis and incorporation I	2	2	1
polyphosphate metabolism	2	2	1
arsenite to oxygen electron transfer	2	1	1
lipoate biosynthesis and incorporation IV (yeast)	7	4	3
lipoate biosynthesis and incorporation III (Bacillus)	3	2	1
lipoate biosynthesis and incorporation V (mammals)	3	2	1
lipoate biosynthesis and incorporation II	3	1	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
ppGpp metabolism	6	6	1
Fe(II) oxidation	6	2	1
cyanophycin metabolism	6	1	1
anaerobic energy metabolism (invertebrates, cytosol)	7	7	1
Entner-Doudoroff pathway I	9	9	1
Entner-Doudoroff pathway III (semi-phosphorylative)	9	6	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	4	1
Rubisco shunt	10	8	1
glycolysis IV	10	8	1
glycolysis V (Pyrococcus)	10	7	1
glycolysis III (from glucose)	11	11	1
glycolysis II (from fructose 6-phosphate)	11	11	1
glycolysis VI (from fructose)	11	8	1
homolactic fermentation	12	11	1
glycolysis I (from glucose 6-phosphate)	13	12	1
Bifidobacterium shunt	15	14	1
mixed acid fermentation	16	12	1
glycerol degradation to butanol	16	9	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 hexitol degradation (bacteria)	18	13	1
superpathway of anaerobic sucrose degradation	19	16	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	19	1
superpathway of N-acetylneuraminate degradation	22	16	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	23	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	17	1
1-butanol autotrophic biosynthesis (engineered)	27	18	1