Experiment set13S76 for Rhodanobacter denitrificans FW104-10B01

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R2A_PIPES pH 4

Group: pH
Media: R2A_PIPES, pH=4
Culturing: rhodanobacter_10B01_ML12, 96 well deep well block, Aerobic, at 23 (C), shaken=700 rpm
Growth: about 3.2 generations
By: Hans and Hira on 10-Jan-25
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 PIPES sesquisodium salt

Specific Phenotypes

For 33 genes in this experiment

SEED Subsystems

Subsystem #Specific
Oxidative stress 3
Cobalt-zinc-cadmium resistance 1
Multidrug Resistance Efflux Pumps 1
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon) 1
Peptidoglycan Biosynthesis 1
Type IV pilus 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
L-glutamine degradation I 1 1 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 3 3
L-asparagine biosynthesis III (tRNA-dependent) 4 3 3
gondoate biosynthesis (anaerobic) 4 4 2
L-glutamate biosynthesis I 2 2 1
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast) 12 9 6
palmitate biosynthesis III 29 21 13
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate) 9 8 4
tetradecanoate biosynthesis (mitochondria) 25 17 11
oleate biosynthesis IV (anaerobic) 14 13 6
palmitate biosynthesis II (type II fatty acid synthase) 31 29 13
fatty acid elongation -- saturated 5 4 2
superpathway of fatty acids biosynthesis (E. coli) 53 49 20
8-amino-7-oxononanoate biosynthesis I 11 10 4
superpathway of unsaturated fatty acids biosynthesis (E. coli) 20 18 7
superpathway of fatty acid biosynthesis II (plant) 43 38 15
(5Z)-dodecenoate biosynthesis I 6 6 2
ammonia assimilation cycle III 3 3 1
(5Z)-dodecenoate biosynthesis II 6 5 2
stearate biosynthesis II (bacteria and plants) 6 5 2
stearate biosynthesis IV 6 4 2
superpathway of fatty acid biosynthesis I (E. coli) 16 14 5
biotin biosynthesis I 15 14 4
streptorubin B biosynthesis 34 20 9
fatty acid biosynthesis initiation (mitochondria) 4 2 1
8-amino-7-oxononanoate biosynthesis IV 5 4 1
superpathway of fatty acid biosynthesis initiation 5 4 1
cis-vaccenate biosynthesis 5 4 1
odd iso-branched-chain fatty acid biosynthesis 34 24 6
anteiso-branched-chain fatty acid biosynthesis 34 24 6
even iso-branched-chain fatty acid biosynthesis 34 24 6
petroselinate biosynthesis 6 2 1
L-glutamate and L-glutamine biosynthesis 7 6 1
L-citrulline biosynthesis 8 6 1
2-allylmalonyl-CoA biosynthesis 8 2 1
peptidoglycan biosynthesis IV (Enterococcus faecium) 17 11 2
peptidoglycan biosynthesis II (staphylococci) 17 11 2
peptidoglycan biosynthesis V (β-lactam resistance) 17 10 2
peptidoglycan biosynthesis I (meso-diaminopimelate containing) 12 10 1
superpathway of L-citrulline metabolism 12 8 1
peptidoglycan maturation (meso-diaminopimelate containing) 12 4 1
androstenedione degradation I (aerobic) 25 8 2
androstenedione degradation II (anaerobic) 27 6 2
superpathway of testosterone and androsterone degradation 28 8 2
peptidoglycan biosynthesis III (mycobacteria) 15 10 1
superpathway of cholesterol degradation I (cholesterol oxidase) 42 10 2
mycolate biosynthesis 205 20 9
superpathway of cholesterol degradation II (cholesterol dehydrogenase) 47 10 2
superpathway of cholesterol degradation III (oxidase) 49 6 2
superpathway of mycolate biosynthesis 239 21 9