Experiment set1IT039 for Pedobacter sp. GW460-11-11-14-LB5

R2A with copper (II) chloride dihydrate 0.16 mM

Group: stress
Media: R2A + copper (II) chloride dihydrate (0.16 mM)
Culturing: Pedo557_ML3, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
Growth: about 4.9 generations
By: Adam on 17-May-17
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
Growth plate: 1754 B2

Specific Phenotypes

For 19 genes in this experiment

For stress copper (II) chloride dihydrate in Pedobacter sp. GW460-11-11-14-LB5

For stress copper (II) chloride dihydrate across organisms

SEED Subsystems

Subsystem	#Specific
Biotin biosynthesis	1
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	1
Cobalt-zinc-cadmium resistance	1
Control of cell elongation - division cycle in Bacilli	1
Copper homeostasis	1
Copper homeostasis: copper tolerance	1
DNA Repair Base Excision	1
ECF class transporters	1
Folate Biosynthesis	1
Iron acquisition in Vibrio	1
Phosphate metabolism	1
Ton and Tol transport systems	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Valine, leucine and isoleucine degradation
• Valine, leucine and isoleucine biosynthesis
• Pantothenate and CoA biosynthesis
• Folate biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
4-aminobenzoate biosynthesis I	2	2	1
L-alanine biosynthesis I	2	1	1
4-aminobenzoate biosynthesis II	2	1	1
L-valine degradation II	3	2	1
L-isoleucine degradation II	3	2	1
L-isoleucine biosynthesis V	3	2	1
L-leucine degradation III	3	2	1
L-isoleucine degradation III (oxidative Stickland reaction)	3	1	1
L-leucine degradation V (oxidative Stickland reaction)	3	1	1
L-valine degradation III (oxidative Stickland reaction)	3	1	1
L-valine biosynthesis	4	4	1
superpathway of L-alanine biosynthesis	4	2	1
L-leucine degradation IV (reductive Stickland reaction)	5	2	1
superpathway of branched chain amino acid biosynthesis	17	17	3
L-leucine biosynthesis	6	6	1
L-isoleucine degradation I	6	4	1
L-isoleucine biosynthesis IV	6	4	1
L-leucine degradation I	6	4	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-isoleucine biosynthesis III	7	4	1
lipoprotein posttranslational modification (Gram-negative bacteria)	7	2	1
L-isoleucine biosynthesis II	8	6	1
L-valine degradation I	8	3	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
superpathway of candicidin biosynthesis	11	4	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-threonine metabolism	18	12	1
odd iso-branched-chain fatty acid biosynthesis	34	24	1
even iso-branched-chain fatty acid biosynthesis	34	24	1
anteiso-branched-chain fatty acid biosynthesis	34	24	1
superpathway of chorismate metabolism	59	35	1