Experiment set1IT038 for Sinorhizobium meliloti 1021

LB with Nickel (II) chloride hexahydrate 1 mM

Group: stress
Media: LB + Nickel (II) chloride hexahydrate (1 mM)
Culturing: Smeli_ML6, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 4.6 generations
By: Mark on 6/2/2015
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: Smeli_SP2 A2

Specific Phenotypes

For 37 genes in this experiment

For stress Nickel (II) chloride hexahydrate in Sinorhizobium meliloti 1021

For stress Nickel (II) chloride hexahydrate across organisms

SEED Subsystems

Subsystem	#Specific
Choline and Betaine Uptake and Betaine Biosynthesis	3
Phosphate metabolism	3
Copper homeostasis: copper tolerance	2
Polyamine Metabolism	2
Ammonia assimilation	1
Fructose utilization	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glutamine synthetases	1
Glutathione-dependent pathway of formaldehyde detoxification	1
High affinity phosphate transporter and control of PHO regulon	1
Histidine Degradation	1
Mannitol Utilization	1
Orphan regulatory proteins	1
Peptidoglycan Biosynthesis	1
Protein degradation	1
Purine conversions	1
Pyridoxin (Vitamin B6) Biosynthesis	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	1
Sucrose utilization	1
Sucrose utilization Shewanella	1
cAMP signaling in bacteria	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Glycine, serine and threonine metabolism
• Glutathione metabolism
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Oxidative phosphorylation
• Glutamate metabolism
• Arginine and proline metabolism
• Tyrosine metabolism
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Tryptophan metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Pyruvate metabolism
• Biphenyl degradation
• 1- and 2-Methylnaphthalene degradation
• Fluorene degradation
• 3-Chloroacrylic acid degradation
• Methane metabolism
• Vitamin B6 metabolism
• Nitrogen metabolism
• Phenylpropanoid biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
choline degradation I	2	2	2
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	2
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	2
L-glutamine biosynthesis I	1	1	1
choline-O-sulfate degradation	3	3	2
ammonia assimilation cycle I	2	2	1
polyphosphate metabolism	2	2	1
β-alanine biosynthesis I	2	1	1
β-alanine biosynthesis IV	2	1	1
ammonia assimilation cycle II	2	1	1
D-sorbitol degradation I	3	3	1
ammonia assimilation cycle III	3	3	1
formaldehyde oxidation II (glutathione-dependent)	3	3	1
glycine betaine biosynthesis III (plants)	3	2	1
superpathway of ammonia assimilation (plants)	3	2	1
sucrose degradation I (sucrose phosphotransferase)	3	1	1
dimethylsulfoniopropanoate biosynthesis I (Wollastonia)	3	1	1
L-aspartate degradation III (anaerobic)	3	1	1
L-aspartate degradation II (aerobic)	3	1	1
Arg/N-end rule pathway (eukaryotic)	14	8	4
sucrose degradation III (sucrose invertase)	4	3	1
sucrose degradation IV (sucrose phosphorylase)	4	3	1
choline degradation IV	4	2	1
dimethylsulfoniopropanoate biosynthesis II (Spartina)	4	1	1
sucrose degradation VII (sucrose 3-dehydrogenase)	4	1	1
sucrose degradation II (sucrose synthase)	5	4	1
mannitol cycle	5	3	1
pyridoxal 5'-phosphate biosynthesis I	7	6	1
L-glutamate and L-glutamine biosynthesis	7	5	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage	12	10	1
superpathway of C1 compounds oxidation to CO2	12	4	1
heterolactic fermentation	18	13	1
superpathway of anaerobic sucrose degradation	19	14	1