Experiment set2IT060 for Sinorhizobium meliloti 1021

LB

Group: lb
Media: LB
Culturing: Smeli_ML6, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 3.8 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_SP5 D6

Specific Phenotypes

For 12 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Choline and Betaine Uptake and Betaine Biosynthesis	1
Phenylalanine and Tyrosine Branches from Chorismate	1
Pyridoxin (Vitamin B6) Biosynthesis	1
Two cell division clusters relating to chromosome partitioning	1
YcfH	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Pyrimidine metabolism
• Glycine, serine and threonine metabolism
• Methionine metabolism
• Lysine biosynthesis
• Histidine metabolism
• Vitamin B6 metabolism
• Alkaloid biosynthesis I
• 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

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
sulfoquinovosyl diacylglycerol biosynthesis	2	2	2
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-phenylalanine biosynthesis III (cytosolic, plants)	2	2	1
glycogen biosynthesis II (from UDP-D-Glucose)	4	3	2
atromentin biosynthesis	2	1	1
pseudouridine degradation	2	1	1
L-tyrosine degradation II	2	1	1
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
L-phenylalanine degradation II (anaerobic)	3	2	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
glycine betaine degradation I	8	7	2
L-tyrosine biosynthesis III	4	3	1
L-tyrosine biosynthesis II	4	2	1
L-phenylalanine degradation III	4	2	1
creatinine degradation I	4	2	1
L-phenylalanine biosynthesis II	4	2	1
L-tyrosine degradation III	4	2	1
L-tyrosine degradation I	5	5	1
superpathway of plastoquinol biosynthesis	5	2	1
superpathway of L-phenylalanine and L-tyrosine biosynthesis	5	2	1
creatinine degradation II	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
lipid IVA biosynthesis (P. putida)	6	6	1
lipid IVA biosynthesis (Vibrio cholerae serogroup O1 El Tor)	6	6	1
lipid IVA biosynthesis (generic)	6	6	1
lipid IVA biosynthesis (2,3-diamino-2,3-dideoxy-D-glucopyranose-containing)	6	6	1
lipid IVA biosynthesis (H. pylori)	6	6	1
lipid IVA biosynthesis (E. coli)	6	6	1
pyridoxal 5'-phosphate biosynthesis I	7	6	1
superpathway of aromatic amino acid biosynthesis	18	18	2
lipid IVA biosynthesis (P. gingivalis)	9	9	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	4	1
superpathway of L-tyrosine biosynthesis	10	10	1
L-histidine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
rosmarinic acid biosynthesis I	10	2	1
(S)-reticuline biosynthesis I	11	3	1
tropane alkaloids biosynthesis	11	1	1
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage	12	10	1
superpathway of rosmarinic acid biosynthesis	14	3	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	4	1
superpathway of (Kdo)2-lipid A biosynthesis	17	11	1
superpathway of Kdo2-lipid A biosynthesis	25	11	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	3	1
superpathway of chorismate metabolism	59	38	2
superpathway of histidine, purine, and pyrimidine biosynthesis	46	42	1