Experiment set2IT065 for Sinorhizobium meliloti 1021

LB, pH8

Group: pH
Media: LB, pH=8
Culturing: Smeli_ML6, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 4.4 generations
By: Mark on 6/2/2015
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride

Specific Phenotypes

For 28 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Proteasome bacterial	2
Proteolysis in bacteria, ATP-dependent	2
Ammonia assimilation	1
Arginine and Ornithine Degradation	1
Glutamine synthetases	1
Methionine Biosynthesis	1
One-carbon metabolism by tetrahydropterines	1
Peptidoglycan Biosynthesis	1
Serine-glyoxylate cycle	1
Terminal cytochrome O ubiquinol oxidase	1
Terminal cytochrome oxidases	1
Threonine and Homoserine 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:

• Arginine and proline metabolism
• Glutamate metabolism
• Alkaloid biosynthesis I
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• C21-Steroid hormone metabolism
• Urea cycle and metabolism of amino groups
• Puromycin biosynthesis
• Pyrimidine metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Bisphenol A degradation
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Nucleotide sugars metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Linoleic acid metabolism
• Tetrachloroethene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• One carbon pool by folate
• Methane metabolism
• Carbon fixation in photosynthetic organisms
• Retinol metabolism
• Nitrogen metabolism
• Alkaloid biosynthesis II
• Insect hormone biosynthesis
• Drug metabolism - other enzymes
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide products
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
sulfoquinovosyl diacylglycerol biosynthesis	2	2	2
L-glutamine biosynthesis I	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-aspartate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
L-ornithine degradation I (L-proline biosynthesis)	1	1	1
L-arginine degradation VII (arginase 3 pathway)	2	2	1
ammonia assimilation cycle I	2	2	1
malate/L-aspartate shuttle pathway	2	2	1
glycogen biosynthesis II (from UDP-D-Glucose)	4	3	2
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
atromentin biosynthesis	2	1	1
L-proline biosynthesis II (from arginine)	2	1	1
L-tyrosine degradation II	2	1	1
ammonia assimilation cycle II	2	1	1
pseudouridine degradation	2	1	1
L-glutamate degradation II	2	1	1
L-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
ammonia assimilation cycle III	3	3	1
superpathway of ammonia assimilation (plants)	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
L-aspartate degradation III (anaerobic)	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
L-aspartate degradation II (aerobic)	3	1	1
L-asparagine degradation III (mammalian)	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
sulfolactate degradation III	3	1	1
(R)-cysteate degradation	3	1	1
L-tyrosine degradation III	4	2	1
putrescine degradation II	4	2	1
L-phenylalanine degradation III	4	2	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	1	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
L-tyrosine degradation I	5	5	1
trans-4-hydroxy-L-proline degradation I	5	3	1
superpathway of plastoquinol biosynthesis	5	2	1
L-tryptophan degradation XIII (reductive Stickland reaction)	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
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	7	2
TCA cycle VIII (Chlamydia)	6	6	1
superpathway of L-threonine biosynthesis	6	6	1
superpathway of sulfolactate degradation	6	3	1
coenzyme M biosynthesis II	6	1	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
L-glutamate and L-glutamine biosynthesis	7	5	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	8	2
superpathway of ornithine degradation	8	5	1
superpathway of aromatic amino acid biosynthesis	18	18	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	4	1
superpathway of L-tyrosine biosynthesis	10	10	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
reductive acetyl coenzyme A pathway I (homoacetogenic bacteria)	10	4	1
rosmarinic acid biosynthesis I	10	2	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	7	1
(S)-reticuline biosynthesis I	11	3	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	11	1
indole-3-acetate biosynthesis II	12	5	1
superpathway of L-isoleucine biosynthesis I	13	13	1
folate transformations I	13	9	1
superpathway of L-arginine and L-ornithine degradation	13	9	1
superpathway of rosmarinic acid biosynthesis	14	3	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	23	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	3	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	2
superpathway of chorismate metabolism	59	38	2