Experiment set9IT035 for Paraburkholderia graminis OAS925

Motility_chemotaxis, R2A; outer cut

Group: motility_chemotaxis
Media: R2A + Method=compound_throughout_media; Sample=outer; Collection=direct_from_plate
Culturing: Burkholderia_OAS925_ML2, soft agar plate (0.25%), Aerobic, at 30 (C), shaken=0 rpm, (solid)
By: Marta Torres on 29-Jul-21
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

Specific Phenotypes

For 14 genes in this experiment

For motility_chemotaxis Method=compound_throughout_media; Sample=outer; Collection=direct_from_plate in Paraburkholderia graminis OAS925

For motility_chemotaxis Method=compound_throughout_media; Sample=outer; Collection=direct_from_plate across organisms

SEED Subsystems

Subsystem	#Specific
Bacterial Chemotaxis	2
Bacterial hemoglobins	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Flagellar motility	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Threonine and Homoserine Biosynthesis	1
ZZ gjo need homes	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glutamate metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Carbon fixation in photosynthetic organisms
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• 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
L-aspartate biosynthesis	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
malate/L-aspartate shuttle pathway	2	2	1
atromentin biosynthesis	2	1	1
L-tyrosine degradation II	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
L-glutamate degradation II	2	1	1
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
sulfolactate degradation III	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
(R)-cysteate degradation	3	1	1
L-phenylalanine degradation II (anaerobic)	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
L-tyrosine degradation III	4	2	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	2	1
L-phenylalanine degradation III	4	2	1
creatinine degradation I	4	1	1
dimethylsulfoniopropanoate biosynthesis III (algae and phytoplankton)	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
creatinine degradation II	5	2	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	7	2
superpathway of L-threonine biosynthesis	6	6	1
TCA cycle VIII (Chlamydia)	6	5	1
superpathway of sulfolactate degradation	6	3	1
coenzyme M biosynthesis II	6	1	1
anaerobic energy metabolism (invertebrates, cytosol)	7	7	1
ethene biosynthesis III (microbes)	7	6	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	8	2
L-homomethionine biosynthesis	7	2	1
glycine betaine degradation I	8	6	1
superpathway of aromatic amino acid biosynthesis	18	18	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	6	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	3	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
rosmarinic acid biosynthesis I	10	2	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	11	1
indole-3-acetate biosynthesis II	12	4	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of rosmarinic acid biosynthesis	14	2	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	15	1
aspartate superpathway	25	22	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	5	1
superpathway of chorismate metabolism	59	42	2
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	23	1