Experiment set5IT025 for Paraburkholderia graminis OAS925

Plant=Brachypodium_distachyon; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=sterile_soil; Collection=outgrowth_R2A_with_Tween_and_Cycloheximide; Time=21_days

Group: in planta
Media: + Plant=Brachypodium_distachyon; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=sterile_soil; Collection=outgrowth_R2A_with_Tween_and_Cycloheximide; Time=21_days
Culturing: Burkholderia_OAS925_ML2, pot, at 26 (C), (Solid)
By: Marta on 3-Jun-21

Specific Phenotypes

For 24 genes in this experiment

For in planta Plant=Brachypodium_distachyon; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=sterile_soil; Collection=outgrowth_R2A_with_Tween_and_Cycloheximide; Time=21_days in Paraburkholderia graminis OAS925

For in planta Plant=Brachypodium_distachyon; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=sterile_soil; Collection=outgrowth_R2A_with_Tween_and_Cycloheximide; Time=21_days across organisms

SEED Subsystems

Subsystem	#Specific
Arginine Biosynthesis extended	2
L-Arabinose utilization	2
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	2
Carboxysome	1
Chitin and N-acetylglucosamine utilization	1
Cyanate hydrolysis	1
Formate hydrogenase	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Methicillin resistance in Staphylococci	1
Molybdenum cofactor biosynthesis	1
Multidrug Resistance Efflux Pumps	1
Peptidoglycan Biosynthesis	1
Sialic Acid Metabolism	1
Stringent Response, (p)ppGpp metabolism	1
Teichoic and lipoteichoic acids biosynthesis	1
Threonine and Homoserine Biosynthesis	1
Transport of Molybdenum	1
Type IV pilus	1
UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis	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
• Urea cycle and metabolism of amino groups
• Lysine biosynthesis
• Peptidoglycan biosynthesis
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• High-mannose type N-glycan biosynthesis
• Nucleotide sugars metabolism
• Glycerophospholipid metabolism
• Sphingolipid metabolism
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Purine metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Cysteine metabolism
• Geraniol degradation
• Valine, leucine and isoleucine biosynthesis
• Lysine degradation
• Tyrosine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Aminophosphonate metabolism
• Glutathione metabolism
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Aminosugars metabolism
• Keratan sulfate biosynthesis
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Glyoxylate and dicarboxylate metabolism
• Methane metabolism
• Carbon fixation in photosynthetic organisms
• Pantothenate and CoA biosynthesis
• Biotin metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Zeatin biosynthesis
• Nitrogen metabolism
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Flavone and flavonol biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-aspartate degradation I	1	1	1
L-aspartate biosynthesis	1	1	1
formate oxidation to CO2	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
malate/L-aspartate shuttle pathway	2	2	1
N-acetylglucosamine degradation I	2	2	1
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
atromentin biosynthesis	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
L-glutamate degradation II	2	1	1
L-tyrosine degradation II	2	1	1
L-ornithine biosynthesis I	5	5	2
cardiolipin biosynthesis II	3	3	1
N-acetylglucosamine degradation II	3	3	1
L-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
ppGpp metabolism	6	5	2
cardiolipin biosynthesis I	3	2	1
sulfolactate degradation III	3	2	1
cyanate degradation	3	2	1
cardiolipin biosynthesis III	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
(R)-cysteate degradation	3	1	1
L-phenylalanine degradation II (anaerobic)	3	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	7	3
L-valine biosynthesis	4	4	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
D-galactosamine and N-acetyl-D-galactosamine degradation	4	2	1
oxalate degradation VI	4	1	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
L-arginine biosynthesis I (via L-ornithine)	9	9	2
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	2
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	8	3
L-arginine biosynthesis II (acetyl cycle)	10	10	2
L-tyrosine degradation I	5	5	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
trans-4-hydroxy-L-proline degradation I	5	3	1
N-acetyl-D-galactosamine degradation	5	2	1
superpathway of plastoquinol biosynthesis	5	2	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
oxalate degradation III	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
enterobacterial common antigen biosynthesis	5	1	1
Salmonella enterica serotype O:54 O antigen biosynthesis	5	1	1
Escherichia coli serotype O:15 O antigen biosynthesis	5	1	1
superpathway of L-threonine biosynthesis	6	6	1
phosphatidylglycerol biosynthesis II	6	6	1
phosphatidylglycerol biosynthesis I	6	6	1
TCA cycle VIII (Chlamydia)	6	5	1
L-arabinose degradation III	6	5	1
L-arabinose degradation V	6	5	1
L-isoleucine biosynthesis IV	6	4	1
superpathway of sulfolactate degradation	6	3	1
superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation	6	2	1
Escherichia coli serotype O:50 O antigen biosynthesis	6	1	1
Escherichia coli serotype O:77/Salmonella enterica serotype O:6,14 O antigen biosynthesis	6	1	1
coenzyme M biosynthesis II	6	1	1
Salmonella enterica serotype O:13 O antigen biosynthesis	6	1	1
Escherichia coli serotype O:149/Shigella boydii serotype O1 O antigen biosynthesis	6	1	1
Escherichia coli serotype O:56 O antigen biosynthesis	6	1	1
Escherichia coli serotype O:177 O antigen biosynthesis	6	1	1
superpathway of L-isoleucine biosynthesis I	13	13	2
L-isoleucine biosynthesis I (from threonine)	7	7	1
anaerobic energy metabolism (invertebrates, cytosol)	7	7	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
L-isoleucine biosynthesis III	7	4	1
Escherichia coli serotype O:157/Salmonella enterica serotype O:30 O antigen biosynthesis	7	1	1
Escherichia coli serotype O:2 O antigen biosynthesis	7	1	1
Escherichia coli serotype O:7 O antigen biosynthesis	7	1	1
Salmonella enterica serotype O:6,7 O antigen biosynthesis	7	1	1
Escherichia coli serotype O:85/Salmonella enterica serotype O:17 O antigen biosynthesis	7	1	1
Salmonella enterica serotype O:18 O antigen biosynthesis	7	1	1
Escherichia coli serotype O:71/Salmonella enterica serotype O:28ac O antigen biosynthesis	7	1	1
Escherichia coli serotype O:1B/Salmonella enterica serotype O:42 O antigen biosynthesis	7	1	1
Salmonella enterica serotype O:39 O antigen biosynthesis	7	1	1
Escherichia coli serotype O:111/Salmonella enterica serotype O:35 O antigen biosynthesis	7	1	1
Escherichia coli serotype O:152 O antigen biosynthesis	7	1	1
L-arabinose degradation IV	8	6	1
L-isoleucine biosynthesis II	8	5	1
chitin derivatives degradation	8	3	1
Escherichia coli serotype O:52 O antigen biosynthesis	8	1	1
Escherichia coli serotype O:117 O antigen biosynthesis	8	1	1
Escherichia coli serotype O:49 O antigen biosynthesis	8	1	1
Shigella boydii serotype 6 O antigen biosynthesis	8	1	1
Escherichia coli serotype O:55/Salmonella enterica serotype O:50 O antigen biosynthesis	8	1	1
Escherichia coli serotype O:107 O antigen biosynthesis	8	1	1
Escherichia coli serotype O:128 O antigen biosynthesis	8	1	1
Escherichia coli serotype O:104 O antigen biosynthesis	8	1	1
Escherichia coli serotype O:86 O antigen biosynthesis	8	1	1
Escherichia coli serotype O:51/Salmonella enterica serotype O:57 O antigen biosynthesis	8	1	1
Escherichia coli serotype O:21/Salmonella enterica serotype O:38 O antigen biosynthesis	8	1	1
Escherichia coli serotype O:127 O antigen biosynthesis	8	1	1
superpathway of branched chain amino acid biosynthesis	17	17	2
superpathway of arginine and polyamine biosynthesis	17	14	2
peptidoglycan biosynthesis II (staphylococci)	17	12	2
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	2
peptidoglycan biosynthesis V (β-lactam resistance)	17	11	2
superpathway of aromatic amino acid biosynthesis	18	18	2
L-lysine biosynthesis I	9	9	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	15	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	6	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	3	1
Escherichia coli serotype O:8 O antigen biosynthesis	9	1	1
Escherichia coli serotype O:183/Shigella boydii serotype O:10 O antigen biosynthesis	9	1	1
Escherichia coli serotype O:169 O antigen biosynthesis	9	1	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of enterobacterial common antigen biosynthesis	10	3	1
rosmarinic acid biosynthesis I	10	2	1
poly(3-O-β-D-glucopyranosyl-N-acetylgalactosamine 1-phosphate) wall teichoic acid biosynthesis	10	2	1
Escherichia coli serotype O:9 O antigen biosynthesis	10	1	1
Escherichia coli serotype O:9a O antigen biosynthesis	10	1	1
poly(glycerol phosphate) wall teichoic acid biosynthesis	11	2	1
(S)-reticuline biosynthesis I	11	1	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	12	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	11	1
superpathway of phospholipid biosynthesis III (E. coli)	12	10	1
superpathway of C1 compounds oxidation to CO2	12	7	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	1
indole-3-acetate biosynthesis II	12	4	1
poly(ribitol phosphate) wall teichoic acid biosynthesis I (B. subtilis)	12	2	1
aspartate superpathway	25	22	2
superpathway of cardiolipin biosynthesis (bacteria)	13	9	1
3-hydroxypropanoate cycle	13	8	1
glyoxylate assimilation	13	5	1
peptidoglycan recycling I	14	10	1
poly(ribitol phosphate) wall teichoic acid biosynthesis II (S. aureus)	14	2	1
superpathway of rosmarinic acid biosynthesis	14	2	1
peptidoglycan biosynthesis III (mycobacteria)	15	11	1
purine nucleobases degradation I (anaerobic)	15	6	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	1
type I lipoteichoic acid biosynthesis (S. aureus)	17	5	1
superpathway of L-threonine metabolism	18	14	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	11	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	10	1
superpathway of the 3-hydroxypropanoate cycle	18	8	1
H. pylori 26695 O-antigen biosynthesis	21	1	1
superpathway of N-acetylneuraminate degradation	22	15	1
purine nucleobases degradation II (anaerobic)	24	16	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	5	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	23	2
superpathway of phospholipid biosynthesis II (plants)	28	10	1
superpathway of chorismate metabolism	59	42	2
superpathway of pentose and pentitol degradation	42	21	1