Experiment set1S482 for Paraburkholderia sabiae LMG 24235

Plant=Oryza_sativa; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=14_days

Group: in planta
Media:
Culturing: Psabiae_ML3b, pot, at 20 (C), (Solid)
By: Marta Torres on 12/5/24

Specific Phenotypes

For 12 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Ammonia assimilation	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Protein degradation	1
Proteolysis in bacteria, ATP-dependent	1
Threonine and Homoserine Biosynthesis	1
Transcription initiation, bacterial sigma factors	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:

• Glutamate metabolism
• Alanine and aspartate 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
N-end rule pathway I (prokaryotic)	2	2	2
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
L-aspartate biosynthesis	1	1	1
L-glutamate degradation II	2	2	1
malate/L-aspartate shuttle pathway	2	2	1
L-tyrosine degradation II	2	1	1
atromentin biosynthesis	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	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-asparagine degradation III (mammalian)	3	2	1
(R)-cysteate degradation	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
sulfolactate degradation III	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	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	4	1
superpathway of plastoquinol biosynthesis	5	2	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	2	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	2	1
L-tyrosine degradation V (reductive Stickland reaction)	5	2	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	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	2	1
coenzyme M biosynthesis II	6	1	1
anaerobic energy metabolism (invertebrates, cytosol)	7	7	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	8	2
superpathway of aromatic amino acid biosynthesis	18	18	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	8	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
rosmarinic acid biosynthesis I	10	3	1
(S)-reticuline biosynthesis I	11	4	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
indole-3-acetate biosynthesis II	12	6	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of rosmarinic acid biosynthesis	14	4	1
superpathway of anaerobic energy metabolism (invertebrates)	17	13	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	17	1
aspartate superpathway	25	24	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	5	1
superpathway of chorismate metabolism	59	42	2
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	23	1