Experiment set39S313 for Burkholderia phytofirmans PsJN

24hr PHYTO4 MOI 10

Group: phage
Media: LB_plus_SM_buffer + Kan (50 ug/ml)
Culturing: BFirm_ML3b, 48 well microplate; Epoch2, Aerobic, at 30 (C), shaken=double orbital, continuous, 205cpm
By: Marissa on 7/6/24
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride, 100 mM Sodium Chloride, 4 mM Magnesium sulfate, 0.005 vol% Gelatin, 25 mM Tris hydrochloride

Specific Phenotypes

For 20 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Oxidative stress	2
Histidine Biosynthesis	1
Rhamnose containing glycans	1
dTDP-rhamnose synthesis	1
linker unit-arabinogalactan synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Fatty acid biosynthesis
• Biosynthesis of unsaturated fatty acids
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Benzoate degradation via CoA ligation
• Limonene and pinene degradation
• Ubiquinone and menaquinone biosynthesis
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Novobiocin biosynthesis
• Nucleotide sugars metabolism
• Streptomycin biosynthesis
• Polyketide sugar unit biosynthesis
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Butanoate metabolism
• Porphyrin and chlorophyll metabolism
• Nitrogen metabolism
• Alkaloid biosynthesis II
• Biosynthesis of type II polyketide backbone
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• 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
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	12	12	6
gondoate biosynthesis (anaerobic)	4	4	2
atromentin biosynthesis	2	1	1
L-tyrosine degradation II	2	1	1
palmitate biosynthesis III	29	28	13
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	9	4
tetradecanoate biosynthesis (mitochondria)	25	23	11
oleate biosynthesis IV (anaerobic)	14	13	6
palmitate biosynthesis II (type II fatty acid synthase)	31	29	13
fatty acid elongation -- saturated	5	5	2
cis-vaccenate biosynthesis	5	5	2
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	19	8
superpathway of fatty acids biosynthesis (E. coli)	53	50	21
8-amino-7-oxononanoate biosynthesis I	11	9	4
superpathway of fatty acid biosynthesis II (plant)	43	38	15
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
polyhydroxybutanoate biosynthesis	3	3	1
(5Z)-dodecenoate biosynthesis I	6	5	2
stearate biosynthesis II (bacteria and plants)	6	5	2
stearate biosynthesis IV	6	4	2
(5Z)-dodecenoate biosynthesis II	6	4	2
L-phenylalanine degradation II (anaerobic)	3	2	1
petroselinate biosynthesis	6	2	2
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
anteiso-branched-chain fatty acid biosynthesis	34	30	11
even iso-branched-chain fatty acid biosynthesis	34	30	11
odd iso-branched-chain fatty acid biosynthesis	34	30	11
superpathway of fatty acid biosynthesis I (E. coli)	16	14	5
biotin biosynthesis I	15	13	4
streptorubin B biosynthesis	34	20	9
L-histidine degradation I	4	4	1
(2S)-ethylmalonyl-CoA biosynthesis	4	3	1
L-tyrosine degradation III	4	2	1
fatty acid biosynthesis initiation (mitochondria)	4	2	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation I	5	5	1
L-histidine degradation II	5	5	1
dTDP-β-L-rhamnose biosynthesis	5	5	1
8-amino-7-oxononanoate biosynthesis IV	5	4	1
superpathway of fatty acid biosynthesis initiation	5	4	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	3	1
superpathway of plastoquinol biosynthesis	5	2	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
L-histidine degradation III	6	4	1
acetyl-CoA fermentation to butanoate	7	6	1
L-histidine degradation VI	8	7	1
2-allylmalonyl-CoA biosynthesis	8	2	1
superpathway of aromatic amino acid biosynthesis	18	18	2
L-phenylalanine degradation IV (mammalian, via side chain)	9	6	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
L-histidine biosynthesis	10	10	1
rosmarinic acid biosynthesis I	10	1	1
O-antigen building blocks biosynthesis (E. coli)	11	11	1
ethylmalonyl-CoA pathway	11	3	1
(S)-reticuline biosynthesis I	11	3	1
superpathway of rosmarinic acid biosynthesis	14	2	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	5	1
mycolate biosynthesis	205	25	9
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	18	1
superpathway of mycolate biosynthesis	239	26	9
anaerobic aromatic compound degradation (Thauera aromatica)	27	5	1
superpathway of chorismate metabolism	59	42	2
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	13	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	44	1