Experiment set22S225 for Agrobacterium fabrum C58

Plant=Ntabacum; PlantTreatment=None; Sample=leaf; GrowthSubstrate=agar; Collection=Direct; Cocuture=C58C1OD2.0

Group: in planta
Media: + Plant=Ntabacum; PlantTreatment=None; Sample=leaf; GrowthSubstrate=agar; Collection=Direct; Cocuture=C58C1OD2.0
Culturing: Agro_ML11b, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 6/16/2023

Specific Phenotypes

For 26 genes in this experiment

For in planta Plant=Ntabacum; PlantTreatment=None; Sample=leaf; GrowthSubstrate=agar; Collection=Direct; Cocuture=C58C1OD2.0 in Agrobacterium fabrum C58

For in planta Plant=Ntabacum; PlantTreatment=None; Sample=leaf; GrowthSubstrate=agar; Collection=Direct; Cocuture=C58C1OD2.0 across organisms

SEED Subsystems

Subsystem	#Specific
Agrobacterium opine transport	4
Arginine and Ornithine Degradation	4
ABC transporter oligopeptide (TC 3.A.1.5.1)	2
Ribonucleotide reduction	2
Di-Inositol-Phosphate biosynthesis	1
Fatty Acid Biosynthesis FASII	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
L-Arabinose utilization	1
mycolic acid synthesis	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
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Biosynthesis of steroids
• Ubiquinone and menaquinone biosynthesis
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Pyrimidine metabolism
• gamma-Hexachlorocyclohexane degradation
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Glutathione metabolism
• Streptomycin biosynthesis
• Inositol phosphate metabolism
• Glycerophospholipid metabolism
• Sphingolipid metabolism
• Naphthalene and anthracene degradation
• 1,4-Dichlorobenzene degradation
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Brassinosteroid biosynthesis
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones
• Phosphatidylinositol signaling system

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-arginine degradation VII (arginase 3 pathway)	2	2	2
L-ornithine degradation I (L-proline biosynthesis)	1	1	1
putrescine biosynthesis III	2	2	1
glycerophosphodiester degradation	2	2	1
adenosine deoxyribonucleotides de novo biosynthesis I	2	2	1
guanosine deoxyribonucleotides de novo biosynthesis I	2	2	1
2-oxoglutarate-derived opine biosynthesis	2	2	1
adenosine deoxyribonucleotides de novo biosynthesis II	4	3	2
guanosine deoxyribonucleotides de novo biosynthesis II	4	3	2
L-proline biosynthesis II (from arginine)	2	1	1
L-canavanine degradation I	2	1	1
phosphatidylcholine resynthesis via glycerophosphocholine	2	1	1
myo-inositol biosynthesis	2	1	1
L-arginine degradation I (arginase pathway)	3	2	1
D-myo-inositol (1,4,5)-trisphosphate degradation	3	1	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)	14	12	4
superpathway of adenosine nucleotides de novo biosynthesis II	7	6	2
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	12	12	3
superpathway of putrescine biosynthesis	4	4	1
gondoate biosynthesis (anaerobic)	4	4	1
superpathway of guanosine nucleotides de novo biosynthesis II	8	7	2
L-arginine degradation VI (arginase 2 pathway)	4	3	1
glycerol and glycerophosphodiester degradation	4	3	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
palmitate biosynthesis III	29	28	7
tetradecanoate biosynthesis (mitochondria)	25	23	6
palmitate biosynthesis II (type II fatty acid synthase)	31	29	7
pyrimidine deoxyribonucleotides de novo biosynthesis I	9	9	2
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	8	2
pyrimidine deoxyribonucleotides de novo biosynthesis III	9	8	2
oleate biosynthesis IV (anaerobic)	14	13	3
superpathway of fatty acids biosynthesis (E. coli)	53	49	11
8-amino-7-oxononanoate biosynthesis IV	5	5	1
fatty acid elongation -- saturated	5	5	1
superpathway of adenosine nucleotides de novo biosynthesis I	5	5	1
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	18	4
urea cycle	5	4	1
cis-vaccenate biosynthesis	5	4	1
superpathway of fatty acid biosynthesis II (plant)	43	38	8
8-amino-7-oxononanoate biosynthesis I	11	9	2
even iso-branched-chain fatty acid biosynthesis	34	30	6
anteiso-branched-chain fatty acid biosynthesis	34	30	6
odd iso-branched-chain fatty acid biosynthesis	34	30	6
superpathway of guanosine nucleotides de novo biosynthesis I	6	6	1
(5Z)-dodecenoate biosynthesis I	6	6	1
(5Z)-dodecenoate biosynthesis II	6	5	1
stearate biosynthesis II (bacteria and plants)	6	5	1
stearate biosynthesis IV	6	4	1
petroselinate biosynthesis	6	2	1
superpathway of D-myo-inositol (1,4,5)-trisphosphate metabolism	6	1	1
superpathway of purine nucleotides de novo biosynthesis II	26	23	4
streptorubin B biosynthesis	34	20	5
pyrimidine deoxyribonucleotides de novo biosynthesis IV	7	6	1
L-Nδ-acetylornithine biosynthesis	7	5	1
phytate degradation I	14	2	2
biotin biosynthesis I	15	13	2
superpathway of fatty acid biosynthesis I (E. coli)	16	15	2
pyrimidine deoxyribonucleotides biosynthesis from CTP	8	7	1
L-citrulline biosynthesis	8	7	1
superpathway of polyamine biosynthesis I	8	5	1
superpathway of polyamine biosynthesis II	8	3	1
2-allylmalonyl-CoA biosynthesis	8	2	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	18	17	2
superpathway of purine nucleotides de novo biosynthesis I	21	21	2
superpathway of histidine, purine, and pyrimidine biosynthesis	46	42	4
superpathway of L-citrulline metabolism	12	9	1
anandamide biosynthesis I	12	3	1
superpathway of purine nucleotide salvage	14	13	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	4	1
superpathway of arginine and polyamine biosynthesis	17	14	1
mycolate biosynthesis	205	21	5
superpathway of mycolate biosynthesis	239	22	5