Experiment set2IT051 for Herbaspirillum seropedicae SmR1

m-Inositol carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + m-Inositol (20 mM), pH=7
Culturing: HerbieS_ML4, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 3.1 generations
By: Mark on 3/10/2016
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)
Growth plate: CARBON4 A3

Specific Phenotypes

For 10 genes in this experiment

For carbon source m-Inositol in Herbaspirillum seropedicae SmR1

For carbon source m-Inositol across organisms

SEED Subsystems

Subsystem	#Specific
Inositol catabolism	6
D-gluconate and ketogluconates metabolism	1
Folate Biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Threonine and Homoserine Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Inositol phosphate metabolism
• Phenylalanine metabolism
• Nicotinate and nicotinamide metabolism
• Ascorbate and aldarate metabolism
• Purine metabolism
• Pyrimidine metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Cysteine metabolism
• Arginine and proline metabolism
• Tyrosine metabolism
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Benzoate degradation via hydroxylation
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Biphenyl degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Carbon fixation in photosynthetic organisms
• Limonene and pinene degradation
• Caprolactam degradation
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• 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
L-aspartate degradation I	1	1	1
L-aspartate biosynthesis	1	1	1
myo-inositol degradation I	7	7	4
malate/L-aspartate shuttle pathway	2	2	1
β-alanine degradation III	2	1	1
L-glutamate degradation II	2	1	1
atromentin biosynthesis	2	1	1
L-tyrosine degradation II	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
myo-, chiro- and scyllo-inositol degradation	10	7	4
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
L-phenylalanine degradation II (anaerobic)	3	2	1
NAD salvage pathway III (to nicotinamide riboside)	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
(R)-cysteate degradation	3	1	1
sulfolactate degradation III	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
UTP and CTP dephosphorylation I	7	5	2
purine nucleotides degradation II (aerobic)	11	8	3
inosine 5'-phosphate degradation	4	3	1
guanosine nucleotides degradation II	4	3	1
guanosine nucleotides degradation III	4	3	1
adenosine nucleotides degradation I	8	5	2
purine nucleotides degradation I (plants)	12	7	3
L-tyrosine degradation III	4	2	1
guanosine nucleotides degradation I	4	2	1
L-phenylalanine degradation III	4	2	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	2	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
L-tyrosine degradation I	5	5	1
adenosine nucleotides degradation II	5	4	1
trans-4-hydroxy-L-proline degradation I	5	3	1
uracil degradation III	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
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	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	4	1
superpathway of purines degradation in plants	18	9	3
superpathway of guanosine nucleotides degradation (plants)	6	3	1
superpathway of sulfolactate degradation	6	2	1
coenzyme M biosynthesis II	6	1	1
anaerobic energy metabolism (invertebrates, cytosol)	7	7	1
ureide biosynthesis	7	5	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	7	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
tunicamycin biosynthesis	9	1	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
rosmarinic acid biosynthesis I	10	3	1
NAD salvage (plants)	11	6	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	11	1
indole-3-acetate biosynthesis II	12	5	1
superpathway of L-isoleucine biosynthesis I	13	13	1
3-hydroxypropanoate cycle	13	5	1
glyoxylate assimilation	13	5	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	16	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	8	1
superpathway of the 3-hydroxypropanoate cycle	18	6	1
aspartate superpathway	25	23	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	3	1
superpathway of chorismate metabolism	59	43	2
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1