Experiment set1IT062 for Azospirillum brasilense Sp245

LB with D-Cycloserine 0.125 mg/ml

Group: stress
Media: LB + D-Cycloserine (0.125 mg/ml)
Culturing: AzoBra_ML2a, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Mark on 3/5/2015
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 1179 D1,D2

Specific Phenotypes

For 11 genes in this experiment

For stress D-Cycloserine in Azospirillum brasilense Sp245

For stress D-Cycloserine across organisms

SEED Subsystems

Subsystem	#Specific
DNA repair, UvrABC system	2
Formate hydrogenase	2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Molybdenum cofactor biosynthesis	2
Peptidoglycan Biosynthesis	1
Soluble cytochromes and functionally related electron carriers	1
Threonine and Homoserine Biosynthesis	1
Transport of Molybdenum	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glutamate metabolism
• Glyoxylate and dicarboxylate metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones
• Citrate cycle (TCA cycle)
• Alanine and aspartate metabolism
• Cysteine metabolism
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• D-Glutamine and D-glutamate metabolism
• Propanoate metabolism
• Methane metabolism
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-aspartate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
malate/L-aspartate shuttle pathway	2	2	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
L-glutamate degradation II	2	1	1
atromentin biosynthesis	2	1	1
L-tyrosine degradation II	2	1	1
glyoxylate cycle	6	6	2
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
L-phenylalanine degradation II (anaerobic)	3	2	1
indole-3-acetate biosynthesis VI (bacteria)	3	2	1
L-asparagine degradation III (mammalian)	3	1	1
sulfolactate degradation III	3	1	1
(R)-cysteate degradation	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
L-phenylalanine degradation III	4	3	1
partial TCA cycle (obligate autotrophs)	8	5	2
nitrogen remobilization from senescing leaves	8	5	2
L-tryptophan degradation VIII (to tryptophol)	4	2	1
L-tyrosine degradation III	4	2	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	1	1
TCA cycle V (2-oxoglutarate synthase)	9	8	2
TCA cycle VII (acetate-producers)	9	7	2
TCA cycle II (plants and fungi)	9	7	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	6	2
TCA cycle VI (Helicobacter)	9	6	2
TCA cycle III (animals)	10	9	2
TCA cycle I (prokaryotic)	10	8	2
2-methylcitrate cycle I	5	4	1
trans-4-hydroxy-L-proline degradation I	5	3	1
L-tyrosine degradation I	5	2	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
superpathway of plastoquinol biosynthesis	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
reductive TCA cycle I	11	7	2
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	5	2
superpathway of L-threonine biosynthesis	6	6	1
superpathway of glyoxylate bypass and TCA	12	10	2
TCA cycle VIII (Chlamydia)	6	5	1
2-methylcitrate cycle II	6	4	1
reductive TCA cycle II	12	7	2
superpathway of sulfolactate degradation	6	3	1
coenzyme M biosynthesis II	6	1	1
anaerobic energy metabolism (invertebrates, cytosol)	7	6	1
superpathway of glyoxylate cycle and fatty acid degradation	14	10	2
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	6	2
UDP-N-acetylmuramoyl-pentapeptide biosynthesis I (meso-diaminopimelate containing)	8	8	1
UDP-N-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)	8	7	1
mixed acid fermentation	16	13	2
superpathway of aromatic amino acid biosynthesis	18	17	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	8	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	1	1
methylaspartate cycle	19	11	2
superpathway of L-phenylalanine biosynthesis	10	9	1
superpathway of L-tyrosine biosynthesis	10	9	1
rosmarinic acid biosynthesis I	10	2	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	17	2
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	11	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	10	1
indole-3-acetate biosynthesis II	12	3	1
ethene biosynthesis V (engineered)	25	17	2
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	21	2
superpathway of rosmarinic acid biosynthesis	14	3	1
peptidoglycan biosynthesis III (mycobacteria)	15	10	1
superpathway of anaerobic energy metabolism (invertebrates)	17	13	1
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	11	1
peptidoglycan biosynthesis II (staphylococci)	17	11	1
peptidoglycan biosynthesis V (β-lactam resistance)	17	10	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	17	1
aspartate superpathway	25	23	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	3	1
superpathway of chorismate metabolism	59	40	2
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1