Experiment set4IT006 for Desulfovibrio vulgaris Miyazaki F

6 days starvation 37C

Group: starvation
Media: MoYLS4, pH=7.2
Culturing: Miya_ML3_a, 15 mL falcon, Anaerobic, at 37 (C), shaken=0 rpm
By: Jen on 1/9/2015
Media components: 1 g/L Yeast Extract, 30 mM Sodium sulfate, 60 mM Sodium D,L-Lactate, 20 mM Ammonium chloride, 30 mM Tris hydrochloride, 0.12 mM EDTA, 1 mM Sodium sulfide nonahydrate, 8 mM Magnesium chloride hexahydrate, 0.6 mM Calcium chloride, 2 mM Potassium phosphate dibasic, 60 uM Iron (II) chloride tetrahydrate, 15 uM Manganese (II) chloride tetrahydrate, 7.8 uM Cobalt chloride hexahydrate, 9 uM Zinc chloride, 1.26 uM Sodium molybdate, 1.92 uM Boric Acid, 2.28 uM Nickel (II) sulfate hexahydrate, 0.06 uM copper (II) chloride dihydrate, 0.21 uM Sodium selenite pentahydrate, 0.144 uM Sodium tungstate dihydrate, Thauer's vitamin mix (0.01 mg/L Pyridoxine HCl, 0.005 mg/L 4-Aminobenzoic acid, 0.005 mg/L Lipoic acid, 0.005 mg/L Nicotinic Acid, 0.005 mg/L Riboflavin, 0.005 mg/L Thiamine HCl, 0.005 mg/L calcium pantothenate, 0.002 mg/L biotin, 0.002 mg/L Folic Acid, 0.0001 mg/L Cyanocobalamin, 0.2 mg/L Choline chloride)

Specific Phenotypes

For 16 genes in this experiment

SEED Subsystems

Subsystem	#Specific
High affinity phosphate transporter and control of PHO regulon	2
Phosphate metabolism	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
ABC transporter oligopeptide (TC 3.A.1.5.1)	1
Alanine biosynthesis	1
Branched-Chain Amino Acid Biosynthesis	1
Coenzyme B12 biosynthesis	1
Formate hydrogenase	1
Isoleucine degradation	1
Leucine Biosynthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Pyruvate Alanine Serine Interconversions	1
Translation elongation factor G family	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Valine, leucine and isoleucine degradation
• Valine, leucine and isoleucine biosynthesis
• Streptomycin biosynthesis
• Polyketide sugar unit biosynthesis
• Pantothenate and CoA biosynthesis
• Biosynthesis of vancomycin group antibiotics
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
UDP-α-D-xylose biosynthesis	2	2	1
L-alanine biosynthesis I	2	1	1
L-isoleucine degradation II	3	2	1
L-isoleucine biosynthesis V	3	2	1
L-leucine degradation III	3	2	1
L-valine degradation II	3	2	1
L-isoleucine degradation III (oxidative Stickland reaction)	3	1	1
L-leucine degradation V (oxidative Stickland reaction)	3	1	1
L-valine degradation III (oxidative Stickland reaction)	3	1	1
L-valine biosynthesis	4	4	1
superpathway of L-alanine biosynthesis	4	3	1
dTDP-6-deoxy-α-D-allose biosynthesis	4	2	1
dTDP-N-acetylviosamine biosynthesis	4	2	1
dTDP-N-acetylthomosamine biosynthesis	4	2	1
dTDP-β-D-fucofuranose biosynthesis	4	2	1
dTDP-β-L-rhamnose biosynthesis	5	5	1
dTDP-4-O-demethyl-β-L-noviose biosynthesis	5	3	1
dTDP-3-acetamido-3,6-dideoxy-α-D-glucose biosynthesis	5	2	1
dTDP-3-acetamido-α-D-fucose biosynthesis	5	2	1
dTDP-α-D-mycaminose biosynthesis	5	2	1
L-leucine degradation IV (reductive Stickland reaction)	5	1	1
superpathway of branched chain amino acid biosynthesis	17	16	3
L-leucine biosynthesis	6	6	1
L-isoleucine biosynthesis IV	6	4	1
dTDP-sibirosamine biosynthesis	6	3	1
dTDP-L-daunosamine biosynthesis	6	3	1
dTDP-D-desosamine biosynthesis	6	2	1
dTDP-α-D-ravidosamine and dTDP-4-acetyl-α-D-ravidosamine biosynthesis	6	2	1
L-isoleucine degradation I	6	1	1
L-leucine degradation I	6	1	1
L-isoleucine biosynthesis I (from threonine)	7	6	1
L-isoleucine biosynthesis III	7	4	1
dTDP-β-L-digitoxose biosynthesis	7	3	1
dTDP-β-L-olivose biosynthesis	7	3	1
dTDP-β-L-mycarose biosynthesis	7	2	1
L-isoleucine biosynthesis II	8	6	1
dTDP-β-L-megosamine biosynthesis	8	3	1
dTDP-β-L-4-epi-vancosamine biosynthesis	8	3	1
L-valine degradation I	8	2	1
UDP-sugars interconversion	9	3	1
dTDP-α-D-olivose, dTDP-α-D-oliose and dTDP-α-D-mycarose biosynthesis	9	3	1
dTDP-α-D-forosamine biosynthesis	9	3	1
superpathway of enterobacterial common antigen biosynthesis	10	2	1
O-antigen building blocks biosynthesis (E. coli)	11	10	1
superpathway of L-isoleucine biosynthesis I	13	12	1
superpathway of L-threonine metabolism	18	12	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	5	1
superpathway of novobiocin biosynthesis	19	4	1
superpathway of erythromycin biosynthesis	19	2	1
superpathway of megalomicin A biosynthesis	22	3	1
superpathway of dTDP-glucose-derived antibiotic building blocks biosynthesis	23	3	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	1
anteiso-branched-chain fatty acid biosynthesis	34	24	1
even iso-branched-chain fatty acid biosynthesis	34	24	1
odd iso-branched-chain fatty acid biosynthesis	34	24	1