Experiment set3IT025 for Herbaspirillum seropedicae SmR1

L-Fucose carbon source

Group: carbon source
Media: NFbHP_noCarbon + L-Fucose (5 g/L), pH=6.5
Culturing: HerbieS_ML4, flask, Aerobic, at 30 (C), shaken=120 rpm
Growth: about 3.9 generations
By: Thalita Tuleski on 19-May-16

Specific Phenotypes

For 11 genes in this experiment

For carbon source L-Fucose in Herbaspirillum seropedicae SmR1

For carbon source L-Fucose across organisms

SEED Subsystems

Subsystem	#Specific
L-Arabinose utilization	2
D-ribose utilization	1
Fatty Acid Biosynthesis FASII	1
Methionine Biosynthesis	1
Methionine Degradation	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:

• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Valine, leucine and isoleucine biosynthesis
• Lysine biosynthesis
• Pantothenate and CoA biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-arabinose degradation V	6	5	2
L-arabinose degradation III	6	5	2
L-lyxonate degradation	3	2	1
gondoate biosynthesis (anaerobic)	4	4	1
L-valine biosynthesis	4	4	1
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	12	9	3
palmitate biosynthesis III	29	21	7
tetradecanoate biosynthesis (mitochondria)	25	17	6
palmitate biosynthesis II (type II fatty acid synthase)	31	29	7
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	9	2
oleate biosynthesis IV (anaerobic)	14	13	3
superpathway of fatty acids biosynthesis (E. coli)	53	50	11
fatty acid elongation -- saturated	5	5	1
cis-vaccenate biosynthesis	5	5	1
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	19	4
pyruvate fermentation to isobutanol (engineered)	5	4	1
8-amino-7-oxononanoate biosynthesis IV	5	4	1
superpathway of fatty acid biosynthesis II (plant)	43	38	8
8-amino-7-oxononanoate biosynthesis I	11	9	2
odd iso-branched-chain fatty acid biosynthesis	34	24	6
even iso-branched-chain fatty acid biosynthesis	34	24	6
anteiso-branched-chain fatty acid biosynthesis	34	24	6
(5Z)-dodecenoate biosynthesis I	6	5	1
stearate biosynthesis II (bacteria and plants)	6	5	1
stearate biosynthesis IV	6	4	1
L-isoleucine biosynthesis IV	6	4	1
(5Z)-dodecenoate biosynthesis II	6	4	1
petroselinate biosynthesis	6	2	1
streptorubin B biosynthesis	34	20	5
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-isoleucine biosynthesis III	7	4	1
L-rhamnose degradation III	7	3	1
biotin biosynthesis I	15	13	2
superpathway of fatty acid biosynthesis I (E. coli)	16	14	2
L-isoleucine biosynthesis II	8	6	1
L-arabinose degradation IV	8	5	1
2-allylmalonyl-CoA biosynthesis	8	2	1
superpathway of branched chain amino acid biosynthesis	17	17	2
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-threonine metabolism	18	13	1
superpathway of pentose and pentitol degradation	42	19	2
mycolate biosynthesis	205	25	5
superpathway of mycolate biosynthesis	239	26	5