Experiment set2S110 for Escherichia coli ECRC101

L-Arabinose

Group: carbon source
Media: M9_plus_L-Arabinose + L-Arabinose (20 mM)
Culturing: Ecoli_ECRC101_ML1, 48 well microplate, Aerobic, at 37 (C), shaken=double orbital, continuous, 205cpm
By: Lucas on 12/16/24

Specific Phenotypes

For 14 genes in this experiment

For carbon source L-Arabinose in Escherichia coli ECRC101

For carbon source L-Arabinose across organisms

SEED Subsystems

Subsystem	#Specific
L-Arabinose utilization	5
Cysteine Biosynthesis	2
Methionine Biosynthesis	2
Acetoin, butanediol metabolism	1
Branched-Chain Amino Acid Biosynthesis	1
Fermentations: Mixed acid	1
L-ascorbate utilization (and related gene clusters)	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Peptidoglycan Biosynthesis	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Thiamin biosynthesis	1
Type IV pilus	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose and glucuronate interconversions
• Peptidoglycan biosynthesis
• Ascorbate and aldarate metabolism
• Purine metabolism
• Alanine and aspartate metabolism
• Methionine metabolism
• Valine, leucine and isoleucine biosynthesis
• Lysine degradation
• Selenoamino acid metabolism
• Pyruvate metabolism
• Butanoate metabolism
• C5-Branched dibasic acid metabolism
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Thiamine metabolism
• Nicotinate and nicotinamide metabolism
• Pantothenate and CoA biosynthesis
• Biotin metabolism
• Sulfur metabolism
• 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
L-arabinose degradation I	4	4	3
D-arabinose degradation I	2	2	1
thiamine diphosphate biosynthesis I (E. coli)	2	2	1
sulfate activation for sulfonation	2	2	1
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
thiamine diphosphate biosynthesis II (Bacillus)	2	2	1
ribitol degradation I	2	1	1
pyruvate fermentation to (R)-acetoin II	2	1	1
pyruvate fermentation to (S)-acetoin	3	3	1
thiamine diphosphate salvage V	3	3	1
assimilatory sulfate reduction III	3	3	1
S-adenosyl-L-methionine salvage II	3	2	1
pyruvate fermentation to (R)-acetoin I	3	2	1
assimilatory sulfate reduction II	3	1	1
sulfite oxidation III	3	1	1
thiamine diphosphate biosynthesis III (Staphylococcus)	3	1	1
thiamine diphosphate biosynthesis IV (eukaryotes)	3	1	1
D-arabinose degradation V	3	1	1
assimilatory sulfate reduction I	4	4	1
L-valine biosynthesis	4	4	1
S-adenosyl-L-methionine salvage I	4	4	1
assimilatory sulfate reduction IV	4	3	1
L-lyxose degradation	4	3	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	6	3
L-methionine biosynthesis III	4	2	1
L-methionine biosynthesis I	5	5	1
thiamine diphosphate salvage II	5	5	1
L-ascorbate degradation I (bacterial, anaerobic)	5	5	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
seleno-amino acid biosynthesis (plants)	5	3	1
superpathway of (R,R)-butanediol biosynthesis	5	2	1
selenate reduction	5	2	1
dissimilatory sulfate reduction I (to hydrogen sufide))	5	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	10	2
NAD de novo biosynthesis IV (anaerobic)	6	5	1
L-methionine biosynthesis II	6	5	1
NAD de novo biosynthesis I	6	5	1
L-isoleucine biosynthesis IV	6	4	1
superpathway of 2,3-butanediol biosynthesis	6	3	1
superpathway of thiosulfate metabolism (Desulfovibrio sulfodismutans)	6	1	1
superpathway of sulfur metabolism (Desulfocapsa sulfoexigens)	6	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-ascorbate degradation II (bacterial, aerobic)	7	5	1
L-isoleucine biosynthesis III	7	5	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
thiamine diphosphate salvage IV (yeast)	7	4	1
superpathway of thiamine diphosphate biosynthesis III (eukaryotes)	7	3	1
superpathway of L-homoserine and L-methionine biosynthesis	8	8	1
partial TCA cycle (obligate autotrophs)	8	7	1
nitrogen remobilization from senescing leaves	8	5	1
thiamine diphosphate formation from pyrithiamine and oxythiamine (yeast)	8	4	1
L-isoleucine biosynthesis II	8	4	1
superpathway of branched chain amino acid biosynthesis	17	17	2
peptidoglycan biosynthesis II (staphylococci)	17	12	2
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	2
peptidoglycan biosynthesis V (β-lactam resistance)	17	11	2
superpathway of S-adenosyl-L-methionine biosynthesis	9	9	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	9	1
nicotine biosynthesis	9	3	1
superpathway of seleno-compound metabolism	19	6	2
superpathway of thiamine diphosphate biosynthesis I	10	10	1
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae)	10	6	1
superpathway of pentose and pentitol degradation	42	15	4
superpathway of thiamine diphosphate biosynthesis II	11	9	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	8	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	12	1
superpathway of nicotine biosynthesis	12	4	1
superpathway of sulfide oxidation (phototrophic sulfur bacteria)	12	2	1
aspartate superpathway	25	24	2
superpathway of L-isoleucine biosynthesis I	13	13	1
formaldehyde assimilation I (serine pathway)	13	8	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	1
peptidoglycan biosynthesis III (mycobacteria)	15	11	1
mixed acid fermentation	16	16	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	18	1
superpathway of L-threonine metabolism	18	15	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
ethene biosynthesis V (engineered)	25	18	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1