Figure 1.
NIBBS methodology overview; The generic metabolic map is taken and converted into organism specific metabolic map, using the enzyme information of each organism.
These networks along with the other algorithm parameters are used to first construct seed sets. These seed sets are then expanded into the final metabolic subsystem that is output by the algorithm. The details are provided in the Methods section.
Table 1.
Number of organisms per phenotype.
Figure 2.
Schematic of key metabolic pathways for hydrogen production in Clostridium acetobutylicum.
Arrows with larger width indicate a series of reactions. Arrows with narrow width indicate individual reactions. Enzymes: 1, glycolytic enzymes; 2, pyruvate ferredoxin oxidoreductase (E.C. 1.2.7.1); 3, hydrogenase (E.C.1.12.7.2); 4, phosphotransacetylase (E.C. 2.3.1.8); 5, acetate kinase (E.C. 2.7.2.1); 6, acetyl-CoA acetyltransferase (thiolase) (E.C. 2.3.1.9); 7, -hydroxybutyryl-CoA dehydrogenase (E.C. 1.1.1.157); 8, crotonase (E.C. 4.2.1.55); 9, butyryl-CoA dehydrogenase (E.C. 1.3.99.2); 10, phosphotransbutyrylase (E.C.2.3.1.19); 11, butyrate kinase (E.C. 2.7.2.7). Abbreviations: Ferredoxin (Fd); Coenzyme A (CoASH).
Table 2.
Hydrogen-related enzymes detected by different methods.
Figure 3.
General overview of hydrogen production through the formate pathway.
Table 3.
List of top ranking pathways and their enrichment score for the phenotype dark fermentative hydrogen production.
Table 4.
List of top ranking pathways and their enrichment score for the phenotype acid-tolerance.
Table 5.
Known aerobic related enzymes that make up the TCA cycle and the glyoxylate bypass that are present (+) or absent (−) in the data set identified by the NIBBS algorithm and T-Test approach.
Figure 4.
Comparison between NIBBS, T-Test and Mututal Information [4].
Figure 5.
MULE vs. NIBBS runtime comparison.
Runtimes (y-axis), with trendline, of the MULE algorithm for the various support count thresholds (x-axis) used by the MBS-Enum algorithm. Total runtime required by the NIBBS-Search algorithm drawn as horizontal dotted line.
Figure 6.
Approximation Accuracy: The negative log of the statistical significance of the approximation scores has been plotted.
The for
. Gray:
; black:
.
Figure 7.
TCA and rTCA metabolic pathways.
TCA cycle: gray arrows; rTCA: black arrows; EC numbers: white boxes; Pathway specific EC numbers: TCA-specific (gray), rTCA-specific (black).