Metabolic Modeling Tutorial
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BioCyc websites MAYBE down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites MAYBE down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites MAYBE down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites MAYBE down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites MAYBE down
12/28 - 12/31
for maintenance.

Comparative Analysis Summary Results

Note: In addition to reflecting differences in biology of different organisms, these statistics will reflect differences in the levels of curation, data availability, and completeness of the PGDBs for these organisms.

Comparative analysis and statistics were computed for the following organism databases:

Click on any cell of a table to see more detail about the cell (usually an enumeration of all entities represented by the statistic). Click on a row or column header to see a more detailed view of the entire row or column. Click on a table header (the top-left cell of the table), where available, for a more detailed view of the entire table. Mouse over a link in a table (such as a row heading) for a further explanation of that item, or to see a description of what will be displayed if you click on that link.

Table of Contents


Pathways

Table 1: Breakdown of Pathways by Pathway Class

This table presents statistics on the number of pathways present in each pathway class. The two largest top-level classes, Biosynthesis and Degradation/Utilization/Assimilation, are broken down further to show the distribution of pathways among their next-level subclasses. The vast majority of pathways are assigned to only a single class. However, a small number may be assigned to more than one.

To see a list of all individual pathways, indicating which organisms each pathway are present in, click "Pathway Class" in the top-left corner. Click on a class, to see all individual pathways that are members of that class.

Pathway Class A. aeolicus VF5 E. coli K-12 substr. MG1655
Biosynthesis 144 205
Amines and Polyamines Biosynthesis
4 8
Amino Acids Biosynthesis
26 28
Aminoacyl-tRNA Charging
3 1
Aromatic Compounds Biosynthesis
2 4
Carbohydrates Biosynthesis
7 15
Cell Structures Biosynthesis
4 9
Cofactors, Prosthetic Groups, Electron Carriers Biosynthesis
32 47
Fatty Acid and Lipid Biosynthesis
12 19
Hormones Biosynthesis
0 0
Metabolic Regulators Biosynthesis
1 1
Nucleosides and Nucleotides Biosynthesis
25 28
Other Biosynthesis
1 5
Secondary Metabolites Biosynthesis
2 2
Siderophore Biosynthesis
0 0
Degradation/Utilization/Assimilation 45 139
Alcohols Degradation
3 5
Aldehyde Degradation
0 5
Amines and Polyamines Degradation
1 10
Amino Acids Degradation
10 18
Aromatic Compounds Degradation
0 4
C1 Compounds Utilization and Assimilation
3 1
Carbohydrates Degradation
4 23
Carboxylates Degradation
0 20
Chlorinated Compounds Degradation
0 0
Cofactors, Prosthetic Groups, Electron Carriers Degradation
0 0
Degradation/Utilization/Assimilation - Other
0 0
Fatty Acid and Lipids Degradation
1 4
Hormones Degradation
0 0
Inorganic Nutrients Metabolism
13 8
Nucleosides and Nucleotides Degradation
4 13
Polymeric Compounds Degradation
2 2
Protein Degradation
2 0
Secondary Metabolites Degradation
1 16
Steroids Degradation
0 0
Generation of Precursor Metabolites and Energy 20 30
Signal transduction pathways 0 30
Total 175 335

Table 2: Pathway Holes

A pathway hole is a reaction in a pathway for which no corresponding gene has been identified in the genome. Pathway holes may exist for a number of possible reasons: They may represent true enzymatic functions in the organism for which the gene has not yet been found, or they could represent false positive pathway predictions or cases in which the pathway in this organism differs slightly from the reference pathway in MetaCyc. This table counts all the pathway holes in each organism database, and classifies pathways based on their number of pathway holes.

Clicking on the first row (Number of Pathway Holes) will show all reactions that are holes in any selected organism database, plus the corresponding genes in other organism databases.

Pathway Holes A. aeolicus VF5 E. coli K-12 substr. MG1655
Number of Pathway Holes 107 34
Pathway Holes as a percentage of total reactions in pathways 19% 4%
Pathways with No Holes 104 281
Pathways with 1 Hole 42 12
Pathways with 2 Holes 13 4
Pathways with 3 Holes 6 0
Pathways with 4 Holes 2 0
Pathways with 5 Holes 2 0
Pathways with > 5 Holes 2 1
Total Pathways with Holes 67 17



Page generated by SRI International Pathway Tools version 18.5 on Fri Dec 26, 2014, biocyc11.
aaeo224324cyc version 18.5.