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


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 144 203
Amines and Polyamines Biosynthesis
4 8
Amino Acids Biosynthesis
27 28
Aminoacyl-tRNA Charging
3 1
Aromatic Compounds Biosynthesis
2 4
Carbohydrates Biosynthesis
7 15
Cell Structures Biosynthesis
4 10
Cofactors, Prosthetic Groups, Electron Carriers Biosynthesis
32 47
Fatty Acid and Lipid Biosynthesis
12 19
Hormones Biosynthesis
0 0
Metabolic Regulators Biosynthesis
1 2
Nucleosides and Nucleotides Biosynthesis
25 28
Other Biosynthesis
1 0
Secondary Metabolites Biosynthesis
2 3
Siderophore Biosynthesis
0 0
Degradation/Utilization/Assimilation 44 146
Alcohols Degradation
3 5
Aldehyde Degradation
0 5
Amines and Polyamines Degradation
1 10
Amino Acids Degradation
9 17
Aromatic Compounds Degradation
0 4
C1 Compounds Utilization and Assimilation
3 1
Carbohydrates Degradation
5 23
Carboxylates Degradation
0 21
Chlorinated Compounds Degradation
0 0
Cofactors, Prosthetic Groups, Electron Carriers Degradation
0 0
Degradation/Utilization/Assimilation - Other
0 1
Fatty Acid and Lipids Degradation
1 4
Hormones Degradation
0 0
Inorganic Nutrients Metabolism
13 15
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 38
Signal transduction pathways 0 30
Total 176 348

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 112 37
Pathway Holes as a percentage of total reactions in pathways 20% 4%
Pathways with No Holes 104 291
Pathways with 1 Hole 42 11
Pathways with 2 Holes 14 3
Pathways with 3 Holes 7 0
Pathways with 4 Holes 2 0
Pathways with 5 Holes 2 0
Pathways with > 5 Holes 2 2
Total Pathways with Holes 69 16

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aaeo224324cyc version 19.1.