Compounds from KEGG and MetaCyc
Desulfovibrio vulgaris Hildenborough Databases
The Desulfovibrio vulgaris Hildenborough (DvH) compound
database file is a compilation of selected compounds from the
KEGG and
MetaCyc
public databases.
Construction.
This database is a combination of distinct compounds associated with
each DvH pathway on the KEGG Web site, together with matching compounds
from the general MetaCyc compound database and the MetaCyc NIL dvul882cyc
compound database.
The KEGG compounds were compared with compounds in the general
MetaCyc database in order to match MetaCyc compounds with KEGG
compounds.
Compounds were matched by comparing KEGG and MetaCyc common names,
by comparing KEGG names with MetaCyc synonyms, by comparing MetaCyc
common names with KEGG synonyms, by comparing all KEGG synonyms with
all MetaCyc synonyms, and finally, by comparing chemical formulas.
If a KEGG and a MetaCyc compound matched using one of the first four
tests, but the chemical formulas of the compounds differed, then
the KEGG and MetaCyc compounds have been included in the database as
separate compounds with the same common name.
For some KEGG compounds, there was no corresponding entry in the
MetaCyc compound database, and vice versa.
Where available, the KEGG name is used as the common name; otherwise,
the MetaCyc name is used.
Where a KEGG compound has been matched to a MetaCyc compound,
the database entry has both the KEGG Id and the MetaCyc UNIQUE-ID,
as well as the list of synonyms used by each database.
Contents.
There are 1,065 compounds in the database. Of these, 741 are
compounds found in KEGG DvH pathways.
All of the 664 compounds from the MetaCyc NIL dvu882cyc database
were included. In addition, because they match KEGG compounds,
134 compounds from the general MetaCyc database were included.
It was possible to match 480 KEGG and MetaCyc compounds, though eight
of the MetaCyc compounds each match two KEGG compounds.
The breakdown of entries is as follows:
| KEGG Compounds (741 total) |
|---|
| 261 |
KEGG compounds not matched with any MetaCyc compound |
| 8 |
KEGG compounds that match four MetaCyc compounds (2-1) |
| 472 |
KEGG compounds that match exactly one MetaCyc compound |
| MetaCyc Compounds (800 total) |
|---|
| 324 |
MetaCyc compounds not matched with any KEGG compound |
| 4 |
MetaCyc compounds that match eight KEGG compounds (1-2) |
| 472 |
MetaCyc compounds that match exactly one KEGG compound |
Format. The file
format is described separately.
Download.
The DvH compounds database is available as a tab-delimited file,
DvH Compounds Database.
Database versions used: KEGG Release no. 29.0, March 2004;
MetaCyc NIL (dvul882cyc) v. 9.5, November 9, 2005;
MetaCyc v. 9.6, November 22, 2005.
For more information: To display information about a compound on
the KEGG Web site, go to http://www.genome.jp/kegg/ligand.html, and
select and enter a search key under LIGAND Relational Database/Search
COMPOUND.
To display information about a compound on the MetaCyc Web
site, go to http://biocyc.org/META/server.html and select "MetaCyc" as
the dataset, "Compound (by name)" as the type of query, and then enter
all or part of the compound name.
Contact for this Web page: Janet Jacobsen,
JSJacobsen@lbl.gov
This page was last updated on December 7, 2005.