ProDom-CG CG42

Release date = August 2001

Sequence and Family Data

Proteins used to build ProDom CG42: A subset of the proteins used to build ProDom 2001.2	148279
Number of complete genomes	42
domain families with at least 2 sequences	53854
domain families	170857
PDB links	16564
Prosite links (Patterns, Profiles and Prefiles)	7474
Pfam-A links	34513
InterPro links	51524

How is Prodom-CG built ?

ProDom-CG (Complete Genome) is a version of the ProDom database which holds only data originating from the complete genome sequencing projects. This release was builded using the following process:

• Consider the complete genomes whose sequences are included inside Swissprot and Tremble (38 archeal or bacterial genomes, and 4 eukaryotic).
• Start from Prodom Version 2001.2 (data of May 2001)
• Keep only the sequences belonging to one of those genomes
• Delete the domains which are now empty
• Calculate the multalignments and the consensus sequence for each remaining domains
• Calculate the links towards other databases and the statistical data.

About the AC numbers

Because ProDom-CG was built from ProDom v 2001.2, we could use an AC numbering scheme consistent with ProDom 2001.2:

• The AC prefix is CG instead of PD
• When a ProDom family is conserved inside ProDom-CG, its AC number is kept unchanged.
• When a ProDom family is deleted for Prodom-CG, its AC number is marked as invalid in ProDom-CG

For instance, the ProDom family PD000271 (177 sequences) is found in ProDom-CG as CG000271 (104 sequences). But the ProDom family PD000646 (238 sequences) is deleted because it did not content any sequence from the complete genomes, so that there is no CG000646 family in ProDom-CG.

Complete genomes found in ProDom-C

There are 8 archeal, 30 bacterial and 4 eukaryotic genomes in Prodom-CG.