Gene3D - A database of CATH structural domain data projected onto the major sequence repositories.

The files made available here are the copyright of Gene3D.

Whilst we encourage you to download these files and to use them for research we do not permit the resale of this data and if you wish to display it within your own resource please acknowledge the latest NAR database issue publication.

For any help please contact us at gene3d.contact@gmail.com



Files
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Release information:
current_release_version.txt gives the current release number and the
corresponding CATH release code.


HMM files:
* gene3d_hmmsearch.tar.gz  - contains the HMMs and scripts to run the Gene3d assignmnet pipeline



domain_sequences:

There are 4 files each with the same header
4mu3A02|3.30.230.40|7a743bc2106cd9d7bdd1437f03374762|4mu3A02-i2|255-355|255-355|1.1e-40|7.3e-36|

1.HMM seed DOMAIN ID
2.CATH SUPERFAMILY CODE
3.MD5 checksum of the full length parent protein sequence
4.HMM ID
5.start/stop of the HMM assignment on the full length parent protein sequence
6.start/stop of the HMM assignment on the full length parent protein sequence after MDA resolution
7.conditional evalue
8.independent evalue

The files starting  nr_gene3d files are the main set of gene3d sequences swissprot / representative proteomes etc.
The files starting nr_uniref90 are assignments of additional sequences in uniref90 not in the nr_gene3d set

The 2 extra files with "_conditional_" in the name dont pass the indepenent e-value threshold to be included in the Gene3D database
but could be real domain hits because of a significant conditional e-value score so are included here in case they are useful.