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UniProt release 7.0

Published February 7, 2006

Full statistics and release notes

Headlines

UniProtKB/Swiss-Prot major release (49.0)

Release 49.0 of 07-Feb-2006 of UniProtKB/Swiss-Prot contains 207'132 sequence entries, comprising 75'438'310 amino acids abstracted from 139'151 references. 12'815 sequences have been added since release 48, the sequence data of 991 existing entries has been updated and the annotations of all entries have been revised. This represents an increase of 7%.

Many improvements were carried out in the last 5 months. In particular, we have changed from showing only the dates corresponding to full UniProtKB releases in the DT lines to displaying the date of the biweekly release at which an entry is integrated or updated. We dropped the information concerning the release number and introduced entry and sequence version numbers in the DT lines.

Cross-references to several databases have been added, and we have changed our copyright statement. (Please read below for further details)

Full statistics and release notes

UniProtKB News

Dates and Versions

We changed from showing only the dates corresponding to full UniProtKB releases in the DT lines to displaying the date of the biweekly release at which an entry is integrated or updated. We dropped the information concerning the release number and introduced entry and sequence version numbers in the DT lines.

The new format of the three DT lines is:

DT   DD-MMM-YYYY, integrated into UniProtKB/database_name.
DT   DD-MMM-YYYY, sequence version version_number.
DT   DD-MMM-YYYY, entry version version_number.

Example for UniProtKB/Swiss-Prot:

DT   01-JAN-1998, integrated into UniProtKB/Swiss-Prot.
DT   15-OCT-2001, sequence version 3.
DT   01-APR-2004, entry version 14.

Example for UniProtKB/TrEMBL:

DT   01-FEB-1999, integrated into UniProtKB/TrEMBL.
DT   15-OCT-2000, sequence version 2.
DT   15-DEC-2004, entry version 5.

The sequence version number of an entry is incremented by one when its amino acid sequence is modified. The entry version number is incremented by one whenever any data in the flat file representation of the entry is modified.

We retrofitted the entry and sequence version numbers, as well as all dates, using archived UniProtKB releases.

Addition of a feature (FT) key CHAIN over the whole sequence length

The feature key CHAIN was previously only used to describe processed protein sequences. Now we added, in the UniProtKB/Swiss-Prot database, a "FT CHAIN" to all the entries having neither a "FT CHAIN" nor a "FT PEPTIDE". This led to the addition of a "FT CHAIN", covering the full length of the sequence, to more than 170 000 entries. In this way, in UniProtKB/Swiss-Prot, all the mature proteins will be described in the feature lines.

Release of a new document about post-translational modifications

The controlled vocabulary for the post-translational modifications (PTMs) that are annotated in the UniProtKB feature table has moved from the UniProtKB User Manual to a separate document, ptmlist.txt.

The document contains, for each individual modification, the controlled vocabulary term and its associated feature key, and additional information, such as the amino acid that can be modified and the mass difference, the position on the protein sequence, the taxonomic distribution, the protein location, associated keyword(s), as well as links to the UniProtKB entries that contain the annotation, and to the corresponding entry in the RESID Database of Protein Modifications.

Copyright

We have changed the copyright statement in all UniProt Knowledgebase entries. All UniProtKB/Swiss-Prot and UniProtKB/TrEMBL entries, as well as all documents now contain the statement
CC   -----------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution-NoDerivs License
CC   -----------------------------------------------------------------------

Cross-References to PptaseDB

Cross-references have been added to the Prokaryotic Protein Phosphatase Database, a database which provides information concerning prokaryotic and archaeal phosphatases for which experimental evidence exists demonstrating phosphatase activity. The Prokaryotic Protein Phosphatase Database is available at http://vigen.biochem.vt.edu/p3d/p3d.htm.

The format of the explicit links in the flat file is:

Resource abbreviation PptaseDB
Resource identifier PptaseDB unique phosphatase identifier.
Example
O52787:
DR   PptaseDB; P3D040495; -.

Cross-references to BioCyc

Cross-references have been added to BioCyc, a collection of Pathway/Genome Databases. Each Pathway/Genome Database describes the genome and metabolic pathways of a single organism, with the exception of the MetaCyc database, which is a reference source on metabolic pathways from many organisms. BioCyc is available at http://www.biocyc.org/.

Implicit links to the EcoCyc database have already been provided before in the NiceProt view of relevant Swiss-Prot entries on ExPASy.

The format of the explicit links in the flat file is:

Resource abbreviation BioCyc
Resource identifier BioCyc database code and identifier, separated by a colon.
Examples
P21170: 
DR   BioCyc; EcoCyc:ARGDECARBOXBIO-MONOMER; -.

Q9HCC0:
DR   BioCyc; MetaCyc:MONOMER-10082; -.