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Swiss-Prot Protein Knowledgebase
Forthcoming changes

Release 41.1 of 25-Mar-2003


Table of contents

Extension of the entry name format
Reference Comment (RC) line topics may span lines
New feature key 'CROSSLNK'
Continuation of the conversion of Swiss-Prot to mixed-case characters
New format of comment line (CC) topic PATHWAY
New format of comment line (CC) topic COFACTOR

Extension of the entry name format

Not before: 01-Jun-2003

We endeavor to assign meaningful entry names that facilitate the identification of the proteins and the species of origin. Currently the entry name consists of up to ten uppercase alphanumeric characters. Swiss-Prot uses a general purpose naming convention that can be symbolized as X_Y, where X is a mnemonic code of at most 4 alphanumeric characters representing the protein name, the '_' sign serves as a separator, and the Y is a mnemonic species identification code of at most 5 alphanumeric characters representing the biological source of the protein.

We are planning to elongate the mnemonic code for the protein name from up to 4 characters to up to 5 characters. E.g. the mnemonic code for the meiotic recombination protein rec10 is currently 'RE10'. After the introduction of extended entry names it could be modified to the 5-letter code 'REC10'.

Reference Comment (RC) line topics may span lines

Not before: 01-May-2003

The RC (Reference Comment) line store comments relevant to the reference cited, in currently 5 distinct topics: PLASMID, SPECIES, STRAIN, TISSUE and TRANSPOSON. It is not always possible to list all information within one line. Therefore we will allow multiple RC lines, in which one topic might span over a line. Example:

RC   STRAIN=Various strains;
could become
RC   STRAIN=AZ.026, DC.005, GA.039, GA2181, IL.014, IN.018, KY.172, KY2.37,
RC   LA.013, MN.001, MNb027, MS.040, NY.016, OH.036, TN.173, TN2.38,
RC   UT.002, AL.012, AZ.180, MI.035, VA.015, and IL2.17;
New feature key 'CROSSLNK'

Not before: 01-May-2003

The feature key 'CROSSLNK' will be introduced to describe bonds between amino acids, which are formed posttranslationally within a peptide or between peptides, such as isopeptidic bonds, carbon-carbon linkages, carbon-nitrogen linkages, tioether bonds, thiolester bonds, and backbone condensations.

Format:
FT   CROSSLNK    from     to      Description.       
Note:
The feature keys 'THIOETH' and 'THIOLEST' will be removed.
Disulfide bonds occur so often in proteins, that we will keep the special feature key 'DISULFID' to describe this kind of linkage.

Continuation of the conversion of Swiss-Prot to mixed-case characters

Continuous change

We will continue to convert Swiss-Prot entries from all 'UPPER CASE' to 'MiXeD CaSe'. We are proceeding in the conversion of CC (Comment) lines, we will start to convert the GN (Gene Name) lines to mixed case, but also any other line type might be effected.

New format of comment line (CC) topic PATHWAY

Continuous change

We are gradually structuring the comment line topic PATHWAY. To describe the biochemical pathway in which the protein is involved, we use the following format:

CC   -!- PATHWAY: biochemical pathway; nth step.[ Comment.]
Example:

CC   -!- PATHWAY: Coenzyme A (CoA) biosynthesis; first step.
New format of comment line (CC) topic COFACTOR

Continuous change

The comment line topic COFACTOR is gradually being modified to the following format:

CC   -!- COFACTOR: cofactor1[, cofactor2 and cofactor3].[ Comment.]
Examples:

CC   -!- COFACTOR: Magnesium.
CC   -!- COFACTOR: Copper, Manganese and Nickel.
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