ExPASy Proteomics Server

Table of contents

New feature key INTRAMEM
Change of release numbers
Change of release cycle
Change of the comment line (CC) topic INTERACTION

Not before: 23-Mar-2010

In addition to the feature keys TOPO_DOM (which describes the topology of regions for transmembrane proteins that span membrane compartments) and TRANSMEM (which describes the extent of the region spanning a membrane), we will introduce a new feature key INTRAMEM to describe the extent of a region located in a membrane without crossing it.

Not before: 23-Mar-2010

In the past, we have distinguished major and minor releases of the UniProt knowledgebase and this is reflected in the UniProtKB release number format: major releases are numbered x.0, minor releases are x.1, x.2, etc. We are going to abandon this distinction and therefore change the number format to YYYY_XX where YYYY is the calendar year and XX a 2-digit number that is incremented for each release of a given year, e.g. 2010_01, 2010_02, etc. We will archive previous releases on our ftp site for at least 2 years.

Not before: 23-Mar-2010

We are going to change our release cycle from 3 to 4 weeks.

Not before: 01-Aug-2010

The CC line topic INTERACTION conveys information about binary protein-protein interactions. A description of its current format is available in the UniProtKB User Manual. Currently, all interaction data is automatically derived from the IntAct database. In the future, we will start to add manually curated binary protein-protein interactions to this topic (these are currently described in the CC line topic SUBUNIT). In order to represent isoform- and chain-specific interactions (e.g. for viral polyproteins) and to add interactor-specific comments (e.g. PTMs and binding regions), we are going to modify the format of the INTERACTION lines. Each binary interaction will be represented by a block of 3 to 4 lines:

• The first line of a block indicates the experimental evidence for the interaction, the source of the data (literature reference or By similarity) and, optionally, cross-reference(s) to other databases.
• The next line is an optional comment about the interaction.
• The last two lines give details on the interacting proteins: the Protein1= line represents the protein of the currently displayed entry, the Protein2= line the other interacting protein. If Protein2 is from a different organism than Protein1, its organism is indicated in an Organism= field.

Note: Variable values are represented in italics. Perl-style multipliers indicate whether a pattern (as delimited by parentheses) is optional (?), may occur 0 or more times (*), or 1 or more times (+). Alternative values are separated by a pipe symbol (|). Special characters are escaped by a backslash (\).

 CC   -!- INTERACTION:
(CC       Interact=status \(source|By similarity\)( \(Potential\))?;( Xref=xref;)?
(CC         Comment=free_text;)?
 CC         Protein1=name [id(:ft_id)?];( Note=free_text;)?
 CC         Protein2=name( [id(:ft_id)?])?;( Organism=tax_name [NCBI_TaxID:tax_id];)?( Note=free_text;)?)+

• status = Yes | No
  Displays the experimental evidence for the interaction:
  • Yes if there is experimental evidence that the two proteins (or their orthologues) interact. An optional (Potential) qualifier indicates that the physiological relevance of the interaction is uncertain (e.g. the evidence results from a not further validated yeast-two-hybrid experiment).
  • No if there is experimental evidence that the two proteins do not interact under the experimental conditions described in the cited publication.
• source: Literature source for the interaction (PubMed or Ref).
• xref = db:db_id(, db:db_id)*
  List of database cross-references, each consisting of database name and unique database identifier. Currently, we only cross-reference the IntAct database.
• name: Biologically meaningful label or name for the protein.
  Displays the gene name (as shown in the GN line field Name= or OrderedLocusNames= or ORFNames=) or a dash '-' if the gene name is unknown.
  If the protein contains multiple chains (e.g. a viral polyprotein), the chain name (from the FT line) is displayed instead and the identifier which follows in square brackets must contain the FTId of the chain.
• id: UniProt accession number or isoform identifier (IsoId= field).
• ft_id: UniProt feature identifier (FTId= field).
• tax_name: Scientific name of the organism.
• tax_id: NCBI taxonomy database identifier of the organism.
• free_text: Free text.
  • Comment= contains additional information concerning the interaction (like subcellular location).
  • Note= contains additional information concerning the interacting protein (like PTM status, binding domains).

Examples:

CC   -!- INTERACTION:
CC       Interact=Yes (PubMed:11533489);
CC         Comment=HDAC3 mediates the deacetylation of RELA;
CC         Protein1=RELA [Q04206];
CC         Protein2=HDAC3 [O15379];

CC   -!- INTERACTION:
CC       Interact=Yes (Ref.4);
CC         Comment=Heterodimers are called polygalacturonase-1 (PG1);
CC         Protein1=GP1 [Q40161];
CC         Protein2=PG2 [P05117];

CC   -!- INTERACTION:
CC       Interact=Yes (PubMed:11501947) (Potential);
CC          Protein1=ABI3 [Q9P2A4];
CC          Protein2=ABI3BP [Q7Z7G0];

CC   -!- INTERACTION:
CC       Interact=Yes (By similarity);
CC         Protein1=GABRG2 [Q5REA1];
CC         Protein2=GABARAP;

CC   -!- INTERACTION:
CC       Interact=Yes (PubMed:10837489);
CC         Protein1=MCL1 [Q07820-1];
CC         Protein2=BAK1 [Q16611];
CC       Interact=Yes (PubMed:15901672, PubMed:17097560); Xref=IntAct:EBI-1003422,EBI-519866;
CC         Protein1=MCL1 [Q07820];
CC         Protein2=BAK1 [Q16611];

CC   -!- INTERACTION:
CC       Interact=Yes (PubMed:11418237); Xref=IntAct:EBI-375446,EBI-389883;
CC         Protein1=ABI1 [Q8IZP0];
CC         Protein2=NCK1 [P16333]; Note=SH3 1 domain;
CC       Interact=No (PubMed:12681507);
CC         Protein1=ABI1 [Q8IZP0-6];
CC         Protein2=NCK1 [P16333];
CC       Interact=Yes (By similarity);
CC         Protein1=ABI1 [Q8IZP0]; Note=N-terminus;
CC         Protein2=WASF1 [Q92558];

CC   -!- INTERACTION:
CC       Interact=Yes (PubMed:11086025);
CC         Protein1=C1QR1 [Q9NPY3];
CC         Protein2=Core protein p21 [P27958:PRO_0000037566)]; Organism=Hepatitis C virus genotype 1a (isolate H) [NCBI_TaxID=11108]; Note=See also other virus strains;

CC   -!- INTERACTION:
CC       Interact=Yes (PubMed:11086025);
CC         Protein1=Core protein p21 [P27958:PRO_0000037566)];
CC         Protein2=C1QR1 [Q9NPY3]; Organism=Homo sapiens [NCBI_TaxID=9606];

CC   -!- INTERACTION:
CC       Interact=Yes (PubMed:16470652); Xref=IntAct:EBI-907934,EBI-907894;
CC         Protein1=CNP [P06623];
CC         Protein2=CABP1 [Q9NZU7]; Organism=Homo sapiens [NCBI_TaxID=9606];