Table of contents

Change of the protein description (DE line)
Changes in the FASTA header line
New OG (OrGanelle) line value: Chromatophore
Change of the comment line (CC) topic INTERACTION

Not before: 22-Jul-2008

The UniProtKB description (DE) lines list protein names in a computer parsable format, but currently with a minimal amount of structure. In UniProtKB/Swiss-Prot the description starts with the recommended name of the protein and additional alternative names are indicated between parentheses. In UniProtKB/TrEMBL the description is derived directly from the underlying nucleotide entry and its accuracy relies on the information provided by the submitter of the nucleotide entry, unless it has been improved by automatic annotation procedures.

Consistent nomenclature is indispensable for communication, literature searching and entry retrieval. The protein names provided in the description lines of UniProtKB/Swiss-Prot are widely used by life scientists and often propagated during the annotation of new genomic sequences. For these reasons we intend to structure the UniProtKB DE lines more explicitly: We will introduce 3 categories, as well as several subcategories, of protein names:

Category Field	Subcategory Field	Cardinality	Description
RecName:		1 in UniProtKB/Swiss-Prot 0-1 in UniProtKB/TrEMBL	The name recommended by the UniProt consortium.
	Full=	1	The full name.
	Short=	0-n	An abbreviation of the full name or an acronym.
	EC=	0-n	An Enzyme Commission number.
AltName:		0-n	A synonym of the recommended name.
	Full=	0-1	The full name.
	Short=	0-n	An abbreviation of the full name or an acronym.
	EC=	0-n	An Enzyme Commission number.
AltName:	Allergen=	0-1	See allergen.txt.
AltName:	Biotech=	0-1	A name used in a biotechnological context.
AltName:	CD_antigen=	0-n	See cdlist.txt.
AltName:	INN=	0-n	The international nonproprietary name: A generic name for a pharmaceutical substance or active pharmaceutical ingredient that is globally recognized and is a public property.
SubName:		0 in UniProtKB/Swiss-Prot 0-n in UniProtKB/TrEMBL	A name provided by the submitter of the underlying nucleotide sequence.
	Full=	1	The full name.
	EC=	0-n	An Enzyme Commission number.

Each name is shown on a separate line; lines may therefore exceed 75 characters.

A block of DE lines may further contain multiple Includes: and/or Contains: sections and a separate field Flags: to indicate whether the protein sequence is a precursor or a fragment:

Field	Cardinality	Value
Includes:	0-n	A block of protein names as described in the table above.
Contains:	0-n	A block of protein names as described in the table above.
Flags:	0-1	Precursor and/or Fragment or Fragments

Examples:

Current format:

DE   Granulocyte colony-stimulating factor precursor (G-CSF) (Pluripoietin)
DE   (Filgrastim) (Lenograstim).

New format:

DE   RecName: Full=Granulocyte colony-stimulating factor;
DE            Short=G-CSF;
DE   AltName: Full=Pluripoietin;
DE   AltName: INN=Filgrastim;
DE   AltName: INN=Lenograstim;
DE   Flags: Precursor;

Current format:

DE   ADAM 10 precursor (EC 3.4.24.81) (A disintegrin and metalloproteinase
DE   domain 10) (Mammalian disintegrin-metalloprotease) (Kuzbanian protein
DE   homolog) (CD156c antigen) (Fragment).

New format:

DE   RecName: Full=A disintegrin and metalloproteinase domain 10;
DE            Short=ADAM 10;
DE            EC=3.4.24.81;
DE   AltName: Full=Mammalian disintegrin-metalloprotease;
DE   AltName: Full=Kuzbanian protein homolog;
DE   AltName: CD_antigen=CD156c;
DE   Flags: Precursor; Fragment;

Current format:

DE   Arginine biosynthesis bifunctional protein argJ [Includes: Glutamate
DE   N-acetyltransferase (EC 2.3.1.35) (Ornithine acetyltransferase)
DE   (Ornithine transacetylase) (OATase); Amino-acid acetyltransferase
DE   (EC 2.3.1.1) (N-acetylglutamate synthase) (AGS)] [Contains: Arginine
DE   biosynthesis bifunctional protein argJ alpha chain; Arginine
DE   biosynthesis bifunctional protein argJ beta chain].

New format:

DE   RecName: Full=Arginine biosynthesis bifunctional protein argJ;
DE   Includes:
DE     RecName: Full=Glutamate N-acetyltransferase;
DE              EC=2.3.1.35;
DE     AltName: Full=Ornithine acetyltransferase;
DE              Short=OATase;
DE     AltName: Full=Ornithine transacetylase;
DE   Includes:
DE     RecName: Full=Amino-acid acetyltransferase;
DE              EC=2.3.1.1;
DE     AltName: Full=N-acetylglutamate synthase;
DE              Short=AGS;
DE   Contains:
DE     RecName: Full=Arginine biosynthesis bifunctional protein argJ alpha chain;
DE   Contains:
DE     RecName: Full=Arginine biosynthesis bifunctional protein argJ beta chain;

Not before: 22-Jul-2008

The current UniProtKB FASTA headers are unfortunately incompatible with the -o option of the NCBI's program formatdb. We have been working with the NCBI to remedy this and changes are required on both sides. While future versions of formatdb will accept a database code for UniProtKB/TrEMBL, we will also have to modify our UniProtKB FASTA headers. For consistency reasons, we will also change the FASTA headers of the other UniProt databases.

UniProtKB

>db|UniqueIdentifier|EntryName ProteinName OS=OrganismName[ GN=GeneName]PE=ProteinExistence SV=SequenceVersion

• db is 'sp' for UniProtKB/Swiss-Prot and 'tr' for UniProtKB/TrEMBL.
• UniqueIdentifier is the primary accession number of the UniProtKB entry.
• EntryName is the entry name of the UniProtKB entry.
• ProteinName is the recommended name of the UniProtKB entry as annotated in the RecName field from release 14.0 on. For UniProtKB/TrEMBL entries without a RecName field, the SubName field is used. The 'precursor' attribute is excluded, 'Fragment' is included with the name if applicable.
• OrganismName is the scientific name of the organism of the UniProtKB entry.
• GeneName is the first gene name of the UniProtKB entry. If there is no gene name, OrderedLocusName or ORFname, the GN field is not listed.
• ProteinExistence is the numerical value describing the evidence for the existence of the protein.
• SequenceVersion is the version number of the sequence.

Examples:

>sp|Q8I6R7|ACN2_ACAGO Acanthoscurrin-2 (Fragment) OS=Acanthoscurria gomesiana GN=acantho2 PE=1 SV=1
>sp|P27748|ACOX_RALEH Acetoin catabolism protein X OS=Ralstonia eutropha (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) GN=acoX PE=4 SV=2
>sp|P04224|HA22_MOUSE H-2 class II histocompatibility antigen, E-K alpha chain OS=Mus musculus PE=1 SV=1

>tr|A3SA23|A3SA23_9RHOB TonB dependent, hydroxamate-type ferrisiderophore, outer membrane receptor OS=Sulfitobacter sp. EE-36 GN=EE36_08023 PE=3 SV=1
>tr|Q8N2H2|Q8N2H2_HUMAN CDNA FLJ90785 fis, clone THYRO1001457, moderately similar to H.sapiens protein kinase C mu OS=Homo sapiens PE=2 SV=1

>sp|IsoID|EntryName Isoform IsoformName of ProteinName OS=OrganismName[ GN=GeneName]

• IsoID is the isoform identifier as assigned in the ALTERNATIVE PRODUCTS section of the UniProtKB entry.
• IsoformName is the isoform name as annotated in the ALTERNATIVE PRODUCTS Name field of the UniProtKB entry.

Example:

sp|Q4R572-2|1433B_MACFA Isoform Short of 14-3-3 protein beta/alpha OS=Macaca fascicularis GN=YWHAB

UniRef

>UniqueIdentifier ClusterName n=Members Tax=Taxon RepID=RepresentativeMember

• UniqueIdentifier is the primary accession number of the UniRef cluster.
• ClusterName is the name of the UniRef cluster.
• Members is the number of UniRef cluster members.
• Taxon is the scientific name of the lowest common taxon shared by all UniRef cluster members.
• RepresentativeMember is the entry name of the representative member of the UniRef cluster.

Example:

>UniRef100_A5DI11 Elongation factor 2 n=1 Tax=Pichia guilliermondii RepID=EF2_PICGU

UniParc

>UniqueIdentifier status=Status

• UniqueIdentifier is the primary accession number of the UniParc entry.
• Status is 'active' if the UniParc entry has at least one active cross-reference, and 'inactive' if it does not have any active cross-references.

Example:

>UPI0000000005 status=active

UniMES

>UniqueIDentifier ProteinName OS=OrganismName[ Pep=SourcePeptideIdentifier]SV=SequenceVersion

• UniqueIdentifier is the primary accession number of the UniMES entry.
• ProteinName is the protein name of the UniMES entry.
• OrganismName is the scientific name of the organism (group) of the UniMES entry.
• SourcePeptideIdentifier is the (optional) peptide identifier provided by the submitter.
• SequenceVersion is the version number of the sequence.

Example:

>MES00000000005 Putative uncharacterized protein GOS_3018412 (Fragment) OS=marine metagenome Pep=JCVI_PEP_1096688850003 SV=1

Archived UniProtKB sequence versions

>db|UniqueIdentifier archived from Release ReleaseNumber ReleaseDate SV=SequenceVersion

• db is 'sp' for UniProtKB/Swiss-Prot and 'tr' for UniProtKB/TrEMBL.
• UniqueIdentifier is the primary accession number of the UniProtKB entry.
• ReleaseNumber refers to the release from which the sequence was archived (Swiss-Prot or TrEMBL release numbers for releases prior to the first UniProt release, and both UniProt and Swiss-Prot or TrEMBL release numbers for releases after the first UniProt release).
• ReleaseDate is the date of the release form which the sequence was archived.
• SequenceVersion is the version number of the sequence.

Examples:

>sp|P05067 archived from Release 18.0 01-MAY-1991 SV=3
>tr|Q55167 archived from Release 17.0 01-JUN-2001 SV=1

>sp|P05067 archived from Release 9.2/51.2 28-NOV-2006 SV=3
>tr|A0RTJ8 archived from Release 11.0/36.0 29-MAY-2007 SV=1

Not before: 22-Jul-2008

We are going to add Chromatophore to the list of valid plastid values in the OG line. The chromatophore is the photosynthetic inclusion found in Paulinella chromatophora, a photosynthetic thecate amoeba. It encodes and houses the machinery necessary for photosynthesis and CO2 fixation; it also has the genetic capacity to synthesize some amino acids, some fatty acids and a few cofactors. It is not yet clear whether the chromatophore derives from the same endosymbiotic event that is thought to have led to all other plastids. The chromatophore genome of P. chromatophora has been sequenced (PubMed:18356055) and been found to be just over 1 Mb, approximately 9 times larger than the average photosynthetic plastid and approximately 1/3 smaller than the smallest cyanobacterial genome.

Example:

OG   Plastid; Chromatophore.

Not before: 01-Oct-2008

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. Up to now, all interaction data has been automatically derived from the IntAct database. In the future we will start to add manually curated binary protein-protein interactions in UniProtKB/Swiss-Prot (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 and the data source (literature reference or By similarity and/or cross-reference to the database from which the data was derived).
• 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 currently displayed entry, the Protein2= line the other interacting protein. If Protein2 is from a different species than Protein1, its species or taxonomic range is indicated.

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( \(source|By similarity\))?;( Xref=xref;)?
(CC         Comment=free_text;)?
 CC         Protein1=name [id(:subid)?];( Note=free_text;)?
 CC         Protein2=name [id(:subid)?];( Organism=organism;)?( Note=free_text;)?)+

• status = Yes | No | Uncertain
  Displays the experimental evidence for the interaction:
  • Yes if there is experimental evidence that the two proteins (or their homologues) interact in a physiological context.
  • No if there is experimental evidence that the two proteins (or their homologues) do not interact under the experimental conditions described in the cited publication.
  • Uncertain if the experimental evidence for the interaction between the two proteins (or their homologues) is not considered to reliably reflect an interaction in a physiological context (e.g. results from not further validated yeast-two-hybrid or in-vitro experiments).
• db_xref = db:db_id(, db:db_id)*
  List of database cross-references, each consisting of database name and unique database identifier.
• source: A db_xref with db = PubMed
  Literature sources for the interaction.
• xref: A db_xref with db = IntAct
  Database entries from which the interaction was imported (currently only IntAct).
• 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).
• subid: UniProt feature identifier (FTId= field).
• organism: Indicates that the interacting proteins originate from different species. The value of this field is one of the following:
  • tax_name [NCBI_TaxID:tax_id]: Scientific name and NCBI taxonomy database identifier of (group of) species of Protein2. In a host-virus protein interaction this refers to the range of species of Protein2. An entry from a representative virus strain/isolate is displayed in Protein2.
  • Host: In a virus-host protein interaction this refers to the range of species of Protein2 which corresponds to the OH line of Protein1. An entry from a representative host is displayed in Protein2.
• 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 (PubMed:10837489);
CC         Protein1=MCL1 [Q07820-1];
CC         Protein2=BAK1 [Q16611];
CC       Interact=Yes (PubMed:15901672, 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 (By similarity);
CC         Protein1=C1QR1 [Q9NPY3];
CC         Protein2=Core protein p21 [P27955:PRO_0000037583)]; Organism=Hepatitis C virus [NCBI_TaxID=11103]; Note=See also other virus strains;

CC   -!- INTERACTION:
CC       Interact=Yes (By similarity);
CC         Protein1=Core protein p21 [P27955:PRO_0000037583];
CC         Protein2=C1QR1 [Q9NPY3]; Organism=Host; Note=See also other hosts;

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];

CC   -!- INTERACTION:
CC       Interact=Uncertain (PubMed:15231747);
CC          Protein1=NOB1 [Q9ULX3];
CC          Protein2=UPF2 [Q9HAU5];