Table of contents

Change of the protein description (DE line)
Changes in the FASTA header line

Not before: 01-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.
	Allergen=	0-1	See allergen.txt.
	Biotech=	0-1	A name used in a biotechnological context.
	CD_antigen=	0-n	See cdlist.txt.
	INN=	0-1	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   Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)
DE   (Aldesleukin).

New format:

DE   RecName: Full=Interleukin-2;
DE            Short=IL-2;
DE   AltName: Full=T-cell growth factor;
DE            Short=TCGF; 
DE   AltName: INN=Aldesleukin;
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: 01-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