FASTA headers

The following is a description of FASTA headers for UniProtKB (including alternative isoforms), UniRef, UniParc, UniMES and archived UniProtKB versions. NCBI's program formatdb (in particular its -o option) is compatible with the UniProtKB fasta headers.

UniProtKB

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

Where:

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. For UniProtKB/TrEMBL entries without a RecName field, the SubName field is used. In case of multiple SubNames, the first one 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

Alternative isoforms (this only applies to UniProtKB/Swiss-Prot):

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

Where:

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.

ProteinExistence and SequenceVersion do not apply to alternative isoforms (ProteinExistence is dependent on the number of cDNA sequences, which is not known for individual isoforms).

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

Where:

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

Where:

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

Where:

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

Where:

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:

"pre-UniProt":

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

"post-UniProt":

>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