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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:

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: 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:

Example:

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

UniParc

>UniqueIdentifier status=Status
Where:

Example:

>UPI0000000005 status=active

UniMES

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

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:

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