UniProt XML to FASTA (two-line) converter

Convert a UniProt XML sequence file to FASTA (two-line).

Convert from Convert to Choose your sequence file

Maximum file size: 50 MB. The file is checked before conversion.

UniProt XML → FASTA (two-line)

The output keeps sequence records but drops features, references, and other source annotations.

About this conversion

The converter reads records in the input format and writes them in the output format. Data that the output format cannot store may be lost. The notes under the Convert file button list the important limits for this pair.

Run it with Biopython

For batch work, you can use Biopython's SeqIO.convert function. This pair needs no molecule type argument.

from Bio import SeqIO

count = SeqIO.convert("input.uniprot-xml", "uniprot-xml",
                      "output.fasta-2line", "fasta-2line")
print("Converted %i records" % count)

Sample input file: UniProt XML

Copy this example into a file, or download it, to try a UniProt XML conversion.

<?xml version='1.0' encoding='UTF-8'?>
<uniprot xmlns="http://uniprot.org/uniprot" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://uniprot.org/uniprot http://www.uniprot.org/support/docs/uniprot.xsd">
<entry dataset="Swiss-Prot" created="2004-07-19" modified="2015-01-07" version="25">
<accession>P84001</accession>
<name>29C0_ANCSP</name>
<protein>
<recommendedName>
<fullName>U3-ctenitoxin-Asp1a</fullName>
<shortName>U3-CNTX-Asp1a</shortName>
</recommendedName>
<alternativeName>
<fullName>Venom protein ANC29C0</fullName>
</alternativeName>
</protein>
<organism>
<name type="scientific">Ancylometes sp.</name>
<name type="common">South American fishing spider</name>
<dbReference type="NCBI Taxonomy" id="280265"/>
<lineage>
<taxon>Eukaryota</taxon>
<taxon>Metazoa</taxon>
<taxon>Ecdysozoa</taxon>
<taxon>Arthropoda</taxon>
<taxon>Chelicerata</taxon>
<taxon>Arachnida</taxon>
<taxon>Araneae</taxon>
<taxon>Araneomorphae</taxon>
<taxon>Entelegynae</taxon>
<taxon>Lycosoidea</taxon>
<taxon>Ctenidae</taxon>
<taxon>Ancylometes</taxon>
</lineage>
</organism>
<reference key="1" evidence="3">
<citation type="submission" date="2004-06" db="UniProtKB">
<title>Protein ANC29C0 from venom of South American fishing spider (Ancylometes spp.) has sequence similarities to neurotoxic peptide Caeron precursor from Bark spider (Caerostris extrusa).</title>
<authorList>
<person name="Richardson M."/>
<person name="Pimenta A.M.C."/>
<person name="Bemquerer M.P."/>
<person name="Santoro M.M."/>
<person name="Figueiredo S.G."/>
<person name="Cordeiro M.N."/>
</authorList>
</citation>
<scope>PROTEIN SEQUENCE</scope>
<scope>SUBCELLULAR LOCATION</scope>
<scope>TISSUE SPECIFICITY</scope>
<scope>MASS SPECTROMETRY</scope>
<source>
<tissue>Venom</tissue>
</source>
</reference>
<comment type="function">
<text evidence="2">Possible neurotoxin.</text>
</comment>
<comment type="subcellular location">
<subcellularLocation>
<location evidence="1">Secreted</location>
</subcellularLocation>
</comment>
<comment type="tissue specificity">
<text evidence="1">Expressed by the venom gland.</text>
</comment>
<comment type="mass spectrometry" mass="9571" method="Electrospray" evidence="1">
<location>
<begin position="1"/>
<end status="unknown"/>
</location>
</comment>
<dbReference type="ArachnoServer" id="AS000014">
<property type="toxin name" value="U3-ctenitoxin-Asp1a"/>
</dbReference>
<dbReference type="GO" id="GO:0005576">
<property type="term" value="C:extracellular region"/>
<property type="evidence" value="ECO:0000501"/>
<property type="project" value="UniProtKB-SubCell"/>
</dbReference>
<proteinExistence type="evidence at protein level"/>
<keyword id="KW-0903">Direct protein sequencing</keyword>
<keyword id="KW-0528">Neurotoxin</keyword>
<keyword id="KW-0964">Secreted</keyword>
<keyword id="KW-0800">Toxin</keyword>
<feature type="chain" description="U3-ctenitoxin-Asp1a" id="PRO_0000087682">
<location>
<begin position="1"/>
<end position="50" status="greater than"/>
</location>
</feature>
<feature type="non-terminal residue" evidence="2">
<location>
<position position="50"/>
</location>
</feature>
<evidence key="1" type="ECO:0000269">
<source ref="1"/>
</evidence>
<evidence key="2" type="ECO:0000303">
<source ref="1"/>
</evidence>
<evidence key="3" type="ECO:0000305"/>
<sequence length="50" mass="5679" checksum="3B06738CA0940B53" modified="2004-07-19" version="1" fragment="single">
ANACTKQADCAEDECCLDNLFFKRPYCEMRYGAGKRCAAASVYKEDKDLY
</sequence>
</entry>
<copyright>
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
Distributed under the Creative Commons Attribution-NoDerivs License
</copyright>
</uniprot>

Download sample (sample.xml, 3.6 KB)

Samples are small illustrative files. Some come from the Biopython test suite (see the project's sample notes); they are not real study data.

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