新疆时时开奖结果记录:uniprot.org news - Welcome-新疆十一选五开奖结果//www.uniprot.org/news?query=&offset=0&limit=25&sort=&desc=trueen-usCopyright 2018, UniProt Consortium230025Old Swiss-Prot releases - Welcome-新疆十一选五开奖结果Fri, 28 Nov 2003 //www.uniprot.org/news/2003/11/28/release February 28, 2003 to November 28, 2003 <div> <div> <h2>Swiss-Prot release 42.6 of 28-Nov-2003</h2> <h3>New comment line (CC) topic RNA EDITING</h3> <p>We have introduced a new comment (CC) line topic: 'RNA EDITING'. This topic is used to convey information relevant to all types of RNA editing that lead to one or more amino acid changes.</p> <p>The format of this comment block is:</p> <pre> CC -!- RNA EDITING: Modified_positions={x[, y, z, ...] | Not_applicable | Undetermined}[; Note=Text]. </pre> <p>Examples:</p> <pre> CC -!- RNA EDITING: Modified_positions=393, 431, 452, 495. </pre> <pre> CC -!- RNA EDITING: Modified_positions=59, 78, 94, 98, 102, 121; Note=The CC stop codon at position 121 is created by RNA editing. The nonsense CC codon at position 59 is modified to a sense codon. </pre> <pre> CC -!- RNA EDITING: Modified_positions=Not_applicable; Note=Some CC positions are modified by RNA editing via nucleotide insertion or CC deletion. The initiator methionine is created by RNA editing. </pre> <p>The free text in the 'Note' is standardized.</p> <p>All entries with such a topic have the keyword <a href="/keywords/KW-0691">RNA editing</a>.</p> <h3>Changes concerning keywords</h3> <p>New keyword:</p> <ul> <li><a href="/keywords/KW-0894">Sodium channel</a></li> </ul> <h2>Swiss-Prot release 42.5 of 21-Nov-2003</h2> <h3>Headlines: Monkey business! </h3> <p>The comparison of the genome of human with that of higher apes such as chimpanzees, gibbons, gorillas and the orangutans, was for a long time a wish of many life scientists.</p> <p>It is becoming a reality due to various sequencing initiatives targeted toward the elucidation of primate genomic sequences. However it will take some time before a significant amount of high quality complete protein sequences are available. In the meanwhile we are trying to ensure that whenever an existing higher ape sequence is available that correspond to a cognate human protein, that sequence gets annotated very quickly.</p> <p>For example, in the last two weeks, the number of annotated chimpanzees protein sequences in Swiss-Prot has doubled.</p> <h2>Swiss-Prot release 42.4 of 14-Nov-2003</h2> <h3>Content changes in the speclist.txt document file</h3> <p>The <a href="/docs/speclist">speclist.txt</a> file lists the organism identification codes which are used to build the "organism" part of an entry name (Examples: ARATH, BACSU, DROME, HUMAN, etc). This file contains for each organism code, the corresponding NCBI taxonomic database node identifier (TaxID) as well as the specific official (scientific) name and optionally common name and synonym.</p> <p>Up to now organisms identification codes where only used in Swiss-Prot where all species represented in the database are associated with such a code. The TrEMBL section of the combined UniProt knowledgebase will soon also make use of entry names that are based on the species of origin. As it is not possible in a reasonable time frame to manually assign organism codes to all species represented in TrEMBL, it was decided to define "virtual" codes that regroup organisms at a certain taxonomic level. Such codes are prefixed by the number "9" and generally correspond to a "pool" of organisms which can be 'wide' as a kingdom. Here are some examples of such codes:</p> <pre> 9BACT B 2: N=Bacteria 9CNID E 6073: N=Cnidaria 9FUNG E 4751: N=Fungi 9REOV V 10880: N=Reoviridae 9TETR E 32523: N=Tetrapoda 9VIRI E 33090: N=Viridiplantae </pre> <p>The list of all the "9" codes that have been defined are now been integrated as a subsection of the speclist.txt file.</p> <h3>Changes concerning the <a href="/docs/ptmlist">controlled vocabulary for PTMs</a></h3> <p>New terms for the Feature key 'LIPID':</p> <ul> <li>GPI-anchor amidated residue</li> <li>Omega-hydroxyceramide glutamate ester</li> <li>Phosphatidylethanolamine amidated glycine</li> </ul> <h3>Changes concerning keywords</h3> <p>New keyword:</p> <ul> <li><a href="/keywords/KW-0893">Thyroid hormones biosynthesis</a></li> </ul> <h2>Swiss-Prot release 42.3 of 07-Nov-2003</h2> <h3>Headlines: More than 10'000 human proteins have been annotated</h3> <p>In the framework of the <a href="//www.expasy.org/sprot/hpi/">HPI</a> project, we have annotated more than 10'000 proteins (almost 10'300). The exact number of genes represented is not exactly equal to the number of proteins for at least four reasons:</p> <ul> <li>We have entries that describe proteins encoded by more than one gene but whose amino acid sequences are 100% identical;</li> <li>We sometimes are unable to describe highly divergent splice isoforms in one entry and these genes are therefore represented by two or more Swiss-Prot entries;</li> <li>For MHC histocompatibility antigens, immunoglobulin and T cell receptors, we often have several entries representing groups of alleles;</li> <li>A very small number of human entries probably represent "bogus" proteins originating from either pseudogenes or from contaminants.</li> </ul> <p> But even taking the above factors into account, we do have more than 10'000 protein-encoding genes represented in Swiss-Prot.</p> <h3>Cross-references to DictyBase</h3> <p>We have added cross-references to the DictyBase database (available at <a href="//dictybase.org/">//dictybase.org/</a>), an online informatics resource for Dictyostelium discoideum. DictyBase goals are to provide a single portal for access to Dictyostelium genome information, curated Dictyostelium literature, to facilitate access to experimental resources such as the Dictyostelium stock center, and to provide an on-line presence for the Dictyostelium community.</p> <p>The identifiers of the appropriate DR line are:</p> <table> <tr> <th>Resource abbreviation</th> <td>DictyBase</td> </tr> <tr> <th>Resource identifier</th> <td>DictyBase's unique identifier for a gene.</td> </tr> <tr> <th>Optional information 1</th> <td>DictyBase's gene symbol.</td> </tr> <tr> <th>Example</th> <td> <pre><a href="//www.uniprot.org/uniprot/P34092#section_x-ref">P34092</a>: DR DictyBase; DDB0002013; myoB.</pre> </td> </tr> </table> <h3>Cross-refereces to DictyDb</h3> <p>Due to the availability of DictyBase (see above) and in agreement with the maintainers of both databases, we have removed all cross-references to the DictyDb database.</p> <h3>Cross-refereces to PhotoList</h3> <p>We have added cross-references to the PhotoList database (available at <a href="//genolist.pasteur.fr/PhotoList/">//genolist.pasteur.fr/PhotoList/</a>), a database dedicated to the analysis of the genome of Photorhabdus luminescens strain TT01.</p> <p>The identifiers of the appropriate DR line are:</p> <table> <tr> <th>Resource abbreviation</th> <td>PhotoList</td> </tr> <tr> <th>Resource identifier</th> <td>PhotoList's unique identifier for an ORF.</td> </tr> <tr> <th>Example</th> <td> <pre><a href="//www.uniprot.org/uniprot/Q8KM01#section_x-ref">Q8KM01</a>: DR PhotoList; plu1253; -.</pre> </td> </tr> </table> <h3>Changes concerning keywords</h3> <p>New keyword:</p> <ul> <li><a href="/keywords/KW-0892">Osteogenesis</a></li> </ul> <p>Deleted keywords:</p> <ul> <li>B-cell</li> <li>Bone</li> </ul> <h2>Swiss-Prot release 42.1 of 24-Oct-2003</h2> <h3>Format change in the jourlist.txt document file</h3> <p>The <a href="/docs/jourlist">jourlist.txt</a> file lists the titles and abbreviations of all journals cited in Swiss-Prot. This file also includes other type of information such as ISSN and CODEN identifiers, publishers, web sites, etc. As of this release, we have added a field for the ISSN of the electronic (on-line) version of journals. This field which is termed "e-ISSN" is optional.</p> <p>Example:</p> <pre> Abbrev: Acta Haematol. Title : Acta Haematologica ISSN : 0001-5792 <strong>e-ISSN: 1421-9662</strong> CODEN : ACHAAH Publis: Karger AG Server: //www.karger.com/journals/aha/ </pre> <h3>Changes concerning keywords</h3> <p>New keyword:</p> <ul> <li><a href="/keywords/KW-0891">Chondrogenesis</a></li> <li><a href="/keywords/KW-0890">Hereditary spastic paraplegia</a></li> </ul> <p>Deleted keywords:</p> <ul> <li>Alkylation</li> <li>Brain</li> <li>Cartilage</li> </ul> <h2>Swiss-Prot release 42.0 of 10-Oct-2003</h2> <h3>Headlines: New major release is available (42.0)</h3> <p> Release 42.0 of Swiss-Prot contains 135'850 sequence entries, comprising 50'046'799 amino acids abstracted from 109'694 references. 13'374 sequences have been added since release 41, the sequence data of 1'298 existing entries has been updated and the annotations of 45'617 entries have been revised. This represents an increase of 11%.</p> <p>Many improvements were carried out in the last 6 months at the level of the CC and FT lines. All the recent changes to Swiss-Prot format are described in detail in the continuously updated document:</p> <h2>Swiss-Prot release 41.26 of 04-Oct-2003</h2> <h3>Controlled vocabulary in the feature (FT) key LIPID</h3> <p>We have revised the annotation of post-translational modified amino acids in lipoproteins, and made a major overhaul of the controlled vocabulary. Lipid annotation that was covered by other feature (FT) keys than LIPID has been moved accordingly, e.g. cholesterol-binding.</p> <p>The currently defined controlled vocabulary for the feature descriptions of 'LIPID' FT lines is listed below:</p> <pre> Cholesterol glycine ester Cis-14-hydroxy-10,13-dioxo-7-heptadecenoic acid aspartate ester GPI-anchor amidated alanine GPI-anchor amidated asparagine GPI-anchor amidated aspartate GPI-anchor amidated cysteine GPI-anchor amidated glycine GPI-anchor amidated serine GPI-anchor amidated threonine GPI-like-anchor amidated glycine GPI-like-anchor amidated serine N-myristoyl glycine N-palmitoyl cysteine N(6)-myristoyl lysine N(6)-palmitoyl lysine O-octanoyl serine O-palmitoyl serine O-palmitoyl threonine Phosphotidylethanolamine amidated glycine S-12-hydroxyfarnesyl cysteine S-archaeol cysteine S-diacylglycerol cysteine S-farnesyl cysteine S-geranylgeranyl cysteine S-myristoyl cysteine S-palmitoleyl cysteine S-palmitoyl cysteine </pre> <h2>Swiss-Prot release 41.24 of 19-Sep-2003</h2> <h3>Changes concerning keywords </h3> <p>Deleted keyword:</p> <ul> <li>T-DNA</li> </ul> <h2>Swiss-Prot release 41.22 of 29-Aug-2003</h2> <h3>Changes concerning keywords</h3> <p>Modified keywords:</p> <ul> <li><strong>Flagella</strong> was renamed to <a href="/keywords/KW-0282">Flagellum</a></li> <li><strong>Microtubules</strong> was renamed to <a href="/keywords/KW-0493">Microtubule</a></li> </ul> <p>New keyword:</p> <ul> <li><a href="/keywords/KW-0889">Transcription antitermination</a></li> </ul> <h2>Swiss-Prot release 41.21 of 22-Aug-2003</h2> <h3>Changes concerning keywords </h3> <p>Modified keyword:</p> <ul> <li><strong>Capping protein</strong> was renamed to <a href="/keywords/KW-0117">Actin capping</a></li> </ul> <p>New keyword:</p> <ul> <li><a href="/keywords/KW-0888">Threonine protease</a></li> </ul> <h2>Swiss-Prot release 41.20 of 16-Aug-2003</h2> <h3>Case and wording change for submissions to Swiss-Prot in reference location (RL) lines</h3> <p>While proceeding with the conversion to mixed case of the different line types of a Swiss-Prot entry, we have decided to do the same for the name of our database, e.g. we are now using "Swiss-Prot" (instead of previously "SWISS-PROT") as the prevalent way of referring to it. This change affects the Swiss-Prot RL (reference location) lines of entries which were submitted directly to Swiss-Prot, and which the authors have not (yet) published. At the same time, we have changed the wording of those lines.</p> <p>Former format:</p> <pre> RL Submitted (MAY-2002) to the SWISS-PROT data bank. </pre> <p>New format:</p> <pre> RL Submitted (MAY-2002) to Swiss-Prot. </pre> <p>Note: RL lines concerning submissions to EMBL/GenBank/DDBJ, PDB and other databases are not affected by this modification.</p> <h3>New comment line (CC) topic ALLERGEN</h3> <p>We have introduced a new comment (CC) line topic type: ALLERGEN. This topic is used to convey information relevant to allergenic proteins.</p> <p>The format of this comment block is:</p> <pre> CC -!- ALLERGEN: Text. </pre> <p>Examples:</p> <pre> <a href="/uniprot/P19121#section_comments">P19121</a>: CC -!- ALLERGEN: Causes an allergic reaction in human. Binds IgE. It is a CC partially heat-labile allergen that may cause both respiratory and CC food-allergy symptoms in patients with the bird-egg syndrome. </pre> <pre> <a href="/uniprot/Q28050#section_comments">Q28050</a>: CC -!- ALLERGEN: Causes an allergic reaction in human. Minor allergen of CC bovine dander. </pre> <h2>Swiss-Prot release 41.18 of 25-Jul-2003</h2> <h3>Headlines: Annotation of microbial H(+)-translocating pyrophosphatases </h3> <p> We have annotated the microbial H(+)-translocating pyrophosphatases present in the acidocalcisome, the first eukaryotic organelle to be found in bacteria.</p> <p> Acidocalcisomes are organelles that have an acidic nature, high eletronic density and contain high concentrations of calcium, magnesium, pyrophosphate and polyP. They were originally found in unicellular eukaryotes, such as Toxoplasma gondii and trypanosomatids. It has been postulated that acidocalcisomes may have an important role as an energy source and in the regulation of intracellualr pH, calcium concentration and osmotic conditions.</p> <p>Now the group of Roberto Docampo has found them in the bacterium Agrobacterium tumefaciens. This is the first organelle to be found in bacteria that have a direct counterpart in eukaryotes. The typical characteristic of the acidocalcisome is the presence of a number of pumps and exchangers: one of them is the H(+)-translocating pyrophosphatase (H+-PPase). This pump generates a proton motive force and may be responsible for the synthesis of pyrophosphate. They are found in several bacteria and archaea and at present it is unkown whether any of these is also localized in acidocalcisomes. As these pumps are present only in some pathogenic bacteria but not in humans, drugs that target them might be effective against these infections.</p> <h3>Changes concerning keywords </h3> <p>Modified keyword:</p> <ul> <li><strong>Metachromatic leucodystrophy</strong> was renamed to <a href="/keywords/KW-0478">Metachromatic leukodystrophy</a></li> </ul> <h2>Swiss-Prot release 41.17 of 19-Jul-2003</h2> <h3>Cross-references to GermOnline</h3> <p>We have added cross-references to the GermOnline database (available at <a href="//germonline.unibas.ch/">//germonline.unibas.org/</a>), which is maintained by the <a href="//www.isb-sib.ch/groups/genombio.htm">Genome Bioinformatics group</a> of the SIB Swiss Institute of Bioinformatics. GermOnline is a gateway for gametogenesis. Its goals are to provide a rapid access to a comprehensive compilation of genes, expression data and functions implicated in germline development, meiosis, gamete formation, and gamete function in 11 key model systems and H. sapiens. At this time, the majority of cross-references in Swiss-Prot concern Saccharomyces cerevisiae gene expression data.</p> <p>The identifiers of the appropriate DR line are:</p> <table> <tr> <th>Resource abbreviation</th> <td>GermOnline</td> </tr> <tr> <th>Resource identifier</th> <td>GermOnline's identifier for a gene.</td> </tr> <tr> <th>Example</th> <td> <pre><a href="//www.uniprot.org/uniprot/P58012#section_x-ref">P58012</a>: DR GermOnline; 305011; -.</pre> </td> </tr> </table> <h2>Swiss-Prot release 41.16 of 11-Jul-2003</h2> <h3>Changes concerning keywords </h3> <p>New keywords:</p> <ul> <li><a href="/keywords/KW-0887">Epilepsy</a></li> <li><a href="/keywords/KW-0886">LTQ</a></li> </ul> <h2>Swiss-Prot release 41.14 of 27-Jun-2003</h2> <h3>Changes concerning keywords </h3> <p>New keywords:</p> <ul> <li><a href="/keywords/KW-0885">CTQ</a></li> <li><a href="/keywords/KW-0884">PQQ biosynthesis</a></li> </ul> <h2>Swiss-Prot release 41.12 of 16-Jun-2003</h2> <h3>New feature key CROSSLNK, and removal of the feature keys THIOETH and THIOLEST</h3> <p>The feature key CROSSLNK has been introduced to describe bonds between amino acids, which are formed posttranslationally within a peptide or between peptides, such as isopeptidic bonds, carbon-carbon linkages, carbon-nitrogen linkages, thioether bonds, thiolester bonds, and backbone condensations.</p> <p>Format:</p> <pre> FT CROSSLNK from to Description. </pre> <p>The initially defined controlled vocabulary is listed below:</p> <pre> 1'-histidyl-3'-tyrosine (His-Tyr) 2-cysteinyl-L-phenylalanine (Cys-Phe) 2-cysteinyl-D-phenylalanine (Cys-Phe) 2-cysteinyl-D-allo-threonine (Cys-Thr) 2-iminomethyl-5-imidazolinone (Gln-Gly) 2-oxazoline (Cys-Ser) 2'-(S-cysteinyl)histidine (Cys-His) 3-cysteinyl-aspartic acid (Cys-Asp) 3'-histidyl-3-tyrosine (His-Tyr) 3'-(S-cysteinyl)-tyrosine (Cys-Tyr) 4-cysteinyl-glutamic acid (Cys-Glu) 4'-cysteinyl-tryptophylquinone (Cys-Trp) 5-imidazolinone (Ser-Gly) 5-imidazolinone (Ala-Gly) 5-imidazolinone (Cys-Gly) Beta-methyllanthionine (Cys-Thr) Beta-methyllanthionine (Thr-Cys) Beta-methyllanthionine sulfoxide (Cys-Thr) Isoaspartyl glycine isopeptide (Asn-Gly) Isoaspartyl lysine isopeptide (Lys-Asn) (interchain with N-...) Isoaspartyl lysine isopeptide (Asn-Lys) (interchain with K-...) Isodityrosine (Tyr-Tyr) Isoglutamyl cysteine thioester (Gln-Cys) Isoglutamyl lysine isopeptide (Lys-Gln) Isoglutamyl lysine isopeptide (Gln-Lys) Isoglutamyl lysine isopeptide (Gln-Lys) (interchain with K-...) Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-...) Lanthionine (Ser-Cys) Lanthionine (Cys-Ser) Lysinoalanine (Lys-Ser) Lysine tyrosylquinone (Lys-Tyr) Lysinoalanine (Ser-Lys) Lysyl topaquinone (Lys-Tyr) N-isoaspartyl cysteine isopeptide (Asn-Cys) Oxazole (Cys-Ser) Oxazole (Gly-Ser) Pyrroloquinoline quinone (Glu-Tyr) S-(2-aminovinyl)-D-cysteine (Ser-Cys) S-(2-aminovinyl)-3-methyl-D-cysteine (Thr-Cys) Thiazole (Gly-Cys) Thiazole (Ser-Cys) Thiazole (Phe-Cys) Thiazole (Cys-Cys) Thiazole (Lys-Cys) Tryptophan tryptophylquinone (Trp-Trp) Glycyl lysine isopeptide (Gly-Lys) (interchain with K-...) Glycyl lysine isopeptide (Lys-Gly) (interchain with G-...) Ubiquitinyl cysteine thioester (Cys) </pre> <p>Examples:</p> <pre> <a href="/uniprot/P01024#section_features">P01024</a>: FT CROSSLNK 1010 1013 Isoglutamyl cysteine thioester (Cys-Gln). </pre> <pre> <a href="/uniprot/P29827#section_features">P29827</a>: FT CROSSLNK 60 77 Beta-methyllanthionine (Cys-Thr). FT CROSSLNK 63 73 Lanthionine (Ser-Cys). FT CROSSLNK 64 70 Beta-methyllanthionine (Cys-Thr). FT CROSSLNK 65 78 Lysinoalanine (Ser-Lys). </pre> <p><strong>Note:</strong> The feature keys THIOETH and THIOLEST have been removed. Various bonds between amino-acids that used to be described by the feature keys BINDING, MOD_RES or SITE will progressively, in groups according the type of PTM, be modified and indicated by CROSSLNK. Disulfide bonds occur so often in proteins, that we decided to keep the special feature key DISULFID to annotate this kind of linkage.</p> <h3>Changes concerning keywords </h3> <p>New keywords:</p> <ul> <li><a href="/keywords/KW-0883">Thioether bond</a></li> <li><a href="/keywords/KW-0882">Thioester bond</a></li> </ul> <h2>Swiss-Prot release 41.10 of 30-May-2003</h2> <h3>Reference Comment (RC) line topics may span lines</h3> <p>The RC (Reference Comment) line store comments relevant to the reference cited, in currently 5 distinct topics: PLASMID, SPECIES, STRAIN, TISSUE and TRANSPOSON. It is not always possible to list all information within one line. Therefore we allow multiple RC lines, in which one topic might span over a line. Example:</p> <pre> <a href="/uniprot/Q9EVG8#section_ref">Q9EVG8</a>: RC STRAIN=AZ.026, DC.005, GA.039, GA2181, IL.014, IN.018, KY.172, KY2.37, RC LA.013, MN.001, MNb027, MS.040, NY.016, OH.036, TN.173, TN2.38, RC UT.002, AL.012, AZ.180, MI.035, VA.015, and IL2.17; </pre> <h3> Cross-references to Genome Knowledgebase (GK)</h3> <p>We have added cross-references to the Genome Knowledgebase (GK) (available at <a href="//www.genomeknowledge.org/">//www.genomeknowledge.org/</a>), which is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology.</p> <p>The identifiers of the appropriate DR line are:</p> <table> <tr> <th>Resource abbreviation</th> <td>GK</td> </tr> <tr> <th>Resource identifier</th> <td>GK's unique identifier for a protein, which is identical to the Swiss-Prot primary AC number of that protein.</td> </tr> <tr> <th>Example</th> <td> <pre><a href="//www.uniprot.org/uniprot/Q9BZJ0#section_x-ref">Q9BZJ0</a>: DR GK; Q9BZJ0; -.</pre> </td> </tr> </table> <h3>Cross-references to PIR SuperFamilies of iProClass</h3> <p>We have added cross-references to the PIR SuperFamilies of iProClass (available at <a href="//pir.georgetown.edu/iproclass/">//pir.georgetown.edu/iproclass/</a>), which is an integrated protein classification database.</p> <p>The identifiers of the appropriate DR line are:</p> <table> <tr> <th>Resource abbreviation</th> <td>PIRSF</td> </tr> <tr> <th>Resource identifier</th> <td>iProClass superfamily number.</td> </tr> <tr> <th>Optional information 1</th> <td>Name for a superfamily.</td> </tr> <tr> <td>Optional information 2:</td> <td>Number of hits found in the sequence, which is generally '1'.</td> </tr> <tr> <th>Example</th> <td> <pre><a href="//www.uniprot.org/uniprot/O28076#section_x-ref">O28076</a>: DR PIRSF; PIRSF006414; FTR; 1.</pre> </td> </tr> </table> <h2>Swiss-Prot release 41.9 of 24-May-2003</h2> <h3>Changes concerning keywords </h3> <p>New keyword:</p> <ul> <li><a href="/keywords/KW-0881">Chlorophyll catabolism</a></li> </ul> <h2>Swiss-Prot release 41.5 of 23-Apr-2003</h2> <h3>Headlines: SARS coronavirus protein sequences are available </h3> <p>We have made a first annotation run of the proteins potentially encoded by the SARS (Severe Acute Respiratory Syndrome) coronavirus. The following entries are available:</p> Nucleocapsid protein (<a href="/uniprot/P59595">P59595</a>) E1 glycoprotein (<a href="/uniprot/P59596">P59596</a>) E2 glycoprotein (<a href="/uniprot/P59594">P59594</a> Envelope protein (<a href="/uniprot/P59637">P59637</a>) Replicase polyprotein 1ab (<a href="/uniprot/P59641">P59641</a>) Hypothetical protein X1 (<a href="/uniprot/P59632">P59632</a>) Hypothetical protein X2 (<a href="/uniprot/P59633">P59633</a>) Hypothetical protein X3 (<a href="/uniprot/P59634">P59634</a>) Hypothetical protein X4 (<a href="/uniprot/P59635">P59635</a>) Hypothetical protein 5 (<a href="/uniprot/P59636">P59636</a>) <h3>Changes concerning keywords </h3> <p>New keywords:</p> <ul> <li><a href="/keywords/KW-0880">Kelch repeat</a></li> </ul> <h2>Swiss-Prot release 41.8 of 16-May-2003</h2> <h3>Headlines: Complete update of PDB cross-references</h3> <p>We have completely updated our cross-references to PDB. Thanks to work done by the EBI and Geneva Swiss-Prot groups in collaboration with the EBI MSD (Macromolecular Structure Database) group we have mapped at the atom level PDB structural data to the relevant Swiss-Prot and TrEMBL entries. This work has led to the introduction of cross-references to PDB in TrEMBL and a very significant increase in the number of these cross-references in Swiss-Prot. More than 6'000 cross-references were added and the number of Swiss-Prot entries that are linked to PDB is now above 5'300 (versus about 3'600 before this work was carried out).</p> <h2>Swiss-Prot release 41.3 of 04-Apr-2003</h2> <h3>Changes concerning keywords </h3> <p>New keywords:</p> <ul> <li><a href="/keywords/KW-0879">Wnt signaling pathway</a></li> </ul> <h2>Swiss-Prot release 41.1 of 25-Mar-2003</h2> <h3>New syntax of the CC line topic ALTERNATIVE PRODUCTS</h3> <p>In Swiss-Prot release 41.1 (and in the accompanying TrEMBL release), a new format was introduced for "CC ALTERNATIVE PRODUCTS" lines. The new format is more structured than the previous format. Associated with these changes are the introduction of stable identifiers for each named splice isoform in all entries that describe more than one splice isoform; the extension of feature identifiers, previously only used for human VARIANT and certain CARBOHYD features, to VARSPLIC features in entries from all species.</p> <p>The new format of the CC line topic ALTERNATIVE PRODUCTS is:</p> <pre> CC -!- ALTERNATIVE PRODUCTS: CC Event=Alternative promoter; CC Comment=Free text; CC Event=Alternative splicing; Named isoforms=n; CC Comment=Optional free text; CC Name=Isoform_1; Synonyms=Synonym_1[, Synonym_n]; CC IsoId=Isoform_identifier_1[, Isoform_identifer_n]; CC Sequence=Displayed; CC Note=Free text; CC Name=Isoform_n; Synonyms=Synonym_1[, Synonym_n]; CC IsoId=Isoform_identifier_1[, Isoform_identifer_n]; CC Sequence=VSP_identifier_1 [, VSP_identifier_n]; CC Note=Free text; CC Event=Alternative initiation; CC Comment=Free text; </pre> <p>The qualifiers are described in the table below:</p> <table> <tr> <th>Topic</th> <th>Description</th> </tr> <tr> <td>Event</td> <td>Biological process that results in the production of the alternative forms (Alternative promoter, Alternative splicing, Alternative initiation).<br /> Format: Event=controlled vocabulary;<br /> Example: Event=Alternative splicing;</td> </tr> <tr> <td>Named isoforms</td> <td>Number of isoforms listed in the topics 'Name' currently only for 'Event=Alternative splicing'.<br /> Format: Named isoforms=number;<br /> Example: Named isoforms=6;</td> </tr> <tr> <td>Comment</td> <td>Any comments concerning one or more isoforms; optional for 'Alternative splicing'; in case of 'Alternative promoter' and 'Alternative initiation' there is always a 'Comment' of free text, which includes relevant information on the isoforms.<br /> Format: Comment=free text;<br /> Example: Comment=Experimental confirmation may be lacking for some isoforms;</td> </tr> <tr> <td>Name</td> <td>A common name for an isoform used in the literature or assigned by Swiss-Prot; currenty only available for spliced isoforms.<br /> Format: Name=common name;<br /> Example: Name=Alpha;</td> </tr> <tr> <td>Synonyms</td> <td>Synonyms for an isoform as used in the literature; optional; currently only available for spliced isoforms.<br /> Format: Synonyms=Synonym_1[,&amp;nbsp;Synonym_n];<br /> Example: Synonyms=B, KL5;</td> </tr> <tr> <td>IsoId</td> <td>Unique identifier for an isoform, consisting of the Swiss-Prot accession number, followed by a dash and a number. <br /> Format: IsoId=acc#-isoform_number[, acc#-isoform_number];<br /> Example: IsoId=P05067-1;</td> </tr> <tr> <td>Sequence</td> <td>Information on the isoform sequence; the term <strong>Displayed</strong> indicates, that the sequence is shown in the entry; a list of <a href="/docs/userman.htm#FTID">feature identifiers</a> (VSP_#) indicates that the isoform is annotated in the feature table; the FTIds enable programs to create the sequence of a splice variant; if the accession number of the IsoId does not correspond to the accession number of the current entry, this topic contains the term <strong>External</strong>; <strong>Not described</strong> points out that the sequence of the isoform is unknown.<br /> Format: Sequence=VSP_#[, VSP_#]|Displayed|External|Not described;<br /> Example: Sequence=Displayed;<br /> Example: Sequence=VSP_000013, VSP_000014; Example: Sequence=External;<br /> Example: Sequence=Not described;<br /> </td> </tr> <tr> <td>Note</td> <td>Lists isoform-specific information; optional.<br /> Format: Note=Free text;<br /> Example: Note=No experimental confirmation available;</td> </tr> </table> <p>Example of the CC lines and the corresponding FT lines for an entry with alternative splicing <a href="/uniprot/Q15746">Q15746</a>:</p> <pre> ... CC -!- ALTERNATIVE PRODUCTS: CC Event=Alternative splicing; Named isoforms=6; CC Name=1; CC IsoId=Q15746-4; Sequence=Displayed; CC Name=2; CC IsoId=Q15746-5; Sequence=VSP_000040; CC Name=3A; CC IsoId=Q15746-6; Sequence=VSP_000041, VSP_000043; CC Name=3B; CC IsoId=Q15746-7; Sequence=VSP_000040, VSP_000041, VSP_000042; CC Name=4; CC IsoId=Q15746-8; Sequence=VSP_000041, VSP_000042; CC Name=del-1790; CC IsoId=Q15746-9; Sequence=VSP_000044; ... FT VARSPLIC 437 506 VSGIPKPEVAWFLEGTPVRRQEGSIEVYEDAGSHYLCLLKA FT RTRDSGTYSCTASNAQGQVSCSWTLQVER -&gt; G (in FT isoform 2 and isoform 3B). FT /FTId=VSP_004791. FT VARSPLIC 1433 1439 DEVEVSD -&gt; MKWRCQT (in isoform 3A, FT isoform 3B and isoform 4). FT /FTId=VSP_004792. FT VARSPLIC 1473 1545 Missing (in isoform 4). FT /FTId=VSP_004793. FT VARSPLIC 1655 1705 Missing (in isoform 3A and isoform 3B). FT /FTId=VSP_004794. FT VARSPLIC 1790 1790 Missing (in isoform Del-1790). FT /FTId=VSP_004795. ... </pre> <p>The corresponding modules of the Swiss-Prot parser <a href="//swissknife.sourceforge.net/">Swissknife</a> have been modified, and Release 1.31 of Swissknife can be <a href="ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife/">downloaded</a>. </p> <h3>Cross-references to Gene Ontology (GO)</h3> <p>We have added cross-references to the Gene Ontology (GO) database (available at <a href="//www.geneontology.org/">//www.geneontology.org/</a>), which provides controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products.</p> <p>The identifiers of the appropriate DR line are:</p> <table> <tr> <th>Resource abbreviation</th> <td>GO</td> </tr> <tr> <th>Resource identifier</th> <td>GO's unique identifier for a GO term.</td> </tr> <tr> <th>Optional information 1</th> <td>A 1-letter abbreviation for one of the 3 ontology aspects, separated from the GO term by a column. If the term is longer than 46 characters, the first 43 characters are indicated followed by 3 dots ('...'). The abbreviations for the 3 distinct aspects of the ontology are <strong>P</strong> (biological Process), <strong>F</strong> (molecular Function), and <strong>C</strong> (cellular Component).</td> </tr> <tr> <th>Optional information 2</th> <td>3-character GO evidence code. The meaning of the evidence codes is: <strong>IDA</strong>=inferred from direct assay, <strong>IMP</strong>=inferred from mutant phenotype, <strong>IGI</strong>=inferred from genetic interaction, <strong>IPI</strong>=inferred from physical interaction, <strong>IEP</strong>=inferred from expression pattern, <strong>TAS</strong>=traceable author statement, <strong>NAS</strong>=non-traceable author statement, <strong>IC</strong>=inferred by curator, <strong>ISS</strong>=inferred from sequence or structural similarity. </td> </tr> <tr> <th>Examples</th> <td> <pre><a href="//www.uniprot.org/uniprot/Q9XTD2#section_x-ref">Q9XTD2</a> DR GO; GO:0008601; F:protein phosphatase type 2A, regulator acti...; IPI. DR GO; GO:0000080; P:G1 phase of mitotic cell cycle; IDA. DR GO; GO:0008285; P:negative regulation of cell proliferation; IDA. DR GO; GO:0006470; P:protein amino acid dephosphorylation; IDA. <a href="//www.uniprot.org/uniprot/P04406#section_x-ref">P04406</a>: DR GO; GO:0005737; C:cytoplasm; NAS. DR GO; GO:0004365; F:glyceraldehyde 3-phosphate dehydrogenase (p...; NAS. DR GO; GO:0006096; P:glycolysis; NAS. </pre> </td> </tr> </table> <h3>Changes concerning keywords </h3> <p>New keywords:</p> <ul> <li><a href="/keywords/KW-0877">Alternative promoter usage</a></li> <li><a href="/keywords/KW-0878">Amphibian defense peptide</a></li> </ul> <p>Deleted keyword:</p> <ul> <li>Amphibian skin</li> </ul> <h2>Swiss-Prot release 41.0, 28-Feb-2003</h2> <h3>Progress in the conversion of Swiss-Prot to mixed-case characters</h3> <p>We are gradually converting Swiss-Prot entries from all UPPER CASE to MiXeD CaSe. With this release the RC (Reference Comment) line topic STRAIN and the CC line topic CATALYTIC ACTIVITY have been converted.</p> <h3>"Nucleomorph" added to the OrGanelle (OG) line</h3> <p>The OG (OrGanelle) line indicates from which genome a gene for a protein originates. Until now, defined terms in the OG line where "Chloroplast", "Cyanelle", "Mitochondrion" and "Plasmid". The term "Nucleomorph" has been added, which is the residual nucleus of an algal endosymbiont that resides inside its host cell.</p> <h3>Multiple RP lines</h3> <p>Starting with release 41, there can be more than one RP (Reference Position) line per reference in a Swiss-Prot entry. The RP line describes the extent of the work carried out by the authors of the reference, e.g. the type of molecule that has been sequenced, protein characterization, PTM characterization, protein structure analysis, variation detection, etc.</p> <p>As the number of experimental results per publication has increased over the years, the limitation of using a single RP line per reference no longer allowed to add all the information while maintaining a consistent format. Therefore we decided to permit multiple RP lines.</p> <p>Example:</p> <pre> RP SEQUENCE FROM N.A., SEQUENCE OF 23-42 AND 351-365, AND RP CHARACTERIZATION. </pre> <h3>Cross-references to Schizosaccharomyces pombe GeneDB Prototype</h3> <p>We have added cross-references to the Schizosaccharomyces pombe GeneDB Prototype (available at <a href="//www.genedb.org/genedb/pombe/index.jsp">//www.genedb.org/genedb/pombe/index.jsp</a>), which contains all S. pombe known and predicted protein coding genes, pseudogenes and tRNAs. It is hosted by the Sanger Institute.</p> <p>The identifiers of the appropriate DR line are:</p> <table> <tr> <th>Resource abbreviation</th> <td>GeneDB_SPombe</td> </tr> <tr> <th>Resource identifier</th> <td>GeneDB's unique identifier for a S. pombe gene.</td> </tr> <tr> <th>Example</th> <td><pre>DR GeneDB_SPombe; SPAC9E9.12c; -.</pre></td> </tr> </table> <h3>Cross-referecences to Genew</h3> <p>We have added cross-references to the Human Gene Nomenclature Database Genew (available at <a href="//www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl">//www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl</a>), which provides data for all human genes which have approved symbols. It is managed by the HUGO Gene Nomenclature Committee (HGNC).</p> <p>The identifiers of the appropriate DR line are:</p> <table> <tr> <th>Resource abbreviation</th> <td>Genew</td> </tr> <tr> <th>Resource identifier</th> <td>HGNC's unique identifier for a human gene</td> </tr> <tr> <th>Optional information 1</th> <td>HGNC's approved gene symbol.</td> </tr> <tr> <th>Example</th> <td><pre>DR Genew; HGNC:5217; HSD3B1.</pre></td> </tr> </table> <h3>Cross-references to Gramene</h3> <p>We have added cross-references to the Gramene database, a comparative mapping resource for grains (available at <a href="//www.gramene.org/">//www.gramene.org/</a>).</p> <p>The format of the explicit links in the flat file is:</p> <table> <tr> <th>Resource abbreviation</th> <td>Gramene</td> </tr> <tr> <th>Resource identifier</th> <td>Unique identifier for a protein, which is identical to the Swiss-Prot primary AC number of that protein.</td> </tr> <tr> <th>Example</th> <td><pre>DR Gramene; Q06967; -.</pre></td> </tr> </table> <h3>Cross-references to HAMAP</h3> <p>We have added cross-references to the collection of orthologous microbial protein families, generated manually by expert curators of the HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes) project in the framework of the Swiss-Prot protein knowledgebase. The data is accessible at <a href="//www.expasy.org/sprot/hamap/families.html">/sprot/hamap/families.html</a>.</p> <p>The identifiers of the appropriate DR line are:</p> <table> <tr> <th>Resource abbreviation</th> <td>HAMAP</td> </tr> <tr> <th>Resource identifier</th> <td>HAMAP unique identifier for a microbe protein family</td> </tr> <tr> <th>Optional information 1</th> <td>The values are either '-', 'fused', 'atypical' or 'atypical/fused'. The value '-' is a placeholder for an empty field; the 'fused' value indicates that the family rule does not cover the entire protein; the value 'atypical' points out that the protein is divergent in sequence or has mutated functional sites, and should not be included in family datasets. The value 'atypical/fused' indicates both latter findings.</td> </tr> <tr> <th>Optional information 2</th> <td>Number of domains found in the protein, generally '1', rarely '2' for the fusion of 2 identical domains.</td> </tr> <tr> <th>Example</th> <td><pre>DR HAMAP; MF_00012; -; 1.</pre></td> </tr> </table> <h3>Cross-references to Phosphorylation Site Database</h3> <p>We have added cross-references to the Phosphorylation Site Database, PhosSite (available at <a href="//vigen.biochem.vt.edu/xpd/xpd.htm">//vigen.biochem.vt.edu/xpd/xpd.htm</a>), which provides access to information from scientific literature concerning prokaryotic proteins that undergo covalent phosphorylation on the hydroxyl side chains of serine, threonine or tyrosine residues.</p> <p>The identifiers of the appropriate DR line are:</p> <table> <tr> <th>Resource abbreviation</th> <td>PhosSite</td> </tr> <tr> <th>Resource identifier</th> <td>Unique identifier for a phosphoprotein, which is identical to the Swiss-Prot primary AC number of that protein. </td> </tr> <tr> <th>Example</th> <td><pre>DR PhosSite; P00955; -.</pre></td> </tr> </table> <h3>Cross-references to TIGRFAMs</h3> <p>We have added cross-references to TIGRFAMs, a protein family database available at <a href="//www.tigr.org/TIGRFAMs/">//www.tigr.org/TIGRFAMs/</a>.</p> <p>The identifiers of the appropriate DR line are:</p> <table> <tr> <th>Resource abbreviation</th> <td>TIGRFAMs</td> </tr> <tr> <th>Resource identifier</th> <td>TIGRFAMs' unique identifier for a protein family.</td> </tr> <tr> <th>Optional information 1</th> <td>TIGRFAMs' entry name for a protein family.</td> </tr> <tr> <th>Optional information 2</th> <td>Number of hits found in the sequence.</td> </tr> <tr> <th>Example</th> <td><pre>DR TIGRFAMs; TIGR00630; uvra; 1.</pre></td> </tr> </table> <h3>Cross-references to CarbBank</h3> <p>We have removed the Swiss-Prot cross-references to CarbBank.</p> <h3>Cross-references to GCRDb</h3> <p>We have removed the Swiss-Prot cross-references to GCRDb.</p> <h3>Cross-references to Mendel</h3> <p>We have removed the Swiss-Prot cross-references to Mendel.</p> <h3>Cross-references to YEPD</h3> <p>We have removed the Swiss-Prot cross-references to the yeast electrophoresis protein database (YEPD).</p> <h3>Explicit links to dbSNP in FT VARIANT lines of human sequence entries</h3> <p>In human protein sequence entries we have introduced explicit links to the Single Nucleotide Polymorphism database (<a href="//www.ncbi.nlm.nih.gov/SNP/">dbSNP</a>) from the feature description of FT VARIANT keys.</p> <p>The format of such links is:</p> <pre> FT VARIANT from to description (IN dbSNP:accession_number). FT /FTId=VAR_number. </pre> Example: <pre> FT VARIANT 65 65 T -&gt; I (IN dbSNP:1065419). FT /FTId=VAR_012009. </pre> <h3>Feature key SIMILAR became obsolete</h3> <p>The feature key SIMILAR was used to describe the extent of a similarity with another protein sequence. Nowadays, most domains with similarity to other proteins are known regions described in domain and family databases, which are annotated in Swiss-Prot with the feature key DOMAIN or REPEAT and the comment (CC) line topic SIMILARITY; thus the feature key SIMILAR became obsolete and will not be used again.</p> <h3>Version of SP in XML format</h3> <p>A distribution version of Swiss-Prot and TrEMBL in XML format is being developed. The first draft of the XML specification was released for public review on February 21, 2002.</p> </div> </div> UniProt release 1.0 - Welcome-新疆十一选五开奖结果Mon, 15 Dec 2003 //www.uniprot.org/news/2003/12/15/release &lt;span&gt;First release of UniProt&lt;/span&gt; <div> <div> <h2>Headlines</h2> <h3>First release of UniProt</h3> <p>Release 42.7 of Swiss-Prot is integrated in the first release of UniProt, the Universal Protein Resource. Swiss-Prot and TrEMBL are the two sections of the UniProt Knowledgebase.</p> <p>Further reading about the Uniprot 1st release:</p> <ul> <li><a href="//sciencenow.sciencemag.org/cgi/content/full/2002/1028/3">Science magazine - Protein databases unified</a></li> <li><a href="//www.genome.gov/page.cfm?pageID=10005283">NHGRI PRESS RELEASE: Funding for global protein database will create one reliable resource</a></li> <li><a href="//pir.georgetown.edu/pirwww/otherinfo/102502uniprot.pdf">UniProt PRESS RELEASE - Establishing a universal knowledgebase of proteins</a></li> </ul> </div> </div> UniProt release 1.1 - Welcome-新疆十一选五开奖结果Fri, 16 Jan 2004 //www.uniprot.org/news/2004/01/16/release &lt;span&gt;10,000 different citations for JBC &lt;/span&gt; | Documents on species, deleted entries and EMBL <div> <div> <h2>Headlines</h2> <h3>10,000 different citations for JBC in Swiss-Prot</h3> <p>The <a ref="//www.jbc.org/">Journal of Biological Chemistry</a> (generally known as JBC) has always been a gold mine for publications directly relevant to the scope of Swiss-Prot. Starting with the first release in 1986 and up to now it has always been the most cited journal in Swiss-Prot. We are now citing about 10,000 different JBC papers in Swiss-Prot. This is almost twice the value for the next most cited journal, PNAS (Proceedings of the National Academy of Sciences of the U.S.A.).</p> <p>It is also noteworthy that JBC was the first major life science journal to be available as full text on the WWW. It is therefore a good opportunity to thank the JBC editorial board and its staff for the great service they are providing to the Life Sciences community.</p> <h2>UniProtKB news</h2> <h3>Changes concerning keywords </h3> <p>New keywords:</p> <ul> <li><a href="/keywords/KW-0895">ERV</a></li> <li><a href="/keywords/KW-0896">Oogenesis</a></li> <li><a href="/keywords/KW-0897">Waardenburg syndrome</a></li> </ul> <p>Deleted keywords:</p> <ul> <li>Liver</li> <li>Muscle</li> <li>Nerve</li> <li>Neurone</li> </ul> <h3>New documentation file <a href="/docs/strains">strains.txt</a></h3> <p>The strain information is usually given in the RC line of the reference block, but can also be indicated in the Organism (OS) line of a database entry. Strains are controlled vocabulary and we created a list of the strains and their synonyms. This information is now made available in the documentation file strains.txt, together with the mnemonic species identification code representing the biological source of the protein in the knowledgebase.</p> <h3>New format of the documentation file <a href="/docs/keywlist">keywlist.txt</a></h3> <p>Keywords are controlled vocabulary and the annotation follows strict rules. As biological terms can have several meanings, we added to the list of keywords the definition of their usage in the knowledgebase and further information such as synonyms or relevant GO terms.</p> <p>Please note that the file header changed and the format for each keyword entry looks as follows:</p> <pre> Line code Content Occurrence in an entry ID Identifier (keyword) Once; starts an entry AC Accession (KW-xxxx) Once DE Definition Once or more SY Synonyms Optional; Once or more GO Gene ontology (GO) mapping Optional; Once or more HI Hierarchy Optional; Once or more WW Interesting WWW site Optional; Once or more CA Category Once // Terminator Once; ends an entry </pre> <p>Example of a keyword definition entry:</p> <pre> ID Acetoin catabolism. AC KW-0006 DE Protein involved in the degradation of acetoin (3-hydroxy-2-butanone). DE Acetoin is a component of the butanediol cycle (butanediol DE fermentation) in microorganisms. SY Acetoin degradation. GO GO:0045150; acetoin catabolism CA Biological process; Pathway. // </pre> <h3>Change in the name of the files containing deleted AC numbers</h3> <p>As UniProt knowledgebase documentation now comprises both Swiss-Prot and TrEMBL, we changed the name of the files "deleteac.txt" containing deleted AC numbers to </p> <ul> <li>"delac_sp.txt" (for deleted Swiss-Prot ACs)</li> <li>"delac_tr.txt" (for deleted TrEMBL ACs).</li> </ul> <h3>Discontinuation of the embltosp.txt index file</h3> <p>The embltosp.txt file, which contained an index of EMBL Nucleotide Sequence Database entries referenced in Swiss-Prot, is no longer available.</p> </div> </div> UniProt release 1.2 - Welcome-新疆十一选五开奖结果Mon, 02 Feb 2004 //www.uniprot.org/news/2004/02/02/release &lt;span&gt;SPIN: new tool for sequence submission&lt;/span&gt; <div> <div> <h2>Headlines</h2> <h3>SPIN - the new web tool for sequence submission to Swiss-Prot </h3> <p>A new web-based tool, <a href="//www.ebi.ac.uk/swissprot/Submissions/spin/">SPIN</a>, is available for submitting directly sequenced protein sequences and their biological annotations to the Swiss-Prot Protein Knowledgebase. SPIN guides you through a sequence of WWW forms allowing interactive submission. The information required to create a database entry will be collected during this process. </p> <p>Annotation updates for existing Swiss-Prot entries are highly appreciated and should be submitted via the "Submit Update" button at the top of any entry [<a ref="/uniprot/Q9Y281">example</a>]. User update requests are treated with a high priority by our annotators.</p> </div> </div> UniProt release 1.3 - Welcome-新疆十一选五开奖结果Mon, 16 Feb 2004 //www.uniprot.org/news/2004/02/16/release &lt;span&gt;&lt;/span&gt; <div> <div> <h2>UniProtKB news</h2> <h3>Changes concerning keywords </h3> <p>New keyword:</p> <ul> <li><a href="/keywords/KW-0898">Cataract</a></li> </ul> </div> </div> UniProt release 1.4 - Welcome-新疆十一选五开奖结果Mon, 01 Mar 2004 //www.uniprot.org/news/2004/03/01/release &lt;span&gt;More than 500'000 comment blocks&lt;/span&gt; <div> <div> <h2>Headlines</h2> <h3>More than 500'000 comment blocks in Swiss-Prot</h3> <p>One of the important aspects of the annotation process is to provide, for each protein, a description of a number of meaningful biological elements such as the function or role of a protein, its subcellular location, its membership in a specific family, etc. All of this information is stored in the <a href="/docs/userman.htm#CC_line">comments field (CC)</a>. Comments are organized by topics, 24 types of which are currently defined. A specific comment can consist of several sentences or other textual elements, which are grouped into what we term a comment block. </p> The total number of comment blocks has now reached the 500'000 mark, which corresponds to an average of 3.5 blocks per Swiss-Prot entry. <h2>UniProtKB news</h2> <h3>Changes concerning keywords </h3> <p>New keyword:</p> <ul> <li><a href="/keywords/KW-0899">Viral immunoevasion</a></li> </ul> </div> </div> UniProt release 1.5 - Welcome-新疆十一选五开奖结果Mon, 15 Mar 2004 //www.uniprot.org/news/2004/03/15/release &lt;span&gt;Cross-references to RGD&lt;/span&gt; <div> <div> <h2>UniProtKB news</h2> <h3>Cross-references to Rat Genome Database (RGD)</h3> <p>We have added cross-references to the Rat Genome Database (RGD), available at <a href="//rgd.mcw.edu/">//rgd.mcw.edu/</a>, which collects data from rat genetic and genomic research efforts and provides curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data.</p> <p>The identifiers of the appropriate DR line are:</p> <table> <tr> <th>Resource abbreviation</th> <td>RGD</td> </tr> <tr> <th>Resource identifier</th> <td>RGD's unique identifier for a gene.</td> </tr> <tr> <th>Optional information 1</th> <td>RGD's gene symbol.</td> </tr> <tr> <th>Example</th> <td> <pre><a href="//www.uniprot.org/uniprot/O08557#section_x-ref">O08557</a>: DR RGD; 70968; Ddah1.</pre> </td> </tr> </table> <h3>Changes concerning keywords </h3> <p>New keyword:</p> <ul> <li><a href="/keywords/KW-0900">Congenital disorder of glycosylation</a></li> </ul> <h3>Changes concerning the <a href="/docs/ptmlist">controlled vocabulary for PTMs</a></h3> <p>New terms for the feature key 'CROSSLNK':</p> <ul> <li>Isoaspartyl glycine isopeptide (Gly-Asn)</li> <li>Isoglutamyl glycine isopeptide (Gly-Glu)</li> </ul> <p>New term for the feature key 'LIPID':</p> <ul> <li>GPI-anchor amidated carboxyl end</li> </ul> </div> </div> UniProt release 1.6 - Welcome-新疆十一选五开奖结果Mon, 29 Mar 2004 //www.uniprot.org/news/2004/03/29/release &lt;span&gt;Major release&lt;/span&gt; | User manual in HTML <div> <div> <h2>Headlines</h2> <h3>UniProtKB/Swiss-Prot major release (43.0)</h3> <p> Release 43.0 of Swiss-Prot contains 146'720 sequence entries, comprising 54'093'154 amino acids abstracted from 113'719 references. 10'760 sequences have been added since release 42, the sequence data of 663 existing entries has been updated and the annotations of 44'948 entries have been revised. This represents an increase of 8%.</p> <p> Many improvements were carried out in the last 6 months at the level of the CC and FT lines. </p> <p><a href="//www.expasy.org/txt/old-rel/relnotes.43.htm">Full statistics and release notes</a></p> <h2>UniProtKB news</h2> <h3>Discontinuation of the plain text versions of the user manual and release notes</h3> <p>Both, the userman.txt and relnotes.txt files have been replaced by an HTML-formatted version, userman.html and relnotes.html. The plain text version of these files are no longer available.</p> </div> </div> UniProt release 1.7 - Welcome-新疆十一选五开奖结果Tue, 13 Apr 2004 //www.uniprot.org/news/2004/04/13/release &lt;span&gt;Extinct organisms&lt;/span&gt; | Cross-references to OGP, 2-DE database of rat heart <div> <div> <h2>Headlines</h2> <h3>Extinct organisms and Swiss-Prot...</h3> <p>Did you know that Swiss-Prot contains proteins originating from extinct organisms? Since the beginning of the 90s, various groups have sequenced gene fragments from a variety of extinct organisms. Most of the time, the resulting sequences are too small or too fragmentary to be translated into protein sequences. But this is not always the case, and we harbor a few complete or partial sequences originating from species that existed on earth in various periods of time.</p> <p> For example we have a RuBisCO large subunit from a fossil leaf of a Miocene (17-20 Myr old) Magnolia, <a href="/uniprot/P30828">P30828</a>.</p> <p> Much more recent is a complete cytochrome b sequence from a Siberian mammoth, <a href="/uniprot/P92658">P92658</a>.</p> <p> But what is more interesting for those interested in the longevity of proteins, is the complete sequence of an osteocalcin from a steppe bison. This sequence was ontained by mass spectrometry directly from permafrost fossilized bones, about 55-56 Kyr old, <a href="/uniprot/P83489">P83489</a>. </p> <h2>UniProtKB news</h2> <h3>Cross-references to Oxford GlycoProteomics 2-DE database (OGP)</h3> <p>We have added cross-references to the Oxford GlycoProteomics 2-DE database (OGP), available at <a href="//proteomewww.bioch.ox.ac.uk/2d/2d.html">//proteomewww.bioch.ox.ac.uk/2d/2d.html</a>.</p> <p>The identifiers of the appropriate DR line are:</p> <table> <tr> <th>Resource abbreviation</th> <td>OGP</td> </tr> <tr> <th>Resource identifier</th> <td>OGP's unique identifier for a protein, which is identical to the Swiss-Prot primary AC number of that protein.</td> </tr> <tr> <th>Example</th> <td> <pre><a href="//www.uniprot.org/uniprot/P31946#section_x-ref">P31946</a>: DR OGP; P31946; -.</pre> </td> </tr> </table> <h3>Cross-references to 2-DE database of rat heart</h3> <p>We have added cross-references to the 2-DE database of rat heart, at German Heart Institute Berlin, available at <a href="//www.mpiib-berlin.mpg.de/2D-PAGE/RAT-HEART/2d/">//www.mpiib-berlin.mpg.de/2D-PAGE/RAT-HEART/2d/</a>.</p> <p>The identifiers of the appropriate DR line are:</p> <table> <tr> <th>Resource abbreviation</th> <td>Rat-heart-2DPAGE</td> </tr> <tr> <th>Resource identifier</th> <td>Rat-heart-2DPAGE's unique identifier for a protein, which is identical to the Swiss-Prot primary AC number of that protein.</td> </tr> <tr> <th>Example</th> <td> <pre><a href="//www.uniprot.org/uniprot/P03996#section_x-ref">P03996</a>: DR Rat-heart-2DPAGE; P03996; -.</pre> </td> </tr> </table> <h3>Changes concerning keywords</h3> <p>New keyword:</p> <ul> <li><a href="/keywords/KW-0901">Leber congenital amaurosis</a></li> <li><a href="/keywords/KW-0902">Two-component regulatory system</a></li> </ul><br /> <h3>Changes concerning the <a href="/docs/ptmlist">controlled vocabulary for PTMs</a></h3> <p>We are continuously overhauling the annotation of post-translational modifications (PTMs). Phosphorylation sites are described in the description field of the feature key MOD_RES, all entries with such a site contain the keyword 'Phosphorylation'. The initially defined controlled vocabulary for phosphorylation sites is listed below:</p> <pre> Phosphocysteine 4-aspartylphosphate Phosphohistidine Tele-phosphohistidine Pros-phosphohistidine Phosphoserine Phosphothreonine Phosphotyrosine </pre> </div> </div> UniProt release 1.8 - Welcome-新疆十一选五开奖结果Mon, 26 Apr 2004 //www.uniprot.org/news/2004/04/26/release &lt;span&gt;Two completely annotated microbial proteomes&lt;/span&gt; | Cross-references to Gene Farm <div> <div> <h2>Headlines</h2> <h3>Two new completely annotated microbial proteomes</h3> <p>In the framework of the <a href="//www.expasy.org/sprot/hamap/">HAMAP project</a> we not only annotate specified <a href="//www.expasy.org/sprot/hamap/families.html">microbial protein families</a>, but we also aim to completely annotate all the proteins from a number of selected microbial genomes.</p> <p>We maintain pages that list complete <a href="//www.expasy.org/sprot/hamap/bacteria.html">bacterial</a> and <a href="//www.expasy.org/sprot/hamap/archaea.html">archaeal</a> proteomes and which report the status of completion of the annotations in Swiss-Prot.</p> <p>We have now completed the annotation of two more microbial genomes, namely those of <em>Buchnera aphidicola (subsp. Baizongia pistaciae)</em> and <em>Methanococcus jannaschii</em>. The total number of microbial genomes where all proteins are annotated in Swiss-Prot is now 8 and more are yet to come.</p> <h2>UniProtKB news</h2> <h3>Cross-references to Structural and functional annotation of <em>Arabidopsis thaliana</em> gene and protein families (GeneFarm)</h3> <p>We have added cross-references to the Structural and functional annotation of <em>Arabidopsis thaliana</em> gene and protein families (GeneFarm), available at <a href="//genoplante-info.infobiogen.fr/Genefarm/index.htpl">//genoplante-info.infobiogen.fr/Genefarm/index.htpl</a>.</p> <p>The identifiers of the appropriate DR line are:</p> <table> <tr> <th>Resource abbreviation</th> <td>GeneFarm</td> </tr> <tr> <th>Resource identifier</th> <td>GeneFarm's unique identifier for a gene.</td> </tr> <tr> <th>Optional information 1</th> <td>GeneFarm's identifier for a gene family.</td> </tr> <tr> <th>Example</th> <td> <pre><a href="//www.uniprot.org/uniprot/O04500#section_x-ref">O04500</a>: DR GeneFarm; 1671; 91.</pre> </td> </tr> </table> <h3>Changes concerning the <a href="/docs/ptmlist">controlled vocabulary for PTMs</a></h3> <p>We are continuously overhauling the annotation of post-translational modifications (PTMs). Sulfation sites are described in the description field of the feature key MOD_RES, all entries with such a site contain the keyword 'Sulfation'. The initially defined controlled vocabulary for sulfation sites is listed below:</p> <pre> Sulfotyrosine Sulfoserine Sulfothreonine </pre> </div> </div> UniProt release 1.9 - Welcome-新疆十一选五开奖结果Tue, 04 May 2004 //www.uniprot.org/news/2004/05/04/release &lt;span&gt;150'000 entries&lt;/span&gt; <div> <div> <h2>Headlines</h2> <h3>Swiss-Prot reaches 150'000 entries</h3> <p>With this release the number of Swiss-Prot entries has reached the 150'000 mark. It took about 9.5 years to reach the 50'000 entries mark (January 1996), almost 6 more years to reach 100'000 entries (September 2001) and about 2.5 years to the current 150'000 entries.</p> <p>The continuous increase in the speed of annotation is due to a number of factors among which the increase in the number of annotators working for Swiss-Prot at SIB and EBI, increase in the productivity of the work of these annotators, the implementation and improvement of software tools that help to automate some annotation tasks, facilitated access to many third party resources, and the gradual rise in quality of the underlying DNA sequences as well as the quality of genomic and cDNA annotation.</p> <h2>UniProtKB News</h2> <h3>Changes concerning the <a href="/docs/ptmlist">controlled vocabulary for PTMs</a></h3> <p>We are continuously overhauling the annotation of post-translational modifications (PTMs). Methylation sites are described in the description field of the feature key MOD_RES, all entries with such a site contain the keyword 'Methylation'. The initially defined controlled vocabulary for methylation sites is listed below:</p> <pre> N-methylalanine N,N,N-trimethylalanine Omega-N-methylated arginine Omega-N-methylarginine Asymmetric dimethylarginine Symmetric dimethylarginine 5-methylarginine N5-methylarginine N4-methylasparagine N4,N4-dimethylasparagine S-methylcysteine Cysteine methyl ester 2-methylglutamine N5-methylglutamine Glutamate methyl ester (Gln) Glutamate methyl ester (Glu) Methylhistidine Pros-methylhistidine Tele-methylhistidine N-methylisoleucine N-methylleucine Leucine methyl ester N6-methylated lysine N6-methyllysine N6,N6-dimethyllysine N6,N6,N6-trimethyllysine Lysine methyl ester N-methylmethionine N-methylphenylalanine N,N-dimethylproline N-methyltyrosine </pre> <h3>Changes concerning keywords </h3> <p>Deleted keyword:</p> <ul> <li>Egg white</li> </ul> </div> </div> UniProt release 1.10 - Welcome-新疆十一选五开奖结果Mon, 24 May 2004 //www.uniprot.org/news/2004/05/24/release &lt;span&gt;New topic TOXIC DOSE &lt;/span&gt; <div> <div> <h2>UniProtKB news</h2> <h3>New comment line (CC) topic: TOXIC DOSE</h3> <p>We have introduced a new comment (CC) line topic: TOXIC DOSE. This topic is used to store information on the poisoning potential (acute toxicity) of a toxin.</p> <p>Generally this topic holds information on the LD(50) and PD(50). LD stands for "Lethal Dose". LD(50) is the amount of a toxin, given all at once, which causes the death of 50% (one half) of a group of test animals.</p> <p>PD(50) stands for "Paralytic dose". It is the amount of a toxin, which causes the paralysis of 50% of a group of test animals.</p> <p>Examples:</p> <pre> CC -!- TOXIC DOSE: PD(50) is 1.72 mg/kg by injection in blowfly larvae. </pre> <pre> CC -!- TOXIC DOSE: LD(50) is 0.015 mg/kg by intravenous injection for CC sarafotoxin-A and sarafotoxin-B, and 0.3 mg/kg for sarafotoxin-C. </pre> <h3>Changes concerning keywords </h3> <p>New keywords:</p> <ul> <li><a href="/keywords/KW-0905">Primary microcephaly</a></li> <li><a href="/keywords/KW-0904">Protein phosphatase</a></li> </ul><br /> <h3>Changes concerning the <a href="/docs/ptmlist">controlled vocabulary for PTMs</a></h3> <p>We are continuously overhauling the annotation of post-translational modifications (PTMs). For the feature key <a href="/manual/mod_res">MOD_RES</a>, the new initially introduced controlled vocabularies for PTMs are:</p> <ul> <li> <p>Acetylation: All entries with annotated acetylation sites have the keyword <a href="/keywords/KW-0007">Acetylation</a>.</p> <pre> N-acetylalanine N-acetylaspartate N-acetylcysteine N-acetylglutamate N-acetylglycine N-acetylmethionine N-acetylproline N-acetylserine N-acetylthreonine N-acetyltyrosine N-acetylvaline N2-acetylarginine N6-acetyllysine </pre> </li> <li> <p>Amidation: All entries with annotated amidation sites have the keyword <a href="/keywords/KW-0027">Amidation</a>.</p> <pre> Alanine amide Arginine amide Aspartic acid 1-amide Asparagine amide Cysteine amide Glutamic acid 1-amide Glutamine amide Glycine amide Histidine amide Isoleucine amide Leucine amide Lysine amide Methionine amide Phenylalanine amide Proline amide Serine amide Threonine amide Tryptophan amide Tyrosine amide Valine amide </pre> </li> <li> <p>Isomerization: All entries with annotated isomerization sites have the keyword <a href="/keywords/KW-0208">D-amino acid</a>.</p> <pre> D-alanine (Ala) D-alanine (Ser) D-asparagine D-allo-isoleucine D-leucine D-methionine D-phenylalanine D-serine D-tryptophan </pre> </li> <li> <p>Other new controlled vocabularies for PTMs that are annotated with the feature key MOD_RES:</p> <pre> 2',4',5'-topaquinone (keyword: <a href="/keywords/KW-0801">TPQ</a>) 3-phenyllactic acid N6-1-carboxyethyl lysine 2,3-didehydroalanine (Ser) 2,3-didehydrobutyrine (Z)-2,3-didehydrotyrosine </pre> </li> </ul> </div> </div> UniProt release 1.11 - Welcome-新疆十一选五开奖结果Mon, 07 Jun 2004 //www.uniprot.org/news/2004/06/07/release &lt;span&gt;Fungi and Swiss-Prot&lt;/span&gt; | Keyword Direct protein sequencing <div> <div> <h2>Headlines</h2> <h3>Fungi and Swiss-Prot</h3> <p>As we are reaching the 10'000 entries mark for fungi in Swiss-Prot, we believe it is useful to inform our users that we are actively working in speeding up the annotation and re-annotation of fungal protein sequences and most notably those originating from the two model organisms <a href="taxonomy/4932"><em>Saccharomyces cerevisiae</em></a> and <a href="taxonomy/4896"><em>Schizosaccharomyces pombe</em></a>. We are currently building up a fungal annotation group which will soon consist of four annotators, three in Geneva and one in Hinxton.</p> <h2>UniProt news</h2> <h3>Changes concerning keywords </h3> <p>New keywords:</p> <ul> <li><a href="/keywords/KW-0903">Direct protein sequencing</a></li> <li><a href="/keywords/KW-0906">Nuclear pore complex</a></li> </ul><br /> <h3>Changes concerning the <a href="/docs/ptmlist">controlled vocabulary for PTMs</a></h3> <p>We are continuously overhauling the annotation of post-translational modifications (PTMs). For the feature key <a href="/manual/mod_res">MOD_RES</a>, the new initially introduced controlled vocabularies for PTMs are:</p> <ul> <li> <p>Bromination: All entries with annotated bromination sites have the keyword <a href="/keywords/KW-0102">Bromination</a>.</p> <pre> Bromohistidine 6'-bromotryptophan </pre> </li> <li> <p>Deamidation</p> <pre> Deamidated asparagine Deamidated glutamine </pre> </li> <li> <p>Formylation: All entries with annotated formylation sites have the keyword <a href="/keywords/KW-0291">Formylation</a>.</p> <pre> N-formylmethionine N-formylglycine </pre> </li> <li> <p>Hydroxylation: All entries with annotated hydroxylation sites have the keyword <a href="/keywords/KW-0379">Hydroxylation</a>.</p> <pre> Hydroxyproline 3-hydroxyasparagine 3-hydroxyaspartate 5-hydroxylysine 3-hydroxytryptophan </pre> </li> <li> <p>Iodination: All entries with annotated iodination sites have the keyword <a href="/keywords/KW-0405">Iodination</a>.</p> <pre> Thyroxine Triiodothyronine </pre> </li> <li> <p>Other new controlled vocabularies for PTMs that are annotated with the feature key MOD_RES: </p> <pre> 3',4'-dihydroxyphenylalanine 3-methylthioaspartic acid 3-oxoalanine (Cys) 3-oxoalanine (Ser) 4-carboxyglutamate (Keyword: <a href="/keywords/KW-0301">Gamma-carboxyglutamic acid</a>) ADP-ribosylarginine ADP-ribosylcysteine Allysine Aspartyl isopeptide (Asn) Cysteine persulfide Pentaglycyl murein peptidoglycan amidated threonine PolyADP-ribosyl glutamic acid Pyruvic acid (Ser) Pyruvic acid (Cys) S-nitrosocysteine (Keyword: <a href="/keywords/KW-0702">S-nitrosylation</a>) </pre> </li> <li> <p>Unidentified modifications</p> <pre> Alanine derivative Arginine derivative Cysteine derivative Glutamine derivative Isoleucine derivative Lysine derivative Methionine derivative Tryptophan derivative </pre> </li> </ul> </div> </div> UniProt release 1.12 - Welcome-新疆十一选五开奖结果Mon, 21 Jun 2004 //www.uniprot.org/news/2004/06/21/release &lt;span&gt;Noah's ark or biodiversity&lt;/span&gt; | Digital Object Identifier | New Reference (RG) line | Cross-references to EchoBASE <div> <div> <h2>Headlines</h2> <h3>Noah's ark or biodiversity in Swiss-Prot</h3> <p>While the crux of Swiss-Prot annotation is targeted toward a number of model organisms (human, <em>Arabidopsis</em>, <em>Drosophila</em>, <em>E. coli</em>, etc.), there is a continual increase in the number of species that are represented in the knowledgebase. Currently Swiss-Prot contains sequences originating from about 8'550 different species. For ~50% of these species there is only one associated entry in Swiss-Prot. This is often a protein whose gene is used for building phylogenetic trees, such as RuBisCO, cytochrome b or hemoglobin. On the other end of the spectrum, the 20 most represented species cover about 40% of the database (60'000 sequences). The most represented species is of course ourselves, with <em>Homo sapiens</em> filling up 7% of Swiss-Prot.</p> <h2>UniProtKB News</h2> <h3>Digital Object Identifier (DOI) in the RX line</h3> <p>The <a href="//www.doi.org">Digital Object Identifier (DOI)</a> is a system for identifying and exchanging intellectual property in the digital environment. We introduced the new optional identifier "DOI" to the RX line. It is used to store the Digital Object Identifier of a cited document. The format for this RX line topic is:</p> <pre>DOI=Digital_object_identifier;</pre> <p>The order of the optional topics in an RX line is:</p> <pre>RX [MEDLINE=Medline_identifier; ][PubMed=Pubmed_identifier; ][DOI=Digital_object_identifier;]</pre> <p>Example:</p> <pre>RX MEDLINE=97291283; PubMed=9145897; DOI=10.1007/s00248-002-2038-4;</pre> <p>Note: The length of a DOI is not restricted. If the topic DOI does not fit into an RX line that already contains a topic, a further RX line will be created, which may be longer than 76 characters.</p> <h3>New line type: RG (Reference Group)</h3> <p>The new reference line 'RG' (Reference Group) has been introduced to list the consortium name associated with a given citation. The RG line is mainly used in submission reference blocks, but can also be used in paper references, if the working group is cited as an author in the paper.</p> <p>Note: RA (Reference Author) and RG line can be present in the same reference block; at least one RA or RG line is mandatory per reference block.</p> <p>The same line type has recently been introduced in the EMBL nucleotide sequence database.</p> <p>The format for this line is:</p> <pre> RG Consortium_name; </pre> <p>Examples:</p> <pre> RG The C. elegans sequencing consortium; RG The Brazilian network for HIV isolation and characterization; </pre> <h3>Cross-references to EchoBASE</h3> <p>We have added cross-references to <a href="//www.biolws1.york.ac.uk/echobase/">EchoBASE</a>, the integrated post-genomic database for <em>E. coli</em>, available at <a href="//www.biolws1.york.ac.uk/echobase/">//www.biolws1.york.ac.uk/echobase/</a>.</p> <p>The identifiers of the appropriate DR line are:</p> <table> <tr> <th>Resource abbreviation</th> <td>EchoBASE</td> </tr> <tr> <th>Resource identifier</th> <td>EchoBASE's unique identifier for a gene.</td> </tr> <tr> <th>Example</th> <td> <pre><a href="//www.uniprot.org/uniprot/O32528#section_x-ref">O32528</a>: DR EchoBASE; EB4119; -.</pre> </td> </tr> </table> </div> </div> UniProt release 2.0 - Welcome-新疆十一选五开奖结果Mon, 05 Jul 2004 //www.uniprot.org/news/2004/07/05/release &lt;span&gt;Major release &lt;/span&gt;| TrEMBLnew disappears | New format for the gene (GN) line | Cross-references to IntAct and Reactome <div> <div> <h2>Headlines</h2> <h3>UniProtKB/Swiss-Prot major release (44.0)</h3> <p> Release 44.0 of Swiss-Prot contains 153'825 sequence entries, comprising 56'599'343 amino acids abstracted from 117'387 references. 6'633 sequences have been added since release 43, the sequence data of 582 existing entries has been updated and the annotations of 139'855 entries have been revised. This represents an increase of 4%. </p> <p>Many improvements were carried out in the last 3 months at the level of the GN, RX, CC and FT lines. </p> <p><a href="//www.expasy.org/txt/old-rel/relnotes.44.htm">Full statistics and release notes</a></p> <h2>UniProtKB News</h2> <h3>Incorporation of new entries into the biweekly UniProtKB releases of Swiss-Prot and TrEMBL</h3> <p>The files provided in the ftp directory /databases/uniprot/knowledgebase/new/ (and known as TrEMBL_New) have been removed. These files contained new sequence entries and sequences to be used to update existing Swiss-Prot or TrEMBL entries. Until now, these entries were integrated into Swiss-Prot and TrEMBL mostly only at full releases of these databases. We now incorporate these new and updated sequences into the biweekly UniProtKB releases of Swiss-Prot and TrEMBL (/databases/uniprot/knowledgebase/uniprot_sprot* and /databases/uniprot/knowledgebase/uniprot_trembl*), and, therefore, the distribution of these files is no longer necessary.</p> <h3>New format for the GN (Gene Name) line</h3> <p>We have introduced a new format for the GN (Gene Name) line and all gene names have been converted to mixed case. The new format is more structured than the previous one, in order to distinguish between three types of information:</p> <ol> <li><strong>Gene names</strong> (a.k.a gene symbols). The names(s) used to represent a gene. As there can be more than one name assigned to a gene. We make a distinction between the one which we believe should be used as the official gene name and the other names which are listed as "Synonyms".</li> <li><strong>Ordered locus names</strong> (a.k.a. OLN, ORF numbers, CDS numbers or Gene numbers). A name used to represent an ORF in a completely sequenced genome or chromosome. It is generally based on a prefix representing the organism and a number which usually represents the sequential ordering of genes on the chromosome. Depending on the genome sequencing center, numbers are attributed only to protein-coding genes, or also to pseudogenes, or also to tRNAs and other features. Examples: HI0934, Rv3245c, At5g34500, YER456W.</li> <li><strong>ORF names</strong> (a.k.a. Sequencing names or Contig names or Temporary ORFNames). A name temporarily attributed by a sequencing project to an open reading frame. This name is generally based on a cosmid numbering system. Examples: MtCY277.28c, SYGP-ORF50, SpBC2F12.04, C06E1.1, CG10954.</li> </ol> <p>The new format of the GN line is:</p> <pre> <strong>GN Name=&lt;name&gt;; Synonyms=&lt;name1&gt;[, &lt;name2&gt;...]; OrderedLocusNames=&lt;name1&gt;[, &lt;name2&gt;...]; GN ORFNames=&lt;name1&gt;[, &lt;name2&gt;...];</strong> </pre> <p>None of the above four tokens are mandatory. But a <strong>"Synonyms"</strong> token can only be present if there is a <strong>"Name"</strong> token.</p> <p>If there is more than one gene, GN line blocks for the different genes are separated by the following line:</p> <pre> <strong>GN and</strong> </pre> <p>Wrapping is done preferentially at a semicolon, otherwise at a comma.</p> <p>Examples:</p> <pre> GN Name=atpG; Synonyms=uncG, papC; GN OrderedLocusNames=b3733, c4659, z5231, ECs4675, SF3813, S3955; </pre> <pre> GN ORFNames=SPAC1834.11c; </pre> <pre> GN Name=cysA1; Synonyms=cysA; OrderedLocusNames=Rv3117, MT3199; GN ORFNames=MTCY164.27; GN and GN Name=cysA2; OrderedLocusNames=Rv0815c, MT0837; ORFNames=MTV043.07c; </pre> <h3>Cross-references to IntAct</h3> <p>We have added cross-references to <a href="//www.ebi.ac.uk/intact/">IntAct</a>, the Protein interaction database and analysis system available at <a href="//www.ebi.ac.uk/intact/">//www.ebi.ac.uk/intact/</a>.</p> <p>The identifiers of the appropriate DR line are:</p> <table> <tr> <th>Resource abbreviation</th> <td>IntAct</td> </tr> <tr> <th>Resource identifier</th> <td>The Swiss-Prot primary AC number for the protein. This is used by IntAct as a link to all the interactions in which that protein is involved.</td> </tr> <tr> <th>Example</th> <td> <pre><a href="//www.uniprot.org/uniprot/P14653#section_x-ref">P14653</a>: DR IntAct; P14653; -.</pre></td> </tr> </table> <h3>Change in cross-references to Reactome (former GK)</h3> <p>The Genome Knowledgebase (GK) was renamed to <a href="//www.reactome.org/">Reactome</a>. We changed the database name in the relevant cross-references (DR lines) accordingly.</p> <p>Example:</p> <pre>DR Reactome; Q9BZJ0; -.</pre> <h3>Changes concerning the <a href="/docs/ptmlist">controlled vocabulary for PTMs</a></h3> <p>We are continuously overhauling the annotation of post-translational modifications (PTMs). For the feature key <a href="/manual/mod_res">MOD_RES</a>, the new introduced controlled vocabularies for PTMs are:</p> <ul> <li> <p>Hydroxylation: All entries with annotated hydroxylation sites have the keyword <a href="/keywords/KW-0379">Hydroxylation</a>.</p> <dl> <dd> <pre> 3,4-dihydroxyarginine 3,5-dihydroxylysine </pre> </dd> </dl> </li> <li> <p>Unidentified N-terminal blocking modifications:</p> <dl> <dd> <pre> Blocked amino end (Ala) Blocked amino end (Arg) Blocked amino end (Asp) Blocked amino end (Cys) Blocked amino end (Gln) Blocked amino end (Glu) Blocked amino end (Gly) Blocked amino end (Ile) Blocked amino end (Met) Blocked amino end (Pro) Blocked amino end (Ser) Blocked amino end (Thr) Blocked amino end (Val) </pre> </dd> </dl> </li> <li> <p>Unidentified N-terminal blocking modifications:</p> <dl> <dd> <pre> Blocked carboxyl end (His) </pre> </dd> </dl> </li> </ul> </div> </div> UniProt release 2.1 - Welcome-新疆十一选五开奖结果Mon, 19 Jul 2004 //www.uniprot.org/news/2004/07/19/release &lt;span&gt;HERV proteins&lt;/span&gt;| KW order | Topic MASS SPECTROMETRY | Cross-references to AGD <div> <div> <h2>Headlines</h2> <h3>Annotation of HERV protein sequences</h3> <p>The human genome contains a number of human endogenous retroviruses (HERVs). These proviruses (the integrated form of retroviral DNA) are retroviral sequences that are transmitted vertically as part of the host germ line. A number of HERV 'families' have been identified, each derived from an independent colonisation event.</p> <p>Some proviruses display open reading frames with coding capacity for a variety of viral-like proteins (Env, Gag, Pol, Pro, etc.). We have already annotated in Swiss-Prot a significant number of HERV proteins. We only include such potential proteins if they are meeting one of these three criteria: i) if there is evidence of their expression by the host, ii) if the derived sequence encodes a full-length protein, iii) if the protein has a potential cellular function.</p> <h2>UniProtKB News</h2> <h3>Change in the keyword line (KW)</h3> <p>Keywords are now stored by alphabetical order on the KW lines of both Swiss-Prot and TrEMBL entries.</p> <h3>Format change in the comment line (CC) topic: MASS SPECTROMETRY</h3> <p>We have slightly changed the format for the comment line topic MASS SPECTROMETRY, which reports the exact molecular weight of a protein or part of a protein as determined by mass spectrometric methods. The modifications concern the topic RANGE, which has become mandatory, and the introduction of the new mandatory topic NOTE, which is used to indicate the relevant reference number.</p> <p><strong>New format:</strong></p> <pre> CC -!- MASS SPECTROMETRY: MW=XXX[; MW_ERR=XX][; METHOD=XX]; RANGE=XX-XX[ (Name)]; NOTE={Free text (Ref.n)|Ref.n}. </pre> <p>Where:</p> <ul> <li>'MW=XXX' is the determined molecular weight (MW);</li> <li>'MW_ERR=XX' (optional) is the accuracy or error range of the MW measurement;</li> <li>'METHOD=XX' (optional) is the ionization method;</li> <li>'RANGE=XX-XX[ (Name)]' (mandatory) is used to indicate what part of the protein sequence entry corresponds to the molecular weight. In case of multiple products, the name of the relevant isoform is enclosed.</li> <li>'NOTE={Free text (Ref.n)|Ref.n}' (mandatory) indicates the relevant reference, which optionally can be preceded by a comment in free text format.</li> </ul> <p><strong>Example:</strong></p> <pre> CC -!- MASS SPECTROMETRY: MW=32875.93; METHOD=MALDI; CC RANGE=1-284 (Isoform 3); NOTE=Ref.6. </pre> <h3>Cross-references to AGD</h3> <p>We have added cross-references to <a href="//agd.unibas.ch/">Ashbya genome database</a>, available at <a href="//agd.unibas.ch/">//agd.unibas.ch/</a>.</p> <p>The identifiers of the appropriate DR line are:</p> <table> <tr> <th>Resource abbreviation</th> <td>AGD</td> </tr> <tr> <th>Resource identifier</th> <td>AGD's unique identifier for a gene. This is generally the OLN (Ordered Locus Name) for that gene (eg: AAR059C), except for mitochondrial genes where AGD uses an identifier based on the gene name (eg: AgCOB1).</td> </tr> <tr> <th>Optional information 1</th> <td>None; a dash '-' is stored in that field.</td> </tr> <tr> <th>Example</th> <td> <pre><a href="//www.uniprot.org/uniprot/Q00063#section_x-ref">Q00063</a>: DR AGD; AAR059C; -.</pre> </td> </tr> </table> <h3>Changes concerning the <a href="/docs/ptmlist">controlled vocabulary for PTMs</a></h3> <p>We are continuously overhauling the annotation of post-translational modifications (PTMs). For the feature key <a href="/manual/mod_res">MOD_RES</a>, the new introduced controlled vocabularies for PTMs are:</p> <ul> <li> <p>Hydroxylation: All entries with annotated hydroxylation sites have the keyword <a href="/keywords/KW-0379">Hydroxylation</a>.</p> <dl><dd> <pre> 4-hydroxyproline </pre> </dd> </dl> </li> <li> <p>Unidentified N-terminal blocking modifications:</p> <dl><dd> <pre> Blocked amino end (Asx) Blocked amino end (Xaa) </pre> </dd> </dl> </li> <li> <p>Other new controlled vocabularies for PTMs that are annotated with the feature key MOD_RES: </p> <dl><dd> <pre> Pros-8alpha-FAD-histidine (Keyword: <a href="/keywords/KW-0274">FAD</a>) N6-murein peptidoglycan lysine </pre> </dd> </dl> </li> </ul> </div> </div> UniProt release 2.2 - Welcome-新疆十一选五开奖结果Fri, 30 Jul 2004 //www.uniprot.org/news/2004/07/30/release &lt;span&gt;PTM controlled vocabularies&lt;/span&gt; <div> <div> <h2>UniProtKB News</h2> <h3>Changes concerning the <a href="/docs/ptmlist">controlled vocabulary for PTMs</a></h3> <p>We are continuously overhauling the annotation of post-translational modifications (PTMs). For the feature key <a href="/manual/mod_res">MOD_RES</a>, the new introduced controlled vocabularies for PTMs <a href="/docs/ptmlist">(PTMlist.txt)</a> are:</p> <ul> <li> <p>Methylation: All entries with annotated methylation sites have the keyword <a href="/keywords/KW-0488">Methylation</a>.</p> <dl><dd> <pre> N6,N6,N6-trimethyl-5-hydroxylysine N6-poly(methylaminopropyl)lysine </pre> </dd></dl> </li> <li> <p>Hydroxylation: All entries with annotated hydroxylation sites have the keyword <a href="/keywords/KW-0379">Hydroxylation</a>.</p> <dl><dd> <pre> 3-hydroxyproline 4-hydroxyarginine </pre> </dd> </dl> </li> <li> <p>Unidentified N-terminal blocking modifications:</p> <dl><dd> <pre> Blocked amino end (Leu) </pre> </dd> </dl> </li> <li> <p>Other new controlled vocabularies for PTMs that are annotated with the feature key MOD_RES: </p> <dl><dd> <pre> Glycine radical (Keyword: <a href="/keywords/KW-0556">Organic radical</a>) Pentaglycyl murein peptidoglycan amidated alanine (Keyword: <a href="/keywords/KW-0572">Peptidoglycan-anchor</a>) Tryptophylquinone </pre> </dd> </dl> </li> </ul> </div> </div> UniProt release 2.3 - Welcome-新疆十一选五开奖结果Mon, 16 Aug 2004 //www.uniprot.org/news/2004/08/16/release &lt;span&gt;New Reference (RL) line&lt;/span&gt; | Cross-references to PDB <div> <div> <h2>UniProtKB News</h2> <h3>New RL line structure for electronic publications</h3> <p>Electronic publications have been indicated in the RL line with the '(er)' prefix that stands for electronic resource:</p> <pre>RL <strong>(er)</strong> Free text.</pre> <p>Example:</p> <pre>RL (er) Plant Gene Register PGR98-023.</pre> <h3>Removal of the submission references to HIV data bank</h3> <p>We replaced all submission references to the HIV data bank by publications, thus RL lines of the type:</p> <pre>RL Submitted (XXX-YYYY) to the HIV data bank.</pre> <p><strong>do no longer exist</strong> in Swiss-Prot.</p> <h3>Change in cross-references to PDB</h3> <p>The structure determination method (X-ray, NMR, etc) as well as the mapping of the extent of the cross-reference on the sequence have been introduced as tertiary identifier to the PDB cross-reference line.</p> <p>Former format:</p> <pre>DR PDB; ENTRY_NAME; REVISION_DATE.</pre> <p><strong>New format:</strong></p> <pre><strong>DR PDB; ENTRY_NAME; Method; CHAIN[S]=RANGE.</strong></pre> <p>The methods are controlled vocabulary and currently include:</p> <ul> <li>X-ray (for X-ray crystallography)</li> <li>NMR (for NMR spectroscopy)</li> <li>EM (for electron microscopy and cryo-electron diffraction)</li> <li>Fiber (for fiber diffraction)</li> <li>IR (for infrared spectroscopy)</li> <li>Model (for predicted models)</li> <li>Neutron (for neutron diffraction)</li> </ul> <p>Example:</p> <pre>DR PDB; 1NB3; X-ray; A/B/C/D=116-335, P/R/S/T=98-105.</pre> <p>The tertiary identifier indicates the chain(s) and the corresponding range, of which the structure has been determined. If the range is unknown, a dash is given rather than the range positions. Example:</p> <pre>DR PDB; 1IYJ; X-ray; <strong>B/D=-.</strong></pre> <p>If the chains and the range is unknown, a dash is used. Example:</p> <pre>DR PDB; 1N12; X-ray; <strong>-</strong>.</pre> <p>With the introduction of the new format, DR PDB lines can become <strong>longer than 75 characters</strong>.</p> </div> </div> UniProt release 2.4 - Welcome-新疆十一选五开奖结果Tue, 31 Aug 2004 //www.uniprot.org/news/2004/08/31/release &lt;span&gt;1'500 cited journals&lt;/span&gt; | TrEMBL release notes <div> <div> <h2>Headlines</h2> <h3>1'500 cited journals</h3> <p>It is interesting to note that information relevant to the scope of Swiss-Prot is found in a continuously increasing number of <a href="/docs/jourlist">scientific journals</a>. Currently Swiss-Prot cites 1'500 different journals. Only 5 years ago, this number was slightly less than 1'000. Out of those 1'500 journals, 157 are either no longer published or have changed their names. It is also noteworthy that about 50% of these 1'500 journals are only cited less than four times in the knowledgebase. At the other extreme, only 106 journals are cited more than 100 times.</p> <h2>UniProtKB News</h2> <h3>Release notes: rnote_sp.html &amp; rnote_tr.html</h3> <p>The TrEMBL release notes (rnote_tr.html) were added to the <a href="/docs">documents distributed with the UniProtKB release</a>. The name of the Swiss-Prot release notes changed from relnotes.html to accordingly. These documents can all be downloaded from <a href="ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/docs/">ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/docs/</a>.</p> </div> </div> UniProt release 2.5 - Welcome-新疆十一选五开奖结果Mon, 13 Sep 2004 //www.uniprot.org/news/2004/09/13/release &lt;span&gt;Controlled vocabulary for PTMs&lt;/span&gt; <div> <div> <h2>UniProtKB News</h2> <h3>Changes concerning keywords </h3> <p>Deleted keyword:</p> <ul> <li>Parotid gland</li> </ul> <h3>Changes concerning the <a href="/docs/ptmlist">controlled vocabulary for PTMs</a></h3> <p>We are continuously overhauling the annotation of post-translational modifications (PTMs). For the feature key <a href="/manual/mod_res">MOD_RES</a>, the new introduced controlled vocabularies for PTMs are:</p> <ul> <li> <p>Flavin binding: All entries with annotated flavin-binding sites have the keyword <a href="/keywords/KW-0285">Flavoprotein</a>.</p> <dl><dd> <pre> FMN phosphoryl serine (Keyword: <a href="/keywords/KW-0288">FMN</a>) FMN phosphoryl threonine (Keyword: <a href="/keywords/KW-0288">FMN</a>) O-8alpha-FAD tyrosine (Keyword: <a href="/keywords/KW-0274">FAD</a>) S-4a-FMN cysteine (Keyword: <a href="/keywords/KW-0288">FMN</a>) S-6-FMN cysteine (Keyword: <a href="/keywords/KW-0288">FMN</a>) S-8alpha-FAD cysteine (Keyword: <a href="/keywords/KW-0274">FAD</a>) Tele-8alpha-FAD histidine (Keyword: <a href="/keywords/KW-0274" shape="rect">FAD</a>) Tele-8alpha-FMN histidine (Keyword: <a href="/keywords/KW-0288">FMN</a>) </pre> </dd></dl> </li> <li> <p>Hydroxylation: All entries with annotated hydroxylation sites have the keyword <a href="/keywords/KW-0379">Hydroxylation</a>.</p> <dl><dd> <pre> 4,5-dihydroxylysine 3,4-dihydroxyproline </pre> </dd></dl> </li> <li> <p>Other new controlled vocabularies for PTMs that are annotated with the feature key MOD_RES: </p> <dl><dd> <pre> O-(sn-1-glycerophosphoryl)serine </pre> </dd></dl> </li> </ul> </div> </div> UniProt release 2.6 - Welcome-新疆十一选五开奖结果Mon, 27 Sep 2004 //www.uniprot.org/news/2004/09/27/release <div> <div> <h2>UniProtKB News</h2> <h3>Changes concerning keywords </h3> <p>Deleted keyword:</p> <ul> <li>Connective tissue</li> <li>Eggshell</li> <li>Endothelial cell</li> <li>Eosinophil</li> </ul> </div> </div> UniProt release 2.7 - Welcome-新疆十一选五开奖结果Mon, 11 Oct 2004 //www.uniprot.org/news/2004/10/11/release &lt;span&gt;Cross-references to H-InvDB and WormBase&lt;/span&gt; <div> <div> <h2>UniProtKB News</h2> <h3>Cross-references to H-InvDB</h3> <p>Cross-references have been added to the human gene database <a href="//www.h-invitational.jp/">H-Invitational Database (H-InvDB)</a>, which provides information on annotated full-length cDNA clones available from six high throughput cDNA sequencing projects. The H-Invitational Database is available at <a href="//www.h-invitational.jp/">//www.h-invitational.jp/</a>.</p> <p>The format of the explicit links in the flat file is:</p> <table> <tr> <th>Resource abbreviation</th> <td>H-InvDB</td> </tr> <tr> <th>Resource identifier</th> <td>H-InvDB's unique identifier for a cDNA cluster.</td> </tr> <tr> <th>Example</th> <td> <pre><a href="//www.uniprot.org/uniprot/P78314#section_x-ref">P78314</a>: DR H-InvDB; HIX0004037; -.</pre> </td> </tr> </table> <h3>Cross-references to WormBase</h3> <p>We have added cross-references to <a href="//www.wormbase.org/">WormBase</a>, which provides information concerning the genetics, genomics and biology of <em>C. elegans</em> and some related nematodes. WormBase is available at <a href="//www.wormbase.org/">//www.wormbase.org/</a>.</p> <p>The identifiers of the appropriate DR line are:</p> <table> <tr> <th>Resource abbreviation</th> <td>WormBase</td> </tr> <tr> <th>Resource identifier</th> <td>WormBase's unique identifier for a gene.</td> </tr> <tr> <th>Optional information 1</th> <td>Gene designation.</td> </tr> <tr> <th>Example</th> <td><pre>DR WormBase; WBGene00006806; unc-74.</pre></td> </tr> </table> <h3>Changes concerning keywords </h3> <p>New keywords:</p> <ul> <li><a href="/keywords/KW-0909">Hibernation</a></li> <li><a href="/keywords/KW-0908">Parkinsonism</a></li> <li><a href="/keywords/KW-0907">Parkinson's disease</a></li> </ul> <p>Deleted keyword:</p> <ul> <li>Semen</li> <li>Yolk</li> </ul> </div> </div> UniProt release 3.0 - Welcome-新疆十一选五开奖结果Mon, 25 Oct 2004 //www.uniprot.org/news/2004/10/25/release &lt;span&gt;Major release&lt;/span&gt; | Release note document <div> <div> <h2>Headlines</h2> <h3>UniProtKB/Swiss-Prot major release (45.0)</h3> <p> Release 45.0 of Swiss-Prot contains 163'235 sequence entries, comprising 59'631'787 amino acids abstracted from 120'520 references. 6'183 sequences have been added since release 44, the sequence data of 2'851 existing entries has been updated and the annotations of 71'220 entries have been revised. This represents an increase of 4%.</p> <p> Many improvements were carried out in the last 3 months at the level of the DR, CC, KW and FT lines. </p> <p>UniProt Knowledgebase release 3.0 includes Swiss-Prot release 45.0 and TrEMBL release 28.0.</p> <p><a href="//www.expasy.org/txt/old-rel/relnotes.45.htm">Full statistics and release notes</a></p> <h2>UniProtKB News</h2> <h3>UniProtKB release notes: relnotes.html</h3> <p>With release 3.0 we introduce the UniProtKB release notes, which replaces the Swiss-Prot release notes (rnote_sp.html) and TrEMBL release notes (rnote_tr.html). The UniProtKB release notes includes the release statistics of both databases, the status of the model organisms and various other useful information. It can all be downloaded from <a href="ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/docs/">ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/docs/</a>.</p> <h3>Changes concerning keywords </h3> <p>New keywords:</p> <ul> <li><a href="/keywords/KW-0910">Bartter syndrome</a></li> </ul> </div> </div> UniProt release 3.1 - Welcome-新疆十一选五开奖结果Tue, 09 Nov 2004 //www.uniprot.org/news/2004/11/09/release &lt;span&gt;Conversion to mixed-case&lt;/span&gt; <div> <div> <h2>UniProtKB News</h2> <h3>Conversion of Swiss-Prot to mixed-case characters</h3> <p>The conversion of Swiss-Prot entries from all UPPER CASE to MiXeD CaSe is now completed. This modification does not apply to the following line types:</p> <ul> <li><a href="/manual/entry_name">ID</a> (IDentification) line</li> <li><a href="/manual/accession">AC</a> (ACcession number) line</li> <li><a href="/manual/references">RP</a> (Reference Position) line</li> <li><a href="/manual/sequences">SQ</a> (SeQuence) line</li> <li>Amino acid sequence</li> </ul> <h3>Changes concerning keywords </h3> <p>New keywords:</p> <ul> <li><a href="/keywords/KW-0911">Desmin-related myopathy</a></li> <li><a href="/keywords/KW-0912">Congenital muscular dystrophy</a></li> <li><a href="/keywords/KW-0913">Age-related macular degeneration</a></li> <li><a href="/keywords/KW-0914">Notch signaling pathway</a></li> </ul> </div> </div> UniProt release 3.2 - Welcome-新疆十一选五开奖结果Tue, 23 Nov 2004 //www.uniprot.org/news/2004/11/23/release &lt;span&gt;Major update of C.elegans entries&lt;/span&gt; | File Submit.txt removed <div> <div> <h2>Headlines</h2> <h3>Major update of C.elegans entries</h3> <p>We have recently finished a major update of Caenorhabditis elegans entries in Swiss-Prot. The following tasks were carried out:</p> <ul> <li>Update and "homogeneization" of all references to the genome project and sequence revisions;</li> <li>Addition of cross-references to WormBase;</li> <li>Re-annotation of many existing entries using literature references;</li> <li>Manual annotation of about one hundred new entries.</li> </ul> <h2>UniProtKB News</h2> <h3>Removal of the file submit.txt</h3> <p>The file submit.txt is no longer distributed. Information on how to submit sequence data, updates or corrections can be found in the <a href="/help/submissions">submissions and updates help</a>.</p> </div> </div>
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