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   | UniProt Knowledgebase Swiss-Prot Protein Knowledgebase TrEMBL Protein Database What's new? Release 13.2 of 08-Apr-2008 |
Also read about forthcoming changes, the latest release statistics (Swiss-Prot, TrEMBL), Swiss-Prot headlines, and recent and forthcoming changes for the XML version of the UniProt Knowledgebase.
| UniProtKB release 13.2 of 08-Apr-2008 |
|---|
The document sec_ac.txt, available by ftp and on the Web site, lists all secondary accession numbers in UniProtKB (UniProtKB/Swiss-Prot and UniProtKB/TrEMBL), together with their corresponding current primary accession number(s).
Cross-references to the HIV have been removed.
Cross-references to the TRANSFAC have been removed.
New keywords:
| UniProtKB release 13.1 of 18-Mar-2008 |
|---|
Cross-references have been added to the Protein Mass spectra EXtraction database. ProMEX is a mass spectral library consisting of tryptic peptide product ion spectra generated by liquid chromatography coupled to ion trap mass spectrometry (LC-ITMS) and was developed using samples derived from Arabidopsis thaliana and Medicago truncatula. The database serves as a reference and can be used for protein identification in uncharacterized samples. Protein identification by ProMEX is linked to other molecular levels of biological organization such as metabolite, pathway and transcript data. The database is further connected to annotation and classification services.
The Protein Mass spectra EXtraction database is available at http://promex.mpimp-golm.mpg.de/.
The format of the explicit link is:
Data bank identifier ProMEX Primary identifier The primary identifier consists of a UniProtKB accession number. Secondary identifier None; a dash '-' is stored in that field. Examples
New keywords:
| UniProtKB release 13.0 of 26-Feb-2008 |
|---|
The non-standard amino acid selenocysteine was annotated with the feature key SE_CYS and represented by the one-letter code 'C' in the sequence. Pyrrolysines were annotated with the more generic feature key MOD_RES and represented by the one-letter code 'K' in the sequence. In order to annotate these and future non-standard amino acids in the same fashion, we replaced the feature key SE_CYS and the MOD_RES feature key used with the description Pyrrolysine with the new feature key NON_STD (non-standard) and the descriptions Selenocysteine and Pyrrolysine, as appropriate. At the same time, we changed the sequence to use the IUPAC/IUBMB recommended one-letter codes 'U' for selenocysteine and 'O' for pyrrolysine.
Previous annotation:
ID BTHD_DROME Reviewed; 249 AA.
..
FT SE_CYS 37 37
..
MPPKRNKKAE APIAERDAGE ELDPNAPVLY VEHCRSCRVF RRRAEELHSA LRERGLQQLQ
*
ID MTBB1_METAC Reviewed; 467 AA.
..
FT MOD_RES 356 356 Pyrrolysine (Probable).
..
RAVNFMKAAV QASPIPCHVD MGMGVGGIPM LETPPVDAVT RASKAMVEVA GVDGIKIGVG
*
New annotation:
ID BTHD_DROME Reviewed; 249 AA.
..
FT NON_STD 37 37 Selenocysteine.
..
MPPKRNKKAE APIAERDAGE ELDPNAPVLY VEHCRSURVF RRRAEELHSA LRERGLQQLQ
*
ID MTBB1_METAC Reviewed; 467 AA.
..
FT NON_STD 356 356 Pyrrolysine (Probable).
..
RAVNFMKAAV QASPIPCHVD MGMGVGGIPM LETPPVDAVT RASKAMVEVA GVDGIOIGVG
*
Cross-references have been added to the Phosphorylation site database. PhosphoSite is an expert-curated knowledgebase of information focused on protein phosphorylation mainly in vertebrates. In addition to phosphorylation sites curated from the literature, large numbers of new unpublished sites discovered by MS/MS analyses are being added regularly.
The Phosphorylation site database is available at http://phosphosite.cellsignal.com/.
The format of the explicit link is:
Data bank identifier PhosphoSite Primary identifier The primary identifier consists of a UniProtKB accession number. Secondary identifier None; a dash '-' is stored in that field. Examples
Cross-references have been added to the 2D-PAGE Database of Escherichia coli. The 2DBase-Ecoli database currently contains 12 gels consisting of 1185 protein spots information in which 723 proteins where identified and annotated. Individual protein spots in the existing gels can be displayed, queried, analysed and compared in a tabular format based on various functional categories enabling quick and subsequent analysis.
The 2D-PAGE Database of Escherichia coli is available at http://2dbase.techfak.uni-bielefeld.de/.
The format of the explicit link is:
Data bank identifier 2DBase-Ecoli Primary identifier The primary identifier consists of a UniProtKB accession number. Secondary identifier None; a dash '-' is stored in that field. Examples
New keywords:
New subcellular locations:
Terms introduced:
Terms for the feature key 'MOD_RES':
| UniProtKB release 12.8 of 05-Feb-2008 |
|---|
Cross-references have been added to the public repository of 2D-gel data World-2DPAGE. All 2D gel data to be published in the journal Proteomics needs to be available on the web. The World-2DPAGE repository hosts the data for resources who cannot build and maintain a web interface. There are currently two data sources submitted to World-2DPAGE, which are numbered consecutively:
The format of the explicit link is:
Data bank identifier World-2DPAGE Primary identifier The primary identifier is a combination of the database name and the accession number (usually from UniProtKB) in this database. Both are concatenated by a ":". Secondary identifier None; a dash '-' is stored in that field. Examples
In cross-references to Cornea-2DPAGE, DOSAC-COBS-2DPAGE, HSC-2DPAGE, REPRODUCTION-2DPAGE and SWISS-2DPAGE, the secondary identifier used to be the species origin. The species information has become obsolete/redundant since UniProtKB/Swiss-Prot no longer contains entries describing the same protein from different species (see Release 6.7). We have therefore removed the species information from these secondary identifiers and replaced them by "-".
Examples:
Previous format:
DR SWISS-2DPAGE; P04217; HUMAN. DR Cornea-2DPAGE; P04217; HUMAN. DR DOSAC-COBS-2DPAGE; P04217; HUMAN. DR REPRODUCTION-2DPAGE; P04217; HUMAN.
New format:
DR SWISS-2DPAGE; P04217; -. DR Cornea-2DPAGE; P04217; -. DR DOSAC-COBS-2DPAGE; P04217; -. DR REPRODUCTION-2DPAGE; P04217; -.
The document pkinfam.txt, available by ftp and on the Web site, provides the classification of human and mouse protein kinases into subfamilies or subgroups, as developed by Gerard Manning. The classification from Diego Miranda-Saavedra has also been taken into account.
This document contains all the human and mouse protein kinase UniProtKB/Swiss-Prot entries, subdivided into 10 subfamilies or subgroups. Each gene name is followed by the corresponding human and/or mouse 'UniProtKB/Swiss-Prot entry name (UniProtKB/Swiss-Prot accession number)'.
New keyword:
| UniProtKB release 12.7 of 15-Jan-2008 |
|---|
The UniProt Metagenomic and Environmental Sequences (UniMES) database is a repository specifically developed for metagenomic and environmental data. We now provide UniMES clusters, i.e. clustered sets of sequences, at two resolutions: 100% (unimes_cluster100.fasta) and >90% (unimes_cluster90.fasta). In unimes_cluster100.fasta, identical sequences and subfragments from unimes.fasta are placed into a single cluster. The unimes_cluster90.fasta is built by clustering unimes_cluster100.fasta representative sequences (the longest sequence in a cluster) using the CD-HIT algorithm (Li W., Jaroszewski L., and Godzik A., Bioinformatics, 17: 282-283, 2001) such that each cluster is composed of sequences that have at least 90% sequence identity, to the representative sequence. Only the representative sequences of the clusters are present in these files.
UniMES is available in the subdirectory current_release/unimes of the UniProt ftp servers ftp.uniprot.org/pub/databases/uniprot, ftp.ebi.ac.uk/pub/databases/uniprot and ftp.expasy.org/databases/uniprot.
The DictyBase database was renamed to dictyBase. We changed the database name in the relevant cross-references (DR lines) accordingly.
Example:
DR dictyBase; DDB0201569; manA.
Cross-references have been added to the PDBsum database. PDBsum provides an overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.
The PDBsum database is available at http://www.ebi.ac.uk/pdbsum.
The format of the explicit link is:
Data bank identifier PDBsum Primary identifier The primary identifier consists of a PDB entry name. Secondary identifier None; a dash '-' is stored in that field. Examples
Cross-references have been added to the Invertebrate Vectors of Human Pathogens database. VectorBase is a NIAID Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens. VectorBase annotates and maintains vector genomes providing an integrated resource for the research community.
The VectorBase database is available at http://www.vectorbase.org/index.php.
The format of the explicit link is:
Data bank identifier VectorBase Primary identifier The primary identifier consists of a VectorBase Gene ID. Secondary identifier The secondary identifier consists of a species name. Examples
There are 9 new documents for several Brucella, Rickettsia and Coxiella complete proteomes, listing all the UniProtKB/Swiss-Prot entries from these proteomes and their corresponding gene designations.
The documents contain, for each relevant UniProtKB/Swiss-Prot entry, the corresponding ordered locus name, entry name, accession number, sequence length and gene name(s).
New keywords:
Modified keywords:
New subcellular locations:
| UniProtKB release 12.6 of 04-Dec-2007 |
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Deleted keyword:
| UniProtKB release 12.5 of 13-Nov-2007 |
|---|
The ptmlist.txt document, which is available by ftp and on the Web site, describes the post-translational modifications (PTMs) that are annotated in UniProtKB/Swiss-Prot entries in the feature (FT) keys CROSSLNK, LIPID and MOD_RES. The document was in a format that is suitable for computer applications (e.g. ExPASy's proteomics tools) but which was not very human readable. The new file format should improve this.
Previous format:
N,N-dimethylproline MOD_RES P BB Nter C2H4 28.031300 28.06 in e:6446,7586,33682 Methylation FT=MOD_RES%20dimethylproline&wild=1 AA0066 MOD:00075
New format:
ID N,N-dimethylproline AC PTM-0179 FT MOD_RES TG Proline. PA Amino acid backbone. PP N-terminal. CF C2 H4 MM 28.031300 MA 28.06 LC Intracellular localisation. TR Eukaryota; taxId:6446 (Sipunculus nudus), taxId:7586 (Echinodermata), taxId:33682 (Euglenozoa). KW Methylation. DR RESID:AA0066. DR MOD:00075. //
With the following definitions of the line types:
--------- --------------------------- ----------------------
Line code Content Occurrence in an entry
--------- --------------------------- ----------------------
ID Identifier (FT description) Once; starts a PTM entry.
AC Accession (PTM-xxxx) Once.
FT Feature key Once.
TG Target Once; two targets separated
by a dash in case of intrachain
crosslinks.
PA Position of the modified Optional, once.
amino acid
PP Position of the modification Optional, once.
in the polypeptide
CF Correction formula Optional, once.
MM Monoisotopic mass difference Optional, once.
MA Average mass difference Optional, once.
LC Cellular location Optional, once; alternatives
can be proposed.
TR Taxonomic range Optional, once or more.
KW Keyword Optional, once or more.
DR Cross-reference to PTM Optional, once or more.
databases
// Terminator Once; ends an entry.
We added an additional field to the cross-reference (DR line) to the PDB database to show the resolution of structures that were determined by X-ray crystallography or electron microscopy.
For the chain names we use now the remediated data from wwPDB, therefore the chain names have changed for some entries.
Previous format:
DR PDB; ENTRY_NAME; METHOD; CHAIN.
New format:
DR PDB; ENTRY_NAME; METHOD; RESOLUTION; CHAIN.
Examples:
Q20728:DR PDB; 1LPL; X-ray; 1.77 A; A=135-229.Q5HEB7:
DR PDB; 2I8C; X-ray; 2.46 A; A/B=1-356.
A dash indicates that we found no information about the resolution or that the field is not applicable (for NMR structures and theoretical models).
Examples:
P02768:DR PDB; 2ESG; X-ray; -; C=25-609.P12872:
DR PDB; 1LBJ; NMR; -; A=26-47.P0AC41:
DR PDB; 2AD0; Model; -; A=1-588.
Cross-references have been added to the CleanEx database of gene expression profiles. CleanEx is a database which provides access to public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-dataset comparisons.
The CleanEx database is available at http://www.cleanex.isb-sib.ch/.
The format of the explicit link is:
Data bank identifier CleanEx Primary identifier The primary identifier consists of a combination of a species code and a gene identifier. Secondary identifier None; a dash '-' is stored in that field. Examples
Modified keywords:
| UniProtKB release 12.4 of 23-Oct-2007 |
|---|
The document subcell.txt, available by ftp and on the Web site, lists the controlled vocabularies used in the comment line (CC) topic SUBCELLULAR LOCATION, their definitions and further information such as synonyms or relevant GO terms in the following format:
--------- ------------------------------- ----------------------------------------------
Line code Content Occurrence in an entry
--------- ------------------------------- ----------------------------------------------
ID Identifier (location) Once; starts an entry
IT Identifier (topology) Once; starts a 'topology' entry
IO Identifier (orientation) Once; starts an 'orientation' entry
AC Accession (SL-xxxx) Once
DE Definition Once or more
SY Synonyms Optional; Once or more
SL Content of subc. loc. lines Once
HI Hierarchy ('is-a') Optional; Once or more
HP Hierarchy ('part-of') Optional; Once or more
KW Associated keyword (accession) Optional; Once or more
GO Gene ontology (GO) mapping Optional; Once or more
WW Interesting links or references Optional; Once or more
// Terminator Once; ends an entry
Example:
ID Cyanelle. AC SL-0082 DE A cyanelle is a photosynthetic organelle of glaucocystophyte algae. DE Cyanelles are surrounded by a double membrane and, in between, a DE peptidoglycan wall. Thylakoid membrane architecture and the presence DE of carboxysomes are cyanobacteria-like. Historically, the term DE cyanelle is derived from a classification as endosymbiotic DE cyanobacteria, and thus is not fully correct. SY Muroplast; Cyanoplast. SL Plastid, cyanelle. HI Plastid. KW KW-0194 GO GO:0009842; cyanelle //
We have structured the comment line topic SUBCELLULAR LOCATION in order to improve the consistency of annotation and to allow to parse its content.
The new format of SUBCELLULAR LOCATION is:
CC -!- SUBCELLULAR LOCATION:(( Molecule:)?( Location\.)+)?( Note=Free_text( Flag)?\.)?Where:
Subcellular_location( Flag)?(; Topology( Flag)?)?(; Orientation( Flag)?)?
\(By similarity|Probable|Potential\)Note: Perl-style multipliers indicate whether a pattern (as delimited by parentheses) is optional (?) or may occur 1 or more times (+). Alternative values are separated by a pipe symbol (|).
Examples:
P32755:CC -!- SUBCELLULAR LOCATION: Cytoplasm. Endoplasmic reticulum membrane; CC Peripheral membrane protein. Golgi apparatus membrane; Peripheral CC membrane protein.Q96QV1:
CC -!- SUBCELLULAR LOCATION: Cell membrane; Peripheral membrane protein CC (By similarity). Secreted (By similarity). Note=The last 22 C- CC terminal amino acids may participate in cell membrane attachment. CC -!- SUBCELLULAR LOCATION: Isoform 2: Cytoplasm (Probable).P35670:
CC -!- SUBCELLULAR LOCATION: Golgi apparatus, trans-Golgi network CC membrane; Multi-pass membrane protein (By similarity). CC Note=Predominantly found in the trans-Golgi network (TGN). Not CC redistributed to the plasma membrane in response to elevated CC copper levels. CC -!- SUBCELLULAR LOCATION: Isoform 2: Cytoplasm. CC -!- SUBCELLULAR LOCATION: WND/140 kDa: Mitochondrion.
EC numbers are used to describe enzyme reactions and are based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB). The EC numbers and the reactions they describe are stored in the ENZYME and IntEnz databases.
In the UniProt Knowledgebase some enzymes are assigned so-called partial EC numbers where part of the numbers are replaced by dashes (e.g. EC 3.4.24.-). This happens in the following situations:
To distinguish these two meanings, we have started to use the letter 'n' with a preliminary number instead of a dash '-' for the latter case. The retrofit of those existing EC numbers of proteins in UniProtKB that catalyze a reaction that is known, but not yet included in the IUBMB EC list will be an ongoing process.
Examples:
The catalytic activity of the protein is not known exactly:
Q9VAC5:DE ADAM 17-like protease precursor (EC 3.4.24.-).
The protein catalyzes a reaction that is known, but not yet included in the IUBMB's EC list:
Q9ES52:DE Phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 1 (EC 3.1.3.n1)
| UniProtKB release 12.3 of 02-Oct-2007 |
|---|
To be consistent with other comment line topics, we have changed the field tags of the topic MASS SPECTROMETRY. At the same time, we have extracted literature references into a new field, Source=, and replaced all molecule descriptions by isoform identifiers.
Previous format:
CC -!- MASS SPECTROMETRY: MW=mass(; MW_ERR=error)?; METHOD=method; RANGE=ranges( (molecule))?; NOTE=(references|free_text (references)).
New format:
CC -!- MASS SPECTROMETRY: Mass=mass(; Mass_error=error)?; Method=method; Range=ranges( (IsoformID))?(; Note=free_text)?; Source=references;
Examples:
P61409:Previous format:
CC -!- MASS SPECTROMETRY: MW=3979.9; METHOD=Electrospray; RANGE=1-31; CC NOTE=Ref.1, Ref.2.
New format:
CC -!- MASS SPECTROMETRY: Mass=3979.9; Method=Electrospray; Range=1-31; CC Source=Ref.1, Ref.2;P04653:
Previous format:
CC -!- MASS SPECTROMETRY: MW=23638.14; MW_ERR=3.0; METHOD=Electrospray; CC RANGE=16-214 (P04653-2; Allele A); NOTE=With eleven phosphate CC groups (Ref.2).
New format:
CC -!- MASS SPECTROMETRY: Mass=23638.14; Mass_error=3.0; Method=Electrospray; CC Range=16-214 (P04653-2); Note=Allele A, with 11 phosphate groups; CC Source=PubMed:7601973;
Note that literature references of the form Ref.n are replaced by PubMed identifiers where this is possible.
Cross-references have been added to the NCBI Reference Sequences database. The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products for taxonomically diverse organisms including eukaryotes, bacteria, and viruses. RefSeq is a baseline for medical, functional, and diversity studies; they provide a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses.
The RefSeq database is available at http://www.ncbi.nlm.nih.gov/RefSeq/.
The format of the explicit link is:
Data bank identifier RefSeq Primary identifier The primary identifier consists of a RefSeq protein accession ID. Secondary identifier None; a dash '-' is stored in that field. Examples
Cross-references have been added to the Database of genes from NCBI RefSeq genomes. Entrez Gene is the NCBI's database for gene-specific information. It does not include all known or predicted genes; instead Entrez Gene focuses on the genomes that have been completely sequenced, that have an active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. The content of Entrez Gene represents the result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. The content (nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases) is updated as new information becomes available. Entrez Gene is a step forward from NCBI's LocusLink, with both a major increase in taxonomic scope and improved access through the many tools associated with NCBI Entrez.
The GeneID database is available at http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene.
The format of the explicit link is:
Data bank identifier GeneID Primary identifier The primary identifier consists of a GeneID accession ID. Secondary identifier None; a dash '-' is stored in that field. Examples
We changed the name of the documentation file orysa.txt, which is an index of Oryza sativa subsp. japonica (rice) entries and their corresponding gene designations, to rice.txt
| UniProtKB release 12.2 of 11-Sep-2007 |
|---|
To be consistent with other comment line topics, we have changed the topic WEB RESOURCE from
CC -!- WEB RESOURCE: NAME=resource_name(; NOTE=free_text)?; URL="url".to
CC -!- WEB RESOURCE: Name=resource_name(; Note=free_text)?; URL="url";
The dbxref.txt file lists the names and abbreviations and URLs of all databases cross-referenced in the UniProt Knowledgebase. The jourlist.txt file lists the titles and abbreviations of all journals cited in the Swiss-Prot section of the UniProt Knowledgebase. We have added a new field, AC, to assign a stable identifier to each record in these files.
Examples:
dbxref.txt
AC : DB-0022 Abbrev: EMBL Name : EMBL nucleotide sequence database Ref : Nucleic Acids Res. 35:D16-D20(2007); PubMed=17148479; DOI=10.1093/nar/gkl913; LinkTp: Explicit Server: http://www.ebi.ac.uk/embl/ Db_URL: www.ebi.ac.uk/htbin/expasyfetch?%s Cat : Sequence databases
jourlist.txt
AC : JN-1120 Abbrev: J. Mol. Biol. Title : Journal of Molecular Biology ISSN : 0022-2836 e-ISSN: 1089-8638 CODEN : JMOBAK Short : JMB Publis: Elsevier Science Server: http://www.elsevier.com/locate/issn/00222836
| UniProtKB release 12.1 of 21-Aug-2007 |
|---|
We are changing our release cycle from 2 to 3 weeks, i.e. release 12.2 is going to be published on Sep 11th, 2007.
Cross-references to the RZPD-ProtExp have been removed.
| UniProtKB release 12.0 of 24-Jul-2007 |
|---|
Most protein sequences are derived from translations of gene predictions. Some of them exhibit strong sequence similarity to known proteins in closely related species. For other proteins there is experimental evidence, such as Edman sequencing, clear identification by mass spectrometry (MSI), X-ray or NMR structure, detection by antibodies, etc. To indicate these different levels of evidence for the existence of a protein, we have introduced the PE (Protein Existence) line.
Note that the PE line does not describe the accuracy or correctness of a sequence displayed in UniProtKB, but the evidence for the existence of a protein. It may happen that the protein sequence is not entirely accurate, especially for sequences derived from gene predictions from genomic sequences.
The format of the PE line is:
PE Level: Evidence;With the following values:
Example:
PE 1: Evidence at protein level;
The PE line appears between the DR and KW lines of UniProtKB entries.
The format of the RL line for submissions is:
RL Submitted (MMM-YYYY) to DatabaseName.
We have replaced the DatabaseName value Swiss-Prot by UniProtKB. The full list of valid DatabaseName values is now:
New keywords:
Modified keywords:
Deleted keyword:
| UniProtKB release 11.3 of 10-Jul-2007 |
|---|
Cross-references have been added to the PharmGKB database. PharmGKB curates information that establishes knowledge about the relationships among drugs, diseases and genes, including their variations and gene products. It is a repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.
The PharmGKB database is available at http://www.pharmgkb.org/.
The format of the explicit link is:
Data bank identifier PharmGKB Primary identifier The primary identifier consists of a PharmGKB accession ID. Secondary identifier None; a dash '-' is stored in that field. Example
New keyword:
| UniProtKB release 11.2 of 26-Jun-2007 |
|---|
New keyword:
Modified keywords:
Terms introduced:
Terms for the feature key 'CROSSLNK':
Terms for the feature key 'LIPID':
Terms for the feature key 'MOD_RES':
| UniProtKB release 11.1 of 12-Jun-2007 |
|---|
Cross-references have been added to the PeptideAtlas database. PeptideAtlas is a multi-organism, publicly accessible compendium of peptides that have been identified in a large set of tandem mass spectrometry proteomics experiments. All results of sequence searching have subsequently been processed through PeptideProphet to derive a probability of correct identification for all results in a uniform manner to insure a high quality database. All peptides have been mapped to Ensembl and can be viewed as custom tracks on the Ensembl Genome Browser.
The PeptideAtlas database is available at http://www.peptideatlas.org/.
The format of the explicit link is:
Data bank identifier PeptideAtlas Primary identifier The primary identifier consists of a UniProtKB accession number. Secondary identifier None; a dash '-' is stored in that field. Example
Cross-references have been added to the Database of Protein Disorder (DisProt). The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. DisProt is a collaborative effort between Center for Computational Biology and Bioinformatics at Indiana University School of Medicine and Center for Information Science and Technology at Temple University.
The DisProt database is available at http://www.disprot.org/.
The format of the explicit link is:
Data bank identifier DisProt Primary identifier The primary identifier consists of a DisProt accession number. Secondary identifier None; a dash '-' is stored in that field. Example
| UniProtKB release 11.0 of 29-May-2007 |
|---|
We are pleased to announce a new UniProt database. The UniProt Metagenomic and Environmental Sequences (UniMES) database is a repository specifically developed for metagenomic and environmental data. Currently the database contains only data from the Global Ocean Sampling Expedition (GOS). The environmental sample data contained within this database is not present in either the UniProt Knowledgebase or the UniProt Reference Clusters. UniMES is released in FASTA format and to add further value, we have collaborated with the InterPro team to provide a file containing InterPro matches to UniMES.
UniMES is available in the new subdirectory current_release/unimes of the UniProt ftp servers ftp.uniprot.org/pub/databases/uniprot, ftp.ebi.ac.uk/pub/databases/uniprot and ftp.expasy.org/databases/uniprot.
We have introduced the new CC line topic SEQUENCE CAUTION to describe protein sequence reports that differ from the sequence that is shown in UniProtKB due to conflicts that are not described in FT CONFLICT lines, such as frameshifts, erroneous gene model predictions, etc. This kind of information was before reported in the CC line topic CAUTION together with other warnings that are unrelated to sequence conflicts.
The format of the SEQUENCE CAUTION topic is:
CC -!- SEQUENCE CAUTION:
Sequence=Sequence; Type=Type;[ Positions=Positions;][ Note=Note;]
Where:
These lines are not wrapped and their length may therefore exceed 75 characters.
Examples:
Q93W20:Previous annotation: CC -!- CAUTION: Ref.2 (BAA97015) sequence differs from that shown due to CC erroneous gene model prediction. The predicted gene At5g49940 has CC been split into 2 genes: At5g49940 and At5g49945. New annotation: CC -!- SEQUENCE CAUTION: CC Sequence=BAA97015.1; Type=Erroneous gene model prediction; Note=The predicted gene At5g49940 has been split into 2 genes: At5g49940 and At5g49945;Q83M39:
Previous annotation: CC -!- CAUTION: Ref.1 and Ref.2 sequences differ from that shown due to a CC stop codon at position 273 which was translated as Gln to extend CC the sequence. New annotation: CC -!- SEQUENCE CAUTION: CC Sequence=AAN42076.1; Type=Erroneous termination; Positions=273; Note=Translated as Gln; CC Sequence=AAP15953.1; Type=Erroneous termination; Positions=273; Note=Translated as Gln;P17814:
Previous annotation: CC -!- CAUTION: Ref.1 (CAA36850) sequence differs from that shown due to CC a frameshift in position 496. CC -!- CAUTION: Ref.1 (CAA36850) sequence differs from that shown due to CC erroneous gene model prediction. New annotation: CC -!- SEQUENCE CAUTION: CC Sequence=CAA36850.1; Type=Erroneous gene model prediction; CC Sequence=CAA36850.1; Type=Frameshift; Positions=496;P0A7B3:
Previous annotation: CC -!- CAUTION: Ref.4 (X07863) sequence differs from that shown due to CC several frameshifts. CC -!- CAUTION: Ref.5 (Y00357) sequence differs from that shown due to CC frameshifts in positions 204, 215 and 282. New annotation: CC -!- SEQUENCE CAUTION: CC Sequence=X07863; Type=Frameshift; Positions=Several; CC Sequence=Y00357; Type=Frameshift; Positions=204, 215, 282;P27612:
Previous annotation: CC -!- CAUTION: Ref.2 (AAA39943) sequence differs from that shown due to CC frameshifts in positions 4, 32, and 42. CC -!- CAUTION: Ref.2 (AAA39943) sequence differs from that shown due to CC contaminating sequence. CC -!- CAUTION: Ref.3 sequence differs from that shown due to a CC frameshift in position 697. Current annotation: CC -!- SEQUENCE CAUTION: CC Sequence=AAA39943.1; Type=Miscellaneous discrepancy; Note=Several frameshifts and contaminating sequence; CC Sequence=Ref.3; Type=Frameshift; Positions=697;
From now on, the CC line topic SUBCELLULAR LOCATION may occur more than once per entry.
Cross-references have been added to the Pseudomonas aeruginosa Community Annotation Project database. This database provides genome annotation of P. aeruginosa strain PAO1 and of other Pseudomonas species, acting as a valuable comparative resource for P. aeruginosa research, as well as being useful for the larger Pseudomonas research community. Over the coming year this database will be further enhanced toward more focus on comparative analysis of P. aeruginosa isolates and more specific information about putative drug and vaccine targets.
The Pseudomonas aeruginosa Community Annotation Project database is available at http://www.pseudomonas.com/.
The format of the explicit link is:
Data bank identifier PseudoCAP Primary identifier The primary identifier consists of the ordered locus name. Secondary identifier None; a dash '-' is stored in that field. Example
Cross-references have been added to the Orphanet database. This database is dedicated to information on rare diseases and orphan drugs. It aims to improve management and treatment of genetic, auto-immune or infectious rare diseases, rare cancers, or not yet classified rare diseases. ORPHANET offers services adapted to the needs of patients and their families, health professionals and researchers, support groups and industry.
The Orphanet database is available at http://www.orpha.net/consor/cgi-bin/home.php?Lng=GB.
The format of the explicit link is:
Data bank identifier Orphanet Primary identifier The primary identifier consists of the Orpha unique disease identifier. Secondary identifier The secondary identifier consists of the name of the disease. Example
New keyword:
| UniProtKB release 10.4 of 01-May-2007 |
|---|
Modified keyword:
| UniProtKB release 10.2 of 03-Apr-2007 |
|---|
Cross-references have been added to the Mycobacterium ulcerans genome database. This database is dedicated to the analysis of the genome of Mycobacterium ulcerans, the Buruli ulcer bacillus: BuruList. BuruList provides a complete dataset of DNA and protein sequences derived from the epidemic strain Agy99, linked to the relevant annotations and functional assignments. It allows one to easily browse through these data and retrieve information, using various criteria (gene names, location, keywords, etc.).
The Mycobacterium ulcerans genome database is available at http://genolist.pasteur.fr/BuruList/.
The format of the explicit link is:
Data bank identifier BuruList Primary identifier The primary identifier consists of the ordered locus name. Secondary identifier None; a dash '-' is stored in that field. Example
New keyword:
| UniProtKB release 10.0 of 06-Mar-2007 |
|---|
The dbxref.txt file lists the names and abbreviations and URLs of all databases cross-referenced in the UniProt Knowledgebase. We have added a new optional field, "Ref". This field contains the database reference in the following format:
Ref : Journal_abbrev Volume:First_page-Last_page(YYYY); [PubMed=Pubmed_identifier; ][DOI=Digital_object_identifier;]
Example:
Abbrev: PROSITE Name : PROSITE; a protein domain and family database Ref : Nucleic Acids Res. 34:D227-D230(2006); PubMed=16381852; DOI=10.1093/nar/gkj063; LinkTp: Explicit Server: http://www.expasy.org/prosite/ Db_URL: www.expasy.org/cgi-bin/get-prosite-raw.pl?%s Cat : Family and domain databases
New keyword:
| UniProtKB release 9.7 of 20-Feb-2007 |
|---|
Cross-references have been added to the MIPS Comprehensive Yeast Genome Database. This database aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis.
The CYGD is available at http://mips.gsf.de/genre/proj/yeast.
The format of the explicit links is:
Data bank identifier CYGD Primary identifier The primary identifier consists of the ordered locus name. Example
We added the value Viral_cRNA to the controlled vocabulary of the field MoleculeType of the cross-references to the EMBL nucleotide sequence database. The format of the DR EMBL line is:
DR EMBL; AccessionNumber; ProteinID; StatusIdentifier; MoleculeType.
The controlled vocabulary of the field MoleculeType is:
New keyword:
| UniProtKB release 9.6 of 06-Feb-2007 |
|---|
Cross-references have been added to the Human Cornea 2-DE database, a two-dimensional polyacrylamide gel electrophoresis federated database available at the Aarhus University (Denmark).
The Cornea-2DPAGE is available at http://www.cornea-proteomics.com/.
The format for the explicit links is:
Data bank identifier Cornea-2DPAGE Primary identifier The primary identifier consists of a UniProtKB accession number. Secondary identifier The secondary identifier consists of the organism common name. Example
Cross-references have been added to the DOSAC-COBS 2D Page, a two-dimensional polyacrylamide gel electrophoresis federated database available at the DOSAC and COBS genome and proteome laboratory (La Maddalena, Italy).
The DOSAC-COBS-2DPAGE is available at http://www.dosac.unipa.it/2d/.
The format for the explicit links is:
Data bank identifier DOSAC-COBS-2DPAGE Primary identifier The primary identifier consists of a UniProtKB accession number. Secondary identifier The secondary identifier consists of the organism common name. Example
Cross-references have been added to the REPRODUCTION-2DPAGE, a two-dimensional polyacrylamide gel electrophoresis database available at the laboratory of Reproductive Medicine, Nanjing Medical University, P. R. China.
The REPRODUCTION-2DPAGE is available at http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi.
The format for the explicit links is:
Data bank identifier REPRODUCTION-2DPAGE Primary identifier The primary identifier consists of a UniProtKB accession number. Secondary identifier The secondary identifier consists of the organism common name. Example
| UniProtKB release 9.5 of 23-Jan-2007 |
|---|
The feature key INIT_MET indicates that there is experimental evidence that the initiator methionine has been cleaved off. In the past, the initiator methionine was not included in the sequence of an UniProtKB entry in such a case and the INIT_MET sequence coordinates were therefore 0.
Example:
FT INIT_MET 0 0
FT CHAIN 1 104 Cytochrome c.
FT /FTId=PRO_0000108218.
..
SQ SEQUENCE 104 AA; 11618 MW; D47C9B513DF1C5C2 CRC64;
GDVEKGKKIF IMKCSQCHTV EKGGKHKTGP NLHGLFGRKT GQAPGYSYTA ANKNKGIIWG
EDTLMEYLEN PKKYIPGTKM IFVGIKKKEE RADLIAYLKK ATNE
//
We have added back the initiator methionine to such protein sequences and changed the sequence coordinates of the feature key INIT_MET accordingly to 1.
Example:
FT INIT_MET 1 1
FT CHAIN 2 105 Cytochrome c.
FT /FTId=PRO_0000108218.
..
SQ SEQUENCE 105 AA; 11749 MW; 8EE9689E0102506B CRC64;
MGDVEKGKKI FIMKCSQCHT VEKGGKHKTG PNLHGLFGRK TGQAPGYSYT AANKNKGIIW
GEDTLMEYLE NPKKYIPGTK MIFVGIKKKE ERADLIAYLK KATNE
//
| UniProtKB release 9.4 of 09-Jan-2007 |
|---|
We changed the Data bank identifier for the Maize Genetics and Genomics Database MaizeGDB from MaizeDB to MaizeGDB.
Example:
DR MaizeDB; 58111; -.
has changed to
DR MaizeGDB; 58111; -.
New keyword:
| UniProtKB release 9.3 of 12-Dec-2006 |
|---|
The document protspot.txt, available by ftp and on the Web site, lists the Protein Spotlight articles and cited UniProtKB/Swiss-Prot entries.
This document contains, for each Protein Spotlight article, the corresponding entries cited in that article. Protein Spotlight (ISSN 1424-4721) is a monthly review written by the Swiss-Prot team of the Swiss Institute of Bioinformatics. Spotlight articles describe a specific protein or family of proteins on an informal tone. Protein Spotlight is available at: http://www.expasy.org/spotlight/.
Cross-references have been added to the Database of interacting proteins. The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data.
The DIP is available at http://dip.doe-mbi.ucla.edu/.
The format for the explicit links is:
Data bank identifier DIP Primary identifier The primary identifier consists of the DIP accession number. Secondary identifier None; a dash '-' is stored in that field. Examples
The primary identifier of the cross-references to the Reactome database has been modified. The primary identifier was a Reactome's unique identifier for a protein, which was identical to the Swiss-Prot primary AC number of that protein. Now it is a stable Reactome identifier. In addition, the pathway name is given as a secondary identifier.
Primary identifier The primary identifier consists of the Reactome identifier. Secondary identifier The secondary identifier consists of a Pathway name Examples
The primary identifier of the cross-references to the GermOnline database has been modified. The primary identifier was a GermOnline's identifier for a gene. Now it is a gene identifier from any source, e.g. Ensembl or model organism database. In addition, the organism name is the secondary identifier.
Primary identifier The primary identifier consists of a gene identifier from any source, e.g. Ensembl or model organism database. Secondary identifier The secondary identifier consists of the organism name Examples
New keywords:
Modified keyword:
| UniProtKB release 9.2 of 28-Nov-2006 |
|---|
Cross-references have been added to the Gene3D Structural and Functional Annotation of Protein Families database. Gene3D database provides a combined structural, functional and evolutionary view of the protein world. It is focussed on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species. The protein sequences have also been clustered into whole-chain families so as to aid functional prediction. The structural annotation is generated using HMM models based on the CATH domain families; CATH is a repository for manually deduced protein domains.
The Gene3D is available at http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/.
The format for the explicit links is:
Data bank identifier Gene3D Primary identifier The primary identifier consists of the Gene3D ID. Secondary identifier The secondary identifier consists of a Gene3D entry name Examples
New keyword:
| UniProtKB release 9.1 of 14-Nov-2006 |
|---|
Before release 9.1, UniProtKB accession numbers consisted of 6 alphanumerical characters in the following format:
1 2 3 4 5 6 [O,P,Q] [0-9] [A-Z, 0-9] [A-Z, 0-9] [A-Z, 0-9] [0-9]
Due to the large increase in the number of protein sequences in UniProtKB, we had to extend the existing accession number format by allowing the first character to be any of the 26 letters (instead of only O, P and Q). To avoid assigning accession numbers identical to those which have been used by the International Nucleotide Sequence Database, the extension in the first position goes along with a restriction in the third position which can only be a letter. The new format for UniProtKB accession numbers is therefore:
1 2 3 4 5 6 [A-N,R-Z] [0-9] [A-Z] [A-Z, 0-9] [A-Z, 0-9] [0-9] [O,P,Q] [0-9] [A-Z, 0-9] [A-Z, 0-9] [A-Z, 0-9] [0-9]
Cross-references have been added to the DrugBank database. The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains many drug entries including FDA-approved small molecule drugs, FDA-approved biotech (protein/peptide) drugs, nutraceuticals and experimental drugs. Additionally, protein (i.e. drug target) sequences are linked to these drug entries. Each DrugCard entry contains more than 80 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data.
The DrugBank database is available at http://redpoll.pharmacy.ualberta.ca/drugbank/.
The format for the explicit links is:
Data bank identifier DrugBank Primary identifier The primary identifier consists of the DrugBank ACcession number. Secondary identifier The secondary identifier consists of a generic name Examples
Cross-references have been added to the European Hepatitis C Virus database. The development of the European Hepatitis C Virus database (euHCVdb) started in 1999 as the French HCV Database. The euHCVdb is mainly oriented towards protein sequence, structure and function analyses and structural biology of HCV.
The European Hepatitis C Virus database is available at http://euhcvdb.ibcp.fr/euHCVdb/.
The format for the explicit links is:
Data bank identifier euHCVdb Primary identifier The primary identifier consists of an EMBL ACcession number. Examples
Explicit links are present in the FT VARIANT lines of protein sequence entries of Hominidae to the Single Nucleotide Polymorphism database (dbSNP). We will prefix dbSNP identifiers in human FT VARIANT lines by "rs". NCBI/dbSNP has rs and ss numbers, but we only refer to SNPs with rs numbers.
Examples:
P08185: FT VARIANT 246 246 S -> A (in dbSNP:rs2228541). FT /FTId=VAR_024350.
P06307: FT VARIANT 32 32 G -> E (in dbSNP:rs11571848). FT /FTId=VAR_018818. FT VARIANT 95 95 R -> W (in dbSNP:rs3774395). FT /FTId=VAR_024452.
| UniProtKB release 9.0 of 31-Oct-2006 |
|---|
The format of the ID line was:
ID EntryName DataClass; MoleculeType; SequenceLength.
We have changed the values of the DataClass field as described in this table:
Old DataClass New DataClass Description STANDARD Reviewed Entries that have been manually reviewed and annotated by UniProtKB curators (Swiss-Prot section of the UniProt Knowledgebase). PRELIMINARY Unreviewed Computer-annotated entries that have not been reviewed by UniProtKB curators (TrEMBL section of the UniProt Knowledgebase).
We have also dropped the field MoleculeType, which was a legacy of compatibility with the EMBL flat file format. The new format of the ID line is:
ID EntryName DataClass; SequenceLength.
Examples:
ID CYC_PIG Reviewed; 104 AA.
ID Q3ASY8_CHLCH Unreviewed; 36805 AA.
We have standardized the FASTA header line of UniProtKB and UniRef entries in the following way:
>UniqueIdentifier|EntryName ProteinName - OrganismName
Examples:
>P24856|ANP_NOTCO Ice-structuring glycoprotein (Fragment) - Notothenia coriiceps neglecta >P51650-1|SSDH_RAT Succinate semialdehyde dehydrogenase - Rattus norvegicus
>UniqueIdentifier Cluster: ClusterName; n=Members; Taxon|Rep: ProteinName - OrganismName
Example:
>UniRef50_P24856 Cluster: Ice-structuring glycoprotein (Fragment); n=15; Holacanthopterygii|Rep: Ice-structuring glycoprotein (Fragment) - Notothenia coriiceps neglecta
Cross-references have been added to the Human Protein Atlas. The Human Protein Atlas shows the expression and localization of proteins in a large variety of normal human tissues and cancer cells. The data is presented as high resolution images representing immunohistochemically stained tissue sections. Each antibody in the database has been used for immunohistochemical staining of both normal and cancer tissue. The immunohistochemical protocols used result in a brown-black staining, localized where an antibody has bound to its corresponding antigen.
The Human Protein Atlas is available at http://www.proteinatlas.org/.
The format for the explicit links is:
Data bank identifier HPA Primary identifier The primary identifier consists of the antibody identifier. Examples
The last field of the cross-references to the Gene Ontology (GO) database has been modified. This field displays the GO evidence code and we have appended to this the source database from which the cross-reference was obtained, separated by a colon.
Examples
New keyword:
| UniProtKB release 8.9 of 17-Oct-2006 |
|---|
Modified keywords:
Deleted keyword:
| UniProtKB release 8.7 of 19-Sep-2006 |
|---|
Cross-references have been added to the KEGG database. KEGG: Kyoto Encyclopedia of Genes and Genomes is part of the research projects of the Kanehisa Laboratories in the Bioinformatics Center of Kyoto University and the Human Genome Center of the University of Tokyo. The aim of this bioinformatics resource is to provide as far as possible a complete computer representation of the cell, the organism, and the biosphere, which will enable computational prediction of higher-level complexity of cellular processes and organism behaviors from genomic and molecular information.
The KEGG database is available at http://www.genome.jp/kegg/.
The format for the explicit links is:
Data bank identifier KEGG Primary identifier The primary identifier consists of a (KEGG-)organism code for the genome, colon, gene number. Examples
| UniProtKB release 8.6 of 05-Sep-2006 |
|---|
Cross-references have been added to the ArrayExpress , a public repository database for microarray gene expression data. The ArrayExpress Data Warehouse stores gene-indexed expression profiles from a curated subset of experiments in the repository.
The ArrayExpress database is available at http://www.ebi.ac.uk/arrayexpress/.
The format for the explicit links is:
Data bank identifier ArrayExpress Primary identifier UniProtKB primary AC. Example
Cross-references have been added to the PeroxiBase, a database which centralizes most of the peroxidase superfamilies encoding sequences, to follow the evolution of peroxidase among living organism and to compile the information concerning putative functions and transcription regulation.
The PeroxiBase database is available at http://peroxidase.isb-sib.ch/.
The format for the explicit links is:
Data bank identifier PeroxiBase Primary identifier PeroxiBase's accession number. Secondary identifier PeroxiBase's entry name Example
New keyword:
Terms introduced:
Terms for the feature key 'CROSSLNK':
Terms for the feature key 'LIPID':
Terms for the feature key 'MOD_RES':
| UniProtKB release 8.4 of 25-Jul-2006 |
|---|
The qualifier 'LARGE SCALE ANALYSIS' was added in RP lines for references that report large screen results to indicate that results have not been extensively studied.
P33304: RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-22, AND MASS RP SPECTROMETRY.
| UniProtKB release 8.3 of 11-Jul-2006 |
|---|
Deleted keyword:
| UniProtKB release 8.2 of 27-June-2006 |
|---|
The document orysa.txt, available by