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Sequence Analysis in a Nutshell: A Guide to Tools
A Guide to Common Tools and Databases
By Scott Markel, Darryl León
January 2003
Pages: 302
January 2003
Pages: 302
Cover | Table of Contents | Colophon
Table of Contents
- Chapter 1: FASTA Format
- Content preview·Buy PDF of this chapter|Buy reprint rights for this chapterThe most common sequence format you'll encounter is FASTA. This format is quite simple. The first line of a sequence entry consists of ">", followed by an identifier, which contains no whitespace. This can be followed by whitespace and a comment or description. This first line is referred to as the comment or description line. One or more sequence data lines may follow. The length of the sequence data lines may not be constant. Common line lengths are 60, 70, 72, and 80. For details, see Section 1.3 at the end of this chapter. Example 1-1 contains a sample FASTA entry.Example 1-1. Sample FASTA entry
>gi|29848|emb|X61622.1|HSCDK2MR H.sapiens CDK2 mRNA ATGGAGAACTTCCAAAAGGTGGAAAAGATCGGAGAGGGCACGTACGGAGTTGTGTACAAAGCCAGAAACA AGTTGACGGGAGAGGTGGTGGCGCTTAAGAAAATCCGCCTGGACACTGAGACTGAGGGTGTGCCCAGTAC TGCCATCCGAGAGATCTCTCTGCTTAAGGAGCTTAACCATCCTAATATTGTCAAGCTGCTGGATGTCATT CACACAGAAAATAAACTCTACCTGGTTTTTGAATTTCTGCACCAAGATCTCAAGAAATTCATGGATGCCT CTGCTCTCACTGGCATTCCTCTTCCCCTCATCAAGAGCTATCTGTTCCAGCTGCTCCAGGGCCTAGCTTT CTGCCATTCTCATCGGGTCCTCCACCGAGACCTTAAACCTCAGAATCTGCTTATTAACACAGAGGGGGCC ATCAAGCTAGCAGACTTTGGACTAGCCAGAGCTTTTGGAGTCCCTGTTCGTACTTACACCCATGAGGTGG TGACCCTGTGGTACCGAGCTCCTGAAATCCTCCTGGGCTCGAAATATTATTCCACAGCTGTGGACATCTG GAGCCTGGGCTGCATCTTTGCTGAGATGGTGACTCGCCGGGCCCTGTTCCCTGGAGATTCTGAGATTGAC CAGCTCTTCCGGATCTTTCGGACTCTGGGGACCCCAGATGAGGTGGTGTGGCCAGGAGTTACTTCTATGC CTGATTACAAGCCAAGTTTCCCCAAGTGGGCCCGGCAAGATTTTAGTAAAGTTGTACCTCCCCTGGATGA AGATGGACGGAGCTTGTTATCGCAAATGCTGCACTACGACCCTAACAAGCGGATTTCGGCCAAGGCAGCC CTGGCTCACCCTTTCTTCCAGGATGTGACCAAGCCAGTACCCCATCTTCGACTCTGATAGCCTTCTTGAA GCCCCCGACCCTAATCGGCTCACCCTCTCCTCCAGTGTGGGCTTGACCAGCTTGGCCTTGGGCTATTTGG ACTCAGGTGGGCCCTCTGAACTTGCCTTAAACACTCACCTTCTAGTCTTAACCAGCCAACTCTGGGAATA CAGGGGTGAAAGGGGGGAACCAGTGAAAATGAAAGGAAGTTTCAGTATTAGATGCACTTAAGTTAGCCTC CACCACCCTTTCCCCCTTCTCTTAGTTATTGCTGAAGAGGGTTGGTATAAAAATAATTTTAAAAAAGCCT TCCTACACGTTAGATTTGCCGTACCAATCTCTGAATGCCCCATAATTATTATTTCCAGTGTTTGGGATGA CCAGGATCCCAAGCCTCCTGCTGCCACAATGTTTATAAAGGCCAAATGATAGCGGGGGCTAAGTTGGTGC TTTTGAGAATTAAGTAAAACAAAACCACTGGGAGGAGTCTATTTTAAAGAATTCGGTTAAAAAATAGATC CAATCAGTTTATACCCTAGTTAGTGTTTTCCTCACCTAATAGGCTGGGAGACTGAAGACTCAGCCCGGGT GGGGGT
Additional content appearing in this section has been removed.
Purchase this book now or read it online at Safari to get the whole thing! - NCBI's Sequence Identifier Syntax
- Content preview·Buy PDF of this chapter|Buy reprint rights for this chapterThe National Center for Biotechnology Information (NCBI) uses the following syntax for its BLAST server. NCBI is part of the National Library of Medicine (NLM) at the National Institutes of Health (NIH). The following (including the table) is NCBI's description. See
ftp://ftp.ncbi.nih.gov/blast/db/READMEfor details.The syntax of sequence header lines used by the NCBI BLAST server depends on the database from which each sequence was obtained. The table below lists the identifiers for the databases from which the sequences were derived.Database nameIdentifier syntaxGenBankgb|accession|locusEMBL Data Libraryemb|accession|locusDDBJ, DNA Database of Japandbj|accession|locusNBRF PIRpir||entryProtein Research Foundationprf||nameSWISS-PROTsp|accession|entry nameBrookhaven Protein Data Bankpdb|entry|chainPatentspat|country|numberAdditional content appearing in this section has been removed.
Purchase this book now or read it online at Safari to get the whole thing! - NCBI's Non-Redundant Database Syntax
- Content preview·Buy PDF of this chapter|Buy reprint rights for this chapterYou should be aware of one additional syntax that's used by the NCBI for their non-redundant database. Since the whole point of the database is to have sequence entries listed only once, the description line syntax allows for more than one set of identifier and description. The sets are delimited by Ctrl-A characters. Here's what NCBI has to say about this.These files are all non-redundant; identical sequences are merged into one entry. To be merged two sequences must have identical lengths and every residue (or basepair) at every position must be the same. The FASTA deflines for the different entries that belong to one sequence are separated by control-A's (^A). In the following example, both entries gi|1469284 and gi|1477453 have the same sequence, in every respect.
>gi|1469284 (U05042) afuC gene product [Actinobacillus pleuropneumoniae]^Agi|1477453 (U04954) afuC gene product [Actinobacillus pleuropneumoniae] MNNDFLVLKNITKSFGKATVIDNLDLVIKRGTMVTLLGPSGCGKTTVLRLVAGLENPTSGQIFIDGEDVT KSSIQNRDICIVFQSYALFPHMSIGDNVGYGLRMQGVSNEERKQRVKEALELVDLAGFADRFVDQISGGQ QQRVALARALVLKPKVLILDEPLSNLDANLRRSMREKIRELQQRLGITSLYVTHDQTEAFAVSDEVIVMN KGTIMQKARQKIFIYDRILYSLRNFMGESTICDGNLNQGTVSIGDYRFPLHNAADFSVADGACLVGVRPE AIRLTATGETSQRCQIKSAVYMGNHWEIVANWNGKDVLINANPDQFDPDATKAFIHFTEQGIFLLNKE
Additional content appearing in this section has been removed.
Purchase this book now or read it online at Safari to get the whole thing! - References
- Content preview·Buy PDF of this chapter|Buy reprint rights for this chapter
-
Pearson, W.R., and D. J. Lipman. 1988. Improved Tools for Biological Sequence Analysis. Proceedings of teh National Academy of Sciences 85:2444-2448.
- NCBI Sequence Identifier Syntax
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ftp://ftp.ncbi.nih.gov/blast/db/README - Non-redundant database
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ftp://ftp.ncbi.nih.gov/blast/db/README
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Purchase this book now or read it online at Safari to get the whole thing! -
- Chapter 2: GenBank/EMBL/DDBJ
- Content preview·Buy PDF of this chapter|Buy reprint rights for this chapterGenBank is maintained by the National Center for Biotechnology Information (NCBI). It is joined by the DNA Data Bank of Japan (DDBJ, in Mishima, Japan) and the European Molecular Biology Laboratory (EMBL, in Heidelberg, Germany) nucleotide database from the European Bioinformatics Institute (EBI, in Hinxton, UK) to form the International Nucleotide Sequence Database Collaboration. Although the three repositories have separate sites for data submission, they share sequence data and allow daily downloads of sequence files by the public. We're using GenBank Release 132, EMBL Release 72, and DDBJ Release 51.Sequence flat files are frequently used in many software tools. GenBank, DDBJ, and EMBL each have their own specific flat file format. Flat files from each of these databases are shown in the next several sections, and these examples are used to illustrate the field definitions and the feature table sections for each repository. The sequence from cyclin-dependent kinase-2 (CDK2) is used as the example for all of the sequence flat file entries and the fasta file.Example 2-1 contains a sample sequence entry from GenBank. This entry contains terms from the GenBank Field Definitions and the DDBJ/EMBL/GenBank Feature Table, discussed later in this chapter.Example 2-1. Sample Genbank entry
LOCUS HSCDK2MR 1476 bp mRNA linear PRI 15-JAN-1992 DEFINITION H.sapiens CDK2 mRNA. ACCESSION X61622 VERSION X61622.1 GI:29848 KEYWORDS CDK2 gene; cell cycle regulation protein; cyclin A binding; protein kinase. SOURCE Homo sapiens (human) ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 1476) AUTHORS Elledge,S.J. and Spottswood,M.R. TITLE A new human p34 protein kinase, CDK2, identified by complementation of a cdc28 mutation in Saccharomyces cerevisiae, is a homolog of Xenopus Eg1 JOURNAL EMBO J. 10 (9), 2653-2659 (1991) MEDLINE 91330891 REFERENCE 2 (bases 1 to 1476) AUTHORS Elledge,S.J. TITLE Direct Submission JOURNAL Submitted (28-NOV-1991) S.J. Elledge, Dept. of Biochemistry, Baylor College of Medicine, 1 Baylor Place, Houston, TX 77030, USA FEATURES Location/Qualifiers source 1..1476 /organism="Homo sapiens" /db_xref="taxon:9606" /clone="pSE1000" /cell_line="EBV transformed Human peripheral lymphocyte (B-cell)" /clone_lib="lambda YES-R cDNA library" gene 1..1476 /gene="CDK2" CDS 1..897 /gene="CDK2" /function="protein kinase" /note="cell division kinase. CDC2 homolog" /codon_start=1 /protein_id="CAA43807.1" /db_xref="GI:29849" /db_xref="SWISS-PROT:P24941" /translation="MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGV PSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLP LIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYT HEVVTLWYRAPEILLGSKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRT LGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRIS AKAALAHPFFQDVTKPVPHLRL" BASE COUNT 368 a 372 c 351 g 385 t ORIGIN 1 atggagaact tccaaaaggt ggaaaagatc ggagagggca cgtacggagt tgtgtacaaa 61 gccagaaaca agttgacggg agaggtggtg gcgcttaaga aaatccgcct ggacactgag 121 actgagggtg tgcccagtac tgccatccga gagatctctc tgcttaagga gcttaaccat 181 cctaatattg tcaagctgct ggatgtcatt cacacagaaa ataaactcta cctggttttt 241 gaatttctgc accaagatct caagaaattc atggatgcct ctgctctcac tggcattcct 301 cttcccctca tcaagagcta tctgttccag ctgctccagg gcctagcttt ctgccattct 361 catcgggtcc tccaccgaga ccttaaacct cagaatctgc ttattaacac agagggggcc 421 atcaagctag cagactttgg actagccaga gcttttggag tccctgttcg tacttacacc 481 catgaggtgg tgaccctgtg gtaccgagct cctgaaatcc tcctgggctc gaaatattat 541 tccacagctg tggacatctg gagcctgggc tgcatctttg ctgagatggt gactcgccgg 601 gccctgttcc ctggagattc tgagattgac cagctcttcc ggatctttcg gactctgggg 661 accccagatg aggtggtgtg gccaggagtt acttctatgc ctgattacaa gccaagtttc 721 cccaagtggg cccggcaaga ttttagtaaa gttgtacctc ccctggatga agatggacgg 781 agcttgttat cgcaaatgct gcactacgac cctaacaagc ggatttcggc caaggcagcc 841 ctggctcacc ctttcttcca ggatgtgacc aagccagtac cccatcttcg actctgatag 901 ccttcttgaa gcccccgacc ctaatcggct caccctctcc tccagtgtgg gcttgaccag 961 cttggccttg ggctatttgg actcaggtgg gccctctgaa cttgccttaa acactcacct 1021 tctagtctta accagccaac tctgggaata caggggtgaa aggggggaac cagtgaaaat 1081 gaaaggaagt ttcagtatta gatgcactta agttagcctc caccaccctt tcccccttct 1141 cttagttatt gctgaagagg gttggtataa aaataatttt aaaaaagcct tcctacacgt 1201 tagatttgcc gtaccaatct ctgaatgccc cataattatt atttccagtg tttgggatga 1261 ccaggatccc aagcctcctg ctgccacaat gtttataaag gccaaatgat agcgggggct 1321 aagttggtgc ttttgagaat taagtaaaac aaaaccactg ggaggagtct attttaaaga 1381 attcggttaa aaaatagatc caatcagttt ataccctagt tagtgttttc ctcacctaat 1441 aggctgggag actgaagact cagcccgggt gggggt //Additional content appearing in this section has been removed.
Purchase this book now or read it online at Safari to get the whole thing! - Example Flat Files
- Content preview·Buy PDF of this chapter|Buy reprint rights for this chapterSequence flat files are frequently used in many software tools. GenBank, DDBJ, and EMBL each have their own specific flat file format. Flat files from each of these databases are shown in the next several sections, and these examples are used to illustrate the field definitions and the feature table sections for each repository. The sequence from cyclin-dependent kinase-2 (CDK2) is used as the example for all of the sequence flat file entries and the fasta file.Additional content appearing in this section has been removed.
Purchase this book now or read it online at Safari to get the whole thing! - GenBank Example Flat File
- Content preview·Buy PDF of this chapter|Buy reprint rights for this chapterExample 2-1 contains a sample sequence entry from GenBank. This entry contains terms from the GenBank Field Definitions and the DDBJ/EMBL/GenBank Feature Table, discussed later in this chapter.Example 2-1. Sample Genbank entry
LOCUS HSCDK2MR 1476 bp mRNA linear PRI 15-JAN-1992 DEFINITION H.sapiens CDK2 mRNA. ACCESSION X61622 VERSION X61622.1 GI:29848 KEYWORDS CDK2 gene; cell cycle regulation protein; cyclin A binding; protein kinase. SOURCE Homo sapiens (human) ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 1476) AUTHORS Elledge,S.J. and Spottswood,M.R. TITLE A new human p34 protein kinase, CDK2, identified by complementation of a cdc28 mutation in Saccharomyces cerevisiae, is a homolog of Xenopus Eg1 JOURNAL EMBO J. 10 (9), 2653-2659 (1991) MEDLINE 91330891 REFERENCE 2 (bases 1 to 1476) AUTHORS Elledge,S.J. TITLE Direct Submission JOURNAL Submitted (28-NOV-1991) S.J. Elledge, Dept. of Biochemistry, Baylor College of Medicine, 1 Baylor Place, Houston, TX 77030, USA FEATURES Location/Qualifiers source 1..1476 /organism="Homo sapiens" /db_xref="taxon:9606" /clone="pSE1000" /cell_line="EBV transformed Human peripheral lymphocyte (B-cell)" /clone_lib="lambda YES-R cDNA library" gene 1..1476 /gene="CDK2" CDS 1..897 /gene="CDK2" /function="protein kinase" /note="cell division kinase. CDC2 homolog" /codon_start=1 /protein_id="CAA43807.1" /db_xref="GI:29849" /db_xref="SWISS-PROT:P24941" /translation="MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGV PSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLP LIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYT HEVVTLWYRAPEILLGSKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRT LGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRIS AKAALAHPFFQDVTKPVPHLRL" BASE COUNT 368 a 372 c 351 g 385 t ORIGIN 1 atggagaact tccaaaaggt ggaaaagatc ggagagggca cgtacggagt tgtgtacaaa 61 gccagaaaca agttgacggg agaggtggtg gcgcttaaga aaatccgcct ggacactgag 121 actgagggtg tgcccagtac tgccatccga gagatctctc tgcttaagga gcttaaccat 181 cctaatattg tcaagctgct ggatgtcatt cacacagaaa ataaactcta cctggttttt 241 gaatttctgc accaagatct caagaaattc atggatgcct ctgctctcac tggcattcct 301 cttcccctca tcaagagcta tctgttccag ctgctccagg gcctagcttt ctgccattct 361 catcgggtcc tccaccgaga ccttaaacct cagaatctgc ttattaacac agagggggcc 421 atcaagctag cagactttgg actagccaga gcttttggag tccctgttcg tacttacacc 481 catgaggtgg tgaccctgtg gtaccgagct cctgaaatcc tcctgggctc gaaatattat 541 tccacagctg tggacatctg gagcctgggc tgcatctttg ctgagatggt gactcgccgg 601 gccctgttcc ctggagattc tgagattgac cagctcttcc ggatctttcg gactctgggg 661 accccagatg aggtggtgtg gccaggagtt acttctatgc ctgattacaa gccaagtttc 721 cccaagtggg cccggcaaga ttttagtaaa gttgtacctc ccctggatga agatggacgg 781 agcttgttat cgcaaatgct gcactacgac cctaacaagc ggatttcggc caaggcagcc 841 ctggctcacc ctttcttcca ggatgtgacc aagccagtac cccatcttcg actctgatag 901 ccttcttgaa gcccccgacc ctaatcggct caccctctcc tccagtgtgg gcttgaccag 961 cttggccttg ggctatttgg actcaggtgg gccctctgaa cttgccttaa acactcacct 1021 tctagtctta accagccaac tctgggaata caggggtgaa aggggggaac cagtgaaaat 1081 gaaaggaagt ttcagtatta gatgcactta agttagcctc caccaccctt tcccccttct 1141 cttagttatt gctgaagagg gttggtataa aaataatttt aaaaaagcct tcctacacgt 1201 tagatttgcc gtaccaatct ctgaatgccc cataattatt atttccagtg tttgggatga 1261 ccaggatccc aagcctcctg ctgccacaat gtttataaag gccaaatgat agcgggggct 1321 aagttggtgc ttttgagaat taagtaaaac aaaaccactg ggaggagtct attttaaaga 1381 attcggttaa aaaatagatc caatcagttt ataccctagt tagtgttttc ctcacctaat 1441 aggctgggag actgaagact cagcccgggt gggggt //Additional content appearing in this section has been removed.
Purchase this book now or read it online at Safari to get the whole thing! - DDBJ Example Flat File
- Content preview·Buy PDF of this chapter|Buy reprint rights for this chapterExample 2-2 contains a sample sequence entry from DDBJ. This entry contains terms from the DDBJ Field Definitions and the DDBJ/EMBL/GenBank Feature Table, discussed later in this chapter.Example 2-2. Sample DDBJ entry
LOCUS HSCDK2MR 1476 bp RNA linear HUM 15-JAN-1992 DEFINITION H.sapiens CDK2 mRNA. ACCESSION X61622 VERSION X61622.1 KEYWORDS CDK2 gene; cell cycle regulation protein; cyclin A binding; protein kinase. SOURCE human. ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 1476) AUTHORS Elledge,S.J. and Spottswood,M.R. TITLE A new human p34 protein kinase, CDK2, identified by complementation of a cdc28 mutation in Saccharomyces cerevisiae, is a homolog of Xenopus Eg1 JOURNAL EMBO J. 10, 2653-2659(1991). MEDLINE 91330891 REFERENCE 2 (bases 1 to 1476) AUTHORS Elledge,S.J. JOURNAL Submitted (28-NOV-1991) to the EMBL/GenBank/DDBJ databases. S.J. Elledge, Dept. of Biochemistry, Baylor College of Medicine, 1 Baylor Place, Houston, TX 77030, USA FEATURES Location/Qualifiers source 1..1476 /db_xref="taxon:9606" /organism="Homo sapiens" /cell_line="EBV transformed Human peripheral lymphocyte (B-cell)" /clone_lib="lambda YES-R cDNA library" /clone="pSE1000" CDS 1..897 /db_xref="SWISS-PROT:P24941" /note="cell division kinase. CDC2 homolog" /gene="CDK2" /function="protein kinase" /protein_id="CAA43807.1" /translation="MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVP STAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLI KSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEV VTLWYRAPEILLGSKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTP DEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAAL AHPFFQDVTKPVPHLRL" BASE COUNT 368 a 372 c 351 g 385 t ORIGIN 1 atggagaact tccaaaaggt ggaaaagatc ggagagggca cgtacggagt tgtgtacaaa 61 gccagaaaca agttgacggg agaggtggtg gcgcttaaga aaatccgcct ggacactgag 121 actgagggtg tgcccagtac tgccatccga gagatctctc tgcttaagga gcttaaccat 181 cctaatattg tcaagctgct ggatgtcatt cacacagaaa ataaactcta cctggttttt 241 gaatttctgc accaagatct caagaaattc atggatgcct ctgctctcac tggcattcct 301 cttcccctca tcaagagcta tctgttccag ctgctccagg gcctagcttt ctgccattct 361 catcgggtcc tccaccgaga ccttaaacct cagaatctgc ttattaacac agagggggcc 421 atcaagctag cagactttgg actagccaga gcttttggag tccctgttcg tacttacacc 481 catgaggtgg tgaccctgtg gtaccgagct cctgaaatcc tcctgggctc gaaatattat 541 tccacagctg tggacatctg gagcctgggc tgcatctttg ctgagatggt gactcgccgg 601 gccctgttcc ctggagattc tgagattgac cagctcttcc ggatctttcg gactctgggg 661 accccagatg aggtggtgtg gccaggagtt acttctatgc ctgattacaa gccaagtttc 721 cccaagtggg cccggcaaga ttttagtaaa gttgtacctc ccctggatga agatggacgg 781 agcttgttat cgcaaatgct gcactacgac cctaacaagc ggatttcggc caaggcagcc 841 ctggctcacc ctttcttcca ggatgtgacc aagccagtac cccatcttcg actctgatag 901 ccttcttgaa gcccccgacc ctaatcggct caccctctcc tccagtgtgg gcttgaccag 961 cttggccttg ggctatttgg actcaggtgg gccctctgaa cttgccttaa acactcacct 1021 tctagtctta accagccaac tctgggaata caggggtgaa aggggggaac cagtgaaaat 1081 gaaaggaagt ttcagtatta gatgcactta agttagcctc caccaccctt tcccccttct 1141 cttagttatt gctgaagagg gttggtataa aaataatttt aaaaaagcct tcctacacgt 1201 tagatttgcc gtaccaatct ctgaatgccc cataattatt atttccagtg tttgggatga 1261 ccaggatccc aagcctcctg ctgccacaat gtttataaag gccaaatgat agcgggggct 1321 aagttggtgc ttttgagaat taagtaaaac aaaaccactg ggaggagtct attttaaaga 1381 attcggttaa aaaatagatc caatcagttt ataccctagt tagtgttttc ctcacctaat 1441 aggctgggag actgaagact cagcccgggt gggggt //Additional content appearing in this section has been removed.
Purchase this book now or read it online at Safari to get the whole thing! - GenBank/DDBJ Field Definitions
- Content preview·Buy PDF of this chapter|Buy reprint rights for this chapterThe field terms found in GenBank/DDBJ sequence flat files are used to help organize the information for human readabilty and machine parsing. There are several GenBank/DDBJ field terms found in a sequence flat file, but the repositories themselves share the same field definitions. Table 2-1 summarizes each of the field definitions.
Table 2-1: GenBank/DDBJ field definitions FieldDescriptionLOCUSA short mnemonic name for the entry, chosen to suggest the sequence's definition. Mandatory keyword/exactly one record.DEFINITIONA concise description of the sequence. Mandatory keyword/one or more records.ACCESSIONThe primary accession number is a unique, unchanging code assigned to each entry. Mandatory keyword/one or more records.VERSIONA compound identifier consisting of the primary accession number and a numeric version number associated with the current version of the sequence data in the record. This is followed by an integer key (a "GI") assigned to the sequence by NCBI. Mandatory keyword/exactly one record.NIDAn alternative method of presenting the NCBI GI identifier (described above). The NID is obsolete and was removed from the GenBank flat file format in December 1999.Additional content appearing in this section has been removed.
Purchase this book now or read it online at Safari to get the whole thing! - EMBL Example Flat File
- Content preview·Buy PDF of this chapter|Buy reprint rights for this chapterExample 2-3 contains a sample sequence entry from EMBL. This entry contains terms from the EMBL Field Definitions and the DDBJ/EMBL/GenBank Feature Table, discussed later in this chapter.Example 2-3. Sample EMBL entry
ID HSCDK2MR standard; RNA; HUM; 1476 BP. XX AC X61622; XX SV X61622.1 XX DT 15-JAN-1992 (Rel. 30, Created) DT 15-JAN-1992 (Rel. 30, Last updated, Version 1) XX DE H.sapiens CDK2 mRNA XX KW CDK2 gene; cell cycle regulation protein; cyclin A binding; protein kinase. XX OS Homo sapiens (human) OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Primates; Catarrhini; Hominidae; Homo. XX RN [1] RP 1-1476 RX MEDLINE; 91330891. RA Elledge S.J., Spottswood M.R.; RT "A new human p34 protein kinase, CDK2, identified by complementation of a RT cdc28 mutation in Saccharomyces cerevisiae, is a homolog of Xenopus Eg1"; RL EMBO J. 10:2653-2659(1991). XX RN [2] RP 1-1476 RA Elledge S.J.; RT ; RL Submitted (28-NOV-1991) to the EMBL/GenBank/DDBJ databases. RL S.J. Elledge, Dept. of Biochemistry, Baylor College of Medicine, 1 Baylor RL Place, Houston, TX 77030, USA XX DR GDB; 128984; CDK2. DR SWISS-PROT; P24941; CDK2_HUMAN. XX FH Key Location/Qualifiers FH FT source 1..1476 FT /db_xref="taxon:9606" FT /organism="Homo sapiens" FT /cell_line="EBV transformed Human peripheral lymphocyte FT (B-cell)" FT /clone_lib="lambda YES-R cDNA library" FT /clone="pSE1000" FT CDS 1..897 FT /db_xref="SWISS-PROT:P24941" FT /note="cell division kinase. CDC2 homolog" FT /gene="CDK2" FT /function="protein kinase" FT /protein_id="CAA43807.1" FT /translation="MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVP FT STAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLI FT KSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEV FT VTLWYRAPEILLGSKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTP FT DEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAAL FT AHPFFQDVTKPVPHLRL" XX SQ Sequence 1476 BP; 368 A; 372 C; 351 G; 385 T; 0 other; atggagaact tccaaaaggt ggaaaagatc ggagagggca cgtacggagt tgtgtacaaa 60 gccagaaaca agttgacggg agaggtggtg gcgcttaaga aaatccgcct ggacactgag 120 actgagggtg tgcccagtac tgccatccga gagatctctc tgcttaagga gcttaaccat 180 cctaatattg tcaagctgct ggatgtcatt cacacagaaa ataaactcta cctggttttt 240 gaatttctgc accaagatct caagaaattc atggatgcct ctgctctcac tggcattcct 300 cttcccctca tcaagagcta tctgttccag ctgctccagg gcctagcttt ctgccattct 360 catcgggtcc tccaccgaga ccttaaacct cagaatctgc ttattaacac agagggggcc 420 atcaagctag cagactttgg actagccaga gcttttggag tccctgttcg tacttacacc 480 catgaggtgg tgaccctgtg gtaccgagct cctgaaatcc tcctgggctc gaaatattat 540 tccacagctg tggacatctg gagcctgggc tgcatctttg ctgagatggt gactcgccgg 600 gccctgttcc ctggagattc tgagattgac cagctcttcc ggatctttcg gactctgggg 660 accccagatg aggtggtgtg gccaggagtt acttctatgc ctgattacaa gccaagtttc 720 cccaagtggg cccggcaaga ttttagtaaa gttgtacctc ccctggatga agatggacgg 780 agcttgttat cgcaaatgct gcactacgac cctaacaagc ggatttcggc caaggcagcc 840 ctggctcacc ctttcttcca ggatgtgacc aagccagtac cccatcttcg actctgatag 900 ccttcttgaa gcccccgacc ctaatcggct caccctctcc tccagtgtgg gcttgaccag 960 cttggccttg ggctatttgg actcaggtgg gccctctgaa cttgccttaa acactcacct 1020 tctagtctta accagccaac tctgggaata caggggtgaa aggggggaac cagtgaaaat 1080 gaaaggaagt ttcagtatta gatgcactta agttagcctc caccaccctt tcccccttct 1140 cttagttatt gctgaagagg gttggtataa aaataatttt aaaaaagcct tcctacacgt 1200 tagatttgcc gtaccaatct ctgaatgccc cataattatt atttccagtg tttgggatga 1260 ccaggatccc aagcctcctg ctgccacaat gtttataaag gccaaatgat agcgggggct 1320 aagttggtgc ttttgagaat taagtaaaac aaaaccactg ggaggagtct attttaaaga 1380 attcggttaa aaaatagatc caatcagttt ataccctagt tagtgttttc ctcacctaat 1440 aggctgggag actgaagact cagcccgggt gggggt 1476 //Additional content appearing in this section has been removed.
Purchase this book now or read it online at Safari to get the whole thing! - EMBL Field Definitions
- Content preview·Buy PDF of this chapter|Buy reprint rights for this chapterThe field codes found in EMBL sequence flat files are used to help organize the information for human readability and machine-based parsing. There are several field codes found in an EMBL sequence flat file, and they are designated with a two-letter abbreviation. Table 2-2 summarizes the content of each field code.
Table 2-2: EMBL field definitions Line codeContentIDIdentificationACAccession number(s)SVNew sequence identifierDTDateDEDescriptionKWKeywordOSOrganism speciesOCOrganism classificationOGOrganelleRNReference numberRCReference comment(s)RPAdditional content appearing in this section has been removed.
Purchase this book now or read it online at Safari to get the whole thing! - DDBJ/EMBL/GenBank Feature Table
- Content preview·Buy PDF of this chapter|Buy reprint rights for this chapterIn February 1986, GenBank and EMBL (joined by DDBJ in 1987) started a collaborative effort to create a common feature table format. The overall objective of the feature table was to supply an in-depth vocabulary for describing nucleotide (and protein) features. We're using Version 4 of the feature table.A feature is a single word or abbreviation indicating a functional role or region associated with a sequence. A list of DDBJ/EMBL/GenBank features is presented in Table 2-3. In the Definition column of the table, the appropriate qualifiers for each feature are in brackets. Mandatory qualifiers are highlighted in bold.
Table 2-3: DDBJ/EMBL/GenBank feature key table Feature KeyDefinitionattenuator1) region of DNA at which regulation of termination of transcription occurs, which controls the expression of some bacterial operons.2) sequence segment located between the promoter and the first structural gene that causes partial termination of transcription.[citation, db_xref, evidence, gene, label, map, note, phenotype, usedin]C_regionConstant region of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains; includes one or more exons depending on the particular chain.[citation, db_xref, evidence, gene, label, map, note, product, pseudo, standard_name, usedin]Additional content appearing in this section has been removed.
Purchase this book now or read it online at Safari to get the whole thing! - References
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Tateno, Y., T. Imanishi, S. Miyazaki, K. Fukami-Kobayashi, N. Saitou, H. Sugawara, and T. Gojobori. 2002. DNA Data Bank of Japan (DDBJ) for genome scale research in life science. Nucleic Acids Research 30 (1):27-30.
- Main site
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http://www.ddbj.nig.ac.jp/ - Release notes
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http://www.ddbj.nig.ac.jp/ddbjnew/ddbj_relnote.html - Download
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ftp://ftp.ddbj.nig.ac.jp/database/ddbj/
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Stoesser, G., W. Baker, A. van den Broek, E. Camon, M. Garcia-Pastor, C. Kanz, T. Kulikova, R. Leinonen, Q. Lin, V. Lombard, R. Lopez, N. Redaschi, P. Stoehr, M. A. Tuli, K. Tzouvara, and R. Vaughan. 2002. The EMBL Nucleotide Sequence Database. Nucleic Acids Research 30 (1):21-26.
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- Chapter 3: SWISS-PROT
- Content preview·Buy PDF of this chapter|Buy reprint rights for this chapterSWISS-PROT is an annotated protein sequence database that was started in 1986. It is currently overseen by the Swiss Institute of Bioinformatics (SIB) in association with the European Bioinformatics Institute (EBI). SWISS-PROT is the preferred protein sequence database for most bioinformaticians because many of the sequence annotations are curated by scientists. TrEMBL, another sequence database, is a computer-annotated supplement that contains all the translations of EMBL nucleotide sequence entries not yet integrated in SWISS-PROT. It has essentially the same sequence flat file format as SWISS-PROT. We're using SWISS-PROT Release 40.Example 3-1 contains a sequence entry from SWISS-PROT. This entry contains terms from the SWISS-PROT Field Definitions and Feature Table types, discussed later in this chapter.Example 3-1. Sample SWISS-PROT sequence entry
ID CDK2_HUMAN STANDARD; PRT; 298 AA. AC P24941; DT 01-MAR-1992 (Rel. 21, Created) DT 01-AUG-1992 (Rel. 23, Last sequence update) DT 15-JUN-2002 (Rel. 41, Last annotation update) DE Cell division protein kinase 2 (EC 2.7.1.-) (p33 protein kinase). GN CDK2. OS Homo sapiens (Human). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. OX NCBI_TaxID=9606; RN [1] RP SEQUENCE FROM N.A. RX MEDLINE=91330891; PubMed=1714386; RA Elledge S.J., Spottswood M.R.; RT "A new human p34 protein kinase, CDK2, identified by complementation RT of a cdc28 mutation in Saccharomyces cerevisiae, is a homolog of RT Xenopus Eg1."; RL EMBO J. 10:2653-2659(1991). RN [2] RP SEQUENCE FROM N.A. RX MEDLINE=91367262; PubMed=1653904; RA Tsai L.-H., Harlow E., Meyerson M.; RT "Isolation of the human cdk2 gene that encodes the cyclin A- and RT adenovirus E1A-associated p33 kinase."; RL Nature 353:174-177(1991). RN [3] RP SEQUENCE FROM N.A. RX MEDLINE=92020980; PubMed=1717994; RA Ninomiya-Tsuji J., Nomoto S., Yasuda H., Reed S.I., Matsumoto K.; RT "Cloning of a human cDNA encoding a CDC2-related kinase by RT complementation of a budding yeast cdc28 mutation."; RL Proc. Natl. Acad. Sci. U.S.A. 88:9006-9010(1991). RN [4] RP SEQUENCE FROM N.A. RC TISSUE=Placenta; RA Strausberg R.; RL Submitted (FEB-2001) to the EMBL/GenBank/DDBJ databases. RN [5] RP PHOSPHORYLATION SITES. RX MEDLINE=93010995; PubMed=1396589; RA Gu Y., Rosenblatt J., O'Morgan D.O.; RT "Cell cycle regulation of CDK2 activity by phosphorylation of Thr160 RT and Tyr15."; RL EMBO J. 11:3995-4005(1992). RN [6] RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS). RX MEDLINE=93288132; PubMed=8510751; RA de Bondt H.L., Rosenblatt J., Jancarik J., Jones H.D., RA Morgan D.O., Kim S.-H.; RT "Crystal structure of cyclin-dependent kinase 2."; RL Nature 363:595-602(1993). RN [7] RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF COMPLEX WITH CYCLIN A. RX MEDLINE=95356811; PubMed=7630397; RA Jeffrey P.D., Russo A.A., Polyak K., Gibbs E., Hurwitz J., RA Massague J., Pavletich N.P.; RT "Mechanism of CDK activation revealed by the structure of a RT cyclinA-CDK2 complex."; RL Nature 376:313-320(1995). RN [8] RP X-RAY CRYSTALLOGRAPHY (2.33 ANGSTROMS) OF COMPLEX WITH L868276. RX MEDLINE=96181476; PubMed=8610110; RA de Azevedo W.F. Jr., Muleer-Dieckmann H.-J., Schulze-Gahmen U., RA Worland P.J., Sausville E., Kim S.-H.; RT "Structural basis for specificity and potency of a flavonoid RT inhibitor of human CDK2, a cell cycle kinase."; RL Proc. Natl. Acad. Sci. U.S.A. 93:2735-2740(1996). RN [9] RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF COMPLEX WITH CG2A AND KIP1. RX MEDLINE=96300318; PubMed=8684460; RA Russo A.A., Jeffrey P.D., Patten A.K., Massague J., Pavletich N.P.; RT "Crystal structure of the p27Kip1 cyclin-dependent-kinase inhibitor RT bound to the cyclin A-Cdk2 complex."; RL Nature 382:325-331(1996). RN [10] RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF COMPLEX WITH CG2A. RX MEDLINE=96313126; PubMed=8756328; RA Russo A.A., Jeffrey P.D., Pavletich N.P.; RT "Structural basis of cyclin-dependent kinase activation by RT phosphorylation."; RL Nat. Struct. Biol. 3:696-700(1996). RN [11] RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS). RX MEDLINE=97075215; PubMed=8917641; RA Schulze-Gahmen U., de Bondt H.L., Kim S.-H.; RT "High-resolution crystal structures of human cyclin-dependent kinase RT 2 with and without ATP: bound waters and natural ligand as guides for RT inhibitor design."; RL J. Med. Chem. 39:4540-4546(1996). RN [12] RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS). RX MEDLINE=97475219; PubMed=9334743; RA Lawrie A.M., Noble M.E.M., Tunnah P., Brown N.R., Johnson L.N., RA Endicott J.A.; RT "Protein kinase inhibition by staurosporine revealed in details of RT the molecular interaction with CDK2."; RL Nat. Struct. Biol. 4:796-801(1997). RN [13] RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF COMPLEX WITG CKS1. RX MEDLINE=96182647; PubMed=8601310; RA Bourne Y., Watson M.H., Hickey M.J., Holmes W., Rocque W., Reed S.I., RA Tainer J.A.; RT "Crystal structure and mutational analysis of the human CDK2 kinase RT complex with cell cycle-regulatory protein CksHs1."; RL Cell 84:863-874(1996). RN [14] RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS). RX MEDLINE=98342369; PubMed=9677190; RA Gray N.S., Wodicka L., Thunnissen A.-M.W.H., Norman T.C., Kwon S., RA Espinoza F.H., Morgan D.O., Barnes G., Leclerc S., Meijer L., RA Kim S.H., Lockhart D.J., Schultz P.G.; RT "Exploiting chemical libraries, structure, and genomics in the search RT for kinase inhibitors."; RL Science 281:533-538(1998). CC -!- FUNCTION: PROBABLY INVOLVED IN THE CONTROL OF THE CELL CYCLE. CC INTERACTS WITH CYCLINS A, D, OR E. ACTIVITY OF CDK2 IS MAXIMAL CC DURING S PHASE AND G2. CC -!- ENZYME REGULATION: PHOSPHORYLATION AT THR-14 OR TYR-15 INACTIVATES CC THE ENZYME, WHILE PHOSPHORYLATION AT THR-160 ACTIVATES IT. CC -!- SIMILARITY: BELONGS TO THE SER/THR FAMILY OF PROTEIN KINASES. CC CDC2/CDKX SUBFAMILY. CC -------------------------------------------------------------------------- CC This SWISS-PROT entry is copyright. It is produced through a collaboration CC between the Swiss Institute of Bioinformatics and the EMBL outstation - CC the European Bioinformatics Institute. There are no restrictions on its CC use by non-profit institutions as long as its content is in no way CC modified and this statement is not removed. Usage by and for commercial CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ CC or send an email to license@isb-sib.ch). CC -------------------------------------------------------------------------- DR EMBL; X61622; CAA43807.1; -. DR EMBL; X62071; CAA43985.1; -. DR EMBL; M68520; AAA35667.1; -. DR EMBL; BC003065; AAH03065.1; -. DR PIR; A41227; A41227. DR PIR; S16520; S16520. DR PIR; S17873; S17873. DR PDB; 1FIN; 27-JAN-97. DR PDB; 1HCK; 07-DEC-96. DR PDB; 1HCL; 07-DEC-96. DR PDB; 1AQ1; 12-NOV-97. DR PDB; 1JST; 11-JAN-97. DR PDB; 1JSU; 29-JUL-97. DR PDB; 1BUH; 09-SEP-98. DR PDB; 1B38; 23-DEC-98. DR PDB; 1B39; 23-DEC-98. DR PDB; 1CKP; 13-JAN-99. DR Genew; HGNC:1771; CDK2. DR MIM; 116953; -. DR InterPro; IPR000719; Euk_pkinase. DR InterPro; IPR002290; Ser_thr_pkinase. DR Pfam; PF00069; pkinase; 1. DR ProDom; PD000001; Euk_pkinase; 1. DR SMART; SM00220; S_TKc; 1. DR PROSITE; PS00107; PROTEIN_KINASE_ATP; 1. DR PROSITE; PS00108; PROTEIN_KINASE_ST; 1. DR PROSITE; PS50011; PROTEIN_KINASE_DOM; 1. KW Transferase; Serine/threonine-protein kinase; ATP-binding; KW Cell cycle; Cell division; Mitosis; Phosphorylation; 3D-structure. FT DOMAIN 4 286 PROTEIN KINASE. FT NP_BIND 10 18 ATP (BY SIMILARITY). FT BINDING 33 33 ATP (BY SIMILARITY). FT ACT_SITE 127 127 BY SIMILARITY. FT MOD_RES 14 14 PHOSPHORYLATION. FT MOD_RES 15 15 PHOSPHORYLATION. FT MOD_RES 160 160 PHOSPHORYLATION (BY CAK). FT MUTAGEN 14 14 T->A: INCREASE ACTIVITY 2 FOLD. FT MUTAGEN 15 15 Y->F: INCREASE ACTIVITY 2 FOLD. FT MUTAGEN 160 160 T->A: ABOLISHES ACTIVITY. FT TURN 2 3 FT STRAND 4 12 FT STRAND 17 23 FT TURN 24 26 FT STRAND 29 35 FT HELIX 46 55 FT TURN 56 57 FT TURN 61 62 FT STRAND 63 63 FT STRAND 66 72 FT TURN 73 74 FT STRAND 75 81 FT STRAND 85 86 FT HELIX 87 93 FT TURN 94 97 FT HELIX 101 120 FT TURN 121 122 FT HELIX 130 132 FT STRAND 133 135 FT TURN 137 138 FT STRAND 141 143 FT TURN 146 147 FT HELIX 148 151 FT STRAND 157 157 FT TURN 159 160 FT STRAND 163 163 FT TURN 167 168 FT HELIX 171 174 FT TURN 175 176 FT TURN 182 182 FT HELIX 183 198 FT HELIX 208 219 FT TURN 224 226 FT TURN 228 229 FT HELIX 230 232 FT TURN 234 235 FT TURN 238 239 FT HELIX 248 251 FT TURN 253 254 FT HELIX 257 266 FT TURN 267 267 FT TURN 271 273 FT HELIX 277 280 FT TURN 281 282 FT HELIX 284 286 FT TURN 287 288 SQ SEQUENCE 298 AA; 33929 MW; F90A0F4E70910B51 CRC64; MENFQKVEKI GEGTYGVVYK ARNKLTGEVV ALKKIRLDTE TEGVPSTAIR EISLLKELNH PNIVKLLDVI HTENKLYLVF EFLHQDLKKF MDASALTGIP LPLIKSYLFQ LLQGLAFCHS HRVLHRDLKP QNLLINTEGA IKLADFGLAR AFGVPVRTYT HEVVTLWYRA PEILLGCKYY STAVDIWSLG CIFAEMVTRR ALFPGDSEID QLFRIFRTLG TPDEVVWPGV TSMPDYKPSF PKWARQDFSK VVPPLDEDGR SLLSQMLHYD PNKRISAKAA LAHPFFQDVT KPVPHLRL //Additional content appearing in this section has been removed.
Purchase this book now or read it online at Safari to get the whole thing! - SWISS-PROT Example Flat File
- Content preview·Buy PDF of this chapter|Buy reprint rights for this chapterExample 3-1 contains a sequence entry from SWISS-PROT. This entry contains terms from the SWISS-PROT Field Definitions and Feature Table types, discussed later in this chapter.Example 3-1. Sample SWISS-PROT sequence entry
ID CDK2_HUMAN STANDARD; PRT; 298 AA. AC P24941; DT 01-MAR-1992 (Rel. 21, Created) DT 01-AUG-1992 (Rel. 23, Last sequence update) DT 15-JUN-2002 (Rel. 41, Last annotation update) DE Cell division protein kinase 2 (EC 2.7.1.-) (p33 protein kinase). GN CDK2. OS Homo sapiens (Human). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. OX NCBI_TaxID=9606; RN [1] RP SEQUENCE FROM N.A. RX MEDLINE=91330891; PubMed=1714386; RA Elledge S.J., Spottswood M.R.; RT "A new human p34 protein kinase, CDK2, identified by complementation RT of a cdc28 mutation in Saccharomyces cerevisiae, is a homolog of RT Xenopus Eg1."; RL EMBO J. 10:2653-2659(1991). RN [2] RP SEQUENCE FROM N.A. RX MEDLINE=91367262; PubMed=1653904; RA Tsai L.-H., Harlow E., Meyerson M.; RT "Isolation of the human cdk2 gene that encodes the cyclin A- and RT adenovirus E1A-associated p33 kinase."; RL Nature 353:174-177(1991). RN [3] RP SEQUENCE FROM N.A. RX MEDLINE=92020980; PubMed=1717994; RA Ninomiya-Tsuji J., Nomoto S., Yasuda H., Reed S.I., Matsumoto K.; RT "Cloning of a human cDNA encoding a CDC2-related kinase by RT complementation of a budding yeast cdc28 mutation."; RL Proc. Natl. Acad. Sci. U.S.A. 88:9006-9010(1991). RN [4] RP SEQUENCE FROM N.A. RC TISSUE=Placenta; RA Strausberg R.; RL Submitted (FEB-2001) to the EMBL/GenBank/DDBJ databases. RN [5] RP PHOSPHORYLATION SITES. RX MEDLINE=93010995; PubMed=1396589; RA Gu Y., Rosenblatt J., O'Morgan D.O.; RT "Cell cycle regulation of CDK2 activity by phosphorylation of Thr160 RT and Tyr15."; RL EMBO J. 11:3995-4005(1992). RN [6] RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS). RX MEDLINE=93288132; PubMed=8510751; RA de Bondt H.L., Rosenblatt J., Jancarik J., Jones H.D., RA Morgan D.O., Kim S.-H.; RT "Crystal structure of cyclin-dependent kinase 2."; RL Nature 363:595-602(1993). RN [7] RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF COMPLEX WITH CYCLIN A. RX MEDLINE=95356811; PubMed=7630397; RA Jeffrey P.D., Russo A.A., Polyak K., Gibbs E., Hurwitz J., RA Massague J., Pavletich N.P.; RT "Mechanism of CDK activation revealed by the structure of a RT cyclinA-CDK2 complex."; RL Nature 376:313-320(1995). RN [8] RP X-RAY CRYSTALLOGRAPHY (2.33 ANGSTROMS) OF COMPLEX WITH L868276. RX MEDLINE=96181476; PubMed=8610110; RA de Azevedo W.F. Jr., Muleer-Dieckmann H.-J., Schulze-Gahmen U., RA Worland P.J., Sausville E., Kim S.-H.; RT "Structural basis for specificity and potency of a flavonoid RT inhibitor of human CDK2, a cell cycle kinase."; RL Proc. Natl. Acad. Sci. U.S.A. 93:2735-2740(1996). RN [9] RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF COMPLEX WITH CG2A AND KIP1. RX MEDLINE=96300318; PubMed=8684460; RA Russo A.A., Jeffrey P.D., Patten A.K., Massague J., Pavletich N.P.; RT "Crystal structure of the p27Kip1 cyclin-dependent-kinase inhibitor RT bound to the cyclin A-Cdk2 complex."; RL Nature 382:325-331(1996). RN [10] RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF COMPLEX WITH CG2A. RX MEDLINE=96313126; PubMed=8756328; RA Russo A.A., Jeffrey P.D., Pavletich N.P.; RT "Structural basis of cyclin-dependent kinase activation by RT phosphorylation."; RL Nat. Struct. Biol. 3:696-700(1996). RN [11] RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS). RX MEDLINE=97075215; PubMed=8917641; RA Schulze-Gahmen U., de Bondt H.L., Kim S.-H.; RT "High-resolution crystal structures of human cyclin-dependent kinase RT 2 with and without ATP: bound waters and natural ligand as guides for RT inhibitor design."; RL J. Med. Chem. 39:4540-4546(1996). RN [12] RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS). RX MEDLINE=97475219; PubMed=9334743; RA Lawrie A.M., Noble M.E.M., Tunnah P., Brown N.R., Johnson L.N., RA Endicott J.A.; RT "Protein kinase inhibition by staurosporine revealed in details of RT the molecular interaction with CDK2."; RL Nat. Struct. Biol. 4:796-801(1997). RN [13] RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF COMPLEX WITG CKS1. RX MEDLINE=96182647; PubMed=8601310; RA Bourne Y., Watson M.H., Hickey M.J., Holmes W., Rocque W., Reed S.I., RA Tainer J.A.; RT "Crystal structure and mutational analysis of the human CDK2 kinase RT complex with cell cycle-regulatory protein CksHs1."; RL Cell 84:863-874(1996). RN [14] RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS). RX MEDLINE=98342369; PubMed=9677190; RA Gray N.S., Wodicka L., Thunnissen A.-M.W.H., Norman T.C., Kwon S., RA Espinoza F.H., Morgan D.O., Barnes G., Leclerc S., Meijer L., RA Kim S.H., Lockhart D.J., Schultz P.G.; RT "Exploiting chemical libraries, structure, and genomics in the search RT for kinase inhibitors."; RL Science 281:533-538(1998). CC -!- FUNCTION: PROBABLY INVOLVED IN THE CONTROL OF THE CELL CYCLE. CC INTERACTS WITH CYCLINS A, D, OR E. ACTIVITY OF CDK2 IS MAXIMAL CC DURING S PHASE AND G2. CC -!- ENZYME REGULATION: PHOSPHORYLATION AT THR-14 OR TYR-15 INACTIVATES CC THE ENZYME, WHILE PHOSPHORYLATION AT THR-160 ACTIVATES IT. CC -!- SIMILARITY: BELONGS TO THE SER/THR FAMILY OF PROTEIN KINASES. CC CDC2/CDKX SUBFAMILY. CC -------------------------------------------------------------------------- CC This SWISS-PROT entry is copyright. It is produced through a collaboration CC between the Swiss Institute of Bioinformatics and the EMBL outstation - CC the European Bioinformatics Institute. There are no restrictions on its CC use by non-profit institutions as long as its content is in no way CC modified and this statement is not removed. Usage by and for commercial CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ CC or send an email to license@isb-sib.ch). CC -------------------------------------------------------------------------- DR EMBL; X61622; CAA43807.1; -. DR EMBL; X62071; CAA43985.1; -. DR EMBL; M68520; AAA35667.1; -. DR EMBL; BC003065; AAH03065.1; -. DR PIR; A41227; A41227. DR PIR; S16520; S16520. DR PIR; S17873; S17873. DR PDB; 1FIN; 27-JAN-97. DR PDB; 1HCK; 07-DEC-96. DR PDB; 1HCL; 07-DEC-96. DR PDB; 1AQ1; 12-NOV-97. DR PDB; 1JST; 11-JAN-97. DR PDB; 1JSU; 29-JUL-97. DR PDB; 1BUH; 09-SEP-98. DR PDB; 1B38; 23-DEC-98. DR PDB; 1B39; 23-DEC-98. DR PDB; 1CKP; 13-JAN-99. DR Genew; HGNC:1771; CDK2. DR MIM; 116953; -. DR InterPro; IPR000719; Euk_pkinase. DR InterPro; IPR002290; Ser_thr_pkinase. DR Pfam; PF00069; pkinase; 1. DR ProDom; PD000001; Euk_pkinase; 1. DR SMART; SM00220; S_TKc; 1. DR PROSITE; PS00107; PROTEIN_KINASE_ATP; 1. DR PROSITE; PS00108; PROTEIN_KINASE_ST; 1. DR PROSITE; PS50011; PROTEIN_KINASE_DOM; 1. KW Transferase; Serine/threonine-protein kinase; ATP-binding; KW Cell cycle; Cell division; Mitosis; Phosphorylation; 3D-structure. FT DOMAIN 4 286 PROTEIN KINASE. FT NP_BIND 10 18 ATP (BY SIMILARITY). FT BINDING 33 33 ATP (BY SIMILARITY). FT ACT_SITE 127 127 BY SIMILARITY. FT MOD_RES 14 14 PHOSPHORYLATION. FT MOD_RES 15 15 PHOSPHORYLATION. FT MOD_RES 160 160 PHOSPHORYLATION (BY CAK). FT MUTAGEN 14 14 T->A: INCREASE ACTIVITY 2 FOLD. FT MUTAGEN 15 15 Y->F: INCREASE ACTIVITY 2 FOLD. FT MUTAGEN 160 160 T->A: ABOLISHES ACTIVITY. FT TURN 2 3 FT STRAND 4 12 FT STRAND 17 23 FT TURN 24 26 FT STRAND 29 35 FT HELIX 46 55 FT TURN 56 57 FT TURN 61 62 FT STRAND 63 63 FT STRAND 66 72 FT TURN 73 74 FT STRAND 75 81 FT STRAND 85 86 FT HELIX 87 93 FT TURN 94 97 FT HELIX 101 120 FT TURN 121 122 FT HELIX 130 132 FT STRAND 133 135 FT TURN 137 138 FT STRAND 141 143 FT TURN 146 147 FT HELIX 148 151 FT STRAND 157 157 FT TURN 159 160 FT STRAND 163 163 FT TURN 167 168 FT HELIX 171 174 FT TURN 175 176 FT TURN 182 182 FT HELIX 183 198 FT HELIX 208 219 FT TURN 224 226 FT TURN 228 229 FT HELIX 230 232 FT TURN 234 235 FT TURN 238 239 FT HELIX 248 251 FT TURN 253 254 FT HELIX 257 266 FT TURN 267 267 FT TURN 271 273 FT HELIX 277 280 FT TURN 281 282 FT HELIX 284 286 FT TURN 287 288 SQ SEQUENCE 298 AA; 33929 MW; F90A0F4E70910B51 CRC64; MENFQKVEKI GEGTYGVVYK ARNKLTGEVV ALKKIRLDTE TEGVPSTAIR EISLLKELNH PNIVKLLDVI HTENKLYLVF EFLHQDLKKF MDASALTGIP LPLIKSYLFQ LLQGLAFCHS HRVLHRDLKP QNLLINTEGA IKLADFGLAR AFGVPVRTYT HEVVTLWYRA PEILLGCKYY STAVDIWSLG CIFAEMVTRR ALFPGDSEID QLFRIFRTLG TPDEVVWPGV TSMPDYKPSF PKWARQDFSK VVPPLDEDGR SLLSQMLHYD PNKRISAKAA LAHPFFQDVT KPVPHLRL //Additional content appearing in this section has been removed.
Purchase this book now or read it online at Safari to get the whole thing! - SWISS-PROT Field Definitions
- Content preview·Buy PDF of this chapter|Buy reprint rights for this chapterThe field codes found in a SWISS-PROT (or TrEMBL) sequence flat file are used to help arrange the information for human readabilty and machine-based parsing. There are several SWISS-PROT field codes found in a sequence flat file; they are represented by two-letter abbreviations. Table 3-1 summarizes the contents of each field code.
Table 3-1: SWISS-PROT field definititions Line codeContentIDIdentificationACAccession number(s)DTDateDEDescriptionGNGene name(s)OSOrganism speciesOGOrganelleOCOrganism classificationOXTaxonomy cross-reference(s)RNReference numberRPReference positionAdditional content appearing in this section has been removed.
Purchase this book now or read it online at Safari to get the whole thing! - SWISS-PROT Feature Table
- Content preview·Buy PDF of this chapter|Buy reprint rights for this chapterA feature is a single word or abbreviation indicating a functional role or region associated with a sequence. A list of SWISS-PROT features (organized by feature type) is presented below. An example for each feature is also included to illustrate its use for describing a sequence location or region.
- CONFLICT
-
Different papers report differing sequences:
FT CONFLICT 304 304 MISSING (IN REF. 3).
- MUTAGEN
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Indicates an experimentally altered site:
FT MUTAGEN 65 65 H->F: 100% ACTIVITY LOSS.
- VARIANT
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Authors report that sequence variants exist:
FT VARIANT 136 136 M -> I.
- VARSPLIC
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Describes sequence variants produced by alternative splicing:
FT VARSPLIC 33 49 MISSING (IN SHORT ISOFORM).
- BINDING
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Binding site for chemical group (co-enzyme, prosthetic group, etc.):
FT BINDING 14 14 HEME (COVALENT).
- CARBOHYD
-
Glycosylation site:
FT CARBOHYD 53 53 N-LINKED (GLCNAC...) (POTENTIAL).
Additional content appearing in this section has been removed.
Purchase this book now or read it online at Safari to get the whole thing! - References
- Content preview·Buy PDF of this chapter|Buy reprint rights for this chapter
-
Bairoch, A., and R. Apweiler. 2000. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Research 28:45-48.
- Main page
-
http://us.expasy.org/sprot/ - Release notes
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http://us.expasy.org/sprot/relnotes/ - User manual
-
http://us.expasy.org/sprot/userman.html - Download
-
ftp://us.expasy.org/databases/swiss-prot
Additional content appearing in this section has been removed.
Purchase this book now or read it online at Safari to get the whole thing! -
- Chapter 4: Pfam
- Content preview·Buy PDF of this chapter|Buy reprint rights for this chapterWhile many databases are dedicated to organizing protein families and protein domains, Pfam is our preferred database for predicting the function of newly-discovered proteins. Pfam is unique in that it is a manually curated database of protein families derived from protein multiple sequence alignments and profile hidden Markow models. Pfam is a key database for understanding protein function and structure. It is used in many methods, including phylogenetic analysis, secondary structure prediction, and sequence annotation. We're using Pfam Release 7.8.Example 4-1 shows a Pfam flat file. This entry contains terms from the Pfam Field Definitions, discussed later in this chapter.Example 4-1. Sample Pfam example
# STOCKHOLM 1.0 #=GF ID 14-3-3 #=GF AC PF00244 #=GF DE 14-3-3 proteins #=GF AU Finn RD #=GF AL Clustalw #=GF SE Prosite #=GF GA 25 25 #=GF TC 35.40 35.40 #=GF NC 19.10 19.10 #=GF BM hmmbuild -f HMM SEED #=GF BM hmmcalibrate --seed 0 HMM #=GF RN [1] #=GF RM 95327195 #=GF RT Structure of a 14-3-3 protein and implications for #=GF RT coordination of multiple signalling pathways. #=GF RA Xiao B, Smerdon SJ, Jones DH, Dodson GG, Soneji Y, Aitken #=GF RA A, Gamblin SJ; #=GF RL Nature 1995;376:188-191. #=GF RN [2] #=GF RM 95327196 #=GF RT Crystal structure of the zeta isoform of the 14-3-3 #=GF RT protein. #=GF RA Liu D, Bienkowska J, Petosa C, Collier RJ, Fu H, Liddington #=GF RA R; #=GF RL Nature 1995;376:191-194. #=GF RN [3] #=GF RM 96182649 #=GF RT Interaction of 14-3-3 with signaling proteins is mediated #=GF RT by the recognition of phosphoserine. #=GF RA Muslin AJ, Tanner JW, Allen PM, Shaw AS; #=GF RL Cell 1996;84:889-897. #=GF RN [4] #=GF RM 97424374 #=GF RT The 14-3-3 protein binds its target proteins with a common #=GF RT site located towards the C-terminus. #=GF RA Ichimura T, Ito M, Itagaki C, Takahashi M, Horigome T, #=GF RA Omata S, Ohno S, Isobe T #=GF RL FEBS Lett 1997;413:273-276. #=GF RN [5] #=GF RM 96394689 #=GF RT Molecular evolution of the 14-3-3 protein family. #=GF RA Wang W, Shakes DC #=GF RL J Mol Evol 1996;43:384-398. #=GF RN [6] #=GF RM 96300316 #=GF RT Function of 14-3-3 proteins. #=GF RA Jin DY, Lyu MS, Kozak CA, Jeang KT #=GF RL Nature 1996;382:308-308. #=GF DR PROSITE; PDOC00633; #=GF DR SMART; 14_3_3; #=GF DR PRINTS; PR00305; #=GF DR SCOP; 1a4o; fa; #=GF DR PDB; 1a37 A; 3; 228; #=GF DR PDB; 1a37 B; 3; 228; #=GF DR PDB; 1a38 A; 3; 228; #=GF DR PDB; 1a38 B; 3; 228; #=GF DR PDB; 1a4o A; 3; 228; #=GF DR PDB; 1a4o B; 3; 228; #=GF DR PDB; 1a4o C; 3; 228; #=GF DR PDB; 1a4o D; 3; 228; #=GF DR PDB; 1qja B; 3; 229; #=GF DR PDB; 1qja A; 3; 230; #=GF DR PDB; 1qjb A; 3; 232; #=GF DR PDB; 1qjb B; 3; 232; #=GF DR INTERPRO; IPR000308; #=GF SQ 148 #=GS O61131/11-251 AC O61131 <deleted for brevity> #=GS 143Z_HUMAN/3-236 DR PDB; 1qjb B; 3; 232; O61131/11-251 RSDCTYRSKLAEQAERYDEMADAMRTLVEQCVnn....... dkdELTVEERNLLSVAYKNAVGARRASWRIISSVEQKEMSKA.NVHNKNIAATYRKKVEEELNNIC.QDILN. LLTKKLIPNT..SESESKVFYYKMKGDYYRYISEFS.CDE. GKKEASNFAQEAYQKATDIAENELPSTHPIRLGLALNYSVFFY..EILNQPHQACEMAKRAF...DDAIT