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Content and Report Formats:

Project Target ID

  • A unique identifier for the target sequence defined by each structural genomics center.

Examples:
  • WR90EC
  • NYSGRC-P007
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PDB ID

  • A unique 4 character alphanumeric identifier for the structure that has been deposited in Protein Data Bank (PDB).

Examples:
  • 1EKE
  • 1STZ
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PFAM ID

  • Protein domain accession number from PFAM.

Examples:
  • PF00005
  • PF00137
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Site

  • The Structural Genomics Center.

To search targets from a single Structural Genomics center, select one of the project sites from the list below.

The NIH Structural Genomics Centers: Other Projects: Asia: Europe:
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Status

  • The status of the target sequence.

Examples:
  • Selected
  • Cloned
  • Expressed
  • Soluble
  • Purified
  • Crystallized
  • Diffraction-quality Crystals
  • Diffraction
  • HSQC
  • NMR Assigned
  • Crystal Structure
  • NMR Structure
  • In PDB
  • Work Stopped
  • Test Target
  • Other
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Include Data From

  • The source of sequence data.

To search only target data provided by the NIH Structural Genomics Centers, select Only NIH Centers.
To include sequences from worldwide Structural Genomics Centers in a query, select All Structural Genomics Centers.
To include sequences from the Protein Data Bank (PDB) in a query, select All Structural Genomics Centers + PDB.
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Target Data Updated

  • The latest update of information on a target sequence. This includes update on any data associated with a target entry such as experimental status change, modifications to the protein sequence, external database references, etc. Please note that the date may not always represent the date when a target was deposited to the targetdb or the date of the latest experimental status. To query target experimental status history in the targetdb please use Target Status Summary Query Form. If you need help or have question about target status history please contact target-help@rcsb.rutgers.edu

Examples:
  • Before: 2001-05-10
  • After : 2001-01-21
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Protein Name

  • The name of the protein for the target sequence.

Examples:
  • Glutamate synthase
  • 29-C10
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Source Organism

  • The scientific name of the source organism for the target sequence.

Examples:
  • Arabidopsis thaliana
  • Escherichia coli
  • Caenorhabditis elegans
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Sequence

  • The one-letter code sequence for FASTA comparison

Examples: 
MKTIIALSYIFCLVFAQDLPGNDNNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGKICN
NPHRILDGINCTLIDALLGDPHCDGFQNEKWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFINE
GFNWTGVTQNGGSSACKRGPDSGFFSRLNWLYKSGSTYPVQNVTMPNNDNSDKLYIWGVHHPSTDKEQTN
LYVQASGKVTVSTKRSQQTIIPNVGSRPWVRGLSSRISIYWTIVKPGDILVINSNGNLIAPRGYFKMRTG
KSSI
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FASTA Sequence Comparison Details

  • [Pearson, W.R. and Lipman, D.J. Improved tools for biological sequence comparison.
    PNAS 85:2444-2448(1988)]
The E()-value cutoff limits the number of scores and alignments shown based on the expected number of scores. A cutoff value of 2.0 (-E 2.0) will show all library sequences with scores with an expectation value <= 2.0.

For protein searches, matched sequences with E()-values < 0.01 for searches of 10,000 protein sequences are almost always homologous. Frequently sequences with E()-values from 1 - 10 are related as well. However, E()-values also reflect differences between the amino acid composition of the query sequence and that of the "average" database sequence. Thus, when searches are done with query sequences with "biased" amino-acid composition, unrelated sequences may have "significant" scores because of sequence bias.

FASTA is available from ftp://ftp.virginia.edu/pub/fasta/.
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Report Formats

HTML Format

  • Features of selected targets are displayed in HTML format.

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FASTA Format

  • Sequences of selected targets are output in Pearson/FASTA format.

Examples: 
>Example 001| Protein Kinase (E.C.2.7.1.37) (cAPK) (Catalytic Subunit)
GNAAAAKKGSEQESVKEFLAKAKEDFLKKWETPSQNTAQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYA
MKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIGRFSE
PHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEII
LSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKR
FGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFTEF
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XML Format

  • Features of selected target sequences are output in XML format.

The XML report format follows the recommendations of the Task Force on Target Tracking. | DTD for the XML format

Example target: 
<target>
<id> Pfu-157236-001 </id>
<lab> Southeast Collaboratory for Structural Genomics </lab>
<date> 2001-06-18 </date>
<status> Proposed </status>
<status> Active Target </status>
<sequence>
 MLKIDLSGKLAFTTASSKGIGFGVAKVLAMAGADVIILSRNEENLKKAKEKIKEIADVNVEYIVADLTKKEDLER
 IVEVKNIGDPDIFFYSTGGPKPGYFMEMTMEDWEEAVKLLLYPAVYLTRALVPGMEKKGFGRIIYSTSVAIKEPI
 PNIALSNVVRISLAGLVRTLAKELGPKGITVNGIMPGIIRTDRVIQLAQDKARREGKSLEEALQDYAKPIPLGRL
 GEPEEIGYLVAFLSSELGSYINGAMIPVDGGRLNSVF  
</sequence>
<name> putative alcohol dehydrogenase/reductase </name> 
</target>
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