TargetTrack | Description of TargetTrack Search Options

Biological Search Options Experimental Search Options Ownership Search Options
Sequence Reported Progress Project Target ID
Cutoff E-Value Materials Available Centers
Source Organism Trial Stop Status PSI:Biology Partnerships
Macromolecule Name Protocol Used Project
Database ID Target Updated Result Format
Target Category

Biological Search Options

Sequence

The IUPAC one-letter code sequence of a target, for FASTA comparison.

Example:
MKTIIALSYIFCLVFAQDLPGNDNNSTATLCLGHH
AVPNGTLVKTITNDQIEVTNATELVQSSSTGKICN
NPHRILDGINCTLIDALLGDPHCDGFQNEKWDLFV
ERSKAFSNCYPYDVPDYASLRSLVASSGTLEFINE
GFNWTGVTQNGGSSACKRGPDSGFFSRLNWLYKSG
STYPVQNVTMPNNDNSDKLYIWGVHHPSTDKEQTN
LYVQASGKVTVSTKRSQQTIIPNVGSRPWVRGLSS
RISIYWTIVKPGDILVINSNGNLIAPRGYFKMRTG
KSSI

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Cutoff E-Value

It is useful, particularly when searching large databases, to know how likely (or rather unlikely) it is that an alignment could arise by chance. BLAST gives some measure of this with the E-value it supplies with each alignment.

As an example, "Expect = 1e-63" tells us that, at least as an approximation, the chance of an alignment as good or better than this occurring by chance is tiny (1e-63). By default BLAST shows alignments with E-values up to and including 10. An alignment with an E-value this high does not, in itself, mean very much as it is expected for the search to throw up around 10 matches of this quality or better purely by chance. (From http://www.clarkfrancis.com/blast/)

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Source Organism

Autocomplete text search for the scientific name of the source organism from which a target sequence originated. Enter in the first few letters of a species to see what exists in the database. Continue typing to narrow your results and/or select an option from the resulting drop-down list.

TargetTrack requests depositions follow the nomenclature of the NCBI Taxonomy database.

Examples:
  • Arabidopsis thaliana
  • Escherichia coli
  • Caenorhabditis elegans

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Macromolecule Name

Autocomplete text search for the name of the protein or nucleic acid that a target macromolecule sequence generates.

Examples:
  • transmembrane protein
  • glutamate synthase
  • 29-C10

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Database ID

TargetTrack recognizes the sequence identifiers from a number of key biological resources, including the Protein Data Bank, UniProt, CATH, Pfam, GenBank, etc. (see table below for full list of possible databases). Enter in a database id of interest to see if any targets have been linked to that identifier.

Examples:
Database Name Database ID (what to enter)
PDB 2I9Y
UniProt Q53004
Pfam PF00005

Databases Found in TargetTrack:
  • BMRB
  • CATH
  • Ensembl
  • GenBank
  • GeneDB
  • GeneOntology
  • InterPro
  • NCBI
  • PDB
  • Pfam
  • PharmGKB
  • PlasmoDB
  • TIGR
  • UniProt
  • WormBase

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Target Category

Each target is registered as falling within a research-focus category. See drop-down list for current categories.

Select one or more target category values to customize your query.

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Experimental Search Options

Reported Progress

Any experimental progress reported for a target. Currently accepted target status milestones are given as drop-down options.

Select one or more status values to obtain all targets that have reached that status in one or more of their trials. This query is useful when searching for targets that have reached a particular milestone and may be further along the production pipeline.

For example, select 'expressed' to return all targets that have been successfully expressed, without concern for their current production status.

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Materials Available

Return targets that have experimental material available for use.

Clones Available - returns targets with one or more clones available at the PSI:Biology-Materials Repository.

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Trial Stop Status

Return targets that have one or more trials with the selected stop status. For example, select 'purification failed' for targets where protein cannot be isolated using attempted techniques. You can use this option to look for methods that led to unsuccessful returns so that you don't make the same mistakes in the lab.

Select one or more stop status values to customize your query.

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Protocol Used

The type of protocol provided in one or more trials of a target. Currently accepted protocol types are given as drop-down options.

Select one or more protocol type values to return targets that have the selected protocol types reported in one or more trials.

For example, select 'purification' to return targets which contain a purification protocol in their reported progress.

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Target Updated

Returns targets that have been updated during the timeframe selected. The latest update of information on a target could include an update on any data associated with a target entry such as an experimental status change, modifications to the protein sequence, changes to external database references, etc.

Please note that the date may not always represent the date when a target was deposited to TargetTrack or the date of the latest experimental status. If you need help or have question about target status history, please contact target-help@sbkb.org

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Ownership Search Options

Project Target ID

A unique identifier for the target sequence, defined by the contributing center.

Examples:
  • JCSG-421578
  • MCSG-APC90108
  • NESG-WR90EC
  • NYSGRC-010702

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Centers

The structural biology center or group of centers responsible for a set of targets.
View the contributing centers page for the full name and website of all current and former contributors.

The first three options select targets from the following groups of centers:

  • All Structural Biology Centers - all centers who have deposited target information
  • All PSI Centers - all PSI centers (see table below)
  • All PSI Large Scale Production Centers - JCSG, MCSG, NESG, NYSGRC/NYSGXRC
Select one of the three provided groupings (All centers, PSI only, PSI large scale only) and/or one or more center name to customize your query. PSI centers and the phases they participated in are listed below.

PSI Center PSI Project
ATCG3D PSI-2
BSGC PSI-1
CESG PSI-1, PSI-2
CHTSB PSI-2
CSMP PSI-2, PSI:Biology
GPCR PSI:Biology
ISFI PSI-2
JCSG PSI-1, PSI-2, PSI:Biology
MCSG PSI-1, PSI-2, PSI:Biology
MPID PSI:Biology
MPP PSI:Biology
MPSBC PSI:Biology
MPSbyNMR PSI:Biology
NatPro PSI:Biology
NESG PSI-1, PSI-2, PSI:Biology
NYCOMPS PSI-2, PSI:Biology
NYSGRC PSI:Biology
NYSGXRC PSI-1, PSI-2
SECSG PSI-1
SGPP PSI-1
TBSGC PSI-1
TEMIMPS PSI:Biology
TMPC PSI:Biology
TransportPDB PSI:Biology

 

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PSI:Biology Partnerships

View targets from high-throughput (HT) enabled structural biology partnerships in the PSI:Biology program.

Targets selected here are provided by the HT partner. If available, targets provided directly by a partnership group can be selected in the Contributing Centers drop-down menu.

Currently available partnerships are listed below by project short name.

Short Name Full Name HT Partner
CEBS Chaperone-Enabled Studies of Epigenetic Regulation Enzymes NESG
CELLMAT Assembly, Dynamics and Evolution of Cell-Cell and Cell-Matrix Adhesions NYSGRC
CHSAM Structure, Dynamics and Activation Mechanisms of Chemokine Receptors GPCR
HOMEO Structural Basis of Protein Homeostasis NESG
IFN Atoms-to-Animals: The Immune Function Network NYSGRC
MPP Mitochondrial Protein Partnership NESG
MTBI Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors MCSG
NatPro Enzyme Discovery for Natural Product Biosynthesis MCSG
NHRs Structural Features of the Nuclear Receptor Signaling Code JCSG
NPCXstals Nucleocytoplasmic Transport: a Target for Cellular Control NYSGRC
PCSEP Program for the Characterization of Secreted Effector Proteins MCSG
STEMCELL Partnership for Stem Cell Biology JCSG
TCELL Partnership for T-Cell Biology JCSG
TJMP Structure-Function Studies of Tight Junction Membrane Proteins CSMP
UC4CDI Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes MCSG

 

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Project

Some targets are listed as falling under one or more projects. See drop-down list for current projects available.

Select one or more projects to customize your query.

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Result Format

HTML Format

Features of selected targets are displayed in HTML format.

FASTA Format

Sequences of selected targets are outputted in Pearson/FASTA format. Click link to download the .fa.zip fasta file to your computer.

XML Format (coming soon)

Features of selected target sequences are outputted in XML format.

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

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