TOPO (TMHMM, SOSUI, TargetP, PSORT) Viewer is a tool for viewing both sub-cellular targeting signals predicted by WoLF PSORT1 and TargetP2, as well as the presence trans-membrane helices predicted by SOSUI3, TMHMM4 and PTS15,6
WoLF PSORT http://wolfpsort.seq.cbrc.jp/
Click on the TOPO Viewer icon to open a Java applet to view the prediction results (see point 4.6.6 for details on Java applet).
: TOPO Viewer icon in H-InvDB Locus or cDNA view
The TOPO Viewer window is divided into four tab pages:
(i) The TABLE tab page (Fig. 4.6.1) that displays the prediction results for all programs. The probabilities that a protein may deliver to up to nine distinct subcellular locations are predicted by PSORTII. The TargetP predicts if a protein contain a signal peptide, a mitochondrial targeting signal or another type of signal. For both, TMHMM and SOSUI programs, the location of the predicted transmembrane helices are shown. Additionally, TMHMM predicts regions of a protein that are located either inside or outside the cell. Note that eventually the first TM helix predicted by both programs may represent a 'signal peptide'.
(ii) The MAP tab page that displays sub-cellular localization signals and trans-membrane helices graphically. Three targeting signals can be visualized, namely, signal peptide, mitochondrial and nuclear targeting signals (Predicted by PSORTII). Note that in the MAP page all signals are displayed if at least a 10.0 value was assigned by PSORTII. To see the probabilities that a protein may deliver to one or more locations, review the TABLE page above.
(iii) The FILE tab page that contains the flat files for each of the prediction programs. Select any of the four programs and and click 'Get file' to access the flat file.
(iv) The GFP tab page that displays the subcellular localization of a protein tested experimentally. Note that currently only a reduced number of ORFs have a green fluorescent (GFP) data.
By default the TABLE page is displayed when the TOPO viewer icon is pressed. The TOPO Viewer Table (Fig. 4.6.1) consists of the following items:Query ID
The query's sequence ID is displayed on the left top corner of the window.WoLF PSORT prediction results
The table displays the predicted sub-cellular location to up to twelve compartments for the protein in query protein, and also shows the percentages of the localization sites of neighbors to each sub-cellular location calculated by the WoLF PSORT program. The top hit(s) are outlined with a yellow background color.TargetP prediction results
The next section of the table displays the predicted results for a targeting signal to mitochondria (mTP), signal peptide (SP) and the presence of another type of targeting signal (other) predicted using the Target P program. The top hit displayed with a yellow background.
Note that the threshold value to annotate a protein as possessing a mitochondrial signal or other is at least 0.8.SOSUI prediction results
The SOSUI section of the table shows the prediction results of trans-membrane segments predicted by the SOSUI program. The number of trans-membrane (TM) segments is displayed in the first row, the starting position of the helix is shown on the N-terminal column, while the end position of the TM is shown in the C-terminal column. Two kinds of TM are predicted: primary and secondary (type column), and the TM amino acid sequence is displayed in the trans-membrane region column. Note that the top hit is outlined with a background yellow color.TMHMM prediction results
The TMHMM section of the table presents the predicted trans-membrane helices by the HMHMM program. The results includes: 1) The number (num); 2) the segment composition (kind) as either TM helix, sequence segment located outside the cell (outside) or inside the cell (inside); 3) The start position of the TM (start) ; and 4) The end position of the TM (end).PTS1 prediction results
The last section of the table presents the PTS1 motif prediction results. Peroxisomal matrix proteins have to be imported into their target organelle post-translationally. The major translocation pathway depends on a C-terminal targeting signal, termed PTS1. PTS1 motif revealed at least nine residues directly upstream are important for signal recognition in the PTS1-Pex5 receptor complex. Prediction classification of either "Targeted" or "Not targeted" for PTS1 motif is determined.
On this page a graphical view of the location of a signal peptide, a mitochondrial, and/or a nuclear targeting signal, as well as trans-membrane helices are presented.
The TOPO Viewer MAP page shows the following items:
Click on the 'FILE' icon to access to flat files of all four prediction programs. After choosing 'FILE', press the 'PSORT' icon to scroll down and select other program, and then press 'Get File' icon to get the program flat file.4.6.5 The GFP page
Click on the 'GFP' icon to access to the experimental results of the sub-cellular localization characterization using the green fluorescent protein (GFP). Note that currently a reduced number of H-Inv proteins were experimentally tested for their subcellular localization. Further updates are expected in a near future.4.6.6 The TOPO Viewer's Java applet
All applets are written using Java 1.2 (a.k.a. J2SE 1.3), and theoretically any web browser that fully supports this should work. However in practice, browsers' built-in Java support tends to be outdated, inconsistent, and buggy, so for best compatibility we recommend that you download and install Sun's free Java Plug-in software in your browser. The main page for this product is http://java.sun.com/products/plugin/ (if you aren't running WINDOWS+IE, click on "IT Professional"), and platform-specific links are given below. The plug-in is usually bundled with the Java 2 Runtime Environment (JRE) or the Java 2 Software Development Kit (SDK). If you are given a choice between these, either will do; the JRE is smaller because it doesn't include developer tools, but both of them contain the plug-in. Note that we have tested TOPO Viewer with version 1.4.0 of the plug-in, but newer versions should also work.References