The Transmembrane – TopPred track utilizes hydropathy analysis to propose probable transmembrane regions in a protein sequence, using the methods of von Heijne, 1992, and Claros and von Heijne, 1994. Possible membrane-protein topologies are considered and ranked according to the “positive-inside rule,” an observation that the cytoplasmic parts of membrane proteins more frequently contain positively charged residues compared to non-cytoplasmic parts. Additional considerations are made for eukaryote proteins, including the net charge difference of residues flanking the N-terminal transmembrane segment.
In the Tracks panel, expand Transmembrane and check the box next to TopPred. The track will now be visible in the Analysis view
Select the track in the Tracks panel. Open the Track Options section, which appears as follows:
- Transmembrane threshold – Regions with a maximum hydrophobicity score equal to or greater than this threshold will be reported as transmembrane regions, as long as they are not adjacent to, nor overlap with, other transmembrane regions. A setting of 0.6 will cause Protean 3D to report all putative regions, while a threshold of 1.0 will cause the application to be more selective and only report regions with a higher probability of being transmembrane regions. The default is 1.0.
- Taxonomy – Select the taxonomy of the organism from which the sequence is derived. The selection influences Protean 3D’s prediction of whether a region is cytoplasmic or extracellular.
Click if you wish to return to the default settings.
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