Description of WD-repeat DSMs

These discrete state-space models are for members of the WD-repeat family of proteins. WD-repeat models can handle multi-domain proteins that contain WD repeats together with other structure domains.

There are currently two superclasses: "generic" and "wd repeat". "generic" is designed for proteins not containing WD repeats. Under this superclass, there is only one macroclass, also called "generic". For detailed description of the generic model, see the "Description of Type-2 DSMs" section. Superclass "wd repeat" is designed for the WD-repeat family of proteins. Under this superclass, there are six macroclasses for WD-repeat proteins, each of which contains a different number of repeats, as defined in the following section. Sequences containing fewer than four WD repeats will not be reported as a WD-repeat protein. This is due to the assumption that all WD-repeat proteins adopt a beta-propeller fold, which must have at least four blades to form a circular structure. Notice that the domain length ranges described below are the ranges only for the WD-repeat domain. We added leader and trailer to our models on the fly to handle longer sequences. Therefore, all models can recognize WD repeats within sequences longer than its maximum domain length. The upper limit on sequence length is still 1000 residues long.

Each WD repeat has two conserved profiles denoted "profile 1" and "profile 2" (which may be approximated as "GHXXXVXXVXFX" and "XLASGSXDXTIKVWD", respectively, as shown at http://bmerc-www.bu.edu/wdrepeat/) that are used in the DSM prediction. A more detailed description of the WD repeat itself and the statistics of the profiles can be found on the WD-repeat Family of Proteins page.

• WD4

  The macroclass WD4 has four WD repeats. Four models have been constructed to cover the domain length range from 187 to 279.

• WD5

  The macroclass WD5 has five WD repeats. Four models have been constructed to cover the domain length range from 233 to 332.

• WD6

  The macroclass WD6 has six WD repeats. Four models have been constructed to cover the domain length range from 278 to 385.

• WD7

  The macroclass WD7 has seven WD repeats. Four models have been constructed to cover the domain length range from 323 to 437.

• WD8

  The macroclass WD8 has eight WD repeats. Four models have been constructed to cover the domain length range from 368 to 489.

• WD9

  The macroclass WD9 has nine WD repeats. Four models have been constructed to cover the length range from 413 to 541.

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