Amino acid composition is one of the parameters, which can be used to identify β-barrel membrane proteins. TMB-HUNT is a modified k-nearest neighbor algorithm used to classify the proteins into the transmembrane β-barrel (TMB) and non- TMB. This method showed an accuracy of 92.5% using weighted amino acids and evolutionary information.
AACompSim is a tool which allows the comparison of the amino acid composition of a SWISS-PROT entry with all other SWISS-PROT entries so as to find the proteins whose amino acid compositions are closest to that of the selected entry.
We will have to enter the following data:
- A SWISS-PROT identifier (ID) (e.g. ALBU_HUMAN) or SWISS-PROT accession number (AC) (e.g. P04406).
- Our e-mail address. The search results will be mailed back to us automatically (this should take less than 15 minutes).
- The SWISS-PROT abbreviation for the species for which we would like to perform the search (example: HUMAN). This will produce the list of proteins from this species, as well as a list of proteins independently of species; we may also specify ALL for all SWISS-PROT entries.
- The AACompSim tool allows the theoretical AA composition of one protein in the SWISS-PROT database to be compared to proteins from one or all species in the database. This serves two main purposes. Firstly, to allow the simulation of matching undertaken for identification purposes with AACompIdent. Secondly, it allows the detection of weak similarities between proteins by comparison of their compositions rather than sequences, as explored by Hobohm and Sander.
Use of AACompSim
To use AACompSim, first select the constellation of amino acids we wish to work with. If we wish to simulate matching undertaken with empirical data, we should specify constellation 2. To match against the database for detecting protein similarities, we should use all 20 amino acids in constellation 0. Then specify an email address to where the results can be sent, the SWISS-PROT identification name (e.g. IPIA_TOBAC) or accession number (e.g. Q03198) of the protein we would like to compare against the database, and the SWISS-PROT abbreviation for the species to match against (e.g. ‘SALTY’ for Salmonella typhimurium). If desired, matching can be done against all species in the database by specifying ‘ALL’. Finally, select the ‘Search’ button to submit the match to ExPASy. AACompSim will return three lists of proteins, similar to those from AACompIdent.
- AACompSim automatically uses the theoretical pI and MW of the specified protein in the matching procedure. The pI and MW are calculated as in Compute pI / MW .
- Default windows of pI ± 0.25 and MW ± 20% used by AACompSim in matching, however matches undertaken without these windows are also included in the program output.