If one entry is specified, you will be asked to specify the protein's domain of interest for which the pI and mass should be computed. The domain can be selected from the hypertext link of features shown, if any, or by numerically specifying the domain start and end points.
If more than one Swiss-Prot/TrEMBL identification name is entered, all proteins will automatically be processed to their mature forms, and pI and Mw values calculated for the chains or peptides. If only fragments of the protein of interest are available in the database, no result will be given and an error message will be shown to highlight that the pI and mass cannot be returned accurately. Where database entries have signal sequences or transit peptides of unknown length (e.g. A1CGA8), an average length signal sequence or transit peptide is removed before the pI and mass computation is done. In Swiss-Prot release 35, the average signal sequence length is 22 amino acids for eukaryotes and viruses, 26 amino acids for prokaryotes and bacteriophages, and 30 for archaebacteria. Transit peptides have an average length of 55 amino acids in chloroplasts, 34 for mitochondria, 29 for microbodies, and 51 for cyanelles.
If your protein of interest is not in Swiss-Prot/TrEMBL, you can enter an AA sequence in standard single letter AA code into the text field, and select the "click here to compute pI/Mw" button. The predicted pI and Mw of your sequence will then be displayed. A typical output from the program is shown in figure 2.
Alternatively to the verbose html output, the result for a list of Swiss-Prot/TrEMBL entries can also be retrieved in a numerical format, with minimal documentation. A file containing 4 columns,
ID AC pI Mwis generated and can be loaded into an external application, such as a spreadsheet program.
ARS1_MOUSE O54984 4.80 39065.08 ARSA_MOUSE_1 P50428 5.50 52173.26 ARSB_MOUSE P50429 FRAGMENT 0.00 ARX_MOUSE O35085 5.19 58504.37 ARY1_MOUSE P50294 5.10 33713.36 ARY2_MOUSE P50295 5.63 33701.41 ARY3_MOUSE P50296 6.07 33685.69 ASAH_MOUSE_1 Q9WV54 6.11 13797.05 ASAH_MOUSE_2 Q9WV54 8.87 29017.27 ASH1_MOUSE Q02067 8.56 24755.51 ASM_MOUSE_1 Q04519 6.48 65060.34 ASNS_MOUSE Q61024 6.12 64151.52 ASPG_MOUSE_1 Q64191 5.18 19681.95 ASPG_MOUSE_2 Q64191 7.61 14809.84 ASPX_MOUSE_1 P50289 4.42 26147.04If pI and MW cannot be computed, a value of "0.00" appears in the Mw column, and the reason for this is displayed in the pI column in form of a code, the meaning of which is as follows:
|FRAGMENT||Incomplete $chain_or_peptide: pI/Mw cannot be computed|
|UNDEFINED||Unknown start- or endpoints: pI/Mw cannot be computed|
|XXX||Sequence contains several consecutive undefined AA: pI/Mw cannot be computed|
If a Swiss-Prot/TrEMBL entry has one or more mature chains/peptides documented, this is indicated by "_1", "_2", etc. appended to the ID. An appended "_1", "_2", etc. indicates that the considered sequence is that corresponding to the first, second etc. CHAIN or PEPTIDE documented in the feature table.
B Asx Aspartic acid or Asparagine Z Glx Glutamine or Glutamic acid X Xaa Any amino acidThe mass values used for these residues are mean values of the corresponding masses weighted by their respective frequencies observed in the whole Swiss-Prot protein sequences (check the frequencies observed in the current Swiss-Prot release).