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iep |
Adjusting the pH of an aqueous protein solution to the point where the numbers of positive and negative charges on the protein are equal brings the protein to its isoelectric point. This is often the point of lowest solubility, presumably because it is the point at which there are fewest intermolecular repulsions, so that the molecules tend to form aggregates.
The application can make a plot of the ionization curve with respect to pH and can write an output file of the data.
% iep sw:laci_ecoli Output file [laci_ecoli.iep]:
Mandatory qualifiers (* if not always prompted): [-sequencea] seqall Sequence database USA * -graph xygraph Graph type * -outfile outfile Output file name Optional qualifiers: (none) Advanced qualifiers: -step float pH step value -amino integer Number of N-termini -[no]termini boolean Include charge at N and C terminus -plot boolean Plot charge vs pH -[no]report boolean Write results to a file General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequencea] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
-graph | Graph type | EMBOSS has a list of known devices, including postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows, x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm, png | EMBOSS_GRAPHICS value, or x11 |
-outfile | Output file name | Output file | <sequence>.iep |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-step | pH step value | Number from 0.010 to 1.000 | .5 |
-amino | Number of N-termini | Any integer value | 1 |
-[no]termini | Include charge at N and C terminus | Yes/No | Yes |
-plot | Plot charge vs pH | Yes/No | No |
-[no]report | Write results to a file | Yes/No | Yes |
IEP of LACI_ECOLI from 1 to 360 Isoelectric Point = 6.8820 pH Bound Charge 1.00 81.96 37.96 1.50 81.89 37.89 2.00 81.65 37.65 2.50 80.91 36.91 3.00 78.79 34.79 3.50 73.70 29.70 4.00 65.15 21.15 4.50 56.73 12.73 5.00 51.75 7.75 5.50 49.36 5.36 6.00 47.63 3.63 6.50 45.56 1.56 7.00 43.59 -0.41 7.50 42.27 -1.73 8.00 41.22 -2.78 8.50 39.87 -4.13 9.00 38.26 -5.74 9.50 36.24 -7.76 10.00 33.03 -10.97 10.50 28.46 -15.54 11.00 23.58 -20.42 11.50 19.41 -24.59 12.00 15.19 -28.81 12.50 9.75 -34.25 13.00 4.64 -39.36 13.50 1.75 -42.25 14.00 0.59 -43.41
Program name | Description |
---|---|
backtranseq | Back translate a protein sequence |
charge | Protein charge plot |
checktrans | Reports STOP codons and ORF statistics of a protein sequence |
compseq | Counts the composition of dimer/trimer/etc words in a sequence |
emowse | Protein identification by mass spectrometry |
freak | Residue/base frequency table or plot |
mwcontam | Shows molwts that match across a set of files |
mwfilter | Filter noisy molwts from mass spec output |
octanol | Displays protein hydropathy |
pepinfo | Plots simple amino acid properties in parallel |
pepstats | Protein statistics |
pepwindow | Displays protein hydropathy |
pepwindowall | Displays protein hydropathy of a set of sequences |