![]() |
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 tsw:laci_ecoli Calculates the isoelectric point of a protein Output file [laci_ecoli.iep]: |
Go to the input files for this example
Go to the output files for this example
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 | Boolean value Yes/No | Yes |
-plot | Plot charge vs pH | Boolean value Yes/No | No |
-[no]report | Write results to a file | Boolean value Yes/No | Yes |
iep
reads in any protein sequence USA.
ID LACI_ECOLI STANDARD; PRT; 360 AA. AC P03023; P71309; Q47338; O09196; DT 21-JUL-1986 (Rel. 01, Created) DT 01-NOV-1997 (Rel. 35, Last sequence update) DT 15-DEC-1998 (Rel. 37, Last annotation update) DE LACTOSE OPERON REPRESSOR. GN LACI. OS Escherichia coli. OC Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae; OC Escherichia. RN [1] RP SEQUENCE FROM N.A. RX MEDLINE; 78246991. RA FARABAUGH P.J.; RT "Sequence of the lacI gene."; RL Nature 274:765-769(1978). RN [2] RP SEQUENCE FROM N.A. RC STRAIN=K12 / MG1655; RX MEDLINE; 97426617. RA BLATTNER F.R., PLUNKETT G. III, BLOCH C.A., PERNA N.T., BURLAND V., RA RILEY M., COLLADO-VIDES J., GLASNER F.D., RODE C.K., MAYHEW G.F., RA GREGOR J., DAVIS N.W., KIRKPATRICK H.A., GOEDEN M.A., ROSE D.J., RA MAU B., SHAO Y.; RT "The complete genome sequence of Escherichia coli K-12."; RL Science 277:1453-1474(1997). RN [3] RP SEQUENCE FROM N.A. RC STRAIN=K12 / MG1655; RA DUNCAN M., ALLEN E., ARAUJO R., APARICIO A.M., CHUNG E., DAVIS K., RA FEDERSPIEL N., HYMAN R., KALMAN S., KOMP C., KURDI O., LEW H., RA LIN D., NAMATH A., OEFNER P., ROBERTS D., SCHRAMM S., DAVIS R.W.; RL Submitted (NOV-1996) to the EMBL/GenBank/DDBJ databases. RN [4] RP SEQUENCE FROM N.A. RA CHEN J., MATTHEWS K.K.S.M.; RL Submitted (MAY-1991) to the EMBL/GenBank/DDBJ databases. RN [5] RP SEQUENCE FROM N.A. RA MARSH S.; RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases. RN [6] RP SEQUENCE OF 1-147; 159-230 AND 233-360. RX MEDLINE; 76091932. RA BEYREUTHER K., ADLER K., FANNING E., MURRAY C., KLEMM A., GEISLER N.; RT "Amino-acid sequence of lac repressor from Escherichia coli. RT Isolation, sequence analysis and sequence assembly of tryptic RT peptides and cyanogen-bromide fragments."; RL Eur. J. Biochem. 59:491-509(1975). RN [7] [Part of this file has been deleted for brevity] CC between the Swiss Institute of Bioinformatics and the EMBL outstation - CC the European Bioinformatics Institute. There are no restrictions on its CC use by non-profit institutions as long as its content is in no way CC modified and this statement is not removed. Usage by and for commercial CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ CC or send an email to license@isb-sib.ch). CC -------------------------------------------------------------------------- DR EMBL; V00294; CAA23569.1; -. DR EMBL; J01636; AAA24052.1; -. DR EMBL; AE000141; AAC73448.1; -. DR EMBL; U73857; AAB18069.1; ALT_INIT. DR EMBL; X58469; CAA41383.1; -. DR EMBL; U86347; AAB47270.1; ALT_INIT. DR EMBL; U72488; AAB36549.1; -. DR EMBL; U78872; AAB37348.1; -. DR EMBL; U78873; AAB37351.1; -. DR EMBL; U78874; AAB37354.1; -. DR PIR; A03558; RPECL. DR PIR; S02540; S02540. DR PDB; 1LCC; 31-JAN-94. DR PDB; 1LCD; 31-JAN-94. DR PDB; 1LTP; 31-OCT-93. DR PDB; 1TLF; 31-JUL-95. DR PDB; 1LBG; 11-JUL-96. DR PDB; 1LBH; 11-JUL-96. DR PDB; 1LBI; 11-JUL-96. DR PDB; 1LQC; 12-FEB-97. DR ECO2DBASE; H039.0; 6TH EDITION. DR ECOGENE; EG10525; LACI. DR PFAM; PF00356; lacI; 1. DR PFAM; PF00532; Peripla_BP_like; 1. DR PROSITE; PS00356; HTH_LACI_FAMILY; 1. KW Transcription regulation; DNA-binding; Repressor; 3D-structure. FT DNA_BIND 6 25 H-T-H MOTIF. FT MUTAGEN 17 17 Y->H: BROADENING OF SPECIFICITY. FT MUTAGEN 22 22 R->N: RECOGNIZE AN OPERATOR VARIANT. FT VARIANT 282 282 Y -> D (IN T41 MUTANT). FT CONFLICT 286 286 S -> L (IN AAA24052, REF. 2, 4 AND 5). FT HELIX 6 13 FT TURN 14 14 FT HELIX 17 24 FT HELIX 32 44 FT TURN 49 50 SQ SEQUENCE 360 AA; 38564 MW; 4CA5A1D6 CRC32; MKPVTLYDVA EYAGVSYQTV SRVVNQASHV SAKTREKVEA AMAELNYIPN RVAQQLAGKQ SLLIGVATSS LALHAPSQIV AAIKSRADQL GASVVVSMVE RSGVEACKAA VHNLLAQRVS GLIINYPLDD QDAIAVEAAC TNVPALFLDV SDQTPINSII FSHEDGTRLG VEHLVALGHQ QIALLAGPLS SVSARLRLAG WHKYLTRNQI QPIAEREGDW SAMSGFQQTM QMLNEGIVPT AMLVANDQMA LGAMRAITES GLRVGADISV VGYDDTEDSS CYIPPSTTIK QDFRLLGQTS VDRLLQLSQG QAVKGNQLLP VSLVKRKTTL APNTQTASPR ALADSLMQLA RQVSRLESGQ // |
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 |
For each pH point it gives the number of bound electrons and the charge.
Program name | Description |
---|---|
backtranseq | Back translate a protein sequence |
charge | Protein charge plot |
checktrans | Reports STOP codons and ORF statistics of a protein |
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 |