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pepwindow |
% pepwindow tsw:hba_human Displays protein hydropathy Graph type [x11]: cps Created pepwindow.ps |
Go to the input files for this example
Go to the output files for this example
Mandatory qualifiers: [-sequencea] sequence Sequence USA -graph xygraph Graph type Optional qualifiers: -datafile datafile nakai database file -length integer window size Advanced qualifiers: (none) 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 USA | Readable sequence | 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 |
Optional qualifiers | Allowed values | Default | |
-datafile | nakai database file | Data file | Enakai.dat |
-length | window size | Integer from 1 to 200 | 7 |
Advanced qualifiers | Allowed values | Default | |
(none) |
ID HBA_HUMAN STANDARD; PRT; 141 AA. AC P01922; DT 21-JUL-1986 (Rel. 01, Created) DT 21-JUL-1986 (Rel. 01, Last sequence update) DT 15-JUL-1999 (Rel. 38, Last annotation update) DE HEMOGLOBIN ALPHA CHAIN. GN HBA1 AND HBA2. OS Homo sapiens (Human), Pan troglodytes (Chimpanzee), and OS Pan paniscus (Pygmy chimpanzee) (Bonobo). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia; OC Eutheria; Primates; Catarrhini; Hominidae; Homo. RN [1] RP SEQUENCE FROM N.A. (ALPHA-1). RX MEDLINE; 81088339. RA MICHELSON A.M., ORKIN S.H.; RT "The 3' untranslated regions of the duplicated human alpha-globin RT genes are unexpectedly divergent."; RL Cell 22:371-377(1980). RN [2] RP SEQUENCE FROM N.A. (ALPHA-2). RX MEDLINE; 81175088. RA LIEBHABER S.A., GOOSSENS M.J., KAN Y.W.; RT "Cloning and complete nucleotide sequence of human 5'-alpha-globin RT gene."; RL Proc. Natl. Acad. Sci. U.S.A. 77:7054-7058(1980). RN [3] RP SEQUENCE FROM N.A. (ALPHA-2). RX MEDLINE; 80137531. RA WILSON J.T., WILSON L.B., REDDY V.B., CAVALLESCO C., GHOSH P.K., RA DERIEL J.K., FORGET B.G., WEISSMAN S.M.; RT "Nucleotide sequence of the coding portion of human alpha globin RT messenger RNA."; RL J. Biol. Chem. 255:2807-2815(1980). RN [4] RP SEQUENCE FROM N.A. (ALPHA-1 AND ALPHA-2). RA FLINT J., HIGGS D.R.; RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases. RN [5] RP SEQUENCE. RA BRAUNITZER G., GEHRING-MULLER R., HILSCHMANN N., HILSE K., HOBOM G., RA RUDLOFF V., WITTMANN-LIEBOLD B.; RT "The constitution of normal adult human haemoglobin."; RL Hoppe-Seyler's Z. Physiol. Chem. 325:283-286(1961). RN [6] RP SEQUENCE. RA HILL R.J., KONIGSBERG W.; RT "The structure of human hemoglobin: IV. The chymotryptic digestion of RT the alpha chain of human hemoglobin."; RL J. Biol. Chem. 237:3151-3156(1962). RN [7] [Part of this file has been deleted for brevity] FT /FTId=VAR_002841. FT VARIANT 130 130 A -> D (IN YUDA; O2 AFFINITY DOWN). FT /FTId=VAR_002842. FT VARIANT 131 131 S -> P (IN QUESTEMBERT; HIGHLY UNSTABLE; FT CAUSES ALPHA-THALASSEMIA). FT /FTId=VAR_002843. FT VARIANT 133 133 S -> R (IN VAL DE MARNE; O2 AFFINITY UP). FT /FTId=VAR_002844. FT VARIANT 135 135 V -> E (IN PAVIE). FT /FTId=VAR_002845. FT VARIANT 136 136 L -> M (IN CHICAGO). FT /FTId=VAR_002846. FT VARIANT 136 136 L -> P (IN BIBBA; UNSTABLE; FT CAUSES ALPHA-THALASSEMIA). FT /FTId=VAR_002847. FT VARIANT 138 138 S -> P (IN ATTLEBORO; O2 AFFINITY UP). FT /FTId=VAR_002848. FT VARIANT 139 139 K -> E (IN HANAKAMI; O2 AFFINITY UP). FT /FTId=VAR_002849. FT VARIANT 139 139 K -> T (IN TOKONAME; O2 AFFINITY UP). FT /FTId=VAR_002850. FT VARIANT 140 140 Y -> H (IN ROUEN; O2 AFFINITY UP). FT /FTId=VAR_002851. FT VARIANT 141 141 R -> C (IN NUNOBIKI; O2 AFFINITY UP). FT /FTId=VAR_002852. FT VARIANT 141 141 R -> L (IN LEGNANO; O2 AFFINITY UP). FT /FTId=VAR_002853. FT VARIANT 141 141 R -> H (IN SURESNES; O2 AFFINITY UP). FT /FTId=VAR_002854. FT VARIANT 141 141 R -> P (IN SINGAPORE). FT /FTId=VAR_002855. FT HELIX 4 35 FT HELIX 37 42 FT TURN 44 45 FT TURN 50 51 FT HELIX 53 71 FT TURN 72 74 FT HELIX 76 79 FT TURN 80 80 FT HELIX 81 89 FT TURN 90 91 FT TURN 95 95 FT HELIX 96 112 FT TURN 114 116 FT HELIX 119 136 FT TURN 137 139 SQ SEQUENCE 141 AA; 15126 MW; 5EC7DB1E CRC32; VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA VHASLDKFLA SVSTVLTSKY R // |
The EMBOSS data file 'Enakai.dat' contains :-
D Hydropathy index (Kyte-Doolittle, 1982) R 0807099 A Kyte, J. and Doolittle, R.F. T A simple method for displaying the hydropathic character of a protein J J. Mol. Biol. 157, 105-132 (1982) C CHOC760103 0.964 JANJ780102 0.922 DESM900102 0.898 EISD860103 0.897 CHOC760104 0.889 WOLR810101 0.885 RADA880101 0.884 MANP780101 0.881 EISD840101 0.878 PONP800103 0.870 NAKH920108 0.868 JANJ790101 0.867 JANJ790102 0.866 PONP800102 0.861 MEIH800103 0.856 PONP800101 0.851 PONP800108 0.850 WARP780101 0.845 RADA880108 0.842 ROSG850102 0.841 DESM900101 0.837 BIOV880101 0.829 RADA880107 0.828 LIFS790102 0.824 KANM800104 0.824 CIDH920104 0.824 MIYS850101 0.821 RADA880104 0.819 NAKH900111 0.817 NISK800101 0.812 FAUJ830101 0.811 ARGP820103 0.806 NAKH920105 0.803 ARGP820102 0.803 KRIW790101 -0.805 CHOC760102 -0.838 GUYH850101 -0.843 RACS770102 -0.844 JANJ780103 -0.845 ROSM880101 -0.845 PRAM900101 -0.850 JANJ780101 -0.852 GRAR740102 -0.859 MEIH800102 -0.871 ROSM880102 -0.878 OOBM770101 -0.899 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.8 -4.5 -3.5 -3.5 2.5 -3.5 -3.5 -0.4 -3.2 4.5 3.8 -3.9 1.9 2.8 -1.6 -0.8 -0.7 -0.9 -1.3 4.2 //
Kyte, J. and Doolittle, R.F. A simple method for displaying the hydropathic character of a protein J. Mol. Biol. 157, 105-132 (1982)
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 |
iep | Calculates the isoelectric point of a protein |
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 |
pepwindowall | Displays protein hydropathy of a set of sequences |
Based on Original program by Jack Kyte and Russell F. Doolittle.
Completed 27th May 1999.