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tmap |
tmap reads in one or more aligned protein sequences.
Two sets of propensity values are then used for the calculations: one for the middle, hydrophobic portion and one for the terminal regions of the transmembrane sequence spans. Average propensity values are calculated for each position along the alignment, with the contribution from each sequence weighted according to its dissimilarity relative to the other aligned sequences.
Eight-residue segments are considered as potential cores of transmembrane segments and elongated if thier middle propensity values are above a threshold. End propensity values are also considered as stop signals. Only helices with a length of 15 to 29 residues are allowed and corrections for strictly conserved charged residues are made.
The method is more successful than predictions based upon single sequences alone.
The results are plotted on a graph and written to a text file.
% tmap tsw:opsd_human -out tmap.res -graph cps Displays membrane spanning regions Created tmap.ps |
Go to the input files for this example
Go to the output files for this example
Mandatory qualifiers: [-msf] seqset File containing a sequence alignment -graph xygraph Graph type Optional qualifiers: -outfile outfile Output file name 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 | |
---|---|---|---|
[-msf] (Parameter 1) |
File containing a sequence alignment | Readable sequences | 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 | |
-outfile | Output file name | Output file | tmap.res |
Advanced qualifiers | Allowed values | Default | |
(none) |
ID OPSD_HUMAN STANDARD; PRT; 348 AA. AC P08100; Q16414; DT 01-AUG-1988 (Rel. 08, Created) DT 01-AUG-1988 (Rel. 08, Last sequence update) DT 15-JUL-1999 (Rel. 38, Last annotation update) DE RHODOPSIN. GN RHO. OS Homo sapiens (Human). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia; OC Eutheria; Primates; Catarrhini; Hominidae; Homo. RN [1] RP SEQUENCE FROM N.A. RX MEDLINE; 84272729. RA NATHANS J., HOGNESS D.S.; RT "Isolation and nucleotide sequence of the gene encoding human RT rhodopsin."; RL Proc. Natl. Acad. Sci. U.S.A. 81:4851-4855(1984). RN [2] RP SEQUENCE OF 1-120 FROM N.A. RA BENNETT J., BELLER B., SUN D., KARIKO K.; RL Submitted (NOV-1994) to the EMBL/GenBank/DDBJ databases. RN [3] RP REVIEW ON ADRP VARIANTS. RX MEDLINE; 94004905. RA AL-MAGHTHEH M., GREGORY C., INGLEHEARN C., HARDCASTLE A., RA BHATTACHARYA S.; RT "Rhodopsin mutations in autosomal dominant retinitis pigmentosa."; RL Hum. Mutat. 2:249-255(1993). RN [4] RP VARIANT ADRP HIS-23. RX MEDLINE; 90136922. RA DRYJA T.P., MCGEE T.L., REICHEI E., HAHN L.B., COWLEY G.S., RA YANDELL D.W., SANDBERG M.A., BERSON E.L.; RT "A point mutation of the rhodopsin gene in one form of retinitis RT pigmentosa."; RL Nature 343:364-366(1990). RN [5] RP VARIANTS ADRP. RX MEDLINE; 91051574. RA FARRAR G.J., KENNA P., REDMOND R., MCWILLIAM P., BRADLEY D.G., RA HUMPHRIES M.M., SHARP E.M., INGLEHEARN C.F., BASHIR R., JAY M., RA WATTY A., LUDWIG M., SCHINZEL A., SAMANNS C., GAL A., RA BHATTACHARYA S.S., HUMPHRIES P.; RT "Autosomal dominant retinitis pigmentosa: absence of the rhodopsin RT proline-->histidine substitution (codon 23) in pedigrees from RT Europe."; RL Am. J. Hum. Genet. 47:941-945(1990). RN [6] RP VARIANTS ADRP HIS-23; ARG-58; LEU-347 AND SER-347. RX MEDLINE; 91015273. [Part of this file has been deleted for brevity] FT /FTId=VAR_004816. FT VARIANT 209 209 V -> M (EFFECT NOT KNOWN). FT /FTId=VAR_004817. FT VARIANT 211 211 H -> P (IN ADRP). FT /FTId=VAR_004818. FT VARIANT 211 211 H -> R (IN ADRP). FT /FTId=VAR_004819. FT VARIANT 216 216 M -> K (IN ADRP). FT /FTId=VAR_004820. FT VARIANT 220 220 F -> C (IN ADRP). FT /FTId=VAR_004821. FT VARIANT 222 222 C -> R (IN ADRP). FT /FTId=VAR_004822. FT VARIANT 255 255 MISSING (IN ADRP). FT /FTId=VAR_004823. FT VARIANT 264 264 MISSING (IN ADRP). FT /FTId=VAR_004824. FT VARIANT 267 267 P -> L (IN ADRP). FT /FTId=VAR_004825. FT VARIANT 267 267 P -> R (IN ADRP). FT /FTId=VAR_004826. FT VARIANT 292 292 A -> E (IN CSNB4). FT /FTId=VAR_004827. FT VARIANT 296 296 K -> E (IN ADRP). FT /FTId=VAR_004828. FT VARIANT 297 297 S -> R (IN ADRP). FT /FTId=VAR_004829. FT VARIANT 342 342 T -> M (IN ADRP). FT /FTId=VAR_004830. FT VARIANT 345 345 V -> L (IN ADRP). FT /FTId=VAR_004831. FT VARIANT 345 345 V -> M (IN ADRP). FT /FTId=VAR_004832. FT VARIANT 347 347 P -> A (IN ADRP). FT /FTId=VAR_004833. FT VARIANT 347 347 P -> L (IN ADRP; COMMON VARIANT). FT /FTId=VAR_004834. FT VARIANT 347 347 P -> Q (IN ADRP). FT /FTId=VAR_004835. FT VARIANT 347 347 P -> R (IN ADRP). FT /FTId=VAR_004836. FT VARIANT 347 347 P -> S (IN ADRP). FT /FTId=VAR_004837. SQ SEQUENCE 348 AA; 38892 MW; 07443BEA CRC32; MNGTEGPNFY VPFSNATGVV RSPFEYPQYY LAEPWQFSML AAYMFLLIVL GFPINFLTLY VTVQHKKLRT PLNYILLNLA VADLFMVLGG FTSTLYTSLH GYFVFGPTGC NLEGFFATLG GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLAGWSRYIP EGLQCSCGID YYTLKPEVNN ESFVIYMFVV HFTIPMIIIF FCYGQLVFTV KEAAAQQQES ATTQKAEKEV TRMVIIMVIA FLICWVPYAS VAFYIFTHQG SNFGPIFMTI PAFFAKSAAI YNPVIYIMMN KQFRNCMLTT ICCGKNPLGD DEASATVSKT ETSQVAPA // |
Program TMAP, version 46, to predict transmembrane segments from .msf file. The program reads a multiple alignment file of the GCG multiple sequence format and predicts membrane-spanning regions according to the algorithm in Persson & Argos (1994), J. Mol. Biol. 237, 182-192. RESULTS from program TMAP, edition 46' Numbers give: a) number of transmembrane segment b) start of TM segment (alignment position / residue number) c) end of TM segment (alignment position / residue number) d) length of TM segment within parentheses PREDICTED TRANSMEMBRANE SEGMENTS FOR ALIGNMENT TM 1: 43 - 69 (27.0) TM 2: 73 - 97 (25.0) TM 3: 112 - 140 (29.0) TM 4: 148 - 176 (29.0) TM 5: 201 - 229 (29.0) TM 6: 255 - 275 (21.0) TM 7: 282 - 302 (21.0) PREDICTED TRANSMEMBRANE SEGMENTS FOR PROTEIN OPSD_HUMAN TM 1: 43 - 69 (27) TM 2: 73 - 97 (25) TM 3: 112 - 140 (29) TM 4: 148 - 176 (29) TM 5: 201 - 229 (29) TM 6: 255 - 275 (21) TM 7: 282 - 302 (21) |
A plot of the propensities to form the middle and the end of transmembrane regions is output.
Bars are displayed in the plot above the regions predicted as being most likely to form transmembrane regions.
The text file (specified by the -outfile option) gives a summary of these regions.
The transmembrane regions for the complete alignment are given first, followed by the predictions for each individual sequence in the alignment. (There is only one sequence in the example alignment.)
Program name | Description |
---|---|
garnier | Predicts protein secondary structure |
helixturnhelix | Report nucleic acid binding motifs |
hmoment | Hydrophobic moment calculation |
pepcoil | Predicts coiled coil regions |
pepnet | Displays proteins as a helical net |
pepwheel | Shows protein sequences as helices |
This application was modified for inclusion in EMBOSS by Ian Longden (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.