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topo |
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% topo tsw:aqp1_human -signa -prol=UM -cys=cg -gly=sr -acid=dr -basic=db -ohaa=da -araa=dg -graph ps Draws an image of a transmembrane protein Transmembrane Sections: 18 35 49 67 94 115 136 156 165 184 211 232 First membrane from the outside [Y]: n Signature Sections: 74 82 sy 189 189 hm 239 239 sa 157 157 sa 262 262 sa Created topo.ps |
Go to the input files for this example
Go to the output files for this example
Standard (Mandatory) qualifiers (* if not always prompted):
[-sequence] sequence Protein sequence filename and optional
format, or reference (input USA)
-sections range [(full sequence)] Examples of region
specifications are:
24-45, 56-78
1:45, 67=99;765..888
1,5,8,10,23,45,57,99
-[no]membrane boolean [Y] First membrane from the outside
-signature toggle [N] Are there any signature areas to be
marked
* -sigrange range [(full sequence)] Examples of ranges
specifications are:
10-10 CF, 56-78 SY\ 1:45 SR, 67=99
HY;765..888 SF
1,5,HG,8,10,HY,23,45,SR,57,99,UG
-graph graph [$EMBOSS_GRAPHICS value, or x11] Graph type
(ps, hpgl, hp7470, hp7580, meta, cps, x11,
tekt, tek, none, data, das, xterm, png, gif)
Additional (Optional) qualifiers:
-cyssymbol menu [CF] Code representing shape and colour for
cys
i.e. SR square red, HY hexagon yellow
CF circle NOfill, UG up arrow green (Values:
N (None); CF (circle); SF (square); HF
(hexagon); UF (up arrow); DF (down arrow); C
(black circle); CG (green circle); CR (red
circle); CB (blue circle); CA (aqua circle);
CM (magenta circle); CY (yellow circle); S
(black square); SG (green square); SR (red
square); SB (blue square); SA (aqua square);
SM (magenta square); SY (yellow square); H
(black hexagon); HG (green hexagon); HR (red
hexagon); HB (blue hexagon); HA (aqua
hexagon); HM (magenta hexagon); HY (yellow
hexagon); U (black up arrow); UG (green up
arrow); UR (red up arrow); UB (blue up
arrow); UA (aqua up arrow); UM (magenta up
arrow); UY (yellow up arrow); D (black down
arrow); DG (green down arrow); DR (red down
arrow); DB (blue down arrow); DA (aqua down
arrow); DM (magenta down arrow); DY (yellow
down arrow))
-glysymbol menu [CF] Symbol to display N-glycosylation sites
outside of membrane see cyssymbol for
examples (Values: N (None); CF (circle); SF
(square); HF (hexagon); UF (up arrow); DF
(down arrow); C (black circle); CG (green
circle); CR (red circle); CB (blue circle);
CA (aqua circle); CM (magenta circle); CY
(yellow circle); S (black square); SG (green
square); SR (red square); SB (blue square);
SA (aqua square); SM (magenta square); SY
(yellow square); H (black hexagon); HG
(green hexagon); HR (red hexagon); HB (blue
hexagon); HA (aqua hexagon); HM (magenta
hexagon); HY (yellow hexagon); U (black up
arrow); UG (green up arrow); UR (red up
arrow); UB (blue up arrow); UA (aqua up
arrow); UM (magenta up arrow); UY (yellow up
arrow); D (black down arrow); DG (green
down arrow); DR (red down arrow); DB (blue
down arrow); DA (aqua down arrow); DM
(magenta down arrow); DY (yellow down
arrow))
-acidicaa menu [CF] Symbol to display acidic amino acids
(Values: N (None); CF (circle); SF (square);
HF (hexagon); UF (up arrow); DF (down
arrow); C (black circle); CG (green circle);
CR (red circle); CB (blue circle); CA (aqua
circle); CM (magenta circle); CY (yellow
circle); S (black square); SG (green
square); SR (red square); SB (blue square);
SA (aqua square); SM (magenta square); SY
(yellow square); H (black hexagon); HG
(green hexagon); HR (red hexagon); HB (blue
hexagon); HA (aqua hexagon); HM (magenta
hexagon); HY (yellow hexagon); U (black up
arrow); UG (green up arrow); UR (red up
arrow); UB (blue up arrow); UA (aqua up
arrow); UM (magenta up arrow); UY (yellow up
arrow); D (black down arrow); DG (green
down arrow); DR (red down arrow); DB (blue
down arrow); DA (aqua down arrow); DM
(magenta down arrow); DY (yellow down
arrow))
-basicaa menu [CF] Symbol to display basic amino acids
(Values: N (None); CF (circle); SF (square);
HF (hexagon); UF (up arrow); DF (down
arrow); C (black circle); CG (green circle);
CR (red circle); CB (blue circle); CA (aqua
circle); CM (magenta circle); CY (yellow
circle); S (black square); SG (green
square); SR (red square); SB (blue square);
SA (aqua square); SM (magenta square); SY
(yellow square); H (black hexagon); HG
(green hexagon); HR (red hexagon); HB (blue
hexagon); HA (aqua hexagon); HM (magenta
hexagon); HY (yellow hexagon); U (black up
arrow); UG (green up arrow); UR (red up
arrow); UB (blue up arrow); UA (aqua up
arrow); UM (magenta up arrow); UY (yellow up
arrow); D (black down arrow); DG (green
down arrow); DR (red down arrow); DB (blue
down arrow); DA (aqua down arrow); DM
(magenta down arrow); DY (yellow down
arrow))
-amineaa menu [CF] Symbol to display amine amino acids
(Values: N (None); CF (circle); SF (square);
HF (hexagon); UF (up arrow); DF (down
arrow); C (black circle); CG (green circle);
CR (red circle); CB (blue circle); CA (aqua
circle); CM (magenta circle); CY (yellow
circle); S (black square); SG (green
square); SR (red square); SB (blue square);
SA (aqua square); SM (magenta square); SY
(yellow square); H (black hexagon); HG
(green hexagon); HR (red hexagon); HB (blue
hexagon); HA (aqua hexagon); HM (magenta
hexagon); HY (yellow hexagon); U (black up
arrow); UG (green up arrow); UR (red up
arrow); UB (blue up arrow); UA (aqua up
arrow); UM (magenta up arrow); UY (yellow up
arrow); D (black down arrow); DG (green
down arrow); DR (red down arrow); DB (blue
down arrow); DA (aqua down arrow); DM
(magenta down arrow); DY (yellow down
arrow))
-ohaa menu [CF] Symbol to display OH- amino acids
(Values: N (None); CF (circle); SF (square);
HF (hexagon); UF (up arrow); DF (down
arrow); C (black circle); CG (green circle);
CR (red circle); CB (blue circle); CA (aqua
circle); CM (magenta circle); CY (yellow
circle); S (black square); SG (green
square); SR (red square); SB (blue square);
SA (aqua square); SM (magenta square); SY
(yellow square); H (black hexagon); HG
(green hexagon); HR (red hexagon); HB (blue
hexagon); HA (aqua hexagon); HM (magenta
hexagon); HY (yellow hexagon); U (black up
arrow); UG (green up arrow); UR (red up
arrow); UB (blue up arrow); UA (aqua up
arrow); UM (magenta up arrow); UY (yellow up
arrow); D (black down arrow); DG (green
down arrow); DR (red down arrow); DB (blue
down arrow); DA (aqua down arrow); DM
(magenta down arrow); DY (yellow down
arrow))
-araa menu [CF] Symbol to display aromatic amino acids
(Values: N (None); CF (circle); SF (square);
HF (hexagon); UF (up arrow); DF (down
arrow); C (black circle); CG (green circle);
CR (red circle); CB (blue circle); CA (aqua
circle); CM (magenta circle); CY (yellow
circle); S (black square); SG (green
square); SR (red square); SB (blue square);
SA (aqua square); SM (magenta square); SY
(yellow square); H (black hexagon); HG
(green hexagon); HR (red hexagon); HB (blue
hexagon); HA (aqua hexagon); HM (magenta
hexagon); HY (yellow hexagon); U (black up
arrow); UG (green up arrow); UR (red up
arrow); UB (blue up arrow); UA (aqua up
arrow); UM (magenta up arrow); UY (yellow up
arrow); D (black down arrow); DG (green
down arrow); DR (red down arrow); DB (blue
down arrow); DA (aqua down arrow); DM
(magenta down arrow); DY (yellow down
arrow))
-proline menu [CF] Symbol to display prolines (Values: N
(None); CF (circle); SF (square); HF
(hexagon); UF (up arrow); DF (down arrow); C
(black circle); CG (green circle); CR (red
circle); CB (blue circle); CA (aqua circle);
CM (magenta circle); CY (yellow circle); S
(black square); SG (green square); SR (red
square); SB (blue square); SA (aqua square);
SM (magenta square); SY (yellow square); H
(black hexagon); HG (green hexagon); HR (red
hexagon); HB (blue hexagon); HA (aqua
hexagon); HM (magenta hexagon); HY (yellow
hexagon); U (black up arrow); UG (green up
arrow); UR (red up arrow); UB (blue up
arrow); UA (aqua up arrow); UM (magenta up
arrow); UY (yellow up arrow); D (black down
arrow); DG (green down arrow); DR (red down
arrow); DB (blue down arrow); DA (aqua down
arrow); DM (magenta down arrow); DY (yellow
down arrow))
-draft boolean [N] Is this a draft plot
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of the sequence to be used
-send1 integer End of the sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-sformat1 string Input sequence format
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-graph" associated qualifiers
-gprompt boolean Graph prompting
-gdesc string Graph description
-gtitle string Graph title
-gsubtitle string Graph subtitle
-gxtitle string Graph x axis title
-gytitle string Graph y axis title
-goutfile string Output file for non interactive displays
-gdirectory string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
|
| Standard (Mandatory) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| [-sequence] (Parameter 1) |
Protein sequence filename and optional format, or reference (input USA) | Readable sequence | Required | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -sections | Examples of region specifications are: 24-45, 56-78 1:45, 67=99;765..888 1,5,8,10,23,45,57,99 | Sequence range | full sequence | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -[no]membrane | First membrane from the outside | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -signature | Are there any signature areas to be marked | Toggle value Yes/No | No | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -sigrange | Examples of ranges specifications are: 10-10 CF, 56-78 SY\ 1:45 SR, 67=99 HY;765..888 SF 1,5,HG,8,10,HY,23,45,SR,57,99,UG | Sequence range | full sequence | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -graph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, das, xterm, png, gif | EMBOSS_GRAPHICS value, or x11 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Additional (Optional) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -cyssymbol | Code representing shape and colour for cys i.e. SR square red, HY hexagon yellow CF circle NOfill, UG up arrow green |
|
CF | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -glysymbol | Symbol to display N-glycosylation sites outside of membrane see cyssymbol for examples |
|
CF | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -acidicaa | Symbol to display acidic amino acids |
|
CF | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -basicaa | Symbol to display basic amino acids |
|
CF | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -amineaa | Symbol to display amine amino acids |
|
CF | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -ohaa | Symbol to display OH- amino acids |
|
CF | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -araa | Symbol to display aromatic amino acids |
|
CF | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -proline | Symbol to display prolines |
|
CF | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| -draft | Is this a draft plot | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| (none) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ID AQP1_HUMAN Reviewed; 269 AA.
AC P29972; Q8TBI5; Q8TDC1;
DT 01-APR-1993, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 16-JUN-2009, entry version 108.
DE RecName: Full=Aquaporin-1;
DE Short=AQP-1;
DE AltName: Full=Aquaporin-CHIP;
DE AltName: Full=Water channel protein for red blood cells and kidney proximal tubule;
DE AltName: Full=Urine water channel;
GN Name=AQP1; Synonyms=CHIP28;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND PARTIAL PROTEIN SEQUENCE.
RX MEDLINE=92107900; PubMed=1722319; DOI=10.1073/pnas.88.24.11110;
RA Preston G.M., Agre P.;
RT "Isolation of the cDNA for erythrocyte integral membrane protein of 28
RT kilodaltons: member of an ancient channel family.";
RL Proc. Natl. Acad. Sci. U.S.A. 88:11110-11114(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX MEDLINE=93340184; PubMed=8340403;
RA Moon C., Preston G.M., Griffin C.A., Jabs E.W., Agre P.;
RT "The human aquaporin-CHIP gene. Structure, organization, and
RT chromosomal localization.";
RL J. Biol. Chem. 268:15772-15778(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Retinal pigment epithelium;
RX MEDLINE=96326579; PubMed=8703970; DOI=10.1016/0005-2736(96)00076-4;
RA Ruiz A.C., Bok D.;
RT "Characterization of the 3' UTR sequence encoded by the AQP-1 gene in
RT human retinal pigment epithelium.";
RL Biochim. Biophys. Acta 1282:174-178(1996).
RN [4]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Uterus;
RX MEDLINE=94290349; PubMed=7517253;
RA Li X., Yu H., Koide S.S.;
RT "The water channel gene in human uterus.";
RL Biochem. Mol. Biol. Int. 32:371-377(1994).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANTS VAL-45 AND ASP-165.
RG SeattleSNPs variation discovery resource;
RL Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [6]
[Part of this file has been deleted for brevity]
FT TRANSMEM 137 155 Helix 4.
FT TOPO_DOM 156 166 Cytoplasmic.
FT TRANSMEM 167 183 Helix 5.
FT TOPO_DOM 184 186 Extracellular.
FT TOPO_DOM 187 192 In membrane.
FT TRANSMEM 193 200 Helix E.
FT TOPO_DOM 201 207 Extracellular.
FT TRANSMEM 208 228 Helix 6.
FT TOPO_DOM 229 269 Cytoplasmic.
FT MOTIF 76 78 NPA 1.
FT MOTIF 192 194 NPA 2.
FT COMPBIAS 159 162 Poly-Arg.
FT SITE 56 56 Substrate discrimination.
FT SITE 180 180 Substrate discrimination.
FT SITE 189 189 Hg(2+)-sensitive residue.
FT SITE 195 195 Substrate discrimination.
FT MOD_RES 246 246 Phosphothreonine (By similarity).
FT MOD_RES 247 247 Phosphoserine (By similarity).
FT MOD_RES 262 262 Phosphoserine.
FT CARBOHYD 42 42 N-linked (GlcNAc...).
FT CARBOHYD 205 205 N-linked (GlcNAc...) (Potential).
FT VARIANT 38 38 P -> L (in Co(A-B-) antigen; non
FT functional AQP1; red cells show low
FT osmotic water permeability).
FT /FTId=VAR_013279.
FT VARIANT 45 45 A -> V (in Co(A-B+) antigen;
FT dbSNP:rs28362692).
FT /FTId=VAR_004400.
FT VARIANT 165 165 G -> D (in dbSNP:rs28362731).
FT /FTId=VAR_022318.
FT CONFLICT 45 45 A -> T (in Ref. 7; AAH22486).
FT HELIX 8 35
FT STRAND 37 42
FT HELIX 48 65
FT STRAND 68 71
FT HELIX 76 83
FT HELIX 94 114
FT TURN 119 122
FT STRAND 132 135
FT HELIX 136 154
FT HELIX 166 182
FT TURN 183 185
FT HELIX 192 199
FT HELIX 207 227
SQ SEQUENCE 269 AA; 28526 MW; BA204D82FB26352E CRC64;
MASEFKKKLF WRAVVAEFLA TTLFVFISIG SALGFKYPVG NNQTAVQDNV KVSLAFGLSI
ATLAQSVGHI SGAHLNPAVT LGLLLSCQIS IFRALMYIIA QCVGAIVATA ILSGITSSLT
GNSLGRNDLA DGVNSGQGLG IEIIGTLQLV LCVLATTDRR RRDLGGSAPL AIGLSVALGH
LLAIDYTGCG INPARSFGSA VITHNFSNHW IFWVGPFIGG ALAVLIYDFI LAPRSSDLTD
RVKVWTSGQV EEYDLDADDI NSRVEMKPK
//
|
![[topo results]](topo.1.topo.gif)
One letter codes are black filled shaped EXCEPT for "N" which means NONE (no shape).
For two letter codes the first letter is the shape and the second the colour except for "F" which means NO FILL.
For the signatures you need to input sets of start position, end position and code. For the example given these are 74 82 sy 189 189 hm 239 239 sa 157 157 sa 262 262 sa
So residues 74 to 82 will have Yellow Squares (sy). residue 189 (i.e. 189 to 189) will have a Magenta Hexagon. (hm)
| Program name | Description |
|---|---|
| garnier | Predicts protein secondary structure using GOR method |
| helixturnhelix | Identify nucleic acid-binding motifs in protein sequences |
| hmoment | Calculate and plot hydrophobic moment for protein sequence(s) |
| pepcoil | Predicts coiled coil regions in protein sequences |
| pepnet | Draw a helical net for a protein sequence |
| pepwheel | Draw a helical wheel diagram for a protein sequence |
| tmap | Predict and plot transmembrane segments in protein sequences |
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.
Changes to the functionality in version 2 have been ported to the EMBOSS version.