Difference between revisions of "Secondary Structure Prediction BCKDHA"
From Bioinformatikpedia
(→3. Prediction of transmembrane alpha-helices and signal peptides) |
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== 1. Secondary structure prediction == |
== 1. Secondary structure prediction == |
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+ | |||
+ | === PSIPRED === |
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+ | |||
+ | [[File:Example.jpg]] |
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+ | Secundary Structure |
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+ | {| border="1" style="text-align:center; border-spacing:0;" |
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+ | !start |
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+ | !end |
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+ | !structural element |
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+ | |- |
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+ | | 1 || 1 || C |
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+ | |- |
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+ | | 2 || 16 || A |
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+ | |- |
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+ | | 17 || 17 || C |
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+ | |- |
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+ | |18 || 25 || A |
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+ | |- |
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+ | |26 || 77 || C |
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+ | |- |
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+ | |78 || 82 || E |
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+ | |- |
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+ | |83 || 98 || C |
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+ | |- |
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+ | |99 || 124 || H |
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+ | |- |
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+ | | 125 || 136 ||C |
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+ | |- |
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+ | |137 || 146 || H |
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+ | |- |
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+ | | 147 || 152 || C |
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+ | |- |
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+ | |153 || 155 || E |
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+ | |- |
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+ | | 156 || 159|| C |
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+ | |- |
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+ | |160 || 166 || H |
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+ | |- |
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+ | |167 || 170 || C |
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+ | |- |
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+ | |171 || 178 || H |
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+ | |- |
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+ | |179 || 212 || C |
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+ | |- |
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+ | |213 || 125 || H |
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+ | |- |
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+ | |126 || 130 || C |
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+ | |- |
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+ | |231 || 236 || E |
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+ | |- |
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+ | |237 || 242 || C |
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+ | |- |
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+ | |243 || 256 || H |
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+ | |- |
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+ | |257 || 259 || C |
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+ | |- |
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+ | |260 || 265 || E |
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+ | |- |
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+ | |266 || 276 || C |
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+ | |- |
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+ | |277 || 278 || H |
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+ | |- |
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+ | |279 || 282 || C |
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+ | |- |
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+ | |283 || 287 || H |
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+ | |- |
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+ | |288 || 296 || C |
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+ | |- |
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+ | |297 || 298 || E |
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+ | |- |
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+ | |299 ||300 || C |
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+ | |- |
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+ | |301 || 318 || H |
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+ | |- |
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+ | |319 || 323 || C |
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+ | |- |
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+ | |324 || 329 || E |
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+ | |- |
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+ | |330 || 347 || C |
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+ | |- |
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+ | |348 || 356 || H |
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+ | |- |
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+ | |357 || 360 || C |
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+ | |- |
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+ | |361 || 370 || H |
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+ | |- |
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+ | |371 || 375 || C |
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+ | |- |
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+ | |377 || 399 || H |
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+ | |- |
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+ | |400 || 404 || C |
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+ | |- |
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+ | |405 || 413 || H |
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+ | |- |
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+ | |414 || 417 || C |
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+ | |- |
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+ | |418 || 434 || H |
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+ | |- |
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+ | |435 || 445 || C |
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+ | |} |
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+ | legend: A=alpha helix, E=beta strand, C=coil |
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+ | |||
+ | |||
+ | |||
+ | === Jpred3 === |
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+ | |||
+ | |||
+ | {| border="1" style="text-align:center; border-spacing:0;" |
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+ | !PDB-ID |
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+ | !Score |
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+ | !Identity |
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+ | !Evalue |
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+ | |- |
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+ | |||
+ | |} |
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+ | |||
+ | === DSSP === |
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== 2. Prediction of disordered regions == |
== 2. Prediction of disordered regions == |
Revision as of 15:23, 24 May 2011
Contents
1. Secondary structure prediction
PSIPRED
start | end | structural element |
---|---|---|
1 | 1 | C |
2 | 16 | A |
17 | 17 | C |
18 | 25 | A |
26 | 77 | C |
78 | 82 | E |
83 | 98 | C |
99 | 124 | H |
125 | 136 | C |
137 | 146 | H |
147 | 152 | C |
153 | 155 | E |
156 | 159 | C |
160 | 166 | H |
167 | 170 | C |
171 | 178 | H |
179 | 212 | C |
213 | 125 | H |
126 | 130 | C |
231 | 236 | E |
237 | 242 | C |
243 | 256 | H |
257 | 259 | C |
260 | 265 | E |
266 | 276 | C |
277 | 278 | H |
279 | 282 | C |
283 | 287 | H |
288 | 296 | C |
297 | 298 | E |
299 | 300 | C |
301 | 318 | H |
319 | 323 | C |
324 | 329 | E |
330 | 347 | C |
348 | 356 | H |
357 | 360 | C |
361 | 370 | H |
371 | 375 | C |
377 | 399 | H |
400 | 404 | C |
405 | 413 | H |
414 | 417 | C |
418 | 434 | H |
435 | 445 | C |
legend: A=alpha helix, E=beta strand, C=coil
Jpred3
PDB-ID | Score | Identity | Evalue |
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DSSP
2. Prediction of disordered regions
3. Prediction of transmembrane alpha-helices and signal peptides
Transmembrane topology and signal peptides are features that are likely to be conserved during evolution.
Phobius
Phobius predicted a signal peptide with about 90% probability at the beginning of the sequence. The predicted signal peptide is 34 amino acids long. The rest of the amino acid is a non cytoplasmic protein sequence. No part of the protein is predicted to be transmembrane spanning.
sp|P12694|ODBA_HUMAN (BCKDHA) | |||
---|---|---|---|
Signal | 1 | 34 | |
Region | 1 | 16 | N-Region |
Region | 17 | 25 | H-Region |
Region | 26 | 34 | C-Region |
TOPO_DOM | 35 | 445 | non cytoplasmic |
sp|P02945|BACR_HALSA | ||||
---|---|---|---|---|
TOPO_DOM | 1 | 22 | NON CYTOPLASMIC. | |
TRANSMEM | 23 | 42 | ||
TOPO_DOM | 43 | 53 | CYTOPLASMIC. | |
TRANSMEM | 54 | 76 | ||
TOPO_DOM | 77 | 95 | NON CYTOPLASMIC. | |
TRANSMEM | 96 | 114 | ||
TOPO_DOM | 115 | 120 | CYTOPLASMIC. | |
TRANSMEM | 121 | 142 | ||
TOPO_DOM | 143 | 147 | NON CYTOPLASMIC. | |
TRANSMEM | 148 | 169 | ||
TOPO_DOM | 170 | 189 | CYTOPLASMIC. | |
TRANSMEM | 190 | 212 | ||
TOPO_DOM | 213 | 217 | NON CYTOPLASMIC. | |
TRANSMEM | 218 | 237 | ||
TOPO_DOM | 238 | 262 | CYTOPLASMIC. |
sp|Q9Y5Q6|INSL5_HUMAN | |||
---|---|---|---|
SIGNAL | 1 | 22 | |
REGION | 1 | 5 | N-REGION |
REGION | 6 | 17 | H-REGION |
REGION | 18 | 22 | C-REGION |
TOPO_DOM | 23 | 135 | NON CYTOPLASMIC |
sp|P11279|LAMP1_HUMAN | |||
---|---|---|---|
SIGNAL | 1 | 28 | |
REGION | 1 | 10 | N-REGION |
REGION | 11 | 22 | H-REGION |
REGION | 23 | 28 | C-REGION |
TOPO_DOM | 29 | 381 | NON CYTOPLASMIC |
TRANSMEM | 382 | 405 | |
TOPO_DOM | 405 | 417 | CYTOPLASMIC |
sp|P05067|A4_HUMAN | |||
---|---|---|---|
SIGNAL | 1 | 17 | |
REGION | 1 | 1 | N-REGION |
REGION | 2 | 12 | H-REGION |
REGION | 13 | 17 | C-REGION |
TOPO_DOM | 18 | 700 | NON CYTOPLASMIC |
TRANSMEM | 701 | 723 | |
TOPO_DOM | 724 | 770 | CYTOPLASMIC |
sp|P02753|RET4_HUMAN | |||
---|---|---|---|
SIGNAL | 1 | 18 | |
REGION | 1 | 2 | N-REGION |
REGION | 3 | 13 | H-REGION |
REGION | 14 | 18 | C-REGION |
TOPO_DOM | 19 | 201 | NON CYTOPLASMIC |
Polyphobius
OBDA_HUMAN (BCKDHA) | |||
---|---|---|---|
TOPO_DOM | 1 | 445 | Non cytoplasmic |
sp|P02945|BACR_HALSA | |||
---|---|---|---|
TOPO_DOM | 1 | 21 | NON CYTOPLASMIC. |
TRANSMEM | 22 | 43 | |
TOPO_DOM | 44 | 54 | CYTOPLASMIC. |
TRANSMEM | 55 | 77 | |
TOPO_DOM | 78 | 94 | NON CYTOPLASMIC. |
TRANSMEM | 95 | 114 | |
TOPO_DOM | 115 | 120 | CYTOPLASMIC. |
TRANSMEM | 121 | 141 | |
TOPO_DOM | 142 | 147 | NON CYTOPLASMIC. |
TRANSMEM | 148 | 166 | |
TOPO_DOM | 167 | 186 | CYTOPLASMIC. |
TRANSMEM | 187 | 205 | |
TOPO_DOM | 206 | 215 | NON CYTOPLASMIC. |
TRANSMEM | 216 | 237 | |
TOPO_DOM | 238 | 262 | CYTOPLASMIC. |
sp|Q9Y5Q6|INSL5_HUMAN | |||
---|---|---|---|
SIGNAL | 1 | 22 | |
REGION | 1 | 4 | N-REGION |
REGION | 5 | 16 | H-REGION |
REGION | 17 | 22 | C-REGION |
TOPO_DOM | 23 | 135 | NON CYTOPLASMIC |
sp|P11279|LAMP1_HUMAN | |||
---|---|---|---|
SIGNAL | 1 | 28 | |
REGION | 1 | 9 | N-REGION |
REGION | 10 | 22 | H-REGION |
REGION | 23 | 28 | C-REGION |
TOPO_DOM | 29 | 381 | NON CYTOPLASMIC |
TRANSMEM | 382 | 405 | |
TOPO_DOM | 405 | 417 | CYTOPLASMIC |
sp|P05067|A4_HUMAN | |||
---|---|---|---|
SIGNAL | 1 | 17 | |
REGION | 1 | 3 | N-REGION |
REGION | 4 | 12 | H-REGION |
REGION | 13 | 17 | C-REGION |
TOPO_DOM | 18 | 700 | NON CYTOPLASMIC |
TRANSMEM | 701 | 723 | |
TOPO_DOM | 724 | 770 | CYTOPLASMIC |
sp|P02753|RET4_HUMAN | |||
---|---|---|---|
SIGNAL | 1 | 18 | |
REGION | 1 | 3 | N-REGION |
REGION | 4 | 13 | H-REGION |
REGION | 14 | 18 | C-REGION |
TOPO_DOM | 19 | 201 | NON CYTOPLASMIC |