Difference between revisions of "Secondary Structure Prediction BCKDHA"

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(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 ===
   
 
== 2. Prediction of disordered regions ==
 
== 2. Prediction of disordered regions ==

Revision as of 14:23, 24 May 2011

1. Secondary structure prediction

PSIPRED

Example.jpg Secundary Structure

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

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

4. Prediction of GO terms