Difference between revisions of "Secondary Structure Prediction BCKDHA"

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(3. Prediction of transmembrane alpha-helices and signal peptides)
(4. Prediction of GO terms)
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== 4. Prediction of GO terms ==
 
== 4. Prediction of GO terms ==
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=== Pfam ===
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{|
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!Query
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!Cellular Component
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!Molecular function
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!Biological Process
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|-
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|BCKDHA
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|
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|GO:0016624 (oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor)
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|GO:0008152 (metabolic process)
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|-
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|A4_HUMAN
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|GO:0016021 (integral to membrane)
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|GO:0005488 (bindung)
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|
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|-
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|BACR_HALSA
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|GO:0016020 (membrane)
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|GO:0005216 (ion channel activity)
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|GO: 0006811 (ion transport)
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|-
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|INSL5_HUMAN
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|GO:0005576 (extracellular region)
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|GO:0005179 (hormone activity)
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|
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|-
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|LAMP1_HUMAN
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|
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|
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|
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|
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|-

Revision as of 14:59, 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

OCTOPUS

SPOCTOPUS

4. Prediction of GO terms

Pfam

Query Cellular Component Molecular function Biological Process
BCKDHA GO:0016624 (oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor) GO:0008152 (metabolic process)
A4_HUMAN GO:0016021 (integral to membrane) GO:0005488 (bindung)
BACR_HALSA GO:0016020 (membrane) GO:0005216 (ion channel activity) GO: 0006811 (ion transport)
INSL5_HUMAN GO:0005576 (extracellular region) GO:0005179 (hormone activity)
LAMP1_HUMAN