Difference between revisions of "Secondary Structure Prediction BCKDHA"

From Bioinformatikpedia
(→‎3. Prediction of transmembrane alpha-helices and signal peptides)
(→‎3. Prediction of transmembrane alpha-helices and signal peptides)
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</tt>
  
</tt>
   
  +
<tt>
  +
{|
  +
!colspan="4"|sp|P11279|LAMP1_HUMAN
  +
|-
  +
|SIGNAL||1||28||
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|-
  +
|REGION||1||10||N-REGION
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|-
  +
|REGION||11||22||H-REGION
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|-
  +
|REGION||23||28||C-REGION
  +
|-
  +
|TOPO_DOM||29||381||NON CYTOPLASMIC
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|-
  +
|TRANSMEM||382||405||
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|-
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|TOPO_DOM||405||417||CYTOPLASMIC
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</tt>
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  +
<tt>
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{|
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!colspan="4"|sp|P05067|A4_HUMAN
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|SIGNAL||1||17||
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|-
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|REGION||1||1||N-REGION
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|-
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|REGION||2||12||H-REGION
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|-
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|REGION||13||17||C-REGION
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|-
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|TOPO_DOM||18||700||NON CYTOPLASMIC
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|-
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|TRANSMEM||701||723||
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|-
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|TOPO_DOM||724||770||CYTOPLASMIC
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|}
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</tt>
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<tt>
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{|
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!colspan="4"|sp|P02753|RET4_HUMAN
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|SIGNAL||1||18||
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|-
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|REGION||1||2||N-REGION
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|-
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|REGION||3||13||H-REGION
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|-
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|REGION||14||18||C-REGION
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|-
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|TOPO_DOM||19||201||NON CYTOPLASMIC
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|}
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</tt>
   
 
=== Polyphobius ===
  
=== Polyphobius ===
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!colspan="4"| sp|P02945|BACR_HALSA
  
!colspan="4"| sp|P02945|BACR_HALSA
 
|-
  
|-
  +
|TOPO_DOM||1||21||NON CYTOPLASMIC.
−
| TOPO_DOM
  
−
| 1
  
−
| 21
  
−
| NON CYTOPLASMIC.
  
 
|-
  
|-
−
|TRANSMEM
+
|TRANSMEM||22||43||
−
| 22
  
−
| 43
 
−
|
  
 
|-
 
|-
−
|TOPO_DOM
+
|TOPO_DOM||44||54||CYTOPLASMIC.
−
|44
  
−
|54
 
−
|CYTOPLASMIC.
  
 
|-
  
|-
−
|TRANSMEM
+
|TRANSMEM||55||77||
−
|55
 
−
|77
 
−
|
  
 
|-
  
|-
−
|TOPO_DOM
+
|TOPO_DOM||78||94||NON CYTOPLASMIC.
−
|78
 
−
|94
 
−
|NON CYTOPLASMIC.
  
 
|-
  
|-
−
|TRANSMEM
+
|TRANSMEM||95||114||
−
|95
 
−
|114
 
−
|
  
 
|-
  
|-
−
|TOPO_DOM
+
|TOPO_DOM||115||120||CYTOPLASMIC.
−
|115
 
−
|120
 
−
|CYTOPLASMIC.
  
 
|-
  
|-
−
|TRANSMEM
+
|TRANSMEM||121||141||
−
|121
 
−
|141
 
−
|
  
 
|-
  
|-
−
| TOPO_DOM
+
| TOPO_DOM||142||147||NON CYTOPLASMIC.
−
|142
 
−
|147
 
−
|NON CYTOPLASMIC.
  
−
|
  
 
|-
  
|-
−
|TRANSMEM
+
|TRANSMEM||148||166||
−
| 148
 
−
|166
 
−
|
  
 
|-
 
|-
−
|TOPO_DOM
+
|TOPO_DOM||167||186||CYTOPLASMIC.
−
|167
 
−
|186
 
−
| CYTOPLASMIC.
  
 
|-
  
|-
−
|TRANSMEM
+
|TRANSMEM||187||205||
−
|187
 
−
|205
 
−
|
  
 
|-
  
|-
−
| TOPO_DOM
+
| TOPO_DOM|| 206|| 215|| NON CYTOPLASMIC.
−
| 206
 
−
| 215
 
−
| NON CYTOPLASMIC.
  
 
|-
  
|-
−
| TRANSMEM
+
| TRANSMEM ||216||237||
−
|216
 
−
|237
 
−
|
  
 
|-
 
|-
−
| TOPO_DOM
+
| TOPO_DOM||238||262||CYTOPLASMIC.
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|}
−
|238
 
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</tt>
−
|262
 
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−
|CYTOPLASMIC.
  
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<tt>
  +
{|
  +
!colspan="4"|sp|Q9Y5Q6|INSL5_HUMAN
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|-
  +
|SIGNAL||1||22||
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|-
  +
|REGION||1||4||N-REGION
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|-
  +
|REGION||5||16||H-REGION
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|-
  +
|REGION||17||22||C-REGION
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|-
  +
|TOPO_DOM||23||135||NON CYTOPLASMIC
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|}
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</tt>
  +
  +
<tt>
  +
{|
  +
!colspan="4"|sp|P11279|LAMP1_HUMAN
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|-
  +
|SIGNAL||1||28||
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|-
  +
|REGION||1||9||N-REGION
  +
|-
  +
|REGION||10||22||H-REGION
  +
|-
  +
|REGION||23||28||C-REGION
  +
|-
  +
|TOPO_DOM||29||381||NON CYTOPLASMIC
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|-
  +
|TRANSMEM||382||405||
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|-
  +
|TOPO_DOM||405||417||CYTOPLASMIC
  +
</tt>
  +
  +
<tt>
  +
{|
  +
!colspan="4"|sp|P05067|A4_HUMAN
  +
|SIGNAL||1||17||
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|-
  +
|REGION||1||3||N-REGION
  +
|-
  +
|REGION||4||12||H-REGION
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|-
  +
|REGION||13||17||C-REGION
  +
|-
  +
|TOPO_DOM||18||700||NON CYTOPLASMIC
  +
|-
  +
|TRANSMEM||701||723||
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|-
  +
|TOPO_DOM||724||770||CYTOPLASMIC
  +
|}
  +
</tt>
  +
  +
<tt>
  +
{|
  +
!colspan="4"|sp|P02753|RET4_HUMAN
  +
|SIGNAL||1||18||
  +
|-
  +
|REGION||1||3||N-REGION
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|-
  +
|REGION||4||13||H-REGION
  +
|-
  +
|REGION||14||18||C-REGION
  +
|-
  +
|TOPO_DOM||19||201||NON CYTOPLASMIC
 
|}
  
|}
 
</tt>
  
</tt>

Revision as of 15:03, 24 May 2011

1. Secondary structure prediction

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

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