Difference between revisions of "BZIP study"

From Crop Genomics Lab.
Jump to: navigation, search
Line 5: Line 5:
 
=== HMM domain clans ===
 
=== HMM domain clans ===
  
* [https://pfam.xfam.org/family/PF00170#tabview=tab0 bZIP_1] (PF00170)
+
* [https://pfam.xfam.org/family/PF00170 bZIP_1] (PF00170)
  
 
''Regarded as the main domain'' for bZIP transcription factor. Clearly distinguishes basic region and leucine zipper.
 
''Regarded as the main domain'' for bZIP transcription factor. Clearly distinguishes basic region and leucine zipper.
 +
 +
'''Used for further analysis.'''
  
 
* [https://pfam.xfam.org/family/PF07716 bZIP_2] (PF07716)
 
* [https://pfam.xfam.org/family/PF07716 bZIP_2] (PF07716)
Line 17: Line 19:
 
No distinct basic region. No clear leucine zipper interface.
 
No distinct basic region. No clear leucine zipper interface.
  
===
+
=== Downloading and generating HMM consensus sequence file ===
 +
 
 +
# Download Stockholm alignment file from Pfam bZIP_1 > Alignment > Download options > Seed
 +
 
 +
<pre>Seed: the curated alignment from which the HMM for the family is built</pre>
 +
 
 +
#

Revision as of 04:59, 20 April 2019

Contents

Identification

Pfam-based approach

HMM domain clans

Regarded as the main domain for bZIP transcription factor. Clearly distinguishes basic region and leucine zipper.

Used for further analysis.

Conserved basic region, weaker leucine zipper.

  • bZIP_Maf (PF03131)

No distinct basic region. No clear leucine zipper interface.

Downloading and generating HMM consensus sequence file

  1. Download Stockholm alignment file from Pfam bZIP_1 > Alignment > Download options > Seed
Seed: the curated alignment from which the HMM for the family is built