Difference between revisions of "BZIP study"
From Crop Genomics Lab.
KangHeum Cho (Talk | contribs) |
KangHeum Cho (Talk | contribs) |
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=== HMM domain clans === | === HMM domain clans === | ||
− | * [https://pfam.xfam.org/family/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) | ||
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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
- bZIP_1 (PF00170)
Regarded as the main domain for bZIP transcription factor. Clearly distinguishes basic region and leucine zipper.
Used for further analysis.
- bZIP_2 (PF07716)
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
- 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