Difference between revisions of "HMM PD0145"
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(Created page with "Back to '''List of HMMs''' '''Symbol''': SAC9_NTD1 '''Name''': SAC9, N-Terminal Domain 1 === Why built the HMM? === We noticed Ddis051 ...") |
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Back to '''[[HMM|List of HMMs]]''' | Back to '''[[HMM|List of HMMs]]''' | ||
| − | '''Symbol''': | + | '''Symbol''': SAC9_CTD1 |
| − | '''Name''': SAC9, | + | '''Name''': SAC9, C-Terminal Domain 1 |
=== Why built the HMM? === | === Why built the HMM? === | ||
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=== How the HMM is built === | === How the HMM is built === | ||
| − | We then PSI-BLASTed the tail (from the C-terminal of Sac_PD to the C-terminal of the full sequence) against Swiss-Prot. Because there were very few hits, we then PSI-BLASTed the same region against Ref-Seq. We downloaded the sequences, removed redundant sequences (at threshold 70% identity), aligned the sequences and manually adjusted the alignments. We found there were actually two conserved regions, which we named | + | We then PSI-BLASTed the tail (from the C-terminal of Sac_PD to the C-terminal of the full sequence) against Swiss-Prot. Because there were very few hits, we then PSI-BLASTed the same region against Ref-Seq. We downloaded the sequences, removed redundant sequences (at threshold 70% identity), aligned the sequences and manually adjusted the alignments. We found there were actually two conserved regions, which we named SAC_CTD1 and [[HMM_PD0146|SAC_CTD2]], respectively. We built two HMMs for each of the two regions. |
Latest revision as of 17:53, 9 October 2015
Back to List of HMMs
Symbol: SAC9_CTD1
Name: SAC9, C-Terminal Domain 1
Why built the HMM?
We noticed Ddis051 has a tail not similar to other SACs in the nine genomes.
How the HMM is built
We then PSI-BLASTed the tail (from the C-terminal of Sac_PD to the C-terminal of the full sequence) against Swiss-Prot. Because there were very few hits, we then PSI-BLASTed the same region against Ref-Seq. We downloaded the sequences, removed redundant sequences (at threshold 70% identity), aligned the sequences and manually adjusted the alignments. We found there were actually two conserved regions, which we named SAC_CTD1 and SAC_CTD2, respectively. We built two HMMs for each of the two regions.
