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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Revision as of 05:49, 9 October 2015

Back to List of HMMs

Symbol: SAC9_NTD1

Name: SAC9, N-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_NTD1 and SAC_NTD2, respectively. We built two HMMs for each of the two regions.