Difference between revisions of "HMM PD0149"
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=== Why built the HMM === | === Why built the HMM === | ||
| − | Because our in-house HMM [[ | + | Because our in-house HMM [[HMM_PD0134|MTMR_GRAM]] can not detect all PH domains in myotubularins, we built the PH domain from [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd13223 CDD profile]. |
=== How the HMM was built === | === How the HMM was built === | ||
Revision as of 19:56, 9 October 2015
Back to List of HMMs
Symbol: PH_1
Name: PH domain
Why built the HMM
Because our in-house HMM MTMR_GRAM can not detect all PH domains in myotubularins, we built the PH domain from CDD profile.
How the HMM was built
We downloaded the alignment from CDD, edited the align to get the regions used by CDD to build the profile, built HMM by hmmbuild, and validated by protein phosphatases of the nine genomes.
Using domain E-value threshold 0.1 for both MTMR_GRAM and PD0149 (PH_1) HMMs, among 76 myotubularins in 9 genomes, 58 have PH domains, PD0149 (PH_1) found 2 that were missed by MTMR_GRAM; and MTMR_GRAM found 25 that were missed by PD0149 (PH_1).
