Difference between revisions of "HMM PD0003"
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=== Description === | === Description === | ||
| − | We built the profile because the boundary of phosphatase domain defined by Pfam profile is not the same as the one reported in crystal structure study <cite>Begley03</cite> and SMART does not have the profile for the myotubularin phosphatase domain. The crystal structure shows the phosphatase domain ranges from 205-586 (Figure 6A in <cite>Begley03</cite>). The Pfam profile [http://pfam.xfam.org/family/PF06602.10 Myotub-related (PF06602)] predicted the range from 192-529. | + | We built the profile because the boundary of phosphatase domain defined by Pfam profile is not the same as the one reported in crystal structure study <cite>Begley03</cite> and SMART does not have the profile for the myotubularin phosphatase domain. The crystal structure shows the phosphatase domain ranges from 205-586 in human MTMR2 (Figure 6A in <cite>Begley03</cite>). The Pfam profile [http://pfam.xfam.org/family/PF06602.10 Myotub-related (PF06602)] predicted the range from 192-529. |
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| + | === How the HMM was built === | ||
| + | We PSI-BLASTed the region from 190 to 600 of human MTMR2. The region is the phosphatase domain determined in crystal structure study with flanking regions. | ||
| + | |||
| + | We first PSI-BLASTed the region against RefSeq database via NCBI BLAST server. We found 5000+ hits in 1st round. | ||
| + | |||
| + | Note: In addition to PSI-BLAST, we tried to obtain an alignment from HHPRED, but the quality is pretty bad. | ||
=== References === | === References === | ||
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#Begley03 pmid=14690594 | #Begley03 pmid=14690594 | ||
</biblio> | </biblio> | ||
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=== Supplementary materials === | === Supplementary materials === | ||
Revision as of 17:50, 6 October 2015
Back to List of HMMs
Symbol: MTM_PD
Name: Myotubularin phosphatase domain
Description
We built the profile because the boundary of phosphatase domain defined by Pfam profile is not the same as the one reported in crystal structure study [1] and SMART does not have the profile for the myotubularin phosphatase domain. The crystal structure shows the phosphatase domain ranges from 205-586 in human MTMR2 (Figure 6A in [1]). The Pfam profile Myotub-related (PF06602) predicted the range from 192-529.
How the HMM was built
We PSI-BLASTed the region from 190 to 600 of human MTMR2. The region is the phosphatase domain determined in crystal structure study with flanking regions.
We first PSI-BLASTed the region against RefSeq database via NCBI BLAST server. We found 5000+ hits in 1st round.
Note: In addition to PSI-BLAST, we tried to obtain an alignment from HHPRED, but the quality is pretty bad.
References
- Begley MJ, Taylor GS, Kim SA, Veine DM, Dixon JE, and Stuckey JA. Crystal structure of a phosphoinositide phosphatase, MTMR2: insights into myotubular myopathy and Charcot-Marie-Tooth syndrome. Mol Cell. 2003 Dec;12(6):1391-402. DOI:10.1016/s1097-2765(03)00486-6 |
Supplementary materials
The sequence of the phosphatase domain of human MTMR2 determined by crystal structure [1]:
>Hsap_MTMR2:205-586 id=HsapP048_AA CC1:CC1:Myotubularin:MTMR1 [Homo sapiens] GWKLYDPLLEYRRQGIPNESWRITKINERYELCDTYPALLVVPANIPDEELKRVASFRSRGRIPVLSWIHPESQATITRCSQPMVGVSGKRSKEDEKYLQAIMDSNAQSHKIFIFDARPSVNAVANKAKGGGYESEDAYQNAELVFLDIHNIHVMRESLRKLKEIVYPNIEETHWLSNLESTHWLEHIKLILAGALRIADKVESGKTSVVVHSSDGWDRTAQLTSLAMLMLDGYYRTIRGFEVLVEKEWLSFGHRFQLRVGHGDKNHADADRSPVFLQFIDCVWQMTRQFPTAFEFNEYFLITILDHLYSCLFGTFLCNSEQQRGKENLPKRTVSLWSYINSQLEDFTNPLYGSYSNHVLYPVASMRHLELWVGYYIRWNPR
