Difference between revisions of "HMM PD0003"
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The result shows we can build four individual HMMs for the subfamilies: | The result shows we can build four individual HMMs for the subfamilies: | ||
| − | * MTMR1, MTMR6, MTMR9 (perhaps MTMR3) | + | * [[HMM_PD0138|MTMR_1_PD]] of MTMR1, MTMR6, MTMR9 (perhaps MTMR3) |
| − | * MTMR10 | + | * [[HMM_PD0140|MTMR10_PD]] of MTMR10 |
| − | * MTMR13 | + | * [[HMM_PD0140|MTMR13_PD]] of MTMR13 |
| − | * MTMR14 | + | * [[HMM_PD0140|MTMR14_PD]] of MTMR14 |
Note: In addition to PSI-BLAST, we tried to obtain an alignment from HHPRED, but the quality is pretty bad. | Note: In addition to PSI-BLAST, we tried to obtain an alignment from HHPRED, but the quality is pretty bad. | ||
Revision as of 21:43, 7 October 2015
Back to List of HMMs
Symbol: CC1_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 [1]:
>Hsap_MTMR2:205-586 id=HsapP048_AA CC1:CC1:Myotubularin:MTMR1 [Homo sapiens] GWKLYDPLLEYRRQGIPNESWRITKINERYELCDTYPALLVVPANIPDEELKRVASFRSRGRIPVLSWIHPESQATITRCSQPMVGVSGKRSKEDEKYLQAIMDSNAQSHKIFIFDARPSVNAVANKAKGGGYESEDAYQNAELVFLDIHNIHVMRESLRKLKEIVYPNIEETHWLSNLESTHWLEHIKLILAGALRIADKVESGKTSVVVHSSDGWDRTAQLTSLAMLMLDGYYRTIRGFEVLVEKEWLSFGHRFQLRVGHGDKNHADADRSPVFLQFIDCVWQMTRQFPTAFEFNEYFLITILDHLYSCLFGTFLCNSEQQRGKENLPKRTVSLWSYINSQLEDFTNPLYGSYSNHVLYPVASMRHLELWVGYYIRWNPR
We first PSI-BLASTed the region against RefSeq database via NCBI BLAST server. We found 5000+ hits in 1st round, which is difficult to look into. We then PSI-BLASTed the region against RefSeq database via NCBI BLAST server. The coverage of human myotubularins:
- MTM1, MTMR1, MTMR2: ~190-600, 100%
- MTMR3: ~214-595 (human, rat, mouse); MTMR4: ~225-588 (human, mouse), ~213-598 (xenopus)
- MTMR5: ~317-535 (human), ~317-579 (mouse); MTMR13 (not in swissprot?)
- MTMR6: ~195-595 (human, mouse); MTMR7: 192-592 (human), 203-593 (mouse); 192-593 (human, chicken)
- MTMR9: 192-588 (human, mouse), 204-592 (cow)
- MTMR10 (MTMRA): 214-532 (human, mouse, xenopus, zebra fish); MTMR11 (MTMRB): 214-561 (human, mouse); MTMR12 (MTMRC): 202-556 (human), 225-556 (mouse, rat, zebra fish),
- MTMR13 (MTMRD): 223-581 (human), 345-581 (xenopus)
The result shows we can build four individual HMMs for the subfamilies:
- MTMR_1_PD of MTMR1, MTMR6, MTMR9 (perhaps MTMR3)
- MTMR10_PD of MTMR10
- MTMR13_PD of MTMR13
- MTMR14_PD of MTMR14
Note: In addition to PSI-BLAST, we tried to obtain an alignment from HHPRED, but the quality is pretty bad.
