Difference between revisions of "HMM PD0003"
(→Supplementary materials) |
(→How the HMM was built) |
||
| Line 9: | Line 9: | ||
=== How the HMM was built === | === 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 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 <cite>Begley03</cite>: |
| − | + | >Hsap_MTMR2:205-586 id=HsapP048_AA CC1:CC1:Myotubularin:MTMR1 [Homo sapiens] | |
| + | GWKLYDPLLEYRRQGIPNESWRITKINERYELCDTYPALLVVPANIPDEELKRVASFRSRGRIPVLSWIHPESQATITRCSQPMVGVSGKRSKEDEKYLQAIMDSNAQSHKIFIFDARPSVNAVANKAKGGGYESEDAYQNAELVFLDIHNIHVMRESLRKLKEIVYPNIEETHWLSNLESTHWLEHIKLILAGALRIADKVESGKTSVVVHSSDGWDRTAQLTSLAMLMLDGYYRTIRGFEVLVEKEWLSFGHRFQLRVGHGDKNHADADRSPVFLQFIDCVWQMTRQFPTAFEFNEYFLITILDHLYSCLFGTFLCNSEQQRGKENLPKRTVSLWSYINSQLEDFTNPLYGSYSNHVLYPVASMRHLELWVGYYIRWNPR | ||
| − | We | + | 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 three individual HMMs for the subfamilies: | ||
| + | * MTMR1, MTMR6, MTMR9 (perhaps MTMR3) | ||
| + | * MTMR10 | ||
| + | * MTMR13 | ||
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 18:27, 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 [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 three individual HMMs for the subfamilies:
- MTMR1, MTMR6, MTMR9 (perhaps MTMR3)
- MTMR10
- MTMR13
Note: In addition to PSI-BLAST, we tried to obtain an alignment from HHPRED, but the quality is pretty bad.
