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| | Back to '''[[HMM|List of HMMs]]''' | | Back to '''[[HMM|List of HMMs]]''' |
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| − | '''Symbol''': CC1_MTM_1_PD
| + | See [[HMM_PD0003|CC1_MTM_PD]]. |
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| − | '''Name''': Myotubularin phosphatase domain (group 1)
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| − | === Why built the HMM? ===
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| − | 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, which lacks the C-terminal ~45 aa.
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| − | 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>:
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| − | >Hsap_MTMR2:205-586 id=HsapP048_AA CC1:CC1:Myotubularin:MTMR1 [Homo sapiens]
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| − | GWKLYDPLLEYRRQGIPNESWRITKINERYELCDTYPALLVVPANIPDEELKRVASFRSRGRIPVLSWIHPESQATITRCSQPMVGVSGKRSKEDEKYLQAIMDSNAQSHKIFIFDARPSVNAVANKAKGGGYESEDAYQNAELVFLDIHNIHVMRESLRKLKEIVYPNIEETHWLSNLESTHWLEHIKLILAGALRIADKVESGKTSVVVHSSDGWDRTAQLTSLAMLMLDGYYRTIRGFEVLVEKEWLSFGHRFQLRVGHGDKNHADADRSPVFLQFIDCVWQMTRQFPTAFEFNEYFLITILDHLYSCLFGTFLCNSEQQRGKENLPKRTVSLWSYINSQLEDFTNPLYGSYSNHVLYPVASMRHLELWVGYYIRWNPR
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| − | 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:
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| − | * MTM1, MTMR1, MTMR2: ~190-600, 100%
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| − | * MTMR3: ~214-595 (human, rat, mouse); MTMR4: ~225-588 (human, mouse), ~213-598 (xenopus)
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| − | * MTMR5: ~317-535 (human), ~317-579 (mouse); MTMR13 (not in swissprot?)
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| − | * MTMR6: ~195-595 (human, mouse); MTMR7: 192-592 (human), 203-593 (mouse); 192-593 (human, chicken)
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| − | * MTMR9: 192-588 (human, mouse), 204-592 (cow)
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| − | * 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),
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| − | * MTMR13 (MTMRD): 223-581 (human), 345-581 (xenopus)
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| − | * MTMR14: no hit
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| − | The result shows we can build four individual HMMs for the subfamilies:
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| − | * [[HMM_PD0138|CC1_MTM_1_PD]] of MTMR1, MTMR6, MTMR9 (perhaps MTMR3)
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| − | * [[HMM_PD0140|MTMR5_PD]] of MTMR5
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| − | * [[HMM_PD0141|MTMR10_PD]] of MTMR10
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| − | * [[HMM_PD0142|MTMR14_PD]] of MTMR14
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| − | Note: In addition to PSI-BLAST, we tried to obtain an alignment from HHPRED, but the quality is pretty bad.
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| − | === How was the HMM built? ===
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| − | We PSI-BLASTed the region against PSI-BLASTed, which converged right after 1st round.
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| − | === References ===
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| − | <biblio>
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| − | #Begley03 pmid=14690594
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| − | </biblio>
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