HMM PD0138 - Revision history

Mark: Replaced content with "Back to '''List of HMMs''' See CC1_MTM_PD."

2015-10-08T04:54:17Z

Replaced content with "Back to '''List of HMMs''' See CC1_MTM_PD."

Mark: /* Why built the HMM? */

2015-10-08T04:48:20Z

‎Why built the HMM?

Mark: Created page with "Back to '''List of HMMs''' '''Symbol''': CC1_MTM_1_PD '''Name''': Myotubularin phosphatase domain (group 1) === Why built the HMM? === We built the profile because ..."

2015-10-08T04:39:51Z

Created page with "Back to '''List of HMMs''' '''Symbol''': CC1_MTM_1_PD '''Name''': Myotubularin phosphatase domain (group 1) === Why built the HMM? === We built the profile because ..."

New page

Back to '''[[HMM|List of HMMs]]'''

'''Symbol''': CC1_MTM_1_PD

'''Name''': Myotubularin phosphatase domain (group 1)

=== Why built the HMM? ===
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.

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 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)
* MTMR14: no hit

The result shows we can build four individual HMMs for the subfamilies:
* [[HMM_PD0138|CC1_MTM_1_PD]] of MTMR1, MTMR6, MTMR9 (perhaps MTMR3)
* [[HMM_PD0140|MTMR5_PD]] of MTMR5
* [[HMM_PD0141|MTMR10_PD]] of MTMR10
* [[HMM_PD0142|MTMR14_PD]] of MTMR14

Note: In addition to PSI-BLAST, we tried to obtain an alignment from HHPRED, but the quality is pretty bad.

=== How was the HMM built? ===
We PSI-BLASTed the region against PSI-BLASTed, which converged right after 1st round.

=== References ===
<biblio>
#Begley03 pmid=14690594
</biblio>

@@ Line 1: / Line 1: @@
 Back to '''[[HMM|List of HMMs]]'''
-'''Symbol''': CC1_MTM_1_PD
+See [[HMM_PD0003|CC1_MTM_PD]].
-−
-'''Name''': Myotubularin phosphatase domain (group 1)
-−
-=== Why built the HMM? ===
-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.
-−
-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 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)
-* MTMR14: no hit
-−
-Note: In addition to PSI-BLAST, we tried to obtain an alignment from HHPRED, but the quality is pretty bad.
-−
-=== How was the HMM built? ===
-We PSI-BLASTed the region against PSI-BLASTed, which converged right after 1st round.
-−
-=== References ===
-<biblio>
-#Begley03 pmid=14690594
-</biblio>