HMM PD0003 - Revision history

Mark: /* How the HMM was built */

2015-10-20T04:59:46Z

‎How the HMM was built

2015-10-20T04:56:51Z

2015-10-19T23:23:33Z

‎Why built the HMM?

2015-10-09T21:29:46Z

2015-10-08T04:53:43Z

‎How the HMM was built

2015-10-08T04:17:08Z

‎Description

2015-10-07T21:44:50Z

2015-10-07T21:43:32Z

‎How the HMM was built

2015-10-07T16:48:52Z

2015-10-06T18:28:00Z

‎How the HMM was built

@@ Line 26: / Line 26: @@
 We just built the HMM followed the [[HMM#Guidance_for_HMM_building|general guidance]]. By using the protein phosphatases of the nine genomes, we found the HMM profile can detect the phosphatase domains of all subfamilies with good boundaries except MTMR14. The HMM has a length of 391 aa, all subfamilies except MTMR14 has the domains of > 380 aa long. Because the HMM does not capture MTMR14, we archive the HMM in a separate page [[HMM_PD0138|CC1_MTM_1_PD]].
-See [[HMM_PD0142|MTMR14, full sequence (MTMR14_FS)]] and [[HMM_PD00143|MTMR14, phosphatase domain (MTMR14_PD)]]  for MTMR14 full sequence and phosphatase domain.
+See [[HMM_PD00143|MTMR14, conserved regions (MTMR14_CR)]] and [[HMM_PD0142|MTMR14, phosphatase domain (MTMR14_PD)]]  for MTMR14 conserved regions and phosphatase domain.
 Note:
@@ Line 32: / Line 32: @@
 * In addition to PSI-BLAST, we tried to obtain an alignment from HHPRED, but the quality is pretty bad.
 * The profile overlaps with [http://pfam.xfam.org/family/3-PAP#tabview=tab1 3-PAP] of Pfam database.
 === References ===

@@ Line 26: / Line 26: @@
 We just built the HMM followed the [[HMM#Guidance_for_HMM_building|general guidance]]. By using the protein phosphatases of the nine genomes, we found the HMM profile can detect the phosphatase domains of all subfamilies with good boundaries except MTMR14. The HMM has a length of 391 aa, all subfamilies except MTMR14 has the domains of > 380 aa long. Because the HMM does not capture MTMR14, we archive the HMM in a separate page [[HMM_PD0138|CC1_MTM_1_PD]].
-See [[HMM_PD0142|MTMR14_PD]] for MTMR14 phosphatase domain.
+See [[HMM_PD0142|MTMR14, full sequence (MTMR14_FS)]] and [[HMM_PD00143|MTMR14, phosphatase domain (MTMR14_PD)]]  for MTMR14 full sequence and phosphatase domain.
 Note:

@@ Line 6: / Line 6: @@
 === 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 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. The C-terminal 45 aa consists of helix 15 and a disordered region in crystal structure.
 === How the HMM was built ===

@@ Line 5: / Line 5: @@
 '''Name''': Myotubularin phosphatase domain
-=== Description ===
+=== 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.
@@ Line 28: / Line 28: @@
 See [[HMM_PD0142|MTMR14_PD]] for MTMR14 phosphatase domain.
-Note: In addition to PSI-BLAST, we tried to obtain an alignment from HHPRED, but the quality is pretty bad.
+Note:
 === References ===

@@ Line 24: / Line 24: @@
 * MTMR14: no hit
-The result shows we can build four individual HMMs for the subfamilies:
+We just built the HMM followed the [[HMM#Guidance_for_HMM_building|general guidance]]. By using the protein phosphatases of the nine genomes, we found the HMM profile can detect the phosphatase domains of all subfamilies with good boundaries except MTMR14. The HMM has a length of 391 aa, all subfamilies except MTMR14 has the domains of > 380 aa long. Because the HMM does not capture MTMR14, we archive the HMM in a separate page [[HMM_PD0138|CC1_MTM_1_PD]].
-* [[HMM_PD0138|MTMR_1_PD]] of MTMR1, MTMR6, MTMR9 (perhaps MTMR3)
-* [[HMM_PD0140|MTMR5_PD]] of MTMR5
+See [[HMM_PD0142|MTMR14_PD]] for MTMR14 phosphatase domain.
-* [[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.

@@ Line 24: / Line 24: @@
 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.

@@ Line 1: / Line 1: @@
 Back to '''[[HMM|List of HMMs]]'''
-'''Symbol''': MTM_PD
+'''Symbol''': CC1_MTM_PD
 '''Name''': Myotubularin phosphatase domain