Difference between revisions of "HMM PD00142"
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=== Why built the HMM? === | === Why built the HMM? === | ||
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| − | + | In brief, there is no available HMM profile for human MTMR14. Read [[HMM_PD0138|CC1_MTM_1_PD]] for more information. | |
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=== How was the HMM built? === | === How was the HMM built? === | ||
| − | ==== Conserved region of [[ | + | ==== Conserved region of [[HMM_PD00143|MTMR14]] ==== |
We PSI-BLASTed human MTMR14 full sequence against NR database via NCBI BLAST server. Eyeballing the sequences, the query hit MTMR3 and other myotubularins. To build a HMM for full sequence MTMR14, we chose MTMR14 sequences from description. We removed redundant sequences above the threshold of 70% identity. We then aligned the sequences using Clustal Omega, followed by manual adjustment. We built the HMM (3.1b) using default parameter. By searching against the protein phosphatases of nine genomes, we found it matched to ~70 aa of other myotubularin subfamilies. | We PSI-BLASTed human MTMR14 full sequence against NR database via NCBI BLAST server. Eyeballing the sequences, the query hit MTMR3 and other myotubularins. To build a HMM for full sequence MTMR14, we chose MTMR14 sequences from description. We removed redundant sequences above the threshold of 70% identity. We then aligned the sequences using Clustal Omega, followed by manual adjustment. We built the HMM (3.1b) using default parameter. By searching against the protein phosphatases of nine genomes, we found it matched to ~70 aa of other myotubularin subfamilies. | ||
==== Comparison with [[HMM_PD0138|CC1_MTM_1_PD]] ==== | ==== Comparison with [[HMM_PD0138|CC1_MTM_1_PD]] ==== | ||
We aligned the alignments of CC1_MTM_1_PD and the conserved region of MTMR14. We found the conserved region of MTMR14 is a subset of CC1_MTM_1_PD. | We aligned the alignments of CC1_MTM_1_PD and the conserved region of MTMR14. We found the conserved region of MTMR14 is a subset of CC1_MTM_1_PD. | ||
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| + | ==== Obtain phosphatase domain ==== | ||
| + | The conserved region contains N-termimal GRAM domain and C-terminal phosphatase domain. We define the phosphatase domain as the region adjacent to GRAM domain and retrieve the alignment block. We then built the HMM profile. | ||
Latest revision as of 17:49, 28 October 2015
Back to List of HMMs
Symbol: CC1_MTM_MTMR14_PD
Name: MTMR14 phosphatase domain
Why built the HMM?
In brief, there is no available HMM profile for human MTMR14. Read CC1_MTM_1_PD for more information.
How was the HMM built?
Conserved region of MTMR14
We PSI-BLASTed human MTMR14 full sequence against NR database via NCBI BLAST server. Eyeballing the sequences, the query hit MTMR3 and other myotubularins. To build a HMM for full sequence MTMR14, we chose MTMR14 sequences from description. We removed redundant sequences above the threshold of 70% identity. We then aligned the sequences using Clustal Omega, followed by manual adjustment. We built the HMM (3.1b) using default parameter. By searching against the protein phosphatases of nine genomes, we found it matched to ~70 aa of other myotubularin subfamilies.
Comparison with CC1_MTM_1_PD
We aligned the alignments of CC1_MTM_1_PD and the conserved region of MTMR14. We found the conserved region of MTMR14 is a subset of CC1_MTM_1_PD.
Obtain phosphatase domain
The conserved region contains N-termimal GRAM domain and C-terminal phosphatase domain. We define the phosphatase domain as the region adjacent to GRAM domain and retrieve the alignment block. We then built the HMM profile.
Note: In addition to PSI-BLAST, we tried to obtain an alignment from HHPRED, but the quality is pretty bad.
