Difference between revisions of "HMM PD00148"

Latest revision as of 04:21, 18 October 2015

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Symbol: SSH_NTD

Name: Slingshot, N-terminal domain

Why built the HMM

The Slingshot subfamily has "A" and "B" domain at N-terminal. The "B" domain partially overlaps with DEK_C domain. The other part of "B" domain and/or the "A" domain have no corresponding HMM in Pfam or SMART database, but NCBI Conserved Domains Database (CDD) has a profile named SSH-N which includes the "A" domain and the other part of "B" domain that does not overlap with DEK_C. Below is a brief description of the profile from CDD:

"N-terminal domain conserved in slingshot (SSH) phosphatases; This domain or region conserved in Bilateria is found N-terminal to the DEK_C-like and catalytic domains of slingshot phosphatases. Slingshot is a cofilin-specific phosphatase. Dephosphorylation reactivates cofilin, which in turn depolymerizes actin and is thus required for actin filament reorganization. Slingshot is a member of the dual-specificity protein phosphatase family. This N-terminal SSH region may be involved in P-cofilin binding (the model C-terminus plus the DEK_C-like domain, which are characterized as the "B" domain in some of the literature), and may be required for the F-actin mediated activation of slingshot (the N-terminal region of this model, sometimes referred to as the "A" domain)."

How the HMM was built

We downloaded the alignment from CDD, edited the align to get the regions used by CDD to build the profile, built HMM by hmmbuild, and validated by protein phosphatases of the nine genomes.