HMM PD00144

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Symbol: IPPc

Name: Inositol Polyphosphate Phosphatase, catalytic domain

Description

We built HMM for IPPc domain, because the Pfam profiles Endonuclease/Exonuclease/phosphatase family and DUF1866 is not able to detect IPPc domain in all synaptojanins.

How the HMM was built

First, we validated whether the boundary predicted by the profile is consistent with that defined by crystal structure (PDB ID: 1I9Y). We obtained the sequence from RCSB website, double checked the original paper, and compared the sequence with the profile.

Second, we downloaded the family alignment from SMART database (SM00128), converted to STOCKHOLM format, built the HMM model using HMMBUILD program, and then searched the HMM against protein phosphatase sequences to validate its sensitivity and specificity.