HMM PD00154

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Symbol: VSP_VSD

Name: VSP, voltage sensor domain

Why built the HMM?

Voltage sensing domain is a transmembrane domain consists of four helix. There is no available profile in public database. The region is annotated as a part of much larger conserved region.

How the HMM is built

We PSI-BLASTed the region 65-230 of NP_954870.2, based upon the region defined in [1] which used 71-221. The hits included not only VSPs but also other ion channels. We then removed redundant sequences (threshold of sequence identity 70%), aligned them by Clustal Omega program, manually adjusted the alignment, built the HMM profile, and validated it by protein phosphatases of the nine genomes.

References

1. Sutton KA, Jungnickel MK, Jovine L, and Florman HM. Evolution of the voltage sensor domain of the voltage-sensitive phosphoinositide phosphatase VSP/TPTE suggests a role as a proton channel in eutherian mammals. Mol Biol Evol. 2012 Sep;29(9):2147-55. DOI:10.1093/molbev/mss083 |