Difference between revisions of "HMM PD00171"
From PhosphataseWiki
(Created page with "Back to '''List of HMMs''' '''Symbol''': RA '''Name''': Ras Association === Why built the HMM === Human PHLPPs have RA domains, but they are not found by Pfam, SM...") |
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'''Name''': Ras Association | '''Name''': Ras Association | ||
| − | === Why built the HMM === | + | === Why we built the HMM === |
| − | Human PHLPPs have RA domains, but they are not found by Pfam, SMART or CDD. That motivates us to build a HMM. | + | Human PHLPPs have experimentally characterized RA domains, but they are not found by Pfam, SMART or CDD. That motivates us to build a HMM. |
=== How the HMM was built === | === How the HMM was built === | ||
| + | Invertebrate and fungal PHLPP homologs have hits to the CYR1 CDD domain, which is a member of the [http://pfam.xfam.org/clan/Ubiquitin Ubiquitin fold clan]. These hits were extended by psi-blast and multiple sequence alignment to pick up additional vertebrate and invertebrate homologs, and the resulting MSA used to build a HMMER profile HMM. | ||
Latest revision as of 21:07, 15 March 2017
Back to List of HMMs
Symbol: RA
Name: Ras Association
Why we built the HMM
Human PHLPPs have experimentally characterized RA domains, but they are not found by Pfam, SMART or CDD. That motivates us to build a HMM.
How the HMM was built
Invertebrate and fungal PHLPP homologs have hits to the CYR1 CDD domain, which is a member of the Ubiquitin fold clan. These hits were extended by psi-blast and multiple sequence alignment to pick up additional vertebrate and invertebrate homologs, and the resulting MSA used to build a HMMER profile HMM.
