Difference between revisions of "HMM"
From PhosphataseWiki
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The page is under construction. | The page is under construction. | ||
| − | === List of HMMs === | + | === List of HMMs of phosphatase domains === |
| + | ===== [[HMM_PD0130|SAC]] ===== | ||
| + | |||
| + | === List of HMMs of accessory domains === | ||
===== [[HMM_PD0127|PAP_NTD (Purple Acid Phosphatase, N-Terminal Domain)]] ===== | ===== [[HMM_PD0127|PAP_NTD (Purple Acid Phosphatase, N-Terminal Domain)]] ===== | ||
===== [[HMM_PD0128|CDC25_NTD (CDC25, N-Terminal Domain)]] ===== | ===== [[HMM_PD0128|CDC25_NTD (CDC25, N-Terminal Domain)]] ===== | ||
Revision as of 17:11, 11 September 2015
The page is under construction.
Contents
List of HMMs of phosphatase domains
SAC
List of HMMs of accessory domains
PAP_NTD (Purple Acid Phosphatase, N-Terminal Domain)
CDC25_NTD (CDC25, N-Terminal Domain)
IQ
PP2C_C
The Pfam PP2C_C profile only match to PPP1C subfamily, but not other PPPc subfamilies. It overlaps with our in-house PPPc HMM profile.
General Protocol for HMM building
We usually built the HMMs from PSI-BLAST hits.
To find the domain sequences for building a HMM, we PSI-BLASTed the domain sequence or the full sequence. It sometime matters if you query the region that is supposed to contain the domain (based upon structure or any evidence) or the full sequence. The full sequence is often more sensitive to find weak hits to the domain. We recommended to download the files of Alignment, Search Strategies, and PssmWithParameters of PSI-BLAST result for reproductivity.
