HMM - Revision history

Mark: /* HMMs of accessory domains */

2017-03-15T18:26:06Z

‎HMMs of accessory domains

2017-03-13T17:35:09Z

2016-03-16T18:23:58Z

‎HMMs of accessory domains

2015-10-19T17:45:48Z

‎HMMs for Finding Protein Phosphatase Domain with High Coverage

2015-10-15T20:58:20Z

‎HMMs of accessory domains

2015-10-15T20:42:44Z

‎HMMs of accessory domains

2015-10-15T20:40:11Z

‎HMMs of accessory domains

2015-10-14T21:20:26Z

‎HMMs of accessory domains

2015-10-14T18:50:17Z

‎HMMs of accessory domains

2015-10-12T07:34:52Z

‎HMMs for Determining the Boundaries of Protein Phosphatase Domain

← Older revision		Revision as of 18:26, 15 March 2017
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	* [[HMM_PD00151\|DnaJ_1]]: DnaJ domain (built from SMART alignment)		* [[HMM_PD00151\|DnaJ_1]]: DnaJ domain (built from SMART alignment)
		+
		+	* [[HMM_PD00171\|RA]]: Ras Association (RA)

	== HMMs partially overlap with phosphatase domains ==		== HMMs partially overlap with phosphatase domains ==

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 * PPP fold
 ** [[HMM_PD0018|PAP]]
-** [[HMM_PD0019|PPPc]]
+** [[HMM_PD0019|PPP]]
 * [[HMM_PD0001|AP fold]]
@@ Line 86: / Line 86: @@
 Some domains and their HMM profiles partially over with phosphatase domains. We do not consider them as accessory domains.
-* [http://pfam.xfam.org/family/PF07830.9 PP2C_C]: Pfam HMM specifically matches with PPP1C but not other PPP subfamilies. The Pfam PP2C_C profile only match to PPP1C subfamily, but not other PPPc subfamilies. It overlaps with our in-house PPPc HMM profile.
+* [http://pfam.xfam.org/family/PF07830.9 PP2C_C]: Pfam HMM specifically matches with PPP1C but not other PPP subfamilies. The Pfam PP2C_C profile only matches the PPP1C subfamily. It overlaps with our in-house PPP HMM profile.
 * [http://pfam.xfam.org/family/3-PAP#tabview=tab1 3-PAP]: The Pfam 3-PAP domain has poor quality. As described on the domain "this domain family is found in eukaryotes, and is typically between 115 and 138 amino acids in length". But, it has a length of 132 aa in HMM logo. The profile partially overlaps with our profile of myotubularin phosphatase domain, whose boundaries are determined from crystal structure.

@@ Line 46: / Line 46: @@
 * [[HMM_CA00001|PH domain]]
 ** [[HMM_PD0134|MTMR_GRAM]]: myotubularin, GRAM domain (in-house)
-*** [[HMM_PD00135|MTMR_1_GRAM]]: GRAM domain profile of MTMR1, MTMR5, MTMR6, MTMR9 and MTMR10 subfamilies
+*** [[HMM_PD00135|MTMR_1_GRAM]]: GRAM domain profile of MTMR1, MTMR5, MTMR6, MTMR9 and MTMR10 subfamilies (in-house)
 *** [[HMM_PD00136|MTMR3_GRAM]]:  MTMR3, GRAM domain (in-house)
 *** [[HMM_PD00152|MTMR9_GRAM]]: MTMR9, GRAM domain (built from CDD alignment)

@@ Line 40: / Line 40: @@
 == HMMs for Finding Protein Phosphatase Domain with High Coverage ==
 We have built a semi-redundant HMM profiles to detect phosphatase domains from biological sequences. We first used the HMMs from public databases, Pfam, SMART and SUPERFAMILY to search protein phosphatases we collected from the literature. We found 1) the HMMs from public databases such as Pfam and SMART can not find all human protein phosphatases, 2) some HMMs are redundant, - they captured exactly the same set of protein phosphatases. Thus, we 1) build in-house HMMs to capture the human protein phosphatases missed, 2) remove 100% redundant HMMs. You can [http://phosphatome.net/download/ download the HMMs].
 == HMMs of accessory domains ==

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 * FCP1 C-Terminal Domain: FCP1 has a C-terminal domain which is conserved in individual clades such as vertebrates and arthropods. However, it is hard to built a universal profile to capture all the FCP1 CTD. The best guess is that the region contains several short motifs.
-** [[HMM_PD00155|FCP1_CTD]]: FCP1, C-Terminal Domain (in-house). The profile aims at to detect the presence of FCP1_C domain but not the boundaries. The profile is able to detect FCP1 CTD in eumetazoa, such as nematostella, fruit fly, sea urchin and human.
+** [[HMM_PD00155|FCP1_CTD]]: FCP1, C-Terminal Domain (in-house). The profile aims at to detect the presence of FCP1_C domain but not the boundaries. The profile is able to detect FCP1 CTD in eumetazoa, such as nematostella, fruit fly, some but not all nematodes (e.g. Loa loa), sea urchin, Ciona and human.
 * [[HMM_PD00154|VSP_VSD]]: VSP, Voltage Sensor Domain (in-house)

@@ Line 49: / Line 49: @@
 *** [[HMM_PD00137|MTMR14_GRAM]]: MTMR14, GRAM domain (in-house)
 ** [[HMM_PD0149|PH_1]]: PH domain (built from CDD alignment)
 * [[HMM_PD00154|VSP_VSD]]: VSP, Voltage Sensor Domain (in-house)

@@ Line 50: / Line 50: @@
 ** [[HMM_PD0149|PH_1]]: PH domain (built from CDD alignment)
-* [[HMM_PD00154|VSP_VSD]]: VSP, Voltage Sensing Domain
+* [[HMM_PD00154|VSP_VSD]]: VSP, Voltage Sensor Domain
 * [[HMM_PD0127|PAP_NTD]]: Purple Acid Phosphatase, N-Terminal Domain (in-house)

@@ Line 2: / Line 2: @@
 == HMMs for Determining the Boundaries of Protein Phosphatase Domain ==
 * CC1 Fold
 ** [[HMM_PD0002|DSP]]
@@ Line 24: / Line 23: @@
 * HP fold
-* [[HMM_PD0014|HP1]]
+** [[HMM_PD0014|HP1]]
-* [[HMM_PD0015|HP2]]
+** [[HMM_PD0015|HP2]]
-−
-* [[HMM_PD0016|PHP_PHP]]
-−
-* [[HMM_PD0017|PPM_PPM]]
 * PPP fold
@@ Line 35: / Line 30: @@
 ** [[HMM_PD0019|PPPc]]
-* [[HMM_PD0020|RTR1]]
+* [[HMM_PD0001|AP fold]]
 == HMMs for Finding Protein Phosphatase Domain with High Coverage ==