HMM PD00127 - Revision history

Mark: Mark moved page HMM PD0127 to HMM PD00127

2015-10-18T01:25:09Z

Mark moved page HMM PD0127 to HMM PD00127

Mark: /* Description */

2015-09-10T17:16:13Z

‎Description

Mark at 15:34, 10 September 2015

2015-09-10T15:34:33Z

Mark at 05:54, 10 September 2015

2015-09-10T05:54:36Z

Mark: /* How the HMM is built */

2015-09-10T05:54:14Z

‎How the HMM is built

Mark at 17:48, 9 September 2015

2015-09-09T17:48:38Z

Mark: Created page with "List of HMMs === Description === The HMM extends Pfam profile [http://pfam.xfam.org/family/PF16656.1 Pur_ac_phosph_N], which cannot detect the domain in some phosphat..."

2015-09-09T17:13:02Z

Created page with "List of HMMs === Description === The HMM extends Pfam profile [http://pfam.xfam.org/family/PF16656.1 Pur_ac_phosph_N], which cannot detect the domain in some phosphat..."

New page

[[HMM|List of HMMs]]

=== Description ===
The HMM extends Pfam profile [http://pfam.xfam.org/family/PF16656.1 Pur_ac_phosph_N], which cannot detect the domain in some phosphatases, such as ''C. elegans'' ACP5 ([[Phosphatase_Sequence_CeleP014_AA]]).

=== How the HMM is built ===
We searched the Pfam domains of ''C. elegans'' ACP5 ([[Phosphatase_Sequence_CeleP014_AA]]) and human ACP5 via Pfam server. Based upon the position of Metallophos domain and the length of the linking region between Metallophos and Pur_ac_phosph_N domain, we guessed the region of 1-100 of ''C. elegans'' ACP5 ([[Phosphatase_Sequence_CeleP014_AA]]) may contain the Pur_ac_phosph_N domain.

We then PSI-BLASTed the region against NR database via NCBI BLAST server.

← Older revision		Revision as of 17:16, 10 September 2015
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		+	'''Symbol''': PAP_NTD
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		+	'''Name''': Purple Acid Phosphatase, N-Terminal Domain

	=== Description ===		=== Description ===

← Older revision		Revision as of 15:34, 10 September 2015
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	=== Description ===		=== Description ===

← Older revision		Revision as of 05:54, 10 September 2015
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−	[[HMM\|List of HMMs]]	+	'''[[HMM\|List of HMMs]]'''

	=== Description ===		=== Description ===

← Older revision	Revision as of 01:25, 18 October 2015
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 === How the HMM is built ===
-We searched the Pfam domains of ''C. elegans'' ACP5 ([[Phosphatase_Sequence_CeleP014_AA]]) and human ACP5 via Pfam server. Based upon the position of Metallophos domain and the length of the linking region between Metallophos and Pur_ac_phosph_N domain, we guessed the region of 1-100 of ''C. elegans'' ACP5 ([[Phosphatase_Sequence_CeleP014_AA]]) may contain the Pur_ac_phosph_N domain.
+We searched the Pfam domains of ''C. elegans'' ACP5 ([[Phosphatase_Sequence_CeleP014_AA]]) and human ACP5 via Pfam server. Based upon the position of Metallophos domain and the length of the linking region between Metallophos and Pur_ac_phosph_N domain, we guessed the region of 1-100 of ''C. elegans'' ACP5 ([[Phosphatase_Sequence_CeleP014_AA]]) may contain the Pur_ac_phosph_N domain. We then PSI-BLASTed the region against NR database via NCBI BLAST server.
-We then PSI-BLASTed the region against NR database via NCBI BLAST server.
+We downloaded the sequences. Then, we i) removed redundant sequences above 70% identity using CD-HIT program (parameter -c 0.7, other parameters default), ii) aligned the sequences by MUSCLE program (default parameters), iii) manually curated the alignment by removing low quality columns, iv) removed the sequences shorter than the length of the shortest 25% sequences, v) realigned the sequences by MUSCLE program, vi) manually curated the alignment, vii) build HMM profile using HMMBUILD program (default parameters), viii) validate the HMM profile that whether it was able to detect the domain from protein phosphatases such as ''C. elegans'' ACP5 ([[Phosphatase_Sequence_CeleP014_AA]]).

@@ Line 2: / Line 2: @@
 === Description ===
-The HMM extends Pfam profile [http://pfam.xfam.org/family/PF16656.1 Pur_ac_phosph_N], which cannot detect the domain in some phosphatases, such as ''C. elegans'' ACP5 ([[Phosphatase_Sequence_CeleP014_AA]]).
+The HMM extends Pfam profile [http://pfam.xfam.org/family/PF16656.1 Pur_ac_phosph_N], which cannot detect the domain in some phosphatases, such as ''C. elegans'' ACP5 ([[Phosphatase_Sequence_CeleP014_AA]]) and one of the Monosiga ACP5s ([[Phosphatase_Sequence_MbreP082_AA]]).
 === How the HMM is built ===