HMM PD0133 - Revision history

Mark at 06:18, 12 September 2015

2015-09-12T06:18:39Z

Mark: /* How the HMM is built */

2015-09-11T19:25:53Z

‎How the HMM is built

Mark: /* How the HMM is built */

2015-09-11T19:22:41Z

‎How the HMM is built

Mark at 18:07, 11 September 2015

2015-09-11T18:07:25Z

Mark: /* How the HMM is built */

2015-09-11T18:07:05Z

‎How the HMM is built

Mark at 18:04, 11 September 2015

2015-09-11T18:04:23Z

Mark: Created page with "Back to '''List of HMMs''' '''Symbol''': MTMR5_C1 '''Name''': MTMR5, C1 domain === Description === The MTMR5 has a C1 domain which is able to be detected by [http:/..."

2015-09-11T18:03:05Z

Created page with "Back to '''List of HMMs''' '''Symbol''': MTMR5_C1 '''Name''': MTMR5, C1 domain === Description === The MTMR5 has a C1 domain which is able to be detected by [http:/..."

New page

Back to '''[[HMM|List of HMMs]]'''

'''Symbol''': MTMR5_C1

'''Name''': MTMR5, C1 domain

=== Description ===
The MTMR5 has a C1 domain which is able to be detected by [http://pfam.xfam.org/family/PF00130 Pfam C1_1] profile in C1 clan.

=== How the HMM is built ===
We PSI-BLASTed the sequence that containing the C1 domain in ''C. elegans'' mtm-5 (1540-1590 determined by searching the complete sequence against CDD and Pfam database). However, the search converged right after the 1st round.

@@ Line 6: / Line 6: @@
 === Description ===
-The [[Phosphatase_Subfamily_MTMR5|MTMR5 subfamily]] has a C1 domain which is able to be detected by [http://pfam.xfam.org/family/PF00130 Pfam C1_1] profile in C1 clan. We try to build a HMM, which can detect the C1 domain of MTMR5.
+The [[Phosphatase_Subfamily_MTMR5|MTMR5 subfamily]] has a C1 domain which is able to be detected by [http://pfam.xfam.org/family/PF00130 Pfam C1_1] profile in C1 clan. We try to build a HMM, which can detect the C1 domain of MTMR5. The resulted HMM built based on C1 domain in ''Drosophila Melanogaster'' sbf can find C1 domain in Tensin subfamily.
 === How the HMM is built ===
 We PSI-BLASTed the sequence that containing the C1 domain in ''C. elegans'' mtm-5 (1540-1590 determined by searching the complete sequence against CDD and Pfam database). However, the search against protein NR data set converged right after the 1st round.
-We PSI-BLASTed the sequence that containing the C1 domain in ''Drosophila Melanogaster'' sf (1790-1840 determined by searching the complete sequence against CDD and Pfam database). There are more than 20000 hits (over the maximum of NCBI BLAST server) in the 2nd round, when searched against protein NR dataset. We therefore searched against UniProt, instead.
+We PSI-BLASTed the sequence that containing the C1 domain in ''Drosophila Melanogaster'' sbf (1790-1840 determined by searching the complete sequence against CDD and Pfam database). There are more than 20000 hits (over the maximum of NCBI BLAST server) in the 2nd round, when searched against protein NR dataset. We therefore searched against UniProt, instead.
 Below are the two full sequences used:

@@ Line 9: / Line 9: @@
 === How the HMM is built ===
-We PSI-BLASTed the sequence that containing the C1 domain in ''C. elegans'' mtm-5 (1540-1590 determined by searching the complete sequence against CDD and Pfam database). However, the search converged right after the 1st round.
+We PSI-BLASTed the sequence that containing the C1 domain in ''C. elegans'' mtm-5 (1540-1590 determined by searching the complete sequence against CDD and Pfam database). However, the search against protein NR data set converged right after the 1st round.
-We PSI-BLASTed the sequence that containing the C1 domain in ''Drosophila Melanogaster'' sf (1790-1840 determined by searching the complete sequence against CDD and Pfam database). (it is undergoing)
+We PSI-BLASTed the sequence that containing the C1 domain in ''Drosophila Melanogaster'' sf (1790-1840 determined by searching the complete sequence against CDD and Pfam database). There are more than 20000 hits (over the maximum of NCBI BLAST server) in the 2nd round, when searched against protein NR dataset. We therefore searched against UniProt, instead.
 Below are the two full sequences used:

@@ Line 13: / Line 13: @@
 Below are the two full sequences used:
-''C. elegans'' sequence
+''C. elegans'' sequence:
   MRDPDKVKSGPICDTVAVIVLEESDDENALPDVLHEVQSPHTSDNIPTSSIKKFARPRGWYNQSVSSPSEFFYQILTTERGTRRIAYVLSTWEEDEKTLNFKAVSIVLISQNFHPKAFKEILLEISNDLRTPEFSSSSELIRFLTYELVEEGSTIEIRTKTLHVELGFELIPISPVTGKDVAMLFKMLGFQNVIKIIHALLSDCRIVLASSSLMRLSRCQNAILSLLYPFEYVHSCVTILPDSLAEVLESPTPFLIGVLSEFVTSFGDENIVVYLDNGEVHVPDHAEIYKSDDYYYNSLHQRLRDVMFTTTSQEDLSIPNEERIEVDDFILDKKLRACFIYYFAELLYGYQYYILYTRIKGNFEKKLTTSLTFHVGAFRGFRKLTDMMSSSLLKSVYFQTFILTRALPRRKHDLFDEISCFKELDQLIFKQNSTSSESKKIIEHISCELIQKERYMEKCSARKQEIFTKIHWISGKELAQNNNSIIHTVKPKMRSNVILQAMLPVVNTHAEYHANQFEAYAHRIEALRNCLAAIFEGKVAFASKSLDAVKSSMRFAPLRIELCRLLNQKCSHDKLTDKQFEDIALLMNAALQAECEEDKDGVVRSLMYLSNVYSRKVAQGMQQYMYTAVQEHKVWKNQRFWTSCFYYEVHEMLFSEMLQKDRKITESLWCHTLRPCAMEMINTDDTDQEELVKQENEMIQAQAKHFANILISLQIPLSEEFFEHEDAHRSVLNEKCKWIVNTLDSILGVTGRINGLSLSRIQTYVEAHVESLRDVYVEMSTGEHLKKGNFDPVLAHGEFLISDPIDCYLLTSIEESEMSLNRLENLLPADGSLFLTNYRVIFKGKSVDINATNGTIVQTIPLYSMESFKKLTNKKLIPTQLIEKGVKIEHIISIRSSCASSIIIAFDEDEINNMAIEKFLEVIETNSHNSFAFYNTRKDMKVVENGSHKFGTLNSAIRGFTKKKTDTRRIRSHSSHRGSIQLSFDKMEELDYLKKNAHIRYAVIDYPRIGLNSKIVKLRMSHSNLDYTICPSYPGNFIVPSETNESELAKVAKGFVEHRLPVVVWMNENGALLVRASAFTSIDMVKKLKKVVNYRRNASKLTGSMTGSQQTLHSKASSNEESSSNIVAGAEIKSAEVQMNYIAKLSNSSQRAVSYALPTQYADKFSTFNDGCTLTQNNANGFPTTRIHRKALYVLLEKGHGVKIPIDSNAEAIMVRSVKESELRRSLQRARQICSSEFQVENRTSFLESWNASNWPQCVSRMIELSNSIVALMNLYNSSVAICLEAGRSITTILSSLSQLLSDPYYRTCDGFQVLVEKEWLAFGHYFHKDTETSSPSFICFLDCVYQISQQYPTAFEFSYFYISFLAYHSTAGYFRTFIDDCEEKRLQSDANEFYLPDNLATINVWEFIKLRNRVSAAFYNELYEQIGDIVIPSSSIPQIHMWPFLAETHLKYGSPYDIEPASHEQQLVDPDYEEEEDWSKLNNTDIDERHLNRRVRSPERDPANMDMIRLLQKSYLTELFDASDRKTTTNGESNGKETIHELTPFTVGARPVQCCYCTNILTRWSKAVHCKKCRIHVHEGCVNRNITIGNITHTWDAKPFEDIKMPSGAIQIGTPQAEKMLHSPNNTLTRESMSPPTANTIPPLCTGYLSKRGAKLKLWVPRFFVLYPDSPKVYYYEDFENWKTAEKPSGCIDLVDFKSFNLEQTGRRGLIELHMKNKTHRLLSENINEAIRWKECIEQVIRD
-''Drosophila Melanogaster'' sequence
+''Drosophila Melanogaster'' sequence:
   MSRLADYFVIVGYDSDKEKTASNVGGQPTCGKIVQRFPEKDWPDTPFIEGIEWFCQPLGWSLSYEKQEPKFFVSVLTDIDANKHYCACLSFHETVAITQTRSVDDEDETIGSSRLLGATPSSMDGITTTSTPASITHHSVMYAPKCLVLISRLDCAETFKNCLGTIYTVYIENLAYGLETLIGNILGCIQVPPAGGPQVRFSIGAGDKQSLQPPQSSSLPTTGSGVHFLFKQLGIKNVLILLCSVMTENKILFLSKCYWHLTDSCRALVALMYPFRYTHVYIPILPAPLTEVLSTPTPFIMGIHSSLQTEITDLLDVIVVDLDGGLVTIPESLTPPVPILPSPLWEQTQDLLSMILFPNLAQADLAFPTLERPSAIAKTDAQIDKELRAIFMRLFAQLLQGYRSCLTIIRIHPKPVITFHKAGFLGARDLIESEFLFRVLDSMFFTTFVNERGPPWRSSDAWDELYSSMNELLKSEAQNRNLVGRTQRFKGYFNFTFPSYFQILTHIQELGRVLYENEGTLAHISYAQKVLRPPEGAFQRIHQPAFPRISSEKVELIIQEGIRKNGVPQRFHVTRNQHRIIPMGPRLPEALDVRPNVQNSARRLEVLRICVSYIFENRITDARKLLPAVMRTLMHRDARLILCREFFGYVHGNKAVLDHQQFELVVRFMNKALQKSSGIDEYTVAAALLPMSTIFCRKLSTGVVQFAYTEIQDHAIWKNLQFWESTFFQDVQGQIKALYLLHRRQNEHQKEANCVLDEVPLEEPTALEITAEQLRKSPNIEEEKKAELAKSEESTLYSQAIHFANRMVSLLIPLDVNVDAASKPKPAFRLEENQSVSNSIMGSHSLSEHSDEGFEENNALEIGVTVGKTISRFIDCVCTEGGVTSEHIRNLHDMVPGVVHMHIESLEPVYLEAKRHPHVQKPKIQTPCLLPGEDLVTDHLRCFLMPDGREDETQCLIPAEGALFLTNYRVIFKGSPCDPLFCEQVIVRTFPIASLLKEKKISVLYLAHLDQTLTEGLQLRSSSFQLIKVAFDPEVTPEQIESFRKILSKARHPFDEFEYFAFQSYGTMLQGVAPLKTKEKYSTLKGFAKKTLLRGAKKAGFKQKQQTKRKLVSDYDYGSADAQETQSIDDELEDGDEFETQNNAMPRLLTTKDVERMRERSYVQDWKRLGFDAESQRGFRISNANTSYATCRSYPAIIVAPVQCSDAAIMHLGRCFKGQRIPLPTWRHANGALLIRGGQPNSKSVIGMLKNTTGSTTNAHHDVTHYPEQDKYFLALINTMPKLTPLALNQYSGMNLSMSSLMGHSSSDDRQPLTPELSRKHKNNLDISDGNKSSQGGKGGTMKGNPKNSLAHPFRKMRLYALGEKSQAKSNMNVDFCADFIPVDYPDIRQSRPAFKKLIRACMPSHNTNEADGQSFAKMVEQSDWLQQISSLMQLSGAVVDLIDLQESSVMLSLEDGSDVTAQLSSIAQLCLDPYYRSLDGFRVLVEKEWLAFGHRFAHRSNLKPSHANTNIAFAPTFLQFLDVVHQLQRQFPMAFEFNDFYLRFLAYHSVSCRFRTFLFDCELERSDSGIAAMEDKRGSLNAKHMFGAGGMATNGSDDECSVYPLDIRSQRAPAPLNRIGHSIFDYIERQHNKTPIFYNFLYSGDKSVTLRPQNNVAALDLWCYYTNEELAQGAPYDLEVTTVDDEIDLSETKGKRMVITAGYDNMEKCNPSAYVCLLSEVKQAETERGHLPQKWLQVWNSLEVPQLEPVARNTSLGNIFVQTHQHKRSTLEIIMKGRLAGYQDKYFHPHRFEKHPYTTPTNCNHCTKLLWGPVGYRCMDCGNSYHEKCTEHSMKNCTKYKAIDGAVGPPNVNMSQGDTASIASSAATTARTSSHHFYNQFSSNVAENRTHEGHLYKRGALLKGWKQRWFVLDSIKHQLRYYDTSEDTAPKGIIELAEVQSVTAAQPAQIGAKGVDEKGFFDLKTSKRIYNFYAINANLAQEWIEKLQACLQ

← Older revision		Revision as of 18:07, 11 September 2015
Line 10:		Line 10:
	=== How the HMM is built ===		=== How the HMM is built ===
	We PSI-BLASTed the sequence that containing the C1 domain in ''C. elegans'' mtm-5 (1540-1590 determined by searching the complete sequence against CDD and Pfam database). However, the search converged right after the 1st round.		We PSI-BLASTed the sequence that containing the C1 domain in ''C. elegans'' mtm-5 (1540-1590 determined by searching the complete sequence against CDD and Pfam database). However, the search converged right after the 1st round.
		+
		+	Below are the two full sequences used:
		+
		+	''C. elegans'' sequence
		+	MRDPDKVKSGPICDTVAVIVLEESDDENALPDVLHEVQSPHTSDNIPTSSIKKFARPRGWYNQSVSSPSEFFYQILTTERGTRRIAYVLSTWEEDEKTLNFKAVSIVLISQNFHPKAFKEILLEISNDLRTPEFSSSSELIRFLTYELVEEGSTIEIRTKTLHVELGFELIPISPVTGKDVAMLFKMLGFQNVIKIIHALLSDCRIVLASSSLMRLSRCQNAILSLLYPFEYVHSCVTILPDSLAEVLESPTPFLIGVLSEFVTSFGDENIVVYLDNGEVHVPDHAEIYKSDDYYYNSLHQRLRDVMFTTTSQEDLSIPNEERIEVDDFILDKKLRACFIYYFAELLYGYQYYILYTRIKGNFEKKLTTSLTFHVGAFRGFRKLTDMMSSSLLKSVYFQTFILTRALPRRKHDLFDEISCFKELDQLIFKQNSTSSESKKIIEHISCELIQKERYMEKCSARKQEIFTKIHWISGKELAQNNNSIIHTVKPKMRSNVILQAMLPVVNTHAEYHANQFEAYAHRIEALRNCLAAIFEGKVAFASKSLDAVKSSMRFAPLRIELCRLLNQKCSHDKLTDKQFEDIALLMNAALQAECEEDKDGVVRSLMYLSNVYSRKVAQGMQQYMYTAVQEHKVWKNQRFWTSCFYYEVHEMLFSEMLQKDRKITESLWCHTLRPCAMEMINTDDTDQEELVKQENEMIQAQAKHFANILISLQIPLSEEFFEHEDAHRSVLNEKCKWIVNTLDSILGVTGRINGLSLSRIQTYVEAHVESLRDVYVEMSTGEHLKKGNFDPVLAHGEFLISDPIDCYLLTSIEESEMSLNRLENLLPADGSLFLTNYRVIFKGKSVDINATNGTIVQTIPLYSMESFKKLTNKKLIPTQLIEKGVKIEHIISIRSSCASSIIIAFDEDEINNMAIEKFLEVIETNSHNSFAFYNTRKDMKVVENGSHKFGTLNSAIRGFTKKKTDTRRIRSHSSHRGSIQLSFDKMEELDYLKKNAHIRYAVIDYPRIGLNSKIVKLRMSHSNLDYTICPSYPGNFIVPSETNESELAKVAKGFVEHRLPVVVWMNENGALLVRASAFTSIDMVKKLKKVVNYRRNASKLTGSMTGSQQTLHSKASSNEESSSNIVAGAEIKSAEVQMNYIAKLSNSSQRAVSYALPTQYADKFSTFNDGCTLTQNNANGFPTTRIHRKALYVLLEKGHGVKIPIDSNAEAIMVRSVKESELRRSLQRARQICSSEFQVENRTSFLESWNASNWPQCVSRMIELSNSIVALMNLYNSSVAICLEAGRSITTILSSLSQLLSDPYYRTCDGFQVLVEKEWLAFGHYFHKDTETSSPSFICFLDCVYQISQQYPTAFEFSYFYISFLAYHSTAGYFRTFIDDCEEKRLQSDANEFYLPDNLATINVWEFIKLRNRVSAAFYNELYEQIGDIVIPSSSIPQIHMWPFLAETHLKYGSPYDIEPASHEQQLVDPDYEEEEDWSKLNNTDIDERHLNRRVRSPERDPANMDMIRLLQKSYLTELFDASDRKTTTNGESNGKETIHELTPFTVGARPVQCCYCTNILTRWSKAVHCKKCRIHVHEGCVNRNITIGNITHTWDAKPFEDIKMPSGAIQIGTPQAEKMLHSPNNTLTRESMSPPTANTIPPLCTGYLSKRGAKLKLWVPRFFVLYPDSPKVYYYEDFENWKTAEKPSGCIDLVDFKSFNLEQTGRRGLIELHMKNKTHRLLSENINEAIRWKECIEQVIRD
		+
		+	''Drosophila Melanogaster'' sequence
		+	MSRLADYFVIVGYDSDKEKTASNVGGQPTCGKIVQRFPEKDWPDTPFIEGIEWFCQPLGWSLSYEKQEPKFFVSVLTDIDANKHYCACLSFHETVAITQTRSVDDEDETIGSSRLLGATPSSMDGITTTSTPASITHHSVMYAPKCLVLISRLDCAETFKNCLGTIYTVYIENLAYGLETLIGNILGCIQVPPAGGPQVRFSIGAGDKQSLQPPQSSSLPTTGSGVHFLFKQLGIKNVLILLCSVMTENKILFLSKCYWHLTDSCRALVALMYPFRYTHVYIPILPAPLTEVLSTPTPFIMGIHSSLQTEITDLLDVIVVDLDGGLVTIPESLTPPVPILPSPLWEQTQDLLSMILFPNLAQADLAFPTLERPSAIAKTDAQIDKELRAIFMRLFAQLLQGYRSCLTIIRIHPKPVITFHKAGFLGARDLIESEFLFRVLDSMFFTTFVNERGPPWRSSDAWDELYSSMNELLKSEAQNRNLVGRTQRFKGYFNFTFPSYFQILTHIQELGRVLYENEGTLAHISYAQKVLRPPEGAFQRIHQPAFPRISSEKVELIIQEGIRKNGVPQRFHVTRNQHRIIPMGPRLPEALDVRPNVQNSARRLEVLRICVSYIFENRITDARKLLPAVMRTLMHRDARLILCREFFGYVHGNKAVLDHQQFELVVRFMNKALQKSSGIDEYTVAAALLPMSTIFCRKLSTGVVQFAYTEIQDHAIWKNLQFWESTFFQDVQGQIKALYLLHRRQNEHQKEANCVLDEVPLEEPTALEITAEQLRKSPNIEEEKKAELAKSEESTLYSQAIHFANRMVSLLIPLDVNVDAASKPKPAFRLEENQSVSNSIMGSHSLSEHSDEGFEENNALEIGVTVGKTISRFIDCVCTEGGVTSEHIRNLHDMVPGVVHMHIESLEPVYLEAKRHPHVQKPKIQTPCLLPGEDLVTDHLRCFLMPDGREDETQCLIPAEGALFLTNYRVIFKGSPCDPLFCEQVIVRTFPIASLLKEKKISVLYLAHLDQTLTEGLQLRSSSFQLIKVAFDPEVTPEQIESFRKILSKARHPFDEFEYFAFQSYGTMLQGVAPLKTKEKYSTLKGFAKKTLLRGAKKAGFKQKQQTKRKLVSDYDYGSADAQETQSIDDELEDGDEFETQNNAMPRLLTTKDVERMRERSYVQDWKRLGFDAESQRGFRISNANTSYATCRSYPAIIVAPVQCSDAAIMHLGRCFKGQRIPLPTWRHANGALLIRGGQPNSKSVIGMLKNTTGSTTNAHHDVTHYPEQDKYFLALINTMPKLTPLALNQYSGMNLSMSSLMGHSSSDDRQPLTPELSRKHKNNLDISDGNKSSQGGKGGTMKGNPKNSLAHPFRKMRLYALGEKSQAKSNMNVDFCADFIPVDYPDIRQSRPAFKKLIRACMPSHNTNEADGQSFAKMVEQSDWLQQISSLMQLSGAVVDLIDLQESSVMLSLEDGSDVTAQLSSIAQLCLDPYYRSLDGFRVLVEKEWLAFGHRFAHRSNLKPSHANTNIAFAPTFLQFLDVVHQLQRQFPMAFEFNDFYLRFLAYHSVSCRFRTFLFDCELERSDSGIAAMEDKRGSLNAKHMFGAGGMATNGSDDECSVYPLDIRSQRAPAPLNRIGHSIFDYIERQHNKTPIFYNFLYSGDKSVTLRPQNNVAALDLWCYYTNEELAQGAPYDLEVTTVDDEIDLSETKGKRMVITAGYDNMEKCNPSAYVCLLSEVKQAETERGHLPQKWLQVWNSLEVPQLEPVARNTSLGNIFVQTHQHKRSTLEIIMKGRLAGYQDKYFHPHRFEKHPYTTPTNCNHCTKLLWGPVGYRCMDCGNSYHEKCTEHSMKNCTKYKAIDGAVGPPNVNMSQGDTASIASSAATTARTSSHHFYNQFSSNVAENRTHEGHLYKRGALLKGWKQRWFVLDSIKHQLRYYDTSEDTAPKGIIELAEVQSVTAAQPAQIGAKGVDEKGFFDLKTSKRIYNFYAINANLAQEWIEKLQACLQ