Difference between revisions of "HMM PD0133"
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(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:/...") |
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=== Description === | === 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. | + | 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 === | === 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'' 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: | ||
| + | |||
| + | ''C. elegans'' sequence: | ||
| + | MRDPDKVKSGPICDTVAVIVLEESDDENALPDVLHEVQSPHTSDNIPTSSIKKFARPRGWYNQSVSSPSEFFYQILTTERGTRRIAYVLSTWEEDEKTLNFKAVSIVLISQNFHPKAFKEILLEISNDLRTPEFSSSSELIRFLTYELVEEGSTIEIRTKTLHVELGFELIPISPVTGKDVAMLFKMLGFQNVIKIIHALLSDCRIVLASSSLMRLSRCQNAILSLLYPFEYVHSCVTILPDSLAEVLESPTPFLIGVLSEFVTSFGDENIVVYLDNGEVHVPDHAEIYKSDDYYYNSLHQRLRDVMFTTTSQEDLSIPNEERIEVDDFILDKKLRACFIYYFAELLYGYQYYILYTRIKGNFEKKLTTSLTFHVGAFRGFRKLTDMMSSSLLKSVYFQTFILTRALPRRKHDLFDEISCFKELDQLIFKQNSTSSESKKIIEHISCELIQKERYMEKCSARKQEIFTKIHWISGKELAQNNNSIIHTVKPKMRSNVILQAMLPVVNTHAEYHANQFEAYAHRIEALRNCLAAIFEGKVAFASKSLDAVKSSMRFAPLRIELCRLLNQKCSHDKLTDKQFEDIALLMNAALQAECEEDKDGVVRSLMYLSNVYSRKVAQGMQQYMYTAVQEHKVWKNQRFWTSCFYYEVHEMLFSEMLQKDRKITESLWCHTLRPCAMEMINTDDTDQEELVKQENEMIQAQAKHFANILISLQIPLSEEFFEHEDAHRSVLNEKCKWIVNTLDSILGVTGRINGLSLSRIQTYVEAHVESLRDVYVEMSTGEHLKKGNFDPVLAHGEFLISDPIDCYLLTSIEESEMSLNRLENLLPADGSLFLTNYRVIFKGKSVDINATNGTIVQTIPLYSMESFKKLTNKKLIPTQLIEKGVKIEHIISIRSSCASSIIIAFDEDEINNMAIEKFLEVIETNSHNSFAFYNTRKDMKVVENGSHKFGTLNSAIRGFTKKKTDTRRIRSHSSHRGSIQLSFDKMEELDYLKKNAHIRYAVIDYPRIGLNSKIVKLRMSHSNLDYTICPSYPGNFIVPSETNESELAKVAKGFVEHRLPVVVWMNENGALLVRASAFTSIDMVKKLKKVVNYRRNASKLTGSMTGSQQTLHSKASSNEESSSNIVAGAEIKSAEVQMNYIAKLSNSSQRAVSYALPTQYADKFSTFNDGCTLTQNNANGFPTTRIHRKALYVLLEKGHGVKIPIDSNAEAIMVRSVKESELRRSLQRARQICSSEFQVENRTSFLESWNASNWPQCVSRMIELSNSIVALMNLYNSSVAICLEAGRSITTILSSLSQLLSDPYYRTCDGFQVLVEKEWLAFGHYFHKDTETSSPSFICFLDCVYQISQQYPTAFEFSYFYISFLAYHSTAGYFRTFIDDCEEKRLQSDANEFYLPDNLATINVWEFIKLRNRVSAAFYNELYEQIGDIVIPSSSIPQIHMWPFLAETHLKYGSPYDIEPASHEQQLVDPDYEEEEDWSKLNNTDIDERHLNRRVRSPERDPANMDMIRLLQKSYLTELFDASDRKTTTNGESNGKETIHELTPFTVGARPVQCCYCTNILTRWSKAVHCKKCRIHVHEGCVNRNITIGNITHTWDAKPFEDIKMPSGAIQIGTPQAEKMLHSPNNTLTRESMSPPTANTIPPLCTGYLSKRGAKLKLWVPRFFVLYPDSPKVYYYEDFENWKTAEKPSGCIDLVDFKSFNLEQTGRRGLIELHMKNKTHRLLSENINEAIRWKECIEQVIRD | ||
| + | |||
| + | ''Drosophila Melanogaster'' sequence: | ||
| + | MSRLADYFVIVGYDSDKEKTASNVGGQPTCGKIVQRFPEKDWPDTPFIEGIEWFCQPLGWSLSYEKQEPKFFVSVLTDIDANKHYCACLSFHETVAITQTRSVDDEDETIGSSRLLGATPSSMDGITTTSTPASITHHSVMYAPKCLVLISRLDCAETFKNCLGTIYTVYIENLAYGLETLIGNILGCIQVPPAGGPQVRFSIGAGDKQSLQPPQSSSLPTTGSGVHFLFKQLGIKNVLILLCSVMTENKILFLSKCYWHLTDSCRALVALMYPFRYTHVYIPILPAPLTEVLSTPTPFIMGIHSSLQTEITDLLDVIVVDLDGGLVTIPESLTPPVPILPSPLWEQTQDLLSMILFPNLAQADLAFPTLERPSAIAKTDAQIDKELRAIFMRLFAQLLQGYRSCLTIIRIHPKPVITFHKAGFLGARDLIESEFLFRVLDSMFFTTFVNERGPPWRSSDAWDELYSSMNELLKSEAQNRNLVGRTQRFKGYFNFTFPSYFQILTHIQELGRVLYENEGTLAHISYAQKVLRPPEGAFQRIHQPAFPRISSEKVELIIQEGIRKNGVPQRFHVTRNQHRIIPMGPRLPEALDVRPNVQNSARRLEVLRICVSYIFENRITDARKLLPAVMRTLMHRDARLILCREFFGYVHGNKAVLDHQQFELVVRFMNKALQKSSGIDEYTVAAALLPMSTIFCRKLSTGVVQFAYTEIQDHAIWKNLQFWESTFFQDVQGQIKALYLLHRRQNEHQKEANCVLDEVPLEEPTALEITAEQLRKSPNIEEEKKAELAKSEESTLYSQAIHFANRMVSLLIPLDVNVDAASKPKPAFRLEENQSVSNSIMGSHSLSEHSDEGFEENNALEIGVTVGKTISRFIDCVCTEGGVTSEHIRNLHDMVPGVVHMHIESLEPVYLEAKRHPHVQKPKIQTPCLLPGEDLVTDHLRCFLMPDGREDETQCLIPAEGALFLTNYRVIFKGSPCDPLFCEQVIVRTFPIASLLKEKKISVLYLAHLDQTLTEGLQLRSSSFQLIKVAFDPEVTPEQIESFRKILSKARHPFDEFEYFAFQSYGTMLQGVAPLKTKEKYSTLKGFAKKTLLRGAKKAGFKQKQQTKRKLVSDYDYGSADAQETQSIDDELEDGDEFETQNNAMPRLLTTKDVERMRERSYVQDWKRLGFDAESQRGFRISNANTSYATCRSYPAIIVAPVQCSDAAIMHLGRCFKGQRIPLPTWRHANGALLIRGGQPNSKSVIGMLKNTTGSTTNAHHDVTHYPEQDKYFLALINTMPKLTPLALNQYSGMNLSMSSLMGHSSSDDRQPLTPELSRKHKNNLDISDGNKSSQGGKGGTMKGNPKNSLAHPFRKMRLYALGEKSQAKSNMNVDFCADFIPVDYPDIRQSRPAFKKLIRACMPSHNTNEADGQSFAKMVEQSDWLQQISSLMQLSGAVVDLIDLQESSVMLSLEDGSDVTAQLSSIAQLCLDPYYRSLDGFRVLVEKEWLAFGHRFAHRSNLKPSHANTNIAFAPTFLQFLDVVHQLQRQFPMAFEFNDFYLRFLAYHSVSCRFRTFLFDCELERSDSGIAAMEDKRGSLNAKHMFGAGGMATNGSDDECSVYPLDIRSQRAPAPLNRIGHSIFDYIERQHNKTPIFYNFLYSGDKSVTLRPQNNVAALDLWCYYTNEELAQGAPYDLEVTTVDDEIDLSETKGKRMVITAGYDNMEKCNPSAYVCLLSEVKQAETERGHLPQKWLQVWNSLEVPQLEPVARNTSLGNIFVQTHQHKRSTLEIIMKGRLAGYQDKYFHPHRFEKHPYTTPTNCNHCTKLLWGPVGYRCMDCGNSYHEKCTEHSMKNCTKYKAIDGAVGPPNVNMSQGDTASIASSAATTARTSSHHFYNQFSSNVAENRTHEGHLYKRGALLKGWKQRWFVLDSIKHQLRYYDTSEDTAPKGIIELAEVQSVTAAQPAQIGAKGVDEKGFFDLKTSKRIYNFYAINANLAQEWIEKLQACLQ | ||
Latest revision as of 06:18, 12 September 2015
Back to List of HMMs
Symbol: MTMR5_C1
Name: MTMR5, C1 domain
Description
The MTMR5 subfamily has a C1 domain which is able to be detected by 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 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:
C. elegans sequence:
MRDPDKVKSGPICDTVAVIVLEESDDENALPDVLHEVQSPHTSDNIPTSSIKKFARPRGWYNQSVSSPSEFFYQILTTERGTRRIAYVLSTWEEDEKTLNFKAVSIVLISQNFHPKAFKEILLEISNDLRTPEFSSSSELIRFLTYELVEEGSTIEIRTKTLHVELGFELIPISPVTGKDVAMLFKMLGFQNVIKIIHALLSDCRIVLASSSLMRLSRCQNAILSLLYPFEYVHSCVTILPDSLAEVLESPTPFLIGVLSEFVTSFGDENIVVYLDNGEVHVPDHAEIYKSDDYYYNSLHQRLRDVMFTTTSQEDLSIPNEERIEVDDFILDKKLRACFIYYFAELLYGYQYYILYTRIKGNFEKKLTTSLTFHVGAFRGFRKLTDMMSSSLLKSVYFQTFILTRALPRRKHDLFDEISCFKELDQLIFKQNSTSSESKKIIEHISCELIQKERYMEKCSARKQEIFTKIHWISGKELAQNNNSIIHTVKPKMRSNVILQAMLPVVNTHAEYHANQFEAYAHRIEALRNCLAAIFEGKVAFASKSLDAVKSSMRFAPLRIELCRLLNQKCSHDKLTDKQFEDIALLMNAALQAECEEDKDGVVRSLMYLSNVYSRKVAQGMQQYMYTAVQEHKVWKNQRFWTSCFYYEVHEMLFSEMLQKDRKITESLWCHTLRPCAMEMINTDDTDQEELVKQENEMIQAQAKHFANILISLQIPLSEEFFEHEDAHRSVLNEKCKWIVNTLDSILGVTGRINGLSLSRIQTYVEAHVESLRDVYVEMSTGEHLKKGNFDPVLAHGEFLISDPIDCYLLTSIEESEMSLNRLENLLPADGSLFLTNYRVIFKGKSVDINATNGTIVQTIPLYSMESFKKLTNKKLIPTQLIEKGVKIEHIISIRSSCASSIIIAFDEDEINNMAIEKFLEVIETNSHNSFAFYNTRKDMKVVENGSHKFGTLNSAIRGFTKKKTDTRRIRSHSSHRGSIQLSFDKMEELDYLKKNAHIRYAVIDYPRIGLNSKIVKLRMSHSNLDYTICPSYPGNFIVPSETNESELAKVAKGFVEHRLPVVVWMNENGALLVRASAFTSIDMVKKLKKVVNYRRNASKLTGSMTGSQQTLHSKASSNEESSSNIVAGAEIKSAEVQMNYIAKLSNSSQRAVSYALPTQYADKFSTFNDGCTLTQNNANGFPTTRIHRKALYVLLEKGHGVKIPIDSNAEAIMVRSVKESELRRSLQRARQICSSEFQVENRTSFLESWNASNWPQCVSRMIELSNSIVALMNLYNSSVAICLEAGRSITTILSSLSQLLSDPYYRTCDGFQVLVEKEWLAFGHYFHKDTETSSPSFICFLDCVYQISQQYPTAFEFSYFYISFLAYHSTAGYFRTFIDDCEEKRLQSDANEFYLPDNLATINVWEFIKLRNRVSAAFYNELYEQIGDIVIPSSSIPQIHMWPFLAETHLKYGSPYDIEPASHEQQLVDPDYEEEEDWSKLNNTDIDERHLNRRVRSPERDPANMDMIRLLQKSYLTELFDASDRKTTTNGESNGKETIHELTPFTVGARPVQCCYCTNILTRWSKAVHCKKCRIHVHEGCVNRNITIGNITHTWDAKPFEDIKMPSGAIQIGTPQAEKMLHSPNNTLTRESMSPPTANTIPPLCTGYLSKRGAKLKLWVPRFFVLYPDSPKVYYYEDFENWKTAEKPSGCIDLVDFKSFNLEQTGRRGLIELHMKNKTHRLLSENINEAIRWKECIEQVIRD
Drosophila Melanogaster sequence:
MSRLADYFVIVGYDSDKEKTASNVGGQPTCGKIVQRFPEKDWPDTPFIEGIEWFCQPLGWSLSYEKQEPKFFVSVLTDIDANKHYCACLSFHETVAITQTRSVDDEDETIGSSRLLGATPSSMDGITTTSTPASITHHSVMYAPKCLVLISRLDCAETFKNCLGTIYTVYIENLAYGLETLIGNILGCIQVPPAGGPQVRFSIGAGDKQSLQPPQSSSLPTTGSGVHFLFKQLGIKNVLILLCSVMTENKILFLSKCYWHLTDSCRALVALMYPFRYTHVYIPILPAPLTEVLSTPTPFIMGIHSSLQTEITDLLDVIVVDLDGGLVTIPESLTPPVPILPSPLWEQTQDLLSMILFPNLAQADLAFPTLERPSAIAKTDAQIDKELRAIFMRLFAQLLQGYRSCLTIIRIHPKPVITFHKAGFLGARDLIESEFLFRVLDSMFFTTFVNERGPPWRSSDAWDELYSSMNELLKSEAQNRNLVGRTQRFKGYFNFTFPSYFQILTHIQELGRVLYENEGTLAHISYAQKVLRPPEGAFQRIHQPAFPRISSEKVELIIQEGIRKNGVPQRFHVTRNQHRIIPMGPRLPEALDVRPNVQNSARRLEVLRICVSYIFENRITDARKLLPAVMRTLMHRDARLILCREFFGYVHGNKAVLDHQQFELVVRFMNKALQKSSGIDEYTVAAALLPMSTIFCRKLSTGVVQFAYTEIQDHAIWKNLQFWESTFFQDVQGQIKALYLLHRRQNEHQKEANCVLDEVPLEEPTALEITAEQLRKSPNIEEEKKAELAKSEESTLYSQAIHFANRMVSLLIPLDVNVDAASKPKPAFRLEENQSVSNSIMGSHSLSEHSDEGFEENNALEIGVTVGKTISRFIDCVCTEGGVTSEHIRNLHDMVPGVVHMHIESLEPVYLEAKRHPHVQKPKIQTPCLLPGEDLVTDHLRCFLMPDGREDETQCLIPAEGALFLTNYRVIFKGSPCDPLFCEQVIVRTFPIASLLKEKKISVLYLAHLDQTLTEGLQLRSSSFQLIKVAFDPEVTPEQIESFRKILSKARHPFDEFEYFAFQSYGTMLQGVAPLKTKEKYSTLKGFAKKTLLRGAKKAGFKQKQQTKRKLVSDYDYGSADAQETQSIDDELEDGDEFETQNNAMPRLLTTKDVERMRERSYVQDWKRLGFDAESQRGFRISNANTSYATCRSYPAIIVAPVQCSDAAIMHLGRCFKGQRIPLPTWRHANGALLIRGGQPNSKSVIGMLKNTTGSTTNAHHDVTHYPEQDKYFLALINTMPKLTPLALNQYSGMNLSMSSLMGHSSSDDRQPLTPELSRKHKNNLDISDGNKSSQGGKGGTMKGNPKNSLAHPFRKMRLYALGEKSQAKSNMNVDFCADFIPVDYPDIRQSRPAFKKLIRACMPSHNTNEADGQSFAKMVEQSDWLQQISSLMQLSGAVVDLIDLQESSVMLSLEDGSDVTAQLSSIAQLCLDPYYRSLDGFRVLVEKEWLAFGHRFAHRSNLKPSHANTNIAFAPTFLQFLDVVHQLQRQFPMAFEFNDFYLRFLAYHSVSCRFRTFLFDCELERSDSGIAAMEDKRGSLNAKHMFGAGGMATNGSDDECSVYPLDIRSQRAPAPLNRIGHSIFDYIERQHNKTPIFYNFLYSGDKSVTLRPQNNVAALDLWCYYTNEELAQGAPYDLEVTTVDDEIDLSETKGKRMVITAGYDNMEKCNPSAYVCLLSEVKQAETERGHLPQKWLQVWNSLEVPQLEPVARNTSLGNIFVQTHQHKRSTLEIIMKGRLAGYQDKYFHPHRFEKHPYTTPTNCNHCTKLLWGPVGYRCMDCGNSYHEKCTEHSMKNCTKYKAIDGAVGPPNVNMSQGDTASIASSAATTARTSSHHFYNQFSSNVAENRTHEGHLYKRGALLKGWKQRWFVLDSIKHQLRYYDTSEDTAPKGIIELAEVQSVTAAQPAQIGAKGVDEKGFFDLKTSKRIYNFYAINANLAQEWIEKLQACLQ
