Difference between revisions of "HMM PD0133"
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=== 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. | ||
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| + | 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) | ||
Below are the two full sequences used: | Below are the two full sequences used: | ||
Revision as of 19:22, 11 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.
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 Drosophila Melanogaster sf (1790-1840 determined by searching the complete sequence against CDD and Pfam database). (it is undergoing)
Below are the two full sequences used:
C. elegans sequence:
MRDPDKVKSGPICDTVAVIVLEESDDENALPDVLHEVQSPHTSDNIPTSSIKKFARPRGWYNQSVSSPSEFFYQILTTERGTRRIAYVLSTWEEDEKTLNFKAVSIVLISQNFHPKAFKEILLEISNDLRTPEFSSSSELIRFLTYELVEEGSTIEIRTKTLHVELGFELIPISPVTGKDVAMLFKMLGFQNVIKIIHALLSDCRIVLASSSLMRLSRCQNAILSLLYPFEYVHSCVTILPDSLAEVLESPTPFLIGVLSEFVTSFGDENIVVYLDNGEVHVPDHAEIYKSDDYYYNSLHQRLRDVMFTTTSQEDLSIPNEERIEVDDFILDKKLRACFIYYFAELLYGYQYYILYTRIKGNFEKKLTTSLTFHVGAFRGFRKLTDMMSSSLLKSVYFQTFILTRALPRRKHDLFDEISCFKELDQLIFKQNSTSSESKKIIEHISCELIQKERYMEKCSARKQEIFTKIHWISGKELAQNNNSIIHTVKPKMRSNVILQAMLPVVNTHAEYHANQFEAYAHRIEALRNCLAAIFEGKVAFASKSLDAVKSSMRFAPLRIELCRLLNQKCSHDKLTDKQFEDIALLMNAALQAECEEDKDGVVRSLMYLSNVYSRKVAQGMQQYMYTAVQEHKVWKNQRFWTSCFYYEVHEMLFSEMLQKDRKITESLWCHTLRPCAMEMINTDDTDQEELVKQENEMIQAQAKHFANILISLQIPLSEEFFEHEDAHRSVLNEKCKWIVNTLDSILGVTGRINGLSLSRIQTYVEAHVESLRDVYVEMSTGEHLKKGNFDPVLAHGEFLISDPIDCYLLTSIEESEMSLNRLENLLPADGSLFLTNYRVIFKGKSVDINATNGTIVQTIPLYSMESFKKLTNKKLIPTQLIEKGVKIEHIISIRSSCASSIIIAFDEDEINNMAIEKFLEVIETNSHNSFAFYNTRKDMKVVENGSHKFGTLNSAIRGFTKKKTDTRRIRSHSSHRGSIQLSFDKMEELDYLKKNAHIRYAVIDYPRIGLNSKIVKLRMSHSNLDYTICPSYPGNFIVPSETNESELAKVAKGFVEHRLPVVVWMNENGALLVRASAFTSIDMVKKLKKVVNYRRNASKLTGSMTGSQQTLHSKASSNEESSSNIVAGAEIKSAEVQMNYIAKLSNSSQRAVSYALPTQYADKFSTFNDGCTLTQNNANGFPTTRIHRKALYVLLEKGHGVKIPIDSNAEAIMVRSVKESELRRSLQRARQICSSEFQVENRTSFLESWNASNWPQCVSRMIELSNSIVALMNLYNSSVAICLEAGRSITTILSSLSQLLSDPYYRTCDGFQVLVEKEWLAFGHYFHKDTETSSPSFICFLDCVYQISQQYPTAFEFSYFYISFLAYHSTAGYFRTFIDDCEEKRLQSDANEFYLPDNLATINVWEFIKLRNRVSAAFYNELYEQIGDIVIPSSSIPQIHMWPFLAETHLKYGSPYDIEPASHEQQLVDPDYEEEEDWSKLNNTDIDERHLNRRVRSPERDPANMDMIRLLQKSYLTELFDASDRKTTTNGESNGKETIHELTPFTVGARPVQCCYCTNILTRWSKAVHCKKCRIHVHEGCVNRNITIGNITHTWDAKPFEDIKMPSGAIQIGTPQAEKMLHSPNNTLTRESMSPPTANTIPPLCTGYLSKRGAKLKLWVPRFFVLYPDSPKVYYYEDFENWKTAEKPSGCIDLVDFKSFNLEQTGRRGLIELHMKNKTHRLLSENINEAIRWKECIEQVIRD
Drosophila Melanogaster sequence:
MSRLADYFVIVGYDSDKEKTASNVGGQPTCGKIVQRFPEKDWPDTPFIEGIEWFCQPLGWSLSYEKQEPKFFVSVLTDIDANKHYCACLSFHETVAITQTRSVDDEDETIGSSRLLGATPSSMDGITTTSTPASITHHSVMYAPKCLVLISRLDCAETFKNCLGTIYTVYIENLAYGLETLIGNILGCIQVPPAGGPQVRFSIGAGDKQSLQPPQSSSLPTTGSGVHFLFKQLGIKNVLILLCSVMTENKILFLSKCYWHLTDSCRALVALMYPFRYTHVYIPILPAPLTEVLSTPTPFIMGIHSSLQTEITDLLDVIVVDLDGGLVTIPESLTPPVPILPSPLWEQTQDLLSMILFPNLAQADLAFPTLERPSAIAKTDAQIDKELRAIFMRLFAQLLQGYRSCLTIIRIHPKPVITFHKAGFLGARDLIESEFLFRVLDSMFFTTFVNERGPPWRSSDAWDELYSSMNELLKSEAQNRNLVGRTQRFKGYFNFTFPSYFQILTHIQELGRVLYENEGTLAHISYAQKVLRPPEGAFQRIHQPAFPRISSEKVELIIQEGIRKNGVPQRFHVTRNQHRIIPMGPRLPEALDVRPNVQNSARRLEVLRICVSYIFENRITDARKLLPAVMRTLMHRDARLILCREFFGYVHGNKAVLDHQQFELVVRFMNKALQKSSGIDEYTVAAALLPMSTIFCRKLSTGVVQFAYTEIQDHAIWKNLQFWESTFFQDVQGQIKALYLLHRRQNEHQKEANCVLDEVPLEEPTALEITAEQLRKSPNIEEEKKAELAKSEESTLYSQAIHFANRMVSLLIPLDVNVDAASKPKPAFRLEENQSVSNSIMGSHSLSEHSDEGFEENNALEIGVTVGKTISRFIDCVCTEGGVTSEHIRNLHDMVPGVVHMHIESLEPVYLEAKRHPHVQKPKIQTPCLLPGEDLVTDHLRCFLMPDGREDETQCLIPAEGALFLTNYRVIFKGSPCDPLFCEQVIVRTFPIASLLKEKKISVLYLAHLDQTLTEGLQLRSSSFQLIKVAFDPEVTPEQIESFRKILSKARHPFDEFEYFAFQSYGTMLQGVAPLKTKEKYSTLKGFAKKTLLRGAKKAGFKQKQQTKRKLVSDYDYGSADAQETQSIDDELEDGDEFETQNNAMPRLLTTKDVERMRERSYVQDWKRLGFDAESQRGFRISNANTSYATCRSYPAIIVAPVQCSDAAIMHLGRCFKGQRIPLPTWRHANGALLIRGGQPNSKSVIGMLKNTTGSTTNAHHDVTHYPEQDKYFLALINTMPKLTPLALNQYSGMNLSMSSLMGHSSSDDRQPLTPELSRKHKNNLDISDGNKSSQGGKGGTMKGNPKNSLAHPFRKMRLYALGEKSQAKSNMNVDFCADFIPVDYPDIRQSRPAFKKLIRACMPSHNTNEADGQSFAKMVEQSDWLQQISSLMQLSGAVVDLIDLQESSVMLSLEDGSDVTAQLSSIAQLCLDPYYRSLDGFRVLVEKEWLAFGHRFAHRSNLKPSHANTNIAFAPTFLQFLDVVHQLQRQFPMAFEFNDFYLRFLAYHSVSCRFRTFLFDCELERSDSGIAAMEDKRGSLNAKHMFGAGGMATNGSDDECSVYPLDIRSQRAPAPLNRIGHSIFDYIERQHNKTPIFYNFLYSGDKSVTLRPQNNVAALDLWCYYTNEELAQGAPYDLEVTTVDDEIDLSETKGKRMVITAGYDNMEKCNPSAYVCLLSEVKQAETERGHLPQKWLQVWNSLEVPQLEPVARNTSLGNIFVQTHQHKRSTLEIIMKGRLAGYQDKYFHPHRFEKHPYTTPTNCNHCTKLLWGPVGYRCMDCGNSYHEKCTEHSMKNCTKYKAIDGAVGPPNVNMSQGDTASIASSAATTARTSSHHFYNQFSSNVAENRTHEGHLYKRGALLKGWKQRWFVLDSIKHQLRYYDTSEDTAPKGIIELAEVQSVTAAQPAQIGAKGVDEKGFFDLKTSKRIYNFYAINANLAQEWIEKLQACLQ
