; SAM: prettyalign v3.5 (July 15, 2005) compiled no_date ; (c) 1992-2001 Regents of the University of California, Santa Cruz ; ; Sequence Alignment and Modeling Software System ; http://www.cse.ucsc.edu/research/compbio/sam.html ; ; ----------------- Citations (SAM, SAM-T2K, HMMs) -------------------- ; R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: ; Extension and analysis of the basic method, CABIOS 12:95-107, 1996. ; K. Karplus, et al., What is the value added by human intervention in protein ; structure prediction, Proteins: Stucture, Function, Genetics 45(S5):86--91, 2001. ; A. Krogh et al., Hidden Markov models in computational biology: ; Applications to protein modeling, JMB 235:1501-1531, Feb 1994. ; --------------------------------------------------------------------- 10 20 30 40 50 60 | | | | | | HsapreLMNA_2 m17sSTPLSPTRITRLQEKEDLQELNDRLAVYIDRVRSLETENAGLRLRITESEEVVSREVSGIKAA BflORF121709 m35fVTQLSPTRLTRMQEKQELQWLNDRLAQYIDRVRYLEAENSRLMVQVTSSEEITQREVTNIKSM Smalamin m48e-RSSSPLTISRSEEKDELAHLNDRLAGYIDYVRKLELDKQKLTRRIQTVTEERMSKVEEARKT NmeORF m26gSSPPGSAKFTRAQEKAELQHLNDRLATYIDRVKNLEQENSKLRSEVTVSRKTVEREVDSMKSL CinORF m7nnSGDGDSLVSGRFEEKAQLQSLNQRFSNYVLAVRTRREQEEKANHG---DESRWSEHLDQVRAL SroORF10006 m5taSTPGSPQFRRRVKEREQLDELNNELAAYLVRVRELQKENGELTSQLEAIRFSRKRFESTATIK MbrORF m23dLDNSAAQVSTRELERQRLEDLNHALSRYISRVRALETQVVTLETHIESFASVKAPKNDEVLET 2XV5:A ggs.--------------------------------------------------------------- 3GEF:A ....--------------------------------------------------------------- 70 80 90 100 110 120 130 | | | | | | | HsapreLMNA_2 YEAELGDARKTLDSVAKERARLQLELSKVREEFKELKARNTKKEGDLIAAQARLKDLEALLNSKEAA BflORF121709 FEQELTDARKLLDDTAKEKARVQIEAGKYRAEADELRAKLAKSEGALATAEKKRHQAESALNEKEGR Smalamin YEDEITALRNLVDDLAKQKSKAELDSKQMRDELNDIKMKANKRDQENRNLQRKIENLEREL------ NmeORF YETELADARRLLDETAKEKAKQQIESSKNSNDAQEFKNKFDKEAAARKKAEKELNDVRKLLHDKENQ CinORF YEQQMNDLRSELEERNRRMNEMEASRTKYETASSDFERRILSLNETVLNQNDEITKLQANLSNKEFE SroORF10006 LEGQVNDLLEEIRRKTTEIGTLNHQVQDLRKQLNKTEGDALEATREKDDLAKQLNEALSKVQELEGQ MbrORF LRAQLEQAKAELDDASQRYADLQLEHSNLQEDFKRAEGDIQGLTSLKERLQGRIESLQAMVNRLEGQ 2XV5:A ------------------------------------------------------------------- 3GEF:A ------------------------------------------------------------------- 140 150 160 170 180 190 | | | | | | HsapreLMNA_2 LSTALSEKRTLEGELHDLRGQVAKLEAALGEAKKQLQDEMLRRVDAENRLQTMKEELDFQKNIYSEE BflORF121709 LQNAIADKQRAEGELAALRLEFANLEKQLATARKQLEEETLLRVDLENKVQTLREEVEFNKQVYEQE Smalamin -----SKYKQDHDAYQPLLSDYHVLEKRFEEMKRDLEAETLLRTDLENKILGLKEQLDFRSRLFDEE NmeORF LTRRNQEALNLESVLRELQGECEELKDALKAAKYALEQETLTRVDLENRCQSLQEEQNFKKQMYDKE CinORF LQQVQLQLTGPRTELETYKAEKSDLSKRLAESERRFMMEEKAKLDIQNELTNLHTRCSHELLVYQQE SroORF10006 VSGLQRDVSQRDTTVTNLQRRVASLEADLGRQVDDTKRERLARLEAESRAQGLEDKLSSQDDMYQQQ MbrORF LASAQSSLQEEKEDGDLARQQLKDLKADLVKHRGRADSEAKARVALENEISGLQESFRLKELEHQSE 2XV5:A ------------------------------------------------------------------- 3GEF:A ------------------------------------------------------------------- 200 210 220 230 240 250 260 | | | | | | | HsapreLMNA_2 LRETKRR....HETRLVEIDNGKQREFESRLADALQELRAQHEDQVEQYKKELEKTYSAKLDNARQS BflORF121709 LTESRTR....KEVSITEVDAG-EAAFESRLQEALREMREQHELEARSMREELETMYTQKITSMRTD Smalamin REKLVER....SLYIEEEVEGRKQAEYESRLTEELRSIRDQTASELEEYKIQMEETFESKLGQLKSS NmeORF LSDIRSQlkt.VETKRVVVETDYKDKYEGLMAEKLQELREDYDSDARSFKEETELLYSSKFEELRIQ CinORF INNLNDRl5srQLTLELEETARRSGRKDGEVSEMMRKAREASEMELRRYMQEAEAKHELSISEIKMH SroORF10006 VTALEEQ....-----IKIGGTSGGLSEEDLEAALTEAKEHYKQAVNNFRTQMRSYFAQ--QPIIEP MbrORF TDALQQQlqv.ALSQVVVSVKTTGNQYEEEMSRLLRVAKSSYAEAADAFREKLKKYYQMNPTPSAAP 2XV5:A -------....-------------------------------------------------------- 3GEF:A -------....-------------------------------------------------------- 270 280 290 300 310 320 | | | | | | HsapreLMNA_2 AERNSNLVGAAHEELQQSRIRIDSLSAQLSQLQKQLAAKEAKLRDLEDSLARERDTSRRLLAEKERE BflORF121709 SERGSNALSVAREEMRESRARIDSLMSQVSGLQGQNASLEARCKELEGMMARMSEESRSSAEQYERE Smalamin ANFSAEDASRQRSELLIARKRADELSHDLSKKIAELELLQRRVADLERQLADERKDFESQLLFQRQE NmeORF RERDSEALAKLREENRNLSKSVDELSSQVHQLEAKNNALVSRVSDLQGLRAQDKEKHDNEILLRENE CinORF MDADARNMDALVEENGRLRSDFNNVSTELEGMRSKLDAANSSIKVAQNNLESERKRFESQLHTLNRK SroORF10006 DTRGLEERARLQTEVIEWRSKYEDVKAQGATAQTEIEGLKSKLAGLEDVFAQIKKSHTDEIRHKEDF MbrORF SMMQDPELKRLQAENEALRNRVAARDQDVADLKNEARHAEDKIDRLTHDLASTKAENKAHLANKDME 2XV5:A --------------------------------------------------ARERDTSRRLLAEKERE 3GEF:A ------------------------------------------------------------------- 330 340 350 360 370 380 | | | | | | HsapreLMNA_2 MAEMRARMQQQLDEYQELLDIKLALDMEIHAYRKLLEGE....EERLRL....SPSPTSQRSRGRAS BflORF121709 IRQLREEISQMMVDYQELMDIKIALDLEISAYRTLLEGE....EQRLKL....TPTPSPT-----AS Smalamin VNRLKEELEESFREFTDLMNTKIALDQEILMYRKMLEGE....ESRLNL....TPAPRDSPFNIPVK NmeORF IAELRTSIDDALRDYEDLMGVKVALDMEITAYRKLLESE....ETRLEI....TPPASPV------- CinORF LQETQDMLLIKIKELTASEESNIPLKAEIDFLRNLIEEE....EKRLGLen..NAYSALKNGYGNAG SroORF10006 IFKLTKTMQDKDDLYRDLLDERIALDAEIDRYRRQLESAlrmfEARSPG....TGAPQMVASVRKTT MbrORF IKNLQQRISGLEDQYRVLLDRNLSLDAEIDQYRGLLGEE....YKRLNMh5slDAMDQLVGSPLSAQ 2XV5:A MAEMRARMQQQLDEYQELLDIKLALDMEIHAYRKLLEGE....EERLRL....SPSPTSQRS----- 3GEF:A ---------------------------------------....------....-------------- 390 400 410 420 430 440 | | | | | | HsapreLMNA_2 SHSSQTQGGGSVTKKRKLE....STESRSSFSQHARTSGRVA.VEEVD.EEGKF.VRLRNKS.NEDQ BflORF121709 NHSISHDCRGRTSKRKRVE....----MESEESGSSSSGAVA.VGGVD.LEGKF.VKLQNTSaEKDM Smalamin RRRVDGDFEGDESNASLTGasysSSRTRFAYRVSSTARGPVEfFKEQD.THGKW.IKIHNSS.NDEM NmeORF -----LGGSSSVSQTRRGNkrarTEETESTMTTTTTAEGAIQ.FTEAD.PDGKY.IKIYNSG.EKDE CinORF ANDQPGNISTFFSVDQNKN184sKNGLLWYSGSTASATGSMK.LVQVD.ENGDF.VRVHNTSaTKEE SroORF10006 RELVALSGRRAVSTKRRTAa25rLAEEAHSFTVETNTQGALS.VEDVDyREGQY.ILLKNTT.ASPL MbrORF RDEQAGEQDLDMSVELRHM....TEEVEEAWTQRMSSNGQIQ.IQSVD.LDRGFdLHLQNIG.QEPI 2XV5:A -------------------....-------------------.-----.-----.-------.---- 3GEF:A -------------------....------------STSGRVA.VEEVD.EEGKF.VRLRNKS.NEDQ 450 460 470 480 490 500 510 | | | | | | | HsapreLMNA_2 SMGNWQIKRQNGDDPLLTYRFPPKFTLKAGQVVTIWAAGA.GA.THSPPTDLVWKAQNTWGCGNSLR BflORF121709 SMGGWLLKRTVGGGEEISYKFPSRYVLKAGQSVTVWATEG.GG.THSPPSDLLFRGQASWGSGDDTK Smalamin NLGSWEL-VHEADGHETRFKFSRAFSLKPGAICTIWSQDA.EGnSHNPPADLTMKN-KSFHPGTEVT NmeORF ALGGWTIQRQVGTEDPSVYKFTPKYVLKSQSHVTVWSAQG.GG.THKPPSDLVFKQLPSWGSGNEAR CinORF EIGGFLLQQNVAGHPVAVFRFPPRTRLQPGHSATVWSNNSlNG.AHDPPTHYLWKQLDKWGTGPECT SroORF10006 DLADWAVTVTNRDTQLGTFEFP-AVTLAPGRSTRVIRGAG.DG.AEKLEGDVVWTEFPDLAAQPELA MbrORF NFDDCVLTVDNGRVSE-TLVMPHGHVVAVGQVVRVVSGLG.EQ.SHRP-GDIAWTSFRDFEFDNTIN 2XV5:A ----------------------------------------.--.----------------------- 3GEF:A SMGNWQIKRQNGDDPLLTYWFPPKFTLKAGQVVTIWAAGA.GA.THSPPTDLVWKAQNTWGCGNSLR 520 | HsapreLMNA_2 TALINSTGEEVAMRKLVR-s27r BflORF121709 TLLVNDSGEEMATRSVTR-v39m Smalamin ILLLDTDGEEQAKCTVKR-1518 NmeORF TALVNAGGEEMATLLEEK-v31m CinORF TILCRPNGQAIAWMTSAP-207t SroORF10006 VYAFDPDDNESSTWAIMR-d... MbrORF VQL--ERGSQVICRAEYT-3405 2XV5:A -------------------.... 3GEF:A TALINSTGEEVAMRKLVR-s7ed