; SAM: /projects/compbio/bin/i686/prettyalign v3.3.2 (February, 2001) compiled 06/24/02_10:51:09 ; (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-T99, 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, C. Barrett, R. Hughey, Hidden Markov models for detecting ; remote protein homologies, Bioinformatics 14(10):846-856, 1998. ; A. Krogh et al., Hidden Markov models in computational biology: ; Applications to protein modeling, JMB 235:1501-1531, Feb 1994. ; --------------------------------------------------------------------- ; Sequences correspond to the following labels: ; 1 T0158 ; 2 1a88A ; 3 1a8s ; 4 1auoA ; 5 1aurA ; 6 1broA ; 7 1brt ; 8 1cleA ; 9 1crl ; 10 1ea5A ; 11 1fj2A ; 12 1jjfA ; 13 1jjiA ; 14 1jkmA ; 15 1jkmB ; 16 1qe3A ; 17 1qfmA ; 18 1qidA ; 19 1thg ; 20 1vxrA ; 21 2bce 10 20 30 40 50 | | | | | 1 ........MKPENKLPVLDLISAEMKTVVNTLQPDLPPWPATGTIAEQRQYYTLERRF....... 2 g.......--------------------------------------------------....... 3 ttf.....--------------------------------------------------....... 4 mtep....--------------------------------------------------....... 5 mtep....--------------------------------------------------....... 6 p.......--------------------------------------------------....... 7 p.......--------------------------------------------------....... 8 apt20iin----EAFLGIPFAEPPVGNLRFKDPVPYSGSLNGQKFTSYGPSCMQQNPE....... 9 apt20iin----EAFLGIPFAEPPVGNLRFKDPVPYSGSLDGQKFTSYGPSCMQQNPE....... 10 xxx24vls-SHISAFLGIPFAEPPVGNMRFRRPEPKKPWSGVWNASTYPNNCQQYVDE....... 11 xxm9efms--------------------------------------------------....... 12 xxx12xsl--------------------------PTMPP------------SGYDQVR....... 13 ml......------DMPIDPVYYQLAEYFDSLPKFDQFSSAREYREAINRIYEERNRQ....... 14 pgr57shd--------------------------------------GFQAVYDSIALD....... 15 ytp60shd--------------------------------------GFQAVYDSIALD....... 16 xth21ngv----HKWKGIPYAKPPVGQWRFKAPEPPEVWEDVLDATAYGPIC------....... 17 ml417eel----------------------------------------EPRVFREVTV....... 18 xxx24vls-SHISAFLGIPFAEPPVGNMRFRRPEPKKPWSGVWNASTYPNNCQQYVDE....... 19 xap21gkv----DTFKGIPFADPPLNDLRFKHPQPFTGSYQGLKANDFSPACMQLDPGnsl12lg 20 xxx25lss--HISAFLGIPFAEPPVGNMRFRRPEPKKPWSGVWNASTYPNNCQQYVDE....... 21 akl27dsv----DIFKGIPFAAAPKAL---EKPERHPGWQGTLKAKSFKKRCLQATLT....... 60 70 80 90 100 | | | | | 1 .WNAGAPEMA........TRAYMVPTKYGQVETRLFCPQP.....DSPATLFYLHGGGFILGNLD 2 .---------........---TVTTSDGTNIFYKDWGPRD.....--GLPVVFHHG---WPLSAD 3 .---------........-----TTRDGTQ----IYYKDW.....GSGQPIVFSHG---WPLNAD 4 .---------........---------------LILQPAK.....PADACVIWLHG-----LGAD 5 .---------........---------------LILQPAK.....PADACVIWLHG-----LGAD 6 .---------........---FITVGQENSTSIDLYYEDH.....GTGQPVVLIHG---FPLSGH 7 .---------........---FITVGQENSTSIDLYYEDH.....GTGQPVVLIHG---FPLSGH 8 .GTFEENLGKtal10qskVFQAVLPQSEDCLTINVVRPPGtkag.ANLPVMLWIFGGGFEIGSPT 9 .GTYEENLPKaal10qskVFEAVSPSSEDCLTINVVRPPGtkag.ANLPVMLWIFGGGFEVGGTS 10 .QFPGFSGSE........MWNPNREMSEDCLYLNIWVPSPrp...KSTTVMVWIYGGGFYSGSST 11 .---------........------------TPLPAIVPAAr....KATAAVIFLHG----LGD-- 12 .NGVPRGQVV........NISYFSTATNSTRPARVYLPPGyskd.KKYSVLYLLHG---IGGSEN 13 .LSQHERVER........VEDRTIKGRNGDIRVRVYQQKP.....-DSPVLVYYHGGGFVICSIE 14 .LPTDRDDVEt.......STETILGVDGNEITLHVFRPAGve...GVLPGLVYTHGGGMTILTTD 15 .LPTDRDDVEt.......STETILGVDGNEITLHVFRPAGve...GVLPGLVYTHGGGMTILTTD 16 .PQPSXXXXX........XXXXLPRQSEDCLYVNVFAPDTps...QNLPVMVWIHGGAFYLGAGS 17 .KGIDASDYQt.......VQIFYPSKDGTKIPMFIVHKKGikld.GSHPAFLYGYGGFNISITPN 18 .QFPGFSGSE........MWNPNREMSEDCLYLNIWVPSPrp...KSTTVMVWIYGGGFYSGSST 19 lAKVIPEEFRgplyd...MAKGTVSMNEDCLYLNVFRPAGtkpd.AKLPVMVWIYGGAFVYGSSA 20 .QFPGFSGSE........MWNPNREMSEDCLYLNIWVPSPrp...KSTTVMVWIYGGGFYSGSST 21 .QD-------........----STYGNEDCLYLNIWVPQGrkevsHDLPVMIWIYGGAFLMGXXX 110 120 130 140 | | | | 1 T.......HDRIMRLLASY...SQ....CTVIGIDYTLS........PEARFPQAIEEIVAACCY 2 D.......WDNQMLFFLSH...-G....YRVIAHDRRGHgrs.....-DQPSTGHDMDTYAADVA 3 S.......WESQMIFLAAQ...-G....YRVIAHDRRGHgrss....-QPWSGNDMDTYADDLAQ 4 R.......YDFMPVAEALQeslLT....TRFVLPQAPT-rpv27sis--------LEELEVSAKM 5 R.......YDFMPVAEALQ...ES....LLTTRFVLPQAptr29sis--------LEELEVSAKM 6 S.......WERQSAALLDA...-G....YRVITYDRRGFgqss....-QPTTGYDYDTFAADLNT 7 S.......WERQSAALLDA...-G....YRVITYDRRGFgqss....-QPTTGYDYDTFAADLNT 8 If......PPAQMVTKSVL...MGkp..IIHVAVNYRVAswg12ika-EGSGNAGLKDQRLGMQW 9 Tfpp....AQMITKSIAMG...KP....IIHVSVNYRVSswg12ika-EGSANAGLKDQRLGMQW 10 L.......DVYNGKYLAYT...EE....VVLVSLSYRVGafg11gsq-EAPGNVGLLDQRMALQW 11 T.......GHGWAEAFAGIrs.SH....IKYICPHA---pvr29qed-----ESGIKQAAENIKA 12 DwfegggrANVIADNLIAE...-GkikpLIIVTPNTNAAgpgia...--DGYENFTKDLLNSLIP 13 S.......HDALCRRIARL...SN....STVVSVDYRLA........PEHKFPAAVYDCYDATKW 14 Nrv.....HRRWCTDLAAA...-G....SVVVMVDFRNAwtaeg...-HHPFPSGVEDCLAAVLW 15 Nrv.....HRRWCTDLAAA...-G....SVVVMVDFRNAwtaeg...-HHPFPSGVEDCLAAVLW 16 E.......PLYDGSKLAAQ...GE....VIVVTLNYRLGpfg12fde-AYSDNLGLLDQAAALKW 17 Y.......SVSRLIFVRHM...-G....GVLAVANIRGGgey15lan----KQNCFDDFQCAAEY 18 L.......DVYNGKYLAYT...EE....VVLVSLSYRVGafg11gsq-EAPGNVGLLDQRMALQW 19 Ayp.....GNSYVKESINMg..QP....VVFVSINYRTGpfg12ita-EGNTNAGLHDQRKGLEW 20 L.......DVYNGKYLAYT...EE....VVLVSLSYRVGafg11gsq-EAPGNVGLLDQRMALQW 21 Xxxxlsn.YLYDGEEIATR...GN....VIVVTFNYRVGplg10gds-NLPGNYGLWDQHMAIAW 150 160 170 180 190 200 | | | | | | 1 FHQQ...AEDYQINMSR.IGFAGDSAGAMLALASALWLRDKQID..CG..KVAGVLLWYGLYGLR 2 ALTE...ALDLRG----.AVHIGHSTGGGEVARYVARAEP----..-G..RVAKAVLVSAVPPVM 3 LIEH...-----LDLRD.AVLFGFSTGGGEVARYIGRHGT----..-A..RVAKAGLISAVPPLM 4 VTDLieaQKRTGIDASR.IFLAGFSQGGAVVFHTAFINWQ----..-G..PLGGVIALSTY---- 5 VTDLieaQKRTGIDASR.IFLAGFSQGGAVVFHTAFINWQ----..-G..PLGGVIALSTY---- 6 VLET...-----LDLQD.AVLVGFSMGTGEVARYVSSYGT----..-A..RIAKVAFLASLEPFL 7 VLET...-----LDLQD.AVLVGFSTGTGEVARYVSSYGT----..-A..RIAKVAFLASLEPFL 8 VADN...IAGFGGDPSK.VTIFGESAGSMSVLCHLIWNDGDNTYkgKP..LFRAGIMQSGAMVPS 9 VADN...IAAFGGDPTK.VTIFGESAGSMSVMCHILWNDGDNTYkgKP..LFRAGIMQSGAMVPS 10 VHDN...IQFFGGDPKT.VTIFGESAGGASVGMHILSPGSRDL-..--..-FRRAILQSGSPNCP 11 LIDQ...EVKNGIPSNR.IILGGFSQGGALSLYTALTTQ-----..-Q..KLAGVTALSCWLPLR 12 YIES...NYSVYTDREH.RAIAGLSMGGGQSFNIGLTNLDKFA-..--..------YIGPISAAP 13 VAEN...AEELRIDPSK.IFVGGDSAGGNLAAAVSIMARDSGE-..-D..FIKHQILIYPVVNFV 14 VDEH...RESLGL--SG.VVVQGESGGGNLAIATTLLAKRRGR-..LD..AIDGVYASIPYISGG 15 VDEH...RESLGL--SG.VVVQGESGGGNLAIATTLLAKRRGR-..LD..AIDGVYASIPYISGG 16 VREN...ISAFGGDPDN.VTVFGESAGGMSIAALLAMPAAKGL-..--..-FQKAIMESGASRTM 17 LIKE...---GYTSPKR.LTINGGSNGGLLVATCANQRPD----..--..LFGCVIAQVGVMDML 18 VHDN...IQFFGGDPKT.VTIFGESAGGASVGMHILSPGSRDL-..--..-FRRAILQSGSPNCP 19 VSDN...IANFGGDPDK.VMIFGESAGAMSVAHQLIAYGGDNTYng--kkLFHSAILQSGGPLPY 20 VHDN...IQFFGGDPKT.VTIFGESAGGASVGMHILSPGSRDL-..--..-FRRAILQSGSPNCP 21 VKRN...IEAFGGDPDXqITLFGESAGGASVSLQTLSPYNKGL-..--..-IKRAISQSGVGLCP 210 220 230 240 | | | | 1 DS....VTRRLLGG........VWDGLTQQDLQMYEEAYLSNDADRES........PYYCLFNND 2 VK....SDT-----........NPDGLPLEVFDEFRAALAANRAQFY-idv55dlk--------- 3 LK....TEA-----........NPGGLPMEVFDGIRQASLADRS----qly58dlk--------- 4 --....--------........--------------------------........---APTFGD 5 --....--------........--------------------------........---APTFGD 6 LK....TDDNPDG-........--------------------------aap65aptTWYTDFRAD 7 LK....TDDNPDG-........--------------------------aap65aptTWYTDFRAD 8 DP....VDGTYGN-........-------EIYDLFVSSAGCGSASDK-la201afa--------- 9 DA....VDGIYGNE........--------IFDLLASNAGC-GSASDKla136avl--------- 10 WA....SVSVA---........-------EGRRRAVELGRNLNCNLNSde192fglPLVKELNYT 11 AS....FPQG----........--------------------------........----PIGGA 12 NT....YPNERLFP........DG------------------------........-------GK 13 AP....TPSLLEFGe.......GLWILDQKIMSWFSEQYFSREEDKFN........PLASVIFAD 14 YA....WDHERRLTelpslvenDGYFIENGGMALLVRAYDPTGEHAED........PIAWPYFAS 15 YA....WDHERRLTelpslvenDGYFIENGGMALLVRAYDPTGEHAED........PIAWPYFAS 16 TKeq..--------........------AASTAAAFLQVLGINESQLDrlh35ald--------P 17 KFhkytIGHAWTTD........YGCSDSKQHFEWLIKY------SPLH........NVKLPEADD 18 WA....SVSVA---........-------EGRRRAVELGRNLNCNLNSde192fglPLVKELNYT 19 HD....SSSVGP--........-------DISYNRFAQYAGCDTSASAnd116qtlSVGSPFRTG 20 WA....SV------........----SVAEGRRRAVELGRNLNCNLNSde192fglPLVKELNYT 21 WA....IQQDP---........---------LFWAKRIAEKVGCPVDDts196fgk--------- 250 260 270 280 290 | | | | | 1 L........TREVPPCFIAGAEFD...PLLDDSRLLYQTL.......AAHQQP..CEFKLYPGTL 2 -........-RIDVPVLVAHGTDDqvvPYADAAPKSAELL.......----AN..ATLKSYEGLP 3 -........-KIDVPTLVVHGDADqv.VPIEASGIASAAL.......VK----g.STLKIYSGAP 4 Elelsa...SQQRIPALCLHGQYDdv.VQNAMGRSAFEHL.......KSRGVT..VTWQEYP-MG 5 Elelsa...SQQRIPALCLHGQYDdv.VQNAMGRSAFEHL.......KSRGVT..VTWQEYP-MG 6 I........PRIDVPALILHGTGDrtlPIENTARVFHKAL.......P----S..AEYVEVEGAP 7 I........PRIDVPALILHGTGDrtlPIENTARVFHKAL.......P----S..AEYVEVEGAP 8 -........---------------...-------------.......------..---------- 9 -........---------------...-------------.......------..---------- 10 A........------------EEE...ALSRRIMHYWATF.......AKTGNP..N--------- 11 -........-NRDISILQCHGDCDpl.VPLMFGSLTVEKL.......KTLVNPanVTFKTYEGMM 12 Aa.......REKLKLLFIACGTND...SLIGFGQRVHEYC.......VANNIN..HVYWLIQGGG 13 L........-ENLPPALIITAEYD...PLRDEGEVFGQML.......RRAGVE..ASIVRYRGVL 14 Ede......LRGLPPFVVAVNELD...PLRDEGIAFARRL.......ARAGVD..VAARVNIGLV 15 Ede......LRGLPPFVVAVNELD...PLRDEGIAFARRL.......ARAGVD..VAARVNIGLV 16 Ktlp13aegAASGIPLLIGTTRDEg..-------------.......------..---------- 17 -........-IQYPSMLLLTADHDdr.VVPLHSLKFIATLqyivgrsRKQNNP..LLIHVDTKAG 18 A........------------EEE...ALSRRIMHYWATF.......AKTGNP..N--------- 19 I........LNALTP---------...-------------.......------..---------- 20 A........------------EEE...ALSRRIMHYWATF.......AKTGNP..N--------- 21 -........---------------...-------------.......------..---------- 300 310 320 | | | 1 HAFLHY.SRM.MKTADEALRDGAQFFTAQL......... 2 HGMLST.HPE.-----VLNP----------dllafvks. 3 HGLTDT.H--.---KDQLNADLLAFIK---g........ 4 HEV---.---.---LPQEIHDIGAWL----aarlg.... 5 HEV---.---.---LPQEIHDIGAWL----aarlg.... 6 HGLLWT.---.--HAEEVNTALLAFL----ak....... 7 HGLLWT.---.--HAEEVNTALLAFL----ak....... 8 ------.---.-------------------tdl59ffv. 9 ------.---.-------------------gd124ffv. 10 ------.---.-------------------eph54txx. 11 HSSC--.---.----QQEMMDVKQFIDKL-lppix.... 12 HDFNVW.KPG.LWNFLQMAD----------eag10xxx. 13 HGFINY.YPV.LKAARDAINQIAALL----vfd...... 14 HGADVIfRHW.LPAALESTVRDVA------gfa10rlr. 15 HGADVIfRHW.LPAALESTVRDVA------gfa10rlr. 16 ------.---.-------------------yl178xxx. 17 HGAGKP.TAKvIEEVSDMFAFIARCL----nidwip... 18 ------.---.-------------------eph54txx. 19 ------.---.-------------------qf130lyg. 20 ------.---.-------------------eph54txx. 21 ------.---.-------------------pf134igf.