; SAM: prettyalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:15 ; (c) 1992-1999 Regents of the University of California, Santa Cruz ; ; Sequence Alignment and Modeling Software System ; http://www.cse.ucsc.edu/research/compbio/sam.html ; ; ------ Citations (HMMs, SAM) ------ ; A. Krogh et al., Hidden Markov models in computational biology: ; ------------- 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, 1999. ; A. Krogh et al., Hidden Markov models in computational biology: ; Applications to protein modeling, JMB 235:1501-1531, Feb 1994. ; -------------------------------------------------------------- ; Sequence numbers correspond to the following labels: ; 1 T0105 ; 2 gi|6175041|sp|P23497|SP10_HUMAN_595:686 ; 3 gi|3252911|gb|AAC39790.1|_596:687 ; 4 gi|2340123|gb|AAC53509.1|_360:449 ; 5 gi|2340117|gb|AAC53506.1|_378:467 ; 6 gi|7305513|ref|NP_038701.1|_378:467 ; 7 gi|2340121|gb|AAC53508.1|_378:467 ; 8 gi|2340131|gb|AAC53513.1|_360:449 ; 9 gi|6166538|sp|Q13342|LY10_HUMAN_580:669 ; 10 gi|6005880|ref|NP_009168.1|_466:555 ; 11 gi|4758586|ref|NP_004500.1|_154:245 ; 12 gi|7643905|gb|AAF65538.1|AF205779_1_82:163 ; 13 gi|6331220|dbj|BAA86583.1|_83:164 ; 14 gi|7643903|gb|AAF65537.1|AF205778_1_82:163 ; 15 gi|6912568|ref|NP_036516.1|_82:163 ; 16 gi|7643907|gb|AAF65539.1|AF205780_1_82:163 ; 17 gi|6599186|emb|CAB63765.1|_57:138 ; 18 gi|3746541|gb|AAC64001.1|_81:162 ; 19 gi|3309569|gb|AAC79679.1|_193:273 ; 20 gi|3309567|gb|AAC79678.1|_193:273 ; 21 gi|5764636|gb|AAD51352.1|AF173868_1_76:156 ; 22 gi|7021843|dbj|BAA91410.1|_76:156 ; 23 gi|3309565|gb|AAC79677.1|_179:259 ; 24 gi|5729846|ref|NP_006573.1|_86:166 ; 25 gi|3309563|gb|AAC79676.1|_193:273 ; 26 gi|8393248|ref|NP_058570.1|_194:274 ; 27 gi|1389895|gb|AAC35994.1|_125:205 ; 28 gi|3293446|gb|AAC25717.1|_125:205 ; 29 gi|8118043|gb|AAF72874.1|AF210433_1_77:156 ; 30 gi|2246694|gb|AAB62704.1|_125:205 ; 31 gi|3293444|gb|AAC25716.1|_125:205 ; 32 gi|3293440|gb|AAC25714.1|_125:205 ; 33 gi|3293442|gb|AAC25715.1|_125:205 ; 34 gi|3293448|gb|AAC25718.1|_125:205 ; 35 gi|3293450|gb|AAC25719.1|_125:205 ; 36 gi|1362890|pir||B49515_215:291 ; 37 gi|4758588|ref|NP_004501.1|_252:328 ; 38 gi|2133648|pir||S69214_211:291 ; 39 gi|7497426|pir||T19932_76:151 ; 40 gi|7496508|pir||T19470_72:150 ; 41 gi|7504108|pir||T22598_6:84 ; 42 gi|7239187|gb|AAF43110.1|AF169948_1_2:61 ; 43 gi|7495061|pir||T32370_91:158 ; 44 gi|7108534|gb|AAF36461.1|AF128116_1_190:247 ; 45 gi|7108546|gb|AAF36467.1|AF128122_1_190:247 ; 46 gi|7108536|gb|AAF36462.1|AF128117_1_190:247 ; 47 gi|7108548|gb|AAF36468.1|AF128123_1_190:247 ; 48 gi|7108538|gb|AAF36463.1|AF128118_1_190:247 ; 49 gi|7108550|gb|AAF36469.1|AF128124_1_190:247 ; 50 gi|7108540|gb|AAF36464.1|AF128119_1_190:247 ; 51 gi|6753020|ref|NP_033776.1|_190:247 ; 52 gi|7108552|gb|AAF36470.1|AF128125_1_190:247 ; 53 gi|7108542|gb|AAF36465.1|AF128120_1_190:247 ; 54 gi|7108532|gb|AAF36460.1|AF128115_1_190:247 ; 55 gi|7108544|gb|AAF36466.1|AF128121_1_190:247 10 20 30 40 50 60 | | | | | | 1 DENINFKQSELPVTCGEVKGTLYKERF.KQGTSKKCIQSED..KKWFTPREFEIEGDRGASKNWK 2 DENINFKQSELPVTCGEVKGTLYKERF.KQGTSKKCIQSED..KKWFTPREFEIEGDRGASKNWK 3 -ENINFKQSELPVTCGEVKGTLYKERF.KQGTSKKCIQSED..KKWFTPREFEIEGDRGASKNWK 4 EENADFGGAELPVVCGNVQGFLNKEKF.KQGIYVRSIRSET..GRLFTPMDFEIEGNCEKAKNWR 5 EENADFGGAELPVVCGNVQGFLNKEKF.KQGIYSRSIRSET..GRLFTPMDFEIEGNCEKAKNWR 6 EENADFGGAELPVVCGNAQGFLDKEKF.KQGIYVRSIRGKT..GRLFTPMDFEIEGNCEKAKNWR 7 EENADFGGAELPAVCGNVQGFLNKEKF.KQGIYVRSIRSET..GRLFTPMDFEIEGNCEKAKNWR 8 EENADFGGAELPVVCGNAQGFLDKEKF.KQGIYVRSIRGKT..GRLFTPMDFEIEGNCEKAKNWR 9 DETVDFKAPLLPVTCGGVKGILHKKKL.QQGILVKCIQTED..GKWFTPTEFEIKGGHARSKNWR 10 DETVDFKAPLLPVTCGGVKGILHKKKL.QQGILVKCIQTED..GKWFTPTEFEIKGGHARSKNWR 11 -DTVDFHCSKSPVTCGEAKGILYKKKM.KHGSSVKCIRNED..GTWLTPNEFEVEGKGRNAKNWK 12 EGENLEAEIVYPITCGDSRANLIWRKFvCPGINVKCVQYDE..-HVISPKEFVHLAGKSTLKDWK 13 EGENLEAEIVYPITCGDSRANLIWRKFvCPGINVKCVQYDE..-HVISPKEFVHLAGKSTLKDWK 14 EGENLEAEIVYPITCGDSRANLIWRKFvCPGINVKCVQYDE..-HVISPKEFVHLAGKSTLKDWK 15 EGENLEAEIVYPITCGDSRANLIWRKFvCPGINVKCVQYDE..-HVISPKEFVHLAGKSTLKDWK 16 EGENLEAEIVYPITCGDSRANLIWRKFvCPGINVKCVQYDE..-HVISPKEFVHLAGKSTLKDWK 17 EGENLEAEIVYPITCGDSRANLIWRKFvCPGINVKCVQYDE..-HVISPKEFVHLAGKSTLKDWK 18 EGENLEAEIVYPITCGDSRANLIWRKFvCPGINVKCVQYDE..-HVISPKEFVHLAGKSTLKDWK 19 NWDPSVYDSELPVRCRNISGTLYKSRL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRASSKDWK 20 NWDPSVYDSELPVRCRNISGTLYKNRL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRASSKDWK 21 -EANEDMEIAYPITCGESKAILLWKKFvCPGINVKCVKFND..-QLISPKHFVHLAGKSTLKDWK 22 -EANEDMEIAYPITCGESKAILLWKKFvCPGINVKCVKFND..-QLISPKHFVHLAGKSTLKDWK 23 NWDPSVYDSELPVRCRNISGTLYKNRL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRASSKDWK 24 -EANEDMEIAYPITCGESKAILLWKKFvCPGINVKCVKFND..-QLISPKHFVHLAGKSTLKDWK 25 NWDPSVYDSELPVRCRNISGTLYKNRL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRASSKDWK 26 NWDPSVYDSELPVRCRNISGTLYKSRL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRASSKDWK 27 NWDPSVYDSELPVRCRNISGTLYKSRL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRASSKDWK 28 NWDPSVYDSELPVRCRNISGTLYKNKL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRASSKDWK 29 --GNEDMEIAYPITCGESKAVLLWKKFvCPGINVKCVKFND..-QLISPKHFVHLAGKSTLKDWK 30 NWDPSVYDSELPVRCRNISGTLYKNRL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRTSSKDWK 31 NWDPSVYDSELPVRCRNISGTLYKNKL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRASSKDWK 32 NWDPSVYDSDLPVRCRNISGTLYKNRL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRASSKDWK 33 NWDPSVCDNDLPVRCRNISGTLYKNKL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRASSKDWK 34 NWDPSVYDSELPVRCRNISGTLYKNRL.GSAAGDGASSRGR..-TGTCPTEFEAMAGRASSKDWK 35 NWDPSVYDSELPVRCRNISGTLYKNRL.GSAAGDGASSRGR..-TGTCPTEFEAMAGRASSKDWK 36 -DTVDFHCSKLPVTCGEAKGILYKKKM.KHGSSVKCIRNED..GTWLTPNEFEVEGKGRNAKNWK 37 -DTVDFHCSKLPVTCGEAKGILYKKKM.KHGSSVKCIRNED..GTWLTPNEFEVEGKGRNAKNWK 38 ENPSTQHNEVFQIRCKTTCAELYRSKL.GSGGRGRCVKYKD..-KWHTPSEFEHVCGRGSSKDWK 39 ------NATTVPVTCGYVKGIMHLKLFrCPGIRQACIEYES..-QYLTPKQFTELGGKGRQKDWK 40 ---EGDASPTVPVSCGVVNGKMHLNLFmCPGIHQPCIEVGN..-DLLSPKQFTIRGDKERQKDWK 41 -----LLKIIFQVKCGTLTAKMVTKLFtCPGIHQNCILIDGe.TEYISPKEFTVRANKDKQKDWK 42 ---------------------------.------KCIQSED..KKWFTPREFEIEGDRRASKNWK 43 --------KYMELKCGALVARLHTELFiCPGIREKCIEVLDcpGELLTPVEFTIKAEKSKQKDWK 44 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK--- 45 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK--- 46 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK--- 47 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK--- 48 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK--- 49 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK--- 50 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK--- 51 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK--- 52 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK--- 53 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK--- 54 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK--- 55 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK--- 70 80 90 | | | 1 LSIRCGGYTLKVLMENKFLPEPPSTRKKVTIK 2 LSIRCGGYTLKVLMENKFLPEPPSTRKKVT-- 3 LSIRCGGYTLKVLMENKFLPEPPSTRKKRIL- 4 QTIRCKGWTLRELIQKGVLQDPPRKKKE---- 5 QTIRCKGWTLRELIQQGVLQDPPRKKKE---- 6 QTIRCKGWTLRELIQKGVLQDPPRKKKE---- 7 QTIRCKGWTLRELIQKGVLQDPPRKKKE---- 8 QTIRCKGWTLRELIQKGVLQDPPRKKKE---- 9 LSVRCGGWPLRWLMENGFLPDPPRIRYR---- 10 LSVRCGGWPLRWLMENGFLPDPPRIRYR---- 11 RNIRCEGMTLGELLKSGLLLCPPRINLKREL- 12 RAIRMNGIMLRKIMDSGELD------------ 13 RAIRMNGIMLRKIMDSGELD------------ 14 RAIRMNGIMLRKIMDSGELD------------ 15 RAIRMNGIMLRKIMDSGELD------------ 16 RAIRMNGIMLRKIMDSGELD------------ 17 RAIRMNGIMLRKIMDSGELD------------ 18 RAIRMNGIMLRKIMDSGELD------------ 19 RSIRYAGRPLQCLIQDGILN------------ 20 RSIRYAGRPLQCLIQDGILN------------ 21 RAIRLGGIMLRKMMDSGQID------------ 22 RAIRLGGIMLRKMMDSGQID------------ 23 RSIRYAGRPLQCLIQDGILN------------ 24 RAIRLGGIMLRKMMDSGQID------------ 25 RSIRYAGRPLQCLIQDGILN------------ 26 RSIRYAGRPLQCLIQDGILN------------ 27 RSIRYAGRPLQCLIQDGILN------------ 28 RSIRYAGRPLQCLIQDGILN------------ 29 RAIRLGGIMLRKMMDSGQID------------ 30 RSIRYAGRPLQCLIQDGILN------------ 31 RSIRYAGRPLQCLIQDGILN------------ 32 RSIRYAGRPLQCLIQDGILN------------ 33 RSIRYAGRPLQCLIQDGILN------------ 34 RSIRYAGRPLQCLIQDGILN------------ 35 RSIRYAGRPLQCLIQDGILN------------ 36 RNIRCEGMTLGELLKR---------------- 37 RNIRCEGMTLGELLKR---------------- 38 RSIKYGGKSLQSLIDEGTLT------------ 39 ACIRVENVSLRTLLENKTID------------ 40 ASIRVGRSSLRTHMEAMTID------------ 41 GSIRIGKSNLRTLMEMRSLD------------ 42 LSIRCGGYTLKFLMENKLLPEPPSTRKKRIL- 43 GAIKHNGRMLR--------------------- 44 -------------------------------- 45 -------------------------------- 46 -------------------------------- 47 -------------------------------- 48 -------------------------------- 49 -------------------------------- 50 -------------------------------- 51 -------------------------------- 52 -------------------------------- 53 -------------------------------- 54 -------------------------------- 55 --------------------------------