; SAM: prettyalign v2.1.1 (Apr 24, 1998) compiled 04/27/98_12:32:27. ; SAM: Sequence Alignment and Modeling Software System ; (c) 1992-1998 Regents of the University of California, Santa Cruz ; http://www.cse.ucsc.edu/research/compbio/sam.html ; ; ------ Citations (HMMs, SAM) ------ ; A. Krogh et al., Hidden Markov models in computational biology: ; Applications to protein modeling, JMB 235:1501-1531, Feb 1994. ; R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: ; Extension and analysis of the basic method, CABIOS 12:95-107, 1996. ; ----------------------- ; Sequence numbers correspond to the following labels: ; 1 T0069 ; 2 GP:BTC43_1_145:301 ; 3 SW:CL43_BOVIN_145:301 ; 4 PIR2:A53570_145:301 ; 5 SW:CONG_BOVIN_216:371 ; 6 PIR2:I45878_216:371 ; 7 GP:BOVCO9_1_180:335 ; 8 GP:BTCONGL_1_216:371 ; 9 SW:PSPD_BOVIN_216:369 ; 10 PIR2:S33603_216:369 ; 11 SW:PSPD_MOUSE_221:374 ; 12 SW:PSPD_RAT_221:374 ; 13 SW:PSPD_HUMAN_222:375 ; 14 PIR2:S18382_164:318 ; 15 GP:HSMRNAPD_1_222:375 ; 16 GP:AF022226_1_91:237 ; 17 SW:MABA_MOUSE_87:237 ; 18 3D:1AFAA_1:152 ; 19 GP:RATMABPA2_1_86:236 ; 20 SW:MABA_RAT_86:236 ; 21 3D:1RTMA_1:147 ; 22 3D:1KMBA_1:147 ; 23 3D:1YTTB_1:112 ; 24 3D:2MSBB_1:111 ; 25 3D:1YTTA_1:113 ; 26 3D:2MSBA_1:110 ; 27 GP:MACMBPA_1_93:243 ; 28 GP:D73408_1_98:247 ; 29 GP:MACMBPC_1_103:234 ; 30 SW:MABC_HUMAN_115:246 ; 31 3D:1HUP_8:139 ; 32 SW:MABC_MOUSE_89:242 ; 33 PIR1:LNMSMC_89:242 ; 34 GP:RATMABPC_1_102:242 ; 35 3D:1RDIB_1:111 ; 36 SW:MABC_RAT_102:242 ; 37 3D:1RDIA_1:110 10 20 30 40 50 | | | | | 1 .....A.EAN.AL.KQ.RVT.ILDGHLRRFQNAFSQYKKAVLFPDGQAVGEKIFKTAGAVKSYSD 2 getsvL.EVD.TL.RQ.RMR.NLEGEVQRLQNIVTQYRKAVLFPDGQAVGEKIFKTAGAVKSYSD 3 getsvL.EVD.TL.RQ.RMR.NLEGEVQRLQNIVTQYRKAVLFPDGQAVGEKIFKTAGAVKSYSD 4 getsvL.EVD.TL.RQ.RMR.NLEGEVQRLQNIVTQYRKAVLFPDGQAVGEKIFKTAGAVKSYSD 5 gesglA.EVN.AL.KQ.RVT.ILDGHLRRFQNAFSQYKKAVLFPDGQAVGEKIFKTAGAVKSYSD 6 gesglA.EVN.AL.KQ.RVT.ILDGHLRRFQNAFSQYKKAVLFPDGQAVGEKIFKTAGAVKSYSD 7 gesglA.EVN.AL.KQ.RVT.ILDGHLRRFQNAFSQYKKAVLFPDGQAVGEKIFKTAGAVKSYSD 8 gesglA.EAN.AL.KQ.RVT.ILDGHLRRFQNAFSQYKKAVLFPDGQAVGEKIFKTAGAVKSYSD 9 gesglA.EVN.AL.RQ.RVG.ILEGQLQRLQNAFSQYKKAMLFPNGRSVGEKIFKTVGSEKTFQD 10 gesglA.EVN.AL.RQ.RVG.ILEGQLQRLQNAFSQYKKAMLFPNGRSVGEKIFKTVGSEKTFQD 11 gesglP.DSA.AL.RQ.QME.ALKGKLQRLEVAFSHYQKAALFPDGRSVGDKIFRTADSEKPFED 12 gesglP.DSA.AL.RQ.QME.ALNGKLQRLEAAFSRYKKAALFPDGQSVGDKIFRAANSEEPFED 13 gesglP.DVA.SL.RQ.QVE.ALQGQVQHLQAAFSQYKKVELFPNGQSVGEKIFKTAGFVKPFTE 14 gesglP.DVA.SL.RQ.QVE.ALQGQVQHLQAAFSQYKKVELFPNGQSVGEKIFKTAGFVKPFTE 15 gesglP.DVA.SL.RQ.QVE.ALQGQVQHLQAAFSQYKKVELFPNGQSVGEKIFKTAGFVKPFTE 16 vvtdd-.---.-L.HR.QIT.DLEAKIRVLEDDLSRYKKALSLKDVVNIGKKMFVSTGKKYNFEK 17 qkgdhG.DNR.AI.EE.KLA.NMEAEIRILKSKLQLTNKLHAFSMGKKSGKKLFVTNHEKMPFSK 18 .....-.---.AI.EV.KLA.NMEAEINTLKSKLELTNKLHAFSMGKKSGKKFFVTNHERMPFSK 19 qkgdrG.DSR.AI.EV.KLA.NMEAEINTLKSKLELTNKLHAFSMGKKSGKKFFVTNHERMPFSK 20 qkgdrG.DSR.AI.EV.KLA.NMEAEINTLKSKLELTNKLHAFSMGKKSGKKFFVTNHERMPFSK 21 .....-.---.AI.EV.KLA.NMEAEINTLKSKLELTNKLHAFSMGKKSGKKFFVTNHERMPFSK 22 .....-.---.AI.EV.KLA.NMEAEINTLKSKLELTNKLHAFSMGKKSGKKFFVTNHERMPFSK 23 .....-.---.--.--.---.----------------------------GKKFFVTNHERMPFSK 24 .....-.---.--.--.---.-----------------------------KKFFVTNHERMPFSK 25 .....-.---.--.--.---.---------------------------SGKKFFVTNHERMPFSK 26 .....-.---.--.--.---.------------------------------KFFVTNHERMPFSK 27 qkgdh-.GDN.SVaEA.KLA.NLERQLQSLRSELDHMKKLQAFSLGKMSGKKLFVTNGERMPFSE 28 gqkgdP.GENmGD.YI.RLA.T--SERATLQSELNQIKNWLIFSLGKRVGKKAFFTNGKKMPFNE 29 serka-.---.--.--.---.--------LQTEMARIKKWLTFSLGRQVGNKFFLTNGEMMTFDK 30 serka-.---.--.--.---.--------LQTEMARIKKWLTFSLGKQVGNKFFLTNGEIMTFEK 31 serka-.---.--.--.---.--------LQTEMARIKKWLTFSLGKQVGNKFFLTNGEIMTFEK 32 kgavgPkGDR.GD.RAeFDTsEIDSEIAALRSELRALRNWVLFSLSEKVGKKYFVSSVKKMSLDR 33 kgavgPkGDR.GD.RAeFDTsEIDSEIAALRSELRALRNWVLFSLSEKVGKKYFVSSVKKMSLDR 34 vefdt-.---.--.--.--T.NIDLEIAALRSELRAMRKWVLLSMSENVGKKYFMSSVRRMPLNR 35 .....-.---.--.--.---.-----------------------------KKYFMSSVRRMPLNR 36 vefdt-.---.--.--.--T.NIDLEIAALRSELRAMRKWVLLSMSENVGKKYFMSSVRRMPLNR 37 .....-.---.--.--.---.------------------------------KYFMSSVRRMPLNR 60 70 80 90 100 110 120 | | | | | | | 1 AEQLCREAKGQLASPRSSAENEAVTQMVRAQEKNAYLSMNDISTEGRFTYPTGEILVYSNWADGE 2 AEQLCREAKGQLASPRSSAENEAVTQLVRAKNKHAYLSMNDISKEGKFTYPTGGSLDYSNWAPGE 3 AEQLCREAKGQLASPRSSAENEAVTQLVRAKNKHAYLSMNDISKEGKFTYPTGGSLDYSNWAPGE 4 AEQLCREAKGQLASPRSSAENEAVTQLVRAKNKHAYLSMNDISKEGKFTYPTGGSLDYSNWAPGE 5 AEQLCREAKGQLASPRSSAENEAVTQMVRAQEKNAYLSMNDISTEGRFTYPTGEILVYSNWADGE 6 AEQLCREAKGQLASPRSSAENEAVTQMVRAQEKNAYLSMNDISTEGRFTYPTGEILVYSNWADGE 7 AEQLCREAKGQLASPRSSAENEAVTQMVRAQEKNAYLSMNDISTEGRFTYPTGEILVYSNWADGE 8 AVQLCREAKGQLASPRSSAENEAVTQMVRAQEKNAYLSMNDISTEGRFTYPTGEILVYSNWADGE 9 AQQICTQAGGQLPSPRSGAENEALTQLATAQNKAAFLSMSDTRKEGTFIYPTGEPLVYSNWAPQE 10 AQQICTQAGGQLPSPRSGAENEALTQLATAQNKAAFLSMSDTRKEGTFIYPTGEPLVYSNWAPQE 11 AQEMCKQAGGQLASPRSATENAAIQQLITAHNKAAFLSMTDVGTEGKFTYPTGEPLVYSNWAPGE 12 AKEMCRQAGGQLASPRSATENAAVQQLVTAHSKAAFLSMTDVGTEGKFTYPTGEALVYSNWAPGE 13 AQLLCTQAGGQLASPRSAAENAALQQLVVAKNEAAFLSMTDSKTEGKFTYPTGESLVYSNWAPGE 14 AQLLCTQAGGQLASPRSAAENAALQQLVVAKNEAAFLSMTDSKTEGKFTYPTGESLVYSNWAPGE 15 AQLLCTQAGGQLASPRSAAENAALQQLVVAKNEAAFLSMTDSKTEGKFTYPTGESLVYSNWAPGE 16 GKSLCAKAGSVLASPRNEAENTALKDLI-DPSSQAYIGISDAQTEGRFMYLSGGPLTYSNWKPGE 17 VKSLCTELQGTVAIPRNAEENKAIQEVATG---IAFLGITDEATEGQFMYVTGGRLTYSNWKKDE 18 VKALCSELRGTVAIPRNAEENKAIQEVAK---TSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDQ 19 VKALCSELRGTVAIPKNAEENKAIQEVAK---TSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDE 20 VKALCSELRGTVAIPRNAEENKAIQEVAK---TSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDE 21 VKALCSELRGTVAIPRNAEENKAIQEVAK---TSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDE 22 VKALCSELRGTVAIPRNAEENKAIQEVAK---TSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDE 23 VKALCSELRGTVAIPRNAEENKAIQEVAK---TSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDE 24 VKALCSELRGTVAIPRNAEENKAIQEVAK---TSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDE 25 VKALCSELRGTVAIPRNAEENKAIQEVAK---TSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDE 26 VKALCSELRGTVAIPRNAEENKAIQEVAK---TSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDE 27 VKALCAGLQATVAAPKNAEENKAIQDV--AKDT-AFLGITDEATEGQFMYVTGGRLTYSNWKKDE 28 VKTLCAQFQGRVATPMNAEENRALKDLVT--EE-AFLGITDQETEGKFVDLTGKGVTYQNWNDGE 29 VKALCARFQASVATPRNAAENRAIQNLIK--EE-AFLGITDENTEGEFVDLTGNKLTYTNWNDGE 30 VKALCVKFQASVATPRNAAENGAIQNLIK--EE-AFLGITDEKTEGQFVDLTGNRLTYTNWNEGE 31 VKALCVKFQASVATPRNAAENGAIQNLIK--EE-AFLGITDEKTEGQFVDLTGNRLTYTNWNEGE 32 VKALCSEFQGSVATPRNAEENSAIQKV--AKD-IAYLGITDVRVEGSFEDLTGNRVRYTNWNDGE 33 VKALCSEFQGSVATPRNAEENSAIQKV--AKD-IAYLGITDVRVEGSFEDLTGNRVRYTNWNDGE 34 AKALCSELQGTVATPRNAEENRAIQNV--AKD-VAFLGITDQRTENVFEDLTGNRVRYTNWNEGE 35 AKALCSELQGTVATPRNAEENRAIQNV--AKD-VAFLGITDQRTENVFEDLTGNRVRYTNWNEGE 36 AKALCSELQGTVATPRNAEENRAIQNV--AKD-VAFLGITDQRTENVFEDLTGNRVRYTNWNEGE 37 AKALCSELQGTVATPRNAEENRAIQNV--AKD-VAFLGITDQRTENVFEDLTGNRVRYTNWNEGE 130 140 150 | | | 1 PNNS..DEG..QPENCVEIFPDGKWNDVPCSKQ.LLVICE.F... 2 PGNRakDEG..-PENCLEIYSDGNWNDIECREE.RLVICE.F... 3 PGNRakDEG..-PENCLEIYSDGNWNDIECREE.RLVICE.F... 4 PNNRakDEG..-PENCLEIYSDGNWNDIECREE.RLVICE.F... 5 PNNS..DEG..QPENCVEIFPDGKWNDVPCSKQ.LLVICE.F... 6 PNNS..DEG..QPENCVEIFPDGKWNDVPCSKQ.LLVICE.F... 7 PNNS..DEG..QPENCVEIFPDGKWNDVPCSKQ.LLVICE.F... 8 PNNS..DEG..QPENCVEIFPDGKWNDVPCSKQ.LLVICE.F... 9 PNN-..D-G..GSENCVEIFPNGKWNDKVCGEQ.RLVICE.F... 10 PNN-..D-G..GSENCVEIFPNGKWNDKVCGEQ.RLVICE.F... 11 PNNN..--G..GAENCVEIFTNGQWNDKACGEQ.RLVICE.F... 12 PNNN..--G..GAENCVEIFTNGQWNDKACGEQ.RLVICE.F... 13 PN--..DDG..GSEDCVEIFTNGKWNDRACGEK.RLVVCE.F... 14 PN--..DDG..GSEDCVEIFTNGKWNDRACGEK.RLVVCEhF... 15 PN--..DDG..GSEDCVEIFTNGKWNDRACGEK.RLVVCE.F... 16 PNN-..-H-..KNEDCAVIEDSGKWNDLDCSNSnIFIICE.-l.. 17 PNN-..-HG..SGEDCVIILDNGLWNDISCQAS.FKAVCE.Fpa. 18 PDDWy.GHGlgGGEDCVTIVDNGLWNDISCQAS.HTAVCE.Fpa. 19 PN--..DHG..SGEDCVTIVDNGLWNDISCQAS.HTAVCE.Fpa. 20 PN--..DHG..SGEDCVTIVDNGLWNDISCQAS.HTAVCE.Fpa. 21 PN--..DHG..SGEDCVTIVDNGLWNDISCQAS.HTAVCE.Fpa. 22 PN--..DHG..SGEDCVTIVDNGLWNDISCQKK.KTAVCE.Fpa. 23 PN--..DHG..SGEDCVTIVDNGLWNDISCQAS.HTAVCE.F... 24 PN--..DHG..SGEDCVTIVDNGLWNDISCQAS.HTAVCE.Fpa. 25 PN--..DHG..SGEDCVTIVDNGLWNDISCQAS.HTAVCE.Fpa. 26 PN--..DHG..SGEDCVTIVDNGLWNDISCQAS.HTAVCE.Fp.. 27 PN--..DHG..SGEDCVILLSNGLWNDISCTAS.YIAVCE.Fpa. 28 PNNA..SPG..--EHCVTLLSDGTWNDIACSAS.FLTVCE.Fsl. 29 PNNA..--G..SNEDCVLLLKNGKWNDIPCSSS.HLALCE.Fpi. 30 PNNA..--G..SDEDCVLLLKNGQWNDVPCSTS.HLAVCE.Fpi. 31 PNNA..--G..SDEDCVLLLKNGQWNDVPCSTS.HLAVCE.Fpi. 32 PNNT..GDG..--EDCVVILGNGKWNDVPCSDS.FLAICE.Fsd. 33 PNNT..GDG..--EDCVVILGNGKWNDVPCSDS.FLAICE.Fsd. 34 PNNV..--G..SGENCVVLLTNGKWNDVPCSDS.FLVVCE.Fsd. 35 PNNV..--G..SGENCVVLLTNGKWNDVPCSDS.FLVVCE.Fs.. 36 PNNV..--G..SGENCVVLLTNGKWNDVPCSDS.FLVVCE.Fsd. 37 PNNV..--G..SGENCVVLLTNGKWNDVPCSDS.FLVVCE.Fs..