; 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 gi|2144249|pir||S60879_149:267 ; 2 gi|1711480|sp|P52939|SP0A_CLOIN_149:266 ; 3 gi|7576241|emb|CAB87987.1|_173:292 ; 4 gi|1711473|sp|P52931|SP0A_BACCI_141:210 ; 5 gi|2119858|pir||S60871_142:211 ; 6 gi|2119857|pir||S60868_146:215 ; 7 gi|2119851|pir||S60870_82:151 ; 8 gi|2119852|pir||S60875_77:147 ; 9 gi|2119859|pir||S60872_144:213 ; 10 gi|2119850|pir||S60873_86:191 ; 11 gi|1711475|sp|P52933|SP0A_BACPU_85:190 ; 12 gi|134739|sp|P06534|SP0A_BACSU_148:267 ; 13 gi|2654216|emb|CAA05307.1|_140:259 ; 14 T0098 ; 15 gi|1711476|sp|P52934|SP0A_BACST_76:146 ; 16 gi|1711474|sp|P52932|SP0A_BACME_143:212 ; 17 gi|1711472|sp|P52930|SP0A_BACCE_81:150 ; 18 gi|1711470|sp|P52928|SP0A_BACAN_145:214 ; 19 gi|1711477|sp|P52935|SP0A_BACTU_146:264 ; 20 gi|1711471|sp|P52929|SP0A_BACBR_144:212 ; 21 gi|7576238|emb|CAB87985.1|_154:273 ; 22 gi|1711498|sp|P52936|SP0A_CLOAB_154:223 ; 23 gi|2119861|pir||S60877_155:224 ; 24 gi|2119853|pir||S60878_93:162 ; 25 gi|1711478|sp|P52937|SP0A_CLOBU_92:161 ; 26 gi|2119854|pir||S60876_98:167 ; 27 gi|497963|gb|AAA18879.1|_97:166 ; 28 gi|1020324|gb|AAA79509.1|_85:154 ; 29 gi|1130609|emb|CAA63989.1|_154:255 ; 30 gi|1711479|sp|P52938|SP0A_CLODI_154:270 ; 31 gi|1711481|sp|P52940|SP0A_CLOPA_151:268 ; 32 gi|2119856|pir||S60880_151:269 ; 33 gi|2119855|pir||S60874_145:263 ; 34 gi|1174405|sp|P42012|SP0A_BACSH_145:262 ; 35 gi|1711482|sp|P52941|SP0A_MOOTH_137:206 ; 36 gi|2119862|pir||S60881_138:207 10 20 30 40 50 60 | | | | | | 1 -QKYLELESEITELLHEIGIPAHIKGYMYLRTAILETYLNVDFLGQITKVLYPEIAKKYATTASR 2 --QKLELESEITELLHEIGIPAHIKGYMYLRTAILETYLNVDFLGQITKVLYPEIAKKYATTASR 3 -NTSRSLEVEVTNVMHEIGVPAHIKGYQYLRDAIMMVVKDLDVINSITKLLYPSIAKEYNTTPSR 4 -PKTKNLDASITSIIHEIGVPAHIKGYLYLREAISMVYNDIELLGSITKVLYPDIAKKYNTTASR 5 -KTKKNLDASITSIIHEIGVPAHIKGYLYLREAISMVYNDIELLGSITKVLYPDIAKKYNTTASR 6 -KPKKNLDASITSIIHEIGVPAHIKGYMYLREAISMVYNDIELLGSITKVLYPDIAKKYNTTASR 7 -KPKKNLDASITSIIHEIGVPAHIKGYMYLREAISMVYNDIELLGSITKVLYPDIAKKYNTTASR 8 NKPKKNLDASITSIIHEIGVPAHIKGYLYLREAIAMVYHDIELLGSITKVLYPDIAKKYNTTASR 9 -KPQANLDASITSIIHEIGVPAHIKGYLYLREAISMVYKDIELLGSITKVLYPDIAKKYNTTASR 10 -KRNKNLDASITTIIHEIGVPAHIKGYLYLREAISMVYNDIELLGSITKVLYPDIAKKFNTTASR 11 -PKRKNLDASITTIIHEIGVPAHIKGYLYLREAISMVYNDIELLGSITKVLYPDIAKKFNTTASR 12 -PKKKNLDASITSIIHEIGVPAHIKGYLYLREAISMVYNDIELLGSITKVLYPDIAKKFNTTASR 13 -NKPKNLDASITSIIHEIGVPAHIKGYLYLREAIAMVYHDIELLGSITKVLYPDIAKKYNTTASR 14 DNKPKNLDASITSIIHEIGVPAHIKGYLYLREAIAMVYHDIELLGSITKVLYPDIAKKYNTTASR 15 DNKPKNLDASITSIIHEIGVPAHIKGYLYLREAIAMVYHDIELLGSITKVLYPDIAKKYNTTASR 16 -SKPANLDASITSIIHEIGVPAHIKGYLYLREAISMVYKDIELLGSITKVLYPDIAKKYNTTASR 17 -GKPKNLDASITSIIHEIGVPAHIKGYMYLREAISMVYNDIELLGSITKVLYPDIAKKYNTTASR 18 -GKPKNLDASITSIIHEIGVPAHIKGYMYLREAISMVYNDIELLGSITKVLYPDIAKKYNTTASR 19 --KPKNLDASITSIIHEIGVPAHIKGYMYLREAISMVYNDIELLGSITKVLYPDIAKKYNTTASR 20 --RGRNLDASITSIIHEIGVPAHIKGYLYLREAITMVYNDVELLGSITKVLYPDIAKKFNTTASH 21 -KAPIDLETEITNIIHEVGVPAHIKGYMYLREAITMVVNDMELLSAVTKELYPSIAKKYNTTASR 22 -KAPIDLETEITNIIHEVGVPAHIKGYMYLREAITMVVNDMELLSAVTKELYPSIAKKYNTTASR 23 -APSIDLETEITNIIHEVGVPAHIKGYMYLREAITMVVNDMELLSAVTKELYPSIAKKYNTTASR 24 -TPSVDLETEITNIIHEIGVPAHIKGYMYLREAITMVVNDMELLSAVTKELYPSIAKKYNTTASR 25 -KTPVDLETEITNIIHEIGVPAHIKGYMYLREAITMVVNDMELLSAVTKELYPSIAKKYNTTASR 26 -KANVDLESEITSIIHQIGVPAHIKGYMYLREAITMVVNNMELLSAVTKELYPSIAKKYNTTASR 27 -NKAVDLESEITSIIHQIGVPAHIKGYMYLREAITMVVNNMELLSAVTKELYPSIAKKYNTTASR 28 -KNVGNIETEITNIIHEIGVPAHIKGYLYLREAMKMVIDNVELLGAVTKELYPSIAKKFNTTPSR 29 -KNVGNIETEITNIIHEIGVPAHIKGYLYLREAMKMVIDNVELLGAVTKELYPSIAKKFNTTPSR 30 -KNVGNIETEITNIIHEIGVPAHIKGYLYLREAMKMVIDNVELLGAVTKELYPSIAKKFNTTPSR 31 --QSVPLDLEDESIIHEIGVPAHIKGYMYLREAINMVVDNIELLSAVTKELYPSIAKKYNTTASR 32 -QSNVPLDLEDESIIHEIGVPAHIKGYMYLREAINMVVDNIELLSAVTKELYPSIAKKYNTTASR 33 -NQQHQLDSTITAIIKEIGVPAHIKGYSYLREAIQMVFEDIELLGSVTKILYPEIAKKFNTTPSR 34 --NQHQLDSTITAIIKEIGVPAHIKGYSYLREAIQMVFEDIELLGSVTKILYPEIAKKFNTTPSR 35 -RAGRNMDVEVTKIIHQMGVPAHIKGYQYLREAILMVIDDVSLLGAVTKELYPLIARKYMTTPSR 36 -AGGRNMDVEVTKIIHQMGVPAHIKGYQYLREAILMVIDDVSLLGAVTKELYPLIARKYMTTPSR 70 80 90 100 110 120 | | | | | | 1 VERAIRHAIEVAWNRGNIDAIDDIFGYTISASKAKPTNSEFIAMISDKLRLEHRL- 2 VERAIRHAIEVAWNRGNIDAIDDIFGYTISASKAKPTNSEFIAMISDKLRLEHRL- 3 VERAIRHAIEVAWSRGQVEAIDALFGYTVNIGKGKPTNSEFIAMIADKLRLELKVS 4 VERAIR-------------------------------------------------- 5 VERAIR-------------------------------------------------- 6 VERAIR-------------------------------------------------- 7 VERAIR-------------------------------------------------- 8 VERAIR-------------------------------------------------- 9 VERAIR-------------------------------------------------- 10 VERAIRHAIEVAWSRGNIDSISSLFGYTVSMSKAKPTNSEFI-------------- 11 VERAIRHAIEVAWSRGNIDSISSLFGYTVSMSKAKPTNSEFI-------------- 12 VERAIRHAIEVAWSRGNIDSISSLFGYTVSMTKAKPTNSEFIAMVADKLRLEHKAS 13 VERAIRHAIEVAWSRGNLESISSLFGYTVSVSKAKPTNSEFIAMVADKLRLEHKAS 14 VERAIRHAIEVAWSRGNLESISSLFGYTVSVSKAKPTNSEFIAMVADKLRLEHKAS 15 VERAIR-------------------------------------------------- 16 VERAIR-------------------------------------------------- 17 VERAIR-------------------------------------------------- 18 VERAIR-------------------------------------------------- 19 VERAIRHAIEVAWSRGNIDSISSLFGYTVSMSKAKPTNSEFIAMVADKLRLEHKAS 20 VERAIR-------------------------------------------------- 21 VERAIRHAIEVAWGRGQIEAINRLFGYTVHNDKGKPTNSEFIAIIADKLRLKNKVS 22 VERAIR-------------------------------------------------- 23 VERAIR-------------------------------------------------- 24 VERAIR-------------------------------------------------- 25 VERAIR-------------------------------------------------- 26 VERAIR-------------------------------------------------- 27 VERAIR-------------------------------------------------- 28 VERAIR-------------------------------------------------- 29 VERAIRHAIEVAWSRGKVDTINQLFGYTVHNTKGKPTN------------------ 30 VERAIRHAIEVAWSRGKVDTINQLFGYTVHNTKGKPTNSEFIAMIADKLRLEH--- 31 VERAIRHAIEVAWSRGQVDTINKLFGYTIHNGKGKPTNSEFIAMIADKLRLKNKV- 32 VERAIRHAIEVAWSRGQVDTINKLFGYTIHNGKGKPTNSEFIAMIADKLRLKNKV- 33 VERAIRHAIEVAWNRGNYEYISSMFGYTEHHLKSKPTNSEFIAMIADKIRIDMMA- 34 VERAIRHAIEVAWNRGNYEYISSMFGYTEHHLKSKPTNSEFIAMIADKIRIDMMA- 35 VERAIR-------------------------------------------------- 36 VERAIR--------------------------------------------------