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