# List of top-scoring protein chains for t2k-100-30-alpha hidden Markov model. # HMM and HMM E-value scores computed by SAM (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. # # FSSP representative for each protein chain taken from FSSP: # ------------------Citations (FSSP) ----------------------------------- # L. Holm and C. Sander (1996) Mapping the protein universe. Science 273:595-602. # #SCOP domains found in each protein chain taken from SCOP: # ------------------Citations (SCOP) ----------------------------------- #Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). #SCOP: a structural classification of proteins database for the investigation of sequences and structures. #J. Mol. Biol. 247, 536-540. Sequence_ID Length Target_Evalue FSSP-rep SCOP_domain SCOP_suid 5S 5N 12S 6S 12S 10N 1vsd 152 4.04e-15 1cxqA c.55.3.2 33625 1asu 162 6.58e-15 1cxqA c.55.3.2 33626 1cxqA 162 1.81e-14 1cxqA c.55.3.2 33621 2itg 163 4.37e-11 1b9dA c.55.3.2 33669 1exqA 154 4.50e-10 1b9dA c.55.3.2 33646 1b9dA 163 6.22e-10 1b9dA c.55.3.2 33649 1hyvA 166 7.59e-10 1b9dA c.55.3.2 61424 1bl3A 160 1.37e-09 1b9dA c.55.3.2 33655 1itg 166 1.28e-08 1b9dA c.55.3.2 33661 1f6uA 55 3.89e-04 1a1tA g.40.1.1 45164 1mfs 55 4.42e-04 1mfs g.40.1.1 45167 1a1tA 55 5.37e-04 1a1tA g.40.1.1 45165 1aaf 55 1.13e-03 1aaf g.40.1.1 45166 1nc8 29 4.82e-03 g.40.1.1 45170 1fivA 113 5.57e-03 1fmb b.50.1.1 26764 1a6bB 40 8.98e-03 1a6bB g.40.1.1 45172 1hvc 203 1.07e-02 1hvc b.50.1.1 26614 4fiv 113 1.67e-02 1fmb b.50.1.1 26762 1difA 99 2.39e-02 1fmb b.50.1.1 26503 1dsqA 21 3.65e-02 g.40.1.1 45173 1dazC 99 3.98e-02 1hvc b.50.1.1 26501 1kzkA 99 4.23e-02 b.50.1.1 73371 5hvpA 99 4.48e-02 1fmb b.50.1.1 26605 1k1tA 99 4.61e-02 b.50.1.1 71995 1bveA 99 6.22e-02 1hvc b.50.1.1 26713 1mml 265 6.41e-02 1mml e.8.1.2 43015 3fivA 116 1.90e-01 1fmb b.50.1.1 26768 1idaA 99 2.19e-01 1fmb b.50.1.1 26715 2fivA 116 2.61e-01 1fmb b.50.1.1 26766 1qmyA 167 4.17e-01 1qmyA d.3.1.2 37094 1cl4A 60 4.76e-01 1cl4A g.40.1.1 45171 1dvpA 220 5.25e-01 1dvpA a.118.9.2 19216 g.50.1.1 45358 1dsvA 31 5.87e-01 1dsvA g.40.1.1 45174 1zin 217 6.53e-01 1zin c.37.1.1 31915 g.41.2.1 45178 1lkvX 232 7.30e-01 a.118.14.1 73980 1lnwA 147 8.35e-01 a.4.5.28 78104 1f2eA 201 9.24e-01 1a0fA a.45.1.1 17745 c.47.1.5 33039 1qqtA 551 1.65e+00 1qqtA a.27.1.1 16923 c.26.1.1 31590 g.41.1.1 45175 2ak3A 226 1.69e+00 1zin c.37.1.1 31892 g.41.2.1 45193 1l5zA 155 1.86e+00 c.23.1.1 77722 1giqA 413 1.93e+00 d.166.1.1 76224 d.166.1.1 76225 1mhyG 169 2.24e+00 1mtyG a.23.3.1 16518 1o86A 589 2.25e+00 d.92.1.5 81177 1scfA 273 2.89e+00 1exzA a.26.1.2 16873 1qkkA 155 2.99e+00 1dbwA c.23.1.1 31104 1o0xA 262 2.99e+00 d.127.1.1 80755 1fxzA 476 3.22e+00 b.82.1.2 65059 b.82.1.2 65060 1gk9A 260 3.27e+00 d.153.1.2 65246 1a6r 471 3.27e+00 3gcb d.3.1.1 37033 1jj22 92 3.32e+00 1ffkZ 1f4lA 551 3.37e+00 1qqtA a.27.1.1 59648 c.26.1.1 59649 g.41.1.1 59650 1h09A 338 3.66e+00 1eyvA 156 3.81e+00 1eyvA a.79.1.1 18446 1exzA 141 3.82e+00 1exzA a.26.1.2 16877 1ffkZ 92 3.95e+00 1ffkZ g.41.8.3 45317 1kdxA 81 4.02e+00 1kdxA a.12.1.1 16375 1cg2A 393 4.49e+00 1cg2A c.56.5.4 33844 d.58.19.1 39360 1qciA 262 4.84e+00 1qi7A d.165.1.1 42201 2rspB 124 4.91e+00 2rspB b.50.1.1 26772 1pbyA 489 4.92e+00 1ib2A 349 4.93e+00 1ib2A a.118.1.8 62141 1mhyD 521 5.04e+00 1mhyD a.25.1.2 16780 1n2aA 201 5.05e+00 1iawA 317 5.16e+00 c.52.1.9 62126 1kxpD 458 5.22e+00 a.126.1.1 73160 a.126.1.1 73161 a.126.1.1 73162 1fmb 104 5.42e+00 1fmb b.50.1.1 26777 1b3qA 379 5.47e+00 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1lj5A 379 5.58e+00 e.1.1.1 73928 1l2iA 261 6.14e+00 a.123.1.1 73503 1miqA 375 6.21e+00 b.50.1.2 79151 1ezfA 340 6.32e+00 1ezfA a.128.1.2 19440 1cqxA 403 6.35e+00 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1ev7A 317 6.49e+00 1ev7B c.52.1.9 33315 1jjuA 489 6.61e+00 a.3.1.7 66774 a.3.1.7 66775 b.1.18.14 66776 b.1.18.14 66777 b.61.4.1 66778 1p9vA 310 6.68e+00 1d6aB 262 6.72e+00 1qi7A d.165.1.1 42198 2plc 274 6.72e+00 2plc c.1.18.2 29614 1b4pA 217 6.84e+00 1aky 221 7.29e+00 1zin c.37.1.1 31896 g.41.2.1 45197 1oqcA 125 7.41e+00 1b34B 118 7.65e+00 1b34B b.38.1.1 24797 1kk1A 410 7.94e+00 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 3gcb 470 8.04e+00 3gcb d.3.1.1 37032 1ku2A 241 8.26e+00 a.112.1.1 72998 1gm7A 209 8.31e+00 d.153.1.2 65302 1ev7B 317 8.34e+00 1ev7B c.52.1.9 33316 1mtyG 162 8.35e+00 1mtyG a.23.3.1 16498 1djxB 624 8.49e+00 1djxB a.39.1.7 17343 b.7.1.1 23160 c.1.18.1 29588 1e3aA 260 8.54e+00 1ajqA d.153.1.2 41838 1rypL 212 8.57e+00 d.153.1.4 41880 1ai7A 209 8.65e+00 1ajqA d.153.1.2 41845 1iznA 286 8.93e+00 1osa 148 9.02e+00 1cll a.39.1.5 17300 1qsaA 618 9.17e+00 1qsaA a.118.5.1 19182 d.2.1.6 36988 1gcb 454 9.39e+00 3gcb d.3.1.1 37034 1a7cA 379 9.74e+00 1sek e.1.1.1 42660 1dc1A 323 9.78e+00 1dc1A c.52.1.11 33321 1exkA 79 1.01e+01 1exkA g.54.1.1 45384 3nodB 423 1.01e+01 1nseA d.174.1.1 42513 3erdA 261 1.03e+01 3erdA a.123.1.1 19293 1ajqA 209 1.04e+01 1ajqA d.153.1.2 41840 1foeA 377 1.04e+01 1foeA a.87.1.1 18517 b.55.1.1 26969 3pghA 587 1.07e+01 1cqeA a.93.1.2 18726 g.3.11.1 44269 1btl 263 1.07e+01 1btl e.3.1.1 42691 1mvpA 124 1.09e+01 2rspB b.50.1.1 26775 1mmoG 162 1.11e+01 1mtyG a.23.3.1 16512 1ln1A 214 1.11e+01 d.129.3.2 74038 1floA 422 1.13e+01 1floA a.60.9.1 18106 d.163.1.1 42166 1a0fA 201 1.14e+01 1a0fA a.45.1.1 17737 c.47.1.5 33031 1qjaA 245 1.17e+01 1qjaA a.118.7.1 19204 1exrA 148 1.18e+01 1cll a.39.1.5 17299 1ey2A 471 1.19e+01 1ey2A b.82.1.4 28116 1erjA 393 1.19e+01 1erjA b.69.4.1 27660 1g87A 614 1.19e+01 1g65K 211 1.21e+01 d.153.1.4 41907 1m1hA 248 1.22e+01 b.114.1.1 78415 d.58.42.1 78416 1im3D 95 1.26e+01 1im3D b.1.18.5 62568 1ivyA 452 1.26e+01 1ivyA c.69.1.5 34654 1ermA 263 1.27e+01 1btl e.3.1.1 42690 1mea 28 1.30e+01 g.41.1.1 45176 1dceA 567 1.31e+01 1dceA a.118.6.1 19191 b.7.4.1 23218 c.10.2.2 30867 1aocA 175 1.31e+01 1aocA g.17.1.5 44817 1ao0A 459 1.31e+01 1ecfB c.61.1.1 34049 d.153.1.1 41816 1ee6A 197 1.32e+01 1ee6A b.80.1.1 28024 1m40A 263 1.36e+01 e.3.1.1 74437 1ea0A 1479 1.38e+01 b.80.4.1 64854 c.1.4.1 64855 d.153.1.1 64856 1sly 618 1.38e+01 1qsaA a.118.5.1 19184 d.2.1.6 36990 1aquA 297 1.42e+01 1aquA c.37.1.5 31942 1m3sA 186 1.43e+01 c.80.1.3 78573 1o7tA 309 1.43e+01 1h54B 754 1.44e+01 a.102.1.4 60636 b.30.5.3 60637 1dmuA 299 1.45e+01 1dmuA c.52.1.4 33294 3cln 148 1.45e+01 1cll a.39.1.5 17286 1uch 230 1.46e+01 1uch d.3.1.6 37129 1hz4A 373 1.46e+01 a.118.8.2 65960 2rspA 124 1.47e+01 2rspB b.50.1.1 26771 2bc2A 227 1.49e+01 1a7tA d.157.1.1 42031 1pnkA 209 1.51e+01 1ajqA d.153.1.2 41839 1fqgA 263 1.51e+01 1btl e.3.1.1 42699 1h8lA 380 1.52e+01 b.3.2.1 65737 c.56.5.1 65738 1qmuA 380 1.53e+01 1qmuA b.3.2.1 22534 c.56.5.1 33827 1ig3A 263 1.54e+01 1ig3A b.82.6.1 62358 c.100.1.1 62359 1k8kE 178 1.56e+01 a.148.1.1 68311 1jj2Z 56 1.56e+01 1ffkX g.41.8.2 63111 1m2oA 768 1.59e+01 a.71.2.1 78480 b.2.8.1 78481 c.62.1.2 78482 d.109.2.1 78483 g.41.10.1 78484 1orrA 347 1.60e+01 1lfkA 398 1.63e+01 a.104.1.1 77926 1scmB 145 1.64e+01 1wdcB a.39.1.5 17304 1n99A 166 1.64e+01 1od5A 492 1.66e+01 1g73C 121 1.68e+01 1g3fA g.52.1.1 45375 5eau 548 1.68e+01 5eat a.102.4.1 18851 a.128.1.3 19443 1n7oA 721 1.69e+01 a.102.3.2 80259 b.24.1.1 80260 b.30.5.2 80261 1gvmA 136 1.70e+01 b.109.1.1 70612 1wdcB 156 1.72e+01 1wdcB a.39.1.5 17302 1eguA 731 1.76e+01 1eguA a.102.3.2 18850 b.24.1.1 23899 b.30.5.2 24423 1n67A 359 1.78e+01 1kyaA 499 1.78e+01 b.6.1.3 73203 b.6.1.3 73204 b.6.1.3 73205 1ccg 291 1.79e+01 1ryc a.93.1.1 18627 1ps9A 671 1.83e+01 1f46A 140 1.92e+01 1f46A d.129.4.1 59643 1eybA 471 1.96e+01 1ey2A b.82.1.4 28115 1p2fA 220 1.97e+01 1tadA 324 1.97e+01 1cipA a.66.1.1 18194 c.37.1.8 32077 1zbdB 134 1.98e+01 1zbdB g.50.1.1 45359 1ee8A 266 1.98e+01 1ee8A a.156.1.2 75823 b.113.1.1 75824 g.39.1.8 75825 1hh1A 143 2.02e+01 1gefA c.52.1.18 61036 1bsvA 321 2.02e+01 1bsvA c.2.1.2 29809 1m7vA 363 2.03e+01 d.174.1.1 78748 2bc2B 227 2.04e+01 1a7tA d.157.1.1 42032 1f9xA 120 2.04e+01 1g3fA g.52.1.1 59748 1ki1B 352 2.07e+01 a.87.1.1 72497 b.55.1.1 72498 1oshA 232 2.11e+01 1fwqA 123 2.16e+01 1fwqA b.88.1.1 28394 1nqkA 381 2.16e+01 1pot 325 2.16e+01 1pot c.94.1.1 35807 2gmfA 127 2.16e+01 2gmfA a.26.1.2 16849 1n6zA 105 2.17e+01 1gfsA 321 2.18e+01 c.2.1.2 29811 1h1hA 134 2.20e+01 d.5.1.1 76468 2dabA 282 2.20e+01 1daaA e.17.1.1 43274 1gnlA 544 2.22e+01 e.26.1.1 70287 1iqpA 327 2.25e+01 a.80.1.1 62649 c.37.1.20 62650 1eal 127 2.26e+01 1hmt b.60.1.2 27227 1q16A 1247 2.26e+01 1mp9A 198 2.27e+01 1ffkX 56 2.27e+01 1ffkX g.41.8.2 45316 1csn 298 2.28e+01 1csn d.144.1.1 41664 1qs8A 329 2.30e+01 1smrA b.50.1.2 26887 1daaA 282 2.30e+01 1daaA e.17.1.1 43270 1otkA 249 2.35e+01 1dbhA 354 2.37e+01 1awe a.87.1.1 18514 b.55.1.1 26967 1aew 174 2.40e+01 2fha a.25.1.1 16676 1b78A 193 2.42e+01 1b78A c.51.4.1 33221 1e1dA 553 2.47e+01 1e1dA e.26.1.1 43363 1g4yB 101 2.48e+01 1g4yB f.15.1.1 60251 1go3F 107 2.49e+01 a.60.8.2 65407 16vpA 366 2.56e+01 16vpA d.180.1.1 42601 3daaA 277 2.59e+01 1daaA e.17.1.1 43272 153l 185 2.65e+01 153l d.2.1.5 36984 1by2 119 2.66e+01 1by2 d.170.1.1 42452 1mi0A 65 2.66e+01 d.15.7.1 79135 1o5kA 306 2.68e+01 1f47B 144 2.73e+01 1f46A d.129.4.1 59645 1e2uA 553 2.73e+01 1e1dA e.26.1.1 43362 1igtB 444 2.75e+01 1igtB b.1.1.1 19765 b.1.1.2 20867 b.1.1.2 20868 b.1.1.2 20869 1qkmA 255 2.75e+01 3erdA a.123.1.1 19309 1mat 264 2.76e+01 1c24A d.127.1.1 41152 1bwsA 321 2.78e+01 1bsvA c.2.1.2 29812 1m98A 317 2.78e+01 a.175.1.1 78866 d.17.4.6 78867 1gw5A 621 2.83e+01 a.118.1.10 70629 1rlr 761 2.87e+01 1rlr a.98.1.1 18753 c.7.1.2 30679 1cll 148 2.90e+01 1cll a.39.1.5 17263 1nnfA 309 2.94e+01 1g5hA 454 2.95e+01 1g5hA c.51.1.1 60270 d.104.1.1 60271 1nc5A 373 2.96e+01 1pmt 203 2.99e+01 1a0fA a.45.1.1 17740 c.47.1.5 33034 1tag 324 3.00e+01 1cipA a.66.1.1 18197 c.37.1.8 32080 1a28A 256 3.00e+01 1a28A a.123.1.1 19290 1a0p 290 3.01e+01 1a0p a.60.9.1 18105 d.163.1.1 42165 1hxrA 115 3.03e+01 1fwqA b.88.1.1 28392 1kyoG 126 3.03e+01 f.27.1.1 73259 2mjpA 193 3.03e+01 1b78A c.51.4.1 33223 1o5uA 101 3.04e+01 1mw7A 240 3.09e+01 e.39.1.1 79557 1c24A 263 3.10e+01 1c24A d.127.1.1 41148 1gntA 553 3.14e+01 e.26.1.1 70290 1hqcA 324 3.14e+01 1hqcA a.4.5.11 16127 c.37.1.20 32424 2napA 723 3.17e+01 2napA b.52.2.2 26926 c.81.1.1 35334 1gpl 432 3.18e+01 1gpl b.12.1.2 23645 c.69.1.19 34793 1k3lA 221 3.18e+01 a.45.1.1 77229 c.47.1.5 77230 1igtD 444 3.19e+01 1igtB b.1.1.1 19767 b.1.1.2 20871 b.1.1.2 20872 b.1.1.2 20873 1jsbA 73 3.19e+01 d.15.3.2 67223 1qoyA 318 3.22e+01 1qoyA h.4.4.1 45788 1pa1A 310 3.22e+01 1phd 414 3.25e+01 1phd a.104.1.1 18913 2matA 264 3.26e+01 1c24A d.127.1.1 41146 1qhuA 460 3.31e+01 1qhuA b.66.1.1 27530 b.66.1.1 27531 1cr0A 296 3.34e+01 1cr1A c.37.1.11 32287 1a8s 273 3.40e+01 1brt c.69.1.12 34710 1i5pA 633 3.40e+01 1i5pA b.18.1.3 61817 b.77.2.1 61818 f.1.3.1 61819 1ivhA 394 3.41e+01 3mdeA a.29.3.1 16608 e.6.1.1 42869 1io2A 213 3.42e+01 1ekeA c.55.3.1 62612 2eiaB 206 3.44e+01 1eia a.28.3.1 16950 a.73.1.1 18330 1oxjA 173 3.45e+01 1pvaA 110 3.48e+01 1a75A a.39.1.4 17207 2occE 109 3.53e+01 2occE a.118.11.1 19224 1csgA 127 3.54e+01 2gmfA a.26.1.2 16851 1i78A 297 3.54e+01 f.4.4.1 66046 1kcfA 258 3.57e+01 a.140.2.1 68434 c.55.3.7 68435 1toh 343 3.60e+01 4pah d.178.1.1 42573 1j08A 226 3.64e+01 1r2zA 274 3.65e+01 2rveA 244 3.65e+01 1rvaA c.52.1.2 33283 1jn8B 273 3.70e+01 1lxkA 721 3.71e+01 a.102.3.2 74331 b.24.1.1 74332 b.30.5.2 74333 1qmqA 414 3.73e+01 1phd a.104.1.1 18907 1ksfX 758 3.74e+01 a.174.1.1 77522 c.37.1.20 77523 c.37.1.20 77524 1ac5 483 3.74e+01 1ac5 c.69.1.5 34653 2hdhA 293 3.74e+01 2hdhA a.100.1.3 18795 c.2.1.6 30199 1gseA 221 3.76e+01 1pgtA a.45.1.1 17667 c.47.1.5 32961 1gbs 185 3.85e+01 153l d.2.1.5 36986 1dytA 133 3.86e+01 7rsa d.5.1.1 37288 1axn 323 3.88e+01 1avc a.65.1.1 18149 1qrjB 199 3.91e+01 1qrjB a.28.3.1 16952 1tfe 145 3.96e+01 1tfe d.43.1.1 38680 1ew6A 137 3.99e+01 1ewaA a.1.1.2 15637 1kafA 108 3.99e+01 d.199.1.1 68372