# List of top-scoring protein chains for t04-100-30-bys-scores 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 2f22A 144 3.60e-12 1rxqA 178 1.04e-07 a.213.1.1 105118 1f44A 324 3.00e-01 a.60.9.1,d.163.1.1 64982,64983 4crxA 322 3.70e-01 4crxA a.60.9.1,d.163.1.1 18095,42155 1xo0A 324 3.86e-01 1vjxA 157 4.34e-01 a.25.1.1 100837 1a0fA 201 1.60e+00 1a0fA a.45.1.1,c.47.1.5 17737,33031 1xrsA 516 1.86e+00 1n2aA 201 1.98e+00 a.45.1.1,c.47.1.5 91553,91554 1fecA 490 2.40e+00 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1txoA 237 3.06e+00 1ufoA 238 3.10e+00 c.69.1.27 99344 1vjzA 341 3.21e+00 c.1.8.3 100838 1bolA 222 3.56e+00 1bolA d.124.1.1 41120 1eg5A 384 3.63e+00 1ecxA c.67.1.3 34429 2fflA 756 4.02e+00 1hlb 158 4.07e+00 1hlb a.1.1.2 15625 1w5cF 44 4.12e+00 1xd7A 145 4.24e+00 a.4.5.55 109566 1us7B 265 4.66e+00 a.205.1.1 99858 1u2zA 433 4.77e+00 c.66.1.31 107626 1r2fA 319 5.07e+00 1r2fA a.25.1.2 16800 1aisB 200 5.44e+00 1aisB a.74.1.2,a.74.1.2 18384,18385 1nktA 922 5.50e+00 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 85830,85831,85832,85833 1ovlA 271 5.58e+00 a.123.1.1 87455 1b25A 619 5.58e+00 1b25A a.110.1.1,d.152.1.1 19044,41796 1rfmA 344 6.21e+00 c.122.1.1 97385 1vbuA 328 6.65e+00 1s5lF 45 6.74e+00 1r71A 178 6.91e+00 a.4.14.1 104823 1gk9B 557 6.91e+00 1mhyD 521 6.96e+00 1mhyD a.25.1.2 16780 1yz1A 174 7.02e+00 1q06A 135 7.16e+00 a.6.1.3 95493 2bh4X 134 7.40e+00 2occE 109 7.42e+00 2occE a.118.11.1 19224 1lki 180 7.49e+00 1lki a.26.1.1 16829 2axtF 45 8.02e+00 2g7sA 194 8.14e+00 1u7gA 385 8.43e+00 f.44.1.1 107723 1p68A 102 8.84e+00 k.8.1.1 94158 1c3wA 222 8.90e+00 1c3wA f.13.1.1 43405 1nni1 174 8.91e+00 1it2A 146 9.70e+00 a.1.1.2 66365 1hs6A 611 9.98e+00 1hs6A a.118.1.7,b.98.1.1,d.92.1.13 61233,61234,61235 1go3F 107 1.02e+01 a.60.8.2 65407 1u6tA 121 1.03e+01 1zxiB 809 1.03e+01 1m0kA 262 1.07e+01 f.13.1.1 78344 1kewA 361 1.10e+01 c.2.1.2 68544 1z2iA 358 1.11e+01 1ezfA 340 1.15e+01 1ezfA a.128.1.2 19440 1a41 234 1.17e+01 1a41 d.163.1.2 42174 2essA 248 1.18e+01 2bw3A 534 1.20e+01 1of8A 370 1.23e+01 c.1.10.4 92819 1swvA 267 1.24e+01 1ac5 483 1.27e+01 1ac5 c.69.1.5 34653 1x42A 232 1.32e+01 1sqgA 429 1.34e+01 a.79.1.3,c.66.1.38 105912,105913 1rqlA 267 1.39e+01 c.108.1.3 97750 1t0qA 498 1.39e+01 a.25.1.2 106220 1m48A 133 1.43e+01 a.26.1.2 74443 1rzrA 332 1.46e+01 2dgkA 452 1.47e+01 1j30A 144 1.49e+01 a.25.1.1 90806 1y9iA 178 1.51e+01 1whrA 124 1.55e+01 1po5A 476 1.59e+01 a.104.1.1 94963 1y8oA 419 1.61e+01 1q74A 303 1.62e+01 c.134.1.1 96019 1uteA 313 1.63e+01 1uteA d.159.1.1 42078 1bouB 302 1.65e+01 1bouB c.56.6.1 33859 1e9gA 286 1.67e+01 1wgjA b.40.5.1 59393 1cot 129 1.67e+01 1ycc a.3.1.1 15899 1e3aB 560 1.70e+01 1ajqB 1ia9A 280 1.75e+01 1ia9A d.144.1.5 62113 1p9qC 256 1.75e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1scfA 273 1.76e+01 1exzA a.26.1.2 16873 1w5rA 278 1.78e+01 1zzgA 415 1.86e+01 1t95A 240 1.86e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1g7oA 215 1.87e+01 1g7oA a.45.1.1,c.47.1.5 60332,60333 2gyqA 175 1.87e+01 1ed5A 444 1.93e+01 1nseA d.174.1.1 42530 1tx4A 198 1.93e+01 1tx4A a.116.1.1 19098 1lst 239 1.93e+01 1lst c.94.1.1 35755 1pmmA 466 1.93e+01 c.67.1.6 94901 1u59A 287 1.96e+01 d.144.1.7 107681 1ykhB 132 1.97e+01 1jqnA 883 1.97e+01 c.1.12.3 77159 1ki9A 192 2.00e+01 c.37.1.1 84404 1eemA 241 2.00e+01 1eemA a.45.1.1,c.47.1.5 17717,33011 1oe8A 211 2.01e+01 a.45.1.1,c.47.1.5 86905,86906 1rfzA 168 2.05e+01 a.195.1.1 97411 1t06A 235 2.05e+01 a.118.1.17 106194 1txgA 335 2.05e+01 1jfbA 404 2.11e+01 a.104.1.1 66624 1w6tA 444 2.13e+01 1lrv 244 2.18e+01 1lrv a.118.1.5 19146 1y82A 157 2.20e+01 1xel 338 2.24e+01 1xel c.2.1.2 29786 1x0vA 354 2.25e+01 1h2rL 534 2.28e+01 1h2rL e.18.1.1 43298 1g3mA 294 2.30e+01 c.37.1.5 83268 1mtyD 512 2.30e+01 1mhyD a.25.1.2 16742 1f4lA 551 2.31e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1nlwB 76 2.32e+01 a.38.1.1 80634 1pv9A 348 2.32e+01 c.55.2.1,d.127.1.1 95157,95158 1u67A 600 2.34e+01 a.93.1.2,g.3.11.1 107697,107698 1jboB 172 2.36e+01 a.1.1.3 84151 1pujA 282 2.36e+01 c.37.1.8 88294 1io7A 368 2.37e+01 1f4tA a.104.1.1 18971 1mba 147 2.42e+01 2fal a.1.1.2 15149 1qj2B 809 2.42e+01 1qj2B 1ithA 141 2.42e+01 1ithA a.1.1.2 15623 1n1cA 217 2.43e+01 a.184.1.1 85254 2fuqA 747 2.43e+01 1qmqA 414 2.43e+01 1phd a.104.1.1 18907 1reqB 637 2.43e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1j8yF 297 2.44e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1g7sA 594 2.46e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1jpaA 312 2.51e+01 d.144.1.7 67011 1xioA 261 2.51e+01 1qkmA 255 2.66e+01 3erdA a.123.1.1 19309 1n82A 331 2.66e+01 c.1.8.3 91703 1pfvA 551 2.66e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 2g8yA 385 2.75e+01 1zx4A 192 2.76e+01 1n8fA 350 2.79e+01 c.1.10.4 85397 1udc 338 2.82e+01 1xel c.2.1.2 29785 1fiy 883 2.83e+01 1fiy c.1.12.3 29307 1ubkL 534 2.84e+01 e.18.1.1 88422 2b1eA 564 2.87e+01 1d1vA 444 2.88e+01 1nseA d.174.1.1 59101 1c52 131 2.90e+01 1c52 a.3.1.1 15810 2bkkA 264 2.92e+01 1fm0D 81 2.93e+01 1fmaD d.15.3.1 37642 1t6jA 714 2.95e+01 1o7fA 469 2.96e+01 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 2a65A 519 2.97e+01 1jclA 260 2.99e+01 c.1.10.1 66501 3tmkA 216 3.05e+01 3tmkA c.37.1.1 31920 1rliA 184 3.05e+01 c.23.5.6 97647 2c3nA 247 3.05e+01 1n62B 809 3.08e+01 d.41.1.1,d.133.1.1 80092,80093 1ww9A 392 3.09e+01 1wuiL 534 3.10e+01 1hqz1 141 3.11e+01 1azsA 220 3.13e+01 1azsA d.58.29.1 39416 1tfe 145 3.17e+01 1tfe d.43.1.1 38680 1yf2A 425 3.22e+01 1tn4 159 3.27e+01 1ncx a.39.1.5 17248 1ywrA 360 3.29e+01 1wy2A 351 3.30e+01 1zoyD 103 3.33e+01 1y8qB 640 3.37e+01 1v96A 149 3.38e+01 1cmbA 104 3.41e+01 1cmbA a.43.1.5 17460 1pgjA 478 3.42e+01 2pgd a.100.1.1,c.2.1.6 18783,30195 1ur1A 378 3.43e+01 c.1.8.3 99804 2g2dA 193 3.44e+01 1ut8A 291 3.44e+01 a.60.7.1,c.120.1.2 99908,99909 1okhA 46 3.44e+01 g.13.1.1 93253 1ylmA 144 3.53e+01 1ab8A 220 3.55e+01 1azsA d.58.29.1 39414 1ctf 74 3.55e+01 1ctf d.45.1.1 38759 1gg1A 350 3.59e+01 1qr7A c.1.10.4 29187 1kn1B 161 3.68e+01 a.1.1.3 77456 1v54E 109 3.71e+01 a.118.11.1 100326 1ib2A 349 3.78e+01 1ib2A a.118.1.8 62141 1u2xA 474 3.80e+01 c.72.1.3 107622 1zzlA 351 3.82e+01 1gx3A 284 3.86e+01 d.3.1.5 70678 1wc3A 219 3.86e+01 1j7lA 264 3.87e+01 d.144.1.6 62697 1phnB 172 3.87e+01 1qgwC a.1.1.3 15642 1zs3A 182 3.88e+01 1wrjA 156 3.88e+01 1tc5A 194 3.90e+01 c.110.1.1 106752 2ar0A 541 3.91e+01 1fe0A 68 3.91e+01 1cc8A d.58.17.1 39345 1oaoA 674 3.91e+01 e.26.1.2 86744 1z7dA 433 3.92e+01 1iyxA 432 3.92e+01 c.1.11.1,d.54.1.1 83815,83816 1vkcA 158 3.93e+01 1ad3A 452 3.95e+01 1ad3A c.82.1.1 35335 1wbsA 360 3.95e+01 1yp1A 202 3.96e+01 1vykA 149 3.98e+01 1dcqA 278 4.02e+01 1dcqA d.211.1.1,g.45.1.1 19178,45326 1c9kA 180 4.09e+01 1c9kB c.37.1.11 32363 1zz2A 360 4.10e+01 1tib 269 4.15e+01 3tgl c.69.1.17 34738 1cmcA 104 4.21e+01 1cmbA a.43.1.5 17462 1l5oA 356 4.22e+01 c.39.1.1 77711 1x0rA 249 4.23e+01 1dq3A 454 4.24e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1o0sA 605 4.24e+01 c.2.1.7,c.58.1.3 86540,86541 2gtsA 86 4.25e+01 1qgrA 876 4.30e+01 1qgrA a.118.1.1 19119 1ks9A 291 4.31e+01 a.100.1.7,c.2.1.6 68857,68858 2gwdA 449 4.35e+01 1h6pA 203 4.37e+01 a.146.1.1 60690 1s5lB 510 4.42e+01 1r3cA 366 4.43e+01 d.144.1.7 96906 1qs0B 338 4.43e+01 1qs0B c.36.1.7,c.48.1.2 31830,33103 2au5A 139 4.47e+01 1rpnA 335 4.47e+01 c.2.1.2 97708 1gy8A 397 4.48e+01 c.2.1.2 83376 1xyzA 347 4.53e+01 1taxA c.1.8.3 28804 1qcwA 410 4.56e+01 1gox c.1.4.1 28622 1z3eA 132 4.66e+01 1z8oA 404 4.71e+01 1dceB 331 4.75e+01 1dceB a.102.4.3 18872 1yrcA 414 4.75e+01 1cnt1 187 4.79e+01 1cnt3 1j8mF 297 4.80e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1fezA 256 4.86e+01 1fezA c.108.1.3 43343 1xwmA 217 4.87e+01 2gfsA 372 4.92e+01 2bcgG 453 4.95e+01 1d0cA 444 4.97e+01 d.174.1.1 64769 1m7jA 484 4.98e+01 b.92.1.6,b.92.1.6,c.1.9.11 78732,78733,78734 1rxwA 336 4.99e+01 a.60.7.1,c.120.1.2 98059,98060 1ucpA 91 5.00e+01 a.77.1.5 99186 1p1xA 260 5.01e+01 c.1.10.1 104060 1nq6A 302 5.03e+01 c.1.8.3 92046 1gt6A 269 5.05e+01 c.69.1.17 76342 1oy3D 282 5.06e+01 d.211.1.1 87554 1cpcB 172 5.08e+01 1qgwC a.1.1.3 15644 1bw0A 416 5.08e+01 1bw0A c.67.1.1 34385 2b30A 301 5.10e+01 1ykuA 136 5.12e+01 1xkfA 133 5.15e+01 2fbhA 146 5.31e+01 1a0aA 63 5.33e+01 1a0aA a.38.1.1 17138 1yewB 247 5.42e+01 2d5xB 146 5.44e+01 1fcqA 350 5.44e+01 c.1.8.9 65006 1rk6A 496 5.46e+01 b.92.1.6,b.92.1.6,c.1.9.11 97599,97600,97601 1nzeA 149 5.47e+01 a.24.18.1 92374 2fafA 608 5.47e+01 2genA 197 5.54e+01 2axtB 510 5.56e+01 1kgnA 329 5.58e+01 a.25.1.2 68584 1dz4A 414 5.66e+01 1phd a.104.1.1 18903 1mtpA 323 5.68e+01 e.1.1.1 85107 1szoA 257 5.74e+01 c.14.1.3 106164 1ghpA 258 5.75e+01 1btl e.3.1.1 60520 2sqcA 631 5.78e+01 2sqcA a.102.4.2,a.102.4.2 18854,18855 1ewqA 765 5.79e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1sdiA 213 5.83e+01 a.198.1.1 105437 1eyhA 144 5.86e+01 1eduA a.118.9.1 19214 1wqwA 235 5.89e+01 2g0dA 409 5.92e+01 1g8eA 116 5.94e+01 1g8eA a.145.1.1 60346 1zwxA 301 5.97e+01 1iwhB 146 6.02e+01 a.1.1.2 76883 2gz4A 207 6.03e+01 2a5kA 307 6.07e+01 1w41A 101 6.16e+01 1gu2A 124 6.20e+01 a.3.1.1 76348 1ukvG 453 6.22e+01 c.3.1.3,c.3.1.3,d.16.1.6 107915,107916,107917 1v93A 296 6.29e+01 c.1.23.1 100532 1jmsA 381 6.31e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1f7cA 231 6.42e+01 1f7cA a.116.1.1 19107 2gsfA 373 6.42e+01 2azwA 148 6.43e+01 1o5zA 442 6.46e+01 c.59.1.2,c.72.2.2 92530,92531 1ggzA 148 6.48e+01 a.39.1.5 70176 1ngnA 155 6.62e+01 a.96.1.2 85697 1s5lZ 62 6.62e+01 1r2rA 248 6.65e+01 c.1.1.1 96875 1jipA 403 6.73e+01 a.104.1.1 66748 1nvpB 57 6.74e+01 a.32.1.1 92211 1gp6A 356 6.81e+01 b.82.2.1 65441 2bjbA 462 6.84e+01 830cA 168 6.87e+01 1ck7A d.92.1.11 40400 1azsB 212 6.88e+01 1azsA d.58.29.1 39423 1bg4 302 6.88e+01 1taxA c.1.8.3 28806 2fgoA 82 6.93e+01 1m6kA 251 6.96e+01 e.3.1.1 78695 1winA 143 7.00e+01 1furA 467 7.00e+01 1furA a.127.1.1 19403 1vi0A 206 7.03e+01 a.4.1.9,a.121.1.1 100720,100721 1ne7A 289 7.04e+01 c.124.1.1 91833 1wnlA 235 7.05e+01 1top 162 7.12e+01 1ncx a.39.1.5 17223 1xg9A 260 7.13e+01 1jeyB 565 7.13e+01 1jeqB b.131.1.2,c.62.1.4 90372,90373 1lucA 355 7.14e+01 1lucA c.1.16.1 29547 1zghA 260 7.14e+01 1c7sA 858 7.18e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21812,22408,29011,40410 1gs9A 165 7.21e+01 a.24.1.1 83313 1q4gA 553 7.24e+01 a.93.1.2,g.3.11.1 95789,95790 2bykB 128 7.24e+01 1v37A 177 7.31e+01 1su8A 636 7.33e+01 e.26.1.2 98999 1lkdA 297 7.35e+01 d.32.1.3,d.32.1.3 78059,78060 1w9cA 321 7.39e+01 1qpoA 284 7.69e+01 1qpoA c.1.17.1,d.41.2.1 29561,38597 1d0vA 356 7.70e+01 1d0vA c.39.1.1 32476 1wl8A 189 7.73e+01 1e58A 249 7.74e+01 1qhfA c.60.1.1 59262 1m7vA 363 7.75e+01 d.174.1.1 78748 1gakA 141 7.75e+01 1gakA a.19.1.1 16415 1poiA 317 7.80e+01 1poiA c.124.1.2 34153 1syyA 346 7.83e+01 a.25.1.2 106126 1riiA 265 7.85e+01 1qo7A 394 7.87e+01 1qo7A c.69.1.11 34697 1psuA 140 7.87e+01 d.38.1.5 88285 1qhfA 240 7.88e+01 1qhfA c.60.1.1 33960 3ertA 261 7.95e+01 3erdA a.123.1.1 19292 1y5hA 133 7.96e+01 1urvA 190 7.96e+01 1ut0A 190 7.96e+01 a.1.1.2 108012 2au3A 407 7.99e+01 1pq1A 196 7.99e+01 f.1.4.1 94986 2afdA 88 8.04e+01 1y37A 304 8.05e+01 1d9tA 289 8.05e+01 1deaA 1jjyA 636 8.05e+01 1jjyA 1ycqA 107 8.06e+01 1ycqA a.42.1.1 17419 2fs2A 151 8.13e+01 1yirA 408 8.17e+01 1jpmA 366 8.20e+01 c.1.11.2,d.54.1.1 67031,67032 1cc1L 498 8.22e+01 1h2rL e.18.1.1 43301 1j4aA 333 8.23e+01 c.2.1.4,c.23.12.1 71502,71503 2csbA 519 8.23e+01 1z5zA 271 8.24e+01 1ad1A 266 8.31e+01 1aj2 c.1.21.1 29668 1or7A 194 8.40e+01 a.4.13.2,a.177.1.1 87332,87333 1x1tA 260 8.40e+01 2gpiA 91 8.43e+01 1fohA 664 8.46e+01 1fohA c.3.1.2,c.47.1.10,d.16.1.2 30381,33078,37900 1js3A 486 8.50e+01 c.67.1.6 67215 1xpcA 248 8.53e+01 2b7kA 200 8.54e+01 1otkA 249 8.55e+01 a.25.1.2 93521 1rr7A 129 8.56e+01 a.4.1.14 105075 1va4A 279 8.59e+01 c.69.1.12 108458 1nkpB 83 8.59e+01 a.38.1.1 80574 1td6A 306 8.63e+01 1n93X 375 8.64e+01 a.206.1.1 91707 1kkhA 317 8.65e+01 d.14.1.5,d.58.26.3 72645,72646 1xahA 354 8.73e+01 1lm4A 194 8.73e+01 d.167.1.1 84626 1dixA 208 8.74e+01 1bk7A d.124.1.1 41122 2b61A 377 8.80e+01 1f24A 402 8.83e+01 1rom a.104.1.1 18953 1fcyA 236 8.89e+01 2lbd a.123.1.1 19282 1wmaA 276 8.90e+01 2axtZ 62 8.94e+01 1gwiA 411 8.96e+01 a.104.1.1 76364 1lj8A 493 8.99e+01 a.100.1.9,c.2.1.6 90392,90393