# List of top-scoring protein chains for t2k-100-30-str2 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 1twfA 1733 1.00e-01 1i50A 1733 1.08e-01 e.29.1.2 61754 1keiA 316 4.31e-01 d.92.1.2 77349 1jbwA 428 4.78e-01 c.59.1.2 62860 c.72.2.2 62861 1fgs 428 5.17e-01 1fgs c.59.1.2 33959 c.72.2.2 34962 6tmnE 316 5.66e-01 1hyt d.92.1.2 59071 2tmnE 316 5.83e-01 1hyt d.92.1.2 59055 8tlnE 316 6.07e-01 1hyt d.92.1.2 59075 1hyt 316 6.14e-01 1hyt d.92.1.2 59005 1zkiA 133 6.24e-01 1k28A 584 6.48e-01 b.40.8.1 68049 b.108.1.2 68050 d.2.1.3 68051 1mp1A 111 9.25e-01 a.188.1.1 91382 2fkcA 247 1.30e+00 2fflA 756 1.30e+00 2es4D 332 1.78e+00 2ts1 419 1.87e+00 2ts1 c.26.1.1 31564 1m6yA 301 1.90e+00 a.60.13.1 78716 c.66.1.23 78717 2d7vA 162 2.34e+00 1b9hA 388 2.35e+00 1b9hA c.67.1.4 34488 1ynmA 247 2.94e+00 1lf6A 684 2.95e+00 a.102.1.5 77918 b.30.5.5 77919 1jgcA 161 3.18e+00 a.25.1.1 66673 1zb1A 392 3.40e+00 1wxcA 281 3.61e+00 2bidA 197 3.76e+00 2bidA f.1.4.1 43398 2cq2A 114 3.82e+00 1pgjA 478 3.98e+00 2pgd a.100.1.1 18783 c.2.1.6 30195 2cvxA 888 4.32e+00 1qdbA 473 4.50e+00 1qdbA a.138.1.3 19688 1ntyA 311 4.82e+00 a.87.1.1 103873 b.55.1.1 103874 1y2mA 716 4.92e+00 1ej6B 1275 5.56e+00 i.7.1.1 45968 1sqc 631 5.62e+00 2sqcA a.102.4.2 18858 a.102.4.2 18859 1hm2A 700 5.64e+00 1cb8A a.102.3.2 61083 b.24.1.1 61084 b.30.5.2 61085 1uuqA 440 5.66e+00 c.1.8.3 100015 1e6yA 569 5.71e+00 1mroA a.89.1.1 18529 d.58.31.2 39447 1cb8A 678 6.28e+00 1cb8A a.102.3.2 18849 b.24.1.1 23898 b.30.5.2 24422 2bvlA 543 6.44e+00 1t6jA 714 6.69e+00 1qgrA 876 6.93e+00 1qgrA a.118.1.1 19119 1wa5C 960 7.11e+00 1wovA 250 7.29e+00 1gvfA 286 7.30e+00 c.1.10.2 70599 1sfkA 76 7.60e+00 a.190.1.1 105488 1lmzA 187 7.62e+00 a.96.1.4 74037 2sqcA 631 7.71e+00 2sqcA a.102.4.2 18854 a.102.4.2 18855 1m0kA 262 7.80e+00 f.13.1.1 78344 1e5rA 290 7.80e+00 1e5rA b.82.2.4 59276 1uruA 244 7.87e+00 h.4.14.1 99835 1e6qM 501 8.15e+00 1e70M c.1.8.4 28920 1f6dA 376 8.70e+00 1f6dA c.87.1.3 35467 2arcB 164 8.71e+00 2arcA b.82.4.1 28149 1hw8A 467 8.74e+00 1dqaA d.58.20.1 61298 d.179.1.1 61299 1vjvA 415 8.95e+00 d.3.1.9 108632 1e4mM 501 9.15e+00 1e70M c.1.8.4 59226 4ts1A 319 9.16e+00 2ts1 c.26.1.1 31565 1e70M 501 9.27e+00 1e70M c.1.8.4 28926 1v58A 241 9.62e+00 c.47.1.9 108371 d.17.3.1 108372 2d1eA 248 9.95e+00 1ocnA 362 9.96e+00 c.6.1.1 86808 1vgvA 384 9.97e+00 c.87.1.3 100608 2ao9A 155 1.01e+01 1kgbA 231 1.03e+01 f.13.1.1 68581 2bvwA 362 1.05e+01 1bvwA c.6.1.1 30666 1oc7A 364 1.08e+01 c.6.1.1 86794 2arcA 164 1.10e+01 2arcA b.82.4.1 28148 1jqzA 146 1.12e+01 b.42.1.1 67109 1bvwA 360 1.15e+01 1bvwA c.6.1.1 30668 1dqaC 467 1.17e+01 1dqaA d.58.20.1 39366 d.179.1.1 42587 1m16A 146 1.21e+01 b.42.1.1 91164 1dqaA 467 1.21e+01 1dqaA d.58.20.1 39364 d.179.1.1 42585 2c5uA 375 1.23e+01 5eau 548 1.25e+01 5eat a.102.4.1 18851 a.128.1.3 19443 1jt7A 146 1.25e+01 b.42.1.1 67255 2bcgG 453 1.28e+01 2aacA 177 1.29e+01 2arcA b.82.4.1 28150 1rg8A 146 1.29e+01 1d5tA 433 1.29e+01 1gnd c.3.1.3 30422 d.16.1.6 37986 1lzlA 323 1.31e+01 c.69.1.2 78306 1y0gA 191 1.32e+01 5eat 548 1.36e+01 5eat a.102.4.1 18853 a.128.1.3 19445 2myr 501 1.41e+01 1o9rA 162 1.42e+01 a.25.1.1 86706 1aoa 275 1.50e+01 1aoa a.40.1.1 17396 a.40.1.1 17397 2at9 247 1.52e+01 1c3wA f.13.1.1 43427 1p63A 144 1.53e+01 b.42.1.1 94153 2al6A 375 1.54e+01 1qvzA 237 1.54e+01 c.23.16.2 96453 1qhbA 596 1.55e+01 1qhbA a.111.1.2 19055 1h54A 754 1.56e+01 a.102.1.4 60634 b.30.5.3 60635 1p4xA 250 1.60e+01 a.4.5.28 87784 a.4.5.28 87785 1l8qA 324 1.63e+01 a.4.12.2 77809 c.37.1.20 77810 1pjhA 280 1.66e+01 c.14.1.3 94761 1rw7A 243 1.71e+01 c.23.16.2 97963 16vpA 366 1.73e+01 16vpA d.180.1.1 42601 1o7iA 119 1.74e+01 b.40.4.3 86642 1ekeA 230 1.75e+01 1ekeA c.55.3.1 33572 1r8iA 213 1.81e+01 a.8.7.1 97239 1x8yA 86 1.84e+01 1xjdA 345 1.87e+01 1rkeA 262 1.87e+01 a.24.9.1 97608 a.24.9.1 97609 1jeqB 565 1.87e+01 1jeqB b.131.1.2 90368 c.62.1.4 90369 1y6iA 233 1.90e+01 2cujA 108 1.90e+01 1lt3A 240 1.95e+01 1lt3A d.166.1.1 42230 1f0xA 571 1.96e+01 1f0xA d.58.32.2 39483 d.145.1.1 41746 1vlmA 219 1.96e+01 c.66.1.41 108836 1odoA 408 1.98e+01 a.104.1.1 92783 1nd7A 374 1.98e+01 d.148.1.1 91817 1eexA 554 1.98e+01 1dioA c.1.19.3 29650 1hx0A 496 1.99e+01 b.71.1.1 61346 c.1.8.1 61347 1ojrA 274 2.03e+01 c.74.1.1 93147 1hnoA 280 2.06e+01 1hnoA c.14.1.3 61095 1r1hA 696 2.06e+01 d.92.1.4 104756 1vi0A 206 2.08e+01 a.4.1.9 100720 a.121.1.1 100721 1eypA 222 2.11e+01 1eypA d.36.1.1 38536 1fkoB 440 2.13e+01 1rthA e.8.1.2 43095 1arzC 273 2.13e+01 1drw c.2.1.3 30061 d.81.1.3 39976 1u9aA 160 2.16e+01 1u9aA d.20.1.1 38333 1h4rA 314 2.21e+01 a.11.2.1 65616 b.55.1.5 65617 d.15.1.4 65618 2az4A 429 2.21e+01 137lA 164 2.28e+01 1l92 d.2.1.3 36791 1j0hA 588 2.28e+01 b.1.18.2 77027 b.71.1.1 77028 c.1.8.1 77029 1be3C 379 2.30e+01 1be3C f.32.1.1 75805 f.21.1.2 75806 1eyqA 222 2.31e+01 1eypA d.36.1.1 38534 1jepA 222 2.32e+01 d.36.1.1 66612 1zh5A 195 2.34e+01 2f02A 323 2.36e+01 1jenB 67 2.36e+01 1jenB d.156.1.1 42029 1tzvA 142 2.37e+01 a.79.1.1 107526 1ywfA 296 2.40e+01 2awdA 323 2.40e+01 2bcmA 165 2.41e+01 1f75A 249 2.45e+01 1f75A c.101.1.1 59662 1fzrA 138 2.49e+01 1fzrA c.52.1.17 33336 1xhkA 187 2.52e+01 1va6A 518 2.52e+01 1ukvG 453 2.53e+01 c.3.1.3 107915 c.3.1.3 107916 d.16.1.6 107917 1floA 422 2.56e+01 1floA a.60.9.1 18106 d.163.1.1 42166 1xxqA 161 2.57e+01 1o7xD 377 2.58e+01 a.103.1.1 81174 1hnuA 280 2.59e+01 1hnoA c.14.1.3 61096 1hbnA 549 2.63e+01 1mroA a.89.1.1 60898 d.58.31.2 60899 1mroA 548 2.63e+01 1mroA a.89.1.1 18525 d.58.31.2 39443 2bmhA 455 2.64e+01 1bu7A a.104.1.1 18941 1jpzA 473 2.67e+01 a.104.1.1 67069 2aehA 369 2.80e+01 1azdA 237 2.81e+01 1nls b.29.1.1 24020 1pmi 440 2.82e+01 1pmi b.82.1.3 28114 1chkA 238 2.85e+01 1chkA d.2.1.7 36999 1jeyB 565 2.87e+01 1jeqB b.131.1.2 90372 c.62.1.4 90373 1dg3A 592 2.88e+01 1dg3A a.114.1.1 19078 c.37.1.8 32153 1uedA 406 2.90e+01 a.104.1.1 99256 1flmA 122 2.92e+01 1axj b.45.1.1 25747 1gmlA 178 2.96e+01 c.8.5.2 70273 1afwA 393 2.96e+01 1afwA c.95.1.1 35900 c.95.1.1 35901 1ykdA 398 2.96e+01 1s5dA 240 2.96e+01 d.166.1.1 98541 1jeoA 180 2.99e+01 c.80.1.3 66611 1drw 273 2.99e+01 1drw c.2.1.3 30057 d.81.1.3 39972 1a6cA 513 3.00e+01 1a6cA b.121.4.2 23296 b.121.4.2 23297 b.121.4.2 23298 1r7aA 504 3.00e+01 b.71.1.1 97192 c.1.8.1 97193 1tq4A 413 3.05e+01 c.37.1.8 107201 1lwjA 441 3.06e+01 b.71.1.1 74303 c.1.8.1 74304 1ppjC 379 3.08e+01 f.32.1.1 104256 f.21.1.2 104257 1bu7A 455 3.08e+01 1bu7A a.104.1.1 18937 1h1oA 183 3.09e+01 a.3.1.4 83454 a.3.1.4 83455 1rpyA 114 3.10e+01 d.93.1.1 97718 1eumA 165 3.10e+01 1eumA a.25.1.1 59507 1m7sA 484 3.11e+01 e.5.1.1 74574 1cqxA 403 3.12e+01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1qwnA 1045 3.18e+01 a.8.3.1 96487 b.30.5.6 96488 c.6.2.1 96489 1axj 122 3.18e+01 1axj b.45.1.1 25749 1nxuA 333 3.19e+01 c.122.1.1 86389 1h2rL 534 3.22e+01 1h2rL e.18.1.1 43298 1qk8A 146 3.22e+01 1ewxA c.47.1.10 33061 1dih 273 3.23e+01 1drw c.2.1.3 30056 d.81.1.3 39971 1dioA 554 3.23e+01 1dioA c.1.19.3 29656 1v9dA 340 3.23e+01 a.207.1.1 100535 1llp 343 3.23e+01 1arv a.93.1.1 18578 1m2vB 926 3.25e+01 a.71.2.1 78497 b.2.8.1 78498 c.62.1.2 78499 d.109.2.1 78500 g.41.10.1 78501 1fyeA 229 3.26e+01 1fyeA c.23.16.4 31477 1htyA 1015 3.26e+01 a.8.3.1 83064 b.30.5.6 83065 c.6.2.1 83066 1hxkA 1015 3.27e+01 a.8.3.1 83070 b.30.5.6 83071 c.6.2.1 83072 2afgA 140 3.28e+01 1bfg b.42.1.1 25514 1ykhB 132 3.32e+01 2a3qA 170 3.33e+01 1jfkA 134 3.38e+01 a.39.1.5 66639 1o8xA 146 3.41e+01 c.47.1.10 86681 1ydiA 263 3.42e+01 1szhA 161 3.42e+01 a.226.1.1 106157 1mxgA 435 3.43e+01 b.71.1.1 85193 c.1.8.1 85194 1hwwA 1015 3.44e+01 a.8.3.1 83067 b.30.5.6 83068 c.6.2.1 83069 1q87A 221 3.45e+01 e.47.1.1 96192 1b1yA 500 3.47e+01 1byb c.1.8.1 28796 1gt7A 274 3.50e+01 c.74.1.1 70398 1f5nA 592 3.54e+01 1dg3A a.114.1.1 19077 c.37.1.8 32152 1o7fA 469 3.54e+01 a.4.5.31 81131 b.82.3.2 81132 b.82.3.2 81133 1eqnA 321 3.55e+01 1dd9A e.13.1.1 43256 1evsA 187 3.62e+01 1evsA a.26.1.1 16845 180lA 164 3.70e+01 1l92 d.2.1.3 36867 1iv8A 720 3.77e+01 b.71.1.1 76842 c.1.8.1 76843 1ezvB 352 3.81e+01 1ezvB d.185.1.1 59543 d.185.1.1 59544 1lkcA 364 3.85e+01 c.67.1.1 73978 1vr3A 191 3.86e+01 1o7xB 377 3.88e+01 a.103.1.1 81172 1fy2A 229 3.89e+01 1fyeA c.23.16.4 31478 1kb9B 352 3.90e+01 d.185.1.1 77313 d.185.1.1 77314 2nmbA 160 3.95e+01 2nmbA b.55.1.2 26994 1cwyA 500 3.96e+01 1cwyA c.1.8.1 28789