# List of top-scoring protein chains for t04-100-30-str2-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 2f4qA 346 2.63e-02 1m93C 41 1.65e-01 2a2pA 129 2.68e-01 1xvqA 175 9.13e-01 1lktA 104 1.11e+00 1lktA b.90.1.1 28398 1yaxA 153 1.25e+00 1tp6A 128 1.52e+00 d.17.4.12 107184 1iscA 192 1.56e+00 1avmA a.2.11.1,d.44.1.1 15733,38726 1vq2A 193 1.90e+00 1zkdA 387 1.94e+00 1u0tA 307 1.99e+00 e.52.1.1 107567 1w9hA 427 2.25e+00 1m7xA 617 2.81e+00 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 1pm1X 180 2.89e+00 b.60.1.1 104189 1skoA 143 3.00e+00 d.110.7.1 105676 2c3vA 102 3.28e+00 2cr5A 109 3.51e+00 1sqeA 109 3.88e+00 d.58.4.5 105908 2fa8A 105 3.91e+00 1vetA 124 4.03e+00 d.110.7.1 108553 16pk 415 4.29e+00 16pk c.86.1.1 35454 1l6rA 227 4.39e+00 c.108.1.10 77768 3nul 130 4.48e+00 3nul d.110.1.1 40891 1uhvA 500 4.54e+00 b.71.1.2,c.1.8.3 99402,99403 1jv4A 162 4.58e+00 b.60.1.1 67343 1yx1A 264 4.66e+00 1zndA 174 5.11e+00 1xc3A 302 5.32e+00 1iujA 106 5.33e+00 d.58.4.5 90701 1kllA 130 5.38e+00 d.32.1.2 72720 1v74A 107 5.51e+00 d.243.1.1 100442 1a8q 274 5.54e+00 1brt c.69.1.12 34702 1qy1A 174 5.79e+00 b.60.1.1 96568 1i05A 180 6.07e+00 1mup b.60.1.1 27130 2dg5B 190 6.19e+00 1txkA 498 6.26e+00 b.1.18.2,b.30.5.9 107425,107426 1u6mA 199 6.31e+00 1m65A 245 6.66e+00 c.6.3.1 84847 1i06A 180 6.73e+00 1mup b.60.1.1 27131 2h3jA 75 6.75e+00 1iow 306 6.95e+00 1iow c.30.1.2,d.142.1.1 31713,41481 1th8A 145 7.24e+00 d.122.1.3 106908 1vr9A 213 7.28e+00 1wm3A 72 7.36e+00 1qhoA 686 7.59e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1huxA 270 7.67e+00 1huxA c.55.1.5 61278 2bjfA 329 7.67e+00 1mup 166 7.69e+00 1mup b.60.1.1 27133 1lq9A 112 7.75e+00 d.58.4.3 78129 1bu6O 501 7.95e+00 1glcG c.55.1.4,c.55.1.4 33499,33500 1peeA 180 8.23e+00 b.60.1.1 104126 1qauA 112 8.76e+00 1qauA b.36.1.1 24779 2bs9A 503 8.78e+00 2fh5A 185 8.81e+00 1mtpB 43 8.99e+00 1z0wA 207 8.99e+00 1ttzA 87 9.02e+00 c.47.1.1 107309 1hw6A 278 9.08e+00 1frb c.1.7.1 61296 1cdq 77 9.24e+00 1cds g.7.1.3 44459 1p6oA 161 9.35e+00 c.97.1.2 94185 1cqyA 99 9.60e+00 1b9zA b.3.1.1 22527 3ezmA 101 1.00e+01 3ezmA b.89.1.1 28395 1ui0A 205 1.03e+01 c.18.1.2 99411 1xf1A 926 1.03e+01 1omiA 248 1.04e+01 b.82.3.3,a.4.5.4 87079,87080 1obr 326 1.08e+01 1aye c.56.5.2 33828 1jofA 365 1.11e+01 b.69.10.1 71775 2bfgA 503 1.12e+01 1ffyA 917 1.21e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1am2 199 1.22e+01 1am2 b.86.1.2 28381 1wrvA 308 1.27e+01 2ghrA 302 1.28e+01 1vjfA 180 1.39e+01 d.116.1.1 100809 1xfsA 178 1.43e+01 d.129.3.5 109589 1lrwA 600 1.46e+01 b.70.1.1 91111 1pylA 97 1.46e+01 d.1.1.2 104391 2a25A 193 1.51e+01 1w6sA 599 1.53e+01 1icxA 155 1.53e+01 d.129.3.1 71191 1lwdA 413 1.54e+01 c.77.1.1 78265 1j79A 347 1.54e+01 1j79A c.1.9.4 62675 1b9wA 89 1.56e+01 1b9wA g.3.11.4,g.3.11.4 44334,44335 1euoA 180 1.59e+01 1np1A b.60.1.1 27163 1uasA 362 1.63e+01 b.71.1.1,c.1.8.1 88388,88389 1bywA 110 1.64e+01 1bywA d.110.3.6 40912 1nqcA 217 1.65e+01 d.3.1.1 86024 1cv8 174 1.66e+01 1cv8 d.3.1.1 37089 2dg5A 366 1.69e+01 1xkiA 162 1.70e+01 1wlsA 328 1.75e+01 1l6sA 323 1.76e+01 c.1.10.3 73627 1j5pA 253 1.77e+01 d.81.1.3,c.2.1.3 71577,83092 2a8eA 220 1.78e+01 2fq9A 225 1.79e+01 1e3uA 246 1.81e+01 1fofA e.3.1.1 42755 1kb0A 677 1.83e+01 a.3.1.6,b.70.1.1 68378,68379 2a15A 139 1.85e+01 1qmvA 197 1.85e+01 1qq2A c.47.1.10 33066 2pil 159 1.86e+01 2pil d.24.1.1 38376 1rvkA 382 1.88e+01 c.1.11.2,d.54.1.1 97928,97929 1zyeA 220 1.88e+01 1gv3A 248 1.90e+01 a.2.11.1,d.44.1.1 70585,70586 1gpeA 587 1.92e+01 1gpeA c.3.1.2,d.16.1.1 30387,37951 1dcjA 81 1.92e+01 1dcjA d.68.3.3 59115 1k55A 246 1.92e+01 e.3.1.1 68156 1pqzA 238 1.94e+01 b.1.1.2,d.19.1.1 104297,104298 1ka9H 200 1.97e+01 c.23.16.1 77308 1h4rA 314 2.12e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1zq1A 438 2.13e+01 1kay 381 2.15e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1w44A 331 2.16e+01 1y9wA 140 2.16e+01 1xrkA 124 2.22e+01 1u58A 253 2.23e+01 1wnfA 328 2.23e+01 1xt9A 212 2.24e+01 1bupA 386 2.30e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1c44A 123 2.32e+01 1qndA d.106.1.1 40795 1rewC 135 2.33e+01 g.7.1.3 97336 1vjvA 415 2.33e+01 d.3.1.9 108632 1q0qA 406 2.37e+01 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1b24A 188 2.41e+01 1b24A d.95.2.1,d.95.2.1 40573,40574 1pamA 686 2.49e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21846,22515,27753,28740 1tqzA 133 2.49e+01 1dg9A 157 2.51e+01 1dg9A c.44.1.1 32637 1fjgP 88 2.51e+01 1emwA d.27.1.1 38444 1jvsA 400 2.52e+01 a.69.3.1,c.2.1.3,d.81.1.3 77187,77188,77189 2akrA 285 2.53e+01 1ecfA 504 2.56e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1zg2A 107 2.57e+01 2cwzA 141 2.58e+01 2cu3A 64 2.60e+01 1jtkA 136 2.60e+01 c.97.1.1 71862 1z2mA 155 2.60e+01 1whzA 70 2.62e+01 1h9oA 112 2.63e+01 1qadA d.93.1.1 60837 1kv9A 668 2.66e+01 a.3.1.6,b.70.1.1 73056,73057 1w41A 101 2.67e+01 1xwwA 157 2.69e+01 1pvmA 184 2.77e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1bbt1 213 2.77e+01 1qqp1 1zceA 155 2.81e+01 1xvsA 126 2.83e+01 2a6aA 218 2.85e+01 1qqp1 213 2.86e+01 1qqp1 1mkeA 152 2.90e+01 b.55.1.4 79231 1h6hA 143 2.90e+01 d.189.1.1 65681 1vkcA 158 2.92e+01 1ijqA 316 2.96e+01 1ijqA b.68.5.1,g.3.11.1 62506,62507 1h7mA 102 2.98e+01 d.79.3.1 83485 1qjpA 171 3.00e+01 1bxwA f.4.1.1 43742 1h80A 464 3.01e+01 b.80.1.8 65714 1m22A 503 3.01e+01 c.117.1.1 78464 1k2fA 190 3.06e+01 b.8.1.2 68054 1lrzA 426 3.09e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1yirA 408 3.10e+01 1uwzA 136 3.12e+01 c.97.1.1 108081 2basA 431 3.13e+01 1xgyH 219 3.13e+01 1zbfA 142 3.13e+01 1uh6A 100 3.15e+01 d.15.1.1 99394 1c0eA 157 3.18e+01 1dg9A c.44.1.1 32638 2bgiA 272 3.19e+01 1k8kA 418 3.27e+01 c.55.1.1,c.55.1.1 68305,68306 1gs5A 258 3.29e+01 c.73.1.2 70395 1qgoA 264 3.30e+01 1qgoA c.92.1.2 35596 2ap1A 327 3.31e+01 1or0B 528 3.35e+01 1kngA 156 3.37e+01 c.47.1.10 72777 1z5lA 285 3.38e+01 1i0cA 60 3.39e+01 1aojA b.34.2.1 61485 1wn5A 130 3.40e+01 1e25A 282 3.46e+01 1e25A e.3.1.1 42731 1tyv 542 3.47e+01 1tyv b.80.1.6 28038 1icpA 376 3.48e+01 1oyc c.1.4.1 62270 2ga9D 469 3.53e+01 1xqaA 113 3.56e+01 1e1aA 314 3.62e+01 1e1aA b.68.6.1 59155 4ubpC 570 3.63e+01 1ubpC b.92.1.1,c.1.9.2 28431,29053 2sli 679 3.64e+01 2sli b.29.1.9,b.68.1.1 24274,27611 2dcnA 311 3.66e+01 1qx4A 274 3.66e+01 b.43.4.2,c.25.1.1 104624,104625 1q9iA 571 3.71e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1p2hA 571 3.71e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1y0pA 571 3.71e+01 1e39A 571 3.74e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1kssA 571 3.75e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1xubA 298 3.76e+01 1nrlA 316 3.78e+01 a.123.1.1 92091 2ae5B 528 3.82e+01 1x54A 434 3.84e+01 1g72A 573 3.84e+01 4aahA b.70.1.1 27680 1ndh 272 3.86e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 2b5nA 323 3.87e+01 1x6oA 174 3.89e+01 b.34.5.2,b.40.4.5 109493,109494 1vjlA 164 3.92e+01 d.257.1.1 100822 2crvA 120 3.92e+01 1um5H 217 4.00e+01 1umkA 275 4.01e+01 1ywlA 96 4.01e+01 1fm2B 520 4.04e+01 1fm2B 1wejH 223 4.08e+01 1igtB b.1.1.1,b.1.1.2 20361,21353 1vqoS 85 4.12e+01 1jj2R 84 4.13e+01 1ffkP d.12.1.1 63103 1s72S 85 4.13e+01 d.12.1.1 105338 1gsa 316 4.16e+01 1gsa c.30.1.3,d.142.1.1 31718,41477 1wh5A 80 4.24e+01 1atg 231 4.27e+01 1atg c.94.1.1 35834 2fikA 287 4.28e+01 1njkA 156 4.28e+01 d.38.1.1 85818 2gfoA 396 4.28e+01 1g2rA 100 4.29e+01 1g2rA d.192.1.1 60231 1f00I 282 4.29e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1pjxA 314 4.30e+01 b.68.6.1 104167 1ro5A 201 4.32e+01 d.108.1.3 105023 1lgpA 116 4.43e+01 b.26.1.2 73890 1i7pA 274 4.44e+01 b.43.4.2,c.25.1.1 66048,66049 1ayaA 101 4.47e+01 1qadA d.93.1.1 40460 1xniA 118 4.48e+01 2a5hA 416 4.49e+01 1b77A 228 4.51e+01 1b77A d.131.1.2,d.131.1.2 41362,41363 2be1A 339 4.55e+01 1gtkA 313 4.58e+01 c.94.1.1,d.50.2.1 76346,76347 1pswA 348 4.59e+01 c.87.1.7 88287 1npeA 267 4.62e+01 b.68.5.1 92032 1bx1A 314 4.63e+01 1fnc b.43.4.2,c.25.1.1 25629,31519 1wfyA 104 4.63e+01 2bryA 497 4.69e+01 1tiyA 164 4.73e+01 c.97.1.2 107012 1fnd 314 4.77e+01 1fnc b.43.4.2,c.25.1.1 25626,31516 1q45A 391 4.80e+01 c.1.4.1 95780 1ri9A 102 4.80e+01 b.34.2.1 97506 1xkpC 143 4.81e+01 1a79A 171 4.83e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 2f9zC 159 4.88e+01 1cq0A 28 4.89e+01 j.6.1.1 46108 1npsA 88 4.95e+01 1prs b.11.1.1 23622 2bycA 137 4.95e+01 1sur 215 4.97e+01 1sur c.26.2.2 31620 1vl2A 421 4.98e+01 c.26.2.1,d.210.1.1 108708,108709 1r77A 103 5.00e+01 2gaiA 633 5.02e+01 2gcc 70 5.04e+01 2gcc d.10.1.2 37484 1psdA 409 5.06e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1e2wA 251 5.09e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1b22A 114 5.14e+01 1b22A a.60.4.1 17969 1sgvA 316 5.18e+01 b.122.1.1,d.265.1.2 98858,98859 1qxhA 167 5.20e+01 c.47.1.10 96528 1ro7A 259 5.27e+01 c.130.1.1 97667 1tzaA 134 5.27e+01 b.1.23.1 107468 1glcG 501 5.29e+01 1glcG c.55.1.4,c.55.1.4 33519,33520 1fecA 490 5.29e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1d4tA 104 5.30e+01 1d4tA d.93.1.1 40537 1pl3A 186 5.30e+01 b.1.9.1 88158 1xkgA 312 5.31e+01 2gu3A 136 5.36e+01 1z47A 355 5.43e+01 1d7cA 190 5.45e+01 1d7bA b.1.9.1 22309 2bkqA 212 5.46e+01 1h3qA 140 5.47e+01 d.110.4.3 76652 2cw9A 194 5.47e+01 1xriA 151 5.50e+01 1g38A 393 5.51e+01 2admA c.66.1.27 60235 1i8jA 323 5.57e+01 1b4kA c.1.10.3 61968 1b63A 333 5.60e+01 1b63A d.14.1.3,d.122.1.2 37566,41107 1ru3A 732 5.69e+01 e.26.1.3 97835 1khbA 625 5.76e+01 c.91.1.1,c.109.1.1 68606,68607 1o6aA 96 5.80e+01 b.139.1.1 92562 2bs6A 90 5.82e+01 1zbsA 291 5.86e+01 1ifqA 138 5.92e+01 1ifqA d.110.4.1 62350 1sc6A 404 5.98e+01 1gqzA 274 5.98e+01 d.21.1.1,d.21.1.1 83311,83312 1xhcA 367 5.98e+01 2bgcA 238 5.98e+01 2go8A 122 5.99e+01 1i07A 60 5.99e+01 1aojA b.34.2.1 61477 1u00A 227 5.99e+01 1jtdB 273 6.02e+01 b.69.5.2 67265 1vemA 516 6.03e+01 1xebA 150 6.10e+01 1m7jA 484 6.15e+01 b.92.1.6,b.92.1.6,c.1.9.11 78732,78733,78734 2bt9A 90 6.16e+01 1r6fA 310 6.25e+01 e.46.1.1 97149 1itbB 315 6.31e+01 1itbB b.1.1.4,b.1.1.4,b.1.1.4 21720,21721,21722 1r4pB 70 6.32e+01 b.40.2.1 97026 1rkqA 282 6.32e+01 c.108.1.10 97621 1a7cA 379 6.35e+01 1sek e.1.1.1 42660 1itcA 516 6.35e+01 b.3.1.1,c.1.8.1 83705,83706 1rk6A 496 6.38e+01 b.92.1.6,b.92.1.6,c.1.9.11 97599,97600,97601 1b8aA 438 6.39e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1x8bA 289 6.44e+01 1mdwA 328 6.46e+01 d.3.1.3 84934 1vcdA 126 6.48e+01 2cx5A 158 6.65e+01 1y81A 138 6.68e+01 1bco 327 6.68e+01 1bco b.48.1.1,c.55.3.3 26431,33676 1r13A 148 6.70e+01 d.169.1.1,h.1.1.1 96782,96783 1obpA 159 6.73e+01 1obpA b.60.1.1 27092 1ef1A 294 6.78e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 1te7A 103 6.80e+01 1opy 131 6.80e+01 1opy d.17.4.3 38113 1pufB 73 6.83e+01 a.4.1.1 95132 1vrbA 342 6.87e+01 1oshA 232 6.90e+01 a.123.1.1 93496 1gw5S 142 6.90e+01 d.110.4.2 70633 1rkd 309 6.91e+01 1rkd c.72.1.1 34928 1y88A 199 6.91e+01 2b59B 172 6.93e+01 1k7jA 206 6.94e+01 d.115.1.1 72103 1u1wA 298 6.94e+01 1twfK 120 6.95e+01 1aisA 182 6.96e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1gmyA 261 6.98e+01 d.3.1.1 76236 2pooA 355 7.01e+01 1qlgA b.68.3.1 27626 1op3H 225 7.04e+01 b.1.1.1,b.1.1.2 87208,87209 1cr5A 189 7.08e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1gmuA 143 7.08e+01 b.107.1.1,d.58.38.1 65335,65336 1gk8I 140 7.13e+01 d.73.1.1 65242 1jbwA 428 7.14e+01 c.59.1.2,c.72.2.2 62860,62861 1tqxA 227 7.14e+01 2fauA 341 7.15e+01 1n13A 52 7.16e+01 d.155.1.2 85248 1dmhA 311 7.17e+01 1dmhA b.3.6.1 22633 1ir21 140 7.18e+01 1brt 277 7.21e+01 1brt c.69.1.12 34699 1hd2A 161 7.22e+01 c.47.1.10 60962 1lf7A 182 7.22e+01 b.60.1.1 73878 1fzoA 274 7.28e+01 1agdA b.1.1.2,d.19.1.1 60155,60156 1pj5A 830 7.30e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1lk2A 274 7.32e+01 b.1.1.2,d.19.1.1 91056,91057 1hi9A 274 7.34e+01 1hi9A c.99.1.1 61063 1wgoA 123 7.34e+01 1wywA 230 7.35e+01 1broA 277 7.39e+01 1brt c.69.1.12 34700 1lfdA 87 7.39e+01 1lfdA d.15.1.5 37622 1a9xA 1058 7.39e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1zc6A 305 7.41e+01 2comA 124 7.56e+01 1b72B 87 7.58e+01 1akhA a.4.1.1 16001 1yqtA 538 7.64e+01 1q18A 332 7.65e+01 c.55.1.7,c.55.1.7 104470,104471 1m9sA 605 7.65e+01 b.1.18.15,b.34.11.1,b.34.11.1,b.34.11.1,c.10.2.1 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