# List of top-scoring protein chains for t2k-100-30-n_notor2-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 1zpwX 90 6.73e-09 1ydyA 356 2.55e-02 1iv8A 720 1.24e-01 b.71.1.1,c.1.8.1 76842,76843 1fecA 490 3.06e-01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 2matA 264 3.85e-01 1c24A d.127.1.1 41146 1f83A 425 4.09e-01 1f82A d.92.1.7 40306 1rtu 114 4.83e-01 9rnt d.1.1.4 36139 1oz9A 150 7.30e-01 d.92.1.15 93808 2af4C 333 7.60e-01 1wfxA 186 8.93e-01 1ve3A 227 9.40e-01 1w2wB 191 9.60e-01 2anpA 291 9.94e-01 2g30A 258 1.20e+00 1lokA 291 1.51e+00 c.56.5.4 78122 2bibA 547 1.53e+00 1o26A 232 1.60e+00 d.207.1.1 86566 1xyfA 436 1.63e+00 1taxA b.42.2.1,c.1.8.3 25577,28909 1xovA 326 2.08e+00 1u2zA 433 2.23e+00 c.66.1.31 107626 2as0A 396 2.25e+00 1xkyA 301 2.33e+00 1han 297 2.35e+00 1han d.32.1.3,d.32.1.3 38506,38507 1lcyA 325 2.56e+00 b.36.1.4,b.47.1.1 73834,73835 1up6A 416 2.59e+00 c.2.1.5,d.162.1.2 107976,107977 1ooyA 481 2.80e+00 c.124.1.3,c.124.1.2 93388,93389 1xnzA 264 2.88e+00 1sz7A 200 2.91e+00 1z3eA 132 2.91e+00 1el3A 316 2.94e+00 1frb c.1.7.1 28672 2ftwA 521 3.08e+00 1rtqA 299 3.08e+00 c.56.5.4 97819 1dm0A 287 3.18e+00 1dm0A d.165.1.2 42227 1poiA 317 3.20e+00 1poiA c.124.1.2 34153 1qwgA 251 3.25e+00 c.1.27.1 96473 1e9lA 377 3.25e+00 1e9lA c.1.8.5,d.26.3.1 59395,59396 1h7wD 1025 3.36e+00 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15686,28631,30327,30612,39010 1bw0A 416 3.36e+00 1bw0A c.67.1.1 34385 1ah4 315 3.40e+00 1frb c.1.7.1 28684 1h7wB 1025 3.47e+00 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15684,28629,30325,30610,39008 1h7wA 1025 3.49e+00 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15683,28628,30324,30609,39007 1uw1A 80 3.49e+00 k.42.1.1 100069 1ao0A 459 3.59e+00 1ecfB c.61.1.1,d.153.1.1 34049,41816 2aaa 484 3.65e+00 7taa b.71.1.1,c.1.8.1 27777,28764 1euvA 221 3.83e+00 1euvA d.3.1.7 37133 1huqA 164 3.89e+00 1byuA c.37.1.8 32020 8atcA 310 4.17e+00 3csuA c.78.1.1,c.78.1.1 35132,35133 1r6vA 671 4.28e+00 2ffeA 311 4.52e+00 1gph1 465 4.59e+00 1ecfB 1vdxA 184 4.63e+00 1uc8A 280 4.87e+00 c.30.1.6,d.142.1.7 99165,99166 1h7xD 1025 4.89e+00 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15690,28635,30331,30616,39014 1b7lA 130 4.91e+00 3lzt d.2.1.2 36515 1r2qA 170 4.92e+00 c.37.1.8 96874 1r0mA 375 5.04e+00 c.1.11.2,d.54.1.1 104747,104748 1ve4A 206 5.04e+00 1iyoA 262 5.07e+00 e.3.1.1 76970 1g6aA 271 5.16e+00 1btl e.3.1.1 42704 1pvvA 315 5.26e+00 c.78.1.1,c.78.1.1 95190,95191 1jlwA 219 5.28e+00 a.45.1.1,c.47.1.5 71741,71742 1hdhA 536 5.45e+00 c.76.1.2 65805 1fmtA 314 5.46e+00 1fmtA b.46.1.1,c.65.1.1 25758,34174 1t8qA 336 5.50e+00 c.1.18.3 106669 1qqyA 130 5.67e+00 3lzt d.2.1.2 36586 1l6rA 227 5.75e+00 c.108.1.10 77768 1y4wA 518 5.79e+00 1ntfA 282 5.81e+00 d.151.1.2 92104 1lmt 136 5.88e+00 3lzt d.2.1.2 36416 1jroB 777 5.96e+00 d.41.1.1,d.133.1.1 67141,67142 1zzmA 259 6.01e+00 3csuA 310 6.12e+00 3csuA c.78.1.1,c.78.1.1 35094,35095 3blm 257 6.20e+00 1btl e.3.1.1 42709 1ajsA 412 6.22e+00 1ajsA c.67.1.1 34276 1mucA 373 6.54e+00 1mucA c.1.11.2,d.54.1.1 29236,38880 1v5wA 343 6.80e+00 c.37.1.11 108387 2gdzA 267 6.86e+00 1wyuA 438 6.88e+00 2gbp 309 7.12e+00 1gca c.93.1.1 35657 1gqoB 143 7.34e+00 c.23.13.1 76296 1dmr 823 7.38e+00 1dmr b.52.2.2,c.81.1.1 26904,35312 1b7mA 130 7.43e+00 3lzt d.2.1.2 36569 1fmtB 314 7.55e+00 1fmtA b.46.1.1,c.65.1.1 25759,34175 1lniA 96 7.87e+00 d.1.1.2 74046 1mnaA 298 7.92e+00 c.69.1.22 79322 1ae1A 273 7.93e+00 1bdb c.2.1.2 29943 1n9eA 787 8.01e+00 b.30.2.1,d.17.2.1,d.17.2.1 91708,91709,91710 1reqA 727 8.14e+00 1reqA c.1.19.1,c.23.6.1 29620,31247 1xrtA 467 8.40e+00 1lz1 130 8.46e+00 3lzt d.2.1.2 36415 1a7lA 389 8.54e+00 4mbp c.94.1.1 35787 1og6A 298 8.58e+00 c.1.7.1 86984 2gdqA 382 8.73e+00 2cx9A 387 8.83e+00 1hv8A 367 8.84e+00 1hv8A c.37.1.19,c.37.1.19 32405,32406 2g39A 497 8.98e+00 2bitX 165 8.98e+00 1rqbA 539 9.05e+00 a.5.7.2,c.1.10.5 105057,105058 1um0A 365 9.07e+00 d.258.1.1 107942 1qyiA 384 9.17e+00 c.108.1.13 96595 1o66A 275 9.18e+00 c.1.12.8 92547 1txuA 273 9.18e+00 a.222.1.1 107439 1uslA 170 9.31e+00 c.121.1.1 99871 1qopB 396 9.47e+00 2tysB c.79.1.1 35270 1e1hB 174 9.50e+00 1jsf 130 9.62e+00 3lzt d.2.1.2 36410 1w0pA 781 9.70e+00 b.29.1.8,b.29.1.8,b.68.1.1 109038,109039,109040 1p1xA 260 9.71e+00 c.1.10.1 104060 1bsg 266 9.80e+00 1btl e.3.1.1 42729 1uasA 362 9.88e+00 b.71.1.1,c.1.8.1 88388,88389 1xruA 282 9.89e+00 1b7oA 130 9.96e+00 3lzt d.2.1.2 36491 1k4gA 386 9.99e+00 c.1.20.1 72054 1rlmA 271 1.00e+01 1xviA 275 1.03e+01 1epwA 1290 1.04e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1ve5A 311 1.04e+01 1cye 129 1.05e+01 3chy c.23.1.1 31077 1mxiA 160 1.06e+01 c.116.1.1 79646 1a50B 396 1.07e+01 2tysB c.79.1.1 35280 3psg 370 1.08e+01 1smrA b.50.1.2 26841 1yfsA 465 1.08e+01 1v5eA 590 1.09e+01 1v5iB 76 1.10e+01 1xo7A 166 1.11e+01 1kcxA 518 1.12e+01 b.92.1.3,c.1.9.6 90953,90954 1t7lA 766 1.13e+01 1x88A 359 1.14e+01 2dg5A 366 1.15e+01 1qxoA 388 1.15e+01 d.258.1.1 96539 1xd3A 230 1.15e+01 1b5xA 130 1.15e+01 3lzt d.2.1.2 36550 1k6dA 220 1.16e+01 c.124.1.2 72082 1b5yA 130 1.16e+01 3lzt d.2.1.2 36570 1j31A 262 1.16e+01 d.160.1.2 90808 1hrdA 449 1.16e+01 1k89 c.2.1.7,c.58.1.1 30219,33867 1ea1A 455 1.16e+01 1ea1A a.104.1.1 18970 1x8mA 288 1.17e+01 b.82.1.13 109516 1mi3A 322 1.18e+01 c.1.7.1 91274 1gmpA 96 1.18e+01 1rgeA d.1.1.2 36036 1q35A 320 1.18e+01 c.94.1.1 95661 1ughI 82 1.19e+01 1ugiA d.17.5.1 38133 1rlmB 271 1.19e+01 1ig3A 263 1.20e+01 1ig3A b.82.6.1,c.100.1.1 62358,62359 1vbuA 328 1.20e+01 1xqwA 293 1.21e+01 2cxaA 256 1.21e+01 1h0hA 977 1.22e+01 b.52.2.2,c.81.1.1 76435,76436 1n6hA 170 1.23e+01 c.37.1.8 80197 1b5zA 130 1.24e+01 3lzt d.2.1.2 36567 1htqA 477 1.24e+01 d.15.9.1,d.128.1.1 71035,71036 1b7nA 130 1.25e+01 3lzt d.2.1.2 36468 2bzsA 236 1.26e+01 1ordA 730 1.26e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31274,34503,41124 1b7pA 130 1.28e+01 3lzt d.2.1.2 36551 1tvoA 368 1.29e+01 1b7rA 130 1.29e+01 3lzt d.2.1.2 36436 1qh8A 478 1.29e+01 1qguA c.92.2.3 35633 1auoA 218 1.31e+01 1auoA c.69.1.14 34716 1bb3A 130 1.35e+01 3lzt d.2.1.2 36544 1reoA 486 1.36e+01 c.3.1.2,d.16.1.5 97325,97326 1mioA 534 1.37e+01 1qguA c.92.2.3 35601 3erk 364 1.37e+01 1hcl d.144.1.7 41654 1b5vA 130 1.37e+01 3lzt d.2.1.2 36563 1hizA 379 1.37e+01 c.1.8.3 65841 1t3cA 421 1.40e+01 d.92.1.7 106343 2admA 421 1.40e+01 2admA c.66.1.27 34238 1jcjA 260 1.42e+01 c.1.10.1 66499 1qguA 478 1.44e+01 1qguA c.92.2.3 35625 1th0A 226 1.44e+01 d.3.1.7 106903 1m5sA 297 1.44e+01 d.58.33.1,d.58.33.1 74511,74512 1w2xA 758 1.46e+01 c.14.1.4,c.14.1.4 109134,109135 1apa 266 1.47e+01 1qi7A d.165.1.1 42205 1vzyA 291 1.47e+01 1ox6A 555 1.48e+01 c.1.2.1,c.23.16.1 87505,87506 1ne2A 200 1.49e+01 c.66.1.32 85586 1z0jA 170 1.49e+01 1lyxA 248 1.51e+01 c.1.1.1 78304 7reqA 727 1.53e+01 1reqA c.1.19.1,c.23.6.1 29616,31243 1b5uA 130 1.54e+01 3lzt d.2.1.2 36453 1b08A 158 1.55e+01 1rtm1 d.169.1.1,h.1.1.1 42416,45423 1w1wA 430 1.56e+01 1ecpA 238 1.57e+01 1ecpA c.56.2.1 33775 1r85A 379 1.58e+01 c.1.8.3 104839 134l 130 1.59e+01 3lzt d.2.1.2 36505 1uylA 236 1.59e+01 d.122.1.1 108147 2cfeA 162 1.64e+01 1ibcA 194 1.70e+01 1pauA c.17.1.1 30997 1z3eB 73 1.76e+01 1xwwA 157 1.80e+01 1z5yE 149 1.82e+01 2ghsA 326 1.82e+01 1g3uA 214 1.84e+01 c.37.1.1 65132 2fnuA 375 1.86e+01 1f1xA 322 1.87e+01 d.32.1.3,d.32.1.3 83208,83209 1mxgA 435 1.88e+01 b.71.1.1,c.1.8.1 85193,85194 1aerA 205 1.89e+01 1aerA d.166.1.1 42249 1l9mA 692 1.92e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 73732,73733,73734,73735 2atfA 200 1.93e+01 1coy 507 1.93e+01 1b8sA c.3.1.2,d.16.1.1 30333,37864 1j0dA 341 1.93e+01 c.79.1.1 83902 1f3lA 321 1.94e+01 1g6q2 c.66.1.6 59630 1ydnA 295 1.95e+01 1dtyA 429 1.96e+01 1dtyA c.67.1.4 34495 1t5oA 351 1.96e+01 c.124.1.5 106459 1d3vA 323 1.97e+01 1d3vA c.42.1.1 32559 1ald 363 1.98e+01 1fbaA c.1.10.1 29100 2gu2A 312 1.98e+01 1vnc 609 1.98e+01 1vns a.111.1.3 19065 1b5wA 130 2.00e+01 3lzt d.2.1.2 36557 2adcA 229 2.00e+01 1gw1A 376 2.02e+01 c.1.8.3 76361 1dywA 173 2.03e+01 2cpl b.62.1.1 27505 1mp4A 292 2.04e+01 c.68.1.6 79376 1k8tA 510 2.06e+01 e.41.1.1 68316 1gifA 115 2.12e+01 1dptA d.80.1.3 39837 1ktaA 365 2.13e+01 e.17.1.1 77533 1pp0A 199 2.14e+01 d.103.1.1 104211 1lmq 129 2.15e+01 3lzt d.2.1.2 36588 1tltA 319 2.16e+01 c.2.1.3,d.81.1.5 107135,107136 1x1nA 524 2.17e+01 1esl 162 2.18e+01 1esl d.169.1.1,g.3.11.1 42353,44225 1tfr 305 2.19e+01 1tfr a.60.7.1,c.120.1.2 18081,33351 1ur3M 319 2.21e+01 c.1.7.1 99806 1aoqA 567 2.22e+01 1qksA a.3.1.2,b.70.2.1 15934,27692 2ffcA 353 2.22e+01 1x7oA 287 2.23e+01 1ybiA 288 2.27e+01 1ga8A 311 2.27e+01 1ga8A c.68.1.4 34516 1fwxA 595 2.29e+01 b.6.1.4,b.69.3.1 60069,60070 1g1tA 157 2.30e+01 d.169.1.1,g.3.11.1 65104,65105 1amy 403 2.34e+01 1jdc b.71.1.1,c.1.8.1 27799,28786 1qoiA 177 2.35e+01 2cpl b.62.1.1 27490 1k2yX 463 2.38e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1fdi 715 2.41e+01 2napA b.52.2.2,c.81.1.1 26918,35326 1qu9A 128 2.43e+01 1qu9A d.79.1.1 39755 1qu9C 128 2.43e+01 1qu9A d.79.1.1 39757 1t4gA 322 2.43e+01 a.60.4.1,c.37.1.11 106418,106419 1iysA 262 2.48e+01 e.3.1.1 90723 1wruA 379 2.54e+01 1jeqB 565 2.56e+01 1jeqB b.131.1.2,c.62.1.4 90368,90369 1ibsA 317 2.58e+01 c.61.1.2,c.61.1.2 66107,66108 1l7vC 249 2.59e+01 c.37.1.12 73674 1vm7A 311 2.63e+01 c.72.1.1 108884 1sg0A 230 2.64e+01 1eb7A 323 2.65e+01 1eb7A a.3.1.5,a.3.1.5 59404,59405 1okjA 251 2.66e+01 c.55.1.9,c.55.1.9 103998,103999 1ny1A 240 2.66e+01 c.6.2.3 86395 1gd9A 389 2.70e+01 c.67.1.1 60454 1klqA 197 2.71e+01 d.135.1.1 68689 3rabA 169 2.72e+01 1ctqA c.37.1.8 32018 1u07A 90 2.73e+01 1wr8A 231 2.75e+01 2myr 501 2.76e+01 1fjgD 209 2.78e+01 1c05A d.66.1.2 39553 1ofgA 381 2.79e+01 1ofgA c.2.1.3,d.81.1.5 30064,39979 1r13A 148 2.83e+01 d.169.1.1,h.1.1.1 96782,96783 1ble 163 2.84e+01 1ble c.38.1.1 32475 1fobA 334 2.85e+01 c.1.8.3 83255 2bg1A 494 2.86e+01 1gdeA 389 2.87e+01 c.67.1.1 60456 1s95A 333 2.89e+01 d.159.1.3 105375 1tgoA 773 2.89e+01 1tgoA c.55.3.5,e.8.1.1 33721,43010 1k7qA 479 2.89e+01 b.80.7.1,d.92.1.6 77283,77284 1v7zA 260 2.90e+01 c.125.1.1 100488 1d0cA 444 2.92e+01 d.174.1.1 64769 3cox 507 2.94e+01 1b8sA c.3.1.2,d.16.1.1 30332,37863 1h4pA 408 2.94e+01 c.1.8.3 90617 1axcA 261 2.95e+01 1plq d.131.1.2,d.131.1.2 41392,41393 1x24A 180 3.04e+01 1v7oA 165 3.08e+01 d.67.1.2 100480 2gx9A 129 3.12e+01 1cb1 78 3.19e+01 4icb a.39.1.1 17156 2an3A 289 3.21e+01 1x42A 232 3.21e+01 1xngA 268 3.28e+01 1yymG 313 3.31e+01 1qd9A 124 3.32e+01 1qu9A d.79.1.1 39758 1jv1A 505 3.32e+01 c.68.1.5 71892 1kafA 108 3.32e+01 d.199.1.1 68372 1at1A 310 3.33e+01 3csuA c.78.1.1,c.78.1.1 35168,35169 1skf 262 3.33e+01 1skf e.3.1.1 42684 1x7dA 350 3.39e+01 1mvwB 145 3.39e+01 i.15.1.1 79524 1t6t1 118 3.39e+01 1bza 262 3.42e+01 1btl e.3.1.1 42701 1qsgA 265 3.43e+01 1eny c.2.1.2 29935 2h3bA 494 3.43e+01 1fwrA 213 3.45e+01 1fwrA c.1.10.1 29164 1r9dA 787 3.45e+01 c.7.1.1 104865 1sawA 225 3.46e+01 1k7gA 479 3.49e+01 b.80.7.1,d.92.1.6 77279,77280 2cvhA 220 3.50e+01 1z7xW 461 3.51e+01 1b7qA 130 3.51e+01 3lzt d.2.1.2 36549 1d0vA 356 3.51e+01 1d0vA c.39.1.1 32476 1zbtA 371 3.51e+01 1k4jA 230 3.52e+01 d.108.1.3 72057 1bsjA 168 3.53e+01 1bs4A d.167.1.1 42302 1ak0 270 3.55e+01 1ak0 a.124.1.2 19345 2hbtA 247 3.55e+01 1zz1A 369 3.62e+01 1ypfA 336 3.64e+01 1xr4A 509 3.68e+01 1svcP 365 3.68e+01 1a3qA b.1.18.1,b.2.5.3 21924,22443 1g1sA 162 3.71e+01 d.169.1.1,g.3.11.1 65100,65101 1f3eA 386 3.73e+01 1pud c.1.20.1 29661 1w24A 182 3.74e+01 1tubA 440 3.78e+01 1tubA c.32.1.1,d.79.2.1 31751,39803 1asg 396 3.78e+01 1ajsA c.67.1.1 34335 1jmxA 494 3.80e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66901,66902,66903,66904,66905 1yloA 348 3.82e+01 1hy7A 173 3.88e+01 d.92.1.11 65957 1ii2A 524 3.88e+01 c.91.1.1,c.109.1.1 66146,66147 1xis 387 3.89e+01 4xis c.1.15.3 29422 4xis 387 3.89e+01 4xis c.1.15.3 29421 3xis 387 3.89e+01 4xis c.1.15.3 29423 1vc3B 97 3.90e+01 3htsB 102 3.90e+01 2hts a.4.5.22 16175 2chnA 716 3.90e+01 1cwoA 165 3.91e+01 2cpl b.62.1.1 27445 1q3kA 259 3.92e+01 c.125.1.1 95693 1b4qA 105 3.93e+01 1kte c.47.1.1 32773 2ajfA 597 3.95e+01 1yndA 165 3.96e+01 1zvkA 358 3.97e+01 1askA 127 3.97e+01 1ounA d.17.4.2 38094 2ge3A 170 3.97e+01 1zh2A 121 3.98e+01 1qhxA 178 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