# List of top-scoring protein chains for t2k-100-30-alpha-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 2a9uA 144 1.61e-01 1bvsB 203 4.34e-01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16281,17956,25275 1h5zA 455 6.22e-01 a.104.1.1 90622 1ea1A 455 6.30e-01 1ea1A a.104.1.1 18970 1e9xA 455 6.43e-01 1ea1A a.104.1.1 18969 1u13A 455 8.87e-01 a.104.1.1 107578 1x8vA 455 9.95e-01 1lfkA 398 1.55e+00 a.104.1.1 77926 1hjp 203 1.64e+00 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16274,17947,25266 1gvhA 396 1.85e+00 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1nr6A 473 2.18e+00 a.104.1.1 92085 1dt6A 473 2.38e+00 1dt6A a.104.1.1 18977 1n6bA 473 2.98e+00 a.104.1.1 85359 2bkyX 89 3.65e+00 1trrA 107 4.18e+00 1jhgA a.4.12.1 19017 1jr3E 334 4.22e+00 a.80.1.1,c.37.1.20 63253,63254 1gmpA 96 4.46e+00 1rgeA d.1.1.2 36036 1i8vA 96 4.61e+00 d.1.1.2 61985 1up7A 417 4.67e+00 1lniA 96 4.89e+00 d.1.1.2 74046 1rgeA 96 4.90e+00 1rgeA d.1.1.2 36028 2wrpR 107 4.93e+00 1jhgA a.4.12.1 19010 1up6A 416 5.08e+00 c.2.1.5,d.162.1.2 107976,107977 1udvA 89 5.12e+00 d.68.6.1 99224 1h3nA 878 5.71e+00 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1deeG 54 5.82e+00 1fc2C a.8.1.1 16343 1qlnA 883 6.00e+00 1cezA e.8.1.3 43111 1yn9A 169 6.06e+00 1gl2C 65 6.23e+00 h.1.15.1 65280 1vddA 228 6.81e+00 e.49.1.1 108519 1k3lA 221 6.81e+00 a.45.1.1,c.47.1.5 77229,77230 1mswD 883 6.84e+00 e.8.1.3 79427 1jhgA 101 7.05e+00 1jhgA a.4.12.1 19009 2cwyA 94 7.09e+00 1iq8A 582 7.97e+00 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1y6zA 263 8.47e+00 1ka2A 499 9.32e+00 d.92.1.5 77305 1yucA 255 9.65e+00 1mgrA 99 9.75e+00 d.1.1.2 79106 1uhgA 385 1.03e+01 e.1.1.1 88491 1i4mA 108 1.05e+01 d.6.1.1 66025 1d8cA 723 1.07e+01 1d8cA c.1.13.1 29325 1oyzA 280 1.10e+01 a.118.1.16 93775 1u2wA 122 1.14e+01 1pylA 97 1.18e+01 d.1.1.2 104391 1w7bA 339 1.18e+01 1l0lA 446 1.20e+01 d.185.1.1,d.185.1.1 84482,84483 1ovaA 386 1.21e+01 1ovaA e.1.1.1 42619 1i4yA 114 1.23e+01 2mhr a.24.4.1 61738 1ppjA 446 1.24e+01 d.185.1.1,d.185.1.1 104252,104253 1k3yA 221 1.25e+01 a.45.1.1,c.47.1.5 77245,77246 1cezA 883 1.29e+01 1cezA e.8.1.3 43110 1gseA 221 1.34e+01 1pgtA a.45.1.1,c.47.1.5 17667,32961 1ho8A 480 1.39e+01 1ho8A a.118.1.9 61107 1ibjA 464 1.42e+01 1ibjA c.67.1.3 62162 1kkhA 317 1.45e+01 d.14.1.5,d.58.26.3 72645,72646 1lrv 244 1.45e+01 1lrv a.118.1.5 19146 1wwzA 159 1.46e+01 1y74B 50 1.53e+01 1q5dA 419 1.54e+01 a.104.1.1 95891 4rnpA 883 1.55e+01 1cezA e.8.1.3 43113 1be3A 446 1.56e+01 1be3A d.185.1.1,d.185.1.1 58950,58951 1lnh 857 1.66e+01 1yge a.119.1.1,b.12.1.1 19237,23637 2ah6A 208 1.66e+01 1p5sA 203 1.67e+01 a.40.1.1 94147 1vkuA 100 1.68e+01 a.28.1.1 108690 1tw9A 206 1.69e+01 a.45.1.1,c.47.1.5 107381,107382 1nd4A 264 1.82e+01 d.144.1.6 91815 1w68A 390 1.86e+01 a.25.1.2 109216 1hm6A 346 1.86e+01 1avc a.65.1.1 18147 1j7nB 776 1.94e+01 d.92.1.14,d.92.1.14,d.166.1.1 66412,66413,66414 1g4yB 101 1.98e+01 1g4yB f.15.1.1 60251 1dk5A 322 1.99e+01 1dk5A a.65.1.1 18192 1a5t 334 2.03e+01 1a5t a.80.1.1,c.37.1.20 18450,32423 1q5zA 177 2.03e+01 a.196.1.1 95954 1wloA 136 2.06e+01 1s9pA 227 2.10e+01 a.123.1.1 105384 1zuhA 168 2.14e+01 1rovA 857 2.29e+01 a.119.1.1,b.12.1.1 97674,97675 1yb3A 175 2.32e+01 1quuA 250 2.37e+01 1quuA a.7.1.1,a.7.1.1 16320,16321 1w5tA 412 2.37e+01 1oheA 348 2.39e+01 c.45.1.1,c.45.1.1 87013,87014 1t2bA 397 2.55e+01 1envA 123 2.58e+01 1envA h.3.2.1 45726 1ee4A 423 2.58e+01 1ee4A a.118.1.1 19128 1wljA 189 2.63e+01 1dtoA 221 2.65e+01 1dtoA b.91.1.1 28405 1ztuA 341 2.65e+01 1f7cA 231 2.78e+01 1f7cA a.116.1.1 19107 1pszA 303 2.80e+01 1toaA c.92.2.2 35600 1khdA 345 2.85e+01 a.46.2.1,c.27.1.1 77400,77401 1r1uA 106 2.95e+01 a.4.5.5 104771 1ab4 477 2.95e+01 1ab4 e.11.1.1 43251 1s3cA 141 2.96e+01 1odoA 408 2.98e+01 a.104.1.1 92783 1qcrA 446 3.00e+01 1be3A d.185.1.1,d.185.1.1 59025,59026 2bwbA 46 3.00e+01 1cem 363 3.04e+01 1cem a.102.1.2 18826 1i7kA 179 3.06e+01 1u9aA d.20.1.1 61889 1gxyA 226 3.11e+01 d.166.1.3 76380 1rztA 331 3.31e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 1dm5A 315 3.31e+01 1avc a.65.1.1 18186 1z3xA 238 3.32e+01 1x6zA 123 3.45e+01 2a9iA 113 3.52e+01 1yiiA 320 3.52e+01 1b8pA 329 3.53e+01 1bmdA c.2.1.5,d.162.1.1 30147,42114 1wj7A 104 3.55e+01 1w99A 558 3.58e+01 1kwfA 363 3.58e+01 a.102.1.2 73078 1j9bA 141 3.69e+01 c.47.1.12 66459 1h9fA 57 3.69e+01 1h9fA a.140.1.1 60826 1wr1B 58 3.74e+01 1p7tA 731 3.80e+01 c.1.13.1 94319 1f8nA 839 3.80e+01 1yge a.119.1.1,b.12.1.1 59703,59704 1bl0A 129 3.80e+01 1d5yA a.4.1.8,a.4.1.8 16053,16054 1pk5A 248 3.87e+01 a.123.1.1 88139 1wa5B 530 3.89e+01 1h38C 883 3.90e+01 e.8.1.3 76627 1otkA 249 3.92e+01 a.25.1.2 93521 1aeiA 315 3.92e+01 1avc a.65.1.1 18180 1rzrA 332 3.93e+01 1s8nA 205 3.95e+01 c.23.1.1 105374 1dzoA 123 3.99e+01 1dzoA d.24.1.1 38378 1jk0A 419 4.10e+01 a.25.1.2 63142 1c05A 159 4.12e+01 1c05A d.66.1.2 39559 1or7C 90 4.13e+01 a.180.1.1 87336 1yge 839 4.13e+01 1yge a.119.1.1,b.12.1.1 19234,23634 1jbgA 109 4.14e+01 a.6.1.3 66480 1ala 321 4.18e+01 1avc a.65.1.1 18153 1pmzA 86 4.20e+01 a.39.1.10 104195 1fgqA 839 4.25e+01 1yge a.119.1.1,b.12.1.1 59826,59827 1sqgA 429 4.27e+01 a.79.1.3,c.66.1.38 105912,105913 1uj6A 227 4.28e+01 c.124.1.4,d.58.40.1 107898,107899 1cuk 203 4.28e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1am4A 199 4.37e+01 1tx4A a.116.1.1 19100 1j7nA 776 4.41e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1e94F 449 4.46e+01 1do0A c.37.1.20 32443 1nal1 297 4.57e+01 1nal3 1s72W 154 4.62e+01 d.59.1.1 105342 1kekA 1231 4.63e+01 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 68524,68525,68526,68527,68528 1j3aA 142 4.69e+01 c.21.1.1 77070 2h1nA 567 4.70e+01 2bbhA 269 4.74e+01 1jj2V 154 4.76e+01 1ffkT d.59.1.1 63107 1rm6C 161 4.80e+01 1h38D 883 4.81e+01 e.8.1.3 76628 1qynA 153 4.84e+01 d.33.1.1 96597 1d1rA 116 4.85e+01 1d1rA d.64.1.1 39548 2fd5A 180 4.86e+01 2fuqA 747 4.88e+01 1aii 323 4.96e+01 1avc a.65.1.1 18150 1yf9A 171 5.01e+01 1vhcA 224 5.06e+01 c.1.10.1 100661 1noyA 388 5.08e+01 1clqA c.55.3.5 33713 1w2fA 276 5.09e+01 d.143.1.3 109125 1h0oA 390 5.11e+01 a.25.1.2 70845 1a63 130 5.16e+01 1a62 a.140.3.1,b.40.4.5 64710,64711 1xsm 390 5.16e+01 1xsm a.25.1.2 16804 1vl7A 157 5.20e+01 b.45.1.1 108732 1z91A 147 5.23e+01 1lk9A 448 5.26e+01 c.67.1.1 78057 1oj4A 283 5.27e+01 d.14.1.5,d.58.26.5 93083,93084 1f5aA 513 5.32e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39337,75835,75836 1bk5A 422 5.36e+01 1bk5A a.118.1.1 19130 1vrmA 325 5.39e+01 1ffkT 154 5.42e+01 1ffkT d.59.1.1 39527 1nal3 297 5.45e+01 1nal3 1q79A 514 5.47e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1gjjA 168 5.50e+01 a.140.1.1,a.140.1.1 83291,83292 1cii 602 5.56e+01 1cii f.1.1.1,h.4.3.1 43381,45787 1ybhA 590 5.56e+01 1jfvA 131 5.63e+01 c.44.1.1 66654 1akhA 61 5.68e+01 1akhA a.4.1.1 15980 1tx4A 198 5.68e+01 1tx4A a.116.1.1 19098 1o17A 345 5.71e+01 a.46.2.1,c.27.1.1 80765,80766 1a62 130 5.73e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 2bcqA 335 5.77e+01 1a8vA 121 5.78e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 1sep 261 5.79e+01 1oaa c.2.1.2 29830 1pzlA 237 5.80e+01 a.123.1.1 104393 1vqoW 154 5.94e+01 1oaa 259 6.03e+01 1oaa c.2.1.2 29829 2fiyA 309 6.10e+01 1bo9A 73 6.13e+01 1bo9A a.65.1.1 18146 1hl2A 297 6.17e+01 c.1.10.1 83581 1ej9A 563 6.20e+01 1a36A d.163.1.2,e.15.1.1 42172,43265 1x1nA 524 6.28e+01 2a5yA 204 6.31e+01 1axn 323 6.40e+01 1avc a.65.1.1 18149 1i1iP 681 6.40e+01 1i1iP d.92.1.5 40297 1xqoA 256 6.46e+01 1i17A 107 6.47e+01 1i17A d.6.1.1 61519 1s3jA 155 6.53e+01 a.4.5.28 98437 1aoa 275 6.54e+01 1aoa a.40.1.1,a.40.1.1 17396,17397 1gl2D 65 6.56e+01 h.1.15.1 65281 1y7yA 74 6.60e+01 1ix9A 205 6.66e+01 a.2.11.1,d.44.1.1 76899,76900 1jmsA 381 6.66e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1lwyA 324 6.72e+01 a.96.1.3,d.129.1.2 78285,78286 1i5sA 367 6.73e+01 1bg2 c.37.1.9 61822 1a35A 538 6.77e+01 1a36A d.163.1.2,e.15.1.1 42171,43264 1kr7A 110 6.77e+01 a.1.1.4 72890 1b10A 142 6.78e+01 1b10A d.6.1.1 37306 2a1iA 146 6.79e+01 1lxyA 409 6.79e+01 d.126.1.4 91154 1wurA 220 6.80e+01 1c8kA 842 6.86e+01 1a8i c.87.1.4 35491 1bk6A 422 6.87e+01 1bk5A a.118.1.1 19133 1avc 673 6.93e+01 1avc a.65.1.1,a.65.1.1 18178,18179 1l1zA 274 7.00e+01 a.156.1.2,b.113.1.1,g.39.1.8 75911,75912,75913 2es4D 332 7.03e+01 1qsaA 618 7.06e+01 1qsaA a.118.5.1,d.2.1.6 19182,36988 2fe8A 315 7.11e+01 1h38B 883 7.13e+01 e.8.1.3 76626 1k5dB 201 7.14e+01 b.55.1.3 68169 1ugpA 203 7.15e+01 d.149.1.1 107831 1jf8A 131 7.17e+01 c.44.1.1 66621 1ez0A 510 7.18e+01 1eyyA c.82.1.1 35385 1h1lA 481 7.20e+01 c.92.2.3 70851 3tmkA 216 7.22e+01 3tmkA c.37.1.1 31920 1hz6A 72 7.24e+01 2ptl d.15.7.1 61429 1kmiZ 214 7.26e+01 h.4.11.1 72752 1t3qA 168 7.27e+01 a.56.1.1,d.15.4.2 106367,106368 1nozA 388 7.31e+01 1clqA c.55.3.5 33715 1rcsA 105 7.31e+01 1jhgA a.4.12.1 19025 1nznA 126 7.34e+01 a.118.8.1 92382 2c4wA 176 7.36e+01 1edi 56 7.36e+01 1fc2C a.8.1.1 16349 2a6qA 86 7.42e+01 1ireA 204 7.44e+01 d.149.1.1 76769 1p2xA 159 7.44e+01 a.40.1.1 104062 1s9rA 410 7.45e+01 d.126.1.4 98758 2ccmA 191 7.48e+01 1g6nA 210 7.52e+01 2cgpA a.4.5.4,b.82.3.2 16100,28139 1q35A 320 7.64e+01 c.94.1.1 95661 2cgpA 210 7.74e+01 2cgpA a.4.5.4,b.82.3.2 16102,28141 1hcrA 52 7.77e+01 1hcrA a.4.1.2 16020 1fdyA 297 7.80e+01 1nal3 c.1.10.1 29071 1mugA 168 7.81e+01 1mugA c.18.1.2 31030 2gm5A 139 7.92e+01 1hq1A 105 7.97e+01 1dulA a.36.1.1 17120 1qlzA 210 7.98e+01 1b10A d.6.1.1 37309 1uruA 244 8.02e+01 h.4.14.1 99835 1ko9A 345 8.05e+01 a.96.1.3,d.129.1.2 68717,68718 1x6iA 91 8.08e+01 1eyyA 510 8.10e+01 1eyyA c.82.1.1 35389 2cvxA 888 8.12e+01 1mp1A 111 8.21e+01 a.188.1.1 91382 2cohA 202 8.22e+01 1sfxA 109 8.31e+01 a.4.5.50 105505 1nq7A 244 8.35e+01 a.123.1.1 92047 1ustA 93 8.38e+01 a.4.5.13 99884 1a8i 842 8.41e+01 1a8i c.87.1.4 35490 1k52A 72 8.42e+01 d.15.7.1 68148 1wgzA 510 8.43e+01 1y9bA 90 8.44e+01 1hw5A 210 8.48e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 2tmkA 216 8.52e+01 3tmkA c.37.1.1 31928 1l1eA 287 8.57e+01 c.66.1.18 73454 1dryA 324 8.60e+01 1drtA b.82.2.2 28128 1s28A 132 8.65e+01 d.198.1.1 105223 1m3qA 317 8.66e+01 a.96.1.3,d.129.1.2 91184,91185 1x3kA 152 8.74e+01 1ox3A 109 8.76e+01 h.1.17.1 93668 1b0pA 1231 8.79e+01 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 31831,31832,33104,34157,39003 2cujA 108 8.80e+01 1i1rB 181 8.82e+01 1i1rB a.26.1.1 61548 1muyA 225 8.89e+01 1mun a.96.1.2 18745 1l2tA 235 8.91e+01 c.37.1.12 73514 1h5uA 842 8.94e+01 1a8i c.87.1.4 60655 1ds1A 324 8.97e+01 1drtA b.82.2.2 28127 1qh8A 478 9.00e+01 1qguA c.92.2.3 35633