# List of top-scoring protein chains for t04-100-30-stride-ebghtl-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 1wmaA 276 9.15e-02 1regX 122 1.15e-01 1regX d.58.27.1 39406 1n5dA 288 2.40e-01 c.2.1.2 80030 1hu4A 288 2.40e-01 1hu4A 1t3gA 159 2.88e-01 2bd0A 244 6.15e-01 1k7kA 221 6.82e-01 c.51.4.1 72104 1vjoA 393 7.78e-01 c.67.1.3 100827 2b9dA 52 8.55e-01 1ht6A 405 1.07e+00 b.71.1.1,c.1.8.1 83629,83630 1jixA 351 1.15e+00 1c3jA c.87.1.1 63081 2ew8A 249 1.23e+00 1vig 71 1.48e+00 1vih d.51.1.1 38806 1n40A 396 1.50e+00 a.104.1.1 79977 1ey4A 149 1.55e+00 1snc b.40.1.1 24815 2bgkA 278 1.55e+00 1ijyA 130 1.65e+00 1ijxA a.141.1.1 62517 1s7zA 117 1.74e+00 a.159.3.1 98715 1c3jA 351 1.75e+00 1c3jA c.87.1.1 35459 1wiwA 290 2.05e+00 2f9dA 125 2.46e+00 1yf5L 254 2.62e+00 1r1dA 247 2.79e+00 c.69.1.29 96813 1z6kA 293 2.79e+00 2cw5A 255 3.05e+00 1v76A 96 3.17e+00 1z2wA 192 3.27e+00 12asA 330 3.35e+00 12asA d.104.1.1 40783 1o26A 232 3.58e+00 d.207.1.1 86566 1g61A 228 3.80e+00 1g61A d.126.1.1 41126 1mrzA 293 3.91e+00 b.43.5.1,c.26.1.3 91452,91453 2bh1A 250 4.84e+00 2bwnA 401 4.90e+00 1us8A 147 5.24e+00 c.37.1.12 99859 1vkrA 125 5.54e+00 c.44.2.1 108689 1xhkA 187 5.73e+00 1hdoA 206 6.22e+00 1he2A c.2.1.2 60965 2erfA 209 6.28e+00 2gaxA 135 7.24e+00 1pymA 295 7.35e+00 1pymA c.1.12.7 29308 3csuA 310 7.45e+00 3csuA c.78.1.1,c.78.1.1 35094,35095 2c36A 285 7.69e+00 1tqhA 247 7.71e+00 c.69.1.29 107225 1vcvA 226 7.74e+00 1wdtA 665 8.05e+00 2d4pA 141 8.06e+00 2ci1A 275 8.74e+00 1nmoA 247 9.00e+00 c.135.1.1 91980 1pieA 419 9.31e+00 d.14.1.5,d.58.26.7 94706,94707 1zymA 258 9.32e+00 1zymA a.60.10.1,c.8.1.2 18110,30705 1s1fA 406 9.34e+00 1ve3A 227 9.41e+00 1wimA 94 9.66e+00 1jmaA 290 9.68e+00 b.1.1.1 63177 1f0cA 305 9.73e+00 1c8oA e.1.1.1 42676 1vid 221 9.88e+00 1vid c.66.1.1 34178 1w24A 182 1.01e+01 1yr1A 119 1.04e+01 1z6oM 191 1.05e+01 1ugpA 203 1.06e+01 d.149.1.1 107831 1qrrA 394 1.07e+01 1qrrA c.2.1.2 29824 1zo0A 126 1.07e+01 1i24A 404 1.08e+01 c.2.1.2 83663 1vl8A 267 1.10e+01 c.2.1.2 108733 2ghrA 302 1.11e+01 1ireA 204 1.11e+01 d.149.1.1 76769 1ka8A 100 1.12e+01 a.4.5.20 72241 1snyA 267 1.13e+01 c.2.1.2 105833 1esgA 213 1.23e+01 1bam c.52.1.3 33286 1ws6A 171 1.23e+01 1gefA 123 1.27e+01 1gefA c.52.1.18 60465 1yj7A 171 1.32e+01 1w2wB 191 1.36e+01 1ysjA 404 1.36e+01 3seb 238 1.38e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1w97L 246 1.40e+01 1hz6A 72 1.42e+01 2ptl d.15.7.1 61429 1ash 150 1.43e+01 1ash a.1.1.2 15622 1gegA 256 1.45e+01 1ybvA c.2.1.2 29888 2a0fA 310 1.45e+01 1ihoA 283 1.48e+01 1ihoA c.26.1.4 62390 1dp4A 435 1.50e+01 1dp4A c.93.1.1 35710 1vrvA 101 1.52e+01 1sc3A 178 1.55e+01 c.17.1.1 105416 1xqaA 113 1.55e+01 1bmqA 167 1.57e+01 1pauA c.17.1.1 30998 1i5gA 144 1.58e+01 1ewxA c.47.1.10 61784 1gcqC 70 1.61e+01 1gcpA b.34.2.1 60436 1jae 471 1.70e+01 1smd b.71.1.1,c.1.8.1 27773,28760 1u5mA 73 1.71e+01 1e6pA 499 1.75e+01 1e15A b.72.2.1,c.1.8.5,d.26.3.1 59314,59315,59316 1yp5A 58 1.77e+01 1rwxA 178 1.78e+01 1bkcE 256 1.81e+01 1bkcA d.92.1.10 40333 1cbf 285 1.81e+01 1cbf c.90.1.1 35587 1m8jA 181 1.82e+01 c.26.1.3 84875 1t8sA 484 1.84e+01 c.56.2.1 106679 2bi7A 384 1.92e+01 1m93B 245 1.99e+01 1s5aA 150 2.01e+01 d.17.4.10 98525 1ej2A 181 2.05e+01 1f9aA c.26.1.3 59414 1pyoA 167 2.09e+01 c.17.1.1 95370 1vqvA 306 2.10e+01 1g5aA 628 2.12e+01 b.71.1.1,c.1.8.1 65152,65153 1udxA 416 2.13e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1goiA 499 2.14e+01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 1wd7A 261 2.18e+01 1k3tA 359 2.19e+01 c.2.1.3,d.81.1.1 72022,72023 1tkkA 366 2.19e+01 c.1.11.2,d.54.1.1 107089,107090 2axyA 73 2.20e+01 1kq6A 141 2.21e+01 d.189.1.1 91020 1xaoA 121 2.22e+01 1fsu 492 2.23e+01 1auk c.76.1.2 35032 1m3sA 186 2.35e+01 c.80.1.3 78573 1t5oA 351 2.39e+01 c.124.1.5 106459 1zip 217 2.46e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1n4qB 377 2.47e+01 a.102.4.3 91636 1x9gA 200 2.54e+01 c.33.1.3 109527 1fsz 372 2.54e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1gypA 358 2.55e+01 1dssG c.2.1.3,d.81.1.1 30004,39919 1yxmA 303 2.56e+01 1h30A 422 2.59e+01 b.29.1.4,b.29.1.4 76604,76605 1vh7A 265 2.61e+01 c.1.2.1 100646 2b5gA 171 2.64e+01 1nh1A 330 2.64e+01 e.45.1.1 91871 1ob8A 135 2.68e+01 2d83A 363 2.71e+01 1s2oA 244 2.71e+01 1msk 331 2.71e+01 1msk d.173.1.1 42495 1h1dA 221 2.73e+01 c.66.1.1 83452 2ddfA 257 2.74e+01 1jsdA 319 2.81e+01 b.19.1.2 63258 1t9kA 347 2.84e+01 c.124.1.5 106721 1k3eA 156 2.84e+01 d.198.1.1 68103 2bv5A 282 2.86e+01 1lwjA 441 2.90e+01 b.71.1.1,c.1.8.1 74303,74304 2b67A 204 2.96e+01 1zw8A 64 2.99e+01 1wcwA 261 3.01e+01 1q7zA 566 3.01e+01 c.1.21.2,c.1.26.1 96090,96091 1zxzA 197 3.02e+01 1k87A 669 3.02e+01 a.176.1.1,c.1.23.2 77286,77287 2gzqA 200 3.03e+01 1wxaA 116 3.03e+01 1w78A 422 3.06e+01 1d1qA 161 3.12e+01 1dg9A c.44.1.1 32642 7taa 478 3.12e+01 7taa b.71.1.1,c.1.8.1 27778,28765 1k8kB 394 3.13e+01 c.55.1.1 68307 1xrtA 467 3.20e+01 1gln 468 3.21e+01 1gln a.97.1.1,c.26.1.1 18752,31588 1x1tA 260 3.23e+01 1c5yB 253 3.28e+01 5ptp 1gj7B 253 3.30e+01 1avaA 403 3.31e+01 1jdc b.71.1.1,c.1.8.1 27797,28784 1sdjA 310 3.34e+01 d.21.1.2,d.21.1.2 98807,98808 7a3hA 303 3.35e+01 7a3hA c.1.8.3 28817 1amy 403 3.36e+01 1jdc b.71.1.1,c.1.8.1 27799,28786 1rpxA 230 3.39e+01 1rpxA c.1.2.2 28536 2aaa 484 3.39e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1ko7A 314 3.47e+01 c.98.2.1,c.91.1.2 72797,72798 1cxpA 104 3.49e+01 1d2vA a.93.1.2 18695 1d2vA 104 3.49e+01 1d2vA a.93.1.2 18697 1q6zA 528 3.49e+01 1x9iA 302 3.52e+01 1tzbA 302 3.53e+01 c.80.1.1 107470 1zin 217 3.53e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1ijxA 127 3.53e+01 1ijxA a.141.1.1 62511 2cdcA 366 3.59e+01 1xg5A 279 3.60e+01 1euaA 213 3.74e+01 1fwrA c.1.10.1 29155 1uouA 474 3.77e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 1zud2 66 3.77e+01 1r0pA 312 3.81e+01 d.144.1.7 96734 1n9eA 787 3.83e+01 b.30.2.1,d.17.2.1,d.17.2.1 91708,91709,91710 1uzmA 247 3.83e+01 1wmbA 260 3.83e+01 1lw6I 64 3.84e+01 d.40.1.1 74294 1o7kA 131 3.85e+01 d.189.1.1 81144 1wbhA 214 3.85e+01 2c0aA 214 3.85e+01 1ja9A 274 3.88e+01 c.2.1.2 62817 1zxcA 263 3.91e+01 1ypcI 64 3.92e+01 2sniI d.40.1.1 38570 1qyaA 307 3.93e+01 d.21.1.2,d.21.1.2 104653,104654 2b6cA 220 3.96e+01 1bfd 528 3.98e+01 1bfd c.31.1.3,c.36.1.5,c.36.1.9 31745,31801,31802 2acvA 463 3.98e+01 1x71A 178 4.03e+01 1c3hA 137 4.03e+01 b.22.1.1 90405 1g8fA 511 4.03e+01 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 1zy7A 403 4.07e+01 1jfzA 154 4.07e+01 a.149.1.1 66655 1k9sA 237 4.10e+01 c.56.2.1 68359 1kgyA 181 4.14e+01 b.18.1.4 72449 1hrhA 136 4.19e+01 1rthA c.55.3.1 33577 1fexA 59 4.29e+01 a.4.1.3 59803 1x89A 178 4.31e+01 1r6xA 395 4.38e+01 b.122.1.3,c.26.1.5 97167,97168 1quqB 121 4.39e+01 1quqB b.40.4.3 25305 1rvkA 382 4.45e+01 c.1.11.2,d.54.1.1 97928,97929 1gxrA 337 4.45e+01 b.69.4.1 70722 1ecpA 238 4.54e+01 1ecpA c.56.2.1 33775 1f24A 402 4.55e+01 1rom a.104.1.1 18953 1a8p 258 4.57e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1jfbA 404 4.59e+01 a.104.1.1 66624 1s0uA 408 4.66e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1nukA 183 4.67e+01 1nukA b.18.1.4 23721 1j77A 209 4.67e+01 1j77A a.132.1.2 62674 1qh4A 380 4.67e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 1wehA 171 4.68e+01 2fb0A 94 4.71e+01 1rf6A 427 4.72e+01 d.68.2.2 97366 1m1cA 680 4.73e+01 e.42.1.1 78395 1aie 31 4.74e+01 1aie a.53.1.1 17829 1u3nA 162 4.74e+01 1kv8A 216 4.76e+01 c.1.2.3 73054 3xis 387 4.77e+01 4xis c.1.15.3 29423 1q6oA 216 4.79e+01 c.1.2.3 95986 2fh7A 595 4.84e+01 1yhtA 367 4.84e+01 3bamA 213 4.87e+01 1bam c.52.1.3 33288 1evlA 401 4.88e+01 1qf6A c.51.1.1,d.104.1.1 33202,40751 2a1iA 146 4.91e+01 1f2tA 149 4.92e+01 1f2tA c.37.1.12 32373 1wdyA 285 4.92e+01 1jpmA 366 5.08e+01 c.1.11.2,d.54.1.1 67031,67032 1gxyA 226 5.13e+01 d.166.1.3 76380 1zy1B 197 5.16e+01 1pbyA 489 5.17e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 1gxjA 186 5.17e+01 d.215.1.1 70707 4xis 387 5.19e+01 4xis c.1.15.3 29421 1uzcA 71 5.19e+01 a.159.2.1 100222 1vqoX 92 5.23e+01 1bkcI 256 5.25e+01 1bkcA d.92.1.10 40334 1gcoA 261 5.26e+01 1ybvA c.2.1.2 29884 1fcyA 236 5.27e+01 2lbd a.123.1.1 19282 1oc2A 348 5.30e+01 c.2.1.2 92765 1r94A 118 5.30e+01 b.124.1.1 97251 1muwA 386 5.42e+01 c.1.15.3 79495 1geeA 261 5.42e+01 c.2.1.2 90509 1ruwA 69 5.44e+01 1o8xA 146 5.46e+01 c.47.1.10 86681 1pfsA 78 5.49e+01 1pfsA b.40.4.7 25391 1gjwA 637 5.57e+01 b.71.1.1,c.1.8.1 60582,60583 2fpoA 202 5.59e+01 2fiuA 99 5.68e+01 4eugA 229 5.69e+01 3eugA c.18.1.1 31019 1qk8A 146 5.69e+01 1ewxA c.47.1.10 33061 2anpA 291 5.73e+01 1s2wA 295 5.74e+01 c.1.12.7 98407 1jg8A 347 5.77e+01 1jg8A c.67.1.1 62946 1m6sA 347 5.77e+01 c.67.1.1 78701 1ass 159 5.83e+01 1a6dA c.8.5.2 30818 1nffA 260 5.87e+01 c.2.1.2 80457 2ez9A 603 5.89e+01 2cdnA 201 5.93e+01 1z57A 339 5.96e+01 2cg4A 152 5.98e+01 1kepA 348 6.01e+01 c.2.1.2 68536 2c1xA 456 6.01e+01 1z5nA 242 6.05e+01 2d1pB 119 6.06e+01 1edqA 540 6.09e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1j8mF 297 6.20e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1i37A 260 6.20e+01 1a28A a.123.1.1 61583 2fjbA 643 6.26e+01 1vbkA 307 6.28e+01 1jnrA 643 6.31e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1ctn 540 6.31e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21876,29005,38439 1hskA 326 6.31e+01 2mbr d.145.1.2,d.146.1.1 61241,61242 1j33A 335 6.31e+01 c.39.1.1 77069 2f06A 144 6.32e+01 1nu0A 138 6.32e+01 c.55.3.8 92165 1qqsA 174 6.36e+01 1nglA b.60.1.1 27143 1amp 291 6.37e+01 1amp c.56.5.4 33837 1lokA 291 6.37e+01 c.56.5.4 78122 1rifA 282 6.43e+01 c.37.1.23 97507 1rtqA 299 6.47e+01 c.56.5.4 97819 1kopA 223 6.48e+01 2cba b.74.1.1 27966 1n2eA 300 6.58e+01 c.26.1.4 85268 1utaA 81 6.68e+01 d.58.52.1 108029 830cA 168 6.69e+01 1ck7A d.92.1.11 40400 1qopB 396 6.70e+01 2tysB c.79.1.1 35270 1ro7A 259 6.74e+01 c.130.1.1 97667 2bvfA 459 6.77e+01 1bd8 156 6.77e+01 1bd8 d.211.1.1 19157 1uf3A 228 6.78e+01 d.159.1.6 99317 1m4jA 142 6.85e+01 d.109.1.2 78602 1oz9A 150 6.86e+01 d.92.1.15 93808 2sns 149 6.87e+01 1snc b.40.1.1 24860 1kafA 108 6.92e+01 d.199.1.1 68372 4uagA 437 6.97e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1o57A 291 6.99e+01 a.4.5.40,c.61.1.1 92483,92484 2tmnE 316 7.00e+01 1hyt d.92.1.2 59055 2a2pA 129 7.01e+01 2a84A 300 7.09e+01 1ub3A 220 7.11e+01 c.1.10.1 88395 2fliA 220 7.12e+01 2ez6A 221 7.14e+01 1jlvA 209 7.14e+01 a.45.1.1,c.47.1.5 71729,71730 1vc1A 110 7.14e+01 c.13.2.1 108493 2ax9A 256 7.16e+01 1bdb 277 7.16e+01 1bdb c.2.1.2 29874 1ek8A 185 7.18e+01 1ek8A d.67.3.1 59444 1lla 628 7.20e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18485,18496,21861 1p5hA 428 7.29e+01 c.123.1.1 87802 1xmbA 418 7.29e+01 1yrlA 491 7.29e+01 1cc1L 498 7.36e+01 1h2rL e.18.1.1 43301 1s95A 333 7.39e+01 d.159.1.3 105375 1va0A 239 7.47e+01 1vziA 126 7.51e+01 b.1.13.1,g.41.5.2 108967,108968 1r9wA 145 7.51e+01 d.89.1.2 97264 1tbmA 326 7.51e+01 a.211.1.2 106744 1vg8A 207 7.54e+01 c.37.1.8 108606 1v5aA 28 7.60e+01 2ax8A 256 7.61e+01 1j8yF 297 7.62e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1t7rA 269 7.67e+01 a.123.1.1 106635 1kfwA 435 7.68e+01 c.1.8.5,d.26.3.1 77376,77377 1ocsA 162 7.69e+01 d.189.1.1 92776 1b74A 254 7.71e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1y7bA 542 7.72e+01 1qlpA 394 7.76e+01 1ovaA e.1.1.1 42628 1ckiA 317 7.84e+01 1csn d.144.1.7 41660 8tlnE 316 7.86e+01 1hyt d.92.1.2 59075 1wdaA 670 7.89e+01 b.2.9.1,b.6.1.6,d.126.1.5 109243,109244,109245 1t71A 281 7.90e+01 1u5hA 273 8.11e+01 1ufyA 122 8.12e+01 d.79.1.2 88489 1jj2W 91 8.13e+01 1ffkU d.29.1.1 63108 1m3uA 264 8.16e+01 c.1.12.8 84784 1wt9B 123 8.16e+01 1rz3A 201 8.16e+01 c.37.1.6 98132 1fm4A 159 8.27e+01 1bv1 d.129.3.1 76186 1koqA 253 8.27e+01 2cba b.74.1.1 27964 2c7pA 327 8.32e+01 1s72X 92 8.38e+01 d.29.1.1 105343 1yk4A 52 8.46e+01 1j2jB 45 8.50e+01 a.7.8.1 84017 1zpxA 23 8.50e+01 1po5A 476 8.54e+01 a.104.1.1 94963 1ica 40 8.55e+01 1ica g.3.7.4 44173 1cewI 108 8.56e+01 1cewI d.17.1.2 37999 1jwiB 125 8.67e+01 d.169.1.1 67384 2f0aA 98 8.70e+01 1innA 166 8.71e+01 1j98A d.185.1.2 62608 1vddA 228 8.74e+01 e.49.1.1 108519 1l6oA 95 8.80e+01 b.36.1.1 84534 2dexX 671 8.84e+01 2flsA 132 8.86e+01 1ax4A 467 8.86e+01 1ax4A c.67.1.2 34391 1vjeA 166 8.88e+01 d.185.1.2 100807 1fmcA 255 8.91e+01 1cydA c.2.1.2 29856 2cs3A 93 8.97e+01