# List of top-scoring protein chains for t06-100-30-bys-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 1y8qA 346 8.11e-03 1zu0A 529 9.26e-02 2cybA 323 1.04e-01 1a99A 344 1.20e-01 1pot c.94.1.1 35812 1wm3A 72 2.49e-01 1t0hB 224 4.05e-01 c.37.1.1 106208 1brwA 433 4.06e-01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 2d5cA 263 5.81e-01 1o0xA 262 5.85e-01 d.127.1.1 80755 1xgsA 295 6.15e-01 1bn5 a.4.5.25,d.127.1.1 16216,41153 2mhr 118 6.71e-01 2mhr a.24.4.1 16581 1gefA 123 6.96e-01 1gefA c.52.1.18 60465 1e5dA 402 7.41e-01 1e5dA c.23.5.1,d.157.1.3 31208,42061 1r3eA 309 7.89e-01 b.122.1.1,d.265.1.2 96907,96908 1ldjA 760 9.08e-01 a.4.5.34,a.118.17.1,e.40.1.1 73847,73848,73849 1yqfA 203 9.78e-01 2fb0A 94 9.84e-01 2czrA 226 9.99e-01 1j34B 123 1.10e+00 d.169.1.1 84049 2gtqA 867 1.11e+00 2faoA 309 1.22e+00 1n3lA 372 1.31e+00 c.26.1.1 79966 3il8 72 1.33e+00 1tvxA d.9.1.1 37356 1w41A 101 1.35e+00 1d0cA 444 1.37e+00 d.174.1.1 64769 1n9lA 109 1.41e+00 d.110.3.6 85468 1qo7A 394 1.41e+00 1qo7A c.69.1.11 34697 1j3mA 129 1.43e+00 d.129.7.1 103836 1sgvA 316 1.46e+00 b.122.1.1,d.265.1.2 98858,98859 2aqjA 538 1.49e+00 1xnzA 264 1.51e+00 2cvlA 124 1.59e+00 1jg5A 83 1.70e+00 d.205.1.1 66666 1u46A 291 1.74e+00 d.144.1.7 107656 2fi0A 81 1.88e+00 1vd4A 62 1.96e+00 1obbA 480 2.01e+00 c.2.1.5,d.162.1.2 86760,86761 1u7iA 136 2.07e+00 d.32.1.7 107724 1gmlA 178 2.21e+00 c.8.5.2 70273 1qpcA 279 2.32e+00 1fgkA d.144.1.7 41685 1hh1A 143 2.33e+00 1gefA c.52.1.18 61036 1vp8A 201 2.40e+00 1tqhA 247 2.46e+00 c.69.1.29 107225 1iukA 140 2.51e+00 c.2.1.8 83712 1whi 122 2.51e+00 1whi b.39.1.1 24810 1w6uA 302 2.64e+00 1q5yA 85 2.70e+00 d.58.18.4 95950 1mjhA 162 2.87e+00 1mjhA c.26.2.4 31639 1yemA 179 2.92e+00 2ew8A 249 2.98e+00 2ggcA 263 3.02e+00 1s68A 249 3.04e+00 d.142.2.4 98591 1gy8A 397 3.12e+00 c.2.1.2 83376 2fvhA 120 3.23e+00 1xocA 520 3.32e+00 1ml4A 308 3.35e+00 c.78.1.1,c.78.1.1 79255,79256 1va4A 279 3.56e+00 c.69.1.12 108458 1fukA 165 3.57e+00 1fukA c.37.1.19 32409 1o4vA 183 3.73e+00 c.23.8.1 86628 1ww8A 439 3.89e+00 1l7mA 211 3.93e+00 c.108.1.4 73664 1wurA 220 3.94e+00 1wosA 364 4.07e+00 b.44.2.1,d.250.1.1 109468,109469 2fulA 178 4.08e+00 1e0bA 68 4.09e+00 1e0bA b.34.13.2 37476 1xuuA 349 4.28e+00 2gcfA 73 4.44e+00 1k2eA 156 4.54e+00 d.113.1.1 72010 1vquA 374 4.62e+00 1vqoU 66 4.64e+00 1f1xA 322 4.74e+00 d.32.1.3,d.32.1.3 83208,83209 1m2oA 768 4.99e+00 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78480,78481,78482,78483,78484 1nzjA 298 5.14e+00 c.26.1.1 92377 1nbwA 607 5.26e+00 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1ctqA 166 5.35e+00 1ctqA c.37.1.8 31965 1q77A 138 5.42e+00 c.26.2.4 96023 2gi9A 56 5.43e+00 1np6A 174 5.49e+00 c.37.1.10 85954 2gsfA 373 5.75e+00 1vjeA 166 5.83e+00 d.185.1.2 100807 1jg1A 235 5.89e+00 c.66.1.7 66661 1b24A 188 6.09e+00 1b24A d.95.2.1,d.95.2.1 40573,40574 1me4A 215 6.27e+00 d.3.1.1 79023 2fblA 153 6.30e+00 1f1uA 323 6.37e+00 d.32.1.3,d.32.1.3 83200,83201 2bkrA 212 6.53e+00 1om4A 422 6.56e+00 d.174.1.1 87067 1qwgA 251 6.56e+00 c.1.27.1 96473 1sauA 115 6.62e+00 1v4pA 157 6.75e+00 1g0oA 283 6.76e+00 1ybvA c.2.1.2 60181 1qysA 106 6.79e+00 k.41.1.1 96603 1j8rA 196 6.88e+00 1j8rA b.2.3.3 62745 1zlqA 502 6.91e+00 2f20A 240 6.96e+00 2d4pA 141 7.10e+00 1t6aA 126 7.11e+00 d.129.8.1 106555 1h75A 81 7.13e+00 1h75A c.47.1.1 60716 2b0cA 206 7.20e+00 1o22A 170 7.28e+00 d.238.1.1 86557 2d8sA 80 7.43e+00 1mkiA 330 7.43e+00 e.3.1.2 84994 1wu7A 434 7.88e+00 1x9iA 302 7.90e+00 1jm1A 204 8.32e+00 b.33.1.1 71745 1ooeA 236 8.35e+00 c.2.1.2 87196 1htrB 329 8.40e+00 1smrA 1xqaA 113 8.47e+00 1nv8A 284 8.64e+00 c.66.1.30 86224 1v7rA 186 8.69e+00 c.51.4.1 100482 2eryA 172 8.79e+00 1wvfA 520 9.11e+00 1a9xA 1058 9.18e+00 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 1reqB 637 9.24e+00 1reqB c.1.19.1,c.23.6.1 29621,31248 1tfe 145 9.30e+00 1tfe d.43.1.1 38680 2b8tA 223 9.43e+00 1yj1A 76 9.45e+00 1n13B 113 9.52e+00 2d1pA 140 9.62e+00 1o4wA 147 9.62e+00 c.120.1.1 86629 1u8zA 168 9.62e+00 1fuiA 591 9.68e+00 1fuiA b.43.2.1,c.85.1.1 25674,35444 1ogwA 76 9.71e+00 d.15.1.1 87001 2a14A 263 9.74e+00 1jbeA 128 9.92e+00 3chy c.23.1.1 62845 1fe0A 68 9.99e+00 1cc8A d.58.17.1 39345 1ktbA 405 1.00e+01 b.71.1.1,c.1.8.1 72960,72961 2fwtA 125 1.02e+01 1gnkA 112 1.02e+01 2pii d.58.5.1 39073 1ht6A 405 1.02e+01 b.71.1.1,c.1.8.1 83629,83630 1wojA 214 1.02e+01 2c71A 216 1.03e+01 1oz9A 150 1.05e+01 d.92.1.15 93808 1yzhA 214 1.05e+01 1xreA 217 1.06e+01 1juvA 193 1.08e+01 c.71.1.1 90912 1dq3A 454 1.08e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1t6t1 118 1.08e+01 1ta0A 197 1.08e+01 c.108.1.16 106729 1k8wA 327 1.08e+01 b.122.1.1,d.265.1.2 83094,90388 1jo0A 98 1.10e+01 d.68.4.1 77140 3chbD 104 1.10e+01 3chbD b.40.2.1 24970 2bgcA 238 1.10e+01 1srb 21 1.12e+01 j.28.1.1 46201 1yzyA 413 1.13e+01 2frnA 278 1.14e+01 1tkeA 224 1.14e+01 1qd9A 124 1.15e+01 1qu9A d.79.1.1 39758 1yqdA 366 1.15e+01 1rxyA 253 1.16e+01 c.56.2.1 98065 1ytvA 366 1.17e+01 1p6oA 161 1.18e+01 c.97.1.2 94185 1nddA 76 1.18e+01 1ubi d.15.1.1 37599 1jnrB 150 1.21e+01 d.58.1.5 66969 1qnrA 344 1.21e+01 1qnoA c.1.8.3 28834 1fmb 104 1.24e+01 1fmb b.50.1.1 26777 1r89A 437 1.27e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 2bolA 314 1.27e+01 1li4A 432 1.29e+01 c.2.1.4,c.23.12.3 84616,84617 3tss 194 1.29e+01 1aw7A b.40.2.2,d.15.6.1 25160,37749 1z08A 170 1.29e+01 1nf2A 268 1.30e+01 c.108.1.10 91849 1xmpA 170 1.31e+01 2ctoA 93 1.32e+01 1wd7A 261 1.32e+01 1mlwA 301 1.32e+01 d.178.1.1 79289 1q9uA 130 1.35e+01 d.129.7.1 96314 1vf8A 377 1.37e+01 1jmuB 666 1.37e+01 1djrD 103 1.37e+01 3chbD b.40.2.1 24865 1z02A 446 1.39e+01 1rf6A 427 1.45e+01 d.68.2.2 97366 1e25A 282 1.46e+01 1e25A e.3.1.1 42731 1wv9A 94 1.46e+01 2fhzA 109 1.47e+01 1vchA 175 1.48e+01 1heiA 451 1.48e+01 1heiA c.37.1.14,c.37.1.14 32463,32464 1t4hA 290 1.48e+01 d.144.1.7 106420 2f5gA 133 1.52e+01 1ignA 246 1.52e+01 1ignA a.4.1.6,a.4.1.6 16048,16049 1wcwA 261 1.54e+01 1rypL 212 1.55e+01 d.153.1.4 41880 1g94A 448 1.55e+01 b.71.1.1,c.1.8.1 65169,65170 3seb 238 1.60e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1hywA 68 1.63e+01 1hywA d.186.1.1 61425 1m6kA 251 1.64e+01 e.3.1.1 78695 2f7fA 494 1.65e+01 2a7oA 112 1.65e+01 1r0rI 51 1.68e+01 g.68.1.1 96736 2fexA 188 1.69e+01 1d1gA 168 1.70e+01 1d1gA c.71.1.1 34889 1o1xA 155 1.71e+01 c.121.1.1 86553 2fb6A 117 1.71e+01 1yspA 181 1.75e+01 2ethA 154 1.78e+01 1nrwA 288 1.79e+01 c.108.1.10 86128 1v25A 541 1.79e+01 e.23.1.1 108275 1amf 233 1.79e+01 1wod c.94.1.1 35833 2gshA 414 1.79e+01 1vljA 407 1.83e+01 e.22.1.2 108832 1x74A 360 1.84e+01 1v93A 296 1.85e+01 c.1.23.1 100532 2ewcA 126 1.86e+01 2agaA 190 1.86e+01 1u11A 182 1.88e+01 c.23.8.1 107576 1jykA 254 1.89e+01 c.68.1.13 67458 1k38A 254 1.90e+01 e.3.1.1 84303 1z5yE 149 1.90e+01 1d3bA 75 1.91e+01 1d3bA b.38.1.1 24798 2c31A 568 1.91e+01 1yqzA 438 1.92e+01 1bdmA 327 1.94e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 1njqA 39 1.95e+01 g.37.1.3 85822 1dl5A 317 1.97e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1vk8A 106 1.98e+01 d.58.48.1 108636 2a9sA 171 2.01e+01 1jpaA 312 2.01e+01 d.144.1.7 67011 1xwyA 264 2.03e+01 1k20A 310 2.05e+01 c.107.1.1 68027 1v6tA 255 2.05e+01 1wa3A 205 2.08e+01 1cs0A 1073 2.09e+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 18558,31487,31673,31674,41518,41519 1a6jA 163 2.10e+01 1a6jA d.112.1.1 40915 1i3dA 146 2.11e+01 a.1.1.2 61587 1bkpA 278 2.11e+01 1bkpA d.117.1.1 41029 1mxiA 160 2.11e+01 c.116.1.1 79646 1edn 21 2.15e+01 j.28.1.1 46197 1w85I 49 2.19e+01 1opjA 293 2.20e+01 d.144.1.7 87230 1ksiA 642 2.22e+01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24408,38043,38044 2bswA 146 2.23e+01 1yt8A 539 2.23e+01 1zmaA 118 2.26e+01 1dxrC 336 2.27e+01 6prcC a.138.1.2 19670 1swvA 267 2.29e+01 1ny1A 240 2.30e+01 c.6.2.3 86395 1dd9A 338 2.30e+01 1dd9A e.13.1.1 43254 1f0xA 571 2.31e+01 1f0xA d.58.32.2,d.145.1.1 39483,41746 2f1kA 279 2.33e+01 2an3A 289 2.34e+01 1otkA 249 2.35e+01 a.25.1.2 93521 2gupA 292 2.36e+01 1qo2A 241 2.36e+01 1qo2A c.1.2.1 28533 2cglA 489 2.38e+01 1bi6H 41 2.38e+01 1bi6H g.3.12.1 44340 1zhvA 134 2.38e+01 2acy 98 2.38e+01 2acy d.58.10.1 39298 1i8aA 189 2.42e+01 1i82A b.1.9.2 61951 2culA 232 2.43e+01 1jetA 517 2.43e+01 1jevA c.94.1.1 35718 1m32A 366 2.43e+01 c.67.1.3 78508 1dzkA 157 2.48e+01 1obpA b.60.1.1 27096 1fkqA 124 2.49e+01 3lzt d.2.1.2 36601 1ejgA 46 2.51e+01 1cbn g.13.1.1 44618 1zljA 78 2.55e+01 1fviA 297 2.56e+01 1fviA b.40.4.6,d.142.2.1 25364,41578 2b3yA 888 2.57e+01 2g7jA 124 2.58e+01 1yseA 141 2.61e+01 1nh0A 99 2.62e+01 b.50.1.1 91869 1jnyA 435 2.65e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1j0pA 108 2.67e+01 a.138.1.1 90743 1ohvA 472 2.68e+01 c.67.1.4 93031 1vloA 381 2.68e+01 b.44.2.1,d.250.1.1 108838,108839 1othA 321 2.70e+01 1othA c.78.1.1,c.78.1.1 35260,35261 2glfA 450 2.74e+01 2fsjA 346 2.76e+01 1cvl 319 2.78e+01 1cvl c.69.1.18 34786 1xb4A 202 2.84e+01 1wyuA 438 2.86e+01 1f20A 435 2.89e+01 b.43.4.1,c.25.1.4 64932,64933 1tzyD 103 2.94e+01 a.22.1.1 107533 1wj9A 211 2.96e+01 2dbnA 461 2.97e+01 1t0fA 276 2.99e+01 2bj0A 203 3.00e+01 1y60A 169 3.00e+01 1q68B 29 3.01e+01 j.108.1.1 95963 1g8pA 350 3.02e+01 1g8pA c.37.1.20 60376 1i4uA 181 3.05e+01 b.60.1.1 61732 1qz5A 375 3.05e+01 c.55.1.1,c.55.1.1 96614,96615 1pcxA 810 3.05e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 94497,94498,94499,94500,94501 1u6pA 56 3.07e+01 1nkqA 259 3.07e+01 d.177.1.1 103862 1whzA 70 3.07e+01 1dj7A 117 3.09e+01 1dj7A g.36.1.1 44997 1wohA 305 3.16e+01 c.42.1.1 109446 1xv5A 401 3.16e+01 2c1iA 431 3.20e+01 1k4mA 213 3.21e+01 c.26.1.3 77258 1jidA 128 3.21e+01 d.201.1.1 66735 1u5mA 73 3.23e+01 2bu3A 254 3.23e+01 1wzcA 249 3.23e+01 2ah5A 210 3.24e+01 1wh0A 134 3.24e+01 1eejA 216 3.29e+01 1eejA c.47.1.9,d.17.3.1 33057,38071 1sr4B 261 3.29e+01 d.151.1.1 105949 1f4pA 147 3.30e+01 5nul c.23.5.1 59651 1yrrA 382 3.30e+01 1vjqA 79 3.31e+01 k.43.1.1 100830 1edg 380 3.32e+01 1edg c.1.8.3 28807 1jcfA 344 3.35e+01 c.55.1.1,c.55.1.1 62878,62879 1vlmA 219 3.36e+01 c.66.1.41 108836 2db3A 434 3.37e+01 1i1qB 192 3.40e+01 1qdlB c.23.16.1 61544 2bcgY 206 3.41e+01 1zk8A 183 3.42e+01 1qczA 169 3.42e+01 1qczA c.23.8.1 31276 1ja9A 274 3.46e+01 c.2.1.2 62817 2gs5A 198 3.46e+01 1cl1A 395 3.46e+01 1cl2A c.67.1.3 34395 1oaoC 729 3.47e+01 e.26.1.3 86746 1jfrA 262 3.48e+01 1jfrA c.69.1.16 34724 1wrvA 308 3.49e+01 2c4nA 250 3.56e+01 1ve0A 134 3.56e+01 1sq2N 113 3.63e+01 b.1.1.1 105881 1l8bA 190 3.65e+01 d.86.1.1 73683 2b9eA 303 3.65e+01 2f8aA 208 3.66e+01 2bvcA 486 3.71e+01 1r26A 125 3.76e+01 c.47.1.1 96847 1y9wA 140 3.77e+01 1yllA 200 3.77e+01 2igd 61 3.81e+01 2igd d.15.7.1 37821 1f5vA 240 3.83e+01 1bkjA d.90.1.1 40255 1n57A 291 3.85e+01 c.23.16.2 85328 2bh4X 134 3.88e+01 1vl5A 260 3.88e+01 c.66.1.41 108720 1ta3B 303 3.90e+01 c.1.8.3 106732 1dcfA 136 3.94e+01 1dcfA c.23.1.2 31124 1ynfA 458 3.94e+01 1a0tP 413 3.94e+01 1a0tP f.4.3.2 43794 1ockA 412 3.96e+01 c.117.1.1 86802 1bn7A 294 3.97e+01 1bn6A c.69.1.8 34677 1pj5A 830 3.98e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 2ae0X 345 3.98e+01 1wuiL 534 3.98e+01 1thfD 253 4.02e+01 1thfD c.1.2.1 28535 1ywyA 74 4.03e+01 1r3sA 367 4.04e+01 c.1.22.1 96963 1a12A 413 4.05e+01 1a12A b.69.5.1 27663 2f8lA 344 4.06e+01 2dcnA 311 4.09e+01 2ci9A 102 4.10e+01 1yarH 217 4.11e+01 4bcl 366 4.11e+01 4bcl b.75.1.1 27968 1yovA 537 4.15e+01 2bzgA 232 4.16e+01 1c9oA 66 4.20e+01 1mjc b.40.4.5 25325 2c2nA 339 4.22e+01 1j6wA 175 4.24e+01 1j98A d.185.1.2 62663 1xklA 273 4.25e+01 1byrA 155 4.25e+01 1byrA d.136.1.1 41450 1xkzA 255 4.25e+01 2rslA 140 4.31e+01 2rslA c.53.1.1 33345 1m8jA 181 4.35e+01 c.26.1.3 84875 1hdcA 253 4.35e+01 1e6wA c.2.1.2 29862 1h7zA 194 4.35e+01 1qhvA b.21.1.1 60733 1vkkA 154 4.36e+01 d.109.1.2 108669 5rubA 490 4.37e+01 1burA c.1.14.1,d.58.9.1 29382,39288 1vpbA 451 4.37e+01 1rijA 25 4.38e+01 k.32.1.1 104951 1ku0A 388 4.39e+01 c.69.1.18 72994 1s57A 153 4.39e+01 1oqqA 106 4.39e+01 d.15.4.1 93422 1hqkA 154 4.42e+01 c.16.1.1 65902 1mzbA 136 4.42e+01 a.4.5.42 91497 1n6zA 105 4.45e+01 d.263.1.1 85369 2au3A 407 4.46e+01 1wehA 171 4.53e+01 2cqeA 98 4.58e+01 1vhoA 346 4.60e+01 b.49.3.1,c.56.5.4 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