# List of top-scoring protein chains for t06-100-30-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 1y8qA 346 1.14e-01 1sgvA 316 2.03e-01 b.122.1.1,d.265.1.2 98858,98859 1zu0A 529 2.25e-01 2cybA 323 3.66e-01 1gy8A 397 3.82e-01 c.2.1.2 83376 1jg5A 83 4.54e-01 d.205.1.1 66666 1xgsA 295 6.52e-01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1w41A 101 7.45e-01 1a99A 344 9.27e-01 1pot c.94.1.1 35812 1ldjA 760 1.02e+00 a.4.5.34,a.118.17.1,e.40.1.1 73847,73848,73849 2fb0A 94 1.04e+00 1t0hB 224 1.16e+00 c.37.1.1 106208 2faoA 309 1.24e+00 1qo7A 394 1.25e+00 1qo7A c.69.1.11 34697 1xnzA 264 1.42e+00 2cvlA 124 1.51e+00 1r3eA 309 1.61e+00 b.122.1.1,d.265.1.2 96907,96908 1f1uA 323 1.62e+00 d.32.1.3,d.32.1.3 83200,83201 1n9lA 109 1.66e+00 d.110.3.6 85468 1k2eA 156 1.67e+00 d.113.1.1 72010 2ggcA 263 1.85e+00 1q5yA 85 1.98e+00 d.58.18.4 95950 1gefA 123 2.01e+00 1gefA c.52.1.18 60465 1e5dA 402 2.13e+00 1e5dA c.23.5.1,d.157.1.3 31208,42061 2mhr 118 2.17e+00 2mhr a.24.4.1 16581 2gtqA 867 2.20e+00 1wj9A 211 2.20e+00 1wm3A 72 2.41e+00 2d5cA 263 2.42e+00 1yqfA 203 2.50e+00 1n3lA 372 2.69e+00 c.26.1.1 79966 1m2oA 768 2.70e+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 1y60A 169 2.75e+00 1fukA 165 2.76e+00 1fukA c.37.1.19 32409 1u7iA 136 2.80e+00 d.32.1.7 107724 1o0xA 262 2.89e+00 d.127.1.1 80755 1ignA 246 3.20e+00 1ignA a.4.1.6,a.4.1.6 16048,16049 1va4A 279 3.24e+00 c.69.1.12 108458 1vd4A 62 3.27e+00 1t0fA 276 3.44e+00 1l7mA 211 3.52e+00 c.108.1.4 73664 1ww8A 439 3.72e+00 1gmlA 178 3.77e+00 c.8.5.2 70273 1z08A 170 3.83e+00 1yzhA 214 3.88e+00 1v7rA 186 3.93e+00 c.51.4.1 100482 1f1xA 322 4.12e+00 d.32.1.3,d.32.1.3 83208,83209 1vp8A 201 4.20e+00 1e0bA 68 4.24e+00 1e0bA b.34.13.2 37476 1t6aA 126 4.28e+00 d.129.8.1 106555 1fyhB 229 4.34e+00 1jrhI b.1.2.1,b.1.2.1 22055,22056 3il8 72 4.55e+00 1tvxA d.9.1.1 37356 1ml4A 308 4.75e+00 c.78.1.1,c.78.1.1 79255,79256 1nbwA 607 4.76e+00 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1iukA 140 4.91e+00 c.2.1.8 83712 1nf2A 268 4.97e+00 c.108.1.10 91849 1fjgE 162 5.06e+00 1pkp d.14.1.1,d.50.1.2 37553,38789 1v4pA 157 5.40e+00 1tqhA 247 5.56e+00 c.69.1.29 107225 1j3mA 129 5.79e+00 d.129.7.1 103836 1xwyA 264 5.92e+00 1mjhA 162 5.98e+00 1mjhA c.26.2.4 31639 1wvfA 520 6.11e+00 1u5mA 73 6.12e+00 2ctoA 93 6.25e+00 1ockA 412 6.26e+00 c.117.1.1 86802 2bkrA 212 6.30e+00 1fe0A 68 6.33e+00 1cc8A d.58.17.1 39345 1u6pA 56 6.89e+00 1j8rA 196 6.97e+00 1j8rA b.2.3.3 62745 2fhzA 109 7.17e+00 1bkpA 278 7.45e+00 1bkpA d.117.1.1 41029 2fi0A 81 7.56e+00 1vchA 175 7.65e+00 1qysA 106 7.82e+00 k.41.1.1 96603 2d1pA 140 8.13e+00 1o22A 170 8.25e+00 d.238.1.1 86557 2d8sA 80 8.65e+00 1srb 21 8.69e+00 j.28.1.1 46201 1qy1A 174 8.85e+00 b.60.1.1 96568 1w6uA 302 9.03e+00 1zndA 174 9.06e+00 2frnA 278 9.23e+00 2ew8A 249 9.33e+00 1sauA 115 9.51e+00 1hh1A 143 9.53e+00 1gefA c.52.1.18 61036 1yqzA 438 9.59e+00 1mkiA 330 9.66e+00 e.3.1.2 84994 1othA 321 9.78e+00 1othA c.78.1.1,c.78.1.1 35260,35261 2fulA 178 9.94e+00 1wosA 364 1.01e+01 b.44.2.1,d.250.1.1 109468,109469 1j6wA 175 1.02e+01 1j98A d.185.1.2 62663 1uekA 275 1.07e+01 d.14.1.5,d.58.26.5 88483,88484 1xocA 520 1.11e+01 1whi 122 1.13e+01 1whi b.39.1.1 24810 1rxyA 253 1.13e+01 c.56.2.1 98065 1vqoU 66 1.13e+01 1r31A 428 1.15e+01 d.58.20.1,d.179.1.1 96897,96898 1ogwA 76 1.16e+01 d.15.1.1 87001 1vf8A 377 1.17e+01 2b8tA 223 1.19e+01 1k8wA 327 1.21e+01 b.122.1.1,d.265.1.2 83094,90388 1jidA 128 1.22e+01 d.201.1.1 66735 1nzjA 298 1.24e+01 c.26.1.1 92377 2gupA 292 1.28e+01 1xreA 217 1.28e+01 1v6tA 255 1.30e+01 1y81A 138 1.34e+01 1nv8A 284 1.34e+01 c.66.1.30 86224 1l8bA 190 1.34e+01 d.86.1.1 73683 1wurA 220 1.35e+01 1oz9A 150 1.35e+01 d.92.1.15 93808 1gnkA 112 1.38e+01 2pii d.58.5.1 39073 1swvA 267 1.44e+01 2an3A 289 1.44e+01 1reqB 637 1.45e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1xuuA 349 1.45e+01 1np6A 174 1.49e+01 c.37.1.10 85954 1ihoA 283 1.49e+01 1ihoA c.26.1.4 62390 1rypL 212 1.51e+01 d.153.1.4 41880 1jm1A 204 1.52e+01 b.33.1.1 71745 2ewcA 126 1.55e+01 1ufkA 254 1.55e+01 c.66.1.39 99340 1wzcA 249 1.56e+01 1fviA 297 1.56e+01 1fviA b.40.4.6,d.142.2.1 25364,41578 2b18A 164 1.59e+01 1vjeA 166 1.59e+01 d.185.1.2 100807 3seb 238 1.61e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1wojA 214 1.62e+01 2f7fA 494 1.63e+01 1brwA 433 1.63e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 3chbD 104 1.63e+01 3chbD b.40.2.1 24970 1ispA 181 1.64e+01 c.69.1.18 76778 1jfrA 262 1.65e+01 1jfrA c.69.1.16 34724 1q67A 231 1.66e+01 b.55.1.7 95960 1wu7A 434 1.67e+01 1l1qA 186 1.69e+01 c.61.1.1 77653 1yj1A 76 1.69e+01 1n13B 113 1.72e+01 2bj7A 138 1.73e+01 1a9xA 1058 1.73e+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 2f5gA 133 1.79e+01 2fvhA 120 1.79e+01 1amf 233 1.80e+01 1wod c.94.1.1 35833 2b3yA 888 1.81e+01 1o4wA 147 1.82e+01 c.120.1.1 86629 1gqpA 221 1.82e+01 b.18.1.9 70372 1dzkA 157 1.87e+01 1obpA b.60.1.1 27096 1a3aA 148 1.88e+01 1a3aA d.112.1.1 40917 1z5yE 149 1.91e+01 1cvl 319 1.93e+01 1cvl c.69.1.18 34786 1vpqA 273 1.98e+01 1sqiA 393 2.00e+01 d.32.1.3,d.32.1.3 105914,105915 1u7lA 392 2.01e+01 1zmaA 118 2.04e+01 2b9eA 303 2.04e+01 1w85I 49 2.05e+01 2bgcA 238 2.06e+01 1hmt 132 2.06e+01 1hmt b.60.1.2 27169 2c31A 568 2.07e+01 1wv9A 94 2.08e+01 1wy5A 317 2.08e+01 1k8qA 377 2.09e+01 c.69.1.6 72177 2fb6A 117 2.09e+01 1opjA 293 2.09e+01 d.144.1.7 87230 1d0cA 444 2.10e+01 d.174.1.1 64769 1wcwA 261 2.11e+01 1ubkL 534 2.13e+01 e.18.1.1 88422 1c7nA 399 2.13e+01 1d2fA c.67.1.3 34413 1lkoA 191 2.14e+01 a.25.1.1,g.41.5.1 78063,78064 2bcqA 335 2.16e+01 1s68A 249 2.16e+01 d.142.2.4 98591 1e25A 282 2.18e+01 1e25A e.3.1.1 42731 1v25A 541 2.19e+01 e.23.1.1 108275 2a9sA 171 2.20e+01 2fblA 153 2.21e+01 1wd7A 261 2.22e+01 2bolA 314 2.23e+01 1ooeA 236 2.24e+01 c.2.1.2 87196 2cwkA 160 2.24e+01 1rdfA 267 2.26e+01 c.108.1.3 104884 1yovA 537 2.28e+01 1o5zA 442 2.28e+01 c.59.1.2,c.72.2.2 92530,92531 1ju3A 583 2.32e+01 b.18.1.13,c.69.1.21 67300,67301 1bn7A 294 2.37e+01 1bn6A c.69.1.8 34677 1ctqA 166 2.39e+01 1ctqA c.37.1.8 31965 1jetA 517 2.40e+01 1jevA c.94.1.1 35718 1edn 21 2.41e+01 j.28.1.1 46197 1vl5A 260 2.43e+01 c.66.1.41 108720 1h70A 255 2.43e+01 1h70A d.126.1.3 60711 1dl5A 317 2.43e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 2eryA 172 2.44e+01 1xkzA 255 2.45e+01 2f8aA 208 2.45e+01 1om4A 422 2.45e+01 d.174.1.1 87067 1sgwA 214 2.45e+01 c.37.1.12 105541 1djrD 103 2.48e+01 3chbD b.40.2.1 24865 1fkqA 124 2.50e+01 3lzt d.2.1.2 36601 1obbA 480 2.51e+01 c.2.1.5,d.162.1.2 86760,86761 1zljA 78 2.53e+01 1vkyA 347 2.57e+01 e.53.1.1 108696 2glfA 450 2.58e+01 1bdmA 327 2.59e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 1tc5A 194 2.61e+01 c.110.1.1 106752 1n8yC 608 2.62e+01 c.10.2.5,c.10.2.5,g.3.9.1,g.3.9.1 80314,80315,80316,80317 2d4pA 141 2.62e+01 1nddA 76 2.64e+01 1ubi d.15.1.1 37599 1kkoA 413 2.67e+01 c.1.11.2,d.54.1.1 68675,68676 1z02A 446 2.69e+01 1cs0A 1073 2.72e+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 1u8zA 168 2.72e+01 1o13A 136 2.74e+01 c.55.5.1 80762 1q9uA 130 2.76e+01 d.129.7.1 96314 1x9iA 302 2.77e+01 1t4hA 290 2.78e+01 d.144.1.7 106420 1z1zA 131 2.79e+01 2bv4A 113 2.84e+01 1ekeA 230 2.88e+01 1ekeA c.55.3.1 33572 1j27A 102 2.91e+01 d.58.50.1 90778 1oo0B 110 2.92e+01 d.58.7.1 87183 1jnrB 150 2.93e+01 d.58.1.5 66969 1wyuA 438 2.96e+01 1dj7A 117 2.96e+01 1dj7A g.36.1.1 44997 2fexA 188 2.99e+01 1jykA 254 3.00e+01 c.68.1.13 67458 2c1lA 358 3.00e+01 2bzgA 232 3.01e+01 1t6t1 118 3.03e+01 2bvcA 486 3.05e+01 1vk8A 106 3.07e+01 d.58.48.1 108636 1yp1A 202 3.07e+01 2f20A 240 3.09e+01 1yzyA 413 3.11e+01 2c1iA 431 3.13e+01 1jnyA 435 3.14e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1wuiL 534 3.16e+01 1p57A 114 3.18e+01 d.170.1.2 94125 1zlqA 502 3.19e+01 1xm3A 264 3.21e+01 1xb4A 202 3.21e+01 1q42A 201 3.21e+01 d.17.4.2 95776 1z5hA 780 3.22e+01 1zo2A 129 3.22e+01 1y0bA 197 3.28e+01 1ww9A 392 3.32e+01 1ey4A 149 3.37e+01 1snc b.40.1.1 24815 1zmoA 244 3.38e+01 1jbeA 128 3.39e+01 3chy c.23.1.1 62845 2f1kA 279 3.40e+01 2fxuA 375 3.42e+01 1t5bA 201 3.42e+01 c.23.5.3 106433 2ah5A 210 3.46e+01 1izmA 184 3.46e+01 a.199.1.1 90725 1p4fA 293 3.46e+01 d.144.1.7 104063 1qz5A 375 3.50e+01 c.55.1.1,c.55.1.1 96614,96615 1okhA 46 3.51e+01 g.13.1.1 93253 2adzA 178 3.51e+01 1heiA 451 3.51e+01 1heiA c.37.1.14,c.37.1.14 32463,32464 1pvvA 315 3.52e+01 c.78.1.1,c.78.1.1 95190,95191 1jg1A 235 3.52e+01 c.66.1.7 66661 1ksiA 642 3.54e+01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24408,38043,38044 1cqmA 101 3.56e+01 1ris d.58.14.1 39321 1njqA 39 3.57e+01 g.37.1.3 85822 1tkeA 224 3.58e+01 1p1lA 102 3.65e+01 d.58.5.2 87695 1ng7A 60 3.66e+01 a.178.1.1 85671 1b6a 478 3.66e+01 1bn5 a.4.5.25,d.127.1.1 16223,41160 1q77A 138 3.67e+01 c.26.2.4 96023 1hnjA 317 3.68e+01 1hn9A c.95.1.2,c.95.1.2 35969,35970 1wa3A 205 3.70e+01 1yemA 179 3.72e+01 1l7dA 384 3.72e+01 c.2.1.4,c.23.12.2 77774,77775 1i8aA 189 3.73e+01 1i82A b.1.9.2 61951 1whzA 70 3.77e+01 1ia8A 289 3.78e+01 1ia8A d.144.1.7 62112 2fwtA 125 3.82e+01 1ohvA 472 3.84e+01 c.67.1.4 93031 1r26A 125 3.84e+01 c.47.1.1 96847 2g9zA 348 3.84e+01 1m7gA 211 3.85e+01 c.37.1.4 78724 1b0uA 262 3.85e+01 1b0uA c.37.1.12 32370 1ytvA 366 3.87e+01 1npk 154 3.89e+01 1npk d.58.6.1 39099 1o1xA 155 3.90e+01 c.121.1.1 86553 1vloA 381 3.91e+01 b.44.2.1,d.250.1.1 108838,108839 1yspA 181 3.94e+01 1mp9A 198 3.94e+01 d.129.1.1,d.129.1.1 91385,91386 2cchB 260 3.96e+01 2czrA 226 3.99e+01 1qpcA 279 3.99e+01 1fgkA d.144.1.7 41685 1gu7A 364 4.01e+01 b.35.1.2,c.2.1.1 83321,83322 2acy 98 4.03e+01 2acy d.58.10.1 39298 1z9bA 135 4.03e+01 1jcfA 344 4.05e+01 c.55.1.1,c.55.1.1 62878,62879 2a7oA 112 4.05e+01 1x13A 401 4.05e+01 2gsfA 373 4.09e+01 1vlmA 219 4.13e+01 c.66.1.41 108836 1qwgA 251 4.14e+01 c.1.27.1 96473 1zhvA 134 4.14e+01 1zdzA 302 4.16e+01 1y8tA 324 4.18e+01 1zejA 293 4.18e+01 1o4vA 183 4.20e+01 c.23.8.1 86628 1xlqA 106 4.21e+01 1jmuB 666 4.21e+01 1naqA 112 4.21e+01 d.58.5.2 91761 1l7yA 94 4.27e+01 d.15.1.6 73676 2cglA 489 4.28e+01 1otkA 249 4.29e+01 a.25.1.2 93521 1qstA 160 4.29e+01 1yghA d.108.1.1 40804 1xtqA 177 4.30e+01 1s5aA 150 4.31e+01 d.17.4.10 98525 2f8lA 344 4.33e+01 1tfe 145 4.33e+01 1tfe d.43.1.1 38680 2d29A 387 4.35e+01 1vkiA 181 4.38e+01 d.116.1.1 108664 1yseA 141 4.38e+01 1r89A 437 4.39e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1vjqA 79 4.41e+01 k.43.1.1 100830 1bjaA 95 4.42e+01 1bjaA a.4.5.9 16122 1g8sA 230 4.43e+01 c.66.1.3 90507 2b1xA 470 4.45e+01 1io7A 368 4.45e+01 1f4tA a.104.1.1 18971 1odzA 386 4.46e+01 c.1.8.3 86889 1b24A 188 4.48e+01 1b24A d.95.2.1,d.95.2.1 40573,40574 1zowA 313 4.48e+01 1pa4A 116 4.53e+01 d.52.7.1 94409 1vhoA 346 4.58e+01 b.49.3.1,c.56.5.4 100694,100695 2fgeA 995 4.60e+01 2g30A 258 4.60e+01 1hqkA 154 4.62e+01 c.16.1.1 65902 1pcxA 810 4.64e+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 1ckmA 330 4.66e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 1ywyA 74 4.67e+01 1y80A 210 4.71e+01 1i3dA 146 4.72e+01 a.1.1.2 61587 2gwdA 449 4.75e+01 1nrjB 218 4.76e+01 c.37.1.8 86125 1bi6H 41 4.78e+01 1bi6H g.3.12.1 44340 2bswA 146 4.78e+01 1f7uA 607 4.79e+01 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 59673,59674,59675 1mtpB 43 4.79e+01 1atzA 189 4.79e+01 1atzA c.62.1.1 34132 1zbfA 142 4.82e+01 1xc3A 302 4.85e+01 1jyrA 96 4.86e+01 d.93.1.1 71969 1h75A 81 4.86e+01 1h75A c.47.1.1 60716 1wmuB 146 4.86e+01 a.1.1.2 109417 1ht6A 405 4.87e+01 b.71.1.1,c.1.8.1 83629,83630 1i6pA 220 4.88e+01 1ddzA c.53.2.1 61848 1cl1A 395 4.90e+01 1cl2A c.67.1.3 34395 1mz4A 137 4.91e+01 a.3.1.1 91496 1ivyA 452 4.96e+01 1ivyA c.69.1.5 34654 1dq3A 454 4.96e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1yixA 265 4.97e+01 1vpbA 451 4.97e+01 1ktbA 405 5.01e+01 b.71.1.1,c.1.8.1 72960,72961 1r1qA 100 5.06e+01 d.93.1.1 104763 1ub9A 100 5.10e+01 a.4.5.28 99159 1wqaA 455 5.10e+01 1pdkB 157 5.13e+01 1pdkB b.2.3.2 22427 1mxiA 160 5.14e+01 c.116.1.1 79646 1ny1A 240 5.14e+01 c.6.2.3 86395 1wtjA 343 5.14e+01 2gf9A 189 5.16e+01 1xqaA 113 5.18e+01 1s2oA 244 5.21e+01 1nr4A 71 5.23e+01 d.9.1.1 92077 2bh4X 134 5.24e+01 1jo0A 98 5.27e+01 d.68.4.1 77140 1fiqC 763 5.28e+01 1fiqC 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68372 2g7jA 124 8.78e+01 1f9zA 135 8.80e+01 1qipA d.32.1.1 38484 2c6qA 351 8.80e+01 1kte 105 8.80e+01 1kte c.47.1.1 32771 1dszB 85 8.81e+01 2nllB g.39.1.2 45108 1ta9A 450 8.84e+01 1uu1A 335 8.84e+01 c.67.1.1 99993 1u4bA 580 8.86e+01 c.55.3.5,e.8.1.1 107664,107665 2sak 121 8.91e+01 2sak d.15.5.1 37711 1xmpA 170 8.91e+01 1y1pA 342 8.92e+01 1kb9B 352 8.95e+01 d.185.1.1,d.185.1.1 77313,77314 1ynfA 458 8.95e+01 1f20A 435 8.97e+01 b.43.4.1,c.25.1.4 64932,64933 1y1nA 291 8.97e+01