# List of top-scoring protein chains for t2k-100-30-near-backbone-11-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.soe.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 1wpnA 188 2.03e-14 c.107.1.1 114826 1i74A 309 2.50e-14 1i74A c.107.1.1 61867 2eb0A 307 1.53e-13 1k20A 310 5.98e-13 c.107.1.1 68027 1ir6A 424 1.77e-07 c.107.1.2 71342 2qb7A 397 6.02e-05 2qsfX 171 8.30e-03 1hv8A 367 5.57e-01 1hv8A c.37.1.19,c.37.1.19 32405,32406 2raqA 97 1.36e+00 2psdA 318 1.58e+00 1d4oA 184 1.66e+00 1d4oA c.31.1.4 31748 2i8lA 156 2.09e+00 2ivyA 101 2.51e+00 2p8tA 200 2.88e+00 1cuk 203 3.07e+00 1hjp 1cukA 203 3.07e+00 a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 2a5dA 175 3.10e+00 c.37.1.8 126172 1jeoA 180 3.73e+00 c.80.1.3 66611 1sazA 381 3.91e+00 c.55.1.2,c.55.1.2 118925,118926 1h4pA 408 3.93e+00 c.1.8.3 90617 1zfjA 491 3.98e+00 1ak5 c.1.5.1,d.37.1.1,d.37.1.1 28638,38540,38541 1fpzA 212 4.24e+00 1fpzA c.45.1.1 59976 2p0oA 372 4.37e+00 2cp8A 54 4.58e+00 a.5.2.1 130695 1vdmA 153 4.80e+00 c.61.1.1 119994 1eps 427 4.93e+00 1eps 2v7bA 529 5.13e+00 1f6bA 198 5.25e+00 c.37.1.8 64986 1lvaA 258 5.53e+00 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1r4wA 226 5.66e+00 c.47.1.13 97050 2e85A 159 5.83e+00 1tf0B 53 5.94e+00 a.8.1.2 106825 3c3pA 210 6.05e+00 1o5kA 306 6.46e+00 c.1.10.1 92504 2ejaA 338 6.48e+00 2d0oA 610 6.83e+00 c.8.6.1,c.55.1.6,c.55.1.6 131075,131076,131077 2jgzB 260 7.21e+00 1p5jA 372 7.79e+00 c.79.1.1 104067 2anuA 255 7.93e+00 c.6.3.1 127058 2f2lX 167 8.04e+00 d.118.1.1 132844 1o66A 275 8.45e+00 c.1.12.8 92547 1m2oB 190 9.25e+00 c.37.1.8 78485 2j5yA 61 9.26e+00 1hmcB 148 9.68e+00 1hmcB a.26.1.2 16868 1pgyA 47 9.72e+00 a.5.2.1 94696 1noyA 388 9.96e+00 1clqA c.55.3.5 33713 1sfxA 109 1.01e+01 a.4.5.50 105505 1hmcA 148 1.01e+01 1hmcB a.26.1.2 16867 1ro2A 216 1.05e+01 d.264.1.2 97665 1bywA 110 1.05e+01 1bywA d.110.3.6 40912 2dykA 161 1.10e+01 2bvwA 362 1.11e+01 1bvwA c.6.1.1 30666 1u5tA 233 1.13e+01 a.4.5.54,a.4.5.54 107684,107685 2qs7A 144 1.16e+01 1mj5A 302 1.17e+01 c.69.1.8 91285 1sxrA 183 1.18e+01 d.118.1.1 106101 1wzaA 488 1.21e+01 b.71.1.1,c.1.8.1 121489,121490 2dstA 131 1.23e+01 1fgkA 310 1.24e+01 1fgkA d.144.1.7 41693 1bvwA 360 1.25e+01 1bvwA c.6.1.1 30668 2prvA 153 1.25e+01 2c8eE 211 1.26e+01 2i3dA 249 1.27e+01 1vqoS 85 1.30e+01 d.12.1.1 120380 1ivnA 190 1.32e+01 c.23.10.5 83719 1egaA 301 1.36e+01 1egaA c.37.1.8,d.52.3.1 32150,38836 3ctdA 213 1.37e+01 1im5A 180 1.41e+01 c.33.1.3 66211 1pv1A 299 1.43e+01 c.69.1.34 111639 2a2cA 478 1.48e+01 2gduA 504 1.53e+01 b.71.1.1,c.1.8.1 135032,135033 2oe3A 114 1.54e+01 1maz 221 1.55e+01 1maz 1ro0A 216 1.56e+01 d.264.1.2 97664 2pbzA 320 1.57e+01 1va0A 239 1.61e+01 c.90.1.1 119899 2ij0C 118 1.64e+01 1lamA 484 1.65e+01 c.50.1.1,c.56.5.3 33166,33829 1lam 484 1.65e+01 1lam 1clc 639 1.66e+01 1clc 1sviA 195 1.66e+01 c.37.1.8 106048 1iz7A 295 1.66e+01 c.69.1.8 76982 2p0lA 288 1.68e+01 1clcA 639 1.69e+01 a.102.1.2,b.1.18.2 18835,21872 2a9kB 223 1.71e+01 d.166.1.1 126443 3b2nA 133 1.73e+01 1e58A 249 1.75e+01 1qhfA c.60.1.1 59262 1jr2A 286 1.82e+01 c.113.1.1 67111 1jp4A 308 1.83e+01 1jp4A e.7.1.1 63223 1jj2R 84 1.84e+01 1ffkP d.12.1.1 63103 2q8uA 336 1.88e+01 1ki9A 192 1.92e+01 c.37.1.1 84404 2d5cA 263 1.94e+01 2rkqA 169 1.96e+01 2jabA 136 1.97e+01 1cqwA 295 1.98e+01 1b6g c.69.1.8 34679 3brsA 289 1.99e+01 1r7aA 504 2.01e+01 b.71.1.1,c.1.8.1 97192,97193 1yrbA 262 2.03e+01 c.37.1.10 123915 1ps1A 337 2.07e+01 1ps1A a.128.1.4 19450 1bllE 488 2.08e+01 1lam c.50.1.1,c.56.5.3 33170,33833 1zp4A 304 2.08e+01 2hwkA 320 2.10e+01 1bn6A 294 2.16e+01 1bn6A c.69.1.8 34678 1z96A 40 2.17e+01 1qi9A 556 2.20e+01 1qhbA a.111.1.2 19053 2ca9A 148 2.22e+01 1y10A 407 2.25e+01 1bn7A 294 2.29e+01 1bn6A c.69.1.8 34677 2cmgA 262 2.34e+01 1t5iA 172 2.38e+01 c.37.1.19 106450 1cv2A 296 2.40e+01 1bn6A c.69.1.8 34680 1t2aA 375 2.41e+01 c.2.1.2 99078 2cmuA 342 2.42e+01 1o54A 277 2.46e+01 c.66.1.13 92482 1k1xA 659 2.50e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1bvzA 585 2.50e+01 1bvzA b.1.18.2,b.71.1.1,c.1.8.1 21856,27783,28770 1r8sA 164 2.51e+01 c.37.1.8 97247 3c5rA 137 2.52e+01 2yy3A 91 2.53e+01 1n0qA 93 2.55e+01 k.37.1.1 79754 2rdpA 150 2.55e+01 1i36A 264 2.58e+01 a.100.1.8,c.2.1.6 71108,71109 1o3yA 166 2.59e+01 c.37.1.8 86618 1yxyA 234 2.63e+01 c.1.2.5 124203 1yzxA 226 2.63e+01 3b9pA 297 2.63e+01 1u4bA 580 2.63e+01 c.55.3.5,e.8.1.1 107664,107665 2f2lA 167 2.64e+01 d.118.1.1 132843 1bfd 528 2.69e+01 1bfd 1je8A 82 2.69e+01 a.4.6.2 77108 2dznA 228 2.71e+01 3ciwA 348 2.74e+01 2j22A 148 2.75e+01 1ktbA 405 2.75e+01 b.71.1.1,c.1.8.1 72960,72961 1awcB 153 2.75e+01 1bd8 d.211.1.1 19156 1wsuA 124 2.77e+01 a.4.5.35,a.4.5.35 121245,121246 1ble 163 2.77e+01 1ble 1hurA 180 2.78e+01 1hurA c.37.1.8 32052 1iukA 140 2.80e+01 c.2.1.8 83712 1fqvA 336 2.80e+01 1fqvA a.158.1.1,c.10.1.3 19254,30856 1rxxA 421 2.85e+01 d.126.1.4 98061 1oc7A 364 2.90e+01 c.6.1.1 86794 3brqA 296 2.95e+01 1khtA 192 2.96e+01 c.37.1.1 84401 1wzlA 585 2.96e+01 b.1.18.2,b.71.1.1,c.1.8.1 121513,121514,121515 1wgnA 63 2.96e+01 a.5.2.1 114617 1t5jA 313 2.97e+01 a.209.1.1 99125 1bccJ 62 2.99e+01 1be3J f.23.14.1 43703 2eo2A 71 3.02e+01 2h5eA 529 3.02e+01 2g1iA 563 3.03e+01 1xhcA 367 3.05e+01 c.3.1.5,c.3.1.5,d.87.1.1 115292,115293,115294 2nydA 370 3.10e+01 2iuyA 342 3.15e+01 3b46A 447 3.16e+01 1v7zA 260 3.19e+01 c.125.1.1 100488 2hhvA 580 3.20e+01 c.55.3.5,e.8.1.1 136514,136515 2qzjA 136 3.20e+01 2o8gI 225 3.25e+01 1yckA 175 3.26e+01 d.118.1.1 122968 1lmeA 176 3.33e+01 d.167.1.1 84629 1uohA 226 3.36e+01 d.211.1.1 99690 1yaaA 412 3.36e+01 1ajsA c.67.1.1 34280 2e18A 257 3.37e+01 1ja9A 274 3.37e+01 c.2.1.2 62817 2hf2A 283 3.37e+01 2orwA 184 3.38e+01 2cjqA 720 3.38e+01 1xwl 580 3.40e+01 1xwl 1vkhA 273 3.46e+01 c.69.1.32 108662 1lwjA 441 3.51e+01 b.71.1.1,c.1.8.1 74303,74304 2rfmA 192 3.57e+01 2vd8A 391 3.62e+01 2cosA 54 3.72e+01 a.5.2.1 130683 1im4A 221 3.73e+01 e.8.1.7 62581 1vl5A 260 3.75e+01 c.66.1.41 108720 2bdpA 580 3.75e+01 1xwl c.55.3.5,e.8.1.1 33709,43002 1jaeA 471 3.77e+01 b.71.1.1,c.1.8.1 27773,28760 1o0sA 605 3.80e+01 c.2.1.7,c.58.1.3 86540,86541 1j3aA 142 3.84e+01 c.21.1.1 77070 2ze0A 555 3.85e+01 2bdqA 224 3.86e+01 2cxxA 190 3.87e+01 c.37.1.8 131013 2az4A 429 3.89e+01 d.157.1.10 127597 1q6zA 528 3.89e+01 c.31.1.3,c.36.1.5,c.36.1.9 111655,111656,111657 1k66A 149 3.91e+01 c.23.1.1 90941 2g3mA 693 3.94e+01 2ev1A 222 3.95e+01 2gptA 523 3.98e+01 1mgsA 73 4.01e+01 1tvxA d.9.1.1 37389 2yy8A 201 4.02e+01 1wlsA 328 4.03e+01 1ji2A 585 4.04e+01 b.1.18.2,b.71.1.1,c.1.8.1 71672,71673,71674 1y14A 187 4.06e+01 a.60.8.2 116322 1rlmA 271 4.19e+01 c.108.1.10 111860 1z5vA 474 4.25e+01 2j0fA 482 4.29e+01 1q3kA 259 4.31e+01 c.125.1.1 95693 1zp2A 235 4.37e+01 1jmsA 381 4.37e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1g7sA 594 4.38e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1ws0A 156 4.39e+01 1vimA 200 4.43e+01 c.80.1.3 100758 1a1vA 476 4.51e+01 1heiA c.37.1.14,c.37.1.14 32467,32468 1l3sA 580 4.57e+01 c.55.3.5,e.8.1.1 84521,84522 2vg0A 227 4.65e+01 2f20A 240 4.80e+01 d.303.1.1 132791 1tufA 434 4.80e+01 b.49.2.3,c.1.6.1 107335,107336 1xbfA 140 4.84e+01 d.273.1.1 109538 1kpgA 287 4.86e+01 c.66.1.18 68735 1ohtA 215 4.92e+01 d.118.1.1 87036 2cw6A 298 4.94e+01 2reb 352 4.98e+01 2reb 2rebA 352 4.98e+01 c.37.1.11,d.48.1.1 32282,38767 1q1hA 110 4.98e+01 a.4.5.41 95580 2iswA 323 5.02e+01 1ofuA 320 5.03e+01 c.32.1.1,d.79.2.1 86972,86973 1rvv1 154 5.03e+01 1rvv1 1q8fA 313 5.05e+01 c.70.1.1 96203 1dfmA 223 5.07e+01 1d2iA c.52.1.5 33295 1mw7A 240 5.08e+01 e.39.1.1 79557 1om4A 422 5.08e+01 d.174.1.1 87067 1uouA 474 5.08e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 1sflA 238 5.09e+01 c.1.10.1 112077 1m3uA 264 5.10e+01 c.1.12.8 84784 1kshA 186 5.11e+01 c.37.1.8 72914 2yvyA 278 5.13e+01 1nk4A 580 5.20e+01 c.55.3.5,e.8.1.1 91923,91924 1go4A 205 5.20e+01 d.135.1.1 70292 2dgdA 223 5.21e+01 2gj8A 172 5.22e+01 c.37.1.8 135270 1b74A 254 5.22e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1i1qA 520 5.23e+01 1qdlA d.161.1.1 61543 2yzhA 171 5.24e+01 1h9mA 145 5.30e+01 1h9jA b.40.6.2,b.40.6.2 60833,60834 2ilrA 264 5.40e+01 1p7gA 222 5.44e+01 a.2.11.1,d.44.1.1 94223,94224 1iknD 236 5.45e+01 1iknD d.211.1.1 19171 1kllA 130 5.49e+01 d.32.1.2 72720 2ix2A 249 5.55e+01 1souA 194 5.66e+01 c.124.1.6 105858 2jnsA 90 5.66e+01 2gagB 405 5.66e+01 2nzcA 86 5.71e+01 2ntiA 249 5.76e+01 2qedA 258 5.80e+01 2qtsA 438 5.82e+01 2hmcA 344 5.82e+01 1w30A 201 5.84e+01 c.61.1.1 114118 2d6yA 202 5.84e+01 a.4.1.9,a.121.1.1 131313,131314 2ei9A 240 5.86e+01 1fsoA 139 5.87e+01 1rhoA b.1.18.8 60007 2hnxA 136 5.91e+01 b.60.1.2 136633 1s3jA 155 5.94e+01 a.4.5.28 98437 2b6hA 192 5.95e+01 c.37.1.8 127994 1kkcA 221 5.97e+01 a.2.11.1,d.44.1.1 68660,68661 2d59A 144 5.99e+01 c.2.1.8 131266 1bs4A 168 6.00e+01 1bs4A d.167.1.1 42287 1j3nA 408 6.04e+01 c.95.1.1,c.95.1.1 84074,84075 1m6yA 301 6.06e+01 a.60.13.1,c.66.1.23 78716,78717 2o5hA 136 6.07e+01 2q8nA 460 6.09e+01 1hf2A 210 6.15e+01 1hf2A b.80.3.1,c.102.1.1 60992,60993 1rkuA 206 6.17e+01 c.108.1.11 97627 3bg2A 444 6.17e+01 1pydA 556 6.26e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31735,31773,31774 2pa8L 92 6.27e+01 2a9gA 418 6.31e+01 d.126.1.4 126435 1sr9A 644 6.37e+01 a.5.7.1,c.1.10.5,d.270.1.1 105960,105961,105962 2ondA 308 6.38e+01 1zxzA 197 6.42e+01 1x3mA 415 6.45e+01 c.55.1.2,c.55.1.2 121664,121665 2pc8A 400 6.50e+01 1b85A 351 6.52e+01 1arv a.93.1.1 18581 1vmeA 410 6.56e+01 c.23.5.1,d.157.1.3 108893,108894 2dkyA 91 6.57e+01 3bgeA 201 6.59e+01 1nrzA 164 6.63e+01 c.38.1.1 86131 3bwaA 276 6.65e+01 2p5iA 288 6.65e+01 1twiA 434 6.69e+01 b.49.2.3,c.1.6.1 107399,107400 1cz1A 394 6.73e+01 1cz1A c.1.8.3 28839 2vktA 289 6.74e+01 1zjjA 263 6.77e+01 1qaxA 428 6.77e+01 1qaxA d.58.20.1,d.179.1.1 39376,42597 1aj2A 282 6.80e+01 c.1.21.1 29665 1aj2 282 6.80e+01 1aj2 1x3lA 440 6.80e+01 2hk0A 309 6.88e+01 2c4nA 250 6.91e+01 c.108.1.14 129837 1ppjJ 62 7.02e+01 f.23.14.1 104266 1ru8A 232 7.06e+01 c.26.2.1 97849 1q0rA 298 7.09e+01 c.69.1.28 95508 1y9iA 178 7.10e+01 a.195.1.1 116586 1ve1A 304 7.11e+01 c.79.1.1 120007 1s5lU 134 7.18e+01 1af3 196 7.19e+01 1maz 1k3zD 282 7.21e+01 d.211.1.1 77251 1xfjA 261 7.24e+01 d.194.1.2 109585 2a7mA 250 7.25e+01 1mw9X 592 7.26e+01 e.10.1.1 91480 1ltm 320 7.32e+01 1ltm 1csh 435 7.34e+01 1csh 1cshA 435 7.34e+01 a.103.1.1 18880 1snyA 267 7.35e+01 c.2.1.2 105833 2astB 336 7.41e+01 a.158.1.1,c.10.1.3 127273,127274 1nzjA 298 7.42e+01 c.26.1.1 92377 1i8fA 81 7.44e+01 1i8fA b.38.1.1 61959 2jgqA 233 7.51e+01 1t46A 313 7.53e+01 d.144.1.7 106397 1heiA 451 7.56e+01 1heiA c.37.1.14,c.37.1.14 32463,32464 2vfxA 206 7.63e+01 1yyaA 250 7.66e+01 1booA 323 7.66e+01 1booA c.66.1.11 34248 1vcvA 226 7.68e+01 c.1.10.1 119988 1oy3D 282 7.71e+01 d.211.1.1 87554 3b2tA 311 7.72e+01 2obwA 258 7.78e+01 1ls1A 295 7.81e+01 a.24.13.1,c.37.1.10 78170,78171 1bg6 359 7.82e+01 1bg6 1kyqA 274 7.84e+01 c.2.1.11,e.37.1.1 73281,73282 2mysB 166 7.87e+01 1wdcB a.39.1.5 17308 1g7nA 131 7.91e+01 b.60.1.2 83274 1bd8 156 7.93e+01 1bd8 2gopA 347 7.97e+01 2pcsA 162 7.99e+01