# 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.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 1o20A 427 6.04e-75 c.82.1.1 86556 1ad3A 452 5.14e-59 1ad3A c.82.1.1 35335 1qi6A 475 1.14e-52 1euhA c.82.1.1 35373 1euhA 475 1.86e-52 1euhA c.82.1.1 35369 1bxsA 501 2.81e-52 1bpwA c.82.1.1 35357 1ag8A 499 3.10e-52 1bpwA c.82.1.1 35341 1a4sA 503 8.18e-52 1bpwA c.82.1.1 35361 1bpwA 503 1.19e-51 1bpwA c.82.1.1 35365 1o04A 500 1.75e-51 c.82.1.1 86508 1wndA 495 2.24e-49 1uzbA 516 7.20e-49 c.82.1.1 100220 2bjkA 516 8.88e-49 1uxtA 501 2.26e-42 c.82.1.1 108125 1ez0A 510 8.47e-28 1eyyA c.82.1.1 35385 1eyyA 510 1.27e-27 1eyyA c.82.1.1 35389 2c3zA 222 6.04e-02 2be3A 226 1.16e-01 1go3F 107 1.42e-01 a.60.8.2 65407 1dt9A 437 2.71e-01 1dt9A c.55.4.2,d.79.3.2,d.91.1.1 33738,39815,40257 8dfr 189 4.40e-01 1aoeA c.71.1.1 34895 1juk 248 4.45e-01 1a53 c.1.2.4 28567 6pfkA 319 4.76e-01 3pfk c.89.1.1 35583 1vjuA 309 4.83e-01 d.248.1.1 100835 3pfk 319 5.07e-01 3pfk c.89.1.1 35581 1a53 247 5.45e-01 1a53 c.1.2.4 28564 1j6oA 268 5.94e-01 c.1.9.12 77088 1igs 248 7.71e-01 1a53 c.1.2.4 28565 1kmvA 186 9.51e-01 c.71.1.1 72757 1k75A 434 9.59e-01 c.82.1.2 68253 1z0sA 278 1.20e+00 4pfk 319 1.41e+00 3pfk c.89.1.1 35582 1kaeA 434 1.47e+00 c.82.1.2 72247 1d4oA 184 2.03e+00 1d4oA c.31.1.4 31748 1z6fA 363 2.28e+00 1suwA 249 2.43e+00 e.52.1.1 106027 1nzoA 363 2.49e+00 b.105.1.1,e.3.1.1 92383,92384 1y5eA 169 2.73e+00 1zxxA 319 2.83e+00 2rveA 244 2.84e+00 1rvaA c.52.1.2 33283 1iy8A 267 3.11e+00 c.2.1.2 83774 1l0iA 78 3.36e+00 a.28.1.1 77643 1u7pA 164 3.37e+00 1zckA 154 4.10e+00 1rxdA 159 4.25e+00 1jigA 146 4.28e+00 a.25.1.1 71685 1wwkA 307 4.49e+00 1t8kA 77 4.55e+00 a.28.1.1 106666 1z8uA 102 5.12e+00 1kqyA 273 5.16e+00 c.1.8.5 68843 2gasA 307 5.59e+00 1kq8A 100 5.74e+00 a.4.5.14 68797 2c60A 111 5.77e+00 1hf2A 210 6.45e+00 1hf2A b.80.3.1,c.102.1.1 60992,60993 1x24A 180 6.54e+00 1gxjA 186 6.98e+00 d.215.1.1 70707 1oi7A 288 7.13e+00 c.2.1.8,c.23.4.1 87049,87050 1llnA 262 7.13e+00 d.165.1.1 84625 1kqzA 273 7.34e+00 c.1.8.5 68844 1ww9A 392 7.41e+00 1x42A 232 7.53e+00 1bu2A 229 7.59e+00 1bu2A a.74.1.1,a.74.1.1 18360,18361 2hvm 273 8.93e+00 1cnv c.1.8.5 28985 1itkA 731 9.15e+00 a.93.1.3,a.93.1.3 71417,71418 1nf2A 268 9.64e+00 c.108.1.10 91849 1chuA 540 9.65e+00 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 2bbhA 269 1.01e+01 1dl2A 511 1.01e+01 1dl2A a.102.2.1 18844 1wolA 122 1.04e+01 1ttzA 87 1.06e+01 c.47.1.1 107309 1vcsA 102 1.06e+01 1zbmA 280 1.07e+01 1xkuA 330 1.11e+01 1zclA 180 1.12e+01 1ugpA 203 1.13e+01 d.149.1.1 107831 1ss4A 153 1.19e+01 d.32.1.6 105976 1uw4B 248 1.20e+01 a.118.1.14 100072 2bhoA 130 1.20e+01 1y01A 102 1.22e+01 2br9A 234 1.23e+01 1r89A 437 1.30e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1uetA 437 1.35e+01 a.160.1.3,d.218.1.7,d.58.16.2 99272,99273,99274 1g61A 228 1.41e+01 1g61A d.126.1.1 41126 1pczA 191 1.46e+01 1ytbA d.129.1.1,d.129.1.1 41292,41293 2b5dX 528 1.54e+01 1p4fA 293 1.54e+01 d.144.1.7 104063 1g2iA 166 1.55e+01 1g2iA c.23.16.2 31438 2dkaA 544 1.59e+01 1nv8A 284 1.61e+01 c.66.1.30 86224 2fgeA 995 1.61e+01 2a61A 145 1.63e+01 1wloA 136 1.66e+01 1o5hA 214 1.67e+01 a.191.1.1 92497 1d3uA 181 1.69e+01 1ytbA d.129.1.1,d.129.1.1 41290,41291 2an1A 292 1.77e+01 2az2A 73 1.83e+01 1jclA 260 1.84e+01 c.1.10.1 66501 2bshA 125 1.84e+01 1xqiA 195 1.84e+01 2a5hA 416 1.93e+01 2bsjA 133 1.93e+01 1lj5A 379 1.93e+01 e.1.1.1 73928 2a6cA 83 1.95e+01 1v8gA 329 2.00e+01 a.46.2.1,c.27.1.1 100505,100506 1cjbA 231 2.00e+01 1qk3A c.61.1.1 34079 1xuuA 349 2.02e+01 1f9zA 135 2.03e+01 1qipA d.32.1.1 38484 1gw5M 435 2.07e+01 b.2.7.1,d.110.4.2 70631,70632 1ireA 204 2.10e+01 d.149.1.1 76769 1aisA 182 2.14e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1tjoA 182 2.18e+01 1jcjA 260 2.21e+01 c.1.10.1 66499 1hqkA 154 2.22e+01 c.16.1.1 65902 1w9hA 427 2.23e+01 1uqtA 482 2.27e+01 c.87.1.6 99794 1a3c 181 2.27e+01 1a3c c.61.1.1 34095 1r5pA 108 2.30e+01 c.47.1.15 97101 1dyr 206 2.35e+01 1aoeA c.71.1.1 34916 1gz0A 253 2.35e+01 c.116.1.1,d.79.3.3 76391,76392 2cxcA 144 2.40e+01 1uquA 482 2.44e+01 c.87.1.6 99796 1jnyA 435 2.51e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1b4aA 149 2.55e+01 1b4aA a.4.5.3,d.74.2.1 16088,39721 1fc2C 58 2.57e+01 1fc2C a.8.1.1 16345 8abp 306 2.65e+01 8abp c.93.1.1 35647 1pe0A 197 2.66e+01 c.23.16.2 88045 1nj4A 363 2.72e+01 b.105.1.1,e.3.1.1 80545,80546 1ny1A 240 2.73e+01 c.6.2.3 86395 1p1xA 260 2.83e+01 c.1.10.1 104060 1lox 662 2.84e+01 1lox a.119.1.2,b.12.1.1 19238,23638 2ab5A 269 2.85e+01 1zs3A 182 2.89e+01 2scuA 288 2.96e+01 2scuA c.2.1.8,c.23.4.1 30303,31131 1pv5A 264 3.04e+01 d.251.1.1 95150 1wgwA 99 3.05e+01 1gnkA 112 3.07e+01 2pii d.58.5.1 39073 1h5wA 309 3.09e+01 e.27.1.1 65635 1rw6A 210 3.09e+01 a.47.4.1 105113 1vzsA 76 3.15e+01 f.45.1.1 108972 1scuA 288 3.18e+01 2scuA c.2.1.8,c.23.4.1 30307,31135 1rlmB 271 3.19e+01 1pbwA 216 3.30e+01 1pbwA a.116.1.1 19103 1vbkA 307 3.34e+01 1kbqA 273 3.38e+01 c.23.5.3 68391 1rvaA 244 3.41e+01 1rvaA c.52.1.2 33240 1o5kA 306 3.41e+01 c.1.10.1 92504 1rpl 251 3.43e+01 1bpyA a.60.12.1,d.218.1.2 75933,75934 1eucA 311 3.50e+01 2scuA c.2.1.8,c.23.4.1 30311,31139 2b4aA 138 3.51e+01 1wmuA 141 3.55e+01 a.1.1.2 109416 1w0bA 102 3.55e+01 a.7.11.1 108985 1ymqA 261 3.56e+01 1vl4A 447 3.61e+01 d.283.1.1 108718 1o98A 511 3.62e+01 c.105.1.1,c.76.1.3 86684,86685 1abe 306 3.65e+01 8abp c.93.1.1 35648 1eduA 149 3.68e+01 1eduA a.118.9.1 19215 1bssA 244 3.72e+01 1rvaA c.52.1.2 33256 1b96A 244 3.75e+01 1rvaA c.52.1.2 33268 1xg4A 295 3.83e+01 1i5pA 633 3.87e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 1pea 385 3.91e+01 1pea c.93.1.1 35662 1xznA 179 3.95e+01 1jakA 512 3.96e+01 c.1.8.6,d.92.2.1 66472,66473 5abp 306 3.98e+01 8abp c.93.1.1 35651 1h3gA 601 3.98e+01 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1eonA 245 4.02e+01 1rvaA c.52.1.2 33238 1ryqA 69 4.03e+01 g.41.9.3 105126 2f06A 144 4.06e+01 1sx5A 244 4.06e+01 c.52.1.2 99023 1e3pA 757 4.08e+01 1e3hA a.4.9.1,b.40.4.5,d.14.1.4,d.14.1.4,d.52.3.1,d.101.1.1,d.101.1.1 16258,25328,37574,37575,38811,40697,40698 3ygsP 97 4.09e+01 3ygsP a.77.1.3 18435 1eudA 311 4.09e+01 2scuA c.2.1.8,c.23.4.1 30312,31140 1bap 306 4.11e+01 8abp c.93.1.1 35654 1t98A 287 4.22e+01 1okrA 123 4.23e+01 a.4.5.39 93269 1f60A 458 4.27e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1ra9 159 4.30e+01 1vdrA c.71.1.1 34820 2ddrA 306 4.37e+01 1z2lA 423 4.39e+01 1m2xA 223 4.46e+01 d.157.1.1 84764 1yt5A 258 4.48e+01 1b94A 244 4.49e+01 1rvaA c.52.1.2 33250 1bmbA 123 4.51e+01 1griA d.93.1.1 40466 1rzuA 485 4.51e+01 c.87.1.8 105140 1b97A 244 4.57e+01 1rvaA c.52.1.2 33252 1d4aA 273 4.57e+01 1d4aA c.23.5.3 31219 1draA 159 4.59e+01 1vdrA c.71.1.1 34831 2cwkA 160 4.59e+01 1vrvA 101 4.61e+01 1mojA 182 4.63e+01 a.25.1.1 91367 1xhbA 472 4.66e+01 1qbgA 272 4.67e+01 1d4aA c.23.5.3 31227 1xel 338 4.70e+01 1xel c.2.1.2 29786 1nonA 179 4.72e+01 c.61.1.1 103868 1hssA 124 4.76e+01 1bea a.52.1.2 17819 1ta8A 332 4.78e+01 1mdbA 539 4.82e+01 e.23.1.1 79008 1obr 326 4.82e+01 1aye c.56.5.2 33828 1vmbA 140 4.90e+01 1j7nA 776 5.00e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1yozA 116 5.02e+01 1qgjA 300 5.06e+01 1bgp a.93.1.1 18691 1hp4A 512 5.07e+01 1hp4A c.1.8.6,d.92.2.1 61111,61112 1xkfA 133 5.10e+01 1hskA 326 5.10e+01 2mbr d.145.1.2,d.146.1.1 61241,61242 1l5zA 155 5.12e+01 c.23.1.1 77722 1avu 181 5.12e+01 1wba b.42.4.1 25603 1uohA 226 5.13e+01 d.211.1.1 99690 256bA 106 5.17e+01 256bA a.24.3.1 16539 2udpA 338 5.19e+01 1xel c.2.1.2 29791 1bax 94 5.20e+01 1bax a.61.1.3 18133 1fsgA 233 5.21e+01 1qk3A c.61.1.1 34029 1rloA 271 5.21e+01 1ijgA 309 5.21e+01 1fouA e.27.1.1 62493 1im8A 244 5.26e+01 c.66.1.14 66212 1q5qA 259 5.26e+01 d.153.1.4 95904 2az0A 73 5.29e+01 1ejjA 511 5.33e+01 1ejjA c.105.1.1,c.76.1.3 59422,59423 1j7nB 776 5.33e+01 d.92.1.14,d.92.1.14,d.166.1.1 66412,66413,66414 1sqiA 393 5.33e+01 d.32.1.3,d.32.1.3 105914,105915 2a7wA 116 5.35e+01 1hp5A 512 5.36e+01 1hp4A c.1.8.6,d.92.2.1 61113,61114 1m3uA 264 5.38e+01 c.1.12.8 84784 1mkyA 439 5.38e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1aoeA 192 5.40e+01 1aoeA c.71.1.1 34923 1di0A 158 5.44e+01 1di0A c.16.1.1 30957 1dowA 205 5.45e+01 1dovA a.24.9.1 16626 1hh2P 344 5.49e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 65835,65836,65837,65838 1jvsA 400 5.49e+01 a.69.3.1,c.2.1.3,d.81.1.3 77187,77188,77189 1a0cA 438 5.55e+01 1a0cA c.1.15.3 29529 1brwA 433 5.56e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 2dhqA 146 5.57e+01 2dhqA c.23.13.1 31382 1rlmA 271 5.57e+01 1bo9A 73 5.61e+01 1bo9A a.65.1.1 18146 2gaxA 135 5.62e+01 2ah6A 208 5.64e+01 1zfpE 98 5.68e+01 1griA d.93.1.1 40465 1a7cA 379 5.68e+01 1sek e.1.1.1 42660 2d0iA 333 5.72e+01 1avaA 403 5.72e+01 1jdc b.71.1.1,c.1.8.1 27797,28784 1jmtA 104 5.73e+01 d.58.7.3 63180 1jksA 294 5.80e+01 d.144.1.7 71710 1h05A 146 5.86e+01 c.23.13.1 76433 1dhy 292 5.88e+01 1han d.32.1.3,d.32.1.3 38504,38505 1ad6 185 5.88e+01 1guxA a.74.1.3 18390 1lh0A 213 5.88e+01 c.61.1.1 73896 1k5hA 398 6.00e+01 a.69.3.1,c.2.1.3,d.81.1.3 68192,68193,68194 1eumA 165 6.01e+01 1eumA a.25.1.1 59507 1p5fA 189 6.05e+01 c.23.16.2 94142 1liaA 164 6.06e+01 1cpcA a.1.1.3 15661 1uesA 191 6.07e+01 a.2.11.1,d.44.1.1 107798,107799 1wy0A 342 6.09e+01 1kw3B 292 6.11e+01 d.32.1.3,d.32.1.3 77549,77550 1hy5A 136 6.13e+01 a.24.11.1 65955 1qk3A 233 6.13e+01 1qk3A c.61.1.1 34031 1ddsA 159 6.18e+01 1vdrA c.71.1.1 34858 1qapA 296 6.19e+01 1qpoA c.1.17.1,d.41.2.1 29559,38595 1dj7A 117 6.20e+01 1dj7A g.36.1.1 44997 1eljA 381 6.29e+01 4mbp c.94.1.1 35791 1dovA 181 6.29e+01 1dovA a.24.9.1 16627 4dfrA 159 6.31e+01 1vdrA c.71.1.1 34822 1kvs 338 6.33e+01 1xel c.2.1.2 29799 1y4tA 322 6.33e+01 1jadA 251 6.44e+01 h.4.10.1 66461 1aep 161 6.49e+01 1aep a.63.1.1 18139 1uzcA 71 6.50e+01 a.159.2.1 100222 6dfr 159 6.53e+01 1vdrA c.71.1.1 34874 1hd8A 363 6.56e+01 b.105.1.1,e.3.1.1 65803,65804 1j8yF 297 6.58e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1sg6A 393 6.59e+01 e.22.1.1 105522 1cx4A 305 6.63e+01 b.82.3.2,b.82.3.2 59099,59100 1wy1A 172 6.64e+01 1dc7A 124 6.66e+01 1dbwA c.23.1.1 31093 1n2zA 245 6.75e+01 c.92.2.2 79865 1yqtA 538 6.76e+01 1udb 338 6.78e+01 1xel c.2.1.2 29787 1neeA 138 6.81e+01 d.241.1.1,g.59.1.1 91841,91842 1amuA 563 6.86e+01 1amuA e.23.1.1 43351 1mw5A 187 6.95e+01 d.259.1.1 91477 1e4yA 214 6.95e+01 1zin c.37.1.1,g.41.2.1 31901,45181 1rvgA 305 7.00e+01 c.1.10.2 97920 2gk3A 256 7.04e+01 1e25A 282 7.07e+01 1e25A e.3.1.1 42731 2ax3A 502 7.13e+01 1xv5A 401 7.17e+01 1o2dA 371 7.18e+01 e.22.1.2 86591 1dmtA 696 7.29e+01 1dmtA d.92.1.4 40296 1qghA 156 7.32e+01 1qghA a.25.1.1 16728 1fi4A 416 7.32e+01 1fi4A d.14.1.5,d.58.26.2 59847,59848 1edi 56 7.45e+01 1fc2C a.8.1.1 16349 1h0aA 158 7.46e+01 a.118.9.1 76434 1e3hA 757 7.53e+01 1e3hA a.4.9.1,d.14.1.4,d.14.1.4,d.52.3.1,d.101.1.1,d.101.1.1 16257,37572,37573,38810,40695,40696 1xhkA 187 7.53e+01 1zzmA 259 7.55e+01 2rslA 140 7.55e+01 2rslA c.53.1.1 33345 1mkzA 172 7.58e+01 c.57.1.1 84998 1ugjA 141 7.58e+01 b.41.1.3 107826 2exnA 136 7.63e+01 1db2A 377 7.63e+01 1sek e.1.1.1 42672 1hl8A 449 7.64e+01 b.71.1.3,c.1.8.11 90646,90647 1wzcA 249 7.66e+01 2dpmA 284 7.70e+01 2dpmA c.66.1.28 34246 1aew 174 7.71e+01 2fha a.25.1.1 16676 1nqzA 194 7.76e+01 d.113.1.1 86077 2axhA 242 7.87e+01 1otgA 125 7.89e+01 1otgA d.80.1.2 39831 1i19A 561 7.91e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 1qkkA 155 7.91e+01 1dbwA c.23.1.1 31104 1igwA 434 7.93e+01 c.1.12.7 62370 1udc 338 7.97e+01 1xel c.2.1.2 29785 1dbrA 231 8.03e+01 1qk3A c.61.1.1 34041 1xkyA 301 8.03e+01 1c4kA 730 8.06e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 1cmkE 350 8.08e+01 1cdkA d.144.1.7 41623 1a9z 338 8.09e+01 1xel c.2.1.2 29795 2cfuA 658 8.10e+01 1pil 112 8.11e+01 2pii d.58.5.1 39072 1vk9A 151 8.14e+01 c.139.1.1 108640 1fq0A 213 8.17e+01 1fwrA c.1.10.1 29161 1rqjA 299 8.17e+01 a.128.1.1 97744 1vdmA 153 8.17e+01 1a9y 338 8.19e+01 1xel c.2.1.2 29789 1zbfA 142 8.20e+01 1bwzA 274 8.25e+01 1bwzA d.21.1.1,d.21.1.1 38337,38338 2pii 112 8.28e+01 2pii d.58.5.1 39071 1k07A 263 8.29e+01 d.157.1.1 77218 1fa8A 135 8.36e+01 1qipA d.32.1.1 38486 1dat 174 8.57e+01 2fha a.25.1.1 16677 1oi0A 124 8.59e+01 c.97.3.1 93045 2ae0X 345 8.64e+01 1m41A 380 8.67e+01 c.1.16.4 78595 2a4aA 281 8.68e+01 1ge9A 184 8.68e+01 1dd5A d.67.3.1 60463 1l8dA 112 8.70e+01 h.4.12.1 73687 1j8mF 297 8.82e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1ejbA 168 8.87e+01 1rvv1 c.16.1.1 59417 1g0sA 209 8.96e+01 1g0sA d.113.1.1 60187 1g7tA 594 8.99e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25714,25715,31033,32148 1hl9A 449 9.00e+01 b.71.1.3,c.1.8.11 90650,90651