# List of top-scoring protein chains for t2k-100-30-dssp-ehl2-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 1bg2 325 5.78e-56 1bg2 c.37.1.9 32189 1i5sA 367 1.09e-53 1bg2 c.37.1.9 61822 1ii6A 368 6.43e-53 1bg2 c.37.1.9 62413 1q0bA 367 1.61e-51 c.37.1.9 95502 1x88A 359 1.64e-51 1i6iA 366 2.14e-51 1bg2 c.37.1.9 61844 1vfvA 366 1.28e-49 c.37.1.9 108592 3kar 346 2.22e-49 1bg2 c.37.1.9 32198 1cz7A 406 2.56e-48 1bg2 c.37.1.9 32194 1f9vA 347 3.56e-48 1bg2 c.37.1.9 59745 1ry6A 360 1.55e-43 c.37.1.9 98090 2kinA 238 2.28e-39 1bg2 c.37.1.9 32190 2kinB 100 1.41e-14 3kinB 3kinB 117 2.17e-14 3kinB 2akaB 299 1.77e-01 1fw9A 164 9.59e-01 1fw9A d.190.1.1 60059 1tt8A 164 9.59e-01 1p9rA 418 1.70e+00 c.37.1.11 94399 1l8qA 324 1.82e+00 a.4.12.2,c.37.1.20 77809,77810 1f60A 458 2.10e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1d2mA 665 2.34e+00 1d2mA c.37.1.19,c.37.1.19 32417,32418 1odfA 290 2.68e+00 c.37.1.6 92782 1tljA 213 3.74e+00 d.282.1.1 107126 1vraB 215 5.26e+00 1zk7A 467 5.40e+00 1gvnB 287 5.45e+00 c.37.1.21 76354 1jx2B 315 6.25e+00 c.37.1.8 67404 2azqA 311 6.35e+00 1c4oA 664 6.94e+00 1d2mA c.37.1.19,c.37.1.19 32415,32416 1wdtA 665 6.97e+00 1yagG 125 8.03e+00 1d0nA d.109.1.1 40846 1nm1G 125 8.04e+00 d.109.1.1 80653 1d4xG 126 8.09e+00 1d0nA d.109.1.1 59109 2ghpA 292 8.46e+00 1udsA 255 8.81e+00 d.14.1.4,d.101.1.1 99219,99220 1wf3A 301 8.94e+00 2aq4A 434 9.31e+00 2afwA 329 9.47e+00 1bucA 383 9.86e+00 3mdeA a.29.3.1,e.6.1.1 16590,42851 2ao0A 324 1.00e+01 1cr5A 189 1.01e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1bmlC 362 1.04e+01 1bmlC d.15.5.1,d.15.5.1,d.15.5.1 37729,37730,37731 1vnc 609 1.08e+01 1vns a.111.1.3 19065 1f3iA 481 1.10e+01 1b7eA 2fsjA 346 1.11e+01 1hv8A 367 1.12e+01 1hv8A c.37.1.19,c.37.1.19 32405,32406 1thtA 305 1.12e+01 1thtA c.69.1.13 34711 1ng1 294 1.13e+01 1ng1 a.24.13.1,c.37.1.10 16961,32272 1ebdA 455 1.17e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 1vns 609 1.18e+01 1vns a.111.1.3 19061 1ex2A 189 1.20e+01 1ex2A c.51.4.2 33225 1nb8A 353 1.22e+01 d.3.1.9 80385 1esgA 213 1.22e+01 1bam c.52.1.3 33286 1tmxA 293 1.25e+01 1j8mF 297 1.28e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1jwyB 315 1.29e+01 c.37.1.8 67401 2bf6A 449 1.29e+01 1y8cA 246 1.39e+01 2bwvA 440 1.42e+01 1pzgA 331 1.43e+01 c.2.1.5,d.162.1.1 95425,95426 1ffh 294 1.44e+01 1ng1 a.24.13.1,c.37.1.10 16960,32271 1ls1A 295 1.47e+01 a.24.13.1,c.37.1.10 78170,78171 2b3yA 888 1.51e+01 1i6pA 220 1.53e+01 1ddzA c.53.2.1 61848 1htjF 210 1.54e+01 1htjF a.91.1.1 61254 1wl9A 440 1.54e+01 3bamB 213 1.54e+01 1bam c.52.1.3 33289 1muhA 481 1.59e+01 c.55.3.4 79485 1a16 440 1.61e+01 1az9 c.55.2.1,d.127.1.1 33548,41165 1jpnA 296 1.66e+01 a.24.13.1,c.37.1.10 67039,67040 3bamA 213 1.70e+01 1bam c.52.1.3 33288 1ka1A 357 1.72e+01 e.7.1.1 68369 1qgxA 357 1.72e+01 1qgxA e.7.1.1 42973 1f42A 306 1.73e+01 1f42A b.1.1.4,b.1.2.1,b.1.2.1 59636,59637,59638 1g6q2 328 1.73e+01 1g6q2 2bycA 137 1.75e+01 1bglA 1023 1.76e+01 1bglA b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 22097,22098,23734,24358,28857 2ng1 293 1.77e+01 1ng1 a.24.13.1,c.37.1.10 16962,32273 1aerA 205 1.87e+01 1aerA d.166.1.1 42249 1x38A 602 1.89e+01 1iexA 605 1.91e+01 c.1.8.7,c.23.11.1 66127,66128 1yuwA 554 1.95e+01 2bh9A 489 1.95e+01 1xwiA 322 1.96e+01 1jz8A 1023 1.98e+01 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 67830,67831,67832,67833,67834 1t0gA 109 2.01e+01 d.120.1.2 99063 1dp0A 1023 2.05e+01 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 22073,22074,23722,24346,28845 2fytA 340 2.05e+01 1ex1A 605 2.06e+01 1ex1A c.1.8.7,c.23.11.1 29013,31347 1d2gA 292 2.09e+01 1xvaA c.66.1.5 34187 2a9sA 171 2.14e+01 1e58A 249 2.20e+01 1qhfA c.60.1.1 59262 1m2oB 190 2.21e+01 c.37.1.8 78485 2bd0A 244 2.21e+01 1h2vZ 156 2.30e+01 d.58.7.1 76595 1h6kZ 98 2.39e+01 d.58.7.1 60686 1qx4A 274 2.44e+01 b.43.4.2,c.25.1.1 104624,104625 1h6kX 97 2.49e+01 d.58.7.1 60684 1fnmA 691 2.49e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 25709,32144,37546,39302,39303 1g291 372 2.49e+01 1g291 1azwA 313 2.51e+01 1qtrA c.69.1.7 34658 1inlA 296 2.52e+01 c.66.1.17 66220 1u2eA 289 2.52e+01 1vz6A 393 2.54e+01 d.154.1.2 108949 5ukdA 194 2.55e+01 1zin c.37.1.1 31851 2fsrA 195 2.58e+01 1yobA 179 2.74e+01 1qf9A 194 2.76e+01 1zin c.37.1.1 31848 1v3eA 431 2.85e+01 b.68.1.1 100287 2a5yB 549 3.05e+01 1wm1A 317 3.06e+01 c.69.1.7 109405 1f06A 320 3.09e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 1jq3A 296 3.11e+01 c.66.1.17 67079 1e19A 314 3.13e+01 1b7bA c.73.1.1 34967 1ca4A 168 3.14e+01 1d0aB b.8.1.1,h.1.2.1 23238,45445 1xkwA 665 3.20e+01 1fg7A 356 3.25e+01 1gewA c.67.1.1 59819 1az9 457 3.25e+01 1az9 c.55.2.1,d.127.1.1 33547,41164 1cf1A 404 3.33e+01 1cf1A b.1.18.11,b.1.18.11 21907,21908 1ifrA 121 3.37e+01 b.1.16.1 71203 1j03A 102 3.38e+01 d.120.1.2 90733 1qyiA 384 3.38e+01 c.108.1.13 96595 1q5qA 259 3.40e+01 d.153.1.4 95904 1um8A 376 3.43e+01 c.37.1.20 99580 1r6lA 239 3.43e+01 d.14.1.4,d.101.1.1 97153,97154 1dapA 320 3.44e+01 1dapA c.2.1.3,d.81.1.3 30053,39968 1jmxA 494 3.47e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66901,66902,66903,66904,66905 1xtzA 264 3.66e+01 2aynA 404 3.66e+01 1jhfA 202 3.80e+01 a.4.5.2,b.87.1.1 63057,63058 1nv8A 284 3.80e+01 c.66.1.30 86224 1ca9A 192 3.82e+01 1d0aB b.8.1.1,h.1.2.1 23244,45451 1n6hA 170 3.83e+01 c.37.1.8 80197 2aegA 268 3.86e+01 1lv7A 257 3.93e+01 c.37.1.20 78232 2dg5B 190 3.95e+01 2cy7A 396 3.95e+01 1wn5A 130 4.04e+01 2b7oA 464 4.05e+01 1on3A 523 4.07e+01 c.14.1.4,c.14.1.4 87107,87108 1r2qA 170 4.09e+01 c.37.1.8 96874 2f7fA 494 4.16e+01 1ll1 590 4.20e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18488,18499,21864 1qfjA 232 4.20e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 1vkmA 297 4.37e+01 c.138.1.1 108670 1gewA 356 4.40e+01 1gewA c.67.1.1 60470 2b67A 204 4.45e+01 1h8eG 272 4.49e+01 1e79G c.49.2.1 60756 1xvaA 292 4.52e+01 1xvaA c.66.1.5 34183 1nbfA 353 4.56e+01 d.3.1.9 80387 1dj0A 264 4.58e+01 1dj0A d.265.1.1 90337 1dar 691 4.61e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1 25707,32142,37547,39300 1sr9A 644 4.65e+01 a.5.7.1,c.1.10.5,d.270.1.1 105960,105961,105962 2pia 321 4.66e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1lla 628 4.67e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18485,18496,21861 1ayrB 363 4.71e+01 1cf1A b.1.18.11,b.1.18.11 21917,21918 1gosA 520 4.71e+01 c.3.1.2,d.16.1.5 65425,65426 1oacA 727 4.73e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24390,38007,38008,40003 1kfiA 572 4.74e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68555,68556,68557,68558 1ak6 174 4.74e+01 1cof d.109.1.2 40865 2fqxA 318 4.74e+01 1spuB 727 4.76e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24399,38025,38026,40012 1dbrA 231 4.77e+01 1qk3A c.61.1.1 34041 1vzyA 291 4.82e+01 1f3lA 321 4.91e+01 1g6q2 c.66.1.6 59630 1oe9A 795 5.01e+01 b.34.3.1,c.37.1.9 92792,92793 1d6zA 727 5.03e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24394,38015,38016,40007 1jb7B 260 5.07e+01 1otcB b.40.4.3 62839 1kjvB 100 5.09e+01 b.1.1.2 77423 1mdl 359 5.13e+01 2mnr c.1.11.2,d.54.1.1 29247,38891 1jv1A 505 5.18e+01 c.68.1.5 71892 2bmaA 470 5.29e+01 1hm2A 700 5.31e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 61083,61084,61085 1d0nA 729 5.33e+01 1d0nA d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1 40834,40835,40836,40837,40838,40839 1owqA 361 5.47e+01 c.1.8.5,d.26.3.1 104041,104042 1jx4A 352 5.51e+01 d.240.1.1,e.8.1.7 90378,90379 1fpxA 352 5.56e+01 1fpxA a.4.5.29,c.66.1.12 59950,59951 1xe0A 114 5.74e+01 1vdc 333 5.75e+01 1trb c.3.1.5,c.3.1.5 30545,30546 1dmaA 214 5.77e+01 1aerA d.166.1.1 42251 1sheA 103 5.86e+01 d.274.1.1 105551 1fzaB 328 5.91e+01 3fib d.171.1.1,h.1.8.1 42480,45621 2b1xB 172 5.94e+01 1z0jA 170 5.95e+01 1k2yX 463 6.03e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1mi8A 158 6.09e+01 b.86.1.2 91279 1tp9A 162 6.12e+01 1mp9A 198 6.15e+01 d.129.1.1,d.129.1.1 91385,91386 1e79G 272 6.27e+01 1e79G c.49.2.1 33158 2atrA 138 6.32e+01 1h4uA 265 6.37e+01 1h4uA d.22.1.2,g.3.11.5 60622,60623 1n7oA 721 6.47e+01 a.102.3.2,b.24.1.1,b.30.5.2 80259,80260,80261 1dl5A 317 6.49e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1qwkA 317 6.53e+01 c.1.7.1 96482 1k3sA 113 6.53e+01 d.198.1.1 68120 1fp2A 352 6.58e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1xkqA 280 6.65e+01 2bifA 469 6.65e+01 1bif c.37.1.7,c.60.1.4 31963,34009 2bsxA 253 6.74e+01 1itxA 419 6.76e+01 c.1.8.5,d.26.3.1 71425,71426 1p5dX 463 6.83e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1efcA 393 6.84e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1tc6A 236 6.88e+01 d.122.1.1 106756 1s3eA 520 6.91e+01 c.3.1.2,d.16.1.5 98426,98427 1egaA 301 6.94e+01 1egaA c.37.1.8,d.52.3.1 32150,38836 3bifA 468 7.08e+01 1bif c.37.1.7,c.60.1.4 31962,34008 2cwlA 302 7.13e+01 1o6jA 150 7.19e+01 c.47.1.10 81089 2cb5A 453 7.21e+01 3gcb d.3.1.1 37035 1kkuA 279 7.23e+01 c.26.1.3 72661 2cdnA 201 7.25e+01 1f7sA 139 7.26e+01 1cof d.109.1.2 40857 1qy5A 269 7.29e+01 d.122.1.1 96573 1g6oA 330 7.32e+01 1g6oA c.37.1.11 32430 3dapA 320 7.34e+01 1dapA c.2.1.3,d.81.1.3 30051,39966 1vom 762 7.39e+01 1lvk b.34.3.1,c.37.1.9 24577,32174 1b44D 129 7.44e+01 3chbD b.40.2.1 24960 2akrA 285 7.52e+01 1q7zA 566 7.59e+01 c.1.21.2,c.1.26.1 96090,96091 1iqpA 327 7.61e+01 a.80.1.1,c.37.1.20 62649,62650 1stzA 338 7.61e+01 a.4.5.51,d.110.2.3 106009,106010 2ca6A 386 7.65e+01 1w7jA 795 7.69e+01 2g39A 497 7.70e+01 1y14A 187 7.71e+01 1eujA 166 7.73e+01 1eujA b.40.4.4 25316 1hjxA 362 7.73e+01 c.1.8.5,d.26.3.1 83512,83513 1j5sA 463 7.80e+01 c.1.9.8 71580 1bxsA 501 7.83e+01 1bpwA c.82.1.1 35357 1ycoA 279 7.84e+01 1yrgA 385 7.86e+01 1yrgA c.10.1.2 30854 1u9iA 519 7.95e+01 2ch4A 320 7.95e+01 1ayrA 368 7.97e+01 1cf1A b.1.18.11,b.1.18.11 21915,21916 1zoiA 276 7.99e+01 1w4tA 299 8.03e+01 1wy2A 351 8.05e+01 1b3qA 379 8.15e+01 1b3qA a.30.2.1,b.40.7.1,d.122.1.3 16993,25454,41112 1fuiA 591 8.16e+01 1fuiA b.43.2.1,c.85.1.1 25674,35444 1ti6A 875 8.18e+01 b.52.2.2,c.81.1.1 106974,106975 1ytfB 53 8.18e+01 1ytfB a.32.1.1 16997 2bjvA 265 8.25e+01 1t71A 281 8.26e+01 1ddzA 496 8.37e+01 1ddzA c.53.2.1,c.53.2.1 33372,33373 1epwA 1290 8.49e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1vjjA 692 8.50e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 1cb8A 678 8.54e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1f6bA 198 8.57e+01 c.37.1.8 64986 1a8s 273 8.64e+01 1brt c.69.1.12 34710 1bueA 265 8.78e+01 1btl e.3.1.1 42727 1d5cA 162 8.90e+01 1ctqA c.37.1.8 32021 1i5gA 144 8.94e+01 1ewxA c.47.1.10 61784 1bhjA 292 8.94e+01 1xvaA c.66.1.5 34189 1fo4A 1332 8.96e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 17910,37695,38586,40227,41416,41758