# List of top-scoring protein chains for t2k-100-30-stride-ebghtl-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 1.03e-50 1bg2 c.37.1.9 32189 1i5sA 367 1.16e-48 1bg2 c.37.1.9 61822 1ii6A 368 4.44e-47 1bg2 c.37.1.9 62413 1i6iA 366 9.80e-47 1bg2 c.37.1.9 61844 1x88A 359 1.35e-46 1q0bA 367 1.60e-46 c.37.1.9 95502 1vfvA 366 1.44e-45 c.37.1.9 108592 3kar 346 9.97e-45 1bg2 c.37.1.9 32198 1cz7A 406 2.72e-44 1bg2 c.37.1.9 32194 1f9vA 347 5.07e-43 1bg2 c.37.1.9 59745 1ry6A 360 1.10e-39 c.37.1.9 98090 2kinA 238 1.20e-35 1bg2 c.37.1.9 32190 2kinB 100 1.14e-12 3kinB 3kinB 117 2.21e-12 3kinB 2akaB 299 1.21e-01 1p9rA 418 3.98e-01 c.37.1.11 94399 2azqA 311 9.30e-01 1l8qA 324 1.53e+00 a.4.12.2,c.37.1.20 77809,77810 1odfA 290 1.60e+00 c.37.1.6 92782 1f60A 458 1.85e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1lv7A 257 1.94e+00 c.37.1.20 78232 1wf3A 301 2.58e+00 1vnc 609 2.88e+00 1vns a.111.1.3 19065 1vns 609 3.40e+00 1vns a.111.1.3 19061 1vraB 215 3.48e+00 1on3A 523 3.72e+00 c.14.1.4,c.14.1.4 87107,87108 1j8mF 297 3.80e+00 1ng1 a.24.13.1,c.37.1.10 62742,62743 1thtA 305 4.47e+00 1thtA c.69.1.13 34711 1nm1G 125 4.51e+00 d.109.1.1 80653 1d4xG 126 4.52e+00 1d0nA d.109.1.1 59109 1yagG 125 4.53e+00 1d0nA d.109.1.1 40846 1fw9A 164 4.72e+00 1fw9A d.190.1.1 60059 1tt8A 164 4.72e+00 1xwiA 322 5.71e+00 1jwyB 315 7.73e+00 c.37.1.8 67401 2cb5A 453 8.08e+00 3gcb d.3.1.1 37035 1jhfA 202 8.41e+00 a.4.5.2,b.87.1.1 63057,63058 1esgA 213 8.43e+00 1bam c.52.1.3 33286 1jx2B 315 8.48e+00 c.37.1.8 67404 2bf6A 449 8.54e+00 1bmlC 362 8.56e+00 1bmlC d.15.5.1,d.15.5.1,d.15.5.1 37729,37730,37731 1y8cA 246 8.92e+00 1tljA 213 9.57e+00 d.282.1.1 107126 1f3iA 481 1.03e+01 1b7eA 1vm8A 534 1.06e+01 1bucA 383 1.06e+01 3mdeA a.29.3.1,e.6.1.1 16590,42851 1pzgA 331 1.15e+01 c.2.1.5,d.162.1.1 95425,95426 1inlA 296 1.19e+01 c.66.1.17 66220 2bycA 137 1.20e+01 1r88A 280 1.23e+01 c.69.1.3 97219 1gvnB 287 1.28e+01 c.37.1.21 76354 1dbrA 231 1.31e+01 1qk3A c.61.1.1 34041 1nb8A 353 1.32e+01 d.3.1.9 80385 1jb7B 260 1.34e+01 1otcB b.40.4.3 62839 1h2vZ 156 1.35e+01 d.58.7.1 76595 1taq 832 1.36e+01 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18082,33352,33698,42991 1jq3A 296 1.46e+01 c.66.1.17 67079 1tmxA 293 1.46e+01 2bh9A 489 1.46e+01 1um8A 376 1.47e+01 c.37.1.20 99580 1c4oA 664 1.48e+01 1d2mA c.37.1.19,c.37.1.19 32415,32416 1wdtA 665 1.50e+01 1cr5A 189 1.53e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1vjjA 692 1.63e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 1efcA 393 1.64e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1zk7A 467 1.66e+01 1ng1 294 1.66e+01 1ng1 a.24.13.1,c.37.1.10 16961,32272 1htjF 210 1.69e+01 1htjF a.91.1.1 61254 2fytA 340 1.70e+01 1fuiA 591 1.71e+01 1fuiA b.43.2.1,c.85.1.1 25674,35444 1k2yX 463 1.72e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1efuA 385 1.73e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1e58A 249 1.78e+01 1qhfA c.60.1.1 59262 1jpnA 296 1.81e+01 a.24.13.1,c.37.1.10 67039,67040 1d2mA 665 1.83e+01 1d2mA c.37.1.19,c.37.1.19 32417,32418 1hm2A 700 1.87e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 61083,61084,61085 1u9iA 519 1.94e+01 2ng1 293 1.96e+01 1ng1 a.24.13.1,c.37.1.10 16962,32273 1d0nA 729 1.99e+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 1ex2A 189 2.00e+01 1ex2A c.51.4.2 33225 1ugiA 84 2.01e+01 1ugiA d.17.5.1 38125 1d3uA 181 2.06e+01 1ytbA d.129.1.1,d.129.1.1 41290,41291 2b1xB 172 2.06e+01 1p5dX 463 2.07e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1ffh 294 2.09e+01 1ng1 a.24.13.1,c.37.1.10 16960,32271 1m3jA 471 2.15e+01 f.9.1.1 91182 1ls1A 295 2.17e+01 a.24.13.1,c.37.1.10 78170,78171 1ng4A 390 2.38e+01 c.3.1.2,d.16.1.3 85666,85667 2napA 723 2.39e+01 2napA b.52.2.2,c.81.1.1 26926,35334 1g291 372 2.43e+01 1g291 1bouB 302 2.44e+01 1bouB c.56.6.1 33859 1ofuA 320 2.48e+01 c.32.1.1,d.79.2.1 86972,86973 1q5qA 259 2.51e+01 d.153.1.4 95904 1hv8A 367 2.55e+01 1hv8A c.37.1.19,c.37.1.19 32405,32406 1muhA 481 2.59e+01 c.55.3.4 79485 1oe9A 795 2.59e+01 b.34.3.1,c.37.1.9 92792,92793 1qf6A 642 2.66e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1cb8A 678 2.70e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1g6q2 328 2.71e+01 1g6q2 1tm0A 350 2.85e+01 d.21.1.3 107147 1l9mA 692 2.88e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 73732,73733,73734,73735 2a5yB 549 2.95e+01 1u2eA 289 2.98e+01 1bvoA 175 2.99e+01 1a3qA b.2.5.3 22457 1s7kA 182 3.07e+01 1p8xA 344 3.09e+01 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 1jv1A 505 3.14e+01 c.68.1.5 71892 1ak7 174 3.14e+01 1cof d.109.1.2 40864 2ao0A 324 3.16e+01 1udiI 83 3.21e+01 1ugiA d.17.5.1 38124 2fsjA 346 3.23e+01 1h6kZ 98 3.33e+01 d.58.7.1 60686 2bmaA 470 3.37e+01 1ihuA 589 3.43e+01 c.37.1.10,c.37.1.10 62394,62395 1wd3A 482 3.44e+01 b.29.1.21,b.42.8.1 109233,109234 2b3yA 888 3.44e+01 1b4uB 302 3.49e+01 1bouB c.56.6.1 33861 1w7jA 795 3.50e+01 1mi8A 158 3.51e+01 b.86.1.2 91279 1tc6A 236 3.52e+01 d.122.1.1 106756 1j5sA 463 3.56e+01 c.1.9.8 71580 1yuwA 554 3.62e+01 1j1iA 296 3.65e+01 c.69.1.10 83977 1gguA 731 3.76e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21885,22179,22180,37115 1j03A 102 3.83e+01 d.120.1.2 90733 1fg7A 356 3.86e+01 1gewA c.67.1.1 59819 1ddzA 496 3.86e+01 1ddzA c.53.2.1,c.53.2.1 33372,33373 2afwA 329 3.86e+01 1egaA 301 3.90e+01 1egaA c.37.1.8,d.52.3.1 32150,38836 1c0pA 363 3.95e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 2bwvA 440 3.95e+01 1jmxA 494 3.96e+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 1br2A 791 3.97e+01 1lvk b.34.3.1,c.37.1.9 24558,32155 1sup 275 4.10e+01 1gci c.41.1.1 32510 2cy7A 396 4.11e+01 1nhp 447 4.12e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 1vom 762 4.16e+01 1lvk b.34.3.1,c.37.1.9 24577,32174 1owqA 361 4.17e+01 c.1.8.5,d.26.3.1 104041,104042 2f7fA 494 4.18e+01 1d2eA 397 4.26e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1wn5A 130 4.27e+01 3bifA 468 4.27e+01 1bif c.37.1.7,c.60.1.4 31962,34008 1hjxA 362 4.27e+01 c.1.8.5,d.26.3.1 83512,83513 1joa 447 4.31e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30563,30564,40203 1fnmA 691 4.41e+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 1wl9A 440 4.42e+01 1unnC 115 4.43e+01 d.240.1.1 99680 1w4tA 299 4.46e+01 1aisA 182 4.47e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1cjbA 231 4.51e+01 1qk3A c.61.1.1 34079 1nv8A 284 4.54e+01 c.66.1.30 86224 1r5jA 337 4.60e+01 c.77.1.5 97097 1siqA 392 4.62e+01 a.29.3.1,e.6.1.1 105585,105586 1to2E 281 4.62e+01 1evuA 731 4.62e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1exmA 405 4.65e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1y08A 323 4.69e+01 1iexA 605 4.77e+01 c.1.8.7,c.23.11.1 66127,66128 1ughI 82 4.81e+01 1ugiA d.17.5.1 38133 1lw6E 281 4.83e+01 c.41.1.1 74293 1bueA 265 4.87e+01 1btl e.3.1.1 42727 1ak6 174 4.91e+01 1cof d.109.1.2 40865 1mpyA 307 4.99e+01 1mpyA d.32.1.3,d.32.1.3 38508,38509 1fp2A 352 5.03e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1g6oA 330 5.05e+01 1g6oA c.37.1.11 32430 1f48A 589 5.07e+01 1f48A c.37.1.10,c.37.1.10 32280,32281 1x38A 602 5.16e+01 1dl2A 511 5.19e+01 1dl2A a.102.2.1 18844 1ayrB 363 5.21e+01 1cf1A b.1.18.11,b.1.18.11 21917,21918 1dbhA 354 5.24e+01 1awe a.87.1.1,b.55.1.1 18514,26967 1stzA 338 5.28e+01 a.4.5.51,d.110.2.3 106009,106010 1orrA 347 5.38e+01 c.2.1.2 93460 1t8hA 277 5.42e+01 d.194.1.2 106664 1l2lA 457 5.44e+01 c.72.1.3 77656 1wmhA 89 5.44e+01 3aig 202 5.45e+01 1atlA d.92.1.9 40321 1pkhA 204 5.54e+01 b.85.4.1 94832 1fyeA 229 5.54e+01 1fyeA c.23.16.4 31477 1dmhA 311 5.54e+01 1dmhA b.3.6.1 22633 2ewrA 170 5.55e+01 1ebdA 455 5.55e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 1a8s 273 5.59e+01 1brt c.69.1.12 34710 3bamB 213 5.61e+01 1bam c.52.1.3 33289 1esmA 316 5.68e+01 1esmA c.37.1.6 31953 1azsC 388 5.71e+01 1cipA a.66.1.1,c.37.1.8 18203,32086 1ex1A 605 5.72e+01 1ex1A c.1.8.7,c.23.11.1 29013,31347 1ck7A 631 5.78e+01 1ck7A b.66.1.1,g.14.1.2,g.14.1.2,g.14.1.2,a.20.1.2,d.92.1.11 27538,44674,44675,44676,58969,58970 1cf1A 404 5.87e+01 1cf1A b.1.18.11,b.1.18.11 21907,21908 1uptA 171 5.96e+01 c.37.1.8 99767 2ch4A 320 6.02e+01 1qksA 567 6.03e+01 1qksA a.3.1.2,b.70.2.1 15951,27710 1gesA 450 6.04e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 1ifrA 121 6.08e+01 b.1.16.1 71203 1nhs 447 6.10e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 1qfjA 232 6.11e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 2b6hA 192 6.11e+01 1ibvB 229 6.14e+01 1svcP 365 6.14e+01 1a3qA b.1.18.1,b.2.5.3 21924,22443 1onxA 390 6.14e+01 b.92.1.7,c.1.9.13 87176,87177 2akaA 776 6.17e+01 1uxtA 501 6.17e+01 c.82.1.1 108125 1o6jA 150 6.19e+01 c.47.1.10 81089 1mp9A 198 6.31e+01 d.129.1.1,d.129.1.1 91385,91386 1g7tA 594 6.48e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25714,25715,31033,32148 1tuoA 464 6.49e+01 1otcB 260 6.51e+01 1otcB b.40.4.3 25310 1fpxA 352 6.51e+01 1fpxA a.4.5.29,c.66.1.12 59950,59951 1mnd 762 6.57e+01 1lvk b.34.3.1,c.37.1.9 24591,32188 1hurA 180 6.61e+01 1hurA c.37.1.8 32052 1m1cA 680 6.65e+01 e.42.1.1 78395 1d6jA 211 6.68e+01 1d6jA c.37.1.4 31940 2bd0A 244 6.70e+01 1t0gA 109 6.70e+01 d.120.1.2 99063 1musA 477 6.72e+01 c.55.3.4 79494 1ex0A 731 6.74e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 2db3A 434 6.79e+01 1ei1A 391 6.85e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 1xkwA 665 6.89e+01 1i5gA 144 6.89e+01 1ewxA c.47.1.10 61784 1aoqA 567 6.90e+01 1qksA a.3.1.2,b.70.2.1 15934,27692 1i6pA 220 6.98e+01 1ddzA c.53.2.1 61848 2aefA 234 6.98e+01 1zoiA 276 7.01e+01 1g8pA 350 7.04e+01 1g8pA c.37.1.20 60376 1pczA 191 7.06e+01 1ytbA d.129.1.1,d.129.1.1 41292,41293 1pyaB 228 7.10e+01 1pyaB 1qy5A 269 7.16e+01 d.122.1.1 96573 2fclA 169 7.17e+01 2ghpA 292 7.23e+01 1oghA 204 7.28e+01 b.85.4.1 86994 2bsxA 253 7.34e+01 2c78A 405 7.41e+01 2bcgY 206 7.49e+01 1d0yA 761 7.55e+01 1lvk b.34.3.1,c.37.1.9 24581,32178 1z0jA 170 7.60e+01 1bob 320 7.61e+01 1bob d.108.1.1 40816 1ms9A 648 7.61e+01 b.29.1.15,b.68.1.1 85088,85089 1fjhB 257 7.64e+01 1fjhB c.2.1.2 29871 1ukvY 206 7.87e+01 c.37.1.8 107918 1z57A 339 7.91e+01 1fgyA 127 7.95e+01 1faoA b.55.1.1 26976 1vdc 333 7.96e+01 1trb c.3.1.5,c.3.1.5 30545,30546 1xksA 450 7.96e+01 1f3lA 321 8.03e+01 1g6q2 c.66.1.6 59630 1qcxA 359 8.14e+01 1qcxA b.80.1.2 28028 1u9jA 358 8.19e+01 1w9iA 770 8.23e+01 1ta9A 450 8.26e+01 1tzfA 259 8.31e+01 c.68.1.13 107476 1z5zA 271 8.37e+01 1r9cA 139 8.43e+01 d.32.1.2 97255 1lvk 762 8.48e+01 1lvk b.34.3.1,c.37.1.9 24576,32173 2bllA 345 8.50e+01 3bamA 213 8.50e+01 1bam c.52.1.3 33288 1g8jA 825 8.53e+01 1g8jA b.52.2.2,c.81.1.1 26924,35332 1f42A 306 8.55e+01 1f42A b.1.1.4,b.1.2.1,b.1.2.1 59636,59637,59638 1m33A 258 8.59e+01 c.69.1.26 78514 1lg2A 365 8.64e+01 c.1.8.5,d.26.3.1 77950,77951 1woqA 267 8.69e+01 c.55.1.10,c.55.1.10 109462,109463 1qrkA 731 8.74e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21889,22187,22188,37119 1gewA 356 8.75e+01 1gewA c.67.1.1 60470 2afbA 351 8.78e+01 1fy2A 229 8.89e+01 1fyeA c.23.16.4 31478 1s28A 132 8.92e+01 d.198.1.1 105223 1zc6A 305 8.95e+01