# 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 1t95A 240 3.16e-01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1f7wA 144 4.47e-01 1f46A d.129.4.1 59679 1f46A 140 5.99e-01 1f46A d.129.4.1 59643 2b1eA 564 6.06e-01 1f47B 144 6.18e-01 1f46A d.129.4.1 59645 1o6dA 163 7.01e-01 c.116.1.3 92567 2aexA 346 7.03e-01 2h0uA 217 8.53e-01 1oyb 400 8.84e-01 1oyc c.1.4.1 28602 1oyc 400 8.88e-01 1oyc c.1.4.1 28603 1a8h 500 8.89e-01 1a8h a.27.1.1,c.26.1.1 16922,31589 1oya 400 8.96e-01 1oyc c.1.4.1 28604 1tn4 159 1.86e+00 1ncx a.39.1.5 17248 1avsA 90 2.19e+00 1cll a.39.1.5 17226 1wdpA 495 2.36e+00 1byb 495 2.37e+00 1byb c.1.8.1 28790 1q6cA 495 2.37e+00 c.1.8.1 95970 1v3hA 495 2.38e+00 c.1.8.1 108303 2c5kT 95 2.46e+00 1p9qC 256 2.48e+00 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1y96B 85 2.65e+00 1b1yA 500 2.78e+00 1byb c.1.8.1 28796 1tzzA 392 2.82e+00 2aukA 190 2.90e+00 1woyA 500 3.10e+00 1y1xA 191 3.39e+00 1eca 136 3.45e+00 1flp a.1.1.2 15209 1eco 136 3.71e+00 1flp a.1.1.2 15208 2a5vA 213 3.89e+00 1ym3A 215 4.01e+00 1ecd 136 4.05e+00 1flp a.1.1.2 15211 1gzqA 300 4.05e+00 b.1.1.2,d.19.1.1 70818,70819 2amdA 311 4.12e+00 1omrA 201 4.41e+00 a.39.1.5 93349 1vgoA 253 4.60e+00 1aj4 161 4.73e+00 1ncx a.39.1.5 17244 1id3B 102 5.02e+00 a.22.1.1 66113 1lj9A 144 5.18e+00 a.4.5.28 78035 1g5pA 289 5.67e+00 1cp2A c.37.1.10 32253 1q6aA 107 5.85e+00 a.186.1.1 95966 1cvrA 435 5.92e+00 1cvrA b.1.18.12,c.17.1.2 21949,31006 1uw4A 91 6.12e+00 d.58.7.4 100071 1e5pA 151 6.21e+00 1bj7 b.60.1.1 59272 1grj 158 6.50e+00 1grj a.2.1.1,d.26.1.2 15691,38433 2cvhA 220 6.53e+00 1txnA 328 6.73e+00 1b5sA 242 6.85e+00 1eaf c.43.1.1 32626 1tw9A 206 7.19e+00 a.45.1.1,c.47.1.5 107381,107382 1ekqA 272 7.21e+00 1c3qA c.72.1.2 34941 1c3qA 272 7.46e+00 1c3qA c.72.1.2 34948 2tmkA 216 7.75e+00 3tmkA c.37.1.1 31928 1p5jA 372 7.78e+00 c.79.1.1 104067 2a5kA 307 8.13e+00 2au5A 139 8.29e+00 1q0sA 259 8.57e+00 c.66.1.28 95509 2tpsA 227 8.63e+00 2tpsA c.1.3.1 28591 1xd8A 289 8.87e+00 1hwtC 81 9.04e+00 1hwtC g.38.1.1,h.1.3.1 45085,45518 2amyA 246 9.59e+00 2cq2A 114 9.69e+00 1fw1A 216 9.74e+00 a.45.1.1,c.47.1.5 60051,60052 1v2zA 111 9.78e+00 a.186.1.1 108300 2beqD 48 9.79e+00 1jixA 351 9.80e+00 1c3jA c.87.1.1 63081 1jg7A 351 9.80e+00 1c3jA c.87.1.1 62945 1bj7 156 9.93e+00 1bj7 b.60.1.1 27113 1c3jA 351 1.01e+01 1c3jA c.87.1.1 35459 2bgu 351 1.01e+01 1c3jA c.87.1.1 35460 1ut8A 291 1.01e+01 a.60.7.1,c.120.1.2 99908,99909 2fbhA 146 1.02e+01 1aj8A 371 1.03e+01 1aj8A a.103.1.1 18900 1xhdA 173 1.04e+01 1zac 90 1.05e+01 1ncx a.39.1.5 17236 1exnA 290 1.07e+01 1exnA a.60.7.1,c.120.1.2 18088,33358 1k2xB 143 1.07e+01 1o5zA 442 1.08e+01 c.59.1.2,c.72.2.2 92530,92531 1j93A 353 1.11e+01 c.1.22.1 66454 1m1eB 81 1.12e+01 a.161.1.1 78400 1ockA 412 1.15e+01 c.117.1.1 86802 2af4C 333 1.15e+01 1eijA 80 1.16e+01 1eijA a.5.6.1 16298 2b18A 164 1.16e+01 1pkhA 204 1.18e+01 b.85.4.1 94832 1pvmA 184 1.23e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1e3pA 757 1.25e+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 1oghA 204 1.28e+01 b.85.4.1 86994 1y791 680 1.30e+01 1a6q 382 1.31e+01 1a6q a.159.1.1,d.219.1.1 75801,75802 1pgvA 197 1.32e+01 c.10.1.1 88073 1ydmA 187 1.36e+01 1y9qA 192 1.41e+01 1vd2A 89 1.41e+01 d.15.2.2 108517 2bkaA 242 1.42e+01 1bbhA 131 1.44e+01 1bbhA a.24.3.2 16546 2adoA 196 1.45e+01 1ajsA 412 1.48e+01 1ajsA c.67.1.1 34276 2fu2A 102 1.51e+01 2etxA 209 1.51e+01 2di4A 238 1.51e+01 1h97A 147 1.52e+01 1h97A a.1.1.2 60812 1e3hA 757 1.55e+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 1fp6A 289 1.56e+01 1cp2A c.37.1.10 32243 2c3nA 247 1.62e+01 1tqhA 247 1.70e+01 c.69.1.29 107225 1q2wA 308 1.71e+01 b.47.1.4 88355 1ap4 89 1.79e+01 1ncx a.39.1.5 17253 2erbA 125 1.81e+01 1snnA 227 1.85e+01 d.115.1.2 105821 1pvyA 227 1.86e+01 d.115.1.2 95195 1kn1B 161 1.87e+01 a.1.1.3 77456 1wdtA 665 1.88e+01 1kx5B 102 1.90e+01 a.22.1.1 77594 1aoiB 87 1.90e+01 1aoiB a.22.1.1 16470 1hq3D 103 1.90e+01 1aoiB a.22.1.1 16464 1tzyD 103 1.90e+01 a.22.1.1 107533 1aoiF 87 1.90e+01 1aoiB a.22.1.1 16471 3tmkA 216 1.93e+01 3tmkA c.37.1.1 31920 2cqsA 842 1.99e+01 1xfxO 149 2.00e+01 1upvA 257 2.03e+01 2c4jA 218 2.06e+01 1b33B 161 2.07e+01 1qgwC a.1.1.3 15650 1jsxA 207 2.11e+01 c.66.1.20 71846 2fueA 262 2.15e+01 1u53A 196 2.16e+01 1b0nA 111 2.17e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 2f6mA 65 2.29e+01 1zuhA 168 2.31e+01 1g0cA 364 2.31e+01 7a3hA c.1.8.3 60165 1sczA 233 2.33e+01 c.43.1.1 98802 1ofcX 304 2.40e+01 a.4.1.3,a.4.1.13,a.187.1.1 92826,92827,92828 2a6sA 84 2.42e+01 1ap6A 198 2.45e+01 1avmA a.2.11.1,d.44.1.1 15746,38705 1a52A 258 2.48e+01 3erdA a.123.1.1 19296 1g01A 364 2.52e+01 7a3hA c.1.8.3 60161 1dekA 241 2.52e+01 1dekA c.37.1.1 31842 1xgwA 176 2.53e+01 1pq9A 253 2.53e+01 a.123.1.1 95004 1j79A 347 2.55e+01 1j79A c.1.9.4 62675 1t3wA 148 2.57e+01 2a4vA 159 2.58e+01 1h6pA 203 2.59e+01 a.146.1.1 60690 1a32 88 2.60e+01 1a32 a.16.1.2 16384 1qgxA 357 2.61e+01 1qgxA e.7.1.1 42973 1ka1A 357 2.61e+01 e.7.1.1 68369 1n4kA 381 2.61e+01 a.118.22.1,b.42.6.1 79992,79993 2c8vA 288 2.67e+01 1jo0A 98 2.69e+01 d.68.4.1 77140 1pyfA 312 2.73e+01 c.1.7.1 95334 1fosF 57 2.74e+01 h.1.3.1 45538 1qhtA 775 2.75e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1gwcA 230 2.75e+01 a.45.1.1,c.47.1.5 70660,70661 1z0xA 220 2.77e+01 1kkuA 279 2.82e+01 c.26.1.3 72661 1bfmA 69 2.85e+01 1a7w a.22.1.2 16479 2bnh 457 2.92e+01 1a4yA c.10.1.1 30850 1zbsA 291 2.98e+01 1n9dA 199 3.01e+01 a.26.1.1 85464 1h0aA 158 3.05e+01 a.118.9.1 76434 1pmzA 86 3.06e+01 a.39.1.10 104195 1xfxA 777 3.11e+01 1sauA 115 3.13e+01 1r0mA 375 3.15e+01 c.1.11.2,d.54.1.1 104747,104748 1allA 160 3.17e+01 1qgwC a.1.1.3 15647 1a7w 69 3.23e+01 1a7w a.22.1.2 16477 1jbaA 204 3.23e+01 1rec a.39.1.5 17330 1vflA 356 3.28e+01 2fcwA 109 3.28e+01 1izmA 184 3.28e+01 a.199.1.1 90725 1eyhA 144 3.30e+01 1eduA a.118.9.1 19214 1wy1A 172 3.37e+01 1q74A 303 3.40e+01 c.134.1.1 96019 2fbmA 291 3.44e+01 1tfjA 219 3.44e+01 1hta 69 3.46e+01 1a7w a.22.1.2 16476 1wbeA 209 3.47e+01 1eduA 149 3.48e+01 1eduA a.118.9.1 19215 2gl5A 410 3.53e+01 1oe8A 211 3.54e+01 a.45.1.1,c.47.1.5 86905,86906 1s48A 609 3.55e+01 e.8.1.4 98475 1dugA 234 3.58e+01 1b8xA a.45.1.1,c.47.1.5 17718,33012 1g4yR 148 3.59e+01 1cll a.39.1.5 60252 1b67A 68 3.59e+01 1a7w a.22.1.2 16474 1xw5A 217 3.61e+01 1yzyA 413 3.62e+01 1r1dA 247 3.63e+01 c.69.1.29 96813 1kqnA 279 3.70e+01 c.26.1.3 77492 2fhfA 1083 3.75e+01 1add 349 3.75e+01 1a4mA c.1.9.1 29020 1fkx 349 3.76e+01 1a4mA c.1.9.1 29018 1cpcL 172 3.78e+01 1qgwC a.1.1.3 15646 1mfqC 129 3.78e+01 a.36.1.1 79046 1f37A 110 3.79e+01 1f37A c.47.1.11 33088 1r9lA 309 3.80e+01 c.94.1.1 97262 1xeuA 263 3.82e+01 1miwA 404 3.90e+01 a.173.1.1,d.218.1.4 79162,79163 1t3qB 788 3.92e+01 d.41.1.1,d.133.1.1 106369,106370 1nvmA 345 3.93e+01 a.5.7.1,c.1.10.5 86249,86250 1srqA 341 4.12e+01 e.55.1.1 105967 1innA 166 4.19e+01 1j98A d.185.1.2 62608 1vjeA 166 4.20e+01 d.185.1.2 100807 1z7xW 461 4.23e+01 1imoA 88 4.29e+01 1imoA c.15.1.2 62590 2fefA 294 4.30e+01 1icpA 376 4.32e+01 1oyc c.1.4.1 62270 1y74A 57 4.34e+01 1zckA 154 4.35e+01 1qznA 173 4.38e+01 b.2.2.2 104669 1u8bA 133 4.40e+01 1v1dA 31 4.44e+01 1exnB 290 4.47e+01 1exnA a.60.7.1,c.120.1.2 18089,33359 1mj3A 260 4.58e+01 c.14.1.3 79183 2fliA 220 4.61e+01 1w1iE 357 4.63e+01 c.1.9.1 109051 1yf3A 259 4.63e+01 2b3yA 888 4.63e+01 1qwgA 251 4.66e+01 c.1.27.1 96473 1yirA 408 4.66e+01 1allB 161 4.69e+01 1qgwC a.1.1.3 15648 1flp 142 4.71e+01 1flp a.1.1.2 15011 1ltaC 49 4.74e+01 1ltaC 1moh 142 4.74e+01 1flp a.1.1.2 15012 2ay1A 394 4.75e+01 1ajsA c.67.1.1 34357 1delA 241 4.76e+01 1dekA c.37.1.1 31844 2dubE 261 4.90e+01 1nzyA c.14.1.3 30916 1v3wA 173 4.93e+01 b.81.1.5 100291 2db0A 253 4.94e+01 1foeA 377 4.96e+01 1foeA a.87.1.1,b.55.1.1 18517,26969 1ztpA 251 4.96e+01 1ug6A 431 4.97e+01 c.1.8.4 88490 1aoqA 567 4.98e+01 1qksA a.3.1.2,b.70.2.1 15934,27692 1qksA 567 4.99e+01 1qksA a.3.1.2,b.70.2.1 15951,27710 1vjuA 309 5.00e+01 d.248.1.1 100835 2gokA 429 5.05e+01 1pl4A 198 5.09e+01 a.2.11.1,d.44.1.1 94854,94855 1abmA 198 5.09e+01 1avmA 1xfuA 747 5.11e+01 1auoA 218 5.12e+01 1auoA c.69.1.14 34716 1q8cA 151 5.12e+01 a.79.1.2 96202 1cmcA 104 5.16e+01 1cmbA a.43.1.5 17462 2bskB 90 5.16e+01 1a4yA 460 5.18e+01 1a4yA c.10.1.1 30852 3ertA 261 5.19e+01 3erdA a.123.1.1 19292 2bexA 460 5.21e+01 1ywfA 296 5.21e+01 1vjvA 415 5.28e+01 d.3.1.9 108632 1keaA 221 5.29e+01 a.96.1.2 68491 1xpcA 248 5.36e+01 1woqA 267 5.40e+01 c.55.1.10,c.55.1.10 109462,109463 2bezF 42 5.41e+01 2cw6A 298 5.49e+01 1b0b 142 5.50e+01 2fal a.1.1.2 15010 2b5aA 77 5.51e+01 2ax8A 256 5.54e+01 1ezvB 352 5.58e+01 1ezvB d.185.1.1,d.185.1.1 59543,59544 1i37A 260 5.61e+01 1a28A a.123.1.1 61583 1fo9A 348 5.69e+01 1foaA c.68.1.10 59928 2a15A 139 5.73e+01 2aclB 244 5.77e+01 1prq 125 5.77e+01 3nul d.110.1.1 40883 1yfbA 59 5.81e+01 1dqsA 393 5.84e+01 1dqsA e.22.1.1 43347 1dp3A 55 5.93e+01 1dp3A a.55.1.2 59128 1gnxA 479 5.97e+01 c.1.8.4 76241 2f3yA 148 6.03e+01 1cpcB 172 6.05e+01 1qgwC a.1.1.3 15644 1rhd 293 6.06e+01 1rhs c.46.1.2,c.46.1.2 32715,32716 1foaA 348 6.11e+01 1foaA c.68.1.10 59929 1n0wA 243 6.11e+01 c.37.1.11 79772 1o50A 157 6.17e+01 d.37.1.1,d.37.1.1 92478,92479 1gln 468 6.19e+01 1gln a.97.1.1,c.26.1.1 18752,31588 1lt4A 247 6.19e+01 1lt3A d.166.1.1 42231 1uvqB 198 6.23e+01 b.1.1.2,d.19.1.1 100064,100065 1p5zB 263 6.26e+01 c.37.1.1 87815 1a4mA 349 6.28e+01 1a4mA c.1.9.1 29014 1k8tA 510 6.28e+01 e.41.1.1 68316 1zgmA 248 6.29e+01 1hr6B 443 6.32e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1rt8A 513 6.33e+01 a.40.1.1 105095 1fr2A 86 6.33e+01 a.28.2.1 83256 1nogA 177 6.35e+01 a.25.2.2 85923 1b33A 160 6.41e+01 1qgwC a.1.1.3 15649 1emvA 86 6.49e+01 1cei a.28.2.1 16944 1nkpA 88 6.50e+01 a.38.1.1 80573 3erdA 261 6.53e+01 3erdA a.123.1.1 19293 2aaoA 166 6.54e+01 1t5bA 201 6.64e+01 c.23.5.3 106433 2a7oA 112 6.65e+01 1c52 131 6.66e+01 1c52 a.3.1.1 15810 2mysB 166 6.71e+01 1wdcB a.39.1.5 17308 1qjtA 99 6.72e+01 1eh2 a.39.1.6 17335 1fo8A 343 6.75e+01 1foaA c.68.1.10 59927 2es9A 115 6.76e+01 1mp4A 292 6.80e+01 c.68.1.6 79376 1jthD 77 6.83e+01 h.1.15.1 67273 2basA 431 6.84e+01 1sbp 310 6.84e+01 1sbp c.94.1.1 35760 1ncx 162 6.92e+01 1ncx a.39.1.5 17222 1top 162 6.93e+01 1ncx a.39.1.5 17223 1rhs 296 6.95e+01 1rhs c.46.1.2,c.46.1.2 32703,32704 1ynfA 458 6.97e+01 1y0eA 223 6.99e+01 1z0kB 69 6.99e+01 1wouA 123 7.03e+01 c.47.1.16 109471 1yozA 116 7.05e+01 1cdb 105 7.11e+01 1qa9A b.1.1.1 19744 1gv3A 248 7.13e+01 a.2.11.1,d.44.1.1 70585,70586 1tqnA 486 7.14e+01 a.104.1.1 107238 1t7rA 269 7.20e+01 a.123.1.1 106635 2cfxA 144 7.27e+01 1cmaA 104 7.27e+01 1cmbA a.43.1.5 17486 2cwoA 197 7.30e+01 1tr0A 108 7.37e+01 d.58.4.4 107261 1cqa 133 7.38e+01 3nul d.110.1.1 40890 1bmfA 510 7.41e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18281,26446,32326 2a07F 93 7.42e+01 1aow 309 7.44e+01 1avc a.65.1.1 18152 1whzA 70 7.44e+01 1n83A 270 7.50e+01 a.123.1.1 80276 1g24A 211 7.55e+01 1g24A d.166.1.1 42270 1afrA 345 7.59e+01 1afrA a.25.1.2 16805 1iscA 192 7.59e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1oq9A 363 7.61e+01 a.25.1.2 87257 1y7yA 74 7.63e+01 1y0vH 146 7.65e+01 1zs4A 83 7.66e+01 1q1hA 110 7.67e+01 a.4.5.41 95580 1h4pA 408 7.69e+01 c.1.8.3 90617 1g6hA 257 7.70e+01 1gajA c.37.1.12 60318 1ku2A 241 7.71e+01 a.4.13.1,a.177.1.1 83096,83097 1b8xA 280 7.77e+01 1b8xA a.45.1.1,c.47.1.5 17739,33033 1eluB 390 7.80e+01 1elqA c.67.1.3 34435 1q1fA 151 7.85e+01 a.1.1.2 104476 1ds9A 198 7.88e+01 1ds9A c.10.3.1 30879 1elqA 390 7.94e+01 1elqA c.67.1.3 34436 2f6uA 234 8.09e+01 1qh5A 260 8.11e+01 1qh5A d.157.1.2 42057 1h5rA 293 8.13e+01 c.68.1.6 65623 2cybA 323 8.14e+01 1wpkA 146 8.18e+01 1regX 122 8.24e+01 1regX d.58.27.1 39406 1idrA 136 8.25e+01 1dlyA a.1.1.1 62301 1jk0B 345 8.29e+01 a.25.1.2 63143 1eluA 390 8.31e+01 1elqA c.67.1.3 34434 1qbgA 272 8.31e+01 1d4aA c.23.5.3 31227 2fnoA 248 8.32e+01 1acf 125 8.35e+01 3nul d.110.1.1 40882 1zl8A 53 8.37e+01 1r5jA 337 8.40e+01 c.77.1.5 97097 1nsyA 271 8.41e+01 2nsyA c.26.2.1 31614 2nsyA 271 8.41e+01 2nsyA c.26.2.1 31612 1hloA 150 8.44e+01 1an4A a.38.1.1 17128 1kq8A 100 8.55e+01 a.4.5.14 68797 1qh3A 260 8.62e+01 1qh5A d.157.1.2 42059 2eulA 156 8.65e+01 1brwA 433 8.69e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1g59A 468 8.72e+01 a.97.1.1,c.26.1.1 60257,60258 1be3B 439 8.78e+01 1be3B d.185.1.1,d.185.1.1 58952,58953 2ax6A 256 8.81e+01 1ypyA 184 8.83e+01 2ftuA 118 8.83e+01 1sr9A 644 8.84e+01 a.5.7.1,c.1.10.5,d.270.1.1 105960,105961,105962 1ih8A 271 8.88e+01 2nsyA c.26.2.1 62377 1lkcA 364 8.88e+01 c.67.1.1 73978 1ak0 270 8.89e+01 1ak0 a.124.1.2 19345 1fviA 297 8.89e+01 1fviA b.40.4.6,d.142.2.1 25364,41578 1rpxA 230 8.89e+01 1rpxA c.1.2.2 28536 1kqpA 271 8.94e+01 c.26.2.1 72883