# List of top-scoring protein chains for t2k-100-30-bys-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 1l0qA 391 3.01e-12 b.1.3.1,b.69.2.3 77644,77645 2c4xA 260 1.95e-10 1b4rA 80 2.96e-04 1b4rA b.1.3.1 22072 1wgoA 123 1.38e-03 b.1.3.1 114618 2yrlA 102 1.45e-02 2kpnA 103 1.76e-01 1ofzA 312 4.48e-01 b.68.8.1 86978 1wcqA 601 9.25e-01 b.1.18.2,b.18.1.1,b.68.1.1 120894,120895,120896 2brqA 97 9.34e-01 b.1.18.10 129008 3c12A 138 9.38e-01 1cfb 205 9.41e-01 1cfb 1cfbA 205 9.41e-01 b.1.2.1,b.1.2.1 21991,21992 2w0pA 94 1.13e+00 b.1.18.10 153738 3ecrA 364 1.28e+00 1w8oA 601 1.38e+00 b.1.18.2,b.18.1.1,b.68.1.1 114374,114375,114376 3b9eA 584 1.72e+00 3h6jA 438 1.76e+00 2iouG 535 1.82e+00 3iswA 99 1.84e+00 1fsoA 139 1.84e+00 1rhoA b.1.18.8 60007 1tlk 154 1.89e+00 1tlk 1ejeA 192 1.96e+00 1ejeA b.45.1.2 25757 1ev2E 220 2.08e+00 1cvsC b.1.1.4,b.1.1.4 21738,21739 2vn4A 599 2.18e+00 1ctn 540 2.26e+00 1ctn 3greA 437 2.52e+00 1f97A 212 2.73e+00 1f97A b.1.1.1,b.1.1.4 19763,21764 1sqsA 242 3.02e+00 c.23.5.5 98968 2dbjA 124 3.05e+00 1fhgA 154 3.06e+00 1tlk b.1.1.4 21706 2k7qA 191 3.07e+00 3kg7A 293 3.38e+00 1edqA 540 3.40e+00 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1dabA 539 3.56e+00 1dabA b.80.1.7 28049 2w38A 438 3.59e+00 1wit 93 3.75e+00 1wit 2wk2A 540 4.21e+00 1aqkH 226 4.43e+00 1igtB b.1.1.1,b.1.1.2 20193,21209 2iepA 192 4.66e+00 2vxsH 225 4.95e+00 1k9tA 540 5.02e+00 b.1.18.2,c.1.8.5,d.26.3.1 77298,77299,77300 1cvsC 225 5.32e+00 1cvsC b.1.1.4,b.1.1.4 21726,21727 3f7pC 248 5.34e+00 1u58A 253 5.53e+00 b.1.1.2,d.19.1.1 144387,144388 1pguA 615 5.59e+00 b.69.4.1,b.69.4.1 88069,88070 2bwrA 401 6.00e+00 1um5H 217 6.20e+00 b.1.1.1,b.1.1.2 113302,113303 3ejjX 289 6.30e+00 1zvfA 176 6.42e+00 b.82.1.20 146029 1jwhA 337 6.47e+00 d.144.1.7 71913 1vjuA 309 6.54e+00 d.248.1.1 100835 2jllA 389 6.55e+00 3duiA 135 6.90e+00 2rikA 284 6.98e+00 1d2oA 187 7.25e+00 1d2oA b.3.5.1,b.3.5.1 22625,22626 1kmtA 141 7.28e+00 b.1.18.8 77442 3bmvA 683 7.36e+00 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 155416,155417,155418,155419 2w18A 356 7.75e+00 1yrzA 528 7.80e+00 b.29.1.23,b.67.2.1 123948,123949 1d2pA 373 8.04e+00 1d2oA b.3.5.1,b.3.5.1,b.3.5.1,b.3.5.1 22629,22630,22631,22632 2oxgA 108 8.30e+00 2bvyA 475 8.37e+00 b.1.18.2,c.1.8.3 129301,129302 1rhfA 182 8.38e+00 b.1.1.1,b.1.1.4 97469,97470 3ii1A 535 8.68e+00 2wlzA 548 8.68e+00 1t62A 166 8.74e+00 b.122.1.4 106541 1ngzB 220 8.76e+00 b.1.1.1,b.1.1.2 80502,80503 3hr5B 226 9.09e+00 1c5cH 215 9.15e+00 1igtB b.1.1.1,b.1.1.2 20475,21439 3f7rA 249 9.15e+00 1vqoB 338 9.17e+00 b.43.3.2 120363 1eut 605 9.25e+00 1eut 2gfaA 119 9.28e+00 b.34.9.1,b.34.9.1 135089,135090 1bqk 124 9.37e+00 1bqk 1bqkA 124 9.37e+00 b.6.1.1 22889 2wjsA 608 9.71e+00 1f6fB 210 1.01e+01 1axiB b.1.2.1,b.1.2.1 22033,22034 3mgaA 407 1.03e+01 3fw6A 534 1.04e+01 1qg3A 195 1.05e+01 1qg3A b.1.2.1,b.1.2.1 21993,21994 3grwA 241 1.06e+01 3emwA 217 1.06e+01 3f7qA 234 1.13e+01 1v8hA 107 1.16e+01 b.1.18.19 119870 1jj2B 337 1.19e+01 1ffkB b.43.3.2 63086 3lmjH 231 1.19e+01 1erxA 184 1.25e+01 1np1A b.60.1.1 27164 1a4jB 219 1.27e+01 1igtB b.1.1.1,b.1.1.2 20233,21245 3cjjA 219 1.35e+01 2r55A 231 1.36e+01 3g7dA 443 1.37e+01 1a6tB 217 1.39e+01 1igtB b.1.1.1,b.1.1.2 20249,21259 2w9qA 87 1.39e+01 3bp5B 202 1.39e+01 1pqzA 238 1.53e+01 b.1.1.2,d.19.1.1 104297,104298 1rhoA 145 1.53e+01 1rhoA b.1.18.8 21899 1xodA 118 1.58e+01 b.55.1.4 122202 1hnf 182 1.58e+01 1qa9A 1hnfA 182 1.58e+01 b.1.1.1,b.1.1.3 19741,21680 1dceA 567 1.62e+01 1dceA a.118.6.1,b.7.4.1,c.10.2.2 19191,23218,30867 3l95B 227 1.66e+01 1b2pA 119 1.73e+01 1b2pA b.78.1.1 27998 1iznB 277 1.74e+01 e.43.1.2 83848 2v4vA 129 1.75e+01 3kldA 384 1.79e+01 2a38A 194 1.82e+01 1v8yA 170 1.82e+01 d.113.1.1 113581 2j97A 109 1.85e+01 3bp6B 202 1.91e+01 3lk42 277 1.94e+01 2grgA 120 1.99e+01 d.110.10.1 147159 1q9rB 222 2.01e+01 b.1.1.1,b.1.1.2 96307,96308 3g0bA 740 2.12e+01 2fhzB 108 2.15e+01 d.243.1.2 133506 1n0xH 230 2.17e+01 b.1.1.1,b.1.1.2 91528,91529 3mi6A 745 2.18e+01 3ednA 299 2.18e+01 1bev1 281 2.19e+01 1aym1 3dm3A 105 2.20e+01 2gm6A 208 2.27e+01 b.82.1.19 147130 2qqrA 118 2.33e+01 b.34.9.1,b.34.9.1 151226,151227 3hacA 728 2.35e+01 1h30A 422 2.35e+01 b.29.1.4,b.29.1.4 76604,76605 1qx4A 274 2.37e+01 b.43.4.2,c.25.1.1 104624,104625 2uubK 129 2.41e+01 c.55.4.1 139942 2va4A 192 2.49e+01 2nnrA 110 2.54e+01 b.1.26.1 148321 3es6B 118 2.59e+01 b.1.18.23 158195 1g5hA 454 2.61e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 1xksA 450 2.63e+01 b.69.14.1 115422 1am2 199 2.64e+01 1am2 1am2A 199 2.64e+01 b.86.1.2 28381 2ux7A 122 2.66e+01 3ivkA 224 2.67e+01 1x99A 145 2.73e+01 b.97.1.2 114978 3mmyA 368 2.73e+01 1qm9A 198 2.79e+01 1qm9A d.58.7.1,d.58.7.1 39207,39208 3gldA 295 2.80e+01 1d5bB 221 2.86e+01 8fabA b.1.1.1,b.1.1.2 20205,21221 2v5sA 394 2.86e+01 1q55A 880 2.89e+01 i.20.1.1 95862 2d7vA 162 3.02e+01 d.227.1.1 146468 3fv3A 339 3.07e+01 3ejvA 179 3.07e+01 d.17.4.28 158181 2v24A 208 3.10e+01 3e8vA 82 3.21e+01 3fq3A 197 3.25e+01 1p5vA 235 3.27e+01 b.1.11.1,b.7.2.1 87812,87813 3g12A 128 3.27e+01 3f1zA 133 3.30e+01 2a8kA 108 3.30e+01 d.243.1.2 126404 1onqA 283 3.37e+01 b.1.1.2,d.19.1.1 93365,93366 1cs6A 382 3.40e+01 1cs6A b.1.1.4,b.1.1.4,b.1.1.4,b.1.1.4 21760,21761,21762,21763 1bxvA 91 3.41e+01 1aac b.6.1.1 22875 2w80C 253 3.48e+01 1cd0A 111 3.51e+01 8fabA b.1.1.1 20559 3kstA 306 3.53e+01 3dlqR 211 3.53e+01 1kdj 102 3.57e+01 1plc 1kdjA 102 3.57e+01 b.6.1.1 22864 2h1tA 188 3.60e+01 b.178.1.1 147215 2a22A 215 3.60e+01 d.159.1.7 126025 2zgyA 320 3.62e+01 c.55.1.1,c.55.1.1 154425,154426 1id2A 106 3.63e+01 1aac b.6.1.1 62288 1wbiA 129 3.63e+01 2bk8A 97 3.66e+01 3ktzA 251 3.68e+01 1sy3A 184 3.77e+01 b.60.1.1 106110 3kykH 227 3.79e+01 3k6iA 99 3.82e+01 1mixA 206 3.83e+01 a.11.2.1,b.55.1.5 79166,79167 3bjqA 316 3.84e+01 1b2wH 220 3.87e+01 1igtB b.1.1.1,b.1.1.2 20307,21299 1zq1A 438 3.90e+01 b.38.3.1,c.88.1.1 125489,125490 1axsB 221 3.91e+01 1mfa b.1.1.1,b.1.1.2 20201,21217 1c76A 136 3.91e+01 2sak d.15.5.1 37718 3bpoC 314 3.91e+01 2zwrA 207 3.94e+01 1qqhA 144 3.97e+01 1dtoA b.91.1.1 28404 4pazA 123 3.99e+01 b.6.1.1 22881 3fn0H 231 4.00e+01 3h51A 156 4.00e+01 1prn 289 4.01e+01 3prn 2v5mA 388 4.09e+01 3b2mA 295 4.11e+01 2vqeK 129 4.12e+01 c.55.4.1 153435 2ow6A 1045 4.12e+01 a.8.3.1,b.30.5.6,c.6.2.1 149039,149040,149041 1je5A 206 4.13e+01 1je5A b.40.4.7 62909 1wwcA 118 4.15e+01 1wwcA b.1.1.4 21778 1d7cA 190 4.16e+01 1d7bA b.1.9.1 22309 3lk2B 243 4.21e+01 3fdrA 94 4.25e+01 3fbuA 168 4.25e+01 2wngA 327 4.26e+01 3i3vA 405 4.29e+01 1x6zA 123 4.29e+01 d.24.1.1 121763 3cfbB 213 4.29e+01 2uvfA 608 4.34e+01 1pz5B 220 4.36e+01 b.1.1.1,b.1.1.2 95403,95404 1io1A 398 4.39e+01 1io1A e.32.1.1 62611 3c8dA 403 4.41e+01 b.1.18.20,c.69.1.2 156025,156026 1j83A 180 4.41e+01 b.18.1.12 66430 3eifA 936 4.45e+01 2bklA 695 4.51e+01 1f15B 218 4.58e+01 1f15B b.121.4.5 23321 1xf1A 926 4.64e+01 2nvwA 479 4.65e+01 c.2.1.3,d.81.1.5 138665,138666 1u7iA 136 4.67e+01 d.32.1.7 107724 1rzfH 235 4.68e+01 b.1.1.1,b.1.1.2 98150,98151 2ajuH 219 4.70e+01 3gleA 295 4.73e+01 2egeA 75 4.73e+01 2z5wA 136 4.73e+01 2zfuA 215 4.75e+01 3kymB 227 4.78e+01 3d48R 211 4.80e+01 b.1.2.1,b.1.2.1 157289,157290 2a74B 188 4.84e+01 1vc3B 97 5.00e+01 8fabB 224 5.00e+01 1igtB b.1.1.1,b.1.1.2 19773,20883 1i7pA 274 5.00e+01 b.43.4.2,c.25.1.1 66048,66049 3e0eA 97 5.01e+01 1gwyA 175 5.02e+01 b.97.1.1 83356 3eesA 153 5.03e+01 2imlA 199 5.08e+01 b.45.1.4 147729 1oe8A 211 5.10e+01 a.45.1.1,c.47.1.5 86905,86906 2bh0A 208 5.13e+01 2g35A 100 5.17e+01 b.55.1.5 134548 2woyA 356 5.19e+01 1jhnA 424 5.20e+01 b.104.1.1,b.29.1.12 66722,70060 3c5pA 197 5.23e+01 2frgP 106 5.23e+01 3idgB 237 5.26e+01 1gzqA 300 5.31e+01 b.1.1.2,d.19.1.1 70818,70819 1ukgA 252 5.43e+01 b.29.1.1 99489 3gi9H 223 5.44e+01 2nr4A 213 5.44e+01 b.45.1.4 148347 2tbvA 387 5.45e+01 2tbvA b.121.4.7 23302 2cdpA 160 5.49e+01 2x10A 545 5.52e+01 1zr6A 503 5.58e+01 2vxvH 223 5.64e+01 1nd6A 354 5.65e+01 c.60.1.2 80407 1op3H 225 5.66e+01 b.1.1.1,b.1.1.2 87208,87209 1oi6A 205 5.66e+01 b.82.1.1 103940 1iq9A 61 5.71e+01 g.7.1.1 90669 3hsuA 503 5.78e+01 2jk9A 212 5.79e+01 3i2cH 222 5.79e+01 3jysA 499 5.79e+01 3ey8A 133 5.82e+01 2fx7H 228 5.83e+01 b.1.1.1,b.1.1.2 134276,134277 1gc1H 229 5.83e+01 1gc1H b.1.1.1,b.1.1.2 20265,21265 2cm5A 166 5.87e+01 b.7.1.2 130613 3holA 509 5.89e+01 3eqnA 758 6.01e+01 2ns9A 157 6.01e+01 d.129.3.10 148382 3lpmA 259 6.04e+01 3c2uA 538 6.05e+01 1qwnA 1045 6.05e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1ej6A 1289 6.09e+01 i.7.1.1 45967 2sak 121 6.13e+01 2sak 2sakA 121 6.13e+01 d.15.5.1 37711 1ojjA 402 6.17e+01 b.29.1.10 93130 2qj8A 332 6.24e+01 2h7wA 131 6.26e+01 b.1.26.1 136225 1htyA 1015 6.35e+01 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 1dzoA 123 6.35e+01 1dzoA d.24.1.1 38378 2aq5A 402 6.38e+01 2qkiB 188 6.44e+01 1ghfH 212 6.45e+01 1igtB b.1.1.1,b.1.1.2 20109,21139 1afvH 220 6.52e+01 1mfa b.1.1.1,b.1.1.2 20131,21161 3kebA 224 6.56e+01 3d30A 208 6.58e+01 3d9aH 210 6.63e+01 3hv9A 265 6.67e+01 1seqL 213 6.72e+01 3imhA 338 6.74e+01 2zw2A 92 6.79e+01 1y55X 126 6.82e+01 2g3rA 123 6.84e+01 b.34.9.1,b.34.9.1 134570,134571 1fi2A 201 6.88e+01 1fi2A b.82.1.2 59845 1xgyH 219 6.89e+01 b.1.1.2 121985 3a5xA 494 6.90e+01 3m4rA 222 6.94e+01 2wb9A 211 6.95e+01 1v6iA 232 6.97e+01 b.29.1.1 100383 2vqaA 361 6.98e+01 1a22B 238 6.99e+01 1axiB b.1.2.1,b.1.2.1 22003,22004 1l6zA 216 7.03e+01 b.1.1.1,b.1.1.4 77770,77771 3fycA 265 7.12e+01 1ad0B 220 7.13e+01 1igtB b.1.1.1,b.1.1.2 20125,21155 1xe1A 116 7.18e+01 b.43.3.1 109571 3k2mC 101 7.18e+01 1a0qH 217 7.21e+01 1mfa b.1.1.1,b.1.1.2 20287,21279 3l4cA 220 7.25e+01 1d7bA 186 7.28e+01 1d7bA b.1.9.1 22307 1iuzA 98 7.31e+01 b.6.1.1 22861 2yz8A 103 7.41e+01 2w60A 218 7.45e+01 2d37A 176 7.61e+01 2jtmA 60 7.66e+01 2whxA 618 7.68e+01 1mwmA 320 7.70e+01 c.55.1.1,c.55.1.1 79580,79581 2gudA 122 7.78e+01 b.77.3.1 135732 1vprA 374 7.83e+01 b.60.1.7 120066 1f00I 282 7.85e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1yn3A 98 7.87e+01 1f8eA 388 7.89e+01 2qwc b.68.1.1 59694 2dwcA 433 7.90e+01