# List of top-scoring protein chains for t2k.w0.5 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 3h3lA 241 1.66e-27 3hbkA 245 8.84e-27 3immA 201 4.58e-21 1z0hA 438 4.76e-03 b.29.1.6 124314 b.42.4.2 124315 2nm1A 436 4.80e-03 b.29.1.6 138369 b.42.4.2 138370 1epwA 1290 1.16e-02 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 2a6zA 222 5.90e-02 b.29.1.13 126319 2a6yA 256 6.41e-02 b.29.1.13 126318 1kdkA 177 1.18e-01 b.29.1.4 72351 1lhwA 189 1.18e-01 b.29.1.4 77966 1f5fA 205 1.29e-01 1d2sA b.29.1.4 24222 1d2sA 170 2.07e-01 1d2sA b.29.1.4 24221 2d93A 134 5.08e-01 1ky9A 448 1.18e+00 b.36.1.4 73198 b.47.1.1 73199 3cs0A 448 1.26e+00 b.36.1.4 156951 b.36.1.4 156952 b.47.1.1 156953 1qu0A 191 1.29e+00 1dykA b.29.1.4 24225 1dykA 394 1.39e+00 1dykA b.29.1.4 24223 b.29.1.4 24224 1okqA 394 1.41e+00 b.29.1.4 93267 b.29.1.4 93268 2cb6A 291 1.42e+00 2dfuA 264 2.36e+00 2b1mA 246 2.36e+00 2cb4A 291 3.10e+00 3butA 136 3.19e+00 2ohfA 396 3.76e+00 3jzjA 409 4.61e+00 3k01A 412 4.66e+00 1r1zA 263 5.04e+00 b.29.1.13 96840 3lcpA 247 5.14e+00 3a4uA 255 5.16e+00 1oq1A 223 5.23e+00 b.29.1.17 93408 1pn5A 159 5.35e+00 a.77.1.5 94948 3cx5A 431 5.41e+00 d.185.1.1 157076 d.185.1.1 157077 1kb9A 431 5.41e+00 d.185.1.1 77311 d.185.1.1 77312 1ezvA 430 5.42e+00 1be3A d.185.1.1 59541 d.185.1.1 59542 1gv9A 260 5.50e+00 b.29.1.13 70596 1sznA 417 5.64e+00 b.71.1.1 106162 c.1.8.1 106163 2vseA 841 5.92e+00 2ddmA 283 5.92e+00 2i0kA 561 6.19e+00 d.58.32.3 147480 d.145.1.1 147481 1i19A 561 6.20e+00 1i19A d.58.32.3 61522 d.145.1.1 61523 1zud1 251 6.23e+00 1zfnA 253 6.27e+00 1e19A 314 6.80e+00 1b7bA c.73.1.1 34967 2bjrA 368 7.52e+00 b.169.1.1 128628 b.169.1.1 128629 1x50A 164 7.71e+00 2cq2A 114 8.41e+00 d.58.7.1 130713 2r16A 182 8.53e+00 3kt1A 633 8.56e+00 3kt7A 633 8.72e+00 2iyeA 263 8.75e+00 2vxrA 482 8.90e+00 2fb6A 117 8.96e+00 1m3yA 413 9.26e+00 b.121.2.3 78579 b.121.2.3 78580 1m4xA 413 9.26e+00 i.6.1.1 78627 1uaiA 224 9.95e+00 b.29.1.18 107761 1j5qA 437 1.02e+01 b.121.2.3 77084 b.121.2.3 77085 2p9xA 99 1.04e+01 2hs5A 239 1.05e+01 a.4.5.6 147379 a.78.1.1 147380 1ej0A 180 1.09e+01 1ej0A c.66.1.2 34179 2glsA 469 1.14e+01 1lgr d.15.9.1 37851 d.128.1.1 41181 1f52A 468 1.14e+01 1lgr d.15.9.1 37839 d.128.1.1 41169 2dulA 378 1.16e+01 c.66.1.58 146588 2c9wA 169 1.17e+01 a.271.1.1 145023 d.93.1.1 145024 2jj6A 134 1.18e+01 2wjrA 214 1.27e+01 2wjqA 215 1.27e+01 3cwvA 369 1.28e+01 3dhpA 496 1.33e+01 b.71.1.1 157725 c.1.8.1 157726 1viwA 471 1.37e+01 1smd b.71.1.1 27776 c.1.8.1 28763 2d40A 354 1.39e+01 b.82.1.23 146454 1xxeA 282 1.45e+01 d.14.1.7 116157 d.14.1.7 116158 1ji1A 637 1.52e+01 b.1.18.2 71666 b.71.1.1 71667 c.1.8.1 71668 2d0fA 637 1.53e+01 b.1.18.2 131064 b.71.1.1 131065 c.1.8.1 131066 1uh4A 637 1.53e+01 b.1.18.2 99391 b.71.1.1 99392 c.1.8.1 99393 3blpX 496 1.54e+01 1izjA 637 1.56e+01 b.1.18.2 83841 b.71.1.1 83842 c.1.8.1 83843 2go3A 267 1.57e+01 d.14.1.7 135422 d.14.1.7 135423 1p42A 270 1.57e+01 d.14.1.7 87754 d.14.1.7 87755 2j65A 271 1.58e+01 d.14.1.7 138074 d.14.1.7 138075 2jt2A 274 1.58e+01 d.14.1.7 148195 d.14.1.7 148196 2apnA 114 1.59e+01 1izkA 637 1.61e+01 b.1.18.2 83844 b.71.1.1 83845 c.1.8.1 83846 3c5zA 202 1.62e+01 1kguA 496 1.62e+01 b.71.1.1 68598 c.1.8.1 68599 1zcyA 353 1.71e+01 c.68.1.14 124922 1kgwA 496 1.77e+01 b.71.1.1 68600 c.1.8.1 68601 2cpuA 496 1.78e+01 1smd b.71.1.1 63334 c.1.8.1 63335 1kgxA 496 1.80e+01 b.71.1.1 68602 c.1.8.1 68603 1zcvA 353 1.81e+01 c.68.1.14 124919 1kb3A 496 1.81e+01 b.71.1.1 72269 c.1.8.1 72270 1kbkA 496 1.83e+01 b.71.1.1 72282 c.1.8.1 72283 3ij8A 496 1.83e+01 2k46A 190 1.84e+01 2jwpA 174 1.84e+01 1kbbA 496 1.84e+01 b.71.1.1 72275 c.1.8.1 72276 153lA 185 1.86e+01 d.2.1.5 36984 2gh1A 301 1.89e+01 c.66.1.49 135170 3baxA 496 1.91e+01 b.71.1.1 155041 c.1.8.1 155042 3egwB 509 1.93e+01 1y4zB 512 1.95e+01 d.58.1.5 144594 1y5iB 512 1.95e+01 d.58.1.5 122641 3ncmA 92 1.96e+01 3ncmA b.1.1.4 21702 1jxkA 491 2.03e+01 b.71.1.1 63316 c.1.8.1 63317 3hx3A 316 2.07e+01 1x44A 103 2.10e+01 b.1.1.4 121678 1z32X 496 2.10e+01 b.71.1.1 124394 c.1.8.1 124395 1nm9A 496 2.11e+01 b.71.1.1 91974 c.1.8.1 91975 1smdA 496 2.11e+01 b.71.1.1 27768 c.1.8.1 28755 1jxjA 496 2.12e+01 b.71.1.1 63314 c.1.8.1 63315 3jyvL 118 2.12e+01 3hy5A 316 2.18e+01 1ldgA 316 2.18e+01 c.2.1.5 30165 d.162.1.1 42132 1q4nX 496 2.19e+01 b.71.1.1 95807 c.1.8.1 95808 1v29A 220 2.21e+01 d.149.1.1 113493 1qw1A 121 2.26e+01 b.34.1.2 145772 3blkA 496 2.26e+01 2dckA 354 2.30e+01 1b0aA 288 2.37e+01 1a4iA c.2.1.7 30286 c.58.1.2 33934 1qqoA 378 2.48e+01 1ba1 c.55.1.1 33395 c.55.1.1 33396 1vclA 432 2.49e+01 b.42.2.1 108498 b.42.2.1 108499 d.281.1.1 108500 3gbaA 257 2.49e+01 2wkyA 258 2.53e+01 2qs4A 258 2.54e+01 3c31A 258 2.54e+01 1zctA 290 2.61e+01 c.68.1.14 124916 1gbsA 185 2.62e+01 d.2.1.5 36986 3czcA 110 2.63e+01 2eiyA 308 2.65e+01 1wrvA 308 2.65e+01 1dypA 271 2.68e+01 1dypA b.29.1.2 24185 2c6uA 122 2.68e+01 1ll2A 333 2.71e+01 c.68.1.14 74005 1ll0A 339 2.75e+01 c.68.1.14 73995 3bdmF 287 2.77e+01 d.153.1.4 155134 1qvzA 237 2.78e+01 c.23.16.2 96453 1z7qG 288 2.78e+01 d.153.1.4 124654 1wmxA 205 2.79e+01 b.18.1.24 109418 2c24A 206 2.80e+01 b.18.1.24 129657 2qndA 144 2.86e+01 2po6A 278 2.89e+01 b.1.1.2 149710 d.19.1.1 149711 1uhkA 191 2.92e+01 a.39.1.5 119681 1ej3A 191 2.92e+01 1ej3A a.39.1.5 17259 3hujA 284 2.94e+01 1zt4A 281 2.95e+01 b.1.1.2 144763 d.19.1.1 144764 2zkql 143 2.95e+01 2pd4A 275 2.96e+01 c.2.1.2 139660 2pc8A 400 2.99e+01 3fvoA 256 3.02e+01 2zntA 256 3.02e+01 2qyvA 487 3.04e+01 1yecL 219 3.04e+01 8fabA b.1.1.1 20144 b.1.1.2 21174 1qvvA 237 3.06e+01 c.23.16.2 96442 1rw7A 243 3.07e+01 c.23.16.2 97963 2a92A 321 3.08e+01 1tvnA 293 3.11e+01 c.1.8.3 119360 3glxA 226 3.13e+01 3dsmA 328 3.15e+01 2ixcA 202 3.22e+01 b.82.1.1 137765 3c5eA 570 3.28e+01 2wd9A 569 3.28e+01 1g3tA 226 3.29e+01 a.4.5.24 65127 a.76.1.1 65128 b.34.1.2 65129 3kx6A 379 3.32e+01 2tdxA 226 3.32e+01 a.4.5.24 16201 a.76.1.1 18407 2qqbA 226 3.32e+01 2qq9A 226 3.32e+01 2qqaA 226 3.32e+01 1eqpA 394 3.33e+01 1cz1A c.1.8.3 28812 1c0wA 225 3.35e+01 1bi0 a.4.5.24 16211 a.76.1.1 18417 b.34.1.2 24455 2dtrA 226 3.35e+01 a.4.5.24 16193 a.76.1.1 18399 b.34.1.2 24450 1fwzA 226 3.35e+01 a.4.5.24 60077 a.76.1.1 60078 b.34.1.2 60079 1eqcA 394 3.38e+01 1cz1A c.1.8.3 28811 1cz1A 394 3.38e+01 1cz1A c.1.8.3 28839 2pboA 400 3.39e+01 1g3yA 226 3.39e+01 a.4.5.24 65136 a.76.1.1 65137 b.34.1.2 65138 1upiA 225 3.39e+01 b.82.1.1 99757 2pb1A 400 3.40e+01 c.1.8.3 139645 1p92A 226 3.41e+01 a.4.5.24 104085 a.76.1.1 104086 b.34.1.2 104087 2qwoA 394 3.43e+01 c.55.1.1 151430 c.55.1.1 151431 3i2wA 290 3.47e+01 2npiA 460 3.47e+01 1d1rA 116 3.59e+01 1d1rA d.64.1.1 39548 1xe7A 203 3.60e+01 b.82.1.16 115213 1bymA 97 3.62e+01 1bi0 b.34.1.2 24458 1piwA 360 3.63e+01 b.35.1.2 104156 c.2.1.1 104157 1qvpA 87 3.66e+01 b.34.1.2 111659 1g8wA 233 3.73e+01 1led b.29.1.1 24160 1fatA 252 3.76e+01 1led b.29.1.1 24164 1pk8A 422 3.79e+01 c.30.1.5 94807 d.142.1.3 94808 1atsA 386 3.80e+01 c.55.1.1 33423 c.55.1.1 33424 2zaaA 236 3.83e+01 2fvuA 222 3.87e+01 2uxtA 451 3.89e+01 3b9cA 144 3.92e+01 2w40A 503 3.92e+01 2w41A 507 3.92e+01 2zacA 236 3.94e+01 1hwmB 266 3.95e+01 1abrB b.42.2.1 25569 b.42.2.1 25570 2fl7A 232 3.97e+01