# List of top-scoring protein chains for t2k-100-30-str2-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 1e54A 332 5.48e-23 1e54A f.4.3.1 59258 2fgqX 332 1.38e-22 f.4.3.1 133439 2omf 340 1.54e-20 2omf 1hxxA 340 1.63e-20 2omf f.4.3.1 61385 2j1nA 346 2.14e-20 2por 301 6.63e-08 2por 2porA 301 6.63e-08 f.4.3.1 43759 1prn 289 2.01e-07 3prn 3prn 289 2.40e-07 3prn 3prnA 289 2.40e-07 f.4.3.1 43761 2o4vA 411 2.24e-06 1a0tP 413 1.01e-04 1a0tP f.4.3.2 43794 1i78A 297 6.59e-03 f.4.4.1 66046 2odjA 428 1.24e-02 1qd6C 240 2.17e-02 1qd5A 1p4tA 155 2.17e-02 f.4.1.1 87779 2iwvA 281 2.19e-02 1kmoA 774 2.41e-02 f.4.3.3 72753 1t16A 427 2.43e-02 f.4.3.4 106242 1qd5A 275 2.73e-02 1qd5A f.4.2.1 43748 1po0A 751 4.18e-02 f.4.3.3 94960 2mprA 421 6.73e-02 2mprA f.4.3.2 43788 2f1cX 286 1.32e-01 1qfgA 725 1.41e-01 1by5A f.4.3.3 43803 1qj8A 148 1.90e-01 1qj8A f.4.1.1 43744 2fcpA 723 2.47e-01 1by5A f.4.3.3 43802 1hn0A 1021 3.19e-01 a.102.3.2,b.18.1.17,b.24.1.1,b.30.5.2 83616,83617,83618,83619 2jqyA 280 3.69e-01 1by5A 714 4.67e-01 1by5A f.4.3.3 43800 1ux6A 350 6.23e-01 b.29.1.16,g.75.1.1 100145,100146 1sdwA 314 8.34e-01 b.121.1.2,b.121.1.2 98810,98811 1af6A 421 9.12e-01 2mprA f.4.3.2 43772 1phm 310 1.10e+00 1phm 3bk5A 237 1.18e+00 1yi9A 309 1.20e+00 b.121.1.2,b.121.1.2 123276,123277 1h54A 754 1.40e+00 a.102.1.4,b.30.5.3 60634,60635 1q40B 219 1.84e+00 d.17.4.2 95771 2dddA 225 1.89e+00 1w99A 558 2.01e+00 1yo8A 634 2.16e+00 1qnxA 209 2.20e+00 1qnxA d.111.1.1 40914 2h5oA 234 2.42e+00 1qjpA 171 2.84e+00 1bxwA f.4.1.1 43742 2f1vA 197 2.92e+00 2vadA 223 3.01e+00 2qdrA 303 3.22e+00 1w61A 414 3.72e+00 1yq2A 1024 3.80e+00 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 123843,123844,123845,123846,123847 1k1xA 659 3.87e+00 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1txnA 328 4.23e+00 d.248.1.1 112779 1h2xA 710 4.25e+00 b.69.7.1,c.69.1.4 76598,76599 1ggxA 223 4.40e+00 1ggxA d.22.1.1 38367 1xssA 225 4.47e+00 1zgoA 223 4.53e+00 1o6gA 710 5.01e+00 b.69.7.1,c.69.1.4 81087,81088 1e8nA 710 5.10e+00 1qfmA b.69.7.1,c.69.1.4 27675,34643 1h2wA 710 5.19e+00 b.69.7.1,c.69.1.4 76596,76597 1qfmA 710 5.21e+00 1qfmA b.69.7.1,c.69.1.4 27673,34641 1ryp2 233 5.56e+00 1ryp2 2rh7A 239 6.19e+00 1g0u1 266 6.33e+00 1m26A 133 6.38e+00 1r0uA 148 6.55e+00 b.60.1.5 96741 2o62A 270 6.63e+00 2ie2A 222 7.21e+00 1tk1A 260 7.70e+00 d.248.1.1 107066 1v7wA 807 7.72e+00 a.102.1.4,b.30.5.3 108411,108412 2qn6A 414 7.83e+00 1cb8A 678 7.84e+00 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1usyA 275 8.05e+00 d.104.1.1 113422 1ymmA 191 8.15e+00 b.1.1.2,d.19.1.1 123701,123702 1fx5A 242 8.25e+00 1led b.29.1.1 24135 2a46A 238 8.33e+00 1ugxA 133 8.45e+00 1ei5A 520 8.86e+00 1ei5A b.61.3.1,b.61.3.1,e.3.1.1 27418,27419,42772 1ww7A 160 9.38e+00 2p4mA 219 9.42e+00 1c3mA 147 9.62e+00 1jotA b.77.3.1 27983 1xmzA 241 9.72e+00 2zaiA 497 9.94e+00 2hpwA 233 1.01e+01 1jssA 224 1.04e+01 d.129.3.2 71844 1oacA 727 1.08e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24390,38007,38008,40003 1gc1H 229 1.10e+01 1gc1H b.1.1.1,b.1.1.2 20265,21265 1i31A 314 1.11e+01 1bw8A b.2.7.1 22481 1diwA 441 1.26e+01 1a8d b.29.1.6,b.42.4.2 24264,25609 1f60A 458 1.26e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 3bgaA 1010 1.36e+01 1uisA 231 1.37e+01 d.22.1.1 99431 2hzmB 317 1.38e+01 1y43B 173 1.42e+01 1d0hA 469 1.51e+01 1a8d b.29.1.6,b.42.4.2 24265,25610 1mkfA 382 1.57e+01 b.116.1.1 79232 2ejoA 223 1.65e+01 1bw8A 321 1.72e+01 1bw8A b.2.7.1 22482 1a8d 452 1.76e+01 1a8d 1a8dA 452 1.76e+01 b.29.1.6,b.42.4.2 24262,25607 1xxqA 161 1.78e+01 1zuxA 224 1.82e+01 1rhi3 236 1.83e+01 1aym3 2ahoA 414 1.83e+01 b.43.3.1,b.44.1.1,c.37.1.8 126767,126768,126769 2b3rA 134 1.85e+01 2nutA 769 1.92e+01 2oy7A 320 1.95e+01 2petA 231 1.96e+01 2oitA 434 1.98e+01 2qk0A 74 1.98e+01 2vpjA 301 2.03e+01 1k2eA 156 2.04e+01 d.113.1.1 72010 1of5A 221 2.04e+01 d.17.4.2 86933 1cid 177 2.04e+01 1cid 1cidA 177 2.04e+01 b.1.1.1,b.1.1.3 19740,21679 2go2A 163 2.12e+01 2fgtA 417 2.13e+01 1vbgA 876 2.22e+01 c.1.12.2,c.8.1.1,d.142.1.5 119951,119952,119953 2ehzA 302 2.23e+01 1zgsA 447 2.29e+01 2ib5A 233 2.36e+01 2eenA 183 2.41e+01 2hdiA 639 2.44e+01 1opoA 348 2.49e+01 b.121.4.7 87240 2hxdA 204 2.58e+01 3b9tA 484 2.60e+01 1vcaA 202 2.63e+01 1vcaA b.1.1.3,b.1.1.4 21649,21685 2o1qA 145 2.68e+01 2fauA 341 2.70e+01 2re9A 181 2.71e+01 1r1a1 287 2.76e+01 1aym1 2c0cA 362 2.89e+01 2sli 679 2.91e+01 2sli 2sliA 679 2.91e+01 b.29.1.9,b.68.1.1 24274,27611 2rg4A 216 2.93e+01 2a5zA 262 3.05e+01 b.29.1.24 126184 2dd7A 216 3.07e+01 2fs2A 151 3.09e+01 d.38.1.5 134003 1psuA 140 3.27e+01 d.38.1.5 88285 2qxlA 658 3.31e+01 2hkdA 320 3.32e+01 2rhsB 800 3.38e+01 2uurA 245 3.43e+01 1pvxA 194 3.43e+01 1axkA b.29.1.11 24341 2e26A 725 3.51e+01 1bxxA 285 3.53e+01 1bw8A b.2.7.1 22483 2gzbA 166 3.54e+01 3b3qE 197 3.67e+01 2pbeA 294 3.69e+01 2oggA 152 3.71e+01 1vyfA 135 3.74e+01 b.60.1.2 108902 1lj5A 379 3.78e+01 e.1.1.1 73928 2cxaA 256 3.87e+01 d.108.1.6 130993 2mev1 277 3.87e+01 2mev1 2r7dA 469 3.88e+01 2qf4A 172 3.89e+01 2oajA 902 3.93e+01 2v74B 346 3.95e+01 2otnA 308 3.97e+01 2f9zC 159 4.01e+01 2q86B 254 4.02e+01 2hyxA 352 4.02e+01 3b9cA 144 4.04e+01 1aqdA 192 4.06e+01 1iakA b.1.1.2,d.19.1.1 21585,38159 1pkhA 204 4.09e+01 b.85.4.1 94832 1uldA 150 4.10e+01 b.29.1.3 99545 2gw3A 225 4.11e+01 1jjoC 261 4.13e+01 1o59A 355 4.29e+01 b.18.1.22,b.18.1.22 92495,92496 2hqkA 219 4.30e+01 1cov3 238 4.30e+01 1aym3 1a6aA 176 4.36e+01 1iakA b.1.1.2,d.19.1.1 21615,38189 2qnkA 286 4.39e+01 2gufA 594 4.40e+01 f.4.3.3 135736 2odiA 238 4.40e+01 2gf3A 389 4.42e+01 c.3.1.2,d.16.1.3 135070,135071 1c8cA 64 4.43e+01 1azpA b.34.13.1 59084 3c0tA 207 4.44e+01 1hxs3 237 4.46e+01 1f1sA 814 4.47e+01 a.102.3.2,b.1.18.2,b.24.1.1,b.30.5.2 64928,64929,64930,64931 1t4wA 196 4.55e+01 b.2.5.2 106427 1bf4A 63 4.55e+01 1azpA b.34.13.1 37461 1sh8A 154 4.62e+01 d.38.1.5 105549 3bodA 178 4.76e+01 2fi3I 58 4.76e+01 2ch8A 201 4.77e+01 1lfwA 470 4.79e+01 c.56.5.4,d.58.19.1 77942,77943 2amdA 311 4.81e+01 1g1kA 143 4.83e+01 1aohA b.2.2.2 22404 2r55A 231 4.84e+01 1jeyB 565 4.87e+01 1jeqB b.131.1.2,c.62.1.4 90372,90373 2c4xA 260 4.90e+01 1ij8A 128 5.08e+01 b.61.1.1 62480 2a9dA 372 5.12e+01 b.1.18.6,d.176.1.1 126431,126432 1el5A 389 5.13e+01 1b3mA c.3.1.2,d.16.1.3 30369,37937 1ej6A 1289 5.16e+01 i.7.1.1 45967 2h2zA 306 5.19e+01 1th8A 145 5.24e+01 d.122.1.3 106908 2b3nA 159 5.27e+01 d.38.1.4 127792 1yr2A 741 5.28e+01 2qkpA 151 5.31e+01 1zq1C 633 5.45e+01 a.182.1.2,d.74.4.1,d.128.1.5 125493,125494,125495 1jotA 133 5.47e+01 1jotA 1bnzA 64 5.55e+01 1azpA b.34.13.1 37468 2o3oA 254 5.57e+01 2cqsA 842 5.61e+01 2aexA 346 5.66e+01 2a22A 215 5.67e+01 d.159.1.7 126025 1w15A 153 5.74e+01 b.7.1.2 109041 1l9cA 389 5.80e+01 c.3.1.2,d.16.1.3 77815,77816 1wmxA 205 5.88e+01 b.18.1.24 109418 1u1zA 168 5.91e+01 d.38.1.6 107602 1c4rA 182 5.96e+01 1c4rA b.29.1.4 24229 2rb8A 104 6.07e+01 2q6kA 283 6.08e+01 1nqnA 122 6.11e+01 b.61.1.1 86042 2rdgA 196 6.16e+01 1jnyA 435 6.21e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1h3iA 293 6.21e+01 b.76.2.1,b.85.7.1 76635,76636 2dy1A 665 6.22e+01 1tv8A 340 6.30e+01 c.1.28.3 107352 2fytA 340 6.30e+01 c.66.1.6 134391 1bxwA 172 6.34e+01 1bxwA f.4.1.1 43743 1jmmA 377 6.34e+01 b.30.6.1 71749 1gw5S 142 6.39e+01 d.110.4.2 70633 1upsA 420 6.39e+01 b.29.1.2,b.42.2.3 113394,113395 3b3fA 341 6.40e+01 2ogrA 229 6.48e+01 2q8oA 136 6.49e+01 1who 96 6.50e+01 1who 1whoA 96 6.50e+01 b.7.3.1 23215 2vglS 142 6.50e+01 1gmuA 143 6.55e+01 b.107.1.1,d.58.38.1 65335,65336 1xniA 118 6.57e+01 b.34.9.1,b.34.9.1 115582,115583 1yiqA 689 6.64e+01 1dr9A 201 6.67e+01 1dr9A b.1.1.1,b.1.1.3 19762,21684 3c8xA 206 6.85e+01 1lkeA 184 6.85e+01 b.60.1.1 84622 2cm5A 166 6.88e+01 b.7.1.2 130613 2dfbA 190 7.03e+01 b.29.1.11 131470 2h1tA 188 7.22e+01 2g6yA 217 7.25e+01 1xs1A 193 7.26e+01 b.85.4.1 115892 1y0gA 191 7.29e+01 b.61.6.1 116299 2ii1A 301 7.32e+01 1pvc1 301 7.34e+01 1pov1 1nqeA 594 7.46e+01 f.4.3.3 86027 1xnaA 183 7.49e+01 1xnaA b.18.1.8 23773 2a50B 168 7.67e+01 1tjxA 159 7.69e+01 b.7.1.2 112465 2p0wA 324 7.74e+01 1q2wA 308 7.81e+01 b.47.1.4 88355 2cc3A 150 7.92e+01 1a25A 149 7.95e+01 1rsy b.7.1.2 23197