# List of top-scoring protein chains for t04-100-40-40-str2+CB_burial_14_7-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 1gefA 123 3.67e-02 1gefA c.52.1.18 60465 1cliA 345 1.25e-01 1cliA d.79.4.1,d.139.1.1 39816,41459 1ob8A 135 5.05e-01 c.52.1.18 111627 1wdjA 187 6.63e-01 c.52.1.27 114536 2jg1A 330 7.75e-01 1hh1A 143 8.01e-01 1gefA c.52.1.18 61036 1gmlA 178 8.72e-01 c.8.5.2 70273 2ixsA 323 1.08e+00 2gb7A 305 1.45e+00 2q8zA 342 1.53e+00 1mxiA 160 1.53e+00 c.116.1.1 79646 2fokA 579 1.90e+00 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16131,16132,16133,33323 1sw5B 275 1.94e+00 c.94.1.1 106070 1tyyA 339 2.08e+00 c.72.1.1 112850 2btuA 346 2.12e+00 1sw2A 275 2.49e+00 c.94.1.1 106064 2eo0A 147 2.67e+00 1xmxA 385 2.80e+00 c.52.1.26 115568 1vk3A 615 2.92e+00 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 1ohvA 472 2.97e+00 c.67.1.4 93031 2g37A 327 3.14e+00 2ajrA 331 3.16e+00 c.72.1.1 126892 2j8gA 339 3.24e+00 2ggoA 401 3.67e+00 2f02A 323 4.43e+00 c.72.1.1 132649 2vhlA 396 4.62e+00 1h09A 338 4.81e+00 b.109.1.1,c.1.8.8 83420,83421 1e4eA 343 5.20e+00 1iow c.30.1.2,d.142.1.1 59221,59222 1sx5A 244 5.75e+00 c.52.1.2 99023 2hs3A 603 5.79e+00 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 136712,136713,136714,136715 1uteA 313 6.01e+00 1uteA d.159.1.1 42078 1y88A 199 6.17e+00 a.60.4.3,c.52.1.30 116560,116561 1nekA 588 6.40e+00 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 1c0pA 363 6.49e+00 1an9A c.4.1.2,d.16.1.3 30647,37934 2ewfA 610 6.65e+00 2cc1A 262 6.88e+00 e.3.1.1 130211 1sw5A 275 7.36e+00 c.94.1.1 106069 1yx2A 365 7.68e+00 1o12A 376 8.19e+00 b.92.1.5,c.1.9.10 80758,80759 1iow 306 8.48e+00 1iow 1iowA 306 8.48e+00 c.30.1.2,d.142.1.1 31713,41481 2jerA 389 8.72e+00 1ybqB 390 8.76e+00 1m3sA 186 8.79e+00 c.80.1.3 78573 1mkmA 249 9.38e+00 a.4.5.33,d.110.2.2 79242,79243 2bx2L 517 9.77e+00 2p14A 192 9.83e+00 1onxA 390 9.89e+00 b.92.1.7,c.1.9.13 87176,87177 1p3wA 404 9.89e+00 c.67.1.3 87752 2ffcA 353 9.98e+00 c.1.2.3 133378 1vhyA 257 1.00e+01 b.122.1.2,c.116.1.5 100714,100715 3cz8A 319 1.03e+01 1we0A 187 1.07e+01 c.47.1.10 120930 2rb9A 334 1.11e+01 2dyuA 334 1.20e+01 1xdwA 331 1.21e+01 1fxoA 293 1.22e+01 1g0rA c.68.1.6 34524 1mp4A 292 1.22e+01 c.68.1.6 79376 2okfA 140 1.22e+01 2avxA 171 1.23e+01 1to3A 304 1.26e+01 c.1.10.1 107161 2hk0A 309 1.30e+01 1vplA 256 1.31e+01 c.37.1.12 113966 1senA 164 1.33e+01 c.47.1.1 105465 1gqeA 365 1.33e+01 e.38.1.1 70351 1b0aA 288 1.34e+01 1a4iA c.2.1.7,c.58.1.2 30286,33934 1atlA 202 1.34e+01 1atlA d.92.1.9 40322 1g6hA 257 1.42e+01 1gajA c.37.1.12 60318 2zctA 249 1.43e+01 2fdsA 352 1.44e+01 c.1.2.3 133320 2v9yA 334 1.44e+01 2fa8A 105 1.45e+01 c.47.1.23 133185 2aqwA 332 1.46e+01 c.1.2.3 127184 1qmvA 197 1.49e+01 1qq2A c.47.1.10 33066 1k7jA 206 1.49e+01 d.115.1.1 72103 2tpsA 227 1.51e+01 2tpsA c.1.3.1 28591 2cjgA 449 1.52e+01 2exrA 524 1.53e+01 1m1lA 236 1.55e+01 d.260.1.1 91166 1xi3A 215 1.56e+01 c.1.3.1 109601 1onwA 390 1.57e+01 b.92.1.7,c.1.9.13 87172,87173 1r0vA 305 1.57e+01 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 2c5uA 375 1.61e+01 1w9hA 427 1.61e+01 c.55.3.10 120785 2jc5A 259 1.63e+01 1gvfA 286 1.67e+01 c.1.10.2 70599 1nxzA 246 1.69e+01 b.122.1.2,c.116.1.5 86391,86392 2p67A 341 1.69e+01 2inbA 140 1.73e+01 1eg5A 384 1.79e+01 1ecxA c.67.1.3 34429 2ha8A 184 1.79e+01 1zoyA 622 1.80e+01 1h5rA 293 1.81e+01 c.68.1.6 65623 1zq7A 207 1.83e+01 d.309.1.1 125501 2qziA 103 1.84e+01 1liiA 363 1.85e+01 c.72.1.1 73921 1qdlA 422 1.88e+01 1qdlA d.161.1.1 42088 1k0wA 231 1.93e+01 c.74.1.1 77220 1q8iA 783 1.94e+01 c.55.3.5,e.8.1.1 96208,96209 1t7lA 766 1.94e+01 1yrtA 364 1.97e+01 1x6vA 630 2.00e+01 b.122.1.3,c.26.1.5,c.37.1.4 121755,121756,121757 1p2fA 220 2.04e+01 a.4.6.1,c.23.1.1 87720,87721 2q18X 293 2.05e+01 9gafA 295 2.05e+01 1apyA d.153.1.5 42008 1tl2A 236 2.07e+01 1tl2A b.67.1.1 27541 2z3zA 706 2.17e+01 1dmgA 225 2.19e+01 1dmgA c.22.1.1 31036 1vhnA 318 2.20e+01 c.1.4.1 100693 2a9sA 171 2.21e+01 c.51.5.1 126448 3d02A 303 2.26e+01 2jgyA 279 2.26e+01 2uxyA 341 2.34e+01 2a40B 260 2.38e+01 d.151.1.1 126139 1lt3A 240 2.41e+01 1lt3A d.166.1.1 42230 2akaB 299 2.42e+01 c.37.1.8 126914 2cghA 268 2.43e+01 1o7fA 469 2.43e+01 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 1x0rA 249 2.44e+01 c.47.1.10 121562 1g67A 225 2.44e+01 c.1.3.1 60311 1sczA 233 2.51e+01 c.43.1.1 98802 2z1uA 343 2.53e+01 1p4kA 295 2.55e+01 d.153.1.5 87772 2abqA 306 2.57e+01 c.72.1.1 126528 1jk7A 323 2.61e+01 1auiA d.159.1.3 63144 1u5vA 273 2.63e+01 c.1.12.5 113054 2ew2A 316 2.64e+01 1g57A 217 2.65e+01 1g57A d.115.1.2 60253 2q0oA 236 2.67e+01 3brcA 156 2.75e+01 1u2zA 433 2.76e+01 c.66.1.31 107626 2bwrA 401 2.76e+01 1x8qA 184 2.78e+01 b.60.1.1 114966 2pm7B 297 2.78e+01 2hc5A 117 2.80e+01 1ujpA 271 2.83e+01 c.1.2.4 99462 2z2uA 311 2.87e+01 1lvwA 295 2.88e+01 c.68.1.6 84723 1eexB 224 2.94e+01 1dioB c.51.3.1 33213 1u5hA 273 3.00e+01 c.1.12.5 113037 3by4A 212 3.01e+01 2ff7A 247 3.02e+01 c.37.1.12 133377 1y1pA 342 3.02e+01 c.2.1.2 122550 1tib 269 3.04e+01 3tgl 1tibA 269 3.04e+01 c.69.1.17 34738 2qz7A 194 3.06e+01 1iukA 140 3.12e+01 c.2.1.8 83712 1v95A 130 3.17e+01 c.51.1.1 108435 2q4wA 524 3.29e+01 2z9wA 392 3.33e+01 2hjpA 290 3.34e+01 1sy3A 184 3.40e+01 b.60.1.1 106110 1eyqA 222 3.45e+01 1eypA d.36.1.1 38534 2i4lA 458 3.49e+01 2c81A 418 3.52e+01 1zupA 315 3.52e+01 c.55.3.11 125681 2pajA 492 3.53e+01 1ijxA 127 3.55e+01 1ijxA a.141.1.1 62511 1aroL 151 3.59e+01 1lba d.118.1.1 41063 2absA 383 3.59e+01 c.72.1.1 126534 1q79A 514 3.68e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1xrtA 467 3.73e+01 b.92.1.3,c.1.9.6 122258,122259 2h88A 621 3.75e+01 2oodA 475 3.76e+01 1lba 146 3.79e+01 1lba 1lbaA 146 3.79e+01 d.118.1.1 41062 2oz8A 389 3.79e+01 1u9iA 519 3.80e+01 c.37.1.11,c.37.1.11 119637,119638 1j9yA 385 3.81e+01 1j9yA c.1.8.3 62791 2av4A 162 3.83e+01 1budA 197 3.84e+01 1atlA d.92.1.9 40328 2g5fA 450 3.90e+01 d.161.1.1 134654 2c2xA 281 3.90e+01 1vrpA 381 3.96e+01 a.83.1.1,d.128.1.2 120473,120474 2h6rA 219 4.00e+01 2gx5A 170 4.01e+01 1a4iA 301 4.02e+01 1a4iA c.2.1.7,c.58.1.2 30278,33926 1j31A 262 4.03e+01 d.160.1.2 90808 2pvaA 345 4.07e+01 3pvaA d.153.1.3 41850 1a9xA 1058 4.07e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1f5aA 513 4.07e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39337,75835,75836 1cs0A 1073 4.08e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1yrrA 382 4.09e+01 b.92.1.5,c.1.9.10 123935,123936 1z6kA 293 4.09e+01 2iyaA 424 4.09e+01 3dni 260 4.11e+01 3dni 3bn1A 373 4.18e+01 1zczA 464 4.18e+01 c.24.1.3,c.97.1.4 124923,124924 1r6lA 239 4.21e+01 d.14.1.4,d.101.1.1 97153,97154 2h8lA 252 4.38e+01 1w0mA 226 4.40e+01 c.1.1.1 109027 2hq1A 247 4.41e+01 2f57A 317 4.41e+01 2irpA 208 4.43e+01 1tqjA 230 4.44e+01 c.1.2.2 107228 1rd5A 262 4.47e+01 c.1.2.4 111772 2bcqA 335 4.52e+01 a.60.6.1,a.60.12.1,d.218.1.2 128304,128305,128306 1zx5A 300 4.55e+01 b.82.1.3 125763 1erxA 184 4.56e+01 1np1A b.60.1.1 27164 1xjdA 345 4.57e+01 d.144.1.7 115388 1eceA 358 4.63e+01 1eceA c.1.8.3 28813 3d0cA 314 4.67e+01 1o6dA 163 4.68e+01 c.116.1.3 92567 1eonA 245 4.73e+01 1rvaA c.52.1.2 33238 2dnjA 260 4.73e+01 3dni d.151.1.1 41790 3pvaA 335 4.76e+01 3pvaA d.153.1.3 41854 1gsa 316 4.79e+01 1gsa 1gsaA 316 4.79e+01 c.30.1.3,d.142.1.1 31718,41477 2q49A 359 4.83e+01 c.2.1.3,d.81.1.1 139831,139832 1k2yX 463 4.86e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 2pmkA 243 4.88e+01 1mpyA 307 4.91e+01 1mpyA d.32.1.3,d.32.1.3 38508,38509 1i1nA 226 4.92e+01 c.66.1.7 71102 2nrrA 159 4.92e+01 2q02A 272 4.94e+01 2d5lA 706 4.97e+01 1y6hA 177 5.22e+01 d.167.1.1 116505 1nulA 152 5.23e+01 1nulA c.61.1.1 34011 2po1B 277 5.23e+01 2i3dA 249 5.25e+01 1vbiA 344 5.31e+01 1sbp 310 5.32e+01 1sbp 1sbpA 310 5.32e+01 c.94.1.1 35760 2it1A 362 5.37e+01 2cy8A 453 5.37e+01 2bjfA 329 5.45e+01 1tc5A 194 5.50e+01 c.110.1.1 106752 1eaf 243 5.51e+01 1eaf 1zotA 358 5.57e+01 3citA 160 5.57e+01 3cbwA 353 5.58e+01 1ysjA 404 5.68e+01 c.56.5.4,d.58.19.1 123975,123976 1vdwA 254 5.72e+01 e.7.1.1 100569 2e52A 300 5.74e+01 2bvyA 475 5.74e+01 b.1.18.2,c.1.8.3 129301,129302 2i87A 364 5.81e+01 1ibjA 464 5.85e+01 1ibjA c.67.1.3 62162 2qkoA 215 5.89e+01 2aqjA 538 5.90e+01 2d2rA 245 5.94e+01 1f1uA 323 5.98e+01 d.32.1.3,d.32.1.3 83200,83201 2au7A 175 5.99e+01 2nuwA 288 6.08e+01 2fv7A 331 6.08e+01 c.72.1.1 134197 1qo8A 566 6.08e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19696,30433,42316 2bqxA 173 6.16e+01 1hrdA 449 6.19e+01 1k89 c.2.1.7,c.58.1.1 30219,33867 1dpbA 243 6.25e+01 c.43.1.1 32618 1jsxA 207 6.46e+01 c.66.1.20 71846 2gwnA 452 6.48e+01 1nrjA 158 6.51e+01 d.110.4.4 86124 2pjdA 343 6.51e+01 2f9zC 159 6.52e+01 1xw8A 252 6.57e+01 c.6.2.5 116111 1c4kA 730 6.58e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 3c8xA 206 6.58e+01 1gkpA 458 6.59e+01 b.92.1.3,c.1.9.6 70231,70232 1snnA 227 6.60e+01 d.115.1.2 105821 2pa4A 323 6.63e+01 3bq5A 766 6.67e+01 1eokA 290 6.68e+01 1eokA c.1.8.5 28991 1x1nA 524 6.69e+01 c.1.8.1 121593 2eh6A 375 6.76e+01 2a5lA 200 6.80e+01 c.23.5.8 126176 1rztA 331 6.83e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 2ex4A 241 6.85e+01 c.66.1.42 132516 1v3wA 173 6.93e+01 b.81.1.5 100291 2gsjA 271 6.98e+01 2nw0A 189 6.99e+01 2bycA 137 7.00e+01 d.58.10.2 129476 1dxrH 258 7.00e+01 6prcH b.41.1.1,f.23.10.1 25456,43433 2bw3A 534 7.04e+01 a.270.1.1,c.55.3.12 129317,129318 2e7jA 371 7.06e+01 1rwiA 270 7.12e+01 b.68.9.1 97987 2e67A 264 7.14e+01 1w85A 368 7.17e+01 c.36.1.11 114335 1ju2A 536 7.18e+01 c.3.1.2,d.16.1.1 77169,77170 1y4iA 398 7.22e+01 c.67.1.3 122619 2ordA 397 7.25e+01 1xf1A 926 7.26e+01 1sc3A 178 7.27e+01 c.17.1.1 105416 1qh4A 380 7.40e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 3cvjA 243 7.43e+01 1pvdA 537 7.44e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 2gsaA 432 7.46e+01 2gsaA c.67.1.4 34446 2ganA 190 7.50e+01 d.108.1.1 134889 1j3wA 163 7.52e+01 d.110.7.1 90833 1oruA 195 7.53e+01 b.58.1.2 93464 1byb 495 7.62e+01 1byb 2j0iA 303 7.69e+01 2ax4A 198 7.71e+01 2f5tX 233 7.73e+01 1tqyA 424 7.75e+01 c.95.1.1,c.95.1.1 107245,107246 2hp1A 432 7.75e+01 1m7xA 617 7.87e+01 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 3bixA 574 7.89e+01 1v4vA 376 7.90e+01 c.87.1.3 100313 1eluA 390 7.97e+01 1elqA c.67.1.3 34434 1vkmA 297 7.98e+01 c.138.1.1 108670 2avwA 311 8.00e+01