# List of top-scoring protein chains for t2k-100-30-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 2oasA 436 1.20e-31 2g39A 497 7.27e-29 c.124.1.2,c.124.1.2 134553,134554 1xr4A 509 2.04e-21 c.124.1.2,c.124.1.2 115860,115861 2hj0A 519 3.61e-21 1ooyA 481 3.39e-19 c.124.1.3,c.124.1.2 93388,93389 2ahuA 531 1.37e-08 c.124.1.3,c.124.1.2 126785,126786 1k6dA 220 1.62e-04 c.124.1.2 72082 2pjmA 226 9.56e-03 1lk5A 229 9.87e-03 c.124.1.4,d.58.40.1 73960,73961 1poiA 317 1.86e-02 1poiA c.124.1.2 34153 1poiB 260 3.31e-02 1poiB c.124.1.3 34155 1vb5A 276 1.71e-01 c.124.1.5 113604 1uj6A 227 1.80e-01 c.124.1.4,d.58.40.1 107898,107899 2f8mA 244 3.79e-01 2hf9A 226 4.00e-01 2gnpA 266 5.04e-01 1o98A 511 8.11e-01 c.105.1.1,c.76.1.3 86684,86685 1eg7A 557 1.29e+00 1eg7A c.37.1.10 32241 1xtzA 264 1.55e+00 1f2dA 341 1.63e+00 1f2dA c.79.1.1 35298 1ejjA 511 2.88e+00 1ejjA c.105.1.1,c.76.1.3 59422,59423 1t9kA 347 3.01e+00 c.124.1.5 106721 1tzfA 259 3.15e+00 c.68.1.13 107476 1j0dA 341 3.83e+00 c.79.1.1 83902 1x1nA 524 4.53e+00 c.1.8.1 121593 1ox6A 555 5.82e+00 c.1.2.1,c.23.16.1 87505,87506 2c71A 216 6.00e+00 c.6.2.3 130017 1gnlA 544 6.27e+00 e.26.1.1 70287 1b7bA 310 6.43e+00 1b7bA c.73.1.1 34963 1zj8A 566 6.43e+00 1cv8 174 6.49e+00 1cv8 1cv8A 174 6.49e+00 d.3.1.1 37089 1jvnA 555 6.80e+00 c.1.2.1,c.23.16.1 67355,67356 3c4vA 426 6.91e+00 1nfp 228 7.04e+00 1nfp 1nfpA 228 7.04e+00 c.1.16.2 29555 2e55A 208 7.11e+00 1ur5A 309 7.38e+00 c.2.1.5,d.162.1.1 99807,99808 1sbzA 197 7.47e+00 c.34.1.1 112068 1uxjA 309 7.54e+00 c.2.1.5,d.162.1.1 108112,108113 1ur1A 378 7.95e+00 c.1.8.3 99804 2c7yA 404 8.00e+00 2c40A 312 8.28e+00 3beoA 375 8.30e+00 1nnwA 252 8.34e+00 d.159.1.5 80674 1yfoA 302 8.51e+00 2shpA c.45.1.2 32681 2efjA 384 8.71e+00 2bkxA 242 8.90e+00 1hd2A 161 9.08e+00 c.47.1.10 60962 2yxbA 161 9.24e+00 1pyfA 312 9.31e+00 c.1.7.1 95334 1zx0A 236 9.51e+00 c.66.1.16 125757 1l5wA 796 9.60e+00 c.87.1.4 73605 2pqmA 343 9.69e+00 2qjwA 176 9.80e+00 1a12A 413 1.00e+01 1a12A b.69.5.1 27663 1cj3A 392 1.04e+01 1pbe c.3.1.2,d.16.1.2 30347,37878 1reqA 727 1.07e+01 1reqA c.1.19.1,c.23.6.1 29620,31247 1ccwA 137 1.09e+01 1be1 c.23.6.1 31238 1pbe 394 1.17e+01 1pbe 1pbeA 394 1.17e+01 c.3.1.2,d.16.1.2 30338,37869 2qbuA 232 1.19e+01 1ahpA 797 1.20e+01 1a8i c.87.1.4 35544 2hzbA 333 1.23e+01 c.143.1.1 136911 2yvuA 186 1.26e+01 5reqA 727 1.28e+01 1reqA c.1.19.1,c.23.6.1 29632,31259 1u9yA 284 1.29e+01 c.61.1.2,c.61.1.2 119655,119656 1qo7A 394 1.31e+01 1qo7A c.69.1.11 34697 1e5xA 486 1.35e+01 c.79.1.1 59283 2ejaA 338 1.45e+01 1gz5A 456 1.48e+01 c.87.1.6 76406 1q7zA 566 1.48e+01 c.1.21.2,c.1.26.1 96090,96091 1tk9A 188 1.53e+01 c.80.1.3 107082 2iidA 498 1.53e+01 c.3.1.2,d.16.1.5 137426,137427 2cjpA 328 1.53e+01 1f8rA 498 1.56e+01 1f8rA c.3.1.2,d.16.1.5 30410,37974 1ve1A 304 1.60e+01 c.79.1.1 120007 1x92A 199 1.63e+01 c.80.1.3 114976 1jbwA 428 1.63e+01 c.59.1.2,c.72.2.2 62860,62861 2i7vA 459 1.65e+01 1tllA 688 1.66e+01 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 2bneA 241 1.68e+01 c.73.1.3 128824 2p5qA 170 1.72e+01 1c3oA 1073 1.75e+01 1c3oA a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18562,31491,31681,31682,41526,41527 1uqtA 482 1.76e+01 c.87.1.6 99794 2cb9A 244 1.78e+01 1ykjA 394 1.79e+01 2nx2A 181 1.79e+01 1hyhA 309 1.82e+01 1hyhA c.2.1.5,d.162.1.1 30150,42117 1w4xA 542 1.82e+01 c.3.1.5,c.3.1.5 109171,109172 1be1 137 1.85e+01 1be1 2cvbA 188 1.86e+01 c.47.1.10 130859 2c4mA 796 1.87e+01 1cs0A 1073 1.88e+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 1f07A 321 1.89e+01 1ezwA c.1.16.3 59560 1rypC 244 1.90e+01 1rypC d.153.1.4 41934 1k2wA 256 1.94e+01 c.2.1.2 90927 1jlnA 297 1.95e+01 1pty c.45.1.2 63172 1g8sA 230 2.01e+01 c.66.1.3 90507 1fcjA 322 2.10e+01 1oasA c.79.1.1 35289 1y1pA 342 2.12e+01 c.2.1.2 122550 1uaaA 673 2.12e+01 1pjr c.37.1.19,c.37.1.19 32401,32402 1pl8A 356 2.13e+01 b.35.1.2,c.2.1.1 94878,94879 1x0oA 119 2.16e+01 2vm6A 150 2.19e+01 1gsa 316 2.22e+01 1gsa 1gsaA 316 2.22e+01 c.30.1.3,d.142.1.1 31718,41477 1fbnA 230 2.27e+01 1fbnA c.66.1.3 34181 2ywdA 191 2.28e+01 3bofA 566 2.31e+01 1oasA 322 2.31e+01 1oasA c.79.1.1 35293 1o4sA 389 2.34e+01 c.67.1.1 86620 6ldhA 329 2.35e+01 c.2.1.5,d.162.1.1 30161,42128 2i2wA 212 2.43e+01 1vm8A 534 2.44e+01 c.68.1.5 113670 1ycdA 243 2.46e+01 1a8y 367 2.50e+01 1a8y 1a8yA 367 2.50e+01 c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1yxyA 234 2.50e+01 c.1.2.5 124203 1cjbA 231 2.52e+01 1qk3A c.61.1.1 34079 2b02A 119 2.52e+01 1h4pA 408 2.54e+01 c.1.8.3 90617 3cox 507 2.54e+01 1b8sA 3coxA 507 2.54e+01 c.3.1.2,d.16.1.1 30332,37863 2aq4A 434 2.56e+01 2q3bA 313 2.62e+01 2v9dA 343 2.66e+01 1rh9A 373 2.68e+01 c.1.8.3 118773 1xclA 235 2.70e+01 c.66.1.16 115127 2himA 358 2.71e+01 1e58A 249 2.72e+01 1qhfA c.60.1.1 59262 2z1mA 345 2.78e+01 1nofA 383 2.80e+01 b.71.1.2,c.1.8.3 92020,92021 2hhjA 267 2.82e+01 c.60.1.1 136497 1qwjA 229 2.83e+01 c.68.1.13 96478 1deoA 233 2.83e+01 1deoA c.23.10.4 31345 2bbsA 290 2.84e+01 1fgs 428 2.86e+01 1fgs 2gaiA 633 2.86e+01 3b85A 208 2.86e+01 1g7fA 298 2.87e+01 1pty c.45.1.2 60330 2dgdA 223 2.88e+01 1q52A 314 2.88e+01 c.14.1.3 95846 1k7cA 233 2.94e+01 c.23.10.4 68267 1pbtA 244 2.97e+01 c.124.1.1 94416 1v0eA 666 3.00e+01 b.68.1.2,b.108.1.3 113466,113467 2cm2A 304 3.07e+01 c.45.1.2 130610 1rlr 761 3.13e+01 1rlr 1rlrA 761 3.13e+01 a.98.1.1,c.7.1.2 18753,30679 1u0mA 382 3.14e+01 c.95.1.2,c.95.1.2 107557,107558 1rwiA 270 3.14e+01 b.68.9.1 97987 1kmmA 424 3.16e+01 1adjA c.51.1.1,d.104.1.1 33174,40723 3bq9A 460 3.21e+01 2d4wA 504 3.26e+01 1fs5A 266 3.26e+01 c.124.1.1 65044 1p1cA 199 3.26e+01 c.66.1.16 87669 2o2zA 323 3.27e+01 1ne2A 200 3.30e+01 c.66.1.32 85586 2hufA 393 3.37e+01 1k0iA 394 3.39e+01 c.3.1.2,d.16.1.2 67942,67943 1kfiA 572 3.40e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68555,68556,68557,68558 1rcuA 195 3.41e+01 c.129.1.1 97295 2vefA 314 3.43e+01 1vl1A 232 3.44e+01 c.124.1.1 108707 1wzaA 488 3.44e+01 b.71.1.1,c.1.8.1 121489,121490 1khhA 198 3.45e+01 c.66.1.16 68615 1gzgA 337 3.49e+01 c.1.10.3 70805 1e19A 314 3.49e+01 1b7bA c.73.1.1 34967 1wkrA 340 3.50e+01 b.50.1.2 109395 1ufoA 238 3.51e+01 c.69.1.27 99344 1pnsB 234 3.53e+01 i.1.1.1 88169 1a6dA 545 3.57e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19488,30819,38936 2ahrA 259 3.60e+01 a.100.1.10,c.2.1.6 126775,126776 1tb3A 352 3.61e+01 c.1.4.1 119205 1nc5A 373 3.69e+01 a.102.1.6 85548 1kcxA 518 3.70e+01 b.92.1.3,c.1.9.6 90953,90954 1yzhA 214 3.73e+01 c.66.1.53 124277 2rgxA 206 3.74e+01 2uubB 256 3.74e+01 c.23.15.1 139932 2oosA 338 3.77e+01 2va8A 715 3.78e+01 2hcrA 326 3.80e+01 2o9pA 454 3.87e+01 1eeoA 321 3.88e+01 1pty c.45.1.2 32655 2o2yA 349 3.89e+01 c.2.1.2 138894 1b4kA 337 3.89e+01 1b4kA c.1.10.3 29184 2fcaA 213 3.89e+01 c.66.1.53 133262 1hjsA 332 3.90e+01 c.1.8.3 83492 2vqeB 256 3.91e+01 1vdmA 153 3.91e+01 c.61.1.1 119994 2j5iA 276 4.09e+01 1bg6 359 4.13e+01 1bg6 1bg6A 359 4.13e+01 a.100.1.5,c.2.1.6 18810,30214 1pty 321 4.16e+01 1pty 1w5fA 353 4.16e+01 c.32.1.1,d.79.2.1 114247,114248 2ehhA 294 4.17e+01 2z1nA 260 4.25e+01 2qjcA 262 4.26e+01 1f3lA 321 4.28e+01 1g6q2 c.66.1.6 59630 1sw5A 275 4.41e+01 c.94.1.1 106069 1fsz 372 4.43e+01 1fsz 3cdxA 354 4.45e+01 2jfgA 445 4.45e+01 c.5.1.1,c.59.1.1,c.72.2.1 138306,138307,138308 2nloA 302 4.47e+01 1orrA 347 4.51e+01 c.2.1.2 93460 2pn8A 211 4.52e+01 2hqbA 296 4.52e+01 2imrA 420 4.54e+01 2p35A 259 4.55e+01 2b8nA 429 4.57e+01 c.118.1.1 128093 1aipA 405 4.58e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 1f6dA 376 4.64e+01 1f6dA c.87.1.3 35467 2ehjA 208 4.65e+01 2qgyA 391 4.69e+01 2e58A 308 4.71e+01 2cz2A 223 4.73e+01 1r0wA 286 4.82e+01 c.37.1.12 96754 2depA 356 4.87e+01 2fssA 365 4.88e+01 2pt7A 330 4.90e+01 1jb9A 316 4.94e+01 1fnc b.43.4.2,c.25.1.1 62840,62841 1pa1A 310 4.99e+01 c.45.1.2 94404 1sjdA 368 5.01e+01 c.1.11.2,d.54.1.1 105632,105633 2po1B 277 5.02e+01 1zdsA 336 5.08e+01 b.6.1.3,b.6.1.3 124952,124953 2bd0A 244 5.12e+01 c.2.1.2 128321 2f71A 298 5.13e+01 c.45.1.2 133070 1xccA 220 5.15e+01 c.47.1.10 115113 1g6oA 330 5.18e+01 1g6oA c.37.1.11 32430 1yovA 537 5.20e+01 c.111.1.2 123785 1fioA 196 5.21e+01 1fioA a.47.2.1 17773 1vp4A 425 5.28e+01 c.67.1.1 113935 1o57A 291 5.33e+01 a.4.5.40,c.61.1.1 92483,92484 2p67A 341 5.39e+01 2ajrA 331 5.42e+01 c.72.1.1 126892 2iw1A 374 5.43e+01 c.87.1.8 137738 1t9hA 307 5.43e+01 b.40.4.5,c.37.1.8 112358,112359 1gntA 553 5.46e+01 e.26.1.1 70290 1ygyA 529 5.46e+01 c.2.1.4,c.23.12.1,d.58.18.1,d.81.2.2 123150,123151,123152,123153 2pi1A 334 5.47e+01 2hbvA 334 5.48e+01 c.1.9.15 136320 1jnyA 435 5.51e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1vgvA 384 5.53e+01 c.87.1.3 100608 1hm9A 468 5.55e+01 b.81.1.4,c.68.1.5 65866,65867 1ixkA 315 5.61e+01 c.66.1.38 90716 2g9zA 348 5.70e+01 2ivfA 976 5.71e+01 1qvbA 481 5.73e+01 1qvbA c.1.8.4 28983 1q32A 544 5.78e+01 d.136.1.3,d.136.1.3 104507,104508 1jflA 228 5.81e+01 c.78.2.1,c.78.2.1 71656,71657 2oz3A 404 5.87e+01 1tcoA 375 5.89e+01 1auiA d.159.1.3 42084 1tz7A 505 5.94e+01 c.1.8.1 119394 1mw9X 592 5.97e+01 e.10.1.1 91480 1l3iA 192 6.02e+01 c.66.1.22 77676 2uxyA 341 6.04e+01 1j6oA 268 6.06e+01 c.1.9.12 77088 1c4oA 664 6.07e+01 1d2mA c.37.1.19,c.37.1.19 32415,32416 1womA 271 6.07e+01 1pz1A 333 6.08e+01 c.1.7.1 95390 2hzmB 317 6.08e+01 1z7wA 322 6.09e+01 c.79.1.1 124674 1mi3A 322 6.10e+01 c.1.7.1 91274 1wmuA 141 6.10e+01 a.1.1.2 109416 1btmA 252 6.13e+01 1amk c.1.1.1 28513 1vp8A 201 6.13e+01 c.49.1.2 113947 2f9fA 177 6.14e+01 c.87.1.8 133161 2j6iA 364 6.15e+01 1odkA 235 6.15e+01 c.56.2.1 86863 1l1qA 186 6.16e+01 c.61.1.1 77653 1np3A 338 6.16e+01 a.100.1.2,c.2.1.6 85946,85947 1b5pA 385 6.17e+01 c.67.1.1 90403 1f20A 435 6.18e+01 b.43.4.1,c.25.1.4 64932,64933 1m3sA 186 6.20e+01 c.80.1.3 78573 2z1dA 372 6.21e+01 1v4vA 376 6.23e+01 c.87.1.3 100313 1a8pA 258 6.29e+01 b.43.4.2,c.25.1.1 25654,31544 2b3yA 888 6.31e+01 c.8.2.1,c.83.1.1 127803,127804 1z7yA 322 6.32e+01 c.79.1.1 124679 1pgjA 478 6.35e+01 2pgd a.100.1.1,c.2.1.6 18783,30195 1snrA 341 6.37e+01 b.6.1.3,b.6.1.3 105823,105824 1qq2A 199 6.39e+01 1qq2A c.47.1.10 33064 1o58A 303 6.40e+01 c.79.1.1 92491 2oe3A 114 6.42e+01 1zr6A 503 6.44e+01 1h5uA 842 6.48e+01 1a8i c.87.1.4 60655 2reeA 224 6.49e+01 2obiA 183 6.49e+01 1up7A 417 6.49e+01 c.2.1.5,d.162.1.2 113374,113375 1ptvA 321 6.51e+01 1pty c.45.1.2 32665 2b78A 385 6.52e+01 b.122.1.9,c.66.1.51 128025,128026 2hp1A 432 6.52e+01 1fjgB 256 6.52e+01 1fjfB c.23.15.1 31400 1udsA 255 6.53e+01 d.14.1.4,d.101.1.1 99219,99220 2ppvA 332 6.57e+01 2j0iA 303 6.57e+01 2a8lA 420 6.58e+01 2ooqA 286 6.61e+01 1zetA 388 6.61e+01 d.240.1.1,e.8.1.7 124997,124998 1ybdA 239 6.62e+01 c.73.1.3 122884 2qahA 303 6.69e+01 2o7rA 338 6.70e+01 1up6A 416 6.72e+01 c.2.1.5,d.162.1.2 107976,107977 2z1aA 552 6.84e+01 1b1cA 181 6.85e+01 1amoA c.23.5.2 31212 2pcnA 161 6.88e+01 1zyeA 220 6.88e+01 c.47.1.10 125817 1e1dA 553 6.91e+01 1e1dA e.26.1.1 43363 2a8jA 420 6.97e+01 2dp3A 257 7.02e+01 1q41A 424 7.04e+01 d.144.1.7 95774 2a1fA 247 7.05e+01 c.73.1.3 125991 1lgyA 269 7.12e+01 3tgl c.69.1.17 34758 1abbA 828 7.15e+01 1a8i c.87.1.4 35536 2jj7A 186 7.18e+01 1sw2A 275 7.21e+01 c.94.1.1 106064 2pfkA 320 7.22e+01 3pfk c.89.1.1 35577 1hv8A 367 7.23e+01 1hv8A c.37.1.19,c.37.1.19 32405,32406 1in6A 334 7.27e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 2f57A 317 7.28e+01 2nygA 273 7.29e+01 1httA 423 7.30e+01 1adjA c.51.1.1,d.104.1.1 33178,40727 1j9qA 341 7.33e+01 1nif b.6.1.3,b.6.1.3 62765,62766 1oc2A 348 7.34e+01 c.2.1.2 92765 1v71A 323 7.34e+01 c.79.1.1 119859 1as6A 343 7.37e+01 1nif b.6.1.3,b.6.1.3 23090,23091 1jmvA 141 7.40e+01 c.26.2.4 66897 1oj7A 408 7.42e+01 e.22.1.2 103971 1pwhA 327 7.50e+01 c.79.1.1 95224 1gt6A 269 7.51e+01 c.69.1.17 76342 1xx6A 191 7.53e+01 c.37.1.24,g.39.1.14 116139,116140 1auiA 521 7.53e+01 1auiA d.159.1.3 42085 1o5kA 306 7.53e+01 c.1.10.1 92504 2iumA 248 7.57e+01 2qhpA 296 7.62e+01 1ng4A 390 7.66e+01 c.3.1.2,d.16.1.3 85666,85667 1vgwA 231 7.67e+01 c.68.1.13 100612 2ebdA 309 7.68e+01 2pa5A 314 7.72e+01 1g97A 459 7.79e+01 1fwyA b.81.1.4,c.68.1.5 60394,60395 1bjwA 382 7.80e+01 1bjwA c.67.1.1 34349 1w5nA 337 7.83e+01 2gekA 406 7.83e+01 2r5nA 669 7.86e+01 2bmfA 451 7.88e+01 c.37.1.14,c.37.1.14 128791,128792 1gc5A 467 7.94e+01 1gc5A c.72.1.3 60429