# List of top-scoring protein chains for t2k-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 2drhA 361 4.70e-33 1b65A 375 4.43e-31 1b65A d.154.1.1 42020 1vz6A 393 1.87e-01 d.154.1.2 108949 1uf5A 303 2.75e-01 d.160.1.2 107808 2dyuA 334 3.22e-01 1erzA 303 3.40e-01 1erzA d.160.1.2 59498 3io1A 445 5.95e-01 1t70A 255 6.59e-01 d.159.1.9 112275 1zjkA 403 9.60e-01 b.47.1.2,g.18.1.1,g.18.1.1 125149,125150,125151 1h7wA 1025 1.07e+00 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15683,28628,30324,30609,39007 1h7xA 1025 1.20e+00 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15687,28632,30328,30613,39011 1ede 310 1.28e+00 1b6g 2i7xA 717 1.35e+00 d.157.1.10 147560 1qz9A 416 1.58e+00 c.67.1.3 96621 1b6g 310 1.67e+00 1b6g 1b6gA 310 1.67e+00 c.69.1.8 34661 1evlA 401 1.91e+00 1qf6A c.51.1.1,d.104.1.1 33202,40751 2vchA 480 2.42e+00 c.87.1.10 152917 2f2hA 773 2.43e+00 b.150.1.1,b.30.5.11,b.71.1.4,c.1.8.13 132818,132819,132820,132821 1cx8A 639 2.82e+00 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17782,30763,33851 1lucB 324 2.85e+00 1lucA c.1.16.1 29548 3bczA 293 3.07e+00 1cl8A 276 3.31e+00 1ckqA c.52.1.1 33230 2vnuD 760 3.36e+00 b.40.4.5,b.40.4.5,b.40.4.5,b.40.4.16 153344,153345,153346,153347 1gteA 1025 3.51e+00 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70440,70441,70442,70443,70444 1cx8B 639 3.70e+00 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17783,30764,33852 2b0tA 738 3.80e+00 1xsjA 778 4.01e+00 b.150.1.1,b.30.5.11,b.71.1.4,c.1.8.13 115951,115952,115953,115954 1f89A 291 4.06e+00 d.160.1.1 64988 2reeA 224 4.27e+00 1eg5A 384 4.57e+00 1ecxA c.67.1.3 34429 1ckqA 276 4.81e+00 1ckqA c.52.1.1 33229 3kasA 640 4.94e+00 2w9mA 578 4.94e+00 1xfjA 261 5.26e+00 d.194.1.2 109585 2ch5A 347 5.60e+00 c.55.1.5,c.55.1.5 130453,130454 3gsiA 827 5.61e+00 2wtmA 251 5.73e+00 1ecxA 384 5.81e+00 1ecxA c.67.1.3 34431 3bb1A 274 5.88e+00 1knwA 425 6.27e+00 b.49.2.3,c.1.6.1 90969,90970 3ie0A 431 6.46e+00 1pj5A 830 6.73e+00 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1ukcA 522 7.10e+00 c.69.1.17 107911 3kpkA 434 7.41e+00 1kdgA 546 7.42e+00 c.3.1.2,d.16.1.1 77337,77338 1ac5 483 7.47e+00 1ac5 1ac5A 483 7.47e+00 c.69.1.5 34653 1kcbA 340 7.47e+00 b.6.1.3,b.6.1.3 90951,90952 1nif 340 7.68e+00 1nif 1de4C 640 7.68e+00 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17779,30760,33848 2c78A 405 7.70e+00 b.43.3.1,b.44.1.1,c.37.1.8 130037,130038,130039 1de5A 426 7.90e+00 1de5A c.1.15.2 29402 2h6eA 344 8.07e+00 1et7A 341 8.25e+00 1nif b.6.1.3,b.6.1.3 23070,23071 3b9tA 484 8.91e+00 1moq 368 8.99e+00 1moq 1moqA 368 8.99e+00 c.80.1.1 35302 2zogA 479 9.09e+00 1lfwA 470 9.16e+00 c.56.5.4,d.58.19.1 77942,77943 1cp3A 277 9.35e+00 1pauA c.17.1.1 30992 1wmdA 434 9.38e+00 b.18.1.20,c.41.1.1 109408,109409 2e7yA 280 9.65e+00 d.157.1.7 146706 1h65A 270 9.97e+00 c.37.1.8 65640 2nsmA 439 1.02e+01 1ecfB 504 1.05e+01 1ecfB c.61.1.1,d.153.1.1 34054,41821 1qpsA 261 1.05e+01 1ckqA c.52.1.1 33234 3h9eA 346 1.05e+01 2bklA 695 1.07e+01 2vdaA 828 1.10e+01 1ub3A 220 1.10e+01 c.1.10.1 88395 1u0mA 382 1.12e+01 c.95.1.2,c.95.1.2 107557,107558 3hywA 430 1.14e+01 3iibA 444 1.17e+01 2bw4A 340 1.20e+01 b.6.1.3,b.6.1.3 129320,129321 2dy1A 665 1.21e+01 b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 146607,146608,146609,146610,146611 2jgdA 933 1.22e+01 1ku0A 388 1.22e+01 c.69.1.18 72994 3cuzA 532 1.26e+01 2b3yA 888 1.27e+01 c.8.2.1,c.83.1.1 127803,127804 3a4yA 431 1.29e+01 1m33A 258 1.37e+01 c.69.1.26 78514 1q1gA 276 1.42e+01 c.56.2.1 95574 1qfmA 710 1.42e+01 1qfmA b.69.7.1,c.69.1.4 27673,34641 1l5wA 796 1.43e+01 c.87.1.4 73605 2aunA 317 1.45e+01 c.8.10.1,c.23.16.7 127334,127335 1a6q 382 1.45e+01 1a6q 1a6qA 382 1.45e+01 a.159.1.1,d.219.1.1 75801,75802 1zrsA 317 1.51e+01 c.8.10.1,c.23.16.7 125556,125557 2v4wA 460 1.55e+01 2uxyA 341 1.56e+01 3ie1A 431 1.57e+01 3iqwA 334 1.58e+01 1rk6A 496 1.62e+01 b.92.1.6,b.92.1.6,c.1.9.11 97599,97600,97601 2gvhA 288 1.63e+01 d.38.1.1,d.38.1.1 135776,135777 3futA 271 1.64e+01 2wyaA 460 1.65e+01 1qe3A 489 1.70e+01 2bce c.69.1.1 34630 1tkjA 284 1.72e+01 c.56.5.4 119296 3bk2A 562 1.73e+01 2qy6A 257 1.75e+01 2ja2A 498 1.76e+01 1xtpA 254 1.76e+01 c.66.1.42 116031 1d8wA 426 1.77e+01 1de5A c.1.15.2 29394 1f0iA 504 1.77e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 1i74A 309 1.78e+01 1i74A c.107.1.1 61867 3ilvA 634 1.80e+01 3egeA 261 1.82e+01 1mzjA 339 1.83e+01 c.95.1.2,c.95.1.2 79700,79701 1euzA 419 1.85e+01 1k89 c.2.1.7,c.58.1.1 59513,59514 1m7jA 484 1.86e+01 b.92.1.6,b.92.1.6,c.1.9.11 78732,78733,78734 1i88A 389 1.87e+01 c.95.1.2,c.95.1.2 66070,66071 1v0wA 506 1.87e+01 d.136.1.2,d.136.1.2 108220,108221 1w5tA 412 1.88e+01 a.4.5.11,c.37.1.20 114255,114256 1e8nA 710 1.88e+01 1qfmA b.69.7.1,c.69.1.4 27675,34643 2epgA 487 1.89e+01 3fj0A 465 1.89e+01 2jbwA 386 1.90e+01 c.69.1.41 147962 1tqyB 415 1.92e+01 c.95.1.1,c.95.1.1 107247,107248 1um0A 365 1.94e+01 d.258.1.1 107942 1xadA 345 1.96e+01 c.77.1.1 35055 3ie2A 431 1.98e+01 1h2xA 710 1.98e+01 b.69.7.1,c.69.1.4 76598,76599 3cmjA 465 1.99e+01 3defA 262 2.02e+01 1sazA 381 2.06e+01 c.55.1.2,c.55.1.2 118925,118926 2zbwA 335 2.06e+01 3htvA 310 2.08e+01 1kmqA 184 2.09e+01 c.37.1.8 84412 2aumA 317 2.10e+01 c.8.10.1,c.23.16.7 127330,127331 1vhwA 253 2.12e+01 c.56.2.1 100706 1rtqA 299 2.15e+01 c.56.5.4 97819 1kdvA 370 2.18e+01 c.41.1.2 68486 1gypA 358 2.18e+01 1dssG c.2.1.3,d.81.1.1 30004,39919 1t71A 281 2.19e+01 d.159.1.9 112283 1mnaA 298 2.21e+01 c.69.1.22 79322 3emvA 253 2.21e+01 3ju7A 377 2.24e+01 1i86A 389 2.26e+01 c.95.1.2,c.95.1.2 66068,66069 2anpA 291 2.28e+01 c.56.5.4 127056 1jy1A 464 2.34e+01 d.136.1.3,d.136.1.3 67438,67439 1sh7A 284 2.36e+01 3kpiA 434 2.38e+01 1usuA 260 2.40e+01 d.14.1.8 99885 2vr4A 846 2.41e+01 b.1.4.1,b.1.4.1,b.1.4.1,b.18.1.5,c.1.8.3 153495,153496,153497,153498,153499 1mkyA 439 2.43e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 3idzA 431 2.45e+01 1o6gA 710 2.48e+01 b.69.7.1,c.69.1.4 81087,81088 2e11A 266 2.48e+01 1ga6A 372 2.50e+01 1ga1A c.41.1.2 32556 1itxA 419 2.53e+01 c.1.8.5,d.26.3.1 71425,71426 1h2wA 710 2.56e+01 b.69.7.1,c.69.1.4 76596,76597 3h4fA 336 2.58e+01 1ga1A 372 2.59e+01 1ga1A c.41.1.2 32557 1nnwA 252 2.60e+01 d.159.1.5 80674 1kxrA 339 2.68e+01 d.3.1.3 73175 1pfkA 320 2.70e+01 3pfk c.89.1.1 35575 1h4pA 408 2.72e+01 c.1.8.3 90617 1ahpA 797 2.74e+01 1a8i c.87.1.4 35544 2f48A 555 2.74e+01 c.89.1.1 132915 2eq6A 464 2.77e+01 1jkeA 145 2.77e+01 c.110.1.1 66791 2dr1A 386 2.78e+01 1r3dA 264 2.78e+01 c.69.1.35 111680 3g5tA 299 2.78e+01 1k20A 310 2.83e+01 c.107.1.1 68027 2ek8A 421 2.88e+01 1lokA 291 2.93e+01 c.56.5.4 78122 1qxoA 388 3.00e+01 d.258.1.1 96539 2hfkA 319 3.01e+01 1mpxA 615 3.05e+01 b.18.1.13,c.69.1.21 85041,85042 1ecfA 504 3.08e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 3k8tA 888 3.11e+01 1iweA 457 3.18e+01 c.37.1.10 71486 1lluA 342 3.19e+01 b.35.1.2,c.2.1.1 91064,91065 2bo9A 308 3.22e+01 c.56.5.1 128897 3l04A 359 3.25e+01 2gn4A 344 3.27e+01 1o5zA 442 3.28e+01 c.59.1.2,c.72.2.2 92530,92531 3mi6A 745 3.28e+01 1l1jA 239 3.31e+01 b.47.1.1 84516 1zbqA 327 3.32e+01 c.2.1.2 124862 1bi5A 389 3.40e+01 1bi5A c.95.1.2,c.95.1.2 35985,35986 2yxoA 267 3.46e+01 1gz6A 319 3.48e+01 c.2.1.2 76410 1zl0A 311 3.50e+01 c.8.10.1,c.23.16.7 125231,125232 2vhhA 405 3.51e+01 2vycA 755 3.52e+01 1rrvA 416 3.53e+01 c.87.1.5 105083 1vjtA 483 3.55e+01 c.2.1.5,d.162.1.2 100833,100834 1fnnA 389 3.59e+01 1fnnA a.4.5.11,c.37.1.20 16129,32426 1cvrA 435 3.61e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 2je8A 848 3.62e+01 b.1.4.1,b.1.4.1,b.1.4.1,b.18.1.5,c.1.8.3 147998,147999,148000,148001,148002 1hyuA 521 3.63e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1xwwA 157 3.63e+01 1x88A 359 3.65e+01 c.37.1.9 121797 2hhiA 204 3.67e+01 2gcoA 201 3.67e+01 3lxrA 185 3.73e+01 1odfA 290 3.73e+01 c.37.1.6 92782 2wafA 682 3.74e+01 1amp 291 3.75e+01 1amp 1cz1A 394 3.75e+01 1cz1A c.1.8.3 28839 1mz5A 638 3.75e+01 b.29.1.15,b.68.1.1 79679,79680 2a1fA 247 3.76e+01 c.73.1.3 125991 2wojA 354 3.81e+01 2c4eA 302 3.84e+01 1ug6A 431 3.85e+01 c.1.8.4 88490 3hlkA 446 3.86e+01 1gadO 330 3.90e+01 1dssG c.2.1.3,d.81.1.1 29950,39865 1yrzA 528 3.91e+01 b.29.1.23,b.67.2.1 123948,123949 1xrjA 261 3.95e+01 c.37.1.6 122256 3c8yA 574 3.97e+01 c.96.1.1,d.15.4.2,d.58.1.5 156057,156058,156059 2pfkA 320 3.97e+01 3pfk c.89.1.1 35577 1qf6A 642 3.99e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1efcA 393 3.99e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1nf3A 195 3.99e+01 c.37.1.8 85594 1uj2A 252 4.00e+01 c.37.1.6 99452 1ybqB 390 4.02e+01 2fx5A 258 4.02e+01 1xjo 284 4.06e+01 1xjo 1j9qA 341 4.14e+01 1nif b.6.1.3,b.6.1.3 62765,62766 2fkbA 180 4.17e+01 d.113.1.2 133650 1c7iA 489 4.20e+01 1thg c.69.1.1 34632 1lnsA 763 4.22e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1d2eA 397 4.24e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 2f82A 450 4.25e+01 2bsxA 253 4.27e+01 c.56.2.1 129128 1rm6A 769 4.28e+01 d.41.1.1,d.133.1.1 111872,111873 2b69A 343 4.29e+01 c.2.1.2 127974 1exmA 405 4.30e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 2dkfA 431 4.33e+01 d.157.1.10 146536 1jvsA 400 4.34e+01 a.69.3.1,c.2.1.3,d.81.1.3 77187,77188,77189 3fd0A 409 4.38e+01 2vjxA 846 4.42e+01 b.1.4.1,b.1.4.1,b.1.4.1,b.18.1.5,c.1.8.3 153203,153204,153205,153206,153207 1y56A 493 4.44e+01 3ecrA 364 4.46e+01 2fshA 853 4.49e+01 2zfnA 460 4.52e+01 1w61A 414 4.56e+01 2byjA 439 4.57e+01 c.67.1.4 129483 2r9fA 339 4.58e+01 d.3.1.3 151767 2cjpA 328 4.58e+01 3k8xA 758 4.60e+01 2ashA 381 4.64e+01 3l05A 359 4.65e+01 1hn9A 317 4.70e+01 1hn9A c.95.1.2,c.95.1.2 35977,35978 2akaB 299 4.72e+01 c.37.1.8 126914 2g8jA 339 4.73e+01 d.3.1.3 134773 2pq6A 482 4.73e+01 c.87.1.10 149785 3h0sA 769 4.74e+01 3gzxA 457 4.79e+01 1itwA 741 4.79e+01 c.77.1.2 76793 2z1aA 552 4.82e+01 d.114.1.1,d.159.1.2 153927,153928 1oe1A 336 4.82e+01 b.6.1.3,b.6.1.3 86891,86892 1w2xA 758 4.82e+01 c.14.1.4,c.14.1.4 109134,109135 3go2A 409 4.85e+01 1tx4B 178 4.85e+01 1ctqA c.37.1.8 32045 2fk6A 320 4.85e+01 d.157.1.7 133646 3itnA 250 4.86e+01 1kezA 300 4.88e+01 c.69.1.22 68546 1a4rA 191 4.89e+01 1ctqA c.37.1.8 32063 2if6A 186 4.90e+01 d.3.1.21 147651 2e0cA 409 4.90e+01 2rhwA 283 4.91e+01 c.69.1.10 152053 1r3nA 462 4.92e+01 c.56.5.4,d.58.19.1 96945,96946 3fobA 281 4.94e+01 2qaeA 468 4.95e+01 3e4rA 324 4.95e+01 1qq9A 284 4.98e+01 1xjo c.56.5.4 33841 1i3kA 348 5.04e+01 1xel c.2.1.2 61595 3ddkA 462 5.04e+01 2oatA 439 5.04e+01 2dkb c.67.1.4 34452 3js2A 317 5.04e+01 1a0cA 438 5.06e+01 1a0cA c.1.15.3 29529 1x0lA 333 5.07e+01 1vaoA 560 5.08e+01 1qltA d.58.32.1,d.145.1.1 39461,41724 1hynP 379 5.08e+01 1hynP d.112.1.2 61408 1nhp 447 5.08e+01 1nhp 1nhpA 447 5.08e+01 c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 2yvtA 260 5.09e+01 d.159.1.6 153779 3fbuA 168 5.12e+01 1u8fO 335 5.12e+01 c.2.1.3,d.81.1.1 119626,119627 3gqiA 326 5.14e+01 2otnA 308 5.16e+01 1musA 477 5.20e+01 c.55.3.4 79494 2i7vA 459 5.27e+01 3k2kA 403 5.27e+01 2afwA 329 5.30e+01 c.56.5.8 126707 2wkqA 332 5.33e+01 2wkrA 332 5.37e+01 1snrA 341 5.37e+01 b.6.1.3,b.6.1.3 105823,105824 1as6A 343 5.42e+01 1nif b.6.1.3,b.6.1.3 23090,23091 3l02A 359 5.43e+01 1n1tA 641 5.48e+01 b.29.1.15,b.68.1.1 79821,79822 3k7mX 431 5.53e+01 3bqwA 351 5.55e+01 1pjjA 271 5.59e+01 a.156.1.2,b.113.1.1,g.39.1.8 104164,104165,104166 2v1pA 467 5.60e+01 c.67.1.2 152410 2ph5A 480 5.62e+01 1a88A 275 5.64e+01 1brt c.69.1.12 34707 2bg5A 324 5.68e+01 2pujA 286 5.76e+01 1oixA 191 5.77e+01 c.37.1.8 118710 1ek6A 348 5.77e+01 1xel c.2.1.2 29800 3k9tA 435 5.78e+01 1hkhA 279 5.79e+01 c.69.1.12 90628 3h3eA 267 5.81e+01 3ii0A 422 5.82e+01 2cvxA 888 5.83e+01 1mg7A 417 5.85e+01 d.14.1.6,d.58.26.6 84954,84955 2pc8A 400 5.92e+01 1rv9A 259 5.97e+01 d.194.1.2 105105 3mebA 448 6.02e+01 1q0bA 367 6.02e+01 c.37.1.9 95502 1vrmA 325 6.06e+01 d.96.2.1 120472 3du6A 596 6.09e+01 1h8lA 380 6.09e+01 b.3.2.1,c.56.5.1 65737,65738 3fbsA 297 6.09e+01 1g3qA 237 6.10e+01 1hyqA c.37.1.10 60237 3hm7A 448 6.12e+01 1eqcA 394 6.12e+01 1cz1A c.1.8.3 28811 1r64A 481 6.13e+01 b.18.1.20,c.41.1.1 97140,97141 2gokA 429 6.17e+01 b.92.1.10,c.1.9.17 147145,147146 2wkpA 332 6.17e+01 2oo6A 409 6.19e+01 2ppeA 343 6.19e+01 b.6.1.3,b.6.1.3 149769,149770 1mdwA 328 6.20e+01 d.3.1.3 84934 1dg9A 157 6.20e+01 1dg9A 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7.61e+01 b.97.1.1 68459 1uyrA 737 7.64e+01 c.14.1.4,c.14.1.4 100188,100189 1cz7A 406 7.64e+01 1bg2 c.37.1.9 32194 3iv7A 364 7.68e+01 3l06A 359 7.70e+01 1f20A 435 7.70e+01 b.43.4.1,c.25.1.4 64932,64933 1crwG 333 7.77e+01 1dssG c.2.1.3,d.81.1.1 30026,39941 2c0cA 362 7.78e+01 1hcz 252 7.82e+01 1hcz 1btmA 252 7.90e+01 1amk c.1.1.1 28513 3frkA 373 7.92e+01 2v5cA 594 8.00e+01