# List of top-scoring protein chains for t2k-100-30-str 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.cse.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 1k30A 368 8.45e-03 c.112.1.1 68067 1fvaA 217 2.92e-02 1fvaA d.58.28.1 39409 1fvgA 199 6.28e-02 1fvaA d.58.28.1 39408 1e1dA 553 1.52e-01 1e1dA e.26.1.1 43363 1b3qA 379 2.98e-01 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1i58A 189 3.78e-01 1b3qA d.122.1.3 61773 1gntA 553 5.90e-01 1e2uA 553 5.95e-01 1e1dA e.26.1.1 43362 1f89A 291 6.51e-01 d.160.1.1 64988 1gnlA 544 7.13e-01 3bifA 468 7.42e-01 1bif c.37.1.7 31962 c.60.1.4 34008 1a3aC 148 8.84e-01 1a3aA d.112.1.1 40919 1bjwA 382 9.40e-01 1bjwA c.67.1.1 34349 1gumA 222 1.18e+00 1pgtA a.45.1.1 17683 c.47.1.5 32977 1vhh 162 1.30e+00 1vhh d.65.1.2 39550 1cleA 534 1.37e+00 1thg c.69.1.17 34771 1a3aA 148 1.39e+00 1a3aA d.112.1.1 40917 1pioA 257 1.40e+00 1btl e.3.1.1 42719 1hizA 379 1.68e+00 c.1.8.3 65841 1ghpA 258 1.70e+00 1btl e.3.1.1 60520 1auiA 521 1.70e+00 1auiA d.159.1.3 42085 1f0xA 571 1.77e+00 1f0xA d.58.32.2 39483 d.145.1.1 41746 1iw7C 1119 1.90e+00 1bif 469 1.93e+00 1bif c.37.1.7 31961 c.60.1.4 34003 1gqeA 365 2.01e+00 1e6yC 247 2.10e+00 1mroC d.58.31.1 39441 3blm 257 2.10e+00 1btl e.3.1.1 42709 1c3wA 222 2.40e+00 1c3wA f.2.1.1 43405 1kijA 390 2.47e+00 1dbwA 126 2.57e+00 1dbwA c.23.1.1 31095 1d5wC 126 2.73e+00 1dbwA c.23.1.1 31101 1tdj 514 2.76e+00 1tdj c.79.1.1 35297 d.58.18.2 39356 d.58.18.2 39357 1cg2A 393 2.83e+00 1cg2A c.56.5.4 33844 d.58.19.1 39360 3minB 522 2.98e+00 1qguB c.92.2.3 35606 1lc0A 294 3.24e+00 1jyaA 130 3.26e+00 d.198.1.1 67453 1dckA 126 3.39e+00 1dbwA c.23.1.1 31097 1f3mC 297 3.63e+00 1hcl d.144.1.1 41677 1qkkA 155 3.76e+00 1dbwA c.23.1.1 31104 1ewkA 490 3.87e+00 1ewkA c.93.1.1 35712 1moq 368 4.16e+00 1moq c.80.1.1 35302 2minB 522 4.43e+00 1qguB c.92.2.3 35610 1b3rA 431 4.52e+00 1b3rA c.2.1.4 30106 c.23.12.3 31366 1a6q 382 4.56e+00 1a6q d.158.1.1 42063 1gulA 222 4.89e+00 1pgtA a.45.1.1 17675 c.47.1.5 32969 1k8eA 345 5.17e+00 1dpb 243 5.26e+00 1eaf c.43.1.1 32618 1l2tA 235 5.47e+00 1egaA 301 5.52e+00 1egaA c.37.1.8 32150 d.52.3.1 38836 1esmA 316 5.60e+00 1esmA c.37.1.6 31953 1gcuA 295 5.64e+00 1gcuA c.2.1.3 30063 d.81.1.4 39978 1iso 416 5.98e+00 1iso c.77.1.1 35065 1d02A 202 6.03e+00 1d02A c.52.1.8 33313 7icd 416 6.19e+00 1iso c.77.1.1 35072 1l5zA 155 6.22e+00 1svy 114 6.27e+00 1svy d.109.1.1 40831 1tlfA 301 6.33e+00 1tlfA c.93.1.1 35687 1dfaA 454 6.46e+00 1vdeA b.86.1.2 28375 d.95.2.2 40575 d.95.2.2 40576 1f7tA 122 6.58e+00 1f7lA d.150.1.2 59667 1nfp 228 6.86e+00 1nfp c.1.16.2 29555 1i0lA 221 6.98e+00 1f75A 249 7.11e+00 1f75A c.101.1.1 59662 1jztA 246 7.27e+00 c.104.1.1 63319 2aop 497 7.36e+00 2aop d.58.36.1 39503 d.58.36.1 39504 d.134.1.1 41427 d.134.1.1 41428 7timA 247 7.37e+00 1amk c.1.1.1 28457 1k6zA 141 7.63e+00 d.198.1.1 68247 1cliA 345 8.16e+00 1cliA d.79.4.1 39816 d.139.1.1 41459 1jyeA 349 8.18e+00 c.93.1.1 67455 1mdbA 539 8.20e+00 1aop 497 8.42e+00 2aop d.58.36.1 39501 d.58.36.1 39502 d.134.1.1 41425 d.134.1.1 41426 1pty 321 8.52e+00 1pty c.45.1.2 32656 1al3 324 8.68e+00 1al3 c.94.1.1 35835 1f7lA 121 8.96e+00 1f7lA d.150.1.2 59666 1l0bA 229 9.02e+00 1qlmA 316 9.16e+00 1qlmA d.147.1.1 41765 1crzA 403 9.31e+00 1crzA b.68.4.1 27629 c.51.2.1 33211 2hnp 321 9.38e+00 1pty c.45.1.2 32678 1a1s 314 9.91e+00 1othA c.78.1.1 35258 c.78.1.1 35259 1e2fA 215 1.01e+01 3tmkA c.37.1.1 59164 1f2eA 201 1.02e+01 1a0fA a.45.1.1 17745 c.47.1.5 33039 1a4iA 301 1.04e+01 1a4iA c.2.1.7 30278 c.58.1.2 33926 1h70A 255 1.05e+01 1h70A d.126.1.3 60711 1jeoA 180 1.07e+01 c.80.1.3 66611 1eeoA 321 1.07e+01 1pty c.45.1.2 32655 1f1eA 154 1.08e+01 a.22.1.2 64927 1azo 232 1.10e+01 1azo c.52.1.14 33329 2at9 247 1.10e+01 1c3wA f.2.1.1 43427 1a8y 367 1.11e+01 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1i7dA 659 1.11e+01 1d6mA e.10.1.1 61886 1eaf 243 1.11e+01 1eaf c.43.1.1 32617 1qtnA 164 1.16e+01 1pauA c.17.1.1 30999 1h72C 296 1.17e+01 d.14.1.5 60712 d.58.26.1 60713 1d3uB 201 1.19e+01 1aisB a.74.1.2 18386 a.74.1.2 18387 1fnoA 417 1.20e+01 1dceB 331 1.20e+01 1dceB a.102.4.3 18872 1b67A 68 1.20e+01 1a7w a.22.1.2 16474 1diaA 306 1.21e+01 1a4iA c.2.1.7 30280 c.58.1.2 33928 1kgbA 231 1.22e+01 f.2.1.1 68581 1pd21 199 1.22e+01 1pd21 1d8wA 426 1.24e+01 1de5A c.1.15.2 29394 1svr 114 1.24e+01 1svy d.109.1.1 40833 1e9cA 215 1.24e+01 c.37.1.1 64808 1e9eA 215 1.24e+01 c.37.1.1 64810 1ptvA 321 1.25e+01 1pty c.45.1.2 32665 1bmtA 246 1.25e+01 1bmtA a.46.1.1 17757 c.23.6.1 31235 1cfzA 162 1.26e+01 1cfzA c.56.1.1 33754 1i45A 248 1.26e+01 1amk c.1.1.1 61665 1mmoD 512 1.27e+01 1mhyD a.25.1.2 16770 1m0kA 262 1.28e+01 1e2gA 215 1.28e+01 3tmkA c.37.1.1 59165 1eudB 396 1.29e+01 2scuB c.23.4.1 31150 d.142.1.4 41571 1k7yA 577 1.30e+01 a.46.1.1 68272 c.23.6.1 68273 d.173.1.1 68274 1fzrA 138 1.31e+01 1fzrA c.52.1.17 33336 1a53 247 1.32e+01 1a53 c.1.2.4 28564 1igs 248 1.32e+01 1a53 c.1.2.4 28565 1jvwA 167 1.34e+01 1biqA 375 1.40e+01 1xikA a.25.1.2 16786 1jjyA 636 1.40e+01 1jjyA e.26.1.2 63141 1f9aA 168 1.41e+01 1f9aA c.26.1.3 31602 1g7fA 298 1.44e+01 1pty c.45.1.2 60330 1m0dA 138 1.49e+01 1ltqA 301 1.50e+01 1fthA 122 1.52e+01 d.150.1.2 60028 1lu9A 287 1.55e+01 1mxa 383 1.56e+01 1mxb d.130.1.1 41326 d.130.1.1 41327 d.130.1.1 41328 1e5xA 486 1.59e+01 c.79.1.1 59283 1oxa 403 1.60e+01 1f4tA a.104.1.1 18965 2ifeA 100 1.62e+01 1tig d.68.1.1 39567 1ly1A 181 1.63e+01 1i2sA 282 1.65e+01 1de5A 426 1.66e+01 1de5A c.1.15.2 29402 1vxrA 537 1.66e+01 2bce c.69.1.1 34595 1xyzA 347 1.67e+01 1taxA c.1.8.3 28804 2tmkA 216 1.68e+01 3tmkA c.37.1.1 31928 1geqA 248 1.69e+01 2tysA c.1.2.4 28589 1d0nA 729 1.69e+01 1d0nA d.109.1.1 40834 d.109.1.1 40835 d.109.1.1 40836 d.109.1.1 40837 d.109.1.1 40838 d.109.1.1 40839 1ea5A 537 1.79e+01 2bce c.69.1.1 34592 1eucB 396 1.80e+01 2scuB c.23.4.1 31149 d.142.1.4 41570 1aisB 200 1.81e+01 1aisB a.74.1.2 18384 a.74.1.2 18385 1js1X 324 1.81e+01 1c9kA 180 1.82e+01 1c9kB c.37.1.11 32363 1a7aA 432 1.85e+01 1b3rA c.2.1.4 30104 c.23.12.3 31364 1bvzA 585 1.87e+01 1bvzA b.1.1.5 21856 b.71.1.1 27783 c.1.8.1 28770 1kmvA 186 1.87e+01 1c5kA 439 1.88e+01 1crzA b.68.4.1 27630 c.51.2.1 33212 1sesA 421 1.88e+01 1sesA a.2.7.1 15710 d.104.1.1 40710 1fts 295 1.89e+01 1ng1 a.24.13.1 16968 c.37.1.10 32279 1ep3B 262 1.92e+01 1ep2B b.43.4.2 25664 c.25.1.3 31554 1dar 691 1.95e+01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1juk 248 1.97e+01 1a53 c.1.2.4 28567 1hp5A 512 1.97e+01 1hp4A c.1.8.6 61113 d.92.2.1 61114 1hp4A 512 1.99e+01 1hp4A c.1.8.6 61111 d.92.2.1 61112 1jipA 403 2.00e+01 a.104.1.1 66748 1e66A 543 2.02e+01 c.69.1.1 59291 1jakA 512 2.03e+01 c.1.8.6 66472 d.92.2.1 66473 1xikA 375 2.03e+01 1xikA a.25.1.2 16784 1b9lA 120 2.07e+01 1b9lA d.96.1.3 40665 1jmeA 455 2.10e+01 a.104.1.1 66885 1dmuA 299 2.13e+01 1dmuA c.52.1.4 33294 1bj7 156 2.14e+01 1bj7 b.60.1.1 27113 1svq 114 2.14e+01 1svy d.109.1.1 40832 1gox 370 2.15e+01 1gox c.1.4.1 28607 1crl 534 2.16e+01 1thg c.69.1.17 34765 1j5pA 253 2.18e+01 1a79A 171 2.19e+01 1a79A c.52.2.1 33340 d.75.1.1 39739 1eupA 403 2.22e+01 1rom a.104.1.1 18967 1bi0 226 2.24e+01 1bi0 a.4.5.24 16202 a.76.1.1 18408 b.34.1.2 24453 1pcfA 66 2.25e+01 1pcfA d.18.1.1 38142 1adeA 431 2.29e+01 1adeA c.37.1.10 32213 1asx 159 2.31e+01 1a6dA c.8.5.2 30821 1php 394 2.38e+01 16pk c.86.1.1 35452 2dtr 226 2.42e+01 1bi0 a.4.5.24 16193 a.76.1.1 18399 b.34.1.2 24450 1mvoA 136 2.42e+01 1hta 69 2.43e+01 1a7w a.22.1.2 16476 1jpnA 296 2.44e+01 a.24.13.1 67039 c.37.1.10 67040 1auoA 218 2.45e+01 1auoA c.69.1.14 34716 1hyeA 313 2.47e+01 2cmd c.2.1.5 61400 d.162.1.1 61401 1psdA 409 2.49e+01 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1amuA 563 2.49e+01 1amuA e.23.1.1 43351 1jeyB 565 2.49e+01 1jeqB e.31.1.2 62925 1aurA 218 2.50e+01 1auoA c.69.1.14 34718 1jobA 162 2.51e+01 1f35A b.94.1.1 63207 1yacA 208 2.51e+01 1yacA c.33.1.2 31757 1cch 82 2.57e+01 451c a.3.1.1 15902 1i19A 561 2.58e+01 1i19A d.58.32.3 61522 d.145.1.1 61523 1rpjA 288 2.58e+01 2dri c.93.1.1 35656 1qh8B 519 2.61e+01 1qguB c.92.2.3 35634 1dt9A 437 2.63e+01 1dt9A c.55.4.2 33738 d.79.3.2 39815 d.91.1.1 40257 1bjz 207 2.64e+01 2tct a.4.1.9 16065 a.121.1.1 19242 1jqcA 375 2.69e+01 1xikA a.25.1.2 63229 1qd9A 124 2.71e+01 1qu9A d.79.1.1 39758 1de6A 426 2.81e+01 1de5A c.1.15.2 29398 1nhs 447 2.84e+01 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1b35A 260 2.87e+01 1b35A b.10.1.3 23333 1e3jA 352 2.87e+01 1e3jA b.35.1.2 24765 c.2.1.1 29781 1fwkA 296 2.89e+01 1fwkA d.14.1.5 37576 d.58.26.1 39398 1egzA 291 2.90e+01 7a3hA c.1.8.3 28828 1ae7 119 2.90e+01 1poa a.133.1.2 19553 1qf5A 431 2.97e+01 1adeA c.37.1.10 32212 1k75A 434 2.98e+01 c.82.1.2 68253 1e3mA 800 3.01e+01 1ewqA a.113.1.1 19075 c.37.1.12 32389 c.55.6.1 33746 d.75.2.1 39747 1thg 544 3.02e+01 1thg c.69.1.17 34763 1qguB 519 3.03e+01 1qguB c.92.2.3 35626 1bfmA 69 3.06e+01 1a7w a.22.1.2 16479 1eiyB 785 3.09e+01 1pysB a.6.1.1 16305 a.6.1.1 16306 b.40.4.4 25314 d.58.13.1 39313 d.104.1.1 40782 d.138.1.1 41458 1a4iB 301 3.09e+01 1a4iA c.2.1.7 30279 c.58.1.2 33927 1h3nA 878 3.11e+01 1cf2O 337 3.12e+01 1b7gO c.2.1.3 29994 d.81.1.1 39909 8dfr 189 3.15e+01 1aoeA c.71.1.1 34895 1m7bA 184 3.18e+01 1qidA 537 3.19e+01 2bce c.69.1.1 34593 1cbuA 180 3.24e+01 1c9kB c.37.1.11 32360 1k8tA 510 3.24e+01 e.9.1.4 68316 1joa 447 3.27e+01 1nhp c.3.1.5 30563 c.3.1.5 30564 d.87.1.1 40203 1j8mF 297 3.30e+01 1ng1 a.24.13.1 62742 c.37.1.10 62743 1dyr 206 3.30e+01 1aoeA c.71.1.1 34916 1lfwA 470 3.35e+01 1jlm 192 3.39e+01 1ido c.62.1.1 34140 1cb7B 483 3.39e+01 1cb7B c.1.19.2 29648 1pszA 303 3.40e+01 1toaA c.92.2.2 35600 1g61A 228 3.40e+01 1g61A d.126.1.1 41126 1qrdA 273 3.41e+01 1d4aA c.23.5.3 31217 2cmkA 227 3.41e+01 1ckeA c.37.1.1 31847 2ng1 293 3.50e+01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1jj2M 186 3.51e+01 1ffkK c.55.4.1 63098 1fokA 568 3.52e+01 2fokA a.4.5.12 16137 a.4.5.12 16138 a.4.5.12 16139 c.52.1.12 33325 1ebdC 41 3.53e+01 1ebdC a.9.1.1 16355 1ng1 294 3.61e+01 1ng1 a.24.13.1 16961 c.37.1.10 32272 1bu7A 455 3.67e+01 1bu7A a.104.1.1 18937 1ga6A 372 3.68e+01 1ga1A c.41.1.2 32556 1h6zA 913 3.72e+01 1f93A 104 3.72e+01 1dcpA d.74.1.1 39688 1kaeA 434 3.77e+01 4blmA 265 3.85e+01 1btl e.3.1.1 42721 1dcoA 104 3.90e+01 1dcpA d.74.1.1 39680 1jeqB 565 3.92e+01 1jeqB e.31.1.2 62922 1jf9A 408 3.94e+01 1c0nA c.67.1.3 62931 2sqcA 631 3.94e+01 2sqcA a.102.4.2 18854 a.102.4.2 18855 1lbvA 252 3.95e+01 1fw9A 164 3.96e+01 1fw9A d.190.1.1 60059 1hv2A 99 3.97e+01 d.42.1.1 61287 1en7A 157 3.98e+01 1en7A a.140.4.1 64733 d.4.1.5 64734