# List of top-scoring protein chains for t04-100-30-str2 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 1h2kA 349 8.64e-33 b.82.2.6 76572 1fi2A 201 2.19e-05 1fi2A b.82.1.2 59845 1o4tA 133 2.25e-04 b.82.1.9 86622 1dgwA 178 5.42e-04 1dgwA b.82.1.2 28090 2arcA 164 3.73e-03 2arcA b.82.4.1 28148 1lr5A 163 3.89e-03 b.82.1.2 74215 1nxmA 197 1.34e-02 b.82.1.1 86385 1qxrA 189 1.66e-02 1plzA 189 1.68e-02 b.82.1.7 88160 1j58A 385 4.16e-02 b.82.1.2 71531 1qhoA 686 4.75e-02 1cxlA b.1.18.2 21844 b.3.1.1 22513 b.71.1.1 27751 c.1.8.1 28738 1e5rA 290 5.27e-02 1e5rA b.82.2.4 59276 1htqA 477 5.47e-02 d.15.9.1 71035 d.128.1.1 71036 1od5A 492 5.77e-02 b.82.1.2 86832 b.82.1.2 86833 1o1yA 239 5.78e-02 c.23.16.1 86554 1uok 558 6.05e-02 1uok b.71.1.1 27801 c.1.8.1 28788 1d2eA 397 6.33e-02 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1a8s 273 8.27e-02 1brt c.69.1.12 34710 1knwA 425 8.28e-02 2phlA 397 9.51e-02 1dgwA b.82.1.2 28082 b.82.1.2 28083 1nrfA 262 1.11e-01 1g291 372 1.21e-01 1g291 1ojxA 263 1.31e-01 1mrzA 293 1.65e-01 1e8gA 560 1.67e-01 1qltA d.58.32.1 39455 d.145.1.1 41718 1byqA 228 1.87e-01 1yer d.122.1.1 41100 1az9 457 2.66e-01 1az9 c.55.2.1 33547 d.127.1.1 41164 1qwrA 319 4.02e-01 1dgwY 93 4.64e-01 1caxB 1dmlA 319 4.76e-01 1dmlA d.131.1.2 41380 d.131.1.2 41381 1ofnA 205 5.61e-01 1oi6A 205 6.00e-01 1o2dA 371 6.14e-01 e.22.1.2 86591 1v8gA 329 6.74e-01 1exmA 405 7.46e-01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1ha3A 405 7.50e-01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1dar 691 7.79e-01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1uwvA 433 7.82e-01 1cb8A 678 8.02e-01 1cb8A a.102.3.2 18849 b.24.1.1 23898 b.30.5.2 24422 1cznA 169 8.11e-01 1rcf c.23.5.1 31181 1rcf 169 9.37e-01 1rcf c.23.5.1 31170 1oboA 169 1.21e+00 c.23.5.1 86776 1dgwX 79 1.44e+00 1caxB b.82.1.2 28091 1amy 403 1.45e+00 1jdc b.71.1.1 27799 c.1.8.1 28786 1yacA 208 1.71e+00 1yacA c.33.1.2 31757 1j8fA 323 1.72e+00 1j8fA c.31.1.5 62738 1pmmA 466 1.78e+00 1g71A 347 1.91e+00 1g71A e.16.1.1 43268 1m7jA 484 1.93e+00 b.92.1.6 78732 b.92.1.6 78733 c.1.9.11 78734 1ax4A 467 1.98e+00 1ax4A c.67.1.2 34391 1s0uA 408 2.00e+00 1avaA 403 2.03e+00 1jdc b.71.1.1 27797 c.1.8.1 28784 1d3vA 323 2.12e+00 1d3vA c.42.1.1 32559 1jm6A 407 2.14e+00 a.29.5.1 66876 d.122.1.4 66877 1fsu 492 2.52e+00 1auk c.76.1.2 35032 1mkeA 152 2.68e+00 b.55.1.4 79231 1d2fA 390 2.84e+00 1d2fA c.67.1.3 34411 1ht6A 405 2.89e+00 b.71.1.1 83629 c.1.8.1 83630 1iupA 282 3.13e+00 c.69.1.10 76815 1kjvA 284 3.15e+00 b.1.1.2 77421 d.19.1.1 77422 1rk6A 496 3.44e+00 1hkhA 279 3.56e+00 1fiy 883 3.92e+00 1fiy c.1.12.3 29307 1mdbA 539 3.95e+00 e.23.1.1 79008 1m2kA 249 3.97e+00 c.31.1.5 84754 1su4A 994 4.13e+00 1p4cA 380 4.20e+00 1gp6A 356 4.53e+00 b.82.2.1 65441 1jmsA 381 4.59e+00 a.60.6.1 66889 a.60.12.1 75862 d.218.1.2 75863 1tf4A 605 4.62e+00 1tf4A a.102.1.2 18827 b.2.2.2 22393 1kk1A 410 4.79e+00 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 1id2A 106 4.79e+00 1aac b.6.1.1 62288 1uumA 372 4.94e+00 1ca1 370 4.98e+00 1ca1 a.124.1.1 19340 b.12.1.3 23648 1ngvA 534 5.18e+00 c.111.1.2 85698 1kyqA 274 5.20e+00 c.2.1.11 73281 e.37.1.1 73282 1a53 247 5.22e+00 1a53 c.1.2.4 28564 1igs 248 5.46e+00 1a53 c.1.2.4 28565 1ad2 228 5.63e+00 1ad2 e.24.1.1 43353 1o17A 345 5.65e+00 a.46.2.1 80765 c.27.1.1 80766 1qa7A 217 5.67e+00 1havA b.47.1.4 26425 1d3cA 686 5.68e+00 1cxlA b.1.18.2 21827 b.3.1.1 22496 b.71.1.1 27734 c.1.8.1 28721 1k8kD 300 5.75e+00 d.198.2.1 68309 d.198.2.1 68310 1d2nA 272 5.85e+00 1d2nA c.37.1.20 32428 1xo1A 291 5.86e+00 1exnA a.60.7.1 18086 c.120.1.2 33356 1ju3A 583 6.10e+00 b.18.1.13 67300 c.69.1.21 67301 1nsf 273 6.14e+00 1d2nA c.37.1.20 32429 1sdwA 314 6.21e+00 1nofA 383 6.37e+00 1jqeA 292 6.38e+00 c.66.1.19 71789 1i1qB 192 6.38e+00 1qdlB c.23.16.1 61544 1bqk 124 6.47e+00 1bqk b.6.1.1 22889 1mxgA 435 6.53e+00 b.71.1.1 85193 c.1.8.1 85194 1jqnA 883 6.54e+00 c.1.12.3 77159 1rypB 250 6.81e+00 1rypB d.153.1.4 41933 1s3eA 520 6.96e+00 1v33A 366 7.22e+00 1oe4A 247 7.30e+00 c.18.1.3 86895 1elqA 390 7.46e+00 1elqA c.67.1.3 34436 1paz 123 7.53e+00 1bqk b.6.1.1 22878 1ojaA 520 7.56e+00 1fs5A 266 7.58e+00 c.35.1.1 65044 1v7zA 260 7.64e+00 1f0cA 305 7.65e+00 1c8oA e.1.1.1 42676 1pamA 686 7.67e+00 1cxlA b.1.18.2 21846 b.3.1.1 22515 b.71.1.1 27753 c.1.8.1 28740 1a8q 274 7.72e+00 1brt c.69.1.12 34702 1eluA 390 7.77e+00 1elqA c.67.1.3 34434 1qwlA 505 7.80e+00 1i7qB 193 8.13e+00 1qdlB c.23.16.1 61902 1hl9A 449 8.17e+00 1jykA 254 8.52e+00 c.68.1.13 67458 1ihkA 174 8.66e+00 1bfg b.42.1.1 62384 1vhcA 224 8.99e+00 1jmkC 230 9.00e+00 c.69.1.22 71747 1qs1A 462 9.49e+00 1qs1A d.166.1.1 42260 d.166.1.1 42261 1pjcA 361 9.61e+00 1sayA c.2.1.4 30101 c.23.12.2 31361 1hbzA 498 9.66e+00 1cf9A e.5.1.1 60937 1qjcA 158 1.01e+01 1b6tA c.26.1.3 63328 1hnjA 317 1.03e+01 1hn9A c.95.1.1 35969 c.95.1.1 35970 1n7oA 721 1.04e+01 a.102.3.2 80259 b.24.1.1 80260 b.30.5.2 80261 1k1xA 659 1.08e+01 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1uyrA 737 1.10e+01 1m22A 503 1.11e+01 c.117.1.1 78464 1mu5A 471 1.12e+01 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1euwA 152 1.15e+01 1dupA b.85.4.1 28349 1evhA 112 1.18e+01 1evhA b.55.1.4 26997 1ly1A 181 1.22e+01 c.37.1.1 74334 1l1lA 739 1.24e+01 c.7.1.4 73470 1ne9A 335 1.28e+01 2fcr 173 1.29e+01 1rcf c.23.5.1 31151 1ep0A 185 1.30e+01 1dzrA b.82.1.1 28080 1hlgA 371 1.32e+01 1hlgA c.69.1.6 34656 1rn5A 177 1.32e+01 1js8A 394 1.38e+01 a.86.1.1 67219 b.112.1.1 67220 1iirA 415 1.44e+01 1iirA c.87.1.5 62453 1ifqA 138 1.46e+01 1ifqA d.110.4.1 62350 1ve9A 347 1.46e+01 1a88A 275 1.46e+01 1brt c.69.1.12 34707 1ptmA 329 1.46e+01 1dhr 241 1.48e+01 1dhr c.2.1.2 29832 1d1gA 168 1.49e+01 1d1gA c.71.1.1 34889 1gpuA 680 1.53e+01 c.36.1.6 65455 c.36.1.10 65454 c.48.1.1 65456 1shwA 138 1.54e+01 1trkA 680 1.55e+01 1trkA c.36.1.6 31804 c.36.1.10 31803 c.48.1.1 33090 1ra9 159 1.56e+01 1vdrA c.71.1.1 34820 1eguA 731 1.56e+01 1eguA a.102.3.2 18850 b.24.1.1 23899 b.30.5.2 24423 1o0xA 262 1.57e+01 d.127.1.1 80755 1vjrA 271 1.57e+01 1dgfA 497 1.57e+01 1cf9A e.5.1.1 42782 1v5lA 103 1.59e+01 1ejdA 419 1.59e+01 1uae d.68.2.2 39576 1rl2A 137 1.59e+01 1rl2A b.34.5.3 24610 b.40.4.5 25342 1khdA 345 1.66e+01 a.46.2.1 77400 c.27.1.1 77401 1zpdA 568 1.68e+01 1zpdA c.31.1.3 31741 c.36.1.5 31785 c.36.1.9 31786 1hdhA 536 1.69e+01 c.76.1.2 65805 1gdeA 389 1.71e+01 c.67.1.1 60456 1eokA 290 1.76e+01 1eokA c.1.8.5 28991 1uvjA 664 1.82e+01 1o91A 178 1.84e+01 1pvvA 315 1.87e+01 1cqxA 403 1.89e+01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1a05A 358 1.90e+01 1cnzA c.77.1.1 35059 1e7uA 961 1.92e+01 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1bia 321 1.92e+01 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1gmxA 108 1.99e+01 c.46.1.3 65355 1g6sA 427 2.01e+01 1eps d.68.2.2 39584 1an9A 340 2.02e+01 1an9A c.4.1.2 30617 d.16.1.3 37904 1jx2B 315 2.06e+01 c.37.1.8 67404 1aohA 147 2.09e+01 1aohA b.2.2.2 22401 1dcs 311 2.10e+01 1dcs b.82.2.1 28124 1mh1 186 2.11e+01 1eesA c.37.1.8 32002 1hhsA 664 2.14e+01 1hi0P e.8.1.6 61045 1rc6A 261 2.14e+01 1jy5A 212 2.18e+01 d.124.1.1 71940 1gvfA 286 2.21e+01 c.1.10.2 70599 1phm 310 2.22e+01 1phm b.121.1.2 59015 b.121.1.2 59016 1jopA 155 2.28e+01 b.82.2.7 84187 1d3gA 367 2.30e+01 1d3gA c.1.4.1 28600 1ei9A 279 2.37e+01 1ei9A c.69.1.13 34713 1j99A 293 2.39e+01 c.37.1.5 71618 1hynP 379 2.42e+01 1hynP d.112.1.2 61408 1cv8 174 2.45e+01 1cv8 d.3.1.1 37089 1iukA 140 2.48e+01 c.2.1.8 83712 1pv9A 348 2.50e+01 1kv5A 250 2.50e+01 c.1.1.1 73052 1gy8A 397 2.51e+01 c.2.1.2 83376 1g87A 614 2.52e+01 a.102.1.2 83275 b.2.2.2 83276 1h0hB 214 2.52e+01 d.58.1.5 76437 1kl1A 419 2.53e+01 c.67.1.4 72663 1o5uA 101 2.55e+01 1edzA 320 2.55e+01 1ee9A c.2.1.7 30287 c.58.1.2 33935 1havA 217 2.57e+01 1havA b.47.1.4 26423 12asA 330 2.58e+01 12asA d.104.1.1 40783 1kgsA 225 2.61e+01 a.4.6.1 68596 c.23.1.1 68597 1pii 452 2.63e+01 1pii c.1.2.4 28559 c.1.2.4 28563 1v7rA 186 2.67e+01 1jdpA 441 2.73e+01 c.93.1.1 62906 1gweA 503 2.76e+01 e.5.1.1 70667 1har 216 2.79e+01 1rthA e.8.1.2 43025 1gqzA 274 2.79e+01 d.21.1.1 83311 d.21.1.1 83312 1te5A 257 2.81e+01 1bxvA 91 2.89e+01 1aac b.6.1.1 22875 1eerB 227 2.91e+01 1eerB b.1.2.1 22011 b.1.2.1 22012 1pymA 295 2.96e+01 1pymA c.1.12.7 29308 1egaA 301 2.99e+01 1egaA c.37.1.8 32150 d.52.3.1 38836 1pa2A 306 3.05e+01 1bgp a.93.1.1 18693 1ab4 477 3.05e+01 1ab4 e.11.1.1 43251 1ajsA 412 3.09e+01 1ajsA c.67.1.1 34276 1s2wA 295 3.10e+01 1rypF 233 3.10e+01 1rypF d.153.1.4 41937 1ko7A 314 3.18e+01 c.98.2.1 72797 c.91.1.2 72798 1idk 359 3.20e+01 1qcxA b.80.1.2 28025 1aa8A 347 3.20e+01 1an9A c.4.1.2 30619 d.16.1.3 37906 1czaN 917 3.23e+01 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1bjwA 382 3.24e+01 1bjwA c.67.1.1 34349 1b5pA 385 3.25e+01 1lv7A 257 3.25e+01 c.37.1.20 78232 1vpt 348 3.26e+01 3mag c.66.1.25 34207 1ut8A 291 3.26e+01 1squA 155 3.34e+01 1k7iA 479 3.35e+01 b.79.1.1 77281 d.92.1.6 77282 1qo2A 241 3.35e+01 1qo2A c.1.2.1 28533 1pvtA 238 3.36e+01 1b5tA 275 3.37e+01 1b5tA c.1.23.1 29676 2ng1 293 3.38e+01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1epwA 1290 3.44e+01 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1plc 99 3.47e+01 1plc b.6.1.1 22846 1qw9A 502 3.48e+01 1a7cA 379 3.51e+01 1sek e.1.1.1 42660 1go7P 462 3.52e+01 b.79.1.1 76245 d.92.1.6 76246 1jpzA 473 3.53e+01 a.104.1.1 67069 1j5sA 463 3.55e+01 c.1.9.8 71580 1iz0A 302 3.56e+01 b.35.1.2 83821 c.2.1.1 83822 1whtA 256 3.58e+01 1ivyA c.69.1.5 34646 1o08A 221 3.59e+01 c.108.1.6 86525 1itcA 516 3.64e+01 b.3.1.1 83705 c.1.8.1 83706 1lk2A 274 3.64e+01 1pmy 123 3.64e+01 1bqk b.6.1.1 22888 1e8yA 966 3.66e+01 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 41715 1omzA 293 3.68e+01 c.68.1.15 87093 1mkiA 330 3.69e+01 e.3.1.2 84994 1tpfA 250 3.70e+01 1amk c.1.1.1 28467 1i45A 248 3.71e+01 1amk c.1.1.1 61665 1whsA 255 3.74e+01 1ivyA c.69.1.5 34649 2sqcA 631 3.74e+01 2sqcA a.102.4.2 18854 a.102.4.2 18855 1gx3A 284 3.78e+01 d.3.1.5 70678 1ogpA 393 3.78e+01 1ls6A 295 3.78e+01 1b24A 188 3.79e+01 1b24A d.95.2.1 40573 d.95.2.1 40574 1v84A 253 3.80e+01 1eyzA 392 3.85e+01 1ez1A b.84.2.1 28246 c.30.1.1 31653 d.142.1.2 41498 1qtqA 553 3.86e+01 1gtrA b.53.1.2 26940 c.26.1.1 31579 1ns5A 155 3.91e+01 c.116.1.3 80705 1l5xA 280 3.96e+01 c.106.1.1 77718 1cvl 319 3.96e+01 1cvl c.69.1.18 34786 1bf6A 291 3.98e+01 1pscA c.1.9.3 29065