# List of top-scoring protein chains for t04-100-30-alpha 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 1bkjA 240 1.41e-23 1bkjA d.90.1.1 40243 1f5vA 240 1.45e-22 1bkjA d.90.1.1 40255 1nox 205 3.55e-15 1nox d.90.1.1 40242 1icrA 217 3.82e-09 1vfrA d.90.1.1 62274 1vfrA 218 2.36e-05 1vfrA d.90.1.1 40247 1ig8A 486 1.57e-02 2yhx c.55.1.3 64746 c.55.1.3 64747 1fts 295 1.59e-02 1ng1 a.24.13.1 16968 c.37.1.10 32279 1n81A 186 2.08e-02 a.185.1.1 85388 1nijA 318 4.48e-02 c.37.1.10 85741 d.237.1.1 85742 1dozA 309 5.14e-02 1ak1 c.92.1.1 35592 1qyaA 307 5.54e-02 1qo7A 394 6.14e-02 1qo7A c.69.1.11 34697 1ks8A 433 7.63e-02 a.102.1.2 77519 1gkmA 509 7.87e-02 a.127.1.2 70228 1b8fA 509 8.42e-02 1b8fA a.127.1.2 19434 1l2uA 245 1.49e-01 c.1.2.3 73516 1sdjA 310 2.70e-01 1ld8B 437 3.11e-01 a.102.4.3 73839 1uanA 227 3.33e-01 1jkmB 361 4.05e-01 1jkmA c.69.1.2 34634 1q7lA 198 4.57e-01 1dqaA 467 4.68e-01 1dqaA d.58.20.1 39364 d.179.1.1 42585 1q7zA 566 4.72e-01 1e7uA 961 4.84e-01 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1vk3A 615 5.49e-01 1g8pA 350 5.75e-01 1g8pA c.37.1.20 60376 1lzlA 323 6.26e-01 c.69.1.2 78306 1vizA 240 6.40e-01 1oaoA 674 7.82e-01 e.26.1.2 86744 1gqeA 365 8.29e-01 e.38.1.1 70351 1aq0A 306 9.76e-01 1aq0A c.1.8.3 28842 1a9xA 1058 1.06e+00 a.92.1.1 18550 c.24.1.1 31479 c.30.1.1 31657 c.30.1.1 31658 d.142.1.2 41502 d.142.1.2 41503 1d8dB 437 1.21e+00 1ft1B a.102.4.3 18866 1k3eA 156 1.27e+00 d.198.1.1 68103 1ojxA 263 1.35e+00 1hl9A 449 1.36e+00 1nf2A 268 1.39e+00 1hrdA 449 1.44e+00 1k89 c.2.1.7 30219 c.58.1.1 33867 1bgvA 449 1.54e+00 1k89 c.2.1.7 30217 c.58.1.1 33865 1bgc 174 1.58e+00 1bgc a.26.1.1 16822 1rg9A 383 1.65e+00 1ddgA 374 1.65e+00 1amoA b.43.4.1 25671 c.25.1.4 31559 1brwA 433 1.69e+00 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1i50A 1733 1.85e+00 e.29.1.1 61754 1f3mC 297 2.32e+00 1hcl d.144.1.7 41677 1vrtA 560 2.49e+00 1rthA c.55.3.1 33574 e.8.1.2 43023 1sfsA 240 2.61e+00 1k0rA 366 2.68e+00 b.40.4.5 67961 d.52.3.1 67962 d.52.3.1 67963 d.202.1.1 67964 1lwjA 441 2.72e+00 b.71.1.1 74303 c.1.8.1 74304 1o8uA 257 2.81e+00 c.14.1.3 81194 1g8iA 190 3.08e+00 1rec a.39.1.5 60363 1nnvA 110 3.13e+00 1ayl 541 3.31e+00 1ayl c.91.1.1 64718 c.109.1.1 64719 1pvtA 238 3.32e+00 1n08A 163 3.58e+00 b.43.5.1 79730 1f0kA 364 3.61e+00 1f0kA c.87.1.2 35465 1o5zA 442 3.63e+00 1fmjA 351 3.90e+00 c.37.1.5 59879 1uz5A 402 3.91e+00 1g2qA 187 3.92e+00 c.61.1.1 65117 1auk 489 3.96e+00 1auk c.76.1.2 35030 1r72A 211 3.98e+00 1m5wA 243 4.19e+00 c.1.24.1 84836 1j0aA 325 4.23e+00 c.79.1.1 83871 1kblA 873 4.40e+00 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1jnyA 435 4.50e+00 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1e25A 282 4.61e+00 1e25A e.3.1.1 42731 1iu4A 331 4.64e+00 d.3.1.8 71430 1ll2A 333 4.72e+00 c.68.1.14 74005 1h6zA 913 4.85e+00 c.1.12.2 70906 c.8.1.1 70907 d.142.1.5 70908 1eg7A 557 4.92e+00 1eg7A c.37.1.10 32241 1vjgA 218 5.03e+00 1h09A 338 5.13e+00 b.109.1.1 83420 c.1.8.8 83421 1e8yA 966 5.23e+00 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 41715 1edt 271 5.93e+00 2ebn c.1.8.5 28993 1psdA 409 5.98e+00 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 2lbp 346 6.00e+00 2liv c.93.1.1 35709 1qs0A 407 6.02e+00 1qs0A c.36.1.11 31829 1iatA 557 6.81e+00 1dqrA c.80.1.2 62123 1rypJ 204 6.87e+00 d.153.1.4 41878 1dik 874 6.99e+00 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 1ho1A 242 7.14e+00 1ho1A c.1.24.1 61097 1vimA 200 7.37e+00 1hdoA 206 7.40e+00 1he2A c.2.1.2 60965 1hcl 298 7.44e+00 1hcl d.144.1.7 41593 2yhx 457 7.62e+00 2yhx i.12.1.1 46024 1dv1A 449 7.74e+00 1bncA b.84.2.1 28234 c.30.1.1 31641 d.142.1.2 41486 1d0qA 103 7.85e+00 1d0qA g.41.3.2 45208 1fsz 372 8.20e+00 1fsz c.32.1.1 31750 d.79.2.1 39802 1vj1A 363 8.35e+00 1mx3A 347 8.54e+00 c.2.1.4 79638 c.23.12.1 79639 1o08A 221 8.64e+00 c.108.1.6 86525 1gz8A 299 8.94e+00 d.144.1.7 83405 1hc7A 477 9.14e+00 1hc7A c.51.1.1 60938 d.68.5.1 60940 d.104.1.1 60939 1id1A 153 9.69e+00 1id1A c.2.1.9 62286 1b7gO 340 1.00e+01 1b7gO c.2.1.3 29992 d.81.1.1 39907 2tysA 268 1.01e+01 2tysA c.1.2.4 28572 1g5cA 170 1.02e+01 1g5cA c.53.2.1 60264 1b7yB 785 1.05e+01 1pysB a.6.1.1 16301 a.6.1.1 16302 b.40.4.4 25312 d.58.13.1 39311 d.104.1.1 40780 d.138.1.1 41456 1kf6C 130 1.06e+01 f.21.2.2 72399 1mml 265 1.06e+01 1mml e.8.1.2 43015 1kyhA 276 1.07e+01 c.72.1.4 73222 1qr0A 228 1.09e+01 1qr0A d.150.1.1 59038 d.150.1.1 59039 1e0tA 470 1.13e+01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1g71A 347 1.16e+01 1g71A e.16.1.1 43268 2shpA 525 1.16e+01 2shpA c.45.1.2 32683 d.93.1.1 40533 d.93.1.1 40534 1ec7A 446 1.17e+01 1bqg c.1.11.2 29218 d.54.1.1 38862 1bykA 255 1.17e+01 1bykA c.93.1.1 35706 1m1nA 491 1.18e+01 c.92.2.3 78417 1odzA 386 1.20e+01 c.1.8.3 86889 1rthA 560 1.20e+01 1rthA c.55.3.1 33576 e.8.1.2 43028 1psuA 140 1.21e+01 d.38.1.5 88285 1me8A 503 1.23e+01 c.1.5.1 79028 1ofuA 320 1.26e+01 c.32.1.1 86972 d.79.2.1 86973 1i2aA 219 1.27e+01 1v7oA 165 1.31e+01 1a8rA 221 1.34e+01 1a8rA d.96.1.1 40587 1n0wA 243 1.34e+01 c.37.1.11 79772 1idrA 136 1.35e+01 1dlyA a.1.1.1 62301 1gtmA 419 1.35e+01 1hwyA c.2.1.7 30223 c.58.1.1 33871 1a8q 274 1.37e+01 1brt c.69.1.12 34702 1f20A 435 1.37e+01 b.43.4.1 64932 c.25.1.4 64933 1vhsA 175 1.40e+01 1q9uA 130 1.40e+01 1j9yA 385 1.41e+01 1j9yA c.1.8.3 62791 1ea7A 310 1.41e+01 c.41.1.1 70086 1p0hA 318 1.42e+01 1d02A 202 1.44e+01 1d02A c.52.1.8 33313 6paxA 133 1.45e+01 6paxA a.4.1.5 64758 a.4.1.5 64759 1hqsA 423 1.45e+01 1iso c.77.1.1 61154 1kqzA 273 1.46e+01 c.1.8.5 68844 1adjA 421 1.48e+01 1adjA c.51.1.1 33188 d.104.1.1 40737 1bpoA 494 1.49e+01 1bpoA a.118.1.4 19143 b.69.6.1 27670 1atiA 505 1.52e+01 1atiA c.51.1.1 33196 d.104.1.1 40745 1gg4A 452 1.53e+01 1gg4A c.98.1.1 58985 c.59.1.1 33957 c.72.2.1 58986 1uu1A 335 1.54e+01 1f8rA 498 1.57e+01 1f8rA c.3.1.2 30410 d.16.1.5 37974 1dd9A 338 1.62e+01 1dd9A e.13.1.1 43254 1d2rA 326 1.63e+01 1d2rB c.26.1.1 31572 3bamA 213 1.65e+01 1bam c.52.1.3 33288 1nx8A 273 1.68e+01 b.82.2.8 86374 1fc6A 388 1.68e+01 1fc6A b.36.1.3 64738 c.14.1.2 64739 1edg 380 1.73e+01 1edg c.1.8.3 28807 1utcA 363 1.75e+01 1eb7A 323 1.76e+01 1eb7A a.3.1.5 59404 a.3.1.5 59405 1l1qA 186 1.78e+01 c.61.1.1 77653 1j2rA 199 1.78e+01 1ia8A 289 1.80e+01 1ia8A d.144.1.7 62112 1i19A 561 1.81e+01 1i19A d.58.32.3 61522 d.145.1.1 61523 1sdsA 117 1.84e+01 1a7tA 232 1.84e+01 1a7tA d.157.1.1 42041 1bsg 266 1.85e+01 1btl e.3.1.1 42729 2apr 325 1.86e+01 2er7E b.50.1.2 26819 1usgA 346 1.87e+01 2hvm 273 1.87e+01 1cnv c.1.8.5 28985 1ga0A 364 1.89e+01 1gceA e.3.1.1 60410 3aprE 325 1.92e+01 2er7E b.50.1.2 26820 1eudB 396 1.98e+01 2scuB c.23.4.1 31150 d.142.1.4 41571 1qtrA 317 1.98e+01 1qtrA c.69.1.7 34660 1fr2B 134 1.98e+01 d.4.1.1 83257 1otjA 283 1.99e+01 1hbnC 248 2.00e+01 1mroC d.58.31.1 60902 1eyzA 392 2.04e+01 1ez1A b.84.2.1 28246 c.30.1.1 31653 d.142.1.2 41498 1acc 735 2.13e+01 1acc f.11.1.1 43828 1hxhA 253 2.14e+01 c.2.1.2 76725 1lucB 324 2.15e+01 1lucA c.1.16.1 29548 1o20A 427 2.16e+01 c.82.1.1 86556 1czaN 917 2.17e+01 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1qqqA 264 2.19e+01 1bkpA d.117.1.1 40931 1o4uA 285 2.19e+01 c.1.17.1 86624 d.41.2.1 86625 1ikpA 613 2.21e+01 b.29.1.7 66182 d.166.1.1 66183 f.1.5.1 66184 1q45A 391 2.27e+01 1mroC 247 2.29e+01 1mroC d.58.31.1 39437 1v1rA 400 2.29e+01 1g5hA 454 2.31e+01 1g5hA c.51.1.1 60270 d.104.1.1 60271 1kjqA 391 2.31e+01 b.84.2.1 72616 c.30.1.1 72617 d.142.1.2 72618 2masA 314 2.34e+01 2masA c.70.1.1 34810 1kwgA 645 2.38e+01 b.71.1.1 77561 c.1.8.1 77562 c.23.16.5 77563 1j6oA 268 2.40e+01 c.1.9.12 77088 1j97A 211 2.45e+01 1f5sA c.108.1.4 62753 1d3gA 367 2.45e+01 1d3gA c.1.4.1 28600 1vddA 228 2.45e+01 1qdeA 224 2.46e+01 1qvaA c.37.1.19 32410 1o17A 345 2.50e+01 a.46.2.1 80765 c.27.1.1 80766 1dp4A 435 2.53e+01 1dp4A c.93.1.1 35710 1r4kA 169 2.53e+01 1dfmA 223 2.56e+01 1d2iA c.52.1.5 33295 1esiA 262 2.57e+01 1skf e.3.1.1 42682 1nqkA 381 2.57e+01 1oi2A 366 2.57e+01 c.32.1.2 87039 d.79.2.2 87040 2tpsA 227 2.58e+01 2tpsA c.1.3.1 28591 1eg5A 384 2.60e+01 1ecxA c.67.1.3 34429 1tafB 70 2.62e+01 1tafB a.22.1.3 16482 1reqB 637 2.63e+01 1reqB c.1.19.1 29621 c.23.6.1 31248 1r6dA 337 2.64e+01 1q4rA 112 2.64e+01 1epuA 591 2.65e+01 1dn1A e.25.1.1 43358 2ptd 298 2.65e+01 2plc c.1.18.2 29605 1j9bA 141 2.66e+01 c.47.1.12 66459 1pb1A 416 2.67e+01 c.77.1.1 88014 1e8aA 91 2.69e+01 1b4cA a.39.1.2 17188 1uroA 367 2.72e+01 1uroA c.1.22.1 29675 1evfA 264 2.72e+01 1bkpA d.117.1.1 40932 1gs5A 258 2.76e+01 c.73.1.2 70395 1r3sA 367 2.79e+01 1jdlA 121 2.79e+01 a.3.1.1 66557 1cpcB 172 2.80e+01 1qgwC a.1.1.3 15644 1j5xA 342 2.82e+01 c.80.1.1 71591 1ng6A 148 2.82e+01 a.182.1.1 85670 1smrA 335 2.83e+01 1smrA b.50.1.2 26878 1ov9A 50 2.83e+01 1rgzA 363 2.84e+01 1dbiA 280 2.88e+01 1gci c.41.1.1 32543 1l7mA 211 2.92e+01 c.108.1.4 73664 1v33A 366 2.93e+01 1aj8A 371 2.94e+01 1aj8A a.103.1.1 18900 1nvpB 57 2.95e+01 1emvB 134 2.95e+01 1bxiB d.4.1.1 37135 1lktA 104 2.96e+01 1lktA b.90.1.1 28398 1f75A 249 2.97e+01 1f75A c.101.1.1 59662 1qopA 268 3.09e+01 2tysA c.1.2.4 28570 1es5A 262 3.10e+01 1skf e.3.1.1 42679 1p3wA 404 3.11e+01 c.67.1.3 87752 1rybA 212 3.11e+01 1d8wA 426 3.13e+01 1de5A c.1.15.2 29394 1vhtA 218 3.14e+01 1o0uA 429 3.14e+01 c.118.1.1 80743 1rfzA 168 3.20e+01 1i1dA 161 3.21e+01 1i21A d.108.1.1 61526 1q74A 303 3.22e+01 1m6yA 301 3.29e+01 a.60.13.1 78716 c.66.1.23 78717 1dcfA 136 3.31e+01 1dcfA c.23.1.2 31124 1gdhA 320 3.31e+01 1gdhA c.2.1.4 30095 c.23.12.1 31355 1scuA 288 3.34e+01 2scuA c.2.1.8 30307 c.23.4.1 31135 1s48A 609 3.35e+01 1j3bA 529 3.38e+01 c.91.1.1 77071 c.109.1.1 77072 1kqfB 294 3.39e+01 d.58.1.5 75900 f.23.22.1 75901 1efyA 350 3.40e+01 1a26 a.41.1.1 17413 d.166.1.2 42275 1ojrA 274 3.42e+01 1f5aA 513 3.43e+01 1fa0B a.160.1.1 75835 d.218.1.3 75836 d.58.16.1 39337 1iuqA 367 3.45e+01 2sas 185 3.48e+01 2sas a.39.1.5 17258 1vapA 123 3.51e+01 1poa a.133.1.2 19548 1n0uA 842 3.52e+01 b.43.3.1 79757 c.37.1.8 79758 d.14.1.1 79759 d.58.11.1 79760 d.58.11.1 79761 1g6hA 257 3.53e+01 1gajA c.37.1.12 60318 2ak3A 226 3.53e+01 1zin c.37.1.1 31892 g.41.2.1 45193 1d0vA 356 3.53e+01 1d0vA c.39.1.1 32476 1h8uA 117 3.55e+01 1h8uA d.169.1.1 60793 1vdeA 454 3.57e+01 1vdeA b.86.1.2 28378 d.95.2.2 40581 d.95.2.2 40582 1on3A 523 3.57e+01 c.14.1.4 87107 c.14.1.4 87108 1g61A 228 3.58e+01 1g61A d.126.1.1 41126 1r9dA 787 3.58e+01 1v6fA 151 3.64e+01 1i4fA 275 3.64e+01 1agdA b.1.1.2 61687 d.19.1.1 61688 1liiA 363 3.64e+01 c.72.1.1 73921 1na6A 404 3.68e+01 1hkhA 279 3.70e+01 1adoA 363 3.70e+01 1fbaA c.1.10.1 29124 1ef1A 294 3.77e+01 1ef1A a.11.2.1 16368 b.55.1.5 27003 d.15.1.4 37611 1k6wA 426 3.80e+01 b.92.1.2 68236 c.1.9.5 68237 1jbwA 428 3.81e+01 c.59.1.2 62860 c.72.2.2 62861 1f2dA 341 3.81e+01 1f2dA c.79.1.1 35298 1dpgA 485 3.82e+01 1dpgA c.2.1.3 30074 d.81.1.5 39989 1nh2B 53 3.84e+01 1sqhA 312 3.85e+01 1e20A 209 3.86e+01 1e20A c.34.1.1 31759 1rcqA 357 3.89e+01 1s9rA 410 3.91e+01 1wdcC 156 3.92e+01 1wdcC a.39.1.5 17317 1j33A 335 4.00e+01 c.39.1.1 77069