# List of top-scoring protein chains for t04-100-30-bys-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.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 1sumB 235 1.10e-06 a.7.12.1 106025 1xwmA 217 2.69e-05 1vctA 205 6.05e-03 1wkbA 810 1.05e-01 2f6hX 419 3.69e-01 1j1vA 94 4.09e-01 a.4.12.2 83981 2c6cA 707 6.62e-01 1afrA 345 7.59e-01 1afrA a.25.1.2 16805 2dc3A 193 1.03e+00 1oq9A 363 1.03e+00 a.25.1.2 87257 1wphA 201 1.12e+00 1urvA 190 1.36e+00 1ut0A 190 1.36e+00 a.1.1.2 108012 1n81A 186 1.43e+00 a.185.1.1 85388 2b05A 246 1.61e+00 2ah6A 208 1.75e+00 1ouvA 273 1.78e+00 a.118.18.1 93570 1tn6A 382 1.87e+00 1ithA 141 2.07e+00 1ithA a.1.1.2 15623 1dowA 205 2.13e+00 1dovA a.24.9.1 16626 1hw1A 239 2.27e+00 1e2xA a.4.5.6,a.78.1.1 16111,18441 1o5hA 214 2.32e+00 a.191.1.1 92497 2awiA 317 2.44e+00 1ld8A 382 2.49e+00 a.118.6.1 73838 1u13A 455 2.81e+00 a.104.1.1 107578 1d8dA 377 2.97e+00 1ft1A a.118.6.1 19185 1woyA 500 3.02e+00 2avpA 70 3.20e+00 2bptA 861 3.29e+00 1dkzA 219 3.75e+00 1dkzA a.8.4.1,b.130.1.1 90345,90346 2c12A 439 3.89e+00 1w2yA 229 3.89e+00 a.204.1.1 109140 1wixA 164 4.25e+00 1yozA 116 4.40e+00 1a8i 842 4.51e+00 1a8i c.87.1.4 35490 1x8vA 455 4.55e+00 1kgnA 329 4.96e+00 a.25.1.2 68584 1n7sA 63 4.98e+00 h.1.15.1 80271 2b7aA 293 5.10e+00 1a8h 500 5.38e+00 1a8h a.27.1.1,c.26.1.1 16922,31589 1i1iP 681 5.72e+00 1i1iP d.92.1.5 40297 1na3A 91 5.84e+00 k.38.1.1 85481 1zgmA 248 6.26e+00 1gw5A 621 6.37e+00 a.118.1.10 70629 1tqgA 105 6.43e+00 a.24.10.3 107224 1wy6A 172 6.60e+00 2dh4A 340 6.99e+00 2cj4A 150 7.02e+00 1ku1A 230 7.09e+00 a.118.3.1 72996 1wwpA 119 7.13e+00 2fpqA 444 7.26e+00 1h5uA 842 7.26e+00 1a8i c.87.1.4 60655 1wucA 250 7.60e+00 1tffA 234 7.69e+00 d.3.1.11 106854 1ash 150 7.75e+00 1ash a.1.1.2 15622 1h3nA 878 7.77e+00 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1wa5B 530 7.82e+00 2fnoA 248 8.00e+00 2e2aA 105 8.60e+00 a.7.2.1 88499 1i5pA 633 8.63e+00 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 1abrA 251 8.68e+00 1mrj d.165.1.1 42196 1z72A 225 9.04e+00 1txuA 273 9.25e+00 a.222.1.1 107439 1wcrA 103 9.88e+00 1s4bP 674 9.97e+00 d.92.1.5 105252 1ajsA 412 1.02e+01 1ajsA c.67.1.1 34276 1paqA 189 1.03e+01 a.118.1.14 94413 2be3A 226 1.04e+01 1wy0A 342 1.04e+01 1xv5A 401 1.05e+01 1n4kA 381 1.06e+01 a.118.22.1,b.42.6.1 79992,79993 1orjA 130 1.10e+01 a.24.19.1 93456 1mhqA 148 1.15e+01 a.118.9.2 84973 1xgwA 176 1.15e+01 2aplA 157 1.18e+01 1cojA 212 1.20e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1v4eA 299 1.21e+01 a.128.1.1 100296 1np3A 338 1.24e+01 a.100.1.2,c.2.1.6 85946,85947 2bw3A 534 1.26e+01 1ug3A 339 1.27e+01 1lshA 1056 1.30e+01 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 1a17 166 1.30e+01 1a17 a.118.8.1 19206 1hz4A 373 1.32e+01 a.118.8.2 65960 2g5cA 281 1.33e+01 1eexG 173 1.33e+01 1dioG a.23.2.1 16490 1wmuB 146 1.34e+01 a.1.1.2 109417 1jk0B 345 1.36e+01 a.25.1.2 63143 16vpA 366 1.36e+01 16vpA d.180.1.1 42601 1rj1A 151 1.39e+01 a.29.6.1 97526 1keaA 221 1.43e+01 a.96.1.2 68491 1qqeA 292 1.45e+01 1qqeA a.118.8.1 19210 1qmqA 414 1.50e+01 1phd a.104.1.1 18907 1lf6A 684 1.50e+01 a.102.1.5,b.30.5.5 77918,77919 1hx1B 114 1.50e+01 1hx1B a.7.7.1 61350 1ka2A 499 1.52e+01 d.92.1.5 77305 2fuqA 747 1.53e+01 1hr6B 443 1.56e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1fqiA 147 1.58e+01 1agrE a.91.1.1 18542 1xqsA 280 1.61e+01 1o5kA 306 1.66e+01 c.1.10.1 92504 1j1jA 240 1.66e+01 a.118.16.1 90762 1mroA 548 1.69e+01 1mroA a.89.1.1,d.58.31.2 18525,39443 1nznA 126 1.71e+01 a.118.8.1 92382 1r2fA 319 1.73e+01 1r2fA a.25.1.2 16800 2btdA 210 1.75e+01 1vls 146 1.77e+01 1vls a.24.2.1 16532 2az0A 73 1.81e+01 2ayuA 417 1.89e+01 1xqrA 296 1.90e+01 1i50A 1733 1.90e+01 e.29.1.2 61754 1x9mA 698 1.91e+01 2fupA 168 1.91e+01 1hbnA 549 1.91e+01 1mroA a.89.1.1,d.58.31.2 60898,60899 1q0gA 117 1.91e+01 a.24.22.1 104428 1mkiA 330 1.94e+01 e.3.1.2 84994 1cpt 412 2.00e+01 1cpt a.104.1.1 18968 1jr8A 117 2.01e+01 a.24.15.1 67115 1wqgA 185 2.03e+01 1elrA 131 2.04e+01 1a17 a.118.8.1 19209 1cnt1 187 2.04e+01 1cnt3 1wlmA 151 2.05e+01 1qkrA 188 2.05e+01 1qkrA a.24.9.1 16628 1vjxA 157 2.05e+01 a.25.1.1 100837 1ez0A 510 2.09e+01 1eyyA c.82.1.1 35385 1l3aA 228 2.11e+01 d.18.1.2 73531 1s0pA 176 2.11e+01 a.192.1.1 98300 1vljA 407 2.14e+01 e.22.1.2 108832 1t0qA 498 2.15e+01 a.25.1.2 106220 2es4D 332 2.17e+01 2btoA 473 2.20e+01 1keyA 235 2.21e+01 a.118.16.1 72389 1hs6A 611 2.23e+01 1hs6A a.118.1.7,b.98.1.1,d.92.1.13 61233,61234,61235 2occA 514 2.24e+01 2occA f.24.1.1 43518 1cuk 203 2.28e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1k3yA 221 2.29e+01 a.45.1.1,c.47.1.5 77245,77246 1ciy 590 2.31e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1nf3A 195 2.32e+01 c.37.1.8 85594 1q5dA 419 2.33e+01 a.104.1.1 95891 1spgA 144 2.33e+01 1abwA a.1.1.2 15409 1jdpA 441 2.37e+01 c.93.1.1 62906 1wleA 501 2.39e+01 1pgjA 478 2.39e+01 2pgd a.100.1.1,c.2.1.6 18783,30195 1kq3A 376 2.43e+01 e.22.1.2 68790 1sgmA 191 2.44e+01 a.4.1.9,a.121.1.1 105537,105538 1sd4A 126 2.46e+01 a.4.5.39 105428 1elwA 118 2.49e+01 1a17 a.118.8.1 19207 1bu7A 455 2.54e+01 1bu7A a.104.1.1 18937 1dofA 403 2.60e+01 1c3cA a.127.1.1 19429 1dz4A 414 2.61e+01 1phd a.104.1.1 18903 1gmjA 84 2.62e+01 h.4.8.1 65310 1gqeA 365 2.63e+01 e.38.1.1 70351 1utg 70 2.75e+01 1utg a.101.1.1 18813 1x42A 232 2.76e+01 1ir6A 424 2.77e+01 c.107.1.2 71342 1t7pA 698 2.77e+01 1t7pA c.55.3.5,e.8.1.1 33712,43005 2az2A 73 2.78e+01 1o17A 345 2.79e+01 a.46.2.1,c.27.1.1 80765,80766 1v54A 514 2.80e+01 f.24.1.1 100321 2utgA 70 2.83e+01 1utg a.101.1.1 18814 1zs9A 261 2.84e+01 1yrcA 414 2.87e+01 1po5A 476 2.87e+01 a.104.1.1 94963 1h5zA 455 2.88e+01 a.104.1.1 90622 1ofcX 304 2.89e+01 a.4.1.3,a.4.1.13,a.187.1.1 92826,92827,92828 2aelA 374 2.97e+01 2d0tA 406 2.99e+01 2cfuA 658 3.00e+01 1h2kA 349 3.07e+01 b.82.2.6 76572 2gokA 429 3.08e+01 1ei1A 391 3.09e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 1mtyB 384 3.11e+01 1mtyB a.25.1.2 16740 1qf8A 182 3.12e+01 1qf8A g.41.4.1 45212 1re9A 414 3.12e+01 1jdhA 529 3.13e+01 a.118.1.1 66549 1qlnA 883 3.13e+01 1cezA e.8.1.3 43111 2bs3C 256 3.15e+01 1rcwA 231 3.21e+01 a.132.1.4 97299 1aisB 200 3.23e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 1qusA 322 3.25e+01 1ltm d.2.1.6 36991 1spgB 147 3.28e+01 1cg5B a.1.1.2 15588 6gsvA 217 3.31e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 1t9kA 347 3.39e+01 c.124.1.5 106721 2bk9A 153 3.46e+01 1f3aA 222 3.46e+01 1pgtA a.45.1.1,c.47.1.5 17701,32995 2f1kA 279 3.54e+01 1twfA 1733 3.57e+01 1or3A 165 3.58e+01 1nfn a.24.1.1 16522 1phnA 162 3.60e+01 1cpcA a.1.1.3 15641 2ashA 381 3.66e+01 1yyqA 374 3.66e+01 1opc 110 3.69e+01 1opc a.4.6.1 16231 1r9kA 172 3.69e+01 a.168.1.1 104869 2aaxA 275 3.74e+01 1nekC 129 3.75e+01 f.21.2.2 80431 1m48A 133 3.75e+01 a.26.1.2 74443 1sfjA 238 3.75e+01 1ee4A 423 3.76e+01 1ee4A a.118.1.1 19128 3ertA 261 3.77e+01 3erdA a.123.1.1 19292 2b0jA 358 3.79e+01 1nzeA 149 3.85e+01 a.24.18.1 92374 1v54J 59 3.85e+01 f.23.4.1 100331 1pf4A 582 3.85e+01 c.37.1.12,f.37.1.1 88052,88053 1vdkA 466 3.86e+01 a.127.1.1 100561 2fbqA 235 3.94e+01 1vp7A 100 3.96e+01 1yoyA 175 3.99e+01 1iwhA 141 4.01e+01 a.1.1.2 76882 1qlaC 256 4.07e+01 1qlaC f.21.2.1 43722 1z5hA 780 4.10e+01 1qjbA 245 4.14e+01 1qjaA a.118.7.1 19202 1h0oA 390 4.18e+01 a.25.1.2 70845 2fnaA 357 4.21e+01 2occJ 59 4.24e+01 2occJ f.23.4.1 43524 1om0A 274 4.30e+01 c.1.8.5 87058 2br9A 234 4.30e+01 1n9dA 199 4.36e+01 a.26.1.1 85464 1odoA 408 4.37e+01 a.104.1.1 92783 1sflA 238 4.38e+01 1xsm 390 4.41e+01 1xsm a.25.1.2 16804 1h3lA 87 4.44e+01 a.177.1.1 76639 2ct8A 497 4.45e+01 1oyzA 280 4.49e+01 a.118.1.16 93775 1z1lA 345 4.52e+01 1na6A 404 4.61e+01 b.142.1.1,c.52.1.22 91748,91749 1ppjA 446 4.66e+01 d.185.1.1,d.185.1.1 104252,104253 1w68A 390 4.67e+01 a.25.1.2 109216 1vh6A 145 4.74e+01 a.24.19.1 100644 1jsdB 176 4.75e+01 h.3.1.1 63259 1jk0A 419 4.76e+01 a.25.1.2 63142 1pveA 72 4.83e+01 a.189.1.1 104322 1a0fA 201 4.83e+01 1a0fA a.45.1.1,c.47.1.5 17737,33031 1e9xA 455 4.84e+01 1ea1A a.104.1.1 18969 1ylmA 144 4.88e+01 1em8B 112 4.92e+01 c.126.1.1 90458 2fcwA 109 4.92e+01 1ta3A 274 4.93e+01 c.1.8.5 106731 1vykA 149 4.94e+01 1z2cB 383 5.07e+01 1jq0A 84 5.09e+01 h.3.2.1 71786 1irdA 141 5.09e+01 a.1.1.2 66286 1siqA 392 5.11e+01 a.29.3.1,e.6.1.1 105585,105586 1a9xA 1058 5.11e+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 18550,31479,31657,31658,41502,41503 1g8iA 190 5.13e+01 1rec a.39.1.5 60363 1x0vA 354 5.15e+01 1oglA 283 5.16e+01 a.204.1.1 92922 1pjr 724 5.17e+01 1pjr c.37.1.19,c.37.1.19 32391,32392 2fefA 294 5.19e+01 1xgkA 352 5.21e+01 1umnA 165 5.23e+01 a.25.1.1 99607 1uouA 474 5.23e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 1n97A 389 5.31e+01 a.104.1.1 80335 1u7lA 392 5.32e+01 2frnA 278 5.32e+01 1xlyA 234 5.38e+01 1pa7A 130 5.39e+01 a.40.1.1 94410 1nvmA 345 5.40e+01 a.5.7.1,c.1.10.5 86249,86250 1rpa 342 5.40e+01 1cviA c.60.1.2 33983 1vj7A 393 5.41e+01 a.211.1.1,d.218.1.8 100801,100802 1t33A 224 5.43e+01 a.4.1.9,a.121.1.1 106295,106296 1h6gA 256 5.47e+01 1h6gA a.24.9.1,a.24.9.1 60669,60670 1ulyA 192 5.50e+01 1l0lA 446 5.52e+01 d.185.1.1,d.185.1.1 84482,84483 1jpzA 473 5.52e+01 a.104.1.1 67069 1o26A 232 5.53e+01 d.207.1.1 86566 1yakA 263 5.53e+01 1qbzA 123 5.54e+01 1qbzA h.3.2.1 45729 1ykuA 136 5.58e+01 1zc6A 305 5.59e+01 2btzA 394 5.65e+01 1q5nA 454 5.78e+01 a.127.1.1 95901 1rkpA 326 5.83e+01 a.211.1.2 97620 2fk8A 318 5.86e+01 1fxxA 482 5.88e+01 1fxxA c.55.3.5 33726 1v2zA 111 5.91e+01 a.186.1.1 108300 1gntA 553 5.96e+01 e.26.1.1 70290 1z0kB 69 5.98e+01 1lh0A 213 5.99e+01 c.61.1.1 73896 2etdA 171 6.00e+01 2dtr 226 6.00e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 1vkeA 133 6.01e+01 a.152.1.2 108650 2b8iA 77 6.04e+01 1pbwA 216 6.05e+01 1pbwA a.116.1.1 19103 1k3pA 426 6.06e+01 a.103.1.1 77237 1cs0A 1073 6.14e+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 2fmpA 335 6.19e+01 2dbnA 461 6.19e+01 1f0yA 302 6.23e+01 2hdhA a.100.1.3,c.2.1.6 18793,30197 1rp4A 389 6.24e+01 a.227.1.1 105027 1gvhA 396 6.25e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1ho8A 480 6.25e+01 1ho8A a.118.1.9 61107 1tv9A 335 6.29e+01 2cwcA 303 6.31e+01 1h99A 224 6.33e+01 a.142.1.1,a.142.1.1 60814,60815 1fvkA 189 6.36e+01 1fvkA c.47.1.13 90351 1dk8A 147 6.38e+01 1agrE a.91.1.1 18548 1wwjA 105 6.39e+01 1e2uA 553 6.40e+01 1e1dA e.26.1.1 43362 1eyhA 144 6.42e+01 1eduA a.118.9.1 19214 1kf6C 130 6.44e+01 f.21.2.2 72399 1hg7A 66 6.47e+01 1msi b.85.1.1 28280 1e85A 127 6.51e+01 1bbhA a.24.3.2 16549 1mojA 182 6.53e+01 a.25.1.1 91367 1yrlA 491 6.57e+01 1e2aA 105 6.63e+01 1e2aA a.7.2.1 16322 1q77A 138 6.70e+01 c.26.2.4 96023 1jhgA 101 6.73e+01 1jhgA a.4.12.1 19009 1v66A 65 6.83e+01 2g8lA 299 6.93e+01 1xpcA 248 6.98e+01 1mqsA 671 7.12e+01 e.25.1.1 79414 2anxA 146 7.18e+01 2fbnA 198 7.22e+01 1eguA 731 7.22e+01 1eguA a.102.3.2,b.24.1.1,b.30.5.2 18850,23899,24423 1ffyA 917 7.30e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1n2aA 201 7.31e+01 a.45.1.1,c.47.1.5 91553,91554 2bnxA 386 7.32e+01 1r71A 178 7.33e+01 a.4.14.1 104823 1k6xA 352 7.41e+01 c.2.1.2 68238 1t6uA 117 7.47e+01 a.24.22.1 106584 1sesA 421 7.69e+01 1sesA a.2.7.1,d.104.1.1 15710,40710 1mtyG 162 7.70e+01 1mtyG a.23.3.1 16498 2bh7A 261 7.73e+01 2g40A 224 7.82e+01 1wchA 315 7.82e+01 1azsA 220 8.10e+01 1azsA d.58.29.1 39416 1mq4A 272 8.13e+01 d.144.1.7 91391 2g3kA 94 8.16e+01 1o86A 589 8.18e+01 d.92.1.5 81177 1peh 35 8.21e+01 1peh j.14.1.1 46151 1c3wA 222 8.24e+01 1c3wA f.13.1.1 43405 1go3F 107 8.26e+01 a.60.8.2 65407 1kiyA 374 8.28e+01 a.128.1.5 72555 1f52A 468 8.30e+01 1lgr d.15.9.1,d.128.1.1 37839,41169 1q9uA 130 8.32e+01 d.129.7.1 96314 2bngA 149 8.33e+01 1w2qA 127 8.34e+01 1qfeA 252 8.34e+01 1qfeA c.1.10.1 29167 1wovA 250 8.40e+01 1bbhA 131 8.40e+01 1bbhA a.24.3.2 16546 1uf2A 1019 8.41e+01 e.28.1.2 99289 1kvkA 395 8.42e+01 d.14.1.5,d.58.26.3 73060,73061 2c8vA 288 8.42e+01 1z82A 335 8.43e+01 1gqnA 252 8.44e+01 c.1.10.1 90514 2a5yA 204 8.46e+01 1jt6A 188 8.46e+01 a.4.1.9,a.121.1.1 67247,67248 1winA 143 8.51e+01 1mh1 186 8.52e+01 1eesA c.37.1.8 32002 1uzeA 589 8.56e+01 d.92.1.5 108174 2abk 211 8.58e+01 2abk a.96.1.1 18743 2gmyA 153 8.64e+01 1zbpA 273 8.71e+01 1owcA 427 8.77e+01 a.103.1.1 104039 1zb1A 392 8.78e+01 1u5pA 216 8.80e+01 1mxrA 375 8.82e+01 a.25.1.2 85197 1mtyD 512 8.86e+01 1mhyD a.25.1.2 16742 1wusA 180 8.87e+01 1yiiA 320 8.90e+01 1wrrA 301 8.97e+01 1r4uA 301 8.97e+01 d.96.1.4,d.96.1.4 97047,97048 1ygtA 111 9.00e+01