# 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 1v7lA 163 2.13e-03 2gp4A 628 1.04e-01 1dl5A 317 3.04e-01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1kqfA 1015 4.38e-01 b.52.2.2,c.81.1.1 72871,72872 1fx2A 235 5.82e-01 1fx2A d.58.29.1 39430 1ivyA 452 6.54e-01 1ivyA c.69.1.5 34654 1ndh 272 8.17e-01 1ndh b.43.4.2,c.25.1.1 25662,31552 2napA 723 9.68e-01 2napA b.52.2.2,c.81.1.1 26926,35334 1yb5A 351 9.76e-01 1ju3A 583 1.03e+00 b.18.1.13,c.69.1.21 67300,67301 1k7jA 206 1.18e+00 d.115.1.1 72103 1e58A 249 1.29e+00 1qhfA c.60.1.1 59262 3ullA 132 1.50e+00 3ullA b.40.4.3 25282 1owfA 99 1.56e+00 a.55.1.1 87487 1zvyA 136 1.58e+00 1kblA 873 1.70e+00 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1tk9A 188 1.72e+00 c.80.1.3 107082 1q7hA 153 1.74e+00 b.122.1.1,d.17.6.2 96042,96043 1i1dA 161 1.77e+00 1i21A d.108.1.1 61526 1amx 180 1.84e+00 1amx b.2.3.1 22410 1o54A 277 1.88e+00 c.66.1.13 92482 1wmmA 145 1.92e+00 1t0hB 224 2.03e+00 c.37.1.1 106208 1pueE 89 2.17e+00 1awcA a.4.5.21 16165 1a88A 275 2.27e+00 1brt c.69.1.12 34707 1ii2A 524 2.35e+00 c.91.1.1,c.109.1.1 66146,66147 1x13A 401 2.70e+00 1huuA 90 3.06e+00 1huuA a.55.1.1 17897 1fltX 95 3.35e+00 1fltX b.1.1.4 21765 2viuA 328 3.39e+00 1hgeA b.19.1.2 23797 1jsdA 319 3.41e+00 b.19.1.2 63258 1iz6A 138 3.54e+00 b.34.5.2,b.40.4.5 76976,76977 2gjgA 248 3.62e+00 1viuA 203 3.87e+00 d.113.1.1 100771 2be1A 339 4.26e+00 1sb8A 352 4.53e+00 c.2.1.2 105410 1se8A 301 4.67e+00 b.40.4.3 105448 2ccjA 205 4.69e+00 1tksA 204 4.80e+00 d.115.1.2 107114 2bf5A 98 4.85e+00 1eu3A 210 4.90e+00 1an8 b.40.2.2,d.15.6.1 25206,37795 1qvcA 145 4.99e+00 3ullA b.40.4.3 25284 2ew2A 316 5.07e+00 1tuaA 191 5.09e+00 d.51.1.1,d.51.1.1 107321,107322 2g76A 335 5.25e+00 1uebA 184 5.31e+00 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1g8fA 511 5.31e+00 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 1aquA 297 5.53e+00 1aquA c.37.1.5 31942 1v74A 107 5.89e+00 d.243.1.1 100442 1vpjA 192 6.04e+00 1tvxA 75 6.31e+00 1tvxA d.9.1.1 37441 1i1nA 226 6.52e+00 c.66.1.7 71102 1erjA 393 6.53e+00 1erjA b.69.4.1 27660 1i12A 160 6.58e+00 1i21A d.108.1.1 61515 1ti6A 875 6.60e+00 b.52.2.2,c.81.1.1 106974,106975 1vjlA 164 6.79e+00 d.257.1.1 100822 1e19A 314 7.42e+00 1b7bA c.73.1.1 34967 1wr4A 36 7.57e+00 2f1rA 171 7.76e+00 1vs0A 310 8.25e+00 1zoiA 276 8.38e+00 2gnqA 336 8.64e+00 1z85A 234 8.76e+00 1k8wA 327 9.16e+00 b.122.1.1,d.265.1.2 83094,90388 1r6xA 395 9.28e+00 b.122.1.3,c.26.1.5 97167,97168 1kl9A 182 9.33e+00 b.40.4.5 72681 2h14A 317 9.43e+00 1lrwA 600 9.43e+00 b.70.1.1 91111 1o0xA 262 9.79e+00 d.127.1.1 80755 1t3lA 337 9.82e+00 b.34.2.1,c.37.1.1 106358,106359 1b34B 118 9.85e+00 1b34B b.38.1.1 24797 2cz1B 212 9.85e+00 1lucB 324 1.00e+01 1lucA c.1.16.1 29548 1h0hA 977 1.01e+01 b.52.2.2,c.81.1.1 76435,76436 1yn3A 98 1.01e+01 1q7fA 286 1.02e+01 b.68.9.1 96036 1em8A 147 1.03e+01 c.128.1.1 90457 2cb5A 453 1.09e+01 3gcb d.3.1.1 37035 1umkA 275 1.11e+01 1yizA 429 1.13e+01 1pvyA 227 1.13e+01 d.115.1.2 95195 2gfaA 119 1.14e+01 1qfgA 725 1.14e+01 1by5A f.4.3.3 43803 1e3jA 352 1.16e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 2bnfB 241 1.16e+01 1snnA 227 1.17e+01 d.115.1.2 105821 1lgpA 116 1.19e+01 b.26.1.2 73890 1uxtA 501 1.20e+01 c.82.1.1 108125 1wjnA 97 1.20e+01 1wl4A 397 1.24e+01 1jf9A 408 1.27e+01 1c0nA c.67.1.3 62931 2f2eA 146 1.28e+01 1a8p 258 1.29e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1xu9A 286 1.31e+01 1ybdA 239 1.32e+01 1xovA 326 1.35e+01 1k4iA 233 1.36e+01 d.115.1.2 72056 1lf2A 331 1.36e+01 b.50.1.2 77914 1zaiA 363 1.36e+01 1fseA 74 1.36e+01 1fseA a.4.6.2 60000 1ko7A 314 1.36e+01 c.98.2.1,c.91.1.2 72797,72798 1adoA 363 1.37e+01 1fbaA c.1.10.1 29124 1wn2A 121 1.37e+01 1o60A 292 1.39e+01 c.1.10.4 92532 1knwA 425 1.40e+01 b.49.2.3,c.1.6.1 90969,90970 2gk3A 256 1.40e+01 1p57A 114 1.40e+01 d.170.1.2 94125 1nrfA 262 1.41e+01 e.3.1.1 92086 2fxqA 264 1.43e+01 1owfB 94 1.44e+01 a.55.1.1 87488 1bia 321 1.45e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1mvfA 135 1.45e+01 b.1.1.1 85141 1am2 199 1.47e+01 1am2 b.86.1.2 28381 1zd0A 150 1.47e+01 2fb6A 117 1.48e+01 1qauA 112 1.53e+01 1qauA b.36.1.1 24779 1ss4A 153 1.54e+01 d.32.1.6 105976 2bneA 241 1.60e+01 2bwvA 440 1.62e+01 1gcuA 295 1.62e+01 1gcuA c.2.1.3,d.81.1.4 30063,39978 1rcqA 357 1.62e+01 b.49.2.2,c.1.6.1 104882,104883 2cblA 305 1.62e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17380,17774,40528 1whzA 70 1.64e+01 2ha8A 184 1.64e+01 1rl6A 177 1.69e+01 1rl6A d.141.1.1,d.141.1.1 41473,41474 6paxA 133 1.72e+01 6paxA a.4.1.5,a.4.1.5 64758,64759 1yr2A 741 1.72e+01 1d3bA 75 1.73e+01 1d3bA b.38.1.1 24798 2absA 383 1.74e+01 1zx8A 136 1.76e+01 1uv4A 293 1.78e+01 1kzlA 208 1.81e+01 b.43.4.3,b.43.4.3 77635,77636 1v8yA 170 1.81e+01 2cwaA 263 1.81e+01 1o20A 427 1.82e+01 c.82.1.1 86556 1ddgA 374 1.83e+01 1amoA b.43.4.1,c.25.1.4 25671,31559 1x3eA 165 1.85e+01 1k78A 149 1.86e+01 a.4.1.5,a.4.1.5 68255,68256 1kevA 351 1.89e+01 1pedA b.35.1.2,c.2.1.1 24749,29765 1luzA 88 1.93e+01 b.40.4.5 74271 1k6dA 220 1.94e+01 c.124.1.2 72082 1s21A 206 1.95e+01 d.166.1.4 105222 1k2yX 463 1.97e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 2as0A 396 1.98e+01 1aonO 97 2.01e+01 b.35.1.1 24642 1dzfA 215 2.02e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 2a19A 175 2.02e+01 1jqbA 351 2.07e+01 b.35.1.2,c.2.1.1 77151,77152 1bkb 136 2.11e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 1gc0A 398 2.14e+01 c.67.1.3 70168 2ahjB 212 2.14e+01 2ahjB b.34.4.4 24599 1w96A 554 2.16e+01 1jsdB 176 2.17e+01 h.3.1.1 63259 1y9lA 115 2.17e+01 1vioA 243 2.17e+01 d.265.1.3,d.66.1.5 100762,100763 1xseA 295 2.17e+01 1g72A 573 2.19e+01 4aahA b.70.1.1 27680 7ahlA 293 2.21e+01 7ahlA f.6.1.1 43812 1df7A 159 2.21e+01 3dfr c.71.1.1 34885 1a6f 119 2.26e+01 1a6f d.14.1.2 37564 1yvhA 329 2.26e+01 5abp 306 2.27e+01 8abp c.93.1.1 35651 1xtoA 311 2.28e+01 1kjkA 64 2.29e+01 d.10.1.4 72613 1tig 94 2.31e+01 1tig d.68.1.1 39566 1nktA 922 2.35e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 85830,85831,85832,85833 1r17A 343 2.40e+01 b.2.3.4,b.2.3.4 96796,96797 1vqoA 240 2.40e+01 2f23A 156 2.42e+01 1wnfA 328 2.42e+01 1t46A 313 2.44e+01 d.144.1.7 106397 1fdr 248 2.44e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 1x7dA 350 2.46e+01 1okgA 373 2.46e+01 c.46.1.2,c.46.1.2,d.26.1.3 93250,93251,93252 1iw7C 1119 2.47e+01 e.29.1.1 71474 1c30B 382 2.49e+01 c.8.3.1,c.23.16.1 30736,31413 1uu1A 335 2.54e+01 c.67.1.1 99993 1iqzA 81 2.54e+01 d.58.1.4 66281 2nacA 393 2.56e+01 2nadA c.2.1.4,c.23.12.1 30088,31348 1i7pA 274 2.64e+01 b.43.4.2,c.25.1.1 66048,66049 2b0cA 206 2.64e+01 2czsA 80 2.65e+01 1zpsA 138 2.65e+01 1xnzA 264 2.65e+01 1vchA 175 2.73e+01 1ywnA 316 2.73e+01 1tf5A 844 2.73e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 106834,106835,106836,106837 1deoA 233 2.80e+01 1deoA c.23.10.4 31345 2gnoA 305 2.80e+01 2bz8A 58 2.80e+01 1k3sA 113 2.82e+01 d.198.1.1 68120 1a9xB 379 2.83e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 1wr7A 41 2.83e+01 2alaA 391 2.91e+01 1liiA 363 2.92e+01 c.72.1.1 73921 3il8 72 2.93e+01 1tvxA d.9.1.1 37356 1cqxA 403 2.93e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1jb9A 316 2.94e+01 1fnc b.43.4.2,c.25.1.1 62840,62841 1bjx 110 2.95e+01 1bjx c.47.1.2 32774 1y0nA 78 2.97e+01 1wl9A 440 2.99e+01 1z9fA 153 2.99e+01 1kv9A 668 3.00e+01 a.3.1.6,b.70.1.1 73056,73057 1k7cA 233 3.01e+01 c.23.10.4 68267 1nqzA 194 3.02e+01 d.113.1.1 86077 1afp 51 3.03e+01 1afp g.26.1.1 44947 1c24A 263 3.04e+01 1c24A d.127.1.1 41148 1vkfA 188 3.06e+01 c.1.29.1 108656 1oyzA 280 3.07e+01 a.118.1.16 93775 1wlyA 333 3.07e+01 1t3iA 420 3.08e+01 c.67.1.3 106354 1rijA 25 3.08e+01 k.32.1.1 104951 1lc0A 294 3.09e+01 c.2.1.3,d.81.1.4 73823,73824 1go2A 304 3.12e+01 b.43.4.2,c.25.1.1 76243,76244 1kb0A 677 3.16e+01 a.3.1.6,b.70.1.1 68378,68379 1qx4A 274 3.17e+01 b.43.4.2,c.25.1.1 104624,104625 1pv9A 348 3.17e+01 c.55.2.1,d.127.1.1 95157,95158 1zvhA 134 3.17e+01 1cruA 454 3.19e+01 1c9uA b.68.2.1 27617 2fbyA 205 3.20e+01 1az9 457 3.20e+01 1az9 c.55.2.1,d.127.1.1 33547,41164 1o4sA 389 3.22e+01 c.67.1.1 86620 2b3gA 123 3.22e+01 2dpmA 284 3.22e+01 2dpmA c.66.1.28 34246 1q1gA 276 3.23e+01 c.56.2.1 95574 2ggcA 263 3.24e+01 1hbzA 498 3.29e+01 1cf9A e.5.1.1 60937 1ir6A 424 3.34e+01 c.107.1.2 71342 2bdrA 175 3.34e+01 1lt8A 406 3.37e+01 c.1.26.1 78186 1w34A 304 3.39e+01 2gm5A 139 3.41e+01 1ei6A 406 3.44e+01 c.76.1.4 90443 2iw2A 494 3.45e+01 1ydxA 406 3.46e+01 2bsaA 303 3.46e+01 1xneA 113 3.48e+01 2bmwA 304 3.50e+01 1ogiA 303 3.54e+01 b.43.4.2,c.25.1.1 92914,92915 2b59B 172 3.56e+01 1sbp 310 3.60e+01 1sbp c.94.1.1 35760 2bikB 313 3.62e+01 1cpt 412 3.63e+01 1cpt a.104.1.1 18968 1jm1A 204 3.66e+01 b.33.1.1 71745 1qxrA 189 3.67e+01 b.82.1.7 96552 1twfF 155 3.69e+01 1gxrA 337 3.71e+01 b.69.4.1 70722 1w41A 101 3.75e+01 2ctdA 96 3.78e+01 1x6oA 174 3.81e+01 b.34.5.2,b.40.4.5 109493,109494 1dxy 333 3.85e+01 1dxy c.2.1.4,c.23.12.1 30094,31354 1r5mA 425 3.89e+01 1nqcA 217 3.92e+01 d.3.1.1 86024 1b8zA 90 3.94e+01 1huuA a.55.1.1 17902 1lplA 95 4.00e+01 b.34.10.1 74173 1xdwA 331 4.00e+01 1que 303 4.00e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1zeqX 84 4.01e+01 2b29A 123 4.01e+01 1zd8A 227 4.01e+01 1j54A 186 4.03e+01 c.55.3.5 77077 1pl8A 356 4.05e+01 b.35.1.2,c.2.1.1 94878,94879 1smrA 335 4.05e+01 1smrA b.50.1.2 26878 1gdeA 389 4.08e+01 c.67.1.1 60456 1smxA 96 4.10e+01 b.40.4.5 105772 2g50A 530 4.12e+01 1qorA 327 4.13e+01 1qorA b.35.1.2,c.2.1.1 24766,29782 1umuA 116 4.16e+01 1umuA b.87.1.1 28382 1g0oA 283 4.17e+01 1ybvA c.2.1.2 60181 1zatA 250 4.17e+01 1pwhA 327 4.24e+01 c.79.1.1 95224 1p5dX 463 4.25e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1l2yA 20 4.26e+01 k.32.1.1 73530 1wdjA 187 4.28e+01 1t5oA 351 4.43e+01 c.124.1.5 106459 1rkxA 357 4.43e+01 c.2.1.2 97631 1jb0D 138 4.45e+01 1jb0D d.187.1.1 62823 1jcxA 267 4.47e+01 c.1.10.4 66510 1oahA 519 4.49e+01 a.138.1.3 86736 1gwmA 153 4.54e+01 b.18.1.19 83348 1vf8A 377 4.54e+01 2a8kA 108 4.55e+01 1hn2A 159 4.57e+01 b.60.1.1 65890 1m7sA 484 4.60e+01 e.5.1.1 74574 1gt1A 159 4.66e+01 b.60.1.1 90515 1n9lA 109 4.69e+01 d.110.3.6 85468 1h59B 54 4.70e+01 g.3.9.1 70881 1e0nA 27 4.70e+01 b.72.1.1 27807 1kjnA 157 4.77e+01 c.115.1.1 72614 1kqfB 294 4.77e+01 d.58.1.5,f.23.22.1 75900,75901 1dqeA 137 4.79e+01 1dqeA a.39.2.1 17388 1xmbA 418 4.79e+01 2c1lA 358 4.81e+01 1k28A 584 4.81e+01 b.40.8.1,b.108.1.2,d.2.1.3 68049,68050,68051 1tovA 98 4.88e+01 b.34.10.1 107179 1ue1A 164 4.89e+01 b.40.4.3 99243 1fd3A 41 4.90e+01 1fd3A g.9.1.1 44572 1k4mA 213 4.91e+01 c.26.1.3 77258 1gweA 503 4.93e+01 e.5.1.1 70667 1ituA 369 4.94e+01 c.1.9.7 71423 2cw5A 255 4.99e+01 2fq9A 225 4.99e+01 1lzlA 323 5.06e+01 c.69.1.2 78306 1ghpA 258 5.08e+01 1btl e.3.1.1 60520 2bklA 695 5.10e+01 1l7dA 384 5.13e+01 c.2.1.4,c.23.12.2 77774,77775 2b4gA 317 5.15e+01 1e5eA 404 5.15e+01 1ibjA c.67.1.3 59265 1e9lA 377 5.15e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 1vkyA 347 5.17e+01 e.53.1.1 108696 1fxqA 267 5.17e+01 1d9eA c.1.10.4 60108 1im5A 180 5.18e+01 c.33.1.3 66211 2aorA 223 5.19e+01 1fb6A 105 5.20e+01 1thx c.47.1.1 32739 1zq1C 633 5.22e+01 1va0A 239 5.23e+01 1h6dA 433 5.25e+01 c.2.1.3,d.81.1.5 65656,65657 1fwsA 267 5.27e+01 1d9eA c.1.10.4 60063 1x82A 190 5.27e+01 1vdmA 153 5.28e+01 1ltlA 279 5.29e+01 b.40.4.11 84701 1bg6 359 5.31e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 1i6pA 220 5.32e+01 1ddzA c.53.2.1 61848 1hkhA 279 5.32e+01 c.69.1.12 90628 1t9kA 347 5.33e+01 c.124.1.5 106721 2ak3A 226 5.33e+01 1zin c.37.1.1,g.41.2.1 31892,45193 2bjuA 453 5.35e+01 1obpA 159 5.41e+01 1obpA b.60.1.1 27092 1ro2A 216 5.43e+01 d.264.1.2 97665 1v3vA 333 5.48e+01 b.35.1.2,c.2.1.1 108345,108346 2g1lA 104 5.51e+01 1ofdA 1520 5.53e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1qvzA 237 5.54e+01 c.23.16.2 96453 1w0uA 55 5.67e+01 1a6wH 120 5.68e+01 1mfa b.1.1.1 20253 2b5iD 217 5.69e+01 2cw8A 537 5.69e+01 1vi2A 300 5.71e+01 c.2.1.7,c.58.1.5 100726,100727 1e0tA 470 5.73e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1im8A 244 5.76e+01 c.66.1.14 66212 1vkmA 297 5.77e+01 c.138.1.1 108670 1k0wA 231 5.79e+01 c.74.1.1 77220 1a62 130 5.80e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1ja9A 274 5.81e+01 c.2.1.2 62817 1zbqA 327 5.82e+01 1nnsA 326 5.84e+01 c.88.1.1 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