# List of top-scoring protein chains for t04-100-30-alpha-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 1din 236 2.70e-02 1din c.69.1.9 34682 1zi8A 236 3.99e-02 1kshA 186 1.56e-01 c.37.1.8 72914 2cb2A 318 1.70e-01 1o17A 345 4.14e-01 a.46.2.1,c.27.1.1 80765,80766 1vemA 516 4.70e-01 1itcA 516 4.87e-01 b.3.1.1,c.1.8.1 83705,83706 1yyaA 250 5.10e-01 1o50A 157 9.22e-01 d.37.1.1,d.37.1.1 92478,92479 1voqa 90 1.01e+00 1nmoA 247 1.21e+00 c.135.1.1 91980 1b35B 255 1.84e+00 1b35B b.121.4.1 23334 1jr7A 311 1.90e+00 b.82.2.3 63255 1e55A 512 1.96e+00 1e70M c.1.8.4 28934 2brcA 214 2.00e+00 1j1hA 144 2.16e+00 b.111.1.1 77056 1h49A 512 2.19e+00 c.1.8.4 83477 1bb8 71 2.44e+00 2bb8 d.10.1.1 37478 1v02A 565 2.58e+00 c.1.8.4 108194 1ah6 220 2.86e+00 1yer d.122.1.1 41094 2breA 219 2.90e+00 1oo0A 147 2.97e+00 d.232.1.1 87182 1neiA 60 3.11e+00 d.253.1.1 91843 2cbuA 468 3.24e+00 1sfxA 109 3.39e+00 a.4.5.50 105505 2a5dA 175 3.84e+00 1wzvA 155 3.91e+00 2bkdN 134 3.91e+00 1nvpD 108 4.33e+00 a.32.1.1,b.56.1.1 92213,92214 1qvbA 481 4.47e+00 1qvbA c.1.8.4 28983 1w3jA 468 4.49e+00 c.1.8.4 109156 1jlyA 304 4.69e+00 1jlyA b.42.3.1,b.42.3.1 25587,25588 1zd9A 188 5.06e+00 1q15A 503 5.09e+00 c.26.2.1,d.153.1.1 95538,95539 1sqsA 242 5.35e+00 c.23.5.5 98968 1pbgA 468 5.73e+00 1e70M c.1.8.4 28946 4icb 76 6.24e+00 4icb a.39.1.1 17145 2cfaA 217 6.51e+00 2d2jA 329 6.52e+00 1zbpA 273 6.73e+00 1kolA 398 7.06e+00 b.35.1.2,c.2.1.1 77474,77475 1aerA 205 7.10e+00 1aerA d.166.1.1 42249 1n3gA 113 7.14e+00 d.204.1.1 79962 1jmcA 246 7.20e+00 1jmcA b.40.4.3,b.40.4.3 25300,25301 1l2lA 457 7.36e+00 c.72.1.3 77656 2f9dA 125 7.78e+00 1nlfA 279 7.92e+00 c.37.1.11 85850 1g2iA 166 8.01e+00 1g2iA c.23.16.2 31438 2agyA 361 8.22e+00 1y1uA 585 8.70e+00 1mml 265 8.88e+00 1mml e.8.1.2 43015 1xniA 118 8.88e+00 1bf5A 545 9.40e+00 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 1ikpA 613 9.43e+00 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1xnb 185 9.45e+00 1axkA b.29.1.11 24308 1fy7A 278 9.53e+00 1fy7A d.108.1.1 40817 1txgA 335 9.59e+00 1ig5A 75 1.02e+01 4icb a.39.1.1 62363 1t2jA 116 1.07e+01 1f9zA 135 1.10e+01 1qipA d.32.1.1 38484 1g8yA 279 1.13e+01 1g8yA c.37.1.11 32302 1r7lA 110 1.16e+01 d.277.1.1 104837 1qfxA 460 1.17e+01 1qfxA c.60.1.2 33994 1mr7A 209 1.22e+01 b.81.1.3 91430 1z5zA 271 1.27e+01 1o3yA 166 1.28e+01 c.37.1.8 86618 2chnA 716 1.30e+01 1irsA 112 1.32e+01 1qqgA b.55.1.2 26991 2fm8A 135 1.35e+01 1d8wA 426 1.36e+01 1de5A c.1.15.2 29394 1fa8A 135 1.40e+01 1qipA d.32.1.1 38486 1cipA 353 1.41e+01 1cipA a.66.1.1,c.37.1.8 18210,32093 2aclB 244 1.43e+01 2c1gA 431 1.47e+01 2ew0A 192 1.49e+01 1yc9A 442 1.51e+01 1fj2A 232 1.52e+01 1auoA c.69.1.14 34720 1uw4A 91 1.59e+01 d.58.7.4 100071 1k0sA 151 1.62e+01 b.40.7.1 67969 1p4kA 295 1.64e+01 d.153.1.5 87772 2dcyA 185 1.68e+01 1zt2B 212 1.73e+01 1mo9A 523 1.73e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1vizA 240 1.76e+01 c.1.4.1 100784 1f6bA 198 1.81e+01 c.37.1.8 64986 1svsA 353 1.81e+01 c.37.1.8 106051 1y80A 210 1.83e+01 1uz1A 468 1.89e+01 1xahA 354 1.92e+01 1wjxA 122 1.95e+01 1kveB 77 1.96e+01 1kveB 1r9fA 136 2.01e+01 d.255.1.1 97257 2gaiA 633 2.03e+01 1zfuA 40 2.08e+01 1ssfA 156 2.09e+01 b.34.9.1,b.34.9.1 105982,105983 2c1iA 431 2.09e+01 2acaA 189 2.19e+01 1whzA 70 2.24e+01 1vg5A 73 2.27e+01 4pgaA 337 2.30e+01 4pgaA c.88.1.1 35565 2fsrA 195 2.31e+01 1uurA 473 2.33e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1qzgA 187 2.34e+01 b.40.4.3 96643 1i50C 318 2.39e+01 d.74.3.1,d.181.1.1 61756,61757 2bj7A 138 2.39e+01 1weoA 93 2.41e+01 1yfnA 118 2.43e+01 1csn 298 2.45e+01 1csn d.144.1.7 41664 1zpuA 534 2.47e+01 1tfzA 424 2.48e+01 d.32.1.3,d.32.1.3 106886,106887 1r8sA 164 2.53e+01 c.37.1.8 97247 2gtrA 261 2.55e+01 1go2A 304 2.59e+01 b.43.4.2,c.25.1.1 76243,76244 1lyxA 248 2.63e+01 c.1.1.1 78304 1rypL 212 2.65e+01 d.153.1.4 41880 1i0dA 332 2.71e+01 1pscA c.1.9.3 61487 1q5hA 147 2.72e+01 b.85.4.1 95893 1seiA 130 2.75e+01 1seiA d.140.1.1 41463 2bsaA 303 2.75e+01 2fa8A 105 2.78e+01 1thjA 214 2.79e+01 1qreA b.81.1.5 28072 2b7eA 59 2.81e+01 2fcjA 119 2.83e+01 1kwnA 207 2.84e+01 b.25.1.1 77568 2ahjA 206 2.84e+01 2ahjA d.149.1.1 41772 1hskA 326 2.90e+01 2mbr d.145.1.2,d.146.1.1 61241,61242 2sak 121 2.92e+01 2sak d.15.5.1 37711 1mwwA 128 2.92e+01 d.80.1.4 91483 1n2sA 299 2.97e+01 c.2.1.2 79857 1xxnA 185 3.00e+01 1nw1A 429 3.00e+01 d.144.1.8 86286 1r29A 127 3.01e+01 d.42.1.1 96856 1flcA 432 3.03e+01 1flcA b.19.1.3,c.23.10.2 23837,31337 1thv 207 3.04e+01 1thv b.25.1.1 23904 1krs 120 3.04e+01 1krs b.40.4.1 25256 1qreA 247 3.05e+01 1qreA b.81.1.5 28066 1htwA 158 3.06e+01 c.37.1.18 71083 1x3pA 54 3.12e+01 1j55A 95 3.12e+01 a.39.1.2 77078 1yzbA 182 3.13e+01 1jykA 254 3.16e+01 c.68.1.13 67458 2f1kA 279 3.18e+01 1jyoA 130 3.20e+01 d.198.1.1 67483 1azo 232 3.34e+01 1azo c.52.1.14 33329 1rypF 233 3.37e+01 1rypF d.153.1.4 41937 2d1eA 248 3.37e+01 1o7iA 119 3.38e+01 b.40.4.3 86642 1a4pA 96 3.39e+01 1b4cA a.39.1.2 17176 1xypA 190 3.41e+01 1axkA b.29.1.11 24327 1xrkA 124 3.45e+01 1w34A 304 3.46e+01 1cojA 212 3.48e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 2basA 431 3.50e+01 1pcfA 66 3.51e+01 1pcfA d.18.1.1 38142 2cz1A 206 3.53e+01 1w32A 348 3.57e+01 1oxcA 114 3.58e+01 b.115.1.1 93683 1zl0A 311 3.58e+01 1ap6A 198 3.64e+01 1avmA a.2.11.1,d.44.1.1 15746,38705 1x6vA 630 3.66e+01 1i3zA 103 3.67e+01 d.93.1.1 83667 2ftbA 125 3.70e+01 2bh1A 250 3.71e+01 1o5xA 248 3.71e+01 c.1.1.1 92528 1ef1A 294 3.75e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 2fw2A 260 3.77e+01 1zkpA 268 3.77e+01 1sy6A 204 3.80e+01 b.1.1.4,b.1.1.4 106111,106112 2aegA 268 3.80e+01 1wwzA 159 3.86e+01 1dabA 539 3.86e+01 1dabA b.80.1.7 28049 2gqrA 237 3.89e+01 1gpr 162 3.90e+01 1gpr b.84.3.1 28267 1g38A 393 3.91e+01 2admA c.66.1.27 60235 1ab4 477 3.91e+01 1ab4 e.11.1.1 43251 1twfC 318 3.92e+01 1q7zA 566 3.96e+01 c.1.21.2,c.1.26.1 96090,96091 1e3uA 246 4.06e+01 1fofA e.3.1.1 42755 2fz4A 237 4.08e+01 1ywhA 313 4.10e+01 2aumA 317 4.12e+01 1zrsA 317 4.18e+01 1x54A 434 4.20e+01 1c2pA 576 4.21e+01 1quvA e.8.1.4 43117 1n0nA 199 4.23e+01 a.2.11.1,d.44.1.1 79750,79751 1kskA 234 4.26e+01 d.66.1.5,d.265.1.3 72920,90389 1rlzA 369 4.27e+01 c.31.1.1 104989 1qcsA 211 4.32e+01 1qcsA b.52.2.3,d.31.1.1 26927,38461 1k1aA 241 4.42e+01 d.211.1.1 67992 1rpyA 114 4.43e+01 d.93.1.1 97718 1igqA 62 4.45e+01 b.34.1.3 66130 1v5iB 76 4.50e+01 1g291 372 4.50e+01 1g291 2aunA 317 4.51e+01 1pl4A 198 4.52e+01 a.2.11.1,d.44.1.1 94854,94855 1suuA 312 4.52e+01 b.68.10.1 99006 1r6jA 82 4.54e+01 b.36.1.1 97151 1pq9A 253 4.54e+01 a.123.1.1 95004 2f57A 317 4.56e+01 1upvA 257 4.58e+01 2a0jA 149 4.60e+01 1osdA 72 4.63e+01 d.58.17.1 104022 1rrmA 386 4.65e+01 e.22.1.2 105081 1z4eA 153 4.66e+01 1wdyA 285 4.66e+01 1clxA 347 4.74e+01 1taxA c.1.8.3 28899 1uzvA 114 4.75e+01 1nteA 82 4.75e+01 b.36.1.1 86163 1mkfA 382 4.77e+01 b.116.1.1 79232 2bh8A 101 4.79e+01 2cx5A 158 4.84e+01 1wp5A 323 4.88e+01 1zc6A 305 4.91e+01 1rqwA 207 4.92e+01 b.25.1.1 97781 1xubA 298 5.01e+01 2blrA 206 5.01e+01 2b69A 343 5.01e+01 1vj5A 555 5.06e+01 c.108.1.2,c.69.1.11 100799,100800 1wnaA 131 5.07e+01 1zj6A 187 5.08e+01 1mtzA 293 5.10e+01 c.69.1.7 79467 1m1zA 513 5.10e+01 c.26.2.1,d.153.1.1 78457,78458 1zsxA 347 5.13e+01 1wh8A 111 5.16e+01 1dmmA 131 5.16e+01 1opy d.17.4.3 38114 1hdmA 201 5.17e+01 1iakA b.1.1.2,d.19.1.1 21583,38157 2bvcA 486 5.18e+01 2ey4C 82 5.18e+01 1jj2R 84 5.19e+01 1ffkP d.12.1.1 63103 1vjrA 271 5.20e+01 c.108.1.14 100832 2evrA 246 5.21e+01 1nz0A 118 5.21e+01 d.14.1.2 86433 1lc5A 364 5.23e+01 c.67.1.1 73827 1po0A 751 5.26e+01 f.4.3.3 94960 1sg7A 96 5.26e+01 2b6hA 192 5.27e+01 1s72S 85 5.29e+01 d.12.1.1 105338 1vqoS 85 5.32e+01 2fd6U 276 5.36e+01 1rypI 222 5.36e+01 d.153.1.4 41877 1gztA 115 5.41e+01 b.115.1.1 76428 1m22A 503 5.44e+01 c.117.1.1 78464 1ycdA 243 5.44e+01 1bylA 125 5.50e+01 1bylA d.32.1.2 38495 2fbmA 291 5.51e+01 1ir6A 424 5.53e+01 c.107.1.2 71342 1exbA 332 5.56e+01 1qrqA c.1.7.1 28666 2bwvA 440 5.60e+01 1f32A 149 5.62e+01 1f32A d.62.1.1 39539 1kbjA 412 5.63e+01 c.1.4.1 72280 1u1wA 298 5.65e+01 1kmoA 774 5.69e+01 f.4.3.3 72753 9gafA 295 5.71e+01 1apyA d.153.1.5 42008 1q3lA 69 5.72e+01 1hurA 180 5.74e+01 1hurA c.37.1.8 32052 2aamA 309 5.74e+01 2fdiA 211 5.76e+01 2bkyA 97 5.80e+01 2gfaA 119 5.80e+01 1hzyA 332 5.82e+01 1pscA c.1.9.3 61468 1wl9A 440 5.83e+01 1at0 145 5.83e+01 1at0 b.86.1.1 28374 1fzqA 181 5.89e+01 1hurA c.37.1.8 32060 1p65A 73 5.90e+01 d.254.1.1 94156 1bykA 255 5.94e+01 1bykA c.93.1.1 35706 1g31A 111 5.98e+01 1g31A b.35.1.1 24656 1k55A 246 5.99e+01 e.3.1.1 68156 1x74A 360 6.01e+01 1xqwA 293 6.04e+01 1ykhB 132 6.05e+01 1h4rA 314 6.07e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1ihnA 113 6.10e+01 1ihnA c.103.1.1 62388 2axjA 242 6.11e+01 1m1sA 116 6.12e+01 b.1.11.2 84747 1z2nX 324 6.22e+01 1g5bA 221 6.29e+01 1g5bA d.159.1.3 60261 1xcbA 211 6.29e+01 a.4.5.38,c.2.1.12 109552,109553 1awd 94 6.32e+01 1awd d.15.4.1 37673 1z8gA 372 6.35e+01 1whtB 153 6.37e+01 1whtB 1que 303 6.43e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1lv7A 257 6.44e+01 c.37.1.20 78232 2f5yA 91 6.48e+01 2pgd 482 6.53e+01 2pgd a.100.1.1,c.2.1.6 18778,30190 1t2bA 397 6.61e+01 1wmmA 145 6.62e+01 1v72A 356 6.63e+01 1u3oA 82 6.69e+01 1xiuA 230 6.69e+01 1c52 131 6.73e+01 1c52 a.3.1.1 15810 1t6kA 278 6.75e+01 1t3qB 788 6.87e+01 d.41.1.1,d.133.1.1 106369,106370 2aieP 203 6.96e+01 2fp7B 172 6.96e+01 1gx5A 536 6.96e+01 e.8.1.4 70682 1nar 290 7.01e+01 1nar c.1.8.5 28988 1a8y 367 7.02e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1kx5C 128 7.03e+01 a.22.1.1 77595 2agcA 162 7.03e+01 1evfA 264 7.06e+01 1bkpA d.117.1.1 40932 1y3tA 337 7.07e+01 1ywnA 316 7.08e+01 1qx4A 274 7.12e+01 b.43.4.2,c.25.1.1 104624,104625 1oh0A 131 7.13e+01 d.17.4.3 87004 1k20A 310 7.13e+01 c.107.1.1 68027 1yarA 233 7.13e+01 1amk 251 7.20e+01 1amk c.1.1.1 28503 1n55A 251 7.28e+01 c.1.1.1 80007 1tw9A 206 7.30e+01 a.45.1.1,c.47.1.5 107381,107382 1zhvA 134 7.34e+01 1fb6A 105 7.40e+01 1thx c.47.1.1 32739 1e0fI 57 7.40e+01 1e0fI g.3.15.2 44377 1moq 368 7.41e+01 1moq c.80.1.1 35302 1e1hA 287 7.44e+01 d.92.1.7 83167 1ex1A 605 7.45e+01 1ex1A c.1.8.7,c.23.11.1 29013,31347 1uv4A 293 7.54e+01 1wpiA 133 7.61e+01 1x75A 132 7.61e+01 1sgoA 139 7.62e+01 d.82.3.1 98857 2sas 185 7.65e+01 2sas a.39.1.5 17258 1i7pA 274 7.70e+01 b.43.4.2,c.25.1.1 66048,66049 2czlA 272 7.72e+01 1y4lA 121 7.74e+01 1nzjA 298 7.75e+01 c.26.1.1 92377 1qqgA 264 7.82e+01 1qqgA b.55.1.2,b.55.1.2 26987,26988 1qcwA 410 7.82e+01 1gox c.1.4.1 28622 1byqA 228 7.83e+01 1yer d.122.1.1 41100 1el6A 219 7.89e+01 1el6B d.182.1.1 42606 1w9yA 319 7.90e+01 1uylA 236 7.96e+01 d.122.1.1 108147 1pv0A 46 7.98e+01 a.2.12.1 95141 3aprE 325 7.99e+01 2er7E b.50.1.2 26820 1ka8A 100 8.00e+01 a.4.5.20 72241 1vpi 122 8.01e+01 1poa a.133.1.2 19559 1zbxB 141 8.03e+01 1x0vA 354 8.09e+01 1ejxC 567 8.11e+01 b.92.1.1,c.1.9.2 83184,83185 2bsjA 133 8.13e+01 2bshA 125 8.18e+01 1v66A 65 8.20e+01 1g2oA 268 8.20e+01 1b8oA c.56.2.1 60228 1r4yA 136 8.30e+01 d.1.1.3 97056 1zd0A 150 8.36e+01 1tqmA 282 8.39e+01 a.4.5.56,d.144.1.9 107236,107237 1tidB 119 8.39e+01 c.13.2.1 107000 1tzyA 129 8.40e+01 a.22.1.1 107530 1nv8A 284 8.41e+01 c.66.1.30 86224 1qd9A 124 8.44e+01 1qu9A d.79.1.1 39758 1jltA 122 8.44e+01 a.133.1.2 66867 1yf5L 254 8.49e+01 1tqhA 247 8.52e+01 c.69.1.29 107225 1deoA 233 8.53e+01 1deoA c.23.10.4 31345 1lci 550 8.59e+01 1lci e.23.1.1 43349 1mr3F 181 8.64e+01 c.37.1.8 79422 1n0wB 35 8.71e+01 j.97.1.1 79773 1h0xA 100 8.72e+01 d.68.6.1 76451 1qqqA 264 8.73e+01 1bkpA d.117.1.1 40931 1y14B 171 8.75e+01 1ogiA 303 8.77e+01 b.43.4.2,c.25.1.1 92914,92915 1ghj 79 8.79e+01 1ghj b.84.1.1 28232 1uz5A 402 8.86e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1whsB 153 8.88e+01 1whtB 1lm6A 215 8.89e+01 d.167.1.1 84628 1p57B 255 8.94e+01 b.47.1.2 94126 1bmtA 246 8.96e+01 1bmtA a.46.1.1,c.23.6.1 17757,31235