# 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 2a9uA 144 2.24e-03 1x8vA 455 1.54e-01 1h5zA 455 1.96e-01 a.104.1.1 90622 1e9xA 455 2.99e-01 1ea1A a.104.1.1 18969 1u13A 455 3.15e-01 a.104.1.1 107578 1u2wA 122 3.84e-01 1gvhA 396 9.96e-01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1oyzA 280 1.10e+00 a.118.1.16 93775 2cwyA 94 1.29e+00 1yn9A 169 1.42e+00 2h1nA 567 1.51e+00 1lrv 244 1.90e+00 1lrv a.118.1.5 19146 1w68A 390 1.98e+00 a.25.1.2 109216 1gmjA 84 2.03e+00 h.4.8.1 65310 1mswD 883 2.07e+00 e.8.1.3 79427 1vddA 228 2.21e+00 e.49.1.1 108519 1jhgA 101 2.46e+00 1jhgA a.4.12.1 19009 1lfkA 398 2.67e+00 a.104.1.1 77926 1rgeA 96 2.72e+00 1rgeA d.1.1.2 36028 1r1uA 106 2.73e+00 a.4.5.5 104771 1lniA 96 2.73e+00 d.1.1.2 74046 2ah6A 208 3.19e+00 1ka2A 499 3.41e+00 d.92.1.5 77305 1qlnA 883 3.53e+00 1cezA e.8.1.3 43111 1ho8A 480 3.59e+00 1ho8A a.118.1.9 61107 1kkhA 317 3.93e+00 d.14.1.5,d.58.26.3 72645,72646 1gl2C 65 3.98e+00 h.1.15.1 65280 1vrmA 325 4.14e+00 1wwzA 159 4.29e+00 2c12A 439 4.30e+00 1tw9A 206 4.41e+00 a.45.1.1,c.47.1.5 107381,107382 1up7A 417 4.63e+00 1i4mA 108 4.63e+00 d.6.1.1 66025 1hm6A 346 5.18e+00 1avc a.65.1.1 18147 2cohA 202 5.33e+00 1l9lA 74 5.47e+00 a.64.1.1 77827 1up6A 416 5.47e+00 c.2.1.5,d.162.1.2 107976,107977 1deeG 54 5.83e+00 1fc2C a.8.1.1 16343 1a5t 334 5.88e+00 1a5t a.80.1.1,c.37.1.20 18450,32423 1rztA 331 5.99e+00 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 1xsm 390 6.06e+00 1xsm a.25.1.2 16804 1h0oA 390 6.17e+00 a.25.1.2 70845 1ab4 477 6.22e+00 1ab4 e.11.1.1 43251 1s9pA 227 7.51e+00 a.123.1.1 105384 1h3nA 878 7.56e+00 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1odoA 408 8.05e+00 a.104.1.1 92783 1pylA 97 8.11e+00 d.1.1.2 104391 1yucA 255 8.33e+00 1kekA 1231 8.35e+00 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 68524,68525,68526,68527,68528 1om2A 95 8.48e+00 1om2A a.23.4.1 16520 1y6zA 263 8.85e+00 1y7yA 74 8.94e+00 1tffA 234 9.18e+00 d.3.1.11 106854 1f7cA 231 9.41e+00 1f7cA a.116.1.1 19107 1mgrA 99 9.56e+00 d.1.1.2 79106 1q35A 320 9.60e+00 c.94.1.1 95661 1rkpA 326 1.10e+01 a.211.1.2 97620 2bbhA 269 1.17e+01 1ee4A 423 1.18e+01 1ee4A a.118.1.1 19128 1yb3A 175 1.29e+01 1l1eA 287 1.39e+01 c.66.1.18 73454 2bcqA 335 1.41e+01 1o17A 345 1.45e+01 a.46.2.1,c.27.1.1 80765,80766 1oaa 259 1.46e+01 1oaa c.2.1.2 29829 1b3uA 588 1.49e+01 1b3uA a.118.1.2 19135 1wj7A 104 1.55e+01 1cuk 203 1.56e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1q2zA 120 1.61e+01 a.118.19.1 95656 1wa5B 530 1.62e+01 1keaA 221 1.64e+01 a.96.1.2 68491 1ibrB 462 1.64e+01 1qgrA a.118.1.1 19120 1b0pA 1231 1.65e+01 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 31831,31832,33104,34157,39003 1vkeA 133 1.66e+01 a.152.1.2 108650 1tx4A 198 1.67e+01 1tx4A a.116.1.1 19098 1jj2V 154 1.68e+01 1ffkT d.59.1.1 63107 1tqmA 282 1.68e+01 a.4.5.56,d.144.1.9 107236,107237 1k3yA 221 1.68e+01 a.45.1.1,c.47.1.5 77245,77246 1s8nA 205 1.70e+01 c.23.1.1 105374 1i52A 236 1.71e+01 1i52A c.68.1.13 61767 1f3aA 222 1.71e+01 1pgtA a.45.1.1,c.47.1.5 17701,32995 1n3gA 113 1.72e+01 d.204.1.1 79962 1o9rA 162 1.75e+01 a.25.1.1 86706 1sqgA 429 1.79e+01 a.79.1.3,c.66.1.38 105912,105913 1mun 225 1.79e+01 1mun a.96.1.2 18744 1uhgA 385 1.79e+01 e.1.1.1 88491 2gf4A 100 1.81e+01 1s72W 154 1.87e+01 d.59.1.1 105342 2es4D 332 1.93e+01 2f23A 156 1.97e+01 1w5tA 412 1.98e+01 2a1iA 146 1.99e+01 1z72A 225 2.02e+01 1hq1A 105 2.02e+01 1dulA a.36.1.1 17120 1pmzA 86 2.04e+01 a.39.1.10 104195 2fk8A 318 2.04e+01 1o86A 589 2.06e+01 d.92.1.5 81177 1wmwA 330 2.07e+01 1i7wA 538 2.09e+01 3bct a.118.1.1 61909 1or7C 90 2.10e+01 a.180.1.1 87336 1z7lA 276 2.10e+01 1zuhA 168 2.17e+01 2fuqA 747 2.18e+01 1hcrA 52 2.19e+01 1hcrA a.4.1.2 16020 1gw5A 621 2.22e+01 a.118.1.10 70629 1ne9A 335 2.22e+01 d.108.1.4,d.108.1.4 91839,91840 1pk5A 248 2.24e+01 a.123.1.1 88139 1l8dA 112 2.28e+01 h.4.12.1 73687 1y8aA 332 2.30e+01 1p5sA 203 2.36e+01 a.40.1.1 94147 1dowA 205 2.36e+01 1dovA a.24.9.1 16626 1skvA 69 2.39e+01 a.30.5.1 105690 2c3mA 1231 2.40e+01 1dtoA 221 2.43e+01 1dtoA b.91.1.1 28405 1uj6A 227 2.46e+01 c.124.1.4,d.58.40.1 107898,107899 1ztuA 341 2.49e+01 2ccmA 191 2.49e+01 1vkuA 100 2.55e+01 a.28.1.1 108690 1uzeA 589 2.58e+01 d.92.1.5 108174 2b5aA 77 2.60e+01 1wljA 189 2.65e+01 1orjA 130 2.67e+01 a.24.19.1 93456 1iq8A 582 2.70e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 2bkyX 89 2.70e+01 1s28A 132 2.71e+01 d.198.1.1 105223 1zarA 282 2.74e+01 1flcB 175 2.74e+01 1flcB h.3.1.1 45716 1fjgD 209 2.75e+01 1c05A d.66.1.2 39553 1gtkA 313 2.78e+01 c.94.1.1,d.50.2.1 76346,76347 1wgzA 510 2.81e+01 1gnwA 211 2.83e+01 1gnwA a.45.1.1,c.47.1.5 17727,33021 1lj9A 144 2.83e+01 a.4.5.28 78035 1i39A 225 2.85e+01 1ekeA c.55.3.1 61585 1ew4A 106 2.87e+01 1ew4A d.82.2.1 40023 1pda 315 2.88e+01 1pda c.94.1.1,d.50.2.1 35751,38794 1wa8A 99 2.89e+01 1fpzA 212 2.93e+01 1fpzA c.45.1.1 59976 1z91A 147 3.02e+01 2b0oE 301 3.03e+01 1jk0A 419 3.13e+01 a.25.1.2 63142 1colA 204 3.16e+01 1a87 f.1.1.1 43378 1cem 363 3.16e+01 1cem a.102.1.2 18826 1y9bA 90 3.17e+01 1x6zA 123 3.20e+01 1g5aA 628 3.33e+01 b.71.1.1,c.1.8.1 65152,65153 1s3jA 155 3.33e+01 a.4.5.28 98437 1lm5A 214 3.37e+01 d.211.2.1 74029 1z3xA 238 3.37e+01 1w7bA 339 3.41e+01 1jhfA 202 3.43e+01 a.4.5.2,b.87.1.1 63057,63058 2h58A 330 3.45e+01 1nd4A 264 3.45e+01 d.144.1.6 91815 1nal1 297 3.46e+01 1nal3 1s3cA 141 3.47e+01 1kwfA 363 3.47e+01 a.102.1.2 73078 1hg4A 279 3.50e+01 1lbd a.123.1.1 19333 1wt4A 73 3.51e+01 1jkoC 52 3.54e+01 a.4.1.2 66809 1zhxA 438 3.54e+01 1gs9A 165 3.57e+01 a.24.1.1 83313 1yodA 30 3.58e+01 1heiA 451 3.59e+01 1heiA c.37.1.14,c.37.1.14 32463,32464 1rw2A 152 3.59e+01 a.118.19.1 97961 2b0tA 738 3.60e+01 1vhcA 224 3.60e+01 c.1.10.1 100661 1nkpA 88 3.61e+01 a.38.1.1 80573 1khdA 345 3.68e+01 a.46.2.1,c.27.1.1 77400,77401 2cujA 108 3.70e+01 1u4bA 580 3.72e+01 c.55.3.5,e.8.1.1 107664,107665 2ahmA 88 3.75e+01 1vl7A 157 3.76e+01 b.45.1.1 108732 1ovaA 386 3.77e+01 1ovaA e.1.1.1 42619 1l1zA 274 3.79e+01 a.156.1.2,b.113.1.1,g.39.1.8 75911,75912,75913 1oj4A 283 3.79e+01 d.14.1.5,d.58.26.5 93083,93084 1ds1A 324 3.81e+01 1drtA b.82.2.2 28127 1wwpA 119 3.85e+01 1nk4A 580 3.85e+01 c.55.3.5,e.8.1.1 91923,91924 1qh8A 478 3.87e+01 1qguA c.92.2.3 35633 1f83A 425 3.89e+01 1f82A d.92.1.7 40306 1g4yB 101 3.89e+01 1g4yB f.15.1.1 60251 1l3sA 580 3.92e+01 c.55.3.5,e.8.1.1 84521,84522 1bl0A 129 3.92e+01 1d5yA a.4.1.8,a.4.1.8 16053,16054 2bb6A 414 3.94e+01 1wpaA 114 3.99e+01 1hl2A 297 4.01e+01 c.1.10.1 83581 1fe6A 52 4.01e+01 1fe6A h.1.19.1 45662 2cg4A 152 4.01e+01 1dzoA 123 4.02e+01 1dzoA d.24.1.1 38378 2fupA 168 4.02e+01 1zq4A 693 4.04e+01 1sheA 103 4.09e+01 d.274.1.1 105551 1x23A 155 4.13e+01 1tbfA 347 4.13e+01 a.211.1.2 106743 1y9qA 192 4.15e+01 1xwl 580 4.15e+01 1xwl c.55.3.5,e.8.1.1 33708,43001 1j9bA 141 4.17e+01 c.47.1.12 66459 1io2A 213 4.18e+01 1ekeA c.55.3.1 62612 1xsnA 335 4.18e+01 1yarA 233 4.23e+01 1or3A 165 4.25e+01 1nfn a.24.1.1 16522 1yi8A 351 4.26e+01 1vqoW 154 4.32e+01 1x3kA 152 4.32e+01 1ybhA 590 4.33e+01 1pszA 303 4.36e+01 1toaA c.92.2.2 35600 1pjqA 457 4.39e+01 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 1yiiA 320 4.42e+01 1kmiZ 214 4.44e+01 h.4.11.1 72752 1ew6A 137 4.49e+01 1ewaA a.1.1.2 15637 2gaeA 346 4.50e+01 2f6hX 419 4.50e+01 1ybkA 52 4.52e+01 1opc 110 4.53e+01 1opc a.4.6.1 16231 1hbzA 498 4.60e+01 1cf9A e.5.1.1 60937 2db0A 253 4.64e+01 1gweA 503 4.65e+01 e.5.1.1 70667 1fjgN 61 4.66e+01 1fjfN g.39.1.7 45154 1quuA 250 4.71e+01 1quuA a.7.1.1,a.7.1.1 16320,16321 2cwxA 430 4.74e+01 1xqoA 256 4.76e+01 1po5A 476 4.86e+01 a.104.1.1 94963 1i4yA 114 4.93e+01 2mhr a.24.4.1 61738 1cqxA 403 4.93e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1gxyA 226 4.95e+01 d.166.1.3 76380 1f45B 197 4.95e+01 1f45B a.26.1.1 59642 2f4mA 295 4.96e+01 2c9wA 169 4.97e+01 1knzA 164 4.99e+01 e.34.1.1 68709 2g03A 194 5.06e+01 1kpgA 287 5.08e+01 c.66.1.18 68735 1go3F 107 5.09e+01 a.60.8.2 65407 1o4sA 389 5.10e+01 c.67.1.1 86620 1izcA 339 5.13e+01 c.1.12.5 83838 1no1A 126 5.15e+01 a.179.1.1 85913 1ez0A 510 5.19e+01 1eyyA c.82.1.1 35385 2ar0A 541 5.26e+01 1wkqA 164 5.33e+01 c.97.1.2 109393 1udvA 89 5.38e+01 d.68.6.1 99224 2c5kT 95 5.41e+01 1ix9A 205 5.42e+01 a.2.11.1,d.44.1.1 76899,76900 1p4wA 99 5.42e+01 a.4.6.2 87783 1g8pA 350 5.44e+01 1g8pA c.37.1.20 60376 1ee8A 266 5.47e+01 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1ta8A 332 5.48e+01 1gakA 141 5.50e+01 1gakA a.19.1.1 16415 1vmaA 306 5.51e+01 a.24.13.1,c.37.1.10 108887,108888 2fd5A 180 5.53e+01 1e68A 70 5.58e+01 1e68A a.64.2.1 18144 1elwA 118 5.60e+01 1a17 a.118.8.1 19207 1uouA 474 5.60e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 2ajfA 597 5.66e+01 1u9tA 354 5.67e+01 1k6kA 143 5.67e+01 a.174.1.1 77274 1v7bA 185 5.68e+01 1xi1A 575 5.71e+01 1nrlA 316 5.74e+01 a.123.1.1 92091 1adr 76 5.75e+01 1r69 a.35.1.2 17042 1i1iP 681 5.84e+01 1i1iP d.92.1.5 40297 1r2zA 274 5.86e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 2bwbA 46 5.86e+01 1rlkA 117 5.88e+01 c.131.1.1 97651 1pq4A 291 5.89e+01 c.92.2.2 94995 2ff4A 388 5.92e+01 1xqrA 296 5.96e+01 2d00A 109 6.01e+01 2fq4A 192 6.01e+01 1jdhA 529 6.08e+01 a.118.1.1 66549 2ae0X 345 6.10e+01 2fn0A 437 6.11e+01 1qtrA 317 6.13e+01 1qtrA c.69.1.7 34660 1rovA 857 6.24e+01 a.119.1.1,b.12.1.1 97674,97675 1wkbA 810 6.30e+01 1qsaA 618 6.32e+01 1qsaA a.118.5.1,d.2.1.6 19182,36988 1s6bB 119 6.42e+01 a.133.1.2 98593 1yf9A 171 6.49e+01 1hw1A 239 6.54e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1sfxA 109 6.56e+01 a.4.5.50 105505 1pzlA 237 6.65e+01 a.123.1.1 104393 1vmgA 95 6.68e+01 1sdsA 117 6.72e+01 d.79.3.1 105439 2gauA 232 6.74e+01 2if1 126 6.77e+01 2if1 d.64.1.1 39547 1hz6A 72 6.78e+01 2ptl d.15.7.1 61429 2bjcA 62 6.80e+01 1q0gA 117 6.81e+01 a.24.22.1 104428 1ezvA 430 6.82e+01 1be3A d.185.1.1,d.185.1.1 59541,59542 2cviA 83 6.83e+01 1yf2A 425 6.87e+01 1xg2B 153 6.90e+01 1zejA 293 6.91e+01 1zs3A 182 6.91e+01 2ex5A 207 6.94e+01 1kb9A 431 6.94e+01 d.185.1.1,d.185.1.1 77311,77312 1r6fA 310 7.05e+01 e.46.1.1 97149 1r55A 214 7.10e+01 1u2kA 309 7.12e+01 1s6yA 450 7.15e+01 c.2.1.5,d.162.1.2 105314,105315 1aoa 275 7.22e+01 1aoa a.40.1.1,a.40.1.1 17396,17397 1i1rB 181 7.23e+01 1i1rB a.26.1.1 61548 1lshA 1056 7.24e+01 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 1obbA 480 7.26e+01 c.2.1.5,d.162.1.2 86760,86761 1b0xA 94 7.31e+01 1b4fA a.60.1.2 17933 2gpiA 91 7.35e+01 1f20A 435 7.37e+01 b.43.4.1,c.25.1.4 64932,64933 1p3wA 404 7.45e+01 c.67.1.3 87752 1myt 146 7.50e+01 1a6m a.1.1.2 15207 1bjt 793 7.54e+01 1bjt e.11.1.1 43249 1wx1A 335 7.56e+01 1nznA 126 7.61e+01 a.118.8.1 92382 2b1xB 172 7.63e+01 2d69A 430 7.64e+01 1pi1A 185 7.65e+01 a.29.7.1 94699 2b1eA 564 7.73e+01 1y7tA 327 7.76e+01 1ks8A 433 7.78e+01 a.102.1.2 77519 1wusA 180 7.84e+01 1hbnA 549 7.85e+01 1mroA a.89.1.1,d.58.31.2 60898,60899 1sly 618 7.86e+01 1qsaA a.118.5.1,d.2.1.6 19184,36990 1vqrA 297 7.87e+01 1h1dA 221 7.89e+01 c.66.1.1 83452 1x6iA 91 7.95e+01 1s4kA 120 7.97e+01 a.35.1.6 105254 1vejA 74 7.97e+01 1rzrA 332 8.00e+01 1j7nA 776 8.01e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1vid 221 8.04e+01 1vid c.66.1.1 34178 1dkgA 197 8.05e+01 1dkgA b.73.1.1,h.1.9.1 27812,45626 1tiiC 53 8.09e+01 1tiiC 1ez3A 127 8.10e+01 1dn1B a.47.2.1 17768 1evyA 366 8.11e+01 1evyA a.100.1.6,c.2.1.6 18811,30215 1yljA 263 8.11e+01 1htjF 210 8.14e+01 1htjF a.91.1.1 61254 1q3lA 69 8.22e+01 3pviA 157 8.28e+01 3pviA c.52.1.6 33300 1ug3A 339 8.28e+01 1xawA 140 8.33e+01 2dbyA 368 8.34e+01 1qexA 288 8.34e+01 1qexA b.32.1.1 24425 1k78A 149 8.40e+01 a.4.1.5,a.4.1.5 68255,68256 2fbqA 235 8.41e+01 1rtwA 220 8.41e+01 a.132.1.3 97823 2auaA 224 8.46e+01 1dcs 311 8.49e+01 1dcs b.82.2.1 28124 1mp1A 111 8.62e+01 a.188.1.1 91382 2cglA 489 8.70e+01 1xbiA 120 8.70e+01 1m6kA 251 8.73e+01 e.3.1.1 78695 1tllA 688 8.74e+01 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1h7cA 108 8.75e+01 a.7.5.1 70914 1a0p 290 8.80e+01 1a0p a.60.9.1,d.163.1.1 18105,42165 1yge 839 8.81e+01 1yge a.119.1.1,b.12.1.1 19234,23634 1sumB 235 8.87e+01 a.7.12.1 106025 2axtF 45 8.87e+01 2f6sA 201 8.89e+01 1wr1B 58 8.93e+01 1n1bA 549 8.95e+01 a.102.4.1,a.128.1.3 79799,79800 1s6lA 212 8.95e+01 1kl9A 182 8.98e+01 b.40.4.5 72681 1r31A 428 9.00e+01 d.58.20.1,d.179.1.1 96897,96898