# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl-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 2.36e-01 1ea1A 455 3.43e-01 1ea1A a.104.1.1 18970 1u13A 455 3.57e-01 a.104.1.1 107578 1h5zA 455 4.37e-01 a.104.1.1 90622 1e9xA 455 4.62e-01 1ea1A a.104.1.1 18969 1x8vA 455 5.80e-01 1bvsB 203 6.63e-01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16281,17956,25275 1yn9A 169 9.35e-01 1dt6A 473 1.66e+00 1dt6A a.104.1.1 18977 1up7A 417 2.22e+00 1up6A 416 2.48e+00 c.2.1.5,d.162.1.2 107976,107977 1hjp 203 2.50e+00 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16274,17947,25266 1trrA 107 2.63e+00 1jhgA a.4.12.1 19017 1rcsA 105 2.84e+00 1jhgA a.4.12.1 19025 1jk0A 419 3.20e+00 a.25.1.2 63142 1rztA 331 3.22e+00 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 2bb6A 414 3.44e+00 1n6bA 473 3.55e+00 a.104.1.1 85359 2bcqA 335 4.45e+00 1lniA 96 4.84e+00 d.1.1.2 74046 1uhgA 385 5.02e+00 e.1.1.1 88491 1ovaA 386 5.02e+00 1ovaA e.1.1.1 42619 1gmpA 96 5.08e+00 1rgeA d.1.1.2 36036 1i8vA 96 5.08e+00 d.1.1.2 61985 1rgeA 96 5.08e+00 1rgeA d.1.1.2 36028 1nr6A 473 6.51e+00 a.104.1.1 92085 4rnpA 883 6.65e+00 1cezA e.8.1.3 43113 1ka2A 499 6.79e+00 d.92.1.5 77305 1cezA 883 7.42e+00 1cezA e.8.1.3 43110 1jhgA 101 7.63e+00 1jhgA a.4.12.1 19009 2wrpR 107 7.66e+00 1jhgA a.4.12.1 19010 1qlnA 883 7.78e+00 1cezA e.8.1.3 43111 1w27A 714 7.98e+00 1kkhA 317 8.01e+00 d.14.1.5,d.58.26.3 72645,72646 1muyA 225 8.07e+00 1mun a.96.1.2 18745 1mun 225 8.55e+00 1mun a.96.1.2 18744 2fbnA 198 8.57e+00 1h38D 883 8.59e+00 e.8.1.3 76628 1u2wA 122 8.67e+00 1h38B 883 8.84e+00 e.8.1.3 76626 1h38C 883 8.90e+00 e.8.1.3 76627 1mgrA 99 9.09e+00 d.1.1.2 79106 1xsm 390 9.13e+00 1xsm a.25.1.2 16804 1pylA 97 1.02e+01 d.1.1.2 104391 1jr3E 334 1.03e+01 a.80.1.1,c.37.1.20 63253,63254 1p7tA 731 1.03e+01 c.1.13.1 94319 1mp1A 111 1.03e+01 a.188.1.1 91382 1sqgA 429 1.08e+01 a.79.1.3,c.66.1.38 105912,105913 1d8cA 723 1.12e+01 1d8cA c.1.13.1 29325 1w5tA 412 1.14e+01 1b8pA 329 1.15e+01 1bmdA c.2.1.5,d.162.1.1 30147,42114 1k3lA 221 1.15e+01 a.45.1.1,c.47.1.5 77229,77230 1k3yA 221 1.15e+01 a.45.1.1,c.47.1.5 77245,77246 1ee4A 423 1.17e+01 1ee4A a.118.1.1 19128 1gseA 221 1.17e+01 1pgtA a.45.1.1,c.47.1.5 17667,32961 1x3kA 152 1.22e+01 1lfkA 398 1.24e+01 a.104.1.1 77926 1r1uA 106 1.28e+01 a.4.5.5 104771 1zl8B 54 1.31e+01 1s9rA 410 1.32e+01 d.126.1.4 98758 1rktA 205 1.34e+01 a.4.1.9,a.121.1.1 97623,97624 1wj7A 104 1.41e+01 1kwfA 363 1.41e+01 a.102.1.2 73078 2cwyA 94 1.43e+01 1avoB 140 1.43e+01 1avoB 1lxyA 409 1.45e+01 d.126.1.4 91154 1z3xA 238 1.46e+01 1iygA 133 1.50e+01 a.118.8.1 76947 1w68A 390 1.51e+01 a.25.1.2 109216 1wjbA 55 1.51e+01 1wjcA a.4.10.1 16265 1wu7A 434 1.55e+01 2cohA 202 1.58e+01 2cujA 108 1.62e+01 1cuk 203 1.62e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1vrmA 325 1.65e+01 1rm6C 161 1.66e+01 1i7kA 179 1.66e+01 1u9aA d.20.1.1 61889 1bqbA 301 1.70e+01 1hyt d.92.1.2 58962 1sly 618 1.72e+01 1qsaA a.118.5.1,d.2.1.6 19184,36990 1rzrA 332 1.72e+01 1j7nA 776 1.74e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 2c3mA 1231 1.74e+01 1p5sA 203 1.74e+01 a.40.1.1 94147 1yucA 255 1.80e+01 1kyoA 430 1.88e+01 d.185.1.1,d.185.1.1 73249,73250 1i4mA 108 1.90e+01 d.6.1.1 66025 1fx7A 230 1.90e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 1h3nA 878 1.96e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1lrv 244 1.96e+01 1lrv a.118.1.5 19146 1cem 363 2.05e+01 1cem a.102.1.2 18826 1as0 353 2.09e+01 1cipA a.66.1.1,c.37.1.8 18212,32095 1deeG 54 2.18e+01 1fc2C a.8.1.1 16343 1y74B 50 2.19e+01 1dowA 205 2.20e+01 1dovA a.24.9.1 16626 2ah6A 208 2.23e+01 6gsvA 217 2.29e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 1ho8A 480 2.32e+01 1ho8A a.118.1.9 61107 1kekA 1231 2.33e+01 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 1h0oA 390 2.38e+01 a.25.1.2 70845 2a9iA 113 2.38e+01 1qcrA 446 2.47e+01 1be3A d.185.1.1,d.185.1.1 59025,59026 1f7cA 231 2.50e+01 1f7cA a.116.1.1 19107 1c8kA 842 2.53e+01 1a8i c.87.1.4 35491 2b1eA 564 2.54e+01 1ag2 103 2.56e+01 1b10A d.6.1.1 37305 1bl0A 129 2.57e+01 1d5yA a.4.1.8,a.4.1.8 16053,16054 1k87A 669 2.57e+01 a.176.1.1,c.1.23.2 77286,77287 1be3A 446 2.59e+01 1be3A d.185.1.1,d.185.1.1 58950,58951 1yb3A 175 2.59e+01 1d1rA 116 2.59e+01 1d1rA d.64.1.1 39548 1f1oA 431 2.70e+01 1f1oA a.127.1.1 19433 1i4yA 114 2.73e+01 2mhr a.24.4.1 61738 1l0lA 446 2.79e+01 d.185.1.1,d.185.1.1 84482,84483 1qr6A 584 2.84e+01 1qr6A c.2.1.7,c.58.1.3 30293,33941 1axn 323 2.87e+01 1avc a.65.1.1 18149 1fpzA 212 2.94e+01 1fpzA c.45.1.1 59976 1kb9A 431 2.97e+01 d.185.1.1,d.185.1.1 77311,77312 1pmzA 86 2.99e+01 a.39.1.10 104195 1aii 323 2.99e+01 1avc a.65.1.1 18150 1a5t 334 3.00e+01 1a5t a.80.1.1,c.37.1.20 18450,32423 1a8i 842 3.00e+01 1a8i c.87.1.4 35490 1pszA 303 3.02e+01 1toaA c.92.2.2 35600 1zarA 282 3.02e+01 1cipA 353 3.02e+01 1cipA a.66.1.1,c.37.1.8 18210,32093 2ccmA 191 3.04e+01 1ezvA 430 3.09e+01 1be3A d.185.1.1,d.185.1.1 59541,59542 1ppjA 446 3.11e+01 d.185.1.1,d.185.1.1 104252,104253 2cfuA 658 3.14e+01 1hm6A 346 3.15e+01 1avc a.65.1.1 18147 1gl2C 65 3.16e+01 h.1.15.1 65280 1b10A 142 3.17e+01 1b10A d.6.1.1 37306 1oyzA 280 3.24e+01 a.118.1.16 93775 1j7nB 776 3.28e+01 d.92.1.14,d.92.1.14,d.166.1.1 66412,66413,66414 1h5uA 842 3.28e+01 1a8i c.87.1.4 60655 1tqmA 282 3.35e+01 a.4.5.56,d.144.1.9 107236,107237 1odoA 408 3.37e+01 a.104.1.1 92783 1hm5A 558 3.38e+01 c.80.1.2 76717 1vmaA 306 3.41e+01 a.24.13.1,c.37.1.10 108887,108888 2fuqA 747 3.45e+01 1vkuA 100 3.46e+01 a.28.1.1 108690 1nznA 126 3.47e+01 a.118.8.1 92382 1vddA 228 3.56e+01 e.49.1.1 108519 1fm2A 169 3.59e+01 1fm2A d.153.1.2 59877 1or0A 160 3.61e+01 d.153.1.2 93445 1aroP 883 3.67e+01 1cezA e.8.1.3 43112 1qm1A 143 3.67e+01 1b10A d.6.1.1 37312 1lshA 1056 3.68e+01 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 1q5dA 419 3.76e+01 a.104.1.1 95891 1wa5B 530 3.79e+01 2fd5A 180 3.84e+01 1dqrA 557 3.85e+01 1dqrA c.80.1.2 35305 2c12A 439 3.95e+01 1gvhA 396 3.96e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1wloA 136 4.00e+01 1bk6A 422 4.05e+01 1bk5A a.118.1.1 19133 1wgzA 510 4.12e+01 1colA 204 4.18e+01 1a87 f.1.1.1 43378 1lkvX 232 4.19e+01 a.118.14.1 73980 1quuA 250 4.22e+01 1quuA a.7.1.1,a.7.1.1 16320,16321 1i17A 107 4.23e+01 1i17A d.6.1.1 61519 1y7yA 74 4.24e+01 1nd4A 264 4.24e+01 d.144.1.6 91815 1kpsB 171 4.25e+01 a.118.12.1 68787 1s8nA 205 4.26e+01 c.23.1.1 105374 2cp8A 54 4.26e+01 1dkgA 197 4.30e+01 1dkgA b.73.1.1,h.1.9.1 27812,45626 2h58A 330 4.39e+01 1ibjA 464 4.50e+01 1ibjA c.67.1.3 62162 1n1bA 549 4.53e+01 a.102.4.1,a.128.1.3 79799,79800 1xszA 356 4.58e+01 1kr7A 110 4.62e+01 a.1.1.4 72890 1s3cA 141 4.63e+01 1b1bA 140 4.64e+01 1bi0 a.4.5.24,a.76.1.1 16215,18421 1xg7A 250 4.65e+01 1ll2A 333 4.71e+01 c.68.1.14 74005 1yarA 233 4.75e+01 1jk0B 345 4.77e+01 a.25.1.2 63143 1pk5A 248 4.82e+01 a.123.1.1 88139 1qm3A 112 4.83e+01 1b10A d.6.1.1 37313 1dovA 181 4.86e+01 1dovA a.24.9.1 16627 1jbgA 109 4.87e+01 a.6.1.3 66480 1r31A 428 4.93e+01 d.58.20.1,d.179.1.1 96897,96898 1khdA 345 4.99e+01 a.46.2.1,c.27.1.1 77400,77401 1le4 144 5.02e+01 1nfn a.24.1.1 16528 1z67A 135 5.03e+01 1p2xA 159 5.08e+01 a.40.1.1 104062 2gi3A 476 5.14e+01 1bed 181 5.15e+01 1fvkA c.47.1.13 90330 1zymA 258 5.17e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 1d3uB 201 5.26e+01 1aisB a.74.1.2,a.74.1.2 18386,18387 1zbdB 134 5.28e+01 1zbdB g.50.1.1 45359 1xqoA 256 5.28e+01 1utxA 66 5.30e+01 a.35.1.3 108034 1hkcA 917 5.32e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33475,33476,33477,33478 1qaxA 428 5.32e+01 1qaxA d.58.20.1,d.179.1.1 39376,42597 1eyyA 510 5.33e+01 1eyyA c.82.1.1 35389 1ez0A 510 5.36e+01 1eyyA c.82.1.1 35385 1mojA 182 5.43e+01 a.25.1.1 91367 1tjoA 182 5.43e+01 1xsnA 335 5.47e+01 2c1xA 456 5.51e+01 2comA 124 5.53e+01 1keaA 221 5.54e+01 a.96.1.2 68491 1bz4A 144 5.56e+01 1nfn a.24.1.1 16521 2d8dA 90 5.60e+01 1t3qA 168 5.69e+01 a.56.1.1,d.15.4.2 106367,106368 1pmaA 233 5.72e+01 1pmaA d.153.1.4 41918 1flcB 175 5.91e+01 1flcB h.3.1.1 45716 1uouA 474 5.91e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 1j9bA 141 5.93e+01 c.47.1.12 66459 1iatA 557 6.08e+01 1dqrA c.80.1.2 62123 1ztuA 341 6.17e+01 1w33A 181 6.17e+01 1oaa 259 6.25e+01 1oaa c.2.1.2 29829 1bmdA 327 6.28e+01 1bmdA c.2.1.5,d.162.1.1 30139,42106 1sep 261 6.30e+01 1oaa c.2.1.2 29830 1etxA 98 6.32e+01 1fipA a.4.1.12 18978 1tn6A 382 6.38e+01 2bwbA 46 6.42e+01 1k1xA 659 6.43e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1rovA 857 6.55e+01 a.119.1.1,b.12.1.1 97674,97675 1nd9A 49 6.59e+01 a.6.1.6 85575 1tx4A 198 6.62e+01 1tx4A a.116.1.1 19098 1udvA 89 6.72e+01 d.68.6.1 99224 2bkyX 89 6.78e+01 1lj9A 144 6.78e+01 a.4.5.28 78035 1q2zA 120 6.84e+01 a.118.19.1 95656 1gxyA 226 6.85e+01 d.166.1.3 76380 1kl9A 182 6.87e+01 b.40.4.5 72681 2cxnA 557 6.88e+01 1sdoA 203 6.89e+01 c.52.1.21 98809 1y7tA 327 6.91e+01 1iq8A 582 6.96e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 2b5aA 77 7.01e+01 1i1iP 681 7.03e+01 1i1iP d.92.1.5 40297 1u0fA 564 7.04e+01 2a1iA 146 7.05e+01 1bdmB 327 7.06e+01 1bmdA c.2.1.5,d.162.1.1 30138,42105 2b4jC 98 7.09e+01 1rkpA 326 7.11e+01 a.211.1.2 97620 1xpxA 163 7.17e+01 1i1rB 181 7.20e+01 1i1rB a.26.1.1 61548 1z7lA 276 7.21e+01 1ll0A 339 7.21e+01 c.68.1.14 73995 1dk5A 322 7.26e+01 1dk5A a.65.1.1 18192 1w99A 558 7.28e+01 1ireA 204 7.28e+01 d.149.1.1 76769 1lpe 144 7.33e+01 1nfn a.24.1.1 16524 1wr1B 58 7.33e+01 1uptB 60 7.35e+01 a.193.1.1 99768 1g24A 211 7.36e+01 1g24A d.166.1.1 42270 1wljA 189 7.37e+01 1kbuA 349 7.38e+01 a.60.9.1,d.163.1.1 72284,72285 1sumB 235 7.44e+01 a.7.12.1 106025 1ig6A 107 7.46e+01 1ig6A a.4.3.1 62364 1go3F 107 7.47e+01 a.60.8.2 65407 2a9kB 223 7.49e+01 1qayA 428 7.49e+01 1qaxA d.58.20.1,d.179.1.1 39378,42599 2cbiA 594 7.56e+01 1b68A 191 7.61e+01 1nfn a.24.1.1 59076 2f6hX 419 7.62e+01 3crxA 343 7.70e+01 4crxA a.60.9.1,d.163.1.1 18101,42161 1ujcA 161 7.71e+01 1vs0A 310 7.75e+01 1ugpA 203 7.76e+01 d.149.1.1 107831 1zy4A 303 7.77e+01 1hg4A 279 7.79e+01 1lbd a.123.1.1 19333 1qsaA 618 7.86e+01 1qsaA a.118.5.1,d.2.1.6 19182,36988 1s6lA 212 7.89e+01 1b0pA 1231 7.91e+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 1bk5A 422 7.96e+01 1bk5A a.118.1.1 19130 1b4uA 139 7.96e+01 1bouA a.88.1.1 18523 1ab4 477 7.97e+01 1ab4 e.11.1.1 43251 1l1eA 287 7.99e+01 c.66.1.18 73454 2bjcA 62 8.00e+01 1smtB 122 8.00e+01 1smtA a.4.5.5 16110 1jmsA 381 8.07e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1qlzA 210 8.09e+01 1b10A d.6.1.1 37309 1ywrA 360 8.12e+01 1o4sA 389 8.13e+01 c.67.1.1 86620 1ykiA 217 8.29e+01 1svsA 353 8.30e+01 c.37.1.8 106051 1ew4A 106 8.34e+01 1ew4A d.82.2.1 40023 2bbhA 269 8.36e+01 1no1A 126 8.41e+01 a.179.1.1 85913 1h16A 759 8.45e+01 c.7.1.1 76462 1k6kA 143 8.49e+01 a.174.1.1 77274 1yf9A 171 8.50e+01 1elwA 118 8.52e+01 1a17 a.118.8.1 19207 1lliA 92 8.52e+01 1lmb3 a.35.1.2 17025 1nal1 297 8.56e+01 1nal3 1i50C 318 8.71e+01 d.74.3.1,d.181.1.1 61756,61757 1vi0A 206 8.75e+01 a.4.1.9,a.121.1.1 100720,100721 1zz2A 360 8.85e+01 1qhaA 917 8.88e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33467,33468,33469,33470 1jqjC 343 8.93e+01 a.80.1.1,c.37.1.20 67097,67098 1i5sA 367 8.95e+01 1bg2 c.37.1.9 61822