# List of top-scoring protein chains for t2k-100-30-str2-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 1.88e-01 1ea1A 455 8.52e-01 1ea1A a.104.1.1 18970 1bvsB 203 1.18e+00 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16281,17956,25275 1yn9A 169 1.23e+00 1u13A 455 1.24e+00 a.104.1.1 107578 1h5zA 455 1.49e+00 a.104.1.1 90622 1e9xA 455 1.58e+00 1ea1A a.104.1.1 18969 1dt6A 473 1.72e+00 1dt6A a.104.1.1 18977 1trrA 107 1.81e+00 1jhgA a.4.12.1 19017 1x8vA 455 2.10e+00 1n6bA 473 2.77e+00 a.104.1.1 85359 1up7A 417 2.90e+00 1rcsA 105 3.18e+00 1jhgA a.4.12.1 19025 1up6A 416 3.27e+00 c.2.1.5,d.162.1.2 107976,107977 1jk0A 419 3.83e+00 a.25.1.2 63142 1hjp 203 3.99e+00 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16274,17947,25266 1jhgA 101 4.39e+00 1jhgA a.4.12.1 19009 2wrpR 107 4.47e+00 1jhgA a.4.12.1 19010 1ho8A 480 4.79e+00 1ho8A a.118.1.9 61107 1nr6A 473 5.61e+00 a.104.1.1 92085 1jr3E 334 6.11e+00 a.80.1.1,c.37.1.20 63253,63254 1ovaA 386 7.13e+00 1ovaA e.1.1.1 42619 1uhgA 385 7.19e+00 e.1.1.1 88491 1fx7A 230 7.30e+00 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 1z3xA 238 8.33e+00 1lniA 96 9.06e+00 d.1.1.2 74046 1avoB 140 9.62e+00 1avoB 1rgeA 96 9.71e+00 1rgeA d.1.1.2 36028 1gmpA 96 9.71e+00 1rgeA d.1.1.2 36036 1i8vA 96 9.71e+00 d.1.1.2 61985 2b1eA 564 1.01e+01 1ee4A 423 1.05e+01 1ee4A a.118.1.1 19128 1xsm 390 1.08e+01 1xsm a.25.1.2 16804 1h38B 883 1.13e+01 e.8.1.3 76626 1h38D 883 1.15e+01 e.8.1.3 76628 1h38C 883 1.16e+01 e.8.1.3 76627 6gsvA 217 1.19e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 1vddA 228 1.19e+01 e.49.1.1 108519 1rztA 331 1.19e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 1kkhA 317 1.22e+01 d.14.1.5,d.58.26.3 72645,72646 1cezA 883 1.26e+01 1cezA e.8.1.3 43110 1pylA 97 1.26e+01 d.1.1.2 104391 1bqbA 301 1.26e+01 1hyt d.92.1.2 58962 4rnpA 883 1.27e+01 1cezA e.8.1.3 43113 1qlnA 883 1.28e+01 1cezA e.8.1.3 43111 1mgrA 99 1.29e+01 d.1.1.2 79106 1h3nA 878 1.29e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1rm6C 161 1.41e+01 1ka2A 499 1.43e+01 d.92.1.5 77305 1w27A 714 1.44e+01 2c3mA 1231 1.46e+01 2bcqA 335 1.46e+01 1zl8B 54 1.48e+01 1w68A 390 1.48e+01 a.25.1.2 109216 1lrv 244 1.51e+01 1lrv a.118.1.5 19146 1b8pA 329 1.52e+01 1bmdA c.2.1.5,d.162.1.1 30147,42114 2bb6A 414 1.53e+01 2cohA 202 1.53e+01 1as0 353 1.53e+01 1cipA a.66.1.1,c.37.1.8 18212,32095 1wjbA 55 1.53e+01 1wjcA a.4.10.1 16265 2cwyA 94 1.54e+01 1oyzA 280 1.64e+01 a.118.1.16 93775 1muyA 225 1.69e+01 1mun a.96.1.2 18745 1wj7A 104 1.75e+01 1fm2A 169 1.77e+01 1fm2A d.153.1.2 59877 1or0A 160 1.78e+01 d.153.1.2 93445 1mun 225 1.79e+01 1mun a.96.1.2 18744 2fbnA 198 1.81e+01 1h0oA 390 1.83e+01 a.25.1.2 70845 1qr6A 584 1.90e+01 1qr6A c.2.1.7,c.58.1.3 30293,33941 1cipA 353 1.97e+01 1cipA a.66.1.1,c.37.1.8 18210,32093 1dowA 205 1.99e+01 1dovA a.24.9.1 16626 1p5sA 203 2.03e+01 a.40.1.1 94147 1i4mA 108 2.04e+01 d.6.1.1 66025 1kekA 1231 2.05e+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 1k87A 669 2.06e+01 a.176.1.1,c.1.23.2 77286,77287 1mp1A 111 2.20e+01 a.188.1.1 91382 1f7cA 231 2.27e+01 1f7cA a.116.1.1 19107 1hm6A 346 2.31e+01 1avc a.65.1.1 18147 1n1bA 549 2.41e+01 a.102.4.1,a.128.1.3 79799,79800 1bl0A 129 2.45e+01 1d5yA a.4.1.8,a.4.1.8 16053,16054 1sly 618 2.49e+01 1qsaA a.118.5.1,d.2.1.6 19184,36990 2cujA 108 2.49e+01 1cem 363 2.51e+01 1cem a.102.1.2 18826 2ccmA 191 2.53e+01 1u2wA 122 2.57e+01 1kwfA 363 2.57e+01 a.102.1.2 73078 1b1bA 140 2.58e+01 1bi0 a.4.5.24,a.76.1.1 16215,18421 1deeG 54 2.66e+01 1fc2C a.8.1.1 16343 1kyoA 430 2.67e+01 d.185.1.1,d.185.1.1 73249,73250 1p7tA 731 2.70e+01 c.1.13.1 94319 1d8cA 723 2.71e+01 1d8cA c.1.13.1 29325 1colA 204 2.73e+01 1a87 f.1.1.1 43378 1xszA 356 2.75e+01 1cuk 203 2.79e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1s9rA 410 2.82e+01 d.126.1.4 98758 1yb3A 175 3.02e+01 1fpzA 212 3.07e+01 1fpzA c.45.1.1 59976 1lxyA 409 3.08e+01 d.126.1.4 91154 1rzrA 332 3.09e+01 1pmzA 86 3.11e+01 a.39.1.10 104195 1wu7A 434 3.19e+01 1zarA 282 3.23e+01 2c12A 439 3.24e+01 1otkA 249 3.26e+01 a.25.1.2 93521 1a5t 334 3.27e+01 1a5t a.80.1.1,c.37.1.20 18450,32423 1t3qA 168 3.28e+01 a.56.1.1,d.15.4.2 106367,106368 1w99A 558 3.28e+01 1iq8A 582 3.30e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1r1uA 106 3.30e+01 a.4.5.5 104771 1vmaA 306 3.33e+01 a.24.13.1,c.37.1.10 108887,108888 1be3A 446 3.35e+01 1be3A d.185.1.1,d.185.1.1 58950,58951 1wgzA 510 3.36e+01 2a9iA 113 3.42e+01 1gl2C 65 3.43e+01 h.1.15.1 65280 1tqmA 282 3.45e+01 a.4.5.56,d.144.1.9 107236,107237 1a8i 842 3.48e+01 1a8i c.87.1.4 35490 1kb9A 431 3.52e+01 d.185.1.1,d.185.1.1 77311,77312 1iygA 133 3.56e+01 a.118.8.1 76947 1ezvA 430 3.63e+01 1be3A d.185.1.1,d.185.1.1 59541,59542 1dovA 181 3.65e+01 1dovA a.24.9.1 16627 1yucA 255 3.71e+01 1xg7A 250 3.72e+01 1l0lA 446 3.76e+01 d.185.1.1,d.185.1.1 84482,84483 1qcrA 446 3.81e+01 1be3A d.185.1.1,d.185.1.1 59025,59026 2c1xA 456 3.81e+01 1khdA 345 3.82e+01 a.46.2.1,c.27.1.1 77400,77401 1b10A 142 3.84e+01 1b10A d.6.1.1 37306 1c8kA 842 3.91e+01 1a8i c.87.1.4 35491 1zymA 258 3.92e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 1sqgA 429 3.95e+01 a.79.1.3,c.66.1.38 105912,105913 1ppjA 446 3.96e+01 d.185.1.1,d.185.1.1 104252,104253 1s8nA 205 3.98e+01 c.23.1.1 105374 1eyyA 510 3.99e+01 1eyyA c.82.1.1 35389 1d1rA 116 4.00e+01 1d1rA d.64.1.1 39548 1vrmA 325 4.16e+01 1y7yA 74 4.17e+01 1gvhA 396 4.18e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1zbdB 134 4.19e+01 1zbdB g.50.1.1 45359 1tw9A 206 4.20e+01 a.45.1.1,c.47.1.5 107381,107382 1wa8A 99 4.29e+01 1s3cA 141 4.48e+01 1kl9A 182 4.52e+01 b.40.4.5 72681 1y74B 50 4.57e+01 1h5uA 842 4.61e+01 1a8i c.87.1.4 60655 1svsA 353 4.62e+01 c.37.1.8 106051 2d8dA 90 4.63e+01 1wloA 136 4.66e+01 1p2xA 159 4.68e+01 a.40.1.1 104062 1odoA 408 4.68e+01 a.104.1.1 92783 168lA 164 4.69e+01 1l92 d.2.1.3 36975 1k3lA 221 4.76e+01 a.45.1.1,c.47.1.5 77229,77230 1k3yA 221 4.76e+01 a.45.1.1,c.47.1.5 77245,77246 1gseA 221 4.82e+01 1pgtA a.45.1.1,c.47.1.5 17667,32961 1pszA 303 4.92e+01 1toaA c.92.2.2 35600 1ej9A 563 4.94e+01 1a36A d.163.1.2,e.15.1.1 42172,43265 2fuqA 747 5.01e+01 1ag2 103 5.07e+01 1b10A d.6.1.1 37305 1bz4A 144 5.15e+01 1nfn a.24.1.1 16521 1go3F 107 5.19e+01 a.60.8.2 65407 1lkvX 232 5.21e+01 a.118.14.1 73980 2gi3A 476 5.23e+01 2f6hX 419 5.27e+01 1bi0 226 5.30e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16202,18408,24453 1ibjA 464 5.33e+01 1ibjA c.67.1.3 62162 1ez0A 510 5.40e+01 1eyyA c.82.1.1 35385 1po5A 476 5.46e+01 a.104.1.1 94963 2bjcA 62 5.52e+01 1gxyA 226 5.53e+01 d.166.1.3 76380 1dkgA 197 5.55e+01 1dkgA b.73.1.1,h.1.9.1 27812,45626 1ig6A 107 5.55e+01 1ig6A a.4.3.1 62364 1j9bA 141 5.65e+01 c.47.1.12 66459 1i7kA 179 5.74e+01 1u9aA d.20.1.1 61889 1lshA 1056 5.75e+01 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 2h58A 330 5.80e+01 1x3kA 152 5.80e+01 1no1A 126 5.80e+01 a.179.1.1 85913 1c0wA 225 5.81e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16211,18417,24455 2a1iA 146 5.83e+01 1le4 144 5.93e+01 1nfn a.24.1.1 16528 1qm1A 143 5.93e+01 1b10A d.6.1.1 37312 1ialA 453 5.94e+01 1bk5A a.118.1.1 19116 1p99A 295 5.97e+01 c.94.1.1 94384 1aeiA 315 5.99e+01 1avc a.65.1.1 18180 1hcrA 52 6.18e+01 1hcrA a.4.1.2 16020 1bk6A 422 6.25e+01 1bk5A a.118.1.1 19133 1wa5B 530 6.31e+01 1keaA 221 6.33e+01 a.96.1.2 68491 1hq1A 105 6.34e+01 1dulA a.36.1.1 17120 1r31A 428 6.41e+01 d.58.20.1,d.179.1.1 96897,96898 1kbuA 349 6.42e+01 a.60.9.1,d.163.1.1 72284,72285 2fd5A 180 6.44e+01 1nd9A 49 6.46e+01 a.6.1.6 85575 1uptB 60 6.47e+01 a.193.1.1 99768 1z7lA 276 6.58e+01 3crxA 343 6.65e+01 4crxA a.60.9.1,d.163.1.1 18101,42161 1kpsB 171 6.65e+01 a.118.12.1 68787 1utg 70 6.67e+01 1utg a.101.1.1 18813 1qaxA 428 6.79e+01 1qaxA d.58.20.1,d.179.1.1 39376,42597 1sumB 235 6.80e+01 a.7.12.1 106025 1z67A 135 6.83e+01 1k1xA 659 6.87e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1dtoA 221 6.88e+01 1dtoA b.91.1.1 28405 1dm5A 315 6.88e+01 1avc a.65.1.1 18186 1xqoA 256 6.90e+01 1zs3A 182 6.92e+01 1ab4 477 7.04e+01 1ab4 e.11.1.1 43251 1i4yA 114 7.09e+01 2mhr a.24.4.1 61738 1qsaA 618 7.14e+01 1qsaA a.118.5.1,d.2.1.6 19182,36988 1jbgA 109 7.15e+01 a.6.1.3 66480 1lfkA 398 7.19e+01 a.104.1.1 77926 1ll2A 333 7.20e+01 c.68.1.14 74005 1b68A 191 7.21e+01 1nfn a.24.1.1 59076 1qryA 80 7.21e+01 2hddA a.4.1.1 16016 1dqrA 557 7.28e+01 1dqrA c.80.1.2 35305 1nznA 126 7.29e+01 a.118.8.1 92382 1whxA 111 7.35e+01 1k6kA 143 7.35e+01 a.174.1.1 77274 1ztuA 341 7.38e+01 1b0pA 1231 7.39e+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 1f1oA 431 7.63e+01 1f1oA a.127.1.1 19433 1cii 602 7.66e+01 1cii f.1.1.1,h.4.3.1 43381,45787 1dk5A 322 7.71e+01 1dk5A a.65.1.1 18192 1w2fA 276 7.80e+01 d.143.1.3 109125 1ftt 68 7.82e+01 2hddA a.4.1.1 15997 1hm5A 558 7.83e+01 c.80.1.2 76717 2utgA 70 7.87e+01 1utg a.101.1.1 18814 1qm3A 112 7.89e+01 1b10A d.6.1.1 37313 1g24A 211 7.93e+01 1g24A d.166.1.1 42270 2a9kB 223 7.94e+01 1jkoC 52 7.95e+01 a.4.1.2 66809 1lpe 144 7.97e+01 1nfn a.24.1.1 16524 1bmdA 327 7.99e+01 1bmdA c.2.1.5,d.162.1.1 30139,42106 1j7nA 776 7.99e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1k38A 254 8.07e+01 e.3.1.1 84303 1gs9A 165 8.07e+01 a.24.1.1 83313 1sdoA 203 8.12e+01 c.52.1.21 98809 1h0pA 182 8.28e+01 b.62.1.1 76450 2b4jC 98 8.34e+01 1yz8P 68 8.34e+01 1x6iA 91 8.43e+01 2d0eA 407 8.45e+01 1tn6A 382 8.51e+01 1mh3A 421 8.54e+01 a.4.1.1,c.94.1.1 79112,79113 2dtr 226 8.64e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 1y7tA 327 8.68e+01 1mojA 182 8.75e+01 a.25.1.1 91367 1tjoA 182 8.75e+01 1or7C 90 8.76e+01 a.180.1.1 87336 1vkuA 100 8.80e+01 a.28.1.1 108690 1bdmB 327 8.80e+01 1bmdA c.2.1.5,d.162.1.1 30138,42105 2ct8A 497 8.83e+01 1wm5A 208 8.90e+01 2cxnA 557 8.93e+01