# 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 2gvkA 317 4.77e-29 1t0tV 248 1.05e+00 d.58.4.10 106229 1o12A 376 1.31e+00 b.92.1.5,c.1.9.10 80758,80759 1r9jA 673 2.05e+00 1fo8A 343 2.16e+00 1foaA c.68.1.10 59927 1q2lA 939 2.42e+00 1moq 368 2.51e+00 1moq c.80.1.1 35302 1omzA 293 2.84e+00 c.68.1.15 87093 1v5vA 401 2.91e+00 1czaN 917 3.03e+00 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 1gcb 454 3.07e+00 3gcb d.3.1.1 37034 2bklA 695 3.80e+00 3gcb 470 3.88e+00 3gcb d.3.1.1 37032 1esc 306 4.00e+00 1esc c.23.10.1 31334 1xkrA 206 4.05e+00 1jk7A 323 4.27e+00 1auiA d.159.1.3 63144 1fm0E 150 4.84e+00 1fmaE d.41.5.1 38629 1jeoA 180 4.94e+00 c.80.1.3 66611 2c7pA 327 5.23e+00 2cg4A 152 5.24e+00 1iirA 415 5.39e+00 1iirA c.87.1.5 62453 1o08A 221 5.91e+00 c.108.1.6 86525 1dciA 275 6.02e+00 1dciA c.14.1.3 30918 1u32A 293 6.08e+00 d.159.1.3 107631 1zdzA 302 7.01e+00 1chmA 401 7.61e+00 1chmA c.55.2.1,d.127.1.1 33545,41142 1r8gA 372 8.90e+00 d.128.1.3 104845 1x1nA 524 8.93e+00 1t5jA 313 9.05e+00 a.209.1.1 99125 1nriA 306 9.27e+00 c.80.1.3 86123 2bkyX 89 9.62e+00 1nt4A 391 9.69e+00 c.60.1.2 92102 1u8xX 472 9.91e+00 c.2.1.5,d.162.1.2 107741,107742 1fjmA 330 9.93e+00 1auiA d.159.1.3 42082 1jyhA 157 9.94e+00 d.60.1.3 71956 1uf2A 1019 1.01e+01 e.28.1.2 99289 1l1sA 113 1.03e+01 c.114.1.1 73484 1y8aA 332 1.04e+01 6mhtA 327 1.04e+01 6mhtA c.66.1.26 34226 2b25A 336 1.12e+01 1rlhA 173 1.13e+01 d.256.1.1 97646 1z6kA 293 1.14e+01 1f0xA 571 1.17e+01 1f0xA d.58.32.2,d.145.1.1 39483,41746 1p7tA 731 1.20e+01 c.1.13.1 94319 1zvdA 380 1.28e+01 1ow1A 195 1.29e+01 b.131.1.3 93625 1d2mA 665 1.29e+01 1d2mA c.37.1.19,c.37.1.19 32417,32418 1vdwA 254 1.32e+01 e.7.1.1 100569 1yfsA 465 1.33e+01 2cb2A 318 1.33e+01 1jg1A 235 1.36e+01 c.66.1.7 66661 1nnhA 294 1.37e+01 d.104.1.1 92005 1m3sA 186 1.39e+01 c.80.1.3 78573 1jmsA 381 1.40e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1bk0 331 1.42e+01 1bk0 b.82.2.1 28118 1x7yB 342 1.43e+01 1d4xG 126 1.43e+01 1d0nA d.109.1.1 59109 1vimA 200 1.49e+01 c.80.1.3 100758 2g8lA 299 1.50e+01 2bkkA 264 1.53e+01 1zjcA 418 1.56e+01 1v9mA 323 1.56e+01 f.40.1.1 100543 1r5zA 323 1.57e+01 f.40.1.1 97135 2gasA 307 1.60e+01 1qd1A 325 1.65e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 2b34A 199 1.65e+01 1o0xA 262 1.71e+01 d.127.1.1 80755 1odmA 331 1.72e+01 b.82.2.1 86875 2b5dX 528 1.73e+01 2bfdB 345 1.83e+01 1ewqA 765 1.86e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 2ga9D 469 1.89e+01 1ofdA 1520 1.90e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 2gfhA 260 1.92e+01 1zejA 293 1.93e+01 1kaeA 434 1.94e+01 c.82.1.2 72247 1jj2H 167 1.96e+01 1ffkF d.41.4.1 63093 2fug7 129 1.98e+01 1c4oA 664 2.00e+01 1d2mA c.37.1.19,c.37.1.19 32415,32416 1udvA 89 2.04e+01 d.68.6.1 99224 1nm1G 125 2.14e+01 d.109.1.1 80653 1ss9A 311 2.16e+01 c.68.1.4 105978 1zhxA 438 2.17e+01 1dtwB 342 2.22e+01 1qs0B c.36.1.7,c.48.1.2 31828,33102 2calA 154 2.27e+01 1olsB 342 2.34e+01 c.36.1.7,c.48.1.2 93332,93333 2gwhA 298 2.35e+01 1j1lA 290 2.35e+01 b.82.1.12 90766 1r89A 437 2.36e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1uxtA 501 2.40e+01 c.82.1.1 108125 1t1dA 100 2.42e+01 1t1dA d.42.1.2 38637 1riqA 465 2.43e+01 a.203.1.1,d.104.1.1 97516,97517 1n83A 270 2.46e+01 a.123.1.1 80276 1wruA 379 2.48e+01 1fw9A 164 2.50e+01 1fw9A d.190.1.1 60059 1w6tA 444 2.55e+01 1tv9A 335 2.55e+01 1a6jA 163 2.55e+01 1a6jA d.112.1.1 40915 1a68 95 2.65e+01 1t1dA d.42.1.2 38639 1qwrA 319 2.68e+01 b.82.1.3 96491 1bbpA 173 2.69e+01 1bbpA b.60.1.1 27147 1wi1A 126 2.69e+01 1jjyA 636 2.70e+01 1jjyA 1xrsA 516 2.70e+01 2ffjA 300 2.72e+01 1tt8A 164 2.73e+01 1pch 88 2.74e+01 1ptf d.94.1.1 40564 1g0hA 252 2.81e+01 1dk4A e.7.1.1 60171 1ga8A 311 2.81e+01 1ga8A c.68.1.4 34516 1ys4A 354 2.84e+01 2bgiA 272 2.85e+01 1uc2A 481 2.92e+01 d.261.1.1 99161 1bia 321 2.94e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1n7vA 555 2.96e+01 b.126.1.1 85377 1rhs 296 3.00e+01 1rhs c.46.1.2,c.46.1.2 32703,32704 1aoeA 192 3.00e+01 1aoeA c.71.1.1 34923 1tl9A 339 3.06e+01 1cjxA 357 3.06e+01 1cjxA d.32.1.3,d.32.1.3 38516,38517 1ffyA 917 3.09e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1v1rB 342 3.20e+01 c.36.1.7,c.48.1.2 108273,108274 1p4cA 380 3.22e+01 c.1.4.1 94100 1grj 158 3.22e+01 1grj a.2.1.1,d.26.1.2 15691,38433 1vqwA 457 3.24e+01 1it2A 146 3.30e+01 a.1.1.2 66365 1o20A 427 3.38e+01 c.82.1.1 86556 1mml 265 3.41e+01 1mml e.8.1.2 43015 1jpzA 473 3.42e+01 a.104.1.1 67069 1s6yA 450 3.46e+01 c.2.1.5,d.162.1.2 105314,105315 2bhwA 232 3.57e+01 1y7pA 223 3.58e+01 1fj2A 232 3.66e+01 1auoA c.69.1.14 34720 1vjqA 79 3.73e+01 k.43.1.1 100830 1e30A 155 3.75e+01 1rcy b.6.1.1 23016 1ht6A 405 3.78e+01 b.71.1.1,c.1.8.1 83629,83630 2fmpA 335 3.79e+01 1vcbA 118 3.80e+01 1vcbA d.15.1.1 37603 1rwtA 232 3.87e+01 f.43.1.1 97992 1gnxA 479 3.88e+01 c.1.8.4 76241 1bpyA 335 3.90e+01 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 17980,75819,75820 1wdnA 226 4.04e+01 1lst c.94.1.1 35816 1p4xA 250 4.07e+01 a.4.5.28,a.4.5.28 87784,87785 1vggA 161 4.10e+01 1d8cA 723 4.10e+01 1d8cA c.1.13.1 29325 1sc6A 404 4.15e+01 1zj8A 566 4.16e+01 1ofuX 119 4.20e+01 c.37.1.22 86976 1ub3A 220 4.22e+01 c.1.10.1 88395 1gtvA 214 4.23e+01 c.37.1.1 70537 2a5dA 175 4.27e+01 2fnjB 118 4.28e+01 1hgxA 183 4.29e+01 1tc1A c.61.1.1 34027 1aqcA 172 4.39e+01 1x11A b.55.1.2 26983 1wvqA 167 4.43e+01 1l8nA 679 4.45e+01 c.1.8.10,d.92.2.2 84564,84565 1c4kA 730 4.47e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 1w30A 201 4.49e+01 1gkzA 388 4.50e+01 a.29.5.1,d.122.1.4 65268,65269 2fp8A 322 4.50e+01 1e1oA 504 4.52e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1hr6B 443 4.53e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1cs8A 316 4.65e+01 1cs8A d.3.1.1 37065 2ae6A 166 4.66e+01 1ijgA 309 4.71e+01 1fouA e.27.1.1 62493 1bkpA 278 4.74e+01 1bkpA d.117.1.1 41029 1j5uA 136 4.84e+01 d.208.1.1 71584 1bgvA 449 4.84e+01 1k89 c.2.1.7,c.58.1.1 30217,33865 1w5tA 412 4.87e+01 1g03A 134 4.88e+01 1qrjB a.73.1.1 60162 1lm8B 118 4.92e+01 d.15.1.1 74033 1sqiA 393 4.95e+01 d.32.1.3,d.32.1.3 105914,105915 1v3yA 192 4.96e+01 2c2aA 258 4.99e+01 2bcgY 206 5.00e+01 1yirA 408 5.01e+01 1sqgA 429 5.02e+01 a.79.1.3,c.66.1.38 105912,105913 1f5jA 199 5.05e+01 1axkA b.29.1.11 24342 1rq2A 382 5.06e+01 c.32.1.1,d.79.2.1 105048,105049 1jayA 212 5.20e+01 c.2.1.6 66478 2bfwA 200 5.21e+01 2c30A 321 5.22e+01 1vehA 92 5.25e+01 1e8cA 498 5.30e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1su8A 636 5.31e+01 e.26.1.2 98999 2chnA 716 5.39e+01 1j7lA 264 5.41e+01 d.144.1.6 62697 1ftrA 296 5.42e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1gy8A 397 5.47e+01 c.2.1.2 83376 1lucA 355 5.48e+01 1lucA c.1.16.1 29547 2b67A 204 5.49e+01 1fvuB 125 5.49e+01 1ixxB d.169.1.1 42346 1iu4A 331 5.50e+01 d.3.1.8 71430 1bf5A 545 5.50e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 1v4pA 157 5.55e+01 1h4gA 207 5.57e+01 b.29.1.11 70863 1rv9A 259 5.59e+01 d.194.1.2 105105 1qh7A 207 5.61e+01 1axkA b.29.1.11 24317 1v6fA 151 5.62e+01 d.109.1.2 108395 1gqeA 365 5.63e+01 e.38.1.1 70351 1bvyF 191 5.73e+01 1bvyF c.23.5.1 31207 1lopA 164 5.73e+01 2cpl b.62.1.1 27510 1vi2A 300 5.89e+01 c.2.1.7,c.58.1.5 100726,100727 2auaA 224 5.90e+01 1qsmA 152 5.93e+01 1qsmA d.108.1.1 40808 1hcrA 52 5.93e+01 1hcrA a.4.1.2 16020 1l5wA 796 5.94e+01 c.87.1.4 73605 1csh 435 6.00e+01 1csh a.103.1.1 18880 1qipA 183 6.04e+01 1qipA d.32.1.1 38470 1evyA 366 6.07e+01 1evyA a.100.1.6,c.2.1.6 18811,30215 1nd4A 264 6.07e+01 d.144.1.6 91815 1azo 232 6.11e+01 1azo c.52.1.14 33329 1r9fA 136 6.13e+01 d.255.1.1 97257 1d3yA 301 6.16e+01 1d3yA e.12.1.1 43252 1o0uA 429 6.16e+01 c.118.1.1 80743 1jakA 512 6.18e+01 c.1.8.6,d.92.2.1 66472,66473 1gggA 226 6.19e+01 1lst c.94.1.1 35817 1y6iA 233 6.20e+01 2c2nA 339 6.27e+01 1vpkA 378 6.31e+01 1iatA 557 6.41e+01 1dqrA c.80.1.2 62123 1w5fA 353 6.43e+01 1v4aA 440 6.44e+01 a.24.16.4,d.218.1.9 108350,108351 1zxzA 197 6.48e+01 1wmuA 141 6.53e+01 a.1.1.2 109416 1orvA 728 6.61e+01 b.70.3.1,c.69.1.24 87354,87355 1vloA 381 6.65e+01 b.44.2.1,d.250.1.1 108838,108839 1rcy 151 6.68e+01 1rcy b.6.1.1 23018 1wsrA 375 6.70e+01 1udxA 416 6.72e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 3ladA 476 6.73e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30573,30574,40208 1zkcA 197 6.80e+01 1z6mA 175 6.80e+01 1sq5A 308 6.81e+01 c.37.1.6 105882 1v4xA 144 6.82e+01 a.1.1.2 108363 1esmA 316 6.83e+01 1esmA c.37.1.6 31953 2givA 295 6.88e+01 1n8fA 350 6.89e+01 c.1.10.4 85397 2cwlA 302 6.92e+01 1l1qA 186 6.95e+01 c.61.1.1 77653 1b00A 127 6.96e+01 3chy c.23.1.1 31122 1jfrA 262 6.97e+01 1jfrA c.69.1.16 34724 1gg1A 350 7.01e+01 1qr7A c.1.10.4 29187 1o86A 589 7.02e+01 d.92.1.5 81177 1rf8B 100 7.03e+01 a.210.1.1 97371 1c3gA 170 7.04e+01 1c3gA b.4.1.1,b.4.1.1 22831,22832 2dlbA 80 7.14e+01 1uzeA 589 7.18e+01 d.92.1.5 108174 2gnpA 266 7.19e+01 1as4B 37 7.19e+01 1as4B 1fkmA 396 7.20e+01 1fkmA a.69.2.1,a.69.2.1 18315,18316 1iyxA 432 7.24e+01 c.1.11.1,d.54.1.1 83815,83816 1j27A 102 7.26e+01 d.58.50.1 90778 1ud9A 245 7.28e+01 d.131.1.2,d.131.1.2 107768,107769 1rr7A 129 7.29e+01 a.4.1.14 105075 1vlpA 441 7.32e+01 d.41.2.2,d.41.2.3 108840,108841 1hp5A 512 7.34e+01 1hp4A c.1.8.6,d.92.2.1 61113,61114 1wb0A 445 7.34e+01 1ntyA 311 7.37e+01 a.87.1.1,b.55.1.1 103873,103874 5reqA 727 7.41e+01 1reqA c.1.19.1,c.23.6.1 29632,31259 1w19A 160 7.42e+01 2ajfA 597 7.44e+01 1vmbA 140 7.44e+01 1wvgA 359 7.46e+01 1ckeA 227 7.49e+01 1ckeA c.37.1.1 31846 1wviA 257 7.52e+01 1v64A 108 7.53e+01 a.21.1.1 108392 2gf6A 135 7.58e+01 1hfuA 503 7.59e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1bu7A 455 7.60e+01 1bu7A a.104.1.1 18937 1rlkA 117 7.62e+01 c.131.1.1 97651 1wphA 201 7.66e+01 1wkaA 147 7.66e+01 1pvdA 537 7.67e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 1ipaA 274 7.70e+01 c.116.1.1,d.79.3.3 71254,71255 1q79A 514 7.71e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1rwzA 245 7.71e+01 d.131.1.2,d.131.1.2 98005,98006 1wy6A 172 7.76e+01 1ukvY 206 7.77e+01 c.37.1.8 107918 1ru3A 732 7.81e+01 e.26.1.3 97835 1lm6A 215 7.86e+01 d.167.1.1 84628 2a8jA 420 7.88e+01 1b56 135 7.91e+01 1hmt b.60.1.2 27183 1psdA 409 8.02e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1z0jA 170 8.06e+01 1foeA 377 8.09e+01 1foeA a.87.1.1,b.55.1.1 18517,26969 1oe4A 247 8.20e+01 c.18.1.3 86895 1q4gA 553 8.22e+01 a.93.1.2,g.3.11.1 95789,95790 1q7zA 566 8.29e+01 c.1.21.2,c.1.26.1 96090,96091 1ufbA 127 8.32e+01 a.24.16.3 99331 1r8oB 71 8.53e+01 1dsxA 87 8.57e+01 1t1dA d.42.1.2 38644 1j58A 385 8.58e+01 b.82.1.2 71531 1ka2A 499 8.59e+01 d.92.1.5 77305 1o97D 320 8.64e+01 c.26.2.3,c.31.1.2 81233,81234 1ve6A 582 8.67e+01 2ah6A 208 8.71e+01 1l7mA 211 8.79e+01 c.108.1.4 73664 1j97A 211 8.87e+01 1f5sA c.108.1.4 62753 1h5wA 309 8.89e+01 e.27.1.1 65635 1fy7A 278 8.90e+01 1fy7A d.108.1.1 40817 1efyA 350 8.95e+01 1a26 a.41.1.1,d.166.1.2 17413,42275