# List of top-scoring protein chains for T0284.t04-w0.5 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 1mumA 295 2.24e-36 c.1.12.7 85108 1xg4A 295 7.16e-36 1ujqA 305 2.35e-35 c.1.12.7 99463 1m3uA 264 4.58e-33 c.1.12.8 84784 1zlpA 318 5.68e-32 1o66A 275 6.20e-32 c.1.12.8 92547 1oy0A 281 1.00e-31 c.1.12.8 87543 1igwA 434 4.87e-30 c.1.12.7 62370 1f8mA 429 2.69e-28 1dquA c.1.12.7 29315 1f8iA 429 7.84e-28 1dquA c.1.12.7 29321 1s2wA 295 8.98e-28 c.1.12.7 98407 1s2uA 295 4.17e-27 c.1.12.7 98401 1dquA 538 3.34e-26 1dquA c.1.12.7 29314 1rvkA 382 1.60e-02 c.1.11.2,d.54.1.1 97928,97929 1h5yA 253 3.68e-02 c.1.2.1 65638 1vhnA 318 4.23e-02 c.1.4.1 100693 1tygA 253 6.10e-02 c.1.31.1 107454 1xm3A 264 6.13e-02 c.1.31.1 115461 1znnA 325 6.56e-02 c.1.2.6 125386 1o1zA 234 1.51e-01 c.1.18.3 86555 6xia 387 1.97e-01 4xis 1xylA 386 2.01e-01 4xis c.1.15.3 29413 2gyiA 386 2.08e-01 4xis c.1.15.3 29409 1tx2A 297 2.11e-01 c.1.21.1 107420 1muwA 386 2.19e-01 c.1.15.3 79495 1clkA 387 2.30e-01 4xis c.1.15.3 29438 1rd5A 262 2.39e-01 c.1.2.4 111772 1o1hA 387 2.59e-01 c.1.15.3 81044 1mnzA 388 2.62e-01 c.1.15.3 79328 1oadA 388 2.77e-01 c.1.15.3 81253 1b4kA 337 2.81e-01 1b4kA c.1.10.3 29184 1w5nA 337 3.10e-01 1gzgA 337 3.30e-01 c.1.10.3 70805 1w5oA 337 3.33e-01 1w56A 337 3.34e-01 1w54A 337 3.36e-01 1w5pA 337 3.53e-01 1w5mA 337 3.62e-01 1w5qA 337 4.14e-01 1tjrA 261 4.70e-01 c.1.2.4 119292 1xi3A 215 5.08e-01 c.1.3.1 109601 1gw9A 388 5.45e-01 c.1.15.3 70658 1qt1A 387 6.37e-01 4xis c.1.15.3 29436 2c1hA 328 6.40e-01 c.1.10.3 129634 1dxiA 388 6.85e-01 4xis c.1.15.3 29407 2a0nA 265 7.13e-01 c.1.2.1 125961 1zfjA 491 7.70e-01 1ak5 c.1.5.1,d.37.1.1,d.37.1.1 28638,38540,38541 1vh7A 265 8.40e-01 c.1.2.1 100646 1thfD 253 9.21e-01 1thfD c.1.2.1 28535 1ep3A 311 1.00e+00 2dorA c.1.4.1 28597 1gpwA 253 1.05e+00 c.1.2.1 65460 1o4uA 285 1.09e+00 c.1.17.1,d.41.2.1 86624,86625 1vjiA 372 1.12e+00 c.1.4.1 100813 1o5kA 306 1.40e+00 c.1.10.1 92504 1jflA 228 1.56e+00 c.78.2.1,c.78.2.1 71656,71657 2at2A 300 1.76e+00 3csuA c.78.1.1,c.78.1.1 35196,35197 1rvgA 305 2.72e+00 c.1.10.2 97920 1mzhA 225 2.86e+00 c.1.10.1 79698 1aj2 282 3.01e+00 1aj2 1ub3A 220 3.67e+00 c.1.10.1 88395 1jpdX 324 4.09e+00 c.1.11.2,d.54.1.1 67014,67015 1ktbA 405 4.12e+00 b.71.1.1,c.1.8.1 72960,72961 1wv2A 265 4.77e+00 c.1.31.1 114910 1f2jA 370 4.89e+00 1fbaA c.1.10.1 29154 1xxxA 303 4.94e+00 c.1.10.1 122433 1yxyA 234 5.65e+00 c.1.2.5 124203 9ximA 393 5.72e+00 4xis c.1.15.3 29505 1x1oA 286 5.90e+00 1k7yA 577 6.11e+00 a.46.1.1,c.23.6.1,d.173.1.1 68272,68273,68274 2xinA 393 6.38e+00 4xis c.1.15.3 29493 1rpxA 230 6.44e+00 1rpxA c.1.2.2 28536 1xinA 393 6.46e+00 4xis c.1.15.3 29513 1ximA 393 6.48e+00 4xis c.1.15.3 29473 5xinA 393 6.53e+00 4xis c.1.15.3 29481 2ximA 393 6.54e+00 4xis c.1.15.3 29497 3xinA 393 6.70e+00 4xis c.1.15.3 29489 2b7nA 273 6.72e+00 1km1A 247 7.02e+00 c.1.2.3 72736 1r1dA 247 7.92e+00 c.69.1.29 96813 1m5wA 243 9.12e+00 c.1.24.1 84836 1ho1A 242 9.28e+00 1ho1A c.1.24.1 61097 1dv7A 227 9.48e+00 1dvjA c.1.2.3 28550 1loqA 228 9.56e+00 c.1.2.3 74155 1rhcA 330 9.58e+00 c.1.16.3 97468 1xkyA 301 9.78e+00 c.1.10.1 122094 1km6A 247 1.01e+01 c.1.2.3 72742 1qapA 296 1.03e+01 1qpoA c.1.17.1,d.41.2.1 29559,38595 1v8fA 276 1.04e+01 c.26.1.4 100503 1gpmA 525 1.04e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 2cv9A 252 1.04e+01 d.159.1.10 130855 3ximA 393 1.05e+01 4xis c.1.15.3 29477 1km4A 247 1.06e+01 c.1.2.3 72740 1p0kA 349 1.08e+01 c.1.4.1 87648 1dvjA 246 1.09e+01 1dvjA c.1.2.3 28546 1q7zA 566 1.14e+01 c.1.21.2,c.1.26.1 96090,96091 1lp6A 229 1.16e+01 c.1.2.3 74171 1l6sA 323 1.21e+01 c.1.10.3 73627 1km2A 247 1.33e+01 c.1.2.3 72738 1x1zA 252 1.33e+01 c.1.2.3 121613 1ka9F 252 1.35e+01 c.1.2.1 77307 1bxbA 387 1.36e+01 4xis c.1.15.3 29543 1km3A 247 1.37e+01 c.1.2.3 72739 1jxhA 288 1.37e+01 c.72.1.2 67415 1tqjA 230 1.38e+01 c.1.2.2 107228 1mra 359 1.39e+01 2mnr 1ve2A 235 1.41e+01 c.90.1.1 120008 1ufvA 276 1.41e+01 c.26.1.4 88487 1losA 224 1.54e+01 c.1.2.3 74157 1b4eA 323 1.57e+01 1b4kA c.1.10.3 29186 2b81A 323 1.80e+01 1zhaA 267 1.81e+01 1ox6A 555 1.86e+01 c.1.2.1,c.23.16.1 87505,87506 1jvnA 555 1.87e+01 c.1.2.1,c.23.16.1 67355,67356 1u59A 287 1.87e+01 d.144.1.7 107681 1f8fA 371 2.03e+01 b.35.1.2,c.2.1.1 83246,83247 1wdtA 665 2.18e+01 b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 120911,120912,120913,120914,120915 2czdA 208 2.19e+01 c.1.2.3 131045 2g8yA 385 2.27e+01 2cunA 410 2.33e+01 1ujpA 271 2.35e+01 c.1.2.4 99462 1zcoA 262 2.39e+01 2a9fA 398 2.41e+01 1texA 287 2.42e+01 c.37.1.5 106818 1jofA 365 2.45e+01 b.69.10.1 71775 1lsuA 147 2.45e+01 c.2.1.9 74250 1wx0A 223 2.62e+01 c.1.10.1 121382 1mrzA 293 2.72e+01 b.43.5.1,c.26.1.3 91452,91453 1u0kA 288 2.96e+01 d.21.1.2,d.21.1.2 107547,107548 1eyeA 280 2.98e+01 1aj2 c.1.21.1 29672 1klzA 247 2.99e+01 c.1.2.3 72731 1v6sA 390 3.02e+01 c.86.1.1 100424 1vzwA 244 3.03e+01 c.1.2.1 120553 1vzyA 291 3.07e+01 d.193.1.1,g.81.1.1 114042,114043 1f5vA 240 3.15e+01 1bkjA d.90.1.1 40255 1t70A 255 3.19e+01 d.159.1.9 112275 1mdl 359 3.20e+01 2mnr 1km5A 247 3.25e+01 c.1.2.3 72741 1fjgC 239 3.26e+01 1fjfC d.52.3.1,d.53.1.1 38831,38839 1v9cA 218 3.27e+01 c.23.17.1 100533 1i94C 238 3.28e+01 1fjfC d.52.3.1,d.53.1.1 61992,61993 1n82A 331 3.31e+01 c.1.8.3 91703 1lroA 267 3.31e+01 c.1.10.4 78161 1dtn 359 3.37e+01 2mnr 1pe1A 267 3.40e+01 c.1.10.4 94591 1reqB 637 3.53e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1g2oA 268 3.54e+01 1b8oA c.56.2.1 60228 1o5iA 249 3.54e+01 c.2.1.2 92499 1tqhA 247 3.59e+01 c.69.1.29 107225 1o59A 355 3.62e+01 b.18.1.22,b.18.1.22 92495,92496 1vhqA 232 3.64e+01 c.23.16.2 100696 1uouA 474 3.65e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 1gmvA 143 3.74e+01 b.107.1.1,d.58.38.1 65343,65344 2mnr 357 3.91e+01 2mnr 1mdr 359 3.93e+01 2mnr 1wcwA 261 4.01e+01 1pkxA 592 4.08e+01 c.24.1.3,c.97.1.4 94838,94839 1i2qA 316 4.10e+01 1onrA c.1.10.1 61578 1vd6A 224 4.11e+01 c.1.18.3 119991 1km0A 247 4.13e+01 c.1.2.3 72732 1ad1A 266 4.16e+01 1aj2 c.1.21.1 29668 1i2oA 316 4.18e+01 1onrA c.1.10.1 61574 1i2rA 316 4.30e+01 1onrA c.1.10.1 61580 1lrtA 376 4.31e+01 c.1.5.1 84685 1sg3A 349 4.33e+01 b.18.1.22,b.18.1.22 98847,98848 1ve6A 582 4.34e+01 b.69.7.2,c.69.1.33 113626,113627 1pc5A 107 4.37e+01 d.58.1.2 94429 1vlwA 217 4.42e+01 c.1.10.1 108868 1pvnA 376 4.44e+01 c.1.5.1 88312 1n0rA 126 4.46e+01 k.37.1.1 79756 1i2pA 316 4.56e+01 1onrA c.1.10.1 61576 1gc5A 467 4.56e+01 1gc5A c.72.1.3 60429 1i2nA 316 4.60e+01 1onrA c.1.10.1 61572 1ucwA 317 4.65e+01 1onrA c.1.10.1 29171 1onrA 316 4.65e+01 1onrA c.1.10.1 29169 1kqpA 271 4.77e+01 c.26.2.1 72883 1wa3A 205 4.77e+01 c.1.10.1 120802 1to3A 304 4.88e+01 c.1.10.1 107161 1pnsC 206 4.93e+01 i.1.1.1 88170 2bz3A 418 4.95e+01 c.95.1.1,c.95.1.1 129534,129535 1t7lA 766 5.00e+01 1xdjA 766 5.04e+01 1m65A 245 5.11e+01 c.6.3.1 84847 1x31A 964 5.15e+01 2ajtA 500 5.18e+01 b.43.2.2,c.85.1.2 126894,126895 1klyA 247 5.21e+01 c.1.2.3 72730 1ml4A 308 5.24e+01 c.78.1.1,c.78.1.1 79255,79256 1umkA 275 5.37e+01 b.43.4.2,c.25.1.1 113312,113313 1v5eA 590 5.37e+01 c.31.1.3,c.36.1.5,c.36.1.9 119844,119845,119846 1v5fA 589 5.44e+01 c.31.1.3,c.36.1.5,c.36.1.9 119847,119848,119849 1gqiA 708 5.55e+01 c.1.8.10,d.92.2.2 76279,76280 1h41A 708 5.55e+01 c.1.8.10,d.92.2.2 83472,83473 1oy1A 228 5.59e+01 c.23.16.2 87548 1pn3A 404 5.62e+01 c.87.1.5 94938 1urjA 1136 5.64e+01 e.58.1.1 113410 1qe5A 266 5.67e+01 1b8oA c.56.2.1 33784 1brwA 433 5.73e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1s7mA 174 5.80e+01 b.144.1.1 98649 2g0tA 350 5.84e+01 c.37.1.10 134499 1vkfA 188 6.09e+01 c.1.29.1 108656 1wcxA 261 6.14e+01 1xpgA 765 6.18e+01 1gvfA 286 6.27e+01 c.1.10.2 70599 1lvl 458 6.29e+01 1lvl 1bgeA 175 6.33e+01 1bgc a.26.1.1 16823 1o5lA 213 6.45e+01 b.82.3.2 92506 4xiaA 393 6.53e+01 4xis c.1.15.3 29439 1h8eH 146 6.58e+01 1e79H b.93.1.1 60757 1ypfA 336 6.79e+01 2cwzA 141 6.81e+01 d.38.1.7 130961 1twdA 256 6.83e+01 c.1.30.1 107397 1rttA 193 6.90e+01 c.23.5.4 105098 1bxcA 387 6.94e+01 4xis c.1.15.3 29539 1bdfA 235 7.00e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1ps9A 671 7.04e+01 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 1v10A 521 7.24e+01 b.6.1.3,b.6.1.3,b.6.1.3 108224,108225,108226 2bz4A 418 7.34e+01 c.95.1.1,c.95.1.1 129542,129543 1mxsA 225 7.36e+01 c.1.10.1 91494 2a47A 238 7.38e+01 1m4zA 238 7.40e+01 b.34.12.1 78630 1xlmA 394 7.40e+01 4xis c.1.15.3 29441 1m41A 380 7.47e+01 c.1.16.4 78595 2g5cA 281 7.47e+01 a.100.1.12,c.2.1.6 134646,134647 1nqkA 381 7.47e+01 c.1.16.4 92050 1dd8A 406 7.48e+01 1dd8A c.95.1.1,c.95.1.1 35932,35933 1hg3A 225 7.50e+01 1hg3A c.1.1.1 61025 1xa3A 437 7.53e+01 c.123.1.1 115025 1dj2A 443 7.55e+01 1adeA c.37.1.10 32237 1vc2A 331 7.55e+01 c.2.1.3,d.81.1.1 100555,100556 2buhA 406 7.60e+01 c.95.1.1,c.95.1.1 129204,129205 1me8A 503 7.67e+01 c.1.5.1 79028 1xlaA 394 7.76e+01 4xis c.1.15.3 29445 1ualA 274 7.79e+01 c.116.1.4 88383 1tkkA 366 7.83e+01 c.1.11.2,d.54.1.1 107089,107090 1zy8A 474 7.87e+01 1g3qA 237 7.92e+01 1hyqA c.37.1.10 60237 1y0eA 223 7.98e+01 c.1.2.5 116297 1f76A 336 8.04e+01 c.1.4.1 76160 1rvv1 154 8.05e+01 1rvv1 1jul 248 8.12e+01 1a53 1jvbA 347 8.13e+01 b.35.1.2,c.2.1.1 77181,77182 1a53 247 8.14e+01 1a53 1w8rA 263 8.23e+01 c.1.10.1 120734 1v7cA 351 8.27e+01 c.79.1.1 100446 1w9pA 433 8.38e+01 c.1.8.5,d.26.3.1 114412,114413 1h9mA 145 8.38e+01 1h9jA b.40.6.2,b.40.6.2 60833,60834 1w8sA 263 8.42e+01 c.1.10.1 120744 1ojxA 263 8.45e+01 c.1.10.1 93164 2fug5 207 8.48e+01 1dj3A 442 8.55e+01 1adeA c.37.1.10 32239 1jkmA 358 8.61e+01 1jkmA c.69.1.2 34633 1f91A 406 8.62e+01 1dd8A c.95.1.1,c.95.1.1 59713,59714 1ek4A 418 8.62e+01 1dd8A c.95.1.1,c.95.1.1 59436,59437 1jkmB 361 8.62e+01 1jkmA c.69.1.2 34634 1qftB 171 8.80e+01 1qftA b.60.1.1 27152 1hl2A 297 8.80e+01 c.1.10.1 83581 1pv8A 330 8.84e+01 c.1.10.3 95155