# List of top-scoring protein chains for t06-100-30-near-backbone-11-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 1xg4A 295 4.66e-30 1m3uA 264 1.87e-26 c.1.12.8 84784 1o66A 275 4.71e-25 c.1.12.8 92547 1s2wA 295 3.37e-24 c.1.12.7 98407 1f8mA 429 1.14e-23 1dquA c.1.12.7 29315 1gvfA 286 1.48e-08 c.1.10.2 70599 1rvgA 305 2.64e-06 c.1.10.2 97920 1rvkA 382 1.01e-05 c.1.11.2,d.54.1.1 97928,97929 1hl2A 297 5.56e-05 c.1.10.1 83581 1xm3A 264 6.47e-05 c.1.31.1 115461 1mdl 359 7.03e-05 2mnr 1o1zA 234 7.30e-05 c.1.18.3 86555 1zfjA 491 7.63e-05 1ak5 c.1.5.1,d.37.1.1,d.37.1.1 28638,38540,38541 1xi3A 215 1.00e-04 c.1.3.1 109601 1ep3A 311 1.17e-04 2dorA c.1.4.1 28597 1nvmA 345 1.37e-04 a.5.7.1,c.1.10.5 86249,86250 1w5qA 337 1.40e-04 1rd5A 262 1.52e-04 c.1.2.4 111772 1gqnA 252 2.50e-04 c.1.10.1 90514 1xkyA 301 2.79e-04 c.1.10.1 122094 1w8sA 263 5.19e-04 c.1.10.1 120744 1o5kA 306 5.91e-04 c.1.10.1 92504 1rhcA 330 6.30e-04 c.1.16.3 97468 1x1oA 286 1.40e-03 1ub3A 220 1.43e-03 c.1.10.1 88395 1l6sA 323 1.48e-03 c.1.10.3 73627 1nqkA 381 1.52e-03 c.1.16.4 92050 1vr6A 350 1.93e-03 c.1.10.4 120439 1n7kA 234 2.16e-03 c.1.10.1 85374 1q7zA 566 2.64e-03 c.1.21.2,c.1.26.1 96090,96091 1p0kA 349 2.66e-03 c.1.4.1 87648 2b7nA 273 4.08e-03 1vzwA 244 4.68e-03 c.1.2.1 120553 1wv2A 265 5.15e-03 c.1.31.1 114910 1ad1A 266 5.73e-03 1aj2 c.1.21.1 29668 1vliA 385 5.84e-03 b.85.1.1,c.1.10.6 108830,108831 1y0eA 223 5.99e-03 c.1.2.5 116297 1ypfA 336 6.17e-03 1m5wA 243 6.24e-03 c.1.24.1 84836 1twdA 256 6.25e-03 c.1.30.1 107397 1yxyA 234 6.38e-03 c.1.2.5 124203 1vc4A 254 7.01e-03 c.1.2.4 100557 1tx2A 297 7.23e-03 c.1.21.1 107420 1tkkA 366 7.91e-03 c.1.11.2,d.54.1.1 107089,107090 1muwA 386 8.19e-03 c.1.15.3 79495 1thfD 253 8.21e-03 1thfD c.1.2.1 28535 2czdA 208 8.41e-03 c.1.2.3 131045 1aj2 282 8.78e-03 1aj2 1qwgA 251 9.74e-03 c.1.27.1 96473 1jflA 228 1.05e-02 c.78.2.1,c.78.2.1 71656,71657 1v93A 296 1.05e-02 c.1.23.1 100532 2gl5A 410 1.09e-02 c.1.11.2,d.54.1.1 135336,135337 1ujpA 271 1.31e-02 c.1.2.4 99462 1h1yA 228 1.32e-02 c.1.2.2 76506 1ktbA 405 1.39e-02 b.71.1.1,c.1.8.1 72960,72961 2b81A 323 1.74e-02 2gjlA 328 1.77e-02 1me8A 503 1.79e-02 c.1.5.1 79028 1vhnA 318 2.04e-02 c.1.4.1 100693 1eyeA 280 2.13e-02 1aj2 c.1.21.1 29672 1q6oA 216 2.23e-02 c.1.2.3 95986 1mzhA 225 2.72e-02 c.1.10.1 79698 1nu5A 370 3.06e-02 c.1.11.2,d.54.1.1 92183,92184 1gox 370 4.24e-02 1gox 1a53 247 4.36e-02 1a53 1reqA 727 5.23e-02 1reqA c.1.19.1,c.23.6.1 29620,31247 1zhaA 267 5.68e-02 1vhcA 224 5.71e-02 c.1.10.1 100661 1wbhA 214 5.89e-02 c.1.10.1 120845 1qopA 268 6.51e-02 2tysA c.1.2.4 28570 1ykwA 435 7.10e-02 c.1.14.1,d.58.9.1 123565,123566 1kfcA 268 8.61e-02 c.1.2.4 77371 1geqA 248 9.24e-02 2tysA c.1.2.4 28589 1mucA 373 9.71e-02 1mucA c.1.11.2,d.54.1.1 29236,38880 1yxcA 292 9.96e-02 c.1.10.1 124183 1x1zA 252 1.01e-01 c.1.2.3 121613 1ve3A 227 1.04e-01 c.66.1.43 120010 1km4A 247 1.04e-01 c.1.2.3 72740 1z41A 338 1.21e-01 c.1.4.1 124421 1wa3A 205 1.29e-01 c.1.10.1 120802 1sflA 238 1.37e-01 c.1.10.1 112077 2cw6A 298 1.47e-01 1w0mA 226 1.59e-01 c.1.1.1 109027 1o60A 292 1.64e-01 c.1.10.4 92532 2fr1A 486 1.66e-01 c.2.1.2,c.2.1.2 133961,133962 1xuuA 349 1.76e-01 b.85.1.1,c.1.10.6 116067,116068 1uasA 362 1.77e-01 b.71.1.1,c.1.8.1 88388,88389 1m6jA 261 1.78e-01 c.1.1.1 78693 1reqB 637 1.81e-01 1reqB c.1.19.1,c.23.6.1 29621,31248 1pe1A 267 1.87e-01 c.1.10.4 94591 1vcvA 226 1.98e-01 c.1.10.1 119988 1brwA 433 1.99e-01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1tr9A 341 2.60e-01 c.1.8.7 112617 1zp4A 304 2.80e-01 1vizA 240 2.83e-01 c.1.4.1 100784 1ezwA 349 2.92e-01 1ezwA c.1.16.3 29558 2tpsA 227 3.10e-01 2tpsA c.1.3.1 28591 1vhqA 232 3.25e-01 c.23.16.2 100696 1vyrA 364 3.29e-01 c.1.4.1 108906 1uk8A 282 3.46e-01 c.69.1.10 107907 1ub0A 258 3.75e-01 c.72.1.2 88394 1nsj 205 4.11e-01 1nsj 1izcA 339 4.14e-01 c.1.12.5 83838 1vkfA 188 4.24e-01 c.1.29.1 108656 2g50A 530 4.27e-01 b.58.1.1,c.1.12.1,c.49.1.1 134618,134619,134620 1epxA 370 4.81e-01 1fbaA c.1.10.1 29150 1tqjA 230 5.05e-01 c.1.2.2 107228 1ml4A 308 5.07e-01 c.78.1.1,c.78.1.1 79255,79256 1ufkA 254 5.32e-01 c.66.1.39 99340 1lt8A 406 5.58e-01 c.1.26.1 78186 1gdhA 320 5.77e-01 1gdhA c.2.1.4,c.23.12.1 30095,31355 1f6yA 262 5.99e-01 1f6yA c.1.21.2 29673 1w3iA 293 6.13e-01 c.1.10.1 109152 1j1iA 296 6.14e-01 c.69.1.10 83977 1p4cA 380 6.58e-01 c.1.4.1 94100 1wcwA 261 6.94e-01 1ohlA 342 7.52e-01 c.1.10.3 87035 1p1xA 260 8.19e-01 c.1.10.1 104060 2cunA 410 8.26e-01 1pszA 303 8.83e-01 1toaA c.92.2.2 35600 1dxeA 256 9.07e-01 1dxeA c.1.12.5 29310 2d13A 227 9.18e-01 c.26.2.1 131121 1othA 321 9.65e-01 1othA c.78.1.1,c.78.1.1 35260,35261 1mi3A 322 9.72e-01 c.1.7.1 91274 1m65A 245 1.07e+00 c.6.3.1 84847 1f5vA 240 1.08e+00 1bkjA d.90.1.1 40255 1onrA 316 1.08e+00 1onrA c.1.10.1 29169 1j7xA 302 1.10e+00 c.14.1.2 66425 1f74A 293 1.11e+00 1nal3 c.1.10.1 29079 1zxxA 319 1.16e+00 1p9bA 442 1.16e+00 c.37.1.10 94385 1php 394 1.16e+00 16pk 1wddA 477 1.23e+00 c.1.14.1,d.58.9.1 114528,114529 1pii 452 1.26e+00 1pii 1rxwA 336 1.28e+00 a.60.7.1,c.120.1.2 98059,98060 2fiqA 420 1.45e+00 c.1.10.7 133527 1q45A 391 1.46e+00 c.1.4.1 95780 2fepA 289 1.46e+00 1r3sA 367 1.54e+00 c.1.22.1 96963 1yyaA 250 1.55e+00 1mo0A 275 1.57e+00 c.1.1.1 79329 1j2rA 199 1.66e+00 c.33.1.3 90788 1ynpA 317 1.71e+00 1fcqA 350 1.73e+00 c.1.8.9 65006 1k7jA 206 1.73e+00 d.115.1.1 72103 1qf5A 431 1.76e+00 1adeA c.37.1.10 32212 1d3gA 367 1.77e+00 1d3gA c.1.4.1 28600 2ashA 381 1.78e+00 1wdpA 495 1.93e+00 c.1.8.1 120907 1o0yA 260 1.96e+00 c.1.10.1 80756 1dkuA 317 1.96e+00 1dkuA c.61.1.2,c.61.1.2 34118,34119 1k0wA 231 1.97e+00 c.74.1.1 77220 1o4vA 183 1.98e+00 c.23.8.1 86628 2gefA 217 2.01e+00 1zmdA 474 2.07e+00 2ag5A 246 2.12e+00 c.2.1.2 126719 1svdA 473 2.19e+00 c.1.14.1,d.58.9.1 119057,119058 1x7oA 287 2.32e+00 2fliA 220 2.37e+00 c.1.2.2 133714 1icpA 376 2.41e+00 1oyc c.1.4.1 62270 2fv7A 331 2.46e+00 c.72.1.1 134197 2g8yA 385 2.48e+00 1zgzA 122 2.50e+00 c.23.1.1 125065 1oyc 400 2.76e+00 1oyc 2frnA 278 2.82e+00 c.66.1.47 133993 1rcqA 357 2.85e+00 b.49.2.2,c.1.6.1 104882,104883 7a3hA 303 2.85e+00 7a3hA c.1.8.3 28817 1pswA 348 2.86e+00 c.87.1.7 88287 1j93A 353 2.88e+00 c.1.22.1 66454 1pvvA 315 2.88e+00 c.78.1.1,c.78.1.1 95190,95191 1v6sA 390 2.89e+00 c.86.1.1 100424 1lucB 324 2.91e+00 1lucA c.1.16.1 29548 1yeyA 444 2.96e+00 c.1.11.2,d.54.1.1 116664,116665 1zjjA 263 3.00e+00 1t7lA 766 3.12e+00 1jvbA 347 3.16e+00 b.35.1.2,c.2.1.1 77181,77182 1f8fA 371 3.22e+00 b.35.1.2,c.2.1.1 83246,83247 1e0tA 470 3.28e+00 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1tqxA 227 3.28e+00 c.1.2.2 112614 1j24A 143 3.31e+00 c.52.1.20 84008 1y81A 138 3.32e+00 c.2.1.8 122731 1qwkA 317 3.41e+00 c.1.7.1 96482 1shuX 182 3.42e+00 c.62.1.1 98882 1g8mA 593 3.45e+00 1g8mA c.24.1.3,c.97.1.4 60371,60372 2iw0A 254 3.51e+00 c.6.2.3 137737 1cb0A 283 3.61e+00 1cb0A c.56.2.1 33790 2aq8A 269 3.69e+00 c.2.1.2 127166 1uozA 315 3.75e+00 c.6.1.1 113354 2f6uA 234 3.78e+00 c.1.4.1 133061 1kaeA 434 3.82e+00 c.82.1.2 72247 1e5dA 402 3.92e+00 1e5dA c.23.5.1,d.157.1.3 31208,42061 1tzzA 392 3.94e+00 c.1.11.2,d.54.1.1 112896,112897 2gptA 523 3.95e+00 1pl8A 356 3.96e+00 b.35.1.2,c.2.1.1 94878,94879 1tp9A 162 4.02e+00 c.47.1.10 119306 1k0fA 277 4.03e+00 c.92.2.2 71974 1gpjA 404 4.04e+00 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1tvnA 293 4.15e+00 c.1.8.3 119360 1k0iA 394 4.20e+00 c.3.1.2,d.16.1.2 67942,67943 1kqpA 271 4.29e+00 c.26.2.1 72883 1v6tA 255 4.30e+00 c.6.2.5 113550 1gx3A 284 4.32e+00 d.3.1.5 70678 2anuA 255 4.49e+00 c.6.3.1 127058 1umdB 324 4.58e+00 c.36.1.7,c.48.1.2 99600,99601 1t0tV 248 4.58e+00 d.58.4.10 106229 1n82A 331 4.62e+00 c.1.8.3 91703 1pyfA 312 4.64e+00 c.1.7.1 95334 1u7pA 164 4.67e+00 c.108.1.17 113095 1eny 268 4.68e+00 1eny 1uf3A 228 4.76e+00 d.159.1.6 99317 1w4tA 299 4.86e+00 d.3.1.5 120639 2f96A 224 4.89e+00 c.55.3.5 133153 1mf7A 194 5.01e+00 c.62.1.1 84937 1b8oA 284 5.14e+00 1b8oA c.56.2.1 33762 1vk4A 298 5.28e+00 c.72.1.1 100850 1n4wA 504 5.29e+00 c.3.1.2,d.16.1.1 91676,91677 1v8fA 276 5.47e+00 c.26.1.4 100503 2gokA 429 5.77e+00 1sjdA 368 5.96e+00 c.1.11.2,d.54.1.1 105632,105633 1un7A 400 6.01e+00 b.92.1.5,c.1.9.10 99657,99658 1hkhA 279 6.03e+00 c.69.1.12 90628 1vk3A 615 6.04e+00 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 1qd1A 325 6.13e+00 1qd1A d.58.34.1,d.58.34.1 39493,39494 1oxkB 134 6.40e+00 c.23.1.1 93691 2a7kA 250 6.48e+00 c.14.1.3 126341 2cglA 489 6.50e+00 2acfA 182 6.51e+00 c.50.1.2 126547 2cjpA 328 6.64e+00 1rqbA 539 6.95e+00 a.5.7.2,c.1.10.5 105057,105058 8abp 306 7.06e+00 8abp 1vi9A 299 7.19e+00 c.72.1.5 100750 1i0dA 332 7.23e+00 1pscA c.1.9.3 61487 1brt 277 7.39e+00 1brt 1n0qA 93 7.54e+00 k.37.1.1 79754 1oi7A 288 7.57e+00 c.2.1.8,c.23.4.1 87049,87050 1rkd 309 7.58e+00 1rkd 1vflA 356 7.59e+00 c.1.9.1 120041 2ffcA 353 7.66e+00 c.1.2.3 133378 1bn7A 294 7.67e+00 1bn6A c.69.1.8 34677 1ny1A 240 7.72e+00 c.6.2.3 86395 1w5rA 278 7.84e+00 d.3.1.5 120643 1wdtA 665 8.17e+00 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 1oi2A 366 8.25e+00 c.119.1.2 103802 1r0mA 375 8.37e+00 c.1.11.2,d.54.1.1 104747,104748 1srvA 145 8.54e+00 1derA c.8.5.1 30817 2rslA 140 8.59e+00 2rslA c.53.1.1 33345 1pfvA 551 8.77e+00 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1ypqA 135 8.78e+00 d.169.1.1 123833 2gm5A 139 8.79e+00 1ja9A 274 8.96e+00 c.2.1.2 62817 7aatA 401 8.96e+00 1ajsA c.67.1.1 34250 1cs0A 1073 8.98e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1j5sA 463 9.01e+00 c.1.9.8 71580 1vmaA 306 9.05e+00 a.24.13.1,c.37.1.10 108887,108888 1mvoA 136 9.23e+00 c.23.1.1 79513 1vk1A 242 9.25e+00 d.268.1.2 108634 1zh2A 121 9.45e+00 c.23.1.1 125069 2faoA 309 9.46e+00 1tv8A 340 9.48e+00 c.1.28.3 107352 1ni9A 338 9.62e+00 e.7.1.2 85739 1toaA 313 9.76e+00 1toaA c.92.2.2 35598 1duvG 333 9.76e+00 1othA c.78.1.1,c.78.1.1 35228,35229 1wd7A 261 9.76e+00 c.113.1.1 114526 1e5kA 201 9.78e+00 1fr9A c.68.1.8 34578 1i1wA 303 9.81e+00 c.1.8.3 76732 1imjA 210 9.81e+00 c.69.1.23 71246 1qopB 396 1.00e+01 2tysB c.79.1.1 35270 2cvzA 289 1.01e+01 a.100.1.1,c.2.1.6 130890,130891 1hruA 188 1.01e+01 1hruA d.115.1.1 40926 1bw0A 416 1.02e+01 1bw0A c.67.1.1 34385 1bd0A 388 1.05e+01 1bd0A b.49.2.2,c.1.6.1 26480,28642 1xmpA 170 1.05e+01 c.23.8.1 115521 1gk8A 475 1.06e+01 c.1.14.1,d.58.9.1 65234,65235 1id1A 153 1.06e+01 1id1A c.2.1.9 62286 2gshA 414 1.06e+01 1qo2A 241 1.07e+01 1qo2A c.1.2.1 28533 1nlfA 279 1.11e+01 c.37.1.11 85850 1gg4A 452 1.11e+01 1gg4A c.59.1.1,c.98.1.1,c.72.2.1 33957,58985,58986 1vd6A 224 1.12e+01 c.1.18.3 119991 1wteA 272 1.14e+01 c.52.1.29 114876 1r5yA 386 1.14e+01 c.1.20.1 97134 1uwvA 433 1.15e+01 b.40.4.12,c.66.1.40 100128,100129 2aeeA 211 1.17e+01 c.61.1.1 126620 1nnsA 326 1.17e+01 c.88.1.1 85910 1r6wA 322 1.18e+01 c.1.11.2,d.54.1.1 97165,97166 2cwzA 141 1.22e+01 d.38.1.7 130961 1uc8A 280 1.23e+01 c.30.1.6,d.142.1.7 99165,99166 1mjhA 162 1.24e+01 1mjhA c.26.2.4 31639 2bneA 241 1.24e+01 c.73.1.3 128824 1nbaA 264 1.27e+01 1nbaA c.33.1.3 31753 1bf6A 291 1.27e+01 1pscA c.1.9.3 29065 1ykjA 394 1.28e+01 1h8eD 482 1.31e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 1jyeA 349 1.31e+01 c.93.1.1 67455 1x9iA 302 1.31e+01 c.80.1.1 114997 1sgjA 284 1.35e+01 c.1.12.5 105535 1lucA 355 1.38e+01 1lucA c.1.16.1 29547 1vgmA 378 1.38e+01 2ajrA 331 1.39e+01 c.72.1.1 126892 2c4nA 250 1.39e+01 c.108.1.14 129837 1a7j 290 1.40e+01 1a7j 1f2vA 219 1.40e+01 1f2vA c.23.17.1 59627 2ck3D 482 1.41e+01 a.69.1.1,b.49.1.1,c.37.1.11 130553,130554,130555 1lhpA 312 1.42e+01 c.72.1.5 77960 1kv5A 250 1.44e+01 c.1.1.1 73052 1j0dA 341 1.45e+01 c.79.1.1 83902 1zzmA 259 1.47e+01 c.1.9.12 125911 1bueA 265 1.48e+01 1btl e.3.1.1 42727 1gd1O 334 1.49e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 1t5iA 172 1.51e+01 c.37.1.19 106450 1v5eA 590 1.51e+01 c.31.1.3,c.36.1.5,c.36.1.9 119844,119845,119846 2a9sA 171 1.56e+01 c.51.5.1 126448 1ec7A 446 1.58e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1qauA 112 1.58e+01 1qauA b.36.1.1 24779 1rxyA 253 1.59e+01 c.56.2.1 98065 1mqoA 227 1.59e+01 d.157.1.1 103846 2bpqA 373 1.60e+01 1ek6A 348 1.62e+01 1xel 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