# List of top-scoring protein chains for t06-100-40-40-str2+CB_burial_14_7-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 1dnlA 199 7.01e-17 1ci0A b.45.1.1 25753 1g79A 218 9.08e-17 1ci0A b.45.1.1 25752 1nrgA 261 1.97e-15 b.45.1.1 80694 2fhqA 141 1.07e-14 1rfeA 162 1.64e-14 1ty9A 222 2.52e-14 1vl7A 157 1.24e-12 b.45.1.1 108732 2fg9A 178 1.94e-12 2asfA 137 5.13e-12 2aq6A 147 1.49e-10 2arzA 247 1.74e-10 1w9aA 147 4.34e-10 2furA 209 2.10e-09 1w3oA 216 4.22e-09 1xhnA 184 1.06e-08 1flmA 122 3.62e-08 1axj b.45.1.1 25747 1ejeA 192 4.09e-05 1ejeA b.45.1.2 25757 1rz1A 161 1.89e-03 b.45.1.2 98124 1yoaA 159 6.36e-03 1i0rA 169 9.04e-03 1i0rA b.45.1.2 61489 1uscA 178 1.93e-02 b.45.1.2 99860 2d37A 176 9.35e-02 1y08A 323 1.19e-01 1z4vA 532 3.73e-01 1ylnA 252 4.61e-01 1b8aA 438 4.74e-01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1lrzA 426 4.86e-01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1gt1A 159 5.50e-01 b.60.1.1 90515 1ww7A 160 9.01e-01 1ko3A 230 1.06e+00 d.157.1.1 90974 1vyoA 128 1.24e+00 1q6uA 245 1.30e+00 d.26.1.1 95998 2bu3A 254 1.38e+00 2cwsA 237 1.39e+00 1ex2A 189 1.75e+00 1ex2A c.51.4.2 33225 2bkrA 212 1.87e+00 1y55X 126 2.00e+00 1rypK 198 2.03e+00 d.153.1.4 41879 1f8eA 388 2.20e+00 2qwc b.68.1.1 59694 2a1vA 144 2.27e+00 1l0wA 580 2.32e+00 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1x54A 434 2.40e+00 1lq9A 112 2.52e+00 d.58.4.3 78129 2gjgA 248 2.69e+00 1q6hA 224 2.83e+00 d.26.1.1 95975 1u04A 771 2.96e+00 b.34.14.1,c.55.3.10 107539,107540 2d1sA 548 2.98e+00 1wbiA 129 3.37e+00 2bwrA 401 3.37e+00 2ftrA 108 3.38e+00 1pg4A 652 3.43e+00 e.23.1.1 88067 1mw7A 240 3.43e+00 e.39.1.1 79557 2ffyA 358 3.46e+00 1rocA 155 3.71e+00 b.1.22.1 97673 1cruA 454 3.81e+00 1c9uA b.68.2.1 27617 1rgyA 360 3.89e+00 e.3.1.1 97456 2cwzA 141 3.89e+00 1rypJ 204 4.11e+00 d.153.1.4 41878 1o7fA 469 4.55e+00 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 1qhdA 398 4.55e+00 1qhdA a.115.1.2,b.19.1.1 63324,63325 1t6gC 184 4.89e+00 b.29.1.11 106569 1yqyA 523 5.12e+00 1cr5A 189 5.57e+00 1cr5A b.52.2.3,d.31.1.1 26931,38465 1tuhA 156 5.78e+00 d.17.4.11 107345 1jhdA 396 5.91e+00 b.122.1.3,c.26.1.5 66712,66713 1vmfA 145 5.96e+00 1s5jA 847 6.10e+00 1wj9A 211 6.12e+00 2bgiA 272 6.14e+00 1xffA 240 6.44e+00 d.153.1.1 109580 1rlmA 271 6.70e+00 1quqB 121 7.35e+00 1quqB b.40.4.3 25305 1mdbA 539 7.69e+00 e.23.1.1 79008 1ksiA 642 7.72e+00 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24408,38043,38044 1b4bA 71 7.83e+00 1b4aA d.74.2.1 39718 1wubA 178 7.90e+00 1z52A 470 8.20e+00 1y7bA 542 8.40e+00 2fp8A 322 8.42e+00 1uocA 289 8.43e+00 c.55.3.9 99686 2cveA 191 8.55e+00 1sq9A 397 8.56e+00 b.69.4.1 105889 1h2wA 710 8.69e+00 b.69.7.1,c.69.1.4 76596,76597 1rgzA 363 8.96e+00 e.3.1.1 97457 2bjrA 368 9.00e+00 1wosA 364 9.04e+00 b.44.2.1,d.250.1.1 109468,109469 1vlyA 338 9.29e+00 b.44.2.1,d.250.1.1 108871,108872 1r5mA 425 9.61e+00 1pgl2 370 1.00e+01 2cxcA 144 1.02e+01 1dpgA 485 1.07e+01 1dpgA c.2.1.3,d.81.1.5 30074,39989 1t5hX 504 1.08e+01 e.23.1.1 106449 2c78A 405 1.08e+01 1ecfA 504 1.09e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1tuvA 114 1.13e+01 1qfoA 119 1.14e+01 1qfoA b.1.1.1 19708 1eyqA 222 1.14e+01 1eypA d.36.1.1 38534 1sdjA 310 1.25e+01 d.21.1.2,d.21.1.2 98807,98808 2b4yA 271 1.30e+01 1i31A 314 1.33e+01 1bw8A b.2.7.1 22481 1l3kA 196 1.34e+01 d.58.7.1,d.58.7.1 73539,73540 1wocA 103 1.35e+01 2b20A 403 1.38e+01 2cxvA 219 1.43e+01 2cb2A 318 1.44e+01 2db1A 118 1.45e+01 1vggA 161 1.48e+01 1nlfA 279 1.52e+01 c.37.1.11 85850 2c4xA 260 1.53e+01 1kolA 398 1.56e+01 b.35.1.2,c.2.1.1 77474,77475 1n08A 163 1.56e+01 b.43.5.1 79730 1htwA 158 1.60e+01 c.37.1.18 71083 1ri6A 343 1.60e+01 b.69.11.1 97503 1vh5A 148 1.61e+01 d.38.1.5 100642 1cl1A 395 1.62e+01 1cl2A c.67.1.3 34395 1z02A 446 1.64e+01 3fib 249 1.65e+01 3fib d.171.1.1 42455 1rypA 243 1.67e+01 1pmaA d.153.1.4 41932 1vkkA 154 1.68e+01 d.109.1.2 108669 1w0dA 337 1.69e+01 1qyaA 307 1.73e+01 d.21.1.2,d.21.1.2 104653,104654 1i5gA 144 1.74e+01 1ewxA c.47.1.10 61784 1inp 400 1.76e+01 1inp e.7.1.1 42972 1ycoA 279 1.76e+01 2c43A 323 1.76e+01 1xfkA 336 1.78e+01 1ct9A 553 1.79e+01 1ct9A c.26.2.1,d.153.1.1 31616,41834 1vajA 214 1.80e+01 1rypI 222 1.80e+01 d.153.1.4 41877 1rloA 271 1.82e+01 1wdtA 665 1.83e+01 1cv8 174 1.85e+01 1cv8 d.3.1.1 37089 1nb9A 147 1.88e+01 b.43.5.1 85515 2fgtA 417 1.91e+01 1vclA 432 1.93e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 2eveA 157 1.94e+01 1e1oA 504 1.94e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 2bjfA 329 1.96e+01 1dzkA 157 1.98e+01 1obpA b.60.1.1 27096 1bj7 156 2.01e+01 1bj7 b.60.1.1 27113 1ms9A 648 2.01e+01 b.29.1.15,b.68.1.1 85088,85089 1fljA 260 2.02e+01 2cba b.74.1.1 27954 1qwzA 235 2.03e+01 b.100.1.1 96510 1i8dA 213 2.03e+01 b.43.4.3,b.43.4.3 61953,61954 1v3eA 431 2.03e+01 b.68.1.1 100287 2exrA 524 2.05e+01 7ahlA 293 2.07e+01 7ahlA f.6.1.1 43812 1vavA 222 2.10e+01 b.29.1.18 108472 2a9sA 171 2.10e+01 1s5aA 150 2.18e+01 d.17.4.10 98525 2dlbA 80 2.21e+01 1r45A 204 2.25e+01 1zkkA 167 2.29e+01 1wmmA 145 2.32e+01 1chuA 540 2.34e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1lw7A 365 2.36e+01 c.26.1.3,c.37.1.1 74295,74296 1xedA 117 2.39e+01 1f06A 320 2.43e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 1f60A 458 2.43e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1m2kA 249 2.44e+01 c.31.1.5 84754 1sqwA 188 2.44e+01 1z4rA 168 2.46e+01 1bvoA 175 2.48e+01 1a3qA b.2.5.3 22457 1mkyA 439 2.49e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 2f06A 144 2.50e+01 1t17A 148 2.53e+01 1p4uA 153 2.54e+01 b.1.10.2 87780 1p32A 209 2.55e+01 1p32A d.25.1.1 38379 1l0qA 391 2.60e+01 b.1.3.1,b.69.2.3 77644,77645 1mqeA 207 2.62e+01 d.113.1.1 91394 1m40A 263 2.67e+01 e.3.1.1 74437 1lcyA 325 2.68e+01 b.36.1.4,b.47.1.1 73834,73835 1va0A 239 2.69e+01 2ex4A 241 2.69e+01 1npk 154 2.69e+01 1npk d.58.6.1 39099 1pbyA 489 2.70e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 1lbvA 252 2.71e+01 e.7.1.1 73813 1xv2A 237 2.71e+01 1dkzA 219 2.72e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1uaiA 224 2.75e+01 b.29.1.18 107761 1rg8A 146 2.75e+01 1npeA 267 2.77e+01 b.68.5.1 92032 2amhA 207 2.79e+01 2bneA 241 2.80e+01 1on0A 158 2.84e+01 d.108.1.1 87095 1nnvA 110 2.86e+01 d.17.7.1 92012 1tdhA 364 2.86e+01 a.156.1.2,b.113.1.1,g.39.1.8 106772,106773,106774 1amuA 563 2.87e+01 1amuA e.23.1.1 43351 1r1mA 164 2.88e+01 d.79.7.1 96820 2cviA 83 2.88e+01 1ta3A 274 2.88e+01 c.1.8.5 106731 1jkgA 140 2.89e+01 d.17.4.2 66795 1qwrA 319 2.91e+01 b.82.1.3 96491 1w5fA 353 2.91e+01 2f4mA 295 2.94e+01 1e5dA 402 2.96e+01 1e5dA c.23.5.1,d.157.1.3 31208,42061 1at0 145 2.98e+01 1at0 b.86.1.1 28374 1s3rA 535 3.01e+01 1jfuA 186 3.05e+01 c.47.1.10 62940 1z90A 469 3.05e+01 2fjrA 189 3.08e+01 1v4pA 157 3.09e+01 2fhfA 1083 3.11e+01 2ga9A 297 3.11e+01 2bklA 695 3.12e+01 1hxn 219 3.13e+01 1hxn b.66.1.1 27529 1u60A 310 3.15e+01 e.3.1.2 107692 2f9zC 159 3.16e+01 1mixA 206 3.16e+01 a.11.2.1,b.55.1.5 79166,79167 1gskA 513 3.19e+01 b.6.1.3,b.6.1.3,b.6.1.3 83314,83315,83316 1jalA 363 3.19e+01 c.37.1.8,d.15.10.2 84138,84139 1ckmA 330 3.22e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 1vmhA 144 3.22e+01 1sdoA 203 3.28e+01 c.52.1.21 98809 1u6tA 121 3.29e+01 1b6a 478 3.31e+01 1bn5 a.4.5.25,d.127.1.1 16223,41160 1yt3A 375 3.32e+01 1llnA 262 3.32e+01 d.165.1.1 84625 1o98A 511 3.34e+01 c.105.1.1,c.76.1.3 86684,86685 1q40B 219 3.36e+01 d.17.4.2 95771 1tu6A 215 3.37e+01 d.3.1.1 107318 2cx5A 158 3.38e+01 1wp5A 323 3.38e+01 2sli 679 3.39e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1zzoA 136 3.43e+01 1orvA 728 3.44e+01 b.70.3.1,c.69.1.24 87354,87355 1vqoD 177 3.45e+01 1p2hA 571 3.45e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1vhsA 175 3.46e+01 d.108.1.1 100698 1efyA 350 3.46e+01 1a26 a.41.1.1,d.166.1.2 17413,42275 1s57A 153 3.49e+01 1y89A 238 3.49e+01 1y4hA 188 3.51e+01 2bkkA 264 3.51e+01 1a8d 452 3.52e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 1vjvA 415 3.53e+01 d.3.1.9 108632 1giqA 413 3.53e+01 d.166.1.1,d.166.1.1 76224,76225 2gviA 204 3.55e+01 1vheA 373 3.59e+01 b.49.3.1,c.56.5.4 100669,100670 1pxvA 183 3.61e+01 d.3.1.1 95301 1ci9A 392 3.62e+01 e.3.1.1 64767 1quqA 129 3.63e+01 1quqA b.40.4.3 25303 1ry9A 145 3.64e+01 d.198.1.1 98094 1uldA 150 3.65e+01 b.29.1.3 99545 1ii7A 333 3.65e+01 1ii7A d.159.1.4 62415 1zzkA 82 3.66e+01 1qhlA 227 3.67e+01 1qhlA c.37.1.12 32382 1or0B 528 3.67e+01 1jkxA 212 3.68e+01 c.65.1.1 66813 3pviA 157 3.69e+01 3pviA c.52.1.6 33300 1g291 372 3.70e+01 1g291 1uesA 191 3.72e+01 a.2.11.1,d.44.1.1 107798,107799 2bdeA 470 3.77e+01 2bi7A 384 3.81e+01 1p4kA 295 3.82e+01 d.153.1.5 87772 1ijqA 316 3.82e+01 1ijqA b.68.5.1,g.3.11.1 62506,62507 1q4rA 112 3.83e+01 d.58.4.4 95823 1upiA 225 3.85e+01 b.82.1.1 99757 1ka1A 357 3.87e+01 e.7.1.1 68369 1ybiA 288 3.90e+01 2f8aA 208 3.93e+01 1wn5A 130 3.96e+01 1tkeA 224 3.99e+01 1x67A 146 4.04e+01 1vk8A 106 4.07e+01 d.58.48.1 108636 2dbsA 90 4.08e+01 1u58A 253 4.09e+01 1pvtA 238 4.09e+01 c.74.1.1 95189 1ihoA 283 4.10e+01 1ihoA c.26.1.4 62390 1aisA 182 4.11e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 2gnqA 336 4.14e+01 1in0A 163 4.17e+01 d.58.49.1,d.58.49.1 83694,83695 1vqzA 341 4.18e+01 1goiA 499 4.18e+01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 1wvqA 167 4.19e+01 1vmbA 140 4.22e+01 2gibA 103 4.26e+01 1nwwA 149 4.28e+01 d.17.4.8 86306 1jrrA 382 4.29e+01 e.1.1.1 63256 1j1yA 136 4.31e+01 d.38.1.5 90776 2ebn 289 4.37e+01 2ebn c.1.8.5 28990 1pytA 94 4.38e+01 1pytA d.58.3.1 39064 1ne8A 117 4.38e+01 b.34.6.2 80424 1wlgA 299 4.39e+01 1ryp1 222 4.40e+01 1ryp1 1xw3A 110 4.41e+01 2c2nA 339 4.41e+01 1k8kD 300 4.45e+01 d.198.2.1,d.198.2.1 68309,68310 2erfA 209 4.46e+01 1zdyA 307 4.47e+01 1t77A 414 4.49e+01 1rypL 212 4.50e+01 d.153.1.4 41880 1iznA 286 4.50e+01 e.43.1.1 83847 1iirA 415 4.54e+01 1iirA c.87.1.5 62453 1o5uA 101 4.55e+01 b.82.1.8 92518 1v0wA 506 4.55e+01 d.136.1.2,d.136.1.2 108220,108221 1h54A 754 4.67e+01 a.102.1.4,b.30.5.3 60634,60635 1e4fT 419 4.68e+01 1e4fT c.55.1.1,c.55.1.1 33453,33454 1xqbA 247 4.70e+01 1wluA 136 4.71e+01 1poiB 260 4.71e+01 1poiB c.124.1.3 34155 1x6vA 630 4.75e+01 1tdzA 272 4.77e+01 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 1n8jA 186 4.78e+01 c.47.1.10 85401 1sa3A 262 4.79e+01 c.52.1.23 105400 2a1rA 430 4.86e+01 1v04A 355 4.87e+01 b.68.6.2 100240 2f5tX 233 4.88e+01 1nnwA 252 4.89e+01 d.159.1.5 80674 1i3zA 103 4.89e+01 d.93.1.1 83667 1otjA 283 4.90e+01 b.82.2.5 93517 1qd9A 124 4.91e+01 1qu9A d.79.1.1 39758 2g76A 335 4.92e+01 1vgjA 184 4.98e+01 1cuk 203 5.02e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1wsrA 375 5.03e+01 1cbf 285 5.03e+01 1cbf c.90.1.1 35587 1ti6B 274 5.04e+01 b.3.5.1,d.58.1.5 106976,106977 1qzzA 374 5.04e+01 a.4.5.29,c.66.1.12 96719,96720 1wv2A 265 5.07e+01 1yymG 313 5.08e+01 1xwyA 264 5.08e+01 1ei5A 520 5.09e+01 1ei5A b.61.3.1,b.61.3.1,e.3.1.1 27418,27419,42772 1zkjA 359 5.10e+01 1rypD 241 5.12e+01 1rypD d.153.1.4 41935 1ikpA 613 5.14e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1h6lA 353 5.21e+01 b.68.3.1 60687 1oo0A 147 5.21e+01 d.232.1.1 87182 1ynlH 219 5.22e+01 2cu5A 129 5.23e+01 1j98A 157 5.30e+01 1j98A d.185.1.2 62755 1nu0A 138 5.33e+01 c.55.3.8 92165 1lml 478 5.34e+01 1lml d.92.1.3 40295 2ae5B 528 5.46e+01 1c0pA 363 5.49e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1naqA 112 5.57e+01 d.58.5.2 91761 2fiuA 99 5.59e+01 1jmsA 381 5.61e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1pqhA 143 5.64e+01 b.52.2.1 95017 1yarH 217 5.66e+01 2bbeA 108 5.69e+01 1cyx 205 5.72e+01 1cyx b.6.1.2 23023 1r2zA 274 5.74e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1r6lA 239 5.75e+01 d.14.1.4,d.101.1.1 97153,97154 1crzA 403 5.80e+01 1crzA b.68.4.1,c.51.2.1 27629,33211 1f60B 94 5.81e+01 1b64 d.58.12.1 39307 1ab8A 220 5.85e+01 1azsA d.58.29.1 39414 2d8rA 99 5.86e+01 2apoA 357 5.87e+01 1xdfA 157 5.88e+01 1p5vA 235 6.03e+01 b.1.11.1,b.7.2.1 87812,87813 1k32A 1045 6.04e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1ewkA 490 6.05e+01 1ewkA c.93.1.1 35712 1t5bA 201 6.06e+01 c.23.5.3 106433 1x89A 178 6.07e+01 1xdpA 687 6.10e+01 1rv9A 259 6.12e+01 d.194.1.2 105105 2a1fA 247 6.14e+01 1rliA 184 6.14e+01 c.23.5.6 97647 1ysjA 404 6.15e+01 1w94A 156 6.20e+01 2gdnA 267 6.23e+01 1feuA 206 6.23e+01 1feuA b.53.1.1 59801 1yzsA 121 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