# List of top-scoring protein chains for t04-100-30-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 1hq0A 295 7.46e-02 1hzgA d.194.1.1 61122 2bkqA 212 5.75e-01 3cla 213 6.06e-01 3cla c.43.1.1 32610 2bkrA 212 6.99e-01 1fhuA 320 9.17e-01 1fhuA c.1.11.2,d.54.1.1 29234,38878 2b49A 287 1.34e+00 2g8yA 385 1.37e+00 2dg5B 190 1.45e+00 1r6wA 322 1.48e+00 c.1.11.2,d.54.1.1 97165,97166 2ap1A 327 1.52e+00 1wbpA 397 1.84e+00 1gc5A 467 1.87e+00 1gc5A c.72.1.3 60429 1mpxA 615 1.96e+00 b.18.1.13,c.69.1.21 85041,85042 1uwzA 136 2.35e+00 c.97.1.1 108081 1dc1A 323 2.43e+00 1dc1A c.52.1.11 33321 1q18A 332 2.46e+00 c.55.1.7,c.55.1.7 104470,104471 1sz2A 332 2.61e+00 1u6dX 308 2.63e+00 1zgkA 308 2.65e+00 1y74A 57 2.70e+00 1gw5S 142 2.73e+00 d.110.4.2 70633 1xt9A 212 3.07e+00 1q8yA 373 3.79e+00 d.144.1.7 96234 1ayoA 130 4.01e+00 1ayoA b.2.4.1 22431 2cayA 145 4.43e+00 1pgs 314 4.81e+00 1pgs b.121.1.1,b.121.1.1 23653,23654 2az4A 429 4.83e+00 1y88A 199 4.89e+00 1poiB 260 5.08e+00 1poiB c.124.1.3 34155 1howA 373 5.11e+00 1hcl d.144.1.7 41679 1wnaA 131 5.13e+00 2eu9A 355 5.53e+00 1zxuA 217 5.58e+00 1vljA 407 5.68e+00 e.22.1.2 108832 1jtkA 136 5.80e+00 c.97.1.1 71862 1ia9A 280 5.92e+00 1ia9A d.144.1.5 62113 1jx4A 352 5.96e+00 d.240.1.1,e.8.1.7 90378,90379 2fm8A 135 6.19e+00 1w9cA 321 6.53e+00 1k2eA 156 6.97e+00 d.113.1.1 72010 1io1A 398 7.12e+00 1io1A e.32.1.1 62611 1lqaA 346 7.38e+00 c.1.7.1 84674 1ckaA 57 7.48e+00 1ckaA b.34.2.1 24459 1mkp 144 7.57e+00 1vhrA c.45.1.1 32654 1qxoA 388 8.03e+00 d.258.1.1 96539 1o5kA 306 8.12e+00 c.1.10.1 92504 1dhs 344 8.20e+00 1dhs c.31.1.1 31727 1ofuX 119 8.44e+00 c.37.1.22 86976 2gx9A 129 8.46e+00 2h1tA 188 8.67e+00 1p90A 145 9.03e+00 c.55.5.2 94377 2cvbA 188 9.10e+00 1tfr 305 9.89e+00 1tfr a.60.7.1,c.120.1.2 18081,33351 1tyyA 339 9.93e+00 1wsrA 375 1.01e+01 2g6bA 180 1.06e+01 1vrbA 342 1.07e+01 1u5tC 202 1.12e+01 a.4.5.54,a.4.5.54 107688,107689 1zc6A 305 1.12e+01 1v4sA 455 1.16e+01 c.55.1.3,c.55.1.3 100309,100310 1z2mA 155 1.20e+01 1on0A 158 1.23e+01 d.108.1.1 87095 1nw3A 416 1.28e+01 c.66.1.31 86288 1j5pA 253 1.32e+01 d.81.1.3,c.2.1.3 71577,83092 1pu5A 164 1.37e+01 b.95.1.1 104310 1ytqA 204 1.40e+01 3bamA 213 1.45e+01 1bam c.52.1.3 33288 1kcqA 104 1.45e+01 d.109.1.1 68449 1uanA 227 1.48e+01 c.134.1.1 99135 1euvA 221 1.49e+01 1euvA d.3.1.7 37133 1vicA 262 1.53e+01 c.68.1.13 100756 1uheA 97 1.55e+01 1vl4A 447 1.55e+01 d.283.1.1 108718 2b7aA 293 1.55e+01 2tysA 268 1.57e+01 2tysA c.1.2.4 28572 1xrhA 351 1.58e+01 1g13A 162 1.61e+01 1g13A b.95.1.1 60194 1iw7C 1119 1.73e+01 e.29.1.1 71474 1rlzA 369 1.73e+01 c.31.1.1 104989 1udxA 416 1.76e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1id1A 153 2.00e+01 1id1A c.2.1.9 62286 1hw6A 278 2.02e+01 1frb c.1.7.1 61296 1qopA 268 2.03e+01 2tysA c.1.2.4 28570 1cq3A 233 2.11e+01 1cq3A b.27.1.1 23923 1wdnA 226 2.13e+01 1lst c.94.1.1 35816 2atzA 180 2.13e+01 1uj0A 62 2.15e+01 b.34.2.1 99449 1u9tA 354 2.19e+01 1xngA 268 2.22e+01 1kfcA 268 2.26e+01 c.1.2.4 77371 2bb2 181 2.27e+01 2bb2 b.11.1.1,b.11.1.1 23604,23605 2cn3A 737 2.28e+01 1nriA 306 2.29e+01 c.80.1.3 86123 1qz9A 416 2.30e+01 c.67.1.3 96621 1xd5A 112 2.39e+01 1jlwA 219 2.41e+01 a.45.1.1,c.47.1.5 71741,71742 1z57A 339 2.44e+01 1vpjA 192 2.44e+01 1w2xA 758 2.45e+01 c.14.1.4,c.14.1.4 109134,109135 2b5eA 504 2.48e+01 2bswA 146 2.50e+01 1ua4A 455 2.56e+01 c.72.1.3 99128 1gcoA 261 2.57e+01 1ybvA c.2.1.2 29884 1geeA 261 2.57e+01 c.2.1.2 90509 1uoyA 64 2.60e+01 g.3.19.1 99709 1ooeA 236 2.61e+01 c.2.1.2 87196 1e8yA 966 2.65e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1m1hA 248 2.67e+01 b.114.1.1,d.58.42.1 78415,78416 1n8fA 350 2.70e+01 c.1.10.4 85397 1hqz1 141 2.70e+01 1ztpA 251 2.72e+01 1ydnA 295 2.73e+01 1c93A 265 2.73e+01 2ebn c.1.8.5 28998 1lehA 364 2.74e+01 1bw9A c.2.1.7,c.58.1.1 30268,33916 1z6nA 167 2.75e+01 1ad1A 266 2.86e+01 1aj2 c.1.21.1 29668 2fp4B 395 2.88e+01 1hywA 68 2.90e+01 1hywA d.186.1.1 61425 1jv4A 162 2.95e+01 b.60.1.1 67343 1zrzA 364 2.96e+01 1khdA 345 3.04e+01 a.46.2.1,c.27.1.1 77400,77401 1k8kC 372 3.06e+01 b.69.4.1 68308 1i05A 180 3.08e+01 1mup b.60.1.1 27130 1pme 380 3.08e+01 1hcl d.144.1.7 41653 1sd4A 126 3.15e+01 a.4.5.39 105428 1edt 271 3.16e+01 2ebn c.1.8.5 28993 2aehA 369 3.16e+01 1mqeA 207 3.18e+01 d.113.1.1 91394 1gg1A 350 3.24e+01 1qr7A c.1.10.4 29187 1zg2A 107 3.24e+01 1aj2 282 3.26e+01 1aj2 c.1.21.1 29665 1spgA 144 3.28e+01 1abwA a.1.1.2 15409 2adzA 178 3.30e+01 1ad4A 266 3.38e+01 1aj2 c.1.21.1 29670 1nnwA 252 3.38e+01 d.159.1.5 80674 1gci 269 3.41e+01 1gci c.41.1.1 32503 1uyrA 737 3.43e+01 c.14.1.4,c.14.1.4 100188,100189 2a6hC 1119 3.46e+01 1n7oA 721 3.47e+01 a.102.3.2,b.24.1.1,b.30.5.2 80259,80260,80261 1lnsA 763 3.48e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1huuA 90 3.48e+01 1huuA a.55.1.1 17897 1pi1A 185 3.49e+01 a.29.7.1 94699 1mup 166 3.50e+01 1mup b.60.1.1 27133 1wqwA 235 3.50e+01 1o2dA 371 3.54e+01 e.22.1.2 86591 1iyxA 432 3.56e+01 c.1.11.1,d.54.1.1 83815,83816 1sh7A 284 3.56e+01 1u7zA 226 3.59e+01 1m2dA 110 3.64e+01 c.47.1.11 78476 1yw5A 177 3.66e+01 1v52A 133 3.72e+01 1k2yX 463 3.73e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1qmeA 702 3.76e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1pov1 302 3.84e+01 1pov1 1wa3A 205 3.84e+01 1jpc 109 3.88e+01 1b2pA b.78.1.1 27986 1ydgA 211 3.89e+01 1p5dX 463 3.90e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1z8gA 372 3.93e+01 2bc2A 227 3.97e+01 1a7tA d.157.1.1 42031 2beiA 170 3.99e+01 1x72A 334 4.00e+01 d.126.1.6 109495 1jhgA 101 4.04e+01 1jhgA a.4.12.1 19009 1nbwB 117 4.06e+01 c.51.3.2 80396 1eguA 731 4.07e+01 1eguA a.102.3.2,b.24.1.1,b.30.5.2 18850,23899,24423 2al6A 375 4.14e+01 1knvA 293 4.15e+01 c.52.1.7 68707 1e9mA 106 4.15e+01 1ayfA d.15.4.1 59397 1f2rI 100 4.16e+01 1c9fA d.15.2.1 37641 1sup 275 4.18e+01 1gci c.41.1.1 32510 1rz2A 254 4.26e+01 b.100.1.1 105130 1t46A 313 4.26e+01 d.144.1.7 106397 1i7qA 519 4.27e+01 1qdlA d.161.1.1 61901 1xb4A 202 4.29e+01 1h8gA 95 4.37e+01 b.109.1.1 65735 1x6oA 174 4.38e+01 b.34.5.2,b.40.4.5 109493,109494 1woqA 267 4.38e+01 c.55.1.10,c.55.1.10 109462,109463 1hh1A 143 4.39e+01 1gefA c.52.1.18 61036 2ex3B 264 4.39e+01 1wguA 136 4.39e+01 1hxs1 302 4.41e+01 1zndA 174 4.54e+01 1h32A 261 4.57e+01 a.3.1.8,a.3.1.8 76618,76619 2alaA 391 4.58e+01 1lba 146 4.59e+01 1lba d.118.1.1 41062 1tuaA 191 4.65e+01 d.51.1.1,d.51.1.1 107321,107322 1lw6E 281 4.66e+01 c.41.1.1 74293 1tbfA 347 4.67e+01 a.211.1.2 106743 3nul 130 4.68e+01 3nul d.110.1.1 40891 1tmy 120 4.69e+01 1dbwA c.23.1.1 31083 1zclA 180 4.75e+01 1f37A 110 4.76e+01 1f37A c.47.1.11 33088 1x9mA 698 4.76e+01 2f51A 118 4.78e+01 1xg8A 111 4.84e+01 1g5cA 170 4.85e+01 1g5cA c.53.2.1 60264 1p57A 114 4.87e+01 d.170.1.2 94125 1z83A 196 4.89e+01 1j9bA 141 4.89e+01 c.47.1.12 66459 1yzbA 182 4.90e+01 1frb 315 4.93e+01 1frb c.1.7.1 28665 1kjkA 64 4.94e+01 d.10.1.4 72613 1svdM 110 4.95e+01 1vsd 152 4.98e+01 1cxqA c.55.3.2 33625 1s3cA 141 4.99e+01 1u0sY 118 5.00e+01 c.23.1.1 107566 1o5zA 442 5.01e+01 c.59.1.2,c.72.2.2 92530,92531 1rypA 243 5.03e+01 1pmaA d.153.1.4 41932 1t7pA 698 5.06e+01 1t7pA c.55.3.5,e.8.1.1 33712,43005 2pia 321 5.14e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1uilA 113 5.18e+01 1auk 489 5.23e+01 1auk c.76.1.2 35030 1e2kA 331 5.24e+01 1qhiA c.37.1.1 31854 1wrmA 165 5.29e+01 1uwmA 106 5.29e+01 1zkrA 153 5.30e+01 1q0pA 223 5.35e+01 c.62.1.1 95507 1qhiA 366 5.36e+01 1qhiA c.37.1.1 31860 1qy1A 174 5.36e+01 b.60.1.1 96568 2gtrA 261 5.41e+01 1xjdA 345 5.41e+01 1zdrA 164 5.43e+01 1i06A 180 5.45e+01 1mup b.60.1.1 27131 1qc7A 101 5.47e+01 1qc7A a.118.14.1 18456 1pbyB 337 5.49e+01 b.69.2.2 94422 1to2E 281 5.50e+01 1wnlA 235 5.54e+01 1jj2B 337 5.60e+01 1ffkB b.43.3.2 63086 1s72B 338 5.61e+01 b.43.3.2 105320 1txoA 237 5.61e+01 1g0uG 252 5.64e+01 d.153.1.4 41952 1xs0A 136 5.64e+01 1r7cA 31 5.67e+01 j.35.1.1 104831 1q7zA 566 5.73e+01 c.1.21.2,c.1.26.1 96090,96091 1t95A 240 5.74e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 2al2A 436 5.74e+01 1rjdA 334 5.75e+01 c.66.1.37 97558 2al1A 436 5.75e+01 1ukmB 128 5.78e+01 d.169.1.1 99500 1v7pB 128 5.79e+01 d.169.1.1 108407 2ebn 289 5.81e+01 2ebn c.1.8.5 28990 1vqvA 306 5.82e+01 1vlwA 217 5.87e+01 c.1.10.1 108868 1euvB 86 5.90e+01 1a5r d.15.1.1 37598 1oneA 436 6.02e+01 4enl c.1.11.1,d.54.1.1 29200,38844 1xx1A 285 6.04e+01 1tvoA 368 6.06e+01 1dkzA 219 6.09e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 2cmuA 342 6.10e+01 1eo1A 124 6.12e+01 1eo1A c.55.5.1 33739 1z08A 170 6.13e+01 1jfuA 186 6.19e+01 c.47.1.10 62940 1rkpA 326 6.22e+01 a.211.1.2 97620 1nb8A 353 6.26e+01 d.3.1.9 80385 1xviA 275 6.32e+01 1qlmA 316 6.33e+01 1qlmA d.147.1.1 41765 1x3mA 415 6.34e+01 1rybA 212 6.36e+01 c.56.3.1 98098 1pbwA 216 6.39e+01 1pbwA a.116.1.1 19103 1shfA 59 6.40e+01 1bbzA b.34.2.1 24462 1eudB 396 6.47e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 1whzA 70 6.51e+01 1yd0A 96 6.51e+01 2a5yB 549 6.53e+01 1w15A 153 6.63e+01 b.7.1.2 109041 1m8uA 173 6.64e+01 b.11.1.1,b.11.1.1 91233,91234 1ek9A 428 6.64e+01 1ek9A f.5.1.1 43809 1oihA 301 6.66e+01 b.82.2.5 93051 1cxqA 162 6.71e+01 1cxqA c.55.3.2 33621 1oxkB 134 6.71e+01 c.23.1.1 93691 1fkx 349 6.71e+01 1a4mA c.1.9.1 29018 1i0cA 60 6.74e+01 1aojA b.34.2.1 61485 2agaA 190 6.74e+01 1vqoB 338 6.75e+01 2a1kA 233 6.78e+01 1bif 469 6.81e+01 1bif c.37.1.7,c.60.1.4 31961,34003 1h2eA 207 6.81e+01 c.60.1.1 70857 1ne9A 335 6.86e+01 d.108.1.4,d.108.1.4 91839,91840 1h10A 125 6.88e+01 b.55.1.1 83446 1unqA 125 6.88e+01 b.55.1.1 107968 2f62A 161 6.95e+01 1kinA 366 6.95e+01 1vlaA 150 6.96e+01 d.227.1.2 108735 2djkA 133 6.98e+01 2a0kA 161 6.98e+01 2f2tA 161 6.98e+01 1p8xA 344 6.99e+01 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 2a10A 125 6.99e+01 1yu6A 275 6.99e+01 1va4A 279 7.01e+01 c.69.1.12 108458 2f9lA 199 7.03e+01 1ybdA 239 7.08e+01 1m5yA 408 7.11e+01 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 1oacA 727 7.12e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24390,38007,38008,40003 2fpmA 322 7.14e+01 1zxfA 155 7.17e+01 1z9zA 60 7.21e+01 1o1zA 234 7.22e+01 c.1.18.3 86555 1cseE 274 7.29e+01 1gci c.41.1.1 32481 1usgA 346 7.30e+01 c.93.1.1 99864 1hruA 188 7.30e+01 1hruA d.115.1.1 40926 1w66A 232 7.30e+01 1qb5D 99 7.33e+01 b.40.2.1 88357 1k4mA 213 7.35e+01 c.26.1.3 77258 1onxA 390 7.36e+01 b.92.1.7,c.1.9.13 87176,87177 1g99A 408 7.39e+01 1g99A c.55.1.2,c.55.1.2 33457,33458 1tzjA 338 7.45e+01 4enl 436 7.52e+01 4enl c.1.11.1,d.54.1.1 29202,38846 1eajA 126 7.53e+01 1f5wA b.1.1.1 59401 1mqoA 227 7.54e+01 d.157.1.1 103846 1gpc 218 7.56e+01 1gpc b.40.4.7 25393 1gpmA 525 7.58e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1u9cA 224 7.60e+01 1r6yA 115 7.63e+01 1jm1A 204 7.64e+01 b.33.1.1 71745 1hzpA 335 7.64e+01 1hn9A c.95.1.2,c.95.1.2 61455,61456 1xyzA 347 7.65e+01 1taxA c.1.8.3 28804 1ms9A 648 7.69e+01 b.29.1.15,b.68.1.1 85088,85089 1wdtA 665 7.78e+01 1gz6A 319 7.80e+01 c.2.1.2 76410 1tiiD 99 7.83e+01 1tiiD b.40.2.1 24965 1dbiA 280 7.86e+01 1gci c.41.1.1 32543 1x2kA 68 7.90e+01 1r5jA 337 7.90e+01 c.77.1.5 97097 1p9qC 256 7.91e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1fmtA 314 7.94e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 1d7uA 433 8.00e+01 2dkb c.67.1.4 34439 1jhdA 396 8.04e+01 b.122.1.3,c.26.1.5 66712,66713 1twdA 256 8.04e+01 c.1.30.1 107397 5nul 138 8.04e+01 5nul c.23.5.1 31191 1fc4A 401 8.07e+01 1bs0A c.67.1.4 59760 1g73C 121 8.10e+01 1g3fA g.52.1.1 45375 1ctt 294 8.17e+01 1ctt c.97.1.1,c.97.1.1 36022,36023 1pfvA 551 8.21e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 2abqA 306 8.21e+01 1frd 98 8.24e+01 1awd d.15.4.1 37648 1ohfA 644 8.27e+01 b.121.4.8 93014 1wosA 364 8.28e+01 b.44.2.1,d.250.1.1 109468,109469 1sqhA 312 8.32e+01 d.108.1.5 98966 1vkkA 154 8.35e+01 d.109.1.2 108669 1s3aA 102 8.35e+01 1f4lA 551 8.37e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1tmxA 293 8.40e+01 1bqcA 302 8.41e+01 1bqcA c.1.8.3 28831 1z2nX 324 8.47e+01 1wdcB 156 8.47e+01 1wdcB a.39.1.5 17302 2biiA 424 8.47e+01 1qmvA 197 8.48e+01 1qq2A c.47.1.10 33066 1r0rE 274 8.53e+01 c.41.1.1 96735 1yo8A 634 8.59e+01 2a0mA 316 8.66e+01 1tc5A 194 8.68e+01 c.110.1.1 106752 2fpoA 202 8.70e+01 1r31A 428 8.70e+01 d.58.20.1,d.179.1.1 96897,96898 1zpyA 95 8.77e+01 2ag4A 164 8.77e+01 1uv4A 293 8.77e+01 1p6xA 334 8.83e+01 c.37.1.1 94195 1mkeA 152 8.86e+01 b.55.1.4 79231 1pinA 163 8.90e+01 1pinA b.72.1.1,d.26.1.1 27802,38431 1zd8A 227 8.96e+01 1qo3C 137 8.98e+01 1qo3C d.169.1.1 42350