# List of top-scoring protein chains for t2k-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 1tbxA 99 5.63e-04 a.4.5.48 106748 1yyvA 131 8.70e-04 1xmaA 145 1.42e-03 2fbiA 142 1.61e-03 1ub9A 100 4.65e-03 a.4.5.28 99159 1jgsA 138 5.75e-03 a.4.5.28 66683 2g7uA 257 6.60e-03 3rubS 123 1.05e-02 1rboC d.73.1.1 39616 1z7uA 112 1.62e-02 2fswA 107 2.61e-02 1an7A 136 3.40e-02 1seiA d.140.1.1 41465 1hw1A 239 4.65e-02 1e2xA a.4.5.6,a.78.1.1 16111,18441 1e2xA 243 4.70e-02 1e2xA a.4.5.6,a.78.1.1 16113,18443 2f2eA 146 6.14e-02 1rboC 123 8.06e-02 1rboC d.73.1.1 39634 8rucI 123 8.89e-02 1rboC d.73.1.1 39629 2a61A 145 1.01e-01 1seiA 130 1.83e-01 1seiA d.140.1.1 41463 1ir21 140 2.60e-01 1q1hA 110 2.71e-01 a.4.5.41 95580 2eshA 118 3.55e-01 1sfxA 109 3.55e-01 a.4.5.50 105505 1gk8I 140 3.75e-01 d.73.1.1 65242 2c5uA 375 3.81e-01 1wddS 128 4.38e-01 1f4kA 122 4.76e-01 1bm9A a.4.5.7 59646 1b1bA 140 4.85e-01 1bi0 a.4.5.24,a.76.1.1 16215,18421 2cfxA 144 5.10e-01 1r7jA 95 5.14e-01 a.4.5.49 104836 1i6uA 130 5.31e-01 d.140.1.1 61850 2fbhA 146 5.37e-01 1lj9A 144 5.87e-01 a.4.5.28 78035 1xgsA 295 6.16e-01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1sd4A 126 7.05e-01 a.4.5.39 105428 2dkaA 544 7.53e-01 1okrA 123 7.60e-01 a.4.5.39 93269 1yzbA 182 1.05e+00 1mkmA 249 1.05e+00 a.4.5.33,d.110.2.2 79242,79243 1lddA 74 1.19e+00 a.4.5.34 73841 2cq2A 114 1.22e+00 1fx7A 230 1.31e+00 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 1bm9A 122 1.33e+00 1bm9A a.4.5.7 16116 2cg4A 152 1.51e+00 1qvbA 481 1.53e+00 1qvbA c.1.8.4 28983 1p4xA 250 1.64e+00 a.4.5.28,a.4.5.28 87784,87785 1duxC 94 1.64e+00 1awcA a.4.5.21 16170 1wxxA 382 1.78e+00 1itwA 741 1.91e+00 c.77.1.2 76793 1hl8A 449 2.01e+00 b.71.1.3,c.1.8.11 90646,90647 2ethA 154 2.14e+00 1u5tA 233 2.16e+00 a.4.5.54,a.4.5.54 107684,107685 2fu4A 83 2.17e+00 1cm7A 363 2.38e+00 1cnzA c.77.1.1 35063 1flmA 122 2.39e+00 1axj b.45.1.1 25747 2b0tA 738 2.55e+00 1q2lA 939 2.71e+00 1wwiA 148 2.73e+00 2dtr 226 2.83e+00 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 1zybA 232 2.89e+00 1yg2A 179 3.11e+00 1f5tA 121 3.15e+00 1bi0 a.4.5.24,a.76.1.1 16203,18409 1mml 265 3.25e+00 1mml e.8.1.2 43015 1xb4A 202 3.32e+00 1bi0 226 3.32e+00 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16202,18408,24453 1k1xA 659 3.56e+00 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 2atzA 180 3.57e+00 2agaA 190 3.59e+00 2cohA 202 3.62e+00 1hl9A 449 3.67e+00 b.71.1.3,c.1.8.11 90650,90651 1qqtA 551 3.90e+00 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 16923,31590,45175 1f4lA 551 3.99e+00 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1pfvA 551 4.01e+00 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1sfuA 75 4.02e+00 a.4.5.19 105503 1wj5A 120 4.23e+00 1h1yA 228 4.52e+00 c.1.2.2 76506 1mwrA 646 4.55e+00 d.17.4.5,d.175.1.1,e.3.1.1 79586,79587,79588 1s3jA 155 4.56e+00 a.4.5.28 98437 1qm9A 198 4.57e+00 1qm9A d.58.7.1,d.58.7.1 39207,39208 2d09A 407 4.72e+00 1axj 122 4.81e+00 1axj b.45.1.1 25749 1bjaA 95 4.88e+00 1bjaA a.4.5.9 16122 1s1fA 406 4.91e+00 1c0wA 225 4.94e+00 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16211,18417,24455 1xewY 172 5.04e+00 1lvaA 258 5.07e+00 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1vqqA 646 5.12e+00 1ft9A 222 5.15e+00 1ft9A a.4.5.4,b.82.3.1 16107,28131 1i6xA 209 5.31e+00 a.4.5.4,b.82.3.2 83673,83674 2cgpA 210 5.34e+00 2cgpA a.4.5.4,b.82.3.2 16102,28141 1p5sA 203 5.39e+00 a.40.1.1 94147 1xmrA 243 5.42e+00 2b0lA 102 5.62e+00 2cujA 108 5.71e+00 1xqaA 113 5.86e+00 1qmeA 702 5.92e+00 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1g6nA 210 5.95e+00 2cgpA a.4.5.4,b.82.3.2 16100,28139 1iz1A 294 5.97e+00 a.4.5.37,c.94.1.1 83823,83824 1b4uB 302 5.99e+00 1bouB c.56.6.1 33861 1bouB 302 6.00e+00 1bouB c.56.6.1 33859 2b8tA 223 6.18e+00 1h7nA 342 6.39e+00 1b4kA c.1.10.3 60726 1nrwA 288 6.39e+00 c.108.1.10 86128 1lea 84 6.43e+00 1lea a.4.5.2 16085 1a9eA 277 6.44e+00 1agdA b.1.1.2,d.19.1.1 20757,38268 1s2oA 244 6.57e+00 1ylvA 342 6.70e+00 1b4kA c.1.10.3 29180 1p2xA 159 6.83e+00 a.40.1.1 104062 1t6cA 315 7.13e+00 c.55.1.8,c.55.1.8 106558,106559 1m2oA 768 7.22e+00 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78480,78481,78482,78483,78484 1yxcA 292 7.29e+00 2a6nA 292 7.30e+00 2a6lA 292 7.35e+00 1mzbA 136 7.41e+00 a.4.5.42 91497 1ddnA 226 7.66e+00 1bi0 a.4.5.24,a.76.1.1 16207,18413 1avyC 74 7.70e+00 1avyB h.1.17.1 45658 1hbxG 157 8.17e+00 1awcA a.4.5.21 60934 1stzA 338 8.47e+00 a.4.5.51,d.110.2.3 106009,106010 1ohlA 342 8.55e+00 c.1.10.3 87035 1jhfA 202 8.87e+00 a.4.5.2,b.87.1.1 63057,63058 1a1nA 276 9.06e+00 1agdA b.1.1.2,d.19.1.1 20755,38267 1y4oA 104 9.14e+00 1y8cA 246 9.22e+00 2bvcA 486 9.70e+00 1aa0 113 9.87e+00 1aa0 h.1.17.1 45659 2b95A 106 1.01e+01 1mnmC 87 1.01e+01 1akhB a.4.1.1 15983 1smtA 122 1.04e+01 1smtA a.4.5.5 16109 1eeoA 321 1.04e+01 1pty c.45.1.2 32655 1i0dA 332 1.05e+01 1pscA c.1.9.3 61487 2d0eA 407 1.05e+01 1eywA 331 1.06e+01 1pscA c.1.9.3 29057 1mwsA 646 1.08e+01 d.17.4.5,d.175.1.1,e.3.1.1 79592,79593,79594 1avyA 74 1.09e+01 1avyB h.1.17.1 45656 1xh3A 276 1.11e+01 1pa1A 310 1.11e+01 c.45.1.2 94404 1on2A 142 1.11e+01 a.4.5.24,a.76.1.1 87103,87104 1tiyA 164 1.13e+01 c.97.1.2 107012 1rxwA 336 1.13e+01 a.60.7.1,c.120.1.2 98059,98060 1i1gA 141 1.14e+01 a.4.5.32,d.58.4.2 65982,65983 1u9tA 354 1.14e+01 2fpoA 202 1.14e+01 1hzyA 332 1.17e+01 1pscA c.1.9.3 61468 1hw5A 210 1.17e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 1aax 321 1.19e+01 1pty c.45.1.2 32657 1a1mA 278 1.21e+01 1agdA b.1.1.2,d.19.1.1 20753,38266 1a88A 275 1.21e+01 1brt c.69.1.12 34707 1a1oA 276 1.22e+01 1agdA b.1.1.2,d.19.1.1 20751,38265 1ggvA 232 1.22e+01 1din c.69.1.9 34683 1ptvA 321 1.22e+01 1pty c.45.1.2 32665 1uz5A 402 1.23e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1aerB 195 1.24e+01 1aerA d.166.1.1 42250 1pscA 365 1.26e+01 1pscA c.1.9.3 29058 1vbiA 344 1.27e+01 1ixcA 294 1.27e+01 a.4.5.37,c.94.1.1 83764,83765 1r1uA 106 1.38e+01 a.4.5.5 104771 2f71A 298 1.41e+01 2fokA 579 1.43e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16131,16132,16133,33323 1bv8A 138 1.47e+01 1ayoA b.2.4.1 22430 1k61A 60 1.47e+01 a.4.1.1 77270 1eaxA 241 1.50e+01 b.47.1.2 64889 1wkbA 810 1.54e+01 1cnzA 363 1.57e+01 1cnzA c.77.1.1 35061 2hnp 321 1.58e+01 1pty c.45.1.2 32678 1tmcA 175 1.60e+01 1agdA d.19.1.1 38258 1dhpA 292 1.62e+01 1dhpA c.1.10.1 29097 1ubeA 349 1.62e+01 c.37.1.11,d.48.1.1 88412,88413 1y88A 199 1.62e+01 2fhzA 109 1.64e+01 1smtB 122 1.65e+01 1smtA a.4.5.5 16110 1pty 321 1.67e+01 1pty c.45.1.2 32656 1zi8A 236 1.69e+01 1wkqA 164 1.73e+01 c.97.1.2 109393 1b6sA 355 1.74e+01 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28242,31649,41494 1gs5A 258 1.74e+01 c.73.1.2 70395 1nw1A 429 1.75e+01 d.144.1.8 86286 1qbjA 81 1.77e+01 1qbjA a.4.5.19 16155 2a2dA 478 1.78e+01 2adcA 229 1.78e+01 1xrhA 351 1.81e+01 1din 236 1.83e+01 1din c.69.1.9 34682 2d1sA 548 1.88e+01 2ae6A 166 1.89e+01 1gd5A 130 1.90e+01 1gd5A d.189.1.1 60439 1j5eK 129 1.91e+01 c.55.4.1 71554 1vljA 407 1.92e+01 e.22.1.2 108832 1avyB 74 1.93e+01 1avyB h.1.17.1 45657 1fjgK 129 1.94e+01 1fjfK c.55.4.1 33733 1zoiA 276 1.95e+01 1nt2A 210 1.95e+01 c.66.1.3 86149 1wdjA 187 1.96e+01 1hsbA 270 1.96e+01 1agdA b.1.1.2,d.19.1.1 20736,38257 1frb 315 1.99e+01 1frb c.1.7.1 28665 1dlwA 116 2.00e+01 1dlyA a.1.1.1 14982 2acjA 66 2.00e+01 1pls 113 2.03e+01 1pls b.55.1.1 26965 1aerA 205 2.06e+01 1aerA d.166.1.1 42249 1iyxA 432 2.06e+01 c.1.11.1,d.54.1.1 83815,83816 1j1hA 144 2.09e+01 b.111.1.1 77056 1yrnB 83 2.11e+01 1akhB a.4.1.1 15986 1udmA 149 2.12e+01 d.109.1.2 107780 1tfr 305 2.12e+01 1tfr a.60.7.1,c.120.1.2 18081,33351 1aw5 326 2.12e+01 1b4kA c.1.10.3 29181 1vmeA 410 2.14e+01 c.23.5.1,d.157.1.3 108893,108894 1xnpA 202 2.14e+01 1b66A 140 2.15e+01 1b66A d.96.1.2 40657 2fhqA 141 2.17e+01 1k77A 260 2.21e+01 c.1.15.5 72096 1qwgA 251 2.21e+01 c.1.27.1 96473 1r1tA 122 2.22e+01 a.4.5.5 104769 1lnwA 147 2.22e+01 a.4.5.28 78104 1kcxA 518 2.23e+01 b.92.1.3,c.1.9.6 90953,90954 1k78A 149 2.23e+01 a.4.1.5,a.4.1.5 68255,68256 1xviA 275 2.24e+01 1wojA 214 2.24e+01 1gtqA 140 2.25e+01 1b66A d.96.1.2 40661 1yj7A 171 2.27e+01 1fzdA 201 2.27e+01 3fib d.171.1.1 42484 1gefA 123 2.29e+01 1gefA c.52.1.18 60465 1pz7A 204 2.32e+01 b.29.1.4 95405 1vjqA 79 2.34e+01 k.43.1.1 100830 1akhB 83 2.37e+01 1akhB a.4.1.1 15985 1w2lA 99 2.39e+01 1ois 223 2.39e+01 1a36A e.15.1.1 43267 1vfqA 143 2.39e+01 1a5y 330 2.40e+01 1pty c.45.1.2 32673 2gjgA 248 2.44e+01 1uxc 65 2.46e+01 1uxc a.35.1.5 17119 2asfA 137 2.47e+01 2av1A 275 2.49e+01 1a8s 273 2.51e+01 1brt c.69.1.12 34710 1or7C 90 2.53e+01 a.180.1.1 87336 1m32A 366 2.59e+01 c.67.1.3 78508 1fokA 568 2.61e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16137,16138,16139,33325 1s3eA 520 2.64e+01 c.3.1.2,d.16.1.5 98426,98427 1w85I 49 2.69e+01 1o97C 264 2.70e+01 c.26.2.3 81232 1uxd 65 2.70e+01 1uxc a.35.1.5 17118 2av7A 275 2.73e+01 1m5yA 408 2.73e+01 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 1ezeA 38 2.75e+01 1ezeA j.39.1.1 46302 1cojA 212 2.77e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1ah0 316 2.78e+01 1frb c.1.7.1 28685 1kafA 108 2.79e+01 d.199.1.1 68372 1zh5A 195 2.80e+01 1dpuA 99 2.80e+01 1dpuA a.4.5.16 16150 1ex7A 186 2.81e+01 1gky c.37.1.1 59537 1pdnC 128 2.86e+01 6paxA a.4.1.5 16047 1wwhA 119 2.87e+01 1qwkA 317 2.87e+01 c.1.7.1 96482 1mla 309 2.89e+01 1mla c.19.1.1,d.58.23.1 31031,39383 1tr1A 447 2.90e+01 1e70M c.1.8.4 28957 1z1dA 103 2.90e+01 2fdoA 94 2.93e+01 1ojaA 520 2.95e+01 c.3.1.2,d.16.1.5 93096,93097 2a2cA 478 3.00e+01 1brt 277 3.02e+01 1brt c.69.1.12 34699 1a8uA 277 3.05e+01 1brt c.69.1.12 34703 1mukA 1267 3.06e+01 e.8.1.4 79492 2nef 136 3.07e+01 1efnB d.102.1.1 40704 1ytfD 121 3.09e+01 1ytfD a.32.1.1,b.56.1.1 16998,27011 1sfsA 240 3.09e+01 c.1.8.8 98846 1kx5B 102 3.09e+01 a.22.1.1 77594 1ai7A 209 3.12e+01 1ajqA d.153.1.2 41845 1a3gA 308 3.13e+01 1daaA e.17.1.1 43286 1kxrA 339 3.15e+01 d.3.1.3 73175 1hq3D 103 3.15e+01 1aoiB a.22.1.1 16464 1tzyD 103 3.15e+01 a.22.1.1 107533 1w9hA 427 3.18e+01 1i1sA 96 3.19e+01 1bjaA a.4.5.9 16124 1xsnA 335 3.20e+01 1s1hC 192 3.20e+01 i.1.1.1 105156 1jksA 294 3.20e+01 d.144.1.7 71710 1q8dA 108 3.23e+01 a.228.1.1 104554 1agdA 276 3.24e+01 1agdA b.1.1.2,d.19.1.1 20741,38260 1siqA 392 3.25e+01 a.29.3.1,e.6.1.1 105585,105586 1broA 277 3.26e+01 1brt c.69.1.12 34700 1e1hB 174 3.29e+01 1f6kA 293 3.31e+01 1nal3 c.1.10.1 29081 2fnaA 357 3.36e+01 1j75A 67 3.37e+01 a.4.5.19 62673 1f74A 293 3.38e+01 1nal3 c.1.10.1 29079 1jofA 365 3.45e+01 b.69.10.1 71775 2aqjA 538 3.45e+01 2c30A 321 3.47e+01 2etjA 250 3.50e+01 2f06A 144 3.51e+01 1z91A 147 3.55e+01 1u04A 771 3.56e+01 b.34.14.1,c.55.3.10 107539,107540 1zhvA 134 3.56e+01 1a76 326 3.59e+01 1a76 a.60.7.1,c.120.1.2 18091,33361 2bvpA 276 3.59e+01 1bc8C 93 3.60e+01 1awcA a.4.5.21 16168 1a8q 274 3.60e+01 1brt c.69.1.12 34702 1te0A 318 3.60e+01 1scmA 60 3.63e+01 1wdcA 1n35A 1267 3.68e+01 e.8.1.4 79935 1gm7A 209 3.70e+01 d.153.1.2 65302 2avuE 192 3.72e+01 1wa3A 205 3.74e+01 1j1iA 296 3.75e+01 c.69.1.10 83977 2fbyA 205 3.77e+01 1bia 321 3.79e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1xh9A 350 3.84e+01 2g0uA 92 3.87e+01 1ucrA 78 3.87e+01 a.4.5.45 99188 1gky 187 3.90e+01 1gky c.37.1.1 31839 1ynuA 473 3.93e+01 1qauA 112 3.93e+01 1qauA b.36.1.1 24779 1pieA 419 3.97e+01 d.14.1.5,d.58.26.7 94706,94707 1bib 321 3.97e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16084,24448,40788 1xn7A 78 3.97e+01 1b6rA 355 3.99e+01 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28241,31648,41493 2bcqA 335 4.02e+01 1ipiA 123 4.04e+01 c.52.1.18 66255 1g5aA 628 4.04e+01 b.71.1.1,c.1.8.1 65152,65153 1uufA 369 4.06e+01 b.35.1.2,c.2.1.1 100006,100007 1whzA 70 4.06e+01 1ikpA 613 4.09e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 2czrA 226 4.17e+01 1kdgA 546 4.25e+01 c.3.1.2,d.16.1.1 77337,77338 1f93A 104 4.26e+01 1dcpA d.74.1.1 39688 1f7wA 144 4.27e+01 1f46A d.129.4.1 59679 1xriA 151 4.29e+01 1i1kA 309 4.29e+01 1daaA e.17.1.1 61533 1ru0A 105 4.32e+01 1gk9A 260 4.34e+01 d.153.1.2 65246 1y0uA 96 4.36e+01 1g19A 350 4.38e+01 2reb c.37.1.11,d.48.1.1 32284,38770 1u5tC 202 4.38e+01 a.4.5.54,a.4.5.54 107688,107689 1wy7A 207 4.39e+01 2bneA 241 4.41e+01 1b8gA 429 4.42e+01 1b8gA c.67.1.4 34499 2d42A 249 4.43e+01 1tlgA 125 4.44e+01 1byfA d.169.1.1 42421 1mdwA 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