# List of top-scoring protein chains for t04-100-30-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 1huuA 90 2.31e-01 1huuA a.55.1.1 17897 1hlvA 131 2.83e-01 a.4.1.7,a.4.1.7 65854,65855 1x3lA 440 3.68e-01 1w2yA 229 4.35e-01 a.204.1.1 109140 1b8zA 90 4.95e-01 1huuA a.55.1.1 17902 1y2mA 716 6.14e-01 1t6jA 714 8.61e-01 1x42A 232 1.21e+00 2aaxA 275 1.28e+00 1pyaB 228 1.54e+00 1pyaB 2ax9A 256 1.54e+00 1l6xB 34 1.79e+00 k.13.1.1 73644 1z8uA 102 1.84e+00 1jt6A 188 1.94e+00 a.4.1.9,a.121.1.1 67247,67248 1zdc 35 1.95e+00 1fc2C k.13.1.1 46434 1i37A 260 2.12e+00 1a28A a.123.1.1 61583 1whzA 70 2.19e+00 2ax8A 256 2.36e+00 1y01A 102 2.46e+00 1wkaA 147 2.69e+00 2ax6A 256 2.82e+00 2g09A 297 3.03e+00 1t7rA 269 3.17e+00 a.123.1.1 106635 1zbsA 291 3.42e+00 2cfxA 144 3.63e+00 1paqA 189 3.69e+00 a.118.1.14 94413 2au5A 139 3.87e+00 1sd4A 126 4.20e+00 a.4.5.39 105428 1rkbA 173 4.40e+00 1tqhA 247 5.15e+00 c.69.1.29 107225 2cu3A 64 5.17e+00 1t3qA 168 5.23e+00 a.56.1.1,d.15.4.2 106367,106368 1szwA 379 5.24e+00 d.265.1.4 99047 2vhbA 146 5.25e+00 2vhbA a.1.1.2 15629 1p5hA 428 5.42e+00 c.123.1.1 87802 1oxsC 353 5.87e+00 b.40.6.3,c.37.1.12 87519,87520 2bduA 297 5.93e+00 1oxxK 353 6.08e+00 b.40.6.3,c.37.1.12 93715,93716 1w0bA 102 6.12e+00 a.7.11.1 108985 1kdgA 546 6.15e+00 c.3.1.2,d.16.1.1 77337,77338 1vqzA 341 6.78e+00 1vj7A 393 6.82e+00 a.211.1.1,d.218.1.8 100801,100802 1s7oA 113 6.87e+00 a.4.13.3 105354 4bcl 366 7.08e+00 4bcl b.75.1.1 27968 1g99A 408 7.13e+00 1g99A c.55.1.2,c.55.1.2 33457,33458 1s69A 124 7.23e+00 a.1.1.1 105305 1qc7A 101 7.25e+00 1qc7A a.118.14.1 18456 1ui0A 205 7.36e+00 c.18.1.2 99411 1l9vA 317 7.39e+00 d.13.2.1,d.216.1.1 73760,73761 1r1dA 247 7.52e+00 c.69.1.29 96813 2bshA 125 7.58e+00 1u3aA 189 7.63e+00 1t1jA 125 7.80e+00 c.137.1.1 106249 1ugjA 141 7.80e+00 b.41.1.3 107826 1sr7A 259 7.90e+00 a.123.1.1 105957 2bsjA 133 8.01e+00 1a28A 256 8.09e+00 1a28A a.123.1.1 19290 1lw6E 281 8.11e+00 c.41.1.1 74293 1to2E 281 8.27e+00 1rtxA 123 8.52e+00 a.1.1.1 97827 1e6bA 221 8.55e+00 1e6bA a.45.1.1,c.47.1.5 59294,59295 2fpnA 216 8.66e+00 1pgjA 478 8.83e+00 2pgd a.100.1.1,c.2.1.6 18783,30195 1sqnA 261 8.89e+00 a.123.1.1 105944 1zv1A 65 9.03e+00 1zklA 353 9.03e+00 1fvkA 189 9.15e+00 1fvkA c.47.1.13 90351 1u5tB 169 9.27e+00 a.4.5.54,a.4.5.54 107686,107687 1sup 275 9.57e+00 1gci c.41.1.1 32510 1uz5A 402 9.71e+00 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 2cg4A 152 9.82e+00 1sedA 117 9.91e+00 a.219.1.1 105449 2f1lA 187 1.03e+01 1ej6D 418 1.04e+01 i.7.1.1 45970 1neeA 138 1.09e+01 d.241.1.1,g.59.1.1 91841,91842 1o4sA 389 1.14e+01 c.67.1.1 86620 1v7bA 185 1.15e+01 1pufA 77 1.18e+01 a.4.1.1 95131 2f4mB 61 1.20e+01 1ri7A 171 1.22e+01 a.4.5.32,d.58.4.2 97504,97505 2bhoA 130 1.25e+01 1u9lA 70 1.26e+01 a.60.4.2 107751 1p7tA 731 1.27e+01 c.1.13.1 94319 1sur 215 1.27e+01 1sur c.26.2.2 31620 1pveA 72 1.29e+01 a.189.1.1 104322 1qu1A 155 1.30e+01 1qu1A h.3.1.1 45670 1khyA 148 1.35e+01 a.174.1.1 77410 1wu4A 396 1.40e+01 2a6cA 83 1.41e+01 2afaA 425 1.42e+01 2atxA 194 1.43e+01 2aplA 157 1.43e+01 1v7nV 163 1.46e+01 a.26.1.2 100476 1dcs 311 1.46e+01 1dcs b.82.2.1 28124 1my6A 199 1.49e+01 a.2.11.1,d.44.1.1 85232,85233 2cwzA 141 1.52e+01 1nq6A 302 1.53e+01 c.1.8.3 92046 1v96A 149 1.53e+01 1ctf 74 1.56e+01 1ctf d.45.1.1 38759 1u20A 212 1.61e+01 1tkeA 224 1.62e+01 1lghB 45 1.62e+01 1lghB f.3.1.1 43734 1acvA 189 1.63e+01 1fvkA c.47.1.13 90328 1d8cA 723 1.64e+01 1d8cA c.1.13.1 29325 2cr5A 109 1.64e+01 1txjA 171 1.66e+01 b.88.1.2 107424 1xqwA 293 1.71e+01 1b72B 87 1.74e+01 1akhA a.4.1.1 16001 2dbbA 151 1.76e+01 1r1uA 106 1.77e+01 a.4.5.5 104771 1nrlA 316 1.77e+01 a.123.1.1 92091 1cxzB 86 1.80e+01 1cxzB a.2.6.1 15705 2fu2A 102 1.83e+01 1e54A 332 1.83e+01 1e54A f.4.3.1 59258 2fgqX 332 1.90e+01 1xpxA 163 1.94e+01 1pu1A 94 1.95e+01 d.266.1.1 104307 1whvA 100 1.95e+01 2f2sA 406 2.01e+01 1ybzA 91 2.03e+01 1q7eA 428 2.11e+01 c.123.1.1 96035 1vf6C 72 2.12e+01 a.194.1.1 100602 2hddA 61 2.14e+01 2hddA a.4.1.1 15971 1fc3A 120 2.23e+01 1fc3A a.4.6.3 16237 1tedA 393 2.28e+01 c.95.1.2 106807 1res 43 2.32e+01 1ret a.4.1.2 16023 1i0lA 221 2.35e+01 c.61.1.1 71096 1xsvA 113 2.36e+01 2scpA 174 2.40e+01 2scpA a.39.1.5 17256 1vkeA 133 2.45e+01 a.152.1.2 108650 1mijA 152 2.47e+01 a.4.1.1 79150 2as0A 396 2.49e+01 1ayl 541 2.51e+01 1ayl c.91.1.1,c.109.1.1 64718,64719 1c3wA 222 2.52e+01 1c3wA f.13.1.1 43405 1b74A 254 2.55e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1ustA 93 2.56e+01 a.4.5.13 99884 2bh1X 96 2.61e+01 1smtA 122 2.67e+01 1smtA a.4.5.5 16109 1pne 140 2.72e+01 1pne d.110.1.1 40866 1bed 181 2.73e+01 1fvkA c.47.1.13 90330 1i6wA 181 2.77e+01 1i6wA c.69.1.18 61859 1fvzA 271 2.79e+01 1fvzA 1lj9A 144 2.82e+01 a.4.5.28 78035 1ztrA 61 2.84e+01 1o26A 232 2.84e+01 d.207.1.1 86566 1u7kA 131 2.92e+01 1w0hA 204 2.93e+01 1zk8A 183 2.93e+01 1hgxA 183 2.95e+01 1tc1A c.61.1.1 34027 1rlkA 117 3.02e+01 c.131.1.1 97651 2af6A 258 3.05e+01 1dofA 403 3.07e+01 1c3cA a.127.1.1 19429 1g291 372 3.10e+01 1g291 2fm9A 215 3.13e+01 1rqlA 267 3.16e+01 c.108.1.3 97750 1s7zA 117 3.22e+01 a.159.3.1 98715 2aeuA 374 3.22e+01 1z54A 132 3.22e+01 2bniA 34 3.29e+01 1vi0A 206 3.30e+01 a.4.1.9,a.121.1.1 100720,100721 1xk7A 408 3.30e+01 1utuA 108 3.32e+01 1xg2B 153 3.36e+01 1adjA 421 3.41e+01 1adjA c.51.1.1,d.104.1.1 33188,40737 1fjlA 81 3.41e+01 2hddA a.4.1.1 16017 1yruB 74 3.42e+01 1yemA 179 3.45e+01 1s6cA 183 3.50e+01 a.39.1.5 98594 1or4A 178 3.51e+01 a.1.1.2 93447 1vzlA 34 3.51e+01 1oeyJ 107 3.55e+01 d.15.2.2 92804 1m0kA 262 3.59e+01 f.13.1.1 78344 1wqgA 185 3.60e+01 1wmiB 67 3.64e+01 1dik 874 3.65e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1iv3A 152 3.66e+01 d.79.5.1 76828 1aua 296 3.69e+01 1aua a.5.3.1,c.13.1.1 16290,30882 1n0wA 243 3.69e+01 c.37.1.11 79772 1z96A 40 3.72e+01 1xa3A 437 3.75e+01 1afwA 393 3.77e+01 1afwA c.95.1.1,c.95.1.1 35900,35901 1tca 317 3.80e+01 1tca c.69.1.17 34726 1h3qA 140 3.82e+01 d.110.4.3 76652 1fezA 256 3.92e+01 1fezA c.108.1.3 43343 1okrA 123 3.93e+01 a.4.5.39 93269 1zd0A 150 3.97e+01 1nmeA 146 3.98e+01 c.17.1.1 85874 1q16B 512 4.01e+01 d.58.1.5 95548 1a41 234 4.04e+01 1a41 d.163.1.2 42174 1tv8A 340 4.07e+01 c.1.28.3 107352 2ah5A 210 4.07e+01 1v32A 101 4.08e+01 a.42.1.1 100277 1hs7A 97 4.12e+01 1hs7A a.47.2.1 61236 1wy5A 317 4.13e+01 1x58A 62 4.21e+01 1wrdA 103 4.23e+01 1kblA 873 4.29e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1a8b 318 4.29e+01 1avc a.65.1.1 18171 2g40A 224 4.31e+01 1k0eA 453 4.33e+01 d.161.1.1 67938 1q6uA 245 4.34e+01 d.26.1.1 95998 1k8kC 372 4.35e+01 b.69.4.1 68308 1yu6A 275 4.36e+01 2ran 316 4.36e+01 1avc a.65.1.1 18170 1y5iB 512 4.39e+01 1l0wA 580 4.41e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1cseE 274 4.44e+01 1gci c.41.1.1 32481 2d1pC 95 4.50e+01 1es5A 262 4.56e+01 1skf e.3.1.1 42679 1vmeA 410 4.57e+01 c.23.5.1,d.157.1.3 108893,108894 1yn4A 99 4.59e+01 1gpmA 525 4.60e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1ispA 181 4.61e+01 c.69.1.18 76778 1ecmA 109 4.63e+01 1ecmA a.130.1.1 19492 2f5uA 447 4.74e+01 1g5cA 170 4.75e+01 1g5cA c.53.2.1 60264 1tig 94 4.77e+01 1tig d.68.1.1 39566 1q6hA 224 4.79e+01 d.26.1.1 95975 1vjtA 483 4.81e+01 c.2.1.5,d.162.1.2 100833,100834 1y43B 173 4.94e+01 1r0rE 274 5.06e+01 c.41.1.1 96735 1mdc 133 5.06e+01 1hmt b.60.1.2 27198 1q8bA 105 5.12e+01 d.58.4.6 96201 1txnA 328 5.12e+01 1t7lA 766 5.14e+01 1colA 204 5.27e+01 1a87 f.1.1.1 43378 2cb5A 453 5.31e+01 3gcb d.3.1.1 37035 1useA 45 5.40e+01 2glzA 153 5.41e+01 1oyiA 82 5.42e+01 a.4.5.19 93729 1u14A 172 5.51e+01 c.51.4.3 107579 1pgyA 47 5.51e+01 a.5.2.1 94696 1ml8A 134 5.51e+01 d.227.1.2 85013 1wddS 128 5.59e+01 2gfgA 193 5.64e+01 1yzbA 182 5.67e+01 1ifqA 138 5.70e+01 1ifqA d.110.4.1 62350 2af4C 333 5.76e+01 2kinB 100 5.78e+01 3kinB 1pt7A 437 5.79e+01 c.123.1.1 95093 1zchA 255 5.81e+01 1xg7A 250 5.89e+01 1kdxA 81 5.90e+01 1kdxA a.12.1.1 16375 2cw9A 194 5.91e+01 1vkcA 158 5.91e+01 1wdgA 94 5.94e+01 h.3.3.1 109248 1lxa 262 5.94e+01 1lxa b.81.1.1 28052 2agaA 190 6.04e+01 1tfjA 219 6.04e+01 1pufB 73 6.11e+01 a.4.1.1 95132 1qf6A 642 6.11e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1k61A 60 6.15e+01 a.4.1.1 77270 2f4eA 180 6.21e+01 1o08A 221 6.22e+01 c.108.1.6 86525 1bg4 302 6.24e+01 1taxA c.1.8.3 28806 1r6jA 82 6.24e+01 b.36.1.1 97151 2acjA 66 6.25e+01 1mtyB 384 6.29e+01 1mtyB a.25.1.2 16740 1wveC 80 6.29e+01 2fexA 188 6.38e+01 1fnoA 417 6.41e+01 d.58.19.1,c.56.5.4 70145,75841 1cs1A 386 6.46e+01 1ibjA c.67.1.3 34399 2ccmA 191 6.46e+01 1y9iA 178 6.50e+01 1wl4A 397 6.60e+01 1v3wA 173 6.61e+01 b.81.1.5 100291 1qrvA 73 6.63e+01 1cktA a.21.1.1 16425 3tmkA 216 6.66e+01 3tmkA c.37.1.1 31920 1htwA 158 6.68e+01 c.37.1.18 71083 1yh2A 175 6.70e+01 2b1eA 564 6.71e+01 1ve4A 206 6.75e+01 1v63A 101 6.80e+01 a.21.1.1 108391 1tgrA 52 6.81e+01 5eau 548 6.83e+01 5eat a.102.4.1,a.128.1.3 18851,19443 1k1xA 659 6.89e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1pd3A 58 6.92e+01 a.30.3.1 94512 1i74A 309 6.95e+01 1i74A c.107.1.1 61867 1j1vA 94 7.12e+01 a.4.12.2 83981 2bh9A 489 7.13e+01 1ic8A 194 7.16e+01 a.4.1.1,a.35.1.1 76740,76741 2ctc 307 7.18e+01 1aye c.56.5.1 33802 3kvt 115 7.26e+01 1t1dA d.42.1.2 38642 1wm3A 72 7.28e+01 1ukxA 137 7.28e+01 d.20.1.3 107919 1t56A 216 7.29e+01 a.4.1.9,a.121.1.1 106428,106429 2atfA 200 7.33e+01 2b5hA 200 7.33e+01 1gz2A 142 7.37e+01 d.169.1.1 83392 1j5wA 298 7.38e+01 d.104.1.1 71589 1q0pA 223 7.39e+01 c.62.1.1 95507 1wzcA 249 7.40e+01 1k8uA 90 7.44e+01 a.39.1.2 72181 1wviA 257 7.45e+01 1eexG 173 7.47e+01 1dioG a.23.2.1 16490 1esiA 262 7.52e+01 1skf e.3.1.1 42682 1mw5A 187 7.54e+01 d.259.1.1 91477 1s28A 132 7.59e+01 d.198.1.1 105223 1r1tA 122 7.61e+01 a.4.5.5 104769 1t9bA 677 7.61e+01 1zljA 78 7.65e+01 2dafA 118 7.67e+01 2blkA 122 7.75e+01 2glfA 450 7.84e+01 1m4tA 392 7.87e+01 c.95.1.1,c.95.1.1 78617,78618 2cxxA 190 7.89e+01 1xjuA 163 7.91e+01 1fpoA 171 7.91e+01 1fpoA a.2.3.1,a.23.1.1 15693,16487 2bvlA 543 7.96e+01 1lb2B 84 7.99e+01 a.60.3.1 77871 2d9kA 75 8.01e+01 2d2mB 142 8.07e+01 1ufwA 95 8.09e+01 d.58.7.1 99358 1m1hA 248 8.09e+01 b.114.1.1,d.58.42.1 78415,78416 2pgd 482 8.11e+01 2pgd a.100.1.1,c.2.1.6 18778,30190 2fd5A 180 8.11e+01 1z2kA 109 8.20e+01 1ji8A 111 8.20e+01 d.203.1.1 66733 1vcc 77 8.25e+01 1vcc d.121.1.1 41092 1qbjA 81 8.28e+01 1qbjA a.4.5.19 16155 1g8qA 90 8.35e+01 1g8qA a.135.1.1 19621 1bebA 162 8.39e+01 1bebA b.60.1.1 27115 1dciA 275 8.44e+01 1dciA c.14.1.3 30918 1swvA 267 8.47e+01 1gpeA 587 8.48e+01 1gpeA c.3.1.2,d.16.1.1 30387,37951 1w85A 368 8.51e+01 1r2qA 170 8.52e+01 c.37.1.8 96874 1r5jA 337 8.54e+01 c.77.1.5 97097 2av5A 120 8.55e+01 1acc 735 8.60e+01 1acc f.11.1.1 43828 2cmd 312 8.61e+01 2cmd c.2.1.5,d.162.1.1 30135,42102 1oaiA 59 8.63e+01 a.5.2.3 81255 1u5pA 216 8.65e+01 2ftbA 125 8.70e+01 1ef1A 294 8.74e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 1ypyA 184 8.76e+01 1zq1C 633 8.76e+01 1hlb 158 8.78e+01 1hlb a.1.1.2 15625 1ekgA 127 8.81e+01 1dlxA d.82.2.1 40021 1ukfA 188 8.86e+01 d.3.1.10 99488 1u55A 188 8.88e+01 d.278.1.1 107677 1nxzA 246 8.92e+01 b.122.1.2,c.116.1.5 86391,86392 2fswA 107 8.95e+01 1js8A 394 8.96e+01 a.86.1.1,b.112.1.1 67219,67220 1ywfA 296 9.00e+01