# List of top-scoring protein chains for t2k-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 1awqA 164 5.14e-34 2cpl b.62.1.1 27461 2cpl 165 5.47e-34 2cpl b.62.1.1 27420 1yndA 165 8.57e-34 1cwoA 165 9.31e-34 2cpl b.62.1.1 27445 2bitX 165 1.16e-33 1awsA 164 1.18e-33 2cpl b.62.1.1 27431 1a58 177 1.29e-33 2cpl b.62.1.1 27495 1dywA 173 1.47e-33 2cpl b.62.1.1 27505 2rmcA 182 2.01e-33 2cpl b.62.1.1 27491 1qoiA 177 5.12e-33 2cpl b.62.1.1 27490 1zcxA 178 9.44e-33 1xo7A 166 9.99e-33 2cfeA 162 1.37e-32 1vdnA 162 2.48e-32 1h0pA 182 9.93e-32 b.62.1.1 76450 1ihgA 370 1.22e-31 2cpl a.118.8.1,b.62.1.1 62380,62381 2a2nA 176 1.74e-29 1zkcA 197 5.28e-29 1xwnA 174 1.93e-28 2fu0A 160 2.16e-28 2b71A 196 7.48e-28 1j2aA 166 3.77e-25 b.62.1.1 90779 1v9tA 166 5.71e-25 b.62.1.1 108451 1lopA 164 3.79e-24 2cpl b.62.1.1 27510 1clh 166 1.11e-21 2cpl b.62.1.1 27512 1zx8A 136 2.42e-02 1zoxA 113 2.05e+00 1ewnA 219 2.36e+00 1bnkA b.46.1.2 25762 1uscA 178 3.44e+00 b.45.1.2 99860 1jjuA 489 3.79e+00 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66774,66775,66776,66777,66778 1pbyA 489 4.05e+00 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 2bf6A 449 4.18e+00 1eudB 396 4.36e+00 2scuB c.23.4.1,d.142.1.4 31150,41571 1eucB 396 4.41e+00 2scuB c.23.4.1,d.142.1.4 31149,41570 1mxiA 160 5.23e+00 c.116.1.1 79646 1shcA 195 5.77e+00 1shcA b.55.1.2 26992 1nbfA 353 6.49e+00 d.3.1.9 80387 1f6oA 219 7.26e+00 1bnkA b.46.1.2 25763 1kskA 234 7.80e+00 d.66.1.5,d.265.1.3 72920,90389 2fp4B 395 8.14e+00 1qlpA 394 8.38e+00 1ovaA e.1.1.1 42628 1nnsA 326 9.65e+00 c.88.1.1 85910 12ca 260 1.02e+01 2cba b.74.1.1 27942 2b4wA 315 1.08e+01 1h3iA 293 1.11e+01 b.76.2.1,b.85.7.1 76635,76636 1zkoA 136 1.11e+01 1mua 256 1.14e+01 2cba b.74.1.1 27831 1fr7A 260 1.14e+01 2cba b.74.1.1 27828 1u5uA 374 1.15e+01 1m1hA 248 1.19e+01 b.114.1.1,d.58.42.1 78415,78416 1uovA 159 1.21e+01 b.7.1.2 107974 1xdpA 687 1.27e+01 1vqvA 306 1.28e+01 1uowA 159 1.28e+01 b.7.1.2 107975 1oa4A 222 1.33e+01 b.29.1.11 86731 1mooA 260 1.36e+01 b.74.1.1 79359 1yo1A 260 1.40e+01 2a1rA 430 1.45e+01 1vioA 243 1.48e+01 d.265.1.3,d.66.1.5 100762,100763 1tjxA 159 1.53e+01 1caj 260 1.53e+01 2cba b.74.1.1 27841 1sglA 209 1.54e+01 d.124.1.1 105536 1lugA 259 1.58e+01 b.74.1.1 91127 1mdbA 539 1.62e+01 e.23.1.1 79008 1c3hA 137 1.69e+01 b.22.1.1 90405 2gdzA 267 1.91e+01 2gfoA 396 1.94e+01 1fcdA 401 1.96e+01 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 1ylnA 252 2.07e+01 1mt6A 280 2.08e+01 b.76.2.1,b.85.7.1 79446,79447 2cba 260 2.19e+01 2cba b.74.1.1 27821 1pswA 348 2.23e+01 c.87.1.7 88287 1xebA 150 2.29e+01 1paz 123 2.33e+01 1bqk b.6.1.1 22878 1pmd 675 2.33e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37491,37492,42562,42771 1c28A 135 2.36e+01 1c28A b.22.1.1 23857 3grs 478 2.38e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30441,30442,40152 1djnA 729 2.42e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 1yphC 131 2.43e+01 1m2oA 768 2.44e+01 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 1vr8A 142 2.63e+01 1fljA 260 2.65e+01 2cba b.74.1.1 27954 2arzA 247 2.66e+01 1bqk 124 2.66e+01 1bqk b.6.1.1 22889 1o91A 178 2.78e+01 b.22.1.1 92656 2awaA 390 2.80e+01 2bx6A 350 2.86e+01 1vfjA 116 3.00e+01 1ffk1 177 3.02e+01 1ffk1 4gr1 478 3.10e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30461,30462,40162 1o94A 729 3.21e+01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 1qmeA 702 3.24e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1aps 98 3.24e+01 2acy d.58.10.1 39299 1bnkA 216 3.37e+01 1bnkA b.46.1.2 25765 1ju2A 536 3.37e+01 c.3.1.2,d.16.1.1 77169,77170 1np1A 184 3.43e+01 1np1A b.60.1.1 27155 1fi2A 201 3.45e+01 1fi2A b.82.1.2 59845 1afcA 140 3.53e+01 1bfg b.42.1.1 25506 1wvqA 167 3.53e+01 1djqA 729 3.56e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 2et1A 201 3.57e+01 1d5rA 324 3.62e+01 1d5rA b.7.1.1,c.45.1.1 23181,32697 1bqg 451 3.65e+01 1bqg c.1.11.2,d.54.1.1 29217,38861 2aexA 346 3.70e+01 1xe7A 203 3.78e+01 1k2i1 245 3.88e+01 1pmy 123 3.90e+01 1bqk b.6.1.1 22888 1sxvA 172 4.01e+01 2fxqA 264 4.06e+01 2gk3A 256 4.11e+01 1yq5A 144 4.15e+01 1xyfA 436 4.17e+01 1taxA b.42.2.1,c.1.8.3 25577,28909 2tmdA 729 4.36e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28616,30317,30602 1gggA 226 4.44e+01 1lst c.94.1.1 35817 1rypI 222 4.46e+01 d.153.1.4 41877 1oktA 211 4.55e+01 a.45.1.1,c.47.1.5 93272,93273 1x8qA 184 4.82e+01 1r77A 103 4.88e+01 1cz7A 406 4.92e+01 1bg2 c.37.1.9 32194 1gctA 245 4.99e+01 5ptp b.47.1.2 26021 1at3A 247 5.05e+01 1at3A b.57.1.1 27021 1fvuB 125 5.12e+01 1ixxB d.169.1.1 42346 1vctA 205 5.18e+01 1qmtA 134 5.20e+01 7rsa d.5.1.1 37290 1lp4A 332 5.20e+01 d.144.1.7 74170 1m2rA 327 5.23e+01 d.144.1.7 84760 1n25A 368 5.23e+01 c.37.1.20 85264 1l1oC 181 5.23e+01 b.40.4.3 73480 1d3uA 181 5.34e+01 1ytbA d.129.1.1,d.129.1.1 41290,41291 1ciy 590 5.36e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1btkA 169 5.40e+01 1btkA b.55.1.1 26959 2b7oA 464 5.48e+01 1gg6B 131 5.49e+01 5ptp 2c26A 260 5.60e+01 1ymiA 334 5.61e+01 2ae0X 345 5.62e+01 1h1hA 134 5.66e+01 d.5.1.1 76468 1om1A 332 5.77e+01 d.144.1.7 93347 1qwyA 291 5.79e+01 b.84.3.2 96509 1h8uA 117 5.91e+01 1h8uA d.169.1.1 60793 1bqcA 302 5.94e+01 1bqcA c.1.8.3 28831 1i7oA 429 5.95e+01 1i7oA d.177.1.1,d.177.1.1 61893,61894 2c4xA 260 5.98e+01 2avtA 378 6.36e+01 1jmxA 494 6.36e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66901,66902,66903,66904,66905 1eerB 227 6.43e+01 1eerB b.1.2.1,b.1.2.1 22011,22012 1rc9A 221 6.44e+01 2ew0A 192 6.44e+01 1nb8A 353 6.46e+01 d.3.1.9 80385 1a6o 332 6.48e+01 1a6o 2bw2A 140 6.49e+01 1bev1 281 6.49e+01 1aym1 1e6mA 128 6.49e+01 3chy c.23.1.1 31039 1lpuA 332 6.50e+01 d.144.1.7 74177 1wpoB 256 6.52e+01 1lay b.57.1.1 27013 1ot5A 477 6.56e+01 b.18.1.20,c.41.1.1 87409,87410 1esiA 262 6.74e+01 1skf e.3.1.1 42682 1barA 140 6.76e+01 1bfg b.42.1.1 25504 1xipA 388 6.83e+01 1gvkB 240 7.02e+01 b.47.1.2 70610 1e5kA 201 7.03e+01 1fr9A c.68.1.8 34578 1g0u1 266 7.14e+01 1qnjA 240 7.14e+01 5ptp b.47.1.2 26238 2gaeA 346 7.19e+01 1gz2A 142 7.20e+01 d.169.1.1 83392 1h38B 883 7.24e+01 e.8.1.3 76626 1skf 262 7.27e+01 1skf e.3.1.1 42684 1gggB 226 7.34e+01 1lst c.94.1.1 35818 1qmpA 130 7.60e+01 1dz3A c.23.1.1 31106 1aroP 883 7.63e+01 1cezA e.8.1.3 43112 1hylA 230 7.65e+01 5ptp b.47.1.2 26076 2cgaA 245 7.67e+01 5ptp b.47.1.2 26028 1y1nA 291 7.78e+01 1o9wA 177 7.81e+01 b.2.3.5 86713 1ok7A 366 7.83e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1ej8A 140 7.92e+01 1qupA b.1.8.1 22300 1gesA 450 7.96e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 1np4A 184 7.96e+01 1np1A b.60.1.1 27166 1f97A 212 7.98e+01 1f97A b.1.1.1,b.1.1.4 19763,21764 1q5qA 259 7.99e+01 d.153.1.4 95904 1z7gA 217 8.02e+01 2b25A 336 8.06e+01 1iz1A 294 8.07e+01 a.4.5.37,c.94.1.1 83823,83824 1q7sA 117 8.16e+01 c.131.1.1 96055 1adwA 123 8.25e+01 1bqk b.6.1.1 22893 1p9uA 302 8.26e+01 b.47.1.4 88001 1mmiA 366 8.30e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1eaxA 241 8.39e+01 b.47.1.2 64889 1h38C 883 8.43e+01 e.8.1.3 76627 1wpuA 147 8.50e+01 1gvoA 364 8.53e+01 c.1.4.1 76357 1at0 145 8.58e+01 1at0 b.86.1.1 28374 1h61A 364 8.67e+01 1oyc c.1.4.1 60657 1npuA 117 8.78e+01 b.1.1.1 92038 1a5dA 173 8.80e+01 1amm b.11.1.1,b.11.1.1 23614,23615 1w99A 558 8.82e+01 1ay1H 213 8.83e+01 1igtB b.1.1.1,b.1.1.2 20243,21255 1r64A 481 8.89e+01 b.18.1.20,c.41.1.1 97140,97141 1ve4A 206 8.93e+01 1gttA 429 8.98e+01 d.177.1.1,d.177.1.1 70529,70530