# 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 2gkeA 274 2.10e-03 1w61A 414 2.53e-03 1bwzA 274 6.92e-03 1bwzA d.21.1.1,d.21.1.1 38337,38338 1gqzA 274 1.17e-02 d.21.1.1,d.21.1.1 83311,83312 1u1wA 298 1.89e-02 1xubA 298 2.76e-02 1t6kA 278 3.24e-02 1tm0A 350 7.81e-02 d.21.1.3 107147 1qyaA 307 8.02e-02 d.21.1.2,d.21.1.2 104653,104654 1sdjA 310 1.31e-01 d.21.1.2,d.21.1.2 98807,98808 2g6yA 217 4.99e-01 2azpA 318 5.22e-01 1ym5A 300 5.83e-01 1p4uA 153 1.09e+00 b.1.10.2 87780 1v7wA 807 2.38e+00 a.102.1.4,b.30.5.3 108411,108412 1lm4A 194 2.46e+00 d.167.1.1 84626 1ci3M 249 2.51e+00 1hcz b.2.6.1,b.84.2.2 22480,28266 1jz8A 1023 3.41e+00 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 67830,67831,67832,67833,67834 1dp0A 1023 3.48e+00 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 22073,22074,23722,24346,28845 2exrA 524 3.55e+00 1lmhA 184 3.81e+00 d.167.1.1 74036 2a7bA 120 4.63e+00 1gyvA 120 4.87e+00 b.1.10.2 70790 1lqwA 183 5.14e+00 d.167.1.1 74210 1spiA 358 5.19e+00 1frpA e.7.1.1 42939 1g86A 142 5.26e+00 b.29.1.3 70161 2ghsA 326 5.43e+00 1lcl 142 5.45e+00 1lcl b.29.1.3 24216 2pcfB 250 5.74e+00 1hcz i.4.1.1 45911 1orvA 728 6.40e+00 b.70.3.1,c.69.1.24 87354,87355 2fbeA 201 7.30e+00 1hdkA 141 7.39e+00 b.29.1.3 65807 1iu1A 146 7.79e+00 b.1.10.2 71428 1bglA 1023 8.04e+00 1bglA b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 22097,22098,23734,24358,28857 1y43B 173 8.93e+00 1ciy 590 9.09e+00 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1kn9A 249 9.34e+00 b.87.1.2 68699 1gywA 128 9.45e+00 b.1.10.2 70791 1b12A 248 9.81e+00 1b12A b.87.1.2 28388 2a6zA 222 1.07e+01 1e2wA 251 1.13e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1ax0 239 1.18e+01 1led b.29.1.1 24042 2bh9A 489 1.22e+01 1xe0A 114 1.24e+01 1cv8 174 1.25e+01 1cv8 d.3.1.1 37089 1hcz 252 1.27e+01 1hcz b.2.6.1,b.84.2.2 22464,28250 1oygA 447 1.31e+01 b.67.2.2 93726 1n5nA 180 1.33e+01 d.167.1.1 85336 1z0sA 278 1.49e+01 2erfA 209 1.51e+01 2def 147 1.57e+01 1bs4A d.167.1.1 42305 1n9pA 207 1.57e+01 b.1.18.16 80343 1gttA 429 1.57e+01 d.177.1.1,d.177.1.1 70529,70530 1s7jA 262 1.61e+01 d.21.1.2 98647 2cfuA 658 1.66e+01 1viwB 198 1.68e+01 1led b.29.1.1 24170 1t0qC 86 1.68e+01 d.15.12.1 106222 1ats 386 1.72e+01 1ba1 c.55.1.1,c.55.1.1 33423,33424 1d2sA 170 1.75e+01 1d2sA b.29.1.4 24221 1wzoA 246 1.76e+01 1gzcA 239 1.77e+01 b.29.1.1 70803 2a74A 643 1.88e+01 1z5bA 469 1.90e+01 1yua 122 1.91e+01 1yua g.41.3.3,g.41.3.3 45210,45211 1f5fA 205 1.95e+01 1d2sA b.29.1.4 24222 1j1tA 233 2.04e+01 b.29.1.18 90771 1w4tA 299 2.06e+01 1suwA 249 2.15e+01 e.52.1.1 106027 1dceA 567 2.16e+01 1dceA a.118.6.1,b.7.4.1,c.10.2.2 19191,23218,30867 1oacA 727 2.16e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24390,38007,38008,40003 1bs4A 168 2.19e+01 1bs4A d.167.1.1 42287 1d6zA 727 2.21e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24394,38015,38016,40007 1s14A 194 2.26e+01 d.122.1.2 98329 1bsjA 168 2.27e+01 1bs4A d.167.1.1 42302 1ca1 370 2.38e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1ap8 213 2.41e+01 1ap8 d.86.1.1 40151 2amhA 207 2.46e+01 1khxA 227 2.51e+01 b.26.1.1 68631 1s2kA 206 2.71e+01 b.29.1.20 98389 1dykA 394 2.71e+01 1dykA b.29.1.4,b.29.1.4 24223,24224 3mddA 385 2.75e+01 3mdeA a.29.3.1,e.6.1.1 16592,42853 1dhkB 223 2.76e+01 1led b.29.1.1 24157 1xeoA 168 2.79e+01 3mdeA 385 2.82e+01 3mdeA a.29.3.1,e.6.1.1 16594,42855 1a02N 301 2.86e+01 1a02N b.1.18.1,b.2.5.3 21923,22440 2a6hD 1524 2.99e+01 1i7oA 429 3.04e+01 1i7oA d.177.1.1,d.177.1.1 61893,61894 1w24A 182 3.14e+01 1spuB 727 3.34e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24399,38025,38026,40012 1azdA 237 3.34e+01 1nls b.29.1.1 24020 1k42A 168 3.35e+01 b.18.1.14 72032 1qupA 222 3.40e+01 1qupA b.1.8.1,d.58.17.1 22301,39352 1knvA 293 3.41e+01 c.52.1.7 68707 1lj5A 379 3.55e+01 e.1.1.1 73928 1qqsA 174 3.57e+01 1nglA b.60.1.1 27143 1voqa 90 3.57e+01 1l4sA 112 3.57e+01 d.204.1.1 77693 1vl2A 421 3.80e+01 c.26.2.1,d.210.1.1 108708,108709 1y6hA 177 3.84e+01 1z2wA 192 3.87e+01 1omrA 201 3.90e+01 a.39.1.5 93349 1rec 201 3.92e+01 1rec a.39.1.5 17326 1pz7A 204 3.94e+01 b.29.1.4 95405 1icjA 168 3.99e+01 1bs4A d.167.1.1 42284 1nc5A 373 4.05e+01 a.102.1.6 85548 1noa 113 4.21e+01 2mcm b.1.7.1 22208 1g2aA 168 4.37e+01 d.167.1.1 65109 1def 147 4.42e+01 1bs4A d.167.1.1 42306 1ba1 386 4.48e+01 1ba1 c.55.1.1,c.55.1.1 33387,33388 1ksgB 152 4.65e+01 b.1.18.8 72913 1kdkA 177 4.66e+01 b.29.1.4 72351 1e8xA 961 4.75e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19148,23183,37631,41711 1kbpA 432 4.87e+01 4kbpA b.1.12.1,d.159.1.1 22349,42068 2cr4A 126 4.93e+01 2ab5A 269 4.93e+01 1umzA 278 5.02e+01 b.29.1.2 99639 1d3bA 75 5.09e+01 1d3bA b.38.1.1 24798 1kcfA 258 5.11e+01 a.140.2.1,c.55.3.7 68434,68435 1p7hL 286 5.12e+01 b.1.18.1,b.2.5.3 94271,94272 2qwc 388 5.14e+01 2qwc b.68.1.1 27547 1cknA 330 5.15e+01 1ckmA b.40.4.6,d.142.2.3 25360,41587 1atr 386 5.16e+01 1ba1 c.55.1.1,c.55.1.1 33421,33422 1n3gA 113 5.35e+01 d.204.1.1 79962 1b0tA 106 5.35e+01 1a6l d.58.1.2 38965 2f4lA 297 5.40e+01 1ckmA 330 5.43e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 1a6l 106 5.44e+01 1a6l d.58.1.2 38966 2a84A 300 5.44e+01 1led 243 5.58e+01 1led b.29.1.1 24039 1ds6B 180 5.60e+01 1rhoA b.1.18.8 21898 1c4rA 182 5.60e+01 1c4rA b.29.1.4 24229 3ait 74 5.65e+01 1hoe b.5.1.1 22835 1iznB 277 5.69e+01 e.43.1.2 83848 1hka 158 5.69e+01 1hka d.58.30.1 39433 2ncm 99 5.71e+01 2ncm b.1.1.4 21703 1or0B 528 5.71e+01 1feuA 206 5.89e+01 1feuA b.53.1.1 59801 1wgoA 123 5.98e+01 1cid 177 6.17e+01 1cid b.1.1.1,b.1.1.3 19740,21679 1c9uA 454 6.22e+01 1c9uA b.68.2.1 27623 1frpA 335 6.27e+01 1frpA e.7.1.1 42875 1gya 105 6.35e+01 1qa9A b.1.1.1 19745 1grj 158 6.39e+01 1grj a.2.1.1,d.26.1.2 15691,38433 1kskA 234 6.44e+01 d.66.1.5,d.265.1.3 72920,90389 1xfoA 357 6.50e+01 1rdzA 337 6.51e+01 1frpA e.7.1.1 42882 1qi9A 556 6.53e+01 1qhbA a.111.1.2 19053 1avbA 226 6.55e+01 1led b.29.1.1 24158 1dlc 584 6.56e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23719,27976,43391 1gr3A 160 6.59e+01 b.22.1.1 65476 1bupA 386 6.62e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1e0tA 470 6.63e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1cruA 454 6.65e+01 1c9uA b.68.2.1 27617 1cxlA 686 6.81e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21829,22498,27736,28723 1o7eA 276 6.82e+01 e.3.1.1 92622 1f8eA 388 6.84e+01 2qwc b.68.1.1 59694 1t5rA 284 6.88e+01 f.6.1.1 106465 1hl8A 449 6.99e+01 b.71.1.3,c.1.8.11 90646,90647 1kay 381 7.01e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1lr0A 129 7.04e+01 d.212.1.1 74213 1kshB 152 7.04e+01 b.1.18.8 72915 1btkB 169 7.05e+01 1btkA b.55.1.1 26960 2d0oA 610 7.11e+01 1rhoA 145 7.12e+01 1rhoA b.1.18.8 21899 1x71A 178 7.18e+01 1cr1A 296 7.20e+01 1cr1A c.37.1.11 32286 1nbwA 607 7.31e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 3nn9 388 7.40e+01 2qwc b.68.1.1 27566 1x89A 178 7.43e+01 1mmiA 366 7.45e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1d3cA 686 7.48e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21827,22496,27734,28721 1y7bA 542 7.56e+01 1fsoA 139 7.61e+01 1rhoA b.1.18.8 60007 1mu5A 471 7.78e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1cr0A 296 7.80e+01 1cr1A c.37.1.11 32287 1l1nA 183 7.80e+01 b.47.1.4 73476 1hzgA 295 7.87e+01 1hzgA d.194.1.1 61436 1a4eA 488 8.07e+01 1cf9A e.5.1.1 42806 1v61A 132 8.10e+01 b.55.1.1 108389 1pamA 686 8.11e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21846,22515,27753,28740 1tnrA 144 8.19e+01 2tnfA b.22.1.1 23867 1nglA 179 8.23e+01 1nglA b.60.1.1 27146 1ot1A 686 8.29e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 87392,87393,87394,87395 2bf6A 449 8.29e+01 1bqnB 430 8.30e+01 1rthA e.8.1.2 43065 2fcbA 173 8.31e+01 2fcbA b.1.1.4,b.1.1.4 21781,21782 1qz8A 113 8.31e+01 b.140.1.1 96619 1qbiA 454 8.34e+01 1c9uA b.68.2.1 27619 1fdd 106 8.49e+01 1a6l d.58.1.2 38960 1t9xA 1049 8.50e+01 2a6vA 226 8.66e+01 1c5kA 439 8.71e+01 1crzA b.68.4.1,c.51.2.1 27630,33212 1fd2 106 8.75e+01 1a6l d.58.1.2 38962 1h30A 422 8.75e+01 b.29.1.4,b.29.1.4 76604,76605 1qwdA 177 8.80e+01 b.60.1.1 96471