# List of top-scoring protein chains for t06-100-40-40-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 1dk0A 188 9.22e-02 1b2vA d.35.1.1 38530 1cy5A 97 1.10e-01 1cy5A a.77.1.3 18430 1ox0A 430 1.26e-01 c.95.1.1,c.95.1.1 87495,87496 1g6hA 257 2.36e-01 1gajA c.37.1.12 60318 1dvoA 152 4.78e-01 1dvoA a.136.1.1 19623 1a7s 221 5.43e-01 1a7s b.47.1.2 26284 1jk7A 323 5.63e-01 1auiA d.159.1.3 63144 1i58A 189 6.03e-01 1b3qA d.122.1.3 61773 1hlvA 131 6.39e-01 a.4.1.7,a.4.1.7 65854,65855 1h3nA 878 7.11e-01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1eejA 216 7.28e-01 1eejA c.47.1.9,d.17.3.1 33057,38071 1cxqA 162 7.35e-01 1cxqA c.55.3.2 33621 1m65A 245 1.27e+00 c.6.3.1 84847 1cpcA 162 1.28e+00 1cpcA a.1.1.3 15643 1dc1A 323 1.28e+00 1dc1A c.52.1.11 33321 1elvA 333 1.38e+00 5ptp b.47.1.2,g.18.1.1 59454,59455 1g2cB 43 1.39e+00 1g2cB 1m7yA 435 1.41e+00 c.67.1.4 78761 1cnzA 363 1.57e+00 1cnzA c.77.1.1 35061 1wmaA 276 1.80e+00 1ctj 89 1.89e+00 1ctj a.3.1.1 15798 1qwgA 251 2.01e+00 c.1.27.1 96473 1epwA 1290 2.08e+00 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1h8dH 260 2.10e+00 5ptp 1gdvA 85 2.34e+00 1ctj a.3.1.1 60458 1sgwA 214 2.51e+00 c.37.1.12 105541 1gtmA 419 2.52e+00 1hwyA c.2.1.7,c.58.1.1 30223,33871 1kid 203 2.89e+00 1derA c.8.5.1 30771 1orvA 728 2.91e+00 b.70.3.1,c.69.1.24 87354,87355 1jalA 363 2.99e+00 c.37.1.8,d.15.10.2 84138,84139 1axn 323 3.26e+00 1avc a.65.1.1 18149 1e3oC 160 3.83e+00 1au7A a.4.1.1,a.35.1.1 59197,59198 1h6gA 256 3.91e+00 1h6gA a.24.9.1,a.24.9.1 60669,60670 1ls9A 91 3.98e+00 a.3.1.1 78177 1mk0A 97 4.13e+00 d.226.1.1 79216 1fiqC 763 5.07e+00 1fiqC d.41.1.1,d.133.1.1 38588,41418 1mzbA 136 5.08e+00 a.4.5.42 91497 1i4wA 353 5.20e+00 c.66.1.24 66028 1dpe 507 5.36e+00 1dpe c.94.1.1 35799 1oxjA 173 5.40e+00 a.60.1.2,a.118.1.13 87517,87518 1jb9A 316 5.42e+00 1fnc b.43.4.2,c.25.1.1 62840,62841 1k5nA 276 5.51e+00 b.1.1.2,d.19.1.1 77266,77267 1qy1A 174 6.22e+00 b.60.1.1 96568 1jdlA 121 6.23e+00 a.3.1.1 66557 1i4fA 275 6.23e+00 1agdA b.1.1.2,d.19.1.1 61687,61688 1psrA 100 6.46e+00 1psrA a.39.1.2 17180 1o8bA 219 6.59e+00 c.124.1.4,d.58.40.1 81180,81181 1b8aA 438 6.60e+00 1b8aA b.40.4.1,d.104.1.1 25244,40765 1ddjA 247 6.65e+00 5ptp b.47.1.2 26362 1b8dA 164 6.69e+00 1cpcA a.1.1.3 15665 1e4mM 501 7.52e+00 1e70M c.1.8.4 59226 1j1jA 240 7.63e+00 a.118.16.1 90762 1huw 166 7.70e+00 1huw a.26.1.1 16831 1jsuC 84 7.79e+00 1jsuC j.55.1.1 46339 1fexA 59 7.90e+00 a.4.1.3 59803 1vjvA 415 8.05e+00 d.3.1.9 108632 1fnd 314 8.47e+00 1fnc b.43.4.2,c.25.1.1 25626,31516 1dp3A 55 9.14e+00 1dp3A a.55.1.2 59128 1bx1A 314 9.80e+00 1fnc b.43.4.2,c.25.1.1 25629,31519 1gcvB 136 9.91e+00 1cg5B a.1.1.2 15589 1jeoA 180 9.93e+00 c.80.1.3 66611 1bd3A 243 1.06e+01 1bd3A c.61.1.1 34098 1j30A 144 1.06e+01 a.25.1.1 90806 1xx1A 285 1.07e+01 1ccwB 483 1.08e+01 1cb7B c.1.19.2 29646 1h0hB 214 1.11e+01 d.58.1.5 76437 1kq3A 376 1.11e+01 e.22.1.2 68790 1g8pA 350 1.12e+01 1g8pA c.37.1.20 60376 1m1nB 522 1.15e+01 c.92.2.3 78418 1jboA 162 1.15e+01 a.1.1.3 84150 2bjfA 329 1.16e+01 1a0jA 223 1.20e+01 5ptp b.47.1.2 26002 1whzA 70 1.22e+01 1q7zA 566 1.29e+01 c.1.21.2,c.1.26.1 96090,96091 1oywA 523 1.33e+01 a.4.5.43,c.37.1.19,c.37.1.19 93760,93761,93762 1woqA 267 1.35e+01 c.55.1.10,c.55.1.10 109462,109463 1it2A 146 1.38e+01 a.1.1.2 66365 1jmtA 104 1.39e+01 d.58.7.3 63180 1g8kA 825 1.46e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 1hj8A 222 1.48e+01 b.47.1.2 65844 1js3A 486 1.48e+01 c.67.1.6 67215 1a4pA 96 1.48e+01 1b4cA a.39.1.2 17176 1hdoA 206 1.54e+01 1he2A c.2.1.2 60965 1h3lA 87 1.56e+01 a.177.1.1 76639 1aj8A 371 1.56e+01 1aj8A a.103.1.1 18900 1u60A 310 1.58e+01 e.3.1.2 107692 1hm6A 346 1.60e+01 1avc a.65.1.1 18147 1jg1A 235 1.61e+01 c.66.1.7 66661 1a8s 273 1.61e+01 1brt c.69.1.12 34710 1dpo 223 1.61e+01 5ptp b.47.1.2 25975 1ji6A 589 1.64e+01 b.18.1.3,b.77.2.1,f.1.3.1 63066,63067,63068 1fcyA 236 1.65e+01 2lbd a.123.1.1 19282 1bqk 124 1.70e+01 1bqk b.6.1.1 22889 1e12A 253 1.70e+01 1c3wA f.13.1.1 43428 1rhcA 330 1.72e+01 c.1.16.3 97468 1i8oA 114 1.72e+01 1ycc a.3.1.1 61979 2sak 121 1.83e+01 2sak d.15.5.1 37711 1nn5A 215 1.84e+01 c.37.1.1 85892 1h8eD 482 1.87e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 1mnaA 298 1.87e+01 c.69.1.22 79322 1dcs 311 1.88e+01 1dcs b.82.2.1 28124 1o2dA 371 1.89e+01 e.22.1.2 86591 1byrA 155 1.91e+01 1byrA d.136.1.1 41450 1bn7A 294 1.92e+01 1bn6A c.69.1.8 34677 1hr6A 475 1.93e+01 1hr6A d.185.1.1,d.185.1.1 61164,61165 1jflA 228 1.94e+01 c.78.2.1,c.78.2.1 71656,71657 1d3vA 323 1.97e+01 1d3vA c.42.1.1 32559 1a3aA 148 2.04e+01 1a3aA d.112.1.1 40917 1ispA 181 2.05e+01 c.69.1.18 76778 1c1yB 77 2.07e+01 1c1yB d.15.1.5 37618 1exrA 148 2.23e+01 1cll a.39.1.5 17299 1fs1B 141 2.28e+01 1vcbB a.157.1.1,d.42.1.1 19252,38664 1dw0A 112 2.29e+01 1dw0A a.3.1.1 15911 1h3gA 601 2.29e+01 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1b3uA 588 2.32e+01 1b3uA a.118.1.2 19135 1g2hA 61 2.34e+01 1g2hA a.4.1.12 60224 1vicA 262 2.41e+01 c.68.1.13 100756 1d2fA 390 2.41e+01 1d2fA c.67.1.3 34411 1f45B 197 2.42e+01 1f45B a.26.1.1 59642 1z57A 339 2.43e+01 1uehA 253 2.48e+01 c.101.1.1 99259 1fxlA 167 2.50e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1f0lA 535 2.51e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22377,42239,43382 1wb4A 297 2.51e+01 1vljA 407 2.53e+01 e.22.1.2 108832 1dpgA 485 2.53e+01 1dpgA c.2.1.3,d.81.1.5 30074,39989 1uzbA 516 2.54e+01 c.82.1.1 100220 1ex2A 189 2.59e+01 1ex2A c.51.4.2 33225 1gvzA 237 2.60e+01 b.47.1.2 76360 1pyoB 105 2.61e+01 1bif 469 2.63e+01 1bif c.37.1.7,c.60.1.4 31961,34003 1f7zA 233 2.66e+01 5ptp b.47.1.2 59681 1dxrC 336 2.70e+01 6prcC a.138.1.2 19670 1d3gA 367 2.71e+01 1d3gA c.1.4.1 28600 1wmqA 147 2.75e+01 1a62 130 2.76e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 2gfgA 193 2.89e+01 1uj8A 77 2.90e+01 1jfzA 154 2.93e+01 a.149.1.1 66655 1mtyB 384 2.95e+01 1mtyB a.25.1.2 16740 1i3dA 146 2.95e+01 a.1.1.2 61587 1j2zA 270 2.98e+01 b.81.1.1 90805 1i4uA 181 3.00e+01 b.60.1.1 61732 1gu9A 177 3.01e+01 a.152.1.1 65540 1dlyA 164 3.10e+01 1dlyA a.1.1.1 14983 1vmgA 95 3.10e+01 1jihA 531 3.11e+01 d.240.1.1,e.8.1.7 90374,90375 1o1yA 239 3.19e+01 c.23.16.1 86554 1hekA 131 3.20e+01 a.61.1.5 65818 1gc0A 398 3.32e+01 c.67.1.3 70168 1jjfA 268 3.33e+01 c.69.1.2 66765 1fl1A 230 3.42e+01 1at3A b.57.1.1 27023 1pvmA 184 3.45e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1rzhH 260 3.52e+01 b.41.1.1,f.23.10.1 98162,98163 1uptB 60 3.54e+01 a.193.1.1 99768 1jakA 512 3.55e+01 c.1.8.6,d.92.2.1 66472,66473 1xocA 520 3.58e+01 1k04A 162 3.62e+01 a.24.14.1 67904 1d9uA 154 3.63e+01 1am7A d.2.1.4 59111 1fi4A 416 3.70e+01 1fi4A d.14.1.5,d.58.26.2 59847,59848 1floA 422 3.71e+01 1floA a.60.9.1,d.163.1.1 18106,42166 1r6jA 82 3.74e+01 b.36.1.1 97151 1uuqA 440 3.80e+01 c.1.8.3 100015 1dq3A 454 3.82e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1f7cA 231 3.90e+01 1f7cA a.116.1.1 19107 1pmi 440 4.02e+01 1pmi b.82.1.3 28114 1eg2A 319 4.04e+01 1eg2A c.66.1.11 34249 1eo1A 124 4.09e+01 1eo1A c.55.5.1 33739 1hw1A 239 4.09e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1mba 147 4.13e+01 2fal a.1.1.2 15149 1vlaA 150 4.18e+01 d.227.1.2 108735 1ash 150 4.19e+01 1ash a.1.1.2 15622 1h4wA 224 4.22e+01 b.47.1.2 65622 1y9iA 178 4.24e+01 1qe3A 489 4.27e+01 2bce c.69.1.1 34630 1f1eA 154 4.37e+01 a.22.1.2 64927 1b65A 375 4.38e+01 1b65A d.154.1.1 42020 1g8mA 593 4.38e+01 1g8mA c.24.1.3,c.97.2.1 60371,60372 1h6pA 203 4.41e+01 a.146.1.1 60690 1j09A 468 4.49e+01 a.97.1.1,c.26.1.1 77025,77026 1tukA 67 4.50e+01 1ecmA 109 4.50e+01 1ecmA a.130.1.1 19492 1khcA 147 4.51e+01 b.34.9.2 68608 1am2 199 4.55e+01 1am2 b.86.1.2 28381 1ccr 112 4.56e+01 1ycc a.3.1.1 15877 1m15A 357 4.60e+01 a.83.1.1,d.128.1.2 78368,78369 1kv7A 488 4.61e+01 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 1uwcA 261 4.64e+01 c.69.1.17 100101 1ars 396 4.65e+01 1ajsA c.67.1.1 34287 1dzkA 157 4.66e+01 1obpA b.60.1.1 27096 1elkA 157 4.70e+01 1dvpA a.118.9.2 19217 2bhuA 602 4.74e+01 1kveA 63 4.81e+01 1kveA d.70.1.2 39590 1irdA 141 4.81e+01 a.1.1.2 66286 1jboB 172 4.82e+01 a.1.1.3 84151 1eaxA 241 4.82e+01 b.47.1.2 64889 1eg3A 261 4.83e+01 1eg3A a.39.1.7,a.39.1.7,b.72.1.1 17376,17377,27805 1gk8A 475 4.89e+01 c.1.14.1,d.58.9.1 65234,65235 1vr5A 547 4.94e+01 1xg5A 279 4.97e+01 1sc3A 178 5.01e+01 c.17.1.1 105416 1e85A 127 5.03e+01 1bbhA a.24.3.2 16549 1p4cA 380 5.07e+01 c.1.4.1 94100 1oygA 447 5.09e+01 b.67.2.2 93726 1qb7A 236 5.14e+01 1qb7A c.61.1.1 34087 1ejxA 100 5.18e+01 d.8.1.1 83182 1dmgA 225 5.23e+01 1dmgA c.22.1.1 31036 1dxeA 256 5.24e+01 1dxeA c.1.12.5 29310 1xpcA 248 5.26e+01 1vr8A 142 5.35e+01 1qazA 351 5.39e+01 1qazA a.102.3.1 18848 1geeA 261 5.49e+01 c.2.1.2 90509 1ga8A 311 5.50e+01 1ga8A c.68.1.4 34516 2nlrA 234 5.54e+01 2nlrA b.29.1.11 24344 1h72C 296 5.55e+01 d.14.1.5,d.58.26.1 60712,60713 1tn6B 437 5.57e+01 1gteA 1025 5.57e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70440,70441,70442,70443,70444 1a8o 70 5.58e+01 1a8o a.28.3.1 16953 1pp0A 199 5.58e+01 d.103.1.1 104211 1ra0A 430 5.59e+01 1ockA 412 5.69e+01 c.117.1.1 86802 1nfp 228 5.77e+01 1nfp c.1.16.2 29555 1eg5A 384 5.79e+01 1ecxA c.67.1.3 34429 1gu2A 124 5.83e+01 a.3.1.1 76348 1cz4A 185 5.85e+01 1cz4A b.52.2.3,d.31.1.1 26934,38468 1dbxA 158 5.87e+01 1dbuA d.116.1.1 40928 1ogiA 303 5.88e+01 b.43.4.2,c.25.1.1 92914,92915 1bxyA 60 5.94e+01 1bxyA d.59.1.1 39525 1senA 164 5.94e+01 c.47.1.1 105465 1ukfA 188 5.99e+01 d.3.1.10 99488 1p4oA 322 6.05e+01 d.144.1.7 87775 1izcA 339 6.11e+01 c.1.12.5 83838 1dqaA 467 6.17e+01 1dqaA d.58.20.1,d.179.1.1 39364,42585 1fiuA 286 6.18e+01 1fiuA c.52.1.10 33317 1o54A 277 6.25e+01 c.66.1.13 92482 1in4A 334 6.27e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 1vpdA 299 6.33e+01 1fonA 240 6.34e+01 5ptp b.47.1.2 26231 1ji1A 637 6.34e+01 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 1d5rA 324 6.39e+01 1d5rA b.7.1.1,c.45.1.1 23181,32697 1fg7A 356 6.53e+01 1gewA c.67.1.1 59819 1g3qA 237 6.53e+01 1hyqA c.37.1.10 60237 1iyrA 111 6.55e+01 a.164.1.1 76973 1lc5A 364 6.64e+01 c.67.1.1 73827 1q4uA 151 6.72e+01 d.38.1.5 95828 1dg9A 157 6.75e+01 1dg9A c.44.1.1 32637 2f42A 179 6.79e+01 2pvbA 107 6.80e+01 1a75A a.39.1.4 17205 1wdpA 495 6.81e+01 1fipA 98 6.82e+01 1fipA a.4.1.12 18980 1e5kA 201 6.84e+01 1fr9A c.68.1.8 34578 1h6kA 757 6.84e+01 a.118.1.14,a.118.1.14,a.118.1.14 60675,60676,60677 1ne9A 335 6.93e+01 d.108.1.4,d.108.1.4 91839,91840 1hq1A 105 6.94e+01 1dulA a.36.1.1 17120 1lfwA 470 6.95e+01 c.56.5.4,d.58.19.1 77942,77943 1p9aG 290 7.00e+01 c.10.2.7 87990 1bjt 793 7.02e+01 1bjt e.11.1.1 43249 1fobA 334 7.04e+01 c.1.8.3 83255 1k55A 246 7.05e+01 e.3.1.1 68156 1hj9A 226 7.07e+01 b.47.1.2 65845 1w27A 714 7.08e+01 1uufA 369 7.08e+01 b.35.1.2,c.2.1.1 100006,100007 1aisA 182 7.09e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1ggzA 148 7.19e+01 a.39.1.5 70176 2arcA 164 7.24e+01 2arcA b.82.4.1 28148 1ddgA 374 7.25e+01 1amoA b.43.4.1,c.25.1.4 25671,31559 1jbeA 128 7.28e+01 3chy c.23.1.1 62845 1oohA 126 7.33e+01 a.39.2.1 93383 1em2A 229 7.34e+01 1em2A d.129.3.2 41321 4ubpA 101 7.40e+01 1ubpA d.8.1.1 37352 1f20A 435 7.50e+01 b.43.4.1,c.25.1.4 64932,64933 1fcqA 350 7.50e+01 c.1.8.9 65006 1atlA 202 7.51e+01 1atlA d.92.1.9 40322 1kkoA 413 7.54e+01 c.1.11.2,d.54.1.1 68675,68676 1d0qA 103 7.57e+01 1d0qA g.41.3.2 45208 1h9hE 223 7.58e+01 b.47.1.2 103810 1dmhA 311 7.62e+01 1dmhA b.3.6.1 22633 1ro7A 259 7.65e+01 c.130.1.1 97667 1b9oA 123 7.68e+01 3lzt d.2.1.2 36597 1su8A 636 7.76e+01 e.26.1.2 98999 1hw7A 255 7.76e+01 1i7fA d.193.1.1 61297 1pu6A 218 7.79e+01 a.96.1.5 95123 1zceA 155 7.81e+01 1ihgA 370 7.84e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 1eljA 381 7.86e+01 4mbp c.94.1.1 35791 1ny1A 240 7.89e+01 c.6.2.3 86395 1oqvA 192 7.91e+01 d.24.1.2 87320 1vkiA 181 7.92e+01 d.116.1.1 108664 1y80A 210 7.95e+01 1j0hA 588 8.02e+01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 1jwqA 179 8.08e+01 c.56.5.6 90921 1jvbA 347 8.09e+01 b.35.1.2,c.2.1.1 77181,77182 1j75A 67 8.11e+01 a.4.5.19 62673 1rkqA 282 8.12e+01 c.108.1.10 97621 1aba 87 8.14e+01 1aba c.47.1.1 32760 1f46A 140 8.14e+01 1f46A d.129.4.1 59643 1in6A 334 8.19e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 1gvkB 240 8.19e+01 b.47.1.2 70610 1s9uA 207 8.29e+01 a.184.1.1 105390 1ji7A 89 8.32e+01 a.60.1.1 71682 1bw0A 416 8.33e+01 1bw0A c.67.1.1 34385 1lst 239 8.36e+01 1lst c.94.1.1 35755 1hn4A 131 8.45e+01 a.133.1.2 65893 7a3hA 303 8.59e+01 7a3hA c.1.8.3 28817 1jl2A 156 8.61e+01 c.55.3.1 66822 1j98A 157 8.70e+01 1j98A d.185.1.2 62755 1cg5A 141 8.76e+01 1abwA a.1.1.2 15406 1jkoC 52 8.82e+01 a.4.1.2 66809 1kzfA 230 8.99e+01 d.108.1.3 73354