# 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 1regX 122 4.32e-01 1regX d.58.27.1 39406 1t3gA 159 5.98e-01 1n40A 396 6.70e-01 a.104.1.1 79977 1c8oA 300 1.08e+00 1c8oA e.1.1.1 42677 1qlpA 394 1.17e+00 1ovaA e.1.1.1 42628 1wmaA 276 1.38e+00 9apiA 347 1.51e+00 1ovaA e.1.1.1 42630 1f0cA 305 1.67e+00 1c8oA e.1.1.1 42676 1mpyA 307 1.75e+00 1mpyA d.32.1.3,d.32.1.3 38508,38509 1hu4A 288 2.32e+00 1hu4A 1n5dA 288 2.32e+00 c.2.1.2 80030 1m93B 245 2.33e+00 2b9dA 52 3.10e+00 1gln 468 3.13e+00 1gln a.97.1.1,c.26.1.1 18752,31588 2ci1A 275 3.17e+00 1wiwA 290 3.40e+00 2f9dA 125 3.79e+00 1coaI 64 4.18e+00 2sniI d.40.1.1 38574 1s7zA 117 4.41e+00 a.159.3.1 98715 1us8A 147 4.58e+00 c.37.1.12 99859 1k7kA 221 4.83e+00 c.51.4.1 72104 1vjoA 393 4.83e+00 c.67.1.3 100827 1tqhA 247 4.87e+00 c.69.1.29 107225 1f8vA 355 5.49e+00 2bbvA b.121.4.4 23329 1j77A 209 5.86e+00 1j77A a.132.1.2 62674 1ypcI 64 5.88e+00 2sniI d.40.1.1 38570 1jae 471 6.02e+00 1smd b.71.1.1,c.1.8.1 27773,28760 1u5mA 73 6.21e+00 1kq6A 141 6.40e+00 d.189.1.1 91020 1fshA 105 7.60e+00 1fshA a.4.5.31 60006 2achA 360 7.65e+00 1c8oA e.1.1.1 42626 1o7kA 131 8.08e+00 d.189.1.1 81144 1xaoA 121 8.24e+00 1o57A 291 8.51e+00 a.4.5.40,c.61.1.1 92483,92484 2d4pA 141 9.06e+00 2a0fA 310 9.55e+00 1keiA 316 9.76e+00 d.92.1.2 77349 2d83A 363 9.96e+00 2bd0A 244 1.03e+01 8tlnE 316 1.05e+01 1hyt d.92.1.2 59075 1hyt 316 1.06e+01 1hyt d.92.1.2 59005 1tqyA 424 1.06e+01 c.95.1.1,c.95.1.1 107245,107246 2tmnE 316 1.07e+01 1hyt d.92.1.2 59055 1tzbA 302 1.08e+01 c.80.1.1 107470 1x9iA 302 1.08e+01 6tmnE 316 1.09e+01 1hyt d.92.1.2 59071 1jg7A 351 1.15e+01 1c3jA c.87.1.1 62945 1as4A 341 1.18e+01 1sek e.1.1.1 42623 1v76A 96 1.18e+01 1xqaA 113 1.19e+01 1eza 259 1.19e+01 1zymA a.60.10.1,c.8.1.2 18113,30708 1b2jA 54 1.20e+01 1rb9 g.41.5.1 45231 1b2oA 54 1.20e+01 1rb9 g.41.5.1 45233 1r1hA 696 1.23e+01 d.92.1.4 104756 1wdyA 285 1.27e+01 1l0wA 580 1.27e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1b13A 54 1.28e+01 1rb9 g.41.5.1 45227 1bd8 156 1.29e+01 1bd8 d.211.1.1 19157 2bgu 351 1.30e+01 1c3jA c.87.1.1 35460 12asA 330 1.31e+01 12asA d.104.1.1 40783 1ws6A 171 1.33e+01 1c3jA 351 1.34e+01 1c3jA c.87.1.1 35459 1gd5A 130 1.34e+01 1gd5A d.189.1.1 60439 1r1dA 247 1.35e+01 c.69.1.29 96813 1k3eA 156 1.40e+01 d.198.1.1 68103 1iro 54 1.40e+01 1rb9 g.41.5.1 45223 1udxA 416 1.41e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1g59A 468 1.42e+01 a.97.1.1,c.26.1.1 60257,60258 1yr1A 119 1.44e+01 2bwnA 401 1.45e+01 1ve3A 227 1.46e+01 1msk 331 1.52e+01 1msk d.173.1.1 42495 1t77A 414 1.52e+01 1pbyA 489 1.54e+01 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 2c36A 285 1.55e+01 1jixA 351 1.55e+01 1c3jA c.87.1.1 63081 1vl8A 267 1.56e+01 c.2.1.2 108733 1aroL 151 1.59e+01 1lba d.118.1.1 41063 1yk4A 52 1.60e+01 2cw5A 255 1.64e+01 2fjbA 643 1.65e+01 1jnrA 643 1.65e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1ash 150 1.66e+01 1ash a.1.1.2 15622 4rxn 54 1.67e+01 1rb9 g.41.5.1 45226 5rxn 54 1.67e+01 1rb9 g.41.5.1 45225 1yzxA 226 1.70e+01 1m3sA 186 1.71e+01 c.80.1.3 78573 1g61A 228 1.75e+01 1g61A d.126.1.1 41126 1zymA 258 1.81e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 1v65A 64 1.83e+01 a.212.1.1 108393 1db2A 377 1.84e+01 1sek e.1.1.1 42672 1ob8A 135 1.88e+01 1wdtA 665 1.89e+01 1k8kB 394 1.94e+01 c.55.1.1 68307 1l4aE 79 1.97e+01 h.1.15.1 73563 1o26A 232 1.99e+01 d.207.1.1 86566 1ocsA 162 1.99e+01 d.189.1.1 92776 1ijyA 130 2.02e+01 1ijxA a.141.1.1 62517 1evlA 401 2.04e+01 1qf6A c.51.1.1,d.104.1.1 33202,40751 1gxrA 337 2.05e+01 b.69.4.1 70722 2ghrA 302 2.11e+01 1y0gA 191 2.12e+01 1brfA 53 2.13e+01 1rb9 g.41.5.1 45236 1bq8A 54 2.14e+01 1rb9 g.41.5.1 45237 1bq9A 54 2.14e+01 1rb9 g.41.5.1 45238 1ciqA 40 2.23e+01 2sniI d.40.1.1 38576 1a7cA 379 2.26e+01 1sek e.1.1.1 42660 1ht6A 405 2.27e+01 b.71.1.1,c.1.8.1 83629,83630 1mtpA 323 2.32e+01 e.1.1.1 85107 1htwA 158 2.45e+01 c.37.1.18 71083 1lj5A 379 2.45e+01 e.1.1.1 73928 1lw6I 64 2.45e+01 d.40.1.1 74294 1jmoA 480 2.46e+01 e.1.1.1 77138 1pieA 419 2.46e+01 d.14.1.5,d.58.26.7 94706,94707 1sep 261 2.46e+01 1oaa c.2.1.2 29830 1lba 146 2.47e+01 1lba d.118.1.1 41062 2bbvA 363 2.48e+01 2bbvA b.121.4.4 23323 1oaa 259 2.50e+01 1oaa c.2.1.2 29829 2aaa 484 2.50e+01 7taa b.71.1.1,c.1.8.1 27777,28764 3blm 257 2.52e+01 1btl e.3.1.1 42709 1ooeA 236 2.53e+01 c.2.1.2 87196 1jjuA 489 2.57e+01 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 1ihoA 283 2.57e+01 1ihoA c.26.1.4 62390 2g03A 194 2.58e+01 1jmaA 290 2.66e+01 b.1.1.1 63177 1yj7A 171 2.70e+01 1v7rA 186 2.71e+01 c.51.4.1 100482 2a1iA 146 2.73e+01 2bgkA 278 2.73e+01 1jfbA 404 2.74e+01 a.104.1.1 66624 1f24A 402 2.78e+01 1rom a.104.1.1 18953 1se4 239 2.78e+01 3seb b.40.2.2,d.15.6.1 25187,37776 1pioA 257 2.79e+01 1btl e.3.1.1 42719 1a8p 258 2.80e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1y7mA 164 2.85e+01 2bbvC 363 2.85e+01 2bbvA b.121.4.4 23325 1zo0A 126 2.89e+01 1f2tA 149 2.90e+01 1f2tA c.37.1.12 32373 1ufyA 122 2.91e+01 d.79.1.2 88489 1o4uA 285 2.92e+01 c.1.17.1,d.41.2.1 86624,86625 1hfoA 113 2.93e+01 d.80.1.3 61006 1mkeA 152 2.98e+01 b.55.1.4 79231 2cs3A 93 2.99e+01 1ukuA 102 2.99e+01 d.58.5.2 99533 1ksfX 758 3.01e+01 a.174.1.1,c.37.1.20,c.37.1.20 77522,77523,77524 1v5aA 28 3.01e+01 2bh1A 250 3.09e+01 2fb0A 94 3.10e+01 1id0A 152 3.12e+01 d.122.1.3 66111 1k7yA 577 3.14e+01 a.46.1.1,c.23.6.1,d.173.1.1 68272,68273,68274 1rvkA 382 3.18e+01 c.1.11.2,d.54.1.1 97928,97929 1m1cA 680 3.29e+01 e.42.1.1 78395 3seb 238 3.35e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1d5mC 239 3.37e+01 3seb b.40.2.2,d.15.6.1 25185,37774 1g26A 31 3.40e+01 1g26A g.3.16.1 44381 2f6sA 201 3.40e+01 1b5qA 472 3.44e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 1acmA 310 3.44e+01 3csuA c.78.1.1,c.78.1.1 35180,35181 1b37A 472 3.46e+01 1b37B c.3.1.2,d.16.1.5 30389,37953 1rdg 53 3.46e+01 1rb9 g.41.5.1 45221 1oz9A 150 3.48e+01 d.92.1.15 93808 1b37B 472 3.52e+01 1b37B c.3.1.2,d.16.1.5 30390,37954 1vkyA 347 3.59e+01 e.53.1.1 108696 7taa 478 3.61e+01 7taa b.71.1.1,c.1.8.1 27778,28765 1e3tA 203 3.66e+01 1d4oA c.31.1.4 31749 1dmtA 696 3.68e+01 1dmtA d.92.1.4 40296 1odeA 122 3.70e+01 d.79.1.2 86846 2sniI 83 3.71e+01 2sniI d.40.1.1 38573 2bi7A 384 3.76e+01 1ab5A 125 3.78e+01 3chy c.23.1.1 31056 1brmA 367 3.79e+01 1brmA c.2.1.3,d.81.1.1 30030,39945 1ugpA 203 3.87e+01 d.149.1.1 107831 1uzcA 71 3.89e+01 a.159.2.1 100222 1ireA 204 3.90e+01 d.149.1.1 76769 2ew8A 249 3.92e+01 1nzaA 103 3.96e+01 d.58.5.2 86444 1xc3A 302 4.02e+01 1ek8A 185 4.02e+01 1ek8A d.67.3.1 59444 1innA 166 4.14e+01 1j98A d.185.1.2 62608 1hc7A 477 4.14e+01 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 1ha9A 34 4.15e+01 1ha9A g.3.2.1 60876 2madH 373 4.17e+01 2bbkH b.69.2.1 27639 1vjeA 166 4.17e+01 d.185.1.2 100807 6rxn 46 4.17e+01 1rb9 g.41.5.1 45222 1bkcI 256 4.21e+01 1bkcA d.92.1.10 40334 1bmv2 374 4.26e+01 1bmv2 1ovqA 138 4.26e+01 c.55.3.8 93607 1v54K 56 4.31e+01 f.23.5.1 100332 2occK 56 4.31e+01 2occK f.23.5.1 43525 1kllA 130 4.32e+01 d.32.1.2 72720 1s1fA 406 4.40e+01 1lea 84 4.44e+01 1lea a.4.5.2 16085 1i5gA 144 4.52e+01 1ewxA c.47.1.10 61784 1o8xA 146 4.56e+01 c.47.1.10 86681 1q7zA 566 4.59e+01 c.1.21.2,c.1.26.1 96090,96091 2aq5A 402 4.60e+01 1bkcA 255 4.77e+01 1bkcA d.92.1.10 40331 1skz 119 4.80e+01 1skz g.3.15.1,g.3.15.1 44366,44367 1fl9A 161 4.85e+01 c.37.1.18 70137 1o6jA 150 4.89e+01 c.47.1.10 81089 1e5mA 416 4.91e+01 1dd8A c.95.1.1,c.95.1.1 58973,58974 2end 138 4.97e+01 2end a.18.1.1 16400 1nh1A 330 5.07e+01 e.45.1.1 91871 2bduA 297 5.08e+01 1bm8 99 5.09e+01 1bm8 d.34.1.1 38528 1ass 159 5.10e+01 1a6dA c.8.5.2 30818 1vkrA 125 5.11e+01 c.44.2.1 108689 1fe0A 68 5.14e+01 1cc8A d.58.17.1 39345 1xrtA 467 5.18e+01 2gaxA 135 5.24e+01 1qk8A 146 5.25e+01 1ewxA c.47.1.10 33061 2ddfA 257 5.34e+01 1alq 266 5.34e+01 1btl e.3.1.1 42707 1wxaA 116 5.36e+01 1kr4A 125 5.43e+01 d.58.5.2 72889 1chmA 401 5.47e+01 1chmA c.55.2.1,d.127.1.1 33545,41142 1wr7A 41 5.50e+01 1lxdA 100 5.50e+01 1lfdA d.15.1.5 37624 1ej2A 181 5.53e+01 1f9aA c.26.1.3 59414 1ka8A 100 5.53e+01 a.4.5.20 72241 1gqiA 708 5.58e+01 c.1.8.10,d.92.2.2 76279,76280 1zxcA 263 5.58e+01 1nrzA 164 5.58e+01 c.38.1.1 86131 1v5mA 136 5.59e+01 b.55.1.1 108379 1j5pA 253 5.59e+01 d.81.1.3,c.2.1.3 71577,83092 1lb2B 84 5.60e+01 a.60.3.1 77871 8rxnA 52 5.62e+01 1rb9 g.41.5.1 45215 2g2dA 193 5.63e+01 1rb9 53 5.65e+01 1rb9 g.41.5.1 45214 1eno 312 5.69e+01 1enp c.2.1.2 29905 3csuA 310 5.73e+01 3csuA c.78.1.1,c.78.1.1 35094,35095 1u7iA 136 5.80e+01 d.32.1.7 107724 1wimA 94 5.80e+01 2azeC 46 5.81e+01 8atcA 310 5.81e+01 3csuA c.78.1.1,c.78.1.1 35132,35133 1wlqC 201 5.82e+01 a.4.5.52 109400 1c0aA 585 5.82e+01 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1j6rA 214 5.83e+01 d.173.1.2 71598 1sfxA 109 5.84e+01 a.4.5.50 105505 2c07A 285 5.85e+01 1f02T 66 5.87e+01 1f02T j.67.1.1 46360 1hybA 181 5.87e+01 1f9aA c.26.1.3 61399 1m4vA 204 5.88e+01 b.40.2.2,d.15.6.1 74459,74460 1vig 71 5.88e+01 1vih d.51.1.1 38806 1asx 159 5.93e+01 1a6dA c.8.5.2 30821 1ufzA 83 5.93e+01 a.5.9.1 107821 1iseA 185 5.93e+01 d.67.3.1 90691 1ghpA 258 5.95e+01 1btl e.3.1.1 60520 1du3A 130 5.98e+01 1d4vA g.24.1.1,g.24.1.1,g.24.1.1 44927,44928,44929 1f2vA 219 6.01e+01 1f2vA c.23.17.1 59627 1sek 378 6.01e+01 1sek e.1.1.1 42675 1tqzA 133 6.05e+01 1sc3A 178 6.09e+01 c.17.1.1 105416 1bkcE 256 6.09e+01 1bkcA d.92.1.10 40333 1xodA 118 6.10e+01 1yovA 537 6.12e+01 1to2I 64 6.15e+01 1nw1A 429 6.19e+01 d.144.1.8 86286 1j2zA 270 6.23e+01 b.81.1.1 90805 1z57A 339 6.23e+01 1axh 37 6.25e+01 1axh g.3.6.2 44109 1i8xA 30 6.27e+01 g.3.16.1 71132 1ewxA 146 6.29e+01 1ewxA c.47.1.10 33062 1y7bA 542 6.31e+01 2d09A 407 6.31e+01 1vasA 137 6.34e+01 2end a.18.1.1 16404 1wu4A 396 6.38e+01 1m8jA 181 6.41e+01 c.26.1.3 84875 1gab 53 6.42e+01 1gab a.8.1.2 16353 1xqoA 256 6.44e+01 1eni 138 6.46e+01 2end a.18.1.1 16403 1qh8B 519 6.48e+01 1qguB c.92.2.3 35634 6cts 433 6.48e+01 1csh a.103.1.1 18891 1csc 433 6.48e+01 1csh a.103.1.1 18886 1rwxA 178 6.50e+01 1enj 138 6.55e+01 2end a.18.1.1 16401 1qguB 519 6.58e+01 1qguB c.92.2.3 35626 1r4wA 226 6.62e+01 c.47.1.13 97050 3ssi 113 6.68e+01 3ssi d.84.1.1 40032 1b7gO 340 6.69e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907 1y51A 88 6.69e+01 1ycdA 243 6.72e+01 1zbyA 294 6.75e+01 1r5pA 108 6.75e+01 c.47.1.15 97101 1ekxA 311 6.77e+01 3csuA c.78.1.1,c.78.1.1 35088,35089 1wwjA 105 6.79e+01 1fx2A 235 6.81e+01 1fx2A d.58.29.1 39430 1csh 435 6.86e+01 1csh a.103.1.1 18880 2c30A 321 6.89e+01 1amz 435 6.90e+01 1csh a.103.1.1 18884 1s2oA 244 6.93e+01 1unlD 208 6.94e+01 1k3tA 359 6.95e+01 c.2.1.3,d.81.1.1 72022,72023 2d0eA 407 6.97e+01 1z53A 294 6.99e+01 1al6 437 6.99e+01 1csh a.103.1.1 18885 1cbf 285 7.03e+01 1cbf c.90.1.1 35587 2csgA 424 7.04e+01 1w6tA 444 7.05e+01 2furA 209 7.07e+01 1gcqC 70 7.08e+01 1gcpA b.34.2.1 60436 1tbmA 326 7.09e+01 a.211.1.2 106744 1g2rA 100 7.09e+01 1g2rA d.192.1.1 60231 1fvaA 217 7.12e+01 1fvaA d.58.28.1 39409 1enk 138 7.14e+01 2end a.18.1.1 16402 2bbhA 269 7.15e+01 1blxA 326 7.18e+01 1hcl d.144.1.7 41596 1hmcB 148 7.19e+01 1hmcB a.26.1.2 16868 1jj2M 186 7.20e+01 1ffkK c.55.4.1 63098 830cA 168 7.21e+01 1ck7A d.92.1.11 40400 1d7oA 297 7.23e+01 1enp c.2.1.2 29907 1foaA 348 7.26e+01 1foaA c.68.1.10 59929 1jdrA 294 7.28e+01 1ryc a.93.1.1 62908 1g9uA 454 7.30e+01 c.10.2.6 65172 1b8gA 429 7.32e+01 1b8gA c.67.1.4 34499 1xa3A 437 7.34e+01 1n4qB 377 7.34e+01 a.102.4.3 91636 1h3gA 601 7.40e+01 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 2eutA 294 7.43e+01 1mpgA 282 7.46e+01 1mpgA a.96.1.3,d.129.1.2 18747,41296 1fexA 59 7.50e+01 a.4.1.3 59803 1atu 374 7.53e+01 1ovaA e.1.1.1 42636 1bpwA 503 7.58e+01 1bpwA c.82.1.1 35365 2f8lA 344 7.59e+01 1knvA 293 7.61e+01 c.52.1.7 68707 1c28A 135 7.61e+01 1c28A b.22.1.1 23857 1cis 66 7.62e+01 2sniI k.1.1.1 46375 2bv5A 282 7.64e+01 1m7yA 435 7.65e+01 c.67.1.4 78761 1yoyA 175 7.70e+01 1aie 31 7.73e+01 1aie a.53.1.1 17829 1jl5A 454 7.74e+01 c.10.2.6 66830 1cxvA 164 7.75e+01 1ck7A d.92.1.11 40404 1mkrA 294 7.76e+01 a.93.1.1 84997 1b8pA 329 7.77e+01 1bmdA c.2.1.5,d.162.1.1 30147,42114 1uouA 474 7.77e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 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