# List of top-scoring protein chains for t2k-100-30-n_sep-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 1elqA 390 2.29e-01 1elqA c.67.1.3 34436 1eluA 390 2.57e-01 1elqA c.67.1.3 34434 1eluB 390 2.60e-01 1elqA c.67.1.3 34435 1ogiA 303 3.48e-01 b.43.4.2,c.25.1.1 92914,92915 2bsaA 303 3.60e-01 1qh0A 295 4.03e-01 b.43.4.2,c.25.1.1 68891,68892 1w34A 304 4.39e-01 1que 303 4.61e-01 1fnc b.43.4.2,c.25.1.1 25647,31537 1go2A 304 4.65e-01 b.43.4.2,c.25.1.1 76243,76244 2bmwA 304 4.85e-01 2chgA 226 4.92e-01 1b2rA 304 6.73e-01 1fnc b.43.4.2,c.25.1.1 25648,31538 1j5sA 463 1.12e+00 c.1.9.8 71580 1yb2A 275 1.19e+00 1o5hA 214 1.69e+00 a.191.1.1 92497 1fnb 314 1.89e+00 1fnc b.43.4.2,c.25.1.1 25628,31518 1x11A 172 2.06e+00 1x11A b.55.1.2 26985 1bx1A 314 2.24e+00 1fnc b.43.4.2,c.25.1.1 25629,31519 1jztA 246 2.41e+00 c.104.1.1 63319 1b7aA 186 2.54e+00 1a44 b.17.1.1 23705 1fnd 314 2.55e+00 1fnc b.43.4.2,c.25.1.1 25626,31516 1a44 185 2.66e+00 1a44 b.17.1.1 23704 1ytlA 174 2.71e+00 1fnc 314 2.84e+00 1fnc b.43.4.2,c.25.1.1 25627,31517 1tqyB 415 2.95e+00 c.95.1.1,c.95.1.1 107247,107248 1cs0B 382 3.08e+00 1c3oB c.8.3.1,c.23.16.1 30740,31417 1e79A 510 3.12e+00 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 1bmfA 510 3.61e+00 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18281,26446,32326 2azpA 318 3.63e+00 1yt3A 375 3.63e+00 1c3oB 382 3.88e+00 1c3oB c.8.3.1,c.23.16.1 30744,31421 1h8eA 510 4.70e+00 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 2b5oA 402 4.78e+00 1jb9A 316 5.24e+00 1fnc b.43.4.2,c.25.1.1 62840,62841 1aoxA 203 5.57e+00 1aoxA c.62.1.1 34151 2gw2A 198 5.69e+00 1c30B 382 5.69e+00 c.8.3.1,c.23.16.1 30736,31413 2ck3A 510 5.76e+00 1v7pC 200 5.77e+00 c.62.1.1 108408 1rhcA 330 5.86e+00 c.1.16.3 97468 1zelA 298 5.96e+00 1behA 187 5.97e+00 1a44 b.17.1.1 23700 2cw8A 537 6.63e+00 1a9xB 379 7.17e+00 1c3oB c.8.3.1,c.23.16.1 30732,31409 1ro7A 259 7.21e+00 c.130.1.1 97667 2fibA 269 7.32e+00 3fib d.171.1.1 42457 1qg0A 308 7.39e+00 1fnc b.43.4.2,c.25.1.1 25639,31529 3fib 249 7.63e+00 3fib d.171.1.1 42455 1j3aA 142 8.11e+00 c.21.1.1 77070 2bijA 305 8.42e+00 1fib 269 8.43e+00 3fib d.171.1.1 42456 1oaoC 729 9.18e+00 e.26.1.3 86746 1gydB 315 9.93e+00 b.67.2.1 70751 1dfaA 454 1.00e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28375,40575,40576 1yb5A 351 1.03e+01 1sfnA 246 1.03e+01 b.82.1.11 105496 1a8p 258 1.05e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1yoaA 159 1.09e+01 1aqcA 172 1.10e+01 1x11A b.55.1.2 26983 1u8zA 168 1.12e+01 2bv5A 282 1.12e+01 1zd9A 188 1.13e+01 2fi9A 128 1.15e+01 1gyhA 318 1.15e+01 b.67.2.1 70757 5abp 306 1.25e+01 8abp c.93.1.1 35651 1ivhA 394 1.26e+01 3mdeA a.29.3.1,e.6.1.1 16608,42869 2a9kA 187 1.27e+01 8abp 306 1.28e+01 8abp c.93.1.1 35647 1sk4A 163 1.29e+01 d.118.1.1 105664 1v1aA 309 1.29e+01 c.72.1.1 100249 1vdeA 454 1.33e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28378,40581,40582 1tc1A 220 1.34e+01 1tc1A c.61.1.1 34083 1abe 306 1.38e+01 8abp c.93.1.1 35648 1i0lA 221 1.39e+01 c.61.1.1 71096 2a35A 215 1.40e+01 1gtdA 85 1.42e+01 d.284.1.1 76344 2b29A 123 1.46e+01 1wgbA 159 1.67e+01 2b3gA 123 1.71e+01 1w2fA 276 1.72e+01 d.143.1.3 109125 1bap 306 1.76e+01 8abp c.93.1.1 35654 1ecfA 504 1.77e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1necA 216 1.87e+01 1vfrA d.90.1.1 40249 2fbhA 146 1.93e+01 1iqpA 327 1.96e+01 a.80.1.1,c.37.1.20 62649,62650 1e5pA 151 2.07e+01 1bj7 b.60.1.1 59272 1ecfB 504 2.10e+01 1ecfB c.61.1.1,d.153.1.1 34054,41821 1icrA 217 2.13e+01 1vfrA d.90.1.1 62274 1nkiA 135 2.13e+01 d.32.1.2 91941 1d6mA 653 2.15e+01 1d6mA e.10.1.1 43248 1qpxA 218 2.18e+01 1qpxA b.1.11.1,b.7.2.1 22318,23200 1a85A 158 2.21e+01 1hfc d.92.1.11 40355 1i7dA 659 2.26e+01 1d6mA e.10.1.1 61886 1um8A 376 2.28e+01 c.37.1.20 99580 1bzsA 165 2.28e+01 1hfc d.92.1.11 40348 1lqpA 135 2.40e+01 d.32.1.2 78151 1skyB 502 2.48e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18313,26478,32358 1e2wA 251 2.48e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1sgvA 316 2.55e+01 b.122.1.1,d.265.1.2 98858,98859 1i85A 110 2.57e+01 1i85A b.1.1.1 61946 1mjgM 729 2.66e+01 e.26.1.3 79204 1z98A 281 2.73e+01 1v8gA 329 2.75e+01 a.46.2.1,c.27.1.1 100505,100506 1a8l 226 2.78e+01 1a8l c.47.1.2,c.47.1.2 32777,32778 1i76A 163 2.82e+01 1hfc d.92.1.11 61877 1a76 326 2.88e+01 1a76 a.60.7.1,c.120.1.2 18091,33361 1hfc 169 2.88e+01 1hfc d.92.1.11 40335 2bm3A 166 2.92e+01 1ojrA 274 2.93e+01 c.74.1.1 93147 1c2pA 576 3.03e+01 1quvA e.8.1.4 43117 1ykiA 217 3.06e+01 1edoA 244 3.10e+01 1ybvA c.2.1.2 29896 1yckA 175 3.14e+01 1xccA 220 3.18e+01 1mho 88 3.18e+01 1b4cA a.39.1.2 17171 1l9xA 315 3.23e+01 c.23.16.1 73762 1tx4B 178 3.27e+01 1ctqA c.37.1.8 32045 1nxiA 132 3.35e+01 d.58.47.1 86381 2b25A 336 3.39e+01 2a0mA 316 3.45e+01 2apqA 139 3.46e+01 2cvjA 180 3.48e+01 1eaf 243 3.80e+01 1eaf c.43.1.1 32617 1gzcA 239 3.86e+01 b.29.1.1 70803 1t0hB 224 3.87e+01 c.37.1.1 106208 1v7lA 163 3.87e+01 1fdpA 235 3.88e+01 5ptp b.47.1.2 26322 1kmqA 184 3.98e+01 c.37.1.8 84412 1zsqA 528 4.02e+01 1y51A 88 4.04e+01 1m1fA 110 4.08e+01 b.34.6.2 78401 2fh5A 185 4.13e+01 1udh 244 4.19e+01 3eugA c.18.1.1 31015 1xahA 354 4.20e+01 1wmhA 89 4.32e+01 1uarA 285 4.35e+01 c.46.1.2,c.46.1.2 107762,107763 1mh1 186 4.40e+01 1eesA c.37.1.8 32002 2f8aA 208 4.43e+01 1w3oA 216 4.46e+01 1twjA 84 4.47e+01 d.284.1.1 107407 1l8nA 679 4.49e+01 c.1.8.10,d.92.2.2 84564,84565 1udg 244 4.50e+01 3eugA c.18.1.1 31016 1u0jA 267 4.50e+01 c.37.1.20 107546 1r5lA 262 4.60e+01 a.5.3.1,c.13.1.1 97099,97100 2bo4A 397 4.64e+01 1a2xA 159 4.67e+01 1ncx a.39.1.5 17251 1gt7A 274 4.69e+01 c.74.1.1 70398 1fqtA 112 4.76e+01 1fqtA b.33.1.1 24441 2fpqA 444 4.77e+01 1mwvA 714 4.78e+01 a.93.1.3,a.93.1.3 85161,85162 1ax0 239 4.80e+01 1led b.29.1.1 24042 1earA 147 4.82e+01 b.107.1.1,d.58.38.1 64875,64876 1r5tA 142 4.82e+01 c.97.1.1 104812 1cfpA 92 4.92e+01 1b4cA a.39.1.2 17172 1dzaA 129 4.94e+01 7rsa d.5.1.1 37275 1yyaA 250 4.97e+01 1t71A 281 5.02e+01 1lam 484 5.12e+01 1lam c.50.1.1,c.56.5.3 33166,33829 1v2yA 105 5.12e+01 d.15.1.1 100275 1lw3A 657 5.19e+01 b.55.1.8,c.45.1.3 91152,91153 2b59A 187 5.29e+01 1qg3A 195 5.36e+01 1qg3A b.1.2.1,b.1.2.1 21993,21994 1t4aA 84 5.37e+01 d.284.1.1 106404 1dpb 243 5.38e+01 1eaf c.43.1.1 32618 1gp1A 198 5.41e+01 1gp1A c.47.1.10 33059 1jkmA 358 5.45e+01 1jkmA c.69.1.2 34633 1ujxA 119 5.52e+01 b.26.1.2 99473 1j27A 102 5.53e+01 d.58.50.1 90778 7rsa 124 5.62e+01 7rsa d.5.1.1 37165 2fhqA 141 5.66e+01 2h00A 254 5.67e+01 2fj6A 82 5.70e+01 7ahlA 293 5.77e+01 7ahlA f.6.1.1 43812 2axyA 73 5.78e+01 2bl0C 142 5.80e+01 1idsA 207 5.81e+01 1avmA a.2.11.1,d.44.1.1 15722,38730 1ywmA 200 5.84e+01 1of5A 221 5.88e+01 d.17.4.2 86933 2kauB 106 5.93e+01 1ubpB b.85.3.1 28328 1ooeA 236 5.96e+01 c.2.1.2 87196 1b25A 619 5.96e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1se0A 116 6.01e+01 g.52.1.1 98814 1eb0A 147 6.02e+01 b.107.1.1,d.58.38.1 64890,64891 1cx8A 639 6.06e+01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17782,30763,33851 1e1hA 287 6.11e+01 d.92.1.7 83167 1k0hA 117 6.21e+01 b.106.1.2 71975 1afrA 345 6.21e+01 1afrA a.25.1.2 16805 1q32A 544 6.22e+01 d.136.1.3,d.136.1.3 104507,104508 2liv 344 6.22e+01 2liv c.93.1.1 35708 2gnoA 305 6.26e+01 1fwcB 106 6.34e+01 1ubpB b.85.3.1 28324 1wn2A 121 6.35e+01 2a6aA 218 6.38e+01 1ip9A 85 6.44e+01 1ip9A d.15.2.2 62638 1dy5A 124 6.59e+01 7rsa d.5.1.1 37163 1zwwA 256 6.60e+01 1euhA 475 6.69e+01 1euhA c.82.1.1 35369 1jqaA 370 6.73e+01 e.22.1.2 67085 1sefA 274 6.75e+01 b.82.1.11 105452 2f2lA 167 6.76e+01 1e9iA 431 6.78e+01 c.1.11.1,d.54.1.1 64818,64819 1ejxB 101 6.79e+01 b.85.3.1 83183 1sesA 421 6.80e+01 1sesA a.2.7.1,d.104.1.1 15710,40710 1rnd 124 7.00e+01 7rsa d.5.1.1 37178 1jvwA 167 7.11e+01 d.26.1.1 71907 1kum 108 7.13e+01 1kum b.3.1.1 22525 2adzA 178 7.14e+01 1ve3A 227 7.16e+01 1go4A 205 7.21e+01 d.135.1.1 70292 1bllE 488 7.21e+01 1lam c.50.1.1,c.56.5.3 33170,33833 2cvzA 289 7.28e+01 1bncB 449 7.30e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28237,31644,41489 1bt4A 362 7.39e+01 1bjnA c.67.1.4 34468 1xg5A 279 7.39e+01 1w3uA 362 7.41e+01 1qppA 218 7.42e+01 1qpxA b.1.11.1,b.7.2.1 22320,23202 1ejrB 101 7.50e+01 1ubpB b.85.3.1 28320 1nbwA 607 7.50e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1l9gA 192 7.51e+01 c.18.1.2 84568 2evwX 166 7.66e+01 1j08A 226 7.73e+01 c.47.1.2,c.47.1.2 83855,83856 2occA 514 7.83e+01 2occA f.24.1.1 43518 1x1oA 286 7.85e+01 1h6hA 143 7.86e+01 d.189.1.1 65681 1jy1A 464 7.87e+01 d.136.1.3,d.136.1.3 67438,67439 1cvrA 435 7.87e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 1dp7P 76 7.91e+01 1dp7P a.4.5.20 16159 1whxA 111 7.91e+01 1qi6A 475 7.93e+01 1euhA c.82.1.1 35373 1fzqA 181 8.09e+01 1hurA c.37.1.8 32060 1a5p 124 8.15e+01 7rsa d.5.1.1 37201 1lap 488 8.15e+01 1lam c.50.1.1,c.56.5.3 33171,33834 1qd1A 325 8.18e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1k87A 669 8.18e+01 a.176.1.1,c.1.23.2 77286,77287 1lxjA 104 8.21e+01 d.58.48.1 84736 1usmA 80 8.28e+01 d.74.1.1 99876 1uj2A 252 8.31e+01 c.37.1.6 99452 1ffkO 154 8.36e+01 1ffkO d.55.1.1 38899 1ydmA 187 8.42e+01 1w23A 360 8.44e+01 1sffA 426 8.49e+01 c.67.1.4 105482 1b93B 152 8.49e+01 1b93A c.24.1.2 31508 1tx4A 198 8.53e+01 1tx4A a.116.1.1 19098 1gcf 109 8.60e+01 1cto b.1.2.1 22053 2bcoA 350 8.61e+01 1ri6A 343 8.68e+01 b.69.11.1 97503 1qc5A 192 8.73e+01 1aoxA c.62.1.1 34147 1bwwA 109 8.74e+01 8fabA b.1.1.1 20518 1hqz9 141 8.78e+01 1ewkA 490 8.91e+01 1ewkA c.93.1.1 35712 1yjmA 110 8.92e+01 1jq5A 370 9.00e+01 e.22.1.2 67084