# 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 1gmxA 108 3.53e-01 c.46.1.3 65355 1gn0A 108 3.96e-01 c.46.1.3 65358 1qapA 296 4.48e-01 1qpoA c.1.17.1 29559 d.41.2.1 38595 1i58A 189 1.34e+00 1b3qA d.122.1.3 61773 1dbtA 239 1.62e+00 1dbtA c.1.2.3 28539 2rslA 140 1.63e+00 2rslA c.53.1.1 33345 1v95A 130 1.65e+00 1vj7A 393 2.11e+00 unknown_sccs -1265 unknown_sccs -9814 1eljA 381 2.13e+00 4mbp c.94.1.1 35791 1bjaA 95 2.76e+00 1bjaA a.4.5.9 16122 1fzrA 138 2.78e+00 1fzrA c.52.1.17 33336 1m0dA 138 2.88e+00 c.52.1.17 74354 1uae 419 3.04e+00 1uae d.68.2.2 39574 1q0rA 298 3.07e+00 unknown_sccs -8330 1vid 221 3.09e+00 1vid c.66.1.1 34178 1qopA 268 3.16e+00 2tysA c.1.2.4 28570 1ejdA 419 3.18e+00 1uae d.68.2.2 39576 1fd8A 73 3.27e+00 1cc8A d.58.17.1 59770 2tysA 268 3.28e+00 2tysA c.1.2.4 28572 1qz9A 416 3.42e+00 c.67.1.3 -8180 1h1dA 221 3.57e+00 c.66.1.1 83452 1geqA 248 3.59e+00 2tysA c.1.2.4 28589 1ao8 162 3.62e+00 3dfr c.71.1.1 34883 1odkA 235 3.83e+00 c.56.2.1 86863 1bksA 268 3.85e+00 2tysA c.1.2.4 28585 1dcfA 136 3.96e+00 1dcfA c.23.1.2 31124 1im5A 180 3.99e+00 unknown_sccs 66211 1jmmA 377 4.10e+00 b.30.6.1 71749 1eblA 317 4.19e+00 1hn9A c.95.1.1 35973 c.95.1.1 35974 1giqA 413 4.21e+00 d.166.1.1 76224 d.166.1.1 76225 1g6sA 427 4.23e+00 1eps d.68.2.2 39584 1hn9A 317 4.25e+00 1hn9A c.95.1.1 35977 c.95.1.1 35978 1b7gO 340 4.53e+00 1b7gO c.2.1.3 29992 d.81.1.1 39907 1hnjA 317 4.53e+00 1hn9A c.95.1.1 35969 c.95.1.1 35970 1mo2A 294 4.64e+00 c.69.1.22 79331 1g73C 121 4.71e+00 1g3fA g.52.1.1 45375 1eblB 317 4.78e+00 1hn9A c.95.1.1 35975 c.95.1.1 35976 1cc8A 73 4.85e+00 1cc8A d.58.17.1 39343 1sheA 103 5.45e+00 1euhA 475 5.54e+00 1euhA c.82.1.1 35369 1o4uA 285 5.59e+00 c.1.17.1 86624 d.41.2.1 86625 1gln 468 5.64e+00 1gln a.97.1.1 18752 c.26.1.1 31588 1m6dA 214 5.68e+00 d.3.1.1 84849 1c9qA 117 5.69e+00 1c9qA g.52.1.1 45377 1iba 101 5.92e+00 1iba d.95.1.1 40567 1eps 427 6.12e+00 1eps d.68.2.2 39586 1ub3A 220 6.22e+00 c.1.10.1 88395 1omhA 293 7.73e+00 unknown_sccs -10527 1brt 277 7.73e+00 1brt c.69.1.12 34699 1l5zA 155 7.84e+00 c.23.1.1 77722 1qi6A 475 7.87e+00 1euhA c.82.1.1 35373 1qtqA 553 7.88e+00 1gtrA b.53.1.2 26940 c.26.1.1 31579 1b3qA 379 7.90e+00 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1broA 277 7.93e+00 1brt c.69.1.12 34700 1qniA 581 8.04e+00 1qniA b.6.1.4 23042 b.69.3.1 27642 2scuB 388 8.37e+00 2scuB c.23.4.1 31141 d.142.1.4 41562 1f89A 291 8.44e+00 d.160.1.1 64988 1li5A 461 8.60e+00 a.27.1.1 73912 c.26.1.1 73913 1aj6 219 8.62e+00 1aj6 d.122.1.2 41106 1uiuA 502 8.64e+00 c.94.1.1 -8674 1atiA 505 8.65e+00 1atiA c.51.1.1 33196 d.104.1.1 40745 1o6eA 235 9.00e+00 b.57.1.1 81083 1fg7A 356 9.19e+00 1gewA c.67.1.1 59819 1dv2A 452 9.29e+00 1bncA b.84.2.1 28238 c.30.1.1 31645 d.142.1.2 41490 1ojxA 263 9.47e+00 c.1.10.1 -5445 1qavA 90 9.53e+00 1qauA b.36.1.1 24777 1e0tA 470 9.73e+00 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1kgsA 225 1.01e+01 a.4.6.1 68596 c.23.1.1 68597 1jbwA 428 1.05e+01 c.59.1.2 62860 c.72.2.2 62861 1n99A 166 1.06e+01 b.36.1.1 85459 b.36.1.1 85460 1upaA 573 1.06e+01 c.31.1.3 -6745 c.36.1.5 -6903 c.36.1.9 -6943 1gtrA 553 1.07e+01 1gtrA b.53.1.2 26939 c.26.1.1 31578 1j1yA 136 1.08e+01 d.38.1.5 -9671 1e4cP 215 1.08e+01 2fua c.74.1.1 34969 1eu8A 409 1.11e+01 1eu8A c.94.1.1 59502 1ui0A 205 1.12e+01 c.18.1.2 -6328 1fgs 428 1.13e+01 1fgs c.59.1.2 33959 c.72.2.2 34962 1ygs 234 1.15e+01 1ygs b.26.1.1 23907 1fl1A 230 1.17e+01 1at3A b.57.1.1 27023 1fua 215 1.21e+01 2fua c.74.1.1 34973 1l2uA 245 1.21e+01 c.1.2.3 73516 1gmeA 151 1.27e+01 b.15.1.1 65305 2fua 215 1.28e+01 2fua c.74.1.1 34977 1atiB 505 1.29e+01 1atiA c.51.1.1 33197 d.104.1.1 40746 1g57A 217 1.30e+01 1g57A d.115.1.2 60253 1nrzA 164 1.33e+01 c.38.1.1 86131 2wsyA 268 1.34e+01 2tysA c.1.2.4 28588 7reqB 637 1.35e+01 1reqB c.1.19.1 29617 c.23.6.1 31244 1i1sA 96 1.41e+01 1bjaA a.4.5.9 16124 1rf6A 427 1.41e+01 d.68.2.2 -10314 1ixkA 315 1.42e+01 unknown_sccs -8099 1rvgA 305 1.43e+01 c.1.10.2 -5500 1mrzA 293 1.44e+01 b.43.5.1 -4048 c.26.1.3 -6616 1oyc 400 1.47e+01 1oyc c.1.4.1 28603 1oya 400 1.48e+01 1oyc c.1.4.1 28604 1g59A 468 1.51e+01 a.97.1.1 60257 c.26.1.1 60258 1akeA 214 1.51e+01 1zin c.37.1.1 31905 g.41.2.1 45185 1se0A 116 1.51e+01 g.52.1.1 -12841 1qgdA 662 1.54e+01 c.36.1.6 88367 c.36.1.10 88368 c.48.1.1 88369 1rxwA 336 1.57e+01 a.60.7.1 -1041 c.120.1.2 -6680 1erv 105 1.58e+01 1erv c.47.1.1 32743 1gx1A 160 1.59e+01 d.79.5.1 70675 1i50A 1733 1.62e+01 e.29.1.2 61754 1a53 247 1.63e+01 1a53 c.1.2.4 28564 1eudB 396 1.64e+01 2scuB c.23.4.1 31150 d.142.1.4 41571 1oi7A 288 1.66e+01 c.2.1.8 87049 c.23.4.1 87050 1v5xA 203 1.66e+01 c.1.2.4 -5169 1uf3A 228 1.67e+01 unknown_sccs -11463 1ky3A 182 1.69e+01 c.37.1.8 73193 1lfpA 249 1.72e+01 e.39.1.1 73885 1obdA 306 1.72e+01 d.143.1.1 86767 1j09A 468 1.74e+01 a.97.1.1 77025 c.26.1.1 77026 1jy8A 159 1.76e+01 d.79.5.1 67452 1ti6B 274 1.77e+01 1l6rA 227 1.77e+01 c.108.1.10 77768 1cqzA 554 1.77e+01 1cr6B c.108.1.2 43339 c.69.1.11 34689 1eo1A 124 1.79e+01 1eo1A c.55.5.1 33739 1qd1A 325 1.79e+01 1qd1A d.58.34.1 39493 d.58.34.1 39494 1ufkA 254 1.80e+01 unknown_sccs -8103 1cv8 174 1.80e+01 1cv8 d.3.1.1 37089 1rpjA 288 1.83e+01 2dri c.93.1.1 35656 1xtcA 194 1.84e+01 1lt3A d.166.1.1 42259 1r13A 148 1.85e+01 d.169.1.1 -11646 h.1.1.1 -12895 1scuA 288 1.85e+01 2scuA c.2.1.8 30307 c.23.4.1 31135 1kmmA 424 1.88e+01 1adjA c.51.1.1 33174 d.104.1.1 40723 1juk 248 1.89e+01 1a53 c.1.2.4 28567 1xyzA 347 1.91e+01 1taxA c.1.8.3 28804 1ra9 159 1.91e+01 1vdrA c.71.1.1 34820 1e5dA 402 1.93e+01 1e5dA c.23.5.1 31208 d.157.1.3 42061 1s5dA 240 1.94e+01 d.166.1.1 -11563 1d2eA 397 1.94e+01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1gxuA 91 1.95e+01 d.58.10.1 76378 1eb0A 147 1.97e+01 b.107.1.1 64890 d.58.38.1 64891 6dfr 159 1.98e+01 1vdrA c.71.1.1 34874 1nm2A 317 1.98e+01 c.19.1.1 80654 d.58.23.1 80655 1j1hA 144 1.99e+01 b.111.1.1 77056 1t5yA 190 2.00e+01 1qkkA 155 2.01e+01 1dbwA c.23.1.1 31104 1hkhA 279 2.02e+01 c.69.1.12 -8342 1jm1A 204 2.02e+01 b.33.1.1 71745 1s4qA 228 2.03e+01 c.37.1.1 -6975 1mdiA 105 2.03e+01 1erv c.47.1.1 32755 1igs 248 2.04e+01 1a53 c.1.2.4 28565 1amuA 563 2.05e+01 1amuA e.23.1.1 43351 1g2iA 166 2.06e+01 1g2iA c.23.16.2 31438 1tif 78 2.06e+01 1tif d.15.8.1 37836 1b9mA 265 2.08e+01 1b9mA a.4.5.8 16118 b.40.6.2 58938 b.40.6.2 58939 1i1qB 192 2.09e+01 1qdlB c.23.16.1 61544 1i8dA 213 2.09e+01 b.43.4.3 61953 b.43.4.3 61954 1eucB 396 2.12e+01 2scuB c.23.4.1 31149 d.142.1.4 41570 1uu1A 335 2.12e+01 c.67.1.1 -8146 1qamA 244 2.14e+01 2ercA c.66.1.24 34220 1ble 163 2.15e+01 1ble c.38.1.1 32475 1i16 130 2.15e+01 1i16 b.36.1.2 24787 1dcuA 357 2.15e+01 1frpA e.7.1.1 42943 1oyb 400 2.15e+01 1oyc c.1.4.1 28602 1qdeA 224 2.21e+01 1qvaA c.37.1.19 32410 1ks2A 219 2.23e+01 unknown_sccs 72908 d.58.40.1 72909 1q35A 320 2.23e+01 c.94.1.1 -8658 1qwgA 251 2.24e+01 unknown_sccs -5678 1i7qB 193 2.27e+01 1qdlB c.23.16.1 61902 1djnA 729 2.31e+01 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 1oltA 457 2.31e+01 unknown_sccs -5688 1o8bA 219 2.31e+01 unknown_sccs 81180 d.58.40.1 81181 1qh3A 260 2.33e+01 1qh5A d.157.1.2 42059 1pytA 94 2.33e+01 1pytA d.58.3.1 39064 1jidA 128 2.36e+01 d.201.1.1 66735 1hwyA 501 2.36e+01 1hwyA c.2.1.7 30262 c.58.1.1 33910 1plq 258 2.37e+01 1plq d.131.1.2 41388 d.131.1.2 41389 1vpsA 289 2.38e+01 1vpsA b.121.6.1 23336 1dbs 224 2.41e+01 1byi c.37.1.10 32209 1draA 159 2.42e+01 1vdrA c.71.1.1 34831 1vdrA 162 2.45e+01 1vdrA c.71.1.1 34893 1kamA 194 2.46e+01 c.26.1.3 72254 1bv8A 138 2.49e+01 1ayoA b.2.4.1 22430 1qjvA 342 2.52e+01 1qjvA b.80.1.5 28035 1itzA 675 2.53e+01 c.36.1.6 76798 c.36.1.10 76797 c.48.1.1 76799 1vkfA 188 2.61e+01 1erw 105 2.64e+01 1erv c.47.1.1 32745 2scuA 288 2.64e+01 2scuA c.2.1.8 30303 c.23.4.1 31131 1vk4A 298 2.64e+01 c.72.1.1 -8414 1jg8A 347 2.65e+01 1jg8A c.67.1.1 62946 1evyA 366 2.65e+01 1evyA a.100.1.6 18811 c.2.1.6 30215 1nw2A 105 2.65e+01 c.47.1.1 -7380 1dts 221 2.66e+01 1byi c.37.1.10 32200 1earA 147 2.70e+01 b.107.1.1 64875 d.58.38.1 64876 1vfrA 218 2.71e+01 1vfrA d.90.1.1 40247 1qv9A 283 2.76e+01 unknown_sccs -6888 2tmdA 729 2.77e+01 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1an9A 340 2.77e+01 1an9A c.4.1.2 30617 d.16.1.3 37904 1a48 306 2.78e+01 1a48 d.143.1.1 41590 1m2dA 110 2.78e+01 c.47.1.11 78476 1lcyA 325 2.81e+01 b.36.1.4 73834 b.47.1.1 73835 1f37A 110 2.81e+01 1f37A c.47.1.11 33088 1ko7A 314 2.81e+01 c.98.2.1 72797 c.91.1.2 72798 3dfr 162 2.82e+01 3dfr c.71.1.1 34880 1hwxA 501 2.83e+01 1hwyA c.2.1.7 30250 c.58.1.1 33898 1bjt 793 2.84e+01 1bjt e.11.1.1 43249 487dH 224 2.87e+01 1ad2 i.1.1.2 45835 1m2bA 110 2.88e+01 c.47.1.11 78474 1ffkI 194 2.88e+01 1ffkI d.12.1.2 37494 1ad2 228 2.88e+01 1ad2 e.24.1.1 43353 1mpb 370 2.91e+01 4mbp c.94.1.1 35780 1ezoA 370 2.92e+01 4mbp c.94.1.1 59539 1pot 325 2.92e+01 1pot c.94.1.1 35807 1e5mA 416 2.92e+01 1dd8A c.95.1.1 58973 c.95.1.1 58974 1ptoA 244 2.93e+01 1bcpA d.166.1.1 42257 1pwhA 327 2.94e+01 c.79.1.1 -8524 1s72M 194 2.94e+01 1o1zA 234 2.97e+01 c.1.18.3 86555 1ne9A 335 2.98e+01 d.108.1.4 -10805 d.108.1.4 -10806 2cbf 234 2.98e+01 1cbf c.90.1.1 35588 1tiqA 180 2.98e+01 1aiu 105 2.99e+01 1erv c.47.1.1 32746 1f32A 149 2.99e+01 1f32A d.62.1.1 39539 1pjr 724 2.99e+01 1pjr c.37.1.19 32391 c.37.1.19 32392 1regX 122 3.04e+01 1regX d.58.27.1 39406 1vpsB 289 3.06e+01 1vpsA b.121.6.1 23337 1ti6A 875 3.08e+01 1e3dA 266 3.09e+01 2frvA e.19.1.1 59188 1m32A 366 3.12e+01 c.67.1.3 78508 1j3mA 129 3.12e+01 1oywA 523 3.13e+01 unknown_sccs -270 c.37.1.19 -7209 c.37.1.19 -7210 1prtA 234 3.21e+01 1bcpA d.166.1.1 42253 1fjhB 257 3.21e+01 1fjhB c.2.1.2 29871 1ha3A 405 3.22e+01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1b00A 127 3.22e+01 3chy c.23.1.1 31122 1lu4A 136 3.26e+01 c.47.1.10 -7509 1gtkA 313 3.27e+01 c.94.1.1 76346 d.50.2.1 76347 1cnv 299 3.28e+01 1cnv c.1.8.5 28989 1aohB 147 3.28e+01 1aohA b.2.2.2 22402 1b5pA 385 3.30e+01 c.67.1.1 -8133 1cvl 319 3.32e+01 1cvl c.69.1.18 34786 1exmA 405 3.34e+01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1reqD 637 3.35e+01 1reqB c.1.19.1 29623 c.23.6.1 31250 1nw1A 429 3.37e+01 d.144.1.8 86286 1r1dA 247 3.41e+01 unknown_sccs -8335 1pe0A 197 3.41e+01 c.23.16.2 88045 1adjA 421 3.43e+01 1adjA c.51.1.1 33188 d.104.1.1 40737 1omp 370 3.44e+01 4mbp c.94.1.1 35778 1aohA 147 3.46e+01 1aohA b.2.2.2 22401 1ro0A 216 3.47e+01 unknown_sccs -11390 1iu8A 206 3.47e+01 c.56.4.1 71436 1kutA 230 3.48e+01 d.143.1.1 73017 1psuA 140 3.49e+01 d.38.1.5 88285 1rie 129 3.50e+01 1rie b.33.1.1 24427 1iu9A 111 3.51e+01 c.78.2.1 -8500 1t0hA 132 3.51e+01 1rl6A 177 3.55e+01 1rl6A d.141.1.1 41473 d.141.1.1 41474 1n57A 291 3.55e+01 c.23.16.2 85328 1p2fA 220 3.55e+01 a.4.6.1 87720 c.23.1.1 87721 1oi2A 366 3.57e+01 c.32.1.2 87039 d.79.2.2 87040 1p5fA 189 3.58e+01 c.23.16.2 -6508 1ad3A 452 3.58e+01 1ad3A c.82.1.1 35335 1jj2L 194 3.58e+01 1ffkI d.12.1.2 63097 1jkiA 533 3.58e+01 c.2.1.3 71704 d.81.1.3 71705 1ok8A 394 3.59e+01 b.1.18.4 -2737 f.10.1.1 -12384 1p0kA 349 3.61e+01 c.1.4.1 87648 1urrA 102 3.62e+01 1m6sA 347 3.65e+01 c.67.1.1 78701 1aa8A 347 3.65e+01 1an9A 1jk7A 323 3.67e+01 1auiA d.159.1.3 63144 1jykA 254 3.68e+01 c.68.1.13 67458 1o5zA 442 3.68e+01 c.59.1.2 -7939 c.72.2.2 -8418 1cipA 353 3.69e+01 1cipA a.66.1.1 18210 c.37.1.8 32093 1dppA 507 3.69e+01 1dpe c.94.1.1 35800 1m3vA 122 3.71e+01 g.39.1.3 84794 g.39.1.3 84795 1npiA 61 3.75e+01 g.3.7.1 80685 1p90A 145 3.75e+01 unknown_sccs -7684 1a88A 275 3.76e+01 1brt c.69.1.12 34707 1iqqA 200 3.77e+01 d.124.1.1 66274 1pswA 348 3.83e+01 c.87.1.7 88287 1q5dA 419 3.83e+01 a.104.1.1 -1454 1gmuA 143 3.85e+01 b.107.1.1 65335 d.58.38.1 65336 1jkmB 361 3.86e+01 1jkmA c.69.1.2 34634 1hnoA 280 3.86e+01 1hnoA c.14.1.3 61095 1uc7A 125 3.86e+01 c.47.1.1 -7414 1jztA 246 3.87e+01 c.104.1.1 63319 1jn5B 250 3.88e+01 d.17.4.2 66922 1s0aA 429 3.88e+01 c.67.1.4 -8201 1o94A 729 3.89e+01 c.1.4.1 81200 c.3.1.1 81201 c.4.1.1 81202 3gcb 470 3.92e+01 3gcb d.3.1.1 37032 1va4A 279 3.95e+01 1pda 315 3.96e+01 1pda c.94.1.1 35751 d.50.2.1 38794 1fjhA 257 3.97e+01 1fjhB c.2.1.2 29870