# List of top-scoring protein chains for t04-100-30-near-backbone-11-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 1y8qA 346 2.72e-02 1t3lA 337 3.83e-02 b.34.2.1,c.37.1.1 106358,106359 1t0hB 224 4.81e-02 c.37.1.1 106208 1n9lA 109 1.11e-01 d.110.3.6 85468 1jnuA 104 3.11e-01 d.110.3.6 71762 1jg1A 235 4.84e-01 c.66.1.7 66661 1tqhA 247 5.74e-01 c.69.1.29 107225 2mhr 118 6.58e-01 2mhr a.24.4.1 16581 1r1dA 247 7.26e-01 c.69.1.29 96813 1h7mA 102 7.79e-01 d.79.3.1 83485 1x4tA 92 8.99e-01 2d8sA 80 9.91e-01 1wojA 214 1.25e+00 1w41A 101 1.35e+00 2cybA 323 1.35e+00 1om4A 422 1.97e+00 d.174.1.1 87067 1jcfA 344 2.26e+00 c.55.1.1,c.55.1.1 62878,62879 1udzA 182 2.37e+00 b.51.1.1 99239 1j3mA 129 2.39e+00 d.129.7.1 103836 1xreA 217 2.46e+00 2faoA 309 2.48e+00 1nb5I 98 2.57e+00 d.17.1.2 80381 1wohA 305 2.77e+00 c.42.1.1 109446 1gefA 123 2.83e+00 1gefA c.52.1.18 60465 1p4fA 293 2.97e+00 d.144.1.7 104063 1mmvB 419 3.04e+00 d.174.1.1 91318 1a99A 344 3.08e+00 1pot c.94.1.1 35812 1hr6B 443 3.11e+00 1be3A d.185.1.1,d.185.1.1 61166,61167 2cthA 107 3.18e+00 3cyr a.138.1.1 19652 1ldjA 760 3.27e+00 a.4.5.34,a.118.17.1,e.40.1.1 73847,73848,73849 2f7fA 494 3.59e+00 1np6A 174 3.94e+00 c.37.1.10 85954 1j0pA 108 4.03e+00 a.138.1.1 90743 1yovA 537 4.15e+00 1vp8A 201 4.27e+00 1cmbA 104 4.38e+00 1cmbA a.43.1.5 17460 1srb 21 4.66e+00 j.28.1.1 46201 1uz1A 468 4.79e+00 2f5gA 133 5.11e+00 1ta3B 303 5.13e+00 c.1.8.3 106732 1w85I 49 5.34e+00 1v4pA 157 5.46e+00 1z7dA 433 5.82e+00 1v7oA 165 6.11e+00 d.67.1.2 100480 1oahA 519 6.39e+00 a.138.1.3 86736 1wh0A 134 6.43e+00 1tzvA 142 6.79e+00 a.79.1.1 107526 1w3jA 468 6.84e+00 c.1.8.4 109156 1a6bB 40 6.84e+00 1a6bB g.40.1.1 45172 1ucnA 152 7.25e+00 d.58.6.1 99183 1s57A 153 7.29e+00 1nigA 152 7.68e+00 a.25.2.1 85740 2aqlA 173 7.73e+00 2cvlA 124 7.76e+00 2cbuA 468 7.77e+00 2fi0A 81 7.86e+00 1u7iA 136 7.96e+00 d.32.1.7 107724 1otkA 249 8.15e+00 a.25.1.2 93521 1njqA 39 8.21e+00 g.37.1.3 85822 1mwyA 73 8.94e+00 d.58.17.1 79616 1n3lA 372 9.24e+00 c.26.1.1 79966 1m32A 366 9.81e+00 c.67.1.3 78508 1iukA 140 9.96e+00 c.2.1.8 83712 1edn 21 9.99e+00 j.28.1.1 46197 1oz9A 150 1.07e+01 d.92.1.15 93808 1eg2A 319 1.08e+01 1eg2A c.66.1.11 34249 1u6pA 56 1.11e+01 2bgcA 238 1.12e+01 1f1uA 323 1.13e+01 d.32.1.3,d.32.1.3 83200,83201 1cmcA 104 1.17e+01 1cmbA a.43.1.5 17462 1jj2T 66 1.17e+01 1ffkR g.39.1.6 63105 1dxrC 336 1.17e+01 6prcC a.138.1.2 19670 1hr6A 475 1.18e+01 1hr6A d.185.1.1,d.185.1.1 61164,61165 1s72U 66 1.18e+01 g.39.1.6 105340 1nqkA 381 1.19e+01 c.1.16.4 92050 1vqoU 66 1.20e+01 1brwA 433 1.21e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1ryqA 69 1.21e+01 g.41.9.3 105126 1jm1A 204 1.23e+01 b.33.1.1 71745 1s1hN 36 1.26e+01 i.1.1.1 105166 1jg5A 83 1.28e+01 d.205.1.1 66666 2fhzA 109 1.28e+01 1s5dA 240 1.31e+01 d.166.1.1 98541 1l0lA 446 1.32e+01 d.185.1.1,d.185.1.1 84482,84483 1nc5A 373 1.32e+01 a.102.1.6 85548 1sgvA 316 1.35e+01 b.122.1.1,d.265.1.2 98858,98859 1hw1A 239 1.37e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1ebmA 317 1.41e+01 1ebmA a.96.1.3,d.129.1.2 18751,41300 1vd4A 62 1.44e+01 1xgsA 295 1.45e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1ebdC 41 1.45e+01 1ebdC a.9.1.1 16355 1oyeA 1049 1.48e+01 d.58.44.1,d.58.44.1,d.58.44.1,d.58.44.1,d.225.1.1,d.225.1.1,f.35.1.1,f.35.1.1 87587,87588,87589,87590,87591,87592,87593,87594 2g9zA 348 1.50e+01 1wcwA 261 1.53e+01 1k4mA 213 1.54e+01 c.26.1.3 77258 1h70A 255 1.58e+01 1h70A d.126.1.3 60711 2fb0A 94 1.58e+01 1qpcA 279 1.60e+01 1fgkA d.144.1.7 41685 1wy6A 172 1.61e+01 1klrA 30 1.64e+01 g.37.1.1 72722 2mtaC 147 1.65e+01 2mtaC a.3.1.1 15908 1i3dA 146 1.66e+01 a.1.1.2 61587 2flsA 132 1.66e+01 1t9xA 1049 1.70e+01 1f1xA 322 1.72e+01 d.32.1.3,d.32.1.3 83208,83209 1usuB 170 1.74e+01 d.83.2.1 99886 2ezh 75 1.76e+01 2ezh a.4.1.2 16029 2a7oA 112 1.77e+01 1tf4A 605 1.82e+01 1tf4A a.102.1.2,b.2.2.2 18827,22393 1diiC 80 1.85e+01 1diiC a.3.1.1 15925 1wnyA 186 1.87e+01 1m3uA 264 1.89e+01 c.1.12.8 84784 1fukA 165 1.91e+01 1fukA c.37.1.19 32409 2a3mA 130 1.93e+01 1yseA 141 1.93e+01 1mxmA 254 1.95e+01 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1w4xA 542 1.95e+01 c.3.1.5,c.3.1.5 109171,109172 1innA 166 1.96e+01 1j98A d.185.1.2 62608 1m3qA 317 2.01e+01 a.96.1.3,d.129.1.2 91184,91185 1dszA 86 2.04e+01 2nllB g.39.1.2 45129 1npk 154 2.06e+01 1npk d.58.6.1 39099 1j5yA 187 2.08e+01 a.4.5.1,d.94.2.1 71592,71593 1wd7A 261 2.08e+01 1hh1A 143 2.10e+01 1gefA c.52.1.18 61036 2an3A 289 2.14e+01 1exkA 79 2.16e+01 1exkA g.54.1.1 45384 1oniA 137 2.28e+01 d.79.1.1 87144 2bv4A 113 2.33e+01 1kjwA 295 2.34e+01 b.34.2.1,c.37.1.1 68643,68644 1wveC 80 2.40e+01 1r4wA 226 2.50e+01 c.47.1.13 97050 1gu7A 364 2.53e+01 b.35.1.2,c.2.1.1 83321,83322 1vekA 84 2.53e+01 1ppjA 446 2.54e+01 d.185.1.1,d.185.1.1 104252,104253 1vjeA 166 2.55e+01 d.185.1.2 100807 1k2eA 156 2.66e+01 d.113.1.1 72010 1ngnA 155 2.66e+01 a.96.1.2 85697 1ocyA 198 2.67e+01 d.231.1.1 86817 1rfzA 168 2.68e+01 a.195.1.1 97411 1t64A 377 2.68e+01 c.42.1.2 106543 1yqfA 203 2.72e+01 1dl5A 317 2.75e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1iwhB 146 2.77e+01 a.1.1.2 76883 1q5yA 85 2.80e+01 d.58.18.4 95950 1y4tA 322 2.89e+01 2bolA 314 2.89e+01 1ccwA 137 2.89e+01 1be1 c.23.6.1 31238 1yzbA 182 2.92e+01 2d5xB 146 2.93e+01 1b0uA 262 2.96e+01 1b0uA c.37.1.12 32370 1vpgA 192 3.04e+01 1z84A 351 3.04e+01 2cwkA 160 3.07e+01 1wc9A 169 3.12e+01 1muwA 386 3.14e+01 c.1.15.3 79495 1dszB 85 3.17e+01 2nllB g.39.1.2 45108 1vkyA 347 3.17e+01 e.53.1.1 108696 1vydA 116 3.24e+01 a.3.1.1 108900 1dbfA 127 3.25e+01 2chsA d.79.1.2 39761 1jvnA 555 3.38e+01 c.1.2.1,c.23.16.1 67355,67356 1lucB 324 3.40e+01 1lucA c.1.16.1 29548 1fe0A 68 3.49e+01 1cc8A d.58.17.1 39345 1xqiA 195 3.50e+01 1vhzA 198 3.54e+01 d.113.1.1 100718 1omiA 248 3.54e+01 b.82.3.3,a.4.5.4 87079,87080 1kb9B 352 3.58e+01 d.185.1.1,d.185.1.1 77313,77314 2d8qA 70 3.58e+01 1a6i 217 3.59e+01 2tct a.4.1.9,a.121.1.1 16066,19243 1jf3A 147 3.59e+01 a.1.1.2 71642 2ewcA 126 3.61e+01 1n13B 113 3.61e+01 1mngA 203 3.62e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1m36A 33 3.66e+01 g.37.1.2 91172 1kamA 194 3.69e+01 c.26.1.3 72254 1zzpA 130 3.70e+01 1vlwA 217 3.70e+01 c.1.10.1 108868 2bryA 497 3.71e+01 2ew8A 249 3.74e+01 1zdzA 302 3.75e+01 1wimA 94 3.75e+01 1r3eA 309 3.77e+01 b.122.1.1,d.265.1.2 96907,96908 2bu3A 254 3.86e+01 1v8gA 329 3.90e+01 a.46.2.1,c.27.1.1 100505,100506 2f8lA 344 3.92e+01 1wmuB 146 3.93e+01 a.1.1.2 109417 2ggcA 263 3.94e+01 1h75A 81 3.95e+01 1h75A c.47.1.1 60716 1gnkA 112 3.99e+01 2pii d.58.5.1 39073 1r0rI 51 4.02e+01 g.68.1.1 96736 2d00A 109 4.02e+01 1tqxA 227 4.06e+01 1wm3A 72 4.19e+01 1poiA 317 4.23e+01 1poiA c.124.1.2 34153 1qo7A 394 4.25e+01 1qo7A c.69.1.11 34697 1t6t1 118 4.26e+01 1bjaA 95 4.26e+01 1bjaA a.4.5.9 16122 1uroA 367 4.29e+01 1uroA c.1.22.1 29675 2tct 207 4.29e+01 2tct a.4.1.9,a.121.1.1 16063,19240 1i50I 122 4.31e+01 g.41.3.1,g.41.3.1 61762,61763 1ox6A 555 4.31e+01 c.1.2.1,c.23.16.1 87505,87506 1xb4A 202 4.31e+01 1adjA 421 4.33e+01 1adjA c.51.1.1,d.104.1.1 33188,40737 1sgpI 51 4.38e+01 2ovo g.68.1.1 44678 1tksA 204 4.42e+01 d.115.1.2 107114 1vloA 381 4.44e+01 b.44.2.1,d.250.1.1 108838,108839 1tkkA 366 4.47e+01 c.1.11.2,d.54.1.1 107089,107090 1sz7A 200 4.50e+01 2bq4A 116 4.52e+01 1hs7A 97 4.53e+01 1hs7A a.47.2.1 61236 1ekeA 230 4.58e+01 1ekeA c.55.3.1 33572 1t4wA 196 4.61e+01 b.2.5.2 106427 1fr2A 86 4.61e+01 a.28.2.1 83256 1pu6A 218 4.67e+01 a.96.1.5 95123 1vqwA 457 4.69e+01 1o5zA 442 4.69e+01 c.59.1.2,c.72.2.2 92530,92531 1jkgA 140 4.70e+01 d.17.4.2 66795 1wwhA 119 4.71e+01 1o4wA 147 4.72e+01 c.120.1.1 86629 1mg2D 155 4.82e+01 a.3.1.1 79062 1qhtA 775 4.82e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 2bh4X 134 4.86e+01 1q9uA 130 4.90e+01 d.129.7.1 96314 1c24A 263 4.91e+01 1c24A d.127.1.1 41148 2c1gA 431 4.91e+01 1o4vA 183 4.93e+01 c.23.8.1 86628 1hnnA 282 4.97e+01 c.66.1.15 65895 2cvcA 545 4.99e+01 1ezvB 352 5.00e+01 1ezvB d.185.1.1,d.185.1.1 59543,59544 2dbnA 461 5.00e+01 2gtqA 867 5.04e+01 2gs5A 198 5.06e+01 1ehyA 294 5.12e+01 1ehyA c.69.1.11 34693 1b65A 375 5.24e+01 1b65A d.154.1.1 42020 1unlD 208 5.27e+01 2ax3A 502 5.28e+01 1flmA 122 5.29e+01 1axj b.45.1.1 25747 2ah5A 210 5.39e+01 1wk8A 194 5.42e+01 1eyqA 222 5.46e+01 1eypA d.36.1.1 38534 1xnzA 264 5.48e+01 1r3sA 367 5.49e+01 c.1.22.1 96963 1xsvA 113 5.54e+01 1i6wA 181 5.60e+01 1i6wA c.69.1.18 61859 1qe3A 489 5.62e+01 2bce c.69.1.1 34630 1owtA 66 5.65e+01 d.230.3.1 87493 1y7rA 133 5.67e+01 1w85A 368 5.68e+01 1rk8A 165 5.70e+01 d.58.7.1 97603 2c8sA 172 5.75e+01 1j1uA 306 5.75e+01 c.26.1.1 83980 1oejA 193 5.75e+01 b.60.1.4 92798 2hbg 147 5.77e+01 2hbg a.1.1.2 15014 1k4iA 233 5.79e+01 d.115.1.2 72056 1yarH 217 5.84e+01 1heiA 451 5.84e+01 1heiA c.37.1.14,c.37.1.14 32463,32464 2ethA 154 5.88e+01 2ffeA 311 5.94e+01 1kqpA 271 6.05e+01 c.26.2.1 72883 5rubA 490 6.05e+01 1burA c.1.14.1,d.58.9.1 29382,39288 1whi 122 6.06e+01 1whi b.39.1.1 24810 4xis 387 6.09e+01 4xis c.1.15.3 29421 1ih8A 271 6.10e+01 2nsyA c.26.2.1 62377 1r45A 204 6.10e+01 2bg1A 494 6.15e+01 1s68A 249 6.19e+01 d.142.2.4 98591 1fseA 74 6.22e+01 1fseA a.4.6.2 60000 2ex5A 207 6.23e+01 1avpA 204 6.27e+01 1avpA d.3.1.7 37132 1zljA 78 6.31e+01 1nrfA 262 6.31e+01 e.3.1.1 92086 1z08A 170 6.32e+01 1wa3A 205 6.38e+01 1xa1A 255 6.38e+01 e.3.1.1 109529 1v7pC 200 6.42e+01 c.62.1.1 108408 1jidA 128 6.50e+01 d.201.1.1 66735 1wurA 220 6.52e+01 1y3nA 490 6.55e+01 1nuuA 252 6.56e+01 c.26.1.3 86209 2cqeA 98 6.56e+01 1ld8B 437 6.59e+01 a.102.4.3 73839 1ojqA 212 6.60e+01 d.166.1.1 93146 2gz4A 207 6.60e+01 1wd2A 60 6.61e+01 g.44.1.1 109232 1jzuA 157 6.62e+01 b.60.1.1 84271 1jpmA 366 6.63e+01 c.1.11.2,d.54.1.1 67031,67032 1nznA 126 6.68e+01 a.118.8.1 92382 2acy 98 6.74e+01 2acy d.58.10.1 39298 1txlA 215 6.77e+01 b.60.1.4 107429 1ri5A 298 6.79e+01 c.66.1.34 97502 3xis 387 6.84e+01 4xis c.1.15.3 29423 1qusA 322 6.91e+01 1ltm d.2.1.6 36991 1fjsL 52 6.92e+01 1hcgB g.3.11.1 44226 1u46A 291 6.99e+01 d.144.1.7 107656 1xjo 284 6.99e+01 1xjo c.56.5.4 33843 1f20A 435 7.03e+01 b.43.4.1,c.25.1.4 64932,64933 1htwA 158 7.08e+01 c.37.1.18 71083 1sl8A 191 7.12e+01 1wvfA 520 7.21e+01 1q68B 29 7.21e+01 j.108.1.1 95963 1pt6A 213 7.24e+01 c.62.1.1 95091 1zhvA 134 7.26e+01 1ispA 181 7.28e+01 c.69.1.18 76778 1cxqA 162 7.29e+01 1cxqA c.55.3.2 33621 1bag 425 7.33e+01 1bag b.71.1.1,c.1.8.1 27720,28707 1ukcA 522 7.37e+01 c.69.1.17 107911 1h1oA 183 7.41e+01 a.3.1.4,a.3.1.4 83454,83455 1gps 47 7.43e+01 1gpt g.3.7.5 44176 1fxrA 64 7.44e+01 1fxd d.58.1.4 38993 2gi9A 56 7.45e+01 1hekA 131 7.56e+01 a.61.1.5 65818 1twfI 122 7.56e+01 1y9kA 157 7.56e+01 1nv8A 284 7.57e+01 c.66.1.30 86224 1hn6A 110 7.58e+01 g.61.1.1 76721 1l6rA 227 7.63e+01 c.108.1.10 77768 1rcwA 231 7.65e+01 a.132.1.4 97299 1yz1A 174 7.68e+01 1j6wA 175 7.68e+01 1j98A d.185.1.2 62663 2axoA 270 7.76e+01 1emvA 86 7.77e+01 1cei a.28.2.1 16944 1fviA 297 7.83e+01 1fviA b.40.4.6,d.142.2.1 25364,41578 1lj2A 110 7.86e+01 h.1.13.2 73926 1u6mA 199 7.88e+01 1z6eB 52 7.93e+01 2ffwA 78 7.93e+01 1yqzA 438 7.94e+01 1atzA 189 7.95e+01 1atzA c.62.1.1 34132 1lmzA 187 7.97e+01 a.96.1.4 74037 1aw7A 194 7.97e+01 1aw7A b.40.2.2,d.15.6.1 25164,37753 1i1nA 226 7.97e+01 c.66.1.7 71102 1juvA 193 7.98e+01 c.71.1.1 90912 1cmiA 85 8.01e+01 1cmiA d.39.1.1 38551 1pv5A 264 8.05e+01 d.251.1.1 95150 1oaoC 729 8.07e+01 e.26.1.3 86746 1x2iA 75 8.08e+01 1ua7A 422 8.08e+01 b.71.1.1,c.1.8.1 107759,107760 2c1iA 431 8.08e+01 1zcjA 463 8.29e+01 1miwA 404 8.37e+01 a.173.1.1,d.218.1.4 79162,79163 2bogX 286 8.38e+01 1cyj 90 8.38e+01 1ctj a.3.1.1 15805 1zdrA 164 8.42e+01 1zczA 464 8.43e+01 1v77A 212 8.51e+01 c.6.3.2 108402 1r89A 437 8.52e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1mml 265 8.56e+01 1mml e.8.1.2 43015 1w68A 390 8.57e+01 a.25.1.2 109216 1bkpA 278 8.66e+01 1bkpA d.117.1.1 41029 1fp0A 88 8.71e+01 1fp0A g.50.1.2 45361 2gwdA 449 8.72e+01 1xmpA 170 8.74e+01 1i8aA 189 8.81e+01 1i82A b.1.9.2 61951 2ganA 190 8.82e+01 1dj7A 117 8.87e+01 1dj7A g.36.1.1 44997 2f1rA 171 8.90e+01 1i8oA 114 8.92e+01 1ycc a.3.1.1 61979