# List of top-scoring protein chains for t2k-80-60-80-str2+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 2aa4A 289 5.89e-03 1vhxA 150 6.41e-02 c.55.3.8 100712 2fr1A 486 6.56e-02 1mucA 373 1.18e-01 1mucA c.1.11.2,d.54.1.1 29236,38880 1nu5A 370 2.17e-01 c.1.11.2,d.54.1.1 92183,92184 1g99A 408 2.67e-01 1g99A c.55.1.2,c.55.1.2 33457,33458 1awcA 110 2.72e-01 1awcA a.4.5.21 16167 1ovqA 138 2.86e-01 c.55.3.8 93607 1ko9A 345 3.17e-01 a.96.1.3,d.129.1.2 68717,68718 1mdl 359 3.36e-01 2mnr c.1.11.2,d.54.1.1 29247,38891 2gl5A 410 4.22e-01 1sjdA 368 4.37e-01 c.1.11.2,d.54.1.1 105632,105633 1jpaA 312 4.64e-01 d.144.1.7 67011 2cygA 312 4.77e-01 1jtdB 273 5.22e-01 b.69.5.2 67265 1fjhB 257 5.48e-01 1fjhB c.2.1.2 29871 2ae6A 166 6.38e-01 1x3mA 415 6.39e-01 1xxbA 78 6.56e-01 1xxaA d.74.2.1 39706 1ufhA 180 6.84e-01 d.108.1.1 88485 1a62 130 6.84e-01 1a62 a.140.3.1,b.40.4.5 64708,64709 1vbuA 328 6.87e-01 1qo7A 394 7.25e-01 1qo7A c.69.1.11 34697 1sftA 388 7.77e-01 1bd0A b.49.2.2,c.1.6.1 26482,28644 1r0mA 375 7.79e-01 c.1.11.2,d.54.1.1 104747,104748 1fjhA 257 7.90e-01 1fjhB c.2.1.2 29870 1isiA 265 8.22e-01 e.4.1.1 71394 1xxaA 78 8.53e-01 1xxaA d.74.2.1 39700 1hufA 140 8.60e-01 1hufA d.195.1.1 61272 1udh 244 9.03e-01 3eugA c.18.1.1 31015 1dtdA 303 9.56e-01 1aye c.56.5.1 33823 1fsu 492 9.68e-01 1auk c.76.1.2 35032 1aye 401 1.10e+00 1aye c.56.5.1,d.58.3.1 33824,39065 1m5yA 408 1.14e+00 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 2bvwA 362 1.18e+00 1bvwA c.6.1.1 30666 1r6wA 322 1.23e+00 c.1.11.2,d.54.1.1 97165,97166 1nnwA 252 1.29e+00 d.159.1.5 80674 2a1vA 144 1.31e+00 1a12A 413 1.32e+00 1a12A b.69.5.1 27663 1udg 244 1.37e+00 3eugA c.18.1.1 31016 1obr 326 1.39e+00 1aye c.56.5.2 33828 1m3qA 317 1.40e+00 a.96.1.3,d.129.1.2 91184,91185 1mv8A 436 1.45e+00 a.100.1.4,c.2.1.6,c.26.3.1 85128,85129,85130 1jug 125 1.51e+00 3lzt d.2.1.2 36587 2ctc 307 1.56e+00 1aye c.56.5.1 33802 1rvkA 382 1.58e+00 c.1.11.2,d.54.1.1 97928,97929 1dysA 348 1.61e+00 1bvwA c.6.1.1 30669 1hfx 123 1.69e+00 3lzt d.2.1.2 36600 2jdxA 385 1.73e+00 1jdw d.126.1.2 41139 2ctb 307 1.75e+00 1aye c.56.5.1 33803 2mnr 357 1.80e+00 2mnr c.1.11.2,d.54.1.1 29245,38889 1fhvA 323 1.84e+00 1fhuA c.1.11.2,d.54.1.1 29235,38879 1s3eA 520 1.87e+00 c.3.1.2,d.16.1.5 98426,98427 1nw8A 319 1.87e+00 c.66.1.11 86292 1ojaA 520 1.88e+00 c.3.1.2,d.16.1.5 93096,93097 6cpa 307 1.94e+00 1aye c.56.5.1 33816 1mqsA 671 2.02e+00 e.25.1.1 79414 1ocnA 362 2.04e+00 c.6.1.1 86808 1on0A 158 2.07e+00 d.108.1.1 87095 1gheA 177 2.10e+00 d.108.1.1 76222 1n57A 291 2.11e+00 c.23.16.2 85328 1ckiA 317 2.17e+00 1csn d.144.1.7 41660 2dcnA 311 2.17e+00 1fhuA 320 2.18e+00 1fhuA c.1.11.2,d.54.1.1 29234,38878 1vk9A 151 2.30e+00 c.139.1.1 108640 1vs0A 310 2.35e+00 1r6dA 337 2.42e+00 c.2.1.2 97148 1bavA 309 2.46e+00 1aye c.56.5.1 33806 1mp8A 281 2.51e+00 d.144.1.7 91384 1el6A 219 2.54e+00 1el6B d.182.1.1 42606 1bvwA 360 2.57e+00 1bvwA c.6.1.1 30668 1qs0A 407 2.58e+00 1qs0A c.36.1.11 31829 1eg2A 319 2.59e+00 1eg2A c.66.1.11 34249 1uj6A 227 2.59e+00 c.124.1.4,d.58.40.1 107898,107899 2bbhA 269 2.60e+00 1hjsA 332 2.63e+00 c.1.8.3 83492 1ehiA 377 2.64e+00 1iow c.30.1.2,d.142.1.1 31716,41484 1x3sA 195 2.66e+00 1el6B 219 2.68e+00 1el6B d.182.1.1 42607 1k6aA 303 2.69e+00 c.1.8.3 72081 1yh3A 256 2.70e+00 1zhvA 134 2.71e+00 1tufA 434 2.73e+00 b.49.2.3,c.1.6.1 107335,107336 2fsrA 195 2.77e+00 2a5hA 416 2.80e+00 1fobA 334 2.84e+00 c.1.8.3 83255 1jdw 423 2.86e+00 1jdw d.126.1.2 41129 1ebmA 317 2.90e+00 1ebmA a.96.1.3,d.129.1.2 18751,41300 1uxoA 192 2.92e+00 c.69.1.31 108121 4matA 278 2.98e+00 1c24A d.127.1.1 41150 1fo4A 1332 3.01e+00 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 17910,37695,38586,40227,41416,41758 1jpmA 366 3.08e+00 c.1.11.2,d.54.1.1 67031,67032 1b4uB 302 3.14e+00 1bouB c.56.6.1 33861 1yme 309 3.19e+00 1aye c.56.5.1 33804 1m4lA 307 3.19e+00 c.56.5.1 78604 2abqA 306 3.20e+00 1lwyA 324 3.47e+00 a.96.1.3,d.129.1.2 78285,78286 1wg8A 285 3.50e+00 1m4zA 238 3.55e+00 b.34.12.1 78630 2c5aA 379 3.56e+00 1gokA 303 3.65e+00 c.1.8.3 65420 1oc7A 364 3.68e+00 c.6.1.1 86794 1h5qA 265 3.68e+00 1cydA c.2.1.2 60643 1bd0A 388 3.68e+00 1bd0A b.49.2.2,c.1.6.1 26480,28642 1ebfA 358 3.72e+00 1ebuA c.2.1.3,d.81.1.2 30033,39948 2d1pA 140 3.73e+00 1taxA 302 3.75e+00 1taxA 2ap1A 327 3.81e+00 1booA 323 3.85e+00 1booA c.66.1.11 34248 1tgoA 773 4.20e+00 1tgoA c.55.3.5,e.8.1.1 33721,43010 1aq0A 306 4.22e+00 1aq0A c.1.8.3 28842 1xbbA 291 4.26e+00 1l3iA 192 4.33e+00 c.66.1.22 77676 3pbgA 468 4.36e+00 1e70M c.1.8.4 28951 1mwmA 320 4.43e+00 c.55.1.1,c.55.1.1 79580,79581 1a63 130 4.45e+00 1a62 a.140.3.1,b.40.4.5 64710,64711 1u9aA 160 4.53e+00 1u9aA d.20.1.1 38333 1w2lA 99 4.55e+00 2fcr 173 4.81e+00 1rcf c.23.5.1 31151 1b94A 244 4.82e+00 1rvaA c.52.1.2 33250 1xm9A 457 4.85e+00 1vkcA 158 4.89e+00 1tkkA 366 4.89e+00 c.1.11.2,d.54.1.1 107089,107090 1lkzA 219 4.92e+00 c.124.1.4,d.58.40.1 73991,73992 1ebuA 358 4.93e+00 1ebuA c.2.1.3,d.81.1.2 30035,39950 1kwmA 402 4.99e+00 c.56.5.1,d.58.3.1 73079,73080 1z5rA 306 5.01e+00 1rypE 242 5.06e+00 1rypE d.153.1.4 41936 1w0hA 204 5.07e+00 1v93A 296 5.09e+00 c.1.23.1 100532 1twiA 434 5.16e+00 b.49.2.3,c.1.6.1 107399,107400 1rwzA 245 5.17e+00 d.131.1.2,d.131.1.2 98005,98006 1ng2A 193 5.29e+00 b.34.2.1,b.34.2.1 85660,85661 1ituA 369 5.30e+00 c.1.9.7 71423 7ceiB 206 5.38e+00 1bxiB d.4.1.1 37134 1pujA 282 5.50e+00 c.37.1.8 88294 1zh5A 195 5.54e+00 1uteA 313 5.58e+00 1uteA d.159.1.1 42078 1tph1 247 5.68e+00 1amk 1qadA 111 5.72e+00 1qadA d.93.1.1 40498 1ghsA 306 5.79e+00 1aq0A c.1.8.3 28840 1cydA 244 5.86e+00 1cydA c.2.1.2 29825 2bnjA 303 5.90e+00 1h9oA 112 5.94e+00 1qadA d.93.1.1 60837 1guqA 348 5.97e+00 1guqA d.13.1.2,d.13.1.2 37522,37523 1w78A 422 5.99e+00 1i1wA 303 6.04e+00 c.1.8.3 76732 1xyzA 347 6.04e+00 1taxA c.1.8.3 28804 1i6pA 220 6.13e+00 1ddzA c.53.2.1 61848 1guaB 81 6.18e+00 1c1yB d.15.1.5 37619 2cy2A 174 6.23e+00 1pf5A 131 6.23e+00 d.79.1.1 94604 1lbeA 258 6.26e+00 1lbeA e.4.1.1 42773 1zmoA 244 6.31e+00 1b97A 244 6.31e+00 1rvaA c.52.1.2 33252 1yvkA 163 6.32e+00 1bouB 302 6.36e+00 1bouB c.56.6.1 33859 1od8A 313 6.41e+00 c.1.8.3 86838 1ns5A 155 6.42e+00 c.116.1.3 80705 1wijA 140 6.52e+00 1ehyA 294 6.63e+00 1ehyA c.69.1.11 34693 2pth 193 6.74e+00 2pth c.56.3.1 33793 1tpfA 250 6.91e+00 1amk c.1.1.1 28467 2g8lA 299 6.93e+00 2azpA 318 6.96e+00 1cr0A 296 6.96e+00 1cr1A c.37.1.11 32287 1b96A 244 6.98e+00 1rvaA c.52.1.2 33268 2cmd 312 7.01e+00 2cmd c.2.1.5,d.162.1.1 30135,42102 1dqeA 137 7.02e+00 1dqeA a.39.2.1 17388 1ekjB 221 7.06e+00 1ekjB c.53.2.1 33365 1a2oA 349 7.10e+00 1chd c.23.1.1,c.40.1.1 31120,32479 2sniI 83 7.20e+00 2sniI d.40.1.1 38573 1v97A 1332 7.26e+00 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 108436,108437,108438,108439,108440,108441 1y9kA 157 7.32e+00 1cr1A 296 7.41e+00 1cr1A c.37.1.11 32286 2c0hA 353 7.50e+00 1hynP 379 7.55e+00 1hynP d.112.1.2 61408 1yr0A 175 7.56e+00 1i7qB 193 7.75e+00 1qdlB c.23.16.1 61902 1nq6A 302 7.78e+00 c.1.8.3 92046 1fa0A 537 7.85e+00 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 2bwnA 401 7.87e+00 1ufbA 127 7.95e+00 a.24.16.3 99331 1yixA 265 7.96e+00 2c1cA 312 7.99e+00 1ac5 483 8.03e+00 1ac5 c.69.1.5 34653 1tiqA 180 8.11e+00 d.108.1.1 107010 1hkvA 453 8.15e+00 b.49.2.3,c.1.6.1 83559,83560 3lck 271 8.25e+00 1fmk d.144.1.7 41686 1uk8A 282 8.29e+00 c.69.1.10 107907 1dvh 79 8.30e+00 1c53 a.3.1.1 15802 1tzzA 392 8.47e+00 1yw5A 177 8.48e+00 1r3nA 462 8.48e+00 c.56.5.4,d.58.19.1 96945,96946 1qtnA 164 8.49e+00 1pauA c.17.1.1 30999 1fdt 327 8.51e+00 1fds c.2.1.2 29841 2b6cA 220 8.52e+00 1uayA 242 8.66e+00 c.2.1.2 88390 2grrA 161 8.68e+00 2h1tA 188 8.73e+00 1nu0A 138 8.75e+00 c.55.3.8 92165 1c24A 263 8.78e+00 1c24A d.127.1.1 41148 2g6tA 306 8.87e+00 3lzt 129 8.92e+00 3lzt d.2.1.2 36245 1yeyA 444 8.97e+00 1j3wA 163 8.99e+00 d.110.7.1 90833 1o5xA 248 9.04e+00 c.1.1.1 92528 1e0wA 313 9.08e+00 1taxA c.1.8.3 59150 1q0rA 298 9.08e+00 c.69.1.28 95508 3eugA 229 9.09e+00 3eugA c.18.1.1 31018 1v0lA 313 9.15e+00 c.1.8.3 108207 1xuqA 212 9.17e+00 1hxpA 348 9.27e+00 1guqA d.13.1.2,d.13.1.2 37530,37531 1u2xA 474 9.33e+00 c.72.1.3 107622 1ta3B 303 9.35e+00 c.1.8.3 106732 1ng4A 390 9.35e+00 c.3.1.2,d.16.1.3 85666,85667 1vjzA 341 9.41e+00 c.1.8.3 100838 1behA 187 9.46e+00 1a44 b.17.1.1 23700 2d1eA 248 9.50e+00 1c1yB 77 9.60e+00 1c1yB d.15.1.5 37618 1g2qA 187 9.60e+00 c.61.1.1 65117 1xiyA 182 9.79e+00 1pwhA 327 9.81e+00 c.79.1.1 95224 1frb 315 9.99e+00 1frb c.1.7.1 28665 1ur4A 399 1.00e+01 1floA 422 1.00e+01 1floA a.60.9.1,d.163.1.1 18106,42166 1a3s 160 1.01e+01 1u9aA d.20.1.1 38335 1yzfA 195 1.02e+01 1a44 185 1.03e+01 1a44 b.17.1.1 23704 1c1bB 440 1.03e+01 1rthA e.8.1.2 43077 1xkqA 280 1.03e+01 1y9aA 360 1.03e+01 1c93A 265 1.03e+01 2ebn c.1.8.5 28998 1lyvA 306 1.05e+01 c.45.1.2 74348 1p9yA 121 1.05e+01 d.241.2.1 94402 1b31A 302 1.06e+01 1taxA c.1.8.3 28892 1xc3A 302 1.07e+01 1dwmA 70 1.07e+01 1hymA d.40.1.1 38583 1pioA 257 1.08e+01 1btl e.3.1.1 42719 2e2c 156 1.08e+01 1u9aA d.20.1.1 38336 1q5qA 259 1.10e+01 d.153.1.4 95904 1rz3A 201 1.10e+01 c.37.1.6 98132 1jtvA 327 1.11e+01 c.2.1.2 84230 1jepA 222 1.12e+01 d.36.1.1 66612 2bjdA 101 1.12e+01 1azwA 313 1.13e+01 1qtrA c.69.1.7 34658 1xqoA 256 1.13e+01 1jfxA 217 1.13e+01 c.1.8.8 62943 2astA 159 1.14e+01 1my6A 199 1.15e+01 a.2.11.1,d.44.1.1 85232,85233 1ufyA 122 1.15e+01 d.79.1.2 88489 1eq0A 158 1.16e+01 d.58.30.1 64909 1fehA 574 1.16e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1w1iE 357 1.17e+01 c.1.9.1 109051 1r2rA 248 1.17e+01 c.1.1.1 96875 1flzA 228 1.18e+01 3eugA c.18.1.1 31027 1dliA 402 1.18e+01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18809,30213,31622 1g4iA 123 1.19e+01 1poa a.133.1.2 60241 1mat 264 1.19e+01 1c24A d.127.1.1 41152 2b0jA 358 1.20e+01 2cyjA 118 1.21e+01 1znbA 232 1.22e+01 1a7tA d.157.1.1 42039 1eerA 166 1.22e+01 1eerA a.26.1.2 16846 2matA 264 1.23e+01 1c24A d.127.1.1 41146 1i5rA 327 1.24e+01 c.2.1.2 83668 1v8gA 329 1.24e+01 a.46.2.1,c.27.1.1 100505,100506 1sx5A 244 1.24e+01 c.52.1.2 99023 1unnC 115 1.26e+01 d.240.1.1 99680 1dljA 402 1.26e+01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1z7gA 217 1.26e+01 1qwgA 251 1.27e+01 c.1.27.1 96473 1j1iA 296 1.27e+01 c.69.1.10 83977 1h2vZ 156 1.27e+01 d.58.7.1 76595 3timA 250 1.28e+01 1amk c.1.1.1 28483 1fdi 715 1.29e+01 2napA b.52.2.2,c.81.1.1 26918,35326 1iupA 282 1.30e+01 c.69.1.10 76815 1l1qA 186 1.30e+01 c.61.1.1 77653 1tt7A 330 1.32e+01 1ghr 306 1.33e+01 1aq0A c.1.8.3 28844 1rvaA 244 1.35e+01 1rvaA c.52.1.2 33240 1vixA 420 1.35e+01 c.56.5.4,d.58.19.1 100777,100778 1i2sA 282 1.36e+01 e.3.1.1 71104 1vetA 124 1.38e+01 d.110.7.1 108553 2fo3A 125 1.39e+01 1n55A 251 1.39e+01 c.1.1.1 80007 3blm 257 1.39e+01 1btl e.3.1.1 42709 4eugA 229 1.40e+01 3eugA c.18.1.1 31019 1spa 396 1.40e+01 1ajsA c.67.1.1 34291 1lyxA 248 1.41e+01 c.1.1.1 78304 1a27 289 1.41e+01 1fds c.2.1.2 29839 1bb4A 130 1.42e+01 3lzt d.2.1.2 36583 1sz2A 332 1.42e+01 1wljA 189 1.42e+01 1k8cA 322 1.43e+01 c.1.7.1 72172 1ta9A 450 1.44e+01 2b61A 377 1.44e+01 2fl7A 232 1.44e+01 1a8vA 121 1.45e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 1dd6A 228 1.48e+01 1a7tA d.157.1.1 42054 1ks2A 219 1.48e+01 c.124.1.4,d.58.40.1 72908,72909 1y9wA 140 1.49e+01 1eugA 229 1.49e+01 3eugA c.18.1.1 31021 1rypH 205 1.50e+01 d.153.1.4 41876 1mi3A 322 1.50e+01 c.1.7.1 91274 2fz0A 149 1.50e+01 2ghrA 302 1.50e+01 1pauA 147 1.51e+01 1pauA c.17.1.1 30994 1bg4 302 1.52e+01 1taxA c.1.8.3 28806 1gosA 520 1.53e+01 c.3.1.2,d.16.1.5 65425,65426 1sspE 223 1.54e+01 3eugA c.18.1.1 31009 1bo4B 168 1.54e+01 1bo4A d.108.1.1 40799 2cfqA 417 1.54e+01 1ykdA 398 1.55e+01 1k68A 140 1.55e+01 c.23.1.1 90943 1fkoB 440 1.56e+01 1rthA e.8.1.2 43095 1fr2B 134 1.56e+01 d.4.1.1 83257 1jjtA 228 1.57e+01 1a7tA d.157.1.1 63139 1lk5A 229 1.58e+01 c.124.1.4,d.58.40.1 73960,73961 1q18A 332 1.58e+01 c.55.1.7,c.55.1.7 104470,104471 1lw6I 64 1.58e+01 d.40.1.1 74294 1klqA 197 1.59e+01 d.135.1.1 68689 1gupA 348 1.60e+01 1guqA d.13.1.2,d.13.1.2 37534,37535 1de5A 426 1.61e+01 1de5A c.1.15.2 29402 1eyqA 222 1.62e+01 1eypA d.36.1.1 38534 1i3zA 103 1.64e+01 d.93.1.1 83667 1rm6B 324 1.65e+01 1to2I 64 1.65e+01 2cvjA 180 1.65e+01 1ptmA 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