# List of top-scoring protein chains for t04-100-40-40-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 1rypI 222 1.99e-01 d.153.1.4 41877 2b06A 155 8.64e-01 1tjyA 316 1.69e+00 c.93.1.1 107062 1ofdA 1520 2.67e+00 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1pswA 348 2.69e+00 c.87.1.7 88287 1r13A 148 3.14e+00 d.169.1.1,h.1.1.1 96782,96783 1wdjA 187 3.49e+00 1jv1A 505 3.77e+00 c.68.1.5 71892 1khtA 192 4.42e+00 c.37.1.1 84401 1vm8A 534 4.56e+00 1eqcA 394 4.83e+00 1cz1A c.1.8.3 28811 1ryp2 233 5.39e+00 1ryp2 1vicA 262 5.77e+00 c.68.1.13 100756 1z90A 469 5.90e+00 1o50A 157 6.07e+00 d.37.1.1,d.37.1.1 92478,92479 1vquA 374 6.08e+00 1m22A 503 6.16e+00 c.117.1.1 78464 1amuA 563 6.29e+00 1amuA e.23.1.1 43351 1g97A 459 6.36e+00 1fwyA b.81.1.4,c.68.1.5 60394,60395 1yzbA 182 6.68e+00 1fkmA 396 6.76e+00 1fkmA a.69.2.1,a.69.2.1 18315,18316 1j5sA 463 6.82e+00 c.1.9.8 71580 3cox 507 6.99e+00 1b8sA c.3.1.2,d.16.1.1 30332,37863 1bj4A 470 7.11e+00 1bj4A c.67.1.4 34479 1zxxA 319 7.82e+00 1pbyB 337 8.35e+00 b.69.2.2 94422 1ksiA 642 9.13e+00 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24408,38043,38044 1qwrA 319 9.26e+00 b.82.1.3 96491 1om4A 422 1.01e+01 d.174.1.1 87067 1hm9A 468 1.02e+01 b.81.1.4,c.68.1.5 65866,65867 1tedA 393 1.03e+01 c.95.1.2 106807 1d0cA 444 1.08e+01 d.174.1.1 64769 1z94A 147 1.13e+01 1hdr 244 1.14e+01 1dhr c.2.1.2 29837 1vjoA 393 1.15e+01 c.67.1.3 100827 1wq3A 322 1.16e+01 1xr4A 509 1.19e+01 4pfk 319 1.19e+01 3pfk c.89.1.1 35582 1mmvB 419 1.19e+01 d.174.1.1 91318 1jmxB 349 1.24e+01 b.69.2.2 66906 1xfiA 367 1.27e+01 e.50.1.1 109584 2bvyA 475 1.29e+01 1r9gA 216 1.29e+01 c.23.16.1 97258 1dhr 241 1.30e+01 1dhr c.2.1.2 29832 1xffA 240 1.32e+01 d.153.1.1 109580 1d1vA 444 1.45e+01 1nseA d.174.1.1 59101 1af7 274 1.50e+01 1af7 a.58.1.1,c.66.1.8 17928,34203 1scuA 288 1.53e+01 2scuA c.2.1.8,c.23.4.1 30307,31135 1sl4A 155 1.58e+01 d.169.1.1 105710 1gdoA 240 1.60e+01 1gdoA 2ffjA 300 1.60e+01 1sdjA 310 1.60e+01 d.21.1.2,d.21.1.2 98807,98808 1tvjA 166 1.62e+01 1zowA 313 1.66e+01 1lm4A 194 1.67e+01 d.167.1.1 84626 1ed5A 444 1.67e+01 1nseA d.174.1.1 42530 1vb5A 276 1.69e+01 1rv3A 483 1.70e+01 c.67.1.4 105101 1vjpA 394 1.82e+01 c.2.1.3,d.81.1.3 100828,100829 2awfA 172 1.89e+01 2dorA 311 1.91e+01 2dorA c.1.4.1 28593 1hnjA 317 1.93e+01 1hn9A c.95.1.2,c.95.1.2 35969,35970 1hjsA 332 1.98e+01 c.1.8.3 83492 1rlzA 369 2.00e+01 c.31.1.1 104989 1zzmA 259 2.28e+01 1ui8A 638 2.37e+01 b.30.2.1,d.17.2.1,d.17.2.1 99419,99420,99421 1p6oA 161 2.39e+01 c.97.1.2 94185 1f6fB 210 2.48e+01 1axiB b.1.2.1,b.1.2.1 22033,22034 1vdwA 254 2.50e+01 e.7.1.1 100569 1go4A 205 2.53e+01 d.135.1.1 70292 1o0xA 262 2.54e+01 d.127.1.1 80755 1zc6A 305 2.55e+01 1u7nA 336 2.57e+01 c.77.1.4 107726 1wzaA 488 2.58e+01 1w6gA 646 2.62e+01 1q18A 332 2.63e+01 c.55.1.7,c.55.1.7 104470,104471 1qyaA 307 2.69e+01 d.21.1.2,d.21.1.2 104653,104654 2f6rA 281 2.74e+01 1vjzA 341 2.75e+01 c.1.8.3 100838 1rypH 205 2.76e+01 d.153.1.4 41876 1iqyA 638 2.80e+01 b.30.2.1,d.17.2.1,d.17.2.1 76763,76764,76765 1p1mA 406 2.83e+01 b.92.1.4,c.1.9.9 87696,87697 1k6wA 426 2.83e+01 b.92.1.2,c.1.9.5 68236,68237 1i1nA 226 2.87e+01 c.66.1.7 71102 1n57A 291 2.90e+01 c.23.16.2 85328 1ldg 316 2.93e+01 1ceqA c.2.1.5,d.162.1.1 30165,42132 1n4wA 504 2.95e+01 c.3.1.2,d.16.1.1 91676,91677 1siiA 646 2.97e+01 b.30.2.1,d.17.2.1,d.17.2.1 105578,105579,105580 1kfwA 435 3.03e+01 c.1.8.5,d.26.3.1 77376,77377 1r5jA 337 3.05e+01 c.77.1.5 97097 1bc5A 269 3.12e+01 1af7 a.58.1.1,c.66.1.8 17929,34204 1mxtA 504 3.13e+01 c.3.1.2,d.16.1.1 79671,79672 1t9kA 347 3.18e+01 c.124.1.5 106721 1j79A 347 3.29e+01 1j79A c.1.9.4 62675 1pfkA 320 3.46e+01 3pfk c.89.1.1 35575 1ev7A 317 3.53e+01 1ev7B c.52.1.9 33315 1u9iA 519 3.53e+01 2au3A 407 3.54e+01 1r9dA 787 3.54e+01 c.7.1.1 104865 1uj6A 227 3.55e+01 c.124.1.4,d.58.40.1 107898,107899 1m7vA 363 3.56e+01 d.174.1.1 78748 1xzoA 174 3.58e+01 1ki9A 192 3.63e+01 c.37.1.1 84404 1t2dA 322 3.64e+01 c.2.1.5,d.162.1.1 99084,99085 2c2aA 258 3.71e+01 1nksA 194 3.72e+01 1nksA c.37.1.1 31886 1pzgA 331 3.72e+01 c.2.1.5,d.162.1.1 95425,95426 2bw0A 329 3.76e+01 1g31A 111 3.84e+01 1g31A b.35.1.1 24656 1c24A 263 3.87e+01 1c24A d.127.1.1 41148 1dorA 311 3.87e+01 2dorA c.1.4.1 28595 1ui7A 638 3.93e+01 b.30.2.1,d.17.2.1,d.17.2.1 99413,99414,99415 1s3iA 310 4.12e+01 b.46.1.1,c.65.1.1 98435,98436 1ykiA 217 4.22e+01 1h8eD 482 4.23e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 1f8yA 157 4.25e+01 1f8xA c.23.14.1 31395 1wmzA 140 4.27e+01 d.169.1.1 109422 1fhdA 312 4.33e+01 1taxA c.1.8.3 28915 1n7kA 234 4.33e+01 c.1.10.1 85374 1amf 233 4.34e+01 1wod c.94.1.1 35833 1a62 130 4.35e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 2afwA 329 4.36e+01 1uasA 362 4.38e+01 b.71.1.1,c.1.8.1 88388,88389 2b0lA 102 4.43e+01 1v0lA 313 4.46e+01 c.1.8.3 108207 1icrA 217 4.46e+01 1vfrA d.90.1.1 62274 2pfkA 320 4.53e+01 3pfk c.89.1.1 35577 1sz2A 332 4.55e+01 1edqA 540 4.58e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1ex1A 605 4.62e+01 1ex1A c.1.8.7,c.23.11.1 29013,31347 1s0yA 76 4.65e+01 d.80.1.1 98314 1jflA 228 4.65e+01 c.78.2.1,c.78.2.1 71656,71657 1frb 315 4.65e+01 1frb c.1.7.1 28665 1yixA 265 4.66e+01 1zjjA 263 4.73e+01 1wznA 252 4.73e+01 1ha3A 405 4.75e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 2g9zA 348 4.78e+01 1lucA 355 4.81e+01 1lucA c.1.16.1 29547 1v72A 356 4.92e+01 1a2vA 655 4.94e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24416,38059,38060 1k7jA 206 4.94e+01 d.115.1.1 72103 1ig0A 319 4.97e+01 1ig0A b.82.6.1,c.100.1.1 62354,62355 1j09A 468 5.03e+01 a.97.1.1,c.26.1.1 77025,77026 1pj5A 830 5.05e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1y8qA 346 5.07e+01 1z8sA 146 5.10e+01 1v25A 541 5.13e+01 e.23.1.1 108275 1ws6A 171 5.20e+01 1xneA 113 5.20e+01 1k9jA 139 5.21e+01 d.169.1.1 68353 7taa 478 5.28e+01 7taa b.71.1.1,c.1.8.1 27778,28765 1ycoA 279 5.33e+01 1wviA 257 5.34e+01 1o6zA 303 5.39e+01 c.2.1.5,d.162.1.1 81107,81108 1j2rA 199 5.40e+01 c.33.1.3 90788 1w32A 348 5.46e+01 1clxA 347 5.47e+01 1taxA c.1.8.3 28899 2azwA 148 5.50e+01 1gpmA 525 5.52e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1ra0A 430 5.55e+01 2msbA 115 5.64e+01 1rtm1 d.169.1.1 42355 1xnzA 264 5.65e+01 1brwA 433 5.73e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1od8A 313 5.82e+01 c.1.8.3 86838 1o13A 136 5.83e+01 c.55.5.1 80762 1rjoA 646 5.83e+01 1s72E 178 5.85e+01 d.141.1.1,d.141.1.1 105323,105324 1wsrA 375 5.85e+01 1jmsA 381 5.85e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1b4vA 504 5.89e+01 1b8sA c.3.1.2,d.16.1.1 30334,37865 2a6hC 1119 5.95e+01 1u9cA 224 5.97e+01 2fo3A 125 5.97e+01 1dhs 344 6.02e+01 1dhs c.31.1.1 31727 1e0wA 313 6.07e+01 1taxA c.1.8.3 59150 1w44A 331 6.07e+01 2fctA 313 6.08e+01 1jubA 311 6.09e+01 c.1.4.1 90908 1fxjA 331 6.21e+01 1fwyA b.81.1.4,c.68.1.5 28062,34520 1jnrA 643 6.21e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1xs5A 241 6.24e+01 1e5mA 416 6.35e+01 1dd8A c.95.1.1,c.95.1.1 58973,58974 1tk9A 188 6.37e+01 c.80.1.3 107082 1zp4A 304 6.43e+01 1wg8A 285 6.44e+01 2f46A 156 6.44e+01 1j2gA 319 6.51e+01 d.96.1.4,d.96.1.4,d.96.1.4,d.96.1.4,d.96.1.4 103824,103825,103826,103827,103828 1k47A 337 6.51e+01 d.14.1.5,d.58.26.4 72040,72041 1whi 122 6.59e+01 1whi b.39.1.1 24810 1ztdA 133 6.61e+01 2fjbA 643 6.61e+01 2a1kA 233 6.65e+01 1pmmA 466 6.69e+01 c.67.1.6 94901 1j6pA 418 6.70e+01 b.92.1.4,c.1.9.9 77089,77090 1dosA 358 6.74e+01 1dosA c.1.10.2 29175 1jg1A 235 6.87e+01 c.66.1.7 66661 1zgzA 122 6.89e+01 2amhA 207 6.93e+01 2mgb 154 6.93e+01 1a6m a.1.1.2 15102 2g7uA 257 6.95e+01 1vljA 407 6.97e+01 e.22.1.2 108832 1gpc 218 7.08e+01 1gpc b.40.4.7 25393 1iw7C 1119 7.10e+01 e.29.1.1 71474 1s0uA 408 7.18e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 2fq3A 104 7.21e+01 1molA 94 7.25e+01 1molA d.17.1.1 37988 1rkbA 173 7.33e+01 1li5A 461 7.35e+01 a.27.1.1,c.26.1.1 73912,73913 1jlnA 297 7.35e+01 1pty c.45.1.2 63172 1r6lA 239 7.39e+01 d.14.1.4,d.101.1.1 97153,97154 1rxxA 421 7.41e+01 d.126.1.4 98061 1ht6A 405 7.45e+01 b.71.1.1,c.1.8.1 83629,83630 1tv8A 340 7.53e+01 c.1.28.3 107352 1frpA 335 7.53e+01 1frpA e.7.1.1 42875 1xc3A 302 7.54e+01 1shuX 182 7.57e+01 c.62.1.1 98882 2d09A 407 7.58e+01 1swxA 209 7.63e+01 a.224.1.1 106075 1anv 356 7.65e+01 1anv a.54.1.1,g.51.1.1,g.51.1.1 17890,45365,45371 1ayaA 101 7.66e+01 1qadA d.93.1.1 40460 1xrsA 516 7.69e+01 1g38A 393 7.71e+01 2admA c.66.1.27 60235 1e79D 482 7.74e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18272,26437,32317 1exmA 405 7.74e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 2awpA 198 7.77e+01 1sw5B 275 7.77e+01 c.94.1.1 106070 1ckmA 330 7.79e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 1v8dA 235 7.85e+01 c.140.1.1 108425 1ykdA 398 7.87e+01 1j9lA 247 7.91e+01 c.106.1.1 62762 1rkpA 326 7.92e+01 a.211.1.2 97620 1ooeA 236 7.93e+01 c.2.1.2 87196 1x38A 602 7.95e+01 2d0eA 407 8.16e+01 1sr4C 166 8.20e+01 b.42.2.1 105950 1lrzA 426 8.21e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1mhnA 59 8.27e+01 b.34.9.1 84964 1dd9A 338 8.27e+01 1dd9A e.13.1.1 43254 1fobA 334 8.35e+01 c.1.8.3 83255 2fb5A 205 8.40e+01 1i88A 389 8.41e+01 c.95.1.2,c.95.1.2 66070,66071 2fhzA 109 8.42e+01 2cu3A 64 8.45e+01 1w0mA 226 8.52e+01 c.1.1.1 109027 1fh9A 312 8.52e+01 1taxA c.1.8.3 28913 2frfA 153 8.60e+01 1dpjA 329 8.74e+01 1smrA b.50.1.2 26828 1vjrA 271 8.78e+01 c.108.1.14 100832 1ub3A 220 8.79e+01 c.1.10.1 88395 1iu4A 331 8.82e+01 d.3.1.8 71430 1e4yA 214 8.83e+01 1zin c.37.1.1,g.41.2.1 31901,45181 1xvaA 292 8.87e+01 1xvaA c.66.1.5 34183