# List of top-scoring protein chains for t04-w0.5-1-bys-0.1-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. # #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 SCOP_domain SCOP_suid 5S 5N 12S 12S 10N 2ahrA 259 2.79e-06 a.100.1.10,c.2.1.6 126775,126776 1vpdA 299 3.39e-06 a.100.1.1,c.2.1.6 113951,113952 2f1kA 279 3.39e-06 a.100.1.12,c.2.1.6 132772,132773 2h78A 302 3.46e-06 1yb4A 295 3.79e-06 2pgdA 482 6.15e-06 a.100.1.1,c.2.1.6 18778,30190 2izzA 322 7.06e-06 2g5cA 281 7.10e-06 a.100.1.12,c.2.1.6 134646,134647 1np3A 338 7.10e-06 a.100.1.2,c.2.1.6 85946,85947 2p4qA 497 8.40e-06 1bg6 359 1.41e-05 2cvzA 289 1.47e-05 a.100.1.1,c.2.1.6 130890,130891 1yqgA 263 1.56e-05 2graA 277 1.90e-05 2pv7A 298 2.08e-05 1pgjA 478 2.29e-05 a.100.1.1,c.2.1.6 18783,30195 1qmgA 524 2.42e-05 a.100.1.2,c.2.1.6 18785,30182 2pgd 482 3.01e-05 1yrlA 491 3.21e-05 3c24A 286 4.27e-05 1ks9A 291 4.90e-05 a.100.1.7,c.2.1.6 68857,68858 2rcyA 262 5.62e-05 2ew2A 316 9.63e-05 1zejA 293 0.000130 2i76A 276 0.000157 1evyA 366 0.000200 a.100.1.6,c.2.1.6 18811,30215 1f0yA 302 0.000307 a.100.1.3,c.2.1.6 18793,30197 1txgA 335 0.000311 a.100.1.6,c.2.1.6 112775,112776 1i36A 264 0.000316 a.100.1.8,c.2.1.6 71108,71109 1jayA 212 0.000442 c.2.1.6 66478 1zcjA 463 0.000999 1z82A 335 0.001049 1bg6A 359 0.001788 a.100.1.5,c.2.1.6 18810,30214 1mv8A 436 0.002271 a.100.1.4,c.2.1.6,c.26.3.1 85128,85129,85130 1dljA 402 0.004997 a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 2o3jA 481 0.007190 2dpoA 319 0.007554 1ff9A 450 0.01297 c.2.1.3,d.81.1.2 30039,39954 1dliA 402 0.01347 a.100.1.4,c.2.1.6,c.26.3.1 18809,30213,31622 1gdhA 320 0.02296 c.2.1.4,c.23.12.1 30095,31355 2nacA 393 0.02944 c.2.1.4,c.23.12.1 30088,31348 1x0vA 354 0.03412 2qytA 317 0.03665 2fssA 365 0.04184 1u8xX 472 0.05646 c.2.1.5,d.162.1.2 107741,107742 1s6yA 450 0.06760 c.2.1.5,d.162.1.2 105314,105315 2j6iA 364 0.08127 1wwkA 307 0.08252 1mx3A 347 0.09859 c.2.1.4,c.23.12.1 79638,79639 1tltA 319 0.09894 c.2.1.3,d.81.1.5 107135,107136 1gpjA 404 0.1028 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1psdA 409 0.1196 c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1qv9A 283 0.1201 c.127.1.1 96356 1xdwA 331 0.1341 1pzgA 331 0.1368 c.2.1.5,d.162.1.1 95425,95426 1vllA 334 0.1411 c.2.1.13 108834 1j4aA 333 0.1677 c.2.1.4,c.23.12.1 71502,71503 1xwfA 431 0.1687 c.2.1.4,c.23.12.3 122392,122393 2hk9A 275 0.1786 1uxjA 309 0.1869 c.2.1.5,d.162.1.1 108112,108113 2g76A 335 0.1871 2o4cA 380 0.1987 1ldg 316 0.1990 1t2dA 322 0.2090 c.2.1.5,d.162.1.1 99084,99085 1dxy 333 0.2225 1x7dA 350 0.2271 c.2.1.13 114927 1lssA 140 0.2465 c.2.1.9 74246 2d0iA 333 0.2516 1ur5A 309 0.2613 c.2.1.5,d.162.1.1 99807,99808 2b0jA 358 0.2808 a.100.1.11,c.2.1.6 127639,127640 1xeaA 323 0.2872 c.2.1.3,d.81.1.5 109572,109573 1d4fA 431 0.2946 c.2.1.4,c.23.12.3 30110,31370 1omoA 322 0.3024 c.2.1.13 104017 2dbqA 334 0.3026 1qp8A 303 0.3630 c.2.1.4,c.23.12.1 30092,31352 1lldA 319 0.4073 c.2.1.5,d.162.1.1 30177,42144 1li4A 432 0.4114 c.2.1.4,c.23.12.3 84616,84617 2vhxA 377 0.4230 1up6A 416 0.4771 c.2.1.5,d.162.1.2 107976,107977 2pi1A 334 0.5086 1v8bA 479 0.5261 c.2.1.4,c.23.12.3 113564,113565 1obbA 480 0.5333 c.2.1.5,d.162.1.2 86760,86761 1sc6A 404 0.5482 c.2.1.4,c.23.12.1,d.58.18.1 118932,118933,118934 1ygyA 529 0.6328 c.2.1.4,c.23.12.1,d.58.18.1,d.81.2.2 123150,123151,123152,123153 1up7A 417 0.7697 c.2.1.5,d.162.1.2 113374,113375 2gcgA 330 0.7867 1nytA 271 0.8010 c.2.1.7,c.58.1.5 86417,86418 2cukA 311 0.8861 2i6tA 303 0.8963 2eklA 313 0.9118 2d5cA 263 0.9334 1guzA 310 0.9939 c.2.1.5,d.162.1.1 65586,65587 2eggA 297 1.028 1f06A 320 1.073 c.2.1.3,d.81.1.3 59556,59557 1hyhA 309 1.087 c.2.1.5,d.162.1.1 30150,42117 1gcuA 295 1.094 c.2.1.3,d.81.1.4 30063,39978 1vjtA 483 1.164 c.2.1.5,d.162.1.2 100833,100834 2ewdA 317 1.229 1dxyA 333 1.245 c.2.1.4,c.23.12.1 30094,31354 1p77A 272 1.314 c.2.1.7,c.58.1.5 94214,94215 2nloA 302 1.419 3ceaA 346 1.539 2nvwA 479 1.717 c.2.1.3,d.81.1.5 138665,138666 1pjcA 361 1.741 c.2.1.4,c.23.12.2 30101,31361 2glxA 332 1.767 6ldhA 329 1.835 c.2.1.5,d.162.1.1 30161,42128 1vknA 351 1.854 c.2.1.3,d.81.1.1 108676,108677 2aefA 234 1.946 2ho3A 325 1.968 1lehA 364 2.112 c.2.1.7,c.58.1.1 30268,33916 2dc1A 236 2.202 1npyA 271 2.220 c.2.1.7,c.58.1.5 85995,85996 2vojA 371 2.267 2axqA 467 2.602 2v7pA 310 2.680 1nvtA 287 2.702 c.2.1.7,c.58.1.5 86270,86271 1lsuA 147 2.977 c.2.1.9 74250 2d59A 144 3.022 c.2.1.8 131266 2q4eA 362 3.258 1ofgA 381 3.269 c.2.1.3,d.81.1.5 30064,39979 1hdoA 206 3.298 c.2.1.2 60965 2p2sA 336 3.767 1qydA 313 3.850 c.2.1.2 96583 2gptA 523 3.887 3c1aA 315 3.985 1ez4A 318 4.241 c.2.1.5,d.162.1.1 64917,64918 1h6dA 433 4.286 c.2.1.3,d.81.1.5 65656,65657 1y81A 138 4.451 c.2.1.8 122731 2hmvA 144 4.625 c.2.1.9 136615 1a5zA 319 4.663 c.2.1.5,d.162.1.1 30181,42148 1a4iA 301 4.751 c.2.1.7,c.58.1.2 30278,33926 3c85A 183 4.859 1j5pA 253 5.054 d.81.1.3,c.2.1.3 71577,83092 1iukA 140 5.200 c.2.1.8 83712 1k6xA 352 5.346 c.2.1.2 68238 1zh8A 340 5.391 c.2.1.3,d.81.1.5 125077,125078 2o7sA 523 5.459 2hjsA 340 5.803 c.2.1.3,d.81.1.1 136547,136548 1c1dA 355 5.958 c.2.1.7,c.58.1.1 30270,33918 2g1uA 155 6.395 2g17A 337 6.595 c.2.1.3,d.81.1.1 134512,134513 1rydA 387 6.876 c.2.1.3,d.81.1.5 118801,118802 1nvmB 312 6.883 c.2.1.3,d.81.1.1 86251,86252 3bioA 304 6.931 2nqtA 352 7.740 1drwA 273 7.940 c.2.1.3,d.81.1.3 30057,39972 1l7dA 384 8.398 c.2.1.4,c.23.12.2 77774,77775 2o4uX 334 8.521 1drw 273 8.649 1scuA 288 9.435 c.2.1.8,c.23.4.1 30307,31135 1cf2O 337 9.459 c.2.1.3,d.81.1.1 29994,39909 2cmdA 312 9.808 c.2.1.5,d.162.1.1 30135,42102 1xq6A 253 10.26 c.2.1.2 115829 2a4kA 263 10.34 c.2.1.2 126156 2r6jA 318 10.66 1xgkA 352 11.09 c.2.1.2 115286 2ixaA 444 11.83 1yqdA 366 11.98 2gz1A 366 12.26 c.2.1.3,d.81.1.1 135887,135888 2bryA 497 12.34 1lc0A 294 13.16 c.2.1.3,d.81.1.4 73823,73824 2exxA 306 13.77 2ph5A 480 14.13 2csuA 457 14.33 c.2.1.8,c.23.4.1,c.23.4.1 130781,130782,130783 1vi2A 300 15.62 c.2.1.7,c.58.1.5 100726,100727 2gasA 307 15.65 2r00A 336 15.72 2ozpA 345 15.94 2z1nA 260 15.97 1qycA 308 16.34 c.2.1.2 96581 2czcA 334 17.21 d.81.1.1 131044 1k2wA 256 17.29 c.2.1.2 90927 1uufA 369 18.01 b.35.1.2,c.2.1.1 100006,100007 1x13A 401 18.08 1kyqA 274 20.24 c.2.1.11,e.37.1.1 73281,73282 2jfgA 445 21.02 c.5.1.1,c.59.1.1,c.72.2.1 138306,138307,138308 2pd6A 264 21.40 2q49A 359 21.43 c.2.1.3,d.81.1.1 139831,139832 2cf5A 357 21.87 2cdcA 366 22.09 2nxcA 254 23.11 c.66.1.39 138739 1xhlA 297 24.19 c.2.1.2 109591 1yb1A 272 24.54 c.2.1.2 116599 2v3aA 384 24.57 1b0aA 288 24.91 c.2.1.7,c.58.1.2 30286,33934 1luaA 287 25.59 c.2.1.7,c.58.1.4 78216,78217 1ys4A 354 26.38 1x7gA 261 27.44 c.2.1.2 114929 1ydeA 270 27.48 c.2.1.2 122980 1e7wA 291 27.61 c.2.1.2 59373 2p5yA 311 27.74 2qa1A 500 28.14 2bzgA 232 28.75 c.66.1.36 129559 1orrA 347 28.96 c.2.1.2 93460 1y9aA 360 29.32 1zud1 251 29.80 2c5aA 379 29.96 c.2.1.2 129894 1pvvA 315 30.09 c.78.1.1,c.78.1.1 95190,95191 1pwxA 254 30.52 c.2.1.2 95262 1w6uA 302 31.27 c.2.1.2 114288 1vj0A 380 31.92 b.35.1.2,c.2.1.1 100786,100787 2jahA 247 32.02 1xseA 295 33.27 c.2.1.2 115925 1othA 321 35.33 c.78.1.1,c.78.1.1 35260,35261 2ph3A 245 35.38 1hwxA 501 36.11 c.2.1.7,c.58.1.1 30250,33898 1zk4A 251 36.35 c.2.1.2 125176 1zmtA 254 36.70 c.2.1.2 125363 2r0cA 549 36.86 1fl2A 310 37.05 c.3.1.5,c.3.1.5 59869,59870 1yxmA 303 37.95 c.2.1.2 124192 1zk7A 467 38.95 3grs 478 39.26 2bkaA 242 39.89 c.2.1.2 128666 1zmdA 474 39.99 1nhp 447 40.24 2d8aA 348 40.53 2hcyA 347 41.08 1jw9B 249 41.29 c.111.1.1 67377 2pnfA 248 41.40 1pbeA 394 42.26 c.3.1.2,d.16.1.2 30338,37869 2o23A 265 42.33 c.2.1.2 138884 1xkqA 280 42.34 c.2.1.2 115417 1bdbA 277 44.72 c.2.1.2 29874 1xg5A 279 44.77 c.2.1.2 115277 2z5lA 511 44.82 1yqzA 438 45.96 1vl8A 267 46.30 c.2.1.2 108733 2nwqA 272 46.31 1d7yA 408 46.77 c.3.1.5,c.3.1.5,d.87.1.1 30565,30566,40204 1zq9A 285 47.32 c.66.1.24 125505 1pl8A 356 48.35 b.35.1.2,c.2.1.1 94878,94879 1n7hA 381 48.42 c.2.1.2 80250 1lluA 342 48.57 b.35.1.2,c.2.1.1 91064,91065 1gesA 450 48.60 c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 1dv2A 452 48.85 b.84.2.1,c.30.1.1,d.142.1.2 28238,31645,41490 2ouiA 360 48.93 2h6eA 344 50.27 2b69A 343 50.79 c.2.1.2 127974 3ladA 476 50.95 c.3.1.5,c.3.1.5,d.87.1.1 30573,30574,40208 1spxA 278 51.41 c.2.1.2 98958 2bgkA 278 51.62 c.2.1.2 128480 1eyzA 392 52.06 b.84.2.1,c.30.1.1,d.142.1.2 28246,31653,41498 2b5wA 357 52.66 1y1pA 342 52.92 c.2.1.2 122550 1fmcA 255 53.21 c.2.1.2 29856 2dwcA 433 53.90 1b6rA 355 54.94 b.84.2.1,c.30.1.1,d.142.1.2 28241,31648,41493 1f8fA 371 55.16 b.35.1.2,c.2.1.1 83246,83247 1gegA 256 55.52 c.2.1.2 29888 2gdzA 267 56.39 c.2.1.2 135043 1q7gA 359 56.41 c.2.1.3,d.81.1.2 96038,96039 2yqzA 263 56.74 1mo9A 523 56.82 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1e3jA 352 56.86 b.35.1.2,c.2.1.1 24765,29781 2ekpA 239 56.99 1xel 338 57.04 1b7gO 340 57.60 c.2.1.3,d.81.1.1 29992,39907 1t2aA 375 57.91 c.2.1.2 99078 1pjqA 457 59.01 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 1xhcA 367 59.42 c.3.1.5,c.3.1.5,d.87.1.1 115292,115293,115294 1i2cA 404 59.79 c.2.1.2 83666 1nhpA 447 61.04 c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 1iz0A 302 61.05 b.35.1.2,c.2.1.1 83821,83822 1jqbA 351 62.21 b.35.1.2,c.2.1.1 77151,77152 1o6zA 303 62.64 c.2.1.5,d.162.1.1 81107,81108 2gqwA 408 63.27 1nhsA 447 63.45 c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 1kevA 351 64.34 b.35.1.2,c.2.1.1 24749,29765 2c07A 285 64.39 c.2.1.2 129577 2cmd 312 65.33 2ejwA 332 65.69 1sb8A 352 66.10 c.2.1.2 105410 2cduA 452 70.12 1ykjA 394 71.29 1b16A 254 71.40 c.2.1.2 29875 2z1mA 345 71.97 2p4hX 322 72.31 2qq5A 260 72.40 1db3A 372 72.71 c.2.1.2 29813 1q1rA 431 73.25 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 2h1rA 299 73.75 1rkxA 357 74.05 c.2.1.2 97631 1zemA 262 74.31 c.2.1.2 124984 3cc8A 230 75.57 1hxhA 253 77.56 c.2.1.2 76725 1y5mA 276 77.59 c.2.1.2 122645 2fdxA 138 78.24 c.23.5.1 31192 1kjqA 391 78.27 b.84.2.1,c.30.1.1,d.142.1.2 72616,72617,72618 1e6wA 260 78.56 c.2.1.2 59326 1ja9A 274 78.62 c.2.1.2 62817 1qrrA 394 78.89 c.2.1.2 29824 1cydA 244 79.28 c.2.1.2 29825 1vm6A 228 79.77 d.81.1.3,c.2.1.3 108877,118631 1xu9A 286 80.42 c.2.1.2 116052 1h7wA 1025 80.93 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15683,28628,30324,30609,39007 1oc2A 348 81.25 c.2.1.2 92765 1trb 320 83.70 1q9iA 571 84.05 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1i24A 404 84.87 c.2.1.2 83663 3c4aA 381 86.93 1q7bA 244 87.00 c.2.1.2 96026 2dt5A 211 87.29 a.4.5.38,c.2.1.12 131708,131709 1jzuA 157 87.68 b.60.1.1 84271 1y8cA 246 89.73 c.66.1.43 116563