# List of top-scoring protein chains for t04-w0.5-1-str4-0.1-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 2h78A 302 3.11e-06 1vpdA 299 4.29e-06 a.100.1.1,c.2.1.6 113951,113952 2ahrA 259 5.04e-06 a.100.1.10,c.2.1.6 126775,126776 2f1kA 279 5.35e-06 a.100.1.12,c.2.1.6 132772,132773 1yb4A 295 5.97e-06 2g5cA 281 6.44e-06 a.100.1.12,c.2.1.6 134646,134647 2izzA 322 7.38e-06 1np3A 338 1.11e-05 a.100.1.2,c.2.1.6 85946,85947 2pgdA 482 1.57e-05 a.100.1.1,c.2.1.6 18778,30190 1yqgA 263 1.65e-05 2p4qA 497 2.18e-05 1bg6 359 2.41e-05 2cvzA 289 2.47e-05 a.100.1.1,c.2.1.6 130890,130891 2pv7A 298 2.96e-05 1qmgA 524 3.34e-05 a.100.1.2,c.2.1.6 18785,30182 1pgjA 478 3.47e-05 a.100.1.1,c.2.1.6 18783,30195 2graA 277 3.94e-05 3c24A 286 4.20e-05 2pgd 482 6.22e-05 1ks9A 291 7.63e-05 a.100.1.7,c.2.1.6 68857,68858 2ew2A 316 9.46e-05 2rcyA 262 9.83e-05 1yrlA 491 9.91e-05 2i76A 276 0.000144 1txgA 335 0.000218 a.100.1.6,c.2.1.6 112775,112776 1zejA 293 0.000220 1evyA 366 0.000261 a.100.1.6,c.2.1.6 18811,30215 1f0yA 302 0.000264 a.100.1.3,c.2.1.6 18793,30197 1i36A 264 0.000421 a.100.1.8,c.2.1.6 71108,71109 1jayA 212 0.000751 c.2.1.6 66478 1zcjA 463 0.000847 1z82A 335 0.000857 1mv8A 436 0.001788 a.100.1.4,c.2.1.6,c.26.3.1 85128,85129,85130 1bg6A 359 0.002082 a.100.1.5,c.2.1.6 18810,30214 2dpoA 319 0.005705 2o3jA 481 0.006039 1dljA 402 0.006383 a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1dliA 402 0.009754 a.100.1.4,c.2.1.6,c.26.3.1 18809,30213,31622 2qytA 317 0.01675 1ff9A 450 0.01711 c.2.1.3,d.81.1.2 30039,39954 1x0vA 354 0.02151 2nacA 393 0.02543 c.2.1.4,c.23.12.1 30088,31348 1gdhA 320 0.02710 c.2.1.4,c.23.12.1 30095,31355 2fssA 365 0.03681 2j6iA 364 0.04604 1u8xX 472 0.05867 c.2.1.5,d.162.1.2 107741,107742 1tltA 319 0.06749 c.2.1.3,d.81.1.5 107135,107136 1ldg 316 0.07173 1gpjA 404 0.08195 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1psdA 409 0.08268 c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1vllA 334 0.08639 c.2.1.13 108834 1s6yA 450 0.08983 c.2.1.5,d.162.1.2 105314,105315 2g76A 335 0.09500 1pzgA 331 0.09742 c.2.1.5,d.162.1.1 95425,95426 1wwkA 307 0.1003 1t2dA 322 0.1093 c.2.1.5,d.162.1.1 99084,99085 1xwfA 431 0.1112 c.2.1.4,c.23.12.3 122392,122393 1j4aA 333 0.1129 c.2.1.4,c.23.12.1 71502,71503 1mx3A 347 0.1182 c.2.1.4,c.23.12.1 79638,79639 1x7dA 350 0.1277 c.2.1.13 114927 1uxjA 309 0.1308 c.2.1.5,d.162.1.1 108112,108113 1xdwA 331 0.1404 2hk9A 275 0.1417 1lssA 140 0.1455 c.2.1.9 74246 2o4cA 380 0.1571 1omoA 322 0.1726 c.2.1.13 104017 1qv9A 283 0.1842 c.127.1.1 96356 1ur5A 309 0.2124 c.2.1.5,d.162.1.1 99807,99808 2b0jA 358 0.2125 a.100.1.11,c.2.1.6 127639,127640 1d4fA 431 0.2201 c.2.1.4,c.23.12.3 30110,31370 1qp8A 303 0.2207 c.2.1.4,c.23.12.1 30092,31352 1xeaA 323 0.2350 c.2.1.3,d.81.1.5 109572,109573 1lldA 319 0.2600 c.2.1.5,d.162.1.1 30177,42144 1li4A 432 0.2756 c.2.1.4,c.23.12.3 84616,84617 2d0iA 333 0.2787 1up6A 416 0.2790 c.2.1.5,d.162.1.2 107976,107977 1dxy 333 0.2859 2pi1A 334 0.3098 1ygyA 529 0.3345 c.2.1.4,c.23.12.1,d.58.18.1,d.81.2.2 123150,123151,123152,123153 2dbqA 334 0.3549 2gcgA 330 0.4634 2d5cA 263 0.4670 1v8bA 479 0.4734 c.2.1.4,c.23.12.3 113564,113565 1up7A 417 0.4994 c.2.1.5,d.162.1.2 113374,113375 1guzA 310 0.5078 c.2.1.5,d.162.1.1 65586,65587 1nytA 271 0.5182 c.2.1.7,c.58.1.5 86417,86418 2cukA 311 0.5529 1obbA 480 0.5678 c.2.1.5,d.162.1.2 86760,86761 2eggA 297 0.5903 1dxyA 333 0.5988 c.2.1.4,c.23.12.1 30094,31354 1hyhA 309 0.6854 c.2.1.5,d.162.1.1 30150,42117 1p77A 272 0.7074 c.2.1.7,c.58.1.5 94214,94215 2nloA 302 0.7205 2vhxA 377 0.7368 6ldhA 329 0.7465 c.2.1.5,d.162.1.1 30161,42128 2ewdA 317 0.7605 1sc6A 404 0.7819 c.2.1.4,c.23.12.1,d.58.18.1 118932,118933,118934 2i6tA 303 0.8511 1npyA 271 0.8581 c.2.1.7,c.58.1.5 85995,85996 1f06A 320 0.9664 c.2.1.3,d.81.1.3 59556,59557 1vjtA 483 1.144 c.2.1.5,d.162.1.2 100833,100834 1gcuA 295 1.153 c.2.1.3,d.81.1.4 30063,39978 1pjcA 361 1.168 c.2.1.4,c.23.12.2 30101,31361 3ceaA 346 1.260 2ho3A 325 1.320 2axqA 467 1.365 2nvwA 479 1.442 c.2.1.3,d.81.1.5 138665,138666 1vknA 351 1.476 c.2.1.3,d.81.1.1 108676,108677 2glxA 332 1.547 2dc1A 236 1.688 1nvtA 287 1.741 c.2.1.7,c.58.1.5 86270,86271 1hdoA 206 1.751 c.2.1.2 60965 2gptA 523 1.890 2hmvA 144 1.919 c.2.1.9 136615 2v7pA 310 2.035 1lehA 364 2.051 c.2.1.7,c.58.1.1 30268,33916 2q4eA 362 2.178 2d59A 144 2.294 c.2.1.8 131266 2p2sA 336 2.351 1c1dA 355 2.494 c.2.1.7,c.58.1.1 30270,33918 1ez4A 318 2.625 c.2.1.5,d.162.1.1 64917,64918 1ofgA 381 2.661 c.2.1.3,d.81.1.5 30064,39979 2nqtA 352 2.673 1a5zA 319 2.706 c.2.1.5,d.162.1.1 30181,42148 1qydA 313 2.814 c.2.1.2 96583 1a4iA 301 2.846 c.2.1.7,c.58.1.2 30278,33926 1nvmB 312 3.083 c.2.1.3,d.81.1.1 86251,86252 1k6xA 352 3.086 c.2.1.2 68238 1j5pA 253 3.194 d.81.1.3,c.2.1.3 71577,83092 3c1aA 315 3.217 2g1uA 155 3.238 2hjsA 340 3.366 c.2.1.3,d.81.1.1 136547,136548 1iukA 140 3.410 c.2.1.8 83712 1h6dA 433 3.491 c.2.1.3,d.81.1.5 65656,65657 2o7sA 523 3.521 1l7dA 384 3.806 c.2.1.4,c.23.12.2 77774,77775 1cf2O 337 3.931 c.2.1.3,d.81.1.1 29994,39909 1vi2A 300 3.955 c.2.1.7,c.58.1.5 100726,100727 2eklA 313 3.988 1y81A 138 4.075 c.2.1.8 122731 1lsuA 147 4.098 c.2.1.9 74250 2vojA 371 4.099 2g17A 337 4.114 c.2.1.3,d.81.1.1 134512,134513 3bioA 304 4.379 2o4uX 334 4.415 1zh8A 340 4.521 c.2.1.3,d.81.1.5 125077,125078 2aefA 234 5.089 2gz1A 366 5.266 c.2.1.3,d.81.1.1 135887,135888 1xq6A 253 5.288 c.2.1.2 115829 3c85A 183 5.303 1rydA 387 5.314 c.2.1.3,d.81.1.5 118801,118802 1scuA 288 5.617 c.2.1.8,c.23.4.1 30307,31135 2cmdA 312 5.640 c.2.1.5,d.162.1.1 30135,42102 2exxA 306 6.277 2a4kA 263 6.686 c.2.1.2 126156 1drwA 273 6.788 c.2.1.3,d.81.1.3 30057,39972 1x13A 401 7.781 1luaA 287 7.818 c.2.1.7,c.58.1.4 78216,78217 1uufA 369 7.858 b.35.1.2,c.2.1.1 100006,100007 2ixaA 444 7.957 2r00A 336 8.090 2czcA 334 8.164 d.81.1.1 131044 1lc0A 294 9.031 c.2.1.3,d.81.1.4 73823,73824 1yqdA 366 9.544 2csuA 457 10.77 c.2.1.8,c.23.4.1,c.23.4.1 130781,130782,130783 1xgkA 352 11.32 c.2.1.2 115286 1hwxA 501 11.82 c.2.1.7,c.58.1.1 30250,33898 1drw 273 12.35 2jfgA 445 13.10 c.5.1.1,c.59.1.1,c.72.2.1 138306,138307,138308 2r6jA 318 13.41 2cdcA 366 13.49 2z1nA 260 13.75 2ph5A 480 13.91 1b0aA 288 14.00 c.2.1.7,c.58.1.2 30286,33934 2nxcA 254 14.12 c.66.1.39 138739 1qycA 308 14.97 c.2.1.2 96581 2ozpA 345 15.13 1othA 321 16.48 c.78.1.1,c.78.1.1 35260,35261 1ys4A 354 17.32 1k2wA 256 17.40 c.2.1.2 90927 2gasA 307 17.59 2bryA 497 18.22 1pl8A 356 19.39 b.35.1.2,c.2.1.1 94878,94879 2cf5A 357 19.47 1orrA 347 19.72 c.2.1.2 93460 2h6eA 344 20.20 1vj0A 380 20.70 b.35.1.2,c.2.1.1 100786,100787 1b7gO 340 21.34 c.2.1.3,d.81.1.1 29992,39907 1ydeA 270 21.73 c.2.1.2 122980 1kyqA 274 22.01 c.2.1.11,e.37.1.1 73281,73282 2pd6A 264 22.23 1e3jA 352 22.76 b.35.1.2,c.2.1.1 24765,29781 2v3aA 384 22.79 1x7gA 261 23.69 c.2.1.2 114929 1yb1A 272 24.35 c.2.1.2 116599 1o6zA 303 25.38 c.2.1.5,d.162.1.1 81107,81108 2ejwA 332 26.35 2q46A 253 26.40 c.2.1.2 139825 1f8fA 371 26.55 b.35.1.2,c.2.1.1 83246,83247 2bzgA 232 26.61 c.66.1.36 129559 1pvvA 315 26.61 c.78.1.1,c.78.1.1 95190,95191 2q49A 359 26.76 c.2.1.3,d.81.1.1 139831,139832 1xhlA 297 26.94 c.2.1.2 109591 1fl2A 310 27.03 c.3.1.5,c.3.1.5 59869,59870 1xhcA 367 27.47 c.3.1.5,c.3.1.5,d.87.1.1 115292,115293,115294 1nhp 447 27.67 1q7gA 359 27.77 c.2.1.3,d.81.1.2 96038,96039 1gegA 256 28.17 c.2.1.2 29888 2jahA 247 28.60 2yyyA 343 28.87 1yqzA 438 29.17 1sb8A 352 29.29 c.2.1.2 105410 2cduA 452 29.70 1bdbA 277 30.15 c.2.1.2 29874 1zud1 251 30.61 1pbeA 394 30.84 c.3.1.2,d.16.1.2 30338,37869 2p5yA 311 31.14 1xseA 295 31.61 c.2.1.2 115925 1zk4A 251 31.79 c.2.1.2 125176 2qa1A 500 32.14 1d7yA 408 32.23 c.3.1.5,c.3.1.5,d.87.1.1 30565,30566,40204 1lluA 342 32.40 b.35.1.2,c.2.1.1 91064,91065 1vm6A 228 32.47 d.81.1.3,c.2.1.3 108877,118631 1y1pA 342 32.93 c.2.1.2 122550 1e7wA 291 33.22 c.2.1.2 59373 1fmcA 255 34.42 c.2.1.2 29856 1gesA 450 35.12 c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 2ph3A 245 35.31 1w6uA 302 35.51 c.2.1.2 114288 1hxhA 253 36.35 c.2.1.2 76725 1zq9A 285 36.51 c.66.1.24 125505 3grs 478 36.84 1spxA 278 37.03 c.2.1.2 98958 1q1rA 431 37.53 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1zmdA 474 37.66 1n7hA 381 37.71 c.2.1.2 80250 1nffA 260 37.80 c.2.1.2 80457 1yxmA 303 37.86 c.2.1.2 124192 1b16A 254 37.88 c.2.1.2 29875 2b69A 343 37.96 c.2.1.2 127974 1cydA 244 38.13 c.2.1.2 29825 1xkqA 280 38.20 c.2.1.2 115417 2h1rA 299 38.34 2gqwA 408 38.49 2d8aA 348 38.52 2a9fA 398 39.00 1y56B 382 39.21 1jw9B 249 40.01 c.111.1.1 67377 1hdcA 253 40.29 c.2.1.2 29862 2c29D 337 40.41 2o23A 265 40.51 c.2.1.2 138884 1q7bA 244 41.07 c.2.1.2 96026 2nwqA 272 41.49 2cmd 312 41.78 2bgkA 278 41.92 c.2.1.2 128480 1zmtA 254 42.14 c.2.1.2 125363 1vl8A 267 43.70 c.2.1.2 108733 2r0cA 549 43.99 1rkxA 357 44.30 c.2.1.2 97631 1y8cA 246 44.74 c.66.1.43 116563 3cc8A 230 45.51 1xa0A 328 45.87 b.35.1.2,c.2.1.1 115021,115022 1ja9A 274 46.45 c.2.1.2 62817 1zk7A 467 46.50 1nhsA 447 46.52 c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 1db3A 372 46.99 c.2.1.2 29813 2pnfA 248 47.09 1duvG 333 48.27 c.78.1.1,c.78.1.1 35228,35229 1eudA 311 48.56 c.2.1.8,c.23.4.1 30312,31140 1vl6A 388 49.03 c.2.1.7,c.58.1.3 108724,108725 2b5wA 357 49.09 1qyrA 252 49.20 c.66.1.24 104657 2bkaA 242 49.56 c.2.1.2 128666 2hcyA 347 49.74 2avnA 260 50.05 c.66.1.41 127380 2ag5A 246 50.11 c.2.1.2 126719 1nhpA 447 50.14 c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 1n8kA 374 50.96 b.35.1.2,c.2.1.1 80298,80299 1y5mA 276 51.12 c.2.1.2 122645 1iz0A 302 51.64 b.35.1.2,c.2.1.1 83821,83822 1l1eA 287 51.73 c.66.1.18 73454 2fk8A 318 52.17 c.66.1.18 133648 2c5aA 379 52.27 c.2.1.2 129894 1pwxA 254 53.03 c.2.1.2 95262 1jqbA 351 53.04 b.35.1.2,c.2.1.1 77151,77152 3c4aA 381 53.81 1xu9A 286 54.00 c.2.1.2 116052 1qrrA 394 54.23 c.2.1.2 29824 2iidA 498 54.64 c.3.1.2,d.16.1.5 137426,137427 1hyuA 521 56.01 c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1oc2A 348 56.26 c.2.1.2 92765 2gdzA 267 57.00 c.2.1.2 135043 1e6wA 260 57.40 c.2.1.2 59326 2p4hX 322 57.49 3c8mA 331 57.61 1t2aA 375 58.23 c.2.1.2 99078 1dv2A 452 58.77 b.84.2.1,c.30.1.1,d.142.1.2 28238,31645,41490 1id1A 153 58.87 c.2.1.9 62286 3ladA 476 59.15 c.3.1.5,c.3.1.5,d.87.1.1 30573,30574,40208 1gtmA 419 59.75 c.2.1.7,c.58.1.1 30223,33871 1ve3A 227 60.46 c.66.1.43 120010 1ebfA 358 60.67 c.2.1.3,d.81.1.2 30033,39948 1wznA 252 60.79 c.66.1.43 121525 2z5lA 511 60.96 2cfcA 250 62.19 1xcbA 211 62.98 a.4.5.38,c.2.1.12 109552,109553 1wmaA 276 63.25 c.2.1.2 121042 1pjqA 457 63.49 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 2blnA 305 63.70 b.46.1.1,c.65.1.1 128734,128735 1b3bA 415 63.88 c.2.1.7,c.58.1.1 30244,33892 2g82A 331 64.20 c.2.1.3,d.81.1.1 134746,134747 1dssG 333 64.75 c.2.1.3,d.81.1.1 30022,39937 1y9aA 360 65.31 1eny 268 65.53 1mo9A 523 66.04 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 2p91A 285 66.99 1b6rA 355 67.40 b.84.2.1,c.30.1.1,d.142.1.2 28241,31648,41493 2gf3A 389 67.89 c.3.1.2,d.16.1.3 135070,135071 2jaeA 489 68.25 1i24A 404 70.11 c.2.1.2 83663 1b26A 416 70.51 c.2.1.7,c.58.1.1 30232,33880 2c7pA 327 71.11 c.66.1.26 130080 1h5qA 265 71.17 c.2.1.2 60643 1xel 338 71.18 1z45A 699 72.08 b.30.5.4,c.2.1.2 124427,124428 1i2cA 404 72.10 c.2.1.2 83666 1wvgA 359 72.82 c.2.1.2 121339 1zd8A 227 72.98 1z7bA 358 74.34 c.2.1.2 124599 3c96A 415 74.62 2dvmA 439 74.88 2z1mA 345 75.38 2yutA 207 76.77 1xg5A 279 77.35 c.2.1.2 115277 1bmdA 327 78.30 c.2.1.5,d.162.1.1 30139,42106 2dwcA 433 78.35 1p0fA 373 78.75 b.35.1.2,c.2.1.1 87642,87643 1kevA 351 78.77 b.35.1.2,c.2.1.1 24749,29765 2h7mA 269 79.22 c.2.1.2 136219 2c07A 285 79.27 c.2.1.2 129577 1mb4A 370 79.55 c.2.1.3,d.81.1.1 78908,78909 3bkwA 243 79.90 1mldA 314 81.95 c.2.1.5,d.162.1.1 30122,42089 1ek6A 348 82.11 c.2.1.2 29800 1y8qA 346 82.79 1x9iA 302 84.51 c.80.1.1 114997 1rpnA 335 85.39 c.2.1.2 97708 1e6uA 321 86.84 c.2.1.2 29805 1x1tA 260 89.18 c.2.1.2 121597