# List of top-scoring protein chains for t04-w0.5-1-pb-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 2c2xA 281 8.96e-08 1b0aA 288 4.42e-07 c.2.1.7,c.58.1.2 30286,33934 2g76A 335 4.60e-07 2eklA 313 5.17e-07 1ygyA 529 5.50e-07 c.2.1.4,c.23.12.1,d.58.18.1,d.81.2.2 123150,123151,123152,123153 2gcgA 330 6.45e-07 2cukA 311 6.46e-07 1gdhA 320 8.00e-07 c.2.1.4,c.23.12.1 30095,31355 2nacA 393 8.02e-07 c.2.1.4,c.23.12.1 30088,31348 1wwkA 307 9.15e-07 1a4iA 301 1.23e-06 c.2.1.7,c.58.1.2 30278,33926 2pi1A 334 1.26e-06 1psdA 409 1.30e-06 c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 2dbqA 334 1.32e-06 1mx3A 347 1.71e-06 c.2.1.4,c.23.12.1 79638,79639 1j4aA 333 1.84e-06 c.2.1.4,c.23.12.1 71502,71503 2vojA 371 2.98e-06 1dxyA 333 3.33e-06 c.2.1.4,c.23.12.1 30094,31354 2j6iA 364 3.55e-06 2fssA 365 3.60e-06 2d0iA 333 3.66e-06 1sc6A 404 3.83e-06 c.2.1.4,c.23.12.1,d.58.18.1 118932,118933,118934 1xdwA 331 4.21e-06 1dxy 333 4.39e-06 2vhxA 377 5.70e-06 1li4A 432 7.13e-06 c.2.1.4,c.23.12.3 84616,84617 1qp8A 303 7.63e-06 c.2.1.4,c.23.12.1 30092,31352 1v8bA 479 8.55e-06 c.2.1.4,c.23.12.3 113564,113565 2o4cA 380 9.84e-06 1xwfA 431 1.13e-05 c.2.1.4,c.23.12.3 122392,122393 1d4fA 431 1.43e-05 c.2.1.4,c.23.12.3 30110,31370 1edzA 320 1.81e-05 c.2.1.7,c.58.1.2 30287,33935 2qrlA 394 4.79e-05 1pjcA 361 0.000301 c.2.1.4,c.23.12.2 30101,31361 1l7dA 384 0.002001 c.2.1.4,c.23.12.2 77774,77775 1lehA 364 0.003249 c.2.1.7,c.58.1.1 30268,33916 1x13A 401 0.005835 1gpjA 404 0.007816 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1x7dA 350 0.03032 c.2.1.13 114927 1c1dA 355 0.03764 c.2.1.7,c.58.1.1 30270,33918 2hk9A 275 0.06029 1nytA 271 0.06962 c.2.1.7,c.58.1.5 86417,86418 1p77A 272 0.07701 c.2.1.7,c.58.1.5 94214,94215 1vpdA 299 0.09607 a.100.1.1,c.2.1.6 113951,113952 1np3A 338 0.1218 a.100.1.2,c.2.1.6 85946,85947 1vllA 334 0.1307 c.2.1.13 108834 2d5cA 263 0.1710 1e3jA 352 0.1881 b.35.1.2,c.2.1.1 24765,29781 2nloA 302 0.2051 1yrlA 491 0.2227 1omoA 322 0.2956 c.2.1.13 104017 2ahrA 259 0.3075 a.100.1.10,c.2.1.6 126775,126776 1bg6 359 0.3171 1uufA 369 0.3219 b.35.1.2,c.2.1.1 100006,100007 2f1kA 279 0.3423 a.100.1.12,c.2.1.6 132772,132773 2eggA 297 0.3713 1jqbA 351 0.4310 b.35.1.2,c.2.1.1 77151,77152 2cf5A 357 0.4463 1vj0A 380 0.4656 b.35.1.2,c.2.1.1 100786,100787 1f8fA 371 0.4734 b.35.1.2,c.2.1.1 83246,83247 1kevA 351 0.5115 b.35.1.2,c.2.1.1 24749,29765 3c24A 286 0.5753 1lluA 342 0.5898 b.35.1.2,c.2.1.1 91064,91065 2dvmA 439 0.5943 1y9aA 360 0.6092 2pgd 482 0.6526 1vi2A 300 0.6552 c.2.1.7,c.58.1.5 100726,100727 1bg6A 359 0.6716 a.100.1.5,c.2.1.6 18810,30214 1yqdA 366 0.6764 1luaA 287 0.6838 c.2.1.7,c.58.1.4 78216,78217 2ew2A 316 0.7145 1nvtA 287 0.7255 c.2.1.7,c.58.1.5 86270,86271 2hcyA 347 0.7294 1pl8A 356 0.7412 b.35.1.2,c.2.1.1 94878,94879 2h78A 302 0.7485 2cdcA 366 0.7861 1h2bA 359 0.8175 b.35.1.2,c.2.1.1 90543,90544 2g5cA 281 0.9107 a.100.1.12,c.2.1.6 134646,134647 1u3wA 374 1.012 b.35.1.2,c.2.1.1 113013,113014 2eihA 343 1.029 2d8aA 348 1.051 1qorA 327 1.081 b.35.1.2,c.2.1.1 24766,29782 1p0fA 373 1.092 b.35.1.2,c.2.1.1 87642,87643 1iz0A 302 1.096 b.35.1.2,c.2.1.1 83821,83822 1npyA 271 1.122 c.2.1.7,c.58.1.5 85995,85996 2izzA 322 1.281 2h6eA 344 1.291 1n8kA 374 1.380 b.35.1.2,c.2.1.1 80298,80299 1othA 321 1.595 c.78.1.1,c.78.1.1 35260,35261 1evyA 366 1.676 a.100.1.6,c.2.1.6 18811,30215 1pvvA 315 1.703 c.78.1.1,c.78.1.1 95190,95191 1yqgA 263 1.722 1qmgA 524 1.954 a.100.1.2,c.2.1.6 18785,30182 1ks9A 291 1.954 a.100.1.7,c.2.1.6 68857,68858 2pv7A 298 1.988 1ff9A 450 2.091 c.2.1.3,d.81.1.2 30039,39954 2b5wA 357 2.101 2ouiA 360 2.168 1d7yA 408 2.534 c.3.1.5,c.3.1.5,d.87.1.1 30565,30566,40204 2graA 277 2.553 1kolA 398 2.596 b.35.1.2,c.2.1.1 77474,77475 2cvzA 289 2.716 a.100.1.1,c.2.1.6 130890,130891 2jhfA 374 2.847 b.35.1.2,c.2.1.1 138314,138315 2ohxA 374 2.941 b.35.1.2,c.2.1.1 24669,29685 1mo9A 523 2.989 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1kyqA 274 3.166 c.2.1.11,e.37.1.1 73281,73282 1jayA 212 3.171 c.2.1.6 66478 3grs 478 3.337 2a4kA 263 3.380 c.2.1.2 126156 1jvbA 347 3.429 b.35.1.2,c.2.1.1 77181,77182 3ladA 476 3.472 c.3.1.5,c.3.1.5,d.87.1.1 30573,30574,40208 1lsuA 147 3.535 c.2.1.9 74250 1i36A 264 3.552 a.100.1.8,c.2.1.6 71108,71109 2p4qA 497 3.619 1g0oA 283 3.825 c.2.1.2 60181 1yb5A 351 3.851 b.35.1.2,c.2.1.1 116601,116602 1pgjA 478 3.854 a.100.1.1,c.2.1.6 18783,30195 1zmdA 474 3.958 1gesA 450 4.390 c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 1z82A 335 4.546 2gptA 523 4.558 1txgA 335 4.714 a.100.1.6,c.2.1.6 112775,112776 1tt7A 330 4.918 b.35.1.2,c.2.1.1 112623,112624 2pgdA 482 4.933 a.100.1.1,c.2.1.6 18778,30190 1q1rA 431 5.065 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 3c85A 183 5.282 2hmvA 144 5.459 c.2.1.9 136615 1vl6A 388 5.469 c.2.1.7,c.58.1.3 108724,108725 2o7sA 523 5.628 1dliA 402 5.733 a.100.1.4,c.2.1.6,c.26.3.1 18809,30213,31622 1gu7A 364 5.831 b.35.1.2,c.2.1.1 83321,83322 2c0cA 362 6.245 1ps9A 671 6.270 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 2j3hA 345 6.664 1mv8A 436 6.665 a.100.1.4,c.2.1.6,c.26.3.1 85128,85129,85130 1yb4A 295 6.696 1zcjA 463 7.001 1enp 312 7.198 1fl2A 310 7.221 c.3.1.5,c.3.1.5 59869,59870 2gqwA 408 7.248 1wlyA 333 7.346 1f0yA 302 7.611 a.100.1.3,c.2.1.6 18793,30197 2yquA 455 7.780 1xeaA 323 7.842 c.2.1.3,d.81.1.5 109572,109573 1dljA 402 7.918 a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1lssA 140 7.928 c.2.1.9 74246 1hrdA 449 8.275 c.2.1.7,c.58.1.1 30219,33867 2o3jA 481 8.318 1ml4A 308 8.332 c.78.1.1,c.78.1.1 79255,79256 1yb1A 272 8.436 c.2.1.2 116599 1ja9A 274 8.467 c.2.1.2 62817 1jg1A 235 8.763 c.66.1.7 66661 2aefA 234 8.894 2axqA 467 8.903 1hyuA 521 8.931 c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1xhcA 367 9.227 c.3.1.5,c.3.1.5,d.87.1.1 115292,115293,115294 2dpoA 319 9.294 1zk7A 467 9.298 2g1uA 155 9.824 1o89A 345 9.897 b.35.1.2,c.2.1.1 92644,92645 1b26A 416 10.25 c.2.1.7,c.58.1.1 30232,33880 1trb 320 10.38 2jfgA 445 10.51 c.5.1.1,c.59.1.1,c.72.2.1 138306,138307,138308 1b3bA 415 10.59 c.2.1.7,c.58.1.1 30244,33892 1d7oA 297 10.82 c.2.1.2 29907 2jahA 247 10.87 1yqzA 438 11.05 1xa0A 328 11.15 b.35.1.2,c.2.1.1 115021,115022 1h7wA 1025 11.23 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 2a9fA 398 11.82 1uluA 261 12.07 c.2.1.2 113292 2h7mA 269 12.86 c.2.1.2 136219 1bdbA 277 13.11 c.2.1.2 29874 2rcyA 262 13.16 2ae2A 260 13.26 c.2.1.2 29945 1hwxA 501 13.30 c.2.1.7,c.58.1.1 30250,33898 2v3aA 384 13.32 2ag5A 246 13.72 c.2.1.2 126719 1vl8A 267 13.76 c.2.1.2 108733 1zsyA 357 13.85 1tltA 319 13.89 c.2.1.3,d.81.1.5 107135,107136 3csuA 310 13.94 c.78.1.1,c.78.1.1 35094,35095 1ydeA 270 13.96 c.2.1.2 122980 1gteA 1025 14.09 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70440,70441,70442,70443,70444 2q0lA 311 14.20 2r9zA 463 14.21 1o5iA 249 14.45 c.2.1.2 92499 2d1yA 256 14.56 c.2.1.2 131151 2pnfA 248 14.56 1bgvA 449 14.59 c.2.1.7,c.58.1.1 30217,33865 2v6oA 596 14.77 1h5qA 265 15.24 c.2.1.2 60643 1qsgA 265 15.64 c.2.1.2 29935 1ooeA 236 15.73 c.2.1.2 87196 2ew8A 249 15.93 c.2.1.2 132447 1xseA 295 16.20 c.2.1.2 115925 2cduA 452 16.27 1fecA 490 16.41 c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1zejA 293 16.45 1cjcA 460 16.51 c.3.1.1,c.4.1.1 30319,30604 1xu9A 286 16.74 c.2.1.2 116052 2i6uA 307 16.84 1k2wA 256 17.05 c.2.1.2 90927 2gagA 965 17.39 2dm6A 333 17.53 b.35.1.2,c.2.1.1 131567,131568 1y5mA 276 17.63 c.2.1.2 122645 1fmcA 255 17.67 c.2.1.2 29856 1xhlA 297 17.73 c.2.1.2 109591 1cydA 244 17.77 c.2.1.2 29825 1zemA 262 17.91 c.2.1.2 124984 1h6vA 499 18.26 c.3.1.5,c.3.1.5,d.87.1.1 60693,60694,60695 2eq6A 464 18.29 1nhp 447 18.32 1m6iA 493 18.59 c.3.1.5,c.3.1.5,d.87.1.1 74533,74534,74535 3grsA 478 18.83 c.3.1.5,c.3.1.5,d.87.1.1 30441,30442,40152 1pjqA 457 18.85 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 1wmaA 276 19.27 c.2.1.2 121042 1w6uA 302 19.41 c.2.1.2 114288 1yxmA 303 19.53 c.2.1.2 124192 1duvG 333 19.76 c.78.1.1,c.78.1.1 35228,35229 1pzgA 331 20.17 c.2.1.5,d.162.1.1 95425,95426 1dhr 241 20.52 1vj1A 363 20.59 b.35.1.2,c.2.1.1 100794,100795 1trbA 320 21.42 c.3.1.5,c.3.1.5 30529,30530 1q7bA 244 21.92 c.2.1.2 96026 1x7gA 261 21.96 c.2.1.2 114929 1lvlA 458 22.25 c.3.1.5,c.3.1.5,d.87.1.1 30567,30568,40205 1o94A 729 22.81 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 1hdcA 253 22.96 c.2.1.2 29862 1qo8A 566 23.02 a.138.1.3,c.3.1.4,d.168.1.1 19696,30433,42316 1xg5A 279 23.08 c.2.1.2 115277 2zbwA 335 23.10 2qytA 317 23.15 1nffA 260 23.21 c.2.1.2 80457 2ef0A 301 23.53 1uh5A 329 23.57 c.2.1.2 107840 1bdb 277 23.85 2o23A 265 24.02 c.2.1.2 138884 1nhpA 447 24.10 c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 4uagA 437 24.11 c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1zbqA 327 24.21 c.2.1.2 124862 2bgkA 278 24.29 c.2.1.2 128480 2hq1A 247 25.53 1zq6A 359 25.66 1w4xA 542 25.93 c.3.1.5,c.3.1.5 109171,109172 2tmdA 729 26.01 c.1.4.1,c.3.1.1,c.4.1.1 28616,30317,30602 2ekpA 239 26.03 1xdzA 240 26.76 c.66.1.20 115196 1e6wA 260 26.91 c.2.1.2 59326 1nhsA 447 27.05 c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 1reoA 486 27.79 c.3.1.2,d.16.1.5 97325,97326 1gcoA 261 28.21 c.2.1.2 29884 1geeA 261 28.21 c.2.1.2 90509 1ykjA 394 28.69 1djqA 729 28.84 c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 1uxjA 309 29.37 c.2.1.5,d.162.1.1 108112,108113 1eny 268 29.38 1nvmB 312 29.41 c.2.1.3,d.81.1.1 86251,86252 1hxhA 253 29.57 c.2.1.2 76725 2gdzA 267 29.62 c.2.1.2 135043 1hdoA 206 29.73 c.2.1.2 60965 2c07A 285 30.98 c.2.1.2 129577 1gegA 256 31.34 c.2.1.2 29888 2p91A 285 31.34 1iy8A 267 31.92 c.2.1.2 83774 1xdiA 499 32.74 c.3.1.5,d.87.1.1 115160,115161 2iidA 498 33.60 c.3.1.2,d.16.1.5 137426,137427 2nm0A 253 33.85 1kpgA 287 34.23 c.66.1.18 68735 1n5dA 288 34.50 c.2.1.2 80030 2yxeA 215 34.55 1xkqA 280 34.73 c.2.1.2 115417 2bi7A 384 34.93 1gtmA 419 35.51 c.2.1.7,c.58.1.1 30223,33871 1i1nA 226 36.39 c.66.1.7 71102 1vjtA 483 36.39 c.2.1.5,d.162.1.2 100833,100834 1spxA 278 37.86 c.2.1.2 98958 3cc8A 230 38.53 1t2dA 322 39.40 c.2.1.5,d.162.1.1 99084,99085 1gz6A 319 39.90 c.2.1.2 76410 1zk4A 251 40.12 c.2.1.2 125176 2i76A 276 40.58 1h1dA 221 40.81 c.66.1.1 83452 1pbe 394 41.92 1dl5A 317 42.09 c.66.1.7,d.197.1.1 64720,64721 1x1eA 239 42.39 1id1A 153 42.63 c.2.1.9 62286 1s6yA 450 42.86 c.2.1.5,d.162.1.2 105314,105315 1up7A 417 43.05 c.2.1.5,d.162.1.2 113374,113375 1vid 221 44.26 2dtxA 264 44.45 1fjhA 257 44.53 c.2.1.2 29870 1uzmA 247 44.67 c.2.1.2 119811 2glxA 332 45.10 3ceaA 346 45.15 1kjqA 391 45.55 b.84.2.1,c.30.1.1,d.142.1.2 72616,72617,72618 1b4vA 504 45.59 c.3.1.2,d.16.1.1 30334,37865 1yb2A 275 45.72 c.66.1.13 122868 1b16A 254 45.94 c.2.1.2 29875 1x1tA 260 46.07 c.2.1.2 121597 2z1nA 260 46.65 2cvjA 180 47.44 2qq5A 260 48.93 2pd6A 264 49.10 1up6A 416 49.15 c.2.1.5,d.162.1.2 107976,107977 2i6tA 303 49.34 1d5tA 433 49.57 c.3.1.3,d.16.1.6 30422,37986 2ywlA 180 49.73 1yzhA 214 50.47 c.66.1.53 124277 1k0iA 394 50.79 c.3.1.2,d.16.1.2 67942,67943 1zud1 251 51.44 1eyzA 392 51.49 b.84.2.1,c.30.1.1,d.142.1.2 28246,31653,41498 1pbeA 394 51.56 c.3.1.2,d.16.1.2 30338,37869 1pg5A 299 51.67 c.78.1.1,c.78.1.1 104146,104147 1yovA 537 51.68 c.111.1.2 123785 1s3eA 520 52.33 c.3.1.2,d.16.1.5 98426,98427 2o2yA 349 53.35 c.2.1.2 138894 1l1eA 287 54.05 c.66.1.18 73454 2ho3A 325 54.81 1obbA 480 55.28 c.2.1.5,d.162.1.2 86760,86761 2fwmX 250 55.30 1jw9B 249 55.65 c.111.1.1 67377 1f8rA 498 56.78 c.3.1.2,d.16.1.5 30410,37974 2exxA 306 56.94 2jaeA 489 58.43 2gv8A 447 60.27 c.3.1.5,c.3.1.5 135759,135760 1i9gA 280 61.79 c.66.1.13 62090 1xtpA 254 61.86 c.66.1.42 116031 2nxcA 254 62.62 c.66.1.39 138739 1ofgA 381 63.80 c.2.1.3,d.81.1.5 30064,39979 1y8qA 346 63.92 2v7pA 310 64.77 1jsxA 207 64.80 c.66.1.20 71846 2dknA 255 65.36 1ldg 316 65.48 2gb4A 252 66.35 2bryA 497 67.87 1yvvA 336 68.53 1k6xA 352 70.29 c.2.1.2 68238 2bcgG 453 70.43 c.3.1.3,c.3.1.3,d.16.1.6 128282,128283,128284 2cfcA 250 70.73 2fk8A 318 71.23 c.66.1.18 133648 1cf2O 337 71.45 c.2.1.3,d.81.1.1 29994,39909 1ur5A 309 72.09 c.2.1.5,d.162.1.1 99807,99808 2o57A 297 72.96 3cox 507 73.25 1tt0A 623 73.39 1f06A 320 74.36 c.2.1.3,d.81.1.3 59556,59557 1hyhA 309 75.53 c.2.1.5,d.162.1.1 30150,42117 2r0cA 549 75.62 1gcuA 295 75.81 c.2.1.3,d.81.1.4 30063,39978 2oosA 338 76.95 1vqwA 457 77.37 c.3.1.5,c.3.1.5 114028,114029 6ldhA 329 77.67 c.2.1.5,d.162.1.1 30161,42128 1c0pA 363 77.75 c.4.1.2,d.16.1.3 30647,37934 2qa1A 500 79.59 1v0jA 399 80.03 1lc0A 294 80.19 c.2.1.3,d.81.1.4 73823,73824 2z3yA 662 80.25 2qfmA 364 82.48 1qydA 313 84.71 c.2.1.2 96583 2dc1A 236 84.96 1o0sA 605 85.53 c.2.1.7,c.58.1.3 86540,86541 1l9cA 389 85.65 c.3.1.2,d.16.1.3 77815,77816 1zmoA 244 86.28 5nul 138 86.31 2nwqA 272 88.70