# List of top-scoring protein chains for t04-100-30-bys-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 1p3wA 404 1.15e-40 c.67.1.3 87752 1t3iA 420 1.41e-37 c.67.1.3 106354 1eg5A 384 3.46e-37 1ecxA c.67.1.3 34429 1jf9A 408 6.14e-37 1c0nA c.67.1.3 62931 1e5eA 404 2.23e-28 1ibjA c.67.1.3 59265 1gc0A 398 5.65e-28 c.67.1.3 70168 1eluA 390 1.18e-26 1elqA c.67.1.3 34434 1elqA 390 1.39e-26 1elqA c.67.1.3 34436 1cs1A 386 1.45e-26 1ibjA c.67.1.3 34399 1qz9A 416 7.37e-25 c.67.1.3 96621 1vjoA 393 1.91e-20 c.67.1.3 100827 1cl1A 395 1.83e-19 1cl2A c.67.1.3 34395 1v2dA 381 1.07e-17 c.67.1.1 108281 1m32A 366 1.18e-15 c.67.1.3 78508 1o4sA 389 2.99e-14 c.67.1.1 86620 1jg8A 347 3.12e-14 1jg8A c.67.1.1 62946 1m6sA 347 3.18e-14 c.67.1.1 78701 1iugA 352 5.26e-14 c.67.1.3 90699 1mdoA 393 9.58e-14 c.67.1.4 79013 1b5pA 385 7.50e-13 c.67.1.1 90403 1bjwA 382 1.45e-12 1bjwA c.67.1.1 34349 1wyuB 474 1.80e-12 1gdeA 389 2.23e-12 c.67.1.1 60456 1lc5A 364 2.42e-12 c.67.1.1 73827 1wyuA 438 6.13e-12 1z7dA 433 6.24e-12 1w7lA 422 6.60e-12 c.67.1.1 109226 1pmmA 466 8.92e-12 c.67.1.6 94901 1bw0A 416 1.26e-11 1bw0A c.67.1.1 34385 1kl1A 419 2.32e-11 c.67.1.4 72663 1b9hA 388 4.41e-11 1b9hA c.67.1.4 34488 1gewA 356 5.57e-11 1gewA c.67.1.1 60470 1yjsA 419 5.98e-11 2bwnA 401 7.15e-11 1fg7A 356 1.11e-10 1gewA c.67.1.1 59819 1yiyA 429 1.16e-10 1yizA 429 1.39e-10 1vefA 395 1.44e-10 1bs0A 384 1.50e-10 1bs0A c.67.1.4 34490 1fc4A 401 1.72e-10 1bs0A c.67.1.4 59760 1b8gA 429 1.84e-10 1b8gA c.67.1.4 34499 1dfoA 417 2.90e-10 1bj4A c.67.1.4 34480 1m7yA 435 3.06e-10 c.67.1.4 78761 1u08A 386 5.41e-10 c.67.1.1 107543 1ynuA 473 7.02e-10 2aeuA 374 7.47e-10 1svvA 359 1.07e-09 c.67.1.1 106054 1w23A 360 1.80e-09 2fnuA 375 1.89e-09 1wstA 417 1.90e-09 1oatA 439 2.07e-09 2dkb c.67.1.4 34461 2oatA 439 2.59e-09 2dkb c.67.1.4 34452 2bylA 439 2.94e-09 1o69A 394 3.24e-09 c.67.1.4 92560 2byjA 439 3.80e-09 1vp4A 425 4.27e-09 1ax4A 467 1.22e-08 1ax4A c.67.1.2 34391 1js3A 486 1.92e-08 c.67.1.6 67215 1rv3A 483 2.50e-08 c.67.1.4 105101 1v72A 356 3.22e-08 1bj4A 470 5.40e-08 1bj4A c.67.1.4 34479 1sffA 426 8.48e-08 c.67.1.4 105482 1uu1A 335 9.59e-08 c.67.1.1 99993 1w3uA 362 1.13e-07 2c0rA 362 1.35e-07 1c7gA 456 1.64e-07 c.67.1.2 90415 1bjnA 360 1.72e-07 1bjnA c.67.1.4 34469 1lk9A 448 1.70e-06 c.67.1.1 78057 2gsaA 432 1.74e-06 2gsaA c.67.1.4 34446 1d2fA 390 1.82e-06 1d2fA c.67.1.3 34411 1c7nA 399 3.35e-06 1d2fA c.67.1.3 34413 1qisA 396 7.16e-06 1ajsA c.67.1.1 34284 1ars 396 1.67e-05 1ajsA c.67.1.1 34287 1ahxA 396 2.44e-05 1ajsA c.67.1.1 34293 2dkb 433 5.59e-05 2dkb c.67.1.4 34438 1d7uA 433 7.46e-05 2dkb c.67.1.4 34439 7aatA 401 3.98e-04 1ajsA c.67.1.1 34250 1ohvA 472 1.61e-03 c.67.1.4 93031 1c4kA 730 1.71e-03 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 1s0aA 429 3.92e-03 c.67.1.4 98263 1qj5A 429 4.47e-03 1dtyA c.67.1.4 34493 1ajsA 412 9.38e-03 1ajsA c.67.1.1 34276 1e5dA 402 3.08e-02 1e5dA c.23.5.1,d.157.1.3 31208,42061 1mvoA 136 8.35e-02 c.23.1.1 79513 2ng1 293 1.64e-01 1ng1 a.24.13.1,c.37.1.10 16962,32273 1f2tB 148 4.31e-01 1f2tB 1uqrA 154 4.55e-01 c.23.13.1 99779 1vljA 407 4.96e-01 e.22.1.2 108832 1iq8A 582 5.12e-01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1k2eA 156 5.23e-01 d.113.1.1 72010 1ls1A 295 6.58e-01 a.24.13.1,c.37.1.10 78170,78171 2fexA 188 7.83e-01 1tqjA 230 9.17e-01 c.1.2.2 107228 1nu0A 138 1.06e+00 c.55.3.8 92165 7taa 478 1.08e+00 7taa b.71.1.1,c.1.8.1 27778,28765 1rd5A 262 1.12e+00 1bag 425 1.22e+00 1bag b.71.1.1,c.1.8.1 27720,28707 1j8yF 297 1.29e+00 1ng1 a.24.13.1,c.37.1.10 62747,62748 1l3iA 192 1.38e+00 c.66.1.22 77676 1oapA 109 1.46e+00 d.79.7.1 92706 1ua7A 422 1.57e+00 b.71.1.1,c.1.8.1 107759,107760 2cbiA 594 1.59e+00 1qs0B 338 1.77e+00 1qs0B c.36.1.7,c.48.1.2 31830,33103 1ut9A 609 1.78e+00 a.102.1.2,b.1.18.2 99912,99913 1j8mF 297 1.87e+00 1ng1 a.24.13.1,c.37.1.10 62742,62743 1vmaA 306 1.89e+00 a.24.13.1,c.37.1.10 108887,108888 1vcoA 550 1.94e+00 c.23.16.1,c.37.1.10 108508,108509 1o58A 303 2.16e+00 c.79.1.1 92491 1ko7A 314 2.20e+00 c.98.2.1,c.91.1.2 72797,72798 2bznA 351 2.76e+00 1kv7A 488 2.93e+00 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 1pamA 686 3.01e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21846,22515,27753,28740 1vm7A 311 3.11e+00 c.72.1.1 108884 1tp6A 128 3.33e+00 d.17.4.12 107184 1eziA 228 3.54e+00 1eyrA c.68.1.13 34512 1wl8A 189 3.70e+00 1xi3A 215 3.75e+00 c.1.3.1 109601 2gjlA 328 4.01e+00 2cy7A 396 4.06e+00 1vl8A 267 4.22e+00 c.2.1.2 108733 2c6qA 351 4.53e+00 1q7lA 198 4.59e+00 c.56.5.4 96044 2aawA 222 4.83e+00 1wkvA 389 5.25e+00 1pea 385 5.46e+00 1pea c.93.1.1 35662 2ag5A 246 6.24e+00 2cwxA 430 6.26e+00 1wmaA 276 6.28e+00 1wwkA 307 6.31e+00 1ltqA 301 6.35e+00 c.108.1.9,c.37.1.1 78208,78209 1vb5A 276 6.38e+00 1z7lA 276 6.46e+00 2d69A 430 6.47e+00 1r1tA 122 6.48e+00 a.4.5.5 104769 1m1nA 491 6.64e+00 c.92.2.3 78417 1t2dA 322 6.84e+00 c.2.1.5,d.162.1.1 99084,99085 1lwdA 413 7.41e+00 c.77.1.1 78265 1wzaA 488 7.47e+00 1wznA 252 7.78e+00 2fsxA 148 8.02e+00 1xx1A 285 8.12e+00 1y80A 210 8.35e+00 1lw3A 657 8.36e+00 b.55.1.8,c.45.1.3 91152,91153 1zu4A 320 8.49e+00 1tksA 204 8.52e+00 d.115.1.2 107114 1vicA 262 8.52e+00 c.68.1.13 100756 1iukA 140 9.06e+00 c.2.1.8 83712 1qopB 396 9.25e+00 2tysB c.79.1.1 35270 1rvgA 305 9.43e+00 c.1.10.2 97920 1ve1A 304 9.69e+00 2fueA 262 9.70e+00 2cxcA 144 9.80e+00 1jdpA 441 1.00e+01 c.93.1.1 62906 1tluA 130 1.03e+01 d.156.1.2 107139 1yrbA 262 1.04e+01 1ebdC 41 1.06e+01 1ebdC a.9.1.1 16355 2bd0A 244 1.08e+01 1t0aA 159 1.10e+01 1sur 215 1.11e+01 1sur c.26.2.2 31620 2adbA 148 1.12e+01 2blkA 122 1.15e+01 1qhtA 775 1.17e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1kfuL 699 1.17e+01 a.39.1.8,b.14.1.1,d.3.1.3 68571,68572,68573 1pda 315 1.20e+01 1pda c.94.1.1,d.50.2.1 35751,38794 1xm8A 254 1.21e+01 1srrA 124 1.22e+01 1dz3A c.23.1.1 31110 1nsj 205 1.25e+01 1nsj c.1.2.4 28560 1edqA 540 1.29e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1v4aA 440 1.30e+01 a.24.16.4,d.218.1.9 108350,108351 1k8kB 394 1.31e+01 c.55.1.1 68307 1wa3A 205 1.37e+01 2ap1A 327 1.38e+01 1wkbA 810 1.40e+01 1zq4A 693 1.40e+01 2fhpA 187 1.41e+01 1oxkB 134 1.43e+01 c.23.1.1 93691 1uvjA 664 1.43e+01 e.8.1.6 100045 1w77A 228 1.45e+01 1hhsA 664 1.47e+01 1hi0P e.8.1.6 61045 1yarH 217 1.47e+01 1qlaA 656 1.48e+01 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 16328,30427,42310 1szwA 379 1.50e+01 d.265.1.4 99047 2afbA 351 1.52e+01 1um0A 365 1.52e+01 d.258.1.1 107942 1vlwA 217 1.53e+01 c.1.10.1 108868 1xngA 268 1.55e+01 1jj2W 91 1.55e+01 1ffkU d.29.1.1 63108 1wdkC 390 1.57e+01 c.95.1.1,c.95.1.1 109258,109259 1dl5A 317 1.58e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1s72X 92 1.58e+01 d.29.1.1 105343 1m65A 245 1.58e+01 c.6.3.1 84847 1x42A 232 1.59e+01 1e19A 314 1.59e+01 1b7bA c.73.1.1 34967 1ea9C 583 1.61e+01 b.1.18.2,b.71.1.1,c.1.8.1 70087,70088,70089 1geqA 248 1.61e+01 2tysA c.1.2.4 28589 1zaiA 363 1.62e+01 1i5gA 144 1.65e+01 1ewxA c.47.1.10 61784 1adoA 363 1.67e+01 1fbaA c.1.10.1 29124 1ju2A 536 1.67e+01 c.3.1.2,d.16.1.1 77169,77170 2ashA 381 1.69e+01 1smtA 122 1.69e+01 1smtA a.4.5.5 16109 2d13A 227 1.69e+01 1vqoX 92 1.70e+01 1ctn 540 1.71e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21876,29005,38439 1mwmA 320 1.71e+01 c.55.1.1,c.55.1.1 79580,79581 1chd 203 1.72e+01 1chd c.40.1.1 32478 2gshA 414 1.72e+01 1k92A 455 1.73e+01 c.26.2.1,d.210.1.1 68325,68326 1i1qA 520 1.73e+01 1qdlA d.161.1.1 61543 2cveA 191 1.74e+01 1jq5A 370 1.77e+01 e.22.1.2 67084 1lfpA 249 1.79e+01 e.39.1.1 73885 1v7cA 351 1.80e+01 c.79.1.1 100446 1gtkA 313 1.80e+01 c.94.1.1,d.50.2.1 76346,76347 1g5tA 196 1.81e+01 1g5rA c.37.1.11 32366 2avnA 260 1.85e+01 1f2dA 341 1.87e+01 1f2dA c.79.1.1 35298 2pth 193 1.88e+01 2pth c.56.3.1 33793 1ww8A 439 1.92e+01 1riqA 465 1.96e+01 a.203.1.1,d.104.1.1 97516,97517 1y8qA 346 1.96e+01 1j5vA 351 1.98e+01 c.72.1.1 71585 1vfgA 390 1.98e+01 a.173.1.1,d.218.1.4 108570,108571 2abqA 306 1.98e+01 2faoA 309 2.01e+01 1ff9A 450 2.01e+01 1ff9A c.2.1.3,d.81.1.2 30039,39954 1bia 321 2.05e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1ak5 503 2.06e+01 1ak5 c.1.5.1 28639 1rpxA 230 2.07e+01 1rpxA c.1.2.2 28536 1u09A 476 2.08e+01 e.8.1.4 107545 2aaa 484 2.10e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1g38A 393 2.12e+01 2admA c.66.1.27 60235 1p0iA 529 2.14e+01 c.69.1.1 93867 1j0dA 341 2.15e+01 c.79.1.1 83902 1x1tA 260 2.17e+01 1wmbA 260 2.19e+01 1eswA 500 2.19e+01 1cwyA c.1.8.1 59500 1vr7A 142 2.21e+01 1w7jA 795 2.21e+01 1a0cA 438 2.24e+01 1a0cA c.1.15.3 29529 1ykwA 435 2.26e+01 1j5yA 187 2.27e+01 a.4.5.1,d.94.2.1 71592,71593 1w9aA 147 2.28e+01 1zs9A 261 2.29e+01 1sa3A 262 2.33e+01 c.52.1.23 105400 1w6tA 444 2.34e+01 1jflA 228 2.38e+01 c.78.2.1,c.78.2.1 71656,71657 1wzlA 585 2.40e+01 1nktA 922 2.41e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 85830,85831,85832,85833 1d3cA 686 2.41e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21827,22496,27734,28721 1reqA 727 2.42e+01 1reqA c.1.19.1,c.23.6.1 29620,31247 1skoA 143 2.42e+01 d.110.7.1 105676 1me8A 503 2.44e+01 c.1.5.1 79028 1v8dA 235 2.45e+01 c.140.1.1 108425 1ve3A 227 2.45e+01 1w78A 422 2.47e+01 1xfkA 336 2.50e+01 2c5uA 375 2.53e+01 1vid 221 2.54e+01 1vid c.66.1.1 34178 1qvbA 481 2.54e+01 1qvbA c.1.8.4 28983 1h1dA 221 2.55e+01 c.66.1.1 83452 1jnrA 643 2.57e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1t3gA 159 2.57e+01 1aba 87 2.58e+01 1aba c.47.1.1 32760 2fjbA 643 2.60e+01 1v8gA 329 2.60e+01 a.46.2.1,c.27.1.1 100505,100506 1z5zA 271 2.66e+01 2anuA 255 2.68e+01 1ldg 316 2.72e+01 1ceqA c.2.1.5,d.162.1.1 30165,42132 1omp 370 2.74e+01 4mbp c.94.1.1 35778 1ejdA 419 2.75e+01 1uae d.68.2.2 39576 5reqA 727 2.77e+01 1reqA c.1.19.1,c.23.6.1 29632,31259 2dexX 671 2.79e+01 2g5cA 281 2.80e+01 2bzlA 325 2.83e+01 1kafA 108 2.83e+01 d.199.1.1 68372 1w30A 201 2.84e+01 1o7jA 327 2.85e+01 c.88.1.1 81140 2bm8A 236 2.85e+01 1qe3A 489 2.86e+01 2bce c.69.1.1 34630 1yfsA 465 2.88e+01 1pg4A 652 2.89e+01 e.23.1.1 88067 1kwgA 645 2.89e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1nvmA 345 2.91e+01 a.5.7.1,c.1.10.5 86249,86250 1wxiA 275 2.92e+01 1wolA 122 2.92e+01 1anf 370 2.93e+01 4mbp c.94.1.1 35776 1zejA 293 3.01e+01 1uv7A 110 3.02e+01 d.67.4.1 100040 1g0uL 241 3.09e+01 d.153.1.4 41894 2f02A 323 3.10e+01 1wdcB 156 3.11e+01 1wdcB a.39.1.5 17302 2dri 271 3.14e+01 2dri c.93.1.1 35637 1n2eA 300 3.15e+01 c.26.1.4 85268 1bmtA 246 3.18e+01 1bmtA a.46.1.1,c.23.6.1 17757,31235 1ihgA 370 3.19e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 1wdgA 94 3.21e+01 h.3.3.1 109248 1tltA 319 3.23e+01 c.2.1.3,d.81.1.5 107135,107136 1yn9A 169 3.25e+01 1sr8A 298 3.26e+01 e.54.1.1 105959 1oe9A 795 3.28e+01 b.34.3.1,c.37.1.9 92792,92793 1wdaA 670 3.28e+01 b.2.9.1,b.6.1.6,d.126.1.5 109243,109244,109245 2f5tX 233 3.29e+01 1u0sA 86 3.31e+01 d.58.24.1 107565 1yt5A 258 3.35e+01 1x1oA 286 3.35e+01 1xxoA 147 3.35e+01 1qqcA 773 3.38e+01 1tgoA c.55.3.5,e.8.1.1 33724,43013 1hdcA 253 3.41e+01 1e6wA c.2.1.2 29862 1udmA 149 3.47e+01 d.109.1.2 107780 1qf5A 431 3.48e+01 1adeA c.37.1.10 32212 1hjsA 332 3.48e+01 c.1.8.3 83492 1t3qB 788 3.49e+01 d.41.1.1,d.133.1.1 106369,106370 1h7eA 245 3.50e+01 c.68.1.13 60717 2fbaA 492 3.52e+01 1uw4A 91 3.54e+01 d.58.7.4 100071 1a9xB 379 3.55e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 2es9A 115 3.56e+01 2bw0A 329 3.56e+01 2fazA 78 3.56e+01 1db3A 372 3.58e+01 1db3A c.2.1.2 29813 1zsqA 528 3.59e+01 1zmaA 118 3.60e+01 2b61A 377 3.61e+01 1z7wA 322 3.61e+01 1w85I 49 3.62e+01 1y81A 138 3.62e+01 2aq6A 147 3.66e+01 1kk8B 139 3.70e+01 a.39.1.5 77430 1ccwB 483 3.70e+01 1cb7B c.1.19.2 29646 1fts 295 3.71e+01 1ng1 a.24.13.1,c.37.1.10 16968,32279 1nal1 297 3.71e+01 1nal3 1pszA 303 3.73e+01 1toaA c.92.2.2 35600 1ecfA 504 3.73e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1wjgA 137 3.75e+01 1vplA 256 3.79e+01 1x72A 334 3.82e+01 d.126.1.6 109495 1j0aA 325 3.83e+01 c.79.1.1 83871 2c3mA 1231 3.83e+01 1z0kB 69 3.87e+01 1ow1A 195 3.90e+01 b.131.1.3 93625 1zjjA 263 3.90e+01 1ufkA 254 3.91e+01 c.66.1.39 99340 1io2A 213 3.92e+01 1ekeA c.55.3.1 62612 1tz9A 367 3.94e+01 c.1.15.6 107466 1nulA 152 4.00e+01 1nulA c.61.1.1 34011 1nk4A 580 4.03e+01 c.55.3.5,e.8.1.1 91923,91924 1ayx 492 4.08e+01 1ayx a.102.1.1 18825 1obbA 480 4.12e+01 c.2.1.5,d.162.1.2 86760,86761 1u4nA 310 4.15e+01 1l3sA 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