# List of top-scoring protein chains for t2k-100-30-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 2bcoA 350 5.81e-20 1yw4A 341 1.43e-18 2bo9A 308 5.71e-05 1h8lA 380 2.59e-04 b.3.2.1,c.56.5.1 65737,65738 1qmuA 380 3.00e-04 1qmuA b.3.2.1,c.56.5.1 22534,33827 2c1cA 312 5.23e-04 1dtdA 303 7.20e-04 1aye c.56.5.1 33823 1aye 401 1.11e-03 1aye c.56.5.1,d.58.3.1 33824,39065 1jqgA 433 3.32e-03 c.56.5.1,d.58.3.1 71791,71792 1m4lA 307 4.63e-03 c.56.5.1 78604 2ctc 307 5.49e-03 1aye c.56.5.1 33802 1yme 309 6.00e-03 1aye c.56.5.1 33804 2ctb 307 7.77e-03 1aye c.56.5.1 33803 6cpa 307 1.07e-02 1aye c.56.5.1 33816 1bavA 309 1.32e-02 1aye c.56.5.1 33806 1kwmA 402 5.81e-02 c.56.5.1,d.58.3.1 73079,73080 1obr 326 1.47e-01 1aye c.56.5.2 33828 1z5rA 306 1.70e-01 1eqcA 394 3.47e-01 1cz1A c.1.8.3 28811 1cz1A 394 3.70e-01 1cz1A c.1.8.3 28839 1h4pA 408 6.67e-01 c.1.8.3 90617 1jvbA 347 6.92e-01 b.35.1.2,c.2.1.1 77181,77182 1x1nA 524 1.16e+00 1po5A 476 1.34e+00 a.104.1.1 94963 1p9bA 442 1.87e+00 c.37.1.10 94385 1xhcA 367 2.07e+00 1wyuB 474 3.19e+00 1keeC 1073 3.70e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68500,68501,68502,68503,68504,68505 1jdbB 1073 3.83e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18574,31503,31705,31706,41550,41551 1keeG 1073 4.16e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68516,68517,68518,68519,68520,68521 2aqjA 538 4.52e+00 1c3oC 1073 4.83e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18563,31492,31683,31684,41528,41529 1keeE 1073 5.03e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68508,68509,68510,68511,68512,68513 1c3oE 1073 5.12e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18564,31493,31685,31686,41530,41531 1cs0A 1073 5.41e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1cs0C 1073 5.50e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18559,31488,31675,31676,41520,41521 1keeA 1073 5.56e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68492,68493,68494,68495,68496,68497 1c3oA 1073 5.60e+00 1c3oA a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18562,31491,31681,31682,41526,41527 1bxrA 1073 5.61e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18570,31499,31697,31698,41542,41543 1c3oG 1073 7.72e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18565,31494,31687,31688,41532,41533 1ag8A 499 8.01e+00 1bpwA c.82.1.1 35341 1dqzA 280 8.76e+00 1dqyA c.69.1.3 34638 2fhpA 187 1.02e+01 1e58A 249 1.06e+01 1qhfA c.60.1.1 59262 1jwqA 179 1.08e+01 c.56.5.6 90921 1dqyA 283 1.09e+01 1dqyA c.69.1.3 34640 1o04A 500 1.11e+01 c.82.1.1 86508 1sv6A 269 1.14e+01 d.177.1.1 106043 1xovA 326 1.14e+01 2b7oA 464 1.16e+01 1qhfA 240 1.20e+01 1qhfA c.60.1.1 33960 2a35A 215 1.21e+01 1pv1A 299 1.23e+01 1cjcA 460 1.23e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1fcdA 401 1.26e+01 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 1i24A 404 1.28e+01 c.2.1.2 83663 1jztA 246 1.30e+01 c.104.1.1 63319 1tdj 514 1.32e+01 1tdj c.79.1.1,d.58.18.2,d.58.18.2 35297,39356,39357 1nbfA 353 1.33e+01 d.3.1.9 80387 1qf5A 431 1.36e+01 1adeA c.37.1.10 32212 2gl5A 410 1.40e+01 1a9xA 1058 1.54e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1qazA 351 1.54e+01 1qazA a.102.3.1 18848 1riiA 265 1.55e+01 1j1iA 296 1.56e+01 c.69.1.10 83977 1spiA 358 1.57e+01 1frpA e.7.1.1 42939 1iweA 457 1.60e+01 c.37.1.10 71486 1b37B 472 1.64e+01 1b37B c.3.1.2,d.16.1.5 30390,37954 1r3dA 264 1.66e+01 1j0dA 341 1.69e+01 c.79.1.1 83902 1b37A 472 1.73e+01 1b37B c.3.1.2,d.16.1.5 30389,37953 1bd3A 243 1.73e+01 1bd3A c.61.1.1 34098 2cq2A 114 1.79e+01 1l3iA 192 1.81e+01 c.66.1.22 77676 1d6mA 653 1.81e+01 1d6mA e.10.1.1 43248 1b5qA 472 1.83e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 1adeA 431 1.88e+01 1adeA c.37.1.10 32213 1vmhA 144 1.89e+01 1xbfA 140 1.89e+01 d.273.1.1 109538 1i7dA 659 1.92e+01 1d6mA e.10.1.1 61886 1dcuA 357 2.02e+01 1frpA e.7.1.1 42943 1eswA 500 2.10e+01 1cwyA c.1.8.1 59500 1qrrA 394 2.12e+01 1qrrA c.2.1.2 29824 1w30A 201 2.13e+01 1f2dA 341 2.16e+01 1f2dA c.79.1.1 35298 1bq3B 246 2.32e+01 1qhfA c.60.1.1 33979 1cwyA 500 2.34e+01 1cwyA c.1.8.1 28789 1kl7A 514 2.39e+01 c.79.1.1 72678 1ey2A 471 2.45e+01 1ey2A b.82.1.4 28116 1nonA 179 2.52e+01 c.61.1.1 103868 1cqwA 295 2.55e+01 1b6g c.69.1.8 34679 1bn7A 294 2.63e+01 1bn6A c.69.1.8 34677 1a3c 181 2.69e+01 1a3c c.61.1.1 34095 1pta 318 2.74e+01 1pscA c.1.9.3 29064 1bn6A 294 2.81e+01 1bn6A c.69.1.8 34678 1vpbA 451 2.85e+01 1hzyA 332 3.09e+01 1pscA c.1.9.3 61468 1wxxA 382 3.09e+01 1pscA 365 3.11e+01 1pscA c.1.9.3 29058 1g0uG 252 3.17e+01 d.153.1.4 41952 1joa 447 3.22e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30563,30564,40203 1g0cA 364 3.24e+01 7a3hA c.1.8.3 60165 1g99A 408 3.27e+01 1g99A c.55.1.2,c.55.1.2 33457,33458 2f9dA 125 3.30e+01 2bv9A 290 3.31e+01 1i0dA 332 3.31e+01 1pscA c.1.9.3 61487 1uirA 314 3.35e+01 c.66.1.17 99429 1qwnA 1045 3.38e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 2hsdA 253 3.39e+01 1e6wA c.2.1.2 29866 1g01A 364 3.40e+01 7a3hA c.1.8.3 60161 1f8rA 498 3.41e+01 1f8rA c.3.1.2,d.16.1.5 30410,37974 1rypA 243 3.48e+01 1pmaA d.153.1.4 41932 1vypX 364 3.51e+01 c.1.4.1 108905 1rliA 184 3.52e+01 c.23.5.6 97647 1ojaA 520 3.65e+01 c.3.1.2,d.16.1.5 93096,93097 1zn8A 180 3.67e+01 1xznA 179 3.70e+01 1v8fA 276 3.74e+01 c.26.1.4 100503 1gxmA 332 3.78e+01 a.102.5.1 76371 1gpjA 404 3.82e+01 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1ddgA 374 3.84e+01 1amoA b.43.4.1,c.25.1.4 25671,31559 1eywA 331 3.89e+01 1pscA c.1.9.3 29057 1ivwA 638 3.98e+01 b.30.2.1,d.17.2.1,d.17.2.1 71456,71457,71458 2b4yA 271 4.00e+01 1rpnA 335 4.02e+01 c.2.1.2 97708 1dik 874 4.03e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 2gsq 202 4.05e+01 1pd21 a.45.1.1,c.47.1.5 17715,33009 1d5yA 292 4.05e+01 1d5yA a.4.1.8,a.4.1.8,d.60.1.2 16055,16056,39532 1hdcA 253 4.07e+01 1e6wA c.2.1.2 29862 1t0iA 191 4.08e+01 c.23.5.4 106209 1eybA 471 4.16e+01 1ey2A b.82.1.4 28115 1xfkA 336 4.18e+01 1ki9A 192 4.21e+01 c.37.1.1 84404 1kblA 873 4.33e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1nhs 447 4.34e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 1xtzA 264 4.39e+01 1rq2A 382 4.65e+01 c.32.1.1,d.79.2.1 105048,105049 1gnxA 479 4.68e+01 c.1.8.4 76241 1s3eA 520 4.73e+01 c.3.1.2,d.16.1.5 98426,98427 1s95A 333 4.75e+01 d.159.1.3 105375 2atvA 196 4.85e+01 1afrA 345 4.97e+01 1afrA a.25.1.2 16805 1oq9A 363 4.99e+01 a.25.1.2 87257 1d6zA 727 5.00e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24394,38015,38016,40007 1gvoA 364 5.00e+01 c.1.4.1 76357 1r6dA 337 5.04e+01 c.2.1.2 97148 1pedA 351 5.07e+01 1pedA b.35.1.2,c.2.1.1 24753,29769 1gosA 520 5.12e+01 c.3.1.2,d.16.1.5 65425,65426 1avk 638 5.19e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24410,38047,38048 1ig0A 319 5.27e+01 1ig0A b.82.6.1,c.100.1.1 62354,62355 2gq1A 332 5.32e+01 2conA 79 5.37e+01 1oacA 727 5.40e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24390,38007,38008,40003 1c4xA 285 5.43e+01 1c4xA c.69.1.10 34684 1gqeA 365 5.43e+01 e.38.1.1 70351 1jqbA 351 5.45e+01 b.35.1.2,c.2.1.1 77151,77152 1jm4B 118 5.46e+01 a.29.2.1 71746 1iqyA 638 5.51e+01 b.30.2.1,d.17.2.1,d.17.2.1 76763,76764,76765 1b6g 310 5.70e+01 1b6g c.69.1.8 34661 2axpA 173 5.72e+01 1yzxA 226 5.92e+01 1za0A 275 6.09e+01 1bxkA 355 6.18e+01 1bxkA c.2.1.2 29803 1hwwA 1015 6.20e+01 a.8.3.1,b.30.5.6,c.6.2.1 83067,83068,83069 2a5zA 262 6.22e+01 1bs9 207 6.26e+01 1bs9 c.69.1.30 31330 1n7hA 381 6.28e+01 c.2.1.2 80250 1vm6A 228 6.31e+01 c.2.1.3,d.81.1.3 108876,108877 1nhp 447 6.42e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 1zhpA 238 6.48e+01 1heiA 451 6.64e+01 1heiA c.37.1.14,c.37.1.14 32463,32464 1nmoA 247 6.70e+01 c.135.1.1 91980 1kgnA 329 6.71e+01 a.25.1.2 68584 1txkA 498 6.77e+01 b.1.18.2,b.30.5.9 107425,107426 1ri6A 343 6.79e+01 b.69.11.1 97503 1c1kA 217 6.80e+01 1c1kA a.120.1.1 19239 2cunA 410 6.84e+01 1htyA 1015 6.98e+01 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 1vyrA 364 6.99e+01 c.1.4.1 108906 1jcxA 267 6.99e+01 c.1.10.4 66510 1pbn 289 7.04e+01 1b8oA c.56.2.1 33771 1hxkA 1015 7.13e+01 a.8.3.1,b.30.5.6,c.6.2.1 83070,83071,83072 2b0cA 206 7.30e+01 2bcgY 206 7.32e+01 2d2jA 329 7.38e+01 1yvcA 70 7.43e+01 1xx9A 238 7.63e+01 1t8xA 267 7.65e+01 2d4rA 147 7.66e+01 1ccwA 137 7.67e+01 1be1 c.23.6.1 31238 1ycdA 243 7.70e+01 1h61A 364 7.72e+01 1oyc c.1.4.1 60657 1un8A 552 7.85e+01 c.119.1.2,a.208.1.1 103806,99661 1fxpA 267 7.86e+01 1d9eA c.1.10.4 60106 1uc8A 280 7.90e+01 c.30.1.6,d.142.1.7 99165,99166 1xklA 273 7.91e+01 1eceA 358 7.95e+01 1eceA c.1.8.3 28813 2citA 282 7.96e+01 1zxoA 291 7.99e+01 1wovA 250 8.03e+01 1cz7A 406 8.04e+01 1bg2 c.37.1.9 32194 1a9t 284 8.04e+01 1b8oA c.56.2.1 33765 1c0dA 358 8.06e+01 1eceA c.1.8.3 28815 1siiA 646 8.11e+01 b.30.2.1,d.17.2.1,d.17.2.1 105578,105579,105580 1zhaA 267 8.22e+01 1iygA 133 8.24e+01 a.118.8.1 76947 1d0nA 729 8.39e+01 1d0nA d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1 40834,40835,40836,40837,40838,40839 1b1a 137 8.40e+01 1be1 c.23.6.1 31242 1spuB 727 8.43e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24399,38025,38026,40012 1xipA 388 8.44e+01 1bglA 1023 8.45e+01 1bglA b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 22097,22098,23734,24358,28857 1fwsA 267 8.47e+01 1d9eA c.1.10.4 60063 1al6 437 8.55e+01 1csh a.103.1.1 18885 1a97A 148 8.57e+01 1nulA c.61.1.1 34023 16pk 415 8.61e+01 16pk c.86.1.1 35454 1zhrA 238 8.62e+01 1gkkA 297 8.68e+01 c.69.1.2 65248 2as0A 396 8.72e+01 1ui7A 638 8.75e+01 b.30.2.1,d.17.2.1,d.17.2.1 99413,99414,99415 1ede 310 8.77e+01 1b6g c.69.1.8 34662 1shwA 138 8.82e+01 b.6.1.5 105562 1gklA 297 8.84e+01 c.69.1.2 65250 1pe1A 267 8.85e+01 c.1.10.4 94591 1wolA 122 8.91e+01 1m98A 317 8.92e+01 a.175.1.1,d.17.4.6 78866,78867 2cvjA 180 8.96e+01