# 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 3.65e-21 1yw4A 341 4.11e-20 2bo9A 308 3.51e-04 1h8lA 380 5.08e-04 b.3.2.1,c.56.5.1 65737,65738 1qmuA 380 5.26e-04 1qmuA b.3.2.1,c.56.5.1 22534,33827 2c1cA 312 9.10e-04 1dtdA 303 3.32e-03 1aye c.56.5.1 33823 1jqgA 433 5.25e-03 c.56.5.1,d.58.3.1 71791,71792 1aye 401 5.36e-03 1aye c.56.5.1,d.58.3.1 33824,39065 1m4lA 307 1.70e-02 c.56.5.1 78604 2ctc 307 2.18e-02 1aye c.56.5.1 33802 1yme 309 2.32e-02 1aye c.56.5.1 33804 2ctb 307 2.95e-02 1aye c.56.5.1 33803 6cpa 307 3.09e-02 1aye c.56.5.1 33816 1bavA 309 3.55e-02 1aye c.56.5.1 33806 1kwmA 402 1.45e-01 c.56.5.1,d.58.3.1 73079,73080 1cz1A 394 3.75e-01 1cz1A c.1.8.3 28839 1z5rA 306 3.88e-01 1eqcA 394 3.97e-01 1cz1A c.1.8.3 28811 1obr 326 4.53e-01 1aye c.56.5.2 33828 1f0yA 302 5.72e-01 2hdhA a.100.1.3,c.2.1.6 18793,30197 2hdhA 293 6.59e-01 2hdhA a.100.1.3,c.2.1.6 18795,30199 1h4pA 408 1.01e+00 c.1.8.3 90617 1x1nA 524 1.30e+00 1jvbA 347 1.41e+00 b.35.1.2,c.2.1.1 77181,77182 1po5A 476 1.44e+00 a.104.1.1 94963 1wyuB 474 3.12e+00 1p9bA 442 4.39e+00 c.37.1.10 94385 1ag8A 499 4.99e+00 1bpwA c.82.1.1 35341 1keeC 1073 6.26e+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 6.34e+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 6.87e+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 1c3oC 1073 7.74e+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 2aqjA 538 7.83e+00 1keeE 1073 8.05e+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 8.11e+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 8.48e+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 8.59e+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 1c3oA 1073 8.86e+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 1keeA 1073 9.10e+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 1bxrA 1073 9.18e+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 1o04A 500 9.52e+00 c.82.1.1 86508 1xhcA 367 9.55e+00 1xovA 326 1.15e+01 1tdj 514 1.18e+01 1tdj c.79.1.1,d.58.18.2,d.58.18.2 35297,39356,39357 2a35A 215 1.22e+01 1c3oG 1073 1.22e+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 18565,31494,31687,31688,41532,41533 1e58A 249 1.27e+01 1qhfA c.60.1.1 59262 1qazA 351 1.32e+01 1qazA a.102.3.1 18848 1qhfA 240 1.41e+01 1qhfA c.60.1.1 33960 1cjcA 460 1.44e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 2fhpA 187 1.71e+01 1ejdA 419 1.75e+01 1uae d.68.2.2 39576 1i24A 404 1.75e+01 c.2.1.2 83663 1nbfA 353 1.76e+01 d.3.1.9 80387 1bd3A 243 1.76e+01 1bd3A c.61.1.1 34098 1vpbA 451 1.89e+01 1fcdA 401 1.92e+01 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 1jwqA 179 2.02e+01 c.56.5.6 90921 1a3c 181 2.25e+01 1a3c c.61.1.1 34095 1ki9A 192 2.34e+01 c.37.1.1 84404 7timA 247 2.36e+01 1amk c.1.1.1 28457 1nonA 179 2.43e+01 c.61.1.1 103868 2b7oA 464 2.44e+01 1dcuA 357 2.60e+01 1frpA e.7.1.1 42943 1a9xA 1058 2.62e+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 2d4rA 147 2.65e+01 1v8fA 276 2.66e+01 c.26.1.4 100503 1neyA 247 2.70e+01 c.1.1.1 80449 1ey2A 471 2.74e+01 1ey2A b.82.1.4 28116 2gl5A 410 2.78e+01 1j1iA 296 2.78e+01 c.69.1.10 83977 1b6g 310 2.88e+01 1b6g c.69.1.8 34661 1l3iA 192 2.93e+01 c.66.1.22 77676 1qf5A 431 2.95e+01 1adeA c.37.1.10 32212 1j0dA 341 3.10e+01 c.79.1.1 83902 1qrrA 394 3.11e+01 1qrrA c.2.1.2 29824 1uirA 314 3.13e+01 c.66.1.17 99429 1eswA 500 3.13e+01 1cwyA c.1.8.1 59500 1dqzA 280 3.14e+01 1dqyA c.69.1.3 34638 1hzyA 332 3.16e+01 1pscA c.1.9.3 61468 1xznA 179 3.21e+01 1pta 318 3.21e+01 1pscA c.1.9.3 29064 1g0uG 252 3.25e+01 d.153.1.4 41952 1bq3B 246 3.28e+01 1qhfA c.60.1.1 33979 1gqeA 365 3.37e+01 e.38.1.1 70351 1i0dA 332 3.42e+01 1pscA c.1.9.3 61487 1adeA 431 3.44e+01 1adeA c.37.1.10 32213 1pscA 365 3.45e+01 1pscA c.1.9.3 29058 1jztA 246 3.46e+01 c.104.1.1 63319 1cwyA 500 3.52e+01 1cwyA c.1.8.1 28789 1a2n 419 3.56e+01 1uae d.68.2.2 39575 1sv6A 269 3.57e+01 d.177.1.1 106043 1iweA 457 3.62e+01 c.37.1.10 71486 2hsdA 253 3.74e+01 1e6wA c.2.1.2 29866 1dqyA 283 3.75e+01 1dqyA c.69.1.3 34640 1b37B 472 3.92e+01 1b37B c.3.1.2,d.16.1.5 30390,37954 1b37A 472 3.94e+01 1b37B c.3.1.2,d.16.1.5 30389,37953 1xbfA 140 4.03e+01 d.273.1.1 109538 1qwnA 1045 4.10e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1b5qA 472 4.14e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 1hdcA 253 4.15e+01 1e6wA c.2.1.2 29862 1lldA 319 4.19e+01 3ldh c.2.1.5,d.162.1.1 30177,42144 1i7gA 287 4.23e+01 a.123.1.1 71121 1spiA 358 4.23e+01 1frpA e.7.1.1 42939 1vmhA 144 4.23e+01 1f2dA 341 4.25e+01 1f2dA c.79.1.1 35298 1vl4A 447 4.33e+01 d.283.1.1 108718 1eybA 471 4.40e+01 1ey2A b.82.1.4 28115 1eywA 331 4.42e+01 1pscA c.1.9.3 29057 1kl7A 514 4.44e+01 c.79.1.1 72678 1pedA 351 4.54e+01 1pedA b.35.1.2,c.2.1.1 24753,29769 1ede 310 4.54e+01 1b6g c.69.1.8 34662 2conA 79 4.54e+01 1rypA 243 4.57e+01 1pmaA d.153.1.4 41932 2b4yA 271 4.61e+01 1gxmA 332 4.63e+01 a.102.5.1 76371 2bv9A 290 4.69e+01 1d5yA 292 4.70e+01 1d5yA a.4.1.8,a.4.1.8,d.60.1.2 16055,16056,39532 1ivwA 638 4.72e+01 b.30.2.1,d.17.2.1,d.17.2.1 71456,71457,71458 1d6zA 727 4.79e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24394,38015,38016,40007 1lqtA 456 4.85e+01 c.3.1.1,c.4.1.1 74198,74199 1jqbA 351 5.03e+01 b.35.1.2,c.2.1.1 77151,77152 1wy7A 207 5.09e+01 1oacA 727 5.13e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24390,38007,38008,40003 1zn8A 180 5.17e+01 1zbsA 291 5.51e+01 1r3dA 264 5.53e+01 1bn7A 294 5.64e+01 1bn6A c.69.1.8 34677 1cqwA 295 5.68e+01 1b6g c.69.1.8 34679 1joa 447 5.68e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30563,30564,40203 1avk 638 5.83e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24410,38047,38048 1ivnA 190 5.86e+01 c.23.10.5 83719 1dxy 333 5.89e+01 1dxy c.2.1.4,c.23.12.1 30094,31354 1h8mA 140 6.00e+01 1h8mA d.110.4.1 60782 1s95A 333 6.02e+01 d.159.1.3 105375 1zxoA 291 6.05e+01 1iqyA 638 6.10e+01 b.30.2.1,d.17.2.1,d.17.2.1 76763,76764,76765 1jkmA 358 6.16e+01 1jkmA c.69.1.2 34633 1c3pA 375 6.17e+01 1c3pA c.42.1.2 32606 1yi8A 351 6.20e+01 1rq2A 382 6.34e+01 c.32.1.1,d.79.2.1 105048,105049 1c4xA 285 6.34e+01 1c4xA c.69.1.10 34684 1bn6A 294 6.37e+01 1bn6A c.69.1.8 34678 1opr 213 6.41e+01 1opr c.61.1.1 34091 1iygA 133 6.42e+01 a.118.8.1 76947 1yvcA 70 6.56e+01 2f9dA 125 6.59e+01 1yzxA 226 6.60e+01 1ccwA 137 6.65e+01 1be1 c.23.6.1 31238 1v3wA 173 6.86e+01 b.81.1.5 100291 1kevA 351 6.90e+01 1pedA b.35.1.2,c.2.1.1 24749,29765 1i5nA 146 6.94e+01 1i5nA a.24.10.3 61805 1nhs 447 6.96e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 2d2jA 329 6.99e+01 2gwxA 267 7.03e+01 2prgA a.123.1.1 19323 1gpjA 404 7.15e+01 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1hwwA 1015 7.17e+01 a.8.3.1,b.30.5.6,c.6.2.1 83067,83068,83069 1pv1A 299 7.18e+01 1wxxA 382 7.26e+01 1txkA 498 7.40e+01 b.1.18.2,b.30.5.9 107425,107426 1xfkA 336 7.46e+01 1yqeA 282 7.47e+01 1wraA 308 7.47e+01 1ddgA 374 7.47e+01 1amoA b.43.4.1,c.25.1.4 25671,31559 2dcnA 311 7.53e+01 1uc8A 280 7.53e+01 c.30.1.6,d.142.1.7 99165,99166 1w30A 201 7.54e+01 1ri6A 343 7.54e+01 b.69.11.1 97503 1spuB 727 7.61e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24399,38025,38026,40012 2fokA 579 7.63e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16131,16132,16133,33323 1rpnA 335 7.65e+01 c.2.1.2 97708 1jbkA 195 7.70e+01 c.37.1.20 71631 1i45A 248 7.74e+01 1amk c.1.1.1 61665 1bxkA 355 7.84e+01 1bxkA c.2.1.2 29803 1b1a 137 7.86e+01 1be1 c.23.6.1 31242 1heiA 451 7.87e+01 1heiA c.37.1.14,c.37.1.14 32463,32464 1jkmB 361 7.92e+01 1jkmA c.69.1.2 34634 1htyA 1015 7.96e+01 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 1ycdA 243 8.11e+01 1dik 874 8.13e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1hxkA 1015 8.14e+01 a.8.3.1,b.30.5.6,c.6.2.1 83070,83071,83072 1kblA 873 8.15e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1riiA 265 8.17e+01 1d2eA 397 8.45e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1jm4B 118 8.45e+01 a.29.2.1 71746 2citA 282 8.46e+01 1rqbA 539 8.48e+01 a.5.7.2,c.1.10.5 105057,105058 1ek0A 170 8.51e+01 1ctqA c.37.1.8 32076 1siiA 646 8.57e+01 b.30.2.1,d.17.2.1,d.17.2.1 105578,105579,105580 1g99A 408 8.62e+01 1g99A c.55.1.2,c.55.1.2 33457,33458 1g0cA 364 8.74e+01 7a3hA c.1.8.3 60165 1gkkA 297 8.88e+01 c.69.1.2 65248 1eugA 229 8.91e+01 3eugA c.18.1.1 31021 1uae 419 8.96e+01 1uae d.68.2.2 39574 1vm6A 228 8.97e+01 c.2.1.3,d.81.1.3 108876,108877