# 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 1bg2 325 4.73e-48 1bg2 c.37.1.9 32189 1i5sA 367 1.01e-45 1bg2 c.37.1.9 61822 1ii6A 368 1.04e-44 1bg2 c.37.1.9 62413 1i6iA 366 1.76e-44 1bg2 c.37.1.9 61844 1x88A 359 7.83e-44 1q0bA 367 8.02e-44 c.37.1.9 95502 1vfvA 366 2.88e-43 c.37.1.9 108592 3kar 346 3.76e-42 1bg2 c.37.1.9 32198 1cz7A 406 3.96e-42 1bg2 c.37.1.9 32194 1f9vA 347 1.77e-41 1bg2 c.37.1.9 59745 1ry6A 360 3.51e-39 c.37.1.9 98090 2kinA 238 3.47e-33 1bg2 c.37.1.9 32190 2kinB 100 6.19e-10 3kinB 3kinB 117 2.12e-09 3kinB 1l8qA 324 2.19e-02 a.4.12.2,c.37.1.20 77809,77810 1odfA 290 3.69e-02 c.37.1.6 92782 2akaB 299 3.87e-02 1p9rA 418 4.40e-02 c.37.1.11 94399 1qf9A 194 4.49e-02 1zin c.37.1.1 31848 5ukdA 194 6.91e-02 1zin c.37.1.1 31851 1ddzA 496 3.00e-01 1ddzA c.53.2.1,c.53.2.1 33372,33373 1jx2B 315 4.06e-01 c.37.1.8 67404 1f5nA 592 5.92e-01 1dg3A a.114.1.1,c.37.1.8 19077,32152 1jwyB 315 6.13e-01 c.37.1.8 67401 1pysB 785 8.15e-01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16299,16300,25311,39310,40779,41455 1p3jA 217 1.09e+00 c.37.1.1,g.41.2.1 94022,94023 1um8A 376 1.10e+00 c.37.1.20 99580 1ihuA 589 1.13e+00 c.37.1.10,c.37.1.10 62394,62395 1d2mA 665 1.17e+00 1d2mA c.37.1.19,c.37.1.19 32417,32418 1ffh 294 1.21e+00 1ng1 a.24.13.1,c.37.1.10 16960,32271 1esmA 316 1.21e+00 1esmA c.37.1.6 31953 1g6oA 330 1.27e+00 1g6oA c.37.1.11 32430 1dg3A 592 1.68e+00 1dg3A a.114.1.1,c.37.1.8 19078,32153 1f48A 589 1.71e+00 1f48A c.37.1.10,c.37.1.10 32280,32281 1ng1 294 1.83e+00 1ng1 a.24.13.1,c.37.1.10 16961,32272 1ls1A 295 1.83e+00 a.24.13.1,c.37.1.10 78170,78171 1ukz 203 1.86e+00 1zin c.37.1.1 31840 3adk 195 1.89e+00 1zin c.37.1.1 31885 3tmkA 216 1.89e+00 3tmkA c.37.1.1 31920 1z83A 196 2.08e+00 2ng1 293 2.10e+00 1ng1 a.24.13.1,c.37.1.10 16962,32273 1b7yB 785 2.24e+00 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16301,16302,25312,39311,40780,41456 1g291 372 2.25e+00 1g291 2fx0A 201 2.25e+00 1jpnA 296 2.31e+00 a.24.13.1,c.37.1.10 67039,67040 1u9iA 519 2.56e+00 1akeA 214 2.79e+00 1zin c.37.1.1,g.41.2.1 31905,45185 1eiyB 785 2.87e+00 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16305,16306,25314,39313,40782,41458 1j8mF 297 2.96e+00 1ng1 a.24.13.1,c.37.1.10 62742,62743 1xrjA 261 3.02e+00 1h65A 270 3.38e+00 c.37.1.8 65640 1z47A 355 3.62e+00 1hf8A 289 3.72e+00 1hg5A a.7.8.2,a.118.9.3 90354,90355 1dq3A 454 4.06e+00 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1bzyA 217 4.09e+00 1qk3A c.61.1.1 34071 1oe9A 795 4.22e+00 b.34.3.1,c.37.1.9 92792,92793 1g8pA 350 4.24e+00 1g8pA c.37.1.20 60376 1lkxA 697 4.38e+00 c.37.1.9 73981 1zin 217 4.49e+00 1zin c.37.1.1,g.41.2.1 31915,45178 1dhs 344 4.67e+00 1dhs c.31.1.1 31727 1hg2A 289 4.68e+00 1hg5A a.7.8.2,a.118.9.3 90358,90359 1htjF 210 5.06e+00 1htjF a.91.1.1 61254 1br2A 791 5.09e+00 1lvk b.34.3.1,c.37.1.9 24558,32155 1xw4X 110 5.55e+00 1mvwA 840 5.66e+00 i.15.1.1 79523 1xwiA 322 5.69e+00 1ih8A 271 5.76e+00 2nsyA c.26.2.1 62377 1f60A 458 6.26e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 2a5yB 549 6.49e+00 1zip 217 6.49e+00 1zin c.37.1.1,g.41.2.1 31916,45179 1ooyA 481 6.54e+00 c.124.1.3,c.124.1.2 93388,93389 1fts 295 6.67e+00 1ng1 a.24.13.1,c.37.1.10 16968,32279 2cdnA 201 6.78e+00 1uj2A 252 6.82e+00 c.37.1.6 99452 1c4oA 664 6.83e+00 1d2mA c.37.1.19,c.37.1.19 32415,32416 1yrbA 262 6.85e+00 1sq5A 308 6.89e+00 c.37.1.6 105882 2bdeA 470 7.14e+00 1hg5A 289 7.32e+00 1hg5A a.7.8.2,a.118.9.3 90360,90361 1ofuA 320 8.10e+00 c.32.1.1,d.79.2.1 86972,86973 1w9iA 770 8.43e+00 1e9rA 437 8.47e+00 c.37.1.11 64827 1m7gA 211 8.49e+00 c.37.1.4 78724 1nsyA 271 8.59e+00 2nsyA c.26.2.1 31614 1f6bA 198 9.67e+00 c.37.1.8 64986 1ycdA 243 9.86e+00 1fztA 211 9.89e+00 1qhfA c.60.1.1 60158 1i9gA 280 1.01e+01 c.66.1.13 62090 1rlzA 369 1.02e+01 c.31.1.1 104989 1v5wA 343 1.03e+01 c.37.1.11 108387 1tq4A 413 1.07e+01 c.37.1.8 107201 1wdtA 665 1.08e+01 1ubpB 122 1.09e+01 1ubpB b.85.3.1 28346 2ahuA 531 1.10e+01 2fji1 399 1.11e+01 1o9lA 481 1.16e+01 c.124.1.2,c.124.1.3 81241,81242 1mv8A 436 1.21e+01 a.100.1.4,c.2.1.6,c.26.3.1 85128,85129,85130 2akaA 776 1.22e+01 1w7jA 795 1.35e+01 2nsyA 271 1.36e+01 2nsyA c.26.2.1 31612 1vom 762 1.39e+01 1lvk b.34.3.1,c.37.1.9 24577,32174 1xw8A 252 1.42e+01 1g9lA 144 1.43e+01 1g9lA a.144.1.1 60399 2d4pA 141 1.50e+01 1e4yA 214 1.56e+01 1zin c.37.1.1,g.41.2.1 31901,45181 1ji0A 240 1.60e+01 c.37.1.12 71665 1w36D 608 1.61e+01 1kqpA 271 1.63e+01 c.26.2.1 72883 1qfjA 232 1.68e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 1mnd 762 1.72e+01 1lvk b.34.3.1,c.37.1.9 24591,32188 2ax4A 198 1.76e+01 1zu4A 320 1.80e+01 1e69B 322 1.81e+01 1e69B c.37.1.12 32377 1m0qA 433 1.84e+01 c.67.1.4 78350 1wi6A 88 1.90e+01 1d7uA 433 1.92e+01 2dkb c.67.1.4 34439 1a5z 319 1.94e+01 1ceqA c.2.1.5,d.162.1.1 30181,42148 1ed1A 135 2.01e+01 1hiwA a.61.1.1 18130 1cbg 490 2.09e+01 1e70M c.1.8.4 28933 1bif 469 2.10e+01 1bif c.37.1.7,c.60.1.4 31961,34003 1vz6A 393 2.13e+01 d.154.1.2 108949 1gvnB 287 2.17e+01 c.37.1.21 76354 2ga9A 297 2.25e+01 1k0dA 260 2.30e+01 a.45.1.1,c.47.1.5 67930,67931 1eft 405 2.34e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1q5dA 419 2.35e+01 a.104.1.1 95891 1fpxA 352 2.39e+01 1fpxA a.4.5.29,c.66.1.12 59950,59951 1ld8A 382 2.40e+01 a.118.6.1 73838 1wn0A 145 2.43e+01 1rj9A 304 2.45e+01 a.24.13.1,c.37.1.10 97553,97554 1exmA 405 2.46e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 2tmkA 216 2.46e+01 3tmkA c.37.1.1 31928 1lvk 762 2.47e+01 1lvk b.34.3.1,c.37.1.9 24576,32173 1d0yA 761 2.48e+01 1lvk b.34.3.1,c.37.1.9 24581,32178 1lw7A 365 2.49e+01 c.26.1.3,c.37.1.1 74295,74296 1xkyA 301 2.49e+01 4ubpB 126 2.55e+01 1ubpB b.85.3.1 28345 1sviA 195 2.56e+01 c.37.1.8 106048 2ccjA 205 2.63e+01 1uptC 170 2.64e+01 c.37.1.8 99769 2bifA 469 2.66e+01 1bif c.37.1.7,c.60.1.4 31963,34009 1h6kZ 98 2.71e+01 d.58.7.1 60686 1nijA 318 2.73e+01 c.37.1.10,d.237.1.1 85741,85742 1i7qA 519 2.81e+01 1qdlA d.161.1.1 61901 1wmhA 89 2.84e+01 1viaA 175 2.86e+01 c.37.1.2 100754 2bd0A 244 2.89e+01 1xw3A 110 2.90e+01 1tn6A 382 2.96e+01 1yuwA 554 3.00e+01 1cjcA 460 3.03e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 2ez9A 603 3.14e+01 1qbqA 333 3.17e+01 1ft1A a.118.6.1 19187 1pfkA 320 3.19e+01 3pfk c.89.1.1 35575 1lwjA 441 3.20e+01 b.71.1.1,c.1.8.1 74303,74304 1iz7A 295 3.23e+01 c.69.1.8 76982 1jcqA 382 3.28e+01 a.118.6.1 66504 2dkb 433 3.32e+01 2dkb c.67.1.4 34438 1ewkA 490 3.33e+01 1ewkA c.93.1.1 35712 1w23A 360 3.33e+01 1jl3A 139 3.39e+01 c.44.1.1 66826 1z5zA 271 3.42e+01 2c78A 405 3.42e+01 1dekA 241 3.49e+01 1dekA c.37.1.1 31842 1yqtA 538 3.51e+01 1cfzA 162 3.54e+01 1cfzA c.56.1.1 33754 1k3eA 156 3.57e+01 d.198.1.1 68103 1r0wA 286 3.58e+01 c.37.1.12 96754 1jihA 531 3.61e+01 d.240.1.1,e.8.1.7 90374,90375 1czyC 168 3.65e+01 1d0aB b.8.1.1,h.1.2.1 23222,45429 1oywA 523 3.66e+01 a.4.5.43,c.37.1.19,c.37.1.19 93760,93761,93762 2comA 124 3.69e+01 1mj5A 302 3.73e+01 c.69.1.8 91285 1poxA 585 3.76e+01 1poxA c.31.1.3,c.36.1.5,c.36.1.9 31731,31793,31794 1ot1A 686 3.76e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 87392,87393,87394,87395 1fcdA 401 3.79e+01 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 1g6hA 257 3.80e+01 1gajA c.37.1.12 60318 2cmd 312 3.83e+01 2cmd c.2.1.5,d.162.1.1 30135,42102 1qoxN 449 3.91e+01 1qoxN c.1.8.4 28978 1rkbA 173 3.91e+01 1cv2A 296 3.94e+01 1bn6A c.69.1.8 34680 1yzsA 121 3.95e+01 1vpt 348 3.98e+01 3mag c.66.1.25 34207 1d3cA 686 3.99e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21827,22496,27734,28721 1m33A 258 4.07e+01 c.69.1.26 78514 1ft1A 377 4.08e+01 1ft1A a.118.6.1 19186 2pfkA 320 4.12e+01 3pfk c.89.1.1 35577 2fpmA 322 4.15e+01 2a9uA 144 4.17e+01 1t5yA 190 4.19e+01 b.122.1.1,d.17.6.3 106495,106496 1fp2A 352 4.24e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1i1qA 520 4.34e+01 1qdlA d.161.1.1 61543 1pamA 686 4.36e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21846,22515,27753,28740 2bbsA 290 4.40e+01 1m2oB 190 4.43e+01 c.37.1.8 78485 1h6kX 97 4.48e+01 d.58.7.1 60684 2ghpA 292 4.48e+01 2a1iA 146 4.51e+01 1vmaA 306 4.51e+01 a.24.13.1,c.37.1.10 108887,108888 3bifA 468 4.55e+01 1bif c.37.1.7,c.60.1.4 31962,34008 1w3iA 293 4.56e+01 c.1.10.1 109152 1jcrA 377 4.56e+01 a.118.6.1 66506 2db3A 434 4.57e+01 1cxlA 686 4.61e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21829,22498,27736,28723 1xmiA 291 4.66e+01 2bmhA 455 4.70e+01 1bu7A a.104.1.1 18941 1omwA 689 4.79e+01 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 1g7sA 594 4.79e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1bouB 302 4.81e+01 1bouB c.56.6.1 33859 1pzgA 331 4.85e+01 c.2.1.5,d.162.1.1 95425,95426 1nsf 273 4.85e+01 1d2nA c.37.1.20 32429 1cjbA 231 4.86e+01 1qk3A c.61.1.1 34079 1vd2A 89 4.87e+01 d.15.2.2 108517 1delA 241 4.94e+01 1dekA c.37.1.1 31844 1w5fA 353 4.96e+01 1fjhA 257 4.97e+01 1fjhB c.2.1.2 29870 1ro2A 216 5.00e+01 d.264.1.2 97665 1qvaA 223 5.07e+01 1qvaA c.37.1.19 32411 1ehiA 377 5.11e+01 1iow c.30.1.2,d.142.1.1 31716,41484 1vg8A 207 5.18e+01 c.37.1.8 108606 1hqoA 258 5.29e+01 1hqoA a.45.1.1,c.47.1.5 17749,33043 1ca9A 192 5.45e+01 1d0aB b.8.1.1,h.1.2.1 23244,45451 1qydA 313 5.46e+01 c.2.1.2 96583 1bu7A 455 5.50e+01 1bu7A a.104.1.1 18937 1m6uA 272 5.52e+01 b.2.5.7 78706 1djqA 729 5.56e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 1jscA 630 5.63e+01 c.31.1.3,c.36.1.5,c.36.1.9 67224,67225,67226 1hl2A 297 5.68e+01 c.1.10.1 83581 2ak3A 226 5.72e+01 1zin c.37.1.1,g.41.2.1 31892,45193 1jfvA 131 5.73e+01 c.44.1.1 66654 1x6vA 630 5.76e+01 1lh0A 213 5.77e+01 c.61.1.1 73896 1ywzA 175 5.80e+01 5tmpA 213 5.84e+01 5tmpA c.37.1.1 31931 1djnA 729 5.87e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 1qhfA 240 5.90e+01 1qhfA c.60.1.1 33960 1h2vC 771 5.94e+01 a.118.1.14,a.118.1.14,a.118.1.14 76592,76593,76594 1xq6A 253 6.11e+01 1opr 213 6.16e+01 1opr c.61.1.1 34091 1ro0A 216 6.17e+01 d.264.1.2 97664 1b4uB 302 6.21e+01 1bouB c.56.6.1 33861 1ej3A 191 6.29e+01 1ej3A a.39.1.5 17259 2b8wA 328 6.30e+01 1rdfA 267 6.34e+01 c.108.1.3 104884 4tmkA 213 6.38e+01 5tmpA c.37.1.1 31930 1hv8A 367 6.42e+01 1hv8A c.37.1.19,c.37.1.19 32405,32406 1nipA 289 6.44e+01 1cp2A c.37.1.10 32263 1tlyA 278 6.56e+01 f.4.6.1 107143 1ok7A 366 6.56e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1tph1 247 6.58e+01 1amk 1jpzA 473 6.66e+01 a.104.1.1 67069 1av6A 289 6.68e+01 3mag c.66.1.25 34218 1fgyA 127 6.68e+01 1faoA b.55.1.1 26976 1h2vZ 156 6.70e+01 d.58.7.1 76595 1adeA 431 6.71e+01 1adeA c.37.1.10 32213 1i7dA 659 6.71e+01 1d6mA e.10.1.1 61886 1g7tA 594 6.79e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25714,25715,31033,32148 1u94A 356 6.82e+01 c.37.1.11,d.48.1.1 107743,107744 1b64 91 6.89e+01 1b64 d.58.12.1 39306 1qhsA 178 6.90e+01 1qhsA c.37.1.3 31938 2azeA 155 6.91e+01 1w2fA 276 6.96e+01 d.143.1.3 109125 1h6kA 757 7.05e+01 a.118.1.14,a.118.1.14,a.118.1.14 60675,60676,60677 1mn4A 282 7.08e+01 b.2.5.7 79313 1ydhA 216 7.11e+01 2cvhA 220 7.13e+01 2pia 321 7.15e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1bq3B 246 7.19e+01 1qhfA c.60.1.1 33979 1eqfA 280 7.19e+01 1eqfA a.29.2.1,a.29.2.1 16972,16973 1hslA 238 7.37e+01 1lst c.94.1.1 35804 1d2nA 272 7.39e+01 1d2nA c.37.1.20 32428 1fp6A 289 7.40e+01 1cp2A c.37.1.10 32243 1r4aA 165 7.55e+01 c.37.1.8 96986 1xdwA 331 7.55e+01 1f4pA 147 7.56e+01 5nul c.23.5.1 59651 1g5pA 289 7.58e+01 1cp2A c.37.1.10 32253 1d8dA 377 7.65e+01 1ft1A a.118.6.1 19185 1taq 832 7.69e+01 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18082,33352,33698,42991 2cbzA 237 7.69e+01 1q60A 99 7.73e+01 1d0aB 168 7.78e+01 1d0aB b.8.1.1,h.1.2.1 23224,45431 1udiI 83 7.79e+01 1ugiA d.17.5.1 38124 1g6wA 261 7.82e+01 1hqoA a.45.1.1,c.47.1.5 17751,33045 3mag 307 7.88e+01 3mag c.66.1.25 34205 1wcwA 261 7.89e+01 1c5kA 439 7.92e+01 1crzA b.68.4.1,c.51.2.1 27630,33212 1yf2A 425 7.96e+01 1gnd 447 7.97e+01 1gnd c.3.1.3,d.16.1.6 30423,37987 1v5eA 590 8.01e+01 1s6yA 450 8.13e+01 c.2.1.5,d.162.1.2 105314,105315 1v39 322 8.15e+01 3mag c.66.1.25 34206 1ughI 82 8.19e+01 1ugiA d.17.5.1 38133 1l7bA 92 8.26e+01 c.15.1.2 91053 2aynA 404 8.32e+01 2tmdA 729 8.37e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28616,30317,30602 1i1nA 226 8.38e+01 c.66.1.7 71102 1b56 135 8.44e+01 1hmt b.60.1.2 27183 2ftuA 118 8.52e+01 1d6mA 653 8.54e+01 1d6mA e.10.1.1 43248 1azsC 388 8.57e+01 1cipA a.66.1.1,c.37.1.8 18203,32086 1ca4A 168 8.59e+01 1d0aB b.8.1.1,h.1.2.1 23238,45445 1ko7A 314 8.60e+01 c.98.2.1,c.91.1.2 72797,72798 1o75A 415 8.63e+01 b.1.20.1,b.1.20.1,b.120.1.1 81117,81118,81119 2gvaA 87 8.67e+01 1gvp b.40.4.7 25389 1sskA 158 8.76e+01 b.148.1.1 105986 1s9aA 257 8.76e+01 b.3.6.1 105379 1fjhB 257 8.78e+01 1fjhB c.2.1.2 29871 1k8tA 510 8.78e+01 e.41.1.1 68316 3bct 457 8.86e+01 3bct a.118.1.1 19112 1dbrA 231 8.86e+01 1qk3A c.61.1.1 34041 2b82A 211 8.87e+01 1mmiA 366 8.87e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1qwtA 255 8.95e+01 b.26.1.3 96501 2azqA 311 8.96e+01 1wvcA 259 8.98e+01