# List of top-scoring protein chains for t2k-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 1ihgA 370 2.07e-37 2cpl a.118.8.1,b.62.1.1 62380,62381 1cwoA 165 3.07e-37 2cpl b.62.1.1 27445 2cpl 165 3.07e-37 2cpl b.62.1.1 27420 1dywA 173 4.29e-37 2cpl b.62.1.1 27505 1qoiA 177 4.76e-37 2cpl b.62.1.1 27490 1a58 177 4.90e-37 2cpl b.62.1.1 27495 1yndA 165 7.39e-37 2bitX 165 9.52e-37 1awqA 164 1.24e-36 2cpl b.62.1.1 27461 1awsA 164 1.50e-36 2cpl b.62.1.1 27431 2rmcA 182 2.29e-36 2cpl b.62.1.1 27491 1xo7A 166 4.19e-36 1zcxA 178 4.67e-36 1h0pA 182 5.65e-36 b.62.1.1 76450 2cfeA 162 6.90e-36 1vdnA 162 2.24e-35 2a2nA 176 7.17e-33 1zkcA 197 4.99e-32 2fu0A 160 1.97e-31 1xwnA 174 4.36e-31 2b71A 196 7.32e-31 1lopA 164 1.41e-27 2cpl b.62.1.1 27510 1v9tA 166 1.74e-27 b.62.1.1 108451 1j2aA 166 2.34e-27 b.62.1.1 90779 1clh 166 3.56e-24 2cpl b.62.1.1 27512 1zx8A 136 4.95e-02 1mxiA 160 8.77e-01 c.116.1.1 79646 2b8mA 117 1.62e+00 2b4wA 315 2.37e+00 1o26A 232 3.97e+00 d.207.1.1 86566 2ex4A 241 4.18e+00 1kq4A 232 4.34e+00 d.207.1.1 68791 3sil 379 4.39e+00 3sil b.68.1.1 27542 1dz3A 130 4.69e+00 1dz3A c.23.1.1 31105 1x9uA 116 5.51e+00 1qmpA 130 5.70e+00 1dz3A c.23.1.1 31106 1gt8A 1025 7.17e+00 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70418,70419,70420,70421,70422 1xe1A 116 8.34e+00 b.43.3.1 109571 1uumA 372 8.81e+00 c.1.4.1 100010 2bdvA 231 9.13e+00 1vj0A 380 9.21e+00 b.35.1.2,c.2.1.1 100786,100787 1s31A 273 9.46e+00 1w96A 554 1.01e+01 1dim 381 1.01e+01 3sil b.68.1.1 27544 1jmmA 377 1.03e+01 b.30.6.1 71749 1xwmA 217 1.06e+01 2sil 381 1.09e+01 3sil b.68.1.1 27543 1tsp 559 1.09e+01 1tyv b.80.1.6 28044 1k2fA 190 1.17e+01 b.8.1.2 68054 1icpA 376 1.19e+01 1oyc c.1.4.1 62270 1wn0A 145 1.22e+01 2bi0A 337 1.30e+01 1tmxA 293 1.36e+01 1vr0A 247 1.36e+01 1wriA 93 1.37e+01 2cbzA 237 1.38e+01 2azpA 318 1.43e+01 1ve4A 206 1.47e+01 1c0eA 157 1.57e+01 1dg9A c.44.1.1 32638 1phr 157 1.60e+01 1dg9A c.44.1.1 32635 1u11A 182 1.66e+01 c.23.8.1 107576 1rypK 198 1.76e+01 d.153.1.4 41879 1o7iA 119 1.91e+01 b.40.4.3 86642 1e8bA 160 1.96e+01 1e8bA g.14.1.2,g.14.1.2,g.27.1.1 44671,44672,44951 1vyrA 364 2.07e+01 c.1.4.1 108906 1dg9A 157 2.10e+01 1dg9A c.44.1.1 32637 1a5dA 173 2.12e+01 1amm b.11.1.1,b.11.1.1 23614,23615 1y89A 238 2.12e+01 1gvoA 364 2.14e+01 c.1.4.1 76357 1oa4A 222 2.25e+01 b.29.1.11 86731 1i69A 219 2.33e+01 c.94.1.1 61825 1qwgA 251 2.35e+01 c.1.27.1 96473 1eeoA 321 2.40e+01 1pty c.45.1.2 32655 1gt91 357 2.40e+01 1vzqH 250 2.40e+01 1v9sA 208 2.46e+01 2bdrA 175 2.48e+01 1xk7A 408 2.50e+01 1ezwA 349 2.51e+01 1ezwA c.1.16.3 29558 1vypX 364 2.54e+01 c.1.4.1 108905 1h61A 364 2.56e+01 1oyc c.1.4.1 60657 1wggA 96 2.64e+01 1i6aA 219 2.65e+01 c.94.1.1 61827 1bf8 205 2.65e+01 1qpxA b.1.11.1,b.7.2.1 22332,23214 1ymmE 249 2.78e+01 1ufbA 127 2.80e+01 a.24.16.3 99331 1uunA 184 2.81e+01 f.6.1.2 100012 1jj2D 176 2.83e+01 1ffkD d.77.1.1 63088 1v6sA 390 2.86e+01 c.86.1.1 100424 1aax 321 2.88e+01 1pty c.45.1.2 32657 1fj2A 232 2.96e+01 1auoA c.69.1.14 34720 1wvqA 167 2.97e+01 1pty 321 3.03e+01 1pty c.45.1.2 32656 1xmpA 170 3.05e+01 1xwwA 157 3.06e+01 2abbA 364 3.11e+01 1xvxA 312 3.22e+01 1qq1A 559 3.25e+01 1tyv b.80.1.6 28041 1qa1A 554 3.26e+01 1tyv b.80.1.6 28047 1z5bA 469 3.30e+01 1fnhA 271 3.32e+01 1fnhA b.1.2.1,b.1.2.1,b.1.2.1 21976,21977,21978 1ltoA 245 3.37e+01 b.47.1.2 84707 2f9nA 245 3.39e+01 1u0sY 118 3.40e+01 c.23.1.1 107566 1z4xA 532 3.47e+01 1tmy 120 3.48e+01 1dbwA c.23.1.1 31083 1knwA 425 3.49e+01 b.49.2.3,c.1.6.1 90969,90970 1xa3A 437 3.49e+01 1ptvA 321 3.51e+01 1pty c.45.1.2 32665 1ahtH 259 3.52e+01 5ptp 1tyu 543 3.52e+01 1tyv b.80.1.6 28037 1tyv 542 3.53e+01 1tyv b.80.1.6 28038 1j2zA 270 3.55e+01 b.81.1.1 90805 1g7fA 298 3.56e+01 1pty c.45.1.2 60330 1h8dH 260 3.57e+01 5ptp 1uwsA 489 3.57e+01 c.1.8.4 108073 1ve2A 235 3.59e+01 1vkdA 338 3.71e+01 b.67.2.4 108644 1tiqA 180 3.76e+01 d.108.1.1 107010 1f6aB 222 3.79e+01 1f6aB b.1.1.2,b.1.1.2 21532,21533 1nxiA 132 3.80e+01 d.58.47.1 86381 1a5y 330 3.81e+01 1pty c.45.1.2 32673 1klnA 605 3.83e+01 1xwl c.55.3.5,e.8.1.1 33693,42986 1rx0A 393 3.84e+01 a.29.3.1,e.6.1.1 98007,98008 1g62A 224 3.85e+01 1g61A d.126.1.1 41128 1pa1A 310 3.87e+01 c.45.1.2 94404 1vfjA 116 3.98e+01 1m8uA 173 4.05e+01 b.11.1.1,b.11.1.1 91233,91234 2b7oA 464 4.05e+01 1j5eE 161 4.08e+01 d.14.1.1,d.50.1.2 71547,71548 1q5fA 156 4.10e+01 d.24.1.1 104536 1mu5A 471 4.12e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1qwyA 291 4.15e+01 b.84.3.2 96509 1kv9A 668 4.25e+01 a.3.1.6,b.70.1.1 73056,73057 1t1gA 364 4.31e+01 c.41.1.2 106246 1tllA 688 4.32e+01 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1uroA 367 4.34e+01 1uroA c.1.22.1 29675 1u5uA 374 4.36e+01 1zirA 173 4.38e+01 1veaA 148 4.41e+01 d.275.1.1 108529 2kfnA 605 4.45e+01 1xwl c.55.3.5,e.8.1.1 33682,42975 1a70 97 4.48e+01 1awd d.15.4.1 37678 1f4pA 147 4.49e+01 5nul c.23.5.1 59651 1d3hA 367 4.50e+01 1d3gA c.1.4.1 28601 1r3sA 367 4.52e+01 c.1.22.1 96963 1yi9A 309 4.59e+01 1s8nA 205 4.60e+01 c.23.1.1 105374 1a0lA 244 4.61e+01 5ptp b.47.1.2 26286 1ze3C 205 4.61e+01 1d8yA 605 4.61e+01 1xwl c.55.3.5,e.8.1.1 33684,42977 1ciy 590 4.63e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1zvkA 358 4.68e+01 2hnp 321 4.71e+01 1pty c.45.1.2 32678 1qpxA 218 4.74e+01 1qpxA b.1.11.1,b.7.2.1 22318,23200 1qcsA 211 4.76e+01 1qcsA b.52.2.3,d.31.1.1 26927,38461 1pswA 348 4.77e+01 c.87.1.7 88287 1tbgE 68 4.78e+01 1tbgE a.137.3.1 19630 1ca4A 168 4.85e+01 1d0aB b.8.1.1,h.1.2.1 23238,45445 1zs9A 261 4.85e+01 1f5yA 85 4.89e+01 1f5yA g.12.1.1,g.12.1.1 44610,44611 1srqA 341 4.99e+01 e.55.1.1 105967 1mh0A 287 5.00e+01 b.47.1.2 79110 1ih7A 903 5.01e+01 1clqA c.55.3.5,e.8.1.1 62375,62376 2b0mA 393 5.03e+01 1dvjA 246 5.19e+01 1dvjA c.1.2.3 28546 1awd 94 5.28e+01 1awd d.15.4.1 37673 2g0cA 76 5.29e+01 1yviA 149 5.30e+01 1zd9A 188 5.41e+01 1n0lA 224 5.44e+01 b.1.11.1,b.7.2.1 79744,79745 1npdA 288 5.51e+01 c.2.1.7,c.58.1.5 80681,80682 2kaiA 80 5.51e+01 2pkaA b.47.1.2 26306 1z4vA 532 5.51e+01 1b77A 228 5.53e+01 1b77A d.131.1.2,d.131.1.2 41362,41363 1xewX 182 5.64e+01 1z41A 338 5.65e+01 1dqiA 124 5.66e+01 1do6A b.1.13.1 22357 1a0rG 65 5.66e+01 1tbgE a.137.3.1 19639 2bibA 547 5.66e+01 1pil 112 5.68e+01 2pii d.58.5.1 39072 1elpA 173 5.69e+01 1amm b.11.1.1,b.11.1.1 23596,23597 1a45 173 5.69e+01 1amm b.11.1.1,b.11.1.1 23602,23603 1sglA 209 5.74e+01 d.124.1.1 105536 1b9xB 68 5.78e+01 1tbgE a.137.3.1 19638 1d3gA 367 5.81e+01 1d3gA c.1.4.1 28600 1np1A 184 5.85e+01 1np1A b.60.1.1 27155 1o4vA 183 5.85e+01 c.23.8.1 86628 1r4wA 226 5.85e+01 c.47.1.13 97050 1v3rA 116 5.90e+01 1gy6A 127 5.92e+01 d.17.4.2 70736 1fjgE 162 5.96e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 1dgrN 79 6.00e+01 1caxB 1amm 174 6.07e+01 1amm b.11.1.1,b.11.1.1 23587,23588 1ca9A 192 6.20e+01 1d0aB b.8.1.1,h.1.2.1 23244,45451 1n0uA 842 6.21e+01 b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 79757,79758,79759,79760,79761 1jjuA 489 6.28e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66774,66775,66776,66777,66778 1y10A 407 6.31e+01 1ntfA 282 6.35e+01 d.151.1.2 92104 1gotG 73 6.36e+01 1tbgE a.137.3.1 19629 1bqcA 302 6.37e+01 1bqcA c.1.8.3 28831 1czyA 168 6.40e+01 1d0aB b.8.1.1,h.1.2.1 23220,45427 1sqkB 25 6.43e+01 j.86.1.1 105924 1km4A 247 6.45e+01 c.1.2.3 72740 1vj2A 126 6.47e+01 b.82.1.10 100796 4gcr 174 6.48e+01 1amm b.11.1.1,b.11.1.1 23589,23590 1bv8A 138 6.50e+01 1ayoA b.2.4.1 22430 1m98A 317 6.73e+01 a.175.1.1,d.17.4.6 78866,78867 1h4aX 173 6.75e+01 b.11.1.1,b.11.1.1 83479,83480 1dgnA 89 6.78e+01 1dgnA a.77.1.3 18436 1w44A 331 6.86e+01 1si6X 282 6.90e+01 1cliA 345 6.92e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1ag8A 499 6.93e+01 1bpwA c.82.1.1 35341 1pa2A 306 6.94e+01 1bgp a.93.1.1 18693 1qr0A 228 6.94e+01 1qr0A d.150.1.1,d.150.1.1 59038,59039 1gt8C 1025 6.97e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70428,70429,70430,70431,70432 2bycA 137 7.02e+01 1cjbA 231 7.06e+01 1qk3A c.61.1.1 34079 2f71A 298 7.13e+01 1dvjC 246 7.20e+01 1dvjA c.1.2.3 28548 1dgwX 79 7.26e+01 1caxB b.82.1.2 28091 1btkB 169 7.31e+01 1btkA b.55.1.1 26960 1gjwA 637 7.37e+01 b.71.1.1,c.1.8.1 60582,60583 1u5kA 244 7.38e+01 1lq9A 112 7.39e+01 d.58.4.3 78129 1crzA 403 7.43e+01 1crzA b.68.4.1,c.51.2.1 27629,33211 2aawA 222 7.47e+01 1pmhX 185 7.47e+01 b.18.1.18 104193 1l4iA 206 7.48e+01 b.1.11.1,b.7.2.1 73564,73565 1c5lH 259 7.48e+01 5ptp 2bm5A 186 7.49e+01 1ffkD 176 7.51e+01 1ffkD d.77.1.1 39750 1wspA 84 7.57e+01 1s2oA 244 7.61e+01 1d0aB 168 7.64e+01 1d0aB b.8.1.1,h.1.2.1 23224,45431 8kme2 259 7.65e+01 1ucyE 2pii 112 7.68e+01 2pii d.58.5.1 39071 1f39A 101 7.69e+01 1umuA b.87.1.1 28386 1akq 147 7.72e+01 5nul c.23.5.1 31159 2fbwA 621 7.76e+01 1u1wA 298 7.99e+01 1xy7A 166 8.04e+01 1czyC 168 8.07e+01 1d0aB b.8.1.1,h.1.2.1 23222,45429 1lf7A 182 8.19e+01 b.60.1.1 73878 1op0A 234 8.21e+01 b.47.1.2 104019 1xdtR 79 8.31e+01 1xdtR g.3.11.1 44296 1y21A 282 8.50e+01 1vqoD 177 8.53e+01 1jb2A 127 8.54e+01 d.17.4.2 71624 1oy1A 228 8.55e+01 c.23.16.2 87548 1mr7A 209 8.63e+01 b.81.1.3 91430 1bftA 101 8.68e+01 1a3qA b.1.18.1 21934 1ckmA 330 8.69e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 2b49A 287 8.75e+01 1iw2A 182 8.92e+01 b.60.1.1 71468 1i2mA 216 8.96e+01 1byuA c.37.1.8 61568 1puoA 170 8.98e+01 a.101.1.1,a.101.1.1 95134,95135