# 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 4.96e-35 2cpl a.118.8.1,b.62.1.1 62380,62381 1dywA 173 1.13e-34 2cpl b.62.1.1 27505 1qoiA 177 1.65e-34 2cpl b.62.1.1 27490 1a58 177 1.95e-34 2cpl b.62.1.1 27495 1cwoA 165 4.34e-34 2cpl b.62.1.1 27445 2cpl 165 4.51e-34 2cpl b.62.1.1 27420 2bitX 165 5.39e-34 2rmcA 182 8.48e-34 2cpl b.62.1.1 27491 1yndA 165 8.90e-34 1h0pA 182 1.07e-33 b.62.1.1 76450 1xo7A 166 1.37e-33 1zcxA 178 1.63e-33 1awsA 164 1.89e-33 2cpl b.62.1.1 27431 1awqA 164 1.90e-33 2cpl b.62.1.1 27461 2cfeA 162 3.22e-33 1vdnA 162 7.65e-33 2a2nA 176 8.03e-31 1zkcA 197 2.89e-30 2fu0A 160 1.41e-29 2b71A 196 3.00e-29 1xwnA 174 4.60e-29 1lopA 164 2.84e-26 2cpl b.62.1.1 27510 1v9tA 166 6.52e-26 b.62.1.1 108451 1j2aA 166 1.01e-25 b.62.1.1 90779 1clh 166 6.97e-23 2cpl b.62.1.1 27512 1zx8A 136 7.34e-02 1mxiA 160 9.32e-01 c.116.1.1 79646 2b8mA 117 1.15e+00 3sil 379 1.72e+00 3sil b.68.1.1 27542 2bdvA 231 1.74e+00 2b4wA 315 2.57e+00 2ex4A 241 3.45e+00 1o26A 232 3.70e+00 d.207.1.1 86566 1dim 381 3.85e+00 3sil b.68.1.1 27544 2sil 381 4.17e+00 3sil b.68.1.1 27543 1kq4A 232 4.28e+00 d.207.1.1 68791 1gt8A 1025 6.74e+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 1dz3A 130 6.96e+00 1dz3A c.23.1.1 31105 1vkdA 338 7.19e+00 b.67.2.4 108644 1qmpA 130 7.21e+00 1dz3A c.23.1.1 31106 1vj0A 380 7.22e+00 b.35.1.2,c.2.1.1 100786,100787 1tmxA 293 7.61e+00 2azpA 318 7.86e+00 1f6aB 222 8.24e+00 1f6aB b.1.1.2,b.1.1.2 21532,21533 1uumA 372 8.31e+00 c.1.4.1 100010 1e8bA 160 8.37e+00 1e8bA g.14.1.2,g.14.1.2,g.27.1.1 44671,44672,44951 1x9uA 116 8.53e+00 1wriA 93 9.02e+00 1wn0A 145 9.29e+00 1vyrA 364 9.35e+00 c.1.4.1 108906 1kv9A 668 9.84e+00 a.3.1.6,b.70.1.1 73056,73057 1xe1A 116 9.90e+00 b.43.3.1 109571 1gvoA 364 1.01e+01 c.1.4.1 76357 1w96A 554 1.10e+01 1jj2D 176 1.14e+01 1ffkD d.77.1.1 63088 1mu5A 471 1.16e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1vypX 364 1.18e+01 c.1.4.1 108905 1icpA 376 1.21e+01 1oyc c.1.4.1 62270 2bi0A 337 1.24e+01 1h61A 364 1.25e+01 1oyc c.1.4.1 60657 2abbA 364 1.34e+01 1c0eA 157 1.36e+01 1dg9A c.44.1.1 32638 1xwmA 217 1.36e+01 1phr 157 1.38e+01 1dg9A c.44.1.1 32635 1z5bA 469 1.39e+01 1s31A 273 1.44e+01 1vzqH 250 1.60e+01 1eeoA 321 1.62e+01 1pty c.45.1.2 32655 1fnhA 271 1.63e+01 1fnhA b.1.2.1,b.1.2.1,b.1.2.1 21976,21977,21978 1ezwA 349 1.65e+01 1ezwA c.1.16.3 29558 1dg9A 157 1.67e+01 1dg9A c.44.1.1 32637 1qwyA 291 1.72e+01 b.84.3.2 96509 1j5eE 161 1.76e+01 d.14.1.1,d.50.1.2 71547,71548 1uwsA 489 1.77e+01 c.1.8.4 108073 1fj2A 232 1.78e+01 1auoA c.69.1.14 34720 1tm0A 350 1.95e+01 d.21.1.3 107147 1aax 321 2.03e+01 1pty c.45.1.2 32657 1oa4A 222 2.05e+01 b.29.1.11 86731 1pty 321 2.10e+01 1pty c.45.1.2 32656 1rypK 198 2.10e+01 d.153.1.4 41879 1u11A 182 2.12e+01 c.23.8.1 107576 1a5dA 173 2.16e+01 1amm b.11.1.1,b.11.1.1 23614,23615 1ahtH 259 2.20e+01 5ptp 1qwgA 251 2.21e+01 c.1.27.1 96473 1fjgE 162 2.23e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 1uunA 184 2.26e+01 f.6.1.2 100012 1g7fA 298 2.37e+01 1pty c.45.1.2 60330 1pswA 348 2.37e+01 c.87.1.7 88287 1pa1A 310 2.40e+01 c.45.1.2 94404 1k2fA 190 2.41e+01 b.8.1.2 68054 1ve4A 206 2.43e+01 1bf8 205 2.49e+01 1qpxA b.1.11.1,b.7.2.1 22332,23214 1m8uA 173 2.51e+01 b.11.1.1,b.11.1.1 91233,91234 1ptvA 321 2.51e+01 1pty c.45.1.2 32665 1j2zA 270 2.54e+01 b.81.1.1 90805 1xwwA 157 2.56e+01 1tiqA 180 2.57e+01 d.108.1.1 107010 1a5y 330 2.59e+01 1pty c.45.1.2 32673 1h8dH 260 2.64e+01 5ptp 1vqoD 177 2.66e+01 1knwA 425 2.70e+01 b.49.2.3,c.1.6.1 90969,90970 1v9sA 208 2.76e+01 1ymmE 249 2.88e+01 2hnp 321 2.94e+01 1pty c.45.1.2 32678 1o7iA 119 2.97e+01 b.40.4.3 86642 1i69A 219 3.03e+01 c.94.1.1 61825 1uroA 367 3.13e+01 1uroA c.1.22.1 29675 1ufbA 127 3.17e+01 a.24.16.3 99331 1r3sA 367 3.26e+01 c.1.22.1 96963 8kme2 259 3.28e+01 1ucyE 1xvxA 312 3.31e+01 1i6aA 219 3.32e+01 c.94.1.1 61827 1mh0A 287 3.35e+01 b.47.1.2 79110 1wggA 96 3.48e+01 1qr0A 228 3.53e+01 1qr0A d.150.1.1,d.150.1.1 59038,59039 1wvqA 167 3.67e+01 2b49A 287 3.68e+01 2f9nA 245 3.69e+01 1np1A 184 3.71e+01 1np1A b.60.1.1 27155 1klnA 605 3.78e+01 1xwl c.55.3.5,e.8.1.1 33693,42986 1g62A 224 3.78e+01 1g61A d.126.1.1 41128 1ltoA 245 3.85e+01 b.47.1.2 84707 1f39A 101 3.86e+01 1umuA b.87.1.1 28386 2bdrA 175 3.86e+01 1zirA 173 3.99e+01 1srqA 341 4.04e+01 e.55.1.1 105967 1yviA 149 4.09e+01 2madH 373 4.15e+01 2bbkH b.69.2.1 27639 1a70 97 4.26e+01 1awd d.15.4.1 37678 1ffkD 176 4.26e+01 1ffkD d.77.1.1 39750 1a45 173 4.35e+01 1amm b.11.1.1,b.11.1.1 23602,23603 1u0sY 118 4.43e+01 c.23.1.1 107566 1c5lH 259 4.45e+01 5ptp 2f71A 298 4.50e+01 1xmpA 170 4.52e+01 1vfjA 116 4.55e+01 1f5yA 85 4.58e+01 1f5yA g.12.1.1,g.12.1.1 44610,44611 1z41A 338 4.59e+01 2bm5A 186 4.64e+01 1tmy 120 4.64e+01 1dbwA c.23.1.1 31083 1ze3C 205 4.64e+01 1jmmA 377 4.66e+01 b.30.6.1 71749 1amm 174 4.68e+01 1amm b.11.1.1,b.11.1.1 23587,23588 1zs9A 261 4.70e+01 1d3hA 367 4.71e+01 1d3gA c.1.4.1 28601 1tbgE 68 4.72e+01 1tbgE a.137.3.1 19630 2b7oA 464 4.81e+01 1ve2A 235 4.98e+01 1ag8A 499 5.05e+01 1bpwA c.82.1.1 35341 1xdtR 79 5.06e+01 1xdtR g.3.11.1 44296 2kfnA 605 5.08e+01 1xwl c.55.3.5,e.8.1.1 33682,42975 1d8yA 605 5.08e+01 1xwl c.55.3.5,e.8.1.1 33684,42977 4gcr 174 5.10e+01 1amm b.11.1.1,b.11.1.1 23589,23590 1cliA 345 5.11e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1ih7A 903 5.21e+01 1clqA c.55.3.5,e.8.1.1 62375,62376 1h4aX 173 5.23e+01 b.11.1.1,b.11.1.1 83479,83480 1u5uA 374 5.29e+01 2b0mA 393 5.30e+01 1a0lA 244 5.31e+01 5ptp b.47.1.2 26286 1qpxA 218 5.35e+01 1qpxA b.1.11.1,b.7.2.1 22318,23200 1zglM 209 5.42e+01 1nfa 178 5.56e+01 1a02N b.2.5.3 22442 1u5kA 244 5.63e+01 1btkA 169 5.63e+01 1btkA b.55.1.1 26959 1ca4A 168 5.63e+01 1d0aB b.8.1.1,h.1.2.1 23238,45445 1btkB 169 5.66e+01 1btkA b.55.1.1 26960 1a0rG 65 5.66e+01 1tbgE a.137.3.1 19639 1vr0A 247 5.66e+01 1b9xB 68 5.77e+01 1tbgE a.137.3.1 19638 1bftA 101 5.84e+01 1a3qA b.1.18.1 21934 1e88A 160 5.90e+01 g.14.1.2,g.14.1.2,g.27.1.1 44669,44670,44950 2biqA 219 5.99e+01 1d3gA 367 6.03e+01 1d3gA c.1.4.1 28600 1gjwA 637 6.06e+01 b.71.1.1,c.1.8.1 60582,60583 2b30A 301 6.08e+01 1op0A 234 6.12e+01 b.47.1.2 104019 2kaiA 80 6.13e+01 2pkaA b.47.1.2 26306 1wspA 84 6.23e+01 1s8nA 205 6.26e+01 c.23.1.1 105374 1u1wA 298 6.27e+01 1dwnA 127 6.28e+01 1dwnA d.85.1.1 40141 1tllA 688 6.36e+01 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1gotG 73 6.41e+01 1tbgE a.137.3.1 19629 1bv8A 138 6.42e+01 1ayoA b.2.4.1 22430 1zd9A 188 6.46e+01 1s2oA 244 6.49e+01 1y89A 238 6.54e+01 1n0lA 224 6.56e+01 b.1.11.1,b.7.2.1 79744,79745 1v3rA 116 6.59e+01 1tq5A 242 6.59e+01 1cjbA 231 6.60e+01 1qk3A c.61.1.1 34079 1si6X 282 6.62e+01 1ucyE 109 6.66e+01 1ucyE 1sqkB 25 6.69e+01 j.86.1.1 105924 1elpA 173 6.71e+01 1amm b.11.1.1,b.11.1.1 23596,23597 1n0uA 842 6.74e+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 1ntfA 282 6.86e+01 d.151.1.2 92104 1d0aB 168 6.87e+01 1d0aB b.8.1.1,h.1.2.1 23224,45431 1iraX 152 6.91e+01 1irp b.42.1.2 25556 1ilr1 152 6.93e+01 1irp 1z4rA 168 6.93e+01 1yo8A 634 6.99e+01 1v6sA 390 7.01e+01 c.86.1.1 100424 1xubA 298 7.10e+01 1ciy 590 7.23e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1k87A 669 7.34e+01 a.176.1.1,c.1.23.2 77286,77287 1czyA 168 7.36e+01 1d0aB b.8.1.1,h.1.2.1 23220,45427 1bfs 106 7.36e+01 1a3qA b.1.18.1 21927 1yi9A 309 7.37e+01 1gt8C 1025 7.39e+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 2aexA 346 7.44e+01 1khvA 516 7.55e+01 e.8.1.4 68627 1q5fA 156 7.58e+01 d.24.1.1 104536 1r4wA 226 7.65e+01 c.47.1.13 97050 1nbaA 264 7.75e+01 1nbaA c.33.1.3 31753 1z4xA 532 7.76e+01 1w44A 331 7.81e+01 1rx0A 393 7.82e+01 a.29.3.1,e.6.1.1 98007,98008 1fjjA 159 7.85e+01 1fjjA b.17.1.2 59852 1xzwA 426 7.86e+01 1ca9A 192 7.88e+01 1d0aB b.8.1.1,h.1.2.1 23244,45451 1qj5A 429 7.96e+01 1dtyA c.67.1.4 34493 1t9fA 187 7.97e+01 b.42.6.1 106710 1gt91 357 7.98e+01 1awd 94 8.00e+01 1awd d.15.4.1 37673 1thx 115 8.10e+01 1thx c.47.1.1 32732 1kb0A 677 8.13e+01 a.3.1.6,b.70.1.1 68378,68379 2pkaA 80 8.25e+01 2pkaA b.47.1.2 26302 2aawA 222 8.25e+01 1puoA 170 8.35e+01 a.101.1.1,a.101.1.1 95134,95135 1pa2A 306 8.44e+01 1bgp a.93.1.1 18693 2gk3A 256 8.48e+01 1dqiA 124 8.49e+01 1do6A b.1.13.1 22357 1czyC 168 8.57e+01 1d0aB b.8.1.1,h.1.2.1 23222,45429 1nxiA 132 8.58e+01 d.58.47.1 86381 1t6kA 278 8.65e+01 1my5A 114 8.65e+01 b.1.18.1 79673 2fbwA 621 8.78e+01 1ldr 43 8.85e+01 1ajj g.12.1.1 44616 1jjuA 489 8.88e+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 1veaA 148 8.92e+01 d.275.1.1 108529