# List of top-scoring protein chains for T0222.t2k-w0.5 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 1pe1A 267 4.34e-10 c.1.10.4 -5553 1lroA 267 1.29e-09 c.1.10.4 78161 1phwA 284 4.70e-07 1g7uA 284 4.92e-07 1d9eA c.1.10.4 60334 1o60A 292 5.59e-07 c.1.10.4 -5549 1a53 247 6.66e-02 1a53 c.1.2.4 28564 1jul 248 6.67e-02 1a53 c.1.2.4 28566 1of8A 370 7.07e-02 c.1.10.4 -5508 1og0A 370 7.12e-02 c.1.10.4 -5532 1v03A 565 6.86e-01 1h1dA 221 7.40e-01 c.66.1.1 83452 1j5tA 242 8.66e-01 c.1.2.4 71583 1i5gA 144 8.70e-01 1ewxA c.47.1.10 61784 1v02A 565 8.85e-01 1v02E 565 8.89e-01 1mzhA 225 9.16e-01 c.1.10.1 79698 1i4nA 251 9.52e-01 c.1.2.4 71114 1fg4A 149 1.01e+00 1ewxA c.47.1.10 59814 1kp8A 547 1.02e+00 a.129.1.1 84414 c.8.5.1 84415 d.56.1.1 84416 1o6jA 150 1.02e+00 c.47.1.10 81089 1jf8A 131 1.02e+00 c.44.1.1 66621 1pcqA 524 1.02e+00 a.129.1.1 -1802 c.8.5.1 -6102 d.56.1.1 -9847 1o81A 152 1.03e+00 c.47.1.10 81175 1mnfA 547 1.04e+00 a.129.1.1 -1788 c.8.5.1 -6088 d.56.1.1 -9833 1gr5A 547 1.06e+00 i.16.1.1 65478 1grlA 548 1.07e+00 1oelA 547 1.08e+00 1derA a.129.1.1 19452 c.8.5.1 30781 d.56.1.1 38900 1oc9A 152 1.10e+00 c.47.1.10 86797 1i2mB 402 1.18e+00 1a12A b.69.5.1 61569 1a12A 413 1.19e+00 1a12A b.69.5.1 27663 1j4zA 547 1.20e+00 a.129.1.1 -1830 c.8.5.1 -6130 d.56.1.1 -9875 1ub3A 220 1.36e+00 c.1.10.1 88395 1ljuA 131 1.40e+00 c.44.1.1 73944 1rxiA 131 1.41e+00 1djpA 330 1.56e+00 4pgaA c.88.1.1 35567 4pgaA 337 1.58e+00 4pgaA c.88.1.1 35565 1ljlA 131 1.65e+00 c.44.1.1 73939 1p4cA 380 1.67e+00 c.1.4.1 -5201 1rvkA 382 1.76e+00 c.1.11.2 -5568 d.54.1.1 -9826 3pga1 337 1.81e+00 4pgaA 1j08A 226 1.84e+00 c.47.1.2 83855 c.47.1.2 83856 1a6dB 543 2.06e+00 1a6dA a.129.1.2 19489 c.8.5.2 30820 d.56.1.2 38937 1tr1A 447 2.11e+00 1e70M c.1.8.4 28957 1e4iA 447 2.11e+00 1e70M c.1.8.4 59225 1vjrA 271 2.15e+00 unknown_sccs -6853 1pw5A 253 2.26e+00 unknown_sccs -6852 1mxsA 225 2.36e+00 c.1.10.1 -5485 1bgaA 447 2.39e+00 1e70M c.1.8.4 28961 1bggA 448 2.39e+00 1e70M c.1.8.4 28953 1o5kA 306 2.57e+00 c.1.10.1 -5482 1qoxA 449 2.62e+00 c.1.8.4 28965 1lk0A 131 2.66e+00 c.44.1.1 73948 1ad1A 266 2.86e+00 1aj2 c.1.21.1 29668 1agx 331 3.13e+00 4pgaA c.88.1.1 35564 1pdo 135 3.15e+00 1pdo c.54.1.1 33376 1ox6A 555 3.22e+00 c.1.2.1 87505 c.23.16.1 87506 1we3A 543 3.25e+00 1h5yA 253 3.41e+00 c.1.2.1 65638 1jvnA 555 3.41e+00 c.1.2.1 67355 c.23.16.1 67356 1j7hA 130 3.63e+00 d.79.1.1 77097 1uyrA 737 3.73e+00 c.14.1.4 -6258 c.14.1.4 -6259 1jr2A 286 3.77e+00 c.113.1.1 67111 1me8A 503 3.78e+00 c.1.5.1 79028 1uyvA 737 3.81e+00 c.14.1.4 -6274 c.14.1.4 -6275 1qgeD 222 3.83e+00 1cvl c.69.1.18 34773 1rvgA 305 3.86e+00 c.1.10.2 -5500 1od2A 805 4.04e+00 c.14.1.4 86821 c.14.1.4 86822 1g69A 228 4.08e+00 c.1.3.1 60313 1g6cA 227 4.09e+00 c.1.3.1 60315 1g4sA 226 4.10e+00 c.1.3.1 60247 1g67A 225 4.10e+00 c.1.3.1 60311 1e5dA 402 4.44e+00 1e5dA c.23.5.1 31208 d.157.1.3 42061 1ovgA 238 4.53e+00 c.56.2.1 -7755 1lrtA 376 4.61e+00 c.1.5.1 84685 1ecpA 238 4.61e+00 1ecpA c.56.2.1 33775 1pk9A 237 4.61e+00 c.56.2.1 -7734 1pw7A 239 4.61e+00 c.56.2.1 -7728 1pvnA 376 4.69e+00 c.1.5.1 88312 1e0rB 159 4.75e+00 1a6dA c.8.5.2 30824 1j6oA 268 4.77e+00 c.1.9.12 77088 1cvl 319 5.39e+00 1cvl c.69.1.18 34786 1tahA 318 5.57e+00 1cvl c.69.1.18 34775 1ea9C 583 5.68e+00 b.1.18.2 70087 b.71.1.1 70088 c.1.8.1 70089 1h0hA 977 5.87e+00 b.52.2.2 76435 c.81.1.1 76436 1ass 159 5.91e+00 1a6dA c.8.5.2 30818 1g8mA 593 5.93e+00 1g8mA c.24.1.3 60371 c.97.2.1 60372 1od0A 468 5.94e+00 c.1.8.4 86818 1m9nA 613 6.35e+00 c.24.1.3 78870 c.97.2.1 78871 2tpsA 227 6.82e+00 2tpsA c.1.3.1 28591 1jm7A 112 7.78e+00 g.44.1.1 66880 1gzgA 337 7.90e+00 c.1.10.3 70805 1mh6A 125 7.94e+00 d.32.1.2 79116 1floA 422 7.95e+00 1floA a.60.9.1 18106 d.163.1.1 42166 1ewjA 126 7.99e+00 1ecsA d.32.1.2 59526 1dtlA 161 8.59e+00 1ncx a.39.1.5 17229 1erzA 303 8.68e+00 1erzA d.160.1.2 59498 1fo6A 304 8.73e+00 1erzA d.160.1.2 59923 1ecsA 126 8.88e+00 1ecsA d.32.1.2 59407 1b4kA 337 8.94e+00 1b4kA c.1.10.3 29184 1m5wA 243 9.34e+00 c.1.24.1 84836 1ho1A 242 9.38e+00 1ho1A c.1.24.1 61097 1aj4 161 9.46e+00 1ncx a.39.1.5 17244 1la0A 161 9.99e+00 a.39.1.5 77864 1m3uA 264 1.00e+01 c.1.12.8 84784 4lipD 320 1.04e+01 1cvl c.69.1.18 34783 1iirA 415 1.06e+01 1iirA c.87.1.5 62453 1p0kA 349 1.09e+01 c.1.4.1 87648 1ojxA 263 1.13e+01 c.1.10.1 -5445 1uf5A 303 1.18e+01 1qu9A 128 1.21e+01 1qu9A d.79.1.1 39755 1rcuA 195 1.24e+01 unknown_sccs -7279 1k8yA 268 1.26e+01 c.1.2.4 72183 1kfbA 268 1.27e+01 c.1.2.4 77369 1o5tA 378 1.32e+01 1eepA 404 1.36e+01 1ak5 c.1.5.1 28636 1q3sA 548 1.37e+01 a.129.1.2 -1872 c.8.5.2 -6172 d.56.1.2 -9917 1beuA 268 1.38e+01 2tysA c.1.2.4 28574 1m6xA 423 1.41e+01 a.60.9.1 78708 d.163.1.1 78709 1m6xC 423 1.41e+01 a.60.9.1 78712 d.163.1.1 78713 1p4eC 429 1.41e+01 a.60.9.1 87768 d.163.1.1 87769 1p4eA 429 1.41e+01 a.60.9.1 87764 d.163.1.1 87765 1ulhA 390 1.43e+01 c.26.1.1 -6596 1va4A 279 1.44e+01 1s5pA 235 1.46e+01 c.31.1.5 -6774 1qopA 268 1.52e+01 2tysA c.1.2.4 28570 1mxmA 254 1.53e+01 b.38.1.3 79647 d.58.43.1 79648 f.34.1.1 79649 1kfcA 268 1.54e+01 c.1.2.4 77371 1np6A 174 1.60e+01 c.37.1.10 85954 1pkxA 592 1.63e+01 c.24.1.3 -6574 c.97.2.1 -8791 1ghtA 105 1.65e+01 2rslA c.53.1.1 60526 1thfD 253 1.76e+01 1thfD c.1.2.1 28535 1gpwA 253 1.76e+01 c.1.2.1 65460 1q3rA 548 1.76e+01 a.129.1.2 -1868 c.8.5.2 -6168 d.56.1.2 -9913 1vh7A 265 1.76e+01 c.1.2.1 -5159 1q3qA 548 1.77e+01 a.129.1.2 -1864 c.8.5.2 -6164 d.56.1.2 -9909 2rslA 140 1.79e+01 2rslA c.53.1.1 33345 1n8nA 212 1.80e+01 unknown_sccs -6830 1km5A 247 1.84e+01 c.1.2.3 72741 1gnxA 479 1.87e+01 c.1.8.4 76241 1p9nA 170 1.87e+01 c.37.1.10 87997 1l5zA 155 1.88e+01 c.23.1.1 77722 1fts 295 1.95e+01 1ng1 a.24.13.1 16968 c.37.1.10 32279 1qkkA 155 2.00e+01 1dbwA c.23.1.1 31104 1eiwA 111 2.00e+01 1eiwA c.23.3.1 31130 1h0pA 182 2.01e+01 b.62.1.1 76450 1gdtA 183 2.04e+01 2rslA a.4.1.2 16021 c.53.1.1 33348 1vhcA 224 2.18e+01 c.1.10.1 -5488 1kq1A 77 2.19e+01 b.38.1.2 72848 1p5dX 463 2.26e+01 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 1brt 277 2.30e+01 1brt c.69.1.12 34699 1ru8A 232 2.30e+01 c.26.2.1 -6635 1cec 343 2.32e+01 1ceo c.1.8.3 28809 1fc4A 401 2.34e+01 1bs0A c.67.1.4 59760 1dk7A 146 2.35e+01 1derA c.8.5.1 30772 1pg5A 299 2.35e+01 1uf3A 228 2.36e+01 unknown_sccs -11463 1ofhA 310 2.37e+01 c.37.1.20 86948 1jon 155 2.38e+01 1derA c.8.5.1 30780 1a6dA 545 2.38e+01 1a6dA a.129.1.2 19488 c.8.5.2 30819 d.56.1.2 38936 1boc 76 2.39e+01 4icb a.39.1.1 17155 1ceo 343 2.42e+01 1ceo c.1.8.3 28808 1la1A 192 2.45e+01 c.8.5.1 73772 1km1A 247 2.47e+01 c.1.2.3 72736 1lw7A 365 2.49e+01 c.26.1.3 74295 c.37.1.1 74296 1lp6A 229 2.49e+01 c.1.2.3 74171 1nx8A 273 2.49e+01 b.82.2.8 86374 1loqA 228 2.49e+01 c.1.2.3 74155 1dv7A 227 2.52e+01 1dvjA c.1.2.3 28550 1losA 224 2.53e+01 c.1.2.3 74157 1km2A 247 2.54e+01 c.1.2.3 72738 1qx2A 76 2.55e+01 1vpe 398 2.59e+01 16pk c.86.1.1 35453 1ktnA 250 2.61e+01 c.1.10.1 72988 1ton 235 2.62e+01 5ptp b.47.1.2 26307 1dvjA 246 2.62e+01 1dvjA c.1.2.3 28546 1kid 203 2.65e+01 1derA c.8.5.1 30771 1d1oA 75 2.68e+01 4icb a.39.1.1 17152 1p1xA 260 2.68e+01 1jcjA 260 2.69e+01 c.1.10.1 66499 1klzA 247 2.70e+01 c.1.2.3 72731 1rd4A 191 2.71e+01 c.62.1.1 -7968 1km0A 247 2.72e+01 c.1.2.3 72732 1f9aA 168 2.75e+01 1f9aA c.26.1.3 31602 1lfaA 187 2.76e+01 1ido c.62.1.1 34122 1q9cA 191 2.79e+01 a.22.1.3 -567 1ht9A 76 2.79e+01 4icb a.39.1.1 61252 1klyA 247 2.87e+01 c.1.2.3 72730 1f74A 293 2.91e+01 1nal3 c.1.10.1 29079 1dgqA 188 2.93e+01 1ido c.62.1.1 34131 1cqpA 182 3.00e+01 1ido c.62.1.1 34127 1nsj 205 3.02e+01 1nsj c.1.2.4 28560 1kcyA 75 3.06e+01 a.39.1.1 68450 1r6uA 437 3.06e+01 c.26.1.1 -6594 1r6tA 477 3.07e+01 c.26.1.1 -6592 1k2yX 463 3.09e+01 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1o4wA 147 3.12e+01 c.120.1.1 86629 1h49A 512 3.13e+01 c.1.8.4 83477 1hxjA 507 3.13e+01 c.1.8.4 76729 1e1eA 512 3.13e+01 1e70M c.1.8.4 28944 1v08A 512 3.13e+01 1q9jA 422 3.19e+01 1l4uA 176 3.21e+01 c.37.1.2 73568 1ypn 313 3.23e+01 1pda c.94.1.1 35754 d.50.2.1 38797 1lte 239 3.25e+01 1led b.29.1.1 24047 1uasA 362 3.27e+01 b.71.1.1 88388 c.1.8.1 88389 1j8mF 297 3.35e+01 1ng1 a.24.13.1 62742 c.37.1.10 62743 1mq9A 180 3.39e+01 c.62.1.1 79411 1jcmP 259 3.39e+01 c.1.2.4 71633 1gtkA 313 3.42e+01 c.94.1.1 76346 d.50.2.1 76347 1mjnA 179 3.47e+01 c.62.1.1 79210 1l2tA 235 3.49e+01 c.37.1.12 73514 1mq8B 177 3.50e+01 c.62.1.1 79407 1viaA 175 3.52e+01 c.37.1.2 -7021 1fa2A 498 3.53e+01 1byb c.1.8.1 28797 1kqvA 79 3.57e+01 a.39.1.1 68842 1n65A 75 3.59e+01 a.39.1.1 -817 1gk9A 260 3.59e+01 d.153.1.2 65246 1i6uA 130 3.60e+01 d.140.1.1 61850 1gdhA 320 3.61e+01 1gdhA c.2.1.4 30095 c.23.12.1 31355 1j2yA 167 3.61e+01 c.23.13.1 84047 1ka9F 252 3.61e+01 c.1.2.1 77307 3lck 271 3.65e+01 1fmk d.144.1.7 41686 1pda 313 3.66e+01 1pda c.94.1.1 35751 d.50.2.1 38794 1km6A 247 3.75e+01 c.1.2.3 72742 1qpcA 279 3.76e+01 1fgkA d.144.1.7 41685 1j8yF 297 3.77e+01 1ng1 a.24.13.1 62747 c.37.1.10 62748 1ax0 239 3.78e+01 1led b.29.1.1 24042 1km4A 247 3.80e+01 c.1.2.3 72740 1hey 128 3.84e+01 3chy c.23.1.1 31061 1r30A 369 3.88e+01 unknown_sccs -5683 1broA 277 3.94e+01 1brt c.69.1.12 34700 1pzgA 331 3.94e+01 c.2.1.5 -5931 d.162.1.1 -11498 1gkpA 458 3.96e+01 b.92.1.3 70231 c.1.9.6 70232 1rkuA 206 3.98e+01 unknown_sccs -6823 1qpdA 279 3.99e+01 1fmk d.144.1.7 41687