# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1hzdA 272 3.74e-03 1hnuA 280 1.48e-02 1hnoA 1j9yA 385 2.29e-02 1j9yA 1ef8A 261 3.38e-02 1ef8A c.14.1.3 30921 1hnoA 280 4.37e-02 1hnoA 2napA 723 6.94e-02 2napA b.52.2.2 26926 c.81.1.1 35334 1ceo 343 7.74e-02 1ceo c.1.8.3 28808 1rpxA 230 1.12e-01 1rpxA c.1.2.2 28536 1fts 295 1.16e-01 1ng1 a.29.1.1 16968 c.37.1.10 32279 1dciA 275 1.18e-01 1dciA c.14.1.3 30918 1cleA 534 1.20e-01 1thg c.69.1.17 34771 1bw0A 416 1.31e-01 1bw0A c.67.1.1 34385 1mil 104 1.39e-01 1d4tA d.93.1.1 40496 1cec 343 1.41e-01 1ceo c.1.8.3 28809 3pnp 289 1.50e-01 1b8oA c.56.2.1 33763 1j8mF 297 1.77e-01 1ng1 1dosA 358 2.34e-01 1dosA c.1.10.2 29175 7odcA 424 2.34e-01 7odcA b.49.2.1 26488 c.1.6.1 28650 1qe3A 489 3.06e-01 2bce c.69.1.1 34630 1ecxA 384 3.20e-01 1ecxA c.67.1.3 34431 1eg5A 384 3.29e-01 1ecxA c.67.1.3 34429 1b8oA 284 3.90e-01 1b8oA c.56.2.1 33762 1k3fA 253 4.37e-01 1pbn 289 4.52e-01 1b8oA c.56.2.1 33771 1ek6A 348 4.67e-01 1xel c.2.1.2 29800 1a3h 300 4.70e-01 7a3hA c.1.8.3 28819 1hzgA 295 4.84e-01 1hzgA 1crl 534 5.13e-01 1thg c.69.1.17 34765 1ecpA 238 5.95e-01 1ecpA c.56.2.1 33775 1aqzA 149 6.12e-01 1aqzA d.1.1.1 36238 1f2tB 148 6.40e-01 1f2tB 7a3hA 303 6.88e-01 7a3hA c.1.8.3 28817 1aqzB 149 7.28e-01 1aqzA d.1.1.1 36239 1e1oA 504 8.42e-01 1lylA b.40.4.1 25258 d.104.1.1 40714 1cs0B 382 9.10e-01 1c3oB c.8.3.1 30740 c.23.16.1 31417 1a9xB 379 9.24e-01 1c3oB c.8.3.1 30732 c.23.16.1 31409 1qgvA 142 9.38e-01 1qgvA c.47.1.8 33056 1k9sA 237 9.57e-01 1hq0A 295 9.64e-01 1hzgA 1poxA 585 1.07e+00 1poxA c.31.1.3 31731 c.36.1.1 31793 c.36.1.1 31794 1ii7A 333 1.13e+00 1ii7A 1cr1A 296 1.18e+00 1cr1A c.37.1.11 32286 1g0cA 364 1.27e+00 7a3hA 1efcA 393 1.28e+00 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1exmA 405 1.36e+00 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1c3oB 382 1.39e+00 1c3oB c.8.3.1 30744 c.23.16.1 31421 1brlB 324 1.44e+00 1lucA c.1.16.1 29554 1lylA 504 1.44e+00 1lylA b.40.4.1 25261 d.104.1.1 40717 1ha3A 405 1.49e+00 1efcA 1lam 484 1.49e+00 1lam c.50.1.1 33166 c.56.5.3 33829 1lap 488 1.50e+00 1lam c.50.1.1 33171 c.56.5.3 33834 1a0cA 438 1.50e+00 1a0cA c.1.15.3 29529 1d7kA 421 1.67e+00 7odcA b.49.2.1 26486 c.1.6.1 28648 1lucB 324 1.68e+00 1lucA c.1.16.1 29548 1cr0A 296 1.87e+00 1cr1A c.37.1.11 32287 1zpdA 568 1.97e+00 1zpdA c.31.1.3 31741 c.36.1.1 31785 c.36.1.1 31786 1d2nA 272 1.99e+00 1d2nA c.37.1.13 32428 1etu 394 2.07e+00 1efcA c.37.1.8 32121 1eiwA 111 2.49e+00 1eiwA c.23.3.1 31130 1nsf 273 2.55e+00 1d2nA c.37.1.13 32429 1k2yX 463 2.72e+00 1fuiA 591 2.74e+00 1fuiA b.43.2.1 25674 c.85.1.1 35444 2shpA 525 2.76e+00 2shpA c.45.1.2 32683 d.93.1.1 40533 d.93.1.1 40534 1ekqA 272 2.88e+00 1c3qA c.72.1.2 34941 1eudA 311 3.03e+00 2scuA c.2.1.8 30312 c.23.4.1 31140 1uroA 367 3.21e+00 1uroA c.1.22.1 29675 1i6wA 181 3.43e+00 1i6wA 5p21 166 3.70e+00 1ctqA c.37.1.8 31966 9ldtA 332 3.72e+00 3ldh c.2.1.5 30154 d.162.1.1 42121 1fjfB 256 4.09e+00 1fjfB c.23.15.1 31399 1bmtA 246 4.28e+00 1bmtA a.46.1.1 17757 c.23.6.1 31235 1ctqA 166 4.45e+00 1ctqA c.37.1.8 31965 1g4uS 383 4.54e+00 1g4uS a.24.11.1 16643 c.45.1.2 32691 1wwaX 109 4.61e+00 1wwcA b.1.1.4 21775 1e55A 512 4.84e+00 1e70M c.1.8.4 28934 1qcwA 410 4.91e+00 1gox c.1.4.1 28622 1fjgB 256 4.96e+00 1fjfB c.23.15.1 31400 1aipE 405 5.00e+00 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1kid 203 5.01e+00 1derA c.8.5.1 30771 1lucA 355 5.24e+00 1lucA c.1.16.1 29547 1pmi 440 5.38e+00 1pmi b.82.1.3 28114 1ejjA 511 5.47e+00 1ejjA 1eqjA 511 5.62e+00 1ejjA 1ax4A 467 5.64e+00 1ax4A c.67.1.2 34391 1g4wR 383 5.93e+00 1g4uS a.24.11.1 16644 c.45.1.2 32692 2dubE 261 6.00e+00 1nzyA c.14.1.3 30916 1g7rA 594 6.32e+00 1g7rA b.43.3.1 25716 b.43.3.1 25717 c.20.1.1 31034 c.37.1.8 32149 2scuB 388 6.53e+00 2scuB c.23.4.1 31141 d.142.1.4 41562 1bhgA 613 6.67e+00 1bhgA b.1.4.1 22161 b.18.1.5 23766 c.1.8.3 28889 1ir3A 306 6.67e+00 1fmk d.144.1.2 41702 1g7tA 594 6.70e+00 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1c3qA 272 6.97e+00 1c3qA c.72.1.2 34948 1byrA 155 7.34e+00 1byrA d.136.1.1 41450 1bqcA 302 7.50e+00 1bqcA c.1.8.3 28831 1srvA 145 7.74e+00 1derA c.8.5.1 30817 1cx8B 639 7.82e+00 1cx8B a.48.2.1 17783 c.8.4.1 30764 c.56.5.5 33852 1i58A 189 7.89e+00 1b3qA 1ep3B 262 7.96e+00 1ep2B b.43.1.3 25664 c.25.1.3 31554 1g7sA 594 8.28e+00 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1qtwA 285 8.33e+00 1qumA c.1.15.1 29392 1fiqC 763 8.35e+00 1fiqC d.41.1.1 38588 d.133.1.1 41418 1b0pA 1231 8.46e+00 c.36.1.4 31831 c.36.1.4 31832 c.48.1.3 33104 c.64.1.1 34157 d.58.1.5 39003 1jy1A 464 8.64e+00 1qumA 285 8.92e+00 1qumA c.1.15.1 29393 1oaa 259 9.01e+00 1oaa c.2.1.2 29829 1theB 260 9.14e+00 1theB d.3.1.1 37057 1bjwA 382 9.23e+00 1bjwA c.67.1.1 34349 3pbgA 468 9.27e+00 1e70M c.1.8.4 28951 1jilA 420 9.30e+00 1hgxA 183 9.73e+00 1tc1A c.61.1.1 34027 1je0A 236 9.77e+00 1jp3A 253 9.81e+00 1f75A 1kcfA 258 1.01e+01 1eq2A 310 1.01e+01 1eq2A c.2.1.2 29814 1he7A 126 1.01e+01 1wwcA 1fm0E 150 1.02e+01 1fmaE d.41.5.1 38629 1devC 196 1.03e+01 1ygs b.26.1.1 23915 1tml 286 1.04e+01 1tml c.6.1.1 30656 1irk 306 1.07e+01 1fmk d.144.1.2 41703 1thg 544 1.08e+01 1thg c.69.1.17 34763 1cx8A 639 1.08e+01 1cx8B a.48.2.1 17782 c.8.4.1 30763 c.56.5.5 33851 1fmaE 150 1.09e+01 1fmaE d.41.5.1 38630 1b1a 137 1.09e+01 1be1 c.23.6.1 31242 1ehiA 377 1.09e+01 1iow c.30.1.2 31716 d.142.1.1 41484 3csuA 310 1.10e+01 3csuA c.78.1.1 35094 c.78.1.1 35095 3grs 478 1.11e+01 3grs c.3.1.5 30441 c.3.1.5 30442 d.87.1.1 40152 1i7qB 193 1.11e+01 1qdlB 1i1qB 192 1.13e+01 1qdlB 1di0A 158 1.13e+01 1di0A c.16.1.1 30957 2dri 271 1.13e+01 2dri c.93.1.1 35637 1edg 380 1.14e+01 1edg c.1.8.3 28807 1igwA 434 1.16e+01 1pyiA 96 1.21e+01 1pyiA g.38.1.1 45079 h.1.3.1 45512 1eudB 396 1.21e+01 2scuB c.23.4.1 31150 d.142.1.4 41571 1a05A 358 1.22e+01 1cnzA c.77.1.1 35059 1d2eA 397 1.22e+01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1gpmA 525 1.22e+01 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 2tpsA 227 1.22e+01 2tpsA c.1.3.1 28591 4gr1 478 1.25e+01 3grs c.3.1.5 30461 c.3.1.5 30462 d.87.1.1 40162 1qciA 262 1.30e+01 1qi7A d.165.1.1 42201 1khxA 227 1.32e+01 1e79D 482 1.32e+01 1skyE a.69.1.1 18272 b.49.1.1 26437 c.37.1.11 32317 1avk 638 1.32e+01 1a2vA b.30.2.1 24410 d.17.2.1 38047 d.17.2.1 38048 1theA 260 1.34e+01 1theB d.3.1.1 37056 1cz1A 394 1.38e+01 1cz1A c.1.8.3 28839 1i6iA 366 1.39e+01 1bg2 1eqcA 394 1.39e+01 1cz1A c.1.8.3 28811 1poiA 317 1.39e+01 1poiA c.63.1.1 34153 1d6aB 262 1.39e+01 1qi7A d.165.1.1 42198 1dbqA 289 1.41e+01 1qpzA c.93.1.1 35666 1ehaA 558 1.42e+01 1ehaA b.1.1.5 21859 b.71.1.1 27786 c.1.8.1 28773 1kao 167 1.43e+01 1ctqA c.37.1.8 32014 1csbB 205 1.43e+01 1theB 1hqkA 154 1.45e+01 1pea 385 1.46e+01 1pea c.93.1.1 35662 1php 394 1.47e+01 16pk c.86.1.1 35452 1qdeA 224 1.47e+01 1qvaA c.37.1.13 32410 1kk1A 410 1.51e+01 1dl5A 317 1.56e+01 1dl5A c.66.1.7 34201 1d3yA 301 1.57e+01 1d3yA e.12.1.1 43252 1i9sA 210 1.58e+01 1i9sA 1ep2B 261 1.59e+01 1ep2B b.43.1.3 25666 c.25.1.3 31556 1e3mA 800 1.63e+01 1ewqA a.113.1.1 19075 c.37.1.12 32389 c.55.6.1 33746 d.75.2.1 39747 1pbgA 468 1.65e+01 1e70M c.1.8.4 28946 1et0A 269 1.67e+01 1et0A e.17.1.1 43289 1jjfA 268 1.68e+01 3pmgA 561 1.70e+01 3pmgA c.84.1.1 35408 c.84.1.1 35409 c.84.1.1 35410 d.129.2.1 41301 1jx4A 352 1.71e+01 1e7uA 961 1.74e+01 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1h61A 364 1.74e+01 1oyc 1dbs 224 1.80e+01 1byi c.37.1.10 32209 1ekjB 221 1.82e+01 1ekjB c.53.2.1 33365 1cbg 490 1.83e+01 1e70M c.1.8.4 28933 1cqwA 295 1.83e+01 1b6g c.69.1.8 34679 1kekA 1231 1.91e+01 1h8eD 482 1.93e+01 1skyE 1nbaA 264 1.98e+01 1nbaA c.33.1.1 31753 1brlA 355 2.04e+01 1lucA c.1.16.1 29553 1hp4A 512 2.04e+01 1hp4A 1jakA 512 2.04e+01 1kq3A 376 2.05e+01 1hdiA 413 2.09e+01 16pk 1g0oA 283 2.11e+01 1ybvA 1bn6A 294 2.13e+01 1bn6A c.69.1.8 34678 1ybvA 283 2.13e+01 1ybvA c.2.1.2 29948 1apa 266 2.17e+01 1qi7A d.165.1.1 42205 1d8cA 723 2.22e+01 1d8cA c.1.13.1 29325 1e5xA 486 2.24e+01 1dar 691 2.26e+01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1dad 224 2.28e+01 1byi c.37.1.10 32204 1bn7A 294 2.29e+01 1bn6A c.69.1.8 34677 1hp5A 512 2.29e+01 1hp4A 1ccwB 483 2.37e+01 1cb7B c.1.19.2 29646 1c4kA 730 2.40e+01 1ordA c.23.7.1 31273 c.67.1.5 34502 d.125.1.1 41123 3pga1 337 2.41e+01 4pgaA 1c2pA 576 2.43e+01 1quvA e.8.1.4 43117 6ldh 330 2.59e+01 3ldh c.2.1.5 30161 d.162.1.1 42128 1dzfA 215 2.61e+01 1dzfA c.52.3.1 33344 d.78.1.1 39753 1ribA 375 2.66e+01 1xikA a.25.1.2 16788 1jj2F 119 2.66e+01 1ffkE 1jqcA 375 2.68e+01 1xikA 1cv8 174 2.73e+01 1cv8 d.3.1.1 37089 1emsA 440 2.74e+01 1emsA d.13.1.1 37520 d.160.1.1 42086 1cb7B 483 2.77e+01 1cb7B c.1.19.2 29648 1ekjA 221 2.79e+01 1ekjB c.53.2.1 33364 2ebn 289 2.83e+01 2ebn c.1.8.5 28990 3ldh 330 2.85e+01 3ldh i.12.1.1 46015 1cfr 285 2.90e+01 1cfr c.52.1.7 33312 1pfkA 320 3.01e+01 3pfk c.89.1.1 35575 1f0kA 364 3.02e+01 1f0kA c.87.1.2 35465 1xikA 375 3.07e+01 1xikA a.25.1.2 16784 1bif 469 3.08e+01 1bif c.37.1.7 31961 c.60.1.4 34003 1b9zA 516 3.09e+01 1b9zA b.3.1.1 22528 c.1.8.2 28798 4pgaA 337 3.09e+01 4pgaA c.88.1.1 35565 1f75A 249 3.11e+01 1f75A 2cy3 118 3.25e+01 3cyr a.138.1.1 19649 1cseE 274 3.25e+01 1gci c.41.1.1 32481 1cliA 345 3.26e+01 1cliA d.79.4.1 39816 d.139.1.1 41459 1smeA 329 3.29e+01 1smrA b.50.1.2 26885 1gtmA 419 3.30e+01 1hwyA c.2.1.7 30223 c.58.1.1 33871 1a27 289 3.31e+01 1fds c.2.1.2 29839 1dkcA 38 3.32e+01 1dkcA g.3.4.2 44082 1kv8A 216 3.33e+01 1e8xA 961 3.34e+01 1e8xA a.118.1.6 19148 b.7.1.1 23183 d.15.1.5 37631 d.144.1.4 41711 2mbr 340 3.36e+01 2mbr d.145.1.2 41749 d.146.1.1 41762 1qo7A 394 3.36e+01 1qo7A c.69.1.11 34697 1ffkE 119 3.36e+01 1ffkE d.79.3.1 39812 1qj2C 285 3.41e+01 1qj2C d.87.2.1 40221 d.145.1.3 41752 1iibA 106 3.46e+01 1iibA c.44.2.1 32648 1qidA 537 3.46e+01 2bce c.69.1.1 34593 1jlnA 297 3.46e+01 1pty 1vhrA 184 3.49e+01 1vhrA c.45.1.1 32651 1aq0A 306 3.49e+01 1aq0A c.1.8.3 28842 1fds 327 3.51e+01 1fds c.2.1.2 29838 1tplA 426 3.52e+01 1ax4A c.67.1.2 34387 1g2qA 187 3.52e+01 1uxy 340 3.53e+01 2mbr d.145.1.2 41748 d.146.1.1 41761 2pfkA 320 3.58e+01 3pfk c.89.1.1 35577 1ezwA 349 3.59e+01 1ezwA c.1.16.3 29558 1lxtA 561 3.65e+01 3pmgA c.84.1.1 35432 c.84.1.1 35433 c.84.1.1 35434 d.129.2.1 41309 1fdd 106 3.66e+01 1a6l d.58.1.2 38960 1d9eA 284 3.76e+01 1d9eA c.1.10.4 29195 1f5mA 180 3.80e+01 1f5mB d.110.2.1 40895 1rkd 309 3.82e+01 1rkd c.72.1.1 34928 1be1 137 3.82e+01 1be1 c.23.6.1 31237 1qvbA 481 3.90e+01 1qvbA c.1.8.4 28983 1cfzA 162 3.92e+01 1cfzA c.56.1.1 33754 1vxrA 537 3.92e+01 2bce c.69.1.1 34595 1pxtB 390 3.95e+01 1afwA c.95.1.1 35906 c.95.1.1 35907