# 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 1cnzA 363 9.49e-61 1cnzA c.77.1.1 35061 1a05A 358 2.47e-59 1cnzA c.77.1.1 35059 1cm7A 363 2.84e-59 1cnzA c.77.1.1 35063 1ipd 345 7.65e-58 1cnzA c.77.1.1 35038 1idm 343 9.20e-58 1cnzA c.77.1.1 35035 1dr8B 344 1.58e-57 1cnzA c.77.1.1 35052 1iso 416 2.23e-54 1iso c.77.1.1 35065 1hqsA 423 3.57e-53 1iso c.77.1.1 61154 7icd 416 5.10e-53 1iso c.77.1.1 35072 1pb1A 416 6.21e-45 c.77.1.1 88014 1lwdA 413 1.64e-43 c.77.1.1 78265 1itwA 741 4.95e-08 c.77.1.2 76793 1aw5 326 2.38e-02 1b4kA c.1.10.3 29181 1ohlA 342 2.46e-02 c.1.10.3 87035 1h7nA 342 2.53e-02 1b4kA c.1.10.3 60726 1ylvA 342 2.62e-02 1b4kA c.1.10.3 29180 1kl7A 514 1.23e-01 c.79.1.1 72678 1fnmA 691 1.29e-01 1dar b.43.3.1 25709 c.37.1.8 32144 d.14.1.1 37546 d.58.11.1 39302 d.58.11.1 39303 1obbA 480 1.42e-01 c.2.1.5 86760 d.162.1.2 86761 1vjoA 393 1.54e-01 c.67.1.3 -8173 1t3lA 337 2.02e-01 1kyqA 274 2.07e-01 c.2.1.11 73281 e.37.1.1 73282 1qapA 296 2.69e-01 1qpoA c.1.17.1 29559 d.41.2.1 38595 1qdlA 422 2.83e-01 1qdlA d.161.1.1 42088 1i9sA 210 3.30e-01 1i9sA c.45.1.1 62099 1l2lA 457 3.87e-01 c.72.1.3 77656 1lkcA 364 4.20e-01 c.67.1.1 73978 1ex1A 605 4.43e-01 1ex1A c.1.8.7 29013 c.23.11.1 31347 1jykA 254 5.19e-01 c.68.1.13 67458 1iexA 605 6.48e-01 c.1.8.7 66127 c.23.11.1 66128 1r5jA 337 6.64e-01 unknown_sccs -8471 1earA 147 8.39e-01 b.107.1.1 64875 d.58.38.1 64876 1ptmA 329 1.01e+00 unknown_sccs -8456 1eb0A 147 1.27e+00 b.107.1.1 64890 d.58.38.1 64891 1k6iA 352 1.49e+00 c.2.1.2 68223 1ursA 402 1.61e+00 c.94.1.1 -8651 1ltqA 301 1.90e+00 c.108.1.9 78208 c.37.1.1 78209 1k6xA 352 1.95e+00 c.2.1.2 68238 1b66A 140 2.42e+00 1b66A d.96.1.2 40657 1dar 691 2.52e+00 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1kwgA 645 2.55e+00 b.71.1.1 77561 c.1.8.1 77562 c.23.16.5 77563 1kwkA 645 2.56e+00 b.71.1.1 77565 c.1.8.1 77566 c.23.16.5 77567 1j5pA 253 2.92e+00 c.2.1.3 83092 d.81.1.3 71577 1h5vA 304 2.95e+00 c.1.8.3 70898 1k4mA 213 3.00e+00 c.26.1.3 77258 1np7A 489 3.14e+00 a.99.1.1 80677 c.28.1.1 80678 1a3h 300 3.18e+00 7a3hA c.1.8.3 28819 2hmiA 558 3.24e+00 1rthA c.55.3.1 33604 e.8.1.2 43106 1g6sA 427 3.82e+00 1eps d.68.2.2 39584 1j2rA 199 3.90e+00 unknown_sccs -6799 1t0hB 224 4.00e+00 1ik6A 369 4.14e+00 c.36.1.7 66174 c.48.1.2 66175 1o5kA 306 4.33e+00 c.1.10.1 -5482 1lp4A 332 4.43e+00 d.144.1.7 74170 1e3mA 800 4.63e+00 1ewqA a.113.1.1 19075 c.37.1.12 32389 c.55.6.1 33746 d.75.2.1 39747 1igs 248 4.74e+00 1a53 c.1.2.4 28565 1hlrA 907 5.09e+00 a.56.1.1 65850 d.15.4.2 65851 d.41.1.1 65852 d.133.1.1 65853 2plc 274 5.12e+00 2plc c.1.18.2 29614 1lc5A 364 5.34e+00 c.67.1.1 73827 1j0aA 325 5.49e+00 c.79.1.1 83871 1dozA 309 5.65e+00 1ak1 c.92.1.1 35592 1gvfA 286 5.74e+00 c.1.10.2 70599 1gtqA 140 5.77e+00 1b66A d.96.1.2 40661 1gr0A 367 5.86e+00 c.2.1.3 70379 d.81.1.3 70380 1rpxA 230 6.00e+00 1rpxA c.1.2.2 28536 1nktA 922 6.02e+00 a.162.1.1 85830 a.172.1.1 85831 c.37.1.19 85832 c.37.1.19 85833 7a3hA 303 6.14e+00 7a3hA c.1.8.3 28817 1hl2A 297 6.23e+00 c.1.10.1 83581 1nal3 297 6.48e+00 1nal3 1a53 247 7.00e+00 1a53 c.1.2.4 28564 12asA 330 7.13e+00 12asA d.104.1.1 40783 1nhs 447 7.27e+00 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1aorA 605 7.36e+00 1b25A a.110.1.1 19042 d.152.1.1 41794 1uedA 406 7.69e+00 a.104.1.1 -1459 1eqcA 394 7.71e+00 1cz1A c.1.8.3 28811 1cz1A 394 7.95e+00 1cz1A c.1.8.3 28839 1pszA 303 7.97e+00 1toaA c.92.2.2 35600 1icpA 376 8.29e+00 1oyc c.1.4.1 62270 1ml9A 302 8.37e+00 b.85.7.1 79282 1juk 248 8.37e+00 1a53 c.1.2.4 28567 1dttA 560 8.44e+00 1rthA c.55.3.1 33611 e.8.1.2 43088 1f60A 458 8.56e+00 1efcA b.43.3.1 25705 b.44.1.1 25745 c.37.1.8 32140 1om1A 332 8.58e+00 d.144.1.7 -11318 1php 394 8.65e+00 16pk c.86.1.1 35452 1lpuA 332 8.77e+00 d.144.1.7 74177 1l8bA 190 8.94e+00 d.86.1.1 73683 1iu8A 206 9.00e+00 c.56.4.1 71436 1ewkA 490 9.07e+00 1ewkA c.93.1.1 35712 1ky3A 182 9.36e+00 c.37.1.8 73193 1opjA 293 9.78e+00 d.144.1.7 87230 1eyeA 280 9.88e+00 1aj2 c.1.21.1 29672 1ejhA 190 9.90e+00 1ejhA d.86.1.1 40147 1eqfA 280 1.01e+01 1eqfA a.29.2.1 16972 a.29.2.1 16973 1rhd 293 1.03e+01 1rhs c.46.1.2 32715 c.46.1.2 32716 1m2rA 327 1.03e+01 d.144.1.7 84760 1ej1A 190 1.07e+01 1ejhA d.86.1.1 40144 1vrtA 560 1.10e+01 1rthA c.55.3.1 33574 e.8.1.2 43023 1s96A 219 1.10e+01 c.37.1.1 -6972 1ecxA 384 1.11e+01 1ecxA c.67.1.3 34431 1nhp 447 1.11e+01 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1h0cA 392 1.19e+01 c.67.1.3 83424 1vgvA 384 1.21e+01 c.87.1.3 -8575 1qnf 484 1.28e+01 1qnf a.99.1.1 18777 c.28.1.1 31632 1ortA 335 1.28e+01 1othA c.78.1.1 35204 c.78.1.1 35205 1o0xA 262 1.32e+01 d.127.1.1 80755 1f6dA 376 1.32e+01 1f6dA c.87.1.3 35467 1e1oA 504 1.32e+01 1lylA b.40.4.1 25258 d.104.1.1 40714 1joa 447 1.35e+01 1nhp c.3.1.5 30563 c.3.1.5 30564 d.87.1.1 40203 1ckaA 57 1.35e+01 1ckaA b.34.2.1 24459 1owlA 484 1.37e+01 a.99.1.1 -1296 c.28.1.1 -6646 1o98A 511 1.37e+01 c.105.1.1 86684 c.76.1.3 86685 1ak1 310 1.38e+01 1ak1 c.92.1.1 35594 1ak5 503 1.39e+01 1ak5 c.1.5.1 28639 1mkyA 439 1.40e+01 c.37.1.8 79250 c.37.1.8 79251 d.52.5.1 79252 1vicA 262 1.47e+01 c.68.1.13 -8252 1hh1A 143 1.48e+01 1gefA c.52.1.18 61036 1k3rA 268 1.49e+01 b.40.4.10 72018 c.116.1.2 72019 1g63A 181 1.49e+01 1g5qA c.34.1.1 60299 1mjfA 281 1.50e+01 c.66.1.17 79198 1cydA 244 1.51e+01 1cydA c.2.1.2 29825 1qgvA 142 1.51e+01 1qgvA c.47.1.8 33056 1jq5A 370 1.52e+01 e.22.1.2 67084 1m56B 264 1.52e+01 b.6.1.2 74472 f.17.2.1 74473 1cb0A 283 1.52e+01 1cb0A c.56.2.1 33790 1pz1A 333 1.56e+01 c.1.7.1 -5255 1mvlA 209 1.57e+01 c.34.1.1 85146 1fxjA 331 1.58e+01 1fwyA b.81.1.4 28062 c.68.1.5 34520 1jihA 531 1.58e+01 unknown_sccs -10212 unknown_sccs -11922 1i5rA 327 1.60e+01 c.2.1.2 83668 1j7rA 86 1.65e+01 1j7rA a.39.1.5 62701 1ejjA 511 1.65e+01 1ejjA c.105.1.1 59422 c.76.1.3 59423 1ii7A 333 1.68e+01 1ii7A d.159.1.4 62415 1eqjA 511 1.70e+01 1ejjA c.105.1.1 59495 c.76.1.3 59496 1oxkB 134 1.71e+01 c.23.1.1 -6411 1fdt 327 1.74e+01 1fds c.2.1.2 29841 1d1qA 161 1.77e+01 1dg9A c.44.1.1 32642 1bu8A 452 1.79e+01 1gpl b.12.1.2 23647 c.69.1.19 34795 1a27 289 1.79e+01 1fds c.2.1.2 29839 1q45A 391 1.79e+01 c.1.4.1 -5199 1asu 162 1.79e+01 1cxqA c.55.3.2 33626 1jb0A 755 1.80e+01 1jb0A f.29.1.1 62820 1hrhA 136 1.81e+01 1rthA c.55.3.1 33577 1pii 452 1.82e+01 1pii c.1.2.4 28559 c.1.2.4 28563 1fds 327 1.82e+01 1fds c.2.1.2 29838 1jtvA 327 1.85e+01 c.2.1.2 84230 1qv9A 283 1.85e+01 unknown_sccs -6888 1aj0 282 1.90e+01 1aj2 c.1.21.1 29667 1dbiA 280 1.91e+01 1gci c.41.1.1 32543 1nmoA 247 1.92e+01 unknown_sccs -8746 1ayaA 101 1.93e+01 1qadA d.93.1.1 40460 1aj2 282 1.97e+01 1aj2 c.1.21.1 29665 1ekqA 272 1.98e+01 1c3qA c.72.1.2 34941 1gm5A 780 2.04e+01 unknown_sccs 65298 b.40.4.9 65299 c.37.1.19 65300 c.37.1.19 65301 1b3qA 379 2.05e+01 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1ps9A 671 2.06e+01 c.1.4.1 -5206 1rkd 309 2.08e+01 1rkd c.72.1.1 34928 1j9yA 385 2.08e+01 1j9yA c.1.8.3 62791 1brwA 433 2.09e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1alvA 173 2.10e+01 1alvA a.39.1.8 17370 1gnxA 479 2.14e+01 c.1.8.4 76241 1v3hA 495 2.15e+01 1frb 315 2.16e+01 1frb c.1.7.1 28665 1t0hA 132 2.20e+01 1gtxA 472 2.24e+01 1gtxA 2end 138 2.31e+01 2end a.18.1.1 16400 1jyoA 130 2.31e+01 d.198.1.1 67483 1vsd 152 2.31e+01 1cxqA c.55.3.2 33625 1ji0A 240 2.35e+01 c.37.1.12 71665 1q6cA 495 2.38e+01 c.1.8.1 -5300 1eg5A 384 2.38e+01 1ecxA c.67.1.3 34429 1j3mA 129 2.41e+01 1c4xA 285 2.41e+01 1c4xA c.69.1.10 34684 1dqwA 267 2.45e+01 1dqwA c.1.2.3 28551 1fp3A 402 2.46e+01 1fp3A a.102.1.3 18842 1p2xA 159 2.51e+01 1q7zA 566 2.52e+01 c.1.21.2 -5638 c.1.26.1 -5666 1hizA 379 2.55e+01 c.1.8.3 65841 1qpoA 284 2.55e+01 1qpoA c.1.17.1 29561 d.41.2.1 38597 1odzA 386 2.55e+01 c.1.8.3 86889 1b37B 472 2.65e+01 1b37B c.3.1.2 30390 d.16.1.5 37954 1s7hA 200 2.66e+01 1jx6A 342 2.69e+01 c.93.1.1 67406 1p5dX 463 2.70e+01 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 1jilA 420 2.73e+01 c.26.1.1 66745 1rhs 296 2.74e+01 1rhs c.46.1.2 32703 c.46.1.2 32704 1rthA 560 2.74e+01 1rthA c.55.3.1 33576 e.8.1.2 43028 1ctt 294 2.76e+01 1ctt c.97.1.1 36022 c.97.1.1 36023 1g8lA 411 2.79e+01 1g8lA b.85.6.1 60365 b.103.1.1 60366 c.57.1.2 60367 1b37A 472 2.80e+01 1b37B c.3.1.2 30389 d.16.1.5 37953 1qxyA 252 2.82e+01 d.127.1.1 -10993 1b5qA 472 2.84e+01 1b37B c.3.1.2 30404 d.16.1.5 37968 1jqsC 68 2.88e+01 i.1.1.1 63239 1cxqA 162 2.91e+01 1cxqA c.55.3.2 33621 1lbd 282 2.91e+01 1lbd a.123.1.1 19279 1e2b 106 2.96e+01 1iibA c.44.2.1 32650 1chmA 401 3.04e+01 1chmA c.55.2.1 33545 d.127.1.1 41142 1yveJ 524 3.06e+01 1qmgA a.100.1.2 18790 c.2.1.6 30187 1po5A 476 3.10e+01 a.104.1.1 -1467 1s72H 171 3.11e+01 1ad1A 266 3.12e+01 1aj2 c.1.21.1 29668 1me8A 503 3.12e+01 c.1.5.1 79028 1e69B 322 3.14e+01 1e69B c.37.1.12 32377 1kn1B 161 3.15e+01 a.1.1.3 77456 1jk3A 158 3.17e+01 d.92.1.11 66790 1cr0A 296 3.21e+01 1cr1A c.37.1.11 32287 1brlB 324 3.29e+01 1lucA c.1.16.1 29554 1auvA 311 3.29e+01 1auvA c.30.1.5 31723 d.142.1.3 41558 1rpmA 278 3.33e+01 2shpA c.45.1.2 32679 1vsrA 136 3.34e+01 1vsrA c.52.1.15 33332 1i39A 225 3.37e+01 1ekeA c.55.3.1 61585 1qcwA 410 3.41e+01 1gox c.1.4.1 28622 1vhzA 198 3.41e+01 d.113.1.1 -10897 1gt7A 274 3.45e+01 c.74.1.1 70398 2at2A 300 3.50e+01 3csuA c.78.1.1 35196 c.78.1.1 35197 1gggB 226 3.53e+01 1lst c.94.1.1 35818 4ts1A 319 3.57e+01 2ts1 c.26.1.1 31565 1ur3M 319 3.57e+01 c.1.7.1 -5248 1i3kA 348 3.59e+01 1xel c.2.1.2 61595 1gakA 141 3.60e+01 1gakA a.19.1.1 16415 1fpxA 352 3.67e+01 1fpxA a.4.5.29 59950 c.66.1.12 59951 1vc4A 254 3.72e+01 c.1.2.4 -5172 1furA 467 3.73e+01 1furA a.127.1.1 19403 1ysc 421 3.83e+01 1ivyA c.69.1.5 34652 1fuoA 467 3.91e+01 1furA a.127.1.1 19411