# List of top-scoring protein chains for 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.soe.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 2el9A 431 8.51e-46 c.51.1.1 146887 d.104.1.1 146888 1kmmA 424 1.11e-45 1adjA c.51.1.1 33174 d.104.1.1 40723 1httA 423 1.14e-45 1adjA c.51.1.1 33178 d.104.1.1 40727 1qe0A 420 2.43e-44 1adjA c.51.1.1 33186 d.104.1.1 40735 1h4vB 421 4.06e-40 1adjA c.51.1.1 60624 d.104.1.1 60625 1adjA 421 4.06e-40 1adjA c.51.1.1 33188 d.104.1.1 40737 1wu7A 434 7.36e-39 c.51.1.1 121275 d.104.1.1 121276 3lc0A 456 4.53e-38 3hriA 456 4.81e-38 1z7mA 344 5.63e-22 d.104.1.1 124632 2i4lA 458 1.77e-08 1nyrA 645 2.27e-08 c.51.1.1 92354 d.15.10.1 92355 d.67.1.1 92356 d.104.1.1 92357 1usyA 275 2.70e-08 d.104.1.1 113422 1usyC 275 2.87e-08 d.104.1.1 113424 1evlA 401 6.23e-08 1qf6A c.51.1.1 33202 d.104.1.1 40751 1qf6A 642 1.40e-07 1qf6A c.51.1.1 33210 d.15.10.1 39551 d.67.1.1 39562 d.104.1.1 40759 2zinA 291 3.17e-06 2zceA 291 3.17e-06 2q7eA 291 3.24e-06 3a32A 471 3.50e-05 1nj8A 459 6.73e-05 c.51.1.1 85769 d.68.5.1 85770 d.104.1.1 85771 2j3mA 572 4.12e-04 1l0wA 580 4.50e-04 b.40.4.1 73426 d.74.4.1 73427 d.104.1.1 73428 1c0aA 585 7.18e-04 1c0aA b.40.4.1 25246 d.74.4.1 39731 d.104.1.1 40767 1il2A 590 7.52e-04 b.40.4.1 66193 d.74.4.1 66194 d.104.1.1 66195 1nj1A 501 1.97e-03 c.51.1.1 85755 d.68.5.1 85756 d.104.1.1 85757 2znjA 308 6.10e-03 3dsqA 288 6.10e-03 1wleA 501 1.13e-02 1b76A 442 1.46e-02 1atiA c.51.1.1 33198 d.104.1.1 40747 3ialA 518 2.11e-02 2alyA 266 2.90e-02 d.104.1.1 126987 1atiA 505 3.00e-02 1atiA c.51.1.1 33196 d.104.1.1 40745 1b7yA 350 3.46e-02 1pysA d.104.1.1 40776 1pysA 350 3.46e-02 1pysA d.104.1.1 40775 2dq3A 425 9.31e-02 3l4gA 508 1.46e-01 3bjuA 521 1.58e-01 1hc7A 477 2.39e-01 1hc7A c.51.1.1 60938 d.68.5.1 60940 d.104.1.1 60939 1v95A 130 3.19e-01 c.51.1.1 108435 1n9wA 422 3.53e-01 b.40.4.1 85473 d.104.1.1 85474 2odrB 648 3.61e-01 2odrA 665 4.46e-01 1b8aA 438 4.59e-01 1b8aA b.40.4.1 25244 d.104.1.1 40765 1wydA 429 4.81e-01 2odrD 685 5.90e-01 2du5A 534 6.99e-01 2du3A 534 7.03e-01 2odrC 701 7.26e-01 3e9hA 493 8.78e-01 3i3tA 355 1.02e+00 2dq0A 455 1.51e+00 2fqxA 318 1.95e+00 3doeA 192 2.38e+00 3i7fA 548 2.58e+00 1kshA 186 2.77e+00 c.37.1.8 72914 1x54A 434 2.96e+00 2rcnA 358 2.98e+00 2du7A 549 3.07e+00 2q5iA 691 3.12e+00 3l7mA 729 3.44e+00 3ikmB 427 3.56e+00 1g5hA 454 3.57e+00 1g5hA c.51.1.1 60270 d.104.1.1 60271 2g4cA 474 3.59e+00 c.51.1.1 134582 d.104.1.1 134583 1pmhX 185 3.77e+00 b.18.1.18 104193 1pmjX 185 3.77e+00 b.18.1.18 104194 2cxxA 190 3.90e+00 c.37.1.8 131013 2cxcA 144 3.95e+00 3l7jA 729 4.55e+00 3l7iA 729 4.56e+00 3ievA 308 4.59e+00 2q5hA 691 4.66e+00 2zt5A 693 4.66e+00 1qh8B 519 4.96e+00 1qguB c.92.2.3 35634 1qguB 519 4.96e+00 1qguB c.92.2.3 35626 1wdnA 226 4.98e+00 1lst c.94.1.1 35816 1gggA 226 4.98e+00 1lst c.94.1.1 35817 1z6xA 180 5.07e+00 c.37.1.8 124571 1poiA 317 5.14e+00 1poiA c.124.1.2 34153 2qgpA 112 5.21e+00 1s1mA 545 5.36e+00 c.23.16.1 105201 c.37.1.10 105202 1xr7A 460 5.86e+00 e.8.1.4 115866 1mjfA 281 5.93e+00 c.66.1.17 79198 1nnhA 294 6.31e+00 d.104.1.1 92005 2al7A 186 6.52e+00 c.37.1.8 126972 1eovA 487 6.80e+00 1b8aA b.40.4.1 25239 d.104.1.1 40760 1asyA 490 6.80e+00 1b8aA b.40.4.1 25242 d.104.1.1 40763 1aszB 490 6.80e+00 1b8aA b.40.4.1 25241 d.104.1.1 40762 1tp7A 460 7.48e+00 3bh6A 164 8.28e+00 3lssA 484 8.51e+00 1aj8A 371 8.53e+00 1aj8A a.103.1.1 18900 2fo1E 373 8.90e+00 d.211.1.1 145176 1ygmA 118 9.09e+00 2gbwB 174 9.61e+00 2a10A 125 9.99e+00 d.58.56.1 125965 1wpgA 994 1.07e+01 b.82.7.1 114806 c.108.1.7 114807 d.220.1.1 114808 f.33.1.1 114809 2zbfA 995 1.07e+01 b.82.7.1 154313 c.108.1.7 154314 d.220.1.1 154315 f.33.1.1 154316 2dqsA 995 1.07e+01 2ijzA 428 1.11e+01 1iyxA 432 1.16e+01 c.1.11.1 83815 d.54.1.1 83816 1o3yA 166 1.25e+01 c.37.1.8 86618 1xmpA 170 1.43e+01 c.23.8.1 115521 2npdA 424 1.44e+01 1obbA 480 1.48e+01 c.2.1.5 86760 d.162.1.2 86761 3msuA 427 1.53e+01 3c1hA 424 1.53e+01 2x77A 189 1.54e+01 2anlA 327 1.55e+01 2nopA 424 1.55e+01 f.44.1.1 138413 3c1jA 424 1.55e+01 3c1iA 424 1.57e+01 2nowA 424 1.57e+01 3gl3A 152 1.58e+01 1mozA 183 1.59e+01 c.37.1.8 79368 2npjA 424 1.62e+01 2pmfA 693 1.62e+01 1xqfA 418 1.64e+01 f.44.1.1 115843 3ijrA 291 1.65e+01 3i3oA 291 1.65e+01 3hbmA 282 1.70e+01 2rhsA 294 1.70e+01 1g0u1 266 1.73e+01 1go3F 107 1.74e+01 a.60.8.2 65407 3fveA 290 1.74e+01 3e3vA 177 1.76e+01 2npeA 424 1.76e+01 2npcA 424 1.82e+01 1yzgA 179 1.83e+01 c.37.1.8 124276 2ckfB 174 1.85e+01 1jqnA 883 1.86e+01 c.1.12.3 77159 3ba1A 333 1.86e+01 1ryp2 233 1.93e+01 1ryp2 2b8eA 273 1.93e+01 c.108.1.7 128068 d.220.1.1 128069 2v3fA 505 1.94e+01 b.71.1.2 152453 c.1.8.3 152454 3a1dA 287 1.97e+01 2wklA 497 1.99e+01 2nt0A 497 1.99e+01 b.71.1.2 138561 c.1.8.3 138562 3a1eA 287 2.02e+01 1kczA 413 2.05e+01 c.1.11.2 68451 d.54.1.1 68452 2npkA 424 2.06e+01 2o2xA 218 2.12e+01 c.108.1.19 148564 2ns1A 412 2.13e+01 f.44.1.1 138545 1g5zA 164 2.18e+01 1ggqA a.24.12.1 60298 3cmqA 415 2.24e+01 1nxeA 427 2.24e+01 a.103.1.1 86377 2h18A 193 2.25e+01 1o4vA 183 2.26e+01 c.23.8.1 86628 1zd9A 188 2.27e+01 c.37.1.8 124938 1wy7A 207 2.30e+01 c.66.1.32 121433 2nuuA 415 2.34e+01 f.44.1.1 138611 1k3pA 426 2.52e+01 a.103.1.1 77237 1owcA 427 2.52e+01 a.103.1.1 104039 3bh7A 164 2.60e+01 c.37.1.8 155255 2x0jA 294 2.60e+01 1typA 487 2.61e+01 3grs c.3.1.5 30509 c.3.1.5 30510 d.87.1.1 40186 2ki3A 126 2.64e+01 1tytA 487 2.64e+01 3grs c.3.1.5 30513 c.3.1.5 30514 d.87.1.1 40188 1ydmA 187 2.67e+01 1noyA 388 2.74e+01 1clqA c.55.3.5 33713 1fzqA 181 2.76e+01 1hurA c.37.1.8 32060 2tprA 490 2.79e+01 3grs c.3.1.5 30505 c.3.1.5 30506 d.87.1.1 40184 1fecA 490 2.79e+01 3grs c.3.1.5 30489 c.3.1.5 30490 d.87.1.1 40176 3efbA 266 2.84e+01 c.124.1.8 158129 2ywwA 149 2.87e+01 3brpB 172 2.89e+01 1ggqA 174 2.90e+01 1ggqA a.24.12.1 60486 2gqpA 236 2.91e+01 d.122.1.1 135513 1t0hB 224 2.94e+01 c.37.1.1 106208 2esaA 236 2.97e+01 1k7hA 476 3.05e+01 c.76.1.1 72101 2bv8B 172 3.06e+01 2iekA 200 3.08e+01 a.4.1.9 147647 a.121.1.1 147648 1z77A 200 3.08e+01 a.4.1.9 124588 a.121.1.1 124589 1zkgA 212 3.08e+01 a.4.1.9 125194 a.121.1.1 125195 2id6A 202 3.08e+01 a.4.1.9 147624 a.121.1.1 147625 2qr6A 393 3.12e+01 1r8sA 164 3.15e+01 c.37.1.8 97247 1qy5A 269 3.16e+01 d.122.1.1 96573 2dy3A 361 3.20e+01 1u0yA 273 3.20e+01 d.122.1.1 119412 2ec5A 746 3.23e+01 a.296.1.1 146778 c.150.1.2 146779 d.3.1.17 146780 2ebfX 746 3.24e+01 a.296.1.1 146766 c.150.1.2 146767 d.3.1.17 146768 3kt5A 203 3.26e+01 1qc6A 130 3.27e+01 1evhA b.55.1.4 26998 2ebhX 746 3.29e+01 a.296.1.1 146769 c.150.1.2 146770 d.3.1.17 146771 1hurA 180 3.33e+01 1hurA c.37.1.8 32052 1r8qA 181 3.35e+01 c.37.1.8 97243 1eq6A 189 3.35e+01 1eq6A d.107.1.1 40796 2vedA 271 3.44e+01 1y7pA 223 3.44e+01 c.23.1.7 122708 d.58.18.12 122709 1lj9A 144 3.46e+01 a.4.5.28 78035 3bfvA 271 3.50e+01 2z01A 348 3.51e+01 3c5wA 232 3.63e+01 1ot7A 229 3.65e+01 a.123.1.1 93505 1osvA 230 3.66e+01 a.123.1.1 93500 1o58A 303 3.71e+01 c.79.1.1 92491 1z6yA 179 3.75e+01 c.37.1.8 124573 1ty4A 170 3.77e+01 f.1.4.1 107452 1tefA 99 3.77e+01 2h16A 183 3.78e+01 1tegA 99 3.79e+01 1zj6A 187 3.82e+01 c.37.1.8 125145 2v8vA 474 3.88e+01 2bdzA 214 3.91e+01 2wa6A 245 3.92e+01 1shqA 478 3.93e+01 c.76.1.1 105560 1h1yA 228 3.97e+01 c.1.2.2 76506