# 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.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 1b57A 358 2.41e-02 1dosA c.1.10.2 29177 1dosA 358 2.50e-02 1dosA c.1.10.2 29175 1efuA 385 1.07e-01 1efcA b.43.3.1 25682 b.44.1.1 25722 c.37.1.8 32115 1efcA 393 1.07e-01 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1dg1G 394 1.07e-01 1efcA b.43.3.1 25684 b.44.1.1 25724 c.37.1.8 32117 1d8tA 393 1.08e-01 1efcA b.43.3.1 25686 b.44.1.1 25726 c.37.1.8 32119 1efm 393 1.15e-01 1efcA c.37.1.8 64732 1etu 394 1.19e-01 1efcA c.37.1.8 64737 2dubE 261 3.36e-01 1nzyA c.14.1.3 30916 1ey3A 258 3.44e-01 c.14.1.3 64911 1qdmA 478 4.13e-01 1smrA a.64.1.2 18141 b.50.1.2 26838 1hzdA 272 7.95e-01 c.14.1.3 65969 1seiA 130 8.03e-01 1seiA d.140.1.1 41463 1dciA 275 9.08e-01 1dciA c.14.1.3 30918 1a5z 319 9.99e-01 1ceqA c.2.1.5 30181 d.162.1.1 42148 1ef8A 261 1.46e+00 1ef8A c.14.1.3 30921 1eqjA 511 1.52e+00 1ejjA c.105.1.1 59495 c.76.1.3 59496 1ejjA 511 1.52e+00 1ejjA c.105.1.1 59422 c.76.1.3 59423 3cox 507 1.69e+00 1b8sA c.3.1.2 30332 d.16.1.1 37863 1mioB 458 1.82e+00 1qguB c.92.2.3 35602 1b23P 405 2.18e+00 1efcA b.43.3.1 25689 b.44.1.1 25729 c.37.1.8 32124 1eft 405 2.23e+00 1efcA b.43.3.1 25688 b.44.1.1 25728 c.37.1.8 32123 1exmA 405 2.74e+00 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1ha3A 405 2.74e+00 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1evyA 366 3.06e+00 1evyA a.100.1.6 18811 c.2.1.6 30215 1aipE 405 3.30e+00 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1augA 215 3.67e+00 1a2zA c.56.4.1 33798 1lucB 324 4.14e+00 1lucA c.1.16.1 29548 1brlB 324 4.14e+00 1lucA c.1.16.1 29554 1yasA 257 4.79e+00 1qj4A c.69.1.20 34801 1qj4A 257 4.79e+00 1qj4A c.69.1.20 34796 1ivyA 452 5.67e+00 1ivyA c.69.1.5 34654 1tgoA 773 6.65e+00 1tgoA c.55.3.5 33721 e.8.1.1 43010 1gbnA 402 6.81e+00 2dkb c.67.1.4 34455 1kid 203 7.04e+00 1derA c.8.5.1 30771 2oatA 439 7.05e+00 2dkb c.67.1.4 34452 1oatA 439 7.05e+00 2dkb c.67.1.4 34461 1e89A 262 7.28e+00 1qj4A c.69.1.20 59375 1ko7A 314 7.71e+00 1cxvA 164 7.93e+00 1ck7A d.92.1.11 40404 1hrb 113 7.98e+00 2mhr a.24.4.1 16580 7odcA 424 8.03e+00 7odcA b.49.2.1 26488 c.1.6.1 28650 1ayyA 151 8.09e+00 1apyA d.153.1.5 42016 9gacA 295 8.17e+00 1apyA d.153.1.5 42010 8pchA 220 8.17e+00 1cs8A d.3.1.1 37084 1jjuB 337 8.65e+00 b.69.2.2 66779 1pmi 440 8.75e+00 1pmi b.82.1.3 28114 1gpmA 525 8.77e+00 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 1dwqA 262 8.87e+00 1qj4A c.69.1.20 34808 9gafA 295 9.03e+00 1apyA d.153.1.5 42008 1dwpA 262 9.03e+00 1qj4A c.69.1.20 34806 9gaaA 295 9.26e+00 1apyA d.153.1.5 42014 1ekqA 272 9.38e+00 1c3qA c.72.1.2 34941 2hhmA 276 9.51e+00 1imbA e.7.1.1 42955 1imbA 277 9.56e+00 1imbA e.7.1.1 42957 1imdA 277 9.56e+00 1imbA e.7.1.1 42968 1eb9A 262 9.60e+00 c.69.1.20 64898 1esjA 284 9.61e+00 1c3qA c.72.1.2 34943 1c3qA 272 9.73e+00 1c3qA c.72.1.2 34948 1qqcA 773 1.01e+01 1tgoA c.55.3.5 33724 e.8.1.1 43013 1ahjA 207 1.05e+01 2ahjA d.149.1.1 41774 1ktbA 405 1.06e+01 1b7tA 835 1.10e+01 1lvk b.34.3.1 24572 c.37.1.9 32169 1dfkA 830 1.16e+01 1lvk b.34.3.1 24573 c.37.1.9 32170 1dflA 831 1.18e+01 1lvk b.34.3.1 24574 c.37.1.9 32171 1dk7A 146 1.18e+01 1derA c.8.5.1 30772 1la1A 192 1.19e+01 1acl 537 1.23e+01 2bce c.69.1.1 34590 1gruA 547 1.25e+01 i.16.1.1 65508 1derA 547 1.26e+01 1derA a.129.1.1 19459 c.8.5.1 30788 d.56.1.1 38907 1gr5A 547 1.26e+01 i.16.1.1 65478 1vxrA 537 1.27e+01 2bce c.69.1.1 34595 1qidA 537 1.27e+01 2bce c.69.1.1 34593 1ea5A 537 1.27e+01 2bce c.69.1.1 34592 1eve 543 1.27e+01 2bce c.69.1.1 34585 1mpp 361 1.28e+01 2rmpA b.50.1.2 26856 1gqsA 532 1.29e+01 2fgwH 232 1.29e+01 1gc1H b.1.1.1 19855 b.1.1.2 20957 1eeaA 534 1.31e+01 2bce c.69.1.1 34609 1jmkC 230 1.33e+01 1az1 315 1.33e+01 1frb c.1.7.1 28677 1jon 155 1.37e+01 1derA c.8.5.1 30780 1abn 315 1.40e+01 1frb c.1.7.1 28683 2acr 315 1.40e+01 1frb c.1.7.1 28674 1ads 315 1.40e+01 1frb c.1.7.1 28671 1el3A 316 1.41e+01 1frb c.1.7.1 28672 1bs0A 384 1.41e+01 1bs0A c.67.1.4 34490 1pft 50 1.46e+01 1pft g.41.3.1 45206 1qhtA 775 1.47e+01 1tgoA c.55.3.5 33722 e.8.1.1 43011 4ubpC 570 1.50e+01 1ubpC b.92.1.1 28431 c.1.9.2 29053 1ubpC 570 1.50e+01 1ubpC b.92.1.1 28432 c.1.9.2 29054 1ie7C 570 1.51e+01 1ubpC b.92.1.1 62315 c.1.9.2 62316 1djeA 384 1.55e+01 1bs0A c.67.1.4 34491 1amn 532 1.59e+01 2bce c.69.1.1 34587 1b5fA 239 1.60e+01 1smrA b.50.1.2 26836 1sbp 310 1.61e+01 1sbp c.94.1.1 35760 2acu 315 1.62e+01 1frb c.1.7.1 28676 1bq3B 246 1.64e+01 1qhfA c.60.1.1 33979 1qhfA 240 1.73e+01 1qhfA c.60.1.1 33960 1em2A 229 1.76e+01 1em2A d.129.3.2 41321 1gpwC 253 1.82e+01 c.1.2.1 65462 1h5sB 586 1.95e+01 c.68.1.6 65628 1gcxA 774 1.98e+01 1tgoA c.55.3.5 33725 e.8.1.1 43014 1hruA 188 1.98e+01 1hruA d.115.1.1 40926 1e1aA 314 1.99e+01 1e1aA b.68.6.1 59155 1thfD 253 2.02e+01 1thfD c.1.2.1 28535 1ose 496 2.06e+01 1smd b.71.1.1 27766 c.1.8.1 28753 1b3bA 415 2.08e+01 1hwyA c.2.1.7 30244 c.58.1.1 33892 1dhkA 496 2.12e+01 1smd b.71.1.1 27761 c.1.8.1 28748 1e9mA 106 2.12e+01 1ayfA d.15.4.1 59397 1bwvA 493 2.14e+01 1burA c.1.14.1 29372 d.58.9.1 39278 2dfpA 534 2.14e+01 2bce c.69.1.1 34597 1d2eA 397 2.15e+01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1eixC 245 2.17e+01 1dbtA c.1.2.3 28544 1ldnA 316 2.19e+01 1hyhA c.2.1.5 30166 d.162.1.1 42133 2ldb 317 2.20e+01 1hyhA c.2.1.5 30175 d.162.1.1 42142 1acc 735 2.22e+01 1acc f.11.1.1 43828 1ksiA 642 2.24e+01 1ksiB b.30.2.1 24408 d.17.2.1 38043 d.17.2.1 38044 1ksiB 642 2.24e+01 1ksiB b.30.2.1 24409 d.17.2.1 38045 d.17.2.1 38046 1grl 548 2.25e+01 1derA a.129.1.1 19487 c.8.5.1 30816 d.56.1.1 38935 1h5sC 586 2.29e+01 c.68.1.6 65629 1f1zA 273 2.31e+01 1f1zA a.4.5.27 16081 c.52.1.16 33334 1i4yA 114 2.34e+01 2mhr a.24.4.1 61738 1oelA 547 2.38e+01 1derA a.129.1.1 19452 c.8.5.1 30781 d.56.1.1 38900 2tmgA 415 2.41e+01 1hwyA c.2.1.7 30238 c.58.1.1 33886 1dw9A 156 2.42e+01 1dw9A a.35.1.4 17065 d.72.1.1 39596 1dwkA 156 2.42e+01 1dw9A a.35.1.4 17075 d.72.1.1 39606 1am2 199 2.57e+01 1am2 b.86.1.2 28381 1hnuA 280 2.74e+01 1hnoA c.14.1.3 61096 1hnoA 280 2.74e+01 1hnoA c.14.1.3 61095 1pgjA 478 2.76e+01 2pgd a.100.1.1 18783 c.2.1.6 30195 1jx2B 315 2.80e+01 c.37.1.8 67404 1i94B 255 2.87e+01 1fjfB c.23.15.1 61991 1fjgB 256 2.87e+01 1fjfB c.23.15.1 31400 2dri 271 2.95e+01 2dri c.93.1.1 35637 1eszA 266 3.03e+01 1dbp 271 3.04e+01 2dri c.93.1.1 35639 1drj 271 3.05e+01 2dri c.93.1.1 35642 1k7sN 265 3.06e+01 1efdN 266 3.09e+01 1efdN c.92.2.1 35597 1cr6B 554 3.13e+01 1cr6B c.108.1.2 43338 c.69.1.11 34688 1ek1A 554 3.13e+01 1cr6B c.108.1.2 43335 c.69.1.11 34685 1cqzA 554 3.13e+01 1cr6B c.108.1.2 43339 c.69.1.11 34689 1b26A 416 3.16e+01 1hwyA c.2.1.7 30232 c.58.1.1 33880 1iexA 605 3.24e+01 c.1.8.7 66127 c.23.11.1 66128 1ex1A 605 3.24e+01 1ex1A c.1.8.7 29013 c.23.11.1 31347 1lgyA 269 3.26e+01 3tgl c.69.1.17 34758 1qo7A 394 3.38e+01 1qo7A c.69.1.11 34697 1drk 271 3.41e+01 2dri c.93.1.1 35638 1e3mA 800 3.43e+01 1ewqA a.113.1.1 19075 c.37.1.12 32389 c.55.6.1 33746 d.75.2.1 39747 1j9yA 385 3.46e+01 1j9yA c.1.8.3 62791 1jk0A 419 3.52e+01 a.25.1.2 63142 1f2dA 341 3.65e+01 1f2dA c.79.1.1 35298 1imjA 210 3.72e+01 2ahjC 206 3.73e+01 2ahjA d.149.1.1 41773 2ahjA 206 3.73e+01 2ahjA d.149.1.1 41772 1i4zA 114 3.78e+01 2mhr a.24.4.1 61746 1bz7B 217 3.79e+01 1igtB b.1.1.1 20403 b.1.1.2 21375 1kkoA 413 3.79e+01 c.1.11.2 68675 d.54.1.1 68676 1egdA 396 3.81e+01 3mdeA a.29.3.1 16596 e.6.1.1 42857 1egeA 396 3.81e+01 3mdeA a.29.3.1 16604 e.6.1.1 42865 1bem 291 3.85e+01 1ryc a.93.1.1 18635 1cjyA 749 3.93e+01 1rlw b.7.1.1 23178 c.75.1.1 34986 1c6vX 81 4.00e+01 1ihvA b.34.7.1 24641