# List of top-scoring protein chains for t2k-100-30-str 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 1lylA 504 4.30e-02 1lylA b.40.4.1 25261 d.104.1.1 40717 1e1oA 504 8.10e-02 1lylA b.40.4.1 25258 d.104.1.1 40714 1viwB 198 1.67e-01 1led b.29.1.1 24170 1dhkB 223 1.77e-01 1led b.29.1.1 24157 4sli 679 3.13e-01 2sli b.29.1.9 24275 b.68.1.1 27612 2sli 679 3.14e-01 2sli b.29.1.9 24274 b.68.1.1 27611 1ruxA 951 6.50e-01 1dhx b.13.2.2 59040 b.13.2.2 59041 1f5jA 199 6.79e-01 1axkA b.29.1.11 24342 1dhx 967 1.61e+00 1dhx b.13.2.2 58971 b.13.2.2 58972 1e7uA 961 1.76e+00 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 2ayh 214 1.77e+00 1axkA b.29.1.2 24172 1eulA 994 1.82e+00 1eulA f.2.1.10 43726 1ixmB 192 2.35e+00 1ixmA d.123.1.1 41115 1k8cA 322 3.33e+00 1e8yA 966 3.43e+00 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 41715 1ly1A 181 3.65e+00 1g5aA 628 3.70e+00 b.71.1.1 65152 c.1.8.1 65153 1ixmA 192 4.33e+00 1ixmA d.123.1.1 41114 3psg 370 4.47e+00 1smrA b.50.1.2 26841 1gg3A 279 4.58e+00 1ef1A a.11.2.1 16372 b.55.1.5 27007 d.15.1.4 37615 1hqz9 141 4.75e+00 1tlfA 301 4.77e+00 1tlfA c.93.1.1 35687 1kblA 873 4.91e+00 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1hqz1 141 5.49e+00 1e8xA 961 5.74e+00 1e8xA a.118.1.6 19148 b.7.1.1 23183 d.15.1.5 37631 d.144.1.4 41711 1exmA 405 6.07e+00 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1lkvX 232 6.18e+00 1gr3A 160 6.39e+00 b.22.1.1 65476 1caxB 184 6.56e+00 1caxB b.82.1.2 28105 1iqpA 327 6.59e+00 a.80.1.1 62649 c.37.1.13 62650 1kkjA 419 6.82e+00 1jwhC 215 6.98e+00 1cawB 184 7.26e+00 1caxB b.82.1.2 28113 1aqjA 421 7.47e+00 2admA c.66.1.10 34242 1cqxA 403 7.48e+00 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1jb0A 755 8.05e+00 1jb0A f.2.1.12 62820 1kz7A 353 8.44e+00 1a6r 471 8.49e+00 3gcb d.3.1.1 37033 1ha3A 405 8.70e+00 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1bn5 478 8.89e+00 1bn5 a.4.5.25 16224 d.127.1.1 41161 2cb5A 453 9.10e+00 3gcb d.3.1.1 37035 1b6a 478 9.23e+00 1bn5 a.4.5.25 16223 d.127.1.1 41160 1k3rA 268 9.26e+00 1f5aA 513 9.73e+00 1fa0B d.58.16.1 39337 e.9.1.2 43231 1dar 691 1.01e+01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1ek1A 554 1.02e+01 1cr6B c.108.1.2 43335 c.69.1.11 34685 1cnt1 187 1.04e+01 1cnt3 1cauB 184 1.07e+01 1caxB b.82.1.2 28103 1aipE 405 1.07e+01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1hgeB 175 1.08e+01 1hgeB h.3.1.1 45680 5nn9 388 1.10e+01 2qwc b.68.1.1 27563 3gcb 470 1.11e+01 3gcb d.3.1.1 37032 1tnrA 144 1.11e+01 2tnfA b.22.1.1 23867 1gcb 454 1.11e+01 3gcb d.3.1.1 37034 1b43A 340 1.13e+01 1a76 a.60.7.1 18092 c.53.1.2 33362 1dc1A 323 1.13e+01 1dc1A c.52.1.11 33321 1kl1A 419 1.15e+01 1qpbA 563 1.18e+01 1zpdA c.31.1.3 31739 c.36.1.1 31781 c.36.1.1 31782 1lenB 52 1.19e+01 2ltnB 1dypA 271 1.20e+01 1dypA b.29.1.2 24185 1b2pA 119 1.27e+01 1b2pA b.78.1.1 27998 1qpxA 218 1.31e+01 1qpxA b.1.11.1 22318 b.7.2.1 23200 1a8d 452 1.32e+01 1a8d b.29.1.6 24262 b.42.4.2 25607 4kbpA 432 1.33e+01 4kbpA b.1.12.1 22345 d.159.1.1 42064 1dd6A 228 1.35e+01 1a7tA d.157.1.1 42054 2cavA 445 1.36e+01 1dgwA b.82.1.2 28094 b.82.1.2 28095 1fxzA 476 1.38e+01 b.82.1.2 65059 b.82.1.2 65060 2viuB 175 1.40e+01 1hgeB h.3.1.1 45676 1kbpA 432 1.40e+01 4kbpA b.1.12.1 22349 d.159.1.1 42068 1cr6B 554 1.41e+01 1cr6B c.108.1.2 43338 c.69.1.11 34688 1tul 108 1.45e+01 1tul b.85.5.1 28373 1d0hA 469 1.48e+01 1a8d b.29.1.6 24265 b.42.4.2 25610 1f8eA 388 1.48e+01 2qwc b.68.1.1 59694 2tmvP 158 1.50e+01 1rmvA a.24.5.1 16586 2qwc 388 1.54e+01 2qwc b.68.1.1 27547 1qbqA 333 1.57e+01 1ft1A a.118.6.1 19187 1jpzA 473 1.59e+01 a.104.1.1 67069 1jyeA 349 1.64e+01 c.93.1.1 67455 1jcqA 382 1.64e+01 a.118.6.1 66504 1ld8A 382 1.65e+01 1dik 874 1.70e+01 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 3hmgB 175 1.70e+01 1hgeB h.3.1.1 45704 1gpiA 431 1.70e+01 b.29.1.10 65450 1erjA 393 1.70e+01 1erjA b.69.4.1 27660 2act 220 1.77e+01 1cs8A d.3.1.1 37002 3nn9 388 1.78e+01 2qwc b.68.1.1 27566 1cqzA 554 1.78e+01 1cr6B c.108.1.2 43339 c.69.1.11 34689 1k4wA 252 1.79e+01 1bxeA 113 1.80e+01 1bxeA d.55.1.1 38898 1ft1A 377 1.82e+01 1ft1A a.118.6.1 19186 1i4jA 110 1.84e+01 1e6pA 499 1.85e+01 1e15A b.72.2.1 59314 c.1.8.5 59315 d.26.3.1 59316 1kdj 102 1.88e+01 1plc b.6.1.1 22864 1fcqA 350 1.96e+01 c.1.8.9 65006 1ki1B 352 1.96e+01 1cnt3 187 1.99e+01 1cnt3 1epuA 591 2.00e+01 1dn1A e.25.1.1 43358 1qlgA 355 2.01e+01 1qlgA b.68.3.1 27627 1e15A 499 2.04e+01 1e15A b.72.2.1 27810 c.1.8.5 29006 d.26.3.1 38440 1gbg 214 2.04e+01 1axkA b.29.1.2 24171 1eysH 259 2.08e+01 6prcH b.41.1.1 25484 f.2.1.2 43517 1iu8A 206 2.08e+01 1dvkA 173 2.10e+01 1dvkA a.72.1.1 18319 1j4aA 333 2.12e+01 1goiA 499 2.13e+01 b.72.2.1 65413 c.1.8.5 65414 d.26.3.1 65415 4pep 326 2.17e+01 1smrA b.50.1.2 26843 1d8dA 377 2.17e+01 1ft1A a.118.6.1 19185 1k8tA 510 2.24e+01 e.9.1.4 68316 1g291 372 2.27e+01 1g291 1jcrA 377 2.27e+01 a.118.6.1 66506 1d2gA 292 2.28e+01 1xvaA c.66.1.5 34187 1qf8A 182 2.29e+01 1qf8A g.41.4.1 45212 1j71A 334 2.34e+01 1eagA b.50.1.2 62669 1ukz 203 2.36e+01 1zin c.37.1.1 31840 1k3tA 359 2.40e+01 2apr 325 2.46e+01 2er7E b.50.1.2 26819 1jg1A 235 2.48e+01 c.66.1.7 66661 1jplA 171 2.56e+01 a.118.9.2 67027 2sqcA 631 2.60e+01 2sqcA a.102.4.2 18854 a.102.4.2 18855 3aprE 325 2.65e+01 2er7E b.50.1.2 26820 1efcA 393 2.70e+01 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1jilA 420 2.72e+01 c.26.1.1 66745 1qcnA 421 2.78e+01 1qcnA b.34.8.1 59017 d.177.1.1 59018 1k0mA 241 2.79e+01 a.45.1.1 67949 c.47.1.5 67950 1qu1A 155 2.84e+01 1qu1A h.3.1.1 45670 1ea2A 131 2.88e+01 d.17.4.3 64860 1c9uA 454 2.94e+01 1c9uA b.68.2.1 27623 1ltqA 301 2.95e+01 2pooA 355 2.97e+01 1qlgA b.68.3.1 27626 1qqjA 419 2.99e+01 1qcnA b.34.8.1 59034 d.177.1.1 59035 1qfcA 306 3.08e+01 1uteA d.159.1.1 42077 1bhjA 292 3.20e+01 1xvaA c.66.1.5 34189 1iweA 457 3.25e+01 1rmvA 157 3.27e+01 1rmvA a.24.5.1 16589 1jjtA 228 3.28e+01 1a7tA d.157.1.1 63139 1t7pA 698 3.34e+01 1t7pA c.55.3.5 33712 e.8.1.1 43005 1bet 107 3.45e+01 1bndA g.17.1.3 44801 1hyoA 421 3.47e+01 1qcnA b.34.8.1 59001 d.177.1.1 59002 1ck7A 631 3.49e+01 1ck7A a.20.1.2 58969 b.66.1.1 27538 d.92.1.11 58970 g.14.1.2 44674 g.14.1.2 44675 g.14.1.2 44676 1qbiA 454 3.50e+01 1c9uA b.68.2.1 27619 1dioA 554 3.51e+01 1dioA c.1.19.3 29656 1js8A 394 3.52e+01 a.86.1.1 67219 b.1.1.5 67220 1h6lA 353 3.53e+01 b.68.3.1 60687 1nozA 388 3.55e+01 1clqA c.55.3.5 33715 1gjuA 637 3.55e+01 b.71.1.1 60580 c.1.8.1 60581 1sqc 631 3.62e+01 2sqcA a.102.4.2 18858 a.102.4.2 18859 1eqkA 102 3.63e+01 1eqkA d.17.1.2 37998 1a2zA 220 3.71e+01 1a2zA c.56.4.1 33794 1eexA 554 3.73e+01 1dioA c.1.19.3 29650 1ig8A 486 3.74e+01 2yhx c.55.1.3 64746 c.55.1.3 64747 1cpcA 162 3.74e+01 1cpcA a.1.1.3 15643 1adjA 421 3.76e+01 1adjA c.51.1.1 33188 d.104.1.1 40737 1qppA 218 3.83e+01 1qpxA b.1.11.1 22320 b.7.2.1 23202 1qcoA 423 3.86e+01 1qcnA b.34.8.1 59021 d.177.1.1 59022 1bu7A 455 3.94e+01 1bu7A a.104.1.1 18937 1cgt 684 3.96e+01 1cxlA b.1.1.5 21815 b.3.1.1 22484 b.71.1.1 27722 c.1.8.1 28709 1lam 484 3.97e+01 1lam c.50.1.1 33166 c.56.5.3 33829