# 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 1iiwA 232 3.30e-01 c.94.1.1 62461 1ii5A 233 3.36e-01 c.94.1.1 62412 1sbp 310 3.93e-01 1sbp c.94.1.1 35760 1f9aA 168 6.52e-01 1f9aA c.26.1.3 31602 1iruC 261 1.08e+00 1ak7 174 1.24e+00 1cof d.109.1.2 40864 1qjhA 101 2.63e+00 1ris d.58.14.1 39326 1ftkA 279 4.09e+00 1gr2A c.94.1.1 35819 1gr2A 279 4.09e+00 1gr2A c.94.1.1 35825 1cdoA 374 4.40e+00 2ohxA b.35.1.2 24747 c.2.1.1 29763 1g19A 350 4.56e+00 2reb c.37.1.11 32284 d.48.1.1 38770 1cl2A 395 4.67e+00 1cl2A c.67.1.3 34397 1wdnA 226 4.73e+00 1lst c.94.1.1 35816 1gggB 226 4.73e+00 1lst c.94.1.1 35818 1cl1A 395 4.79e+00 1cl2A c.67.1.3 34395 1eu8A 409 5.41e+00 1eu8A c.94.1.1 59502 1h7wD 1025 6.07e+00 a.1.2.2 15686 c.1.4.1 28631 c.3.1.1 30327 c.4.1.1 30612 d.58.1.5 39010 1h7wB 1025 6.07e+00 a.1.2.2 15684 c.1.4.1 28629 c.3.1.1 30325 c.4.1.1 30610 d.58.1.5 39008 1h7wA 1025 6.07e+00 1h7wA a.1.2.2 15683 c.1.4.1 28628 c.3.1.1 30324 c.4.1.1 30609 d.58.1.5 39007 1gteA 1025 6.07e+00 1h7xB 1025 6.08e+00 a.1.2.2 15688 c.1.4.1 28633 c.3.1.1 30329 c.4.1.1 30614 d.58.1.5 39012 1h7xC 1025 6.08e+00 a.1.2.2 15689 c.1.4.1 28634 c.3.1.1 30330 c.4.1.1 30615 d.58.1.5 39013 1h7xD 1025 6.08e+00 a.1.2.2 15690 c.1.4.1 28635 c.3.1.1 30331 c.4.1.1 30616 d.58.1.5 39014 1h7xA 1025 6.08e+00 1h7wA a.1.2.2 15687 c.1.4.1 28632 c.3.1.1 30328 c.4.1.1 30613 d.58.1.5 39011 1mabG 270 6.29e+00 1e1qG c.49.2.1 33165 1h6vE 499 6.35e+00 c.3.1.5 60705 c.3.1.5 60706 d.87.1.1 60707 1ej2A 181 7.01e+00 1f9aA c.26.1.3 59414 1hybA 181 7.03e+00 1f9aA c.26.1.3 61399 1pls 113 7.17e+00 1pls b.55.1.1 26965 1cpo 299 7.29e+00 1cpo a.39.3.1 17390 a.39.3.1 17391 1attA 421 7.53e+00 1ovaA e.1.1.1 42638 1b37B 472 7.71e+00 1b37B c.3.1.2 30390 d.16.1.5 37954 1b5qA 472 7.71e+00 1b37B c.3.1.2 30404 d.16.1.5 37968 1k0dA 260 8.88e+00 a.45.1.1 67930 c.47.1.5 67931 1g6wD 261 8.89e+00 1hqoA a.45.1.1 17754 c.47.1.5 33048 1gl8A 104 9.95e+00 c.47.1.1 65290 1c3uA 431 1.02e+01 1c3cA a.127.1.1 19427 1fb6A 105 1.03e+01 1thx c.47.1.1 32739 1vdc 333 1.03e+01 1trb c.3.1.5 30545 c.3.1.5 30546 1nsiA 431 1.04e+01 1nseA d.174.1.1 42522 1c3cA 429 1.05e+01 1c3cA a.127.1.1 19425 4nosA 427 1.07e+01 1nseA d.174.1.1 42516 1eg9A 449 1.08e+01 1ndoA b.33.1.2 24443 d.129.3.3 41322 1ndoA 449 1.08e+01 1ndoA b.33.1.2 24444 d.129.3.3 41323 1lte 239 1.10e+01 1led b.29.1.1 24047 1ek6A 348 1.12e+01 1xel c.2.1.2 29800 1pmi 440 1.12e+01 1pmi b.82.1.3 28114 1i3kA 348 1.19e+01 1xel c.2.1.2 61595 1hzjA 348 1.19e+01 1xel c.2.1.2 61450 1g61A 228 1.20e+01 1g61A d.126.1.1 41126 2reb 352 1.21e+01 2reb c.37.1.11 32282 d.48.1.1 38767 2recA 353 1.22e+01 2reb i.2.1.1 45879 1gpx 106 1.23e+01 1ayfA d.15.4.1 37681 1t7pA 698 1.24e+01 1t7pA c.55.3.5 33712 e.8.1.1 43005 1cof 143 1.26e+01 1cof d.109.1.2 40860 1cfyA 143 1.26e+01 1cof d.109.1.2 40858 1put 106 1.26e+01 1ayfA d.15.4.1 37680 1pdxA 106 1.27e+01 1ayfA d.15.4.1 37682 1attB 411 1.28e+01 1ovaA e.1.1.1 42639 1is2A 661 1.29e+01 1ep8A 112 1.31e+01 c.47.1.1 64907 1d0bA 213 1.31e+01 1d0bA c.10.2.1 30866 1aerB 195 1.33e+01 1aerA d.166.1.1 42250 1pyp 285 1.36e+01 1wgjA b.40.5.1 25409 1qi4A 429 1.40e+01 1jdc b.71.1.1 27791 c.1.8.1 28778 1jdc 429 1.40e+01 1jdc b.71.1.1 27789 c.1.8.1 28776 1qi5A 429 1.42e+01 1jdc b.71.1.1 27792 c.1.8.1 28779 1etzA 215 1.50e+01 8fabA b.1.1.1 20480 b.1.1.2 21444 1lb8A 263 1.52e+01 1lci 550 1.53e+01 1lci e.23.1.1 43349 1lnrE 185 1.54e+01 1qc6A 130 1.55e+01 1evhA b.55.1.4 26998 1amk 251 1.60e+01 1amk c.1.1.1 28503 1qdsA 251 1.60e+01 1amk c.1.1.1 28504 1ax0 239 1.60e+01 1led b.29.1.1 24042 1qi3A 429 1.62e+01 1jdc b.71.1.1 27794 c.1.8.1 28781 1fyuA 255 1.62e+01 1led b.29.1.1 24048 1gcyA 527 1.63e+01 1jdc b.71.1.1 27788 c.1.8.1 28775 1im8A 244 1.66e+01 c.66.1.14 66212 1qpkA 418 1.67e+01 1jdc b.71.1.1 27793 c.1.8.1 28780 1dl5A 317 1.72e+01 1dl5A c.66.1.7 64720 d.197.1.1 64721 1ekeA 230 1.76e+01 1ekeA c.55.3.1 33572 1ep7A 112 1.87e+01 c.47.1.1 64905 1lbcA 263 1.88e+01 1ftjB 263 1.89e+01 1gr2A c.94.1.1 35827 1gmeA 151 1.90e+01 b.15.1.1 65305 1lbbA 263 1.96e+01 1fyeA 229 2.02e+01 1fyeA c.23.16.4 31477 1qj2C 285 2.08e+01 1qj2C d.87.2.1 40221 d.145.1.3 41752 1k6wA 426 2.13e+01 b.92.1.2 68236 c.1.9.5 68237 1lo7A 141 2.22e+01 1bvqA 141 2.22e+01 1bvqA d.38.1.1 38542 6pfkA 319 2.30e+01 3pfk c.89.1.1 35583 1yppA 286 2.32e+01 1wgjA b.40.5.1 25407 1mnc 163 2.34e+01 1hfc d.92.1.11 40353 1e9gB 286 2.40e+01 1wgjA b.40.5.1 59394 1i6zA 135 2.47e+01 a.7.7.1 61861 1fvsA 72 2.47e+01 1aw0 d.58.17.1 60049 8prkB 287 2.48e+01 1wgjA b.40.5.1 25396 8prkA 287 2.48e+01 1wgjA b.40.5.1 25395 1hujA 281 2.51e+01 1wgjA b.40.5.1 25403 1wgjA 286 2.54e+01 1wgjA b.40.5.1 25397 1e9gA 286 2.54e+01 1wgjA b.40.5.1 59393 1hukA 281 2.55e+01 1wgjA b.40.5.1 25405 1g81A 164 2.55e+01 1fw9A d.190.1.1 60336 117eA 286 2.56e+01 1wgjA b.40.5.1 25401 1gehA 444 2.57e+01 c.1.14.1 65181 d.58.9.1 65182 1jbbA 153 2.58e+01 1u9aA d.20.1.1 62842 1jmrA 249 2.59e+01 1jatA 155 2.62e+01 1u9aA d.20.1.1 62818 1g1bA 164 2.63e+01 1fw9A d.190.1.1 60202 1jsqA 582 2.67e+01 i.13.1.1 63270 1e0tA 470 2.68e+01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1e0uA 470 2.71e+01 1a49A b.58.1.1 27072 c.1.12.1 29300 c.49.1.1 33154 1g0uL 241 2.75e+01 d.153.1.4 41894 1gz9A 239 2.76e+01 1jbgA 109 2.79e+01 a.6.1.3 66480 1cqmA 101 2.80e+01 1ris d.58.14.1 39321 1pkyA 470 2.82e+01 1a49A b.58.1.1 27068 c.1.12.1 29296 c.49.1.1 33150 3adk 195 2.86e+01 1zin c.37.1.1 31885 1be3A 446 2.92e+01 1be3A d.185.1.1 58950 d.185.1.1 58951 1ryp1 222 2.96e+01 1ryp1 1qcrA 446 2.97e+01 1be3A d.185.1.1 59025 d.185.1.1 59026 1fna 91 3.11e+01 1fnf b.1.2.1 21971 1qgc2 218 3.13e+01 1qqp2 1i40A 175 3.14e+01 b.40.5.1 66024 1obwA 175 3.14e+01 2prd b.40.5.1 25416 1jr2A 286 3.18e+01 c.113.1.1 67111 1li5A 461 3.19e+01 1hqoA 258 3.20e+01 1hqoA a.45.1.1 17749 c.47.1.5 33043 1jl5A 454 3.23e+01 c.10.2.6 66830 1g9uA 454 3.23e+01 c.10.2.6 65172 1kgsA 225 3.23e+01 a.4.6.1 68596 c.23.1.1 68597 1mldA 314 3.25e+01 2cmd c.2.1.5 30122 d.162.1.1 42089 1aa3 63 3.34e+01 2reb d.48.1.1 38769 1ahsA 126 3.42e+01 1ahsA b.19.1.1 23794 4pfk 319 3.43e+01 3pfk c.89.1.1 35582 3pfk 319 3.43e+01 3pfk c.89.1.1 35581 1fw9A 164 3.48e+01 1fw9A d.190.1.1 60059 1e5tA 710 3.53e+01 1qfmA b.69.7.1 27676 c.69.1.4 34644 1hg3A 225 3.58e+01 1hg3A c.1.1.1 61025 1qqtA 551 3.59e+01 1qqtA a.27.1.1 16923 c.26.1.1 31590 g.41.1.1 45175 1f4lA 551 3.69e+01 1qqtA a.27.1.1 59648 c.26.1.1 59649 g.41.1.1 59650 1jd3A 164 3.69e+01 1fw9A d.190.1.1 62896 1mjwA 175 3.70e+01 2prd b.40.5.1 25419 1qfsA 710 3.71e+01 1qfmA b.69.7.1 27677 c.69.1.4 34645 1ccwA 137 3.72e+01 1be1 c.23.6.1 31238 1and 223 3.75e+01 5ptp b.47.1.2 25985 1udrA 129 3.79e+01 3chy c.23.1.1 31041 1l0oA 150 3.90e+01 1f4yL 210 3.90e+01 8fabA b.1.1.1 20454 b.1.1.2 21418 1h6tA 291 3.93e+01 b.1.1.6 65686 c.10.2.1 65687 1f4xL 210 3.94e+01 8fabA b.1.1.1 20450 b.1.1.2 21414 1ge8A 249 3.97e+01 1plq d.131.1.2 41398 d.131.1.2 41399