# 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 1qvcA 145 6.59e-19 3ullA b.40.4.3 25284 1kawA 135 2.80e-16 3ullA b.40.4.3 25288 3ullA 132 1.61e-14 3ullA b.40.4.3 25282 1a8p 258 1.39e-01 1fdr b.43.4.2 25654 c.25.1.1 31544 1je5A 206 1.81e-01 1je5A b.40.4.7 62909 1be9A 119 3.05e-01 1pdr b.36.1.1 24774 1bfeA 119 3.14e-01 1pdr b.36.1.1 24775 1pdr 99 3.34e-01 1pdr b.36.1.1 24771 1at0 145 4.60e-01 1at0 b.86.1.1 28374 1ndoB 194 8.85e-01 1ndoB d.17.4.4 38121 1d1nA 99 1.05e+00 1d1nA b.43.3.1 25718 1ewjA 126 1.35e+00 1ecsA d.32.1.2 59526 1fnc 314 1.42e+00 1fnc b.43.4.2 25627 c.25.1.1 31517 1ecsA 126 1.63e+00 1ecsA d.32.1.2 59407 1otcA 495 1.65e+00 1otcA b.40.4.3 25307 b.40.4.3 25308 b.40.4.3 25309 1fnd 314 1.80e+00 1fnc b.43.4.2 25626 c.25.1.1 31516 1jj2B 337 2.07e+00 1ffkB b.43.3.2 63086 1d5yA 292 2.11e+00 1d5yA a.4.1.8 16055 a.4.1.8 16056 d.60.1.2 39532 1jb7A 495 2.37e+00 1otcA b.40.4.3 62836 b.40.4.3 62837 b.40.4.3 62838 1que 303 2.46e+00 1fnc b.43.4.2 25647 c.25.1.1 31537 1eg9B 194 2.86e+00 1ndoB d.17.4.4 38120 1fdr 248 2.94e+00 1fdr b.43.4.2 25653 c.25.1.1 31543 1lj5A 379 2.95e+00 1l9mA 692 3.10e+00 1huuA 90 4.32e+00 1huuA a.55.1.1 17897 1gm5A 780 4.40e+00 a.29.4.1 65298 b.40.4.9 65299 c.37.1.13 65300 c.37.1.13 65301 1qg0A 308 4.46e+00 1fnc b.43.4.2 25639 c.25.1.1 31529 1f9zA 135 4.72e+00 1qipA d.32.1.1 38484 1j7xA 302 4.80e+00 c.14.1.2 66425 2prd 174 5.37e+00 2prd b.40.5.1 25435 1cqqA 180 5.89e+00 1cqqA b.47.1.4 26422 2tdt 274 5.89e+00 3tdt b.81.1.2 28054 3tdt 274 5.94e+00 3tdt b.81.1.2 28053 1b8zA 90 6.07e+00 1huuA a.55.1.1 17902 1gmuA 143 6.15e+00 b.107.1.1 65335 d.58.38.1 65336 1fa8A 135 6.41e+00 1qipA d.32.1.1 38486 1e79A 510 6.75e+00 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1wit 93 7.07e+00 1wit b.1.1.4 21714 1bmfA 510 7.37e+00 1skyB a.69.1.1 18281 b.49.1.1 26446 c.37.1.11 32326 1fjgQ 105 7.41e+00 1fjfQ b.40.4.5 25352 1rlw 126 8.33e+00 1rlw b.7.1.1 23177 1gotB 340 8.52e+00 1tbgA b.69.4.1 27648 1b8aA 438 8.71e+00 1b8aA b.40.4.1 25244 d.104.1.1 40765 1gpeA 587 9.04e+00 1gpeA c.3.1.2 30387 d.16.1.4 37951 1tlk 154 9.53e+00 1tlk b.1.1.4 21707 1fhgA 154 9.59e+00 1tlk b.1.1.4 21706 1ff9A 450 1.01e+01 1ff9A c.2.1.3 30039 d.81.1.2 39954 1h8eA 510 1.13e+01 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1ndh 272 1.16e+01 1ndh b.43.4.2 25662 c.25.1.1 31552 1vpsB 289 1.28e+01 1vpsA b.10.1.4 23337 1je0A 236 1.41e+01 c.56.2.1 66581 1qppA 218 1.45e+01 1qpxA b.1.11.1 22320 b.7.2.1 23202 1qpxA 218 1.47e+01 1qpxA b.1.11.1 22318 b.7.2.1 23200 1gd5A 130 1.48e+01 1gd5A d.189.1.1 60439 1h8dH 260 1.52e+01 5ptp 1k28D 391 1.54e+01 b.106.1.1 68052 b.106.1.1 68053 1i40A 175 1.57e+01 b.40.5.1 66024 1sro 76 1.61e+01 1sro b.40.4.5 25327 1tdtA 259 1.68e+01 3tdt b.81.1.2 28055 1bbzA 58 1.77e+01 1bbzA b.34.2.1 24477 1shaA 104 1.78e+01 1fmk d.93.1.1 40424 1qqjA 419 1.79e+01 1qcnA b.34.8.1 59034 d.177.1.1 59035 1hyoA 421 1.79e+01 1qcnA b.34.8.1 59001 d.177.1.1 59002 1qcnA 421 1.79e+01 1qcnA b.34.8.1 59017 d.177.1.1 59018 1a7cA 379 1.81e+01 1sek e.1.1.1 42660 1shbA 104 1.86e+01 1fmk d.93.1.1 40425 1shdA 107 1.86e+01 1fmk d.93.1.1 40440 1aboA 62 1.87e+01 1bbzA b.34.2.1 24474 1qdbA 473 1.87e+01 1qdbA a.138.1.3 19688 1d6mA 653 1.90e+01 1d6mA e.10.1.1 43248 1quqB 121 1.95e+01 1quqB b.40.4.3 25305 1lylA 504 2.01e+01 1lylA b.40.4.1 25261 d.104.1.1 40717 1gqvA 135 2.11e+01 1f15B 218 2.13e+01 1f15B b.10.1.2 23321 1hqkA 154 2.16e+01 c.16.1.1 65902 1f46A 140 2.17e+01 1f46A d.129.4.1 59643 1e1oA 504 2.18e+01 1lylA b.40.4.1 25258 d.104.1.1 40714 1ciy 590 2.20e+01 1ciy b.18.1.3 23720 b.77.2.1 27977 f.1.3.1 43392 1a8vA 121 2.20e+01 1a62 a.140.3.1 64712 b.40.4.5 64713 1hi2A 135 2.23e+01 7rsa d.5.1.1 61057 1fs7A 485 2.28e+01 1qdbA a.138.1.3 19691 2dtr 226 2.31e+01 1bi0 a.4.5.24 16193 a.76.1.1 18399 b.34.1.2 24450 1i7pA 274 2.31e+01 b.43.4.2 66048 c.25.1.1 66049 1d8iA 311 2.32e+01 1d8iA d.63.1.1 39541 1jh2A 99 2.38e+01 b.35.1.1 63038 1a62 130 2.39e+01 1a62 a.140.3.1 64708 b.40.4.5 64709 1jb9A 316 2.42e+01 1fnc b.43.4.2 62840 c.25.1.1 62841 1vpsA 289 2.45e+01 1vpsA b.10.1.4 23336 1an7A 136 2.46e+01 1seiA d.140.1.1 41465 1g13A 162 2.46e+01 1g13A b.95.1.1 60194 1bf8 205 2.49e+01 1qpxA b.1.11.1 22332 b.7.2.1 23214 1obwA 175 2.52e+01 2prd b.40.5.1 25416 1an8 208 2.57e+01 1an8 b.40.2.2 25202 d.15.6.1 37791 1fmk 452 2.58e+01 1fmk b.34.2.1 24511 d.93.1.1 40436 d.144.1.2 41690 1eur 365 2.62e+01 1eut b.68.1.1 27607 1qouA 181 2.62e+01 1qouA b.17.1.1 23707 1sesA 421 2.63e+01 1sesA a.2.7.1 15710 d.104.1.1 40710 1c5lH 259 2.65e+01 5ptp 1jb3A 131 2.66e+01 1jc7A b.40.3.2 62833 1ewnA 219 2.70e+01 1bnkA b.46.1.2 25762 1ahtH 259 2.72e+01 5ptp 1g3jB 61 2.78e+01 1g3jB j.71.1.1 46366 1i1jA 108 2.90e+01 1i1jA b.34.2.1 61531 1behA 187 2.98e+01 1a44 b.17.1.1 23700 8kme2 259 3.01e+01 1ucyE 1uxy 340 3.02e+01 2mbr d.145.1.2 41748 d.146.1.1 41761 1cfzA 162 3.03e+01 1cfzA c.56.1.1 33754 1ucyE 109 3.10e+01 1ucyE 1j8rA 196 3.11e+01 1j8rA b.2.3.3 62745 1eu3A 210 3.12e+01 1an8 b.40.2.2 25206 d.15.6.1 37795 1ihjA 98 3.14e+01 1pdr b.36.1.1 62382 1bnkA 216 3.21e+01 1bnkA b.46.1.2 25765 1fuxA 166 3.24e+01 1fjjA b.17.1.2 60034 1jbuH 254 3.26e+01 5ptp b.47.1.2 62856 1d8hA 311 3.27e+01 1d8iA d.63.1.1 39544 1jb1A 205 3.28e+01 1jb1A c.91.1.2 62832 1euu 605 3.33e+01 1eut b.1.1.5 21892 b.18.1.1 23713 b.68.1.1 27610 2dynA 122 3.34e+01 1dynA b.55.1.1 26957 1tdj 514 3.37e+01 1tdj c.79.1.1 35297 d.58.18.2 39356 d.58.18.2 39357 1qfxA 460 3.38e+01 1qfxA c.60.1.3 33994 1nbcA 155 3.60e+01 1nbcA b.2.2.2 22390 1smrA 335 3.67e+01 1smrA b.50.1.2 26878 2bbkH 355 3.67e+01 2bbkH b.69.2.1 27634 1emwA 88 3.68e+01 1emwA d.27.1.1 38448 1eut 605 3.70e+01 1eut b.1.1.5 21891 b.18.1.1 23712 b.68.1.1 27609 1jc7A 131 3.76e+01 1jc7A b.40.3.2 62873 1kicA 339 3.77e+01 1hozA 339 3.79e+01 c.70.1.1 65898 2ms2A 129 3.81e+01 1msc d.85.1.1 40049 1fnhA 271 3.83e+01 1fnhA b.1.2.1 21976 b.1.2.1 21977 b.1.2.1 21978 4aahA 571 3.83e+01 4aahA b.70.1.1 27678 2rhe 114 3.83e+01 8fabA b.1.1.1 20523 1qd1A 325 3.85e+01 1qd1A d.58.34.1 39493 d.58.34.1 39494 1hh1A 143 3.87e+01 1gefA c.52.1.18 61036 1i6iA 366 3.88e+01 1bg2 c.37.1.9 61844 1g72A 573 3.89e+01 4aahA b.70.1.1 27680 1qlyA 58 3.92e+01 1bbzA b.34.2.1 24530 1a78A 134 3.93e+01 1c1lA b.29.1.3 24212 1dar 691 3.96e+01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300