# 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 2.48e-19 3ullA b.40.4.3 25284 1kawA 135 1.21e-16 3ullA b.40.4.3 25288 3ullA 132 3.21e-15 3ullA b.40.4.3 25282 1a8p 258 1.20e-01 1fdr b.43.4.2 25654 c.25.1.1 31544 1je5A 206 1.69e-01 1je5A b.40.4.7 62909 1be9A 119 2.25e-01 1pdr b.36.1.1 24774 1bfeA 119 2.44e-01 1pdr b.36.1.1 24775 1pdr 99 2.94e-01 1pdr b.36.1.1 24771 1at0 145 5.31e-01 1at0 b.86.1.1 28374 1otcA 495 8.55e-01 1otcA b.40.4.3 25307 b.40.4.3 25308 b.40.4.3 25309 1ewjA 126 1.07e+00 1ecsA d.32.1.2 59526 1jb7A 495 1.25e+00 1otcA b.40.4.3 62836 b.40.4.3 62837 b.40.4.3 62838 1ecsA 126 1.31e+00 1ecsA d.32.1.2 59407 1d1nA 99 1.38e+00 1d1nA b.43.3.1 25718 1fnc 314 1.51e+00 1fnc b.43.4.2 25627 c.25.1.1 31517 1fdr 248 1.57e+00 1fdr b.43.4.2 25653 c.25.1.1 31543 1ndoB 194 1.71e+00 1ndoB d.17.4.4 38121 1fnd 314 1.84e+00 1fnc b.43.4.2 25626 c.25.1.1 31516 1que 303 1.99e+00 1fnc b.43.4.2 25647 c.25.1.1 31537 1d5yA 292 2.36e+00 1d5yA a.4.1.8 16055 a.4.1.8 16056 d.60.1.2 39532 1lj5A 379 2.43e+00 1f9zA 135 2.46e+00 1qipA d.32.1.1 38484 1l9mA 692 3.33e+00 1gm5A 780 3.37e+00 a.29.4.1 65298 b.40.4.9 65299 c.37.1.13 65300 c.37.1.13 65301 1j7xA 302 3.43e+00 c.14.1.2 66425 1fa8A 135 4.01e+00 1qipA d.32.1.1 38486 1e79A 510 4.04e+00 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 2prd 174 4.04e+00 2prd b.40.5.1 25435 1ff9A 450 4.35e+00 1ff9A c.2.1.3 30039 d.81.1.2 39954 1bmfA 510 4.37e+00 1skyB a.69.1.1 18281 b.49.1.1 26446 c.37.1.11 32326 1gpeA 587 4.59e+00 1gpeA c.3.1.2 30387 d.16.1.4 37951 1gmuA 143 4.71e+00 b.107.1.1 65335 d.58.38.1 65336 1huuA 90 5.22e+00 1huuA a.55.1.1 17897 1eg9B 194 5.75e+00 1ndoB d.17.4.4 38120 1fjgQ 105 5.96e+00 1fjfQ b.40.4.5 25352 1qg0A 308 6.46e+00 1fnc b.43.4.2 25639 c.25.1.1 31529 1wit 93 6.84e+00 1wit b.1.1.4 21714 1h8eA 510 7.00e+00 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1gotB 340 7.40e+00 1tbgA b.69.4.1 27648 1rlw 126 7.85e+00 1rlw b.7.1.1 23177 1b8zA 90 8.20e+00 1huuA a.55.1.1 17902 2tdt 274 8.41e+00 3tdt b.81.1.2 28054 3tdt 274 8.51e+00 3tdt b.81.1.2 28053 1vpsB 289 1.02e+01 1vpsA b.10.1.4 23337 1qpxA 218 1.04e+01 1qpxA b.1.11.1 22318 b.7.2.1 23200 1jj2B 337 1.04e+01 1ffkB b.43.3.2 63086 1b8aA 438 1.09e+01 1b8aA b.40.4.1 25244 d.104.1.1 40765 1ndh 272 1.10e+01 1ndh b.43.4.2 25662 c.25.1.1 31552 1cqqA 180 1.14e+01 1cqqA b.47.1.4 26422 1shaA 104 1.19e+01 1fmk d.93.1.1 40424 1qppA 218 1.19e+01 1qpxA b.1.11.1 22320 b.7.2.1 23202 1shbA 104 1.25e+01 1fmk d.93.1.1 40425 1tlk 154 1.29e+01 1tlk b.1.1.4 21707 1fhgA 154 1.30e+01 1tlk b.1.1.4 21706 1tdtA 259 1.33e+01 3tdt b.81.1.2 28055 1shdA 107 1.40e+01 1fmk d.93.1.1 40440 1h8dH 260 1.42e+01 5ptp 1qqjA 419 1.46e+01 1qcnA b.34.8.1 59034 d.177.1.1 59035 1qcnA 421 1.46e+01 1qcnA b.34.8.1 59017 d.177.1.1 59018 1hyoA 421 1.46e+01 1qcnA b.34.8.1 59001 d.177.1.1 59002 1lylA 504 1.49e+01 1lylA b.40.4.1 25261 d.104.1.1 40717 1gd5A 130 1.64e+01 1gd5A d.189.1.1 60439 1i1jA 108 1.64e+01 1i1jA b.34.2.1 61531 1fltV 98 1.67e+01 1vpfA g.17.1.1 44751 1a7cA 379 1.68e+01 1sek e.1.1.1 42660 1bbzA 58 1.75e+01 1bbzA b.34.2.1 24477 1quqB 121 1.76e+01 1quqB b.40.4.3 25305 1fmk 452 1.79e+01 1fmk b.34.2.1 24511 d.93.1.1 40436 d.144.1.2 41690 1sro 76 1.80e+01 1sro b.40.4.5 25327 1aboA 62 1.84e+01 1bbzA b.34.2.1 24474 1an8 208 1.90e+01 1an8 b.40.2.2 25202 d.15.6.1 37791 1kqrA 179 2.01e+01 1qdbA 473 2.03e+01 1qdbA a.138.1.3 19688 1i40A 175 2.04e+01 b.40.5.1 66024 1qouA 181 2.05e+01 1qouA b.17.1.1 23707 1vpsA 289 2.06e+01 1vpsA b.10.1.4 23336 1gqvA 135 2.13e+01 1d8iA 311 2.14e+01 1d8iA d.63.1.1 39541 1i7pA 274 2.16e+01 b.43.4.2 66048 c.25.1.1 66049 1k28D 391 2.17e+01 b.106.1.1 68052 b.106.1.1 68053 1a8vA 121 2.22e+01 1a62 a.140.3.1 64712 b.40.4.5 64713 1i6iA 366 2.22e+01 1bg2 c.37.1.9 61844 1d6mA 653 2.22e+01 1d6mA e.10.1.1 43248 1fs7A 485 2.23e+01 1qdbA a.138.1.3 19691 1g13A 162 2.23e+01 1g13A b.95.1.1 60194 1hi2A 135 2.25e+01 7rsa d.5.1.1 61057 1ihjA 98 2.31e+01 1pdr b.36.1.1 62382 1je0A 236 2.36e+01 c.56.2.1 66581 1a62 130 2.38e+01 1a62 a.140.3.1 64708 b.40.4.5 64709 1ds6B 180 2.40e+01 1rhoA b.1.1.5 21898 1an7A 136 2.42e+01 1seiA d.140.1.1 41465 1f46A 140 2.44e+01 1f46A d.129.4.1 59643 1e1oA 504 2.45e+01 1lylA b.40.4.1 25258 d.104.1.1 40714 1qunB 279 2.46e+01 b.2.3.2 22411 b.2.3.2 22412 1hp1A 516 2.46e+01 1behA 187 2.47e+01 1a44 b.17.1.1 23700 2dtr 226 2.49e+01 1bi0 a.4.5.24 16193 a.76.1.1 18399 b.34.1.2 24450 1c5lH 259 2.50e+01 5ptp 1ahtH 259 2.54e+01 5ptp 1bf8 205 2.55e+01 1qpxA b.1.11.1 22332 b.7.2.1 23214 1mal 421 2.64e+01 2mprA f.4.3.2 43784 1ewnA 219 2.64e+01 1bnkA b.46.1.2 25762 1ush 550 2.65e+01 1ush d.114.1.1 40923 d.159.1.2 42079 1f15B 218 2.68e+01 1f15B b.10.1.2 23321 8kme2 259 2.77e+01 1ucyE 2bbkH 355 2.80e+01 2bbkH b.69.2.1 27634 1bnkA 216 2.81e+01 1bnkA b.46.1.2 25765 1jh2A 99 2.83e+01 b.35.1.1 63038 1eu3A 210 2.86e+01 1an8 b.40.2.2 25206 d.15.6.1 37795 1kicA 339 2.95e+01 1jb3A 131 2.97e+01 1jc7A b.40.3.2 62833 1hozA 339 2.97e+01 c.70.1.1 65898 1fnhA 271 2.98e+01 1fnhA b.1.2.1 21976 b.1.2.1 21977 b.1.2.1 21978 1eur 365 2.99e+01 1eut b.68.1.1 27607 1j8rA 196 2.99e+01 1j8rA b.2.3.3 62745 1hqkA 154 3.01e+01 c.16.1.1 65902 1qlyA 58 3.03e+01 1bbzA b.34.2.1 24530 1sesA 421 3.08e+01 1sesA a.2.7.1 15710 d.104.1.1 40710 1tbgA 340 3.10e+01 1tbgA b.69.4.1 27649 1d8hA 311 3.11e+01 1d8iA d.63.1.1 39544 1jb9A 316 3.15e+01 1fnc b.43.4.2 62840 c.25.1.1 62841 1uxy 340 3.17e+01 2mbr d.145.1.2 41748 d.146.1.1 41761 1ckaA 57 3.24e+01 1ckaA b.34.2.1 24459 1e54A 332 3.25e+01 1e54A f.4.3.1 59258 1aw5 326 3.47e+01 1b4kA c.1.10.3 29181 2aviA 128 3.48e+01 1swuA b.61.1.1 27411 1g3jB 61 3.48e+01 1g3jB j.71.1.1 46366 1a78A 134 3.51e+01 1c1lA b.29.1.3 24212 1vpfA 102 3.52e+01 1vpfA g.17.1.1 44767 1obwA 175 3.52e+01 2prd b.40.5.1 25416 1sty 150 3.57e+01 1snc b.40.1.1 24812 1ucyE 109 3.59e+01 1ucyE 2madH 373 3.66e+01 2bbkH b.69.2.1 27639 1nbcA 155 3.73e+01 1nbcA b.2.2.2 22390 1jc7A 131 3.73e+01 1jc7A b.40.3.2 62873 1cfzA 162 3.74e+01 1cfzA c.56.1.1 33754 2ms2A 129 3.74e+01 1msc d.85.1.1 40049 1fuxA 166 3.77e+01 1fjjA b.17.1.2 60034 4aahA 571 3.84e+01 4aahA b.70.1.1 27678 2hntE 81 3.91e+01 1ucyH 1g72A 573 3.91e+01 4aahA b.70.1.1 27680 1emwA 88 3.95e+01 1emwA d.27.1.1 38448 1aop 497 3.97e+01 2aop d.58.36.1 39501 d.58.36.1 39502 d.134.1.1 41425 d.134.1.1 41426 2aop 497 3.98e+01 2aop d.58.36.1 39503 d.58.36.1 39504 d.134.1.1 41427 d.134.1.1 41428 1euu 605 3.99e+01 1eut b.1.1.5 21892 b.18.1.1 23713 b.68.1.1 27610