# List of top-scoring protein chains for t2k-100-30-bys 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 1gulA 222 6.65e-03 1pgtA a.45.1.1 17675 c.47.1.5 32969 1gumA 222 7.05e-03 1pgtA a.45.1.1 17683 c.47.1.5 32977 1pd21 199 1.76e-02 1pd21 1iyhA 198 3.52e-02 a.45.1.1 83790 c.47.1.5 83791 1r2rA 248 7.18e-02 c.1.1.1 -5147 6gsvA 217 1.42e-01 1b8xA a.45.1.1 17633 c.47.1.5 32925 1oktA 211 2.10e-01 a.45.1.1 -942 c.47.1.5 -7467 1pgtA 210 2.52e-01 1pgtA a.45.1.1 17515 c.47.1.5 32809 1l2lA 457 4.38e-01 c.72.1.3 77656 1ezfA 340 5.22e-01 1ezfA a.128.1.2 19440 1b4pA 217 5.53e-01 a.45.1.1 83158 c.47.1.5 83159 2gsq 202 5.97e-01 1pd21 a.45.1.1 17715 c.47.1.5 33009 1f3aA 222 6.82e-01 1pgtA a.45.1.1 17701 c.47.1.5 32995 1augA 215 9.62e-01 1a2zA c.56.4.1 33798 1ky9A 448 1.05e+00 b.36.1.4 73198 b.47.1.1 73199 1iu8A 206 1.30e+00 c.56.4.1 71436 1o6zA 303 1.53e+00 c.2.1.5 81107 d.162.1.1 81108 1tbmA 326 1.64e+00 1ky9B 448 1.70e+00 b.36.1.4 73200 b.36.1.4 73201 b.47.1.1 73202 1jdlA 121 1.81e+00 a.3.1.1 66557 1kzhA 555 1.91e+00 c.89.1.1 73361 1f47B 144 2.09e+00 1f46A d.129.4.1 59645 1nhyA 219 2.38e+00 a.45.1.1 80520 c.47.1.5 80521 1gseA 221 2.45e+00 1pgtA a.45.1.1 17667 c.47.1.5 32961 1f7wA 144 2.65e+00 1f46A d.129.4.1 59679 1f46A 140 2.87e+00 1f46A d.129.4.1 59643 1oe8A 211 2.89e+00 a.45.1.1 86905 c.47.1.5 86906 1p5dX 463 2.92e+00 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 1q6oA 216 3.20e+00 c.1.2.3 -5162 1fxxA 482 3.71e+00 1fxxA c.55.3.5 33726 1eh2 106 3.82e+00 1eh2 a.39.1.6 17339 1ql3A 99 3.93e+00 1ycc a.3.1.1 15822 1m0uA 249 4.01e+00 a.45.1.1 78359 c.47.1.5 78360 1fwkA 296 4.12e+00 1fwkA d.14.1.5 37576 d.58.26.1 39398 1k3lA 221 4.15e+00 a.45.1.1 77229 c.47.1.5 77230 1k3yA 221 4.25e+00 a.45.1.1 77245 c.47.1.5 77246 1qumA 285 4.35e+00 1qumA c.1.15.1 29393 1d7kA 421 4.64e+00 7odcA b.49.2.3 26486 c.1.6.1 28648 1uekA 275 4.69e+00 d.14.1.5 88483 d.58.26.5 88484 1n55A 251 4.83e+00 c.1.1.1 80007 1kf6C 130 5.06e+00 f.21.2.2 72399 1j93A 353 5.09e+00 c.1.22.1 66454 1qmvA 197 5.27e+00 1qq2A c.47.1.10 33066 1do0A 442 5.57e+00 1do0A c.37.1.20 32432 1eu8A 409 5.60e+00 1eu8A c.94.1.1 59502 1k2yX 463 5.73e+00 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1vaoA 560 5.90e+00 1qltA d.58.32.1 39461 d.145.1.1 41724 1izoA 417 5.92e+00 a.104.1.1 83851 1e8gA 560 5.94e+00 1qltA d.58.32.1 39455 d.145.1.1 41718 1qtwA 285 6.07e+00 1qumA c.1.15.1 29392 1lehA 364 6.12e+00 1bw9A c.2.1.7 30268 c.58.1.1 33916 1mxgA 435 6.15e+00 b.71.1.1 85193 c.1.8.1 85194 1ny1A 240 6.46e+00 c.6.2.3 86395 1amk 251 6.71e+00 1amk c.1.1.1 28503 1qltA 560 6.85e+00 1qltA d.58.32.1 39457 d.145.1.1 41720 1ne2A 200 7.05e+00 c.66.1.32 85586 1kv8A 216 7.54e+00 c.1.2.3 73054 1e9gA 286 7.66e+00 1wgjA b.40.5.1 59393 1im5A 180 7.69e+00 unknown_sccs 66211 1ig3A 263 8.39e+00 1ig3A b.82.6.1 62358 c.100.1.1 62359 1aurA 218 9.63e+00 1auoA c.69.1.14 34718 1ei6A 406 9.77e+00 unknown_sccs -8436 1ugpB 226 1.00e+01 1ireB 228 1.03e+01 b.34.4.4 76770 1h72C 296 1.04e+01 d.14.1.5 60712 d.58.26.1 60713 1wgjA 286 1.06e+01 1wgjA b.40.5.1 25397 1e9gB 286 1.07e+01 1wgjA b.40.5.1 59394 8prkA 287 1.07e+01 1wgjA b.40.5.1 25395 1k7kA 221 1.07e+01 c.51.4.1 72104 1ejxA 100 1.13e+01 d.8.1.1 83182 1dugA 234 1.17e+01 1b8xA a.45.1.1 17718 c.47.1.5 33012 1ozhA 566 1.18e+01 c.31.1.3 -6737 c.36.1.5 -6895 c.36.1.9 -6935 1kwgA 645 1.20e+01 b.71.1.1 77561 c.1.8.1 77562 c.23.16.5 77563 1d5tA 433 1.22e+01 1gnd c.3.1.3 30422 d.16.1.6 37986 1poiB 260 1.25e+01 1poiB unknown_sccs 34155 1uf2A 1019 1.26e+01 unknown_sccs -12036 1auoA 218 1.27e+01 1auoA c.69.1.14 34716 1aijL 281 1.29e+01 6prcL f.26.1.1 43461 1n82A 331 1.31e+01 c.1.8.3 -5306 1fwcA 100 1.31e+01 1ubpA d.8.1.1 37331 2kauA 100 1.32e+01 1ubpA d.8.1.1 37335 1ua4A 455 1.33e+01 c.72.1.3 -8416 1rzhL 281 1.37e+01 f.26.1.1 -12215 1nofA 383 1.39e+01 b.71.1.2 -4668 c.1.8.3 -5339 1okrA 123 1.40e+01 unknown_sccs -235 1bp3A 191 1.40e+01 1huw a.26.1.1 16838 2oatA 439 1.40e+01 2dkb c.67.1.4 34452 8prkB 287 1.45e+01 1wgjA b.40.5.1 25396 1gc5A 467 1.48e+01 1gc5A c.72.1.3 60429 1uocA 289 1.51e+01 unknown_sccs -7671 1gnd 447 1.60e+01 1gnd c.3.1.3 30423 d.16.1.6 37987 1f9aA 168 1.61e+01 1f9aA c.26.1.3 31602 3nul 130 1.62e+01 3nul d.110.1.1 40891 1gu7A 364 1.65e+01 b.35.1.2 83321 c.2.1.1 83322 1n2eA 300 1.66e+01 c.26.1.4 85268 1ltqA 301 1.71e+01 c.108.1.9 78208 c.37.1.1 78209 1g61A 228 1.74e+01 1g61A d.126.1.1 41126 1tph1 247 1.80e+01 1amk 1owfA 99 1.84e+01 a.55.1.1 87487 1ihfA 99 1.91e+01 1huuA a.55.1.1 17893 1cviA 342 1.92e+01 1cviA c.60.1.2 33989 1b8dA 164 1.92e+01 1cpcA a.1.1.3 15665 1gks 78 1.92e+01 1cc5 a.3.1.1 15909 1mopA 300 1.94e+01 c.26.1.4 85035 1nd6A 354 1.95e+01 c.60.1.2 80407 1d9eA 284 1.96e+01 1d9eA c.1.10.4 29195 1q9iA 571 1.98e+01 a.138.1.3 -2051 c.3.1.4 -6041 d.168.1.1 -11607 1dcfA 136 2.07e+01 1dcfA c.23.1.2 31124 1b6g 310 2.15e+01 1b6g c.69.1.8 34661 1hybA 181 2.15e+01 1f9aA c.26.1.3 61399 1ktaA 365 2.17e+01 e.17.1.1 77533 1f0jA 377 2.21e+01 1f0jA a.125.1.1 19346 1e39A 571 2.21e+01 1qjdA a.138.1.3 19694 c.3.1.4 30431 d.168.1.1 42314 1fqjC 42 2.28e+01 1fqjC j.51.1.1 46332 1a0k 131 2.28e+01 3nul d.110.1.1 40892 1jb0L 154 2.29e+01 1jb0L f.31.1.1 62829 1m5q1 130 2.31e+01 1cwvA 492 2.32e+01 1cwvA b.1.14.1 22373 b.1.14.1 22374 b.1.14.1 22375 b.1.14.1 22376 d.169.1.3 42442 2hpaA 342 2.33e+01 1cviA c.60.1.2 33985 1fxqA 267 2.35e+01 1d9eA c.1.10.4 60108 1qz9A 416 2.38e+01 c.67.1.3 -8180 1eexA 554 2.39e+01 1dioA c.1.19.3 29650 1ofcX 304 2.40e+01 a.4.1.3 -195 unknown_sccs -199 unknown_sccs -978 1qjdA 571 2.42e+01 1qjdA a.138.1.3 19695 c.3.1.4 30432 d.168.1.1 42315 1cot 129 2.42e+01 1ycc a.3.1.1 15899 1qciA 262 2.43e+01 1qi7A d.165.1.1 42201 1m64A 571 2.47e+01 a.138.1.3 78683 c.3.1.4 78684 d.168.1.1 78685 1vhqA 232 2.48e+01 c.23.16.2 -6514 1j24A 143 2.50e+01 c.52.1.20 84008 1oatA 439 2.60e+01 2dkb c.67.1.4 34461 1ass 159 2.64e+01 1a6dA c.8.5.2 30818 1nqcA 217 2.67e+01 d.3.1.1 86024 2cevA 299 2.69e+01 1d3vA c.42.1.1 32576 1ede 310 2.71e+01 1b6g c.69.1.8 34662 1d6aB 262 2.74e+01 1qi7A d.165.1.1 42198 1dioA 554 2.75e+01 1dioA c.1.19.3 29656 1f7cA 231 2.76e+01 1f7cA a.116.1.1 19107 1kssA 571 2.76e+01 a.138.1.3 72928 c.3.1.4 72929 d.168.1.1 72930 1iknD 236 2.77e+01 1iknD d.211.1.1 19171 1lb6A 160 2.86e+01 b.8.1.1 73798 1ekfA 365 2.89e+01 1ekfA e.17.1.1 59445 1r1dA 247 2.89e+01 unknown_sccs -8335 1jfbA 404 2.91e+01 a.104.1.1 66624 1eb7A 323 2.93e+01 1eb7A a.3.1.5 59404 a.3.1.5 59405 1v1rB 342 2.98e+01 1lj1A 571 3.03e+01 a.138.1.3 78023 c.3.1.4 78024 d.168.1.1 78025 1kwkA 645 3.07e+01 b.71.1.1 77565 c.1.8.1 77566 c.23.16.5 77567 1l0lK 56 3.08e+01 f.23.15.1 84497 1es6A 296 3.10e+01 1es6A b.31.1.1 83048 b.31.1.1 83049 1cmnA 402 3.14e+01 1rom a.104.1.1 18958 1taq 832 3.16e+01 1taq a.60.7.1 18082 c.120.1.2 33352 c.55.3.5 33698 e.8.1.1 42991 1n16A 381 3.16e+01 a.83.1.1 79781 d.128.1.2 79782 1k4nA 192 3.17e+01 d.32.1.5 72059 1dtwB 342 3.17e+01 1qs0B c.36.1.7 31828 c.48.1.2 33102 1kt8A 365 3.19e+01 e.17.1.1 77531 1kn1B 161 3.21e+01 a.1.1.3 77456 1jg5A 83 3.21e+01 d.205.1.1 66666 1p0hA 318 3.23e+01 d.108.1.1 -10802 1ftpA 133 3.24e+01 1hmt b.60.1.2 27199 1ikoP 178 3.31e+01 b.6.1.5 71243 1kp0A 402 3.32e+01 c.55.2.1 72834 d.127.1.1 72835 1h75A 81 3.36e+01 1h75A c.47.1.1 60716 1h1nA 305 3.36e+01 c.1.8.3 70855 1asx 159 3.41e+01 1a6dA c.8.5.2 30821 1aw9 216 3.43e+01 1gnwA a.45.1.1 17736 c.47.1.5 33030 1ltlA 279 3.52e+01 b.40.4.11 84701 1i45A 248 3.53e+01 1amk c.1.1.1 61665 1ej2A 181 3.60e+01 1f9aA c.26.1.3 59414 1p1cA 199 3.68e+01 c.66.1.16 87669 1ny6A 267 3.76e+01 c.37.1.20 -7221 1cx8A 639 3.80e+01 1cx8B a.48.2.1 17782 c.8.4.1 30763 c.56.5.5 33851 1ufhA 180 3.82e+01 d.108.1.1 88485 1de4C 640 3.92e+01 1cx8B a.48.2.1 17779 c.8.4.1 30760 c.56.5.5 33848 1tbgE 68 3.92e+01 1tbgE a.137.3.1 19630 2apsA 162 3.97e+01 1yaiA b.1.8.1 22298