# List of top-scoring protein chains for t2k-100-30-bys-scores 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 2bcoA 350 9.86e-27 1yw4A 341 4.91e-26 1qmuA 380 1.63e-05 1qmuA b.3.2.1,c.56.5.1 22534,33827 1h8lA 380 1.78e-05 b.3.2.1,c.56.5.1 65737,65738 2bo9A 308 1.99e-02 2c1cA 312 9.86e-02 1aye 401 1.46e-01 1aye c.56.5.1,d.58.3.1 33824,39065 1jqgA 433 1.62e-01 c.56.5.1,d.58.3.1 71791,71792 1ag8A 499 3.27e-01 1bpwA c.82.1.1 35341 1dtdA 303 3.43e-01 1aye c.56.5.1 33823 1f7wA 144 5.30e-01 1f46A d.129.4.1 59679 1o04A 500 1.00e+00 c.82.1.1 86508 1f47B 144 1.06e+00 1f46A d.129.4.1 59645 1vp4A 425 1.24e+00 1b9dA 163 1.28e+00 1b9dA c.55.3.2 33649 1f46A 140 2.51e+00 1f46A d.129.4.1 59643 2aqjA 538 2.82e+00 1nstA 325 3.09e+00 1nstA c.37.1.5 31951 2conA 79 3.70e+00 1akq 147 3.82e+00 5nul c.23.5.1 31159 1kwmA 402 3.92e+00 c.56.5.1,d.58.3.1 73079,73080 1bavA 309 4.09e+00 1aye c.56.5.1 33806 1xwyA 264 4.41e+00 1hdcA 253 4.46e+00 1e6wA c.2.1.2 29862 1azl 147 5.09e+00 5nul c.23.5.1 31154 1yme 309 5.27e+00 1aye c.56.5.1 33804 2ajrA 331 5.29e+00 1m4lA 307 5.35e+00 c.56.5.1 78604 1hyvA 166 5.54e+00 1b9dA c.55.3.2 61424 1akw 147 6.13e+00 5nul c.23.5.1 31153 1j9eA 147 6.14e+00 c.23.5.1 62756 1jvbA 347 6.15e+00 b.35.1.2,c.2.1.1 77181,77182 2ctb 307 6.28e+00 1aye c.56.5.1 33803 1bu5A 147 6.93e+00 5nul c.23.5.1 31155 2fflA 756 6.97e+00 1rpnA 335 7.23e+00 c.2.1.2 97708 2ctc 307 7.25e+00 1aye c.56.5.1 33802 1akr 147 7.35e+00 1rcf c.23.5.1 31152 1t2aA 375 7.46e+00 c.2.1.2 99078 1akt 147 7.66e+00 5nul c.23.5.1 31157 2fx2 147 7.93e+00 1rcf c.23.5.1 31158 1ex2A 189 7.97e+00 1ex2A c.51.4.2 33225 1lam 484 8.53e+00 1lam c.50.1.1,c.56.5.3 33166,33829 1ki9A 192 8.67e+00 c.37.1.1 84404 1u2fA 90 8.88e+00 1u2fA d.58.7.1 39168 1i24A 404 8.89e+00 c.2.1.2 83663 1nmoA 247 8.91e+00 c.135.1.1 91980 1xfjA 261 1.03e+01 d.194.1.2 109585 1f4pA 147 1.03e+01 5nul c.23.5.1 59651 1cz1A 394 1.13e+01 1cz1A c.1.8.3 28839 1hx1B 114 1.20e+01 1hx1B a.7.7.1 61350 1a8y 367 1.21e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1g8lA 411 1.26e+01 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1m2rA 327 1.36e+01 d.144.1.7 84760 1ihnA 113 1.36e+01 1ihnA c.103.1.1 62388 2hsdA 253 1.37e+01 1e6wA c.2.1.2 29866 1gnxA 479 1.37e+01 c.1.8.4 76241 1bl3A 160 1.40e+01 1b9dA c.55.3.2 33655 1bde 35 1.44e+01 1bde j.11.1.1 46142 1xhkA 187 1.45e+01 1h2vZ 156 1.51e+01 d.58.7.1 76595 1wyuB 474 1.51e+01 1yj7A 171 1.53e+01 1wpgA 994 1.55e+01 1cpy 421 1.56e+01 1ivyA c.69.1.5 34651 1tkeA 224 1.56e+01 1lap 488 1.63e+01 1lam c.50.1.1,c.56.5.3 33171,33834 1ysc 421 1.73e+01 1ivyA c.69.1.5 34652 1d6mA 653 1.73e+01 1d6mA e.10.1.1 43248 1h6kZ 98 1.74e+01 d.58.7.1 60686 1oglA 283 1.75e+01 a.204.1.1 92922 1su4A 994 1.78e+01 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 98993,98994,98995,98996 2d1yA 256 1.85e+01 1db3A 372 1.93e+01 1db3A c.2.1.2 29813 1gdhA 320 1.98e+01 1gdhA c.2.1.4,c.23.12.1 30095,31355 1z5rA 306 2.00e+01 1eqcA 394 2.01e+01 1cz1A c.1.8.3 28811 1a6o 332 2.03e+01 1a6o 1qu9A 128 2.04e+01 1qu9A d.79.1.1 39755 1qu9C 128 2.04e+01 1qu9A d.79.1.1 39757 1vpdA 299 2.10e+01 1tyyA 339 2.14e+01 1iyxA 432 2.16e+01 c.1.11.1,d.54.1.1 83815,83816 1gmxA 108 2.17e+01 c.46.1.3 65355 1qo2A 241 2.20e+01 1qo2A c.1.2.1 28533 1djxB 624 2.23e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17343,23160,29588 2sqcA 631 2.24e+01 2sqcA a.102.4.2,a.102.4.2 18854,18855 1xq6A 253 2.26e+01 1qatB 622 2.30e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17355,23172,29600 1d8yA 605 2.36e+01 1xwl c.55.3.5,e.8.1.1 33684,42977 1lp4A 332 2.46e+01 d.144.1.7 74170 1wolA 122 2.50e+01 1dtc 27 2.52e+01 j.7.1.1 46109 1om1A 332 2.55e+01 d.144.1.7 93347 1v8fA 276 2.55e+01 c.26.1.4 100503 2evaA 307 2.56e+01 1x0vA 354 2.59e+01 1x74A 360 2.61e+01 1gqeA 365 2.61e+01 e.38.1.1 70351 1f0kA 364 2.65e+01 1f0kA c.87.1.2 35465 1fp3A 402 2.66e+01 1fp3A a.102.1.3 18842 1bllE 488 2.67e+01 1lam c.50.1.1,c.56.5.3 33170,33833 1rq2A 382 2.75e+01 c.32.1.1,d.79.2.1 105048,105049 1wg8A 285 2.76e+01 2b81A 323 2.76e+01 1qjcA 158 2.79e+01 1b6tA c.26.1.3 63328 1q5yA 85 2.79e+01 d.58.18.4 95950 6cpa 307 2.86e+01 1aye c.56.5.1 33816 1rwrA 301 2.90e+01 b.80.1.11 97990 1qhtA 775 2.94e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1vhuA 211 2.95e+01 c.50.1.2 100703 1dg9A 157 3.01e+01 1dg9A c.44.1.1 32637 1im4A 221 3.04e+01 e.8.1.7 62581 1s95A 333 3.09e+01 d.159.1.3 105375 1eexB 224 3.12e+01 1dioB c.51.3.1 33213 9ldtA 332 3.15e+01 3ldh c.2.1.5,d.162.1.1 30154,42121 1qasA 622 3.16e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17340,23157,29585 1wzcA 249 3.18e+01 1g0cA 364 3.24e+01 7a3hA c.1.8.3 60165 2cvlA 124 3.30e+01 2kfnA 605 3.41e+01 1xwl c.55.3.5,e.8.1.1 33682,42975 1g94A 448 3.47e+01 b.71.1.1,c.1.8.1 65169,65170 1se7A 83 3.50e+01 1dbxA 158 3.52e+01 1dbuA d.116.1.1 40928 1y8qB 640 3.53e+01 1k0dA 260 3.54e+01 a.45.1.1,c.47.1.5 67930,67931 1txpA 28 3.55e+01 1g01A 364 3.56e+01 7a3hA c.1.8.3 60161 1hxhA 253 3.63e+01 c.2.1.2 76725 1dxy 333 3.67e+01 1dxy c.2.1.4,c.23.12.1 30094,31354 1qcxA 359 3.68e+01 1qcxA b.80.1.2 28028 1c3oE 1073 3.69e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18564,31493,31685,31686,41530,41531 1gn0A 108 3.79e+01 c.46.1.3 65358 1kdgA 546 3.80e+01 c.3.1.2,d.16.1.1 77337,77338 1b37B 472 3.82e+01 1b37B c.3.1.2,d.16.1.5 30390,37954 1rkiA 102 3.86e+01 1vqvA 306 3.91e+01 1h3fA 432 3.92e+01 c.26.1.1,d.66.1.4 76631,76632 1b5qA 472 4.04e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 1i7dA 659 4.10e+01 1d6mA e.10.1.1 61886 1ktjA 129 4.10e+01 b.1.18.7 72974 1x59A 73 4.12e+01 1keeE 1073 4.15e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68508,68509,68510,68511,68512,68513 2av5A 120 4.16e+01 1vig 71 4.20e+01 1vih d.51.1.1 38806 2al6A 375 4.27e+01 1h49A 512 4.27e+01 c.1.8.4 83477 1b6tA 159 4.29e+01 1b6tA c.26.1.3 31600 1lbd 282 4.30e+01 1lbd a.123.1.1 19279 1gr5A 547 4.31e+01 i.16.1.1 65478 1p1xA 260 4.42e+01 c.1.10.1 104060 1nhp 447 4.47e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 1vmfA 145 4.49e+01 1xa3A 437 4.50e+01 1jcjA 260 4.51e+01 c.1.10.1 66499 1q1rA 431 4.51e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1hjzA 192 4.55e+01 c.50.1.2 83520 1djqA 729 4.55e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 1lldA 319 4.55e+01 3ldh c.2.1.5,d.162.1.1 30177,42144 1kl7A 514 4.61e+01 c.79.1.1 72678 1h1nA 305 4.62e+01 c.1.8.3 70855 1zy7A 403 4.64e+01 1yfnA 118 4.64e+01 1m4jA 142 4.74e+01 d.109.1.2 78602 2c3zA 222 4.75e+01 2f3nA 76 4.76e+01 2aj7A 163 4.79e+01 1kjnA 157 4.84e+01 c.115.1.1 72614 1djnA 729 4.86e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 1o77D 146 4.87e+01 c.23.2.1 81128 1jdpA 441 4.88e+01 c.93.1.1 62906 1jbkA 195 4.88e+01 c.37.1.20 71631 1fgkA 310 4.90e+01 1fgkA d.144.1.7 41693 1jdbB 1073 4.93e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18574,31503,31705,31706,41550,41551 1dbfA 127 4.96e+01 2chsA d.79.1.2 39761 1diaA 306 4.99e+01 1a4iA c.2.1.7,c.58.1.2 30280,33928 1xjjA 644 5.01e+01 1v7cA 351 5.04e+01 c.79.1.1 100446 1nhs 447 5.05e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 1jclA 260 5.06e+01 c.1.10.1 66501 1vrpA 381 5.07e+01 2cybA 323 5.08e+01 1spvA 184 5.10e+01 c.50.1.2 98957 1tz9A 367 5.11e+01 c.1.15.6 107466 1nonA 179 5.12e+01 c.61.1.1 103868 1vkwA 218 5.15e+01 d.90.1.2 108695 1g6wA 261 5.19e+01 1hqoA a.45.1.1,c.47.1.5 17751,33045 1bdb 277 5.20e+01 1bdb c.2.1.2 29874 2chsA 127 5.29e+01 2chsA d.79.1.2 39764 1hd7A 318 5.29e+01 1bix d.151.1.1 41780 1y14B 171 5.30e+01 2au3A 407 5.31e+01 1qf6A 642 5.33e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1sqc 631 5.35e+01 2sqcA a.102.4.2,a.102.4.2 18858,18859 1ceo 343 5.39e+01 1ceo c.1.8.3 28808 1ou8A 111 5.39e+01 b.136.1.1 93543 1cy9A 264 5.42e+01 1ecl e.10.1.1 43236 1xhcA 367 5.43e+01 1yqeA 282 5.48e+01 2f02A 323 5.54e+01 1zbfA 142 5.61e+01 1fyxA 149 5.62e+01 1fyvA c.23.2.1 31128 1ox8A 107 5.66e+01 b.136.1.1 93671 1rocA 155 5.68e+01 b.1.22.1 97673 1qrrA 394 5.71e+01 1qrrA c.2.1.2 29824 1v71A 323 5.72e+01 2awdA 323 5.72e+01 1guzA 310 5.77e+01 c.2.1.5,d.162.1.1 65586,65587 1h6kX 97 5.77e+01 d.58.7.1 60684 1lpuA 332 5.78e+01 d.144.1.7 74177 1mjc 69 5.79e+01 1mjc b.40.4.5 25319 1t6cA 315 5.81e+01 c.55.1.8,c.55.1.8 106558,106559 1wznA 252 5.82e+01 1b37A 472 5.83e+01 1b37B c.3.1.2,d.16.1.5 30389,37953 1o77E 146 5.85e+01 c.23.2.1 81129 1a4iB 301 5.88e+01 1a4iA c.2.1.7,c.58.1.2 30279,33927 1aj4 161 5.93e+01 1ncx a.39.1.5 17244 1v3wA 173 5.97e+01 b.81.1.5 100291 1p9bA 442 6.02e+01 c.37.1.10 94385 1m6nA 802 6.09e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 78697,78698,78699,78700 2bi7A 384 6.11e+01 1a4iA 301 6.11e+01 1a4iA c.2.1.7,c.58.1.2 30278,33926 1rijA 25 6.13e+01 k.32.1.1 104951 2mhr 118 6.18e+01 2mhr a.24.4.1 16581 1keeC 1073 6.29e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68500,68501,68502,68503,68504,68505 1cs0A 1073 6.29e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1dsj 28 6.31e+01 j.11.1.1 46139 1kkoA 413 6.33e+01 c.1.11.2,d.54.1.1 68675,68676 1phr 157 6.34e+01 1dg9A c.44.1.1 32635 1tf5A 844 6.35e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 106834,106835,106836,106837 1wr8A 231 6.37e+01 1e55A 512 6.37e+01 1e70M c.1.8.4 28934 1xk7A 408 6.37e+01 2d4qA 257 6.43e+01 1cs0C 1073 6.49e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18559,31488,31675,31676,41520,41521 1pyfA 312 6.53e+01 c.1.7.1 95334 1eulA 994 6.53e+01 1eulA 1dbwA 126 6.55e+01 1dbwA c.23.1.1 31095 1c3oA 1073 6.56e+01 1c3oA a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18562,31491,31681,31682,41526,41527 1qh4A 380 6.63e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 1itzA 675 6.78e+01 c.36.1.10,c.36.1.6,c.48.1.1 76797,76798,76799 1kte 105 6.87e+01 1kte c.47.1.1 32771 2a35A 215 6.89e+01 1iqcA 308 6.91e+01 a.3.1.5,a.3.1.5 66266,66267 1derA 547 6.91e+01 1derA 1lwjA 441 6.94e+01 b.71.1.1,c.1.8.1 74303,74304 1vgwA 231 6.95e+01 c.68.1.13 100612 1dcjA 81 6.95e+01 1dcjA d.68.3.3 59115 1kamA 194 6.96e+01 c.26.1.3 72254 1ykfA 352 6.96e+01 1pedA b.35.1.2,c.2.1.1 24757,29773 1x1rA 178 6.96e+01 1cjcA 460 6.98e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1dkuA 317 6.98e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1keeG 1073 6.99e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68516,68517,68518,68519,68520,68521 1klnA 605 7.00e+01 1xwl c.55.3.5,e.8.1.1 33693,42986 1wurA 220 7.03e+01 1fliA 98 7.06e+01 1awcA a.4.5.21 16160 1lqpA 135 7.06e+01 d.32.1.2 78151 1g5cA 170 7.09e+01 1g5cA c.53.2.1 60264 1xovA 326 7.09e+01 1o94A 729 7.11e+01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 1hm6A 346 7.24e+01 1avc a.65.1.1 18147 1b0aA 288 7.28e+01 1a4iA c.2.1.7,c.58.1.2 30286,33934 2gl5A 410 7.28e+01 1esc 306 7.30e+01 1esc c.23.10.1 31334 1iv0A 98 7.30e+01 c.55.3.8 90706 1bxrA 1073 7.31e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18570,31499,31697,31698,41542,41543 1rliA 184 7.33e+01 c.23.5.6 97647 1bix 287 7.34e+01 1bix d.151.1.1 41781 1e9iA 431 7.41e+01 c.1.11.1,d.54.1.1 64818,64819 1ldnA 316 7.42e+01 1hyhA c.2.1.5,d.162.1.1 30166,42133 1xznA 179 7.44e+01 2vil 126 7.46e+01 2vil d.109.1.1 40830 2arkA 188 7.56e+01 1hqoA 258 7.60e+01 1hqoA a.45.1.1,c.47.1.5 17749,33043 1ofwA 296 7.65e+01 a.138.1.1 92850 1w6tA 444 7.69e+01 1c3kA 147 7.84e+01 1jotA b.77.3.1 27984 1ayx 492 7.92e+01 1ayx a.102.1.1 18825 1aqm 453 7.93e+01 1smd b.71.1.1,c.1.8.1 27717,28704 1t0fA 276 7.94e+01 1dbuA 158 7.98e+01 1dbuA d.116.1.1 40930 1ku3A 73 8.11e+01 a.4.13.2 73000 1f6yA 262 8.11e+01 1f6yA c.1.21.2 29673 1xfsA 178 8.13e+01 d.129.3.5 109589 1k3sA 113 8.15e+01 d.198.1.1 68120 1ngkA 128 8.16e+01 a.1.1.1 85673 1h4pA 408 8.19e+01 c.1.8.3 90617 2aehA 369 8.21e+01 1c3mA 147 8.32e+01 1jotA b.77.3.1 27983 1kczA 413 8.32e+01 c.1.11.2,d.54.1.1 68451,68452 1f4tA 368 8.37e+01 1f4tA a.104.1.1 18973 1juk 248 8.41e+01 1a53 c.1.2.4 28567 1dkrA 317 8.42e+01 1dkuA c.61.1.2,c.61.1.2 34114,34115 1f20A 435 8.48e+01 b.43.4.1,c.25.1.4 64932,64933 2pfkA 320 8.49e+01 3pfk c.89.1.1 35577 2cdpA 160 8.49e+01 1kfd 605 8.49e+01 1xwl c.55.3.5,e.8.1.1 33694,42987 1ozjA 144 8.54e+01 d.164.1.1 93846 1gnlA 544 8.58e+01 e.26.1.1 70287 1ynuA 473 8.62e+01 1afrA 345 8.65e+01 1afrA a.25.1.2 16805 2ahxA 617 8.69e+01 1khtA 192 8.83e+01 c.37.1.1 84401 2fvgA 340 8.86e+01 1opjA 293 8.92e+01 d.144.1.7 87230 2d4rA 147 8.94e+01 2bfxA 284 8.98e+01 1obr 326 9.00e+01 1aye c.56.5.2 33828