# List of top-scoring protein chains for t2k-100-30-str2-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 1qdbA 473 8.28e-01 1qdbA a.138.1.3 19688 1klxA 138 1.17e+00 a.118.18.1 77440 1cpt 412 2.54e+00 1cpt a.104.1.1 18968 1josA 128 3.31e+00 d.52.7.1 84191 1aipC 196 3.87e+00 1tfe a.5.2.2,d.43.1.1 58930,58931 2cunA 410 5.03e+00 1io1A 398 5.29e+00 1io1A e.32.1.1 62611 1sz9A 144 6.46e+00 a.118.9.4 106139 1b0b 142 8.63e+00 2fal a.1.1.2 15010 1flp 142 8.72e+00 1flp a.1.1.2 15011 1moh 142 8.72e+00 1flp a.1.1.2 15012 1z3xA 238 1.03e+01 2d7vA 162 1.05e+01 2cy7A 396 1.05e+01 1qi7A 253 1.09e+01 1qi7A d.165.1.1 42210 1tmxA 293 1.11e+01 1ytzT 107 1.15e+01 1fjgI 128 1.24e+01 1fjfI d.14.1.1 37559 1knqA 175 1.30e+01 c.37.1.17 72786 2cwyA 94 1.31e+01 2sas 185 1.36e+01 2sas a.39.1.5 17258 1umgA 362 1.42e+01 d.280.1.1 107956 1opoA 348 1.50e+01 b.121.4.7 87240 1ewqA 765 1.61e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1oneA 436 1.67e+01 4enl c.1.11.1,d.54.1.1 29200,38844 2mgg 154 1.74e+01 1a6m a.1.1.2 15069 1necA 216 1.78e+01 1vfrA d.90.1.1 40249 1qbjA 81 1.83e+01 1qbjA a.4.5.19 16155 1pyp 285 1.87e+01 1wgjA b.40.5.1 25409 1g24A 211 1.93e+01 1g24A d.166.1.1 42270 2a9kB 223 1.93e+01 1q3eA 207 1.99e+01 b.82.3.2 95669 2b7eA 59 2.05e+01 2al1A 436 2.06e+01 1yviA 149 2.09e+01 1sglA 209 2.10e+01 d.124.1.1 105536 1y1xA 191 2.11e+01 2oneA 436 2.13e+01 4enl c.1.11.1,d.54.1.1 29203,38847 102m 154 2.13e+01 1a6m a.1.1.2 15073 1e9gA 286 2.19e+01 1wgjA b.40.5.1 59393 1b3oA 514 2.21e+01 1ak5 c.1.5.1 28640 1c02A 166 2.24e+01 1qspA a.24.10.2 16633 1f3aA 222 2.28e+01 1pgtA a.45.1.1,c.47.1.5 17701,32995 1hh8A 213 2.29e+01 1e96B a.118.8.1 61042 1mod 154 2.30e+01 1a6m a.1.1.2 15107 1wm5A 208 2.35e+01 1e96B 203 2.37e+01 1e96B a.118.8.1 19211 1g4uS 383 2.38e+01 1g4uS a.24.11.1,c.45.1.2 16643,32691 3nul 130 2.54e+01 3nul d.110.1.1 40891 1f52A 468 2.56e+01 1lgr d.15.9.1,d.128.1.1 37839,41169 1e9gB 286 2.56e+01 1wgjA b.40.5.1 59394 1n6bA 473 2.61e+01 a.104.1.1 85359 2al2A 436 2.62e+01 1b4pA 217 2.64e+01 a.45.1.1,c.47.1.5 83158,83159 1g8pA 350 2.66e+01 1g8pA c.37.1.20 60376 3lynA 136 2.66e+01 1lis a.19.1.1 16413 1fo4A 1332 2.70e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 17910,37695,38586,40227,41416,41758 1mll 154 2.74e+01 1a6m a.1.1.2 15057 2spl 154 2.77e+01 1a6m a.1.1.2 15047 1i1rB 181 2.82e+01 1i1rB a.26.1.1 61548 1ytaA 180 2.84e+01 1qspA 165 2.86e+01 1qspA a.24.10.2 16639 1mgn 154 2.91e+01 1a6m a.1.1.2 15097 1v97A 1332 2.92e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 108436,108437,108438,108439,108440,108441 103m 154 2.97e+01 1a6m a.1.1.2 15124 1fzcA 87 2.98e+01 1fzcA h.1.8.1 45590 1yppA 286 3.02e+01 1wgjA b.40.5.1 25407 2glsA 470 3.08e+01 1lgr d.15.9.1,d.128.1.1 37851,41181 4enl 436 3.13e+01 4enl c.1.11.1,d.54.1.1 29202,38846 1alvA 173 3.16e+01 1alvA a.39.1.8 17370 1efyA 350 3.18e+01 1a26 a.41.1.1,d.166.1.2 17413,42275 8prkB 287 3.18e+01 1wgjA b.40.5.1 25396 1qr6A 584 3.20e+01 1qr6A c.2.1.7,c.58.1.3 30293,33941 1eg3A 261 3.21e+01 1eg3A a.39.1.7,a.39.1.7,b.72.1.1 17376,17377,27805 1mym 154 3.23e+01 1a6m a.1.1.2 15054 1feuA 206 3.30e+01 1feuA b.53.1.1 59801 1dc1A 323 3.34e+01 1dc1A c.52.1.11 33321 1e39A 571 3.41e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 8prkA 287 3.43e+01 1wgjA b.40.5.1 25395 1a26 361 3.44e+01 1a26 a.41.1.1,d.166.1.2 17412,42274 1b8pA 329 3.44e+01 1bmdA c.2.1.5,d.162.1.1 30147,42114 1a0k 131 3.49e+01 3nul d.110.1.1 40892 1mlg 154 3.49e+01 1a6m a.1.1.2 15104 1wpuA 147 3.53e+01 2spo 154 3.54e+01 1a6m a.1.1.2 15053 2c5uA 375 3.54e+01 1psrA 100 3.56e+01 1psrA a.39.1.2 17180 1s35A 214 3.57e+01 a.7.1.1,a.7.1.1 98420,98421 1p68A 102 3.65e+01 k.8.1.1 94158 1p2hA 571 3.67e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1qgpA 77 3.68e+01 1qbjA a.4.5.19 16158 1bzpA 153 3.71e+01 1a6m a.1.1.2 15020 117eA 286 3.73e+01 1wgjA b.40.5.1 25401 2mgb 154 3.75e+01 1a6m a.1.1.2 15102 1q9iA 571 3.78e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1y0pA 571 3.80e+01 1qjdA 571 3.83e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19695,30432,42315 1kssA 571 3.83e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1atiA 505 3.84e+01 1atiA c.51.1.1,d.104.1.1 33196,40745 1wgjA 286 3.85e+01 1wgjA b.40.5.1 25397 2gh1A 301 3.88e+01 2ezvA 269 3.89e+01 1mlo 154 3.93e+01 1a6m a.1.1.2 15085 1m64A 571 3.94e+01 a.138.1.3,c.3.1.4,d.168.1.1 78683,78684,78685 1uaaA 673 3.94e+01 1pjr c.37.1.19,c.37.1.19 32401,32402 1k8kD 300 4.01e+01 d.198.2.1,d.198.2.1 68309,68310 1wpbA 172 4.02e+01 1or7A 194 4.04e+01 a.4.13.2,a.177.1.1 87332,87333 2c0rA 362 4.12e+01 1mbd 153 4.24e+01 1a6m a.1.1.2 15033 2d2sA 235 4.24e+01 1wmqA 147 4.26e+01 1xvhA 129 4.30e+01 1k47A 337 4.32e+01 d.14.1.5,d.58.26.4 72040,72041 1mv8A 436 4.33e+01 a.100.1.4,c.2.1.6,c.26.3.1 85128,85129,85130 1q47A 495 4.47e+01 b.69.12.1 104532 1b26A 416 4.49e+01 1hwyA c.2.1.7,c.58.1.1 30232,33880 1okcA 297 4.50e+01 f.42.1.1 93248 1hw1A 239 4.61e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1bf5A 545 4.66e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 1w3uA 362 4.73e+01 2c6qA 351 4.73e+01 1b3bA 415 4.79e+01 1hwyA c.2.1.7,c.58.1.1 30244,33892 2trcP 217 4.80e+01 1b9yC c.47.1.6 33051 1lj1A 571 4.82e+01 a.138.1.3,c.3.1.4,d.168.1.1 78023,78024,78025 1ab4 477 4.85e+01 1ab4 e.11.1.1 43251 1binA 143 4.90e+01 2gdm a.1.1.2 15231 1bt4A 362 4.93e+01 1bjnA c.67.1.4 34468 1xq8A 140 5.01e+01 1r6uA 437 5.01e+01 c.26.1.1 97163 1mla 309 5.21e+01 1mla c.19.1.1,d.58.23.1 31031,39383 1qwnA 1045 5.30e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1dlwA 116 5.32e+01 1dlyA a.1.1.1 14982 1wkoA 180 5.36e+01 1k0dA 260 5.38e+01 a.45.1.1,c.47.1.5 67930,67931 1xk4C 113 5.39e+01 1fiqB 350 5.46e+01 1fiqB d.87.2.1,d.145.1.3 40229,41760 1fslA 143 5.64e+01 2gdm a.1.1.2 15229 1rtxA 123 5.64e+01 a.1.1.1 97827 1y21A 282 5.67e+01 1cojA 212 5.68e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1y9qA 192 5.71e+01 1a6g 151 5.74e+01 1a6m a.1.1.2 15021 1s69A 124 5.76e+01 a.1.1.1 105305 1nr6A 473 5.77e+01 a.104.1.1 92085 1na6A 404 5.79e+01 b.142.1.1,c.52.1.22 91748,91749 1w33A 181 5.84e+01 2ezk 99 5.85e+01 2ezk a.4.1.2 16027 1htyA 1015 6.00e+01 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 1ee4A 423 6.04e+01 1ee4A a.118.1.1 19128 1hxkA 1015 6.05e+01 a.8.3.1,b.30.5.6,c.6.2.1 83070,83071,83072 1quqB 121 6.12e+01 1quqB b.40.4.3 25305 1hwwA 1015 6.12e+01 a.8.3.1,b.30.5.6,c.6.2.1 83067,83068,83069 1ymmA 191 6.17e+01 1a6m 151 6.21e+01 1a6m a.1.1.2 15018 1lgr 468 6.22e+01 1lgr d.15.9.1,d.128.1.1 37837,41167 2c4jA 218 6.23e+01 1dt6A 473 6.30e+01 1dt6A a.104.1.1 18977 2lgsA 468 6.37e+01 1lgr d.15.9.1,d.128.1.1 37838,41168 1e2xA 243 6.37e+01 1e2xA a.4.5.6,a.78.1.1 16113,18443 1lxyA 409 6.47e+01 d.126.1.4 91154 2a6hA 315 6.53e+01 1ly2A 130 6.54e+01 g.18.1.1,g.18.1.1 74335,74336 1icrA 217 6.54e+01 1vfrA d.90.1.1 62274 2ezl 99 6.55e+01 2ezk a.4.1.2 16026 1gpjA 404 6.56e+01 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1kbuA 349 6.58e+01 a.60.9.1,d.163.1.1 72284,72285 1dk0A 188 6.58e+01 1b2vA d.35.1.1 38530 1utuA 108 6.58e+01 1ghqB 134 6.61e+01 1ghqB g.18.1.1,g.18.1.1 60522,60523 1as4B 37 6.68e+01 1as4B 1guxA 218 6.68e+01 1guxA a.74.1.3 18388 1ykiA 217 6.74e+01 1b2vA 188 6.76e+01 1b2vA d.35.1.1 38532 1l9lA 74 6.79e+01 a.64.1.1 77827 1j0mA 752 6.83e+01 a.102.3.2,b.24.1.1,b.30.5.2 83910,83911,83912 1z2iA 358 6.96e+01 1rrmA 386 6.98e+01 e.22.1.2 105081 1tu9A 134 7.00e+01 a.1.1.2 107320 1vcsA 102 7.11e+01 1rsy 152 7.13e+01 1rsy b.7.1.2 23192 1g6wA 261 7.15e+01 1hqoA a.45.1.1,c.47.1.5 17751,33045 1si6X 282 7.16e+01 1ad6 185 7.17e+01 1guxA a.74.1.3 18390 5csmA 256 7.17e+01 5csmA a.130.1.2 19494 1bc3 319 7.30e+01 1avc a.65.1.1 18175 1ixmB 192 7.37e+01 1ixmA d.123.1.1 41115 2bivA 243 7.41e+01 1vqwA 457 7.48e+01 1fs7A 485 7.48e+01 1qdbA a.138.1.3 19691 1kfuS 184 7.57e+01 a.39.1.8 68574 1pa7A 130 7.62e+01 a.40.1.1 94410 1pdz 434 7.65e+01 4enl c.1.11.1,d.54.1.1 29215,38859 2bgiA 272 7.69e+01 1k9uA 78 7.69e+01 a.39.1.10 84348 1be3A 446 7.76e+01 1be3A d.185.1.1,d.185.1.1 58950,58951 1aqdA 192 7.88e+01 1iakA b.1.1.2,d.19.1.1 21585,38159 1h6qA 168 7.90e+01 1h6qA b.88.1.2 60692 1cl2A 395 7.95e+01 1cl2A c.67.1.3 34397 1cl1A 395 8.02e+01 1cl2A c.67.1.3 34395 1i5pA 633 8.03e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 1v9dA 340 8.04e+01 a.207.1.1 100535 1hssA 124 8.10e+01 1bea a.52.1.2 17819 1u6zA 513 8.12e+01 1t3tA 1303 8.12e+01 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 2acjA 66 8.26e+01 1l5aA 436 8.33e+01 c.43.1.2,c.43.1.2 75923,75924 1ntfA 282 8.33e+01 d.151.1.2 92104 1ofcX 304 8.40e+01 a.4.1.3,a.4.1.13,a.187.1.1 92826,92827,92828 1w6kA 732 8.41e+01 1jw3A 140 8.41e+01 d.208.1.1 67373 1zx4A 192 8.42e+01 171l 164 8.50e+01 1l92 d.2.1.3 36962 1xw5A 217 8.54e+01 1tcrA 202 8.56e+01 1tcrA b.1.1.1,b.1.1.2 20605,21549 1k78A 149 8.67e+01 a.4.1.5,a.4.1.5 68255,68256 1m1jA 491 8.70e+01 h.1.8.1 74369 1cb8A 678 8.73e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1b8yA 167 8.82e+01 1hfc d.92.1.11 40377 1s9rA 410 8.83e+01 d.126.1.4 98758 1y74B 50 8.87e+01 1veaA 148 8.92e+01 d.275.1.1 108529 1k3yA 221 8.95e+01 a.45.1.1,c.47.1.5 77245,77246 1k3lA 221 8.96e+01 a.45.1.1,c.47.1.5 77229,77230