# 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 1ufaA 520 8.34e-02 a.8.3.3,c.6.2.4 99329,99330 1ad3A 452 1.87e-01 1ad3A c.82.1.1 35335 2fiyA 309 2.71e-01 1vj5A 555 3.87e-01 c.108.1.2,c.69.1.11 100799,100800 1tbmA 326 4.69e-01 a.211.1.2 106744 2b1eA 564 5.56e-01 1trrA 107 6.16e-01 1jhgA a.4.12.1 19017 1h6zA 913 7.44e-01 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 1sz2A 332 8.04e-01 1qrjB 199 9.09e-01 1qrjB a.28.3.1 16952 1jb0I 38 9.87e-01 1jb0I f.23.17.1 62826 1w1oA 534 1.01e+00 d.58.32.4,d.145.1.1 109071,109072 1cr6B 554 1.12e+00 1cr6B c.69.1.11,c.108.1.2 34688,43338 2wrpR 107 1.21e+00 1jhgA a.4.12.1 19010 1zv1A 65 1.27e+00 1ni3A 392 1.44e+00 c.37.1.8,d.15.10.2 80531,80532 1zd3A 555 1.45e+00 1jhgA 101 1.60e+00 1jhgA a.4.12.1 19009 1q18A 332 2.06e+00 c.55.1.7,c.55.1.7 104470,104471 1jpaA 312 2.18e+00 d.144.1.7 67011 1z2nX 324 2.24e+00 1y3nA 490 2.47e+00 1x91A 153 2.67e+00 2afwA 329 2.96e+00 1hdiA 413 3.01e+00 16pk c.86.1.1 60964 1bf5A 545 3.10e+00 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 2myo 118 3.12e+00 2myo d.211.1.1 19175 1bp1 456 3.43e+00 1bp1 d.83.1.1,d.83.1.1 40026,40027 1fsu 492 3.68e+00 1auk c.76.1.2 35032 1eia 207 3.70e+00 1eia a.28.3.1,a.73.1.1 16951,18331 1ewfA 456 3.89e+00 1bp1 d.83.1.1,d.83.1.1 40024,40025 1e08A 371 4.01e+00 i.4.1.1 45914 1jmxA 494 4.08e+00 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66901,66902,66903,66904,66905 1n2fA 142 4.14e+00 d.227.1.1 79853 1jmtB 28 4.16e+00 1z6uA 150 4.30e+00 2dg5A 366 4.41e+00 2aclB 244 4.51e+00 2ctoA 93 4.54e+00 1v1rA 400 5.01e+00 c.36.1.11 108272 2fmcA 82 5.09e+00 1kblA 873 5.48e+00 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1w07A 659 5.51e+00 1zboA 210 5.80e+00 2mev2 256 5.86e+00 1aym2 1ihp 438 6.01e+00 1ihp c.60.1.2 33993 1tqxA 227 6.55e+00 1kpsB 171 6.67e+00 a.118.12.1 68787 1myo 118 7.01e+00 2myo d.211.1.1 19174 1qfxA 460 7.08e+00 1qfxA c.60.1.2 33994 1m93B 245 7.25e+00 1bd8 156 7.60e+00 1bd8 d.211.1.1 19157 1c8oA 300 7.61e+00 1c8oA e.1.1.1 42677 1x1fA 149 8.07e+00 1hfeL 421 8.32e+00 1fehA c.96.1.1,d.58.1.5 36018,39001 1im5A 180 8.33e+00 c.33.1.3 66211 1iuhA 198 8.97e+00 d.61.1.2 83711 1pa7A 130 9.11e+00 a.40.1.1 94410 1huvA 380 9.52e+00 c.1.4.1 61277 1iciA 256 9.55e+00 1iciA c.31.1.5 62266 2fikA 287 9.84e+00 1z5lA 285 1.03e+01 1bh9B 89 1.05e+01 1bh9B a.22.1.3 16485 2ccmA 191 1.07e+01 2akrA 285 1.08e+01 1x6iA 91 1.09e+01 1hzfA 367 1.12e+01 a.102.4.4 76731 1x74A 360 1.13e+01 1sszA 34 1.14e+01 j.35.1.1 105999 1f0cA 305 1.15e+01 1c8oA e.1.1.1 42676 2eiaB 206 1.17e+01 1eia a.28.3.1,a.73.1.1 16950,18330 1m6jA 261 1.18e+01 c.1.1.1 78693 1q4mA 221 1.19e+01 a.132.1.3 95805 1xioA 261 1.19e+01 1h2vC 771 1.20e+01 a.118.1.14,a.118.1.14,a.118.1.14 76592,76593,76594 1qd9A 124 1.21e+01 1qu9A d.79.1.1 39758 1ohfA 644 1.21e+01 b.121.4.8 93014 1rkd 309 1.22e+01 1rkd c.72.1.1 34928 2fqmA 75 1.23e+01 1i9gA 280 1.28e+01 c.66.1.13 62090 2f2gA 221 1.28e+01 1yy7A 213 1.29e+01 1l1jA 239 1.31e+01 b.47.1.1 84516 1o5hA 214 1.32e+01 a.191.1.1 92497 1cjsA 219 1.33e+01 1cjsA e.24.1.1 43354 1p4cA 380 1.41e+01 c.1.4.1 94100 1yzxA 226 1.42e+01 2gdjA 264 1.47e+01 1wjgA 137 1.49e+01 1k6iA 352 1.50e+01 c.2.1.2 68223 1s7jA 262 1.51e+01 d.21.1.2 98647 1tkeA 224 1.52e+01 1cd1A 315 1.53e+01 1cd1A b.1.1.2,d.19.1.1 21579,38155 2b05A 246 1.56e+01 1i2aA 219 1.79e+01 e.24.1.1 90660 1xmeA 568 1.89e+01 1sphA 88 1.90e+01 1ptf d.94.1.1 40544 2bemA 170 1.91e+01 1yozA 116 2.03e+01 1kfd 605 2.03e+01 1xwl c.55.3.5,e.8.1.1 33694,42987 1dik 874 2.04e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1whrA 124 2.04e+01 2fb6A 117 2.07e+01 1w36C 1122 2.17e+01 1cojA 212 2.21e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1t4gA 322 2.22e+01 a.60.4.1,c.37.1.11 106418,106419 6gsvA 217 2.24e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 1gt8D 1025 2.25e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70433,70434,70435,70436,70437 1t92A 116 2.39e+01 1qh4A 380 2.40e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 1thg 544 2.42e+01 1thg c.69.1.17 34763 1jhdA 396 2.47e+01 b.122.1.3,c.26.1.5 66712,66713 1m98A 317 2.50e+01 a.175.1.1,d.17.4.6 78866,78867 2c5rA 67 2.51e+01 1wmmA 145 2.52e+01 1be3F 110 2.52e+01 1be3F f.27.1.1 43668 1xfjA 261 2.52e+01 d.194.1.2 109585 2f96A 224 2.57e+01 1ka9H 200 2.64e+01 c.23.16.1 77308 2b7aA 293 2.65e+01 2fk8A 318 2.67e+01 1m2kA 249 2.72e+01 c.31.1.5 84754 2fpmA 322 2.79e+01 1h7xC 1025 2.80e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15689,28634,30330,30615,39013 1jk8B 190 2.85e+01 1iakB b.1.1.2,d.19.1.1 63147,63148 1r4wA 226 2.99e+01 c.47.1.13 97050 1h3nA 878 3.04e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1o9wA 177 3.04e+01 b.2.3.5 86713 1gt8B 1025 3.10e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70423,70424,70425,70426,70427 1aq0A 306 3.13e+01 1aq0A c.1.8.3 28842 1muyA 225 3.21e+01 1mun a.96.1.2 18745 1bccF 109 3.25e+01 1be3F f.27.1.1 43700 1adjA 421 3.30e+01 1adjA c.51.1.1,d.104.1.1 33188,40737 1fehA 574 3.30e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 2cygA 312 3.32e+01 1n1jA 93 3.37e+01 a.22.1.3 79813 1gt8C 1025 3.41e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70428,70429,70430,70431,70432 1hz4A 373 3.43e+01 a.118.8.2 65960 1vjkA 98 3.47e+01 d.15.3.1 108631 1zq9A 285 3.58e+01 1gthB 1025 3.61e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70488,70489,70490,70491,70492 1kf6D 119 3.67e+01 f.21.2.2 72400 1nmtA 392 3.71e+01 1nmtA d.108.1.2,d.108.1.2 40823,40824 1ghr 306 3.75e+01 1aq0A c.1.8.3 28844 1x7yA 400 3.85e+01 1efuA 385 3.85e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1efcA 393 3.86e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1de6A 426 3.87e+01 1de5A c.1.15.2 29398 1h4vB 421 3.90e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 2bt2A 161 3.90e+01 2gwgA 350 3.93e+01 1tzpA 255 3.94e+01 d.65.1.3 107520 1y1uA 585 3.96e+01 1sheA 103 3.97e+01 d.274.1.1 105551 1wr7A 41 4.02e+01 1vgmA 378 4.03e+01 1pveA 72 4.07e+01 a.189.1.1 104322 1ordA 730 4.07e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31274,34503,41124 2esnA 310 4.08e+01 1h7wA 1025 4.11e+01 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15683,28628,30324,30609,39007 2lefA 86 4.17e+01 2lefA a.21.1.1 16433 2furA 209 4.23e+01 1gewA 356 4.25e+01 1gewA c.67.1.1 60470 1x4tA 92 4.32e+01 1qahA 136 4.36e+01 d.79.1.1 96338 1nd7A 374 4.41e+01 d.148.1.1 91817 1bs2A 607 4.42e+01 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 16930,31597,39563 1jae 471 4.50e+01 1smd b.71.1.1,c.1.8.1 27773,28760 1zy9A 564 4.57e+01 1mun 225 4.57e+01 1mun a.96.1.2 18744 1p4dA 330 4.59e+01 d.89.1.5 94101 1rcsA 105 4.66e+01 1jhgA a.4.12.1 19025 1d8wA 426 4.68e+01 1de5A c.1.15.2 29394 2aplA 157 4.69e+01 3inkC 133 4.74e+01 3inkC a.26.1.2 16881 1lghA 56 4.76e+01 1lghA f.3.1.1 43733 1ehkA 562 4.77e+01 1ehkA f.24.1.1 43624 2es9A 115 4.88e+01 2fgtA 417 4.88e+01 1qu9A 128 4.88e+01 1qu9A d.79.1.1 39755 1qu9C 128 4.88e+01 1qu9A d.79.1.1 39757 1h9eA 56 4.90e+01 1h9eA a.140.1.1 60825 1okjA 251 4.92e+01 c.55.1.9,c.55.1.9 103998,103999 1gthC 1025 4.94e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70493,70494,70495,70496,70497 1acp 77 4.97e+01 1acp a.28.1.1 16931 2c4jA 218 5.00e+01 1apyA 162 5.21e+01 1apyA d.153.1.5 42004 1qycA 308 5.21e+01 c.2.1.2 96581 1ykhB 132 5.24e+01 2b33A 140 5.32e+01 1amf 233 5.33e+01 1wod c.94.1.1 35833 1w2fA 276 5.36e+01 d.143.1.3 109125 1z6gA 218 5.41e+01 1uurA 473 5.42e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1fhvA 323 5.45e+01 1fhuA c.1.11.2,d.54.1.1 29235,38879 1htxA 32 5.48e+01 1qfdA g.3.2.1 61261 1wod 233 5.51e+01 1wod c.94.1.1 35832 1olsA 400 5.53e+01 c.36.1.11 93331 1m3uA 264 5.57e+01 c.1.12.8 84784 2bnkA 67 5.60e+01 1gthA 1025 5.63e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70483,70484,70485,70486,70487 1rzsA 61 5.65e+01 a.35.1.2 105139 1h7xD 1025 5.67e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15690,28635,30331,30616,39014 1fpoA 171 5.68e+01 1fpoA a.2.3.1,a.23.1.1 15693,16487 1fg7A 356 5.68e+01 1gewA c.67.1.1 59819 1p9aG 290 5.68e+01 c.10.2.7 87990 1cn4C 166 5.70e+01 1eerA a.26.1.2 16847 1r6wA 322 5.73e+01 c.1.11.2,d.54.1.1 97165,97166 1ln4A 104 5.80e+01 d.68.4.1 74043 1hp5A 512 5.80e+01 1hp4A c.1.8.6,d.92.2.1 61113,61114 1bs0A 384 5.83e+01 1bs0A c.67.1.4 34490 2br9A 234 5.86e+01 2ezh 75 5.87e+01 2ezh a.4.1.2 16029 1v2dA 381 5.88e+01 c.67.1.1 108281 2ezi 75 5.95e+01 2ezh a.4.1.2 16028 1gjjA 168 6.06e+01 a.140.1.1,a.140.1.1 83291,83292 1ni5A 433 6.15e+01 c.26.2.5,d.229.1.1 80533,80534 1ppjF 110 6.18e+01 f.27.1.1 104262 2ewcA 126 6.18e+01 1rtwA 220 6.22e+01 a.132.1.3 97823 1x6vA 630 6.28e+01 1cktA 71 6.31e+01 1cktA a.21.1.1 16417 1jakA 512 6.31e+01 c.1.8.6,d.92.2.1 66472,66473 1xb4A 202 6.33e+01 1ats 386 6.35e+01 1ba1 c.55.1.1,c.55.1.1 33423,33424 1mmoD 512 6.35e+01 1mhyD a.25.1.2 16770 1m0zA 290 6.37e+01 c.10.2.7 74359 1gdeA 389 6.38e+01 c.67.1.1 60456 1l0iA 78 6.41e+01 a.28.1.1 77643 1t8kA 77 6.48e+01 a.28.1.1 106666 1hp4A 512 6.48e+01 1hp4A c.1.8.6,d.92.2.1 61111,61112 1tqyB 415 6.50e+01 c.95.1.1,c.95.1.1 107247,107248 1kay 381 6.58e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 2bo9A 308 6.62e+01 1af3 196 6.63e+01 1maz f.1.4.1 43397 1bupA 386 6.63e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1ba1 386 6.67e+01 1ba1 c.55.1.1,c.55.1.1 33387,33388 1hpm 386 6.69e+01 1ba1 c.55.1.1,c.55.1.1 33381,33382 2givA 295 6.69e+01 2atjA 308 6.70e+01 1bgp a.93.1.1 18675 1alvA 173 6.70e+01 1alvA a.39.1.8 17370 1sf8A 126 6.71e+01 d.271.1.1 105472 1gd9A 389 6.72e+01 c.67.1.1 60454 1d5wC 126 6.72e+01 1dbwA c.23.1.1 31101 1gteA 1025 6.74e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70440,70441,70442,70443,70444 1dckA 126 6.77e+01 1dbwA c.23.1.1 31097 1zc6A 305 6.79e+01 1oqcA 125 6.82e+01 a.24.15.1 87264 1vi0A 206 6.82e+01 a.4.1.9,a.121.1.1 100720,100721 1gteD 1025 6.84e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70455,70456,70457,70458,70459 1imuA 107 6.86e+01 d.204.1.1 66218 2mtaC 147 6.87e+01 2mtaC a.3.1.1 15908 1z3eB 73 6.88e+01 1pq1A 196 6.94e+01 f.1.4.1 94986 1mhyB 395 6.96e+01 1mtyB a.25.1.2 16781 1u5dA 108 6.99e+01 1xgkA 352 7.01e+01 2gsfA 373 7.12e+01 2a6sA 84 7.19e+01 1kplA 473 7.22e+01 f.20.1.1 68782 1n3gA 113 7.26e+01 d.204.1.1 79962 1dtdA 303 7.35e+01 1aye c.56.5.1 33823 1yuwA 554 7.36e+01 2bjqA 345 7.38e+01 1l8yA 91 7.49e+01 a.21.1.1 73708 2fywA 267 7.52e+01 1mtyD 512 7.52e+01 1mhyD a.25.1.2 16742 1h7wD 1025 7.62e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15686,28631,30327,30612,39010 1vixA 420 7.65e+01 c.56.5.4,d.58.19.1 100777,100778 1xkmB 25 7.66e+01 1jajA 174 7.68e+01 d.218.1.2 66471 1de5A 426 7.73e+01 1de5A c.1.15.2 29402 2bfdA 400 7.74e+01 1crkA 380 7.83e+01 1qh4A a.83.1.1,d.128.1.2 18458,41193 1jem 87 7.88e+01 1ptf d.94.1.1 40548 1n2zA 245 7.89e+01 c.92.2.2 79865 1g7oA 215 7.90e+01 1g7oA a.45.1.1,c.47.1.5 60332,60333 1xmaA 145 7.91e+01 2cpgA 45 8.08e+01 2cpgA a.43.1.3 17455 1eemA 241 8.11e+01 1eemA a.45.1.1,c.47.1.5 17717,33011 1f07A 321 8.24e+01 1ezwA c.1.16.3 59560 1xk7A 408 8.27e+01 1lkyA 77 8.29e+01 a.60.1.1 73985 4ubpC 570 8.29e+01 1ubpC b.92.1.1,c.1.9.2 28431,29053 1b01A 45 8.31e+01 2cpgA a.43.1.3 17458 1fohA 664 8.34e+01 1fohA c.3.1.2,c.47.1.10,d.16.1.2 30381,33078,37900 1m13A 316 8.37e+01 a.123.1.1 84746 1w85A 368 8.39e+01 1ok7A 366 8.40e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1aihA 170 8.41e+01 1aihA d.163.1.1 42149 2cglA 489 8.46e+01 1zbsA 291 8.53e+01 1b74A 254 8.56e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1irzA 64 8.58e+01 a.4.1.11 76772 2a7mA 250 8.60e+01 1h7xA 1025 8.66e+01 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15687,28632,30328,30613,39011 2a3qA 170 8.72e+01 1ut7A 171 8.75e+01 b.143.1.1 99906 1g8fA 511 8.78e+01 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 1sqgA 429 8.78e+01 a.79.1.3,c.66.1.38 105912,105913 1z6aA 500 8.80e+01 1d3uB 201 8.86e+01 1aisB a.74.1.2,a.74.1.2 18386,18387 1phk 298 8.93e+01 1cdkA d.144.1.7 41635 1axsA 211 8.95e+01 8fabA b.1.1.1,b.1.1.2 20200,21216 1mhyD 521 8.99e+01 1mhyD a.25.1.2 16780