# 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 8.32e-02 a.8.3.3,c.6.2.4 99329,99330 1vj5A 555 2.05e-01 c.108.1.2,c.69.1.11 100799,100800 1ad3A 452 3.23e-01 1ad3A c.82.1.1 35335 1tbmA 326 5.86e-01 a.211.1.2 106744 2fiyA 309 7.13e-01 1zd3A 555 7.17e-01 1cr6B 554 8.69e-01 1cr6B c.69.1.11,c.108.1.2 34688,43338 1h6zA 913 1.15e+00 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 1qrjB 199 1.17e+00 1qrjB a.28.3.1 16952 1jb0I 38 1.28e+00 1jb0I f.23.17.1 62826 1w1oA 534 1.33e+00 d.58.32.4,d.145.1.1 109071,109072 1trrA 107 1.36e+00 1jhgA a.4.12.1 19017 1ni3A 392 1.62e+00 c.37.1.8,d.15.10.2 80531,80532 1sz2A 332 2.04e+00 2b1eA 564 2.51e+00 1z2nX 324 2.60e+00 2wrpR 107 2.78e+00 1jhgA a.4.12.1 19010 1hdiA 413 3.03e+00 16pk c.86.1.1 60964 2myo 118 3.10e+00 2myo d.211.1.1 19175 1bp1 456 3.17e+00 1bp1 d.83.1.1,d.83.1.1 40026,40027 1zv1A 65 3.27e+00 2afwA 329 3.33e+00 1eia 207 3.49e+00 1eia a.28.3.1,a.73.1.1 16951,18331 1bf5A 545 3.59e+00 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 1n2fA 142 3.76e+00 d.227.1.1 79853 1jhgA 101 3.80e+00 1jhgA a.4.12.1 19009 1ewfA 456 3.86e+00 1bp1 d.83.1.1,d.83.1.1 40024,40025 1fsu 492 4.00e+00 1auk c.76.1.2 35032 1e08A 371 4.00e+00 i.4.1.1 45914 1jmtB 28 4.36e+00 1ihp 438 4.43e+00 1ihp c.60.1.2 33993 1jmxA 494 4.95e+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 1q18A 332 5.09e+00 c.55.1.7,c.55.1.7 104470,104471 1bd8 156 5.47e+00 1bd8 d.211.1.1 19157 1qfxA 460 5.77e+00 1qfxA c.60.1.2 33994 2fmcA 82 6.20e+00 1y3nA 490 6.33e+00 2mev2 256 6.35e+00 1aym2 2ccmA 191 6.36e+00 1myo 118 6.51e+00 2myo d.211.1.1 19174 2aclB 244 6.61e+00 1kblA 873 6.82e+00 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1iuhA 198 7.06e+00 d.61.1.2 83711 1v1rA 400 7.06e+00 c.36.1.11 108272 1rkd 309 7.70e+00 1rkd c.72.1.1 34928 1o5hA 214 7.76e+00 a.191.1.1 92497 2ctoA 93 7.86e+00 1x91A 153 7.87e+00 1pa7A 130 7.96e+00 a.40.1.1 94410 1jpaA 312 8.11e+00 d.144.1.7 67011 1m93B 245 8.18e+00 1iciA 256 8.28e+00 1iciA c.31.1.5 62266 1zboA 210 8.41e+00 1hfeL 421 8.62e+00 1fehA c.96.1.1,d.58.1.5 36018,39001 1c8oA 300 8.85e+00 1c8oA e.1.1.1 42677 1efuA 385 9.04e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1tqxA 227 9.11e+00 1efcA 393 9.19e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1kpsB 171 9.46e+00 a.118.12.1 68787 1hzfA 367 9.60e+00 a.102.4.4 76731 1im5A 180 1.01e+01 c.33.1.3 66211 1huvA 380 1.02e+01 c.1.4.1 61277 2dg5A 366 1.05e+01 1x1fA 149 1.06e+01 1w07A 659 1.07e+01 1bh9B 89 1.08e+01 1bh9B a.22.1.3 16485 1z6uA 150 1.10e+01 1yzxA 226 1.10e+01 1cjsA 219 1.10e+01 1cjsA e.24.1.1 43354 2eiaB 206 1.17e+01 1eia a.28.3.1,a.73.1.1 16950,18330 1sszA 34 1.17e+01 j.35.1.1 105999 1q4mA 221 1.21e+01 a.132.1.3 95805 1i2aA 219 1.30e+01 e.24.1.1 90660 2f2gA 221 1.30e+01 1x74A 360 1.39e+01 2b7aA 293 1.40e+01 1f0cA 305 1.41e+01 1c8oA e.1.1.1 42676 1xioA 261 1.42e+01 2fqmA 75 1.43e+01 1p4cA 380 1.46e+01 c.1.4.1 94100 6gsvA 217 1.48e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 1de6A 426 1.62e+01 1de5A c.1.15.2 29398 1i9gA 280 1.62e+01 c.66.1.13 62090 1t92A 116 1.67e+01 2fb6A 117 1.78e+01 1m6jA 261 1.79e+01 c.1.1.1 78693 2gdjA 264 1.82e+01 1x6iA 91 1.82e+01 1be3F 110 1.83e+01 1be3F f.27.1.1 43668 1jhdA 396 1.84e+01 b.122.1.3,c.26.1.5 66712,66713 1yy7A 213 1.91e+01 1gt8D 1025 1.94e+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 1qd9A 124 1.95e+01 1qu9A d.79.1.1 39758 1tkeA 224 1.99e+01 1s7jA 262 2.02e+01 d.21.1.2 98647 1r4wA 226 2.04e+01 c.47.1.13 97050 1d8wA 426 2.06e+01 1de5A c.1.15.2 29394 2fikA 287 2.13e+01 1wjgA 137 2.14e+01 1l1jA 239 2.14e+01 b.47.1.1 84516 1gt8B 1025 2.15e+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 1h2vC 771 2.18e+01 a.118.1.14,a.118.1.14,a.118.1.14 76592,76593,76594 2bemA 170 2.22e+01 1hz4A 373 2.23e+01 a.118.8.2 65960 1sphA 88 2.25e+01 1ptf d.94.1.1 40544 1cojA 212 2.26e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1aq0A 306 2.26e+01 1aq0A c.1.8.3 28842 1z5lA 285 2.28e+01 1ohfA 644 2.28e+01 b.121.4.8 93014 1k6iA 352 2.34e+01 c.2.1.2 68223 2akrA 285 2.37e+01 2cygA 312 2.39e+01 1dik 874 2.39e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 2f96A 224 2.48e+01 1m98A 317 2.53e+01 a.175.1.1,d.17.4.6 78866,78867 1wmmA 145 2.54e+01 1m2kA 249 2.57e+01 c.31.1.5 84754 1h7xC 1025 2.61e+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 2esnA 310 2.64e+01 1ka9H 200 2.69e+01 c.23.16.1 77308 1gthB 1025 2.70e+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 1hp5A 512 2.72e+01 1hp4A c.1.8.6,d.92.2.1 61113,61114 1xfjA 261 2.81e+01 d.194.1.2 109585 1yozA 116 2.87e+01 1kfd 605 2.88e+01 1xwl c.55.3.5,e.8.1.1 33694,42987 1ghr 306 2.89e+01 1aq0A c.1.8.3 28844 1gt8C 1025 2.96e+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 1xmeA 568 2.97e+01 1cd1A 315 2.97e+01 1cd1A b.1.1.2,d.19.1.1 21579,38155 1p4dA 330 3.01e+01 d.89.1.5 94101 2c5rA 67 3.02e+01 1jakA 512 3.06e+01 c.1.8.6,d.92.2.1 66472,66473 1qh4A 380 3.06e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 1thg 544 3.08e+01 1thg c.69.1.17 34763 2furA 209 3.09e+01 1fehA 574 3.10e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1hp4A 512 3.14e+01 1hp4A c.1.8.6,d.92.2.1 61111,61112 1bccF 109 3.18e+01 1be3F f.27.1.1 43700 1w36C 1122 3.35e+01 1adjA 421 3.44e+01 1adjA c.51.1.1,d.104.1.1 33188,40737 1de5A 426 3.48e+01 1de5A c.1.15.2 29402 1nmtA 392 3.52e+01 1nmtA d.108.1.2,d.108.1.2 40823,40824 1kf6D 119 3.55e+01 f.21.2.2 72400 1h3nA 878 3.56e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 2gwgA 350 3.59e+01 1h7wA 1025 3.67e+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 2fpmA 322 3.68e+01 1n1jA 93 3.72e+01 a.22.1.3 79813 1h4vB 421 3.75e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1o9wA 177 3.84e+01 b.2.3.5 86713 1qu9A 128 3.91e+01 1qu9A d.79.1.1 39755 1qu9C 128 3.91e+01 1qu9A d.79.1.1 39757 1zq9A 285 3.91e+01 1m3uA 264 3.96e+01 c.1.12.8 84784 1rtwA 220 3.99e+01 a.132.1.3 97823 1t4gA 322 4.00e+01 a.60.4.1,c.37.1.11 106418,106419 1htxA 32 4.04e+01 1qfdA g.3.2.1 61261 1jae 471 4.08e+01 1smd b.71.1.1,c.1.8.1 27773,28760 1t8kA 77 4.16e+01 a.28.1.1 106666 1vjkA 98 4.19e+01 d.15.3.1 108631 1x7yA 400 4.20e+01 1gthC 1025 4.22e+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 1y1uA 585 4.25e+01 1lghA 56 4.25e+01 1lghA f.3.1.1 43733 2es9A 115 4.27e+01 1whrA 124 4.31e+01 1wr7A 41 4.48e+01 1llmC 88 4.52e+01 g.37.1.1,g.37.1.1 91059,91060 1acp 77 4.55e+01 1acp a.28.1.1 16931 1gthA 1025 4.57e+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 1mmoD 512 4.73e+01 1mhyD a.25.1.2 16770 1l0iA 78 4.74e+01 a.28.1.1 77643 1ordA 730 4.84e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31274,34503,41124 1geeA 261 4.85e+01 c.2.1.2 90509 1gcoA 261 4.85e+01 1ybvA c.2.1.2 29884 1rzsA 61 4.90e+01 a.35.1.2 105139 1b8aA 438 4.92e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1apyA 162 4.93e+01 1apyA d.153.1.5 42004 3inkC 133 5.02e+01 3inkC a.26.1.2 16881 1olsA 400 5.05e+01 c.36.1.11 93331 1nd7A 374 5.05e+01 d.148.1.1 91817 1v2dA 381 5.14e+01 c.67.1.1 108281 1ytaA 180 5.14e+01 2c4jA 218 5.17e+01 1sheA 103 5.17e+01 d.274.1.1 105551 1cn4C 166 5.18e+01 1eerA a.26.1.2 16847 1qmzB 259 5.19e+01 1vin a.74.1.1,a.74.1.1 18338,18339 2givA 295 5.28e+01 1h7xD 1025 5.28e+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 1muyA 225 5.33e+01 1mun a.96.1.2 18745 1fhvA 323 5.35e+01 1fhuA c.1.11.2,d.54.1.1 29235,38879 2aplA 157 5.39e+01 1tzpA 255 5.41e+01 d.65.1.3 107520 2fgtA 417 5.43e+01 2bnkA 67 5.46e+01 2a7mA 250 5.48e+01 1xfsA 178 5.49e+01 d.129.3.5 109589 1h9eA 56 5.56e+01 1h9eA a.140.1.1 60825 1bdc 60 5.60e+01 1fc2C a.8.1.1 16350 1qycA 308 5.64e+01 c.2.1.2 96581 1zbfA 142 5.67e+01 1qahA 136 5.68e+01 d.79.1.1 96338 1tqyB 415 5.74e+01 c.95.1.1,c.95.1.1 107247,107248 1r6wA 322 5.74e+01 c.1.11.2,d.54.1.1 97165,97166 1ppjF 110 5.76e+01 f.27.1.1 104262 1eemA 241 5.87e+01 1eemA a.45.1.1,c.47.1.5 17717,33011 1x4tA 92 5.91e+01 2ezh 75 5.93e+01 2ezh a.4.1.2 16029 1alvA 173 5.95e+01 1alvA a.39.1.8 17370 2ezi 75 5.97e+01 2ezh a.4.1.2 16028 1mtyD 512 5.97e+01 1mhyD a.25.1.2 16742 1mhyD 521 6.08e+01 1mhyD a.25.1.2 16780 2b33A 140 6.11e+01 2cchB 260 6.12e+01 2ewcA 126 6.16e+01 1bs0A 384 6.23e+01 1bs0A c.67.1.4 34490 2mtaC 147 6.23e+01 2mtaC a.3.1.1 15908 1ln4A 104 6.26e+01 d.68.4.1 74043 1amf 233 6.26e+01 1wod c.94.1.1 35833 1sf8A 126 6.27e+01 d.271.1.1 105472 2a3qA 170 6.33e+01 1d3uB 201 6.38e+01 1aisB a.74.1.2,a.74.1.2 18386,18387 1wod 233 6.41e+01 1wod c.94.1.1 35832 1h7wD 1025 6.43e+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 4ubpC 570 6.44e+01 1ubpC b.92.1.1,c.1.9.2 28431,29053 1vi0A 206 6.47e+01 a.4.1.9,a.121.1.1 100720,100721 1zy9A 564 6.48e+01 1uw4B 248 6.49e+01 a.118.1.14 100072 1p2fA 220 6.55e+01 a.4.6.1,c.23.1.1 87720,87721 1gteA 1025 6.55e+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 1b74A 254 6.56e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 2g3kA 94 6.62e+01 1ehaA 558 6.63e+01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21859,27786,28773 1gjjA 168 6.65e+01 a.140.1.1,a.140.1.1 83291,83292 1uurA 473 6.69e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1mgpA 313 6.69e+01 c.119.1.1 79098 1gteD 1025 6.70e+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 1ehkA 562 6.93e+01 1ehkA f.24.1.1 43624 2a2oA 258 7.03e+01 1w85A 368 7.05e+01 1lkyA 77 7.05e+01 a.60.1.1 73985 2bfdA 400 7.17e+01 1g8fA 511 7.17e+01 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 1x6vA 630 7.18e+01 1imuA 107 7.18e+01 d.204.1.1 66218 1ats 386 7.25e+01 1ba1 c.55.1.1,c.55.1.1 33423,33424 1h99A 224 7.28e+01 a.142.1.1,a.142.1.1 60814,60815 1zc6A 305 7.29e+01 1okjA 251 7.36e+01 c.55.1.9,c.55.1.9 103998,103999 1d6mA 653 7.38e+01 1d6mA e.10.1.1 43248 1g7oA 215 7.42e+01 1g7oA a.45.1.1,c.47.1.5 60332,60333 2atjA 308 7.51e+01 1bgp a.93.1.1 18675 2a2mA 258 7.53e+01 2b05A 246 7.55e+01 1z3eB 73 7.59e+01 1bupA 386 7.60e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1ubpC 570 7.63e+01 1ubpC b.92.1.1,c.1.9.2 28432,29054 1kay 381 7.64e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 2fywA 267 7.66e+01 1kezA 300 7.68e+01 c.69.1.22 68546 1hpm 386 7.68e+01 1ba1 c.55.1.1,c.55.1.1 33381,33382 1ba1 386 7.74e+01 1ba1 c.55.1.1,c.55.1.1 33387,33388 1vixA 420 7.80e+01 c.56.5.4,d.58.19.1 100777,100778 1mun 225 7.82e+01 1mun a.96.1.2 18744 3kinB 117 7.85e+01 3kinB 2d00A 109 7.85e+01 1hlvA 131 7.86e+01 a.4.1.7,a.4.1.7 65854,65855 1xk7A 408 7.90e+01 1n3gA 113 7.91e+01 d.204.1.1 79962 1h7xA 1025 7.99e+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 1rcsA 105 8.03e+01 1jhgA a.4.12.1 19025 2lefA 86 8.08e+01 2lefA a.21.1.1 16433 1ie7C 570 8.15e+01 1ubpC b.92.1.1,c.1.9.2 62315,62316 1z6aA 500 8.24e+01 2bjqA 345 8.28e+01 2fk8A 318 8.36e+01 1d5wC 126 8.42e+01 1dbwA c.23.1.1 31101 1crkA 380 8.44e+01 1qh4A a.83.1.1,d.128.1.2 18458,41193 1jajA 174 8.45e+01 d.218.1.2 66471 1guxA 218 8.46e+01 1guxA a.74.1.3 18388 1s5lX 50 8.55e+01 1p3jA 217 8.60e+01 c.37.1.1,g.41.2.1 94022,94023 1z5zA 271 8.60e+01 1u5dA 108 8.61e+01 1vin 268 8.65e+01 1vin a.74.1.1,a.74.1.1 18354,18355 1irzA 64 8.67e+01 a.4.1.11 76772 1yuwA 554 8.68e+01 2aheA 267 8.71e+01 2iu5A 195 8.73e+01 1jy3N 53 8.76e+01 h.1.8.1 67446 1a3k 137 8.87e+01 1a3k b.29.1.3 24218 1b73A 254 8.94e+01 1b74A c.78.2.1,c.78.2.1 35266,35267 1gt8A 1025 8.97e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70418,70419,70420,70421,70422 2occH 85 9.00e+01 2occH a.51.1.1 17796