# 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 1w61A 414 1.12e-01 2gkeA 274 2.81e-01 1bwzA 274 3.06e-01 1bwzA d.21.1.1,d.21.1.1 38337,38338 1gqzA 274 3.31e-01 d.21.1.1,d.21.1.1 83311,83312 1sdjA 310 7.51e-01 d.21.1.2,d.21.1.2 98807,98808 1qyaA 307 1.03e+00 d.21.1.2,d.21.1.2 104653,104654 1mkeA 152 1.08e+00 b.55.1.4 79231 1ats 386 1.09e+00 1ba1 c.55.1.1,c.55.1.1 33423,33424 1b0vA 106 1.70e+00 1a6l d.58.1.2 38982 1u2hA 99 1.79e+00 1vhzA 198 1.98e+00 d.113.1.1 100718 1fd2 106 2.12e+00 1a6l d.58.1.2 38962 1a6l 106 2.15e+00 1a6l d.58.1.2 38966 1b0tA 106 2.15e+00 1a6l d.58.1.2 38965 7fd1A 106 2.56e+00 1a6l d.58.1.2 38953 1orrA 347 2.57e+00 c.2.1.2 93460 2f6uA 234 2.64e+00 1fdd 106 2.76e+00 1a6l d.58.1.2 38960 1hpm 386 2.91e+00 1ba1 c.55.1.1,c.55.1.1 33381,33382 1bupA 386 3.30e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 1kay 381 3.45e+00 1ba1 c.55.1.1,c.55.1.1 33385,33386 1atr 386 3.51e+00 1ba1 c.55.1.1,c.55.1.1 33421,33422 1ba1 386 3.83e+00 1ba1 c.55.1.1,c.55.1.1 33387,33388 1lm6A 215 4.67e+00 d.167.1.1 84628 1ci3M 249 4.74e+00 1hcz b.2.6.1,b.84.2.2 22480,28266 2g6yA 217 5.48e+00 1v58A 241 5.74e+00 c.47.1.9,d.17.3.1 108371,108372 1jjiA 311 6.62e+00 c.69.1.2 66766 1x6zA 123 7.59e+00 1fivA 113 8.12e+00 1fmb b.50.1.1 26764 1rec 201 8.46e+00 1rec a.39.1.5 17326 1omrA 201 8.98e+00 a.39.1.5 93349 1cwvA 492 9.14e+00 1cwvA b.1.14.1,b.1.14.1,b.1.14.1,b.1.14.1,d.169.1.3 22373,22374,22375,22376,42442 1y0gA 191 9.92e+00 1l5jA 865 1.04e+01 a.118.15.1,c.8.2.1,c.83.1.1 73592,73593,73594 1l1nA 183 1.06e+01 b.47.1.4 73476 1bqsA 209 1.06e+01 1bqsA b.1.1.4,b.1.1.4 21704,21705 1k3bB 164 1.09e+01 d.3.1.1 72015 1r7lA 110 1.11e+01 d.277.1.1 104837 1dzoA 123 1.14e+01 1dzoA d.24.1.1 38378 2fivA 116 1.21e+01 1fmb b.50.1.1 26766 1j5qA 437 1.23e+01 b.121.2.3,b.121.2.3 77084,77085 2aieP 203 1.26e+01 1rzl 91 1.45e+01 1rzl a.52.1.1 17817 3fivA 116 1.55e+01 1fmb b.50.1.1 26768 1lj5A 379 1.56e+01 e.1.1.1 73928 2f57A 317 1.63e+01 1vrmA 325 1.63e+01 1gpiA 431 1.65e+01 b.29.1.10 65450 4fiv 113 1.72e+01 1fmb b.50.1.1 26762 2beiA 170 1.75e+01 1eysH 259 1.80e+01 6prcH b.41.1.1,f.23.10.1 25484,43517 1hmr 132 1.84e+01 1hmt b.60.1.2 27170 1a48 306 1.84e+01 1a48 d.143.1.1 41590 1yua 122 1.92e+01 1yua g.41.3.3,g.41.3.3 45210,45211 1ufbA 127 2.00e+01 a.24.16.3 99331 1nzjA 298 2.07e+01 c.26.1.1 92377 1wkvA 389 2.09e+01 1zynA 202 2.12e+01 2ckiA 262 2.15e+01 2sli 679 2.16e+01 2sli b.29.1.9,b.68.1.1 24274,27611 4sli 679 2.21e+01 2sli b.29.1.9,b.68.1.1 24275,27612 1q06A 135 2.23e+01 a.6.1.3 95493 1f76A 336 2.36e+01 c.1.4.1 76160 1wbpA 397 2.38e+01 1m3yA 413 2.40e+01 b.121.2.3,b.121.2.3 78579,78580 1qi9A 556 2.43e+01 1qhbA a.111.1.2 19053 2f15A 96 2.48e+01 1y43A 39 2.59e+01 1f00I 282 2.60e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 2cr4A 126 2.64e+01 2b59B 172 2.66e+01 1dv8A 128 2.70e+01 1ixxB d.169.1.1 42352 1mqoA 227 2.71e+01 d.157.1.1 103846 1qbeA 132 2.72e+01 1qbeA d.85.1.1 40138 1z7wA 322 2.74e+01 1dkxA 219 2.80e+01 1dkzA a.8.4.1,b.130.1.1 90339,90340 1y3nA 490 2.90e+01 2blnA 305 3.01e+01 2calA 154 3.05e+01 1bihA 395 3.06e+01 1bihA b.1.1.4,b.1.1.4,b.1.1.4,b.1.1.4 21752,21753,21754,21755 2g1uA 155 3.10e+01 1xo1A 291 3.13e+01 1exnA a.60.7.1,c.120.1.2 18086,33356 1ut9A 609 3.18e+01 a.102.1.2,b.1.18.2 99912,99913 1obdA 306 3.18e+01 d.143.1.1 86767 1z0mA 96 3.29e+01 2gc9A 179 3.39e+01 1zbpA 273 3.43e+01 1oixA 191 3.48e+01 1z7yA 322 3.50e+01 1vefA 395 3.51e+01 1z0nA 96 3.51e+01 2sak 121 3.53e+01 2sak d.15.5.1 37711 1g99A 408 3.55e+01 1g99A c.55.1.2,c.55.1.2 33457,33458 1a7cA 379 3.58e+01 1sek e.1.1.1 42660 2f6eA 127 3.66e+01 1t6kA 278 3.90e+01 1tukA 67 3.90e+01 1jjuA 489 3.90e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66774,66775,66776,66777,66778 1mroB 442 3.91e+01 1mroB a.89.1.1,d.58.31.2 18531,39449 2stv 195 3.92e+01 2stv b.121.7.1 23287 2bukA 196 3.93e+01 1js8A 394 3.94e+01 a.86.1.1,b.112.1.1 67219,67220 1azdA 237 3.95e+01 1nls b.29.1.1 24020 1i82A 189 3.98e+01 1i82A b.1.9.2 61937 1i8aA 189 4.10e+01 1i82A b.1.9.2 61951 1hms 132 4.20e+01 1hmt b.60.1.2 27168 2bh9A 489 4.22e+01 1e4eA 343 4.27e+01 1iow c.30.1.2,d.142.1.1 59221,59222 1xiwA 105 4.31e+01 1tcrA 202 4.33e+01 1tcrA b.1.1.1,b.1.1.2 20605,21549 1x99A 145 4.35e+01 1voqa 90 4.37e+01 2alaA 391 4.41e+01 1uyjA 296 4.42e+01 f.8.1.2 108143 2fomB 185 4.42e+01 1a8z 153 4.45e+01 1rcy b.6.1.1 23020 1l4sA 112 4.58e+01 d.204.1.1 77693 1ooyA 481 4.61e+01 c.124.1.3,c.124.1.2 93388,93389 1ak0 270 4.67e+01 1ak0 a.124.1.2 19345 1e6yB 433 4.71e+01 1mroB a.89.1.1,d.58.31.2 18535,39453 1cjsA 219 4.76e+01 1cjsA e.24.1.1 43354 1u8zA 168 4.77e+01 1hyuA 521 4.83e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1i2aA 219 4.85e+01 e.24.1.1 90660 1oivA 191 4.94e+01 c.37.1.8 93076 1sy6A 204 4.96e+01 b.1.1.4,b.1.1.4 106111,106112 1u0kA 288 5.02e+01 d.21.1.2,d.21.1.2 107547,107548 1l0sA 90 5.05e+01 b.81.2.1 73408 1qfhA 212 5.09e+01 1qfhA b.1.18.10,b.1.18.10 21893,21894 1hbnB 442 5.10e+01 1mroB a.89.1.1,d.58.31.2 60900,60901 1fe0A 68 5.14e+01 1cc8A d.58.17.1 39345 1kf6B 243 5.14e+01 a.1.2.1,d.15.4.2 72397,72398 1exnA 290 5.22e+01 1exnA a.60.7.1,c.120.1.2 18088,33358 1hf2A 210 5.28e+01 1hf2A b.80.3.1,c.102.1.1 60992,60993 2a8yA 270 5.30e+01 1hynP 379 5.46e+01 1hynP d.112.1.2 61408 2dddA 225 5.49e+01 1g8iA 190 5.50e+01 1rec a.39.1.5 60363 1qhkA 47 5.73e+01 1qhkA d.100.1.2 40694 2fz4A 237 5.74e+01 1q47A 495 5.79e+01 b.69.12.1 104532 1afb1 154 5.82e+01 1rtm1 1yuwA 554 5.87e+01 1iq9A 61 5.89e+01 g.7.1.1 90669 1u3eM 174 5.91e+01 d.4.1.3,d.285.1.1 107640,107641 3nodB 423 5.94e+01 1nseA d.174.1.1 42513 1rl4A 188 5.97e+01 d.167.1.1 97636 1dkzA 219 6.03e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1oc2A 348 6.08e+01 c.2.1.2 92765 1otgA 125 6.11e+01 1otgA d.80.1.2 39831 1bk0 331 6.30e+01 1bk0 b.82.2.1 28118 1e30A 155 6.33e+01 1rcy b.6.1.1 23016 1lci 550 6.33e+01 1lci e.23.1.1 43349 1ihp 438 6.38e+01 1ihp c.60.1.2 33993 1kepA 348 6.42e+01 c.2.1.2 68536 1db2A 377 6.43e+01 1sek e.1.1.1 42672 1ciy 590 6.44e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1i58A 189 6.49e+01 1b3qA d.122.1.3 61773 1exnB 290 6.52e+01 1exnA a.60.7.1,c.120.1.2 18089,33359 1n67A 359 6.54e+01 b.2.3.4,b.2.3.4 85354,85355 1y9kA 157 6.55e+01 1pyiA 96 6.59e+01 1pyiA g.38.1.1,h.1.3.1 45079,45512 1ux8A 132 6.60e+01 2bx2L 517 6.61e+01 1ko3A 230 6.61e+01 d.157.1.1 90974 8rxnA 52 6.62e+01 1rb9 g.41.5.1 45215 2bsaA 303 6.65e+01 1o9lA 481 6.69e+01 c.124.1.2,c.124.1.3 81241,81242 1odmA 331 6.69e+01 b.82.2.1 86875 1ogiA 303 6.72e+01 b.43.4.2,c.25.1.1 92914,92915 1zn6A 227 6.73e+01 1rb9 53 6.79e+01 1rb9 g.41.5.1 45214 1w34A 304 6.83e+01 1y60A 169 6.88e+01 1ut8A 291 6.89e+01 a.60.7.1,c.120.1.2 99908,99909 1sr8A 298 6.91e+01 e.54.1.1 105959 1tq5A 242 6.93e+01 1yqfA 203 6.93e+01 1xewX 182 6.95e+01 1yk4A 52 6.98e+01 1g79A 218 7.01e+01 1ci0A b.45.1.1 25752 1m1eB 81 7.05e+01 a.161.1.1 78400 1oe1A 336 7.08e+01 b.6.1.3,b.6.1.3 86891,86892 1rerA 391 7.27e+01 b.1.18.4,f.10.1.1 97327,97328 1xubA 298 7.27e+01 1djxB 624 7.33e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17343,23160,29588 1pylA 97 7.39e+01 d.1.1.2 104391 1e79G 272 7.41e+01 1e79G c.49.2.1 33158 1y7wA 291 7.42e+01 1wzlA 585 7.52e+01 1mo9A 523 7.54e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1u6zA 513 7.63e+01 1jjeA 222 7.72e+01 1a7tA d.157.1.1 63117 1jjtA 228 7.76e+01 1a7tA d.157.1.1 63139 1h21A 247 7.83e+01 a.138.1.3 76510 1go2A 304 7.83e+01 b.43.4.2,c.25.1.1 76243,76244 1si7A 369 7.86e+01 d.265.1.4 98883 1rpa 342 7.86e+01 1cviA c.60.1.2 33983 1iqsA 88 7.87e+01 d.214.1.1 71278 1rztA 331 7.91e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 1lkkA 105 8.02e+01 1lckA d.93.1.1 40412 2fn2 59 8.03e+01 1e8bA g.14.1.2 44668 1afh 93 8.04e+01 1rzl a.52.1.1 17816 1que 303 8.05e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1b2rA 304 8.12e+01 1fnc b.43.4.2,c.25.1.1 25648,31538 1pdkB 157 8.13e+01 1pdkB b.2.3.2 22427 1fu1B 203 8.13e+01 1fu1B b.59.1.1,h.1.11.1 27077,45631 1hmt 132 8.18e+01 1hmt b.60.1.2 27169 1fk5A 93 8.22e+01 1rzl a.52.1.1 59866 1ukvY 206 8.24e+01 c.37.1.8 107918 1of4A 179 8.27e+01 b.18.1.18 86932 2pcfB 250 8.29e+01 1hcz i.4.1.1 45911 1mzm 93 8.34e+01 1rzl a.52.1.1 17814 2adgA 214 8.35e+01 1zghA 260 8.36e+01 1szwA 379 8.38e+01 d.265.1.4 99047 1diwA 441 8.41e+01 1a8d b.29.1.6,b.42.4.2 24264,25609 1xg9A 260 8.50e+01 2cxkA 95 8.54e+01 1rdg 53 8.56e+01 1rb9 g.41.5.1 45221 2c30A 321 8.59e+01 1tsg 98 8.60e+01 1tsg 1i86A 389 8.65e+01 c.95.1.2,c.95.1.2 66068,66069 2g6tA 306 8.70e+01 1jjfA 268 8.72e+01 c.69.1.2 66765 1ji2A 585 8.72e+01 b.1.18.2,b.71.1.1,c.1.8.1 71672,71673,71674 1ghj 79 8.81e+01 1ghj b.84.1.1 28232 1c76A 136 8.93e+01 2sak d.15.5.1 37718 1bglA 1023 8.96e+01 1bglA b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 22097,22098,23734,24358,28857 1ag6 99 8.97e+01 1plc b.6.1.1 22857