# 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 1ihp 438 5.52e-02 1ihp c.60.1.2 33993 6gsvA 217 1.47e-01 1b8xA a.45.1.1,c.47.1.5 17633,32925 1tbmA 326 3.83e-01 a.211.1.2 106744 1eemA 241 3.89e-01 1eemA a.45.1.1,c.47.1.5 17717,33011 2c4jA 218 4.07e-01 1xw5A 217 4.33e-01 1efcA 393 4.63e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 2myo 118 7.63e-01 2myo d.211.1.1 19175 1qfxA 460 7.95e-01 1qfxA c.60.1.2 33994 1zv1A 65 7.99e-01 1q18A 332 8.09e-01 c.55.1.7,c.55.1.7 104470,104471 1myo 118 8.24e-01 2myo d.211.1.1 19174 2fiyA 309 8.36e-01 1cr6B 554 8.50e-01 1cr6B c.69.1.11,c.108.1.2 34688,43338 1sz2A 332 8.54e-01 1y3nA 490 8.77e-01 1efuA 385 1.02e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1trrA 107 1.09e+00 1jhgA a.4.12.1 19017 1bd8 156 1.17e+00 1bd8 d.211.1.1 19157 1b4pA 217 1.24e+00 a.45.1.1,c.47.1.5 83158,83159 2wrpR 107 1.42e+00 1jhgA a.4.12.1 19010 1jpaA 312 1.49e+00 d.144.1.7 67011 1jhgA 101 1.84e+00 1jhgA a.4.12.1 19009 1qwoA 442 1.94e+00 c.60.1.2 104620 2furA 209 1.97e+00 1zd3A 555 2.01e+00 1x1fA 149 2.09e+00 1ohfA 644 2.46e+00 b.121.4.8 93014 1vj5A 555 2.84e+00 c.108.1.2,c.69.1.11 100799,100800 1axdA 209 2.92e+00 1gnwA a.45.1.1,c.47.1.5 17730,33024 2b1eA 564 3.04e+00 1w1oA 534 3.67e+00 d.58.32.4,d.145.1.1 109071,109072 1im5A 180 3.74e+00 c.33.1.3 66211 1m98A 317 4.02e+00 a.175.1.1,d.17.4.6 78866,78867 1ufaA 520 4.49e+00 a.8.3.3,c.6.2.4 99329,99330 1x6vA 630 5.32e+00 1rcsA 105 5.51e+00 1jhgA a.4.12.1 19025 1gumA 222 5.52e+00 1pgtA a.45.1.1,c.47.1.5 17683,32977 1x91A 153 5.64e+00 1ni3A 392 5.86e+00 c.37.1.8,d.15.10.2 80531,80532 1xmeA 568 6.08e+00 1zejA 293 6.24e+00 1zboA 210 6.84e+00 2gsvA 80 6.96e+00 1p4dA 330 7.09e+00 d.89.1.5 94101 1gewA 356 7.46e+00 1gewA c.67.1.1 60470 1ycsB 239 7.50e+00 1ycsB d.211.1.1,b.34.2.1 19155,24553 1nd7A 374 7.58e+00 d.148.1.1 91817 1w07A 659 7.72e+00 1qrjB 199 7.87e+00 1qrjB a.28.3.1 16952 1fhuA 320 8.15e+00 1fhuA c.1.11.2,d.54.1.1 29234,38878 1fsu 492 8.49e+00 1auk c.76.1.2 35032 2afwA 329 8.52e+00 1z00B 84 8.87e+00 1sszA 34 9.22e+00 j.35.1.1 105999 1n1jA 93 9.22e+00 a.22.1.3 79813 1ad3A 452 9.51e+00 1ad3A c.82.1.1 35335 1f7uA 607 9.63e+00 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 59673,59674,59675 1n45A 233 1.02e+01 a.132.1.1 79981 1jb0I 38 1.05e+01 1jb0I f.23.17.1 62826 2fu4A 83 1.11e+01 1yy7A 213 1.12e+01 1fg7A 356 1.13e+01 1gewA c.67.1.1 59819 1yozA 116 1.13e+01 1etu 394 1.14e+01 1efcA c.37.1.8 64737 2mev2 256 1.17e+01 1aym2 1d5wC 126 1.19e+01 1dbwA c.23.1.1 31101 1t5oA 351 1.20e+01 c.124.1.5 106459 1hdiA 413 1.26e+01 16pk c.86.1.1 60964 2lefA 86 1.30e+01 2lefA a.21.1.1 16433 1whrA 124 1.33e+01 1rh9A 373 1.34e+01 1h6zA 913 1.39e+01 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 2occH 85 1.46e+01 2occH a.51.1.1 17796 2ccmA 191 1.48e+01 2iu5A 195 1.49e+01 1hp5A 512 1.49e+01 1hp4A c.1.8.6,d.92.2.1 61113,61114 1o5hA 214 1.52e+01 a.191.1.1 92497 2fqmA 75 1.53e+01 1z6uA 150 1.57e+01 1rxqA 178 1.58e+01 a.213.1.1 105118 2aplA 157 1.62e+01 1jk8B 190 1.63e+01 1iakB b.1.1.2,d.19.1.1 63147,63148 1eia 207 1.65e+01 1eia a.28.3.1,a.73.1.1 16951,18331 1e08A 371 1.67e+01 i.4.1.1 45914 1h2vC 771 1.77e+01 a.118.1.14,a.118.1.14,a.118.1.14 76592,76593,76594 1ppjF 110 1.77e+01 f.27.1.1 104262 1hp4A 512 1.80e+01 1hp4A c.1.8.6,d.92.2.1 61111,61112 1xioA 261 1.83e+01 1jakA 512 1.84e+01 c.1.8.6,d.92.2.1 66472,66473 1c7nA 399 1.87e+01 1d2fA c.67.1.3 34413 1dbwA 126 1.95e+01 1dbwA c.23.1.1 31095 1vi0A 206 1.96e+01 a.4.1.9,a.121.1.1 100720,100721 1kbuA 349 2.00e+01 a.60.9.1,d.163.1.1 72284,72285 1i9gA 280 2.04e+01 c.66.1.13 62090 2aclB 244 2.04e+01 3crxA 343 2.14e+01 4crxA a.60.9.1,d.163.1.1 18101,42161 1hg2A 289 2.14e+01 1hg5A a.7.8.2,a.118.9.3 90358,90359 1llmC 88 2.15e+01 g.37.1.1,g.37.1.1 91059,91060 1br1B 150 2.16e+01 1wdcC a.39.1.5 17309 1dckA 126 2.18e+01 1dbwA c.23.1.1 31097 1fpoA 171 2.22e+01 1fpoA a.2.3.1,a.23.1.1 15693,16487 4crxA 322 2.30e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 1x74A 360 2.30e+01 1mzbA 136 2.33e+01 a.4.5.42 91497 1b8aA 438 2.34e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1yw0A 276 2.37e+01 1h3nA 878 2.39e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1kpsB 171 2.41e+01 a.118.12.1 68787 1ozhA 566 2.45e+01 c.31.1.3,c.36.1.5,c.36.1.9 93833,93834,93835 1repC 251 2.46e+01 1repC a.4.5.10,a.4.5.10 16125,16126 1jhdA 396 2.49e+01 b.122.1.3,c.26.1.5 66712,66713 1qd9A 124 2.59e+01 1qu9A d.79.1.1 39758 1v9jA 113 2.61e+01 d.52.6.1 100542 1y88A 199 2.66e+01 1gulA 222 2.67e+01 1pgtA a.45.1.1,c.47.1.5 17675,32969 1v9mA 323 2.69e+01 f.40.1.1 100543 1mun 225 2.69e+01 1mun a.96.1.2 18744 1skf 262 2.81e+01 1skf e.3.1.1 42684 1ewfA 456 2.84e+01 1bp1 d.83.1.1,d.83.1.1 40024,40025 2es9A 115 2.85e+01 1bgp 309 2.85e+01 1bgp a.93.1.1 18690 1bp1 456 2.88e+01 1bp1 d.83.1.1,d.83.1.1 40026,40027 1crxA 322 2.89e+01 4crxA a.60.9.1,d.163.1.1 18097,42157 2bo9A 308 2.89e+01 1es5A 262 2.89e+01 1skf e.3.1.1 42679 1esiA 262 2.91e+01 1skf e.3.1.1 42682 1z2nX 324 2.92e+01 1jmtB 28 2.96e+01 1s6lA 212 2.99e+01 2db0A 253 3.10e+01 1ockA 412 3.13e+01 c.117.1.1 86802 1pveA 72 3.13e+01 a.189.1.1 104322 2bbrA 195 3.13e+01 1r5zA 323 3.15e+01 f.40.1.1 97135 1muyA 225 3.15e+01 1mun a.96.1.2 18745 2ctoA 93 3.18e+01 1n0qA 93 3.21e+01 k.37.1.1 79754 2a2fX 325 3.28e+01 1dtdA 303 3.28e+01 1aye c.56.5.1 33823 1zwwA 256 3.28e+01 1z6gA 218 3.32e+01 1jae 471 3.34e+01 1smd b.71.1.1,c.1.8.1 27773,28760 2bykB 128 3.35e+01 1qcrF 103 3.39e+01 1be3F f.27.1.1 43676 1ehkA 562 3.40e+01 1ehkA f.24.1.1 43624 1hmy 327 3.42e+01 6mhtA c.66.1.26 34229 1pq1A 196 3.44e+01 f.1.4.1 94986 1xo0A 324 3.46e+01 1pa7A 130 3.46e+01 a.40.1.1 94410 1ordA 730 3.50e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31274,34503,41124 1okcA 297 3.50e+01 f.42.1.1 93248 1gvhA 396 3.54e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1zrzA 364 3.57e+01 1ugpA 203 3.61e+01 d.149.1.1 107831 2ch0A 133 3.62e+01 2f96A 224 3.63e+01 1r6wA 322 3.65e+01 c.1.11.2,d.54.1.1 97165,97166 1ireA 204 3.66e+01 d.149.1.1 76769 1cn4C 166 3.72e+01 1eerA a.26.1.2 16847 1fhvA 323 3.78e+01 1fhuA c.1.11.2,d.54.1.1 29235,38879 1v54H 85 3.79e+01 a.51.1.1 100329 1r6uA 437 3.80e+01 c.26.1.1 97163 1fxtA 149 3.85e+01 d.20.1.1 65055 1qs2A 401 3.86e+01 1qs1A d.166.1.1,d.166.1.1 42268,42269 1nkl 78 3.88e+01 1nkl a.64.1.1 18140 1noyA 388 3.91e+01 1clqA c.55.3.5 33713 1yzyA 413 3.98e+01 1otsA 465 4.09e+01 f.20.1.1 87415 1hf8A 289 4.10e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1es2A 262 4.23e+01 1skf e.3.1.1 42680 1fjxA 327 4.23e+01 6mhtA c.66.1.26 34228 2aawA 222 4.25e+01 1sheA 103 4.29e+01 d.274.1.1 105551 1s7jA 262 4.30e+01 d.21.1.2 98647 1b35A 260 4.30e+01 1b35A b.121.4.1 23333 1n3kA 130 4.31e+01 a.77.1.4 79965 2fpmA 322 4.31e+01 1kl9A 182 4.31e+01 b.40.4.5 72681 1v1rA 400 4.32e+01 c.36.1.11 108272 1k6iA 352 4.37e+01 c.2.1.2 68223 1fzyA 149 4.44e+01 d.20.1.1 65072 1huvA 380 4.45e+01 c.1.4.1 61277 1xg2B 153 4.50e+01 1qmzB 259 4.51e+01 1vin a.74.1.1,a.74.1.1 18338,18339 1p4cA 380 4.53e+01 c.1.4.1 94100 2g6tA 306 4.53e+01 1aye 401 4.56e+01 1aye c.56.5.1,d.58.3.1 33824,39065 1d6gA 47 4.57e+01 1d6gA g.33.1.1 44976 1qq8A 214 4.70e+01 1qq8A 1g7oA 215 4.73e+01 1g7oA a.45.1.1,c.47.1.5 60332,60333 3mhtA 327 4.75e+01 6mhtA c.66.1.26 34234 1n3gA 113 4.76e+01 d.204.1.1 79962 1ds1A 324 4.80e+01 1drtA b.82.2.2 28127 1bavA 309 4.81e+01 1aye c.56.5.1 33806 6cpa 307 4.84e+01 1aye c.56.5.1 33816 1dryA 324 4.85e+01 1drtA b.82.2.2 28128 1kpkA 473 4.88e+01 f.20.1.1 68776 2fgtA 417 4.89e+01 2aheA 267 4.90e+01 1wovA 250 4.95e+01 1tw9A 206 4.98e+01 a.45.1.1,c.47.1.5 107381,107382 1gdeA 389 4.98e+01 c.67.1.1 60456 1m65A 245 5.01e+01 c.6.3.1 84847 1zq9A 285 5.02e+01 1w2fA 276 5.05e+01 d.143.1.3 109125 1hg5A 289 5.07e+01 1hg5A a.7.8.2,a.118.9.3 90360,90361 1us5A 314 5.10e+01 c.94.1.1 99856 2c7pA 327 5.17e+01 1t7rA 269 5.19e+01 a.123.1.1 106635 1nozA 388 5.20e+01 1clqA c.55.3.5 33715 1pgtA 210 5.23e+01 1pgtA a.45.1.1,c.47.1.5 17515,32809 1x3zA 335 5.26e+01 2gdjA 264 5.31e+01 1qh4A 380 5.34e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 1r4wA 226 5.35e+01 c.47.1.13 97050 2c30A 321 5.36e+01 2ctb 307 5.37e+01 1aye c.56.5.1 33803 2ctc 307 5.37e+01 1aye c.56.5.1 33802 1m4lA 307 5.39e+01 c.56.5.1 78604 1pn0A 665 5.39e+01 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 2b1xA 470 5.42e+01 2cchB 260 5.43e+01 1aab 83 5.44e+01 1cktA a.21.1.1 16420 1be3F 110 5.47e+01 1be3F f.27.1.1 43668 1u08A 386 5.49e+01 c.67.1.1 107543 1tkeA 224 5.49e+01 1im8A 244 5.51e+01 c.66.1.14 66212 1ihbA 162 5.53e+01 1bd8 d.211.1.1 19161 1pd21 199 5.55e+01 1pd21 1tjlA 151 5.57e+01 a.2.14.1,g.39.1.13 107027,107028 1fohA 664 5.58e+01 1fohA c.3.1.2,c.47.1.10,d.16.1.2 30381,33078,37900 6mhtA 327 5.67e+01 6mhtA c.66.1.26 34226 1iw7C 1119 5.68e+01 e.29.1.1 71474 2beiA 170 5.74e+01 1lghA 56 5.74e+01 1lghA f.3.1.1 43733 1uohA 226 5.74e+01 d.211.1.1 99690 2esnA 310 5.79e+01 1vjrA 271 5.82e+01 c.108.1.14 100832 1fi2A 201 5.84e+01 1fi2A b.82.1.2 59845 1yme 309 5.87e+01 1aye c.56.5.1 33804 1hz4A 373 5.89e+01 a.118.8.2 65960 1aj5A 173 5.94e+01 1alvA a.39.1.8 17367 1kfuS 184 5.96e+01 a.39.1.8 68574 1b73A 254 5.99e+01 1b74A c.78.2.1,c.78.2.1 35266,35267 2f1sA 186 6.00e+01 1t7lA 766 6.03e+01 1b74A 254 6.08e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1v2dA 381 6.09e+01 c.67.1.1 108281 1a1iA 90 6.09e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 44998,44999,45000 2btvA 901 6.10e+01 2btvA e.28.1.1 43376 1s72N 187 6.11e+01 c.55.4.1 105333 1tq4A 413 6.16e+01 c.37.1.8 107201 1mhyD 521 6.16e+01 1mhyD a.25.1.2 16780 1e6iA 121 6.17e+01 1b91A a.29.2.1 16969 1ufzA 83 6.31e+01 a.5.9.1 107821 2afaA 425 6.34e+01 1g2fC 90 6.47e+01 k.12.1.1 60222 1ykhB 132 6.49e+01 1sphA 88 6.50e+01 1ptf d.94.1.1 40544 1q87A 221 6.56e+01 e.47.1.1 96192 1mp8A 281 6.61e+01 d.144.1.7 91384 2grrB 170 6.64e+01 1kplA 473 6.67e+01 f.20.1.1 68782 2b7aA 293 6.68e+01 2atjA 308 6.71e+01 1bgp a.93.1.1 18675 1pta 318 6.72e+01 1pscA c.1.9.3 29064 1t92A 116 6.76e+01 1ewqA 765 6.81e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1y5iC 225 6.84e+01 2b33A 140 6.85e+01 2et1A 201 6.91e+01 1mgpA 313 6.91e+01 c.119.1.1 79098 1m3uA 264 6.97e+01 c.1.12.8 84784 1h0aA 158 6.97e+01 a.118.9.1 76434 1x31D 99 7.01e+01 1ngnA 155 7.06e+01 a.96.1.2 85697 1fx8A 281 7.09e+01 f.19.1.1 43651 1gd9A 389 7.19e+01 c.67.1.1 60454 2gsfA 373 7.20e+01 2a2rA 210 7.29e+01 1xfsA 178 7.29e+01 d.129.3.5 109589 1zy9A 564 7.30e+01 1gqeA 365 7.32e+01 e.38.1.1 70351 1vqoN 187 7.35e+01 1m6kA 251 7.36e+01 e.3.1.1 78695 1myf 153 7.39e+01 1a6m a.1.1.2 15147 1bccF 109 7.47e+01 1be3F f.27.1.1 43700 1t1uA 639 7.48e+01 18gsA 210 7.48e+01 1pgtA a.45.1.1,c.47.1.5 17528,32822 1alvA 173 7.54e+01 1alvA a.39.1.8 17370 8ohm 435 7.54e+01 1heiA c.37.1.14,c.37.1.14 32469,32470 1l1jA 239 7.62e+01 b.47.1.1 84516 2aa4A 289 7.62e+01 1gcqC 70 7.70e+01 1gcpA b.34.2.1 60436 1b06A 210 7.70e+01 1avmA a.2.11.1,d.44.1.1 15740,38737 1zvzA 279 7.70e+01 1z63A 500 7.73e+01 1x23A 155 7.76e+01 1xrtA 467 7.79e+01 2f4mB 61 7.81e+01 1okjA 251 7.82e+01 c.55.1.9,c.55.1.9 103998,103999 1guxA 218 7.83e+01 1guxA a.74.1.3 18388 1x8vA 455 7.88e+01 1ldfA 281 7.90e+01 f.19.1.1 73845 2pia 321 7.90e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1ylqA 96 7.97e+01 1xaa 345 8.05e+01 1cnzA c.77.1.1 35033 1kblA 873 8.09e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1wmmA 145 8.10e+01 1vin 268 8.10e+01 1vin a.74.1.1,a.74.1.1 18354,18355 1a1hA 90 8.18e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 45004,45005,45006 1n1jB 97 8.21e+01 a.22.1.3 79814 1wjgA 137 8.22e+01 1z3eB 73 8.22e+01 1rzsA 61 8.23e+01 a.35.1.2 105139 1r29A 127 8.27e+01 d.42.1.1 96856 2c5rA 67 8.30e+01 1kinA 366 8.34e+01 1xikA 375 8.35e+01 1xikA a.25.1.2 16784 1ituA 369 8.35e+01 c.1.9.7 71423 1vzoA 355 8.39e+01 d.144.1.7 108971 1aisB 200 8.41e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 7atjA 308 8.42e+01 1bgp a.93.1.1 18673 1acp 77 8.43e+01 1acp a.28.1.1 16931 1qo7A 394 8.44e+01 1qo7A c.69.1.11 34697 1ipd 345 8.49e+01 1cnzA c.77.1.1 35038 1xjzA 233 8.51e+01 1idm 343 8.53e+01 1cnzA c.77.1.1 35035 1qhhC 115 8.61e+01 1pjr 1no1A 126 8.61e+01 a.179.1.1 85913 1ddzA 496 8.62e+01 1ddzA c.53.2.1,c.53.2.1 33372,33373 1qbhA 101 8.64e+01 1g3fA g.52.1.1 45374 1es4A 262 8.66e+01 1skf e.3.1.1 42683 1ig6A 107 8.76e+01 1ig6A a.4.3.1 62364 1h9eA 56 8.86e+01 1h9eA a.140.1.1 60825 1s72I 162 8.87e+01 a.4.7.1 105328 1buyA 166 8.87e+01 1eerA a.26.1.2 16848 1eyyA 510 8.87e+01 1eyyA c.82.1.1 35389 1ap7 168 8.90e+01 1bd8 d.211.1.1 19170 2adoA 196 8.95e+01 1zbtA 371 8.95e+01 1zaaC 87 8.97e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 45013,45014,45015