# List of top-scoring protein chains for t2k-100-30-stride-ebghtl-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 1gz0A 253 7.65e-36 c.116.1.1,d.79.3.3 76391,76392 1ipaA 274 7.85e-33 c.116.1.1,d.79.3.3 71254,71255 1x7oA 287 1.25e-31 1v2xA 194 2.61e-24 c.116.1.1 100274 1zjrA 211 1.32e-23 1mxiA 160 5.80e-16 c.116.1.1 79646 1rqlA 267 1.32e-02 c.108.1.3 97750 1h1yA 228 1.48e-02 c.1.2.2 76506 1swvA 267 1.75e-02 1k7yA 577 2.26e-02 a.46.1.1,c.23.6.1,d.173.1.1 68272,68273,68274 1wlsA 328 2.54e-02 1j8yF 297 3.55e-02 1ng1 a.24.13.1,c.37.1.10 62747,62748 1bmtA 246 3.77e-02 1bmtA a.46.1.1,c.23.6.1 17757,31235 1rj9A 304 3.84e-02 a.24.13.1,c.37.1.10 97553,97554 1ujpA 271 4.11e-02 c.1.2.4 99462 1zxxA 319 4.32e-02 1zjjA 263 4.41e-02 1wnfA 328 5.33e-02 1fezA 256 6.30e-02 1fezA c.108.1.3 43343 1j8mF 297 8.06e-02 1ng1 a.24.13.1,c.37.1.10 62742,62743 1sdsA 117 8.40e-02 d.79.3.1 105439 1qwgA 251 8.50e-02 c.1.27.1 96473 1rdfA 267 8.79e-02 c.108.1.3 104884 2tpsA 227 9.67e-02 2tpsA c.1.3.1 28591 1pxwA 128 1.03e-01 d.79.3.1 95305 1xf1A 926 1.10e-01 1xbiA 120 1.21e-01 1ojxA 263 1.24e-01 c.1.10.1 93164 1h7mA 102 1.25e-01 d.79.3.1 83485 1w8sA 263 1.35e-01 1w41A 101 1.93e-01 1geqA 248 2.33e-01 2tysA c.1.2.4 28589 1z85A 234 2.45e-01 1js3A 486 2.75e-01 c.67.1.6 67215 1knwA 425 2.91e-01 b.49.2.3,c.1.6.1 90969,90970 1j2rA 199 3.56e-01 c.33.1.3 90788 1dcfA 136 3.69e-01 1dcfA c.23.1.2 31124 2as0A 396 3.72e-01 1tk9A 188 4.12e-01 c.80.1.3 107082 1t0bA 252 4.81e-01 c.23.16.6 106199 2akzA 439 4.90e-01 1twdA 256 5.44e-01 c.1.30.1 107397 1z15A 344 5.51e-01 1te6A 439 5.53e-01 c.1.11.1,d.54.1.1 106797,106798 1xx1A 285 5.68e-01 1tzjA 338 5.77e-01 1lvwA 295 5.79e-01 c.68.1.6 84723 1nxzA 246 6.56e-01 b.122.1.2,c.116.1.5 86391,86392 1xrtA 467 7.14e-01 1vhyA 257 7.16e-01 b.122.1.2,c.116.1.5 100714,100715 1jj2F 119 7.26e-01 1ffkE d.79.3.1 63091 1fts 295 8.52e-01 1ng1 a.24.13.1,c.37.1.10 16968,32279 1jztA 246 9.06e-01 c.104.1.1 63319 1v5xA 203 9.54e-01 c.1.2.4 100377 1gc0A 398 9.63e-01 c.67.1.3 70168 2liv 344 9.67e-01 2liv c.93.1.1 35708 1d7kA 421 9.78e-01 7odcA b.49.2.3,c.1.6.1 26486,28648 1bqcA 302 1.02e+00 1bqcA c.1.8.3 28831 1vlmA 219 1.11e+00 c.66.1.41 108836 2aifA 135 1.12e+00 1o98A 511 1.19e+00 c.105.1.1,c.76.1.3 86684,86685 1gca 309 1.27e+00 1gca c.93.1.1 35659 1pwxA 254 1.29e+00 c.2.1.2 95262 1e9iA 431 1.33e+00 c.1.11.1,d.54.1.1 64818,64819 2ng1 293 1.43e+00 1ng1 a.24.13.1,c.37.1.10 16962,32273 1xi3A 215 1.46e+00 c.1.3.1 109601 1p7tA 731 1.53e+00 c.1.13.1 94319 1d8cA 723 1.56e+00 1d8cA c.1.13.1 29325 1vjrA 271 1.64e+00 c.108.1.14 100832 2fymA 431 1.65e+00 1v6zA 228 1.69e+00 2fr1A 486 1.80e+00 7odcA 424 1.82e+00 7odcA b.49.2.3,c.1.6.1 26488,28650 1nvmA 345 1.87e+00 a.5.7.1,c.1.10.5 86249,86250 2a3nA 355 1.91e+00 1wyuB 474 2.21e+00 1tx2A 297 2.21e+00 c.1.21.1 107420 1eqjA 511 2.23e+00 1ejjA c.105.1.1,c.76.1.3 59495,59496 1i4nA 251 2.24e+00 c.1.2.4 71114 1i3kA 348 2.25e+00 1xel c.2.1.2 61595 1i60A 278 2.29e+00 c.1.15.4 71118 1xg4A 295 2.34e+00 1wqaA 455 2.38e+00 1kngA 156 2.38e+00 c.47.1.10 72777 2dri 271 2.48e+00 2dri c.93.1.1 35637 1k3rA 268 2.54e+00 b.40.4.10,c.116.1.2 72018,72019 1qorA 327 2.56e+00 1qorA b.35.1.2,c.2.1.1 24766,29782 1e7kA 128 2.65e+00 1ffkE d.79.3.1 39813 1tc5A 194 2.92e+00 c.110.1.1 106752 1zmtA 254 2.98e+00 2admA 421 3.02e+00 2admA c.66.1.27 34238 1mumA 295 3.04e+00 c.1.12.7 85108 2b0cA 206 3.10e+00 1mc3A 296 3.10e+00 c.68.1.6 78943 2a67A 167 3.12e+00 1e5eA 404 3.13e+00 1ibjA c.67.1.3 59265 1whtB 153 3.18e+00 1whtB 1z5yE 149 3.26e+00 1aqjA 421 3.29e+00 2admA c.66.1.27 34242 1bcsB 160 3.31e+00 1whtB 1zu4A 320 3.46e+00 1xuuA 349 3.50e+00 1whsB 153 3.55e+00 1whtB 1uu1A 335 3.57e+00 c.67.1.1 99993 1umdB 324 3.69e+00 c.36.1.7,c.48.1.2 99600,99601 1t9kA 347 3.71e+00 c.124.1.5 106721 1ffkE 119 3.87e+00 1ffkE d.79.3.1 39812 1p3dA 475 3.94e+00 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1gqyA 475 4.16e+00 c.5.1.1,c.59.1.1,c.72.2.1 83305,83306,83307 1j5eK 129 4.36e+00 c.55.4.1 71554 1jpnA 296 4.38e+00 a.24.13.1,c.37.1.10 67039,67040 1ea7A 310 4.54e+00 c.41.1.1 70086 1g38A 393 4.55e+00 2admA c.66.1.27 60235 1igs 248 4.76e+00 1a53 c.1.2.4 28565 1qcwA 410 4.78e+00 1gox c.1.4.1 28622 1juk 248 4.80e+00 1a53 c.1.2.4 28567 1qopA 268 4.84e+00 2tysA c.1.2.4 28570 1xs5A 241 4.87e+00 3pfk 319 4.95e+00 3pfk c.89.1.1 35581 1sjdA 368 5.02e+00 c.1.11.2,d.54.1.1 105632,105633 1ejjA 511 5.03e+00 1ejjA c.105.1.1,c.76.1.3 59422,59423 1rlkA 117 5.05e+00 c.131.1.1 97651 1cs0C 1073 5.14e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18559,31488,31675,31676,41520,41521 1nu5A 370 5.14e+00 c.1.11.2,d.54.1.1 92183,92184 1fbnA 230 5.15e+00 1fbnA c.66.1.3 34181 1rbp 182 5.18e+00 1aqb b.60.1.1 27085 1vmeA 410 5.20e+00 c.23.5.1,d.157.1.3 108893,108894 1o66A 275 5.23e+00 c.1.12.8 92547 1ffh 294 5.29e+00 1ng1 a.24.13.1,c.37.1.10 16960,32271 1ujqA 305 5.30e+00 c.1.12.7 99463 1zwzA 126 5.31e+00 1g8sA 230 5.32e+00 c.66.1.3 90507 2fi1A 190 5.34e+00 1keeG 1073 5.37e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68516,68517,68518,68519,68520,68521 1dkrA 317 5.40e+00 1dkuA c.61.1.2,c.61.1.2 34114,34115 1a9xA 1058 5.48e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1c3oE 1073 5.53e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18564,31493,31685,31686,41530,41531 1jdbB 1073 5.60e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18574,31503,31705,31706,41550,41551 1p3wA 404 5.62e+00 c.67.1.3 87752 4pfk 319 5.66e+00 3pfk c.89.1.1 35582 1keeA 1073 5.81e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68492,68493,68494,68495,68496,68497 3chy 128 5.81e+00 3chy c.23.1.1 31038 1dkuA 317 5.91e+00 1dkuA c.61.1.2,c.61.1.2 34118,34119 1o5zA 442 6.04e+00 c.59.1.2,c.72.2.2 92530,92531 1iyxA 432 6.05e+00 c.1.11.1,d.54.1.1 83815,83816 1keeC 1073 6.05e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68500,68501,68502,68503,68504,68505 1c3oG 1073 6.05e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18565,31494,31687,31688,41532,41533 1h75A 81 6.06e+00 1h75A c.47.1.1 60716 1keeE 1073 6.21e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68508,68509,68510,68511,68512,68513 1vquA 374 6.29e+00 1c3oC 1073 6.52e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18563,31492,31683,31684,41528,41529 2gbp 309 6.53e+00 1gca c.93.1.1 35657 1cs0A 1073 6.57e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1z6nA 167 6.60e+00 2gjlA 328 6.63e+00 1a53 247 6.64e+00 1a53 c.1.2.4 28564 1efpB 252 6.71e+00 1efvB c.26.2.3 31636 1j0aA 325 6.85e+00 c.79.1.1 83871 1m65A 245 6.85e+00 c.6.3.1 84847 1ls1A 295 6.90e+00 a.24.13.1,c.37.1.10 78170,78171 1p80A 753 6.91e+00 c.23.16.3,e.5.1.1 94337,94338 1wmmA 145 6.93e+00 1kv8A 216 6.97e+00 c.1.2.3 73054 1w0mA 226 7.15e+00 c.1.1.1 109027 1vimA 200 7.37e+00 c.80.1.3 100758 1cf9A 753 7.41e+00 1cf9A c.23.16.3,e.5.1.1 31441,42815 1vlwA 217 7.43e+00 c.1.10.1 108868 1j6uA 469 7.48e+00 c.5.1.1,c.59.1.1,c.72.2.1 77094,77095,77096 1c3oA 1073 7.53e+00 1c3oA a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18562,31491,31681,31682,41526,41527 1ve5A 311 7.59e+00 1wdaA 670 7.72e+00 b.2.9.1,b.6.1.6,d.126.1.5 109243,109244,109245 1ynpA 317 7.73e+00 1yqdA 366 7.85e+00 2dexX 671 7.88e+00 2aamA 309 7.94e+00 1lc5A 364 7.95e+00 c.67.1.1 73827 1b5pA 385 8.00e+00 c.67.1.1 90403 1p9rA 418 8.01e+00 c.37.1.11 94399 4enl 436 8.08e+00 4enl c.1.11.1,d.54.1.1 29202,38846 1ab5A 125 8.15e+00 3chy c.23.1.1 31056 1is8K 84 8.16e+00 d.205.1.1 66331 1m2kA 249 8.22e+00 c.31.1.5 84754 1ru8A 232 8.26e+00 c.26.2.1 97849 1cozA 129 8.31e+00 1cozA c.26.1.2 31598 1w6tA 444 8.38e+00 1iciA 256 8.42e+00 1iciA c.31.1.5 62266 1uc8A 280 8.55e+00 c.30.1.6,d.142.1.7 99165,99166 1o6dA 163 8.73e+00 c.116.1.3 92567 1o0uA 429 8.89e+00 c.118.1.1 80743 1ihoA 283 8.94e+00 1ihoA c.26.1.4 62390 1jg5A 83 8.96e+00 d.205.1.1 66666 1ab6A 125 9.11e+00 3chy c.23.1.1 31054 2bznA 351 9.18e+00 1ibsA 317 9.23e+00 c.61.1.2,c.61.1.2 66107,66108 1m3sA 186 9.35e+00 c.80.1.3 78573 1vp4A 425 9.45e+00 2ge3A 170 9.62e+00 1zs9A 261 9.78e+00 1xbtA 193 9.80e+00 2gasA 307 9.90e+00 1vs0A 310 9.90e+00 1tjyA 316 1.01e+01 c.93.1.1 107062 1dbiA 280 1.03e+01 1gci c.41.1.1 32543 1h05A 146 1.03e+01 c.23.13.1 76433 1w4rA 195 1.04e+01 1spiA 358 1.04e+01 1frpA e.7.1.1 42939 1x3lA 440 1.04e+01 1fjgK 129 1.04e+01 1fjfK c.55.4.1 33733 1o69A 394 1.07e+01 c.67.1.4 92560 2d0oA 610 1.07e+01 2agaA 190 1.08e+01 2acaA 189 1.08e+01 1p0fA 373 1.09e+01 b.35.1.2,c.2.1.1 87642,87643 1pdz 434 1.09e+01 4enl c.1.11.1,d.54.1.1 29215,38859 1jud 232 1.09e+01 1qq5A c.108.1.1 43325 1o4sA 389 1.10e+01 c.67.1.1 86620 1gxlA 213 1.10e+01 d.215.1.1 70713 1zrn 232 1.10e+01 1qq5A c.108.1.1 43323 1d2nA 272 1.12e+01 1d2nA c.37.1.20 32428 1mrzA 293 1.12e+01 b.43.5.1,c.26.1.3 91452,91453 1ltdA 506 1.14e+01 1gox c.1.4.1,d.120.1.1 28618,41086 1n71A 180 1.14e+01 d.108.1.1 85370 1xklA 273 1.14e+01 1qe5A 266 1.16e+01 1b8oA c.56.2.1 33784 1jbeA 128 1.16e+01 3chy c.23.1.1 62845 1m7xA 617 1.16e+01 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 1mioB 458 1.18e+01 1qguB c.92.2.3 35602 1xfkA 336 1.20e+01 2a4nA 182 1.20e+01 2al1A 436 1.21e+01 1q9jA 422 1.23e+01 c.43.1.2,c.43.1.2 104590,104591 1oneA 436 1.25e+01 4enl c.1.11.1,d.54.1.1 29200,38844 1x42A 232 1.26e+01 1wr2A 238 1.27e+01 1sazA 381 1.27e+01 2fdrA 229 1.29e+01 2oneA 436 1.29e+01 4enl c.1.11.1,d.54.1.1 29203,38847 1eyrA 228 1.30e+01 1eyrA c.68.1.13 34514 1uxtA 501 1.31e+01 c.82.1.1 108125 2b8nA 429 1.32e+01 1miwA 404 1.33e+01 a.173.1.1,d.218.1.4 79162,79163 1ooeA 236 1.36e+01 c.2.1.2 87196 1pta 318 1.36e+01 1pscA c.1.9.3 29064 1ah0 316 1.36e+01 1frb c.1.7.1 28685 1ii7A 333 1.38e+01 1ii7A d.159.1.4 62415 1v4pA 157 1.40e+01 1agnA 373 1.42e+01 2ohxA b.35.1.2,c.2.1.1 24737,29753 1ah4 315 1.43e+01 1frb c.1.7.1 28684 1usgA 346 1.43e+01 c.93.1.1 99864 1ymqA 261 1.45e+01 1uufA 369 1.45e+01 b.35.1.2,c.2.1.1 100006,100007 1bksA 268 1.45e+01 2tysA c.1.2.4 28585 1bjwA 382 1.46e+01 1bjwA c.67.1.1 34349 1uurA 473 1.48e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1u7pA 164 1.49e+01 1tqjA 230 1.50e+01 c.1.2.2 107228 1bxsA 501 1.50e+01 1bpwA c.82.1.1 35357 2a1fA 247 1.51e+01 2al2A 436 1.52e+01 1o7jA 327 1.53e+01 c.88.1.1 81140 1jc4A 148 1.55e+01 1jc4A d.32.1.4 62863 1y9kA 157 1.55e+01 1qo2A 241 1.55e+01 1qo2A c.1.2.1 28533 1ck9A 104 1.56e+01 1ck9A d.79.3.1 39806 1w23A 360 1.56e+01 1n7kA 234 1.56e+01 c.1.10.1 85374 1b87A 181 1.57e+01 1b87A d.108.1.1 40797 1vhh 162 1.59e+01 1vhh d.65.1.2 39550 1rvgA 305 1.59e+01 c.1.10.2 97920 1jm1A 204 1.59e+01 b.33.1.1 71745 2gwgA 350 1.59e+01 1z8fA 228 1.60e+01 1hbp 183 1.60e+01 1aqb b.60.1.1 27079 1fcbA 511 1.61e+01 1gox c.1.4.1,d.120.1.1 28620,41087 1oxkB 134 1.65e+01 c.23.1.1 93691 1t5oA 351 1.66e+01 c.124.1.5 106459 1nsf 273 1.66e+01 1d2nA c.37.1.20 32429 1hbq 183 1.66e+01 1aqb b.60.1.1 27078 1kczA 413 1.66e+01 c.1.11.2,d.54.1.1 68451,68452 1m3uA 264 1.66e+01 c.1.12.8 84784 2c1lA 358 1.67e+01 1qfcA 306 1.67e+01 1uteA d.159.1.1 42077 1q6oA 216 1.68e+01 c.1.2.3 95986 1wdvA 152 1.68e+01 1ck2A 104 1.70e+01 1ck9A d.79.3.1 39809 1imjA 210 1.70e+01 c.69.1.23 71246 2wsyA 268 1.74e+01 2tysA c.1.2.4 28588 1d5wC 126 1.75e+01 1dbwA c.23.1.1 31101 1bxrA 1073 1.75e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18570,31499,31697,31698,41542,41543 6pfkA 319 1.75e+01 3pfk c.89.1.1 35583 1k4jA 230 1.75e+01 d.108.1.3 72057 1vkcA 158 1.76e+01 1im5A 180 1.76e+01 c.33.1.3 66211 1e6mA 128 1.77e+01 3chy c.23.1.1 31039 1s4qA 228 1.79e+01 c.37.1.1 98507 1gt8B 1025 1.80e+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 1km4A 247 1.83e+01 c.1.2.3 72740 1u9cA 224 1.84e+01 1bag 425 1.85e+01 1bag b.71.1.1,c.1.8.1 27720,28707 1xdwA 331 1.85e+01 1nsj 205 1.85e+01 1nsj c.1.2.4 28560 1st9A 143 1.86e+01 c.47.1.10 98987 1dxeA 256 1.88e+01 1dxeA c.1.12.5 29310 1mjhB 162 1.90e+01 1mjhA c.26.2.4 31640 1wdiA 345 1.94e+01 1ox6A 555 1.95e+01 c.1.2.1,c.23.16.1 87505,87506 1rpxA 230 1.95e+01 1rpxA c.1.2.2 28536 1pymA 295 1.95e+01 1pymA c.1.12.7 29308 1ble 163 1.95e+01 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