# List of top-scoring protein chains for t06-100-30-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 2f8aA 208 9.10e-39 1xzoA 174 8.17e-17 1st9A 143 7.22e-14 c.47.1.10 98987 2f9sA 151 9.59e-14 1jfuA 186 1.38e-12 c.47.1.10 62940 1kngA 156 7.91e-08 c.47.1.10 72777 1xvwA 160 1.34e-07 2b7kA 200 1.65e-07 1z5yE 149 6.99e-07 1lu4A 136 9.40e-07 c.47.1.10 91124 2cvbA 188 1.35e-06 1zzoA 136 2.40e-06 1o8xA 146 5.65e-06 c.47.1.10 86681 1qmvA 197 1.29e-05 1qq2A c.47.1.10 33066 1i5gA 144 2.93e-05 1ewxA c.47.1.10 61784 2fy6A 143 4.25e-05 1t00A 112 1.28e-04 1faaA 124 2.35e-04 1erv c.47.1.1 32738 1erv 105 3.12e-04 1erv c.47.1.1 32743 1uf5A 303 5.95e-04 d.160.1.2 107808 1thx 115 7.21e-04 1thx c.47.1.1 32732 1r26A 125 3.31e-03 c.47.1.1 96847 2trxA 108 6.70e-03 1thx c.47.1.1 32719 1x0rA 249 8.38e-03 1erw 105 9.66e-03 1erv c.47.1.1 32745 2a5lA 200 9.94e-03 2a4vA 159 1.07e-02 1vpqA 273 2.05e-02 1vhxA 150 5.92e-02 c.55.3.8 100712 1yvoA 172 7.21e-02 1xccA 220 7.59e-02 1vicA 262 7.87e-02 c.68.1.13 100756 1w4vA 119 8.41e-02 1xvqA 175 9.41e-02 1g3qA 237 9.70e-02 1hyqA c.37.1.10 60237 1n8jA 186 9.71e-02 c.47.1.10 85401 1vmeA 410 1.07e-01 c.23.5.1,d.157.1.3 108893,108894 1eejA 216 1.13e-01 1eejA c.47.1.9,d.17.3.1 33057,38071 1pch 88 1.16e-01 1ptf d.94.1.1 40564 2f51A 118 1.30e-01 2fomB 185 1.73e-01 1n3lA 372 1.87e-01 c.26.1.1 79966 2f2lX 167 2.00e-01 1nswA 105 2.35e-01 c.47.1.1 92097 1v98A 140 2.40e-01 1e4fT 419 2.90e-01 1e4fT c.55.1.1,c.55.1.1 33453,33454 1f1uA 323 3.24e-01 d.32.1.3,d.32.1.3 83200,83201 1ogiA 303 4.01e-01 b.43.4.2,c.25.1.1 92914,92915 2c1lA 358 4.07e-01 8rucI 123 4.32e-01 1rboC d.73.1.1 39629 1hgxA 183 4.67e-01 1tc1A c.61.1.1 34027 1senA 164 4.75e-01 c.47.1.1 105465 2a5dA 175 4.98e-01 1m1nA 491 5.49e-01 c.92.2.3 78417 1heiA 451 5.96e-01 1heiA c.37.1.14,c.37.1.14 32463,32464 3tmkA 216 8.23e-01 3tmkA c.37.1.1 31920 1fsgA 233 8.44e-01 1qk3A c.61.1.1 34029 1wsrA 375 8.84e-01 1uc7A 125 1.01e+00 c.47.1.1 99163 2essA 248 1.04e+00 1hd2A 161 1.14e+00 c.47.1.10 60962 1uf3A 228 1.16e+00 d.159.1.6 99317 1wosA 364 1.16e+00 b.44.2.1,d.250.1.1 109468,109469 1z7gA 217 1.32e+00 2plc 274 1.47e+00 2plc c.1.18.2 29614 1bykA 255 1.49e+00 1bykA c.93.1.1 35706 2fqxA 318 1.52e+00 1umdA 367 1.54e+00 c.36.1.11 99599 1oz9A 150 1.55e+00 d.92.1.15 93808 1fnd 314 1.56e+00 1fnc b.43.4.2,c.25.1.1 25626,31516 1tv8A 340 1.61e+00 c.1.28.3 107352 1f74A 293 1.64e+00 1nal3 c.1.10.1 29079 1m2dA 110 1.69e+00 c.47.1.11 78476 2fp7B 172 1.72e+00 1wxxA 382 1.79e+00 1cozA 129 1.81e+00 1cozA c.26.1.2 31598 2f2lA 167 1.97e+00 2b5eA 504 1.97e+00 1m7yA 435 2.00e+00 c.67.1.4 78761 1nu0A 138 2.00e+00 c.55.3.8 92165 1x1nA 524 2.05e+00 1s95A 333 2.06e+00 d.159.1.3 105375 2b18A 164 2.31e+00 1nn5A 215 2.33e+00 c.37.1.1 85892 2az4A 429 2.34e+00 2fneA 117 2.42e+00 1zo0A 126 2.46e+00 1t5bA 201 2.47e+00 c.23.5.3 106433 1pj5A 830 2.62e+00 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1n9lA 109 2.62e+00 d.110.3.6 85468 1qsgA 265 2.65e+00 1eny c.2.1.2 29935 2cokA 113 2.69e+00 1s1fA 406 2.74e+00 2bw0A 329 2.77e+00 1m98A 317 2.78e+00 a.175.1.1,d.17.4.6 78866,78867 1xc3A 302 2.80e+00 1y81A 138 2.80e+00 1vyrA 364 2.82e+00 c.1.4.1 108906 1jr7A 311 2.84e+00 b.82.2.3 63255 1up7A 417 2.90e+00 1hh1A 143 2.93e+00 1gefA c.52.1.18 61036 1w77A 228 3.04e+00 1r7aA 504 3.04e+00 b.71.1.1,c.1.8.1 97192,97193 1bx1A 314 3.09e+00 1fnc b.43.4.2,c.25.1.1 25629,31519 1gskA 513 3.11e+00 b.6.1.3,b.6.1.3,b.6.1.3 83314,83315,83316 1kllA 130 3.15e+00 d.32.1.2 72720 1kk1A 410 3.15e+00 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1vetA 124 3.29e+00 d.110.7.1 108553 2bkkA 264 3.30e+00 2fvgA 340 3.32e+00 1xo1A 291 3.33e+00 1exnA a.60.7.1,c.120.1.2 18086,33356 1uxaA 194 3.35e+00 b.21.1.1 108091 1nt2A 210 3.36e+00 c.66.1.3 86149 2cybA 323 3.38e+00 1t0iA 191 3.39e+00 c.23.5.4 106209 1ytvA 366 3.39e+00 1o2dA 371 3.44e+00 e.22.1.2 86591 1szwA 379 3.44e+00 d.265.1.4 99047 2rslA 140 3.55e+00 2rslA c.53.1.1 33345 1ykwA 435 3.56e+00 1wbiA 129 3.56e+00 1q3iA 214 3.66e+00 d.220.1.1 104524 1wddS 128 3.66e+00 1va4A 279 3.73e+00 c.69.1.12 108458 1oywA 523 3.74e+00 a.4.5.43,c.37.1.19,c.37.1.19 93760,93761,93762 1d4aA 273 3.75e+00 1d4aA c.23.5.3 31219 2b9wA 424 3.77e+00 1vlbA 907 3.97e+00 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 2gaeA 346 4.02e+00 2c6qA 351 4.09e+00 1e5dA 402 4.34e+00 1e5dA c.23.5.1,d.157.1.3 31208,42061 1qh8A 478 4.35e+00 1qguA c.92.2.3 35633 1obfO 335 4.41e+00 c.2.1.3,d.81.1.1 86768,86769 1y9zA 441 4.49e+00 2g5cA 281 4.52e+00 1xm7A 195 4.70e+00 1y7qA 98 4.86e+00 1zx1A 231 4.90e+00 1qf9A 194 4.91e+00 1zin c.37.1.1 31848 1j05B 121 4.95e+00 b.1.1.1 90736 1vixA 420 4.96e+00 c.56.5.4,d.58.19.1 100777,100778 2fikA 287 4.98e+00 1uptA 171 5.02e+00 c.37.1.8 99767 1rl6A 177 5.04e+00 1rl6A d.141.1.1,d.141.1.1 41473,41474 1acc 735 5.05e+00 1acc f.11.1.1 43828 2h1tA 188 5.13e+00 1ohvA 472 5.14e+00 c.67.1.4 93031 2bgcA 238 5.38e+00 1t6cA 315 5.44e+00 c.55.1.8,c.55.1.8 106558,106559 1mo0A 275 5.45e+00 c.1.1.1 79329 1xg5A 279 5.50e+00 1ag9A 175 5.55e+00 1rcf c.23.5.1 31178 2ae0X 345 5.62e+00 1q7fA 286 5.78e+00 b.68.9.1 96036 1t7lA 766 5.85e+00 1keaA 221 6.00e+00 a.96.1.2 68491 1t71A 281 6.07e+00 1d2fA 390 6.07e+00 1d2fA c.67.1.3 34411 1w0mA 226 6.09e+00 c.1.1.1 109027 1geeA 261 6.12e+00 c.2.1.2 90509 1zxuA 217 6.24e+00 1sg0A 230 6.39e+00 1vjoA 393 6.46e+00 c.67.1.3 100827 1sxrA 183 6.49e+00 d.118.1.1 106101 2ghsA 326 6.51e+00 2ahqA 76 6.54e+00 2axoA 270 6.56e+00 1tjyA 316 6.70e+00 c.93.1.1 107062 2bmaA 470 6.96e+00 1mjhA 162 7.08e+00 1mjhA c.26.2.4 31639 1vemA 516 7.13e+00 1vloA 381 7.29e+00 b.44.2.1,d.250.1.1 108838,108839 1uw4B 248 7.32e+00 a.118.1.14 100072 1qqp2 218 7.39e+00 1qqp2 1ra0A 430 7.42e+00 1w8sA 263 7.43e+00 1zkcA 197 7.71e+00 1wlsA 328 7.75e+00 1fh9A 312 7.84e+00 1taxA c.1.8.3 28913 1vhuA 211 7.86e+00 c.50.1.2 100703 1ek0A 170 7.90e+00 1ctqA c.37.1.8 32076 1z0sA 278 8.03e+00 1fp3A 402 8.17e+00 1fp3A a.102.1.3 18842 1z57A 339 8.29e+00 1utcA 363 8.32e+00 a.118.1.4,b.69.6.1 99914,99915 1n2eA 300 8.32e+00 c.26.1.4 85268 1y55X 126 8.45e+00 1jb9A 316 8.47e+00 1fnc b.43.4.2,c.25.1.1 62840,62841 1wcdJ 441 8.49e+00 1gheA 177 8.50e+00 d.108.1.1 76222 2c7pA 327 8.56e+00 2fdoA 94 8.63e+00 1zemA 262 8.77e+00 2fhzA 109 8.84e+00 2cmuA 342 9.09e+00 1bw0A 416 9.14e+00 1bw0A c.67.1.1 34385 1dy9A 187 9.16e+00 1jxpA b.47.1.3 26400 1b5qA 472 9.17e+00 1b37B c.3.1.2,d.16.1.5 30404,37968 1wkbA 810 9.27e+00 1z6nA 167 9.27e+00 1y0yA 353 9.70e+00 1xtmA 175 9.80e+00 1nsj 205 9.87e+00 1nsj c.1.2.4 28560 1im8A 244 9.89e+00 c.66.1.14 66212 1ecsA 126 9.92e+00 1ecsA d.32.1.2 59407 1c75A 71 9.93e+00 451c a.3.1.1 15796 1f1xA 322 9.98e+00 d.32.1.3,d.32.1.3 83208,83209 1q0uA 219 1.01e+01 c.37.1.19 95512 1rxdA 159 1.02e+01 1zfjA 491 1.06e+01 1ak5 c.1.5.1,d.37.1.1,d.37.1.1 28638,38540,38541 1nrjA 158 1.08e+01 d.110.4.4 86124 1ugmA 125 1.09e+01 d.15.1.3 107827 1io2A 213 1.11e+01 1ekeA c.55.3.1 62612 1o98A 511 1.11e+01 c.105.1.1,c.76.1.3 86684,86685 1p57A 114 1.12e+01 d.170.1.2 94125 1r9jA 673 1.13e+01 2f9lA 199 1.14e+01 1yzfA 195 1.14e+01 1rz3A 201 1.14e+01 c.37.1.6 98132 1f00I 282 1.14e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1pcfA 66 1.17e+01 1pcfA d.18.1.1 38142 1nf2A 268 1.17e+01 c.108.1.10 91849 1iseA 185 1.18e+01 d.67.3.1 90691 1x72A 334 1.20e+01 d.126.1.6 109495 1s4iA 175 1.21e+01 2a97A 439 1.22e+01 1mdbA 539 1.23e+01 e.23.1.1 79008 2bbsA 290 1.23e+01 2fp4B 395 1.24e+01 1lm8V 160 1.24e+01 b.3.3.1 74035 1o5kA 306 1.24e+01 c.1.10.1 92504 1uc2A 481 1.25e+01 d.261.1.1 99161 1vbkA 307 1.29e+01 1ne9A 335 1.30e+01 d.108.1.4,d.108.1.4 91839,91840 2aamA 309 1.31e+01 1xu1R 42 1.32e+01 2b3yA 888 1.35e+01 1in0A 163 1.35e+01 d.58.49.1,d.58.49.1 83694,83695 2a0mA 316 1.37e+01 1rifA 282 1.39e+01 c.37.1.23 97507 1eljA 381 1.42e+01 4mbp c.94.1.1 35791 1zbqA 327 1.44e+01 1xi7A 61 1.44e+01 1oacA 727 1.46e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24390,38007,38008,40003 1yp2A 451 1.46e+01 1ku3A 73 1.49e+01 a.4.13.2 73000 1h54A 754 1.49e+01 a.102.1.4,b.30.5.3 60634,60635 1srvA 145 1.54e+01 1derA c.8.5.1 30817 1sg6A 393 1.54e+01 e.22.1.1 105522 1q35A 320 1.58e+01 c.94.1.1 95661 1h12A 405 1.58e+01 a.102.1.2 83447 2bwqA 129 1.59e+01 1vl1A 232 1.59e+01 c.124.1.1 108707 1nkiA 135 1.61e+01 d.32.1.2 91941 1wy7A 207 1.65e+01 1oboA 169 1.66e+01 c.23.5.1 86776 1o5xA 248 1.66e+01 c.1.1.1 92528 2gqrA 237 1.68e+01 1q6hA 224 1.68e+01 d.26.1.1 95975 1bdb 277 1.71e+01 1bdb c.2.1.2 29874 1fxoA 293 1.72e+01 1g0rA c.68.1.6 34524 1zwyA 185 1.72e+01 1wmhA 89 1.72e+01 2a84A 300 1.74e+01 1h8eG 272 1.75e+01 1e79G c.49.2.1 60756 2f1rA 171 1.77e+01 1x8qA 184 1.79e+01 2a35A 215 1.80e+01 1vflA 356 1.83e+01 1ls1A 295 1.83e+01 a.24.13.1,c.37.1.10 78170,78171 1afp 51 1.84e+01 1afp g.26.1.1 44947 1n55A 251 1.84e+01 c.1.1.1 80007 1j0hA 588 1.86e+01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 1anf 370 1.91e+01 4mbp c.94.1.1 35776 1jflA 228 1.93e+01 c.78.2.1,c.78.2.1 71656,71657 2ffcA 353 1.94e+01 1ow1A 195 1.94e+01 b.131.1.3 93625 1q7hA 153 1.95e+01 b.122.1.1,d.17.6.2 96042,96043 1nbwA 607 1.95e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1zd7A 159 1.98e+01 1y51A 88 2.01e+01 1xyzA 347 2.03e+01 1taxA c.1.8.3 28804 1ihoA 283 2.03e+01 1ihoA c.26.1.4 62390 1bvoA 175 2.04e+01 1a3qA b.2.5.3 22457 1wznA 252 2.04e+01 1gtvA 214 2.04e+01 c.37.1.1 70537 1vqoS 85 2.06e+01 1vdmA 153 2.08e+01 1wleA 501 2.08e+01 1kt6A 183 2.14e+01 b.60.1.1 84466 1vrtA 560 2.17e+01 1rthA c.55.3.1,e.8.1.2 33574,43023 1tp9A 162 2.18e+01 1wehA 171 2.19e+01 1n7kA 234 2.19e+01 c.1.10.1 85374 1tvnA 293 2.20e+01 2axtB 510 2.22e+01 1n67A 359 2.22e+01 b.2.3.4,b.2.3.4 85354,85355 1oeyJ 107 2.23e+01 d.15.2.2 92804 1cqyA 99 2.24e+01 1b9zA b.3.1.1 22527 2as0A 396 2.24e+01 1lba 146 2.25e+01 1lba d.118.1.1 41062 1iq4A 179 2.25e+01 1iq4A d.77.1.1 62641 1wqdA 27 2.26e+01 1uwzA 136 2.27e+01 c.97.1.1 108081 1j3aA 142 2.28e+01 c.21.1.1 77070 1i52A 236 2.33e+01 1i52A c.68.1.13 61767 1xk5A 204 2.33e+01 2acvA 463 2.34e+01 1fvkA 189 2.34e+01 1fvkA c.47.1.13 90351 1tc5A 194 2.34e+01 c.110.1.1 106752 1suwA 249 2.35e+01 e.52.1.1 106027 1vlmA 219 2.36e+01 c.66.1.41 108836 5hpgA 84 2.36e+01 5hpgA g.14.1.1 44642 2c1iA 431 2.39e+01 1vyoA 128 2.41e+01 1yloA 348 2.42e+01 1ad2 228 2.43e+01 1ad2 e.24.1.1 43353 1v6tA 255 2.43e+01 1z3eA 132 2.48e+01 1zavA 180 2.49e+01 1xypA 190 2.50e+01 1axkA b.29.1.11 24327 1ltzA 297 2.51e+01 d.178.1.1 74254 1hxhA 253 2.51e+01 c.2.1.2 76725 1ubkL 534 2.54e+01 e.18.1.1 88422 1z7xW 461 2.54e+01 1pvdA 537 2.54e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 1x1tA 260 2.55e+01 1tl2A 236 2.58e+01 1tl2A b.67.1.1 27541 1uayA 242 2.59e+01 c.2.1.2 88390 2furA 209 2.60e+01 1zj6A 187 2.60e+01 1tuaA 191 2.61e+01 d.51.1.1,d.51.1.1 107321,107322 1v3vA 333 2.62e+01 b.35.1.2,c.2.1.1 108345,108346 1j54A 186 2.68e+01 c.55.3.5 77077 1iibA 106 2.71e+01 1iibA c.44.2.1 32648 1s8nA 205 2.73e+01 c.23.1.1 105374 1lst 239 2.77e+01 1lst c.94.1.1 35755 1p0zA 131 2.77e+01 d.110.6.1 93882 1v8fA 276 2.78e+01 c.26.1.4 100503 1yx1A 264 2.79e+01 1ns5A 155 2.81e+01 c.116.1.3 80705 1p0fA 373 2.84e+01 b.35.1.2,c.2.1.1 87642,87643 1rlhA 173 2.84e+01 d.256.1.1 97646 1mdc 133 2.92e+01 1hmt b.60.1.2 27198 1f5mA 180 2.92e+01 1f5mB d.110.2.1 40895 1t6t1 118 2.93e+01 1sh8A 154 2.95e+01 d.38.1.5 105549 1wuiL 534 2.98e+01 1nf3C 128 2.98e+01 b.36.1.1 85596 1c7nA 399 3.01e+01 1d2fA c.67.1.3 34413 1rypJ 204 3.02e+01 d.153.1.4 41878 1r8eA 278 3.03e+01 a.6.1.3,d.60.1.1 104843,104844 1ecfA 504 3.05e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 2ae2A 260 3.07e+01 1bdb c.2.1.2 29945 1w7bA 339 3.09e+01 1ju2A 536 3.09e+01 c.3.1.2,d.16.1.1 77169,77170 1v5vA 401 3.09e+01 1bqcA 302 3.10e+01 1bqcA c.1.8.3 28831 1tif 78 3.13e+01 1tif d.15.8.1 37836 1sk4A 163 3.14e+01 d.118.1.1 105664 1sazA 381 3.14e+01 1rxyA 253 3.15e+01 c.56.2.1 98065 1ymqA 261 3.16e+01 1svpA 161 3.16e+01 1svpA b.47.1.3 26384 2ez9A 603 3.16e+01 1o6aA 96 3.20e+01 b.139.1.1 92562 1vi4A 174 3.22e+01 c.8.7.1 100731 2f4qA 346 3.22e+01 1wd5A 208 3.23e+01 1ja1A 622 3.24e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1j99A 293 3.24e+01 c.37.1.5 71618 1a8l 226 3.34e+01 1a8l c.47.1.2,c.47.1.2 32777,32778 1fcdA 401 3.34e+01 1fcdA 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