# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl-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 2ah5A 210 5.11e-04 1t5oA 351 4.40e-02 c.124.1.5 106459 1pu6A 218 1.42e-01 a.96.1.5 95123 2go7A 207 8.61e-01 1eexA 554 9.00e-01 1dioA c.1.19.3 29650 1dioA 554 9.15e-01 1dioA c.1.19.3 29656 2f2eA 146 1.12e+00 2ng1 293 1.23e+00 1ng1 a.24.13.1,c.37.1.10 16962,32273 1zkrA 153 1.36e+00 1ihgA 370 1.50e+00 2cpl a.118.8.1,b.62.1.1 62380,62381 1wusA 180 1.80e+00 1e19A 314 1.83e+00 1b7bA c.73.1.1 34967 2fnaA 357 1.89e+00 1jpnA 296 2.56e+00 a.24.13.1,c.37.1.10 67039,67040 1ls1A 295 2.58e+00 a.24.13.1,c.37.1.10 78170,78171 1ffh 294 2.60e+00 1ng1 a.24.13.1,c.37.1.10 16960,32271 1uc8A 280 2.82e+00 c.30.1.6,d.142.1.7 99165,99166 2b49A 287 2.93e+00 1ecmA 109 2.99e+00 1ecmA a.130.1.1 19492 1miwA 404 3.13e+00 a.173.1.1,d.218.1.4 79162,79163 1ng1 294 3.34e+00 1ng1 a.24.13.1,c.37.1.10 16961,32272 1xnfA 275 3.39e+00 1z9hA 290 3.53e+00 1sf8A 126 3.56e+00 d.271.1.1 105472 1rh6A 55 3.91e+00 a.6.1.7 104935 1lx8A 55 4.02e+00 a.6.1.7 84734 2cbiA 594 4.22e+00 1txdA 385 4.50e+00 a.87.1.1,b.55.1.1 107422,107423 111l 164 4.83e+00 1l92 d.2.1.3 36661 1v32A 101 4.85e+00 a.42.1.1 100277 1ekfA 365 5.06e+00 1ekfA e.17.1.1 59445 174lA 164 5.22e+00 1l92 d.2.1.3 36956 1aqwA 209 5.42e+00 1pgtA a.45.1.1,c.47.1.5 17517,32811 1lbkA 208 5.48e+00 a.45.1.1,c.47.1.5 73809,73810 2coiA 386 5.61e+00 1r0dA 206 5.61e+00 a.216.1.1 104715 17gsA 210 5.74e+00 1pgtA a.45.1.1,c.47.1.5 17524,32818 1puoA 170 6.07e+00 a.101.1.1,a.101.1.1 95134,95135 2a1hA 365 6.20e+00 1kt8A 365 6.46e+00 e.17.1.1 77531 1ktaA 365 6.48e+00 e.17.1.1 77533 1cfe 135 6.49e+00 1cfe d.111.1.1 40913 18gsA 210 7.04e+00 1pgtA a.45.1.1,c.47.1.5 17528,32822 1b7yA 350 7.19e+00 1pysA d.104.1.1 40776 2at9 247 7.49e+00 1c3wA f.13.1.1 43427 1y8qB 640 7.55e+00 1pgtA 210 7.59e+00 1pgtA a.45.1.1,c.47.1.5 17515,32809 1sgmA 191 7.64e+00 a.4.1.9,a.121.1.1 105537,105538 1vekA 84 7.65e+00 1pysA 350 7.73e+00 1pysA d.104.1.1 40775 1ygtA 111 7.89e+00 1pbwA 216 7.95e+00 1pbwA a.116.1.1 19103 1is8A 230 8.23e+00 d.96.1.1 66321 2gk3A 256 8.26e+00 1ukz 203 8.56e+00 1zin c.37.1.1 31840 2g7sA 194 8.74e+00 1v54A 514 8.77e+00 f.24.1.1 100321 2occA 514 8.98e+00 2occA f.24.1.1 43518 1pm6A 72 9.02e+00 a.6.1.7 94894 2a5vA 213 9.13e+00 192l 164 9.15e+00 1l92 d.2.1.3 36815 1unlD 208 9.49e+00 1glqA 209 9.56e+00 1pgtA a.45.1.1,c.47.1.5 17588,32882 1dgsA 667 9.69e+00 1dgsA a.60.2.2,b.40.4.6,d.142.2.2 17963,25365,41581 1q6aA 107 9.70e+00 a.186.1.1 95966 1yviA 149 9.74e+00 2grrB 170 9.80e+00 1wy9A 147 1.02e+01 1nxuA 333 1.04e+01 c.122.1.1 86389 1a59 378 1.05e+01 1aj8A a.103.1.1 18902 1vqoV 71 1.05e+01 2f6lA 166 1.06e+01 2fp1A 166 1.06e+01 1izmA 184 1.07e+01 a.199.1.1 90725 1j57A 143 1.08e+01 d.221.1.1 77079 1fj7A 101 1.08e+01 1fj7A d.58.7.1 39209 1wteA 272 1.14e+01 1ezwA 349 1.15e+01 1ezwA c.1.16.3 29558 2a07F 93 1.16e+01 1ys7A 233 1.17e+01 1fc4A 401 1.17e+01 1bs0A c.67.1.4 59760 1q1vA 70 1.22e+01 a.159.4.1 104479 1pq1A 196 1.22e+01 f.1.4.1 94986 1fjeB 175 1.23e+01 1fj7A d.58.7.1,d.58.7.1 39210,39211 1vgoA 253 1.28e+01 1ym3A 215 1.29e+01 1sly 618 1.32e+01 1qsaA a.118.5.1,d.2.1.6 19184,36990 2f1kA 279 1.38e+01 2a5kA 307 1.45e+01 1bkrA 109 1.50e+01 1bkrA a.40.1.1 17394 1q1fA 151 1.50e+01 a.1.1.2 104476 2es4D 332 1.53e+01 1yvrA 538 1.53e+01 1h1nA 305 1.53e+01 c.1.8.3 70855 1c3wA 222 1.54e+01 1c3wA f.13.1.1 43405 1cg5B 141 1.55e+01 1cg5B a.1.1.2 15585 1aa2 108 1.56e+01 1bkrA a.40.1.1 17395 1z6gA 218 1.62e+01 1jj2U 70 1.65e+01 1ffkS a.2.2.1 63106 1s72V 71 1.65e+01 a.2.2.1 105341 1po5A 476 1.65e+01 a.104.1.1 94963 1b8zA 90 1.68e+01 1huuA a.55.1.1 17902 1wy0A 342 1.69e+01 1m0kA 262 1.72e+01 f.13.1.1 78344 1x46A 150 1.73e+01 1jeqA 609 1.77e+01 1jeqA a.140.2.1,b.131.1.1,c.62.1.3 64748,90366,90367 1o06A 20 1.79e+01 j.105.1.1 86524 1g59A 468 1.81e+01 a.97.1.1,c.26.1.1 60257,60258 2bw3A 534 1.82e+01 1v2zA 111 1.85e+01 a.186.1.1 108300 1oj6A 151 1.90e+01 a.1.1.2 93088 2cdnA 201 1.96e+01 1alvA 173 1.96e+01 1alvA a.39.1.8 17370 1sz2A 332 2.00e+01 1qsaA 618 2.03e+01 1qsaA a.118.5.1,d.2.1.6 19182,36988 1kgbA 231 2.04e+01 f.13.1.1 68581 2axtJ 40 2.06e+01 2fiqA 420 2.06e+01 2a2fX 325 2.07e+01 1ft9A 222 2.07e+01 1ft9A a.4.5.4,b.82.3.1 16107,28131 1vqwA 457 2.09e+01 189l 164 2.10e+01 1l92 d.2.1.3 36960 1f3mA 80 2.11e+01 1f3mA j.66.1.1 46358 2gx9A 129 2.12e+01 1q18A 332 2.16e+01 c.55.1.7,c.55.1.7 104470,104471 1ujmA 342 2.16e+01 2fbqA 235 2.18e+01 1wa8B 95 2.20e+01 1y1pA 342 2.24e+01 1kxpD 458 2.25e+01 a.126.1.1,a.126.1.1,a.126.1.1 73160,73161,73162 1ku1A 230 2.27e+01 a.118.3.1 72996 1irxA 523 2.29e+01 a.97.1.2,c.26.1.1 71378,71379 1odoA 408 2.32e+01 a.104.1.1 92783 1qloA 34 2.36e+01 1qloA j.35.1.1 46281 2gtsA 86 2.37e+01 2fdrA 229 2.37e+01 1b3bA 415 2.43e+01 1hwyA c.2.1.7,c.58.1.1 30244,33892 1x24A 180 2.43e+01 1tubA 440 2.47e+01 1tubA c.32.1.1,d.79.2.1 31751,39803 1t9kA 347 2.47e+01 c.124.1.5 106721 1smbA 154 2.52e+01 d.111.1.1 105756 1aisB 200 2.56e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 1f1oA 431 2.57e+01 1f1oA a.127.1.1 19433 1ozjA 144 2.58e+01 d.164.1.1 93846 1ffkS 70 2.59e+01 1ffkS a.2.2.1 15692 1ug0A 88 2.63e+01 a.217.1.1 107822 175lA 164 2.68e+01 1l92 d.2.1.3 36924 1tx4A 198 2.84e+01 1tx4A a.116.1.1 19098 1bhdA 118 2.85e+01 1bkrA a.40.1.1 17398 2bsxA 253 2.89e+01 1zccA 248 2.98e+01 1r1hA 696 2.98e+01 d.92.1.4 104756 1g0uE 234 3.04e+01 d.153.1.4 41950 1jnyA 435 3.06e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1ywfA 296 3.06e+01 2ctoA 93 3.07e+01 171l 164 3.11e+01 1l92 d.2.1.3 36962 172l 164 3.11e+01 1l92 d.2.1.3 36905 1rypF 233 3.12e+01 1rypF d.153.1.4 41937 173l 164 3.17e+01 1l92 d.2.1.3 36728 1k94A 165 3.17e+01 a.39.1.8 68333 2gh1A 301 3.18e+01 142l 164 3.20e+01 1l92 d.2.1.3 36874 128l 164 3.21e+01 1l92 d.2.1.3 36634 152l 164 3.22e+01 1l92 d.2.1.3 36904 129l 164 3.24e+01 1l92 d.2.1.3 36660 138l 164 3.24e+01 1l92 d.2.1.3 36679 1bh9B 89 3.25e+01 1bh9B a.22.1.3 16485 1oaoA 674 3.27e+01 e.26.1.2 86744 118l 164 3.27e+01 1l92 d.2.1.3 36642 1t3tA 1303 3.32e+01 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 1dvkA 173 3.34e+01 1dvkA a.72.1.1 18319 1jgsA 138 3.35e+01 a.4.5.28 66683 163l 164 3.35e+01 1l92 d.2.1.3 36658 1t2bA 397 3.36e+01 1d3uB 201 3.36e+01 1aisB a.74.1.2,a.74.1.2 18386,18387 1l58 164 3.38e+01 1l92 d.2.1.3 36635 2aqwA 332 3.38e+01 107l 164 3.38e+01 1l92 d.2.1.3 36690 1z83A 196 3.41e+01 177l 164 3.41e+01 1l92 d.2.1.3 36958 1jjrA 151 3.42e+01 a.140.2.1 66772 131l 164 3.42e+01 1l92 d.2.1.3 36685 2amxA 376 3.42e+01 147l 164 3.43e+01 1l92 d.2.1.3 36864 130l 164 3.46e+01 1l92 d.2.1.3 36638 125l 164 3.49e+01 1l92 d.2.1.3 36672 1e4yA 214 3.49e+01 1zin c.37.1.1,g.41.2.1 31901,45181 119l 164 3.50e+01 1l92 d.2.1.3 36622 1elrA 131 3.54e+01 1a17 a.118.8.1 19209 1ppjB 439 3.56e+01 d.185.1.1,d.185.1.1 104254,104255 160l 164 3.56e+01 1l92 d.2.1.3 36748 1abwA 283 3.58e+01 1abwA a.1.1.2,a.1.1.2 15288,15289 166l 164 3.58e+01 1l92 d.2.1.3 36681 1io1A 398 3.60e+01 1io1A e.32.1.1 62611 122l 164 3.61e+01 1l92 d.2.1.3 36667 1x42A 232 3.63e+01 161l 164 3.64e+01 1l92 d.2.1.3 36636 1aj6 219 3.66e+01 1aj6 d.122.1.2 41106 1m5yA 408 3.66e+01 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 162l 164 3.69e+01 1l92 d.2.1.3 36749 1j09A 468 3.69e+01 a.97.1.1,c.26.1.1 77025,77026 1nhyA 219 3.73e+01 a.45.1.1,c.47.1.5 80520,80521 2cosA 54 3.75e+01 1zclA 180 3.79e+01 1uedA 406 3.93e+01 a.104.1.1 99256 169lA 164 3.94e+01 1l92 d.2.1.3 36963 157l 164 3.95e+01 1l92 d.2.1.3 36717 1o08A 221 3.95e+01 c.108.1.6 86525 112l 164 4.02e+01 1l92 d.2.1.3 36677 109l 164 4.02e+01 1l92 d.2.1.3 36781 126l 164 4.09e+01 1l92 d.2.1.3 36699 2ccjA 205 4.09e+01 1kpsB 171 4.10e+01 a.118.12.1 68787 191l 164 4.12e+01 1l92 d.2.1.3 36826 3vub 101 4.13e+01 3vub b.34.6.1 24613 2aorA 223 4.13e+01 1am4A 199 4.14e+01 1tx4A a.116.1.1 19100 1f4tA 368 4.18e+01 1f4tA a.104.1.1 18973 159l 164 4.21e+01 1l92 d.2.1.3 36682 1jqSB 32 4.22e+01 1jqsB 32 4.22e+01 i.1.1.1 63238 155l 164 4.22e+01 1l92 d.2.1.3 36762 1wdgA 94 4.22e+01 h.3.3.1 109248 1l0lB 439 4.26e+01 d.185.1.1,d.185.1.1 84484,84485 1h2aL 567 4.28e+01 1h2rL e.18.1.1 43299 1ubkL 534 4.28e+01 e.18.1.1 88422 1wuiL 534 4.28e+01 1h2rL 534 4.29e+01 1h2rL e.18.1.1 43298 1lmzA 187 4.30e+01 a.96.1.4 74037 168lA 164 4.30e+01 1l92 d.2.1.3 36975 123l 164 4.38e+01 1l92 d.2.1.3 36697 156l 164 4.44e+01 1l92 d.2.1.3 36709 1mhdA 132 4.45e+01 1mhdA d.164.1.1 42175 2fi0A 81 4.48e+01 1kekA 1231 4.48e+01 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 68524,68525,68526,68527,68528 1p36A 164 4.53e+01 d.2.1.3 93978 1l0lG 81 4.55e+01 f.23.13.1 84493 1xn8A 131 4.59e+01 1e9rA 437 4.62e+01 c.37.1.11 64827 1kv4A 42 4.64e+01 j.4.1.3 73051 143l 164 4.65e+01 1l92 d.2.1.3 36857 1dw0A 112 4.65e+01 1dw0A a.3.1.1 15911 1l3pA 102 4.67e+01 a.24.17.1 84520 1zd8A 227 4.68e+01 2bykB 128 4.69e+01 2bnkA 67 4.69e+01 1ydnA 295 4.72e+01 1w36C 1122 4.75e+01 1rxdA 159 4.76e+01 2ci1A 275 4.77e+01 1zckA 154 4.77e+01 1ju3A 583 4.79e+01 b.18.1.13,c.69.1.21 67300,67301 167lA 164 4.80e+01 1l92 d.2.1.3 36937 2ffjA 300 4.80e+01 1q1gA 276 4.82e+01 c.56.2.1 95574 1l92 164 4.83e+01 1l92 d.2.1.3 36629 1lw9A 164 4.86e+01 d.2.1.3 84727 113l 164 4.92e+01 1l92 d.2.1.3 36678 165l 164 4.97e+01 1l92 d.2.1.3 36680 1cnsA 243 5.00e+01 1cnsA d.2.1.1 36241 1rcuA 195 5.05e+01 c.129.1.1 97295 1a91 79 5.07e+01 1a91 f.17.1.1 43635 1vhtA 218 5.08e+01 c.37.1.1 100700 2baa 243 5.09e+01 1cnsA d.2.1.1 36243 1qusA 322 5.12e+01 1ltm d.2.1.6 36991 2au5A 139 5.14e+01 1jwwA 80 5.14e+01 d.58.17.1 71919 1ltm 320 5.15e+01 1ltm d.2.1.6 36992 1b6iA 164 5.16e+01 1l92 d.2.1.3 36945 1wn0A 145 5.16e+01 2c5rA 67 5.18e+01 114l 164 5.20e+01 1l92 d.2.1.3 36663 1ntr 124 5.20e+01 1dbwA c.23.1.1 31092 1np8A 159 5.22e+01 a.39.1.8 92022 199l 164 5.25e+01 1l92 d.2.1.3 36855 141l 164 5.26e+01 1l92 d.2.1.3 36863 1ufiA 64 5.29e+01 a.30.4.1 99336 1gyfA 62 5.32e+01 1gyfA d.76.1.1 39749 196l 164 5.36e+01 1l92 d.2.1.3 36927 1kzuB 41 5.39e+01 1kzuB f.3.1.1 43728 1nkzB 41 5.39e+01 f.3.1.1 80612 1d6mA 653 5.43e+01 1d6mA e.10.1.1 43248 1qf9A 194 5.44e+01 1zin c.37.1.1 31848 164l 164 5.45e+01 1l92 d.2.1.3 36714 1rvgA 305 5.45e+01 c.1.10.2 97920 1lc5A 364 5.46e+01 c.67.1.1 73827 1kanA 253 5.47e+01 1knyA a.24.16.1,d.218.1.1 75878,75879 1rv3A 483 5.48e+01 c.67.1.4 105101 140l 164 5.48e+01 1l92 d.2.1.3 36891 1lkyA 77 5.49e+01 a.60.1.1 73985 1nm8A 616 5.50e+01 c.43.1.3,c.43.1.3 85872,85873 1g2cA 52 5.55e+01 1g2cA h.3.2.1 45767 5ukdA 194 5.56e+01 1zin c.37.1.1 31851 1b0pA 1231 5.58e+01 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 31831,31832,33104,34157,39003 1skf 262 5.60e+01 1skf e.3.1.1 42684 1bpoA 494 5.60e+01 1bpoA a.118.1.4,b.69.6.1 19143,27670 1dc7A 124 5.62e+01 1dbwA c.23.1.1 31093 2aboA 136 5.67e+01 1jdhA 529 5.69e+01 a.118.1.1 66549 1es4A 262 5.70e+01 1skf e.3.1.1 42683 2c3mA 1231 5.71e+01 1es5A 262 5.72e+01 1skf e.3.1.1 42679 1r5qA 102 5.74e+01 a.186.1.1 97103 1wzzA 334 5.76e+01 1o5hA 214 5.76e+01 a.191.1.1 92497 1bd3A 243 5.77e+01 1bd3A c.61.1.1 34098 2cfuA 658 5.82e+01 1i7dA 659 5.85e+01 1d6mA e.10.1.1 61886 1bw0A 416 5.86e+01 1bw0A c.67.1.1 34385 2b25A 336 5.89e+01 1h4lD 147 5.89e+01 a.74.1.1 70873 6gsvA 217 5.91e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 1cz4A 185 5.92e+01 1cz4A b.52.2.3,d.31.1.1 26934,38468 120l 164 5.93e+01 1l92 d.2.1.3 36720 1esiA 262 5.96e+01 1skf e.3.1.1 42682 180lA 164 5.96e+01 1l92 d.2.1.3 36867 1r8mE 203 6.00e+01 a.118.3.1 97242 1c52 131 6.08e+01 1c52 a.3.1.1 15810 158l 164 6.12e+01 1l92 d.2.1.3 36747 1f4qA 165 6.14e+01 1alvA a.39.1.8 17360 2g38B 198 6.16e+01 1es2A 262 6.17e+01 1skf e.3.1.1 42680 1latA 82 6.18e+01 2nllB g.39.1.2 45122 1r8sE 203 6.29e+01 a.118.3.1 97248 1otgA 125 6.29e+01 1otgA d.80.1.2 39831 146l 164 6.31e+01 1l92 d.2.1.3 36763 2ao0A 324 6.32e+01 1tedA 393 6.32e+01 c.95.1.2 106807 1hr6B 443 6.35e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1cpt 412 6.36e+01 1cpt a.104.1.1 18968 1y791 680 6.39e+01 2f7tA 227 6.41e+01 145l 164 6.42e+01 1l92 d.2.1.3 36860 2f46A 156 6.44e+01 1mpgA 282 6.45e+01 1mpgA a.96.1.3,d.129.1.2 18747,41296 2aaxA 275 6.46e+01 1lkcA 364 6.47e+01 c.67.1.1 73978 1cc8A 73 6.47e+01 1cc8A d.58.17.1 39343 1gajA 257 6.47e+01 1gajA c.37.1.12 60416 1odkA 235 6.48e+01 c.56.2.1 86863 1tkkA 366 6.49e+01 c.1.11.2,d.54.1.1 107089,107090 2dc3A 193 6.49e+01 1f16A 192 6.52e+01 1f16A f.1.4.1 43400 2fdsA 352 6.54e+01 1aj5A 173 6.58e+01 1alvA a.39.1.8 17367 1fd9A 213 6.62e+01 1fd9A d.26.1.1 59771 1szt 68 6.65e+01 1aikN h.3.2.1 45725 1k8kG 151 6.69e+01 a.118.13.1 68313 1ar1A 558 6.71e+01 2occA f.24.1.1 43618 1ofgA 381 6.75e+01 1ofgA c.2.1.3,d.81.1.5 30064,39979 1ir6A 424 6.75e+01 c.107.1.2 71342 190l 164 6.78e+01 1l92 d.2.1.3 36892 1vg5A 73 6.78e+01 2aq4A 434 6.84e+01 1vsgA 364 6.90e+01 1vsgA h.4.1.1 45782 1mejA 223 6.92e+01 c.65.1.1 79029 1oy1A 228 6.92e+01 c.23.16.2 87548 1g2cK 52 6.92e+01 1g2cK h.3.2.1 45772 1su8A 636 6.93e+01 e.26.1.2 98999 1u59A 287 6.93e+01 d.144.1.7 107681 2a5yA 204 6.94e+01 195l 164 6.97e+01 1l92 d.2.1.3 36841 1pw4A 451 7.01e+01 f.38.1.1 95198 1x0vA 354 7.01e+01 2aexA 346 7.07e+01 1pyfA 312 7.09e+01 c.1.7.1 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