# List of top-scoring protein chains for t2k.100-30-str 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.soe.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 1hzmA 154 3.42e-12 c.46.1.1 65975 1c25 161 3.88e-12 1c25 1qb0A 211 1.77e-11 1c25 c.46.1.1 32699 2oucA 142 2.06e-11 1ymkA 175 2.10e-11 c.46.1.1 123699 2a2kA 175 5.18e-11 1e0cA 271 5.07e-09 1e0cA c.46.1.2 32717 c.46.1.2 32718 1uarA 285 2.17e-08 c.46.1.2 107762 c.46.1.2 107763 1gmxA 108 3.03e-08 c.46.1.3 65355 1yt8A 539 8.54e-08 c.46.1.2 123996 c.46.1.2 123997 c.46.1.2 123998 c.46.1.2 123999 1whbA 157 1.06e-07 c.46.1.4 114639 2gwfA 157 2.09e-07 c.46.1.4 135802 2j6pA 152 2.09e-07 1rhs 296 3.77e-07 1rhs 1rhsA 296 3.77e-07 c.46.1.2 32703 c.46.1.2 32704 2hhgA 139 5.15e-07 2eg4A 230 1.08e-06 1t3kA 152 5.65e-06 c.46.1.1 106357 1okgA 373 3.53e-05 c.46.1.2 93250 c.46.1.2 93251 d.26.1.3 93252 2fsxA 148 1.21e-03 1wv9A 94 3.32e-03 1l2tA 235 1.73e-01 c.37.1.12 73514 1t5bA 201 3.43e-01 c.23.5.3 106433 1azwA 313 3.65e-01 1qtrA c.69.1.7 34658 3b55A 451 3.80e-01 1ns5A 155 3.99e-01 c.116.1.3 80705 1wq3A 322 7.24e-01 1t9kA 347 7.62e-01 c.124.1.5 106721 1g3mA 294 7.62e-01 c.37.1.5 83268 1hy3A 294 8.39e-01 c.37.1.5 71090 1dljA 402 9.37e-01 1dliA a.100.1.4 18808 c.2.1.6 30212 c.26.3.1 31621 2p6xA 309 1.01e+00 2z98A 200 1.02e+00 1dliA 402 1.04e+00 1dliA a.100.1.4 18809 c.2.1.6 30213 c.26.3.1 31622 1nbwB 117 1.05e+00 c.51.3.2 80396 1yrbA 262 1.07e+00 c.37.1.10 123915 1dqyA 283 1.10e+00 1dqyA c.69.1.3 34640 1aq0A 306 1.16e+00 1aq0A c.1.8.3 28842 1tikA 213 1.18e+00 c.23.5.3 107003 1xiyA 182 1.19e+00 c.47.1.10 122022 1npyA 271 1.21e+00 c.2.1.7 85995 c.58.1.5 85996 1vbuA 328 1.26e+00 c.1.8.3 119963 2ooqA 286 1.28e+00 1d1gA 168 1.33e+00 1d1gA c.71.1.1 34889 1dqzA 280 1.44e+00 1dqyA c.69.1.3 34638 2j13A 247 1.49e+00 c.6.2.3 137934 2ps2A 371 1.54e+00 2hxvA 360 1.56e+00 c.71.1.2 136859 c.97.1.2 136860 4ts1A 319 1.67e+00 2ts1 c.26.1.1 31565 1y80A 210 1.79e+00 2uz0A 263 1.86e+00 1sh7A 284 1.88e+00 1vhrA 184 1.93e+00 1vhrA c.45.1.1 32651 2it1A 362 1.95e+00 1jbeA 128 2.01e+00 3chy c.23.1.1 62845 2ts1 419 2.14e+00 2ts1 2f4dA 184 2.17e+00 1nnwA 252 2.22e+00 d.159.1.5 80674 2yvuA 186 2.26e+00 3chy 128 2.31e+00 3chy 1f0nA 285 2.32e+00 1dqyA c.69.1.3 34636 3c97A 140 2.32e+00 1jixA 351 2.35e+00 1c3jA c.87.1.1 63081 1jilA 420 2.40e+00 c.26.1.1 66745 1h09A 338 2.43e+00 b.109.1.1 83420 c.1.8.8 83421 1j8yF 297 2.46e+00 1ng1 a.24.13.1 62747 c.37.1.10 62748 1tb3A 352 2.60e+00 c.1.4.1 119205 1nmuB 104 2.68e+00 d.79.3.1 80666 1e6mA 128 2.74e+00 3chy c.23.1.1 31039 2i1yA 301 2.76e+00 1j24A 143 2.83e+00 c.52.1.20 84008 1u8tA 129 2.84e+00 c.23.1.1 113192 1yasA 257 2.85e+00 1qj4A c.69.1.20 34801 1qj4A 257 2.89e+00 1qj4A c.69.1.20 34796 1vl5A 260 2.93e+00 c.66.1.41 108720 2fh7A 595 3.01e+00 1jq0A 84 3.26e+00 h.3.2.1 71786 1ny1A 240 3.26e+00 c.6.2.3 86395 2dc1A 236 3.32e+00 1on3A 523 3.32e+00 c.14.1.4 87107 c.14.1.4 87108 2i1oA 398 3.37e+00 2j8gA 339 3.41e+00 1xyzA 347 3.57e+00 1taxA c.1.8.3 28804 2bkaA 242 3.61e+00 c.2.1.2 128666 4dfrA 159 3.63e+00 1vdrA c.71.1.1 34822 1lqtA 456 3.65e+00 c.3.1.1 74198 c.4.1.1 74199 1yfoA 302 3.67e+00 2shpA c.45.1.2 32681 1vdmA 153 3.70e+00 c.61.1.1 119994 1agqA 135 3.73e+00 1agqA g.17.1.2 44789 2pidA 356 3.78e+00 1j8mF 297 3.85e+00 1ng1 a.24.13.1 62742 c.37.1.10 62743 2b4pA 334 3.92e+00 2qgmA 445 3.94e+00 1w85A 368 3.97e+00 c.36.1.11 114335 2b3oA 532 4.04e+00 1fc6A 388 4.09e+00 1fc6A b.36.1.3 64738 c.14.1.2 64739 1wm1A 317 4.10e+00 c.69.1.7 109405 2i75A 320 4.16e+00 1clxA 347 4.17e+00 1taxA c.1.8.3 28899 1larA 575 4.19e+00 1larA c.45.1.2 32693 c.45.1.2 32694 1qtrA 317 4.26e+00 1qtrA c.69.1.7 34660 2cyaA 364 4.27e+00 2p1fA 291 4.33e+00 2shpA 525 4.33e+00 2shpA c.45.1.2 32683 d.93.1.1 40533 d.93.1.1 40534 1qo7A 394 4.34e+00 1qo7A c.69.1.11 34697 2c1cA 312 4.45e+00 c.56.5.1 129630 1ab6A 125 4.52e+00 3chy c.23.1.1 31054 1mtzA 293 4.53e+00 c.69.1.7 79467 1oxxK 353 4.63e+00 b.40.6.3 93715 c.37.1.12 93716 1w32A 348 4.65e+00 c.1.8.3 114120 2dr3A 247 4.66e+00 1ecfA 504 4.66e+00 1ecfB c.61.1.1 34053 d.153.1.1 41820 1wznA 252 4.71e+00 c.66.1.43 121525 1b74A 254 4.79e+00 1b74A c.78.2.1 35264 c.78.2.1 35265 1u24A 337 4.79e+00 c.45.1.4 112968 1draA 159 4.80e+00 1vdrA c.71.1.1 34831 1fnmA 691 4.88e+00 1dar b.43.3.1 25709 c.37.1.8 32144 d.14.1.1 37546 d.58.11.1 39302 d.58.11.1 39303 1u0sY 118 4.88e+00 c.23.1.1 107566 1vmeA 410 4.89e+00 c.23.5.1 108893 d.157.1.3 108894 2qcfA 260 4.94e+00 1ddsA 159 5.02e+00 1vdrA c.71.1.1 34858 1rcqA 357 5.03e+00 b.49.2.2 104882 c.1.6.1 104883 2gq0A 303 5.04e+00 1ta3B 303 5.05e+00 c.1.8.3 106732 1oxsC 353 5.07e+00 b.40.6.3 87519 c.37.1.12 87520 1jl3A 139 5.16e+00 c.44.1.1 66826 1yksA 440 5.16e+00 c.37.1.14 123561 c.37.1.14 123562 2blcA 238 5.23e+00 1nvtA 287 5.37e+00 c.2.1.7 86270 c.58.1.5 86271 1h3fA 432 5.37e+00 c.26.1.1 76631 d.66.1.4 76632 1ojxA 263 5.43e+00 c.1.10.1 93164 2hrcA 359 5.47e+00 c.92.1.1 136687 1jpnA 296 5.54e+00 a.24.13.1 67039 c.37.1.10 67040 2f4nA 273 5.60e+00 1wchA 315 5.68e+00 c.45.1.2 114508 1xr4A 509 5.71e+00 c.124.1.2 115860 c.124.1.2 115861 1w5fA 353 5.73e+00 c.32.1.1 114247 d.79.2.1 114248 1cex 214 5.80e+00 1cex 1cexA 214 5.80e+00 c.69.1.30 31285 1ao0A 459 5.84e+00 1ecfB c.61.1.1 34049 d.153.1.1 41816 2jfzA 255 5.84e+00 2ixaA 444 5.88e+00 1gph1 465 5.91e+00 1ecfB 2bm0A 691 5.97e+00 b.43.3.1 128748 c.37.1.8 128749 d.14.1.1 128750 d.58.11.1 128751 d.58.11.1 128752 2f8lA 344 5.97e+00 c.66.1.45 133132 1d5rA 324 6.01e+00 1d5rA b.7.1.1 23181 c.45.1.1 32697 1ecfB 504 6.09e+00 1ecfB c.61.1.1 34054 d.153.1.1 41821 1qdeA 224 6.09e+00 1qvaA c.37.1.19 32410 1xp8A 366 6.12e+00 c.37.1.11 115735 d.48.1.1 115736 1o89A 345 6.22e+00 b.35.1.2 92644 c.2.1.1 92645 2i2xB 258 6.28e+00 3dfrA 162 6.36e+00 c.71.1.1 34880 3dfr 162 6.36e+00 3dfr 2pbnA 313 6.36e+00 1xqwA 293 6.38e+00 3b85A 208 6.46e+00 1wlsA 328 6.50e+00 1vm6A 228 6.58e+00 c.2.1.3 118631 d.81.1.3 108877 2h4vA 320 6.59e+00 2aznA 219 6.60e+00 c.71.1.2 127608 2yvtA 260 6.61e+00 1ra9 159 6.63e+00 1vdrA 1ra9A 159 6.63e+00 c.71.1.1 34820 1gpmA 525 6.68e+00 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 1tp9A 162 6.68e+00 c.47.1.10 119306 1epxA 370 6.74e+00 1fbaA c.1.10.1 29150 2jgyA 279 6.78e+00 1o6dA 163 6.88e+00 c.116.1.3 92567 1id1A 153 6.95e+00 1id1A c.2.1.9 62286 1vmaA 306 7.13e+00 a.24.13.1 108887 c.37.1.10 108888 2hmcA 344 7.28e+00 1tq6A 413 7.34e+00 c.37.1.8 107202 2ffuA 501 7.42e+00 1sjdA 368 7.42e+00 c.1.11.2 105632 d.54.1.1 105633 2gruA 368 7.43e+00 1scuA 288 7.52e+00 2scuA c.2.1.8 30307 c.23.4.1 31135 1zgzA 122 7.62e+00 c.23.1.1 125065 1mvoA 136 7.66e+00 c.23.1.1 79513 2omkA 231 7.86e+00 2scuA 288 7.90e+00 2scuA c.2.1.8 30303 c.23.4.1 31131 1ycdA 243 7.91e+00 2q9uA 414 7.91e+00 2bl9A 238 7.97e+00 1khdA 345 8.00e+00 a.46.2.1 77400 c.27.1.1 77401 2fnaA 357 8.03e+00 a.4.5.11 133809 c.37.1.20 133810 1ng1 294 8.12e+00 1ng1 1im5A 180 8.15e+00 c.33.1.3 66211 1zh2A 121 8.20e+00 c.23.1.1 125069 2px0A 296 8.23e+00 1xq6A 253 8.26e+00 c.2.1.2 115829 2pocA 367 8.26e+00 1ab5A 125 8.26e+00 3chy c.23.1.1 31056 1vheA 373 8.32e+00 b.49.3.1 100669 c.56.5.4 100670 1ush 550 8.32e+00 1ush 2cwdA 161 8.39e+00 2ewsA 287 8.53e+00 2yysA 286 8.65e+00 1rpxA 230 8.70e+00 1rpxA c.1.2.2 28536 1iqpA 327 8.92e+00 a.80.1.1 62649 c.37.1.20 62650 1g291 372 8.95e+00 1g291 2np9A 440 8.97e+00 2pxxA 215 8.99e+00 1vc1A 110 9.04e+00 c.13.2.1 108493 2q1sA 377 9.08e+00 2okgA 255 9.11e+00 1vl6A 388 9.12e+00 c.2.1.7 108724 c.58.1.3 108725 1p3y1 194 9.15e+00 1z47A 355 9.24e+00 2c78A 405 9.25e+00 b.43.3.1 130037 b.44.1.1 130038 c.37.1.8 130039 1dar 691 9.26e+00 1dar 2z1dA 372 9.31e+00 2ocgA 254 9.38e+00 1vlpA 441 9.55e+00 c.1.17.2 108841 d.41.2.2 108840 1j3kA 280 9.73e+00 c.71.1.1 84070 1gox 370 9.78e+00 1gox 1goxA 369 9.78e+00 c.1.4.1 28607 1afsA 323 9.79e+00 1frb c.1.7.1 28694 1sgwA 214 9.86e+00 c.37.1.12 105541 1nnlA 225 9.87e+00 c.108.1.4 85906 1y1lA 124 9.94e+00 c.44.1.1 116341 2pcjA 224 9.97e+00 2ejaA 338 9.99e+00 2dgdA 223 1.00e+01 2h8lA 252 1.00e+01 3c10A 423 1.00e+01 2q46A 253 1.01e+01 c.2.1.2 139825 2e0tA 151 1.01e+01 1kgdA 180 1.02e+01 c.37.1.1 68582 2b6nA 278 1.02e+01 2pqpA 421 1.03e+01 2nvrA 423 1.03e+01 1xseA 295 1.03e+01 c.2.1.2 115925 1vdrA 162 1.04e+01 1vdrA c.71.1.1 34893 1eg7A 557 1.05e+01 1eg7A c.37.1.10 32241 1oi7A 288 1.05e+01 c.2.1.8 87049 c.23.4.1 87050 2orwA 184 1.07e+01 3bf0A 593 1.07e+01 1imjA 210 1.07e+01 c.69.1.23 71246 1ylhA 560 1.07e+01 1vkrA 125 1.08e+01 c.44.2.1 108689 1vgvA 384 1.09e+01 c.87.1.3 100608 1vb3A 428 1.09e+01 c.79.1.1 119942 2cybA 323 1.11e+01 1lbqA 362 1.11e+01 c.92.1.1 77877 2nx9A 464 1.11e+01 1exmA 405 1.12e+01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 2pa5A 314 1.12e+01 2grvA 621 1.13e+01 1aquA 297 1.13e+01 1aquA c.37.1.5 31942 2obnA 349 1.15e+01 1uc7A 125 1.15e+01 c.47.1.1 99163 2qapA 391 1.16e+01 1ztcA 221 1.16e+01 d.157.1.11 125635 1ys7A 233 1.16e+01 a.4.6.1 123961 c.23.1.1 123962 1ls1A 295 1.17e+01 a.24.13.1 78170 c.37.1.10 78171 1u2pA 163 1.17e+01 2bzlA 325 1.17e+01 1ebdA 455 1.19e+01 1lvl c.3.1.5 30577 c.3.1.5 30578 d.87.1.1 40210 1u9iA 519 1.19e+01 c.37.1.11 119637 c.37.1.11 119638 2pth 193 1.19e+01 2pth 2pthA 193 1.19e+01 c.56.3.1 33793 1wekA 217 1.19e+01 c.129.1.1 114553 1k2yX 463 1.20e+01 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 2pzmA 330 1.23e+01 2cygA 312 1.23e+01 c.1.8.3 131025 1v0lA 313 1.24e+01 c.1.8.3 108207 1cwyA 500 1.25e+01 1cwyA c.1.8.1 28789 2f46A 156 1.25e+01 2io8A 619 1.25e+01 c.30.1.7 137549 d.3.1.15 137550 d.142.1.8 137551 1jztA 246 1.26e+01 c.104.1.1 63319 1eswA 500 1.27e+01 1cwyA c.1.8.1 59500 1e5dA 402 1.27e+01 1e5dA c.23.5.1 31208 d.157.1.3 42061 2oz3A 404 1.27e+01 1c3jA 351 1.28e+01 1c3jA c.87.1.1 35459 1b0uA 262 1.28e+01 1b0uA c.37.1.12 32370 1v8bA 479 1.29e+01 c.2.1.4 113564 c.23.12.3 113565 2p3eA 420 1.30e+01 1wu7A 434 1.31e+01 c.51.1.1 121275 d.104.1.1 121276 1vj1A 363 1.32e+01 b.35.1.2 100794 c.2.1.1 100795 1pjqA 457 1.32e+01 c.2.1.11 94766 c.90.1.1 94767 e.37.1.1 94768 1u2eA 289 1.33e+01 2egzA 219 1.34e+01 2iswA 323 1.37e+01 2ex4A 241 1.38e+01 c.66.1.42 132516 1ay7B 89 1.39e+01 1ay7B c.9.1.1 30836 1ztpA 251 1.39e+01 d.86.1.2 125649 3c3mA 138 1.40e+01 2dbyA 368 1.40e+01 1w30A 201 1.41e+01 c.61.1.1 114118 3bfpA 194 1.42e+01 2bgsA 344 1.42e+01 1pj5A 830 1.42e+01 b.44.2.1 94742 c.3.1.2 94743 d.16.1.5 94744 d.250.1.1 94745 1reoA 486 1.42e+01 c.3.1.2 97325 d.16.1.5 97326 1poiA 317 1.42e+01 1poiA c.124.1.2 34153 2qptA 550 1.44e+01 1lsuA 147 1.44e+01 c.2.1.9 74250 1ejjA 511 1.47e+01 1ejjA c.105.1.1 59422 c.76.1.3 59423 1vhyA 257 1.47e+01 b.122.1.2 100714 c.116.1.5 100715 1m7gA 211 1.48e+01 c.37.1.4 78724 2qlcA 126 1.48e+01 2nytA 190 1.49e+01 1ihnA 113 1.49e+01 1ihnA c.103.1.1 62388 2ff7A 247 1.49e+01 c.37.1.12 133377 1a8sA 273 1.50e+01 c.69.1.12 34710 1y81A 138 1.51e+01 c.2.1.8 122731 2pmkA 243 1.51e+01 1xkyA 301 1.52e+01 c.1.10.1 122094 8dfrA 189 1.52e+01 c.71.1.1 34895 1q7gA 359 1.52e+01 c.2.1.3 96038 d.81.1.2 96039 2fokA 579 1.54e+01 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1b43A 340 1.54e+01 1a76 a.60.7.1 18092 c.120.1.2 33362 1yioA 208 1.55e+01 a.4.6.2 123326 c.23.1.1 123327 3cq9A 227 1.55e+01 1u8xX 472 1.55e+01 c.2.1.5 107741 d.162.1.2 107742 2fn9A 290 1.56e+01 2pfuA 99 1.56e+01 1nxzA 246 1.56e+01 b.122.1.2 86391 c.116.1.5 86392 2yxdA 183 1.57e+01 2pfsA 150 1.57e+01 2bijA 305 1.57e+01 1o66A 275 1.59e+01 c.1.12.8 92547 1gajA 257 1.60e+01 1gajA c.37.1.12 60416 1zynA 202 1.60e+01 c.47.1.2 125838 c.47.1.2 125839 1fokA 568 1.60e+01 2fokA a.4.5.12 16137 a.4.5.12 16138 a.4.5.12 16139 c.52.1.12 33325 2q4kA 251 1.62e+01 d.86.1.2 139864 1yqtA 538 1.62e+01 1yn9A 169 1.63e+01 2v9cA 215 1.63e+01 1yzfA 195 1.63e+01 c.23.10.5 124275 1m1nB 522 1.64e+01 c.92.2.3 78418 1fehA 574 1.64e+01 1fehA c.96.1.1 36015 d.15.4.2 37690 d.58.1.5 38998 1ghsA 306 1.66e+01 1aq0A c.1.8.3 28840 1ydgA 211 1.66e+01 c.23.5.8 116614 1zc0A 309 1.67e+01 2f71A 298 1.67e+01 c.45.1.2 133070 2nw0A 189 1.67e+01 2dvmA 439 1.67e+01 2p8jA 209 1.68e+01 2oczA 231 1.69e+01 1o98A 511 1.70e+01 c.105.1.1 86684 c.76.1.3 86685 2mbr 340 1.72e+01 2mbr 2mbrA 340 1.72e+01 d.145.1.2 41749 d.146.1.1 41762 1dquA 538 1.73e+01 1dquA c.1.12.7 29314 1wl8A 189 1.73e+01 c.23.16.1 120997 1t5oA 351 1.73e+01 c.124.1.5 106459 2vduE 254 1.74e+01 1ep2B 261 1.76e+01 1ep2B b.43.4.2 25666 c.25.1.3 31556 1ja9A 274 1.77e+01 c.2.1.2 62817 2ip1A 432 1.77e+01 1ek6A 348 1.78e+01 1xel c.2.1.2 29800 1s8nA 205 1.78e+01 c.23.1.1 105374 1es9A 232 1.79e+01 1wab c.23.10.3 31340 2nygA 273 1.79e+01 1f6dA 376 1.79e+01 1f6dA c.87.1.3 35467 2e9lA 469 1.79e+01 2i57A 438 1.80e+01 1wab 232 1.82e+01 1wab 2deoA 230 1.82e+01 1tt7A 330 1.82e+01 b.35.1.2 112623 c.2.1.1 112624 1c96A 753 1.83e+01 1amj c.8.2.1 30727 c.83.1.1 35403 1fg7A 356 1.83e+01 1gewA c.67.1.1 59819 1tib 269 1.83e+01 3tgl 1tibA 269 1.83e+01 c.69.1.17 34738 2a9fA 398 1.85e+01 1bi5A 389 1.86e+01 1bi5A c.95.1.2 35985 c.95.1.2 35986 1i86A 389 1.86e+01 c.95.1.2 66068 c.95.1.2 66069 1va4A 279 1.88e+01 c.69.1.12 108458 1gewA 356 1.88e+01 1gewA c.67.1.1 60470 1i88A 389 1.88e+01 c.95.1.2 66070 c.95.1.2 66071 2qi9C 249 1.90e+01 1n8fA 350 1.90e+01 c.1.10.4 85397 1rqbA 539 1.91e+01 a.5.7.2 105057 c.1.10.5 105058 2qsfA 533 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