# List of top-scoring protein chains for t04-80-60-80-str2+near-backbone-11-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 1zx4A 192 2.44e-01 1dc1A 323 2.83e-01 1dc1A c.52.1.11 33321 1d5yA 292 3.20e-01 1d5yA a.4.1.8,a.4.1.8,d.60.1.2 16055,16056,39532 1g3mA 294 4.17e-01 c.37.1.5 83268 1aquA 297 5.20e-01 1aquA c.37.1.5 31942 2ayuA 417 5.24e-01 1yz7A 188 7.49e-01 1c02A 166 8.92e-01 1qspA a.24.10.2 16633 2cw9A 194 9.87e-01 1ls6A 295 1.01e+00 c.37.1.5 91115 1g5aA 628 1.06e+00 b.71.1.1,c.1.8.1 65152,65153 1udxA 416 1.10e+00 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1sz9A 144 1.11e+00 a.118.9.4 106139 1i60A 278 1.18e+00 c.1.15.4 71118 1ca1 370 1.27e+00 1ca1 a.124.1.1,b.12.1.3 19340,23648 2d28C 149 1.32e+00 1p4xA 250 1.34e+00 a.4.5.28,a.4.5.28 87784,87785 1m5yA 408 1.39e+00 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 1qqcA 773 1.47e+00 1tgoA c.55.3.5,e.8.1.1 33724,43013 1t0tV 248 1.48e+00 d.58.4.10 106229 1tmxA 293 1.55e+00 1yj7A 171 1.68e+00 1q8iA 783 1.75e+00 c.55.3.5,e.8.1.1 96208,96209 1fvkA 189 1.92e+00 1fvkA c.47.1.13 90351 1kvkA 395 1.94e+00 d.14.1.5,d.58.26.3 73060,73061 1qf6A 642 1.95e+00 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1zcbA 362 2.12e+00 2cz1A 206 2.43e+00 2ahjA 206 2.44e+00 2ahjA d.149.1.1 41772 1czaN 917 2.50e+00 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 1cqxA 403 2.51e+00 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 2d27A 149 2.58e+00 1avqA 228 2.60e+00 1avqA c.52.1.13 33326 1khoA 370 2.64e+00 a.124.1.1,b.12.1.3 72489,72490 1acvA 189 2.72e+00 1fvkA c.47.1.13 90328 1hfoA 113 2.78e+00 d.80.1.3 61006 1uw4B 248 2.80e+00 a.118.1.14 100072 1u3aA 189 2.87e+00 1p5zB 263 2.89e+00 c.37.1.1 87815 1w07A 659 2.91e+00 2bolA 314 3.07e+00 1dmhA 311 3.07e+00 1dmhA b.3.6.1 22633 2aifA 135 3.22e+00 1bw0A 416 3.38e+00 1bw0A c.67.1.1 34385 1eazA 125 3.50e+00 b.55.1.1 70113 1ig8A 486 3.70e+00 2yhx c.55.1.3,c.55.1.3 64746,64747 1ccwB 483 4.15e+00 1cb7B c.1.19.2 29646 1ift 263 4.19e+00 1mrj d.165.1.1 42211 1vp4A 425 4.20e+00 1f5mA 180 4.29e+00 1f5mB d.110.2.1 40895 2cy5A 140 4.38e+00 1r5zA 323 4.40e+00 f.40.1.1 97135 1e25A 282 4.44e+00 1e25A e.3.1.1 42731 1bsmA 201 4.46e+00 1avmA a.2.11.1,d.44.1.1 15780,38743 1m6sA 347 4.93e+00 c.67.1.1 78701 1or7A 194 5.02e+00 a.4.13.2,a.177.1.1 87332,87333 1q6uA 245 5.06e+00 d.26.1.1 95998 1ukfA 188 5.07e+00 d.3.1.10 99488 1u6mA 199 5.24e+00 1q3eA 207 5.38e+00 b.82.3.2 95669 1stzA 338 5.39e+00 a.4.5.51,d.110.2.3 106009,106010 1jmsA 381 5.41e+00 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1h6qA 168 5.47e+00 1h6qA b.88.1.2 60692 2etgA 296 5.49e+00 1q6hA 224 5.60e+00 d.26.1.1 95975 1jg8A 347 5.67e+00 1jg8A c.67.1.1 62946 1gqeA 365 5.71e+00 e.38.1.1 70351 2g09A 297 5.80e+00 1aky 221 5.90e+00 1zin c.37.1.1,g.41.2.1 31896,45197 3nul 130 6.05e+00 3nul d.110.1.1 40891 1zt2B 212 6.06e+00 1j99A 293 6.49e+00 c.37.1.5 71618 1sedA 117 6.50e+00 a.219.1.1 105449 1pysA 350 6.58e+00 1pysA d.104.1.1 40775 1wu7A 434 6.59e+00 1ku1A 230 6.90e+00 a.118.3.1 72996 1g60A 260 6.98e+00 c.66.1.11 70151 1wpbA 172 7.06e+00 2f5xA 312 7.17e+00 1m3sA 186 7.23e+00 c.80.1.3 78573 1knqA 175 7.28e+00 c.37.1.17 72786 2cy7A 396 7.40e+00 1k47A 337 7.48e+00 d.14.1.5,d.58.26.4 72040,72041 2c0rA 362 7.50e+00 1icrA 217 7.63e+00 1vfrA d.90.1.1 62274 1jx4A 352 7.79e+00 d.240.1.1,e.8.1.7 90378,90379 2cygA 312 7.79e+00 1a0rP 245 7.81e+00 1b9yC c.47.1.6 33054 2a9kB 223 7.82e+00 1f7lA 121 7.86e+00 1f7lA d.150.1.2 59666 1z5hA 780 7.88e+00 1ykiA 217 7.91e+00 2bduA 297 8.14e+00 1eb7A 323 8.25e+00 1eb7A a.3.1.5,a.3.1.5 59404,59405 1u2wA 122 8.34e+00 1iugA 352 8.48e+00 c.67.1.3 90699 1vfrA 218 8.57e+00 1vfrA d.90.1.1 40247 1b3tA 147 8.64e+00 1b3tA d.58.8.1 39228 1fthA 122 8.66e+00 d.150.1.2 60028 1s2xA 206 8.77e+00 a.47.3.1 105229 1ykuA 136 8.77e+00 1y1xA 191 8.99e+00 1f3iA 481 9.00e+00 1b7eA 1y9qA 192 9.07e+00 1r31A 428 9.26e+00 d.58.20.1,d.179.1.1 96897,96898 1g24A 211 9.27e+00 1g24A d.166.1.1 42270 1ax8 146 9.28e+00 1ax8 a.26.1.1 16844 1cc1L 498 9.62e+00 1h2rL e.18.1.1 43301 1nstA 325 1.02e+01 1nstA c.37.1.5 31951 1qsaA 618 1.04e+01 1qsaA a.118.5.1,d.2.1.6 19182,36988 2fymA 431 1.05e+01 1k2yX 463 1.06e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1xqiA 195 1.07e+01 2ffjA 300 1.07e+01 1vhiA 142 1.10e+01 1b3tA d.58.8.1 39230 1w6tA 444 1.10e+01 1knvA 293 1.10e+01 c.52.1.7 68707 1qhdA 398 1.13e+01 1qhdA a.115.1.2,b.19.1.1 63324,63325 1qhtA 775 1.14e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1p5dX 463 1.14e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1faoA 126 1.14e+01 1faoA b.55.1.1 26974 1q87A 221 1.16e+01 e.47.1.1 96192 1tueB 218 1.16e+01 b.91.1.1 107324 2b67A 204 1.16e+01 1b7yA 350 1.17e+01 1pysA d.104.1.1 40776 1fa0A 537 1.18e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 1wolA 122 1.24e+01 1w3uA 362 1.25e+01 1pzgA 331 1.28e+01 c.2.1.5,d.162.1.1 95425,95426 1wpuA 147 1.29e+01 2azqA 311 1.29e+01 1twfK 120 1.29e+01 1nm8A 616 1.29e+01 c.43.1.3,c.43.1.3 85872,85873 1z54A 132 1.30e+01 1cojA 212 1.31e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1lm4A 194 1.31e+01 d.167.1.1 84626 2pviA 157 1.31e+01 3pviA c.52.1.6 33302 1wlqC 201 1.31e+01 a.4.5.52 109400 1wy2A 351 1.34e+01 2trcP 217 1.36e+01 1b9yC c.47.1.6 33051 1m33A 258 1.37e+01 c.69.1.26 78514 1r3sA 367 1.37e+01 c.1.22.1 96963 1ed5A 444 1.38e+01 1nseA d.174.1.1 42530 1veaA 148 1.38e+01 d.275.1.1 108529 1m7vA 363 1.39e+01 d.174.1.1 78748 1mzbA 136 1.41e+01 a.4.5.42 91497 1bed 181 1.41e+01 1fvkA c.47.1.13 90330 1gnkA 112 1.42e+01 2pii d.58.5.1 39073 1r8eA 278 1.42e+01 a.6.1.3,d.60.1.1 104843,104844 1yoyA 175 1.43e+01 1uq5A 263 1.44e+01 d.165.1.1 99778 2brcA 214 1.47e+01 1ixmA 192 1.47e+01 1ixmA d.123.1.1 41114 1e9xA 455 1.47e+01 1ea1A a.104.1.1 18969 1oneA 436 1.47e+01 4enl c.1.11.1,d.54.1.1 29200,38844 1pieA 419 1.48e+01 d.14.1.5,d.58.26.7 94706,94707 1gzsB 165 1.49e+01 a.168.1.1 76425 1nrjB 218 1.50e+01 c.37.1.8 86125 2dfkA 402 1.51e+01 1nh1A 330 1.53e+01 e.45.1.1 91871 1bg0 356 1.54e+01 1qh4A a.83.1.1,d.128.1.2 18476,41211 1bm9A 122 1.55e+01 1bm9A a.4.5.7 16116 3pviA 157 1.55e+01 3pviA c.52.1.6 33300 1rq2A 382 1.57e+01 c.32.1.1,d.79.2.1 105048,105049 1tukA 67 1.60e+01 1gs5A 258 1.60e+01 c.73.1.2 70395 1zpvA 91 1.61e+01 1tc6A 236 1.62e+01 d.122.1.1 106756 1d0cA 444 1.63e+01 d.174.1.1 64769 2b7eA 59 1.63e+01 1dptA 117 1.63e+01 1dptA d.80.1.3 39862 1iuqA 367 1.65e+01 c.112.1.1 90703 1jh6A 189 1.65e+01 d.61.1.1 66707 1php 394 1.69e+01 16pk c.86.1.1 35452 1mw7A 240 1.70e+01 e.39.1.1 79557 1uroA 367 1.71e+01 1uroA c.1.22.1 29675 1j7xA 302 1.71e+01 c.14.1.2 66425 1byqA 228 1.72e+01 1yer d.122.1.1 41100 1x75A 132 1.74e+01 1avmA 201 1.75e+01 1avmA a.2.11.1,d.44.1.1 15782,38745 1qtrA 317 1.75e+01 1qtrA c.69.1.7 34660 1m15A 357 1.77e+01 a.83.1.1,d.128.1.2 78368,78369 1ui7A 638 1.77e+01 b.30.2.1,d.17.2.1,d.17.2.1 99413,99414,99415 1x8hA 228 1.78e+01 1snyA 267 1.78e+01 c.2.1.2 105833 1x8gA 227 1.79e+01 1m7yA 435 1.80e+01 c.67.1.4 78761 1wm1A 317 1.80e+01 c.69.1.7 109405 1o5hA 214 1.80e+01 a.191.1.1 92497 1wd5A 208 1.81e+01 1gd0A 122 1.82e+01 1dptA d.80.1.3 39834 2g0wA 296 1.84e+01 1ru8A 232 1.87e+01 c.26.2.1 97849 1hr6A 475 1.87e+01 1hr6A d.185.1.1,d.185.1.1 61164,61165 2cwyA 94 1.91e+01 1xfuA 747 1.91e+01 2a6tA 271 1.93e+01 1xmaA 145 1.94e+01 1k2xA 177 1.94e+01 d.153.1.5 90929 1up7A 417 1.95e+01 1d1vA 444 1.95e+01 1nseA d.174.1.1 59101 1fmjA 351 1.98e+01 c.37.1.5 59879 1wmqA 147 1.98e+01 1wwpA 119 1.99e+01 1snnA 227 2.00e+01 d.115.1.2 105821 1x8vA 455 2.00e+01 1pv9A 348 2.00e+01 c.55.2.1,d.127.1.1 95157,95158 1josA 128 2.01e+01 d.52.7.1 84191 1fs7A 485 2.04e+01 1qdbA a.138.1.3 19691 1ah6 220 2.05e+01 1yer d.122.1.1 41094 2bzgA 232 2.06e+01 1qr6A 584 2.08e+01 1qr6A c.2.1.7,c.58.1.3 30293,33941 1mxmA 254 2.09e+01 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 8abp 306 2.09e+01 8abp c.93.1.1 35647 1qlpA 394 2.11e+01 1ovaA e.1.1.1 42628 1s2oA 244 2.14e+01 1z7uA 112 2.15e+01 1zd8A 227 2.16e+01 2dpmA 284 2.16e+01 2dpmA c.66.1.28 34246 1h6gA 256 2.16e+01 1h6gA a.24.9.1,a.24.9.1 60669,60670 1ul7A 102 2.16e+01 d.129.6.1 99540 1r71A 178 2.16e+01 a.4.14.1 104823 1b4pA 217 2.17e+01 a.45.1.1,c.47.1.5 83158,83159 1r9gA 216 2.19e+01 c.23.16.1 97258 1wl8A 189 2.20e+01 1i5pA 633 2.20e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 1vaxA 287 2.20e+01 2exrA 524 2.21e+01 1a6jA 163 2.22e+01 1a6jA d.112.1.1 40915 1n5uA 585 2.26e+01 a.126.1.1,a.126.1.1,a.126.1.1 85339,85340,85341 1jrrA 382 2.26e+01 e.1.1.1 63256 1pt7A 437 2.27e+01 c.123.1.1 95093 5abp 306 2.32e+01 8abp c.93.1.1 35651 1vh7A 265 2.33e+01 c.1.2.1 100646 1w9yA 319 2.33e+01 1paqA 189 2.34e+01 a.118.1.14 94413 1auyA 189 2.34e+01 1auyA b.121.4.6 23311 1lfpA 249 2.35e+01 e.39.1.1 73885 1ib8A 164 2.37e+01 b.38.2.1,d.52.4.1 71168,71169 1b04A 318 2.39e+01 1b04A d.142.2.2 41579 1htjF 210 2.41e+01 1htjF a.91.1.1 61254 1smtA 122 2.42e+01 1smtA a.4.5.5 16109 2genA 197 2.42e+01 2bleA 367 2.43e+01 2bnkA 67 2.43e+01 1t4gA 322 2.44e+01 a.60.4.1,c.37.1.11 106418,106419 1zzlA 351 2.44e+01 1rztA 331 2.44e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 1y0zA 330 2.44e+01 1ynuA 473 2.44e+01 1rqjA 299 2.45e+01 a.128.1.1 97744 2mgg 154 2.45e+01 1a6m a.1.1.2 15069 1p3jA 217 2.46e+01 c.37.1.1,g.41.2.1 94022,94023 1brt 277 2.48e+01 1brt c.69.1.12 34699 1l5aA 436 2.48e+01 c.43.1.2,c.43.1.2 75923,75924 2cunA 410 2.49e+01 1r1dA 247 2.51e+01 c.69.1.29 96813 2cfxA 144 2.51e+01 1b24A 188 2.51e+01 1b24A d.95.2.1,d.95.2.1 40573,40574 1b6rA 355 2.53e+01 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28241,31648,41493 1u6rA 380 2.54e+01 2ax4A 198 2.55e+01 1q8fA 313 2.55e+01 c.70.1.1 96203 1yarO 237 2.55e+01 1on0A 158 2.57e+01 d.108.1.1 87095 2b3yA 888 2.58e+01 1ireA 204 2.58e+01 d.149.1.1 76769 2al1A 436 2.59e+01 1ixcA 294 2.61e+01 a.4.5.37,c.94.1.1 83764,83765 1bo1A 416 2.62e+01 1bo1A d.143.1.2 41591 1rwxA 178 2.62e+01 1qh4A 380 2.67e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 1xl7A 612 2.67e+01 1vfgA 390 2.67e+01 a.173.1.1,d.218.1.4 108570,108571 2c6qA 351 2.68e+01 1xfxA 777 2.69e+01 1gcb 454 2.70e+01 3gcb d.3.1.1 37034 1ls1A 295 2.71e+01 a.24.13.1,c.37.1.10 78170,78171 5ukdA 194 2.71e+01 1zin c.37.1.1 31851 1pvyA 227 2.72e+01 d.115.1.2 95195 1a8rA 221 2.72e+01 1a8rA d.96.1.1 40587 1b06A 210 2.75e+01 1avmA a.2.11.1,d.44.1.1 15740,38737 1z3eA 132 2.79e+01 1fseA 74 2.79e+01 1fseA a.4.6.2 60000 1xi1A 575 2.81e+01 1pveA 72 2.84e+01 a.189.1.1 104322 1wmwA 330 2.85e+01 2cxxA 190 2.85e+01 1kkhA 317 2.87e+01 d.14.1.5,d.58.26.3 72645,72646 1v8aA 265 2.87e+01 c.72.1.2 100494 1eluA 390 2.88e+01 1elqA c.67.1.3 34434 1dvkA 173 2.89e+01 1dvkA a.72.1.1 18319 1y5eA 169 2.90e+01 1xg0C 177 2.90e+01 1fmcA 255 2.90e+01 1cydA c.2.1.2 29856 1c7nA 399 2.91e+01 1d2fA c.67.1.3 34413 2d7vA 162 2.92e+01 1ztpA 251 2.94e+01 1dlwA 116 2.94e+01 1dlyA a.1.1.1 14982 1psrA 100 2.95e+01 1psrA a.39.1.2 17180 1zchA 255 2.96e+01 1no5A 114 2.97e+01 d.218.1.5 92014 1ujnA 348 2.97e+01 e.22.1.1 99460 1mlo 154 2.97e+01 1a6m a.1.1.2 15085 1lj2A 110 2.97e+01 h.1.13.2 73926 1wphA 201 2.97e+01 1q79A 514 3.00e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1mym 154 3.00e+01 1a6m a.1.1.2 15054 1hfs 160 3.02e+01 1hfc d.92.1.11 40370 1umgA 362 3.02e+01 d.280.1.1 107956 1i50K 120 3.03e+01 d.74.3.2 61765 1fzcA 87 3.05e+01 1fzcA h.1.8.1 45590 1qgwC 177 3.05e+01 1qgwC a.1.1.3 15673 1ftkA 279 3.07e+01 1gr2A c.94.1.1 35819 1woyA 500 3.09e+01 1i7wA 538 3.10e+01 3bct a.118.1.1 61909 2b9hA 353 3.10e+01 1yw4A 341 3.10e+01 1qf9A 194 3.11e+01 1zin c.37.1.1 31848 1q44A 326 3.12e+01 c.37.1.5 95779 1sf9A 128 3.12e+01 b.34.15.1 98831 1b72B 87 3.13e+01 1akhA a.4.1.1 16001 1ugpA 203 3.17e+01 d.149.1.1 107831 2breA 219 3.18e+01 1k38A 254 3.19e+01 e.3.1.1 84303 1f0xA 571 3.19e+01 1f0xA d.58.32.2,d.145.1.1 39483,41746 2eshA 118 3.19e+01 1u0mA 382 3.19e+01 c.95.1.2,c.95.1.2 107557,107558 1gjnA 153 3.20e+01 a.1.1.2 70191 1dv1A 449 3.21e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1w25A 459 3.23e+01 1io1A 398 3.26e+01 1io1A e.32.1.1 62611 1zfjA 491 3.31e+01 1ak5 c.1.5.1,d.37.1.1,d.37.1.1 28638,38540,38541 1a0i 348 3.32e+01 1a0i b.40.4.6,d.142.2.1 25363,41577 1uylA 236 3.34e+01 d.122.1.1 108147 2c07A 285 3.38e+01 1smbA 154 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