# List of top-scoring protein chains for t06-80-60-80-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 1k8kA 418 1.19e-02 c.55.1.1,c.55.1.1 68305,68306 1z9bA 135 9.64e-02 1cfr 285 4.17e-01 1cfr c.52.1.7 33312 1qwoA 442 4.72e-01 c.60.1.2 104620 1ss4A 153 6.69e-01 d.32.1.6 105976 2fsqA 243 9.98e-01 1ud9A 245 1.00e+00 d.131.1.2,d.131.1.2 107768,107769 1lkdA 297 1.10e+00 d.32.1.3,d.32.1.3 78059,78060 1u8sA 192 1.34e+00 d.58.18.5,d.58.18.5 107737,107738 1x7oA 287 1.37e+00 1t6nA 220 1.52e+00 c.37.1.19 106576 1lfpA 249 1.53e+00 e.39.1.1 73885 1qkkA 155 1.81e+00 1dbwA c.23.1.1 31104 1wd6A 123 2.03e+00 1lxjA 104 2.09e+00 d.58.48.1 84736 2b8eA 273 2.11e+00 1x3lA 440 2.58e+00 2f9dA 125 2.59e+00 1vecA 206 2.61e+00 c.37.1.19 100575 1mai 131 2.75e+00 1mai b.55.1.1 26951 1jl1A 155 2.79e+00 c.55.3.1 66821 1kjnA 157 2.82e+00 c.115.1.1 72614 1im8A 244 2.88e+00 c.66.1.14 66212 2esrA 177 2.92e+00 1wf3A 301 3.00e+00 2cxhA 217 3.00e+00 1a8l 226 3.00e+00 1a8l c.47.1.2,c.47.1.2 32777,32778 1yz7A 188 3.07e+00 2fbhA 146 3.16e+00 1gwiA 411 3.29e+00 a.104.1.1 76364 1shuX 182 3.46e+00 c.62.1.1 98882 1u7bA 261 3.48e+00 1b00A 127 3.48e+00 3chy c.23.1.1 31122 1tqyB 415 3.65e+00 c.95.1.1,c.95.1.1 107247,107248 1tc1A 220 3.82e+00 1tc1A c.61.1.1 34083 1ytlA 174 3.88e+00 1vg0A 650 3.94e+00 c.3.1.3,d.16.1.6 108596,108597 1mp9A 198 3.96e+00 d.129.1.1,d.129.1.1 91385,91386 1y5oA 115 4.06e+00 1qfxA 460 4.07e+00 1qfxA c.60.1.2 33994 1ow1A 195 4.20e+00 b.131.1.3 93625 1btkA 169 4.28e+00 1btkA b.55.1.1 26959 1ujnA 348 4.28e+00 e.22.1.1 99460 1qwnA 1045 4.30e+00 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1ftrA 296 4.30e+00 1ftrA d.58.33.1,d.58.33.1 39485,39486 1v58A 241 4.50e+00 c.47.1.9,d.17.3.1 108371,108372 2ftrA 108 4.55e+00 1h6dA 433 4.65e+00 c.2.1.3,d.81.1.5 65656,65657 2f06A 144 4.80e+00 1qvcA 145 4.96e+00 3ullA b.40.4.3 25284 1kw3B 292 5.14e+00 d.32.1.3,d.32.1.3 77549,77550 1vr5A 547 5.24e+00 1ay7B 89 5.30e+00 1ay7B c.9.1.1 30836 1i0lA 221 5.44e+00 c.61.1.1 71096 1jztA 246 5.69e+00 c.104.1.1 63319 1k8rB 110 5.77e+00 d.15.1.5 72180 2c07A 285 5.78e+00 1dkmA 410 5.82e+00 1dklA c.60.1.2 34000 1x67A 146 6.13e+00 1x3sA 195 6.16e+00 1q0uA 219 6.19e+00 c.37.1.19 95512 1pmmA 466 6.35e+00 c.67.1.6 94901 1jetA 517 6.41e+00 1jevA c.94.1.1 35718 1hqz1 141 6.62e+00 1dkqA 410 6.64e+00 1dklA c.60.1.2 33998 1y7qA 98 6.66e+00 2bgiA 272 6.82e+00 1cznA 169 6.90e+00 1rcf c.23.5.1 31181 2ghrA 302 6.90e+00 1urjA 1136 6.92e+00 1ggzA 148 7.41e+00 a.39.1.5 70176 1fxoA 293 7.44e+00 1g0rA c.68.1.6 34524 2b5eA 504 7.52e+00 1u69A 163 7.69e+00 d.32.1.7 107699 1x31C 206 7.91e+00 2be3A 226 8.19e+00 1ky3A 182 8.57e+00 c.37.1.8 73193 2cy7A 396 8.99e+00 1vqoL 165 9.06e+00 1i8dA 213 9.09e+00 b.43.4.3,b.43.4.3 61953,61954 1nrzA 164 9.19e+00 c.38.1.1 86131 1t3yA 141 9.71e+00 1w5fA 353 1.02e+01 1p9yA 121 1.03e+01 d.241.2.1 94402 1jc4A 148 1.03e+01 1jc4A d.32.1.4 62863 1yyaA 250 1.04e+01 2bycA 137 1.04e+01 1x0vA 354 1.05e+01 1vetB 125 1.07e+01 d.110.7.1 108554 1kmvA 186 1.11e+01 c.71.1.1 72757 1kmqA 184 1.14e+01 c.37.1.8 84412 1e5pA 151 1.14e+01 1bj7 b.60.1.1 59272 1vj1A 363 1.14e+01 b.35.1.2,c.2.1.1 100794,100795 1dbwA 126 1.15e+01 1dbwA c.23.1.1 31095 1v6tA 255 1.16e+01 1b3tA 147 1.16e+01 1b3tA d.58.8.1 39228 1iibA 106 1.19e+01 1iibA c.44.2.1 32648 1wiwA 290 1.20e+01 1zlqA 502 1.21e+01 1uw4A 91 1.23e+01 d.58.7.4 100071 1r7mA 235 1.23e+01 1vj7A 393 1.24e+01 a.211.1.1,d.218.1.8 100801,100802 1zyiA 171 1.25e+01 1u4nA 310 1.26e+01 2fug1 438 1.26e+01 1cdzA 96 1.27e+01 1cdzA c.15.1.1 30925 2fsjA 346 1.30e+01 1qysA 106 1.32e+01 k.41.1.1 96603 1mtyB 384 1.34e+01 1mtyB a.25.1.2 16740 1em8A 147 1.34e+01 c.128.1.1 90457 1i4uA 181 1.36e+01 b.60.1.1 61732 1eluA 390 1.36e+01 1elqA c.67.1.3 34434 1l8bA 190 1.38e+01 d.86.1.1 73683 2pii 112 1.41e+01 2pii d.58.5.1 39071 1k8wA 327 1.41e+01 b.122.1.1,d.265.1.2 83094,90388 2d1eA 248 1.43e+01 1f20A 435 1.44e+01 b.43.4.1,c.25.1.4 64932,64933 1d1qA 161 1.45e+01 1dg9A c.44.1.1 32642 1z8oA 404 1.46e+01 1jy1A 464 1.48e+01 d.136.1.3,d.136.1.3 67438,67439 1j58A 385 1.49e+01 b.82.1.2 71531 1s12A 94 1.53e+01 2bfwA 200 1.53e+01 1j55A 95 1.54e+01 a.39.1.2 77078 1y80A 210 1.55e+01 1zkoA 136 1.58e+01 1qahA 136 1.59e+01 d.79.1.1 96338 1c30B 382 1.61e+01 c.8.3.1,c.23.16.1 30736,31413 1vjeA 166 1.61e+01 d.185.1.2 100807 1u7pA 164 1.61e+01 1wu7A 434 1.62e+01 1gx1A 160 1.63e+01 d.79.5.1 70675 1tiqA 180 1.63e+01 d.108.1.1 107010 2ffuA 501 1.65e+01 1aihA 170 1.66e+01 1aihA d.163.1.1 42149 1v7lA 163 1.66e+01 1obbA 480 1.67e+01 c.2.1.5,d.162.1.2 86760,86761 1kzyC 259 1.68e+01 c.15.1.4,c.15.1.4 73383,73384 1u7iA 136 1.72e+01 d.32.1.7 107724 1ywmA 200 1.72e+01 1o54A 277 1.73e+01 c.66.1.13 92482 1rwzA 245 1.73e+01 d.131.1.2,d.131.1.2 98005,98006 1uayA 242 1.73e+01 c.2.1.2 88390 1neyA 247 1.77e+01 c.1.1.1 80449 1i3cA 149 1.82e+01 c.23.1.1 71112 1qyrA 252 1.84e+01 c.66.1.24 104657 1bvyF 191 1.84e+01 1bvyF c.23.5.1 31207 1pjcA 361 1.86e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 1bx4A 345 1.88e+01 1bx4A c.72.1.1 34935 1ttwA 138 1.90e+01 d.198.1.1 107308 2b9eA 303 1.91e+01 1irdB 146 1.94e+01 a.1.1.2 66287 1vlaA 150 1.94e+01 d.227.1.2 108735 1qo0D 196 1.96e+01 1qo0D c.23.1.3 31125 1i4mA 108 1.96e+01 d.6.1.1 66025 2cc0A 195 2.02e+01 2cqsA 842 2.03e+01 1dynA 125 2.03e+01 1dynA b.55.1.1 26955 1qz5A 375 2.04e+01 c.55.1.1,c.55.1.1 96614,96615 1t0tV 248 2.05e+01 d.58.4.10 106229 1h3nA 878 2.08e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1jbeA 128 2.12e+01 3chy c.23.1.1 62845 1d2vA 104 2.14e+01 1d2vA a.93.1.2 18697 1mwvA 714 2.18e+01 a.93.1.3,a.93.1.3 85161,85162 1vrvA 101 2.19e+01 1qf5A 431 2.20e+01 1adeA c.37.1.10 32212 1fmjA 351 2.23e+01 c.37.1.5 59879 1dl5A 317 2.24e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1y81A 138 2.26e+01 2afwA 329 2.26e+01 1ppjD 241 2.28e+01 a.3.1.3,f.23.11.1 104258,104259 1ta3A 274 2.30e+01 c.1.8.5 106731 2c27A 315 2.35e+01 1ogiA 303 2.35e+01 b.43.4.2,c.25.1.1 92914,92915 1i9gA 280 2.38e+01 c.66.1.13 62090 2an1A 292 2.40e+01 1j7gA 144 2.44e+01 c.110.1.1 84130 2b3yA 888 2.47e+01 2cy2A 174 2.48e+01 2cg4A 152 2.53e+01 1pa1A 310 2.55e+01 c.45.1.2 94404 1knvA 293 2.57e+01 c.52.1.7 68707 1toaA 313 2.57e+01 1toaA c.92.2.2 35598 2g0qA 173 2.57e+01 2ahrA 259 2.57e+01 1efvA 315 2.57e+01 1efvA c.26.2.3,c.31.1.2 31633,31728 1ylqA 96 2.60e+01 1w6kA 732 2.63e+01 1dqpA 230 2.66e+01 1dqnA c.61.1.1 34069 1xdzA 240 2.67e+01 1ppjB 439 2.67e+01 d.185.1.1,d.185.1.1 104254,104255 1hb6A 86 2.70e+01 a.11.1.1 70959 1wyuA 438 2.79e+01 1ppjF 110 2.79e+01 f.27.1.1 104262 1n2aA 201 2.79e+01 a.45.1.1,c.47.1.5 91553,91554 1ne7A 289 2.85e+01 c.124.1.1 91833 1n3yA 198 2.86e+01 c.62.1.1 79976 1oqqA 106 2.86e+01 d.15.4.1 93422 1qu9A 128 2.87e+01 1qu9A d.79.1.1 39755 2cq2A 114 2.90e+01 1uqtA 482 2.91e+01 c.87.1.6 99794 1fr2A 86 2.93e+01 a.28.2.1 83256 1dg9A 157 2.95e+01 1dg9A c.44.1.1 32637 1fnnA 389 3.01e+01 1fnnA a.4.5.11,c.37.1.20 16129,32426 1iseA 185 3.06e+01 d.67.3.1 90691 1ohuA 175 3.07e+01 f.1.4.1 93029 1rypA 243 3.07e+01 1pmaA d.153.1.4 41932 2cfaA 217 3.08e+01 1wwiA 148 3.08e+01 2fxuA 375 3.10e+01 1qfjA 232 3.12e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 2pia 321 3.14e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1x7vA 99 3.14e+01 d.58.4.11 109501 1l9vA 317 3.17e+01 d.13.2.1,d.216.1.1 73760,73761 1j2gA 319 3.18e+01 d.96.1.4,d.96.1.4,d.96.1.4,d.96.1.4,d.96.1.4 103824,103825,103826,103827,103828 1m6yA 301 3.20e+01 a.60.13.1,c.66.1.23 78716,78717 1pszA 303 3.20e+01 1toaA c.92.2.2 35600 1h4vB 421 3.20e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1josA 128 3.20e+01 d.52.7.1 84191 1wvqA 167 3.22e+01 1yqfA 203 3.23e+01 1jh6A 189 3.25e+01 d.61.1.1 66707 2c5rA 67 3.26e+01 1jkeA 145 3.27e+01 c.110.1.1 66791 2a2kA 175 3.28e+01 1a9xB 379 3.28e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 2cb2A 318 3.30e+01 1v96A 149 3.33e+01 1x0rA 249 3.33e+01 1a41 234 3.34e+01 1a41 d.163.1.2 42174 2bjvA 265 3.35e+01 1gvhA 396 3.35e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1k2eA 156 3.37e+01 d.113.1.1 72010 2go8A 122 3.37e+01 2ethA 154 3.37e+01 1mwwA 128 3.37e+01 d.80.1.4 91483 1yzhA 214 3.37e+01 2axcA 264 3.44e+01 1twfK 120 3.47e+01 2fyxA 143 3.47e+01 1yb2A 275 3.52e+01 1t6eX 381 3.53e+01 b.50.1.2 106564 2f71A 298 3.53e+01 1vlrA 350 3.54e+01 d.13.1.3,d.246.1.1 108860,108861 2a72A 146 3.57e+01 1feuA 206 3.59e+01 1feuA b.53.1.1 59801 1v71A 323 3.61e+01 8dfr 189 3.63e+01 1aoeA c.71.1.1 34895 1pmhX 185 3.67e+01 b.18.1.18 104193 1dxeA 256 3.68e+01 1dxeA c.1.12.5 29310 1z6nA 167 3.69e+01 1i1nA 226 3.71e+01 c.66.1.7 71102 1zghA 260 3.74e+01 1e8gA 560 3.77e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1cjwA 166 3.77e+01 1cjwA d.108.1.1 40818 1xzzA 246 3.77e+01 2eu9A 355 3.78e+01 1xjvA 294 3.80e+01 2cw8A 537 3.82e+01 2gupA 292 3.86e+01 1orvA 728 3.86e+01 b.70.3.1,c.69.1.24 87354,87355 1m4rA 151 3.89e+01 a.26.1.3 84799 1xttA 216 3.92e+01 2f8lA 344 3.94e+01 1oboA 169 3.94e+01 c.23.5.1 86776 2bcgY 206 3.95e+01 2bnxA 386 3.97e+01 1cipA 353 3.97e+01 1cipA a.66.1.1,c.37.1.8 18210,32093 1h70A 255 3.99e+01 1h70A d.126.1.3 60711 1nw3A 416 3.99e+01 c.66.1.31 86288 1cqxA 403 4.01e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1uyjA 296 4.02e+01 f.8.1.2 108143 1f4pA 147 4.08e+01 5nul c.23.5.1 59651 1rqpA 299 4.11e+01 b.141.1.1,c.132.1.1 97754,97755 1tadA 324 4.11e+01 1cipA a.66.1.1,c.37.1.8 18194,32077 1n0lA 224 4.12e+01 b.1.11.1,b.7.2.1 79744,79745 1e2kA 331 4.13e+01 1qhiA c.37.1.1 31854 1em8B 112 4.13e+01 c.126.1.1 90458 1xg0A 76 4.13e+01 1qz8A 113 4.14e+01 b.140.1.1 96619 1q0qA 406 4.15e+01 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1xmbA 418 4.17e+01 1nox 205 4.20e+01 1nox d.90.1.1 40242 1qsgA 265 4.27e+01 1eny c.2.1.2 29935 1tbxA 99 4.29e+01 a.4.5.48 106748 1qgoA 264 4.30e+01 1qgoA c.92.1.2 35596 1hc7A 477 4.33e+01 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 1oi2A 366 4.33e+01 c.119.1.2 103802 1tfzA 424 4.35e+01 d.32.1.3,d.32.1.3 106886,106887 1zosA 230 4.41e+01 1z5sD 83 4.41e+01 1luaA 287 4.43e+01 c.2.1.7,c.58.1.4 78216,78217 1mkyA 439 4.44e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1euhA 475 4.45e+01 1euhA c.82.1.1 35369 1h3qA 140 4.46e+01 d.110.4.3 76652 1sqeA 109 4.46e+01 d.58.4.5 105908 1xppA 115 4.47e+01 1xeaA 323 4.49e+01 c.2.1.3,d.81.1.5 109572,109573 1xxlA 239 4.50e+01 1rkbA 173 4.50e+01 2fcjA 119 4.57e+01 1b79A 119 4.60e+01 1b79A a.81.1.1 18451 2scpA 174 4.62e+01 2scpA a.39.1.5 17256 1zetA 388 4.62e+01 1w5tA 412 4.63e+01 1k8kF 168 4.67e+01 d.198.2.1 68312 1o08A 221 4.67e+01 c.108.1.6 86525 1exrA 148 4.69e+01 1cll a.39.1.5 17299 1yy7A 213 4.71e+01 1f7dA 136 4.72e+01 1dun b.85.4.1 28353 1utcA 363 4.74e+01 a.118.1.4,b.69.6.1 99914,99915 1x89A 178 4.79e+01 1o7fA 469 4.80e+01 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 1xocA 520 4.82e+01 2d5xB 146 4.83e+01 1nh8A 304 4.84e+01 c.94.1.1,d.58.5.3 80507,80508 1se0A 116 4.88e+01 g.52.1.1 98814 1vrbA 342 4.89e+01 1h5rA 293 4.90e+01 c.68.1.6 65623 1fs0E 138 4.90e+01 1aqt a.2.10.1,b.93.1.1 59997,59998 1jbkA 195 4.92e+01 c.37.1.20 71631 1gdhA 320 4.93e+01 1gdhA c.2.1.4,c.23.12.1 30095,31355 1izmA 184 4.95e+01 a.199.1.1 90725 2atzA 180 4.96e+01 1qdeA 224 5.03e+01 1qvaA c.37.1.19 32410 1sr4B 261 5.04e+01 d.151.1.1 105949 1tljA 213 5.07e+01 d.282.1.1 107126 2f2lX 167 5.10e+01 2gvkA 317 5.16e+01 1zv1A 65 5.19e+01 1udzA 182 5.22e+01 b.51.1.1 99239 1dvoA 152 5.23e+01 1dvoA a.136.1.1 19623 2bx6A 350 5.26e+01 1zx4A 192 5.29e+01 1m1hA 248 5.31e+01 b.114.1.1,d.58.42.1 78415,78416 1z82A 335 5.33e+01 1ga3A 113 5.33e+01 1ga3A a.26.1.2 60411 1jeyA 609 5.37e+01 1jeqA b.131.1.1,c.62.1.3 90370,90371 2rslA 140 5.37e+01 2rslA c.53.1.1 33345 1yb3A 175 5.40e+01 1no5A 114 5.42e+01 d.218.1.5 92014 1pzwA 80 5.42e+01 g.39.1.10 95483 1zndA 174 5.47e+01 1in0A 163 5.49e+01 d.58.49.1,d.58.49.1 83694,83695 1vjkA 98 5.52e+01 d.15.3.1 108631 1kwgA 645 5.54e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1ig5A 75 5.55e+01 4icb a.39.1.1 62363 1usmA 80 5.57e+01 d.74.1.1 99876 1ppjA 446 5.57e+01 d.185.1.1,d.185.1.1 104252,104253 1vq0A 302 5.59e+01 1fo8A 343 5.63e+01 1foaA c.68.1.10 59927 1dyqA 234 5.63e+01 3seb b.40.2.2,d.15.6.1 59140,59141 2gasA 307 5.66e+01 1hrkA 359 5.67e+01 1hrkA c.92.1.1 61228 1w0nA 131 5.67e+01 1sqhA 312 5.68e+01 d.108.1.5 98966 2fliA 220 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