# List of top-scoring protein chains for t06-100-30-str2-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 1gz8A 299 2.20e-39 d.144.1.7 83405 1p4oA 322 2.75e-39 d.144.1.7 87775 1fgkA 310 1.73e-38 1fgkA d.144.1.7 41693 1rdqE 350 5.34e-38 d.144.1.7 97314 2evaA 307 3.54e-37 1ia8A 289 8.98e-36 1ia8A d.144.1.7 62112 1t4hA 290 9.78e-35 d.144.1.7 106420 1j1bA 420 3.08e-33 d.144.1.7 90758 2bikB 313 2.26e-32 1z57A 339 8.67e-32 1csn 298 5.77e-26 1csn d.144.1.7 41664 1e7uA 961 4.31e-03 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1e8yA 966 1.60e-02 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1cjaA 342 3.79e-02 1cjaA d.144.1.3 41708 1gnlA 544 1.26e-01 e.26.1.1 70287 1gw5S 142 6.08e-01 d.110.4.2 70633 1ako 268 7.43e-01 1ako d.151.1.1 41779 1gntA 553 8.16e-01 e.26.1.1 70290 1sfxA 109 8.43e-01 a.4.5.50 105505 1oc7A 364 1.02e+00 c.6.1.1 86794 1f3vA 179 1.21e+00 1f3vA d.58.22.1 39382 1huxA 270 1.35e+00 1huxA c.55.1.5 61278 1je0A 236 1.37e+00 c.56.2.1 66581 1e4fT 419 1.51e+00 1e4fT c.55.1.1,c.55.1.1 33453,33454 1ia9A 280 1.83e+00 1ia9A d.144.1.5 62113 1n4wA 504 1.94e+00 c.3.1.2,d.16.1.1 91676,91677 1btkA 169 2.09e+00 1btkA b.55.1.1 26959 1woqA 267 2.18e+00 c.55.1.10,c.55.1.10 109462,109463 1ex2A 189 2.18e+00 1ex2A c.51.4.2 33225 1f8rA 498 2.32e+00 1f8rA c.3.1.2,d.16.1.5 30410,37974 1omrA 201 2.35e+00 a.39.1.5 93349 1m15A 357 2.59e+00 a.83.1.1,d.128.1.2 78368,78369 1cliA 345 2.60e+00 1cliA d.79.4.1,d.139.1.1 39816,41459 1dzkA 157 2.78e+00 1obpA b.60.1.1 27096 1i2sA 282 3.08e+00 e.3.1.1 71104 1i9zA 347 3.08e+00 1i9yA d.151.1.2 62102 1e8gA 560 3.59e+00 1qltA d.58.32.1,d.145.1.1 39455,41718 1g8iA 190 3.59e+00 1rec a.39.1.5 60363 1hzoA 271 3.63e+00 e.3.1.1 71092 1j98A 157 3.64e+00 1j98A d.185.1.2 62755 1dcoA 104 3.68e+00 1dcpA d.74.1.1 39680 1d4xG 126 3.73e+00 1d0nA d.109.1.1 59109 1jssA 224 3.83e+00 d.129.3.2 71844 1hzdA 272 4.15e+00 c.14.1.3 65969 1a99A 344 4.27e+00 1pot c.94.1.1 35812 1eu8A 409 4.35e+00 1eu8A c.94.1.1 59502 1whzA 70 4.49e+00 1iy8A 267 4.66e+00 c.2.1.2 83774 1w2fA 276 4.91e+00 d.143.1.3 109125 1jl2A 156 4.91e+00 c.55.3.1 66822 2gk9A 426 5.30e+00 1w1oA 534 5.50e+00 d.58.32.4,d.145.1.1 109071,109072 1j6qA 136 5.63e+00 b.40.9.1 77091 1b8oA 284 5.72e+00 1b8oA c.56.2.1 33762 1k94A 165 6.00e+00 a.39.1.8 68333 1r89A 437 6.00e+00 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1dsxA 87 6.15e+00 1t1dA d.42.1.2 38644 1ydyA 356 6.27e+00 1fxkC 133 6.37e+00 1fxkC a.2.5.1 15702 1gtfA 74 6.54e+00 b.82.5.1 70460 1m40A 263 6.62e+00 e.3.1.1 74437 1kw4A 89 6.89e+00 a.60.1.2 73077 1vhwA 253 6.91e+00 c.56.2.1 100706 1qgvA 142 7.27e+00 1qgvA c.47.1.8 33056 1x8qA 184 7.31e+00 1t1dA 100 7.34e+00 1t1dA d.42.1.2 38637 1xszA 356 7.44e+00 1g4wR 383 7.58e+00 1g4uS a.24.11.1,c.45.1.2 16644,32692 1tw6A 133 7.98e+00 1ryaA 160 8.20e+00 d.113.1.5 105122 1qsgA 265 8.20e+00 1eny c.2.1.2 29935 1lfpA 249 8.61e+00 e.39.1.1 73885 1qksA 567 8.62e+00 1qksA a.3.1.2,b.70.2.1 15951,27710 1guiA 155 8.92e+00 b.18.1.14 76351 1sauA 115 9.21e+00 1bupA 386 9.38e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 1dceB 331 9.89e+00 1dceB a.102.4.3 18872 1h6kA 757 9.92e+00 a.118.1.14,a.118.1.14,a.118.1.14 60675,60676,60677 1gen 218 9.95e+00 1gen b.66.1.1 27536 1g6aA 271 1.01e+01 1btl e.3.1.1 42704 1b5pA 385 1.02e+01 c.67.1.1 90403 1umgA 362 1.02e+01 d.280.1.1 107956 1jb3A 131 1.03e+01 1jc7A b.40.3.2 62833 1io2A 213 1.05e+01 1ekeA c.55.3.1 62612 1jl1A 155 1.05e+01 c.55.3.1 66821 1e8aA 91 1.07e+01 1b4cA a.39.1.2 17188 1p0zA 131 1.07e+01 d.110.6.1 93882 1xdzA 240 1.07e+01 1epxA 370 1.08e+01 1fbaA c.1.10.1 29150 1uebA 184 1.11e+01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1tvxA 75 1.11e+01 1tvxA d.9.1.1 37441 1em2A 229 1.14e+01 1em2A d.129.3.2 41321 1xkzA 255 1.15e+01 1hi9A 274 1.16e+01 1hi9A c.99.1.1 61063 1ixkA 315 1.17e+01 c.66.1.38 90716 1nxuA 333 1.18e+01 c.122.1.1 86389 1alvA 173 1.19e+01 1alvA a.39.1.8 17370 1rl0A 255 1.19e+01 1i1qA 520 1.20e+01 1qdlA d.161.1.1 61543 1oxjA 173 1.21e+01 a.60.1.2,a.118.1.13 87517,87518 1qgiA 259 1.22e+01 1qgiA d.2.1.7 37001 1dtdA 303 1.22e+01 1aye c.56.5.1 33823 1bob 320 1.23e+01 1bob d.108.1.1 40816 1f7sA 139 1.24e+01 1cof d.109.1.2 40857 1ggzA 148 1.30e+01 a.39.1.5 70176 1bueA 265 1.31e+01 1btl e.3.1.1 42727 1in6A 334 1.32e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 1f0lA 535 1.33e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22377,42239,43382 1bsg 266 1.35e+01 1btl e.3.1.1 42729 1ckmA 330 1.36e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 1q52A 314 1.37e+01 c.14.1.3 95846 1k07A 263 1.38e+01 d.157.1.1 77218 1kq3A 376 1.45e+01 e.22.1.2 68790 1wy2A 351 1.49e+01 1vmeA 410 1.51e+01 c.23.5.1,d.157.1.3 108893,108894 1x8gA 227 1.54e+01 1w6uA 302 1.56e+01 1h99A 224 1.61e+01 a.142.1.1,a.142.1.1 60814,60815 1rwiA 270 1.63e+01 b.68.9.1 97987 1uzvA 114 1.67e+01 1eyeA 280 1.69e+01 1aj2 c.1.21.1 29672 1oboA 169 1.70e+01 c.23.5.1 86776 2pth 193 1.71e+01 2pth c.56.3.1 33793 1v2bA 177 1.74e+01 d.107.1.2 108279 1ii7A 333 1.76e+01 1ii7A d.159.1.4 62415 1kolA 398 1.79e+01 b.35.1.2,c.2.1.1 77474,77475 1ifrA 121 1.79e+01 b.1.16.1 71203 1cojA 212 1.81e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1m6pA 152 1.82e+01 1m6pA b.64.1.1 27519 1in4A 334 1.82e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 1nykA 165 1.82e+01 b.33.1.1 86408 1lv7A 257 1.83e+01 c.37.1.20 78232 1u07A 90 1.86e+01 1vybA 238 1.91e+01 d.151.1.1 108897 1y7bA 542 1.94e+01 3bamA 213 1.94e+01 1bam c.52.1.3 33288 1lyvA 306 1.94e+01 c.45.1.2 74348 1b8aA 438 1.96e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1gyxA 76 2.02e+01 d.80.1.1 76387 1a8y 367 2.02e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1c75A 71 2.03e+01 451c a.3.1.1 15796 1usmA 80 2.07e+01 d.74.1.1 99876 1b35B 255 2.11e+01 1b35B b.121.4.1 23334 2dpmA 284 2.12e+01 2dpmA c.66.1.28 34246 1vns 609 2.12e+01 1vns a.111.1.3 19061 1v4vA 376 2.14e+01 c.87.1.3 100313 1ifqA 138 2.17e+01 1ifqA d.110.4.1 62350 1rm6A 769 2.21e+01 1vkpA 383 2.21e+01 d.126.1.6 108686 1y0hA 105 2.22e+01 1bd8 156 2.22e+01 1bd8 d.211.1.1 19157 1eu1A 780 2.22e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 1hxhA 253 2.24e+01 c.2.1.2 76725 1twdA 256 2.24e+01 c.1.30.1 107397 1czaN 917 2.28e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 1kqrA 179 2.29e+01 b.29.1.14 72886 1kjwA 295 2.30e+01 b.34.2.1,c.37.1.1 68643,68644 1oywA 523 2.31e+01 a.4.5.43,c.37.1.19,c.37.1.19 93760,93761,93762 1ew6A 137 2.32e+01 1ewaA a.1.1.2 15637 1gqiA 708 2.32e+01 c.1.8.10,d.92.2.2 76279,76280 1o7nA 449 2.34e+01 b.33.1.2,d.129.3.3 81162,81163 1chuA 540 2.36e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1c4qA 69 2.41e+01 2bosA b.40.2.1 25010 1njhA 119 2.42e+01 b.128.1.1 85787 1j54A 186 2.48e+01 c.55.3.5 77077 1iomA 377 2.49e+01 a.103.1.1 83698 1j55A 95 2.52e+01 a.39.1.2 77078 1i4wA 353 2.54e+01 c.66.1.24 66028 1gk8A 475 2.55e+01 c.1.14.1,d.58.9.1 65234,65235 1axn 323 2.58e+01 1avc a.65.1.1 18149 1wddA 477 2.59e+01 1yx1A 264 2.60e+01 1ej2A 181 2.61e+01 1f9aA c.26.1.3 59414 1e2kA 331 2.62e+01 1qhiA c.37.1.1 31854 1gveA 327 2.63e+01 c.1.7.1 70597 1gheA 177 2.63e+01 d.108.1.1 76222 1szhA 161 2.64e+01 a.226.1.1 106157 1vyrA 364 2.66e+01 c.1.4.1 108906 1jhdA 396 2.66e+01 b.122.1.3,c.26.1.5 66712,66713 1uekA 275 2.69e+01 d.14.1.5,d.58.26.5 88483,88484 1xfsA 178 2.71e+01 d.129.3.5 109589 1pdo 135 2.75e+01 1pdo c.54.1.1 33376 1g8sA 230 2.76e+01 c.66.1.3 90507 1g0cA 364 2.76e+01 7a3hA c.1.8.3 60165 1gpiA 431 2.76e+01 b.29.1.10 65450 1vjpA 394 2.78e+01 c.2.1.3,d.81.1.3 100828,100829 1aquA 297 2.78e+01 1aquA c.37.1.5 31942 1n13B 113 2.84e+01 1v5iB 76 2.85e+01 1dm9A 133 2.86e+01 1dm9A d.66.1.3 39560 1yd0A 96 2.88e+01 3nul 130 2.89e+01 3nul d.110.1.1 40891 1cfr 285 2.92e+01 1cfr c.52.1.7 33312 1cjcA 460 2.93e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 7a3hA 303 2.94e+01 7a3hA c.1.8.3 28817 1e5pA 151 2.94e+01 1bj7 b.60.1.1 59272 1gegA 256 2.94e+01 1ybvA c.2.1.2 29888 1oafA 261 2.96e+01 a.93.1.1 86734 1fepA 724 2.97e+01 1fepA f.4.3.3 43808 1dlwA 116 3.01e+01 1dlyA a.1.1.1 14982 1uj8A 77 3.02e+01 1vpt 348 3.02e+01 3mag c.66.1.25 34207 1g3mA 294 3.03e+01 c.37.1.5 83268 1wkqA 164 3.03e+01 c.97.1.2 109393 1f0xA 571 3.07e+01 1f0xA d.58.32.2,d.145.1.1 39483,41746 1byfA 125 3.09e+01 1byfA d.169.1.1 42419 1fs5A 266 3.12e+01 c.124.1.1 65044 1j6wA 175 3.12e+01 1j98A d.185.1.2 62663 1w3iA 293 3.13e+01 c.1.10.1 109152 1im5A 180 3.14e+01 c.33.1.3 66211 1dmgA 225 3.15e+01 1dmgA c.22.1.1 31036 1mtzA 293 3.15e+01 c.69.1.7 79467 1ooyA 481 3.16e+01 c.124.1.3,c.124.1.2 93388,93389 1auiB 169 3.17e+01 1auiB a.39.1.5 17325 1io0A 185 3.18e+01 c.10.1.1 76753 1ls1A 295 3.23e+01 a.24.13.1,c.37.1.10 78170,78171 1icpA 376 3.24e+01 1oyc c.1.4.1 62270 1idrA 136 3.25e+01 1dlyA a.1.1.1 62301 1hw5A 210 3.28e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 1dbqA 289 3.29e+01 1qpzA c.93.1.1 35666 1jyaA 130 3.31e+01 d.198.1.1 67453 1ummA 172 3.32e+01 a.3.1.1 107958 1d7uA 433 3.35e+01 2dkb c.67.1.4 34439 2gfaA 119 3.40e+01 1gsoA 431 3.41e+01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 1i27A 73 3.42e+01 1i27A a.4.5.30 61555 1b24A 188 3.43e+01 1b24A d.95.2.1,d.95.2.1 40573,40574 1anf 370 3.44e+01 4mbp c.94.1.1 35776 1jnyA 435 3.47e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1bu6O 501 3.48e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1j6oA 268 3.48e+01 c.1.9.12 77088 1e25A 282 3.48e+01 1e25A e.3.1.1 42731 1jmvA 141 3.51e+01 c.26.2.4 66897 1j93A 353 3.53e+01 c.1.22.1 66454 1sxrA 183 3.55e+01 d.118.1.1 106101 1ee8A 266 3.55e+01 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1z8kA 193 3.58e+01 2ddrA 306 3.60e+01 1h4rA 314 3.60e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1y8oB 128 3.64e+01 1bjt 793 3.68e+01 1bjt e.11.1.1 43249 1r2qA 170 3.69e+01 c.37.1.8 96874 1evhA 112 3.70e+01 1evhA b.55.1.4 26997 1i76A 163 3.70e+01 1hfc d.92.1.11 61877 1obdA 306 3.70e+01 d.143.1.1 86767 1o08A 221 3.70e+01 c.108.1.6 86525 1rzhH 260 3.75e+01 b.41.1.1,f.23.10.1 98162,98163 1gz2A 142 3.81e+01 d.169.1.1 83392 1nzjA 298 3.81e+01 c.26.1.1 92377 1iq8A 582 3.82e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1xpmA 396 3.93e+01 1gppA 237 3.96e+01 b.86.1.2 76262 1x8vA 455 3.96e+01 1juhA 350 3.96e+01 b.82.1.5 71884 1jfrA 262 4.00e+01 1jfrA c.69.1.16 34724 1nu0A 138 4.00e+01 c.55.3.8 92165 1fmcA 255 4.01e+01 1cydA c.2.1.2 29856 1qnrA 344 4.03e+01 1qnoA c.1.8.3 28834 1oygA 447 4.05e+01 b.67.2.2 93726 1f7zA 233 4.06e+01 5ptp b.47.1.2 59681 1gmyA 261 4.07e+01 d.3.1.1 76236 1xkpC 143 4.09e+01 1vcaA 202 4.09e+01 1vcaA b.1.1.3,b.1.1.4 21649,21685 1xocA 520 4.11e+01 1e3dA 266 4.17e+01 2frvA e.19.1.1 59188 1vlyA 338 4.17e+01 b.44.2.1,d.250.1.1 108871,108872 1yacA 208 4.19e+01 1yacA c.33.1.3 31757 2gkpA 167 4.27e+01 1cl8A 276 4.33e+01 1ckqA c.52.1.1 33230 1rliA 184 4.34e+01 c.23.5.6 97647 1ja9A 274 4.38e+01 c.2.1.2 62817 1b43A 340 4.39e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 1y0yA 353 4.46e+01 1tzpA 255 4.47e+01 d.65.1.3 107520 1d4aA 273 4.48e+01 1d4aA c.23.5.3 31219 1hn0A 1021 4.51e+01 a.102.3.2,b.18.1.17,b.24.1.1,b.30.5.2 83616,83617,83618,83619 1gvjA 146 4.52e+01 a.4.5.21 90525 1h4wA 224 4.56e+01 b.47.1.2 65622 1jqnA 883 4.57e+01 c.1.12.3 77159 1fjjA 159 4.57e+01 1fjjA b.17.1.2 59852 1q7zA 566 4.62e+01 c.1.21.2,c.1.26.1 96090,96091 1tu9A 134 4.71e+01 a.1.1.2 107320 1se8A 301 4.72e+01 b.40.4.3 105448 1m4lA 307 4.73e+01 c.56.5.1 78604 1dv1A 449 4.74e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1jw9B 249 4.76e+01 c.111.1.1 67377 1lkkA 105 4.80e+01 1lckA d.93.1.1 40412 1qf8A 182 4.84e+01 1qf8A g.41.4.1 45212 2trxA 108 4.84e+01 1thx c.47.1.1 32719 1qq5A 253 4.86e+01 1qq5A c.108.1.1 43327 1oohA 126 4.87e+01 a.39.2.1 93383 1g7sA 594 4.89e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1ks9A 291 4.90e+01 a.100.1.7,c.2.1.6 68857,68858 1cb8A 678 4.90e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1atlA 202 4.91e+01 1atlA d.92.1.9 40322 1flcB 175 4.98e+01 1flcB h.3.1.1 45716 1q0rA 298 5.00e+01 c.69.1.28 95508 1jubA 311 5.02e+01 c.1.4.1 90908 1o97D 320 5.05e+01 c.26.2.3,c.31.1.2 81233,81234 1f60A 458 5.07e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1es5A 262 5.08e+01 1skf e.3.1.1 42679 1dpo 223 5.11e+01 5ptp b.47.1.2 25975 1aj2 282 5.20e+01 1aj2 c.1.21.1 29665 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