# List of top-scoring protein chains for t06-100-30-alpha-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 2b99A 156 1.20e-01 1l2tA 235 1.35e-01 c.37.1.12 73514 1jf8A 131 1.37e-01 c.44.1.1 66621 1z47A 355 1.67e-01 1vyrA 364 4.18e-01 c.1.4.1 108906 1fobA 334 5.31e-01 c.1.8.3 83255 1cr1A 296 7.12e-01 1cr1A c.37.1.11 32286 1bupA 386 8.04e-01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1srrA 124 8.21e-01 1dz3A c.23.1.1 31110 1mb3A 124 1.05e+00 c.23.1.1 78907 1c9kA 180 1.07e+00 1c9kB c.37.1.11 32363 2gqrA 237 1.34e+00 2c31A 568 1.50e+00 1vp8A 201 1.56e+00 1z2lA 423 1.60e+00 1yymG 313 1.72e+00 1n2sA 299 1.75e+00 c.2.1.2 79857 1woqA 267 1.79e+00 c.55.1.10,c.55.1.10 109462,109463 1b0uA 262 1.86e+00 1b0uA c.37.1.12 32370 1tmy 120 1.99e+00 1dbwA c.23.1.1 31083 2cqnA 77 2.11e+00 1g7sA 594 2.12e+00 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1n13B 113 2.17e+00 2f5gA 133 2.23e+00 1xubA 298 2.37e+00 1cnzA 363 2.54e+00 1cnzA c.77.1.1 35061 1ek0A 170 2.64e+00 1ctqA c.37.1.8 32076 1bg4 302 2.65e+00 1taxA c.1.8.3 28806 1u0sY 118 2.80e+00 c.23.1.1 107566 1wleA 501 2.87e+00 1eiwA 111 2.89e+00 1eiwA c.23.3.1 31130 1fzqA 181 2.94e+00 1hurA c.37.1.8 32060 7odcA 424 3.36e+00 7odcA b.49.2.3,c.1.6.1 26488,28650 1svfB 38 3.46e+00 1svfB h.3.2.1 45764 2ethA 154 3.53e+00 1z90A 469 3.75e+00 1juhA 350 3.78e+00 b.82.1.5 71884 1q45A 391 3.82e+00 c.1.4.1 95780 1hp1A 516 3.90e+00 d.114.1.1,d.159.1.2 70976,70977 2gclA 261 4.38e+00 1r2qA 170 4.49e+00 c.37.1.8 96874 1i39A 225 4.63e+00 1ekeA c.55.3.1 61585 2anuA 255 4.71e+00 1nxmA 197 4.72e+00 b.82.1.1 86385 1t8tA 271 4.76e+00 c.37.1.5 106685 1zarA 282 4.96e+00 1b6g 310 4.98e+00 1b6g c.69.1.8 34661 2fiuA 99 5.01e+00 1w5fA 353 5.15e+00 1pm3A 78 5.16e+00 b.41.1.2 94889 1e19A 314 5.18e+00 1b7bA c.73.1.1 34967 1nu7D 282 5.24e+00 a.8.6.1,a.8.6.1 92191,92192 1xqwA 293 5.65e+00 1vr3A 191 5.72e+00 1k77A 260 5.96e+00 c.1.15.5 72096 1mvoA 136 6.02e+00 c.23.1.1 79513 2b61A 377 6.18e+00 1g291 372 6.37e+00 1g291 1jmvA 141 6.42e+00 c.26.2.4 66897 1o8xA 146 6.49e+00 c.47.1.10 86681 1k66A 149 6.54e+00 c.23.1.1 90941 1oxxK 353 6.73e+00 b.40.6.3,c.37.1.12 93715,93716 1m6iA 493 6.98e+00 c.3.1.5,c.3.1.5,d.87.1.1 74533,74534,74535 1m8jA 181 7.32e+00 c.26.1.3 84875 1qipA 183 7.49e+00 1qipA d.32.1.1 38470 1i60A 278 7.58e+00 c.1.15.4 71118 1o22A 170 7.70e+00 d.238.1.1 86557 1ti6B 274 7.76e+00 b.3.5.1,d.58.1.5 106976,106977 1nu0A 138 8.05e+00 c.55.3.8 92165 1v02A 565 8.12e+00 c.1.8.4 108194 2fp8A 322 8.12e+00 1kutA 230 8.13e+00 d.143.1.1 73017 2b06A 155 8.14e+00 1ypfA 336 8.15e+00 1vplA 256 8.20e+00 1w78A 422 8.24e+00 1qv9A 283 8.44e+00 c.127.1.1 96356 1amf 233 8.48e+00 1wod c.94.1.1 35833 2cbiA 594 8.60e+00 1qxyA 252 8.69e+00 d.127.1.1 96565 1v33A 366 8.87e+00 d.264.1.1 100278 1s8nA 205 9.05e+00 c.23.1.1 105374 1ne9A 335 9.10e+00 d.108.1.4,d.108.1.4 91839,91840 1j5pA 253 9.37e+00 d.81.1.3,c.2.1.3 71577,83092 1mtzA 293 9.48e+00 c.69.1.7 79467 1v04A 355 9.50e+00 b.68.6.2 100240 1u6tA 121 9.65e+00 2gkeA 274 9.79e+00 1lt8A 406 9.81e+00 c.1.26.1 78186 1q8fA 313 9.89e+00 c.70.1.1 96203 1obdA 306 9.89e+00 d.143.1.1 86767 1lcyA 325 9.94e+00 b.36.1.4,b.47.1.1 73834,73835 1y8tA 324 9.99e+00 1pk6A 133 1.00e+01 b.22.1.1 94801 1kblA 873 1.01e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 2czdA 208 1.02e+01 1g6hA 257 1.05e+01 1gajA c.37.1.12 60318 2azpA 318 1.06e+01 1ccwA 137 1.06e+01 1be1 c.23.6.1 31238 1h5qA 265 1.07e+01 1cydA c.2.1.2 60643 2b0vA 153 1.09e+01 1wosA 364 1.12e+01 b.44.2.1,d.250.1.1 109468,109469 1yd7A 395 1.13e+01 2f5tX 233 1.15e+01 2aefA 234 1.16e+01 1o0iA 138 1.18e+01 d.38.1.5 86532 1z4eA 153 1.18e+01 1atg 231 1.20e+01 1atg c.94.1.1 35834 1n0wA 243 1.20e+01 c.37.1.11 79772 1ta3B 303 1.21e+01 c.1.8.3 106732 1c96A 753 1.21e+01 1amj c.8.2.1,c.83.1.1 30727,35403 1w8iA 156 1.22e+01 1g8sA 230 1.22e+01 c.66.1.3 90507 1u2eA 289 1.24e+01 1f9yA 158 1.24e+01 d.58.30.1 83249 1ej2A 181 1.29e+01 1f9aA c.26.1.3 59414 2avtA 378 1.29e+01 1ig3A 263 1.30e+01 1ig3A b.82.6.1,c.100.1.1 62358,62359 2bbsA 290 1.32e+01 2fyxA 143 1.33e+01 1t0fA 276 1.36e+01 1vf8A 377 1.36e+01 1qsmA 152 1.36e+01 1qsmA d.108.1.1 40808 1zr6A 503 1.36e+01 1pea 385 1.37e+01 1pea c.93.1.1 35662 1vk9A 151 1.38e+01 c.139.1.1 108640 1qd1A 325 1.40e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1wohA 305 1.41e+01 c.42.1.1 109446 1v60A 123 1.41e+01 1gqzA 274 1.43e+01 d.21.1.1,d.21.1.1 83311,83312 1jysA 242 1.46e+01 c.56.2.1 77216 1k4zA 159 1.46e+01 b.80.5.1 72070 1kjqA 391 1.47e+01 b.84.2.1,c.30.1.1,d.142.1.2 72616,72617,72618 2f4nA 273 1.49e+01 1zhhB 242 1.49e+01 2fbiA 142 1.50e+01 1qhtA 775 1.51e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1kyhA 276 1.51e+01 c.72.1.4 73222 2ajrA 331 1.54e+01 1wb0A 445 1.59e+01 1wywA 230 1.61e+01 1ra0A 430 1.65e+01 1h3fA 432 1.67e+01 c.26.1.1,d.66.1.4 76631,76632 1drw 273 1.69e+01 1drw c.2.1.3,d.81.1.3 30057,39972 1n82A 331 1.70e+01 c.1.8.3 91703 1xttA 216 1.72e+01 1qb7A 236 1.74e+01 1qb7A c.61.1.1 34087 1meoA 209 1.74e+01 c.65.1.1 79035 2frnA 278 1.75e+01 1s0aA 429 1.75e+01 c.67.1.4 98263 1pj5A 830 1.77e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1ve1A 304 1.78e+01 1dkiA 371 1.78e+01 1dkiA d.3.1.1 37090 1uh5A 329 1.79e+01 c.2.1.2 107840 2cwxA 430 1.79e+01 1k2eA 156 1.80e+01 d.113.1.1 72010 2gk9A 426 1.89e+01 1p5vA 235 1.89e+01 b.1.11.1,b.7.2.1 87812,87813 2ey4C 82 1.91e+01 2d13A 227 1.92e+01 1z41A 338 1.94e+01 1r4pB 70 1.95e+01 b.40.2.1 97026 1gmlA 178 1.97e+01 c.8.5.2 70273 1e6uA 321 1.98e+01 1bsvA c.2.1.2 29805 1s7iA 124 1.98e+01 d.58.4.9 105353 2a84A 300 1.99e+01 1r0rE 274 2.02e+01 c.41.1.1 96735 2fxqA 264 2.03e+01 1yavA 159 2.05e+01 1ekqA 272 2.10e+01 1c3qA c.72.1.2 34941 1me8A 503 2.13e+01 c.1.5.1 79028 1u94A 356 2.13e+01 c.37.1.11,d.48.1.1 107743,107744 1y9uA 323 2.14e+01 1n2eA 300 2.15e+01 c.26.1.4 85268 1hziA 129 2.16e+01 1rcb a.26.1.2 61449 1mzhA 225 2.16e+01 c.1.10.1 79698 1xhcA 367 2.17e+01 1nnxA 109 2.17e+01 b.40.10.1 92013 2bllA 345 2.18e+01 2ffcA 353 2.18e+01 1s95A 333 2.19e+01 d.159.1.3 105375 1vmoA 163 2.19e+01 1vmoA b.77.1.1 27974 2fexA 188 2.20e+01 1u24A 337 2.21e+01 1qc7A 101 2.22e+01 1qc7A a.118.14.1 18456 2exnA 136 2.22e+01 1zh2A 121 2.23e+01 1st9A 143 2.26e+01 c.47.1.10 98987 1t4hA 290 2.26e+01 d.144.1.7 106420 1vk6A 269 2.26e+01 d.113.1.4,d.113.1.4 100851,100852 2biiA 424 2.26e+01 1o5zA 442 2.31e+01 c.59.1.2,c.72.2.2 92530,92531 1m3uA 264 2.36e+01 c.1.12.8 84784 1dz3A 130 2.37e+01 1dz3A c.23.1.1 31105 2d69A 430 2.41e+01 1ivyA 452 2.41e+01 1ivyA c.69.1.5 34654 1i1wA 303 2.41e+01 c.1.8.3 76732 1jayA 212 2.44e+01 c.2.1.6 66478 1eo1A 124 2.47e+01 1eo1A c.55.5.1 33739 1sg4A 260 2.48e+01 1ltzA 297 2.50e+01 d.178.1.1 74254 1q7zA 566 2.50e+01 c.1.21.2,c.1.26.1 96090,96091 1q35A 320 2.50e+01 c.94.1.1 95661 1a0tP 413 2.50e+01 1a0tP f.4.3.2 43794 1ursA 402 2.52e+01 c.94.1.1 99833 1xjdA 345 2.53e+01 1r31A 428 2.56e+01 d.58.20.1,d.179.1.1 96897,96898 2au3A 407 2.59e+01 1nqjA 119 2.60e+01 b.23.2.1 86031 1nhkL 144 2.63e+01 1npk d.58.6.1 39142 1ff9A 450 2.63e+01 1ff9A c.2.1.3,d.81.1.2 30039,39954 1gheA 177 2.64e+01 d.108.1.1 76222 2fo1D 85 2.69e+01 1aozA 552 2.70e+01 1aozA b.6.1.3,b.6.1.3,b.6.1.3 23124,23125,23126 1nrzA 164 2.71e+01 c.38.1.1 86131 1exqA 154 2.72e+01 1b9dA c.55.3.2 33646 2d48A 129 2.72e+01 1edqA 540 2.72e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1wd5A 208 2.73e+01 2d1uA 104 2.73e+01 1on0A 158 2.73e+01 d.108.1.1 87095 1s12A 94 2.75e+01 2axyA 73 2.75e+01 2gshA 414 2.75e+01 1qg3A 195 2.76e+01 1qg3A b.1.2.1,b.1.2.1 21993,21994 1twfH 146 2.76e+01 1rw7A 243 2.77e+01 c.23.16.2 97963 1ufoA 238 2.78e+01 c.69.1.27 99344 1f9vA 347 2.80e+01 1bg2 c.37.1.9 59745 1d5tA 433 2.85e+01 1gnd c.3.1.3,d.16.1.6 30422,37986 1y1nA 291 2.85e+01 1zgzA 122 2.86e+01 1tv8A 340 2.87e+01 c.1.28.3 107352 1y1oA 203 2.89e+01 1i5gA 144 2.91e+01 1ewxA c.47.1.10 61784 1cfr 285 2.95e+01 1cfr c.52.1.7 33312 1su0B 159 2.96e+01 d.224.1.2 106015 1m98A 317 2.98e+01 a.175.1.1,d.17.4.6 78866,78867 1qwgA 251 3.01e+01 c.1.27.1 96473 1s98A 107 3.05e+01 b.124.1.1 105377 1zmtA 254 3.07e+01 1qy1A 174 3.08e+01 b.60.1.1 96568 1gtmA 419 3.13e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1q8yA 373 3.20e+01 d.144.1.7 96234 1o69A 394 3.21e+01 c.67.1.4 92560 1xg8A 111 3.28e+01 1uehA 253 3.28e+01 c.101.1.1 99259 2fs2A 151 3.29e+01 2f9sA 151 3.34e+01 1rvgA 305 3.35e+01 c.1.10.2 97920 1zn8A 180 3.42e+01 1lv7A 257 3.43e+01 c.37.1.20 78232 1xfsA 178 3.49e+01 d.129.3.5 109589 1l7aA 318 3.50e+01 c.69.1.25 77772 1y10A 407 3.52e+01 2bwnA 401 3.52e+01 1h8eD 482 3.56e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 2f1lA 187 3.59e+01 2bf6A 449 3.65e+01 1h54A 754 3.65e+01 a.102.1.4,b.30.5.3 60634,60635 2cvhA 220 3.65e+01 6ldh 330 3.65e+01 3ldh c.2.1.5,d.162.1.1 30161,42128 1vqoS 85 3.69e+01 1ytvA 366 3.69e+01 1nnfA 309 3.71e+01 c.94.1.1 85903 1zndA 174 3.71e+01 1nnhA 294 3.73e+01 d.104.1.1 92005 1iukA 140 3.75e+01 c.2.1.8 83712 1vetB 125 3.77e+01 d.110.7.1 108554 1w1oA 534 3.83e+01 d.58.32.4,d.145.1.1 109071,109072 1dl5A 317 3.87e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 2aq5A 402 3.91e+01 1ww8A 439 3.92e+01 1v5eA 590 3.92e+01 1ako 268 3.93e+01 1ako d.151.1.1 41779 1pwxA 254 3.99e+01 c.2.1.2 95262 7a3hA 303 4.01e+01 7a3hA c.1.8.3 28817 1t62A 166 4.03e+01 b.122.1.4 106541 1ebfA 358 4.03e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 2gc9A 179 4.05e+01 1wvhA 134 4.05e+01 1on2A 142 4.05e+01 a.4.5.24,a.76.1.1 87103,87104 1zhvA 134 4.05e+01 1vc3B 97 4.06e+01 1v71A 323 4.12e+01 2fuqA 747 4.17e+01 1yoxA 250 4.20e+01 2gdjA 264 4.21e+01 1yb3A 175 4.21e+01 1xfcA 384 4.27e+01 2f42A 179 4.29e+01 1ayoA 130 4.31e+01 1ayoA b.2.4.1 22431 1lam 484 4.35e+01 1lam c.50.1.1,c.56.5.3 33166,33829 1v9nA 360 4.36e+01 1orrA 347 4.36e+01 c.2.1.2 93460 1dxy 333 4.43e+01 1dxy c.2.1.4,c.23.12.1 30094,31354 2etvA 346 4.45e+01 1eciA 37 4.47e+01 1eciA a.33.1.1 16999 1wtaA 275 4.48e+01 1io2A 213 4.52e+01 1ekeA c.55.3.1 62612 1s5aA 150 4.54e+01 d.17.4.10 98525 1pkoA 139 4.55e+01 b.1.1.1 88147 1rkqA 282 4.62e+01 c.108.1.10 97621 1um0A 365 4.63e+01 d.258.1.1 107942 1ghhA 81 4.63e+01 1ghhA d.57.1.1 38940 1l0wA 580 4.68e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1f28A 297 4.70e+01 1bkpA d.117.1.1 59608 1zymA 258 4.70e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 1p9yA 121 4.73e+01 d.241.2.1 94402 1q42A 201 4.76e+01 d.17.4.2 95776 2bbkL 125 4.77e+01 2bbkL g.21.1.1 44882 1hc7A 477 4.78e+01 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 2fhxA 246 4.81e+01 1pqhA 143 4.87e+01 b.52.2.1 95017 1wisA 124 4.88e+01 1s57A 153 4.88e+01 1uwsA 489 4.90e+01 c.1.8.4 108073 2b7nA 273 4.93e+01 1m40A 263 4.98e+01 e.3.1.1 74437 1fh9A 312 4.99e+01 1taxA c.1.8.3 28913 2cb2A 318 5.02e+01 1qvzA 237 5.03e+01 c.23.16.2 96453 1um5H 217 5.09e+01 1es9A 232 5.11e+01 1wab c.23.10.3 31340 1o0xA 262 5.16e+01 d.127.1.1 80755 1ws0A 156 5.18e+01 1w2wB 191 5.19e+01 1jtdB 273 5.22e+01 b.69.5.2 67265 1vcdA 126 5.23e+01 1zgkA 308 5.25e+01 1pmi 440 5.29e+01 1pmi b.82.1.3 28114 1gvhA 396 5.29e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1fjgE 162 5.30e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 1tw7A 99 5.32e+01 1vpqA 273 5.33e+01 1svpA 161 5.34e+01 1svpA b.47.1.3 26384 1th0A 226 5.35e+01 d.3.1.7 106903 1ispA 181 5.36e+01 c.69.1.18 76778 1gh9A 71 5.39e+01 1gh9A g.41.6.1 45266 1in4A 334 5.39e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 1lehA 364 5.42e+01 1bw9A c.2.1.7,c.58.1.1 30268,33916 1z3eA 132 5.44e+01 1hl9A 449 5.45e+01 b.71.1.3,c.1.8.11 90650,90651 1v7lA 163 5.49e+01 1n7kA 234 5.51e+01 c.1.10.1 85374 1rxdA 159 5.53e+01 1anf 370 5.53e+01 4mbp c.94.1.1 35776 1in6A 334 5.53e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 1lk2A 274 5.54e+01 b.1.1.2,d.19.1.1 91056,91057 1vetA 124 5.55e+01 d.110.7.1 108553 1umzA 278 5.59e+01 b.29.1.2 99639 1t7lA 766 5.60e+01 1qp6A 35 5.60e+01 1qp6A k.16.1.1 46443 1z5yE 149 5.61e+01 1o66A 275 5.64e+01 c.1.12.8 92547 1lnsA 763 5.67e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1xteA 154 5.69e+01 1qy6A 274 5.71e+01 b.47.1.1 96574 2b69A 343 5.71e+01 1d3yA 301 5.76e+01 1d3yA e.12.1.1 43252 1lw7A 365 5.77e+01 c.26.1.3,c.37.1.1 74295,74296 1q4uA 151 5.78e+01 d.38.1.5 95828 1w2lA 99 5.79e+01 1ma3A 253 5.80e+01 c.31.1.5 78883 1evlA 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