# 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 1j8uA 325 5.00e-02 d.178.1.1 71611 1m7yA 435 1.51e-01 c.67.1.4 78761 1dk0A 188 3.80e-01 1b2vA d.35.1.1 38530 1hlvA 131 5.19e-01 a.4.1.7,a.4.1.7 65854,65855 1jalA 363 6.01e-01 c.37.1.8,d.15.10.2 84138,84139 1a7s 221 6.05e-01 1a7s b.47.1.2 26284 1cnzA 363 6.67e-01 1cnzA c.77.1.1 35061 1ockA 412 7.99e-01 c.117.1.1 86802 1cxqA 162 8.10e-01 1cxqA c.55.3.2 33621 1p1mA 406 8.52e-01 b.92.1.4,c.1.9.9 87696,87697 1vljA 407 8.96e-01 e.22.1.2 108832 1eljA 381 1.25e+00 4mbp c.94.1.1 35791 1i4wA 353 1.29e+00 c.66.1.24 66028 1dp3A 55 1.31e+00 1dp3A a.55.1.2 59128 1xqoA 256 1.31e+00 1q0rA 298 1.35e+00 c.69.1.28 95508 1ooeA 236 1.36e+00 c.2.1.2 87196 1fiqC 763 1.46e+00 1fiqC d.41.1.1,d.133.1.1 38588,41418 1byrA 155 1.68e+00 1byrA d.136.1.1 41450 1m65A 245 1.82e+00 c.6.3.1 84847 1ctj 89 1.89e+00 1ctj a.3.1.1 15798 1nxuA 333 1.95e+00 c.122.1.1 86389 1senA 164 2.01e+00 c.47.1.1 105465 1rrmA 386 2.14e+00 e.22.1.2 105081 1fnnA 389 2.26e+00 1fnnA a.4.5.11,c.37.1.20 16129,32426 1lqtA 456 2.33e+00 c.3.1.1,c.4.1.1 74198,74199 1g8kA 825 2.41e+00 1g8jA b.52.2.2,c.81.1.1 26920,35328 1im5A 180 2.74e+00 c.33.1.3 66211 1jb9A 316 2.75e+00 1fnc b.43.4.2,c.25.1.1 62840,62841 1cy5A 97 3.16e+00 1cy5A a.77.1.3 18430 1h8dH 260 3.29e+00 5ptp 2bjfA 329 3.54e+00 1i58A 189 3.70e+00 1b3qA d.122.1.3 61773 1kwfA 363 3.91e+00 a.102.1.2 73078 1dqzA 280 4.00e+00 1dqyA c.69.1.3 34638 1eo1A 124 4.03e+00 1eo1A c.55.5.1 33739 1f20A 435 4.12e+00 b.43.4.1,c.25.1.4 64932,64933 1fexA 59 4.20e+00 a.4.1.3 59803 1tl9A 339 4.20e+00 1oxjA 173 4.22e+00 a.60.1.2,a.118.1.13 87517,87518 1hkhA 279 4.34e+00 c.69.1.12 90628 1dvoA 152 4.57e+00 1dvoA a.136.1.1 19623 1ox0A 430 4.62e+00 c.95.1.1,c.95.1.1 87495,87496 1v5vA 401 4.72e+00 1bueA 265 4.72e+00 1btl e.3.1.1 42727 1sfxA 109 5.07e+00 a.4.5.50 105505 1cjcA 460 5.34e+00 1cjcA c.3.1.1,c.4.1.1 30319,30604 1ek6A 348 5.44e+00 1xel c.2.1.2 29800 1fcyA 236 5.64e+00 2lbd a.123.1.1 19282 1t4hA 290 5.76e+00 d.144.1.7 106420 1eq2A 310 6.00e+00 1eq2A c.2.1.2 29814 1gcvB 136 6.02e+00 1cg5B a.1.1.2 15589 1muwA 386 6.05e+00 c.1.15.3 79495 1dugA 234 6.43e+00 1b8xA a.45.1.1,c.47.1.5 17718,33012 1g3qA 237 6.57e+00 1hyqA c.37.1.10 60237 1g6hA 257 7.14e+00 1gajA c.37.1.12 60318 1fnd 314 7.26e+00 1fnc b.43.4.2,c.25.1.1 25626,31516 1h3nA 878 7.70e+00 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1ddgA 374 7.96e+00 1amoA b.43.4.1,c.25.1.4 25671,31559 1qwgA 251 8.03e+00 c.1.27.1 96473 1jeoA 180 8.04e+00 c.80.1.3 66611 1jy5A 212 8.13e+00 d.124.1.1 71940 1ju2A 536 8.16e+00 c.3.1.2,d.16.1.1 77169,77170 1dcs 311 8.25e+00 1dcs b.82.2.1 28124 1bx1A 314 8.42e+00 1fnc b.43.4.2,c.25.1.1 25629,31519 1mgtA 174 8.77e+00 1mgtA a.4.2.1,c.55.7.1 16078,33753 1a4pA 96 9.40e+00 1b4cA a.39.1.2 17176 1j09A 468 9.55e+00 a.97.1.1,c.26.1.1 77025,77026 1pvmA 184 9.61e+00 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1sgwA 214 9.68e+00 c.37.1.12 105541 1h8eD 482 9.74e+00 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 1bn7A 294 1.05e+01 1bn6A c.69.1.8 34677 1iugA 352 1.06e+01 c.67.1.3 90699 1ihgA 370 1.07e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 1ydyA 356 1.08e+01 1fh9A 312 1.11e+01 1taxA c.1.8.3 28913 1s2wA 295 1.14e+01 c.1.12.7 98407 1qy1A 174 1.19e+01 b.60.1.1 96568 1j75A 67 1.22e+01 a.4.5.19 62673 1fiuA 286 1.23e+01 1fiuA c.52.1.10 33317 1wvfA 520 1.30e+01 1vjpA 394 1.35e+01 c.2.1.3,d.81.1.3 100828,100829 1gpeA 587 1.37e+01 1gpeA c.3.1.2,d.16.1.1 30387,37951 1i7dA 659 1.44e+01 1d6mA e.10.1.1 61886 1jl2A 156 1.44e+01 c.55.3.1 66822 1huw 166 1.44e+01 1huw a.26.1.1 16831 1fs1B 141 1.45e+01 1vcbB a.157.1.1,d.42.1.1 19252,38664 1mr7A 209 1.46e+01 b.81.1.3 91430 1d3gA 367 1.46e+01 1d3gA c.1.4.1 28600 1bob 320 1.46e+01 1bob d.108.1.1 40816 1f1eA 154 1.47e+01 a.22.1.2 64927 1efnB 152 1.49e+01 1efnB d.102.1.1 40699 1ji1A 637 1.53e+01 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 1ejxA 100 1.54e+01 d.8.1.1 83182 1jdpA 441 1.55e+01 c.93.1.1 62906 1cnv 299 1.55e+01 1cnv c.1.8.5 28989 1qe3A 489 1.61e+01 2bce c.69.1.1 34630 1f0nA 285 1.62e+01 1dqyA c.69.1.3 34636 1fobA 334 1.62e+01 c.1.8.3 83255 1a3aA 148 1.64e+01 1a3aA d.112.1.1 40917 1ispA 181 1.70e+01 c.69.1.18 76778 1jmsA 381 1.72e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1fehA 574 1.77e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1ojrA 274 1.78e+01 c.74.1.1 93147 1it2A 146 1.81e+01 a.1.1.2 66365 1j30A 144 1.83e+01 a.25.1.1 90806 2nlrA 234 1.84e+01 2nlrA b.29.1.11 24344 1wmqA 147 1.88e+01 1izcA 339 1.97e+01 c.1.12.5 83838 1mtyB 384 1.97e+01 1mtyB a.25.1.2 16740 1vjvA 415 2.04e+01 d.3.1.9 108632 1on2A 142 2.17e+01 a.4.5.24,a.76.1.1 87103,87104 1guxB 152 2.23e+01 1guxB a.74.1.3 18389 1orvA 728 2.23e+01 b.70.3.1,c.69.1.24 87354,87355 1c0pA 363 2.24e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1pyoB 105 2.25e+01 1ls9A 91 2.26e+01 a.3.1.1 78177 1a5t 334 2.26e+01 1a5t a.80.1.1,c.37.1.20 18450,32423 1avsA 90 2.31e+01 1cll a.39.1.5 17226 1wmhB 86 2.43e+01 1ddjA 247 2.44e+01 5ptp b.47.1.2 26362 1exrA 148 2.49e+01 1cll a.39.1.5 17299 1e3oC 160 2.50e+01 1au7A a.4.1.1,a.35.1.1 59197,59198 1wmaA 276 2.52e+01 1jcfA 344 2.53e+01 c.55.1.1,c.55.1.1 62878,62879 1et9A 204 2.54e+01 1an8 b.40.2.2,d.15.6.1 25204,37793 1b43A 340 2.55e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 1i5nA 146 2.58e+01 1i5nA a.24.10.3 61805 1abv 134 2.59e+01 1abv a.70.1.1 18317 2evaA 307 2.59e+01 1j4aA 333 2.61e+01 c.2.1.4,c.23.12.1 71502,71503 1tqhA 247 2.63e+01 c.69.1.29 107225 1a41 234 2.65e+01 1a41 d.163.1.2 42174 1o54A 277 2.67e+01 c.66.1.13 92482 1alvA 173 2.73e+01 1alvA a.39.1.8 17370 1elkA 157 2.76e+01 1dvpA a.118.9.2 19217 1gtmA 419 2.77e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1jdc 429 2.81e+01 1jdc b.71.1.1,c.1.8.1 27789,28776 1v7rA 186 2.84e+01 c.51.4.1 100482 1b0uA 262 2.84e+01 1b0uA c.37.1.12 32370 1whzA 70 2.94e+01 1bw0A 416 2.99e+01 1bw0A c.67.1.1 34385 1b8aA 438 3.02e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1oywA 523 3.03e+01 a.4.5.43,c.37.1.19,c.37.1.19 93760,93761,93762 1h3lA 87 3.04e+01 a.177.1.1 76639 1g2nA 264 3.06e+01 1lbd a.123.1.1 60227 1jpaA 312 3.08e+01 d.144.1.7 67011 1hufA 140 3.13e+01 1hufA d.195.1.1 61272 1wb4A 297 3.14e+01 2nacA 393 3.19e+01 2nadA c.2.1.4,c.23.12.1 30088,31348 1h6gA 256 3.22e+01 1h6gA a.24.9.1,a.24.9.1 60669,60670 1io0A 185 3.23e+01 c.10.1.1 76753 1h0hB 214 3.26e+01 d.58.1.5 76437 1bif 469 3.32e+01 1bif c.37.1.7,c.60.1.4 31961,34003 1evyA 366 3.49e+01 1evyA a.100.1.6,c.2.1.6 18811,30215 1olrA 224 3.50e+01 b.29.1.11 93330 4ubpA 101 3.52e+01 1ubpA d.8.1.1 37352 1iyrA 111 3.57e+01 a.164.1.1 76973 1n8kA 374 3.64e+01 b.35.1.2,c.2.1.1 80298,80299 1nzjA 298 3.65e+01 c.26.1.1 92377 1c8uA 285 3.65e+01 1c8uA d.38.1.3,d.38.1.3 38547,38548 1jjtA 228 3.71e+01 1a7tA d.157.1.1 63139 1a76 326 3.73e+01 1a76 a.60.7.1,c.120.1.2 18091,33361 1u60A 310 3.74e+01 e.3.1.2 107692 1amuA 563 3.75e+01 1amuA e.23.1.1 43351 1sqsA 242 3.78e+01 c.23.5.5 98968 1gk8A 475 3.93e+01 c.1.14.1,d.58.9.1 65234,65235 1g2cB 43 3.95e+01 1g2cB 1eyhA 144 4.01e+01 1eduA a.118.9.1 19214 1uj8A 77 4.01e+01 1y80A 210 4.04e+01 1qgiA 259 4.15e+01 1qgiA d.2.1.7 37001 1ym3A 215 4.31e+01 1ej2A 181 4.31e+01 1f9aA c.26.1.3 59414 1ggzA 148 4.39e+01 a.39.1.5 70176 1dz3A 130 4.40e+01 1dz3A c.23.1.1 31105 1v33A 366 4.49e+01 d.264.1.1 100278 1buoA 121 4.49e+01 1buoA d.42.1.1 38631 1elvA 333 4.53e+01 5ptp b.47.1.2,g.18.1.1 59454,59455 1dmuA 299 4.55e+01 1dmuA c.52.1.4 33294 1fadA 99 4.58e+01 1fadA a.77.1.2 18428 1dmgA 225 4.64e+01 1dmgA c.22.1.1 31036 1j79A 347 4.64e+01 1j79A c.1.9.4 62675 1fipA 98 4.70e+01 1fipA a.4.1.12 18980 1e8cA 498 4.74e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1ogiA 303 4.81e+01 b.43.4.2,c.25.1.1 92914,92915 1vyrA 364 4.92e+01 c.1.4.1 108906 1fp2A 352 4.98e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1bqk 124 5.00e+01 1bqk b.6.1.1 22889 1dmhA 311 5.03e+01 1dmhA b.3.6.1 22633 1gc0A 398 5.06e+01 c.67.1.3 70168 1us5A 314 5.09e+01 c.94.1.1 99856 1hdoA 206 5.13e+01 1he2A c.2.1.2 60965 1khcA 147 5.13e+01 b.34.9.2 68608 1jjfA 268 5.20e+01 c.69.1.2 66765 1h3gA 601 5.22e+01 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1a0jA 223 5.28e+01 5ptp b.47.1.2 26002 1j6rA 214 5.32e+01 d.173.1.2 71598 1wr8A 231 5.34e+01 1orrA 347 5.40e+01 c.2.1.2 93460 1pe1A 267 5.49e+01 c.1.10.4 94591 1jk7A 323 5.51e+01 1auiA d.159.1.3 63144 1dzlA 505 5.52e+01 1dzlA b.121.6.1 23586 1f7uA 607 5.53e+01 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 59673,59674,59675 1mml 265 5.64e+01 1mml e.8.1.2 43015 1hbnA 549 5.66e+01 1mroA a.89.1.1,d.58.31.2 60898,60899 1ukfA 188 5.67e+01 d.3.1.10 99488 1hw1A 239 5.67e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 3seb 238 5.72e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1g5hA 454 5.74e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 1b5fA 239 5.77e+01 1smrA b.50.1.2 26836 1ezwA 349 5.81e+01 1ezwA c.1.16.3 29558 1j9lA 247 5.81e+01 c.106.1.1 62762 1t6t1 118 5.88e+01 1cz4A 185 5.90e+01 1cz4A b.52.2.3,d.31.1.1 26934,38468 1ivnA 190 5.97e+01 c.23.10.5 83719 1gtkA 313 5.98e+01 c.94.1.1,d.50.2.1 76346,76347 1jfzA 154 6.00e+01 a.149.1.1 66655 1a53 247 6.02e+01 1a53 c.1.2.4 28564 1kveA 63 6.03e+01 1kveA d.70.1.2 39590 1b3aA 67 6.03e+01 1b3aA d.9.1.1 37410 1jubA 311 6.06e+01 c.1.4.1 90908 1ra0A 430 6.09e+01 1j2zA 270 6.11e+01 b.81.1.1 90805 1xkzA 255 6.16e+01 1c52 131 6.23e+01 1c52 a.3.1.1 15810 1pp0A 199 6.37e+01 d.103.1.1 104211 1pv5A 264 6.37e+01 d.251.1.1 95150 1bu6O 501 6.43e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1nar 290 6.44e+01 1nar c.1.8.5 28988 1i4uA 181 6.44e+01 b.60.1.1 61732 1f8fA 371 6.57e+01 b.35.1.2,c.2.1.1 83246,83247 1qxyA 252 6.61e+01 d.127.1.1 96565 1pyfA 312 6.96e+01 c.1.7.1 95334 1c1yB 77 6.99e+01 1c1yB d.15.1.5 37618 1gcyA 527 7.01e+01 1jdc b.71.1.1,c.1.8.1 27788,28775 1dqaA 467 7.06e+01 1dqaA d.58.20.1,d.179.1.1 39364,42585 1ee4A 423 7.08e+01 1ee4A a.118.1.1 19128 1ug6A 431 7.10e+01 c.1.8.4 88490 1h2kA 349 7.18e+01 b.82.2.6 76572 1dp4A 435 7.30e+01 1dp4A c.93.1.1 35710 1rtqA 299 7.32e+01 c.56.5.4 97819 1jbkA 195 7.45e+01 c.37.1.20 71631 1gvzA 237 7.46e+01 b.47.1.2 76360 1cfzA 162 7.48e+01 1cfzA c.56.1.1 33754 1eemA 241 7.48e+01 1eemA a.45.1.1,c.47.1.5 17717,33011 1vl2A 421 7.51e+01 c.26.2.1,d.210.1.1 108708,108709 1bli 483 7.57e+01 1bli b.71.1.1,c.1.8.1 27715,28702 2arcA 164 7.61e+01 2arcA b.82.4.1 28148 1u55A 188 7.64e+01 d.278.1.1 107677 1aua 296 7.65e+01 1aua a.5.3.1,c.13.1.1 16290,30882 1s2oA 244 7.72e+01 1k55A 246 7.74e+01 e.3.1.1 68156 1mzbA 136 7.77e+01 a.4.5.42 91497 1p4cA 380 7.78e+01 c.1.4.1 94100 1mk0A 97 7.80e+01 d.226.1.1 79216 1jbeA 128 7.82e+01 3chy c.23.1.1 62845 1rhcA 330 7.82e+01 c.1.16.3 97468 1ntvA 152 7.83e+01 b.55.1.2 86168 1ltzA 297 7.83e+01 d.178.1.1 74254 1r5lA 262 7.83e+01 a.5.3.1,c.13.1.1 97099,97100 1ej0A 180 7.84e+01 1ej0A c.66.1.2 34179 1cq0A 28 7.85e+01 j.6.1.1 46108 1dzkA 157 7.91e+01 1obpA b.60.1.1 27096 1ja9A 274 8.02e+01 c.2.1.2 62817 1ffyA 917 8.04e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1r5rA 119 8.05e+01 a.39.2.1 97104 1ny1A 240 8.07e+01 c.6.2.3 86395 1usgA 346 8.11e+01 c.93.1.1 99864 1dpgA 485 8.12e+01 1dpgA c.2.1.3,d.81.1.5 30074,39989 1j1jA 240 8.16e+01 a.118.16.1 90762 1d3yA 301 8.20e+01 1d3yA e.12.1.1 43252 1ii7A 333 8.20e+01 1ii7A d.159.1.4 62415 1hr6A 475 8.24e+01 1hr6A d.185.1.1,d.185.1.1 61164,61165 1kqpA 271 8.25e+01 c.26.2.1 72883 1jkmB 361 8.25e+01 1jkmA c.69.1.2 34634 1r2qA 170 8.28e+01 c.37.1.8 96874 1pu6A 218 8.38e+01 a.96.1.5 95123 1xx1A 285 8.41e+01 1el5A 389 8.45e+01 1b3mA c.3.1.2,d.16.1.3 30369,37937 1p4oA 322 8.47e+01 d.144.1.7 87775 1wy2A 351 8.48e+01 1b25A 619 8.48e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1gqiA 708 8.48e+01 c.1.8.10,d.92.2.2 76279,76280 1udzA 182 8.52e+01 b.51.1.1 99239 1mqvA 125 8.55e+01 a.24.3.2 79415 1dxrM 323 8.59e+01 6prcM f.26.1.1 43432 1adt 356 8.60e+01 1anv a.54.1.1,g.51.1.1,g.51.1.1 17887,45362,45368 1bd3A 243 8.60e+01 1bd3A c.61.1.1 34098 1dxeA 256 8.67e+01 1dxeA c.1.12.5 29310 1aba 87 8.76e+01 1aba c.47.1.1 32760 1kv7A 488 8.78e+01 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 1b8dA 164 8.80e+01 1cpcA a.1.1.3 15665 1g8iA 190 8.90e+01 1rec a.39.1.5 60363 1vhvA 268 8.92e+01 c.90.1.1 100704 1m6kA 251 8.93e+01 e.3.1.1 78695 1bkrA 109 8.95e+01 1bkrA a.40.1.1 17394 1omrA 201 8.99e+01 a.39.1.5 93349 1twdA 256 8.99e+01 c.1.30.1 107397