# List of top-scoring protein chains for t04-100-30-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 1wqaA 455 1.92e-02 1ri7A 171 9.71e-02 a.4.5.32,d.58.4.2 97504,97505 1fcyA 236 7.02e-01 2lbd a.123.1.1 19282 1e9rA 437 9.19e-01 c.37.1.11 64827 2gj8A 172 9.87e-01 1wdtA 665 1.13e+00 2faoA 309 1.47e+00 2ffuA 501 1.76e+00 2cviA 83 1.96e+00 1fsz 372 2.47e+00 1fsz c.32.1.1,d.79.2.1 31750,39802 1yr0A 175 2.65e+00 1ymqA 261 2.78e+00 1d3yA 301 2.90e+00 1d3yA e.12.1.1 43252 1wi1A 126 3.23e+00 1amy 403 3.31e+00 1jdc b.71.1.1,c.1.8.1 27799,28786 1s0uA 408 3.37e+00 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1qysA 106 3.39e+00 k.41.1.1 96603 2al2A 436 3.69e+00 1zu4A 320 4.50e+00 1yj7A 171 4.50e+00 2dbbA 151 4.55e+00 1avaA 403 4.61e+00 1jdc b.71.1.1,c.1.8.1 27797,28784 1oneA 436 4.98e+00 4enl c.1.11.1,d.54.1.1 29200,38844 1vjeA 166 5.48e+00 d.185.1.2 100807 2akzA 439 5.57e+00 2eueA 279 5.76e+00 1bfd 528 5.76e+00 1bfd c.31.1.3,c.36.1.5,c.36.1.9 31745,31801,31802 1tfr 305 5.77e+00 1tfr a.60.7.1,c.120.1.2 18081,33351 2al1A 436 6.06e+00 1r5tA 142 6.17e+00 c.97.1.1 104812 1az9 457 6.49e+00 1az9 c.55.2.1,d.127.1.1 33547,41164 1oz9A 150 6.81e+00 d.92.1.15 93808 1q6zA 528 6.93e+00 1dar 691 7.01e+00 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1 25707,32142,37547,39300 1wl9A 440 7.44e+00 2f5gA 133 7.46e+00 1yovA 537 7.46e+00 1b3aA 67 7.52e+00 1b3aA d.9.1.1 37410 2bwvA 440 7.76e+00 1w1wA 430 7.79e+00 4enl 436 8.10e+00 4enl c.1.11.1,d.54.1.1 29202,38846 2f4nA 273 8.16e+00 2c1cA 312 8.22e+00 1vggA 161 8.24e+00 1fo8A 343 8.36e+00 1foaA c.68.1.10 59927 1ftrA 296 8.51e+00 1ftrA d.58.33.1,d.58.33.1 39485,39486 1s96A 219 9.33e+00 c.37.1.1 98740 1u7lA 392 9.68e+00 1vl6A 388 9.82e+00 c.2.1.7,c.58.1.3 108724,108725 1ht6A 405 9.84e+00 b.71.1.1,c.1.8.1 83629,83630 1zx4A 192 1.10e+01 1innA 166 1.11e+01 1j98A d.185.1.2 62608 1kepA 348 1.12e+01 c.2.1.2 68536 1zowA 313 1.13e+01 1y9aA 360 1.18e+01 1k2fA 190 1.20e+01 b.8.1.2 68054 1rwzA 245 1.23e+01 d.131.1.2,d.131.1.2 98005,98006 1zbsA 291 1.25e+01 2bitX 165 1.34e+01 2an9A 207 1.34e+01 1q2lA 939 1.35e+01 1eg9A 449 1.37e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1o7nA 449 1.37e+01 b.33.1.2,d.129.3.3 81162,81163 1odkA 235 1.38e+01 c.56.2.1 86863 1phk 298 1.43e+01 1cdkA d.144.1.7 41635 1zpvA 91 1.43e+01 2b61A 377 1.44e+01 1y81A 138 1.45e+01 1u6mA 199 1.49e+01 1y8aA 332 1.51e+01 1oc2A 348 1.51e+01 c.2.1.2 92765 1pdz 434 1.52e+01 4enl c.1.11.1,d.54.1.1 29215,38859 1kicA 339 1.53e+01 c.70.1.1 72510 1w77A 228 1.58e+01 2fckA 181 1.58e+01 2av4A 162 1.63e+01 2fiqA 420 1.68e+01 1bykA 255 1.69e+01 1bykA c.93.1.1 35706 1lmeA 176 1.70e+01 d.167.1.1 84629 1ka1A 357 1.70e+01 e.7.1.1 68369 2cxxA 190 1.71e+01 1uch 230 1.71e+01 1uch d.3.1.6 37129 1nu4A 97 1.72e+01 d.58.7.1 80731 1qwdA 177 1.74e+01 b.60.1.1 96471 1vecA 206 1.75e+01 c.37.1.19 100575 1i05A 180 1.76e+01 1mup b.60.1.1 27130 1aszB 490 1.77e+01 1b8aA b.40.4.1,d.104.1.1 25241,40762 1jx2B 315 1.78e+01 c.37.1.8 67404 1vd5A 377 1.78e+01 a.102.1.7 108518 1jb7B 260 1.80e+01 1otcB b.40.4.3 62839 2eifA 136 1.81e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 2cxcA 144 1.83e+01 1qy1A 174 1.88e+01 b.60.1.1 96568 1qgxA 357 1.91e+01 1qgxA e.7.1.1 42973 1te6A 439 1.95e+01 c.1.11.1,d.54.1.1 106797,106798 1kt6A 183 1.96e+01 b.60.1.1 84466 1r9cA 139 1.98e+01 d.32.1.2 97255 1gegA 256 2.00e+01 1ybvA c.2.1.2 29888 1zndA 174 2.02e+01 1wn5A 130 2.02e+01 2a7mA 250 2.03e+01 1kkeA 210 2.04e+01 b.21.1.2,b.83.1.2 68669,68670 1g55A 343 2.05e+01 1g55A c.66.1.26 34247 2ajrA 331 2.10e+01 1cvrA 435 2.16e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 1xvaA 292 2.16e+01 1xvaA c.66.1.5 34183 1z7mA 344 2.18e+01 2g5cA 281 2.20e+01 1jv4A 162 2.24e+01 b.60.1.1 67343 2di4A 238 2.25e+01 2cw5A 255 2.26e+01 1wvfA 520 2.26e+01 1xhbA 472 2.31e+01 2fuvA 549 2.32e+01 1i06A 180 2.33e+01 1mup b.60.1.1 27131 1urnA 97 2.38e+01 1urnA d.58.7.1 39153 1n5nA 180 2.41e+01 d.167.1.1 85336 2atxA 194 2.43e+01 1guzA 310 2.44e+01 c.2.1.5,d.162.1.1 65586,65587 1pvvA 315 2.44e+01 c.78.1.1,c.78.1.1 95190,95191 1hbq 183 2.47e+01 1aqb b.60.1.1 27078 1wvqA 167 2.49e+01 1vdnA 162 2.51e+01 1ldg 316 2.53e+01 1ceqA c.2.1.5,d.162.1.1 30165,42132 3sdhA 146 2.54e+01 3sdhA a.1.1.2 14984 1pzxA 289 2.57e+01 c.119.1.1 95484 1s2dA 167 2.57e+01 c.23.14.1 98377 1u8sA 192 2.60e+01 d.58.18.5,d.58.18.5 107737,107738 2gzaA 361 2.60e+01 1t3cA 421 2.61e+01 d.92.1.7 106343 2fa8A 105 2.66e+01 1mup 166 2.69e+01 1mup b.60.1.1 27133 2gsaA 432 2.70e+01 2gsaA c.67.1.4 34446 1qb5D 99 2.71e+01 b.40.2.1 88357 1yzvA 204 2.74e+01 1vkjA 285 2.76e+01 c.37.1.5 108666 1dywA 173 2.79e+01 2cpl b.62.1.1 27505 1xwyA 264 2.85e+01 1m1hA 248 2.86e+01 b.114.1.1,d.58.42.1 78415,78416 1l1lA 739 2.87e+01 c.7.1.4 73470 2c0nA 203 2.88e+01 1ub3A 220 2.91e+01 c.1.10.1 88395 1ve0A 134 2.93e+01 1f1zA 273 2.98e+01 1f1zA a.4.5.27,c.52.1.16 16081,33334 1em8A 147 3.00e+01 c.128.1.1 90457 2b99A 156 3.02e+01 1ukuA 102 3.05e+01 d.58.5.2 99533 1nxiA 132 3.06e+01 d.58.47.1 86381 1ztdA 133 3.07e+01 2bo4A 397 3.10e+01 1bco 327 3.14e+01 1bco b.48.1.1,c.55.3.3 26431,33676 1jysA 242 3.14e+01 c.56.2.1 77216 1tcvA 287 3.18e+01 1fzyA 149 3.19e+01 d.20.1.1 65072 1it2A 146 3.27e+01 a.1.1.2 66365 1ws0A 156 3.35e+01 1iyxA 432 3.36e+01 c.1.11.1,d.54.1.1 83815,83816 1lmiA 131 3.38e+01 b.1.19.1 78098 1t2dA 322 3.38e+01 c.2.1.5,d.162.1.1 99084,99085 1utiA 58 3.39e+01 b.34.2.1 99962 2f1fA 164 3.40e+01 1ej1A 190 3.41e+01 1ejhA d.86.1.1 40144 1j0dA 341 3.43e+01 c.79.1.1 83902 1ftkA 279 3.54e+01 1gr2A c.94.1.1 35819 1wduA 245 3.55e+01 d.151.1.1 109286 2b0jA 358 3.56e+01 1u04A 771 3.57e+01 b.34.14.1,c.55.3.10 107539,107540 1aqb 183 3.58e+01 1aqb b.60.1.1 27084 2fv1A 377 3.59e+01 1ursA 402 3.60e+01 c.94.1.1 99833 1mwmA 320 3.62e+01 c.55.1.1,c.55.1.1 79580,79581 1xc3A 302 3.62e+01 2b4aA 138 3.64e+01 2fxaA 207 3.67e+01 1ooeA 236 3.71e+01 c.2.1.2 87196 1ev7A 317 3.71e+01 1ev7B c.52.1.9 33315 1xnzA 264 3.72e+01 1twjA 84 3.73e+01 d.284.1.1 107407 1zsyA 357 3.75e+01 1a3c 181 3.77e+01 1a3c c.61.1.1 34095 1e6yC 247 3.78e+01 1mroC d.58.31.1 39441 1f44A 324 3.82e+01 a.60.9.1,d.163.1.1 64982,64983 1c24A 263 3.85e+01 1c24A d.127.1.1 41148 1t0fA 276 3.87e+01 1wdvA 152 3.88e+01 2ax3A 502 3.94e+01 1zud1 251 4.12e+01 1kk1A 410 4.12e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1bqk 124 4.15e+01 1bqk b.6.1.1 22889 1i9gA 280 4.17e+01 c.66.1.13 62090 1jmsA 381 4.20e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1dekA 241 4.26e+01 1dekA c.37.1.1 31842 1v3rA 116 4.32e+01 1z5bA 469 4.38e+01 2azpA 318 4.39e+01 1rq2A 382 4.41e+01 c.32.1.1,d.79.2.1 105048,105049 2cpgA 45 4.42e+01 2cpgA a.43.1.3 17455 1ysrA 150 4.43e+01 1vehA 92 4.47e+01 2b8nA 429 4.48e+01 2h6dA 276 4.52e+01 1ea9C 583 4.57e+01 b.1.18.2,b.71.1.1,c.1.8.1 70087,70088,70089 1psdA 409 4.61e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1pu6A 218 4.61e+01 a.96.1.5 95123 1f02T 66 4.63e+01 1f02T j.67.1.1 46360 1xi3A 215 4.63e+01 c.1.3.1 109601 2cx5A 158 4.64e+01 1fa0A 537 4.65e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 1xt8A 292 4.65e+01 1cg5A 141 4.69e+01 1abwA a.1.1.2 15406 1yghA 164 4.71e+01 1yghA d.108.1.1 40802 1xdpA 687 4.72e+01 1z08A 170 4.76e+01 1v95A 130 4.77e+01 c.51.1.1 108435 2c2hA 192 4.79e+01 1ob8A 135 4.81e+01 1vp4A 425 4.81e+01 1i50K 120 4.83e+01 d.74.3.2 61765 1eo6A 117 4.84e+01 1eo6A d.15.1.3 37609 1t4aA 84 4.86e+01 d.284.1.1 106404 1zosA 230 4.89e+01 1o0uA 429 4.90e+01 c.118.1.1 80743 1gd0A 122 4.91e+01 1dptA d.80.1.3 39834 1ii2A 524 4.96e+01 c.91.1.1,c.109.1.1 66146,66147 1fzqA 181 4.96e+01 1hurA c.37.1.8 32060 2fcjA 119 5.00e+01 2cfxA 144 5.08e+01 1z5nA 242 5.10e+01 1yvoA 172 5.18e+01 1u6bA 98 5.22e+01 d.58.7.1 107703 2choA 716 5.22e+01 3tmkA 216 5.24e+01 3tmkA c.37.1.1 31920 2chnA 716 5.24e+01 1qahA 136 5.28e+01 d.79.1.1 96338 1tiiD 99 5.29e+01 1tiiD b.40.2.1 24965 2cbiA 594 5.30e+01 1yb0A 159 5.35e+01 1z5oA 242 5.38e+01 1b4bA 71 5.39e+01 1b4aA d.74.2.1 39718 1l6sA 323 5.45e+01 c.1.10.3 73627 2cg4A 152 5.45e+01 1xahA 354 5.47e+01 1f35A 162 5.51e+01 1f35A b.94.1.1 59628 1i12A 160 5.53e+01 1i21A d.108.1.1 61515 2azeA 155 5.54e+01 1sc6A 404 5.57e+01 1xt9A 212 5.57e+01 1oiaA 95 5.59e+01 d.58.7.1 87051 1mu5A 471 5.63e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1yndA 165 5.67e+01 1bazA 53 5.67e+01 1bazA a.43.1.1 17421 2ffsA 157 5.68e+01 1q3iA 214 5.69e+01 d.220.1.1 104524 1twfK 120 5.74e+01 1he7A 126 5.77e+01 1wwcA b.1.1.4 60970 1g2rA 100 5.78e+01 1g2rA d.192.1.1 60231 1qo0D 196 5.79e+01 1qo0D c.23.1.3 31125 1c25 161 5.79e+01 1c25 c.46.1.1 32698 1qkkA 155 5.80e+01 1dbwA c.23.1.1 31104 1z7dA 433 5.80e+01 1u2wA 122 5.82e+01 2gcfA 73 5.83e+01 1q77A 138 5.83e+01 c.26.2.4 96023 1nrfA 262 5.86e+01 e.3.1.1 92086 1qjcA 158 5.90e+01 1b6tA c.26.1.3 63328 1f2tB 148 5.91e+01 1f2tB 1jmtA 104 5.94e+01 d.58.7.3 63180 1jfzA 154 5.95e+01 a.149.1.1 66655 1lfpA 249 5.97e+01 e.39.1.1 73885 1qc5A 192 6.02e+01 1aoxA c.62.1.1 34147 1f2dA 341 6.04e+01 1f2dA c.79.1.1 35298 2bmoA 447 6.07e+01 1o0iA 138 6.12e+01 d.38.1.5 86532 1i4wA 353 6.17e+01 c.66.1.24 66028 1fvgA 199 6.26e+01 1fvaA d.58.28.1 39408 2a0jA 149 6.29e+01 1h6kZ 98 6.32e+01 d.58.7.1 60686 1ko6A 187 6.39e+01 b.119.1.1 77471 1mzbA 136 6.44e+01 a.4.5.42 91497 2fu0A 160 6.45e+01 1czfA 362 6.46e+01 1czfA b.80.1.3 28031 1skoA 143 6.46e+01 d.110.7.1 105676 1avqA 228 6.50e+01 1avqA c.52.1.13 33326 1uirA 314 6.52e+01 c.66.1.17 99429 1at3A 247 6.53e+01 1at3A b.57.1.1 27021 1jjiA 311 6.53e+01 c.69.1.2 66766 1vc3B 97 6.62e+01 1id1A 153 6.63e+01 1id1A c.2.1.9 62286 1xd3A 230 6.64e+01 1vqsA 116 6.64e+01 2b33A 140 6.67e+01 1tr8A 102 6.69e+01 1ro5A 201 6.70e+01 d.108.1.3 105023 2bj7A 138 6.71e+01 1ne8A 117 6.73e+01 b.34.6.2 80424 1tqmA 282 6.75e+01 a.4.5.56,d.144.1.9 107236,107237 1mqiA 263 6.79e+01 c.94.1.1 91398 1f08A 148 6.80e+01 1f08A d.89.1.2 59564 1ow1A 195 6.80e+01 b.131.1.3 93625 1zejA 293 6.87e+01 1xhdA 173 6.87e+01 1wa3A 205 6.93e+01 1lbu 213 7.03e+01 1lbu a.20.1.1,d.65.1.1 16416,39549 1i1dA 161 7.05e+01 1i21A d.108.1.1 61526 1iz6A 138 7.05e+01 b.34.5.2,b.40.4.5 76976,76977 1aun 208 7.06e+01 1thv b.25.1.1 23900 1oebA 62 7.06e+01 b.34.2.1 86909 1z6nA 167 7.09e+01 2ivyA 101 7.15e+01 1i8jA 323 7.17e+01 1b4kA c.1.10.3 61968 2cwzA 141 7.21e+01 1h5rA 293 7.24e+01 c.68.1.6 65623 2bp1A 360 7.25e+01 1w6tA 444 7.26e+01 1nq7A 244 7.27e+01 a.123.1.1 92047 1dzkA 157 7.29e+01 1obpA b.60.1.1 27096 1efpB 252 7.30e+01 1efvB c.26.2.3 31636 1pa7A 130 7.31e+01 a.40.1.1 94410 2a5jA 191 7.31e+01 1cxyA 90 7.33e+01 1cyo d.120.1.1 41085 1xo5A 183 7.35e+01 1x7oA 287 7.35e+01 1q0vA 81 7.43e+01 j.105.1.1 95514 1w36B 1180 7.49e+01 1vkhA 273 7.57e+01 c.69.1.32 108662 3pmgA 561 7.58e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 2btiA 63 7.60e+01 1s6cA 183 7.60e+01 a.39.1.5 98594 1vlwA 217 7.62e+01 c.1.10.1 108868 2gdgA 114 7.64e+01 1xg8A 111 7.64e+01 2ggcA 263 7.68e+01 1jh6A 189 7.70e+01 d.61.1.1 66707 1scuA 288 7.71e+01 2scuA c.2.1.8,c.23.4.1 30307,31135 2ew8A 249 7.78e+01 1g66A 207 7.78e+01 1bs9 c.69.1.30 31329 1m6yA 301 7.79e+01 a.60.13.1,c.66.1.23 78716,78717 1o7zA 77 7.82e+01 d.9.1.1 86660 1rfmA 344 7.83e+01 c.122.1.1 97385 1r13A 148 7.85e+01 d.169.1.1,h.1.1.1 96782,96783 1oniA 137 7.85e+01 d.79.1.1 87144 1wzlA 585 7.87e+01 1xmxA 385 7.89e+01 1gtvA 214 7.91e+01 c.37.1.1 70537 2gw8A 114 7.95e+01 2bl1A 172 7.96e+01 2b6eA 146 7.97e+01 2a72A 146 8.03e+01 1hgxA 183 8.08e+01 1tc1A c.61.1.1 34027 1jj2L 194 8.10e+01 1ffkI d.12.1.2 63097 1x6mA 196 8.14e+01 1g3qA 237 8.14e+01 1hyqA c.37.1.10 60237 1of5B 184 8.15e+01 d.17.4.2 86934 1xo0A 324 8.15e+01 1q0uA 219 8.16e+01 c.37.1.19 95512 1o26A 232 8.17e+01 d.207.1.1 86566 1nijA 318 8.22e+01 c.37.1.10,d.237.1.1 85741,85742 2a5dA 175 8.24e+01 1tl0D 103 8.30e+01 1tph1 247 8.32e+01 1amk 1bn7A 294 8.35e+01 1bn6A c.69.1.8 34677 1pbgA 468 8.36e+01 1e70M c.1.8.4 28946 1ec7A 446 8.36e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 2pii 112 8.40e+01 2pii d.58.5.1 39071 1go4A 205 8.42e+01 d.135.1.1 70292 1bbpA 173 8.44e+01 1bbpA b.60.1.1 27147 1lci 550 8.46e+01 1lci e.23.1.1 43349 1sqsA 242 8.47e+01 c.23.5.5 98968 1fsiA 189 8.48e+01 1fsiA d.61.1.1 39536 2cyeA 133 8.50e+01 1pt6A 213 8.56e+01 c.62.1.1 95091 1mjfA 281 8.56e+01 c.66.1.17 79198 1t3tA 1303 8.57e+01 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 1sviA 195 8.58e+01 c.37.1.8 106048 1j08A 226 8.63e+01 c.47.1.2,c.47.1.2 83855,83856 1k3rA 268 8.65e+01 b.40.4.10,c.116.1.2 72018,72019 1m2rA 327 8.66e+01 d.144.1.7 84760 1v7pC 200 8.70e+01 c.62.1.1 108408 1byqA 228 8.74e+01 1yer d.122.1.1 41100 1c7qA 445 8.74e+01 2pgi c.80.1.2 35307 1tedA 393 8.76e+01 c.95.1.2 106807 1woqA 267 8.76e+01 c.55.1.10,c.55.1.10 109462,109463 1a3k 137 8.81e+01 1a3k b.29.1.3 24218 1v60A 123 8.82e+01 1pxfA 111 8.83e+01 b.40.4.4 88341 1eu8A 409 8.88e+01 1eu8A c.94.1.1 59502 1qi9A 556 8.92e+01 1qhbA a.111.1.2 19053 1oo0B 110 8.94e+01 d.58.7.1 87183 1kjlA 146 8.97e+01