# List of top-scoring protein chains for t04-100-30-bys-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 1y2qA 143 7.56e-03 2gfgA 193 1.16e-01 1mp9A 198 2.70e-01 d.129.1.1,d.129.1.1 91385,91386 1u94A 356 2.97e-01 c.37.1.11,d.48.1.1 107743,107744 1j8yF 297 4.52e-01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1ofuA 320 4.86e-01 c.32.1.1,d.79.2.1 86972,86973 1vgjA 184 5.53e-01 1vljA 407 6.45e-01 e.22.1.2 108832 1wy7A 207 6.60e-01 1rtxA 123 6.63e-01 a.1.1.1 97827 1usgA 346 7.13e-01 c.93.1.1 99864 2reb 352 7.13e-01 2reb c.37.1.11,d.48.1.1 32282,38767 1dlyA 164 8.31e-01 1dlyA a.1.1.1 14983 1vdxA 184 8.41e-01 1ufkA 254 8.41e-01 c.66.1.39 99340 1v6tA 255 8.91e-01 1aisA 182 9.87e-01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1wqaA 455 1.01e+00 1r85A 379 1.03e+00 c.1.8.3 104839 1s69A 124 1.20e+00 a.1.1.1 105305 1qysA 106 1.37e+00 k.41.1.1 96603 1dosA 358 1.52e+00 1dosA c.1.10.2 29175 1zmdA 474 1.55e+00 1xb4A 202 1.63e+00 2ci1A 275 1.76e+00 1yz7A 188 1.84e+00 1fvuB 125 1.98e+00 1ixxB d.169.1.1 42346 1ecsA 126 2.13e+00 1ecsA d.32.1.2 59407 1xmxA 385 2.50e+00 1gntA 553 2.73e+00 e.26.1.1 70290 1e2uA 553 2.81e+00 1e1dA e.26.1.1 43362 1gnlA 544 2.86e+00 e.26.1.1 70287 2b8nA 429 3.01e+00 2b4gA 317 3.13e+00 1z15A 344 3.44e+00 1ivnA 190 3.52e+00 c.23.10.5 83719 1tzjA 338 3.53e+00 1u9iA 519 3.71e+00 1dtwB 342 3.77e+00 1qs0B c.36.1.7,c.48.1.2 31828,33102 1xqaA 113 3.92e+00 1rv3A 483 4.21e+00 c.67.1.4 105101 1cliA 345 4.28e+00 1cliA d.79.4.1,d.139.1.1 39816,41459 1gx5A 536 4.44e+00 e.8.1.4 70682 1gefA 123 4.65e+00 1gefA c.52.1.18 60465 1nf8A 207 4.75e+00 c.33.1.3 85630 1qs0B 338 4.75e+00 1qs0B c.36.1.7,c.48.1.2 31830,33103 1nf9A 207 4.84e+00 c.33.1.3 85631 1yemA 179 4.91e+00 2bfdB 345 5.00e+00 1pvgA 418 5.05e+00 d.14.1.3,d.122.1.2 95161,95162 1bjt 793 5.06e+00 1bjt e.11.1.1 43249 1atiA 505 5.38e+00 1atiA c.51.1.1,d.104.1.1 33196,40745 1xviA 275 5.39e+00 1olsB 342 5.52e+00 c.36.1.7,c.48.1.2 93332,93333 1vmbA 140 5.62e+00 1ow1A 195 5.95e+00 b.131.1.3 93625 1x7yB 342 6.00e+00 1c2pA 576 6.04e+00 1quvA e.8.1.4 43117 1bj4A 470 6.18e+00 1bj4A c.67.1.4 34479 1v5vA 401 6.22e+00 1qtoA 122 6.23e+00 1bylA d.32.1.2 38494 1xg5A 279 6.24e+00 1v1rB 342 6.31e+00 c.36.1.7,c.48.1.2 108273,108274 1b00A 127 6.52e+00 3chy c.23.1.1 31122 1w66A 232 6.63e+00 1r89A 437 6.70e+00 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1o0uA 429 6.72e+00 c.118.1.1 80743 3ladA 476 6.79e+00 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30573,30574,40208 1gudA 288 6.94e+00 c.93.1.1 83326 1xp8A 366 7.04e+00 1rsgA 516 7.20e+00 1zesA 125 7.29e+00 2lbp 346 7.29e+00 2liv c.93.1.1 35709 1ii7A 333 7.58e+00 1ii7A d.159.1.4 62415 2cvlA 124 7.66e+00 1wd3A 482 7.67e+00 b.29.1.21,b.42.8.1 109233,109234 1xg9A 260 7.69e+00 1zghA 260 7.71e+00 1lssA 140 7.74e+00 c.2.1.9 74246 1q9jA 422 7.77e+00 c.43.1.2,c.43.1.2 104590,104591 1fm0E 150 7.84e+00 1fmaE d.41.5.1 38629 1wkvA 389 7.90e+00 1wvfA 520 8.10e+00 2a35A 215 8.21e+00 1ooeA 236 8.22e+00 c.2.1.2 87196 2fhzA 109 8.36e+00 1j34B 123 8.39e+00 d.169.1.1 84049 2fuvA 549 8.44e+00 1yvkA 163 8.58e+00 1jayA 212 8.66e+00 c.2.1.6 66478 2ewtA 71 9.04e+00 1in0A 163 9.08e+00 d.58.49.1,d.58.49.1 83694,83695 1tv8A 340 9.33e+00 c.1.28.3 107352 2f4nA 273 9.34e+00 1sw5B 275 9.53e+00 c.94.1.1 106070 1qhtA 775 9.59e+00 1tgoA c.55.3.5,e.8.1.1 33722,43011 1rpxA 230 9.60e+00 1rpxA c.1.2.2 28536 1bh9B 89 9.67e+00 1bh9B a.22.1.3 16485 1rz3A 201 1.02e+01 c.37.1.6 98132 1x3lA 440 1.06e+01 1jg5A 83 1.06e+01 d.205.1.1 66666 1p5fA 189 1.07e+01 c.23.16.2 94142 2fcr 173 1.08e+01 1rcf c.23.5.1 31151 1jqbA 351 1.10e+01 b.35.1.2,c.2.1.1 77151,77152 1nonA 179 1.12e+01 c.61.1.1 103868 2liv 344 1.15e+01 2liv c.93.1.1 35708 5abp 306 1.15e+01 8abp c.93.1.1 35651 1tk9A 188 1.17e+01 c.80.1.3 107082 2abwA 227 1.17e+01 2dri 271 1.18e+01 2dri c.93.1.1 35637 1u7iA 136 1.19e+01 d.32.1.7 107724 1sw5A 275 1.19e+01 c.94.1.1 106069 1r8eA 278 1.21e+01 a.6.1.3,d.60.1.1 104843,104844 1mjhA 162 1.24e+01 1mjhA c.26.2.4 31639 1tvlA 454 1.24e+01 c.1.16.4 107366 1kyqA 274 1.25e+01 c.2.1.11,e.37.1.1 73281,73282 1et0A 269 1.25e+01 1et0A e.17.1.1 43289 1j98A 157 1.26e+01 1j98A d.185.1.2 62755 1jyhA 157 1.26e+01 d.60.1.3 71956 1yy5B 513 1.27e+01 1z0wA 207 1.33e+01 2c5aA 379 1.33e+01 1bykA 255 1.35e+01 1bykA c.93.1.1 35706 1c7sA 858 1.35e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21812,22408,29011,40410 1fjhA 257 1.35e+01 1fjhB c.2.1.2 29870 1za7A 165 1.36e+01 2h0uA 217 1.36e+01 1eq2A 310 1.36e+01 1eq2A c.2.1.2 29814 1xqiA 195 1.36e+01 1tqjA 230 1.37e+01 c.1.2.2 107228 1nv8A 284 1.38e+01 c.66.1.30 86224 1e19A 314 1.39e+01 1b7bA c.73.1.1 34967 2acvA 463 1.39e+01 1eziA 228 1.40e+01 1eyrA c.68.1.13 34512 1vkhA 273 1.41e+01 c.69.1.32 108662 1u14A 172 1.41e+01 c.51.4.3 107579 1o8bA 219 1.43e+01 c.124.1.4,d.58.40.1 81180,81181 1vhoA 346 1.44e+01 b.49.3.1,c.56.5.4 100694,100695 1vr6A 350 1.44e+01 1qd9A 124 1.45e+01 1qu9A d.79.1.1 39758 1gpmA 525 1.46e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1fyeA 229 1.47e+01 1fyeA c.23.16.4 31477 1o2dA 371 1.48e+01 e.22.1.2 86591 1vimA 200 1.49e+01 c.80.1.3 100758 1ezwA 349 1.50e+01 1ezwA c.1.16.3 29558 2b3nA 159 1.52e+01 1cg2A 393 1.54e+01 1cg2A c.56.5.4,d.58.19.1 33844,39360 1ep3B 262 1.54e+01 1ep2B b.43.4.2,c.25.1.3 25664,31554 1u5tC 202 1.54e+01 a.4.5.54,a.4.5.54 107688,107689 1gxjA 186 1.54e+01 d.215.1.1 70707 1dv1A 449 1.57e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1oltA 457 1.58e+01 c.1.28.2 93334 1cnt1 187 1.60e+01 1cnt3 1w5fA 353 1.60e+01 1ekeA 230 1.62e+01 1ekeA c.55.3.1 33572 1dlwA 116 1.63e+01 1dlyA a.1.1.1 14982 1l6rA 227 1.65e+01 c.108.1.10 77768 1wt9B 123 1.65e+01 1djqA 729 1.66e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 2f5gA 133 1.66e+01 2cb2A 318 1.66e+01 1f20A 435 1.71e+01 b.43.4.1,c.25.1.4 64932,64933 1a8p 258 1.71e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1xzoA 174 1.71e+01 1gesA 450 1.72e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 1rpjA 288 1.74e+01 2dri c.93.1.1 35656 1ubeA 349 1.80e+01 c.37.1.11,d.48.1.1 88412,88413 1i2kA 269 1.82e+01 e.17.1.1 90661 1xhkA 187 1.83e+01 1m0dA 138 1.83e+01 c.52.1.17 74354 1djnA 729 1.84e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 1fzrA 138 1.84e+01 1fzrA c.52.1.17 33336 1vkyA 347 1.85e+01 e.53.1.1 108696 1wryA 121 1.86e+01 1sqiA 393 1.87e+01 d.32.1.3,d.32.1.3 105914,105915 1lqpA 135 1.90e+01 d.32.1.2 78151 2ng1 293 1.92e+01 1ng1 a.24.13.1,c.37.1.10 16962,32273 1kqpA 271 1.92e+01 c.26.2.1 72883 1sesA 421 1.94e+01 1sesA a.2.7.1,d.104.1.1 15710,40710 1fsz 372 1.94e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1c9kA 180 1.95e+01 1c9kB c.37.1.11 32363 2f9zC 159 1.98e+01 1p1lA 102 2.01e+01 d.58.5.2 87695 1qu9A 128 2.06e+01 1qu9A d.79.1.1 39755 1gnxA 479 2.06e+01 c.1.8.4 76241 1kevA 351 2.07e+01 1pedA b.35.1.2,c.2.1.1 24749,29765 1ayaA 101 2.10e+01 1qadA d.93.1.1 40460 1td2A 287 2.10e+01 c.72.1.5 106765 1lfpA 249 2.13e+01 e.39.1.1 73885 1x6vA 630 2.17e+01 1kc6A 257 2.18e+01 c.52.1.19 68419 2pia 321 2.18e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1e8pA 46 2.19e+01 g.55.1.1 59385 1rztA 331 2.19e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 1kwmA 402 2.20e+01 c.56.5.1,d.58.3.1 73079,73080 2fp4B 395 2.21e+01 1bw0A 416 2.21e+01 1bw0A c.67.1.1 34385 1v60A 123 2.21e+01 1pv9A 348 2.22e+01 c.55.2.1,d.127.1.1 95157,95158 1mml 265 2.22e+01 1mml e.8.1.2 43015 2a0kA 161 2.23e+01 1vl8A 267 2.23e+01 c.2.1.2 108733 1l8aA 886 2.23e+01 c.36.1.10,c.36.1.6,c.48.1.1 73677,73678,73679 1ne9A 335 2.24e+01 d.108.1.4,d.108.1.4 91839,91840 1ru8A 232 2.25e+01 c.26.2.1 97849 1v8aA 265 2.25e+01 c.72.1.2 100494 1avyA 74 2.26e+01 1avyB h.1.17.1 45656 1o4sA 389 2.28e+01 c.67.1.1 86620 1t4bA 367 2.28e+01 c.2.1.3,d.81.1.1 106406,106407 1i88A 389 2.28e+01 c.95.1.2,c.95.1.2 66070,66071 2f62A 161 2.31e+01 2b5iD 217 2.33e+01 2f2tA 161 2.35e+01 1cwpA 190 2.35e+01 1cwpA b.121.4.5 23305 2an1A 292 2.35e+01 1hd2A 161 2.36e+01 c.47.1.10 60962 1w3uA 362 2.38e+01 1xrjA 261 2.41e+01 1rypL 212 2.41e+01 d.153.1.4 41880 1hh1A 143 2.44e+01 1gefA c.52.1.18 61036 1a48 306 2.47e+01 1a48 d.143.1.1 41590 1xtqA 177 2.50e+01 2g7zA 282 2.50e+01 1yobA 179 2.53e+01 1uslA 170 2.55e+01 c.121.1.1 99871 1obdA 306 2.55e+01 d.143.1.1 86767 1bi5A 389 2.57e+01 1bi5A c.95.1.2,c.95.1.2 35985,35986 1u0kA 288 2.57e+01 d.21.1.2,d.21.1.2 107547,107548 1ejdA 419 2.57e+01 1uae d.68.2.2 39576 1rqlA 267 2.58e+01 c.108.1.3 97750 1xznA 179 2.60e+01 1i9sA 210 2.61e+01 1i9sA c.45.1.1 62099 2cc6A 68 2.63e+01 2cc9A 68 2.63e+01 1vjqA 79 2.65e+01 k.43.1.1 100830 2a6pA 208 2.73e+01 1fts 295 2.73e+01 1ng1 a.24.13.1,c.37.1.10 16968,32279 1ki9A 192 2.74e+01 c.37.1.1 84404 1ls1A 295 2.79e+01 a.24.13.1,c.37.1.10 78170,78171 1w19A 160 2.79e+01 8abp 306 2.83e+01 8abp c.93.1.1 35647 1oniA 137 2.83e+01 d.79.1.1 87144 1c44A 123 2.84e+01 1qndA d.106.1.1 40795 1mogA 67 2.84e+01 d.230.2.1 85034 1mb4A 370 2.85e+01 c.2.1.3,d.81.1.1 78908,78909 2tmdA 729 2.88e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28616,30317,30602 1jjvA 206 2.89e+01 c.37.1.1 71698 1kutA 230 2.92e+01 d.143.1.1 73017 2akoA 251 2.93e+01 2fjbA 643 2.93e+01 1jkeA 145 2.94e+01 c.110.1.1 66791 2c8vA 288 2.95e+01 1cmiA 85 2.97e+01 1cmiA d.39.1.1 38551 1t6cA 315 2.99e+01 c.55.1.8,c.55.1.8 106558,106559 1j0aA 325 2.99e+01 c.79.1.1 83871 1fjgI 128 3.00e+01 1fjfI d.14.1.1 37559 1u9yA 284 3.01e+01 1iqrA 420 3.01e+01 a.99.1.1,c.28.1.1 66275,66276 1pk6B 132 3.01e+01 b.22.1.1 94802 2freA 200 3.03e+01 2gdjA 264 3.03e+01 1rcf 169 3.03e+01 1rcf c.23.5.1 31170 1brmA 367 3.03e+01 1brmA c.2.1.3,d.81.1.1 30030,39945 1ro5A 201 3.05e+01 d.108.1.3 105023 1us5A 314 3.08e+01 c.94.1.1 99856 2arkA 188 3.08e+01 2fi0A 81 3.09e+01 1wvcA 259 3.09e+01 1zjjA 263 3.10e+01 1yhtA 367 3.14e+01 1xrkA 124 3.15e+01 1ju2A 536 3.16e+01 c.3.1.2,d.16.1.1 77169,77170 1t1uA 639 3.18e+01 1j8mF 297 3.20e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1jnrA 643 3.21e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1vi9A 299 3.22e+01 c.72.1.5 100750 1w41A 101 3.23e+01 1lrrA 131 3.24e+01 d.228.1.1 78165 2gn4A 344 3.24e+01 1cex 214 3.34e+01 1cex c.69.1.30 31285 1am7A 158 3.36e+01 1am7A d.2.1.4 36981 1x9mA 698 3.36e+01 1knmA 130 3.37e+01 b.42.2.1 72781 1vetB 125 3.37e+01 d.110.7.1 108554 1e3jA 352 3.39e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 2ca6A 386 3.39e+01 2audA 257 3.40e+01 1wd7A 261 3.40e+01 1nox 205 3.41e+01 1nox d.90.1.1 40242 2ajrA 331 3.41e+01 2b06A 155 3.43e+01 1icrA 217 3.43e+01 1vfrA d.90.1.1 62274 1w85I 49 3.43e+01 1ta3B 303 3.46e+01 c.1.8.3 106732 1naqA 112 3.48e+01 d.58.5.2 91761 1jznA 135 3.49e+01 d.169.1.1 84262 1ykiA 217 3.50e+01 1y5iA 1246 3.50e+01 2g6tA 306 3.51e+01 1lc5A 364 3.51e+01 c.67.1.1 73827 2a2kA 175 3.51e+01 1u24A 337 3.52e+01 1dkuA 317 3.54e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1ccwA 137 3.54e+01 1be1 c.23.6.1 31238 1kv7A 488 3.54e+01 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 1w9hA 427 3.55e+01 1iapA 211 3.55e+01 a.91.1.1 62119 1pxvA 183 3.56e+01 d.3.1.1 95301 2tpt 440 3.57e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17759,31623,38621 1squA 155 3.58e+01 d.252.1.1 98971 1xocA 520 3.59e+01 1wzcA 249 3.62e+01 1y1pA 342 3.66e+01 1hc7A 477 3.66e+01 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 1htqA 477 3.67e+01 d.15.9.1,d.128.1.1 71035,71036 1g2iA 166 3.74e+01 1g2iA c.23.16.2 31438 1q16A 1247 3.74e+01 b.52.2.2,c.81.1.1 95546,95547 1pwxA 254 3.74e+01 c.2.1.2 95262 1udvA 89 3.75e+01 d.68.6.1 99224 1ujmA 342 3.75e+01 1v3vA 333 3.75e+01 b.35.1.2,c.2.1.1 108345,108346 1vk3A 615 3.77e+01 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 2g76A 335 3.82e+01 1rlr 761 3.82e+01 1rlr a.98.1.1,c.7.1.2 18753,30679 2cwkA 160 3.83e+01 1g5hA 454 3.84e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 1wy2A 351 3.85e+01 1w7lA 422 3.85e+01 c.67.1.1 109226 1ih8A 271 3.86e+01 2nsyA c.26.2.1 62377 1ffa 214 3.92e+01 1cex c.69.1.30 31289 1nkiA 135 3.93e+01 d.32.1.2 91941 1knwA 425 3.94e+01 b.49.2.3,c.1.6.1 90969,90970 1kafA 108 3.94e+01 d.199.1.1 68372 1f4pA 147 3.94e+01 5nul c.23.5.1 59651 1g3qA 237 3.95e+01 1hyqA c.37.1.10 60237 1gcoA 261 3.96e+01 1ybvA c.2.1.2 29884 1xd8A 289 3.96e+01 1geeA 261 3.96e+01 c.2.1.2 90509 1h7mA 102 3.99e+01 d.79.3.1 83485 2fcjA 119 4.00e+01 1b0b 142 4.05e+01 2fal a.1.1.2 15010 1louA 101 4.07e+01 1ris 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