# List of top-scoring protein chains for t04-100-40-40-str2+CB_burial_14_7-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 2a9uA 144 2.03e-03 1colA 204 3.41e-01 1a87 f.1.1.1 43378 1i1rB 181 5.25e-01 1i1rB a.26.1.1 61548 2c3mA 1231 9.05e-01 1q52A 314 1.17e+00 c.14.1.3 95846 1x8vA 455 1.19e+00 1no1A 126 1.28e+00 a.179.1.1 85913 1wm5A 208 1.31e+00 1kekA 1231 1.50e+00 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 68524,68525,68526,68527,68528 1hh8A 213 1.55e+00 1e96B a.118.8.1 61042 2c5uA 375 1.86e+00 1h5zA 455 2.07e+00 a.104.1.1 90622 1s9pA 227 2.09e+00 a.123.1.1 105384 1utg 70 2.21e+00 1utg a.101.1.1 18813 1kpsB 171 2.27e+00 a.118.12.1 68787 1w68A 390 2.34e+00 a.25.1.2 109216 1zs3A 182 2.52e+00 1u13A 455 2.53e+00 a.104.1.1 107578 2cwyA 94 2.68e+00 2utgA 70 2.78e+00 1utg a.101.1.1 18814 2b0jA 358 2.87e+00 1rgeA 96 2.98e+00 1rgeA d.1.1.2 36028 1f5nA 592 3.16e+00 1dg3A a.114.1.1,c.37.1.8 19077,32152 1nznA 126 3.18e+00 a.118.8.1 92382 1cuk 203 3.61e+00 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1ezvA 430 4.03e+00 1be3A d.185.1.1,d.185.1.1 59541,59542 1lniA 96 4.47e+00 d.1.1.2 74046 1kb9A 431 4.47e+00 d.185.1.1,d.185.1.1 77311,77312 1vctA 205 4.83e+00 1mgrA 99 5.08e+00 d.1.1.2 79106 1qghA 156 5.11e+00 1qghA a.25.1.1 16728 1deeG 54 5.20e+00 1fc2C a.8.1.1 16343 1s9rA 410 5.54e+00 d.126.1.4 98758 1xo5A 183 5.62e+00 2f22A 144 5.82e+00 1pylA 97 5.92e+00 d.1.1.2 104391 1b0pA 1231 5.97e+00 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 31831,31832,33104,34157,39003 1lrv 244 5.97e+00 1lrv a.118.1.5 19146 1wa8A 99 6.65e+00 2a72A 146 6.76e+00 1rzsA 61 6.91e+00 a.35.1.2 105139 1e9xA 455 7.20e+00 1ea1A a.104.1.1 18969 2occH 85 7.34e+00 2occH a.51.1.1 17796 1oyzA 280 7.47e+00 a.118.1.16 93775 1mqsA 671 7.65e+00 e.25.1.1 79414 1ll2A 333 7.93e+00 c.68.1.14 74005 2f6lA 166 8.27e+00 1us7B 265 8.29e+00 a.205.1.1 99858 1furA 467 8.55e+00 1furA a.127.1.1 19403 1j7nA 776 8.70e+00 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1q87A 221 9.20e+00 e.47.1.1 96192 1v54H 85 9.43e+00 a.51.1.1 100329 1h0oA 390 9.63e+00 a.25.1.2 70845 2b5aA 77 9.89e+00 1vbiA 344 9.93e+00 1gweA 503 9.93e+00 e.5.1.1 70667 6gsvA 217 1.00e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 2bbhA 269 1.05e+01 1f83A 425 1.07e+01 1f82A d.92.1.7 40306 1p3wA 404 1.07e+01 c.67.1.3 87752 2ae0X 345 1.08e+01 1ujwB 135 1.10e+01 h.4.9.1 99472 1u4bA 580 1.10e+01 c.55.3.5,e.8.1.1 107664,107665 1tfr 305 1.14e+01 1tfr a.60.7.1,c.120.1.2 18081,33351 1jmuB 666 1.16e+01 1mp1A 111 1.17e+01 a.188.1.1 91382 1hbzA 498 1.17e+01 1cf9A e.5.1.1 60937 1yucA 255 1.18e+01 1wz8A 264 1.20e+01 1mpgA 282 1.22e+01 1mpgA a.96.1.3,d.129.1.2 18747,41296 2fp1A 166 1.23e+01 1top 162 1.27e+01 1ncx a.39.1.5 17223 1fseA 74 1.32e+01 1fseA a.4.6.2 60000 1w8iA 156 1.34e+01 1uzeA 589 1.34e+01 d.92.1.5 108174 1pszA 303 1.34e+01 1toaA c.92.2.2 35600 1zroA 602 1.35e+01 2c1xA 456 1.38e+01 1tbfA 347 1.43e+01 a.211.1.2 106743 1zzcA 198 1.45e+01 1o86A 589 1.46e+01 d.92.1.5 81177 1lwbA 122 1.47e+01 a.133.1.3 84728 1xcbA 211 1.51e+01 a.4.5.38,c.2.1.12 109552,109553 1ew4A 106 1.57e+01 1ew4A d.82.2.1 40023 1vmaA 306 1.57e+01 a.24.13.1,c.37.1.10 108887,108888 2fuqA 747 1.58e+01 1go3F 107 1.60e+01 a.60.8.2 65407 1o4sA 389 1.62e+01 c.67.1.1 86620 1hr6B 443 1.66e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1e94F 449 1.71e+01 1do0A c.37.1.20 32443 1tllA 688 1.72e+01 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 2gmyA 153 1.73e+01 1q16B 512 1.74e+01 d.58.1.5 95548 1ohuA 175 1.74e+01 f.1.4.1 93029 1gvhA 396 1.74e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 2a5yA 204 1.78e+01 1vjxA 157 1.81e+01 a.25.1.1 100837 1l3sA 580 1.81e+01 c.55.3.5,e.8.1.1 84521,84522 1yb3A 175 1.82e+01 1y7yA 74 1.86e+01 1p7tA 731 1.90e+01 c.1.13.1 94319 1r1uA 106 1.90e+01 a.4.5.5 104771 1y791 680 1.91e+01 1y5iB 512 1.93e+01 1r2fA 319 1.96e+01 1r2fA a.25.1.2 16800 1r9dA 787 2.02e+01 c.7.1.1 104865 1mr8A 93 2.05e+01 1b4cA a.39.1.2 17186 1uzcA 71 2.08e+01 a.159.2.1 100222 1oaa 259 2.08e+01 1oaa c.2.1.2 29829 2c2xA 281 2.15e+01 1ho8A 480 2.19e+01 1ho8A a.118.1.9 61107 2c0rA 362 2.25e+01 1ox3A 109 2.25e+01 h.1.17.1 93668 1xsm 390 2.26e+01 1xsm a.25.1.2 16804 2eshA 118 2.31e+01 1mkmA 249 2.35e+01 a.4.5.33,d.110.2.2 79242,79243 1hu3A 260 2.36e+01 1hu3A a.118.1.14 19137 1w07A 659 2.42e+01 1zk8A 183 2.51e+01 2bylA 439 2.51e+01 1jhfA 202 2.54e+01 a.4.5.2,b.87.1.1 63057,63058 1d2zB 153 2.55e+01 1d2zB a.77.1.2 18439 1u61A 138 2.60e+01 a.149.1.1 107696 1xszA 356 2.64e+01 1w3uA 362 2.66e+01 1q16A 1247 2.67e+01 b.52.2.2,c.81.1.1 95546,95547 1k7wA 468 2.67e+01 a.127.1.1 72130 1xnfA 275 2.70e+01 1fpzA 212 2.71e+01 1fpzA c.45.1.1 59976 2bnmA 198 2.72e+01 1utxA 66 2.76e+01 a.35.1.3 108034 3pviA 157 2.76e+01 3pviA c.52.1.6 33300 1hx1B 114 2.78e+01 1hx1B a.7.7.1 61350 1wc3A 219 2.80e+01 1ab4 477 2.80e+01 1ab4 e.11.1.1 43251 1zq4A 693 2.81e+01 1wgzA 510 2.82e+01 1y5iA 1246 2.84e+01 1xk4A 93 2.87e+01 1oatA 439 2.89e+01 2dkb c.67.1.4 34461 1v38A 78 2.90e+01 a.60.1.2 100280 1d8cA 723 3.00e+01 1d8cA c.1.13.1 29325 1fjgD 209 3.03e+01 1c05A d.66.1.2 39553 1a5t 334 3.03e+01 1a5t a.80.1.1,c.37.1.20 18450,32423 1orjA 130 3.05e+01 a.24.19.1 93456 1iyhA 198 3.08e+01 a.45.1.1,c.47.1.5 83790,83791 1ng6A 148 3.11e+01 a.182.1.1 85670 1nk4A 580 3.11e+01 c.55.3.5,e.8.1.1 91923,91924 2gaeA 346 3.11e+01 1w2fA 276 3.14e+01 d.143.1.3 109125 2gpiA 91 3.14e+01 1xwl 580 3.17e+01 1xwl c.55.3.5,e.8.1.1 33708,43001 1wgwA 99 3.20e+01 1tjvA 474 3.21e+01 a.127.1.1 107054 1oe8A 211 3.22e+01 a.45.1.1,c.47.1.5 86905,86906 1pd21 199 3.24e+01 1pd21 1dk8A 147 3.25e+01 1agrE a.91.1.1 18548 1k8tA 510 3.27e+01 e.41.1.1 68316 1xqoA 256 3.27e+01 1ka2A 499 3.28e+01 d.92.1.5 77305 1yt3A 375 3.28e+01 1s6yA 450 3.33e+01 c.2.1.5,d.162.1.2 105314,105315 1iw7C 1119 3.35e+01 e.29.1.1 71474 1hm6A 346 3.40e+01 1avc a.65.1.1 18147 1jjyA 636 3.42e+01 1jjyA 1s6lA 212 3.43e+01 1ydiA 263 3.48e+01 1wloA 136 3.49e+01 2pviA 157 3.50e+01 3pviA c.52.1.6 33302 1yz7A 188 3.51e+01 1dgfA 497 3.51e+01 1cf9A e.5.1.1 42782 2oatA 439 3.51e+01 2dkb c.67.1.4 34452 1b9hA 388 3.52e+01 1b9hA c.67.1.4 34488 1u2wA 122 3.56e+01 1dytA 133 3.62e+01 7rsa d.5.1.1 37288 1vi0A 206 3.66e+01 a.4.1.9,a.121.1.1 100720,100721 1cjgA 62 3.66e+01 1pru a.35.1.5 17112 1ki1B 352 3.67e+01 a.87.1.1,b.55.1.1 72497,72498 1e8yA 966 3.68e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 2byjA 439 3.69e+01 1ib2A 349 3.73e+01 1ib2A a.118.1.8 62141 1jqnA 883 3.81e+01 c.1.12.3 77159 1i1iP 681 3.85e+01 1i1iP d.92.1.5 40297 2bjcA 62 3.85e+01 2a6hC 1119 3.88e+01 1v7bA 185 3.90e+01 1fiy 883 3.92e+01 1fiy c.1.12.3 29307 1wt4A 73 3.95e+01 1hw1A 239 3.98e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1rktA 205 4.00e+01 a.4.1.9,a.121.1.1 97623,97624 1of5B 184 4.05e+01 d.17.4.2 86934 2d1eA 248 4.10e+01 1om2A 95 4.12e+01 1om2A a.23.4.1 16520 1q4mA 221 4.19e+01 a.132.1.3 95805 1spgA 144 4.25e+01 1abwA a.1.1.2 15409 1ppjB 439 4.25e+01 d.185.1.1,d.185.1.1 104254,104255 1a0cA 438 4.31e+01 1a0cA c.1.15.3 29529 1t4bA 367 4.33e+01 c.2.1.3,d.81.1.1 106406,106407 1x6iA 91 4.36e+01 1a0p 290 4.38e+01 1a0p a.60.9.1,d.163.1.1 18105,42165 1wa5B 530 4.40e+01 1na3A 91 4.41e+01 k.38.1.1 85481 1m12A 84 4.42e+01 a.64.1.1 84745 1su8A 636 4.44e+01 e.26.1.2 98999 1m98A 317 4.45e+01 a.175.1.1,d.17.4.6 78866,78867 1dvoA 152 4.48e+01 1dvoA a.136.1.1 19623 1omwA 689 4.50e+01 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 1xwoA 465 4.52e+01 1y0uA 96 4.52e+01 1a4sA 503 4.54e+01 1bpwA c.82.1.1 35361 1pq4A 291 4.55e+01 c.92.2.2 94995 1jchA 551 4.56e+01 b.101.1.1,b.110.1.1,h.4.9.1 66491,66492,66493 1yzvA 204 4.62e+01 1zy4A 303 4.63e+01 1sd4A 126 4.68e+01 a.4.5.39 105428 1af3 196 4.69e+01 1maz f.1.4.1 43397 1v63A 101 4.73e+01 a.21.1.1 108391 1gakA 141 4.74e+01 1gakA a.19.1.1 16415 1wzaA 488 4.75e+01 1l0lB 439 4.83e+01 d.185.1.1,d.185.1.1 84484,84485 1ds1A 324 4.85e+01 1drtA b.82.2.2 28127 1gl2C 65 4.91e+01 h.1.15.1 65280 1bouA 139 5.14e+01 1bouA a.88.1.1 18521 1pk5A 248 5.14e+01 a.123.1.1 88139 1t01A 255 5.18e+01 a.24.9.1,a.24.9.1 106188,106189 1wmbA 260 5.24e+01 1vddA 228 5.26e+01 e.49.1.1 108519 3lynA 136 5.28e+01 1lis a.19.1.1 16413 1b68A 191 5.28e+01 1nfn a.24.1.1 59076 2f3nA 76 5.32e+01 2fq4A 192 5.35e+01 1dciA 275 5.36e+01 1dciA c.14.1.3 30918 1s8nA 205 5.38e+01 c.23.1.1 105374 1maz 221 5.41e+01 1maz f.1.4.1 43393 1fazA 122 5.41e+01 1fazA a.133.1.3 59757 2dh4A 340 5.43e+01 1j2mA 99 5.44e+01 a.165.1.1 84018 1iznB 277 5.46e+01 e.43.1.2 83848 1l9lA 74 5.51e+01 a.64.1.1 77827 1g8pA 350 5.53e+01 1g8pA c.37.1.20 60376 1i0aA 466 5.64e+01 1auwA a.127.1.1 61479 2h58A 330 5.65e+01 1zljA 78 5.66e+01 2lisA 136 5.68e+01 1lis a.19.1.1 16405 1zz2A 360 5.71e+01 1hyp 80 5.72e+01 1hyp a.52.1.1 17806 2cg4A 152 5.78e+01 1di1A 300 5.82e+01 1di1A a.128.1.4 19446 1pzlA 237 5.94e+01 a.123.1.1 104393 2au3A 407 6.01e+01 1vh4A 435 6.04e+01 b.80.6.1 100640 1yn9A 169 6.06e+01 1omrA 201 6.18e+01 a.39.1.5 93349 1l8dA 112 6.19e+01 h.4.12.1 73687 1q1hA 110 6.20e+01 a.4.5.41 95580 1m7kA 99 6.20e+01 a.7.7.1 74573 1s4bP 674 6.24e+01 d.92.1.5 105252 1keaA 221 6.25e+01 a.96.1.2 68491 1m0uA 249 6.26e+01 a.45.1.1,c.47.1.5 78359,78360 1rzhH 260 6.28e+01 b.41.1.1,f.23.10.1 98162,98163 1jhgA 101 6.35e+01 1jhgA a.4.12.1 19009 2crbA 97 6.36e+01 1i36A 264 6.38e+01 a.100.1.8,c.2.1.6 71108,71109 1yioA 208 6.41e+01 2cvdA 198 6.42e+01 1usyA 275 6.46e+01 1eg7A 557 6.47e+01 1eg7A c.37.1.10 32241 1l5jA 865 6.58e+01 a.118.15.1,c.8.2.1,c.83.1.1 73592,73593,73594 1hw5A 210 6.69e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 1qovH 260 6.71e+01 6prcH b.41.1.1,f.23.10.1 25464,43457 1kr7A 110 6.78e+01 a.1.1.4 72890 1r5rA 119 6.82e+01 a.39.2.1 97104 2f2gA 221 6.85e+01 1h7nA 342 6.89e+01 1b4kA c.1.10.3 60726 1tqnA 486 6.90e+01 a.104.1.1 107238 1uayA 242 6.92e+01 c.2.1.2 88390 1ee4A 423 6.94e+01 1ee4A a.118.1.1 19128 1tw9A 206 6.98e+01 a.45.1.1,c.47.1.5 107381,107382 2cfxA 144 7.01e+01 1w96A 554 7.02e+01 1ut8A 291 7.04e+01 a.60.7.1,c.120.1.2 99908,99909 1whxA 111 7.06e+01 1zthA 258 7.07e+01 1rm6C 161 7.08e+01 1l0lA 446 7.10e+01 d.185.1.1,d.185.1.1 84482,84483 1i7kA 179 7.10e+01 1u9aA d.20.1.1 61889 1wwzA 159 7.19e+01 1rovA 857 7.20e+01 a.119.1.1,b.12.1.1 97674,97675 1qlnA 883 7.20e+01 1cezA e.8.1.3 43111 1hy0A 466 7.20e+01 1auwA a.127.1.1 61392 1zzlA 351 7.25e+01 1yozA 116 7.33e+01 1ohlA 342 7.36e+01 c.1.10.3 87035 1ufzA 83 7.39e+01 a.5.9.1 107821 1o9iA 266 7.39e+01 a.25.1.3 92671 1yjsA 419 7.39e+01 3ertA 261 7.40e+01 3erdA a.123.1.1 19292 1t3wA 148 7.40e+01 1y8aA 332 7.43e+01 2bl0B 145 7.47e+01 1kqfA 1015 7.48e+01 b.52.2.2,c.81.1.1 72871,72872 1unkA 87 7.49e+01 1cei a.28.2.1 16935 2ts1 419 7.49e+01 2ts1 c.26.1.1 31564 1dtoA 221 7.57e+01 1dtoA b.91.1.1 28405 1uw2A 61 7.61e+01 g.37.1.4 108064 2b1eA 564 7.66e+01 1b71A 191 7.67e+01 1ryt a.25.1.1,g.41.5.1 16647,45246 1dgnA 89 7.71e+01 1dgnA a.77.1.3 18436 2anxA 146 7.73e+01 1sumB 235 7.74e+01 a.7.12.1 106025 1zq1A 438 7.81e+01 1nd4A 264 7.81e+01 d.144.1.6 91815 1lis 136 7.82e+01 1lis a.19.1.1 16406 1bj4A 470 7.86e+01 1bj4A c.67.1.4 34479 5csmA 256 7.90e+01 5csmA a.130.1.2 19494 2fupA 168 7.90e+01 1uby 367 7.90e+01 1uby a.128.1.1 19435 1iy8A 267 7.93e+01 c.2.1.2 83774 1x75A 132 7.98e+01 1ehiA 377 8.03e+01 1iow c.30.1.2,d.142.1.1 31716,41484 1dzoA 123 8.06e+01 1dzoA d.24.1.1 38378 1gqiA 708 8.08e+01 c.1.8.10,d.92.2.2 76279,76280 1no5A 114 8.08e+01 d.218.1.5 92014 1yqyA 523 8.12e+01 1z5hA 780 8.13e+01 1jx4A 352 8.23e+01 d.240.1.1,e.8.1.7 90378,90379 2genA 197 8.29e+01 1xdpA 687 8.29e+01 1nnlA 225 8.31e+01 c.108.1.4 85906 1z7lA 276 8.31e+01 1u11A 182 8.31e+01 c.23.8.1 107576 2a1iA 146 8.33e+01 1xx4A 261 8.33e+01 1fn9A 365 8.34e+01 1fn9A d.196.1.1 59894 1jt6A 188 8.37e+01 a.4.1.9,a.121.1.1 67247,67248 1uptB 60 8.44e+01 a.193.1.1 99768 1rztA 331 8.47e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 1y9qA 192 8.49e+01 1bjt 793 8.54e+01 1bjt e.11.1.1 43249 1kzfA 230 8.61e+01 d.108.1.3 73354 2bcqA 335 8.61e+01 1ualA 274 8.62e+01 c.116.1.4 88383 1sheA 103 8.66e+01 d.274.1.1 105551 1uj6A 227 8.66e+01 c.124.1.4,d.58.40.1 107898,107899 1t3qA 168 8.70e+01 a.56.1.1,d.15.4.2 106367,106368 2avuE 192 8.78e+01 1pbwA 216 8.88e+01 1pbwA a.116.1.1 19103 1wryA 121 8.91e+01 1kl1A 419 8.97e+01 c.67.1.4 72663