# 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 2gkeA 274 1.20e-04 1gqzA 274 1.33e-04 d.21.1.1,d.21.1.1 83311,83312 1bwzA 274 3.24e-04 1bwzA d.21.1.1,d.21.1.1 38337,38338 1tm0A 350 4.26e-04 d.21.1.3 107147 1w61A 414 4.53e-04 1u1wA 298 1.87e-02 1xubA 298 3.75e-02 1ym5A 300 5.72e-02 1t6kA 278 5.85e-02 1z94A 147 1.79e-01 1o0pA 104 2.43e-01 d.58.7.1 86535 1sdjA 310 4.01e-01 d.21.1.2,d.21.1.2 98807,98808 1dp4A 435 6.31e-01 1dp4A c.93.1.1 35710 1p3dA 475 8.26e-01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 2b3nA 159 9.96e-01 1yqfA 203 1.23e+00 1t6aA 126 1.26e+00 d.129.8.1 106555 1qyaA 307 1.36e+00 d.21.1.2,d.21.1.2 104653,104654 2sli 679 1.42e+00 2sli b.29.1.9,b.68.1.1 24274,27611 1j5pA 253 1.53e+00 d.81.1.3,c.2.1.3 71577,83092 1y0gA 191 1.58e+00 1cqqA 180 2.01e+00 1cqqA b.47.1.4 26422 1xhdA 173 2.15e+00 1vrmA 325 2.59e+00 1mkeA 152 2.76e+00 b.55.1.4 79231 1wosA 364 2.99e+00 b.44.2.1,d.250.1.1 109468,109469 1wznA 252 3.00e+00 1ycoA 279 3.30e+00 1ut8A 291 3.39e+00 a.60.7.1,c.120.1.2 99908,99909 2azpA 318 3.79e+00 1nscA 390 4.22e+00 2qwc b.68.1.1 27591 1ut9A 609 4.28e+00 a.102.1.2,b.1.18.2 99912,99913 2cr4A 126 4.36e+00 1wucA 250 4.46e+00 1sr8A 298 4.49e+00 e.54.1.1 105959 1q47A 495 4.51e+00 b.69.12.1 104532 2g6yA 217 4.65e+00 1gtzA 156 4.72e+00 c.23.13.1 70539 1d0iA 156 4.74e+00 2dhqA c.23.13.1 31383 1xtqA 177 4.78e+00 1i1iP 681 4.94e+00 1i1iP d.92.1.5 40297 1w6sA 599 5.12e+00 2aioA 269 5.14e+00 1rzhL 281 5.21e+00 f.26.1.1 98164 1zwxA 301 5.34e+00 1tafB 70 5.50e+00 1tafB a.22.1.3 16482 1tdtA 259 5.51e+00 3tdt b.81.1.2 28055 1wekA 217 5.60e+00 1xo1A 291 6.02e+00 1exnA a.60.7.1,c.120.1.2 18086,33356 1smlA 269 6.17e+00 1smlA d.157.1.1 42053 3tdt 274 6.22e+00 3tdt b.81.1.2 28053 1xeuA 263 6.24e+00 1vdkA 466 6.45e+00 a.127.1.1 100561 2cxcA 144 6.66e+00 1iqaA 160 6.86e+00 b.22.1.1 71274 1v7oA 165 6.91e+00 d.67.1.2 100480 1ci3M 249 6.93e+00 1hcz b.2.6.1,b.84.2.2 22480,28266 1s55A 156 7.15e+00 1cwvA 492 7.16e+00 1cwvA b.1.14.1,b.1.14.1,b.1.14.1,b.1.14.1,d.169.1.3 22373,22374,22375,22376,42442 1yc9A 442 7.24e+00 1uebA 184 7.30e+00 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1pbyA 489 7.47e+00 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 1oe4A 247 7.70e+00 c.18.1.3 86895 1ej8A 140 7.99e+00 1qupA b.1.8.1 22300 1mpp 361 8.69e+00 2rmpA b.50.1.2 26856 1x1nA 524 8.90e+00 1rcy 151 8.92e+00 1rcy b.6.1.1 23018 1kkcA 221 9.08e+00 a.2.11.1,d.44.1.1 68660,68661 1ghj 79 9.09e+00 1ghj b.84.1.1 28232 2a6hC 1119 9.25e+00 2fomB 185 9.44e+00 1umzA 278 9.55e+00 b.29.1.2 99639 2calA 154 1.01e+01 1qhkA 47 1.02e+01 1qhkA d.100.1.2 40694 1x05A 129 1.05e+01 1v10A 521 1.06e+01 b.6.1.3,b.6.1.3,b.6.1.3 108224,108225,108226 1omrA 201 1.12e+01 a.39.1.5 93349 1oixA 191 1.12e+01 2gc9A 179 1.14e+01 1dkqA 410 1.19e+01 1dklA c.60.1.2 33998 1iw7C 1119 1.22e+01 e.29.1.1 71474 1hf2A 210 1.24e+01 1hf2A b.80.3.1,c.102.1.1 60992,60993 1ufbA 127 1.28e+01 a.24.16.3 99331 1f06A 320 1.31e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 1v58A 241 1.32e+01 c.47.1.9,d.17.3.1 108371,108372 1dkmA 410 1.33e+01 1dklA c.60.1.2 34000 1uyjA 296 1.33e+01 f.8.1.2 108143 1js8A 394 1.33e+01 a.86.1.1,b.112.1.1 67219,67220 2bw0A 329 1.34e+01 1kay 381 1.35e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1lurA 339 1.36e+01 b.30.5.4 84717 1y7wA 291 1.37e+01 1rec 201 1.40e+01 1rec a.39.1.5 17326 1josA 128 1.41e+01 d.52.7.1 84191 1o70A 324 1.45e+01 b.118.1.1,b.118.1.1 81115,81116 1ecfA 504 1.47e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1o20A 427 1.50e+01 c.82.1.1 86556 1ffa 214 1.50e+01 1cex c.69.1.30 31289 1kk1A 410 1.50e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1bupA 386 1.54e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1cx1A 153 1.56e+01 1ulo b.18.1.14 23770 1e30A 155 1.59e+01 1rcy b.6.1.1 23016 1mo9A 523 1.61e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 2a74A 643 1.67e+01 2cyeA 133 1.69e+01 1zm0A 114 1.70e+01 1zo2A 129 1.71e+01 1oivA 191 1.72e+01 c.37.1.8 93076 1yi9A 309 1.73e+01 1gpiA 431 1.73e+01 b.29.1.10 65450 1cex 214 1.74e+01 1cex c.69.1.30 31285 4uagA 437 1.75e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1ogsA 497 1.75e+01 b.71.1.2,c.1.8.3 86997,86998 1a8rA 221 1.75e+01 1a8rA d.96.1.1 40587 1xx0A 127 1.75e+01 2fclA 169 1.77e+01 2b5iD 217 1.78e+01 2gf9A 189 1.80e+01 1qwnA 1045 1.81e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1go4A 205 1.82e+01 d.135.1.1 70292 2a1kA 233 1.82e+01 4ubpC 570 1.83e+01 1ubpC b.92.1.1,c.1.9.2 28431,29053 2f6uA 234 1.83e+01 1x6zA 123 1.83e+01 1ukvY 206 1.86e+01 c.37.1.8 107918 1uctA 218 1.89e+01 b.1.1.4,b.1.1.4 88467,88468 2fz4A 237 1.91e+01 1bk0 331 1.91e+01 1bk0 b.82.2.1 28118 2fs2A 151 1.94e+01 2b5nA 323 1.94e+01 1mxmA 254 2.01e+01 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1rzuA 485 2.06e+01 c.87.1.8 105140 2bcgY 206 2.08e+01 2b59B 172 2.08e+01 1b56 135 2.08e+01 1hmt b.60.1.2 27183 1vhzA 198 2.09e+01 d.113.1.1 100718 1qipA 183 2.11e+01 1qipA d.32.1.1 38470 1p7tA 731 2.15e+01 c.1.13.1 94319 1yb3A 175 2.17e+01 1fo8A 343 2.18e+01 1foaA c.68.1.10 59927 1dzoA 123 2.19e+01 1dzoA d.24.1.1 38378 1prxA 224 2.20e+01 1prxA c.47.1.10 33076 1wycA 392 2.21e+01 1e1oA 504 2.21e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1t6cA 315 2.22e+01 c.55.1.8,c.55.1.8 106558,106559 1o17A 345 2.22e+01 a.46.2.1,c.27.1.1 80765,80766 1v3eA 431 2.22e+01 b.68.1.1 100287 2az4A 429 2.24e+01 1s0uA 408 2.26e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 7fd1A 106 2.28e+01 1a6l d.58.1.2 38953 3proC 166 2.29e+01 3proC d.52.1.1,d.52.1.1 38812,38813 1kcxA 518 2.29e+01 b.92.1.3,c.1.9.6 90953,90954 1sdwA 314 2.31e+01 b.121.1.2,b.121.1.2 98810,98811 1b8fA 509 2.31e+01 1b8fA a.127.1.2 19434 2eifA 136 2.32e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1s1fA 406 2.35e+01 1xttA 216 2.35e+01 1xfjA 261 2.36e+01 d.194.1.2 109585 1gkmA 509 2.38e+01 a.127.1.2 70228 1b12A 248 2.42e+01 1b12A b.87.1.2 28388 1zq1A 438 2.42e+01 2a8yA 270 2.45e+01 1r9gA 216 2.47e+01 c.23.16.1 97258 1lylA 504 2.48e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 1xizA 159 2.50e+01 1lj5A 379 2.51e+01 e.1.1.1 73928 1ygs 234 2.51e+01 1ygs b.26.1.1 23907 1htyA 1015 2.51e+01 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 1wlnA 120 2.55e+01 1wybA 392 2.58e+01 1f00I 282 2.61e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 2aliA 158 2.63e+01 1wubA 178 2.67e+01 1uc2A 481 2.68e+01 d.261.1.1 99161 2a6tA 271 2.71e+01 1x88A 359 2.75e+01 1odmA 331 2.75e+01 b.82.2.1 86875 1yg9A 330 2.76e+01 1vljA 407 2.79e+01 e.22.1.2 108832 1f0cA 305 2.83e+01 1c8oA e.1.1.1 42676 2awaA 390 2.84e+01 1a2vA 655 2.87e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24416,38059,38060 1uurA 473 2.89e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1zz1A 369 2.91e+01 1u3wA 374 2.95e+01 1e94F 449 2.97e+01 1do0A c.37.1.20 32443 1h2kA 349 2.97e+01 b.82.2.6 76572 2g6tA 306 2.99e+01 1r7lA 110 2.99e+01 d.277.1.1 104837 1ti6B 274 3.01e+01 b.3.5.1,d.58.1.5 106976,106977 2bx6A 350 3.01e+01 1ixlA 131 3.02e+01 d.38.1.5 90717 1fh0A 221 3.05e+01 1cs8A d.3.1.1 59832 1v4pA 157 3.13e+01 1zcbA 362 3.13e+01 1wudA 89 3.15e+01 1r3eA 309 3.17e+01 b.122.1.1,d.265.1.2 96907,96908 1f3uA 118 3.21e+01 1f3uA b.65.1.1 27521 1yuwA 554 3.22e+01 2rspA 124 3.29e+01 2rspB b.50.1.1 26771 1ciy 590 3.33e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1mqoA 227 3.37e+01 d.157.1.1 103846 1lm8V 160 3.38e+01 b.3.3.1 74035 1a7cA 379 3.40e+01 1sek e.1.1.1 42660 1pj5A 830 3.45e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1sziA 247 3.49e+01 a.24.23.1 106159 1g99A 408 3.51e+01 1g99A c.55.1.2,c.55.1.2 33457,33458 1wtaA 275 3.51e+01 1ejxC 567 3.55e+01 b.92.1.1,c.1.9.2 83184,83185 1vcbC 160 3.57e+01 1vcbC b.3.3.1 22535 1xvaA 292 3.58e+01 1xvaA c.66.1.5 34183 2d09A 407 3.58e+01 1r77A 103 3.61e+01 2a35A 215 3.63e+01 1psuA 140 3.64e+01 d.38.1.5 88285 1i8dA 213 3.70e+01 b.43.4.3,b.43.4.3 61953,61954 1vk1A 242 3.71e+01 d.268.1.2 108634 1jdrA 294 3.72e+01 1ryc a.93.1.1 62908 2bgoA 140 3.73e+01 2pil 159 3.74e+01 2pil d.24.1.1 38376 1ca1 370 3.74e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 2aneA 125 3.76e+01 1hf8A 289 3.77e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1kepA 348 3.78e+01 c.2.1.2 68536 1uwkA 557 3.78e+01 e.51.1.1 108065 1g72A 573 3.82e+01 4aahA b.70.1.1 27680 1qfhA 212 3.84e+01 1qfhA b.1.18.10,b.1.18.10 21893,21894 1xjcA 169 3.84e+01 1oh4A 179 3.86e+01 b.18.1.18 92978 1ko3A 230 3.88e+01 d.157.1.1 90974 1h8gA 95 3.88e+01 b.109.1.1 65735 1oc2A 348 3.89e+01 c.2.1.2 92765 1v1pA 211 3.89e+01 b.40.2.2,d.15.6.1 108268,108269 1d8cA 723 3.90e+01 1d8cA c.1.13.1 29325 1izmA 184 3.93e+01 a.199.1.1 90725 1m3yA 413 3.93e+01 b.121.2.3,b.121.2.3 78579,78580 3rabA 169 3.95e+01 1ctqA c.37.1.8 32018 1u6zA 513 3.95e+01 2fr2A 172 4.00e+01 2ewrA 170 4.00e+01 1nnxA 109 4.00e+01 b.40.10.1 92013 1of4A 179 4.01e+01 b.18.1.18 86932 1n67A 359 4.02e+01 b.2.3.4,b.2.3.4 85354,85355 1dtoA 221 4.06e+01 1dtoA b.91.1.1 28405 1orrA 347 4.08e+01 c.2.1.2 93460 2d4qA 257 4.09e+01 2gf6A 135 4.27e+01 1i5pA 633 4.29e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 2ckiA 262 4.31e+01 2bm5A 186 4.32e+01 1ltsA 185 4.34e+01 1lt3A d.166.1.1 42229 1z08A 170 4.36e+01 1hg8A 349 4.36e+01 b.80.1.3 65830 1orvA 728 4.44e+01 b.70.3.1,c.69.1.24 87354,87355 1sqjA 789 4.48e+01 b.69.13.1,b.69.13.1 105918,105919 1v1qA 134 4.49e+01 1o6vA 466 4.51e+01 b.1.18.15,c.10.2.1 81099,81100 2f4nA 273 4.52e+01 1z54A 132 4.54e+01 1jc9A 269 4.56e+01 d.171.1.1 66490 2fcbA 173 4.57e+01 2fcbA b.1.1.4,b.1.1.4 21781,21782 1q15A 503 4.59e+01 c.26.2.1,d.153.1.1 95538,95539 2af4C 333 4.61e+01 1xruA 282 4.62e+01 1i1nA 226 4.64e+01 c.66.1.7 71102 2bvbA 137 4.66e+01 2gfaA 119 4.69e+01 2fn0A 437 4.70e+01 1gmiA 136 4.71e+01 b.7.1.1 65309 1jcfA 344 4.74e+01 c.55.1.1,c.55.1.1 62878,62879 2ai4A 119 4.77e+01 1u84A 90 4.77e+01 2dcyA 185 4.78e+01 2nlrA 234 4.78e+01 2nlrA b.29.1.11 24344 1h9dB 134 4.81e+01 2jhbA b.54.1.1 60822 1gv3A 248 4.85e+01 a.2.11.1,d.44.1.1 70585,70586 1ut7A 171 4.87e+01 b.143.1.1 99906 1pfsA 78 5.01e+01 1pfsA b.40.4.7 25391 1jb7A 495 5.04e+01 1otcA b.40.4.3,b.40.4.3,b.40.4.3 62836,62837,62838 1czfA 362 5.05e+01 1czfA b.80.1.3 28031 1uisA 231 5.06e+01 d.22.1.1 99431 1e5pA 151 5.06e+01 1bj7 b.60.1.1 59272 1xnb 185 5.08e+01 1axkA b.29.1.11 24308 1z5hA 780 5.09e+01 1q1rA 431 5.12e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1j75A 67 5.14e+01 a.4.5.19 62673 1vi6A 208 5.15e+01 c.23.15.1 100736 1w3fA 315 5.17e+01 2gaeA 346 5.18e+01 1jofA 365 5.18e+01 b.69.10.1 71775 1vm7A 311 5.20e+01 c.72.1.1 108884 1dkzA 219 5.21e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1dykA 394 5.21e+01 1dykA b.29.1.4,b.29.1.4 24223,24224 2etvA 346 5.21e+01 1nksA 194 5.24e+01 1nksA c.37.1.1 31886 1fjgK 129 5.27e+01 1fjfK c.55.4.1 33733 1ycdA 243 5.28e+01 1vh7A 265 5.31e+01 c.1.2.1 100646 1hyoA 421 5.35e+01 1qcnA b.34.8.1,d.177.1.1 59001,59002 2f15A 96 5.40e+01 1ygaA 342 5.40e+01 1ouwA 152 5.45e+01 b.77.3.1 93571 1r4pA 297 5.46e+01 d.165.1.2 97025 1erjA 393 5.48e+01 1erjA b.69.4.1 27660 1vyfA 135 5.54e+01 b.60.1.2 108902 1yua 122 5.58e+01 1yua g.41.3.3,g.41.3.3 45210,45211 1dabA 539 5.59e+01 1dabA b.80.1.7 28049 1tq5A 242 5.63e+01 1qi9A 556 5.65e+01 1qhbA a.111.1.2 19053 1kpf 126 5.67e+01 1kpf d.13.1.1 37507 1usyA 275 5.69e+01 1cb8A 678 5.69e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1kmtA 141 5.71e+01 b.1.18.8 77442 2bf6A 449 5.71e+01 1kbvA 327 5.72e+01 b.6.1.3,b.6.1.3 68395,68396 1tuhA 156 5.82e+01 d.17.4.11 107345 1xksA 450 5.85e+01 1l0sA 90 5.85e+01 b.81.2.1 73408 1bkb 136 5.86e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 1iuhA 198 5.86e+01 d.61.1.2 83711 1f08A 148 5.88e+01 1f08A d.89.1.2 59564 1kq3A 376 5.89e+01 e.22.1.2 68790 1tueB 218 5.89e+01 b.91.1.1 107324 1mkiA 330 5.89e+01 e.3.1.2 84994 1kpeA 126 5.92e+01 1kpf d.13.1.1 37508 1urvA 190 5.92e+01 1ut0A 190 5.92e+01 a.1.1.2 108012 1su0B 159 5.95e+01 d.224.1.2 106015 2f9lA 199 5.98e+01 1zghA 260 6.00e+01 1j1nA 492 6.02e+01 c.94.1.1 83978 1alu 186 6.04e+01 1alu a.26.1.1 16826 1tns 76 6.04e+01 1qpmA a.6.1.7 16228 1cjcA 460 6.05e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1xg9A 260 6.05e+01 1vjrA 271 6.05e+01 c.108.1.14 100832 3ladA 476 6.06e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 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