# List of top-scoring protein chains for t04-100-30-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 1hu4A 288 1.88e-01 1hu4A 1n5dA 288 1.88e-01 c.2.1.2 80030 1wmaA 276 2.01e-01 1n40A 396 2.33e-01 a.104.1.1 79977 1t3gA 159 3.72e-01 1k7kA 221 4.34e-01 c.51.4.1 72104 1c3jA 351 4.65e-01 1c3jA c.87.1.1 35459 1ypcI 64 5.29e-01 2sniI d.40.1.1 38570 1regX 122 5.56e-01 1regX d.58.27.1 39406 1tqhA 247 6.96e-01 c.69.1.29 107225 2aaa 484 6.97e-01 7taa b.71.1.1,c.1.8.1 27777,28764 1jixA 351 7.35e-01 1c3jA c.87.1.1 63081 1lw6I 64 1.06e+00 d.40.1.1 74294 7taa 478 1.47e+00 7taa b.71.1.1,c.1.8.1 27778,28765 2a0fA 310 1.48e+00 2bh1A 250 1.69e+00 1g61A 228 1.80e+00 1g61A d.126.1.1 41126 2b9dA 52 1.91e+00 2bd0A 244 2.03e+00 2ci1A 275 2.08e+00 1u5hA 273 2.42e+00 1v76A 96 2.55e+00 1ihoA 283 2.78e+00 1ihoA c.26.1.4 62390 1xrtA 467 2.82e+00 1pbyA 489 2.99e+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 1z6kA 293 3.08e+00 1f0cA 305 3.16e+00 1c8oA e.1.1.1 42676 1us8A 147 3.17e+00 c.37.1.12 99859 1s7zA 117 3.20e+00 a.159.3.1 98715 1yf5L 254 3.25e+00 1mrzA 293 3.30e+00 b.43.5.1,c.26.1.3 91452,91453 1ws6A 171 3.33e+00 3csuA 310 3.43e+00 3csuA c.78.1.1,c.78.1.1 35094,35095 2d83A 363 3.63e+00 1jae 471 3.64e+00 1smd b.71.1.1,c.1.8.1 27773,28760 1to2I 64 3.89e+00 1kq6A 141 3.90e+00 d.189.1.1 91020 2fqxA 318 3.97e+00 1gln 468 4.38e+00 1gln a.97.1.1,c.26.1.1 18752,31588 1oaa 259 4.72e+00 1oaa c.2.1.2 29829 1id0A 152 4.88e+00 d.122.1.3 66111 1cbf 285 4.90e+00 1cbf c.90.1.1 35587 1h1yA 228 4.93e+00 c.1.2.2 76506 1r1dA 247 5.03e+00 c.69.1.29 96813 1brmA 367 5.44e+00 1brmA c.2.1.3,d.81.1.1 30030,39945 1o26A 232 6.12e+00 d.207.1.1 86566 2ew8A 249 6.14e+00 1udxA 416 6.19e+00 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1lba 146 6.29e+00 1lba d.118.1.1 41062 1t71A 281 6.42e+00 1k3eA 156 6.44e+00 d.198.1.1 68103 1m93B 245 6.45e+00 2d4pA 141 6.48e+00 1rvkA 382 6.75e+00 c.1.11.2,d.54.1.1 97928,97929 1y0gA 191 6.89e+00 1o7kA 131 7.18e+00 d.189.1.1 81144 2bwnA 401 7.32e+00 1amp 291 7.40e+00 1amp c.56.5.4 33837 1v7rA 186 7.45e+00 c.51.4.1 100482 1vl8A 267 7.64e+00 c.2.1.2 108733 2bgkA 278 7.95e+00 1rtqA 299 7.98e+00 c.56.5.4 97819 1ycdA 243 8.10e+00 1vjoA 393 8.17e+00 c.67.1.3 100827 1h3gA 601 8.18e+00 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1ht6A 405 8.20e+00 b.71.1.1,c.1.8.1 83629,83630 1ijyA 130 8.35e+00 1ijxA a.141.1.1 62517 1fsz 372 8.37e+00 1fsz c.32.1.1,d.79.2.1 31750,39802 1ob8A 135 8.39e+00 2cw5A 255 8.50e+00 1qlpA 394 8.82e+00 1ovaA e.1.1.1 42628 1lokA 291 8.86e+00 c.56.5.4 78122 1zz1A 369 8.86e+00 1u5vA 273 8.97e+00 1jfbA 404 8.99e+00 a.104.1.1 66624 1f24A 402 9.16e+00 1rom a.104.1.1 18953 1vcvA 226 9.34e+00 1ve3A 227 9.50e+00 1sc3A 178 9.60e+00 c.17.1.1 105416 2a1iA 146 9.65e+00 1f8vA 355 9.69e+00 2bbvA b.121.4.4 23329 1evlA 401 9.70e+00 1qf6A c.51.1.1,d.104.1.1 33202,40751 1rwxA 178 9.74e+00 2anpA 291 9.76e+00 1xqaA 113 9.93e+00 1bmqA 167 9.99e+00 1pauA c.17.1.1 30998 2ghrA 302 1.01e+01 2fliA 220 1.01e+01 1v65A 64 1.02e+01 a.212.1.1 108393 1wiwA 290 1.02e+01 1w97L 246 1.04e+01 1pyoA 167 1.14e+01 c.17.1.1 95370 1gxjA 186 1.16e+01 d.215.1.1 70707 1w2wB 191 1.17e+01 1uxoA 192 1.18e+01 c.69.1.31 108121 1ooeA 236 1.19e+01 c.2.1.2 87196 3seb 238 1.25e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1iro 54 1.26e+01 1rb9 g.41.5.1 45223 1o57A 291 1.27e+01 a.4.5.40,c.61.1.1 92483,92484 2acvA 463 1.28e+01 1s5aA 150 1.33e+01 d.17.4.10 98525 1f2vA 219 1.34e+01 1f2vA c.23.17.1 59627 1pamA 686 1.35e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21846,22515,27753,28740 1wdyA 285 1.38e+01 1xaoA 121 1.38e+01 1rz3A 201 1.45e+01 c.37.1.6 98132 1rpxA 230 1.46e+01 1rpxA c.1.2.2 28536 1xfdA 723 1.47e+01 1ey4A 149 1.50e+01 1snc b.40.1.1 24815 1ckiA 317 1.53e+01 1csn d.144.1.7 41660 1vig 71 1.55e+01 1vih d.51.1.1 38806 1j77A 209 1.55e+01 1j77A a.132.1.2 62674 1pymA 295 1.58e+01 1pymA c.1.12.7 29308 1qyiA 384 1.62e+01 c.108.1.13 96595 1wwjA 105 1.63e+01 1bd8 156 1.64e+01 1bd8 d.211.1.1 19157 1uzcA 71 1.66e+01 a.159.2.1 100222 2c2aA 258 1.66e+01 3xis 387 1.68e+01 4xis c.1.15.3 29423 1yj7A 171 1.68e+01 1hrhA 136 1.71e+01 1rthA c.55.3.1 33577 1ass 159 1.73e+01 1a6dA c.8.5.2 30818 1gcqC 70 1.75e+01 1gcpA b.34.2.1 60436 1uanA 227 1.77e+01 c.134.1.1 99135 1yk4A 52 1.80e+01 1wdtA 665 1.80e+01 1pieA 419 1.82e+01 d.14.1.5,d.58.26.7 94706,94707 1z2wA 192 1.87e+01 1hdoA 206 1.88e+01 1he2A c.2.1.2 60965 1nmoA 247 1.93e+01 c.135.1.1 91980 4xis 387 1.93e+01 4xis c.1.15.3 29421 1i19A 561 2.07e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 1snyA 267 2.07e+01 c.2.1.2 105833 1xc3A 302 2.08e+01 1h4vB 421 2.09e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1w24A 182 2.11e+01 1kwgA 645 2.12e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 2f1kA 279 2.18e+01 1c7sA 858 2.20e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21812,22408,29011,40410 1u5mA 73 2.28e+01 1semA 58 2.28e+01 1ckaA b.34.2.1 24544 1uouA 474 2.34e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 2f9dA 125 2.40e+01 1vllA 334 2.44e+01 c.2.1.13 108834 1d3cA 686 2.47e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21827,22496,27734,28721 2ca6A 386 2.47e+01 1zo0A 126 2.49e+01 1r5pA 108 2.53e+01 c.47.1.15 97101 1e2fA 215 2.54e+01 3tmkA c.37.1.1 59164 1bdb 277 2.54e+01 1bdb c.2.1.2 29874 1kamA 194 2.54e+01 c.26.1.3 72254 1rq2A 382 2.56e+01 c.32.1.1,d.79.2.1 105048,105049 4uagA 437 2.58e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1z90A 469 2.62e+01 1e2gA 215 2.75e+01 3tmkA c.37.1.1 59165 1brfA 53 2.76e+01 1rb9 g.41.5.1 45236 1mtpA 323 2.78e+01 e.1.1.1 85107 1bq9A 54 2.78e+01 1rb9 g.41.5.1 45238 1nn5A 215 2.78e+01 c.37.1.1 85892 1s2oA 244 2.79e+01 2dexX 671 2.80e+01 2fa8A 105 2.82e+01 2tpt 440 2.83e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17759,31623,38621 1muwA 386 2.84e+01 c.1.15.3 79495 2ahrA 259 2.84e+01 1eokA 290 2.85e+01 1eokA c.1.8.5 28991 1h70A 255 2.87e+01 1h70A d.126.1.3 60711 1yr1A 119 2.91e+01 1ctn 540 2.98e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21876,29005,38439 1lwjA 441 3.01e+01 b.71.1.1,c.1.8.1 74303,74304 1f9aA 168 3.02e+01 1f9aA c.26.1.3 31602 1k8kB 394 3.02e+01 c.55.1.1 68307 1edqA 540 3.05e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 2fb0A 94 3.07e+01 8tlnE 316 3.07e+01 1hyt d.92.1.2 59075 1gxrA 337 3.09e+01 b.69.4.1 70722 1w78A 422 3.10e+01 1k3tA 359 3.11e+01 c.2.1.3,d.81.1.1 72022,72023 1lssA 140 3.13e+01 c.2.1.9 74246 1fukA 165 3.15e+01 1fukA c.37.1.19 32409 1u9cA 224 3.15e+01 2tmnE 316 3.15e+01 1hyt d.92.1.2 59055 1s1fA 406 3.17e+01 2a84A 300 3.17e+01 2c07A 285 3.18e+01 1sdjA 310 3.18e+01 d.21.1.2,d.21.1.2 98807,98808 1gegA 256 3.18e+01 1ybvA c.2.1.2 29888 1x9gA 200 3.19e+01 c.33.1.3 109527 1zymA 258 3.21e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 1tqyA 424 3.23e+01 c.95.1.1,c.95.1.1 107245,107246 1rifA 282 3.25e+01 c.37.1.23 97507 2d09A 407 3.27e+01 1hc7A 477 3.27e+01 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 1yhtA 367 3.29e+01 1h30A 422 3.35e+01 b.29.1.4,b.29.1.4 76604,76605 2g50A 530 3.36e+01 1quqB 121 3.36e+01 1quqB b.40.4.3 25305 1msk 331 3.37e+01 1msk d.173.1.1 42495 1zesA 125 3.37e+01 1oz9A 150 3.39e+01 d.92.1.15 93808 2fqpA 97 3.40e+01 1nh1A 330 3.43e+01 e.45.1.1 91871 1a49A 530 3.43e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27026,29255,33109 1y7lA 316 3.51e+01 1m3sA 186 3.52e+01 c.80.1.3 78573 2d0eA 407 3.57e+01 1wd7A 261 3.60e+01 1j2jB 45 3.62e+01 a.7.8.1 84017 1orvA 728 3.66e+01 b.70.3.1,c.69.1.24 87354,87355 1c28A 135 3.66e+01 1c28A b.22.1.1 23857 1ghsA 306 3.66e+01 1aq0A c.1.8.3 28840 2c1xA 456 3.68e+01 1b8gA 429 3.70e+01 1b8gA c.67.1.4 34499 2ddfA 257 3.73e+01 1zxcA 263 3.74e+01 1jfzA 154 3.75e+01 a.149.1.1 66655 12asA 330 3.75e+01 12asA d.104.1.1 40783 1ukuA 102 3.75e+01 d.58.5.2 99533 1ugpA 203 3.77e+01 d.149.1.1 107831 1kfwA 435 3.77e+01 c.1.8.5,d.26.3.1 77376,77377 1n7hA 381 3.78e+01 c.2.1.2 80250 1ireA 204 3.78e+01 d.149.1.1 76769 1cxpA 104 3.79e+01 1d2vA a.93.1.2 18695 1d2vA 104 3.79e+01 1d2vA a.93.1.2 18697 1qh8B 519 3.81e+01 1qguB c.92.2.3 35634 1x1tA 260 3.83e+01 1jj2M 186 3.89e+01 1ffkK c.55.4.1 63098 1dcfA 136 3.90e+01 1dcfA c.23.1.2 31124 1fexA 59 3.91e+01 a.4.1.3 59803 1feuA 206 3.92e+01 1feuA b.53.1.1 59801 1du3A 130 3.92e+01 1d4vA g.24.1.1,g.24.1.1,g.24.1.1 44927,44928,44929 1qyaA 307 3.93e+01 d.21.1.2,d.21.1.2 104653,104654 1kllA 130 3.94e+01 d.32.1.2 72720 1b00A 127 3.96e+01 3chy c.23.1.1 31122 1mb4A 370 3.97e+01 c.2.1.3,d.81.1.1 78908,78909 2bduA 297 3.98e+01 1ufzA 83 3.99e+01 a.5.9.1 107821 1wehA 171 4.00e+01 2cdcA 366 4.05e+01 1o4vA 183 4.05e+01 c.23.8.1 86628 1q7zA 566 4.07e+01 c.1.21.2,c.1.26.1 96090,96091 1m7yA 435 4.07e+01 c.67.1.4 78761 1mlwA 301 4.10e+01 d.178.1.1 79289 1wkcA 184 4.13e+01 1i5gA 144 4.15e+01 1ewxA c.47.1.10 61784 1cy5A 97 4.17e+01 1cy5A a.77.1.3 18430 1vdwA 254 4.20e+01 e.7.1.1 100569 1lb2B 84 4.20e+01 a.60.3.1 77871 2bllA 345 4.20e+01 2ae2A 260 4.20e+01 1bdb c.2.1.2 29945 1yf3A 259 4.21e+01 2f6kA 307 4.22e+01 2f6sA 201 4.22e+01 1jdc 429 4.23e+01 1jdc b.71.1.1,c.1.8.1 27789,28776 2f06A 144 4.24e+01 1qf6A 642 4.29e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 2flsA 132 4.32e+01 1vc1A 110 4.33e+01 c.13.2.1 108493 1eceA 358 4.37e+01 1eceA c.1.8.3 28813 1wt9B 123 4.42e+01 1g4wR 383 4.43e+01 1g4uS a.24.11.1,c.45.1.2 16644,32692 1mx3A 347 4.49e+01 c.2.1.4,c.23.12.1 79638,79639 2fjbA 643 4.56e+01 1jnrA 643 4.57e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1wn5A 130 4.58e+01 1tkkA 366 4.58e+01 c.1.11.2,d.54.1.1 107089,107090 1n2eA 300 4.60e+01 c.26.1.4 85268 1ka8A 100 4.60e+01 a.4.5.20 72241 1ytlA 174 4.62e+01 1vqoN 187 4.62e+01 1gypA 358 4.64e+01 1dssG c.2.1.3,d.81.1.1 30004,39919 1uedA 406 4.65e+01 a.104.1.1 99256 1jykA 254 4.65e+01 c.68.1.13 67458 1wu7A 434 4.67e+01 1ryaA 160 4.69e+01 d.113.1.5 105122 1ocsA 162 4.70e+01 d.189.1.1 92776 2bzgA 232 4.70e+01 1cseI 71 4.70e+01 1egpA d.40.1.1 38559 1u69A 163 4.71e+01 d.32.1.7 107699 1wnaA 131 4.75e+01 1tjyA 316 4.77e+01 c.93.1.1 107062 1aie 31 4.78e+01 1aie a.53.1.1 17829 2b5gA 171 4.78e+01 1jx7A 117 4.79e+01 c.114.1.1 77195 1ruwA 69 4.80e+01 1tqxA 227 4.84e+01 1kafA 108 4.85e+01 d.199.1.1 68372 1qyrA 252 4.86e+01 c.66.1.24 104657 1va0A 239 4.86e+01 1aboA 62 4.89e+01 1bbzA b.34.2.1 24474 1amy 403 4.90e+01 1jdc b.71.1.1,c.1.8.1 27799,28786 1bkcI 256 4.91e+01 1bkcA d.92.1.10 40334 1uhwA 109 4.91e+01 a.4.5.31 99410 1fvgA 199 4.93e+01 1fvaA d.58.28.1 39408 1t3qC 288 4.96e+01 d.87.2.1,d.145.1.3 106371,106372 1ynuA 473 4.97e+01 2erfA 209 5.00e+01 1wmbA 260 5.01e+01 1jpmA 366 5.01e+01 c.1.11.2,d.54.1.1 67031,67032 1n4qB 377 5.01e+01 a.102.4.3 91636 1e6pA 499 5.04e+01 1e15A b.72.2.1,c.1.8.5,d.26.3.1 59314,59315,59316 1adjA 421 5.12e+01 1adjA c.51.1.1,d.104.1.1 33188,40737 1sw5B 275 5.14e+01 c.94.1.1 106070 1rdg 53 5.14e+01 1rb9 g.41.5.1 45221 1g5aA 628 5.14e+01 b.71.1.1,c.1.8.1 65152,65153 1ysjA 404 5.14e+01 2end 138 5.16e+01 2end a.18.1.1 16400 1yrgA 385 5.16e+01 1yrgA c.10.1.2 30854 2cygA 312 5.16e+01 2c36A 285 5.17e+01 1iirA 415 5.19e+01 1iirA c.87.1.5 62453 1esgA 213 5.19e+01 1bam c.52.1.3 33286 1f02T 66 5.19e+01 1f02T j.67.1.1 46360 1qhoA 686 5.27e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1xkqA 280 5.27e+01 1q9uA 130 5.29e+01 d.129.7.1 96314 1chmA 401 5.29e+01 1chmA c.55.2.1,d.127.1.1 33545,41142 1vq2A 193 5.30e+01 1jwqA 179 5.30e+01 c.56.5.6 90921 1sw5A 275 5.31e+01 c.94.1.1 106069 1x71A 178 5.31e+01 1r6fA 310 5.31e+01 e.46.1.1 97149 1w5fA 353 5.33e+01 1nu0A 138 5.34e+01 c.55.3.8 92165 1bbzA 58 5.34e+01 1bbzA b.34.2.1 24477 2cujA 108 5.34e+01 1e5eA 404 5.35e+01 1ibjA c.67.1.3 59265 1nrzA 164 5.35e+01 c.38.1.1 86131 1g5tA 196 5.35e+01 1g5rA c.37.1.11 32366 1i74A 309 5.37e+01 1i74A c.107.1.1 61867 1z6oM 191 5.38e+01 1i3zA 103 5.41e+01 d.93.1.1 83667 6mhtA 327 5.41e+01 6mhtA c.66.1.26 34226 1m8jA 181 5.42e+01 c.26.1.3 84875 1tqjA 230 5.43e+01 c.1.2.2 107228 2bbhA 269 5.43e+01 1vh7A 265 5.43e+01 c.1.2.1 100646 2ez6A 221 5.45e+01 2gaxA 135 5.49e+01 1f8yA 157 5.50e+01 1f8xA c.23.14.1 31395 1uzbA 516 5.50e+01 c.82.1.1 100220 1kr4A 125 5.50e+01 d.58.5.2 72889 2c7pA 327 5.52e+01 1shfA 59 5.55e+01 1bbzA b.34.2.1 24462 2g03A 194 5.56e+01 1ej2A 181 5.59e+01 1f9aA c.26.1.3 59414 1tw0A 157 5.65e+01 1x89A 178 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