# List of top-scoring protein chains for t06-100-30-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 1xg4A 295 5.66e-38 1s2wA 295 1.66e-30 c.1.12.7 98407 1f8mA 429 6.52e-30 1dquA c.1.12.7 29315 1m3uA 264 8.31e-30 c.1.12.8 84784 1o66A 275 9.14e-29 c.1.12.8 92547 1gvfA 286 2.10e-11 c.1.10.2 70599 1rvgA 305 2.14e-09 c.1.10.2 97920 1rvkA 382 1.05e-06 c.1.11.2,d.54.1.1 97928,97929 1rd5A 262 2.50e-06 c.1.2.4 111772 1zfjA 491 2.73e-06 1ak5 c.1.5.1,d.37.1.1,d.37.1.1 28638,38540,38541 1xm3A 264 4.41e-06 c.1.31.1 115461 1mdl 359 7.24e-06 2mnr 1ad1A 266 9.94e-06 1aj2 c.1.21.1 29668 1xi3A 215 1.21e-05 c.1.3.1 109601 1q7zA 566 1.21e-05 c.1.21.2,c.1.26.1 96090,96091 1p0kA 349 1.62e-05 c.1.4.1 87648 1w5qA 337 3.78e-05 1ep3A 311 5.52e-05 2dorA c.1.4.1 28597 1mzhA 225 6.45e-05 c.1.10.1 79698 1gqnA 252 6.71e-05 c.1.10.1 90514 1xkyA 301 7.36e-05 c.1.10.1 122094 1gox 370 7.70e-05 1gox 1l6sA 323 8.00e-05 c.1.10.3 73627 1tx2A 297 9.51e-05 c.1.21.1 107420 1twdA 256 9.63e-05 c.1.30.1 107397 1ub3A 220 1.03e-04 c.1.10.1 88395 1wv2A 265 1.18e-04 c.1.31.1 114910 1jflA 228 1.18e-04 c.78.2.1,c.78.2.1 71656,71657 1qwgA 251 1.21e-04 c.1.27.1 96473 1o1zA 234 1.62e-04 c.1.18.3 86555 1aj2 282 1.72e-04 1aj2 1w8sA 263 1.99e-04 c.1.10.1 120744 1n7kA 234 2.32e-04 c.1.10.1 85374 1rhcA 330 2.67e-04 c.1.16.3 97468 1thfD 253 2.72e-04 1thfD c.1.2.1 28535 1hl2A 297 3.65e-04 c.1.10.1 83581 1v93A 296 3.79e-04 c.1.23.1 100532 1nvmA 345 3.90e-04 a.5.7.1,c.1.10.5 86249,86250 1vhnA 318 4.47e-04 c.1.4.1 100693 1x1oA 286 4.49e-04 1vhcA 224 4.76e-04 c.1.10.1 100661 2gjlA 328 6.61e-04 1muwA 386 7.42e-04 c.1.15.3 79495 1vr6A 350 8.05e-04 c.1.10.4 120439 1geqA 248 8.78e-04 2tysA c.1.2.4 28589 1ujpA 271 9.39e-04 c.1.2.4 99462 1tkkA 366 9.71e-04 c.1.11.2,d.54.1.1 107089,107090 1yxyA 234 1.07e-03 c.1.2.5 124203 2gptA 523 1.13e-03 1vhqA 232 1.13e-03 c.23.16.2 100696 1vzwA 244 1.17e-03 c.1.2.1 120553 2czdA 208 1.18e-03 c.1.2.3 131045 1ktbA 405 1.42e-03 b.71.1.1,c.1.8.1 72960,72961 2b7nA 273 1.62e-03 1q6oA 216 1.80e-03 c.1.2.3 95986 1ypfA 336 1.80e-03 2fiqA 420 2.40e-03 c.1.10.7 133527 1h1yA 228 3.30e-03 c.1.2.2 76506 1z41A 338 3.48e-03 c.1.4.1 124421 1wa3A 205 3.52e-03 c.1.10.1 120802 1vcvA 226 3.96e-03 c.1.10.1 119988 1zp4A 304 4.08e-03 1o5kA 306 4.67e-03 c.1.10.1 92504 1o0yA 260 4.75e-03 c.1.10.1 80756 1ykwA 435 5.19e-03 c.1.14.1,d.58.9.1 123565,123566 2b81A 323 5.33e-03 1xuuA 349 5.41e-03 b.85.1.1,c.1.10.6 116067,116068 2g8yA 385 6.07e-03 1y0eA 223 6.39e-03 c.1.2.5 116297 1vkfA 188 6.43e-03 c.1.29.1 108656 2gl5A 410 6.80e-03 c.1.11.2,d.54.1.1 135336,135337 1izcA 339 6.95e-03 c.1.12.5 83838 1reqB 637 6.96e-03 1reqB c.1.19.1,c.23.6.1 29621,31248 1x9iA 302 7.00e-03 c.80.1.1 114997 1kfcA 268 7.07e-03 c.1.2.4 77371 1nu5A 370 8.93e-03 c.1.11.2,d.54.1.1 92183,92184 1a53 247 9.20e-03 1a53 1m5wA 243 9.25e-03 c.1.24.1 84836 1zcjA 463 1.11e-02 1ub0A 258 1.33e-02 c.72.1.2 88394 1zhaA 267 1.50e-02 1vi2A 300 1.52e-02 c.2.1.7,c.58.1.5 100726,100727 1wbhA 214 1.53e-02 c.1.10.1 120845 1vliA 385 1.55e-02 b.85.1.1,c.1.10.6 108830,108831 1o4vA 183 1.58e-02 c.23.8.1 86628 1reqA 727 1.63e-02 1reqA c.1.19.1,c.23.6.1 29620,31247 1qopA 268 1.67e-02 2tysA c.1.2.4 28570 1onrA 316 1.68e-02 1onrA c.1.10.1 29169 1vc4A 254 2.20e-02 c.1.2.4 100557 1nsj 205 2.35e-02 1nsj 1fnnA 389 2.37e-02 1fnnA a.4.5.11,c.37.1.20 16129,32426 1o60A 292 2.41e-02 c.1.10.4 92532 1tqjA 230 2.69e-02 c.1.2.2 107228 1pii 452 2.76e-02 1pii 2fepA 289 2.79e-02 2d13A 227 2.86e-02 c.26.2.1 131121 1pe1A 267 2.92e-02 c.1.10.4 94591 1eyeA 280 2.98e-02 1aj2 c.1.21.1 29672 1rqbA 539 3.21e-02 a.5.7.2,c.1.10.5 105057,105058 1p1xA 260 3.35e-02 c.1.10.1 104060 1nqkA 381 3.39e-02 c.1.16.4 92050 1ohlA 342 3.39e-02 c.1.10.3 87035 2tpsA 227 3.66e-02 2tpsA c.1.3.1 28591 1tr9A 341 3.89e-02 c.1.8.7 112617 1sflA 238 4.33e-02 c.1.10.1 112077 2c6qA 351 4.97e-02 2cwxA 430 5.04e-02 c.1.14.1,d.58.9.1 130956,130957 1vqtA 213 6.20e-02 c.1.2.3 120417 1oi7A 288 6.23e-02 c.2.1.8,c.23.4.1 87049,87050 1x1zA 252 6.33e-02 c.1.2.3 121613 2fr1A 486 6.68e-02 c.2.1.2,c.2.1.2 133961,133962 1ezwA 349 6.93e-02 1ezwA c.1.16.3 29558 2d69A 430 7.07e-02 c.1.14.1,d.58.9.1 131292,131293 1d3gA 367 7.08e-02 1d3gA c.1.4.1 28600 2c4nA 250 8.49e-02 c.108.1.14 129837 1gkpA 458 8.55e-02 b.92.1.3,c.1.9.6 70231,70232 1km4A 247 9.04e-02 c.1.2.3 72740 1zjrA 211 9.30e-02 1f74A 293 9.43e-02 1nal3 c.1.10.1 29079 1xmpA 170 1.00e-01 c.23.8.1 115521 1p4cA 380 1.11e-01 c.1.4.1 94100 1n82A 331 1.13e-01 c.1.8.3 91703 1vicA 262 1.18e-01 c.68.1.13 100756 1dosA 358 1.20e-01 1dosA c.1.10.2 29175 1wtjA 343 1.20e-01 1ja9A 274 1.22e-01 c.2.1.2 62817 1gdhA 320 1.30e-01 1gdhA c.2.1.4,c.23.12.1 30095,31355 1v7cA 351 1.32e-01 c.79.1.1 100446 1z2iA 358 1.36e-01 1g2oA 268 1.39e-01 1b8oA c.56.2.1 60228 1brwA 433 1.39e-01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1pl8A 356 1.43e-01 b.35.1.2,c.2.1.1 94878,94879 1tcvA 287 1.46e-01 1xfcA 384 1.47e-01 1wyuA 438 1.50e-01 c.67.1.7 121452 1k0wA 231 1.50e-01 c.74.1.1 77220 1g57A 217 1.51e-01 1g57A d.115.1.2 60253 1zxxA 319 1.53e-01 1jkmB 361 1.57e-01 1jkmA c.69.1.2 34634 1yeyA 444 1.58e-01 c.1.11.2,d.54.1.1 116664,116665 1toaA 313 1.59e-01 1toaA c.92.2.2 35598 1ufkA 254 1.68e-01 c.66.1.39 99340 1mucA 373 1.73e-01 1mucA c.1.11.2,d.54.1.1 29236,38880 1jhdA 396 1.76e-01 b.122.1.3,c.26.1.5 66712,66713 2c4wA 176 1.76e-01 2gokA 429 1.78e-01 1u94A 356 1.80e-01 c.37.1.11,d.48.1.1 107743,107744 2ashA 381 1.85e-01 1v5eA 590 1.87e-01 c.31.1.3,c.36.1.5,c.36.1.9 119844,119845,119846 2chgA 226 1.90e-01 1q74A 303 1.91e-01 c.134.1.1 96019 1v4vA 376 1.94e-01 c.87.1.3 100313 2pth 193 2.07e-01 2pth 2fqxA 318 2.09e-01 1w0mA 226 2.13e-01 c.1.1.1 109027 1j24A 143 2.24e-01 c.52.1.20 84008 1vfsA 386 2.37e-01 b.49.2.2,c.1.6.1 108584,108585 1pswA 348 2.37e-01 c.87.1.7 88287 1x7oA 287 2.39e-01 1j93A 353 2.40e-01 c.1.22.1 66454 1zaiA 363 2.43e-01 c.1.10.1 124828 1gpjA 404 2.45e-01 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1zvkA 358 2.45e-01 1knwA 425 2.48e-01 b.49.2.3,c.1.6.1 90969,90970 1bd0A 388 2.50e-01 1bd0A b.49.2.2,c.1.6.1 26480,28642 2cw6A 298 2.55e-01 1v71A 323 2.63e-01 c.79.1.1 119859 1k0fA 277 2.69e-01 c.92.2.2 71974 1y88A 199 2.71e-01 a.60.4.3,c.52.1.30 116560,116561 2dri 271 2.74e-01 2dri 1zjjA 263 2.75e-01 1lzlA 323 2.78e-01 c.69.1.2 78306 1vd6A 224 2.81e-01 c.1.18.3 119991 1cg2A 393 2.81e-01 1cg2A c.56.5.4,d.58.19.1 33844,39360 1oi2A 366 2.95e-01 c.119.1.2 103802 1me8A 503 2.97e-01 c.1.5.1 79028 2bfdA 400 3.00e-01 1dbqA 289 3.01e-01 1qpzA c.93.1.1 35666 1tzjA 338 3.01e-01 c.79.1.1 112868 1ulyA 192 3.05e-01 a.4.5.58 113297 1ejdA 419 3.05e-01 1uae d.68.2.2 39576 1ls1A 295 3.10e-01 a.24.13.1,c.37.1.10 78170,78171 1qczA 169 3.22e-01 1qczA c.23.8.1 31276 1pszA 303 3.24e-01 1toaA c.92.2.2 35600 1dkuA 317 3.26e-01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1dxeA 256 3.29e-01 1dxeA c.1.12.5 29310 1jbeA 128 3.42e-01 3chy c.23.1.1 62845 1gntA 553 3.54e-01 e.26.1.1 70290 2gm5A 139 3.61e-01 1zud1 251 3.62e-01 1r0mA 375 3.73e-01 c.1.11.2,d.54.1.1 104747,104748 1gca 309 3.78e-01 1gca 1e19A 314 3.86e-01 1b7bA c.73.1.1 34967 1uanA 227 3.89e-01 c.134.1.1 99135 1mi3A 322 4.01e-01 c.1.7.1 91274 1ko3A 230 4.05e-01 d.157.1.1 90974 1umdB 324 4.06e-01 c.36.1.7,c.48.1.2 99600,99601 1uwkA 557 4.07e-01 e.51.1.1 108065 1wd7A 261 4.08e-01 c.113.1.1 114526 1m65A 245 4.13e-01 c.6.3.1 84847 1ml4A 308 4.14e-01 c.78.1.1,c.78.1.1 79255,79256 1php 394 4.26e-01 16pk 1swvA 267 4.43e-01 c.108.1.3 112134 1ve2A 235 4.44e-01 c.90.1.1 120008 1yyaA 250 4.45e-01 1w3iA 293 4.47e-01 c.1.10.1 109152 1epxA 370 4.49e-01 1fbaA c.1.10.1 29150 2bfwA 200 4.49e-01 c.87.1.8 128456 1ve3A 227 4.50e-01 c.66.1.43 120010 2cjpA 328 4.63e-01 2g50A 530 4.64e-01 b.58.1.1,c.1.12.1,c.49.1.1 134618,134619,134620 1z4eA 153 4.64e-01 d.108.1.1 124431 1uasA 362 4.73e-01 b.71.1.1,c.1.8.1 88388,88389 1vizA 240 4.74e-01 c.1.4.1 100784 1vk1A 242 4.78e-01 d.268.1.2 108634 1v6tA 255 4.91e-01 c.6.2.5 113550 1h3fA 432 4.94e-01 c.26.1.1,d.66.1.4 76631,76632 1g55A 343 5.25e-01 1g55A c.66.1.26 34247 1x7yA 400 5.32e-01 c.36.1.11 114944 1qv9A 283 5.34e-01 c.127.1.1 96356 1vi9A 299 5.44e-01 c.72.1.5 100750 2abqA 306 5.60e-01 c.72.1.1 126528 1v8aA 265 5.64e-01 c.72.1.2 100494 1i0dA 332 5.64e-01 1pscA c.1.9.3 61487 1r3sA 367 5.76e-01 c.1.22.1 96963 1wddA 477 5.79e-01 c.1.14.1,d.58.9.1 114528,114529 1ccwA 137 5.83e-01 1be1 c.23.6.1 31238 1yxcA 292 5.84e-01 c.1.10.1 124183 1yt8A 539 5.85e-01 c.46.1.2,c.46.1.2,c.46.1.2,c.46.1.2 123996,123997,123998,123999 7aatA 401 6.22e-01 1ajsA c.67.1.1 34250 1vyrA 364 6.25e-01 c.1.4.1 108906 1lssA 140 6.42e-01 c.2.1.9 74246 2rslA 140 6.62e-01 2rslA c.53.1.1 33345 1yacA 208 6.65e-01 1yacA c.33.1.3 31757 1t5iA 172 6.73e-01 c.37.1.19 106450 1rxdA 159 6.75e-01 c.45.1.1 111959 1u11A 182 6.78e-01 c.23.8.1 107576 1qwkA 317 6.94e-01 c.1.7.1 96482 1mvoA 136 6.94e-01 c.23.1.1 79513 1zh2A 121 7.03e-01 c.23.1.1 125069 1t1gA 364 7.10e-01 c.41.1.2 106246 1rzuA 485 7.23e-01 c.87.1.8 105140 1vj0A 380 7.30e-01 b.35.1.2,c.2.1.1 100786,100787 1e5dA 402 7.45e-01 1e5dA c.23.5.1,d.157.1.3 31208,42061 1fcqA 350 7.46e-01 c.1.8.9 65006 1wdpA 495 7.63e-01 c.1.8.1 120907 1wcwA 261 7.64e-01 1m6jA 261 7.74e-01 c.1.1.1 78693 1jvbA 347 7.80e-01 b.35.1.2,c.2.1.1 77181,77182 1n4wA 504 7.83e-01 c.3.1.2,d.16.1.1 91676,91677 1zgzA 122 7.96e-01 c.23.1.1 125065 2akoA 251 8.06e-01 c.73.1.3 126923 1uf3A 228 8.11e-01 d.159.1.6 99317 1x6vA 630 8.23e-01 b.122.1.3,c.26.1.5,c.37.1.4 121755,121756,121757 1v6sA 390 8.32e-01 c.86.1.1 100424 4uagA 437 8.56e-01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1cb0A 283 8.62e-01 1cb0A c.56.2.1 33790 2cdnA 201 8.66e-01 c.37.1.1 130289 1neyA 247 8.71e-01 c.1.1.1 80449 1hkhA 279 8.75e-01 c.69.1.12 90628 1uuqA 440 8.86e-01 c.1.8.3 100015 1oyc 400 8.86e-01 1oyc 1v1aA 309 9.23e-01 c.72.1.1 100249 1npyA 271 9.39e-01 c.2.1.7,c.58.1.5 85995,85996 1othA 321 9.59e-01 1othA c.78.1.1,c.78.1.1 35260,35261 1orvA 728 9.59e-01 b.70.3.1,c.69.1.24 87354,87355 1ir6A 424 9.61e-01 c.107.1.2 71342 1vk3A 615 9.69e-01 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 1xx1A 285 9.70e-01 1mnaA 298 9.79e-01 c.69.1.22 79322 2cunA 410 1.01e+00 1yzyA 413 1.05e+00 c.146.1.1 124292 1va4A 279 1.10e+00 c.69.1.12 108458 2au3A 407 1.11e+00 2ajrA 331 1.15e+00 c.72.1.1 126892 1g3qA 237 1.16e+00 1hyqA c.37.1.10 60237 1kv5A 250 1.17e+00 c.1.1.1 73052 1jbwA 428 1.19e+00 c.59.1.2,c.72.2.2 62860,62861 1wzlA 585 1.20e+00 b.1.18.2,b.71.1.1,c.1.8.1 121513,121514,121515 1xewY 172 1.20e+00 1qhoA 686 1.21e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 2bsxA 253 1.23e+00 c.56.2.1 129128 1e0tA 470 1.25e+00 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1bf6A 291 1.25e+00 1pscA c.1.9.3 29065 2pgd 482 1.25e+00 2pgd 1zmdA 474 1.25e+00 1y81A 138 1.30e+00 c.2.1.8 122731 2azpA 318 1.30e+00 2fsjA 346 1.30e+00 c.55.1.12,c.55.1.12 134025,134026 1mrzA 293 1.31e+00 b.43.5.1,c.26.1.3 91452,91453 1gg4A 452 1.34e+00 1gg4A c.59.1.1,c.98.1.1,c.72.2.1 33957,58985,58986 2aq8A 269 1.34e+00 c.2.1.2 127166 1ihuA 589 1.35e+00 c.37.1.10,c.37.1.10 62394,62395 1gk8A 475 1.35e+00 c.1.14.1,d.58.9.1 65234,65235 1aky 221 1.35e+00 1zin 2bpqA 373 1.36e+00 1pyfA 312 1.36e+00 c.1.7.1 95334 2axpA 173 1.36e+00 c.37.1.1 127497 1ve6A 582 1.37e+00 b.69.7.2,c.69.1.33 113626,113627 1vbiA 344 1.40e+00 1vhh 162 1.41e+00 1vhh 1tp9A 162 1.42e+00 c.47.1.10 119306 1ec7A 446 1.42e+00 1bqg c.1.11.2,d.54.1.1 29218,38862 2f46A 156 1.43e+00 1eny 268 1.44e+00 1eny 2aeeA 211 1.44e+00 c.61.1.1 126620 1jftA 340 1.47e+00 a.35.1.5,c.93.1.1 66652,66653 1vk4A 298 1.48e+00 c.72.1.1 100850 1tzzA 392 1.49e+00 c.1.11.2,d.54.1.1 112896,112897 1x8gA 227 1.50e+00 d.157.1.1 114960 1uehA 253 1.50e+00 c.101.1.1 99259 1x8hA 228 1.50e+00 d.157.1.1 114961 1zq6A 359 1.50e+00 1wx1A 335 1.52e+00 1j1iA 296 1.55e+00 c.69.1.10 83977 2f6uA 234 1.57e+00 c.1.4.1 133061 1tqhA 247 1.57e+00 c.69.1.29 107225 2fv7A 331 1.60e+00 c.72.1.1 134197 1te2A 226 1.60e+00 c.108.1.6 106792 2frnA 278 1.63e+00 c.66.1.47 133993 1zczA 464 1.69e+00 c.24.1.3,c.97.1.4 124923,124924 1nmoA 247 1.70e+00 c.135.1.1 91980 1i39A 225 1.73e+00 1ekeA c.55.3.1 61585 1zkdA 387 1.73e+00 c.66.1.52 125184 1iirA 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