# List of top-scoring protein chains for t04-100-30-str2 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 1souA 194 8.29e-25 1p80A 753 1.87e-02 c.23.16.3 -6547 e.5.1.1 -11840 1cf9A 753 1.89e-02 1cf9A c.23.16.3 31441 e.5.1.1 42815 1gteA 1025 8.03e-02 a.1.2.2 70440 c.1.4.1 70441 c.3.1.1 70442 c.4.1.1 70443 d.58.1.5 70444 1h7wA 1025 9.27e-02 1h7wA a.1.2.2 15683 c.1.4.1 28628 c.3.1.1 30324 c.4.1.1 30609 d.58.1.5 39007 1poiA 317 2.99e-01 1poiA unknown_sccs 34153 1hgxA 183 3.36e-01 1tc1A c.61.1.1 34027 1f8yA 157 3.58e-01 1f8xA c.23.14.1 31395 1rjdA 334 4.26e-01 unknown_sccs -8079 1b0uA 262 4.94e-01 1b0uA c.37.1.12 32370 1oxxK 353 5.97e-01 b.40.6.3 -3969 c.37.1.12 -7187 1p5dX 463 6.17e-01 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 1k2yX 463 6.38e-01 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1jeyB 565 6.53e-01 1jeqB unknown_sccs -4431 unknown_sccs -7995 1oxsC 353 7.43e-01 b.40.6.3 87519 c.37.1.12 87520 1lk5A 229 8.10e-01 unknown_sccs 73960 d.58.40.1 73961 1g2iA 166 8.43e-01 1g2iA c.23.16.2 31438 1dqwA 267 8.77e-01 1dqwA c.1.2.3 28551 1nhp 447 9.31e-01 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1gc5A 467 9.67e-01 1gc5A c.72.1.3 60429 1uj6A 227 1.19e+00 1vhqA 232 1.44e+00 c.23.16.2 -6514 1s2dA 167 1.56e+00 c.23.14.1 -6469 1u08A 386 1.63e+00 1usgA 346 2.06e+00 c.93.1.1 -8635 1omzA 293 2.08e+00 c.68.1.15 87093 1l2tA 235 2.14e+00 c.37.1.12 73514 1qh8A 478 2.16e+00 1qguA c.92.2.3 35633 1iukA 140 2.23e+00 c.2.1.8 83712 1nhs 447 2.30e+00 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1jq5A 370 2.35e+00 e.22.1.2 67084 2lbp 346 2.69e+00 2liv c.93.1.1 35709 1d3vA 323 2.81e+00 1d3vA c.42.1.1 32559 1v9fA 325 2.91e+00 1q7zA 566 3.11e+00 c.1.21.2 -5638 c.1.26.1 -5666 1rpxA 230 3.23e+00 1rpxA c.1.2.2 28536 1vi6A 208 3.47e+00 c.23.15.1 -6489 1dljA 402 3.56e+00 1dliA a.100.1.4 18808 c.2.1.6 30212 c.26.3.1 31621 1np6A 174 4.08e+00 c.37.1.10 85954 1mk4A 157 4.19e+00 d.108.1.1 84979 1tib 269 4.49e+00 3tgl c.69.1.17 34738 1auvA 311 4.61e+00 1auvA c.30.1.5 31723 d.142.1.3 41558 1fmcA 255 4.66e+00 1cydA c.2.1.2 29856 1ll7A 392 4.81e+00 c.1.8.5 78085 d.26.3.1 78086 1dmhA 311 5.31e+00 1dmhA b.3.6.1 22633 1iv8A 720 5.42e+00 b.71.1.1 76842 c.1.8.1 76843 1sv6A 269 5.68e+00 3tgl 269 5.73e+00 3tgl c.69.1.17 34733 1gt6A 269 5.97e+00 c.69.1.17 76342 1w2wB 191 6.05e+00 2liv 344 6.06e+00 2liv c.93.1.1 35708 1d2kA 392 6.22e+00 1d2kA c.1.8.5 29008 d.26.3.1 38442 1o8bA 219 6.28e+00 unknown_sccs 81180 d.58.40.1 81181 1vhoA 346 6.71e+00 unknown_sccs -4283 c.56.5.4 -7893 1vheA 373 6.79e+00 unknown_sccs -4280 c.56.5.4 -7890 1km4A 247 7.15e+00 c.1.2.3 72740 1ppjA 446 7.82e+00 1to6A 371 7.87e+00 1gcoA 261 7.90e+00 1ybvA c.2.1.2 29884 1geeA 261 7.90e+00 c.2.1.2 -5814 1dvjA 246 8.06e+00 1dvjA c.1.2.3 28546 1rtqA 299 8.07e+00 c.56.5.4 -7864 1dekA 241 8.13e+00 1dekA c.37.1.1 31842 1korA 400 8.23e+00 c.26.2.1 72824 d.210.1.1 72825 1g2qA 187 8.88e+00 c.61.1.1 65117 1m1nB 522 8.88e+00 c.92.2.3 78418 1pg4A 652 8.89e+00 e.23.1.1 88067 1l0lA 446 9.41e+00 d.185.1.1 84482 d.185.1.1 84483 1jvnA 555 9.49e+00 c.1.2.1 67355 c.23.16.1 67356 1lokA 291 9.85e+00 c.56.5.4 78122 1st9A 143 9.87e+00 c.47.1.10 -7503 1qopB 396 1.00e+01 2tysB c.79.1.1 35270 1s0aA 429 1.01e+01 c.67.1.4 -8201 1qj5A 429 1.06e+01 1dtyA c.67.1.4 34493 1vhtA 218 1.07e+01 c.37.1.1 -7004 1i7pA 274 1.07e+01 b.43.4.2 66048 c.25.1.1 66049 1onwA 390 1.08e+01 b.92.1.7 87172 c.1.9.13 87173 1p3wA 404 1.12e+01 c.67.1.3 87752 1mrzA 293 1.14e+01 b.43.5.1 -4048 c.26.1.3 -6616 1o4sA 389 1.16e+01 c.67.1.1 86620 1vicA 262 1.16e+01 c.68.1.13 -8252 1gu7A 364 1.17e+01 b.35.1.2 83321 c.2.1.1 83322 5nul 138 1.19e+01 5nul c.23.5.1 31191 1p1mA 406 1.20e+01 b.92.1.4 87696 c.1.9.9 87697 1gmiA 136 1.23e+01 b.7.1.1 65309 1ixkA 315 1.26e+01 unknown_sccs -8099 1qh8B 519 1.27e+01 1qguB c.92.2.3 35634 1eg7A 557 1.27e+01 1eg7A c.37.1.10 32241 1tltA 319 1.29e+01 1ua4A 455 1.31e+01 c.72.1.3 -8416 1pujA 282 1.33e+01 c.37.1.8 88294 3xis 387 1.35e+01 4xis c.1.15.3 29423 4xis 387 1.36e+01 4xis c.1.15.3 29421 1amp 291 1.36e+01 1amp c.56.5.4 33837 1v3vA 333 1.37e+01 1ls1A 295 1.41e+01 a.24.13.1 78170 c.37.1.10 78171 1ndh 272 1.45e+01 1ndh b.43.4.2 25662 c.25.1.1 31552 1kjnA 157 1.45e+01 c.115.1.1 72614 1bif 469 1.48e+01 1bif c.37.1.7 31961 c.60.1.4 34003 1onxA 390 1.49e+01 b.92.1.7 87176 c.1.9.13 87177 1dozA 309 1.51e+01 1ak1 c.92.1.1 35592 1h09A 338 1.51e+01 b.109.1.1 83420 c.1.8.8 83421 1cnv 299 1.52e+01 1cnv c.1.8.5 28989 1j6pA 418 1.53e+01 b.92.1.4 77089 c.1.9.9 77090 1qb7A 236 1.54e+01 1qb7A c.61.1.1 34087 1gegA 256 1.58e+01 1ybvA c.2.1.2 29888 1k87A 669 1.58e+01 a.176.1.1 77286 c.1.23.2 77287 1ka9H 200 1.58e+01 c.23.16.1 77308 1k3rA 268 1.59e+01 b.40.4.10 72018 c.116.1.2 72019 1hh1A 143 1.63e+01 1gefA c.52.1.18 61036 1jeoA 180 1.65e+01 c.80.1.3 66611 1uteA 313 1.65e+01 1uteA d.159.1.1 42078 1ja9A 274 1.65e+01 c.2.1.2 62817 1jfuA 186 1.65e+01 c.47.1.10 62940 1o7jA 327 1.66e+01 c.88.1.1 81140 1ecfA 504 1.69e+01 1ecfB c.61.1.1 34053 d.153.1.1 41820 4ubpC 570 1.70e+01 1ubpC b.92.1.1 28431 c.1.9.2 29053 1i50F 155 1.70e+01 d.78.1.2 61760 1qsgA 265 1.70e+01 1eny c.2.1.2 29935 1t64A 377 1.74e+01 1tmy 120 1.76e+01 1dbwA c.23.1.1 31083 1ass 159 1.77e+01 1a6dA c.8.5.2 30818 1a04A 215 1.77e+01 1a04A a.4.6.2 16234 c.23.1.1 31089 1a3c 181 1.87e+01 1a3c c.61.1.1 34095 2ng1 293 1.88e+01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1v84A 253 1.95e+01 1ixcA 294 1.96e+01 a.4.5.37 83764 c.94.1.1 83765 1e5dA 402 1.96e+01 1e5dA c.23.5.1 31208 d.157.1.3 42061 1m1nA 491 1.99e+01 c.92.2.3 78417 1l7mA 211 2.02e+01 c.108.1.4 73664 1nnhA 294 2.02e+01 d.104.1.1 -10772 1kqpA 271 2.02e+01 c.26.2.1 72883 1ih8A 271 2.02e+01 2nsyA c.26.2.1 62377 1qk8A 146 2.05e+01 1ewxA c.47.1.10 33061 4pgaA 337 2.07e+01 4pgaA c.88.1.1 35565 2hvm 273 2.11e+01 1cnv c.1.8.5 28985 1fp1D 372 2.13e+01 1fpqA a.4.5.29 59939 c.66.1.12 59940 1g291 372 2.13e+01 1g291 1muwA 386 2.14e+01 c.1.15.3 79495 1dmgA 225 2.15e+01 1dmgA c.22.1.1 31036 1fnsA 196 2.15e+01 1auq c.62.1.1 34136 1gg1A 350 2.16e+01 1qr7A c.1.10.4 29187 1b7gO 340 2.17e+01 1b7gO c.2.1.3 29992 d.81.1.1 39907 1hv9A 456 2.19e+01 1fwyA b.81.1.4 28060 c.68.1.5 34518 1uwzA 136 2.23e+01 1hp5A 512 2.23e+01 1hp4A c.1.8.6 61113 d.92.2.1 61114 1okgA 373 2.25e+01 c.46.1.2 -7367 c.46.1.2 -7368 unknown_sccs -9494 1pg5A 299 2.26e+01 1qstA 160 2.28e+01 1yghA d.108.1.1 40804 1n8fA 350 2.28e+01 c.1.10.4 85397 1gcuA 295 2.28e+01 1gcuA c.2.1.3 30063 d.81.1.4 39978 1e5eA 404 2.29e+01 1ibjA c.67.1.3 59265 1jakA 512 2.29e+01 c.1.8.6 66472 d.92.2.1 66473 1srrA 124 2.32e+01 1dz3A c.23.1.1 31110 1eg5A 384 2.33e+01 1ecxA c.67.1.3 34429 1n2eA 300 2.34e+01 c.26.1.4 85268 1ejxC 567 2.36e+01 b.92.1.1 83184 c.1.9.2 83185 2hpaA 342 2.39e+01 1cviA c.60.1.2 33985 1v88A 130 2.46e+01 1ijbA 202 2.52e+01 c.62.1.1 71229 1jd1A 129 2.55e+01 1qu9A d.79.1.1 62890 1sqgA 429 2.57e+01 1lwjA 441 2.58e+01 b.71.1.1 74303 c.1.8.1 74304 1o8xA 146 2.60e+01 c.47.1.10 86681 1jflA 228 2.63e+01 c.78.2.1 71656 c.78.2.1 71657 1j97A 211 2.70e+01 1f5sA c.108.1.4 62753 1guzA 310 2.71e+01 c.2.1.5 65586 d.162.1.1 65587 1d4fA 431 2.72e+01 1b3rA c.2.1.4 30110 c.23.12.3 31370 1nd6A 354 2.73e+01 c.60.1.2 80407 1dv1A 449 2.77e+01 1bncA b.84.2.1 28234 c.30.1.1 31641 d.142.1.2 41486 1fsz 372 2.78e+01 1fsz c.32.1.1 31750 d.79.2.1 39802 1vgyA 393 2.78e+01 c.56.5.4 -7882 d.58.19.1 -10106 1qgoA 264 2.78e+01 1qgoA c.92.1.2 35596 2ts1 419 2.78e+01 2ts1 c.26.1.1 31564 1ccwA 137 2.81e+01 1be1 c.23.6.1 31238 1tidB 119 2.82e+01 1gca 309 2.83e+01 1gca c.93.1.1 35659 1i60A 278 2.84e+01 c.1.15.4 71118 1c7gA 456 2.84e+01 c.67.1.2 -8153 1aop 497 2.85e+01 2aop d.58.36.1 39501 d.58.36.1 39502 d.134.1.1 41425 d.134.1.1 41426 1kwsA 261 2.86e+01 c.68.1.7 73083 1pswA 348 2.87e+01 c.87.1.7 88287 1vk4A 298 2.87e+01 c.72.1.1 -8414 3chy 128 2.87e+01 3chy c.23.1.1 31038 1nf2A 268 2.87e+01 c.108.1.10 -6842 1qd9A 124 2.92e+01 1qu9A d.79.1.1 39758 1iugA 352 2.96e+01 c.67.1.3 -8176 1gpmA 525 2.99e+01 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 1o59A 355 3.03e+01 unknown_sccs -3132 unknown_sccs -3133 1fukA 165 3.06e+01 1fukA c.37.1.19 32409 1g66A 207 3.08e+01 1bs9 unknown_sccs 31329 1uroA 367 3.18e+01 1uroA c.1.22.1 29675 1r3sA 367 3.19e+01 c.1.22.1 -5648 1lfwA 470 3.20e+01 c.56.5.4 77942 d.58.19.1 77943 1o69A 394 3.21e+01 c.67.1.4 -8209 1hq0A 295 3.24e+01 1hzgA d.194.1.1 61122 1v7zA 260 3.26e+01 unknown_sccs -6353 1k77A 260 3.26e+01 c.1.15.5 72096 1s3iA 310 3.27e+01 b.46.1.1 -4111 c.65.1.1 -8042 1psdA 409 3.28e+01 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1jf9A 408 3.32e+01 1c0nA c.67.1.3 62931 1svy 114 3.36e+01 1svy d.109.1.1 40831 1oaa 259 3.41e+01 1oaa c.2.1.2 29829 1fcjA 322 3.43e+01 1oasA c.79.1.1 35289 1jbeA 128 3.45e+01 3chy c.23.1.1 62845 1gqnA 252 3.48e+01 c.1.10.1 -5494 1wdkC 390 3.49e+01 1kpgA 287 3.52e+01 c.66.1.18 68735 1mdoA 393 3.55e+01 c.67.1.4 79013 1thm 279 3.57e+01 1gci c.41.1.1 32544 1ikpA 613 3.60e+01 b.29.1.7 66182 d.166.1.1 66183 f.1.5.1 66184 1kqzA 273 3.61e+01 c.1.8.5 68844 1sup 275 3.63e+01 1gci c.41.1.1 32510 1kq3A 376 3.64e+01 e.22.1.2 68790 1p5fA 189 3.70e+01 c.23.16.2 -6508 1onrA 316 3.70e+01 1onrA c.1.10.1 29169 1ea7A 310 3.75e+01 c.41.1.1 70086 1dkuA 317 3.78e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1o5zA 442 3.79e+01 c.59.1.2 -7939 c.72.2.2 -8418 1o57A 291 3.81e+01 unknown_sccs -249 c.61.1.1 -7960 1jtkA 136 3.81e+01 c.97.1.1 71862 1p4uA 153 3.83e+01 b.1.10.2 87780 1tk9A 188 3.86e+01 1cvrA 435 3.86e+01 1cvrA b.1.18.12 21949 c.17.1.2 31006 1r13A 148 3.90e+01 d.169.1.1 -11646 h.1.1.1 -12895 1nofA 383 3.91e+01 b.71.1.2 -4668 c.1.8.3 -5339 1ct9A 553 3.94e+01 1ct9A c.26.2.1 31616 d.153.1.1 41834