# List of top-scoring protein chains for t04-100-30-stride-ebghtl 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 1ush 550 7.05e-24 1ush d.114.1.1 40923 d.159.1.2 42079 1hp1A 516 7.98e-24 d.114.1.1 70976 d.159.1.2 70977 1ii7A 333 5.97e-08 1ii7A d.159.1.4 62415 1kbpA 432 4.40e-07 4kbpA b.1.12.1 22349 d.159.1.1 42068 4kbpA 432 5.56e-07 4kbpA b.1.12.1 22345 d.159.1.1 42064 1uteA 313 1.30e-06 1uteA d.159.1.1 42078 1b74A 254 5.12e-03 1b74A c.78.2.1 35264 c.78.2.1 35265 2pfkA 320 1.29e-02 3pfk c.89.1.1 35577 1b1cA 181 1.76e-02 1amoA c.23.5.2 31212 1h65A 270 3.47e-02 c.37.1.8 65640 1eqjA 511 4.10e-02 1ejjA c.105.1.1 59495 c.76.1.3 59496 1o98A 511 4.72e-02 c.105.1.1 86684 c.76.1.3 86685 1ojxA 263 5.59e-02 1r7aA 504 6.21e-02 7odcA 424 6.41e-02 7odcA b.49.2.3 26488 c.1.6.1 28650 1ja1A 622 8.77e-02 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 4pfk 319 9.32e-02 3pfk c.89.1.1 35582 1f89A 291 1.01e-01 d.160.1.1 64988 1lfwA 470 1.09e-01 c.56.5.4 77942 d.58.19.1 77943 1bqcA 302 1.36e-01 1bqcA c.1.8.3 28831 1j7lA 264 1.83e-01 d.144.1.6 62697 1j9lA 247 2.52e-01 c.106.1.1 62762 1jflA 228 3.20e-01 c.78.2.1 71656 c.78.2.1 71657 1uf3A 228 3.72e-01 1ig3A 263 4.06e-01 1ig3A b.82.6.1 62358 c.100.1.1 62359 1qh5A 260 4.37e-01 1qh5A d.157.1.2 42057 1g0cA 364 4.38e-01 7a3hA c.1.8.3 60165 1k6dA 220 4.46e-01 c.63.1.2 72082 1fjmA 330 4.99e-01 1auiA d.159.1.3 42082 1h1nA 305 6.06e-01 c.1.8.3 70855 1jk7A 323 6.09e-01 1auiA d.159.1.3 63144 4pgaA 337 6.22e-01 4pgaA c.88.1.1 35565 1exbA 332 6.23e-01 1qrqA c.1.7.1 28666 1fmtA 314 6.39e-01 1fmtA b.46.1.1 25758 c.65.1.1 34174 1o0uA 429 6.44e-01 c.118.1.1 80743 1j31A 262 6.46e-01 1v02A 565 6.80e-01 1nvmA 345 7.05e-01 a.5.7.1 86249 c.1.10.5 86250 1dkuA 317 7.22e-01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1q9iA 571 7.22e-01 1m65A 245 7.26e-01 c.6.3.1 84847 1ihoA 283 7.74e-01 1ihoA c.26.1.4 62390 1k1xA 659 7.77e-01 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1mkyA 439 8.14e-01 c.37.1.8 79250 c.37.1.8 79251 d.52.5.1 79252 1gr0A 367 8.15e-01 c.2.1.3 70379 d.81.1.3 70380 1usgA 346 8.79e-01 1gln 468 8.88e-01 1gln a.97.1.1 18752 c.26.1.1 31588 1ad1A 266 9.29e-01 1aj2 c.1.21.1 29668 1lwjA 441 9.40e-01 b.71.1.1 74303 c.1.8.1 74304 1e39A 571 1.04e+00 1qjdA a.138.1.3 19694 c.3.1.4 30431 d.168.1.1 42314 1chuA 540 1.05e+00 1chuA a.7.3.1 16325 c.3.1.4 30424 d.168.1.1 42307 1kssA 571 1.08e+00 a.138.1.3 72928 c.3.1.4 72929 d.168.1.1 72930 1fobA 334 1.12e+00 c.1.8.3 83255 1ad4A 266 1.14e+00 1aj2 c.1.21.1 29670 1eudB 396 1.24e+00 2scuB c.23.4.1 31150 d.142.1.4 41571 1ars 396 1.24e+00 1ajsA c.67.1.1 34287 1d7yA 408 1.26e+00 1d7yA c.3.1.5 30565 c.3.1.5 30566 d.87.1.1 40204 1k7jA 206 1.31e+00 d.115.1.1 72103 1czaN 917 1.37e+00 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1cr1A 296 1.46e+00 1cr1A c.37.1.11 32286 1rqpA 299 1.48e+00 1ak5 503 1.53e+00 1ak5 c.1.5.1 28639 1o5zA 442 1.57e+00 1pyfA 312 1.67e+00 1ahxA 396 1.72e+00 1ajsA c.67.1.1 34293 1qisA 396 1.79e+00 1ajsA c.67.1.1 34284 1vjrA 271 1.89e+00 1zfjA 491 1.94e+00 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1d3gA 367 1.96e+00 1d3gA c.1.4.1 28600 1umdB 324 2.00e+00 1g5bA 221 2.02e+00 1g5bA d.159.1.3 60261 1d3vA 323 2.03e+00 1d3vA c.42.1.1 32559 1rpxA 230 2.04e+00 1rpxA c.1.2.2 28536 1lxiA 139 2.05e+00 g.17.1.2 84735 1jhdA 396 2.15e+00 b.122.1.3 66712 c.26.1.5 66713 1qh3A 260 2.16e+00 1qh5A d.157.1.2 42059 1i6pA 220 2.27e+00 1ddzA c.53.2.1 61848 1ezwA 349 2.31e+00 1ezwA c.1.16.3 29558 1srqA 341 2.31e+00 1ii2A 524 2.33e+00 c.91.1.1 66146 c.109.1.1 66147 1vkfA 188 2.36e+00 1o7jA 327 2.40e+00 c.88.1.1 81140 1pg4A 652 2.48e+00 e.23.1.1 88067 1auiA 521 2.51e+00 1auiA d.159.1.3 42085 1h09A 338 2.52e+00 b.109.1.1 83420 c.1.8.8 83421 1pt7A 437 2.53e+00 1bn7A 294 2.55e+00 1bn6A c.69.1.8 34677 1ps9A 671 2.60e+00 1jixA 351 2.66e+00 1c3jA c.87.1.1 63081 1fsz 372 2.69e+00 1fsz c.32.1.1 31750 d.79.2.1 39802 1g4wR 383 2.72e+00 1g4uS a.24.11.1 16644 c.45.1.2 32692 3pmgA 561 2.74e+00 3pmgA c.84.1.1 35408 c.84.1.1 35409 c.84.1.1 35410 d.129.2.1 41301 1deoA 233 2.75e+00 1deoA c.23.10.4 31345 1olsB 342 2.76e+00 1yasA 257 2.80e+00 1qj4A c.69.1.20 34801 1pvvA 315 2.81e+00 1jztA 246 2.86e+00 c.104.1.1 63319 1uumA 372 2.90e+00 1ek6A 348 2.95e+00 1xel c.2.1.2 29800 2fcr 173 2.97e+00 1rcf c.23.5.1 31151 1dtwB 342 2.98e+00 1qs0B c.36.1.7 31828 c.48.1.2 33102 1me8A 503 3.01e+00 c.1.5.1 79028 1ea7A 310 3.01e+00 c.41.1.1 70086 1e8cA 498 3.06e+00 c.98.1.1 59377 c.59.1.1 59378 c.72.2.1 59379 1uqtA 482 3.13e+00 1f9vA 347 3.19e+00 1bg2 c.37.1.9 59745 1gg4A 452 3.26e+00 1gg4A c.98.1.1 58985 c.59.1.1 33957 c.72.2.1 58986 1eceA 358 3.30e+00 1eceA c.1.8.3 28813 2tysA 268 3.34e+00 2tysA c.1.2.4 28572 1ni4B 341 3.37e+00 c.36.1.7 85729 c.48.1.2 85730 1rfmA 344 3.37e+00 1b25A 619 3.38e+00 1b25A a.110.1.1 19044 d.152.1.1 41796 1qj4A 257 3.40e+00 1qj4A c.69.1.20 34796 1mjhA 162 3.44e+00 1mjhA c.26.2.4 31639 1k92A 455 3.45e+00 c.26.2.1 68325 d.210.1.1 68326 1rzjG 321 3.53e+00 1n8fA 350 3.54e+00 c.1.10.4 85397 1gntA 553 3.58e+00 e.26.1.1 70290 1ecpA 238 3.60e+00 1ecpA c.56.2.1 33775 1bvyF 191 3.62e+00 1bvyF c.23.5.1 31207 1k7cA 233 3.67e+00 c.23.10.4 68267 1rvkA 382 3.72e+00 1icpA 376 3.74e+00 1oyc c.1.4.1 62270 1c3jA 351 3.76e+00 1c3jA c.87.1.1 35459 1e2uA 553 3.86e+00 1e1dA e.26.1.1 43362 1ccwB 483 3.90e+00 1cb7B c.1.19.2 29646 2liv 344 3.91e+00 2liv c.93.1.1 35708 1v1rB 342 3.95e+00 1rj9A 304 3.96e+00 1gteA 1025 4.01e+00 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 1k3rA 268 4.02e+00 b.40.4.10 72018 c.116.1.2 72019 1oygA 447 4.09e+00 1h7wA 1025 4.27e+00 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 1ispA 181 4.29e+00 c.69.1.18 76778 1at3A 247 4.37e+00 1at3A b.57.1.1 27021 1k7hA 476 4.44e+00 c.76.1.1 72101 1j4aA 333 4.52e+00 c.2.1.4 71502 c.23.12.1 71503 1vjjA 692 4.54e+00 1l8nA 679 4.57e+00 c.1.8.10 84564 d.92.2.2 84565 1rf6A 427 4.57e+00 1byb 495 4.59e+00 1byb c.1.8.1 28790 1ewqA 765 4.64e+00 1ewqA a.113.1.1 19069 c.37.1.12 32383 c.55.6.1 33740 d.75.2.1 39743 1qycA 308 4.66e+00 1k9sA 237 4.72e+00 c.56.2.1 68359 1k2yX 463 4.79e+00 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1a05A 358 4.85e+00 1cnzA c.77.1.1 35059 1djnA 729 4.88e+00 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 1g9mG 321 4.88e+00 1gc1G d.172.1.1 42492 1hzdA 272 4.89e+00 c.14.1.3 65969 1edg 380 4.90e+00 1edg c.1.8.3 28807 1vkhA 273 4.91e+00 5nul 138 4.91e+00 5nul c.23.5.1 31191 1iukA 140 4.92e+00 c.2.1.8 83712 1q6cA 495 4.95e+00 1puiA 210 4.97e+00 c.37.1.8 88292 1f4pA 147 4.98e+00 5nul c.23.5.1 59651 1i6wA 181 4.98e+00 1i6wA c.69.1.18 61859 1bf6A 291 5.14e+00 1pscA c.1.9.3 29065 1cbf 285 5.15e+00 1cbf c.90.1.1 35587 1p0kA 349 5.18e+00 c.1.4.1 87648 1l5xA 280 5.26e+00 c.106.1.1 77718 1ac5 483 5.29e+00 1ac5 c.69.1.5 34653 1fpzA 212 5.30e+00 1fpzA c.45.1.1 59976 1vhnA 318 5.33e+00 1vhwA 253 5.34e+00 1o60A 292 5.36e+00 1nd4A 264 5.38e+00 1igwA 434 5.43e+00 c.1.12.7 62370 1ek1A 554 5.62e+00 1cr6B c.108.1.2 43335 c.69.1.11 34685 1g2oA 268 5.64e+00 1b8oA c.56.2.1 60228 1lw6E 281 5.72e+00 c.41.1.1 74293 1vjnA 220 5.74e+00 1qs0B 338 5.83e+00 1qs0B c.36.1.7 31830 c.48.1.2 33103 1sup 275 5.89e+00 1gci c.41.1.1 32510 1rcuA 195 6.08e+00 1h1yA 228 6.25e+00 c.1.2.2 76506 1lc5A 364 6.27e+00 c.67.1.1 73827 1rk6A 496 6.27e+00 1p5dX 463 6.31e+00 1j7xA 302 6.41e+00 c.14.1.2 66425 1ed8A 449 6.42e+00 1b8jA c.76.1.1 34988 1rpnA 335 6.45e+00 1pbjA 125 6.51e+00 1e9lA 377 6.55e+00 1e9lA c.1.8.5 59395 d.26.3.1 59396 1r0wA 286 6.72e+00 1ir6A 424 6.74e+00 c.107.1.2 71342 1khdA 345 6.76e+00 a.46.2.1 77400 c.27.1.1 77401 1vizA 240 6.79e+00 1gg1A 350 6.84e+00 1qr7A c.1.10.4 29187 1lvwA 295 6.93e+00 c.68.1.6 84723 2lbp 346 7.01e+00 2liv c.93.1.1 35709 1gnxA 479 7.05e+00 c.1.8.4 76241 1m1nB 522 7.05e+00 c.92.2.3 78418 1vjoA 393 7.06e+00 1ayl 541 7.12e+00 1ayl c.91.1.1 64718 c.109.1.1 64719 1zpdA 568 7.28e+00 1zpdA c.31.1.3 31741 c.36.1.5 31785 c.36.1.9 31786 1r6xA 395 7.55e+00 1rewA 114 7.58e+00 1gpmA 525 7.59e+00 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 1ew2A 513 7.72e+00 1b8jA c.76.1.1 59525 1nnsA 326 7.74e+00 c.88.1.1 85910 1j8mF 297 7.80e+00 1ng1 a.24.13.1 62742 c.37.1.10 62743 1p4cA 380 7.91e+00 1j1uA 306 7.98e+00 c.26.1.1 83980 1bw0A 416 8.01e+00 1bw0A c.67.1.1 34385 1q7zA 566 8.03e+00 1fezA 256 8.08e+00 1fezA c.108.1.3 43343 1sixA 174 8.30e+00 1mv8A 436 8.49e+00 a.100.1.4 85128 c.2.1.6 85129 c.26.3.1 85130 1r3sA 367 8.50e+00 1uroA 367 8.51e+00 1uroA c.1.22.1 29675 1gq6A 313 8.57e+00 c.42.1.1 70341 1o94A 729 8.62e+00 c.1.4.1 81200 c.3.1.1 81201 c.4.1.1 81202 1uok 558 8.62e+00 1uok b.71.1.1 27801 c.1.8.1 28788 4uagA 437 8.64e+00 4uagA c.5.1.1 30651 c.59.1.1 33952 c.72.2.1 34955 1ku0A 388 8.65e+00 c.69.1.18 72994 1pwxA 254 8.67e+00 1pii 452 8.85e+00 1pii c.1.2.4 28559 c.1.2.4 28563 1ursA 402 8.90e+00 1g8mA 593 8.91e+00 1g8mA c.24.1.3 60371 c.97.2.1 60372 1g8lA 411 9.25e+00 1g8lA b.85.6.1 60365 b.103.1.1 60366 c.57.1.2 60367 1jakA 512 9.27e+00 c.1.8.6 66472 d.92.2.1 66473 1h8lA 380 9.30e+00 b.3.2.1 65737 c.56.5.1 65738 1r5yA 386 9.32e+00 1tmy 120 9.37e+00 1dbwA c.23.1.1 31083 1gnlA 544 9.40e+00 e.26.1.1 70287 1l8rA 101 9.40e+00 a.6.1.4 73700 1j09A 468 9.44e+00 a.97.1.1 77025 c.26.1.1 77026 2myr 501 9.50e+00 1v0wA 506 9.53e+00 1rhs 296 9.58e+00 1rhs c.46.1.2 32703 c.46.1.2 32704 1isiA 265 9.70e+00 e.4.1.1 71394 1f8gA 384 9.71e+00 1sayA c.2.1.4 59695 c.23.12.2 59696 1vhcA 224 9.74e+00 1m3uA 264 9.84e+00 c.1.12.8 84784 1od8A 313 9.86e+00 c.1.8.3 86838 1e0wA 313 9.86e+00 1taxA c.1.8.3 59150 1pvmA 184 9.93e+00 1fiuA 286 1.02e+01 1fiuA c.52.1.10 33317 1hp5A 512 1.02e+01 1hp4A c.1.8.6 61113 d.92.2.1 61114 1vjfA 180 1.02e+01 1hxhA 253 1.03e+01 c.2.1.2 76725 1hdoA 206 1.04e+01 1he2A c.2.1.2 60965 1j2rA 199 1.05e+01 1bykA 255 1.05e+01 1bykA c.93.1.1 35706 1m1nA 491 1.06e+01 c.92.2.3 78417 1kbjA 412 1.07e+01 c.1.4.1 72280 1mzjA 339 1.07e+01 c.95.1.1 79700 c.95.1.1 79701 1jf8A 131 1.07e+01 c.44.1.1 66621 1dbtA 239 1.09e+01 1dbtA c.1.2.3 28539 1qo2A 241 1.10e+01 1qo2A c.1.2.1 28533 1o6dA 163 1.10e+01 1sur 215 1.11e+01 1sur c.26.2.2 31620 1qw9A 502 1.11e+01 1h49A 512 1.11e+01 c.1.8.4 83477 1pixA 587 1.12e+01 1mq7A 154 1.13e+01 b.85.4.1 79404 1pxgA 382 1.13e+01 1f0iA 504 1.13e+01 1f0iA d.136.1.2 59566 d.136.1.2 59567 1f74A 293 1.13e+01 1nal3 c.1.10.1 29079 1rqlA 267 1.15e+01 1pswA 348 1.16e+01 c.87.1.7 88287 1ivnA 190 1.20e+01 c.23.10.5 83719 1o66A 275 1.21e+01 1m6kA 251 1.22e+01 e.3.1.1 78695 1dd9A 338 1.22e+01 1dd9A e.13.1.1 43254 1iso 416 1.24e+01 1iso c.77.1.1 35065 1jvnA 555 1.24e+01 c.1.2.1 67355 c.23.16.1 67356 1o5iA 249 1.25e+01 1azsA 220 1.25e+01 1azsA d.58.29.1 39416 1pud 386 1.25e+01 1pud c.1.20.1 29658 1cb0A 283 1.27e+01 1cb0A c.56.2.1 33790 1augA 215 1.28e+01 1a2zA c.56.4.1 33798 1dbiA 280 1.29e+01 1gci c.41.1.1 32543 1b4kA 337 1.30e+01 1b4kA c.1.10.3 29184 1dleA 298 1.30e+01 1dleA b.47.1.2 26312 1smd 496 1.31e+01 1smd b.71.1.1 27768 c.1.8.1 28755 1f0kA 364 1.32e+01 1f0kA c.87.1.2 35465 1o2dA 371 1.32e+01 e.22.1.2 86591 1pymA 295 1.33e+01 1pymA c.1.12.7 29308 1hx0A 496 1.33e+01 b.71.1.1 61346 c.1.8.1 61347 1oywA 523 1.33e+01 1f9aA 168 1.34e+01 1f9aA c.26.1.3 31602 1ll7A 392 1.34e+01 c.1.8.5 78085 d.26.3.1 78086 1goiA 499 1.35e+01 b.72.2.1 65413 c.1.8.5 65414 d.26.3.1 65415 1i74A 309 1.36e+01 1i74A c.107.1.1 61867 3tgl 269 1.37e+01 3tgl c.69.1.17 34733 1r61A 207 1.37e+01 1tif 78 1.38e+01 1tif d.15.8.1 37836 1l6rA 227 1.38e+01 c.108.1.10 77768 1gox 370 1.39e+01 1gox c.1.4.1 28607 1ass 159 1.40e+01 1a6dA c.8.5.2 30818 1byrA 155 1.41e+01 1byrA d.136.1.1 41450 1e55A 512 1.43e+01 1e70M c.1.8.4 28934 2plc 274 1.46e+01 2plc c.1.18.2 29614 1g6oA 330 1.48e+01 1g6oA c.37.1.11 32430 1uouA 474 1.48e+01 2tmdA 729 1.51e+01 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1f8mA 429 1.53e+01 1dquA c.1.12.7 29315 1uqrA 154 1.54e+01 1o4vA 183 1.55e+01 c.23.8.1 86628 1edt 271 1.56e+01 2ebn c.1.8.5 28993 1cf1A 404 1.56e+01 1cf1A b.1.18.11 21907 b.1.18.11 21908 1ceo 343 1.56e+01 1ceo c.1.8.3 28808 1rvgA 305 1.57e+01 1q7eA 428 1.57e+01 1pq4A 291 1.59e+01 1jxhA 288 1.60e+01 c.72.1.2 67415 1pkhA 204 1.61e+01 1d2kA 392 1.62e+01 1d2kA c.1.8.5 29008 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