# List of top-scoring protein chains for t04-100-30-near-backbone-11 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 1pjqA 457 6.71e-37 c.2.1.11 -5904 c.90.1.1 -8611 e.37.1.1 -12004 1cbf 285 1.43e-33 1cbf c.90.1.1 35587 1vhvA 268 2.68e-24 c.90.1.1 -8619 1fsz 372 1.23e-04 1fsz c.32.1.1 31750 d.79.2.1 39802 4pfk 319 1.28e-03 3pfk c.89.1.1 35582 2pfkA 320 1.87e-03 3pfk c.89.1.1 35577 1oi7A 288 2.65e-02 c.2.1.8 87049 c.23.4.1 87050 1c0pA 363 4.18e-02 1an9A c.4.1.2 30647 d.16.1.3 37934 1pwhA 327 4.21e-02 c.79.1.1 -8524 1upaA 573 9.07e-02 c.31.1.3 -6745 c.36.1.5 -6903 c.36.1.9 -6943 1gca 309 1.04e-01 1gca c.93.1.1 35659 1j3vA 289 1.20e-01 a.100.1.1 -1303 c.2.1.6 -5947 1o4vA 183 1.51e-01 c.23.8.1 86628 1jvbA 347 1.93e-01 b.35.1.2 77181 c.2.1.1 77182 1cv2A 296 2.33e-01 1bn6A c.69.1.8 34680 1vkmA 297 2.34e-01 1ig8A 486 2.41e-01 2yhx c.55.1.3 64746 c.55.1.3 64747 1mwmA 320 2.45e-01 c.55.1.1 79580 c.55.1.1 79581 1uf5A 303 2.47e-01 1erzA 303 2.48e-01 1erzA d.160.1.2 59498 1ofuA 320 2.65e-01 c.32.1.1 86972 d.79.2.1 86973 1oaoA 674 2.73e-01 e.26.1.2 86744 1ns5A 155 2.75e-01 c.116.1.3 80705 1mv8A 436 2.89e-01 a.100.1.4 85128 c.2.1.6 85129 c.26.3.1 85130 1p5jA 372 2.97e-01 1cei 94 3.16e-01 1cei a.28.2.1 16939 1unkA 87 3.16e-01 1cei a.28.2.1 16935 1h2bA 359 3.62e-01 b.35.1.2 -3679 c.2.1.1 -5703 1b74A 254 4.43e-01 1b74A c.78.2.1 35264 c.78.2.1 35265 1o57A 291 4.45e-01 unknown_sccs -249 c.61.1.1 -7960 1bg6 359 4.59e-01 1bg6 a.100.1.5 18810 c.2.1.6 30214 1reqA 727 4.94e-01 1reqA c.1.19.1 29620 c.23.6.1 31247 1kq3A 376 5.01e-01 e.22.1.2 68790 1toaA 313 5.33e-01 1toaA c.92.2.2 35598 1v5wA 343 5.45e-01 1ad4A 266 6.11e-01 1aj2 c.1.21.1 29670 1k0fA 277 6.17e-01 c.92.2.2 71974 1mj5A 302 6.21e-01 c.69.1.8 -8326 1qycA 308 6.73e-01 c.2.1.2 -5782 1mtzA 293 7.43e-01 c.69.1.7 79467 1a3c 181 7.90e-01 1a3c c.61.1.1 34095 1pvdA 537 8.10e-01 1zpdA c.31.1.3 31737 c.36.1.5 31777 c.36.1.9 31778 1kaeA 434 8.48e-01 c.82.1.2 72247 1rvkA 382 9.07e-01 c.1.11.2 -5568 d.54.1.1 -9826 1iukA 140 9.20e-01 c.2.1.8 83712 1eudA 311 9.23e-01 2scuA c.2.1.8 30312 c.23.4.1 31140 1tn3 137 9.42e-01 1htn d.169.1.1 42423 1spxA 278 1.13e+00 c.2.1.2 -5870 1l3iA 192 1.23e+00 c.66.1.22 77676 5reqA 727 1.25e+00 1reqA c.1.19.1 29632 c.23.6.1 31259 1jq5A 370 1.31e+00 e.22.1.2 67084 1d3vA 323 1.37e+00 1d3vA c.42.1.1 32559 1km4A 247 1.46e+00 c.1.2.3 72740 1fpzA 212 1.46e+00 1fpzA c.45.1.1 59976 1e55A 512 1.48e+00 1e70M c.1.8.4 28934 1h49A 512 1.53e+00 c.1.8.4 83477 1vhnA 318 1.58e+00 c.1.4.1 -5209 1rxxA 421 1.59e+00 unknown_sccs -10982 1ad1A 266 1.60e+00 1aj2 c.1.21.1 29668 1f06A 320 1.73e+00 1dapA c.2.1.3 59556 d.81.1.3 59557 1n7kA 234 1.78e+00 c.1.10.1 85374 1khdA 345 1.87e+00 a.46.2.1 77400 c.27.1.1 77401 1avaA 403 1.89e+00 1jdc b.71.1.1 27797 c.1.8.1 28784 1uj6A 227 1.96e+00 1vkfA 188 1.99e+00 1pszA 303 2.05e+00 1toaA c.92.2.2 35600 1ewkA 490 2.06e+00 1ewkA c.93.1.1 35712 1knwA 425 2.13e+00 b.49.2.3 -4274 c.1.6.1 -5229 1j0aA 325 2.15e+00 c.79.1.1 83871 1nnlA 225 2.21e+00 c.108.1.4 85906 1a8q 274 2.24e+00 1brt c.69.1.12 34702 1g63A 181 2.29e+00 1g5qA c.34.1.1 60299 1eluA 390 2.30e+00 1elqA c.67.1.3 34434 1senA 164 2.30e+00 1ny1A 240 2.39e+00 c.6.2.3 86395 1b5tA 275 2.41e+00 1b5tA c.1.23.1 29676 1uohA 226 2.45e+00 d.211.1.1 -9572 1dozA 309 2.46e+00 1ak1 c.92.1.1 35592 1v4vA 376 2.63e+00 c.87.1.3 -8583 1hgxA 183 2.67e+00 1tc1A c.61.1.1 34027 1bif 469 2.77e+00 1bif c.37.1.7 31961 c.60.1.4 34003 1i7qB 193 2.87e+00 1qdlB c.23.16.1 61902 1bqcA 302 2.91e+00 1bqcA c.1.8.3 28831 1v93A 296 2.94e+00 c.1.23.1 -5654 1vhcA 224 2.94e+00 c.1.10.1 -5488 1e4iA 447 3.08e+00 1e70M c.1.8.4 59225 1rk6A 496 3.09e+00 b.92.1.6 -5087 b.92.1.6 -5088 c.1.9.11 -5435 1elqA 390 3.09e+00 1elqA c.67.1.3 34436 1s72O 116 3.15e+00 1a8s 273 3.20e+00 1brt c.69.1.12 34710 1pvyA 227 3.26e+00 d.115.1.2 -10937 1snnA 227 3.31e+00 1dbwA 126 3.31e+00 1dbwA c.23.1.1 31095 1m7jA 484 3.32e+00 b.92.1.6 78732 b.92.1.6 78733 c.1.9.11 78734 1dvjA 246 3.32e+00 1dvjA c.1.2.3 28546 1gpmA 525 3.41e+00 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 1h9dB 134 3.47e+00 2jhbA b.54.1.1 60822 1ds1A 324 3.51e+00 1drtA b.82.2.2 28127 1vi9A 299 3.58e+00 c.72.1.5 -8393 1oltA 457 3.60e+00 unknown_sccs -5688 1v02A 565 3.62e+00 1jdpA 441 3.64e+00 c.93.1.1 62906 1bf6A 291 3.75e+00 1pscA c.1.9.3 29065 1fs5A 266 3.86e+00 unknown_sccs 65044 1tph1 247 3.93e+00 1amk 1s6yA 450 4.25e+00 1q7zA 566 4.31e+00 c.1.21.2 -5638 c.1.26.1 -5666 1p3wA 404 4.35e+00 c.67.1.3 87752 1nw3A 416 4.44e+00 c.66.1.31 86288 1amy 403 4.47e+00 1jdc b.71.1.1 27799 c.1.8.1 28786 1r71A 178 4.49e+00 1l4uA 176 4.63e+00 c.37.1.2 73568 1kao 167 4.64e+00 1ctqA c.37.1.8 32014 1mkyA 439 4.79e+00 c.37.1.8 79250 c.37.1.8 79251 d.52.5.1 79252 1gdeA 389 4.87e+00 c.67.1.1 60456 1pv5A 264 4.98e+00 unknown_sccs -10182 1umzA 278 5.12e+00 b.29.1.2 -3398 1a9xB 379 5.21e+00 1c3oB c.8.3.1 30732 c.23.16.1 31409 1rkxA 357 5.38e+00 c.2.1.2 -5770 1dhpA 292 5.59e+00 1dhpA c.1.10.1 29097 1vk3A 615 5.84e+00 d.79.4.1 -10416 d.79.4.1 -10417 d.139.1.1 -11154 d.139.1.1 -11155 1jwiB 125 6.36e+00 d.169.1.1 67384 5rubA 490 6.39e+00 1burA c.1.14.1 29382 d.58.9.1 39288 2liv 344 6.62e+00 2liv c.93.1.1 35708 1qopA 268 6.63e+00 2tysA c.1.2.4 28570 1qs0B 338 6.63e+00 1qs0B c.36.1.7 31830 c.48.1.2 33103 1eyeA 280 6.95e+00 1aj2 c.1.21.1 29672 1kjqA 391 6.99e+00 b.84.2.1 72616 c.30.1.1 72617 d.142.1.2 72618 1pv9A 348 7.04e+00 c.55.2.1 -7610 d.127.1.1 -11000 1neyA 247 7.08e+00 c.1.1.1 80449 1jclA 260 7.10e+00 c.1.10.1 66501 1gdhA 320 7.20e+00 1gdhA c.2.1.4 30095 c.23.12.1 31355 1k1aA 241 7.37e+00 d.211.1.1 67992 1qydA 313 7.46e+00 c.2.1.2 -5786 1tx4B 178 7.52e+00 1ctqA c.37.1.8 32045 1kmqA 184 7.53e+00 c.37.1.8 84412 1nf2A 268 7.62e+00 c.108.1.10 -6842 1gpjA 404 7.73e+00 a.151.1.1 65451 c.2.1.7 65452 d.58.39.1 65453 1nhs 447 7.93e+00 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1k7jA 206 7.95e+00 d.115.1.1 72103 1hjzA 192 8.01e+00 c.50.1.2 83520 1q1rA 431 8.04e+00 c.3.1.5 -6048 c.3.1.5 -6049 d.87.1.1 -10502 1khcA 147 8.05e+00 b.34.9.2 68608 1ou0A 207 8.14e+00 c.23.17.1 -6498 1ftrA 296 8.33e+00 1ftrA d.58.33.1 39485 d.58.33.1 39486 3rabA 169 8.36e+00 1ctqA c.37.1.8 32018 1ht6A 405 8.44e+00 b.71.1.1 83629 c.1.8.1 83630 1usgA 346 8.52e+00 c.93.1.1 -8635 1m3uA 264 8.59e+00 c.1.12.8 84784 1p1xA 260 8.59e+00 1a4mA 349 8.59e+00 1a4mA c.1.9.1 29014 1juvA 193 8.61e+00 c.71.1.1 -8363 1f0xA 571 8.74e+00 1f0xA d.58.32.2 39483 d.145.1.1 41746 1f2dA 341 8.87e+00 1f2dA c.79.1.1 35298 1ptmA 329 8.88e+00 unknown_sccs -8456 1n2sA 299 9.14e+00 c.2.1.2 79857 1hd7A 318 9.14e+00 1bix d.151.1.1 41780 1va4A 279 9.17e+00 1o4sA 389 9.35e+00 c.67.1.1 86620 1q1gA 276 9.38e+00 c.56.2.1 -7846 1d2eA 397 9.50e+00 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1ve9A 347 9.61e+00 c.4.1.2 -6056 d.16.1.3 -9214 1k1xA 659 9.69e+00 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1lj8A 493 9.80e+00 a.100.1.9 78033 c.2.1.6 78034 1ohvA 472 9.90e+00 c.67.1.4 -8181 1dxy 333 1.02e+01 1dxy c.2.1.4 30094 c.23.12.1 31354 1khvA 516 1.03e+01 e.8.1.4 68627 1g60A 260 1.03e+01 c.66.1.11 70151 1db3A 372 1.04e+01 1db3A c.2.1.2 29813 1ijbA 202 1.06e+01 c.62.1.1 71229 1bfd 528 1.06e+01 1bfd c.31.1.3 31745 c.36.1.5 31801 c.36.1.9 31802 1nhyA 219 1.08e+01 a.45.1.1 80520 c.47.1.5 80521 1jb3A 131 1.09e+01 1jc7A b.40.3.2 62833 1a99A 344 1.09e+01 1pot c.94.1.1 35812 1fnsA 196 1.09e+01 1auq c.62.1.1 34136 1ll7A 392 1.11e+01 c.1.8.5 78085 d.26.3.1 78086 1u02A 239 1.11e+01 1nhp 447 1.12e+01 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1r0vA 305 1.12e+01 c.52.2.1 -7572 c.52.2.1 -7573 d.75.1.1 -10344 1o54A 277 1.13e+01 c.66.1.13 -8095 1mw7A 240 1.13e+01 e.39.1.1 79557 1l6rA 227 1.15e+01 c.108.1.10 77768 1augA 215 1.18e+01 1a2zA c.56.4.1 33798 1uirA 314 1.18e+01 c.66.1.17 -8114 1je8A 82 1.19e+01 a.4.6.2 77108 1ma3A 253 1.21e+01 c.31.1.5 78883 1o66A 275 1.22e+01 c.1.12.8 -5590 1e4fT 419 1.22e+01 1e4fT c.55.1.1 33453 c.55.1.1 33454 1gcuA 295 1.23e+01 1gcuA c.2.1.3 30063 d.81.1.4 39978 1krhA 338 1.24e+01 b.43.4.2 72891 c.25.1.2 72892 d.15.4.2 72893 1a8p 258 1.26e+01 1fdr b.43.4.2 25654 c.25.1.1 31544 1b0pA 1231 1.27e+01 c.36.1.8 31831 c.36.1.12 31832 c.48.1.3 33104 c.64.1.1 34157 d.58.1.5 39003 1i1qB 192 1.30e+01 1qdlB c.23.16.1 61544 1pyfA 312 1.31e+01 c.1.7.1 -5251 1vjgA 218 1.34e+01 unknown_sccs -6447 1ezvA 430 1.34e+01 1be3A d.185.1.1 59541 d.185.1.1 59542 1rlhA 173 1.34e+01 unknown_sccs -10786 1hdoA 206 1.35e+01 1he2A c.2.1.2 60965 1vhuA 211 1.38e+01 c.50.1.2 -7934 1qdeA 224 1.38e+01 1qvaA c.37.1.19 32410 1q9iA 571 1.40e+01 a.138.1.3 -2051 c.3.1.4 -6041 d.168.1.1 -11607 1q0rA 298 1.42e+01 unknown_sccs -8330 1qxyA 252 1.45e+01 d.127.1.1 -10993 1php 394 1.46e+01 16pk c.86.1.1 35452 1teaA 299 1.50e+01 1jf8A 131 1.50e+01 c.44.1.1 66621 1d2kA 392 1.51e+01 1d2kA c.1.8.5 29008 d.26.3.1 38442 1t2aA 375 1.51e+01 c.2.1.2 -5764 1pjr 724 1.53e+01 1pjr c.37.1.19 32391 c.37.1.19 32392 1mmsA 140 1.57e+01 1mmsA a.4.7.1 16247 d.47.1.1 38766 1b5qA 472 1.61e+01 1b37B c.3.1.2 30404 d.16.1.5 37968 1rz3A 201 1.61e+01 c.37.1.6 -7048 1i45A 248 1.62e+01 1amk c.1.1.1 61665 1eyzA 392 1.62e+01 1ez1A b.84.2.1 28246 c.30.1.1 31653 d.142.1.2 41498 1jpmA 366 1.63e+01 c.1.11.2 67031 d.54.1.1 67032 1jdc 429 1.63e+01 1jdc b.71.1.1 27789 c.1.8.1 28776 1qfjA 232 1.69e+01 1qfjA b.43.4.2 25655 c.25.1.1 31545 2rslA 140 1.70e+01 2rslA c.53.1.1 33345 1puiA 210 1.73e+01 c.37.1.8 88292 1iibA 106 1.74e+01 1iibA c.44.2.1 32648 1udxA 416 1.74e+01 b.117.1.1 -3546 c.37.1.8 -7101 unknown_sccs -9009 1b6g 310 1.78e+01 1b6g c.69.1.8 34661 1m2kA 249 1.80e+01 c.31.1.5 84754 1tzbA 302 1.82e+01 1k4mA 213 1.83e+01 c.26.1.3 77258 1oywA 523 1.84e+01 unknown_sccs -270 c.37.1.19 -7209 c.37.1.19 -7210 1m3sA 186 1.85e+01 c.80.1.3 78573 1m7bA 184 1.86e+01 c.37.1.8 74572 1rw7A 243 1.87e+01 c.23.16.2 -6530 1tmy 120 1.87e+01 1dbwA c.23.1.1 31083 1v6fA 151 1.87e+01 1qwgA 251 1.90e+01 unknown_sccs -5678 1dbtA 239 1.92e+01 1dbtA c.1.2.3 28539 1o6dA 163 1.92e+01 c.116.1.3 -6689 1gp6A 356 1.93e+01 b.82.2.1 65441 1jl3A 139 1.97e+01 c.44.1.1 66826 2lbp 346 2.00e+01 2liv c.93.1.1 35709 1lqtA 456 2.00e+01 c.3.1.1 74198 c.4.1.1 74199 1e8cA 498 2.01e+01 c.98.1.1 59377 c.59.1.1 59378 c.72.2.1 59379 1ii7A 333 2.01e+01 1ii7A d.159.1.4 62415 1an9A 340 2.02e+01 1an9A c.4.1.2 30617 d.16.1.3 37904 1hr6A 475 2.03e+01 1hr6A d.185.1.1 61164 d.185.1.1 61165 1to6A 371 2.06e+01 1vjnA 220 2.06e+01 unknown_sccs -11458 1qhfA 240 2.08e+01 1qhfA c.60.1.1 33960 1kb9A 431 2.08e+01 d.185.1.1 77311 d.185.1.1 77312 1ton 235 2.09e+01 5ptp b.47.1.2 26307 1kwmA 402 2.09e+01 c.56.5.1 73079 d.58.3.1 73080 1q8iA 783 2.10e+01 c.55.3.5 -7635 e.8.1.1 -11885 1kekA 1231 2.12e+01 c.36.1.8 68524 c.36.1.12 68525 c.48.1.3 68526 c.64.1.1 68527 d.58.1.5 68528 1lyxA 248 2.12e+01 c.1.1.1 78304 1qv9A 283 2.14e+01 unknown_sccs -6888 1jo0A 98 2.15e+01 d.68.4.1 77140 1vizA 240 2.16e+01 c.1.4.1 -5212 1fl1A 230 2.17e+01 1at3A b.57.1.1 27023 1pmi 440 2.17e+01 1pmi b.82.1.3 28114 1lh0A 213 2.18e+01 c.61.1.1 73896 1plq 258 2.18e+01 1plq d.131.1.2 41388 d.131.1.2 41389 1e3dA 266 2.19e+01 2frvA e.19.1.1 59188 2madH 373 2.19e+01 2bbkH b.69.2.1 27639 1r85A 379 2.21e+01 1ujnA 348 2.25e+01 e.22.1.1 -11998 1q5qA 259 2.25e+01 d.153.1.4 -11433 1o60A 292 2.26e+01 c.1.10.4 -5549 2fcr 173 2.30e+01 1rcf c.23.5.1 31151 1uc2A 481 2.30e+01 unknown_sccs -11725 1ag9A 175 2.31e+01 1rcf c.23.5.1 31178 1ipaA 274 2.31e+01 c.116.1.1 71254 d.79.3.3 71255 1fcjA 322 2.34e+01 1oasA c.79.1.1 35289 1gzgA 337 2.43e+01 c.1.10.3 70805 1f6dA 376 2.44e+01 1f6dA c.87.1.3 35467 1fkx 349 2.44e+01 1a4mA c.1.9.1 29018 1pujA 282 2.47e+01 c.37.1.8 88294 1aa8A 347 2.48e+01 1an9A 1el5A 389 2.48e+01 1b3mA c.3.1.2 30369 d.16.1.3 37937 1ek0A 170 2.50e+01 1ctqA c.37.1.8 32076 1e6wA 260 2.50e+01 1e6wA c.2.1.2 59326 1v7wA 807 2.53e+01 1h75A 81 2.56e+01 1h75A c.47.1.1 60716 3tmkA 216 2.56e+01 3tmkA c.37.1.1 31920 1m65A 245 2.63e+01 c.6.3.1 84847 7odcA 424 2.63e+01 7odcA b.49.2.3 26488 c.1.6.1 28650 1rpxA 230 2.67e+01 1rpxA c.1.2.2 28536 1qbjA 81 2.70e+01 1qbjA a.4.5.19 16155 1o5xA 248 2.71e+01 c.1.1.1 -5157 1d1gA 168 2.71e+01 1d1gA c.71.1.1 34889 1ra9 159 2.72e+01 1vdrA c.71.1.1 34820 1hxhA 253 2.72e+01 c.2.1.2 76725 1l8nA 679 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