# List of top-scoring protein chains for t04-100-30-bys 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 1kllA 130 3.19e-10 d.32.1.2 72720 1f9zA 135 4.80e-07 1qipA d.32.1.1 38484 1fa8A 135 1.11e-06 1qipA d.32.1.1 38486 1ecsA 126 2.46e-06 1ecsA d.32.1.2 59407 1nkiA 135 7.44e-06 d.32.1.2 -9544 1lqpA 135 8.11e-06 d.32.1.2 78151 1lkdA 297 6.50e-05 d.32.1.3 78059 d.32.1.3 78060 1kw3B 292 7.76e-05 d.32.1.3 77549 d.32.1.3 77550 1han 297 9.94e-05 1han d.32.1.3 38506 d.32.1.3 38507 1r9cA 139 4.89e-04 d.32.1.2 -9557 1f1uA 323 5.60e-04 d.32.1.3 83200 d.32.1.3 83201 1qipA 183 5.91e-04 1qipA d.32.1.1 38470 1f1xA 322 1.22e-02 d.32.1.3 83208 d.32.1.3 83209 1jc4A 148 5.24e-02 1jc4A d.32.1.4 62863 1dynA 125 6.06e-02 1dynA b.55.1.1 26955 1bylA 125 2.24e-01 1bylA d.32.1.2 38495 1oywA 523 3.10e-01 unknown_sccs -270 c.37.1.19 -7209 c.37.1.19 -7210 1cjxA 357 3.17e-01 1cjxA d.32.1.3 38516 d.32.1.3 38517 1p1lA 102 3.24e-01 d.58.5.2 87695 1egiA 147 3.89e-01 1eggA d.169.1.1 42331 1heiA 451 4.28e-01 1heiA c.37.1.14 32463 c.37.1.14 32464 1uxy 340 4.47e-01 2mbr d.145.1.2 41748 d.146.1.1 41761 1opbA 135 4.88e-01 1hmt b.60.1.2 27216 1qtoA 122 5.60e-01 1bylA d.32.1.2 38494 1ne7A 289 6.95e-01 unknown_sccs -6858 1g9zA 152 7.08e-01 1bp7A d.95.2.1 60408 1tl2A 236 7.98e-01 1tl2A b.67.1.1 27541 1qlpA 394 9.63e-01 1ovaA e.1.1.1 42628 1uuzA 137 1.04e+00 d.233.1.1 -9478 1j5yA 187 1.10e+00 a.4.5.1 71592 d.94.2.1 71593 1ht6A 405 1.27e+00 b.71.1.1 83629 c.1.8.1 83630 1d9tA 289 1.34e+00 1deaA 1sjwA 144 1.35e+00 unknown_sccs -9296 1l6rA 227 1.37e+00 c.108.1.10 77768 1mngA 203 1.37e+00 1avmA a.2.11.1 15776 d.44.1.1 38701 1hkeA 137 1.39e+00 1r8sA 164 1.40e+00 c.37.1.8 -7082 1chd 203 1.43e+00 1chd c.40.1.1 32478 1ftrA 296 1.46e+00 1ftrA d.58.33.1 39485 d.58.33.1 39486 1qqgA 264 1.65e+00 1qqgA b.55.1.2 26987 b.55.1.2 26988 1vhyA 257 1.70e+00 b.122.1.2 -5129 c.116.1.5 -6705 1pvmA 184 2.08e+00 d.37.1.1 -9612 d.37.1.1 -9613 unknown_sccs -12799 1fukA 165 2.54e+00 1fukA c.37.1.19 32409 1bgvA 449 2.72e+00 1k89 c.2.1.7 30217 c.58.1.1 33865 1dxeA 256 2.75e+00 1dxeA c.1.12.5 29310 1f6yA 262 2.75e+00 1f6yA c.1.21.2 29673 1hskA 326 2.76e+00 2mbr d.145.1.2 61241 d.146.1.1 61242 1nqkA 381 2.76e+00 c.1.16.4 -5607 1lvaA 258 3.07e+00 a.4.5.35 74276 a.4.5.35 74277 a.4.5.35 74278 a.4.5.35 74279 1i9gA 280 3.13e+00 c.66.1.13 62090 1q7bA 244 3.13e+00 c.2.1.2 -5826 1q7hA 153 3.17e+00 b.122.1.1 -5124 unknown_sccs -9313 1fo4A 1332 3.22e+00 a.56.1.1 17910 d.15.4.2 37695 d.41.1.1 38586 d.87.2.1 40227 d.133.1.1 41416 d.145.1.3 41758 1fiqC 763 3.25e+00 1fiqC d.41.1.1 38588 d.133.1.1 41418 1v97A 1332 3.46e+00 1vjfA 180 3.92e+00 d.116.1.1 -10941 7aatA 401 3.93e+00 1ajsA c.67.1.1 34250 1oltA 457 3.96e+00 unknown_sccs -5688 1k20A 310 4.05e+00 c.107.1.1 68027 1uekA 275 4.46e+00 d.14.1.5 88483 d.58.26.5 88484 1ptf 88 4.51e+00 1ptf d.94.1.1 40549 1ezwA 349 4.97e+00 1ezwA c.1.16.3 29558 1g0oA 283 5.15e+00 1ybvA c.2.1.2 60181 1gkpA 458 5.20e+00 b.92.1.3 70231 c.1.9.6 70232 1top 162 5.28e+00 1ncx a.39.1.5 17223 1spxA 278 5.30e+00 c.2.1.2 -5870 1a8p 258 5.37e+00 1fdr b.43.4.2 25654 c.25.1.1 31544 2fmr 65 5.37e+00 2fmr d.51.1.1 38808 1ugpB 226 5.42e+00 1kr4A 125 5.43e+00 d.58.5.2 72889 1cf9A 753 5.54e+00 1cf9A c.23.16.3 31441 e.5.1.1 42815 1mu5A 471 5.55e+00 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1o1zA 234 5.99e+00 c.1.18.3 86555 1f6bA 198 6.01e+00 c.37.1.8 64986 1p80A 753 6.03e+00 c.23.16.3 -6547 e.5.1.1 -11840 1miwA 404 6.27e+00 a.173.1.1 79162 d.218.1.4 79163 1ub3A 220 6.46e+00 c.1.10.1 88395 1o3yA 166 6.48e+00 c.37.1.8 86618 1a0i 348 6.51e+00 1a0i b.40.4.6 25363 d.142.2.1 41577 1a8b 318 6.77e+00 1avc a.65.1.1 18171 1ckeA 227 6.79e+00 1ckeA c.37.1.1 31846 1ireB 228 6.80e+00 b.34.4.4 76770 1oh0A 131 6.88e+00 d.17.4.3 87004 1v61A 132 6.93e+00 1na3A 91 6.96e+00 k.38.1.1 85481 1mkiA 330 7.21e+00 e.3.1.2 84994 1f0iA 504 7.32e+00 1f0iA d.136.1.2 59566 d.136.1.2 59567 1o04A 500 7.43e+00 c.82.1.1 86508 1j3wA 163 7.59e+00 unknown_sccs -10870 1sphA 88 7.64e+00 1ptf d.94.1.1 40544 1oo0B 110 7.66e+00 d.58.7.1 87183 1hq0A 295 7.73e+00 1hzgA d.194.1.1 61122 1eazA 125 7.78e+00 b.55.1.1 70113 1mkeA 152 7.92e+00 b.55.1.4 79231 2ran 316 7.92e+00 1avc a.65.1.1 18170 1dp4A 435 8.00e+00 1dp4A c.93.1.1 35710 1vicA 262 8.04e+00 c.68.1.13 -8252 1ko7A 314 8.11e+00 c.98.2.1 72797 c.91.1.2 72798 1sn4A 64 8.21e+00 1aho g.3.7.1 44136 1ci9A 392 8.42e+00 e.3.1.1 64767 1ei6A 406 8.55e+00 unknown_sccs -8436 1byqA 228 8.56e+00 1yer d.122.1.1 41100 1bykA 255 8.70e+00 1bykA c.93.1.1 35706 2rslA 140 8.90e+00 2rslA c.53.1.1 33345 1a9xA 1058 8.96e+00 a.92.1.1 18550 c.24.1.1 31479 c.30.1.1 31657 c.30.1.1 31658 d.142.1.2 41502 d.142.1.2 41503 1q1gA 276 9.20e+00 c.56.2.1 -7846 1ollA 188 9.30e+00 b.1.1.4 -2690 b.1.1.4 -2691 1g5tA 196 9.33e+00 1g5rA c.37.1.11 32366 1oa4A 222 9.36e+00 b.29.1.11 86731 1jfuA 186 9.39e+00 c.47.1.10 62940 1q16B 512 9.39e+00 d.58.1.5 -9938 1szwA 379 9.40e+00 unknown_sccs -10164 1k66A 149 9.45e+00 c.23.1.1 -6406 1uc8A 280 9.61e+00 unknown_sccs -6718 unknown_sccs -11230 1qxoA 388 9.78e+00 unknown_sccs -11161 1xvaA 292 1.01e+01 1xvaA c.66.1.5 34183 1nxzA 246 1.04e+01 b.122.1.2 86391 c.116.1.5 86392 1fg7A 356 1.07e+01 1gewA c.67.1.1 59819 1i9zA 347 1.08e+01 1i9yA d.151.1.2 62102 1k3bA 119 1.11e+01 b.61.5.1 72016 1b8aA 438 1.13e+01 1b8aA b.40.4.1 25244 d.104.1.1 40765 1nqjA 119 1.14e+01 b.23.2.1 86031 1kyfA 247 1.16e+01 b.1.10.1 73220 d.105.1.1 73221 1ja9A 274 1.19e+01 c.2.1.2 62817 1l4dB 122 1.19e+01 d.15.5.1 77684 1h3nA 878 1.20e+01 a.27.1.1 76641 b.51.1.1 76642 c.26.1.1 76643 1pbyA 489 1.20e+01 a.3.1.7 -178 a.3.1.7 -179 b.1.18.14 -2762 b.1.18.14 -2763 b.61.4.1 -4528 1o0uA 429 1.21e+01 c.118.1.1 80743 1jkeA 145 1.22e+01 c.110.1.1 66791 2fokA 579 1.23e+01 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1ttzA 87 1.23e+01 1rkd 309 1.23e+01 1rkd c.72.1.1 34928 1n8jA 186 1.25e+01 c.47.1.10 85401 1o54A 277 1.25e+01 c.66.1.13 -8095 1nxiA 132 1.26e+01 d.58.47.1 86381 1nkqA 259 1.29e+01 1f7lA 121 1.31e+01 1f7lA d.150.1.2 59666 1eiwA 111 1.33e+01 1eiwA c.23.3.1 31130 1hrdA 449 1.37e+01 1k89 c.2.1.7 30219 c.58.1.1 33867 1go3F 107 1.38e+01 a.60.8.2 65407 1t4bA 367 1.41e+01 1rlkA 117 1.41e+01 unknown_sccs -7526 1ukuA 102 1.41e+01 d.58.5.2 -9992 1gewA 356 1.43e+01 1gewA c.67.1.1 60470 1v9kA 228 1.46e+01 1jykA 254 1.46e+01 c.68.1.13 67458 1uzcA 71 1.47e+01 a.159.2.1 -339 1gsoA 431 1.50e+01 1gsoA b.84.2.1 28240 c.30.1.1 31647 d.142.1.2 41492 1awqA 164 1.52e+01 2cpl b.62.1.1 27461 1o0wA 252 1.58e+01 a.149.1.1 80751 d.50.1.1 80752 1fxoA 293 1.59e+01 1g0rA c.68.1.6 34524 1hrhA 136 1.61e+01 1rthA c.55.3.1 33577 1ax4A 467 1.67e+01 1ax4A c.67.1.2 34391 1klxA 138 1.73e+01 a.118.18.1 77440 1p3jA 217 1.74e+01 c.37.1.1 -6996 g.41.2.1 -12769 1v04A 355 1.77e+01 unknown_sccs -4592 1gr3A 160 1.77e+01 b.22.1.1 65476 1cliA 345 1.80e+01 1cliA d.79.4.1 39816 d.139.1.1 41459 1uylA 236 1.80e+01 1mho 88 1.81e+01 1b4cA a.39.1.2 17171 2btfA 375 1.81e+01 1yagA c.55.1.1 33429 c.55.1.1 33430 1pba 81 1.81e+01 1pytA d.58.3.1 39067 1v0wA 506 1.82e+01 2ae2A 260 1.85e+01 1bdb c.2.1.2 29945 2liv 344 1.85e+01 2liv c.93.1.1 35708 1mi3A 322 1.87e+01 c.1.7.1 -5257 1naqA 112 1.88e+01 d.58.5.2 -9984 1nzaA 103 1.92e+01 d.58.5.2 86444 1g5hA 454 1.92e+01 1g5hA c.51.1.1 60270 d.104.1.1 60271 1uwvA 433 1.93e+01 unknown_sccs -3950 unknown_sccs -8107 1jjeA 222 1.93e+01 1a7tA d.157.1.1 63117 1qtsA 247 1.93e+01 1qtsA b.1.10.1 22313 d.105.1.1 40789 1k7kA 221 1.94e+01 c.51.4.1 72104 1v7rA 186 1.96e+01 c.51.4.1 -7546 2dpmA 284 1.97e+01 2dpmA c.66.1.28 34246 1qz9A 416 1.98e+01 c.67.1.3 -8180 1sr9A 644 1.98e+01 1ejdA 419 2.00e+01 1uae d.68.2.2 39576 1qnrA 344 2.01e+01 1qnoA c.1.8.3 28834 1e42A 258 2.01e+01 1e42A b.1.10.1 22316 d.105.1.1 40792 1rthA 560 2.01e+01 1rthA c.55.3.1 33576 e.8.1.2 43028 1lfpA 249 2.02e+01 e.39.1.1 73885 1g2iA 166 2.03e+01 1g2iA c.23.16.2 31438 1mo1A 87 2.04e+01 d.94.1.1 -10640 1brmA 367 2.08e+01 1brmA c.2.1.3 30030 d.81.1.1 39945 1kveB 77 2.10e+01 1kveB 1aozA 552 2.10e+01 1aozA b.6.1.3 23124 b.6.1.3 23125 b.6.1.3 23126 1fqtA 112 2.11e+01 1fqtA b.33.1.1 24441 1s72H 171 2.13e+01 1r4uA 301 2.13e+01 d.96.1.4 -10709 d.96.1.4 -10710 1c7gA 456 2.14e+01 c.67.1.2 -8153 1n6zA 105 2.16e+01 unknown_sccs 85369 2cblA 305 2.16e+01 2cblA a.39.1.7 17380 a.48.1.1 17774 d.93.1.1 40528 1qlaA 656 2.20e+01 1qlaA a.7.3.1 16328 c.3.1.4 30427 d.168.1.1 42310 1fviA 297 2.21e+01 1fviA b.40.4.6 25364 d.142.2.1 41578 1tiqA 180 2.21e+01 1ms9A 648 2.23e+01 b.29.1.15 85088 b.68.1.1 85089 1oe8A 211 2.26e+01 a.45.1.1 86905 c.47.1.5 86906 1ey4A 149 2.27e+01 1snc b.40.1.1 24815 1ho1A 242 2.29e+01 1ho1A c.1.24.1 61097 1i58A 189 2.32e+01 1b3qA d.122.1.3 61773 1jjtA 228 2.34e+01 1a7tA d.157.1.1 63139 1s5lB 510 2.38e+01 1iapA 211 2.38e+01 a.91.1.1 62119 1pj5A 830 2.39e+01 unknown_sccs -4066 c.3.1.2 -6031 d.16.1.5 -9251 unknown_sccs -10171 1f4lA 551 2.40e+01 1qqtA a.27.1.1 59648 c.26.1.1 59649 g.41.1.1 59650 1ru3A 732 2.42e+01 e.26.1.3 -12021 1b93A 152 2.42e+01 1b93A c.24.1.2 31507 1qwgA 251 2.44e+01 unknown_sccs -5678 1j77A 209 2.45e+01 1j77A a.132.1.2 62674 1hurA 180 2.45e+01 1hurA c.37.1.8 32052 1a3aA 148 2.49e+01 1a3aA d.112.1.1 40917 1vf7A 369 2.50e+01 1gtvA 214 2.50e+01 c.37.1.1 70537 1lylA 504 2.51e+01 1lylA b.40.4.1 25261 d.104.1.1 40717 1gz6A 319 2.52e+01 c.2.1.2 76410 1regX 122 2.54e+01 1regX d.58.27.1 39406 1q8rA 120 2.55e+01 unknown_sccs -10422 1nrwA 288 2.57e+01 c.108.1.10 86128 2cpl 165 2.59e+01 2cpl b.62.1.1 27420 1pfvA 551 2.60e+01 a.27.1.1 -727 c.26.1.1 -6603 g.41.1.1 -12765 1v88A 130 2.63e+01 1qjvA 342 2.64e+01 1qjvA b.80.1.5 28035 1p4wA 99 2.65e+01 a.4.6.2 87783 1pv5A 264 2.69e+01 unknown_sccs -10182 1pvtA 238 2.71e+01 c.74.1.1 -8444 1fvrA 327 2.80e+01 d.144.1.7 60047 1a05A 358 2.80e+01 1cnzA c.77.1.1 35059 1fi2A 201 2.81e+01 1fi2A b.82.1.2 59845 1pbgA 468 2.81e+01 1e70M c.1.8.4 28946 1kqzA 273 2.82e+01 c.1.8.5 68844 1t7pA 698 2.83e+01 1t7pA c.55.3.5 33712 e.8.1.1 43005 1s96A 219 2.85e+01 c.37.1.1 -6972 1j7gA 144 2.86e+01 c.110.1.1 84130 1pt7A 437 2.86e+01 c.123.1.1 -8762 1qyiA 384 2.87e+01 unknown_sccs -6836 1apyA 162 2.88e+01 1apyA d.153.1.5 42004 1vdwA 254 2.89e+01 e.7.1.1 -11868 1o97C 264 2.95e+01 c.26.2.3 81232 1uz5A 402 2.97e+01 b.85.6.1 -5029 b.103.1.1 -5069 c.57.1.2 -7902 1n0qA 93 2.97e+01 k.37.1.1 79754 1dd9A 338 2.97e+01 1dd9A e.13.1.1 43254 2hvm 273 2.98e+01 1cnv c.1.8.5 28985 1ecfA 504 3.02e+01 1ecfB c.61.1.1 34053 d.153.1.1 41820 1aisB 200 3.06e+01 1aisB a.74.1.2 18384 a.74.1.2 18385 1kqwA 134 3.07e+01 b.60.1.2 72887 1q7eA 428 3.07e+01 c.123.1.1 -8768 1qbjA 81 3.09e+01 1qbjA a.4.5.19 16155 1tpfA 250 3.12e+01 1amk c.1.1.1 28467 1v1rA 400 3.16e+01 1j6zA 376 3.23e+01 1yagA c.55.1.1 62667 c.55.1.1 62668 1brt 277 3.25e+01 1brt c.69.1.12 34699 1mr3F 181 3.29e+01 c.37.1.8 79422 1em8A 147 3.30e+01 unknown_sccs -7272 1gwmA 153 3.30e+01 b.18.1.19 83348 1anf 370 3.32e+01 4mbp c.94.1.1 35776 1go2A 304 3.34e+01 b.43.4.2 76243 c.25.1.1 76244 1uox 296 3.36e+01 1uox 1vjoA 393 3.36e+01 c.67.1.3 -8173 1b0uA 262 3.38e+01 1b0uA c.37.1.12 32370 1svpA 161 3.44e+01 1svpA b.47.1.3 26384 1drw 273 3.44e+01 1drw c.2.1.3 30057 d.81.1.3 39972 1lshA 1056 3.46e+01 a.118.4.1 74242 f.7.1.1 74243 f.7.1.1 74244 1t5eA 360 3.47e+01 1nnwA 252 3.49e+01 d.159.1.5 80674 1odkA 235 3.49e+01 c.56.2.1 86863 1opd 85 3.54e+01 1ptf d.94.1.1 40560 1aq0A 306 3.62e+01 1aq0A c.1.8.3 28842 1lurA 339 3.63e+01 b.30.5.4 84717 1vk3A 615 3.64e+01 d.79.4.1 -10416 d.79.4.1 -10417 d.139.1.1 -11154 d.139.1.1 -11155 1skoA 143 3.65e+01 1crb 134 3.68e+01 1hmt b.60.1.2 27220 1in0A 163 3.71e+01 d.58.49.1 83694 d.58.49.1 83695 1nkr 201 3.71e+01 1nkr b.1.1.4 21799 b.1.1.4 21800 1dfaA 454 3.74e+01 1vdeA b.86.1.2 28375 d.95.2.2 40575 d.95.2.2 40576 1ha1 184 3.77e+01 1ha1 d.58.7.1 39147 d.58.7.1 39148 1k0eA 453 3.79e+01 d.161.1.1 67938 1nv8A 284 3.79e+01 c.66.1.30 86224 1b8oA 284 3.81e+01 1b8oA c.56.2.1 33762 1qxrA 189 3.82e+01 b.82.1.7 -4834 2fcr 173 3.82e+01 1rcf c.23.5.1 31151 1fezA 256 3.83e+01 1fezA c.108.1.3 43343 1ble 163 3.84e+01 1ble c.38.1.1 32475 1f37A 110 3.85e+01 1f37A c.47.1.11 33088 1n7kA 234 3.86e+01 c.1.10.1 85374 1k9sA 237 3.91e+01 c.56.2.1 68359 1ja1A 622 3.96e+01 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1e1oA 504 3.96e+01 1lylA b.40.4.1 25258 d.104.1.1 40714 1kptA 105 3.99e+01 1kptA d.70.1.1 39588