# List of top-scoring protein chains for t2k-100-30-alpha 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 1hgxA 183 6.84e-01 1tc1A c.61.1.1 34027 1mkp 144 7.10e-01 1vhrA c.45.1.1 32654 1fgxA 288 7.70e-01 1fgxA c.68.1.2 34508 1d8dA 377 8.46e-01 1ft1A a.118.6.1 19185 1jcrA 377 8.99e-01 a.118.6.1 66506 1j8wB 273 1.00e+00 c.68.1.2 66441 1fdi 715 1.08e+00 2napA b.52.2.2 26918 c.81.1.1 35326 2ae2A 260 1.09e+00 1bdb c.2.1.2 29945 1k9sA 237 1.13e+00 c.56.2.1 68359 2ezl 99 1.19e+00 2ezk a.4.1.2 16026 1ft1A 377 1.21e+00 1ft1A a.118.6.1 19186 1qbqA 333 1.33e+00 1ft1A a.118.6.1 19187 1ld8A 382 1.34e+00 1d2nA 272 1.35e+00 1d2nA c.37.1.13 32428 1qd9A 124 1.36e+00 1qu9A d.79.1.1 39758 1thm 279 1.39e+00 1gci c.41.1.1 32544 1zfjA 491 1.42e+00 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1ecpA 238 1.55e+00 1ecpA c.56.2.1 33775 1ja9A 274 1.56e+00 c.2.1.2 62817 1fdo 715 1.58e+00 2napA b.52.2.2 26917 c.81.1.1 35325 1nsf 273 1.62e+00 1d2nA c.37.1.13 32429 1jcqA 382 1.66e+00 a.118.6.1 66504 1cus 200 1.68e+00 1cex c.23.9.1 31287 1f0yA 302 1.69e+00 2hdhA a.100.1.3 18793 c.2.1.6 30197 1dmmA 131 1.71e+00 1opy d.17.4.3 38114 1ltsD 103 1.79e+00 3chbD b.40.2.1 24900 1pkp 150 1.82e+00 1pkp d.14.1.1 37551 d.50.1.2 38787 1ea2A 131 1.82e+00 d.17.4.3 64860 1efiD 103 1.95e+00 3chbD b.40.2.1 24870 1cex 214 2.01e+00 1cex c.23.9.1 31285 1djrD 103 2.01e+00 3chbD b.40.2.1 24865 1fj2A 232 2.27e+00 1auoA c.69.1.14 34720 1bi5A 389 2.32e+00 1bi5A c.95.1.2 35985 c.95.1.2 35986 2ezk 99 2.36e+00 2ezk a.4.1.2 16027 1jd1A 129 2.59e+00 1qu9A d.79.1.1 62890 1aa6 715 3.02e+00 2napA b.52.2.2 26916 c.81.1.1 35324 1geqA 248 3.13e+00 2tysA c.1.2.4 28589 1opy 131 3.23e+00 1opy d.17.4.3 38113 1oasA 322 3.23e+00 1oasA c.79.1.1 35293 1pjr 724 3.40e+00 1pjr c.37.1.13 32391 c.37.1.13 32392 1qu9A 128 3.52e+00 1qu9A d.79.1.1 39755 1qu9C 128 3.52e+00 1qu9A d.79.1.1 39757 1pdz 434 3.53e+00 4enl c.1.11.1 29215 d.54.1.1 38859 3chbD 104 3.78e+00 3chbD b.40.2.1 24970 2hdhA 293 3.78e+00 2hdhA a.100.1.3 18795 c.2.1.6 30199 1g2yA 32 3.83e+00 a.34.1.1 17003 1e0bA 68 3.86e+00 1e0bA d.9.2.2 37476 1b66A 140 3.96e+00 1b66A d.96.1.2 40657 1dbiA 280 4.07e+00 1gci c.41.1.1 32543 1k3fA 253 4.22e+00 c.56.2.1 68105 1cf2O 337 4.37e+00 1b7gO c.2.1.3 29994 d.81.1.1 39909 1je0A 236 4.44e+00 c.56.2.1 66581 1f6dA 376 4.67e+00 1f6dA c.87.1.3 35467 1b0nB 57 4.81e+00 1b0nB a.34.1.1 17002 1b4aA 149 5.10e+00 1b4aA a.4.5.3 16088 d.74.2.1 39721 1g60A 260 5.12e+00 1ekgA 127 5.18e+00 1dlxA d.82.2.1 40021 1dusA 194 5.19e+00 1dusA c.66.1.4 34182 1a4mA 349 5.44e+00 1a4mA c.1.9.1 29014 2ahjB 212 5.71e+00 2ahjB b.34.4.4 24599 2cmd 312 5.81e+00 2cmd c.2.1.5 30135 d.162.1.1 42102 1lx7A 253 5.84e+00 1ahjB 212 5.87e+00 2ahjB b.34.4.4 24601 1add 349 5.91e+00 1a4mA c.1.9.1 29020 2nsyA 271 5.98e+00 2nsyA c.26.2.1 31612 1mpyA 307 6.07e+00 1mpyA d.32.1.3 38508 d.32.1.3 38509 1i88A 389 6.25e+00 c.95.1.2 66070 c.95.1.2 66071 1agi 125 6.27e+00 7rsa d.5.1.1 37303 1fcjA 322 6.42e+00 1oasA c.79.1.1 35289 2matA 264 6.44e+00 1c24A d.127.1.1 41146 1nsyA 271 6.61e+00 2nsyA c.26.2.1 31614 1rpjA 288 6.70e+00 2dri c.93.1.1 35656 1aisA 182 6.73e+00 1ytbA d.129.1.1 41288 d.129.1.1 41289 1kqpA 271 7.05e+00 1jx4A 352 7.16e+00 e.8.1.5 67405 1ekeA 230 7.29e+00 1ekeA c.55.3.1 33572 1ftrA 296 7.29e+00 1ftrA d.58.33.1 39485 d.58.33.1 39486 1gtqA 140 7.31e+00 1b66A d.96.1.2 40661 1f44A 324 7.58e+00 a.60.9.1 64982 d.163.1.1 64983 1f93E 32 7.65e+00 1f93E a.34.1.1 17013 1h7nA 342 7.68e+00 1b4kA c.1.10.3 60726 1i86A 389 7.70e+00 c.95.1.2 66068 c.95.1.2 66069 1heuA 374 7.83e+00 2ohxA b.35.1.2 60979 c.2.1.1 60980 1ahtH 259 7.88e+00 5ptp 1c24A 263 8.27e+00 1c24A d.127.1.1 41148 1ih8A 271 8.64e+00 2nsyA c.26.2.1 62377 3pgm 241 8.76e+00 1qhfA c.60.1.1 33982 1qg8A 255 8.87e+00 1qg8A c.68.1.1 34505 1dmlA 319 9.09e+00 1dmlA d.131.1.2 41380 d.131.1.2 41381 1clqA 903 9.32e+00 1clqA c.55.3.5 33717 e.8.1.1 43006 1bm9A 122 9.32e+00 1bm9A a.4.5.7 16116 1ivhA 394 9.38e+00 3mdeA a.29.3.1 16608 e.6.1.1 42869 1mroA 548 9.67e+00 1mroA a.89.1.1 18525 d.58.31.2 39443 1a8y 367 9.83e+00 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 8abp 306 9.92e+00 8abp c.93.1.1 35647 1b4kA 337 9.99e+00 1b4kA c.1.10.3 29184 4pfk 319 1.01e+01 3pfk c.89.1.1 35582 1mjhB 162 1.01e+01 1mjhA c.29.1.2 31640 1aw5 326 1.01e+01 1b4kA c.1.10.3 29181 1cmiA 85 1.02e+01 1cmiA d.39.1.1 38551 1eyqA 222 1.03e+01 1eypA d.36.1.1 38534 8kme2 259 1.04e+01 1ucyE 1lba 146 1.06e+01 1lba d.118.1.1 41062 1rypE 242 1.06e+01 1rypE d.153.1.4 41936 1gajA 257 1.07e+01 1gajA c.37.1.12 60416 1h8dH 260 1.07e+01 5ptp 1hetA 374 1.08e+01 2ohxA b.35.1.2 60975 c.2.1.1 60976 1fjgC 239 1.09e+01 1fjfC d.52.3.1 38831 d.53.1.1 38839 1eb7A 323 1.09e+01 1eb7A a.3.1.5 59404 a.3.1.5 59405 1d9tA 289 1.09e+01 1deaA c.35.1.1 31767 1whsA 255 1.10e+01 1ivyA c.69.1.5 34649 1mjhA 162 1.10e+01 1mjhA c.29.1.2 31639 1edt 271 1.12e+01 2ebn c.1.8.5 28993 1qhhA 167 1.14e+01 1pjr c.37.1.13 32393 1gzgA 337 1.15e+01 1k2yX 463 1.16e+01 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 c.84.1.1 68066 1hjrA 158 1.17e+01 1hjrA c.55.3.6 33727 1ak1 310 1.18e+01 1ak1 c.92.1.1 35594 1jepA 222 1.22e+01 d.36.1.1 66612 1mla 309 1.22e+01 1mla c.19.1.1 31031 d.58.23.1 39383 1ak5 503 1.25e+01 1ak5 c.1.5.1 28639 1hufA 140 1.25e+01 1hufA d.195.1.1 61272 1ee2A 373 1.26e+01 2ohxA b.35.1.2 24663 c.2.1.1 29679 1qr6A 584 1.28e+01 1qr6A c.2.1.7 30293 c.58.1.3 33941 1j7xA 302 1.29e+01 c.14.1.2 66425 2cb5A 453 1.30e+01 3gcb d.3.1.1 37035 1ucyE 109 1.31e+01 1ucyE 1hbnA 549 1.34e+01 1mroA a.89.1.1 60898 d.58.31.2 60899 1ryp1 222 1.35e+01 1ryp1 1f4kA 122 1.37e+01 1bm9A a.4.5.7 59646 1fjgT 106 1.37e+01 1fjfT a.7.6.1 16338 2rusB 490 1.38e+01 1burA c.1.14.1 29385 d.58.9.1 39291 1ej2A 181 1.38e+01 1f9aA c.26.1.3 59414 1ew4A 106 1.39e+01 1ew4A d.82.2.1 40023 1hz6A 72 1.40e+01 2ptl d.15.7.1 61429 1aisB 200 1.40e+01 1aisB a.74.1.2 18384 a.74.1.2 18385 1qhsA 178 1.43e+01 1qhsA c.37.1.3 31938 1a2zA 220 1.46e+01 1a2zA c.56.4.1 33794 1repC 251 1.46e+01 1repC a.4.5.10 16125 a.4.5.10 16126 1qo2A 241 1.46e+01 1qo2A c.1.2.1 28533 2napA 723 1.49e+01 2napA b.52.2.2 26926 c.81.1.1 35334 1jjuA 489 1.49e+01 a.3.1.7 66774 a.3.1.7 66775 b.1.1.6 66776 b.1.1.6 66777 b.61.4.1 66778 1g6hA 257 1.50e+01 1gajA c.37.1.12 60318 1c5lH 259 1.57e+01 5ptp 1k51A 72 1.57e+01 d.15.7.1 68147 1jsdB 176 1.58e+01 h.3.1.1 63259 1imjA 210 1.58e+01 6pfkA 319 1.59e+01 3pfk c.89.1.1 35583 1qu6A 179 1.61e+01 1qu6A d.50.1.1 38784 d.50.1.1 38785 256bA 106 1.62e+01 256bA a.24.3.1 16539 3pfk 319 1.64e+01 3pfk c.89.1.1 35581 1skyB 502 1.64e+01 1skyB a.69.1.1 18313 b.49.1.1 26478 c.37.1.11 32358 9gafA 295 1.65e+01 1apyA d.153.1.5 42008 1mml 265 1.67e+01 1mml e.8.1.2 43015 1qi6A 475 1.68e+01 1euhA c.82.1.1 35373 1f9mA 112 1.70e+01 1erv c.47.1.1 32736 1yveJ 524 1.71e+01 1qmgA a.100.1.2 18790 c.2.1.6 30187 1jy5A 212 1.71e+01 1bdg 451 1.76e+01 1qhaA c.55.1.3 33461 c.55.1.3 33462 1jfuA 186 1.76e+01 c.47.1.10 62940 8adh 374 1.78e+01 2ohxA b.35.1.2 24690 c.2.1.1 29706 6ldh 330 1.81e+01 3ldh c.2.1.5 30161 d.162.1.1 42128 1e19A 314 1.82e+01 1b7bA c.73.1.1 34967 1mrg 263 1.83e+01 1mrj d.165.1.1 42183 5ldh 334 1.83e+01 3ldh c.2.1.5 30158 d.162.1.1 42125 1yveI 524 1.84e+01 1qmgA a.100.1.2 18789 c.2.1.6 30186 1e79A 510 1.84e+01 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1ek0A 170 1.85e+01 1ctqA c.37.1.8 32076 1whtA 256 1.88e+01 1ivyA c.69.1.5 34646 1k52A 72 1.92e+01 d.15.7.1 68148 1h6pA 203 1.92e+01 a.146.1.1 60690 1bo1A 416 1.93e+01 1bo1A d.143.1.2 41591 1aw0 72 1.94e+01 1aw0 d.58.17.1 39342 1ylvA 342 1.98e+01 1b4kA c.1.10.3 29180 1al3 324 1.98e+01 1al3 c.94.1.1 35835 2tmkA 216 1.99e+01 3tmkA c.37.1.1 31928 1eblA 317 2.00e+01 1hn9A c.95.1.1 35973 c.95.1.1 35974 1dofA 403 2.01e+01 1c3cA a.127.1.1 19429 1tib 269 2.03e+01 3tgl c.69.1.17 34738 1j4wA 174 2.03e+01 1aquA 297 2.04e+01 1aquA c.37.1.5 31942 1hn9A 317 2.04e+01 1hn9A c.95.1.1 35977 c.95.1.1 35978 1qmgA 524 2.06e+01 1qmgA a.100.1.2 18785 c.2.1.6 30182 1h8eA 510 2.06e+01 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1clxA 347 2.07e+01 1taxA c.1.8.3 28899 1dozA 309 2.07e+01 1ak1 c.92.1.1 35592 5rubA 490 2.09e+01 1burA c.1.14.1 29382 d.58.9.1 39288 1j5eC 239 2.10e+01 1eblB 317 2.10e+01 1hn9A c.95.1.1 35975 c.95.1.1 35976 1qhfA 240 2.13e+01 1qhfA c.60.1.1 33960 1jsmB 176 2.13e+01 h.3.1.1 63265 1qhxA 178 2.13e+01 1qhsA c.37.1.3 31936 1ihoA 283 2.14e+01 1ihoA c.26.1.4 62390 1ej0A 180 2.15e+01 1ej0A c.66.1.2 34179 1j5rA 371 2.17e+01 1eypA 222 2.19e+01 1eypA d.36.1.1 38536 1lqtA 456 2.19e+01 1euhA 475 2.21e+01 1euhA c.82.1.1 35369 1h6zA 913 2.22e+01 1hnjA 317 2.23e+01 1hn9A c.95.1.1 35969 c.95.1.1 35970 1hy0A 466 2.25e+01 1auwA a.127.1.1 61392 1fsiA 189 2.26e+01 1fsiA d.61.1.1 39536 1qpoA 284 2.26e+01 1qpoA c.1.17.1 29561 d.41.2.1 38597 1d3vA 323 2.27e+01 1d3vA c.42.1.1 32559 1io2A 213 2.27e+01 1ekeA c.55.3.1 62612 1d2mA 665 2.28e+01 1d2mA c.37.1.13 32417 c.37.1.13 32418 2ohxA 374 2.28e+01 2ohxA b.35.1.2 24669 c.2.1.1 29685 1f2dA 341 2.31e+01 1f2dA c.79.1.1 35298 2cpl 165 2.31e+01 2cpl b.62.1.1 27420 1rlaA 323 2.31e+01 1d3vA c.42.1.1 32561 1alu 186 2.33e+01 1alu a.26.1.1 16826 1b0uA 262 2.37e+01 1b0uA c.37.1.12 32370 1qjwA 365 2.37e+01 1bvwA c.6.1.1 30657 1php 394 2.37e+01 16pk c.86.1.1 35452 1apyB 141 2.39e+01 1apyB 1hme 77 2.41e+01 1cktA a.21.1.1 16418 1qvbA 481 2.43e+01 1qvbA c.1.8.4 28983 1dd9A 338 2.48e+01 1dd9A e.13.1.1 43254 1k77A 260 2.49e+01 1gpmA 525 2.49e+01 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 1jqeA 292 2.52e+01 1go3F 107 2.54e+01 a.60.8.2 65407 1vfrA 218 2.57e+01 1vfrA d.90.1.1 40247 1jeoA 180 2.58e+01 c.80.1.3 66611 1bmfA 510 2.58e+01 1skyB a.69.1.1 18281 b.49.1.1 26446 c.37.1.11 32326 1iibA 106 2.59e+01 1iibA c.44.2.1 32648 1cseE 274 2.59e+01 1gci c.41.1.1 32481 1ljrA 244 2.63e+01 1ljrA a.45.1.1 17707 c.47.1.5 33001 1crxA 322 2.66e+01 4crxA a.60.9.1 18097 d.163.1.1 42157 1lfdA 87 2.67e+01 1lfdA d.15.1.5 37622 1kf6D 119 2.68e+01 1i1gA 141 2.68e+01 a.4.5.32 65982 d.58.37.1 65983 1h5qA 265 2.69e+01 1cydA c.2.1.2 60643 1bq3B 246 2.70e+01 1qhfA c.60.1.1 33979 2gbp 309 2.72e+01 1gca c.93.1.1 35657 1a0i 348 2.72e+01 1a0i b.40.4.6 25363 d.142.2.1 41577 1m5sA 297 2.74e+01 1mat 264 2.75e+01 1c24A d.127.1.1 41152 1faaA 124 2.78e+01 1erv c.47.1.1 32738 1f0kA 364 2.79e+01 1f0kA c.87.1.2 35465 1maz 221 2.84e+01 1maz f.1.4.1 43393 1js1X 324 2.85e+01 2bc2A 227 2.88e+01 1a7tA d.157.1.1 42031 2bc2B 227 2.89e+01 1a7tA d.157.1.1 42032 1is2A 661 2.90e+01 1h6oA 204 2.93e+01 a.146.1.1 60689 2dri 271 2.96e+01 2dri c.93.1.1 35637 1e79D 482 2.98e+01 1skyE a.69.1.1 18272 b.49.1.1 26437 c.37.1.11 32317 2rveA 244 3.02e+01 1rvaA c.52.1.2 33283 1bkpA 278 3.08e+01 1bkpA d.117.1.1 41029 1i6wA 181 3.09e+01 1i6wA c.69.1.18 61859 5ukdA 194 3.11e+01 1zin c.37.1.1 31851 9ldtA 332 3.12e+01 3ldh c.2.1.5 30154 d.162.1.1 42121 3tmkA 216 3.12e+01 3tmkA c.37.1.1 31920 1h8eD 482 3.12e+01 1skyE a.69.1.1 60747 b.49.1.1 60748 c.37.1.11 60749 1hdfA 102 3.13e+01 1ag4 b.11.1.1 23627 1g7tA 594 3.18e+01 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1gjuA 637 3.22e+01 b.71.1.1 60580 c.1.8.1 60581 1cl1A 395 3.25e+01 1cl2A c.67.1.3 34395 1cwoA 165 3.28e+01 2cpl b.62.1.1 27445 1gjwA 637 3.32e+01 b.71.1.1 60582 c.1.8.1 60583 1iexA 605 3.32e+01 c.1.8.7 66127 c.23.11.1 66128 1gq6A 313 3.37e+01 1fs1B 141 3.38e+01 1vcbB a.122.1.1 19252 d.42.1.2 38664 1e4fT 419 3.40e+01 1e4fT c.55.1.1 33453 c.55.1.1 33454 1rec 201 3.41e+01 1rec a.39.1.5 17326 1jx6A 342 3.46e+01 c.93.1.1 67406 1dorA 311 3.47e+01 2dorA c.1.4.1 28595 1edoA 244 3.48e+01 1ybvA c.2.1.2 29896 1jb0D 138 3.52e+01 1jb0D d.187.1.1 62823 1hzpA 335 3.53e+01 1hn9A c.95.1.1 61455 c.95.1.1 61456 1g6oA 330 3.53e+01 1g6oA c.37.1.13 32430 1jkfA 533 3.57e+01 1i9sA 210 3.60e+01 1i9sA c.45.1.1 62099 1hf2A 210 3.60e+01 1hf2A b.80.3.1 60992 c.102.1.1 60993 2dorA 311 3.61e+01 2dorA c.1.4.1 28593 1f06A 320 3.64e+01 1dapA c.2.1.3 59556 d.81.1.3 59557 1eaf 243 3.67e+01 1eaf c.43.1.1 32617 1jh6A 189 3.67e+01 d.61.1.1 66707 3cbh 365 3.67e+01 1bvwA c.6.1.1 30665 1k47A 337 3.70e+01 3pflA 759 3.71e+01 1cm5A c.7.1.1 30673 1hmt 132 3.73e+01 1hmt b.60.1.2 27169 1cm5A 759 3.78e+01 1cm5A c.7.1.1 30671 1esmA 316 3.83e+01 1esmA c.37.1.6 31953 1gu9A 177 3.84e+01 a.152.1.1 65540 1bwyA 132 3.85e+01 1hmt b.60.1.2 27172 2fokA 579 3.85e+01 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1d8cA 723 3.86e+01 1d8cA c.1.13.1 29325 1cseI 71 3.88e+01 1egpA d.40.1.1 38559 1eg5A 384 3.89e+01 1ecxA c.67.1.3 34429 1g72A 573 3.91e+01 4aahA b.70.1.1 27680 1jxmA 301 3.91e+01 b.34.2.1 67420 c.37.1.1 67421 1esgA 213 3.93e+01 1bam c.52.1.3 33286 1iirA 415 3.96e+01 1iirA c.87.1.5 62453 1ffkM 148 3.98e+01 1ffkM a.94.1.1 18740 1pyiA 96 3.99e+01 1pyiA g.38.1.1 45079 h.1.3.1 45512 1rypH 205 3.99e+01 d.153.1.4 41876 1gai 472 3.99e+01 1ayx a.102.1.1 18819