# List of top-scoring protein chains for t2k-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 1kw3B 292 7.93e-04 d.32.1.3 77549 d.32.1.3 77550 1gdgA 293 1.39e-03 1dhy 292 3.93e-03 1han d.32.1.3 38504 d.32.1.3 38505 1lkdA 297 5.12e-03 d.32.1.3 78059 d.32.1.3 78060 1kllA 130 6.06e-03 d.32.1.2 72720 1han 297 6.29e-03 1han d.32.1.3 38506 d.32.1.3 38507 1lgtA 297 6.66e-03 d.32.1.3 77956 d.32.1.3 77957 1qqgA 264 4.09e-01 1qqgA b.55.1.2 26987 b.55.1.2 26988 1q1gA 276 7.81e-01 c.56.2.1 -7846 1egiA 147 7.92e-01 1eggA d.169.1.1 42331 1oltA 457 8.00e-01 unknown_sccs -5688 1dynA 125 8.60e-01 1dynA b.55.1.1 26955 1amoA 615 1.01e+00 1amoA b.43.4.1 25669 c.23.5.2 31210 c.25.1.4 31557 1g9zA 152 1.01e+00 1bp7A d.95.2.1 60408 1f9zA 135 1.04e+00 1qipA d.32.1.1 38484 8ohm 435 1.33e+00 1heiA c.37.1.14 32469 c.37.1.14 32470 1uuzA 137 1.37e+00 d.233.1.1 -9478 1f6bA 198 1.47e+00 c.37.1.8 64986 1q7bA 244 1.53e+00 c.2.1.2 -5826 1hkeA 137 1.54e+00 1eggA 147 1.58e+00 1eggA d.169.1.1 42333 2dynA 122 1.62e+00 1dynA b.55.1.1 26957 1uxy 340 1.73e+00 2mbr d.145.1.2 41748 d.146.1.1 41761 7aatA 401 1.76e+00 1ajsA c.67.1.1 34250 1r9cA 139 1.88e+00 d.32.1.2 -9557 1f20A 435 2.10e+00 b.43.4.1 64932 c.25.1.4 64933 2mbr 340 2.11e+00 2mbr d.145.1.2 41749 d.146.1.1 41762 1b2rA 304 2.12e+00 1fnc b.43.4.2 25648 c.25.1.1 31538 1heiA 451 2.14e+00 1heiA c.37.1.14 32463 c.37.1.14 32464 1go2A 304 2.24e+00 b.43.4.2 76243 c.25.1.1 76244 1bp7A 152 2.40e+00 1bp7A d.95.2.1 40568 1q16B 512 2.45e+00 d.58.1.5 -9938 1hl9A 449 2.62e+00 unknown_sccs -4694 unknown_sccs -5365 1lvaA 258 2.63e+00 a.4.5.35 74276 a.4.5.35 74277 a.4.5.35 74278 a.4.5.35 74279 1bykA 255 2.65e+00 1bykA c.93.1.1 35706 1fa8A 135 2.93e+00 1qipA d.32.1.1 38486 1j5yA 187 3.05e+00 a.4.5.1 71592 d.94.2.1 71593 1a8b 318 3.29e+00 1avc a.65.1.1 18171 1ftrA 296 3.54e+00 1ftrA d.58.33.1 39485 d.58.33.1 39486 1a8a 318 3.89e+00 1avc a.65.1.1 18169 1ogiA 303 3.93e+00 b.43.4.2 -4042 c.25.1.1 -6587 1qh0A 295 3.97e+00 b.43.4.2 68891 c.25.1.1 68892 1awqA 164 4.11e+00 2cpl b.62.1.1 27461 1uslA 170 4.16e+00 c.121.1.1 -6682 2ran 316 4.23e+00 1avc a.65.1.1 18170 1d2kA 392 4.53e+00 1d2kA c.1.8.5 29008 d.26.3.1 38442 1g2iA 166 4.59e+00 1g2iA c.23.16.2 31438 1q7hA 153 4.64e+00 b.122.1.1 -5124 unknown_sccs -9313 2dpmA 284 4.66e+00 2dpmA c.66.1.28 34246 1hl8A 449 4.71e+00 unknown_sccs -4690 unknown_sccs -5361 1ll7A 392 4.72e+00 c.1.8.5 78085 d.26.3.1 78086 1cwoA 165 4.72e+00 2cpl b.62.1.1 27445 1jc4A 148 4.81e+00 1jc4A d.32.1.4 62863 1que 303 4.87e+00 1fnc b.43.4.2 25647 c.25.1.1 31537 2cpl 165 5.23e+00 2cpl b.62.1.1 27420 1oywA 523 5.61e+00 unknown_sccs -270 c.37.1.19 -7209 c.37.1.19 -7210 1snc 149 5.62e+00 1snc b.40.1.1 24813 1fe0A 68 6.04e+00 1cc8A d.58.17.1 39345 1avc 673 6.53e+00 1avc a.65.1.1 18178 a.65.1.1 18179 1fukA 165 6.62e+00 1fukA c.37.1.19 32409 1opbA 135 6.88e+00 1hmt b.60.1.2 27216 1sty 150 7.41e+00 1snc b.40.1.1 24812 1p1lA 102 7.44e+00 d.58.5.2 87695 1anxA 319 7.62e+00 1avc a.65.1.1 18161 1jb1A 205 7.78e+00 1jb1A c.91.1.2 62832 1i9gA 280 7.81e+00 c.66.1.13 62090 1lrzA 426 8.03e+00 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1q9uA 130 8.06e+00 unknown_sccs -11025 1t4bA 367 8.53e+00 1af5 126 8.60e+00 1bp7A d.95.2.1 40572 1p5hA 428 9.01e+00 c.123.1.1 87802 1ey4A 149 9.11e+00 1snc b.40.1.1 24815 1hv8A 367 9.17e+00 1hv8A c.37.1.19 32405 c.37.1.19 32406 1mu5A 471 9.25e+00 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1n2zA 245 9.42e+00 c.92.2.2 79865 1eazA 125 9.60e+00 b.55.1.1 70113 1jotA 133 9.74e+00 1jotA 1g0oA 283 9.77e+00 1ybvA c.2.1.2 60181 1s96A 219 9.78e+00 c.37.1.1 -6972 1brmA 367 9.94e+00 1brmA c.2.1.3 30030 d.81.1.1 39945 1sbp 310 1.00e+01 1sbp c.94.1.1 35760 1qlpA 394 1.03e+01 1ovaA e.1.1.1 42628 1pj5A 830 1.06e+01 unknown_sccs -4066 c.3.1.2 -6031 d.16.1.5 -9251 unknown_sccs -10171 1n97A 389 1.08e+01 a.104.1.1 80335 1ybvA 283 1.10e+01 1ybvA c.2.1.2 29948 1dxeA 256 1.12e+01 1dxeA c.1.12.5 29310 1jjuA 489 1.12e+01 a.3.1.7 66774 a.3.1.7 66775 b.1.18.14 66776 b.1.18.14 66777 b.61.4.1 66778 1lr5A 163 1.12e+01 b.82.1.2 74215 1pswA 348 1.12e+01 c.87.1.7 88287 1mi0A 65 1.13e+01 d.15.7.1 79135 1e42A 258 1.13e+01 1e42A b.1.10.1 22316 d.105.1.1 40792 1kblA 873 1.13e+01 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1qd9A 124 1.15e+01 1qu9A d.79.1.1 39758 1ne7A 289 1.20e+01 unknown_sccs -6858 1o0wA 252 1.22e+01 a.149.1.1 80751 d.50.1.1 80752 1uzcA 71 1.24e+01 a.159.2.1 -339 1h6zA 913 1.30e+01 c.1.12.2 70906 c.8.1.1 70907 d.142.1.5 70908 1awsA 164 1.34e+01 2cpl b.62.1.1 27431 1jroB 777 1.35e+01 d.41.1.1 67141 d.133.1.1 67142 1ur3M 319 1.38e+01 c.1.7.1 -5248 1dik 874 1.40e+01 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 1ja1A 622 1.41e+01 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1ht6A 405 1.45e+01 b.71.1.1 83629 c.1.8.1 83630 1og6A 298 1.46e+01 c.1.7.1 86984 1bk5A 422 1.53e+01 1bk5A a.118.1.1 19130 3fruA 269 1.53e+01 1agdA b.1.1.2 20657 d.19.1.1 38150 1rthA 560 1.56e+01 1rthA c.55.3.1 33576 e.8.1.2 43028 1apyA 162 1.56e+01 1apyA d.153.1.5 42004 1h40A 71 1.57e+01 1nqjA 119 1.57e+01 b.23.2.1 86031 1b4aA 149 1.58e+01 1b4aA a.4.5.3 16088 d.74.2.1 39721 1eiwA 111 1.61e+01 1eiwA c.23.3.1 31130 1ewjA 126 1.62e+01 1ecsA d.32.1.2 59526 1hw1A 239 1.62e+01 1e2xA a.4.5.6 16111 a.78.1.1 18441 1lea 84 1.63e+01 1lea a.4.5.2 16085 1a8p 258 1.66e+01 1fdr b.43.4.2 25654 c.25.1.1 31544 1ecsA 126 1.71e+01 1ecsA d.32.1.2 59407 1b5l 172 1.71e+01 1b5l a.26.1.3 16900 1lqpA 135 1.71e+01 d.32.1.2 78151 1fg7A 356 1.71e+01 1gewA c.67.1.1 59819 1hq0A 295 1.72e+01 1hzgA d.194.1.1 61122 1bk6A 422 1.73e+01 1bk5A a.118.1.1 19133 1aq6A 253 1.74e+01 1qq5A c.108.1.1 43331 1pbyA 489 1.76e+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 1cliA 345 1.76e+01 1cliA d.79.4.1 39816 d.139.1.1 41459 1e2xA 243 1.77e+01 1e2xA a.4.5.6 16113 a.78.1.1 18443 1mveA 243 1.79e+01 b.29.1.2 85140 1cqxA 403 1.85e+01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1lrv 244 1.86e+01 1lrv a.118.1.5 19146 1hrhA 136 1.92e+01 1rthA c.55.3.1 33577 1bed 181 1.95e+01 1fvkA unknown_sccs -7444 1uctA 218 1.97e+01 b.1.1.4 88467 b.1.1.4 88468 1hvd 319 1.98e+01 1avc a.65.1.1 18154 1ee4A 423 1.99e+01 1ee4A a.118.1.1 19128 1yacA 208 1.99e+01 1yacA unknown_sccs 31757 1f0iA 504 2.07e+01 1f0iA d.136.1.2 59566 d.136.1.2 59567 1qbjA 81 2.13e+01 1qbjA a.4.5.19 16155 1f1uA 323 2.14e+01 d.32.1.3 83200 d.32.1.3 83201 1gewA 356 2.17e+01 1gewA c.67.1.1 60470 1jqeA 292 2.18e+01 c.66.1.19 71789 1r8sA 164 2.22e+01 c.37.1.8 -7082 1amz 435 2.24e+01 1csh a.103.1.1 18884 1o9wA 177 2.25e+01 b.2.3.5 86713 1k0gA 453 2.28e+01 d.161.1.1 67940 1ic8A 194 2.29e+01 a.4.1.1 76740 a.35.1.1 76741 1em8A 147 2.34e+01 unknown_sccs -7272 1gz6A 319 2.36e+01 c.2.1.2 76410 1d2gA 292 2.36e+01 1xvaA c.66.1.5 34187 1je6A 275 2.36e+01 b.1.1.2 71638 d.19.1.1 71639 1o54A 277 2.40e+01 c.66.1.13 -8095 1jokA 149 2.40e+01 1snc b.40.1.1 63214 1csh 435 2.41e+01 1csh a.103.1.1 18880 1jkgA 140 2.41e+01 d.17.4.2 66795 1k0eA 453 2.42e+01 d.161.1.1 67938 1luaA 287 2.45e+01 c.2.1.7 78216 c.58.1.4 78217 1v0wA 506 2.49e+01 1b4bA 71 2.50e+01 1b4aA d.74.2.1 39718 1s7oA 113 2.51e+01 1fvrA 327 2.52e+01 d.144.1.7 60047 1vhcA 224 2.52e+01 c.1.10.1 -5488 1vk4A 298 2.54e+01 c.72.1.1 -8414 1i2tA 61 2.60e+01 1i2tA a.144.1.1 61582 1iakA 199 2.64e+01 1iakA b.1.1.2 21625 d.19.1.1 38199 1d9tA 289 2.68e+01 1deaA 1mc3A 296 2.69e+01 c.68.1.6 78943 1of5B 184 2.70e+01 d.17.4.2 86934 1iqbB 89 2.71e+01 g.3.1.1 66264 g.3.1.1 66265 1khdA 345 2.72e+01 a.46.2.1 77400 c.27.1.1 77401 1lcyA 325 2.74e+01 b.36.1.4 73834 b.47.1.1 73835 1ezm 301 2.76e+01 1hyt d.92.1.2 58980 1dcjA 81 2.82e+01 1dcjA d.68.3.3 59115 1jacC 133 2.85e+01 1jotA 1tadA 324 2.86e+01 1cipA a.66.1.1 18194 c.37.1.8 32077 1aoa 275 2.87e+01 1aoa a.40.1.1 17396 a.40.1.1 17397 1rw7A 243 2.89e+01 c.23.16.2 -6530 1nkiA 135 2.89e+01 d.32.1.2 -9544 1k6kA 143 2.90e+01 a.174.1.1 77274 1ihrA 76 2.93e+01 1ihrA d.212.1.2 62392 1f07A 321 2.94e+01 1ezwA c.1.16.3 59560 1ptf 88 2.96e+01 1ptf d.94.1.1 40549 1h0aA 158 2.96e+01 a.118.9.1 76434 1eduA 149 3.01e+01 1eduA a.118.9.1 19215 1ii6A 368 3.01e+01 1bg2 c.37.1.9 62413 1o5nA 126 3.02e+01 1vj2A 126 3.02e+01 unknown_sccs -4850 1ble 163 3.02e+01 1ble c.38.1.1 32475 1ltqA 301 3.07e+01 c.108.1.9 78208 c.37.1.1 78209 1i7wA 538 3.07e+01 3bct a.118.1.1 61909 1ugpB 226 3.11e+01 1btn 106 3.12e+01 1btn b.55.1.1 26952 1mj5A 302 3.15e+01 c.69.1.8 -8326 1uekA 275 3.18e+01 d.14.1.5 88483 d.58.26.5 88484 1go3F 107 3.19e+01 a.60.8.2 65407 1kypA 237 3.23e+01 d.22.1.1 73280 1oqvA 192 3.24e+01 d.24.1.2 87320 1ireB 228 3.27e+01 b.34.4.4 76770 1gkpA 458 3.30e+01 b.92.1.3 70231 c.1.9.6 70232 1top 162 3.30e+01 1ncx a.39.1.5 17223 1hzgA 295 3.33e+01 1hzgA d.194.1.1 61436 1jgsA 138 3.39e+01 a.4.5.28 66683 1bhjA 292 3.40e+01 1xvaA c.66.1.5 34189 1m26A 133 3.42e+01 1brt 277 3.43e+01 1brt c.69.1.12 34699 1kqyA 273 3.47e+01 c.1.8.5 68843 1hkhA 279 3.47e+01 c.69.1.12 -8342 1eg7A 557 3.53e+01 1eg7A c.37.1.10 32241 1pz7A 204 3.54e+01 b.29.1.4 -3439 1k2yX 463 3.57e+01 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1jajA 174 3.63e+01 d.218.1.2 66471 1fxlA 167 3.63e+01 1b7fA d.58.7.1 39183 d.58.7.1 39184 1omp 370 3.65e+01 4mbp c.94.1.1 35778 1qgvA 142 3.66e+01 1qgvA c.47.1.8 33056 1xvaA 292 3.67e+01 1xvaA c.66.1.5 34183 1j2jB 45 3.70e+01 a.7.8.1 84017 1b0uA 262 3.71e+01 1b0uA c.37.1.12 32370 1iznB 277 3.72e+01 e.43.1.2 83848 1gs5A 258 3.73e+01 c.73.1.2 70395 1yagA 375 3.74e+01 1yagA c.55.1.1 33449 c.55.1.1 33450 1ncx 162 3.75e+01 1ncx a.39.1.5 17222 1qp6A 35 3.77e+01 1qp6A k.16.1.1 46443 1ollA 188 3.83e+01 b.1.1.4 -2690 b.1.1.4 -2691 1h0xA 100 3.83e+01 d.68.6.1 76451 1en2A 89 3.84e+01 1hev g.3.1.1 44048 g.3.1.1 44049 1cwwA 102 3.90e+01 1cy5A a.77.1.3 18434 1qa7A 217 3.93e+01 1havA b.47.1.4 26425 1qvzA 237 3.94e+01 c.23.16.2 -6537 1crb 134 3.95e+01 1hmt b.60.1.2 27220