# List of top-scoring protein chains for t2k-100-30-str2 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 1qbkB 890 3.11e-02 1qbkB a.118.1.1 19127 1mhyB 395 5.84e-02 1mtyB a.25.1.2 16781 1e8yA 966 1.15e-01 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 41715 1cjaA 342 1.46e-01 1cjaA d.144.1.3 41708 1e7uA 961 2.82e-01 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1u19A 349 3.81e-01 1fkmA 396 4.48e-01 1fkmA a.69.2.1 18315 a.69.2.1 18316 6cts 433 4.74e-01 1csh a.103.1.1 18891 1t7pA 698 5.14e-01 1t7pA c.55.3.5 33712 e.8.1.1 43005 1fz1C 389 5.76e-01 1mtyB a.25.1.2 16746 1l9hA 349 6.44e-01 f.13.1.2 73720 1gw5B 591 1.07e+00 a.118.1.10 70630 1hzxA 349 1.13e+00 1f88A f.13.1.2 61466 1pu6A 218 1.14e+00 1j0mA 752 1.50e+00 a.102.3.2 83910 b.24.1.1 83911 b.30.5.2 83912 1r9dA 787 1.54e+00 1eguA 731 1.54e+00 1eguA a.102.3.2 18850 b.24.1.1 23899 b.30.5.2 24423 1x9mA 698 1.56e+00 1h2vC 771 1.63e+00 a.118.1.2 76592 a.118.1.2 76593 a.118.1.2 76594 1rmi 160 1.70e+00 1ifa a.26.1.3 16891 1t64A 377 1.85e+00 1n7oA 721 2.04e+00 a.102.3.2 80259 b.24.1.1 80260 b.30.5.2 80261 1eupA 403 2.12e+00 1rom a.104.1.1 18967 1amoA 615 2.33e+00 1amoA b.43.4.1 25669 c.23.5.2 31210 c.25.1.4 31557 1dnpA 471 2.43e+00 1qnf a.99.1.1 18775 c.28.1.1 31630 1mhyG 169 2.59e+00 1mtyG a.23.3.1 16518 1iapA 211 2.88e+00 a.91.1.1 62119 1csc 433 2.97e+00 1csh a.103.1.1 18886 1lxkA 721 3.04e+00 a.102.3.2 74331 b.24.1.1 74332 b.30.5.2 74333 1v4aA 440 3.08e+00 1so2A 420 3.11e+00 1lrv 244 3.21e+00 1lrv a.118.1.5 19146 1g71A 347 3.88e+00 1g71A e.16.1.1 43268 1iqrA 420 4.29e+00 a.99.1.1 66275 c.28.1.1 66276 1e8xA 961 4.33e+00 1e8xA a.118.1.6 19148 b.7.1.1 23183 d.15.1.5 37631 d.144.1.4 41711 1f88A 348 4.58e+00 1f88A f.13.1.2 43429 1csmA 256 4.62e+00 5csmA a.130.1.2 19495 1itcA 516 4.65e+00 b.3.1.1 83705 c.1.8.1 83706 1jipA 403 4.68e+00 a.104.1.1 66748 1r0vA 305 4.79e+00 1s9uA 207 4.82e+00 1ndk 155 5.17e+00 1npk d.58.6.1 39118 1ja1A 622 5.23e+00 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1npk 154 5.34e+00 1npk d.58.6.1 39099 1gaxA 862 5.37e+00 1gaxA a.2.7.3 75842 a.27.1.1 75843 b.51.1.1 26893 c.26.1.1 31595 1ihgA 370 5.49e+00 2cpl a.118.8.1 62380 b.62.1.1 62381 1ppjC 379 5.54e+00 2xis 387 5.56e+00 4xis c.1.15.3 29427 1b9zA 516 5.66e+00 1b9zA b.3.1.1 22528 c.1.8.1 28798 1mxmA 254 5.76e+00 b.38.1.3 79647 d.58.43.1 79648 f.34.1.1 79649 1kqfC 217 5.83e+00 f.21.1.1 72874 1tn6A 382 6.04e+00 1jb0A 755 6.10e+00 1jb0A f.29.1.1 62820 1s2xA 206 6.13e+00 1qjaA 245 6.41e+00 1qjaA a.118.7.1 19204 1hmcB 148 6.47e+00 1hmcB a.26.1.2 16868 1f3fA 155 6.52e+00 1npk d.58.6.1 39101 1ayx 492 6.59e+00 1ayx a.102.1.1 18825 1qjbA 245 6.65e+00 1qjaA a.118.7.1 19202 1nhkL 144 6.77e+00 1npk d.58.6.1 39142 4xis 387 6.84e+00 4xis c.1.15.3 29421 1xis 387 6.86e+00 4xis c.1.15.3 29422 1dofA 403 6.87e+00 1c3cA a.127.1.1 19429 1mnzA 388 6.97e+00 c.1.15.3 79328 2pflA 759 6.98e+00 1cm5A c.7.1.1 30675 1amz 435 6.99e+00 1csh a.103.1.1 18884 1be3C 379 7.14e+00 1be3C f.32.1.1 75805 f.21.1.2 75806 2bidA 197 7.28e+00 2bidA f.1.4.1 43398 1jcqA 382 7.36e+00 a.118.6.1 66504 1ld8A 382 7.48e+00 a.118.6.1 73838 1pw4A 451 7.54e+00 1rr7A 129 7.80e+00 1jk0B 345 8.00e+00 a.25.1.2 63143 1oxa 403 8.77e+00 1f4tA a.104.1.1 18965 1rt8A 513 8.83e+00 1hmcA 148 9.00e+00 1hmcB a.26.1.2 16867 1gw9A 388 9.25e+00 c.1.15.3 70658 1ft1A 377 9.35e+00 1ft1A a.118.6.1 19186 1mmoG 162 9.51e+00 1mtyG a.23.3.1 16512 1csh 435 9.61e+00 1csh a.103.1.1 18880 1tbfA 347 9.92e+00 1ir6A 424 9.94e+00 c.107.1.2 71342 1fuoA 467 1.01e+01 1furA a.127.1.1 19411 1mtyG 162 1.04e+01 1mtyG a.23.3.1 16498 1sig 339 1.06e+01 1sig a.177.1.1 19068 1h6kA 757 1.07e+01 a.118.1.2 60675 a.118.1.2 60676 a.118.1.2 60677 1uddA 226 1.12e+01 1o86A 589 1.16e+01 d.92.1.5 81177 1cpt 412 1.16e+01 1cpt a.104.1.1 18968 5csmA 256 1.18e+01 5csmA a.130.1.2 19494 2ran 316 1.18e+01 1avc a.65.1.1 18170 1a8b 318 1.19e+01 1avc a.65.1.1 18171 3xis 387 1.23e+01 4xis c.1.15.3 29423 1aw9 216 1.27e+01 1gnwA a.45.1.1 17736 c.47.1.5 33030 1a76 326 1.27e+01 1a76 a.60.7.1 18091 c.120.1.2 33361 1u7gA 385 1.30e+01 1l7vA 326 1.30e+01 f.22.1.1 73672 1j4nA 271 1.32e+01 f.19.1.1 71510 1b43A 340 1.33e+01 1a76 a.60.7.1 18092 c.120.1.2 33362 1ea3A 164 1.35e+01 1aa7A a.95.1.1 59398 1n97A 389 1.39e+01 a.104.1.1 80335 1cnsA 243 1.39e+01 1cnsA d.2.1.1 36241 1d8dA 377 1.40e+01 1ft1A a.118.6.1 19185 1pot 325 1.42e+01 1pot c.94.1.1 35807 1j78A 458 1.43e+01 a.126.1.1 66397 a.126.1.1 66398 a.126.1.1 66399 1qmzB 259 1.45e+01 1vin a.74.1.1 18338 a.74.1.1 18339 1aa7A 158 1.48e+01 1aa7A a.95.1.1 18741 1fyhA 258 1.49e+01 1d9cA a.26.1.3 16907 a.26.1.3 16908 1h16A 759 1.56e+01 c.7.1.1 76462 4crxA 322 1.58e+01 4crxA a.60.9.1 18095 d.163.1.1 42155 1qhbA 596 1.59e+01 1qhbA a.111.1.2 19055 1pv6A 417 1.66e+01 1n1bA 549 1.68e+01 a.102.4.1 79799 a.128.1.3 79800 1gcvA 140 1.68e+01 1cg5B a.1.1.2 15410 3crxA 343 1.72e+01 4crxA a.60.9.1 18101 d.163.1.1 42161 1h7eA 245 1.73e+01 c.68.1.13 60717 1f4tA 368 1.79e+01 1f4tA a.104.1.1 18973 1a8a 318 1.91e+01 1avc a.65.1.1 18169 1mmoB 384 1.92e+01 1mtyB a.25.1.2 16768 1r1mA 164 1.96e+01 1dxjA 242 1.97e+01 1cnsA d.2.1.1 36244 1muwA 386 1.99e+01 c.1.15.3 79495 1uzeA 589 2.04e+01 1qlaC 256 2.05e+01 1qlaC f.21.2.1 43722 1j99A 293 2.06e+01 c.37.1.5 71618 1jcrA 377 2.08e+01 a.118.6.1 66506 1mtyB 384 2.09e+01 1mtyB a.25.1.2 16740 1ofcX 304 2.09e+01 1pzlA 237 2.16e+01 1b79A 119 2.19e+01 1b79A a.81.1.1 18451 1cm5A 759 2.20e+01 1cm5A c.7.1.1 30671 1va6A 518 2.25e+01 1fjgD 209 2.26e+01 1c05A d.66.1.2 39553 1up8A 598 2.27e+01 1hvd 319 2.38e+01 1avc a.65.1.1 18154 2baa 243 2.41e+01 1cnsA d.2.1.1 36243 1taq 832 2.43e+01 1taq a.60.7.1 18082 c.120.1.2 33352 c.55.3.5 33698 e.8.1.1 42991 1avc 673 2.46e+01 1avc a.65.1.1 18178 a.65.1.1 18179 1v33A 366 2.48e+01 1ecrA 309 2.50e+01 1ecrA e.2.1.1 42678 1i6lA 328 2.52e+01 c.26.1.1 66041 1kbuA 349 2.56e+01 a.60.9.1 72284 d.163.1.1 72285 1f76A 336 2.56e+01 c.1.4.1 76160 1ifa 158 2.57e+01 1ifa a.26.1.3 16892 1rpa 342 2.62e+01 1cviA c.60.1.2 33983 3pflA 759 2.67e+01 1cm5A c.7.1.1 30673 1lshA 1056 2.70e+01 a.118.4.1 74242 f.7.1.1 74243 f.7.1.1 74244 1lla 628 2.71e+01 1lla a.85.1.1 18485 a.86.1.1 18496 b.1.18.3 21861 1swxA 209 2.71e+01 1br2A 791 2.71e+01 1lvk b.34.3.1 24558 c.37.1.9 32155 1fnnA 389 2.76e+01 1fnnA a.4.5.11 16129 c.37.1.20 32426 1vin 268 2.79e+01 1vin a.74.1.1 18354 a.74.1.1 18355 1aisB 200 2.81e+01 1aisB a.74.1.2 18384 a.74.1.2 18385 1by2 119 2.83e+01 1by2 d.170.1.1 42452 1uf2A 1019 2.86e+01 1ovlA 271 2.97e+01 a.123.1.1 87455 1q8iA 783 3.05e+01 1crxA 322 3.06e+01 4crxA a.60.9.1 18097 d.163.1.1 42157 1pah 308 3.13e+01 4pah d.178.1.1 42578 1nu7D 282 3.17e+01 1i6kA 328 3.20e+01 c.26.1.1 66040 1i36A 264 3.24e+01 a.100.1.8 71108 c.2.1.6 71109 1q52A 314 3.24e+01 1j8uA 325 3.25e+01 d.178.1.1 71611 1nrfA 262 3.29e+01 1rkpA 326 3.31e+01 1lfkA 398 3.36e+01 a.104.1.1 77926 1a0jA 223 3.38e+01 5ptp b.47.1.2 26002 1lkxA 697 3.41e+01 c.37.1.9 73981 1t8qA 336 3.43e+01 1tubA 440 3.49e+01 1tubA c.32.1.1 31751 d.79.2.1 39803 1furA 467 3.50e+01 1furA a.127.1.1 19403 1gnlA 544 3.52e+01 e.26.1.1 70287 1qi9A 556 3.53e+01 1qhbA a.111.1.2 19053 1io7A 368 3.53e+01 1f4tA a.104.1.1 18971 5bcaA 516 3.55e+01 1b9zA b.3.1.1 22529 c.1.8.1 28799 1d5yA 292 3.66e+01 1d5yA a.4.1.8 16055 a.4.1.8 16056 d.60.1.2 39532 1jm7B 117 3.69e+01 g.44.1.1 66881 1fpoA 171 3.72e+01 1fpoA a.2.3.1 15693 a.23.1.1 16487 1etu 394 3.73e+01 1efcA c.37.1.8 64737 1ddbA 195 3.83e+01 1ddbA f.1.4.1 43399 1w68A 390 3.83e+01 1l5wA 796 3.86e+01 c.87.1.4 73605 1h1yA 228 3.87e+01 c.1.2.2 76506 1j1jA 240 3.88e+01 1ht6A 405 3.88e+01 b.71.1.1 83629 c.1.8.1 83630 1rgqC 22 3.88e+01 1uumA 372 3.92e+01