# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 2.40e-52 1qbkB a.118.1.1 19127 1wa5C 960 5.34e-39 1w9cA 321 3.12e-36 1qgrA 876 1.77e-21 1qgrA a.118.1.1 19119 1ibrB 462 9.80e-18 1qgrA a.118.1.1 19120 1gw5B 591 4.85e-07 a.118.1.10 70630 1b3uA 588 2.31e-06 1b3uA a.118.1.2 19135 1bk6A 422 4.28e-05 1bk5A a.118.1.1 19133 1wa5B 530 5.19e-05 1ee4A 423 5.56e-05 1ee4A a.118.1.1 19128 1bk5A 422 1.56e-04 1bk5A a.118.1.1 19130 1fiy 883 6.12e-04 1fiy c.1.12.3 29307 1jqnA 883 6.41e-04 c.1.12.3 77159 1gw5A 621 7.70e-04 a.118.1.10 70629 1qb4A 883 8.70e-04 c.1.12.3 74640 1bj5 585 3.16e-03 1bj5 a.126.1.1 19369 a.126.1.1 19370 a.126.1.1 19371 1ha2A 585 4.47e-03 1bj5 a.126.1.1 60866 a.126.1.1 60867 a.126.1.1 60868 1ao6A 585 5.76e-03 1bj5 a.126.1.1 19354 a.126.1.1 19355 a.126.1.1 19356 1w07A 659 6.23e-03 1n5uA 585 1.15e-02 a.126.1.1 85339 a.126.1.1 85340 a.126.1.1 85341 1jdhA 529 1.54e-02 a.118.1.1 66549 1e7aA 585 1.81e-02 1bj5 a.126.1.1 19360 a.126.1.1 19361 a.126.1.1 19362 1i7wA 538 1.90e-02 3bct a.118.1.1 61909 2sqcA 631 1.96e-02 2sqcA a.102.4.2 18854 a.102.4.2 18855 1ldjA 760 2.54e-02 a.4.5.34 73847 a.118.17.1 73848 e.40.1.1 73849 1jb0A 755 2.72e-02 1jb0A f.29.1.1 62820 1sqc 631 3.05e-02 2sqcA a.102.4.2 18858 a.102.4.2 18859 1avc 673 5.54e-02 1avc a.65.1.1 18178 a.65.1.1 18179 1g3jA 532 6.84e-02 3bct a.118.1.1 19114 1jk0B 345 6.86e-02 a.25.1.2 63143 2btvA 901 8.62e-02 2btvA e.28.1.1 43376 1kxpD 458 9.18e-02 a.126.1.1 73160 a.126.1.1 73161 a.126.1.1 73162 1miwA 404 1.70e-01 a.173.1.1 79162 d.218.1.4 79163 1ehkA 562 2.21e-01 1ehkA f.24.1.1 43624 1l7vA 326 2.48e-01 f.22.1.1 73672 5eat 548 3.10e-01 5eat a.102.4.1 18853 a.128.1.3 19445 1v54A 514 5.28e-01 1j78A 458 5.67e-01 a.126.1.1 66397 a.126.1.1 66398 a.126.1.1 66399 2occA 514 6.22e-01 2occA f.24.1.1 43518 1oohA 126 6.36e-01 1eia 207 7.79e-01 1eia a.28.3.1 16951 a.73.1.1 18331 1jk0A 419 1.39e+00 a.25.1.2 63142 1a36A 592 1.40e+00 1a36A a.2.8.1 15715 d.163.1.2 42173 e.15.1.1 43266 1xikA 375 1.42e+00 1xikA a.25.1.2 16784 1upkA 341 1.53e+00 1afrA 345 1.61e+00 1afrA a.25.1.2 16805 1d8cA 723 1.64e+00 1d8cA c.1.13.1 29325 1kgnA 329 1.80e+00 a.25.1.2 68584 1oyzA 280 1.83e+00 1lj8A 493 1.85e+00 a.100.1.9 78033 c.2.1.6 78034 1jqcA 375 1.89e+00 1xikA a.25.1.2 63229 1k4tA 592 1.92e+00 a.2.8.1 77263 d.163.1.2 77264 e.15.1.1 77265 1upvA 257 1.95e+00 1mxrA 375 2.18e+00 a.25.1.2 85197 1ribA 375 2.19e+00 1xikA a.25.1.2 16788 1e2gA 215 2.40e+00 3tmkA c.37.1.1 59165 1nfiC 301 2.51e+00 b.1.18.1 21943 b.2.5.3 22456 1n46A 258 2.52e+00 a.123.1.1 85315 1e9cA 215 2.58e+00 c.37.1.1 64808 1ezfA 340 2.65e+00 1ezfA a.128.1.2 19440 2eiaB 206 2.65e+00 1eia a.28.3.1 16950 a.73.1.1 18330 1mukA 1267 2.69e+00 e.8.1.4 79492 1e2fA 215 2.75e+00 3tmkA c.37.1.1 59164 1bob 320 2.78e+00 1bob d.108.1.1 40816 1e9eA 215 2.79e+00 c.37.1.1 64810 3bct 457 2.86e+00 3bct a.118.1.1 19112 1biqA 375 3.02e+00 1xikA a.25.1.2 16786 1taq 832 3.12e+00 1taq a.60.7.1 18082 c.120.1.2 33352 c.55.3.5 33698 e.8.1.1 42991 1e8yA 966 3.13e+00 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 41715 1tzvA 142 3.26e+00 1ulyA 192 3.31e+00 1mv8A 436 3.33e+00 a.100.1.4 85128 c.2.1.6 85129 c.26.3.1 85130 1ash 150 3.36e+00 1ash a.1.1.2 15622 1p7tA 731 3.38e+00 1nn5A 215 3.41e+00 c.37.1.1 85892 1nktA 922 3.45e+00 a.162.1.1 85830 a.172.1.1 85831 c.37.1.19 85832 c.37.1.19 85833 1oq9A 363 3.54e+00 a.25.1.2 87257 1y14A 187 3.69e+00 1e8xA 961 3.70e+00 1e8xA a.118.1.6 19148 b.7.1.1 23183 d.15.1.5 37631 d.144.1.4 41711 1kktA 511 3.75e+00 a.102.2.1 68687 5eau 548 3.76e+00 5eat a.102.4.1 18851 a.128.1.3 19443 1nc5A 373 3.88e+00 a.102.1.6 85548 1ft1A 377 3.96e+00 1ft1A a.118.6.1 19186 1fchA 368 4.00e+00 1fchA a.118.8.1 19212 2kfnA 605 4.20e+00 1xwl c.55.3.5 33682 e.8.1.1 42975 1ih7A 903 4.38e+00 1clqA c.55.3.5 62375 e.8.1.1 62376 1clqA 903 4.38e+00 1clqA c.55.3.5 33717 e.8.1.1 43006 1vnc 609 4.42e+00 1vns a.111.1.3 19065 1nfiA 301 4.71e+00 1a3qA b.1.18.1 21942 b.2.5.3 22455 1sctB 151 4.72e+00 3sdhA a.1.1.2 15003 1dmtA 696 5.24e+00 1dmtA d.92.1.4 40296 1ljrA 244 5.36e+00 1ljrA a.45.1.1 17707 c.47.1.5 33001 1guxA 218 5.55e+00 1guxA a.74.1.3 18388 1g5hA 454 5.59e+00 1g5hA c.51.1.1 60270 d.104.1.1 60271 1t7rA 269 5.63e+00 1jffA 451 5.67e+00 c.32.1.1 62932 d.79.2.1 62933 1m6nA 802 5.76e+00 a.162.1.1 78697 a.172.1.1 78698 c.37.1.19 78699 c.37.1.19 78700 1h3fA 432 5.92e+00 c.26.1.1 76631 d.66.1.4 76632 1dceB 331 5.92e+00 1dceB a.102.4.3 18872 1n35A 1267 5.95e+00 e.8.1.4 79935 1evyA 366 6.12e+00 1evyA a.100.1.6 18811 c.2.1.6 30215 1ae1A 273 6.20e+00 1bdb c.2.1.2 29943 1t6jA 714 6.20e+00 1w4xA 542 6.25e+00 1m13A 316 6.33e+00 a.123.1.1 84746 1rx0A 393 6.41e+00 1yfm 488 6.43e+00 1furA a.127.1.1 19413 1lshA 1056 6.81e+00 a.118.4.1 74242 f.7.1.1 74243 f.7.1.1 74244 1lnh 857 6.96e+00 1yge a.119.1.1 19237 b.12.1.1 23637 1ih8A 271 7.00e+00 2nsyA c.26.2.1 62377 1tbmA 326 7.03e+00 1j5sA 463 7.06e+00 c.1.9.8 71580 1gaxA 862 7.32e+00 1gaxA a.2.7.3 75842 a.27.1.1 75843 b.51.1.1 26893 c.26.1.1 31595 1o7nB 194 7.35e+00 d.17.4.4 81164 1h12A 405 7.44e+00 a.102.1.2 83447 1r1hA 696 7.59e+00 1jsqA 582 7.75e+00 i.13.1.1 63270 1nrlA 316 7.88e+00 1kpkA 473 7.88e+00 f.20.1.1 68776 1wmuA 141 7.96e+00 1nekC 129 8.05e+00 f.21.2.2 80431 1a8i 842 8.12e+00 1a8i c.87.1.4 35490 1va6A 518 8.20e+00 1tubA 440 8.21e+00 1tubA c.32.1.1 31751 d.79.2.1 39803 1rtwA 220 8.52e+00 1vns 609 8.61e+00 1vns a.111.1.3 19061 1d8dA 377 8.77e+00 1ft1A a.118.6.1 19185 1oywA 523 8.94e+00 1i4sA 147 8.99e+00 a.149.1.1 66026 1vjoA 393 9.36e+00 1kplA 473 9.50e+00 f.20.1.1 68782 1k7wA 468 9.98e+00 a.127.1.1 72130 1otsA 465 9.99e+00 f.20.1.1 87415 1rec 201 9.99e+00 1rec a.39.1.5 17326 1hcuA 503 1.01e+01 a.102.2.1 65796 1q6hA 224 1.01e+01 1spvA 184 1.04e+01 1tf5A 844 1.05e+01 1dcnD 436 1.05e+01 1auwA a.127.1.1 19423 1htjF 210 1.06e+01 1htjF a.91.1.1 61254 1dn1A 594 1.07e+01 1dn1A e.25.1.1 43357 1kzhA 555 1.07e+01 c.89.1.1 73361 1hskA 326 1.13e+01 2mbr d.145.1.2 61241 d.146.1.1 61242 1irxA 523 1.14e+01 a.97.1.2 71378 c.26.1.1 71379 1jcqA 382 1.15e+01 a.118.6.1 66504 1kv9A 668 1.18e+01 a.3.1.6 73056 b.70.1.1 73057 1c1kA 217 1.18e+01 1c1kA a.120.1.1 19239 1ndoB 194 1.19e+01 1ndoB d.17.4.4 38121 1eg9B 194 1.21e+01 1ndoB d.17.4.4 38120 1ld8A 382 1.23e+01 a.118.6.1 73838 1b8fA 509 1.23e+01 1b8fA a.127.1.2 19434 1hy0A 466 1.24e+01 1auwA a.127.1.1 61392 1riqA 465 1.27e+01 1tjvA 474 1.28e+01 1rovA 857 1.30e+01 1kb9G 125 1.32e+01 f.27.1.1 77322 1kyoG 126 1.36e+01 f.27.1.1 73259 1vp4A 425 1.36e+01 1fqvD 149 1.39e+01 1fqvD a.157.1.1 19263 d.42.1.1 38667 1e3hA 757 1.41e+01 1e3hA a.4.9.1 16257 d.14.1.4 37572 d.14.1.4 37573 d.52.3.1 38810 d.101.1.1 40695 d.101.1.1 40696 1aueA 100 1.42e+01 1nsgB a.24.7.1 16615 1ornA 226 1.43e+01 a.96.1.1 87342 1up8A 598 1.44e+01 1vlpA 441 1.46e+01 1m33A 258 1.46e+01 c.69.1.26 78514 1phk 298 1.49e+01 1cdkA d.144.1.7 41635 1r9kA 172 1.51e+01 1ezvF 125 1.53e+01 1be3F f.27.1.1 59550 1sh0A 510 1.59e+01 1jqiA 388 1.60e+01 a.29.3.1 67087 e.6.1.1 67088 1peqA 714 1.61e+01 1h3nA 878 1.61e+01 a.27.1.1 76641 b.51.1.1 76642 c.26.1.1 76643 1n93X 375 1.62e+01 1vh4A 435 1.66e+01 1clc 639 1.68e+01 1clc a.102.1.2 18835 b.1.18.2 21872 1a6dA 545 1.70e+01 1a6dA a.129.1.2 19488 c.8.5.2 30819 d.56.1.2 38936 1sz2A 332 1.72e+01 1f75A 249 1.72e+01 1f75A c.101.1.1 59662 1vdkA 466 1.73e+01 1eco 136 1.74e+01 1flp a.1.1.2 15208 1vljA 407 1.74e+01 1uor 585 1.77e+01 1bj5 a.126.1.1 19396 a.126.1.1 19397 a.126.1.1 19398 1tqnA 486 1.80e+01 1fqvJ 149 1.82e+01 1fqvD a.157.1.1 19266 d.42.1.1 38670 1j33A 335 1.83e+01 c.39.1.1 77069 1lfpA 249 1.86e+01 e.39.1.1 73885 1kyqA 274 1.88e+01 c.2.1.11 73281 e.37.1.1 73282 1brwA 433 1.89e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1i37A 260 1.92e+01 1a28A a.123.1.1 61583 1qhbA 596 1.93e+01 1qhbA a.111.1.2 19055 1ecd 136 1.93e+01 1flp a.1.1.2 15211 1h5uA 842 1.94e+01 1a8i c.87.1.4 60655 1xlyA 234 1.97e+01 1xfhA 422 1.98e+01 1itkA 731 2.00e+01 a.93.1.3 71417 a.93.1.3 71418 1eca 136 2.00e+01 1flp a.1.1.2 15209 1jfaA 374 2.01e+01 a.128.1.5 66622 1jvpP 298 2.06e+01 d.144.1.7 67371 1tzjA 338 2.07e+01 1omrA 201 2.09e+01 1ucrA 78 2.10e+01 1qhtA 775 2.10e+01 1tgoA c.55.3.5 33722 e.8.1.1 43011 3tmkA 216 2.11e+01 3tmkA c.37.1.1 31920 1mpgA 282 2.14e+01 1mpgA a.96.1.3 18747 d.129.1.2 41296 1dcnA 424 2.15e+01 1auwA a.127.1.1 19420 1wekA 217 2.15e+01 1q87A 221 2.15e+01 1vheA 373 2.16e+01 1auwA 468 2.16e+01 1auwA a.127.1.1 19416 1vmeA 410 2.20e+01 1lw7A 365 2.22e+01 c.26.1.3 74295 c.37.1.1 74296 1fo3A 460 2.22e+01 1dl2A a.102.2.1 18845 1u6mA 199 2.25e+01 2tmkA 216 2.26e+01 3tmkA c.37.1.1 31928 1iv8A 720 2.28e+01 b.71.1.1 76842 c.1.8.1 76843 1jcrA 377 2.30e+01 a.118.6.1 66506 1ks8A 433 2.37e+01 a.102.1.2 77519 1mgn 154 2.39e+01 1a6m a.1.1.2 15097 1aorA 605 2.41e+01 1b25A a.110.1.1 19042 d.152.1.1 41794 1tml 286 2.43e+01 1tml c.6.1.1 30656 1fqiA 147 2.48e+01 1agrE a.91.1.1 18542 1j6oA 268 2.49e+01 c.1.9.12 77088 1vpqA 273 2.49e+01 1u5kA 244 2.52e+01 1bbhA 131 2.53e+01 1bbhA a.24.3.2 16546 1lvk 762 2.54e+01 1lvk b.34.3.1 24576 c.37.1.9 32173 1ceo 343 2.55e+01 1ceo c.1.8.3 28808 1tn6A 382 2.56e+01 1cb8A 678 2.56e+01 1cb8A a.102.3.2 18849 b.24.1.1 23898 b.30.5.2 24422 1kqpA 271 2.57e+01 c.26.2.1 72883 3erk 364 2.59e+01 1hcl d.144.1.7 41654 1exbA 332 2.60e+01 1qrqA c.1.7.1 28666 1lrv 244 2.61e+01 1lrv a.118.1.5 19146 2nsyA 271 2.61e+01 2nsyA c.26.2.1 31612 1nsyA 271 2.62e+01 2nsyA c.26.2.1 31614 1q18A 332 2.68e+01 1i1qA 520 2.70e+01 1qdlA d.161.1.1 61543 1cpq 129 2.71e+01 1cpq a.24.3.2 16556 1pprM 312 2.71e+01 1pprM a.131.1.1 19502 a.131.1.1 19503 1nxcA 478 2.71e+01 1c3cA 429 2.73e+01 1c3cA a.127.1.1 19425 1zymA 258 2.73e+01 1zymA a.60.10.1 18110 c.8.1.2 30705 1f0yA 302 2.79e+01 2hdhA a.100.1.3 18793 c.2.1.6 30197 1mnd 762 2.83e+01 1lvk b.34.3.1 24591 c.37.1.9 32188 1h4vB 421 2.83e+01 1adjA c.51.1.1 60624 d.104.1.1 60625 1f7uA 607 2.84e+01 1bs2A a.27.1.1 59673 c.26.1.1 59674 d.67.2.1 59675 1khoA 370 2.86e+01 a.124.1.1 72489 b.12.1.3 72490 1hm2A 700 2.89e+01 1cb8A a.102.3.2 61083 b.24.1.1 61084 b.30.5.2 61085 1a04A 215 2.90e+01 1a04A a.4.6.2 16234 c.23.1.1 31089 1j79A 347 2.91e+01 1j79A c.1.9.4 62675 1bc5A 269 2.92e+01 1af7 a.58.1.1 17929 c.66.1.8 34204 1qqfA 277 2.93e+01 1c3d a.102.4.4 18875 1d2nA 272 2.94e+01 1d2nA c.37.1.20 32428 1xqoA 256 2.95e+01 2hdhA 293 2.97e+01 2hdhA a.100.1.3 18795 c.2.1.6 30199 1pme 380 2.98e+01 1hcl d.144.1.7 41653 1h6pA 203 3.00e+01 a.146.1.1 60690 1jfzA 154 3.02e+01 a.149.1.1 66655 1r4wA 226 3.04e+01 1ewfA 456 3.07e+01 1bp1 d.83.1.1 40024 d.83.1.1 40025 1qpzA 340 3.08e+01 1qpzA a.35.1.5 17097 c.93.1.1 35673 1vmaA 306 3.10e+01 1ovnA 248 3.12e+01 1adjA 421 3.14e+01 1adjA c.51.1.1 33188 d.104.1.1 40737 1cec 343 3.14e+01 1ceo c.1.8.3 28809 1oe9A 795 3.15e+01 2gsaA 432 3.18e+01 2gsaA c.67.1.4 34446 1f20A 435 3.19e+01 b.43.4.1 64932 c.25.1.4 64933 1qqcA 773 3.20e+01 1tgoA c.55.3.5 33724 e.8.1.1 43013 1l6nA 289 3.23e+01 a.61.1.1 73624 a.73.1.1 73625 1gvnB 287 3.24e+01 c.37.1.21 76354 1e7uA 961 3.24e+01 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1anxA 319 3.28e+01 1avc a.65.1.1 18161 1nsgB 94 3.33e+01 1nsgB a.24.7.1 16613 3fapB 94 3.33e+01 1nsgB a.24.7.1 16612 1u3dA 509 3.33e+01 1af7 274 3.35e+01 1af7 a.58.1.1 17928 c.66.1.8 34203 1f5qB 252 3.43e+01 1f5qB a.74.1.1 18362 a.74.1.1 18363 1uiuA 502 3.45e+01 1gai 472 3.46e+01 1ayx a.102.1.1 18819 1qsgA 265 3.47e+01 1eny c.2.1.2 29935 1bzpA 153 3.48e+01 1a6m a.1.1.2 15020 1gpb 842 3.50e+01 1a8i c.87.1.4 35478 1ohuA 175 3.51e+01 1qkrA 188 3.59e+01 1qkrA a.24.9.1 16628 1vom 762 3.61e+01 1lvk b.34.3.1 24577 c.37.1.9 32174 1dr8B 344 3.62e+01 1cnzA c.77.1.1 35052 1wetA 340 3.65e+01 1qpzA a.35.1.5 17093 c.93.1.1 35670 1xteA 154 3.70e+01 1vpwA 340 3.70e+01 1qpzA a.35.1.5 17087 c.93.1.1 35680 1gggB 226 3.75e+01 1lst c.94.1.1 35818 153l 185 3.79e+01 153l d.2.1.5 36984 1omhA 293 3.80e+01 1qrqA 325 3.87e+01 1qrqA c.1.7.1 28667 1pf4A 582 3.89e+01 c.37.1.12 88052 f.37.1.1 88053 1h6kA 757 3.90e+01 a.118.1.2 60675 a.118.1.2 60676 a.118.1.2 60677 1bk0 331 3.94e+01 1bk0 b.82.2.1 28118 1odmA 331 3.94e+01 b.82.2.1 86875 1cpt 412 3.96e+01 1cpt a.104.1.1 18968 1d1dA 262 3.96e+01 1d1dA a.28.3.1 16958 a.73.1.1 18335 1jwhC 215 3.97e+01 g.41.4.1 71915 1t0qB 330 3.97e+01 1pw4A 451 3.98e+01