# List of top-scoring protein chains for t2k-100-30-n_notor2-scores 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 1na3A 91 4.34e-04 k.38.1.1 85481 1fchA 368 1.06e-03 1fchA a.118.8.1 19212 2avpA 70 2.35e-03 1elwA 118 3.35e-03 1a17 a.118.8.1 19207 1xnfA 275 3.51e-03 1a17 166 4.14e-03 1a17 a.118.8.1 19206 2fbnA 198 4.84e-03 1elrA 131 5.94e-03 1a17 a.118.8.1 19209 1hh8A 213 1.51e-02 1e96B a.118.8.1 61042 1wm5A 208 1.70e-02 1e96B 203 1.82e-02 1e96B a.118.8.1 19211 1hz4A 373 1.71e-01 a.118.8.2 65960 1ihgA 370 1.92e-01 2cpl a.118.8.1,b.62.1.1 62380,62381 1ouvA 273 2.51e-01 a.118.18.1 93570 1hxiA 121 3.42e-01 1hxiA a.118.8.1 61366 2ff4A 388 4.60e-01 1jcqA 382 5.58e-01 a.118.6.1 66504 1tn6A 382 1.43e+00 1ld8A 382 1.45e+00 a.118.6.1 73838 1kit 757 1.48e+00 1kit b.29.1.8,b.29.1.8,b.68.1.1 24272,24273,27616 1qqeA 292 2.14e+00 1qqeA a.118.8.1 19210 1wy6A 172 2.39e+00 1vlbA 907 2.42e+00 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 1hlrA 907 2.43e+00 1dciA 275 2.62e+00 1dciA c.14.1.3 30918 1qbqA 333 2.64e+00 1ft1A a.118.6.1 19187 1clqA 903 2.90e+00 1clqA c.55.3.5,e.8.1.1 33717,43006 1ggzA 148 3.44e+00 a.39.1.5 70176 1zbpA 273 3.44e+00 2f3yA 148 3.86e+00 1aosA 464 4.28e+00 1auwA a.127.1.1 19414 1ft1A 377 5.39e+00 1ft1A a.118.6.1 19186 1xrsA 516 6.58e+00 1cll 148 7.07e+00 1cll a.39.1.5 17263 1lf6A 684 7.09e+00 a.102.1.5,b.30.5.5 77918,77919 1dceA 567 7.37e+00 1dceA a.118.6.1,b.7.4.1,c.10.2.2 19191,23218,30867 1y8qA 346 1.05e+01 1nffA 260 1.18e+01 c.2.1.2 80457 1oyeA 1049 1.18e+01 d.58.44.1,d.58.44.1,d.58.44.1,d.58.44.1,d.225.1.1,d.225.1.1,f.35.1.1,f.35.1.1 87587,87588,87589,87590,87591,87592,87593,87594 2fnaA 357 1.20e+01 1osa 148 1.28e+01 1cll a.39.1.5 17300 1exrA 148 1.31e+01 1cll a.39.1.5 17299 1dx4A 586 1.41e+01 2bce c.69.1.1 34622 2b05A 246 1.48e+01 3minB 522 1.53e+01 1qguB c.92.2.3 35606 1hqsA 423 1.58e+01 1iso c.77.1.1 61154 1i19A 561 1.72e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 1n4qB 377 1.72e+01 a.102.4.3 91636 1nznA 126 1.75e+01 a.118.8.1 92382 2bklA 695 1.78e+01 1ahr 146 1.88e+01 1cll a.39.1.5 17287 1iqpA 327 1.90e+01 a.80.1.1,c.37.1.20 62649,62650 2as0A 396 1.91e+01 7reqB 637 1.94e+01 1reqB c.1.19.1,c.23.6.1 29617,31244 1qsaA 618 2.00e+01 1qsaA a.118.5.1,d.2.1.6 19182,36988 1v7wA 807 2.06e+01 a.102.1.4,b.30.5.3 108411,108412 1nthA 458 2.10e+01 c.1.25.1 80730 1qqcA 773 2.17e+01 1tgoA c.55.3.5,e.8.1.1 33724,43013 1ncx 162 2.18e+01 1ncx a.39.1.5 17222 3cln 148 2.19e+01 1cll a.39.1.5 17286 1b1yA 500 2.22e+01 1byb c.1.8.1 28796 1qlaA 656 2.23e+01 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 16328,30427,42310 1qhtA 775 2.25e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1vf8A 377 2.27e+01 1h54B 754 2.31e+01 a.102.1.4,b.30.5.3 60636,60637 1hkkA 364 2.33e+01 c.1.8.5,d.26.3.1 90634,90635 1gq2A 555 2.37e+01 c.2.1.7,c.58.1.3 70308,70309 1g4yR 148 2.37e+01 1cll a.39.1.5 60252 1wb0A 445 2.40e+01 1ao0A 459 2.47e+01 1ecfB c.61.1.1,d.153.1.1 34049,41816 1w36C 1122 2.52e+01 1reqB 637 2.57e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1j09A 468 2.57e+01 a.97.1.1,c.26.1.1 77025,77026 1xkqA 280 2.60e+01 1hs6A 611 2.65e+01 1hs6A a.118.1.7,b.98.1.1,d.92.1.13 61233,61234,61235 1j7xA 302 2.71e+01 c.14.1.2 66425 1ia6A 441 2.84e+01 a.102.1.2 76738 1d2nA 272 2.96e+01 1d2nA c.37.1.20 32428 2br9A 234 2.97e+01 1bdg 451 2.98e+01 1qhaA c.55.1.3,c.55.1.3 33461,33462 1l2qA 458 3.03e+01 c.1.25.1 73510 1k4gA 386 3.11e+01 c.1.20.1 72054 1vd5A 377 3.15e+01 a.102.1.7 108518 1e5eA 404 3.17e+01 1ibjA c.67.1.3 59265 1goiA 499 3.18e+01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 2bryA 497 3.20e+01 1jqiA 388 3.23e+01 a.29.3.1,e.6.1.1 67087,67088 1p1xA 260 3.27e+01 c.1.10.1 104060 1h8lA 380 3.33e+01 b.3.2.1,c.56.5.1 65737,65738 1cnzA 363 3.34e+01 1cnzA c.77.1.1 35061 1fjgT 106 3.36e+01 1fjfT a.7.6.1 16338 1ezoA 370 3.41e+01 4mbp c.94.1.1 59539 1rlr 761 3.43e+01 1rlr a.98.1.1,c.7.1.2 18753,30679 1ea1A 455 3.46e+01 1ea1A a.104.1.1 18970 1o7eA 276 3.46e+01 e.3.1.1 92622 1bif 469 3.47e+01 1bif c.37.1.7,c.60.1.4 31961,34003 1qjaA 245 3.48e+01 1qjaA a.118.7.1 19204 1fwcC 567 3.56e+01 1ubpC b.92.1.1,c.1.9.2 28410,29032 1ktaA 365 3.59e+01 e.17.1.1 77533 1jlwA 219 3.61e+01 a.45.1.1,c.47.1.5 71741,71742 1ush 550 3.61e+01 1ush d.114.1.1,d.159.1.2 40923,42079 2wsyB 396 3.65e+01 2tysB c.79.1.1 35288 1klxA 138 3.65e+01 a.118.18.1 77440 2ffeA 311 3.70e+01 1u4bA 580 3.74e+01 c.55.3.5,e.8.1.1 107664,107665 1b3bA 415 3.80e+01 1hwyA c.2.1.7,c.58.1.1 30244,33892 1hu3A 260 3.81e+01 1hu3A a.118.1.14 19137 1vr5A 547 3.83e+01 1tn4 159 3.88e+01 1ncx a.39.1.5 17248 1u8vA 490 3.91e+01 1xdpA 687 3.93e+01 1n46A 258 3.94e+01 a.123.1.1 85315 1e8yA 966 3.96e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1ux5A 411 4.11e+01 a.207.1.1 100144 1qf6A 642 4.11e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1qjbA 245 4.11e+01 1qjaA a.118.7.1 19202 1pguA 615 4.18e+01 b.69.4.1,b.69.4.1 88069,88070 1jv1A 505 4.19e+01 c.68.1.5 71892 3vtk 343 4.25e+01 1qhiA c.37.1.1 31884 1q1lA 401 4.31e+01 d.258.1.1 95591 1n6bA 473 4.35e+01 a.104.1.1 85359 1rpjA 288 4.35e+01 2dri c.93.1.1 35656 1dqrA 557 4.37e+01 1dqrA c.80.1.2 35305 1rqbA 539 4.38e+01 a.5.7.2,c.1.10.5 105057,105058 1ido 192 4.51e+01 1ido c.62.1.1 34139 1q0qA 406 4.54e+01 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1ogpA 393 4.54e+01 b.1.18.6,d.176.1.1 92927,92928 1ruxA 951 4.61e+01 1dhx 1qc9A 276 4.64e+01 1ckqA c.52.1.1 33235 1nouA 507 4.65e+01 c.1.8.6,d.92.2.1 85932,85933 1zb1A 392 4.69e+01 1pn0A 665 4.70e+01 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 1g9gA 629 4.70e+01 a.102.1.2 83279 1f3eA 386 4.73e+01 1pud c.1.20.1 29661 1wxcA 281 4.73e+01 1v8fA 276 4.87e+01 c.26.1.4 100503 1e9iA 431 4.89e+01 c.1.11.1,d.54.1.1 64818,64819 1eh9A 558 4.94e+01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21858,27785,28772 1ejxC 567 4.95e+01 b.92.1.1,c.1.9.2 83184,83185 1erjA 393 4.95e+01 1erjA b.69.4.1 27660 1ejrC 567 4.96e+01 1ubpC b.92.1.1,c.1.9.2 28420,29042 1uohA 226 4.98e+01 d.211.1.1 99690 1ezm 301 5.00e+01 1hyt d.92.1.2 58980 2a84A 300 5.10e+01 1iwgA 1053 5.11e+01 d.58.44.1,d.58.44.1,d.58.44.1,d.58.44.1,d.225.1.1,d.225.1.1,f.35.1.1,f.35.1.1 76874,76875,76876,76877,76878,76879,76880,76881 1hbg 147 5.12e+01 2hbg a.1.1.2 15015 2hbg 147 5.14e+01 2hbg a.1.1.2 15014 1qqfA 277 5.16e+01 1c3d a.102.4.4 18875 1amy 403 5.17e+01 1jdc b.71.1.1,c.1.8.1 27799,28786 1peqA 714 5.32e+01 a.98.1.1,c.7.1.2 104131,104132 1c3d 294 5.35e+01 1c3d a.102.4.4 18874 1ewkA 490 5.38e+01 1ewkA c.93.1.1 35712 1jcjA 260 5.42e+01 c.1.10.1 66499 1ozhA 566 5.47e+01 c.31.1.3,c.36.1.5,c.36.1.9 93833,93834,93835 1nr6A 473 5.50e+01 a.104.1.1 92085 1fo4A 1332 5.50e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 17910,37695,38586,40227,41416,41758 1kssA 571 5.58e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1xf1A 926 5.67e+01 1dqsA 393 5.69e+01 1dqsA e.22.1.1 43347 2at2A 300 5.80e+01 3csuA c.78.1.1,c.78.1.1 35196,35197 1x0lA 333 6.03e+01 1bjt 793 6.05e+01 1bjt e.11.1.1 43249 1gdj 153 6.11e+01 2gdm a.1.1.2 15213 1qtqA 553 6.11e+01 1gtrA b.53.1.2,c.26.1.1 26940,31579 1p2xA 159 6.24e+01 a.40.1.1 104062 1riqA 465 6.27e+01 a.203.1.1,d.104.1.1 97516,97517 2c3mA 1231 6.27e+01 1jihA 531 6.28e+01 d.240.1.1,e.8.1.7 90374,90375 1xkyA 301 6.29e+01 1jf3A 147 6.30e+01 a.1.1.2 71642 1hl9A 449 6.33e+01 b.71.1.3,c.1.8.11 90650,90651 1ojrA 274 6.36e+01 c.74.1.1 93147 1u4gA 301 6.51e+01 d.92.1.2 107670 1igwA 434 6.52e+01 c.1.12.7 62370 1ydnA 295 6.53e+01 2cvxA 888 6.57e+01 1b89A 449 6.58e+01 1b89A a.118.1.3 19138 2fgeA 995 6.69e+01 1lh1 153 6.71e+01 2gdm a.1.1.2 15222 2lh2 153 6.71e+01 2gdm a.1.1.2 15220 1lgr 468 6.71e+01 1lgr d.15.9.1,d.128.1.1 37837,41167 2lgsA 468 6.75e+01 1lgr d.15.9.1,d.128.1.1 37838,41168 1g65K 211 6.80e+01 d.153.1.4 41907 1e4mM 501 6.85e+01 1e70M c.1.8.4 59226 1j8wB 273 6.88e+01 2crbA 97 6.93e+01 1h54A 754 6.94e+01 a.102.1.4,b.30.5.3 60634,60635 2a74A 643 7.02e+01 1l5aA 436 7.05e+01 c.43.1.2,c.43.1.2 75923,75924 1b8fA 509 7.12e+01 1b8fA a.127.1.2 19434 1tf4A 605 7.14e+01 1tf4A a.102.1.2,b.2.2.2 18827,22393 1n35A 1267 7.15e+01 e.8.1.4 79935 1e8nA 710 7.25e+01 1qfmA b.69.7.1,c.69.1.4 27675,34643 1iomA 377 7.33e+01 a.103.1.1 83698 1vemA 516 7.38e+01 1qjdA 571 7.44e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19695,30432,42315 180lA 164 7.53e+01 1l92 d.2.1.3 36867 1hyuA 521 7.55e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1y7bA 542 7.61e+01 1top 162 7.62e+01 1ncx a.39.1.5 17223 1musA 477 7.74e+01 c.55.3.4 79494 1j08A 226 7.77e+01 c.47.1.2,c.47.1.2 83855,83856 1udxA 416 7.85e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1wfdA 93 7.86e+01 8atcA 310 7.89e+01 3csuA c.78.1.1,c.78.1.1 35132,35133 2chnA 716 7.90e+01 1i1iP 681 7.94e+01 1i1iP d.92.1.5 40297 1crwG 333 7.95e+01 1dssG c.2.1.3,d.81.1.1 30026,39941 1a2xA 159 8.00e+01 1ncx a.39.1.5 17251 1ynfA 458 8.01e+01 1n62B 809 8.14e+01 d.41.1.1,d.133.1.1 80092,80093 158l 164 8.18e+01 1l92 d.2.1.3 36747 1sk7A 198 8.19e+01 a.132.1.2 105671 5fbpA 335 8.23e+01 1frpA e.7.1.1 42873 1yozA 116 8.24e+01 1u1jA 765 8.26e+01 c.1.22.2,c.1.22.2 107590,107591 1j9yA 385 8.28e+01 1j9yA c.1.8.3 62791 1emy 153 8.36e+01 1a6m a.1.1.2 15204 1iexA 605 8.37e+01 c.1.8.7,c.23.11.1 66127,66128 1abbA 828 8.41e+01 1a8i c.87.1.4 35536 1w9pA 433 8.43e+01 1v97A 1332 8.44e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 108436,108437,108438,108439,108440,108441 1ed8A 449 8.49e+01 1b8jA c.76.1.1 34988 1dosA 358 8.52e+01 1dosA c.1.10.2 29175 1xd3A 230 8.53e+01 1x9dA 538 8.57e+01 1hr6B 443 8.59e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1dtyA 429 8.71e+01 1dtyA c.67.1.4 34495 1yu3A 381 8.80e+01 1xrtA 467 8.89e+01 1c0aA 585 8.98e+01 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767