# List of top-scoring protein chains for t04-100-30-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 1nb8A 353 2.61e-52 d.3.1.9 80385 1ubi 76 1.98e-05 1ubi d.15.1.1 37584 1ogwA 76 2.16e-05 d.15.1.1 87001 1bt0A 76 1.87e-04 1ubi d.15.1.1 37607 1nddA 76 1.41e-03 1ubi d.15.1.1 37599 1vcbA 118 4.58e-03 1vcbA d.15.1.1 37603 1lm8B 118 5.78e-03 d.15.1.1 74033 1hleA 345 1.23e-02 1ovaA e.1.1.1 42618 1euvB 86 4.24e-02 1a5r d.15.1.1 37598 1a7cA 379 1.25e-01 1sek e.1.1.1 42660 1ovaA 386 1.32e-01 1ovaA e.1.1.1 42619 1uhgA 385 1.45e-01 e.1.1.1 88491 1ltlA 279 1.53e-01 b.40.4.11 84701 1dbhA 354 1.62e-01 1awe a.87.1.1 18514 b.55.1.1 26967 1cqxA 403 1.91e-01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1d0cA 444 3.26e-01 d.174.1.1 64769 1n62A 166 3.57e-01 a.56.1.1 80090 d.15.4.2 80091 1nijA 318 4.83e-01 c.37.1.10 85741 d.237.1.1 85742 1d1vA 444 5.23e-01 1nseA d.174.1.1 59101 1qmyA 167 5.36e-01 1qmyA d.3.1.2 37094 1mtpA 323 5.75e-01 e.1.1.1 85107 1ef1A 294 6.11e-01 1ef1A a.11.2.1 16368 b.55.1.5 27003 d.15.1.4 37611 1qwyA 291 6.96e-01 unknown_sccs -5023 1ift 263 7.89e-01 1mrj d.165.1.1 42211 1lj5A 379 8.52e-01 e.1.1.1 73928 1i5pA 633 9.03e-01 1i5pA b.18.1.3 61817 b.77.2.1 61818 f.1.3.1 61819 1jofA 365 9.23e-01 b.69.10.1 71775 1kk1A 410 9.34e-01 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 2cblA 305 9.97e-01 2cblA a.39.1.7 17380 a.48.1.1 17774 d.93.1.1 40528 1uurA 473 1.11e+00 a.47.1.1 -968 b.2.5.5 -2904 d.93.1.1 -10632 1jrrA 382 1.11e+00 e.1.1.1 63256 1phm 310 1.27e+00 1phm b.121.1.2 59015 b.121.1.2 59016 1hkfA 122 1.30e+00 b.1.1.1 83553 1ed5A 444 1.41e+00 1nseA d.174.1.1 42530 1k6kA 143 1.44e+00 a.174.1.1 77274 1f9vA 347 1.51e+00 1bg2 c.37.1.9 59745 1hlrA 907 1.53e+00 a.56.1.1 65850 d.15.4.2 65851 d.41.1.1 65852 d.133.1.1 65853 1oygA 447 1.61e+00 unknown_sccs -4549 1i6iA 366 1.65e+00 1bg2 c.37.1.9 61844 1sdwA 314 1.65e+00 b.121.1.2 -3024 b.121.1.2 -3025 1f83A 425 1.78e+00 1f82A d.92.1.7 40306 2hgsA 474 1.79e+00 2hgsA c.30.1.4 31722 d.142.1.6 75997 1a8h 500 1.95e+00 1a8h a.27.1.1 16922 c.26.1.1 31589 1rwzA 245 2.05e+00 d.131.1.2 -11106 d.131.1.2 -11107 1gg3A 279 2.18e+00 1ef1A a.11.2.1 16372 b.55.1.5 27007 d.15.1.4 37615 1lfdA 87 2.97e+00 1lfdA d.15.1.5 37622 1ryt 190 3.05e+00 1ryt a.25.1.1 16646 g.41.5.1 45245 1b71A 191 3.07e+00 1ryt a.25.1.1 16647 g.41.5.1 45246 1qxfA 66 3.17e+00 g.41.8.4 -12822 1scfA 273 3.18e+00 1exzA a.26.1.2 16873 1uq5A 263 3.18e+00 d.165.1.1 -11555 1rvgA 305 3.50e+00 c.1.10.2 -5500 1exrA 148 3.56e+00 1cll a.39.1.5 17299 1psrA 100 3.76e+00 1psrA a.39.1.2 17180 2cb5A 453 3.94e+00 3gcb d.3.1.1 37035 1n0xH 230 4.10e+00 b.1.1.1 -2201 b.1.1.2 -2473 1bq9A 54 4.22e+00 1rb9 g.41.5.1 45238 1dhkB 223 4.23e+00 1led b.29.1.1 24157 1qpaA 345 4.25e+00 1arv a.93.1.1 18585 1brfA 53 4.45e+00 1rb9 g.41.5.1 45236 1ov3A 138 4.63e+00 b.34.2.1 87451 b.34.2.1 87452 1uch 230 4.72e+00 1uch d.3.1.6 37129 1alo 907 4.81e+00 1alo 1nzjA 298 4.97e+00 c.26.1.1 -6600 1lkoA 191 5.44e+00 a.25.1.1 78063 g.41.5.1 78064 1p4xA 250 5.59e+00 a.4.5.28 87784 a.4.5.28 87785 1oglA 283 5.64e+00 unknown_sccs -1512 1plq 258 5.69e+00 1plq d.131.1.2 41388 d.131.1.2 41389 1rdg 53 5.72e+00 1rb9 g.41.5.1 45221 1avsA 90 5.82e+00 1cll a.39.1.5 17226 1fvuB 125 5.90e+00 1ixxB d.169.1.1 42346 1nc7A 138 6.01e+00 b.123.1.1 85549 1rpa 342 6.04e+00 1cviA c.60.1.2 33983 1t0yA 122 6.08e+00 d.15.1.1 -9151 1ig8A 486 6.34e+00 2yhx c.55.1.3 64746 c.55.1.3 64747 1id0A 152 6.39e+00 d.122.1.3 66111 1f2rI 100 6.75e+00 1c9fA d.15.2.1 37641 1uvqB 198 6.80e+00 b.1.1.2 -2659 d.19.1.1 -9348 1ojjA 402 7.23e+00 b.29.1.10 -3473 1spxA 278 7.53e+00 c.2.1.2 -5870 1dymA 402 7.59e+00 1celA b.29.1.10 24304 1fnnA 389 7.71e+00 1fnnA a.4.5.11 16129 c.37.1.20 32426 1ggzA 148 8.12e+00 a.39.1.5 70176 1ciy 590 8.26e+00 1ciy b.18.1.3 23720 b.77.2.1 27977 f.1.3.1 43392 1f89A 291 9.15e+00 d.160.1.1 64988 1go4A 205 9.21e+00 d.135.1.1 70292 1rzfH 235 9.44e+00 b.1.1.1 -2188 b.1.1.2 -2453 1h3nA 878 9.78e+00 a.27.1.1 76641 b.51.1.1 76642 c.26.1.1 76643 1sqgA 429 9.94e+00 1npuA 117 9.96e+00 b.1.1.1 -2339 1jmtA 104 1.01e+01 d.58.7.3 63180 1s6cA 183 1.02e+01 a.39.1.5 -858 1e4fT 419 1.02e+01 1e4fT c.55.1.1 33453 c.55.1.1 33454 1j1vA 94 1.05e+01 a.4.12.2 83981 1q1aA 289 1.08e+01 c.31.1.5 -6781 1f4lA 551 1.09e+01 1qqtA a.27.1.1 59648 c.26.1.1 59649 g.41.1.1 59650 1mzbA 136 1.14e+01 unknown_sccs -266 1dzoA 123 1.15e+01 1dzoA d.24.1.1 38378 1g5hA 454 1.19e+01 1g5hA c.51.1.1 60270 d.104.1.1 60271 1hq3C 136 1.26e+01 1aoiA a.22.1.1 16454 1pfvA 551 1.30e+01 a.27.1.1 -727 c.26.1.1 -6603 g.41.1.1 -12765 1eg3A 261 1.31e+01 1eg3A a.39.1.7 17376 a.39.1.7 17377 b.72.1.1 27805 1sczA 233 1.31e+01 c.43.1.1 -7326 1vjoA 393 1.34e+01 c.67.1.3 -8173 1kk8B 139 1.34e+01 a.39.1.5 77430 1kz7A 353 1.34e+01 a.87.1.1 73333 b.55.1.1 73334 1jmmA 377 1.37e+01 b.30.6.1 71749 1cb8A 678 1.39e+01 1cb8A a.102.3.2 18849 b.24.1.1 23898 b.30.5.2 24422 1mijA 152 1.40e+01 a.4.1.1 79150 1mu5A 471 1.41e+01 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1a32 88 1.43e+01 1a32 a.16.1.2 16384 1qlpA 394 1.43e+01 1ovaA e.1.1.1 42628 1dazC 99 1.46e+01 1hvc b.50.1.1 26501 1j55A 95 1.50e+01 a.39.1.2 77078 1qwzA 235 1.59e+01 b.100.1.1 -4543 1m0wA 491 1.61e+01 c.30.1.4 78363 d.142.1.6 78364 1hdmB 193 1.70e+01 1hdmB b.1.1.2 21584 d.19.1.1 38158 6rxn 46 1.73e+01 1rb9 g.41.5.1 45222 1mngA 203 1.77e+01 1avmA a.2.11.1 15776 d.44.1.1 38701 1s0uA 408 1.78e+01 b.43.3.1 -4053 b.44.1.1 -4061 c.37.1.8 -7096 1n9eA 787 1.84e+01 b.30.2.1 -3529 d.17.2.1 -9278 d.17.2.1 -9279 1jtvA 327 1.85e+01 c.2.1.2 84230 1p65A 73 1.88e+01 unknown_sccs -10331 1fs1B 141 1.89e+01 1vcbB a.157.1.1 19252 d.42.1.1 38664 1qb2A 109 1.92e+01 1qb2A a.36.1.1 17125 1rhfA 182 1.92e+01 b.1.1.1 -2335 b.1.1.4 -2684 1bf5A 545 1.94e+01 1bg1A a.47.1.1 17766 b.2.5.5 22460 d.93.1.1 40526 1fiy 883 1.97e+01 1fiy c.1.12.3 29307 1wdcB 156 2.02e+01 1wdcB a.39.1.5 17302 2gsaA 432 2.03e+01 2gsaA c.67.1.4 34446 1wer 334 2.06e+01 1wer a.116.1.2 19108 1idaA 99 2.09e+01 1fmb b.50.1.1 26715 1ngzB 220 2.09e+01 b.1.1.1 80502 b.1.1.2 80503 1s8iA 121 2.10e+01 a.133.1.2 -1968 1gcb 454 2.12e+01 3gcb d.3.1.1 37034 1i37A 260 2.15e+01 1a28A a.123.1.1 61583 1gv3A 248 2.15e+01 a.2.11.1 70585 d.44.1.1 70586 1l1oC 181 2.17e+01 b.40.4.3 73480 1p3jA 217 2.17e+01 c.37.1.1 -6996 g.41.2.1 -12769 1jnyA 435 2.17e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1h5uA 842 2.19e+01 1a8i c.87.1.4 60655 1sctB 151 2.21e+01 3sdhA a.1.1.2 15003 1pv5A 264 2.24e+01 unknown_sccs -10182 1fmb 104 2.25e+01 1fmb b.50.1.1 26777 1ldjA 760 2.32e+01 a.4.5.34 73847 a.118.17.1 73848 e.40.1.1 73849 1ryjA 70 2.32e+01 d.15.3.2 -9179 1mg7A 417 2.33e+01 d.14.1.6 84954 d.58.26.6 84955 1bgc 174 2.37e+01 1bgc a.26.1.1 16822 1jqnA 883 2.39e+01 c.1.12.3 77159 1h09A 338 2.40e+01 b.109.1.1 83420 c.1.8.8 83421 1nh0A 99 2.41e+01 b.50.1.1 -4299 2hpaA 342 2.42e+01 1cviA c.60.1.2 33985 1ryp2 233 2.44e+01 1ryp2 1op3H 225 2.50e+01 b.1.1.1 87208 b.1.1.2 87209 1g66A 207 2.50e+01 1bs9 unknown_sccs 31329 1e7uA 961 2.53e+01 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1khvA 516 2.55e+01 e.8.1.4 68627 1o5xA 248 2.65e+01 c.1.1.1 -5157 3gcb 470 2.66e+01 3gcb d.3.1.1 37032 1ngnA 155 2.66e+01 a.96.1.2 85697 1abrA 251 2.72e+01 1mrj d.165.1.1 42196 1a8i 842 2.73e+01 1a8i c.87.1.4 35490 1fds 327 2.76e+01 1fds c.2.1.2 29838 2ng1 293 2.80e+01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1pgs 314 2.82e+01 1pgs b.121.1.1 23653 b.121.1.1 23654 1cv8 174 2.84e+01 1cv8 d.3.1.1 37089 1difA 99 2.87e+01 1fmb b.50.1.1 26503 1g6gA 127 2.90e+01 1g6gA b.26.1.2 23916 1r9fA 136 2.94e+01 unknown_sccs -10736 1ly1A 181 2.95e+01 c.37.1.1 74334 1azpA 66 3.02e+01 1azpA b.34.13.1 37467 1owfA 99 3.10e+01 a.55.1.1 87487 1nw3A 416 3.12e+01 c.66.1.31 86288 1ihoA 283 3.15e+01 1ihoA c.26.1.4 62390 2polA 366 3.16e+01 2polA d.131.1.1 41356 d.131.1.1 41357 d.131.1.1 41358 1e1oA 504 3.19e+01 1lylA b.40.4.1 25258 d.104.1.1 40714 1ki1B 352 3.22e+01 a.87.1.1 72497 b.55.1.1 72498 1jflA 228 3.25e+01 c.78.2.1 71656 c.78.2.1 71657 1epwA 1290 3.27e+01 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1hyeA 313 3.34e+01 2cmd c.2.1.5 61400 d.162.1.1 61401 1furA 467 3.42e+01 1furA a.127.1.1 19403 1gl4A 285 3.43e+01 d.22.1.2 65286 g.3.11.5 65287 1foeA 377 3.46e+01 1foeA a.87.1.1 18517 b.55.1.1 26969 1iwdA 215 3.49e+01 d.3.1.1 83756 1mho 88 3.50e+01 1b4cA a.39.1.2 17171 1mlwA 301 3.59e+01 d.178.1.1 79289 1m2dA 110 3.61e+01 c.47.1.11 78476 1a28A 256 3.66e+01 1a28A a.123.1.1 19290 1n1jB 97 3.72e+01 a.22.1.3 79814 1xvaA 292 3.74e+01 1xvaA c.66.1.5 34183 1r4wA 226 3.75e+01 unknown_sccs -7447 1memA 215 3.75e+01 1cs8A d.3.1.1 37069 1sjwA 144 3.78e+01 unknown_sccs -9296 1kzkA 99 3.78e+01 b.50.1.1 73371 1sr7A 259 3.79e+01 1kx5B 102 3.80e+01 a.22.1.1 77594 1k1xA 659 3.81e+01 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1cmiA 85 3.86e+01 1cmiA d.39.1.1 38551 1auiB 169 3.88e+01 1auiB a.39.1.5 17325 1k9uA 78 3.91e+01 a.39.1.10 84348 1fzvA 132 3.97e+01 1vpfA g.17.1.1 60159 1t2aA 375 3.97e+01 c.2.1.2 -5764 1f37A 110 3.97e+01 1f37A c.47.1.11 33088 1pb6A 212 3.98e+01 a.4.1.9 88017 a.121.1.1 88018