# List of top-scoring protein chains for t04-100-30-stride-ebghtl-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.soe.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 2hztA 107 1.13e-18 1yyvA 131 3.34e-17 a.4.5.69 124254 1z7uA 112 4.15e-17 a.4.5.69 124672 2fswA 107 6.30e-17 a.4.5.69 134042 2f2eA 146 8.21e-16 a.4.5.69 132808 1smtA 122 4.26e-06 1smtA a.4.5.5 16109 1r1tA 122 4.42e-06 a.4.5.5 104769 2oqgA 114 1.50e-05 2a61A 145 2.69e-05 a.4.5.28 126187 3bpvA 138 3.40e-05 1sfxA 109 5.06e-05 a.4.5.50 105505 2fbhA 146 9.07e-05 a.4.5.28 133245 1r1uA 106 2.60e-04 a.4.5.5 104771 2ethA 154 2.90e-04 a.4.5.28 132358 2gxgA 146 2.92e-04 2fbiA 142 5.21e-04 a.4.5.28 133246 2pexA 153 5.81e-04 3cjnA 162 6.11e-04 1ub9A 100 6.47e-04 a.4.5.28 99159 3bj6A 152 7.41e-04 2h09A 155 1.04e-03 1bjaA 95 1.11e-03 1bjaA a.4.5.9 16122 1xmaA 145 1.12e-03 a.4.5.61 115477 2eshA 118 1.19e-03 a.4.5.61 132325 2v7fA 150 1.25e-03 1lnwA 147 1.71e-03 a.4.5.28 78104 1lj9A 144 1.84e-03 a.4.5.28 78035 1jgsA 138 2.81e-03 a.4.5.28 66683 3b73A 111 2.83e-03 3broA 141 3.84e-03 1y0uA 96 3.96e-03 a.4.5.5 116310 2d1hA 109 4.04e-03 a.4.5.50 131125 3cdhA 155 5.12e-03 2v79A 135 6.71e-03 3ctaA 230 7.35e-03 1fx7A 230 8.35e-03 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 2e1nA 138 8.53e-03 3bddA 142 1.00e-02 2bv6A 142 1.04e-02 2dqlA 115 1.05e-02 2nnnA 140 1.06e-02 2hr3A 147 1.18e-02 a.4.5.28 136678 1tw3A 360 1.26e-02 a.4.5.29,c.66.1.12 107373,107374 2pg4A 95 1.30e-02 1ucrA 78 1.79e-02 a.4.5.45 99188 2co5A 99 1.90e-02 1tbxA 99 2.14e-02 a.4.5.48 106748 2obpA 96 2.18e-02 1u2wA 122 2.39e-02 a.4.5.5 119487 1r7jA 95 2.48e-02 a.4.5.49 104836 2fe3A 145 2.51e-02 2qq9A 226 2.92e-02 1s3jA 155 3.13e-02 a.4.5.28 98437 1j75A 67 3.27e-02 a.4.5.19 62673 1on2A 142 3.43e-02 a.4.5.24,a.76.1.1 87103,87104 2ev0A 142 3.52e-02 a.4.5.24,a.76.1.1 132413,132414 2dtrA 226 3.85e-02 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 2p8tA 200 4.05e-02 2e7xA 150 4.15e-02 2cfxA 144 4.17e-02 a.4.5.32,d.58.4.2 130395,130396 2p5vA 162 4.24e-02 2rdpA 150 4.32e-02 1mzbA 136 4.50e-02 a.4.5.42 91497 2pn6A 150 4.57e-02 2qvoA 95 4.72e-02 2dtr 226 5.25e-02 1bi0 2nyxA 168 5.82e-02 1z91A 147 6.30e-02 a.4.5.28 124736 2fu4A 83 7.34e-02 2hgcA 102 9.81e-02 1in4A 334 1.08e-01 1hqcA a.4.5.11,c.37.1.20 62597,62598 1in6A 334 1.35e-01 1hqcA a.4.5.11,c.37.1.20 62601,62602 2cg4A 152 1.60e-01 a.4.5.32,d.58.4.2 130417,130418 2hs5A 239 1.72e-01 1hw1A 239 1.86e-01 1e2xA a.4.5.6,a.78.1.1 16111,18441 2ia0A 171 1.89e-01 2dbbA 151 1.90e-01 1dpuA 99 2.19e-01 1dpuA a.4.5.16 16150 1q1hA 110 2.35e-01 a.4.5.41 95580 2qwwA 154 2.92e-01 2heoA 67 3.01e-01 3boqA 160 3.12e-01 2b0lA 102 3.50e-01 a.4.5.66 127641 1z1dA 103 3.68e-01 a.4.5.16 124351 1zybA 232 3.81e-01 a.4.5.4,b.82.3.2 125815,125816 2cyyA 151 3.83e-01 a.4.5.32,d.58.4.2 131028,131029 1mkmA 249 4.12e-01 a.4.5.33,d.110.2.2 79242,79243 1zarA 282 4.46e-01 a.4.5.56,d.144.1.9 124843,124844 1yg2A 179 4.73e-01 a.4.5.61 116681 3bjaA 139 4.80e-01 1tqmA 282 4.84e-01 a.4.5.56,d.144.1.9 107236,107237 1lvaA 258 5.44e-01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 2i5iA 263 5.53e-01 2jt1A 77 5.99e-01 2ek5A 129 6.21e-01 1wsuA 124 6.70e-01 a.4.5.35,a.4.5.35 121245,121246 2gmgA 105 6.83e-01 1gvjA 146 6.99e-01 a.4.5.21 90525 2fa5A 162 7.38e-01 2pbqA 178 7.41e-01 1oyiA 82 8.14e-01 a.4.5.19 93729 2jtvA 65 8.20e-01 1wj5A 120 8.38e-01 a.4.5.59 114692 1zgdA 312 9.09e-01 1b9mA 265 9.26e-01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1bia 321 9.38e-01 1bia 1biaA 321 9.38e-01 a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1bm9A 122 1.06e+00 1bm9A a.4.5.7 16116 3c7jA 237 1.12e+00 1ulyA 192 1.12e+00 a.4.5.58 113297 2givA 295 1.14e+00 d.108.1.1 135253 1t98A 287 1.19e+00 a.4.5.65,a.47.6.1 119196,119197 2dk5A 91 1.25e+00 2pjpA 121 1.40e+00 1m7jA 484 1.42e+00 b.92.1.6,b.92.1.6,c.1.9.11 78732,78733,78734 1eejA 216 1.43e+00 1eejA c.47.1.9,d.17.3.1 33057,38071 1rk6A 496 1.49e+00 b.92.1.6,b.92.1.6,c.1.9.11 97599,97600,97601 1sfuA 75 1.56e+00 a.4.5.19 105503 2pq8A 278 1.58e+00 1xmkA 79 1.61e+00 a.4.5.19 122165 1ri7A 171 1.77e+00 a.4.5.32,d.58.4.2 97504,97505 3bz6A 183 1.79e+00 2nr3A 183 1.87e+00 1xd7A 145 1.98e+00 a.4.5.55 109566 1oywA 523 1.98e+00 a.4.5.43,c.37.1.19,c.37.1.19 93760,93761,93762 1x19A 359 2.05e+00 1jhfA 202 2.20e+00 a.4.5.2,b.87.1.1 63057,63058 1fp1D 372 2.22e+00 1fpqA a.4.5.29,c.66.1.12 59939,59940 2dqrA 122 2.37e+00 1rztA 331 2.79e+00 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 1c4zA 358 2.81e+00 1c4zA d.148.1.1 41766 1qzzA 374 2.83e+00 a.4.5.29,c.66.1.12 96719,96720 3by6A 126 2.91e+00 1bc8C 93 3.01e+00 1awcA a.4.5.21 16168 2hoeA 380 3.14e+00 a.4.5.63,c.55.1.10,c.55.1.10 136639,136640,136641 2bcqA 335 3.18e+00 a.60.6.1,a.60.12.1,d.218.1.2 128304,128305,128306 1okrA 123 3.27e+00 a.4.5.39 93269 1qz9A 416 3.49e+00 c.67.1.3 96621 1sd4A 126 3.55e+00 a.4.5.39 105428 1i6xA 209 4.10e+00 a.4.5.4,b.82.3.2 83673,83674 3bwgA 239 4.14e+00 2dobA 83 4.15e+00 2fnaA 357 4.37e+00 a.4.5.11,c.37.1.20 133809,133810 1mb4A 370 4.42e+00 c.2.1.3,d.81.1.1 78908,78909 2dk8A 81 4.79e+00 1j5yA 187 5.07e+00 a.4.5.1,d.94.2.1 71592,71593 2qz8A 149 5.18e+00 2g80A 253 5.78e+00 c.108.1.22 134741 1s5jA 847 6.04e+00 c.55.3.5,e.8.1.1 112040,112041 3rubS 123 6.11e+00 1rboC d.73.1.1 39616 1ig0A 319 6.25e+00 1ig0A b.82.6.1,c.100.1.1 62354,62355 2ffjA 300 6.60e+00 e.50.1.1 133387 1xnfA 275 7.17e+00 a.118.8.1 115580 2gqqA 163 7.18e+00 2fokA 579 7.22e+00 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16131,16132,16133,33323 2fbkA 181 7.34e+00 a.4.5.28 133247 1ixcA 294 7.70e+00 a.4.5.37,c.94.1.1 83764,83765 2nxqA 134 7.72e+00 2g7uA 257 7.78e+00 2ia2A 265 8.18e+00 2gwgA 350 8.49e+00 c.1.9.15 135805 1qf5A 431 8.53e+00 1adeA c.37.1.10 32212 1fi4A 416 8.97e+00 1fi4A d.14.1.5,d.58.26.2 59847,59848 3brjA 175 1.04e+01 1xgsA 295 1.08e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1zx4A 192 1.09e+01 1yo5C 97 1.12e+01 a.4.5.21 123768 1t4bA 367 1.13e+01 c.2.1.3,d.81.1.1 106406,106407 1cnzA 363 1.19e+01 1cnzA c.77.1.1 35061 1xn7A 78 1.21e+01 a.4.5.62 115576 1hw5A 210 1.23e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 2h41A 95 1.24e+01 1me4A 215 1.29e+01 d.3.1.1 79023 2dg5A 366 1.31e+01 d.153.1.6 131500 2j5pA 76 1.32e+01 a.4.5.67 138050 1azsA 220 1.34e+01 1azsA d.58.29.1 39416 2fmyA 220 1.37e+01 1m40A 263 1.39e+01 e.3.1.1 74437 2cq2A 114 1.49e+01 d.58.7.1 130713 1p3y1 194 1.51e+01 1p4xA 250 1.52e+01 a.4.5.28,a.4.5.28 87784,87785 2p5tB 253 1.55e+01 2bw3A 534 1.56e+01 a.270.1.1,c.55.3.12 129317,129318 2b7aA 293 1.57e+01 2ivmA 150 1.57e+01 1qbjA 81 1.57e+01 1qbjA a.4.5.19 16155 6paxA 133 1.58e+01 6paxA a.4.1.5,a.4.1.5 64758,64759 2g9zA 348 1.59e+01 1zwwA 256 1.60e+01 a.238.1.1 125750 3bptA 363 1.61e+01 1fp2A 352 1.62e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1stzA 338 1.64e+01 a.4.5.51,d.110.2.3 106009,106010 1t0aA 159 1.67e+01 d.79.5.1 112192 1jhgA 101 1.69e+01 1jhgA a.4.12.1 19009 1xsvA 113 1.73e+01 a.4.13.3 116003 2h2mA 108 1.79e+01 2z2mC 125 1.79e+01 2zc3C 125 1.79e+01 1ua4A 455 1.80e+01 c.72.1.3 99128 2ob0A 170 1.92e+01 1hlvA 131 1.93e+01 a.4.1.7,a.4.1.7 65854,65855 1brmA 367 1.94e+01 1brmA c.2.1.3,d.81.1.1 30030,39945 1omiA 248 1.97e+01 b.82.3.3,a.4.5.4 87079,87080 2gd5A 179 1.98e+01 1whzA 70 2.01e+01 d.50.3.2 114656 2h9dA 101 2.02e+01 a.130.1.1 136250 2qrvA 295 2.07e+01 2pc8A 400 2.08e+01 1eqcA 394 2.09e+01 1cz1A c.1.8.3 28811 2o71A 115 2.11e+01 1ro2A 216 2.12e+01 d.264.1.2 97665 2qdjA 304 2.20e+01 2dr1A 386 2.22e+01 1k78A 149 2.22e+01 a.4.1.5,a.4.1.5 68255,68256 2uzhA 165 2.23e+01 2aelA 374 2.27e+01 8rucI 123 2.28e+01 1rboC d.73.1.1 39629 2qhsA 237 2.30e+01 1j5uA 136 2.34e+01 d.208.1.1 71584 2clqA 295 2.39e+01 1nd4A 264 2.39e+01 d.144.1.6 91815 1ixkA 315 2.48e+01 c.66.1.38 90716 1rblI 109 2.50e+01 d.73.1.1 118599 2cw9A 194 2.50e+01 d.17.4.13 130920 2gbbA 156 2.54e+01 1ro0A 216 2.56e+01 d.264.1.2 97664 1ir21 140 2.56e+01 2v75A 104 2.57e+01 1nexB 464 2.64e+01 a.158.1.1,b.69.4.1 80443,80444 2gm5A 139 2.70e+01 1vi0A 206 2.83e+01 a.4.1.9,a.121.1.1 100720,100721 1aua 296 2.84e+01 1aua 1auaA 296 2.84e+01 a.5.3.1,c.13.1.1 16290,30882 1bh9B 89 2.92e+01 1bh9B a.22.1.3 16485 1rscI 111 2.94e+01 d.73.1.1 118620 1tjoA 182 2.99e+01 a.25.1.1 112461 1e58A 249 3.01e+01 1qhfA c.60.1.1 59262 2cw8A 537 3.06e+01 2qr7A 342 3.13e+01 1mngA 203 3.13e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1v4eA 299 3.20e+01 a.128.1.1 100296 1g0sA 209 3.23e+01 1g0sA d.113.1.1 60187 1vsrA 136 3.23e+01 1vsrA c.52.1.15 33332 1u61A 138 3.26e+01 a.149.1.1 107696 3bzcA 785 3.32e+01 1u5kA 244 3.39e+01 b.40.4.13,g.45.1.2 113038,113039 1bqbA 301 3.40e+01 1hyt d.92.1.2 58962 1a79A 171 3.43e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 2p5kA 64 3.49e+01 2vlaA 285 3.51e+01 1tz9A 367 3.51e+01 c.1.15.6 107466 2hiqA 113 3.58e+01 d.58.4.12 136529 1m32A 366 3.60e+01 c.67.1.3 78508 2di3A 239 3.63e+01 1t6sA 162 3.64e+01 a.4.5.60,a.4.5.60 112271,112272 1ermA 263 3.65e+01 1btl e.3.1.1 42690 1zcoA 262 3.77e+01 1fadA 99 3.83e+01 1fadA a.77.1.2 18428 1khcA 147 3.83e+01 b.34.9.2 68608 2g17A 337 3.87e+01 c.2.1.3,d.81.1.1 134512,134513 1tfzA 424 3.89e+01 d.32.1.3,d.32.1.3 106886,106887 1txgA 335 3.90e+01 a.100.1.6,c.2.1.6 112775,112776 1woyA 500 3.91e+01 a.27.1.1,c.26.1.1 121130,121131 2qr6A 393 3.94e+01 2h6bA 250 3.96e+01 1dlwA 116 3.97e+01 1dlyA a.1.1.1 14982 1y6iA 233 4.09e+01 a.118.1.22,a.261.1.1 122660,122661 2ohhA 404 4.13e+01 2hl0A 143 4.17e+01 1n9bA 265 4.20e+01 e.3.1.1 85463 1fm0E 150 4.26e+01 1fmaE d.41.5.1 38629 2pnwA 380 4.30e+01 1cpcA 162 4.31e+01 1cpcA a.1.1.3 15643 1fnnA 389 4.37e+01 1fnnA a.4.5.11,c.37.1.20 16129,32426 3c2bA 221 4.38e+01 1u5tB 169 4.47e+01 a.4.5.54,a.4.5.54 107686,107687 1sa3A 262 4.49e+01 c.52.1.23 105400 1l2lA 457 4.49e+01 c.72.1.3 77656 1gd2E 70 4.49e+01 1gd2G h.1.3.1 45528 1yyaA 250 4.52e+01 1giqA 413 4.59e+01 d.166.1.1,d.166.1.1 76224,76225 1wd6A 123 4.60e+01 d.58.4.12 114525 2o09A 189 4.65e+01 2ip2A 334 4.67e+01 1faoA 126 4.70e+01 1faoA b.55.1.1 26974 1qmeA 702 4.75e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 2esnA 310 4.75e+01 a.4.5.37,c.94.1.1 132333,132334 1wk8A 194 4.81e+01 1oltA 457 4.81e+01 c.1.28.2 93334 1kafA 108 4.81e+01 d.199.1.1 68372 2r3sA 335 4.83e+01 1qhfA 240 4.88e+01 1qhfA c.60.1.1 33960 3bboO 135 4.89e+01 3bk2A 562 5.01e+01 2iy2A 72 5.07e+01 2uubD 209 5.12e+01 d.66.1.2 139935 1nkzA 53 5.16e+01 f.3.1.1 80611 1qc7A 101 5.17e+01 1qc7A a.118.14.1 18456 1na6A 404 5.28e+01 b.142.1.1,c.52.1.22 91748,91749 3ch3X 265 5.35e+01 2k2rA 129 5.38e+01 1g2hA 61 5.43e+01 1g2hA a.4.1.12 60224 1jboA 162 5.43e+01 a.1.1.3 84150 2ac3A 316 5.48e+01 1htyA 1015 5.51e+01 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 1korA 400 5.59e+01 c.26.2.1,d.210.1.1 72824,72825 1mtyB 384 5.61e+01 1mtyB a.25.1.2 16740 2fxtA 192 5.64e+01 2odsA 265 5.64e+01 1btl 263 5.68e+01 1btl 2duyA 75 5.73e+01 2q09A 416 5.78e+01 2vqeD 209 5.82e+01 2fukA 220 5.82e+01 1j0aA 325 5.89e+01 c.79.1.1 83871 1g41A 444 5.89e+01 1do0A c.37.1.20 32450 1gk8I 140 5.91e+01 d.73.1.1 65242 1fjgD 209 5.92e+01 1c05A d.66.1.2 39553 2jv3A 110 5.92e+01 2rfpA 171 5.95e+01 3cneA 175 5.97e+01 1q3lA 69 5.99e+01 b.34.13.2 111652 1yd9A 193 6.03e+01 c.50.1.2 122976 1a8h 500 6.05e+01 1a8h 3cvjA 243 6.08e+01 2jgzB 260 6.14e+01 2c5uA 375 6.19e+01 2d5bA 500 6.20e+01 a.27.1.1,c.26.1.1 131268,131269 1lbu 213 6.27e+01 1lbu 1lbuA 213 6.27e+01 a.20.1.1,d.65.1.1 16416,39549 2ow6A 1045 6.30e+01 1qwnA 1045 6.30e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1izmA 184 6.34e+01 a.199.1.1 90725 1eexB 224 6.38e+01 1dioB c.51.3.1 33213 2iafA 151 6.39e+01 d.81.2.1 137157 1x2gA 337 6.40e+01 1yz7A 188 6.41e+01 2ga1A 106 6.42e+01 a.4.1.16 134850 2e18A 257 6.47e+01 1ve2A 235 6.48e+01 c.90.1.1 120008 2g8lA 299 6.51e+01 e.50.1.1 134775 1x8hA 228 6.52e+01 d.157.1.1 114961 3bczA 293 6.58e+01 1x8gA 227 6.58e+01 d.157.1.1 114960 2qdsA 227 6.58e+01 2jj7A 186 6.59e+01 1g8iA 190 6.61e+01 1rec a.39.1.5 60363 1z3eB 73 6.65e+01 a.60.3.1 124401 1o6dA 163 6.67e+01 c.116.1.3 92567 2q3bA 313 6.69e+01 2ftwA 521 6.69e+01 b.92.1.3,c.1.9.6 134083,134084 1o6sB 105 6.72e+01 b.1.6.1 81096 1jmoA 480 6.76e+01 e.1.1.1 77138 1ockA 412 6.77e+01 c.117.1.1 86802 2q43A 418 6.78e+01 c.56.5.4,d.58.19.1 139821,139822 2h5gA 463 6.81e+01 2nq5A 755 6.85e+01 2gtqA 867 6.85e+01 1wu7A 434 6.86e+01 c.51.1.1,d.104.1.1 121275,121276 2of3A 266 6.94e+01 2im8A 131 6.95e+01 a.24.26.1 137506 1s2wA 295 7.05e+01 c.1.12.7 98407 2z67A 456 7.06e+01 1wddS 128 7.06e+01 d.73.1.1 114532 1iibA 106 7.07e+01 1iibA c.44.2.1 32648 2exrA 524 7.11e+01 3c19A 186 7.11e+01 1wnyA 186 7.12e+01 1wlsA 328 7.17e+01 2yv9A 291 7.19e+01 1u4bA 580 7.20e+01 c.55.3.5,e.8.1.1 107664,107665 2hhvA 580 7.21e+01 c.55.3.5,e.8.1.1 136514,136515 1r9kA 172 7.23e+01 a.168.1.1 104869 2p86A 215 7.24e+01 1dofA 403 7.26e+01 1c3cA a.127.1.1 19429 2dy1A 665 7.39e+01 1xwiA 322 7.39e+01 1yyqA 374 7.40e+01 1y8qA 346 7.45e+01 2akaA 776 7.45e+01 1gzsB 165 7.50e+01 a.168.1.1 76425 2omzB 105 7.63e+01 1y8cA 246 7.63e+01 c.66.1.43 116563 2ekgA 327 7.66e+01 2g37A 327 7.94e+01 2q4wA 524 7.95e+01