# List of top-scoring protein chains for t2k-100-30-near-backbone-11-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 8.12e-16 2fswA 107 4.30e-15 a.4.5.69 134042 1z7uA 112 9.56e-15 a.4.5.69 124672 1yyvA 131 1.55e-14 a.4.5.69 124254 2f2eA 146 4.60e-14 a.4.5.69 132808 2a61A 145 1.14e-05 a.4.5.28 126187 3bpvA 138 1.35e-05 1ub9A 100 1.50e-05 a.4.5.28 99159 2ethA 154 3.83e-05 a.4.5.28 132358 2fbhA 146 5.94e-05 a.4.5.28 133245 3bj6A 152 7.11e-05 2pexA 153 8.57e-05 1smtA 122 1.12e-04 1smtA a.4.5.5 16109 1r1tA 122 1.63e-04 a.4.5.5 104769 3cjnA 162 1.83e-04 2gxgA 146 1.91e-04 2hr3A 147 2.29e-04 a.4.5.28 136678 2fbiA 142 2.85e-04 a.4.5.28 133246 1r1uA 106 3.48e-04 a.4.5.5 104771 2bv6A 142 3.68e-04 1z91A 147 3.71e-04 a.4.5.28 124736 1i1gA 141 3.93e-04 a.4.5.32,d.58.4.2 65982,65983 1lnwA 147 5.63e-04 a.4.5.28 78104 2d1hA 109 5.83e-04 a.4.5.50 131125 1xmaA 145 5.92e-04 a.4.5.61 115477 1sfxA 109 5.99e-04 a.4.5.50 105505 1lj9A 144 6.00e-04 a.4.5.28 78035 3cdhA 155 6.27e-04 1s3jA 155 9.12e-04 a.4.5.28 98437 3b73A 111 9.46e-04 2h09A 155 9.89e-04 2eshA 118 1.30e-03 a.4.5.61 132325 3ctaA 230 1.41e-03 3bddA 142 1.47e-03 2oqgA 114 1.64e-03 1bjaA 95 1.83e-03 1bjaA a.4.5.9 16122 1i1sA 96 2.22e-03 1bjaA a.4.5.9 16124 2b0lA 102 2.30e-03 a.4.5.66 127641 2co5A 99 2.47e-03 1ucrA 78 2.52e-03 a.4.5.45 99188 3broA 141 3.09e-03 2pn6A 150 3.20e-03 2p5vA 162 3.65e-03 2e7xA 150 3.67e-03 2rdpA 150 5.46e-03 1jgsA 138 5.48e-03 a.4.5.28 66683 3bjaA 139 6.17e-03 2e1nA 138 6.28e-03 2cyyA 151 8.14e-03 a.4.5.32,d.58.4.2 131028,131029 1yg2A 179 9.92e-03 a.4.5.61 116681 2fbkA 181 1.04e-02 a.4.5.28 133247 2nnnA 140 1.07e-02 2qvoA 95 1.15e-02 1b1bA 140 1.15e-02 1bi0 a.4.5.24,a.76.1.1 16215,18421 1j75A 67 1.19e-02 a.4.5.19 62673 2cg4A 152 1.26e-02 a.4.5.32,d.58.4.2 130417,130418 1ri7A 171 1.41e-02 a.4.5.32,d.58.4.2 97504,97505 1tw3A 360 1.41e-02 a.4.5.29,c.66.1.12 107373,107374 2obpA 96 1.45e-02 2pg4A 95 1.66e-02 1f5tA 121 1.67e-02 1bi0 a.4.5.24,a.76.1.1 16203,18409 2nyxA 168 1.96e-02 2p8tA 200 2.03e-02 1tbxA 99 2.56e-02 a.4.5.48 106748 1u2wA 122 3.05e-02 a.4.5.5 119487 2dqlA 115 3.13e-02 2heoA 67 3.17e-02 1fx7A 230 3.79e-02 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 1q1hA 110 4.06e-02 a.4.5.41 95580 2cfxA 144 4.29e-02 a.4.5.32,d.58.4.2 130395,130396 2hgcA 102 4.97e-02 2dbbA 151 5.03e-02 3boqA 160 5.10e-02 1ulyA 192 5.12e-02 a.4.5.58 113297 1y0uA 96 5.53e-02 a.4.5.5 116310 1mzbA 136 6.99e-02 a.4.5.42 91497 2fu4A 83 7.61e-02 1mkmA 249 7.88e-02 a.4.5.33,d.110.2.2 79242,79243 2dtr 226 8.84e-02 1bi0 2dtrA 226 9.21e-02 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 2jtvA 65 9.84e-02 1bi0 226 1.02e-01 1bi0 2qz8A 149 1.15e-01 2ax9A 256 1.21e-01 a.123.1.1 127481 2ax8A 256 1.21e-01 2ev0A 142 1.23e-01 a.4.5.24,a.76.1.1 132413,132414 1r7jA 95 1.25e-01 a.4.5.49 104836 1on2A 142 1.42e-01 a.4.5.24,a.76.1.1 87103,87104 2ia0A 171 1.47e-01 2qwwA 154 1.58e-01 2ivmA 150 1.63e-01 2gqqA 163 1.82e-01 2fa5A 162 1.82e-01 1t98A 287 1.83e-01 a.4.5.65,a.47.6.1 119196,119197 1zybA 232 1.94e-01 a.4.5.4,b.82.3.2 125815,125816 1fp1D 372 2.03e-01 1fpqA a.4.5.29,c.66.1.12 59939,59940 1xmkA 79 2.05e-01 a.4.5.19 122165 1c0wA 225 2.09e-01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16211,18417,24455 2v79A 135 2.15e-01 1e2xA 243 2.30e-01 1e2xA a.4.5.6,a.78.1.1 16113,18443 1dpuA 99 2.45e-01 1dpuA a.4.5.16 16150 2ax6A 256 2.59e-01 a.123.1.1 127479 2hoeA 380 2.61e-01 a.4.5.63,c.55.1.10,c.55.1.10 136639,136640,136641 2qq9A 226 2.71e-01 1hw1A 239 2.75e-01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1z1dA 103 4.58e-01 a.4.5.16 124351 1sfuA 75 5.40e-01 a.4.5.19 105503 1xn7A 78 5.74e-01 a.4.5.62 115576 1jhfA 202 6.11e-01 a.4.5.2,b.87.1.1 63057,63058 1gvjA 146 6.12e-01 a.4.5.21 90525 1t6t1 118 6.20e-01 1tz9A 367 6.46e-01 c.1.15.6 107466 2ek5A 129 7.15e-01 2pjpA 121 7.66e-01 2cgpA 210 8.04e-01 2cgpA a.4.5.4,b.82.3.2 16102,28141 1i6xA 209 8.55e-01 a.4.5.4,b.82.3.2 83673,83674 1lea 84 8.66e-01 1lea 2di3A 239 8.66e-01 1g6nA 210 8.70e-01 2cgpA a.4.5.4,b.82.3.2 16100,28139 3c7jA 237 9.04e-01 3bwgA 239 9.12e-01 2jt1A 77 9.91e-01 1p4xA 250 9.99e-01 a.4.5.28,a.4.5.28 87784,87785 1j5yA 187 1.03e+00 a.4.5.1,d.94.2.1 71592,71593 1hw5A 210 1.14e+00 2cgpA a.4.5.4,b.82.3.2 16098,28137 2nyiA 195 1.16e+00 1wj5A 120 1.23e+00 a.4.5.59 114692 2sttA 96 1.27e+00 1awcA a.4.5.21 16163 1sd4A 126 1.37e+00 a.4.5.39 105428 2ia2A 265 1.56e+00 1qzzA 374 1.63e+00 a.4.5.29,c.66.1.12 96719,96720 1bia 321 1.64e+00 1bia 1biaA 321 1.64e+00 a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1bm9A 122 1.71e+00 1bm9A a.4.5.7 16116 2gmgA 105 1.74e+00 1wsuA 124 1.76e+00 a.4.5.35,a.4.5.35 121245,121246 1a49A 530 2.00e+00 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27026,29255,33109 1ft9A 222 2.03e+00 1ft9A a.4.5.4,b.82.3.1 16107,28131 2g50A 530 2.09e+00 b.58.1.1,c.1.12.1,c.49.1.1 134618,134619,134620 1a79A 171 2.13e+00 1a79A c.52.2.1,d.75.1.1 33340,39739 1hlvA 131 2.27e+00 a.4.1.7,a.4.1.7 65854,65855 1b9mA 265 2.28e+00 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1yzbA 182 2.30e+00 1okrA 123 2.45e+00 a.4.5.39 93269 2qgnA 322 2.45e+00 1t7rA 269 2.60e+00 a.123.1.1 106635 1ixcA 294 2.89e+00 a.4.5.37,c.94.1.1 83764,83765 2cksA 306 2.94e+00 1fliA 98 3.05e+00 1awcA a.4.5.21 16160 2h6bA 250 3.12e+00 1t6sA 162 3.49e+00 a.4.5.60,a.4.5.60 112271,112272 2nr3A 183 3.60e+00 2rkhA 180 3.81e+00 1qbjA 81 4.14e+00 1qbjA a.4.5.19 16155 3bz6A 183 4.16e+00 1s2wA 295 4.23e+00 c.1.12.7 98407 1awcA 110 4.43e+00 1awcA a.4.5.21 16167 1q7zA 566 4.65e+00 c.1.21.2,c.1.26.1 96090,96091 1oyiA 82 4.91e+00 a.4.5.19 93729 1yo5C 97 5.18e+00 a.4.5.21 123768 1wi9A 72 5.30e+00 a.4.5.47 114663 3bofA 566 5.33e+00 1hbxG 157 5.78e+00 1awcA a.4.5.21 60934 2hs5A 239 5.91e+00 1qgpA 77 6.02e+00 1qbjA a.4.5.19 16158 1bc8C 93 6.13e+00 1awcA a.4.5.21 16168 1c4zA 358 6.45e+00 1c4zA d.148.1.1 41766 2pefA 373 7.14e+00 1duxC 94 7.21e+00 1awcA a.4.5.21 16170 2agaA 190 7.34e+00 1r26A 125 7.52e+00 c.47.1.1 96847 2g7uA 257 7.69e+00 2rjbA 455 7.79e+00 1k78A 149 7.81e+00 a.4.1.5,a.4.1.5 68255,68256 1fpqA 372 7.90e+00 1fpqA a.4.5.29,c.66.1.12 59947,59948 1khcA 147 7.90e+00 b.34.9.2 68608 2c5uA 375 8.83e+00 2g9wA 138 9.28e+00 1cw0A 155 9.31e+00 1vsrA c.52.1.15 33333 6paxA 133 9.64e+00 6paxA a.4.1.5,a.4.1.5 64758,64759 1xb4A 202 9.90e+00 a.4.5.54,a.4.5.54 121832,121833 1rkbA 173 1.05e+01 c.37.1.1 111854 3rubS 123 1.08e+01 1rboC d.73.1.1 39616 2cjjA 93 1.14e+01 a.4.1.3 130540 2iu1A 208 1.18e+01 1b00A 127 1.19e+01 3chy c.23.1.1 31122 1w9hA 427 1.23e+01 c.55.3.10 120785 1twfB 1224 1.25e+01 e.29.1.1 112726 1x19A 359 1.26e+01 1pymA 295 1.27e+01 1pymA c.1.12.7 29308 2aaxA 275 1.29e+01 2fnaA 357 1.33e+01 a.4.5.11,c.37.1.20 133809,133810 1rblI 109 1.34e+01 d.73.1.1 118599 1vsrA 136 1.34e+01 1vsrA c.52.1.15 33332 2pq8A 278 1.36e+01 3by6A 126 1.44e+01 1rr7A 129 1.45e+01 a.4.1.14 105075 2qkoA 215 1.45e+01 1lvaA 258 1.46e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1xd7A 145 1.48e+01 a.4.5.55 109566 1g291 372 1.55e+01 1g291 1bw6A 56 1.59e+01 1bw6A a.4.1.7 16052 2gmsA 390 1.65e+01 1jhgA 101 1.67e+01 1jhgA a.4.12.1 19009 1zesA 125 1.68e+01 c.23.1.1 124994 2akaA 776 1.69e+01 2h41A 95 1.69e+01 2o71A 115 1.70e+01 1h8aC 128 1.73e+01 a.4.1.3,a.4.1.3 65731,65732 1eejA 216 1.79e+01 1eejA c.47.1.9,d.17.3.1 33057,38071 2oczA 231 1.83e+01 1pjaA 302 1.86e+01 c.69.1.13 94758 1jqeA 292 1.96e+01 c.66.1.19 71789 1g2hA 61 2.02e+01 1g2hA a.4.1.12 60224 2vgbA 528 2.05e+01 1zarA 282 2.07e+01 a.4.5.56,d.144.1.9 124843,124844 2dqrA 122 2.11e+01 2fxtA 192 2.11e+01 1o51A 114 2.12e+01 d.58.5.4 92480 2aotA 292 2.13e+01 c.66.1.19 127098 1zgdA 312 2.17e+01 2aouA 292 2.18e+01 c.66.1.19 127100 2dk5A 91 2.21e+01 1rscI 111 2.23e+01 d.73.1.1 118620 1z6rA 406 2.26e+01 a.4.5.63,c.55.1.10,c.55.1.10 124557,124558,124559 1b74A 254 2.26e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1w9iA 770 2.27e+01 3b8xA 390 2.33e+01 1iktA 120 2.34e+01 d.106.1.1 66188 2zfdA 226 2.37e+01 2vggA 528 2.40e+01 1v2yA 105 2.46e+01 d.15.1.1 100275 2pfzA 301 2.52e+01 1we0A 187 2.56e+01 c.47.1.10 120930 2frhA 127 2.59e+01 a.4.5.28 133988 1tqmA 282 2.62e+01 a.4.5.56,d.144.1.9 107236,107237 2vgiA 528 2.62e+01 2nn4A 72 2.69e+01 3cg4A 142 2.69e+01 1u5tA 233 2.78e+01 a.4.5.54,a.4.5.54 107684,107685 2vgfA 528 2.80e+01 2b5tI 432 2.80e+01 e.1.1.1 127905 2qrvA 295 2.93e+01 1kyzA 365 2.93e+01 a.4.5.29,c.66.1.12 73312,73313 1xviA 275 2.98e+01 c.108.1.10 116088 2ip2A 334 2.98e+01 1uhnA 189 3.05e+01 a.39.1.5 99399 2qc0A 373 3.05e+01 1rljA 139 3.06e+01 c.23.5.7 104983 1z7gA 217 3.13e+01 c.61.1.1 124624 2jbaA 127 3.20e+01 1l7vC 249 3.26e+01 c.37.1.12 73674 1otrA 49 3.30e+01 a.5.2.4 87413 1i4yA 114 3.30e+01 2mhr a.24.4.1 61738 2yxyA 115 3.31e+01 2bbsA 290 3.39e+01 1w9yA 319 3.43e+01 b.82.2.1 120801 2ftwA 521 3.43e+01 b.92.1.3,c.1.9.6 134083,134084 1m32A 366 3.45e+01 c.67.1.3 78508 2bzgA 232 3.49e+01 c.66.1.36 129559 2i5hA 205 3.51e+01 2scpA 174 3.53e+01 2scpA a.39.1.5 17256 2esrA 177 3.58e+01 c.66.1.46 132344 2iugA 120 3.59e+01 1fpxA 352 3.64e+01 1fpxA a.4.5.29,c.66.1.12 59950,59951 1b59A 370 3.69e+01 1bn5 a.4.5.25,d.127.1.1 16225,41162 1ordA 730 3.69e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31274,34503,41124 2givA 295 3.76e+01 d.108.1.1 135253 1k8tA 510 3.78e+01 e.41.1.1 68316 1fp2A 352 3.82e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1c4kA 730 3.89e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 1hstA 90 3.89e+01 1hstA a.4.5.13 16140 1in6A 334 3.94e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 1o69A 394 3.97e+01 c.67.1.4 92560 2jbhA 225 4.04e+01 1t0iA 191 4.10e+01 c.23.5.4 106209 1in4A 334 4.11e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 1pdnC 128 4.13e+01 6paxA a.4.1.5 16047 1xgsA 295 4.26e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1eokA 290 4.26e+01 1eokA c.1.8.5 28991 1cf7A 76 4.26e+01 1cf7B a.4.5.17 16151 1q3lA 69 4.34e+01 b.34.13.2 111652 1uoyA 64 4.57e+01 g.3.19.1 99709 2v75A 104 4.62e+01 2j2fA 363 4.64e+01 2ilrA 264 4.68e+01 1r9wA 145 4.75e+01 d.89.1.2 97264 1auaA 296 4.78e+01 a.5.3.1,c.13.1.1 16290,30882 1aua 296 4.78e+01 1aua 1cf7B 95 4.89e+01 1cf7B a.4.5.17 16152 2qi9C 249 4.89e+01 2fmyA 220 4.91e+01 2rekA 199 4.91e+01 1w4tA 299 4.95e+01 d.3.1.5 120639 1pazA 123 5.07e+01 b.6.1.1 22878 2nszA 129 5.25e+01 a.118.1.14 138560 1om2A 95 5.25e+01 1om2A a.23.4.1 16520 1iv8A 720 5.43e+01 b.71.1.1,c.1.8.1 76842,76843 1on3A 523 5.55e+01 c.14.1.4,c.14.1.4 87107,87108 2nyuA 196 5.57e+01 2e18A 257 5.66e+01 1tuzA 118 5.74e+01 a.39.1.7 112670 2p1mA 163 5.77e+01 1xbrA 184 5.82e+01 1xbrA b.2.5.4 22458 1trrA 107 5.84e+01 1jhgA a.4.12.1 19017 2oolA 337 5.90e+01 3ygsP 97 5.90e+01 3ygsP a.77.1.3 18435 2iafA 151 5.90e+01 d.81.2.1 137157 1a28A 256 5.94e+01 1a28A a.123.1.1 19290 2q4fA 149 6.06e+01 a.24.10.2 139847 1unkA 87 6.16e+01 1cei a.28.2.1 16935 1lj8A 493 6.17e+01 a.100.1.9,c.2.1.6 90392,90393 1d0yA 761 6.18e+01 1lvk b.34.3.1,c.37.1.9 24581,32178 1py0A 125 6.26e+01 b.6.1.1 111645 1x9bA 53 6.37e+01 a.10.2.1 114982 1egzA 291 6.47e+01 7a3hA c.1.8.3 28828 1qf5A 431 6.64e+01 1adeA c.37.1.10 32212 1e3yA 104 6.68e+01 1fadA a.77.1.2 18426 1afrA 345 6.68e+01 1afrA a.25.1.2 16805 2idbA 505 6.78e+01 b.45.1.3,d.333.1.1 137270,137271 2ev1A 222 6.84e+01 1tfzA 424 6.87e+01 d.32.1.3,d.32.1.3 106886,106887 1od5A 492 6.89e+01 b.82.1.2,b.82.1.2 86832,86833 2himA 358 6.91e+01 1xmiA 291 7.08e+01 c.37.1.12 115489 2vqeR 88 7.12e+01 1bg4A 302 7.17e+01 c.1.8.3 28806 1v54E 109 7.18e+01 a.118.11.1 100326 1h0hB 214 7.33e+01 d.58.1.5 76437 2gbbA 156 7.33e+01 1pea 385 7.35e+01 1pea 1fztA 211 7.38e+01 1qhfA c.60.1.1 60158 1peaA 385 7.38e+01 c.93.1.1 35662 1s7oA 113 7.40e+01 a.4.13.3 105354 1af7 274 7.42e+01 1af7 1af7A 274 7.45e+01 a.58.1.1,c.66.1.8 17928,34203 2cq2A 114 7.46e+01 d.58.7.1 130713 1sqnA 261 7.48e+01 a.123.1.1 105944 2hp0A 466 7.54e+01 2gclA 261 7.57e+01 b.55.1.10 134991 2c2xA 281 7.61e+01 2ajtA 500 7.62e+01 b.43.2.2,c.85.1.2 126894,126895 2qsrA 173 7.65e+01 1wn8A 22 7.69e+01 j.113.1.1 109427 1b3jA 274 7.84e+01 1agdA b.1.1.2,d.19.1.1 20855,38319 2occE 109 7.85e+01 2occE a.118.11.1 19224 1wk8A 194 7.86e+01 2oblA 347 7.90e+01 2ixmA 303 7.91e+01 a.268.1.1 137776 2j01P 150 7.93e+01 1n13B 113 7.93e+01 2od5A 116 7.96e+01