# List of top-scoring protein chains for t04-100-30-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 5.37e-16 2fswA 107 9.53e-15 a.4.5.69 134042 1z7uA 112 2.28e-14 a.4.5.69 124672 1yyvA 131 3.10e-14 a.4.5.69 124254 2f2eA 146 8.20e-14 a.4.5.69 132808 3bpvA 138 4.65e-05 2a61A 145 6.13e-05 a.4.5.28 126187 1ub9A 100 6.25e-05 a.4.5.28 99159 2ethA 154 6.33e-05 a.4.5.28 132358 1smtA 122 1.70e-04 1smtA a.4.5.5 16109 2fbhA 146 1.73e-04 a.4.5.28 133245 3bj6A 152 1.96e-04 1r1tA 122 2.45e-04 a.4.5.5 104769 2pexA 153 4.28e-04 1r1uA 106 6.18e-04 a.4.5.5 104771 2gxgA 146 7.18e-04 2fbiA 142 9.23e-04 a.4.5.28 133246 3cjnA 162 1.13e-03 1xmaA 145 1.34e-03 a.4.5.61 115477 2oqgA 114 1.37e-03 1bjaA 95 2.30e-03 1bjaA a.4.5.9 16122 1sfxA 109 2.71e-03 a.4.5.50 105505 3b73A 111 2.77e-03 2d1hA 109 2.99e-03 a.4.5.50 131125 2bv6A 142 3.06e-03 2hr3A 147 3.13e-03 a.4.5.28 136678 1z91A 147 3.14e-03 a.4.5.28 124736 1lnwA 147 3.31e-03 a.4.5.28 78104 3cdhA 155 3.64e-03 1lj9A 144 3.85e-03 a.4.5.28 78035 2eshA 118 4.48e-03 a.4.5.61 132325 2h09A 155 5.00e-03 3bddA 142 5.76e-03 2co5A 99 7.04e-03 3broA 141 7.77e-03 2b0lA 102 9.89e-03 a.4.5.66 127641 2cg4A 152 1.04e-02 a.4.5.32,d.58.4.2 130417,130418 1ucrA 78 1.06e-02 a.4.5.45 99188 2p5vA 162 1.12e-02 3ctaA 230 1.23e-02 1s3jA 155 1.28e-02 a.4.5.28 98437 2e7xA 150 1.28e-02 2pn6A 150 1.74e-02 2pg4A 95 1.90e-02 2fbkA 181 1.90e-02 a.4.5.28 133247 1yg2A 179 2.11e-02 a.4.5.61 116681 1tw3A 360 2.24e-02 a.4.5.29,c.66.1.12 107373,107374 2p8tA 200 2.80e-02 2obpA 96 3.06e-02 1j75A 67 3.91e-02 a.4.5.19 62673 2e1nA 138 3.94e-02 1fx7A 230 4.07e-02 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 2cyyA 151 4.22e-02 a.4.5.32,d.58.4.2 131028,131029 2rdpA 150 4.26e-02 1jgsA 138 4.36e-02 a.4.5.28 66683 1y0uA 96 4.45e-02 a.4.5.5 116310 3bjaA 139 4.63e-02 1ri7A 171 4.89e-02 a.4.5.32,d.58.4.2 97504,97505 2hgcA 102 6.03e-02 2qvoA 95 6.83e-02 2dtrA 226 8.40e-02 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 2heoA 67 8.65e-02 1mzbA 136 8.69e-02 a.4.5.42 91497 2dtr 226 8.82e-02 1bi0 2v79A 135 9.14e-02 2v7fA 150 9.52e-02 2nnnA 140 9.58e-02 2cfxA 144 9.92e-02 a.4.5.32,d.58.4.2 130395,130396 3boqA 160 1.04e-01 2dbbA 151 1.11e-01 1hw1A 239 1.11e-01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1u2wA 122 1.19e-01 a.4.5.5 119487 1r7jA 95 1.20e-01 a.4.5.49 104836 2ax8A 256 1.24e-01 2qz8A 149 1.27e-01 2ax9A 256 1.29e-01 a.123.1.1 127481 2fu4A 83 1.35e-01 1q1hA 110 1.36e-01 a.4.5.41 95580 2dqlA 115 1.53e-01 2nyxA 168 1.64e-01 2jtvA 65 1.76e-01 1tbxA 99 2.07e-01 a.4.5.48 106748 2ivmA 150 2.20e-01 2ax6A 256 2.68e-01 a.123.1.1 127479 1mkmA 249 2.69e-01 a.4.5.33,d.110.2.2 79242,79243 1zybA 232 3.01e-01 a.4.5.4,b.82.3.2 125815,125816 2gqqA 163 3.07e-01 2fa5A 162 3.26e-01 2ia0A 171 3.42e-01 1t98A 287 3.50e-01 a.4.5.65,a.47.6.1 119196,119197 2ev0A 142 3.55e-01 a.4.5.24,a.76.1.1 132413,132414 2qwwA 154 3.71e-01 1ulyA 192 4.18e-01 a.4.5.58 113297 2qq9A 226 4.36e-01 1xmkA 79 4.52e-01 a.4.5.19 122165 1gvjA 146 4.71e-01 a.4.5.21 90525 1dpuA 99 4.84e-01 1dpuA a.4.5.16 16150 1on2A 142 5.34e-01 a.4.5.24,a.76.1.1 87103,87104 2ek5A 129 5.54e-01 1t7rA 269 5.87e-01 a.123.1.1 106635 2di3A 239 6.04e-01 1sfuA 75 6.09e-01 a.4.5.19 105503 2ia2A 265 6.53e-01 2hoeA 380 7.00e-01 a.4.5.63,c.55.1.10,c.55.1.10 136639,136640,136641 3bwgA 239 7.13e-01 1z1dA 103 7.90e-01 a.4.5.16 124351 1b9mA 265 8.07e-01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1tz9A 367 9.55e-01 c.1.15.6 107466 1wj5A 120 1.01e+00 a.4.5.59 114692 1sd4A 126 1.05e+00 a.4.5.39 105428 1jhfA 202 1.26e+00 a.4.5.2,b.87.1.1 63057,63058 1p4xA 250 1.29e+00 a.4.5.28,a.4.5.28 87784,87785 1yzbA 182 1.45e+00 2jt1A 77 1.47e+00 1w9yA 319 1.73e+00 b.82.2.1 120801 1oyiA 82 1.75e+00 a.4.5.19 93729 2nr3A 183 1.75e+00 1fp1D 372 1.80e+00 1fpqA a.4.5.29,c.66.1.12 59939,59940 1ixcA 294 2.03e+00 a.4.5.37,c.94.1.1 83764,83765 1bm9A 122 2.05e+00 1bm9A a.4.5.7 16116 1s2wA 295 2.09e+00 c.1.12.7 98407 2pjpA 121 2.18e+00 1bia 321 2.31e+00 1bia 1biaA 321 2.31e+00 a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 3bz6A 183 2.42e+00 2gmgA 105 2.52e+00 1xn7A 78 2.86e+00 a.4.5.62 115576 1k78A 149 3.08e+00 a.4.1.5,a.4.1.5 68255,68256 1i6xA 209 3.19e+00 a.4.5.4,b.82.3.2 83673,83674 3c7jA 237 3.47e+00 2hs5A 239 3.53e+00 1hw5A 210 3.60e+00 2cgpA a.4.5.4,b.82.3.2 16098,28137 1wsuA 124 3.67e+00 a.4.5.35,a.4.5.35 121245,121246 2agaA 190 3.72e+00 1qzzA 374 3.80e+00 a.4.5.29,c.66.1.12 96719,96720 1a79A 171 3.94e+00 1a79A c.52.2.1,d.75.1.1 33340,39739 1yo5C 97 4.14e+00 a.4.5.21 123768 1okrA 123 4.28e+00 a.4.5.39 93269 2r3sA 335 5.17e+00 6paxA 133 5.21e+00 6paxA a.4.1.5,a.4.1.5 64758,64759 2qgnA 322 5.42e+00 2pefA 373 5.99e+00 2g7uA 257 6.01e+00 1q7zA 566 6.05e+00 c.1.21.2,c.1.26.1 96090,96091 1r26A 125 6.40e+00 c.47.1.1 96847 1bc8C 93 6.40e+00 1awcA a.4.5.21 16168 1c4zA 358 6.58e+00 1c4zA d.148.1.1 41766 1t6t1 118 6.74e+00 3bofA 566 6.79e+00 2pq8A 278 6.83e+00 1xviA 275 6.86e+00 c.108.1.10 116088 2rkhA 180 6.87e+00 2nyuA 196 7.08e+00 1hlvA 131 7.29e+00 a.4.1.7,a.4.1.7 65854,65855 2h6bA 250 7.41e+00 3rubS 123 8.05e+00 1rboC d.73.1.1 39616 1rkbA 173 8.08e+00 c.37.1.1 111854 1pymA 295 8.29e+00 1pymA c.1.12.7 29308 1x19A 359 8.35e+00 1xb4A 202 8.45e+00 a.4.5.54,a.4.5.54 121832,121833 1j5yA 187 8.96e+00 a.4.5.1,d.94.2.1 71592,71593 1rr7A 129 1.02e+01 a.4.1.14 105075 1hstA 90 1.05e+01 1hstA a.4.5.13 16140 1b74A 254 1.06e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 2aaxA 275 1.08e+01 2qkoA 215 1.10e+01 2oblA 347 1.17e+01 1we0A 187 1.17e+01 c.47.1.10 120930 1wi9A 72 1.19e+01 a.4.5.47 114663 1v2yA 105 1.24e+01 d.15.1.1 100275 2nszA 129 1.27e+01 a.118.1.14 138560 1khcA 147 1.28e+01 b.34.9.2 68608 3by6A 126 1.32e+01 1w9hA 427 1.35e+01 c.55.3.10 120785 1eejA 216 1.40e+01 1eejA c.47.1.9,d.17.3.1 33057,38071 2bbsA 290 1.40e+01 3brjA 175 1.51e+01 2b5tI 432 1.51e+01 e.1.1.1 127905 2pfzA 301 1.54e+01 1t6sA 162 1.56e+01 a.4.5.60,a.4.5.60 112271,112272 2v75A 104 1.62e+01 2v8pA 271 1.62e+01 2rjbA 455 1.68e+01 2givA 295 1.69e+01 d.108.1.1 135253 1qbjA 81 1.77e+01 1qbjA a.4.5.19 16155 1fadA 99 1.80e+01 1fadA a.77.1.2 18428 1jvwA 167 1.80e+01 d.26.1.1 71907 1a49A 530 1.83e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27026,29255,33109 1eokA 290 1.83e+01 1eokA c.1.8.5 28991 1vi0A 206 1.86e+01 a.4.1.9,a.121.1.1 100720,100721 2fnaA 357 1.87e+01 a.4.5.11,c.37.1.20 133809,133810 1zgdA 312 1.89e+01 1b00A 127 1.91e+01 3chy c.23.1.1 31122 2q4fA 149 1.93e+01 a.24.10.2 139847 2g50A 530 1.95e+01 b.58.1.1,c.1.12.1,c.49.1.1 134618,134619,134620 2v1xA 591 2.01e+01 2yxyA 115 2.10e+01 1bkdS 439 2.11e+01 1bkdS a.117.1.1 19111 1g2hA 61 2.11e+01 1g2hA a.4.1.12 60224 1jhgA 101 2.12e+01 1jhgA a.4.12.1 19009 2paqA 201 2.13e+01 a.211.1.1 139643 2c5uA 375 2.13e+01 1on3A 523 2.17e+01 c.14.1.4,c.14.1.4 87107,87108 2ixmA 303 2.19e+01 a.268.1.1 137776 2ajtA 500 2.21e+01 b.43.2.2,c.85.1.2 126894,126895 1vzqH 250 2.21e+01 2cksA 306 2.34e+01 2aelA 374 2.37e+01 3bbpD 71 2.39e+01 2nyiA 195 2.39e+01 1twfB 1224 2.45e+01 e.29.1.1 112726 1s7oA 113 2.48e+01 a.4.13.3 105354 1vr1H 261 2.52e+01 5ptp 2i5hA 205 2.53e+01 1ybzA 91 2.54e+01 a.130.1.1 122901 2cf8H 257 2.61e+01 1m1eB 81 2.62e+01 a.161.1.1 78400 1xmiA 291 2.63e+01 c.37.1.12 115489 2idbA 505 2.64e+01 b.45.1.3,d.333.1.1 137270,137271 1c4kA 730 2.68e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 2dqrA 122 2.77e+01 1iktA 120 2.80e+01 d.106.1.1 66188 2akaA 776 2.82e+01 1jipA 403 2.84e+01 a.104.1.1 66748 2pgbB 259 2.87e+01 2himA 358 2.89e+01 1g291 372 2.92e+01 1g291 1unkA 87 2.93e+01 1cei a.28.2.1 16935 2hr0A 645 2.94e+01 1rblI 109 2.97e+01 d.73.1.1 118599 1lvaA 258 2.97e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1ywwA 85 2.99e+01 2parA 201 3.00e+01 1h0hB 214 3.04e+01 d.58.1.5 76437 2h41A 95 3.07e+01 1d0yA 761 3.12e+01 1lvk b.34.3.1,c.37.1.9 24581,32178 1zesA 125 3.13e+01 c.23.1.1 124994 2ii0A 490 3.25e+01 a.117.1.1 137425 2ps5A 374 3.25e+01 1rscI 111 3.30e+01 d.73.1.1 118620 1yviA 149 3.36e+01 a.24.10.2 124099 2qsfA 533 3.47e+01 2aotA 292 3.47e+01 c.66.1.19 127098 2iugA 120 3.48e+01 2ilrA 264 3.54e+01 2bvrH 252 3.58e+01 2iu1A 208 3.61e+01 1vj1A 363 3.66e+01 b.35.1.2,c.2.1.1 100794,100795 1o51A 114 3.68e+01 d.58.5.4 92480 2p1mA 163 3.68e+01 2rekA 199 3.70e+01 2gmsA 390 3.72e+01 3cg4A 142 3.73e+01 2frhA 127 3.73e+01 a.4.5.28 133988 2ev1A 222 3.80e+01 2q37A 181 3.83e+01 2dk5A 91 3.88e+01 1vsrA 136 3.89e+01 1vsrA c.52.1.15 33332 1r9oA 477 3.91e+01 a.104.1.1 104878 1g1xC 88 3.97e+01 1fjfR a.4.8.1 16249 2cjjA 93 3.97e+01 a.4.1.3 130540 1jqeA 292 3.99e+01 c.66.1.19 71789 1ad3A 452 4.18e+01 1ad3A c.82.1.1 35335 1hh2P 344 4.23e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 65835,65836,65837,65838 1h8dH 260 4.24e+01 5ptp 3b8xA 390 4.32e+01 2fxtA 192 4.32e+01 1yyqA 374 4.32e+01 2py6A 409 4.36e+01 2gbbA 156 4.40e+01 1gytA 503 4.41e+01 c.50.1.1,c.56.5.3 70765,70766 2e18A 257 4.42e+01 1w9iA 770 4.43e+01 1cf7B 95 4.45e+01 1cf7B a.4.5.17 16152 2cq2A 114 4.53e+01 d.58.7.1 130713 2oexA 351 4.54e+01 1sf9A 128 4.65e+01 b.34.15.1 98831 2ip2A 334 4.70e+01 1a28A 256 4.72e+01 1a28A a.123.1.1 19290 1tadA 324 4.76e+01 1cipA a.66.1.1,c.37.1.8 18194,32077 1ufzA 83 4.78e+01 a.5.9.1 107821 1zynA 202 4.78e+01 c.47.1.2,c.47.1.2 125838,125839 2qcoA 210 4.79e+01 1iv8A 720 4.82e+01 b.71.1.1,c.1.8.1 76842,76843 1af3 196 4.85e+01 1maz 2aouA 292 4.89e+01 c.66.1.19 127100 3ygsP 97 4.89e+01 3ygsP a.77.1.3 18435 2qrvA 295 4.93e+01 1z6rA 406 5.08e+01 a.4.5.63,c.55.1.10,c.55.1.10 124557,124558,124559 1m32A 366 5.11e+01 c.67.1.3 78508 1pjaA 302 5.14e+01 c.69.1.13 94758 2o71A 115 5.14e+01 2cveA 191 5.16e+01 d.14.1.11,d.58.11.2 130869,130870 1xbrA 184 5.16e+01 1xbrA b.2.5.4 22458 2vqeR 88 5.19e+01 1k8tA 510 5.31e+01 e.41.1.1 68316 1kiyA 374 5.32e+01 a.128.1.5 72555 1z8oA 404 5.33e+01 a.104.1.1 124722 2fmyA 220 5.39e+01 1oltA 457 5.39e+01 c.1.28.2 93334 1ka2A 499 5.51e+01 d.92.1.5 77305 1pazA 123 5.52e+01 b.6.1.1 22878 3c1mA 473 5.59e+01 1ir21 140 5.67e+01 2c3nA 247 5.67e+01 2g62A 325 5.72e+01 a.268.1.1 134685 1o69A 394 5.84e+01 c.67.1.4 92560 2pijA 67 5.87e+01 2g9wA 138 5.88e+01 2b7aA 293 5.88e+01 2c81A 418 5.95e+01 1xsvA 113 6.06e+01 a.4.13.3 116003 1h6pA 203 6.09e+01 a.146.1.1 60690 1lvk 762 6.09e+01 1lvk 2jbaA 127 6.10e+01 2e3dA 302 6.10e+01 2nq5A 755 6.11e+01 2jbhA 225 6.12e+01 1lfkA 398 6.16e+01 a.104.1.1 77926 2hnhA 910 6.19e+01 1sqnA 261 6.20e+01 a.123.1.1 105944 1gk8I 140 6.27e+01 d.73.1.1 65242 1od5A 492 6.28e+01 b.82.1.2,b.82.1.2 86832,86833 1tfzA 424 6.28e+01 d.32.1.3,d.32.1.3 106886,106887 1hq0A 295 6.28e+01 1hzgA d.194.1.1 61122 1qwkA 317 6.30e+01 c.1.7.1 96482 1gppA 237 6.32e+01 b.86.1.2 76262 1xx7A 184 6.34e+01 a.211.1.1 116143 1g7oA 215 6.35e+01 1g7oA a.45.1.1,c.47.1.5 60332,60333 1cei 94 6.36e+01 1cei 1qf5A 431 6.41e+01 1adeA c.37.1.10 32212 3bk2A 562 6.44e+01 2pzeA 229 6.46e+01 2pbqA 178 6.46e+01 2ftwA 521 6.55e+01 b.92.1.3,c.1.9.6 134083,134084 2qc0A 373 6.60e+01 1t6jA 714 6.61e+01 a.127.1.2 112259 3cfyA 137 6.62e+01 1bdmA 327 6.64e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 1auk 489 6.71e+01 1auk 1aukA 489 6.71e+01 c.76.1.2 35030 1otrA 49 6.80e+01 a.5.2.4 87413 2oqqA 42 6.80e+01 2d5fA 493 6.87e+01 1rkuA 206 7.00e+01 c.108.1.11 97627 2ijmA 281 7.01e+01 1xbtA 193 7.05e+01 c.37.1.24,g.39.1.14 115080,115081 1n13B 113 7.08e+01 1sr7A 259 7.15e+01 a.123.1.1 105957 1maz 221 7.21e+01 1maz 1y8qA 346 7.23e+01 2ieeA 271 7.26e+01 2j01P 150 7.32e+01 1qp6A 35 7.32e+01 1qp6A k.16.1.1 46443 1py0A 125 7.36e+01 b.6.1.1 111645 1tqmA 282 7.41e+01 a.4.5.56,d.144.1.9 107236,107237 2qdjA 304 7.43e+01 1nrvA 105 7.48e+01 d.93.1.1 86126 2oolA 337 7.51e+01 1pq1A 196 7.52e+01 f.1.4.1 94986 1zarA 282 7.59e+01 a.4.5.56,d.144.1.9 124843,124844 2po3A 424 7.61e+01 1qhfA 240 7.65e+01 1qhfA c.60.1.1 33960 1j3mA 129 7.70e+01 d.129.7.1 103836 2fe3A 145 7.72e+01 2nn4A 72 7.72e+01 1r0wA 286 7.73e+01 c.37.1.12 96754 2hp0A 466 7.80e+01 2eqaA 352 7.88e+01 1dofA 403 7.98e+01 1c3cA a.127.1.1 19429