# 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.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 1g9oA 91 2.76e-17 1pdr b.36.1.1 60400 2fneA 117 8.42e-17 2fe5A 94 1.73e-16 1tp5A 119 3.68e-16 1be9A 119 4.02e-16 1pdr b.36.1.1 24774 2fcfA 103 4.34e-16 1qavA 90 3.39e-15 1qauA b.36.1.1 24777 1n7fA 97 3.06e-14 b.36.1.1 91692 1ihjA 98 3.16e-14 1pdr b.36.1.1 62382 1n7eA 97 3.21e-14 b.36.1.1 91691 2f5yA 91 5.83e-14 1qauA 112 6.88e-14 1qauA b.36.1.1 24779 2f0aA 98 1.08e-13 1l6oA 95 1.13e-13 b.36.1.1 84534 1q3oA 109 1.16e-13 b.36.1.1 95700 1mfgA 95 2.19e-13 b.36.1.1 79043 1wf7A 103 2.82e-13 1v5lA 103 5.44e-13 b.36.1.1 108378 1nf3C 128 7.03e-13 b.36.1.1 85596 1kwaA 88 1.68e-12 1kwaA b.36.1.1 24772 1r6jA 82 5.14e-12 b.36.1.1 97151 1nteA 82 1.05e-11 b.36.1.1 86163 1fc6A 388 1.69e-07 1fc6A b.36.1.3,c.14.1.2 64738,64739 1te0A 318 4.64e-07 1lcyA 325 1.59e-06 b.36.1.4,b.47.1.1 73834,73835 1sotA 320 8.47e-06 b.36.1.4,b.47.1.1 105852,105853 1y8tA 324 2.49e-05 1db3A 372 4.52e-02 1db3A c.2.1.2 29813 2bh4X 134 6.14e-01 1cot 129 8.54e-01 1ycc a.3.1.1 15899 1to2I 64 9.24e-01 1lw6I 64 9.90e-01 d.40.1.1 74294 1vpqA 273 1.39e+00 1dxrH 258 1.60e+00 6prcH b.41.1.1,f.23.10.1 25456,43433 1ujxA 119 1.60e+00 b.26.1.2 99473 1a6f 119 1.83e+00 1a6f d.14.1.2 37564 2a6tA 271 1.90e+00 1yjmA 110 1.94e+00 1rypH 205 2.00e+00 d.153.1.4 41876 1xewX 182 2.13e+00 1koe 172 2.84e+00 1koe d.169.1.5 42448 2aefA 234 3.07e+00 2b4aA 138 3.32e+00 1ad3A 452 3.59e+00 1ad3A c.82.1.1 35335 1reqB 637 3.82e+00 1reqB c.1.19.1,c.23.6.1 29621,31248 3tmkA 216 3.84e+00 3tmkA c.37.1.1 31920 2cw8A 537 3.92e+00 1o6dA 163 4.41e+00 c.116.1.3 92567 1jhfA 202 4.44e+00 a.4.5.2,b.87.1.1 63057,63058 1t6t1 118 4.88e+00 1js8A 394 5.01e+00 a.86.1.1,b.112.1.1 67219,67220 1mzbA 136 5.09e+00 a.4.5.42 91497 1evlA 401 5.40e+00 1qf6A c.51.1.1,d.104.1.1 33202,40751 1zckA 154 5.41e+00 1x24A 180 5.76e+00 2bikB 313 5.80e+00 1k4mA 213 5.88e+00 c.26.1.3 77258 2axcA 264 6.13e+00 1rrmA 386 6.45e+00 e.22.1.2 105081 1ypcI 64 6.63e+00 2sniI d.40.1.1 38570 1pk1B 89 6.65e+00 1pueE 89 6.71e+00 1awcA a.4.5.21 16165 1cq3A 233 6.92e+00 1cq3A b.27.1.1 23923 1sflA 238 6.93e+00 1uzcA 71 6.97e+00 a.159.2.1 100222 1rxdA 159 7.05e+00 1sfjA 238 7.21e+00 1qw2A 102 8.51e+00 d.249.1.1 96456 1l1dA 152 8.54e+00 b.88.1.3 73452 2brfA 110 8.72e+00 1xwsA 313 8.94e+00 2f51A 118 8.99e+00 1uh5A 329 9.11e+00 c.2.1.2 107840 1z5yE 149 9.48e+00 1h6kA 757 9.61e+00 a.118.1.14,a.118.1.14,a.118.1.14 60675,60676,60677 1viuA 203 9.74e+00 d.113.1.1 100771 1r13A 148 1.00e+01 d.169.1.1,h.1.1.1 96782,96783 1jvwA 167 1.04e+01 d.26.1.1 71907 1nmeA 146 1.04e+01 c.17.1.1 85874 1nkqA 259 1.09e+01 d.177.1.1 103862 2bw3A 534 1.10e+01 1uc2A 481 1.12e+01 d.261.1.1 99161 1ti6A 875 1.12e+01 b.52.2.2,c.81.1.1 106974,106975 1rxwA 336 1.12e+01 a.60.7.1,c.120.1.2 98059,98060 1bx4A 345 1.13e+01 1bx4A c.72.1.1 34935 1fdr 248 1.19e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 2aa4A 289 1.20e+01 1fm0E 150 1.21e+01 1fmaE d.41.5.1 38629 2bshA 125 1.24e+01 1h05A 146 1.24e+01 c.23.13.1 76433 1zhvA 134 1.25e+01 1zq9A 285 1.25e+01 2bkfA 87 1.28e+01 2bhoA 130 1.31e+01 1dg6A 191 1.36e+01 1d4vB b.22.1.1 23883 1n0qA 93 1.36e+01 k.37.1.1 79754 1zclA 180 1.37e+01 1kw4A 89 1.40e+01 a.60.1.2 73077 1vj0A 380 1.42e+01 b.35.1.2,c.2.1.1 100786,100787 2bsjA 133 1.47e+01 1gjjA 168 1.49e+01 a.140.1.1,a.140.1.1 83291,83292 1fvrA 327 1.52e+01 d.144.1.7 60047 2c9wA 169 1.62e+01 1qyaA 307 1.66e+01 d.21.1.2,d.21.1.2 104653,104654 1unkA 87 1.70e+01 1cei a.28.2.1 16935 1t3qB 788 1.78e+01 d.41.1.1,d.133.1.1 106369,106370 1l3iA 192 1.82e+01 c.66.1.22 77676 1lnzA 342 1.83e+01 b.117.1.1,c.37.1.8 78112,78113 1vheA 373 1.84e+01 b.49.3.1,c.56.5.4 100669,100670 2dhqA 146 1.86e+01 2dhqA c.23.13.1 31382 1fxlA 167 1.88e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1fxkC 133 1.92e+01 1fxkC a.2.5.1 15702 1h9oA 112 1.95e+01 1qadA d.93.1.1 60837 1zyeA 220 1.99e+01 1h3gA 601 2.02e+01 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1t9iA 163 2.02e+01 1y96A 86 2.02e+01 1r6xA 395 2.05e+01 b.122.1.3,c.26.1.5 97167,97168 1h2vC 771 2.15e+01 a.118.1.14,a.118.1.14,a.118.1.14 76592,76593,76594 1a62 130 2.18e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1yeyA 444 2.21e+01 1f9aA 168 2.22e+01 1f9aA c.26.1.3 31602 1x3mA 415 2.23e+01 1sdjA 310 2.24e+01 d.21.1.2,d.21.1.2 98807,98808 2fwkA 121 2.32e+01 2napA 723 2.35e+01 2napA b.52.2.2,c.81.1.1 26926,35334 1ql3A 99 2.36e+01 1ycc a.3.1.1 15822 1csh 435 2.40e+01 1csh a.103.1.1 18880 1hssA 124 2.42e+01 1bea a.52.1.2 17819 1sw5B 275 2.49e+01 c.94.1.1 106070 2covD 104 2.50e+01 1b65A 375 2.59e+01 1b65A d.154.1.1 42020 1v5iB 76 2.64e+01 1m4zA 238 2.66e+01 b.34.12.1 78630 1sw5A 275 2.71e+01 c.94.1.1 106069 1xe0A 114 2.76e+01 1unlD 208 2.78e+01 1xv2A 237 2.82e+01 1um0A 365 2.91e+01 d.258.1.1 107942 1s3aA 102 2.95e+01 2btvA 901 2.98e+01 2btvA e.28.1.1 43376 1a8y 367 2.99e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1h4lD 147 3.01e+01 a.74.1.1 70873 1qhlA 227 3.02e+01 1qhlA c.37.1.12 32382 1q7hA 153 3.03e+01 b.122.1.1,d.17.6.2 96042,96043 1diiC 80 3.06e+01 1diiC a.3.1.1 15925 1dvoA 152 3.08e+01 1dvoA a.136.1.1 19623 1yb2A 275 3.13e+01 1yi9A 309 3.21e+01 2cc0A 195 3.26e+01 1bxaA 105 3.26e+01 1aac b.6.1.1 22839 2c8mA 262 3.27e+01 1hvyA 288 3.35e+01 1bkpA d.117.1.1 41049 1xsvA 113 3.37e+01 1ypvA 313 3.42e+01 1u8vA 490 3.45e+01 1ztdA 133 3.45e+01 1aac 105 3.47e+01 1aac b.6.1.1 22838 1iq8A 582 3.51e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1twfC 318 3.53e+01 1cliA 345 3.54e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1rd5A 262 3.55e+01 1zxxA 319 3.56e+01 1uc8A 280 3.56e+01 c.30.1.6,d.142.1.7 99165,99166 1idk 359 3.69e+01 1qcxA b.80.1.2 28025 1mq7A 154 3.73e+01 b.85.4.1 79404 1cei 94 3.74e+01 1cei a.28.2.1 16939 2d4pA 141 3.78e+01 1sfdA 105 3.80e+01 b.6.1.1 105480 2d00A 109 3.82e+01 1wi9A 72 3.83e+01 2c5qA 240 3.83e+01 1ojhA 65 3.87e+01 a.214.1.1 103976 1viaA 175 3.91e+01 c.37.1.2 100754 1w9gA 104 3.91e+01 2ch4A 320 3.98e+01 1ej2A 181 3.99e+01 1f9aA c.26.1.3 59414 1rlhA 173 4.00e+01 d.256.1.1 97646 1zuoA 186 4.07e+01 1mvoA 136 4.10e+01 c.23.1.1 79513 1phm 310 4.10e+01 1phm b.121.1.2,b.121.1.2 59015,59016 2ahqA 76 4.15e+01 1z1dA 103 4.17e+01 1yloA 348 4.22e+01 1xewY 172 4.24e+01 2bwbA 46 4.27e+01 1yqfA 203 4.32e+01 1tif 78 4.35e+01 1tif d.15.8.1 37836 3ertA 261 4.37e+01 3erdA a.123.1.1 19292 1a8vA 121 4.39e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 1r0vA 305 4.41e+01 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 1fgkA 310 4.54e+01 1fgkA d.144.1.7 41693 2bneA 241 4.56e+01 1iruK 201 4.60e+01 d.153.1.4 71362 1g5tA 196 4.72e+01 1g5rA c.37.1.11 32366 1wveC 80 4.72e+01 1fyxA 149 4.78e+01 1fyvA c.23.2.1 31128 1d4oA 184 4.82e+01 1d4oA c.31.1.4 31748 1x6vA 630 4.83e+01 2bnfB 241 4.86e+01 1l7bA 92 4.88e+01 c.15.1.2 91053 1flmA 122 4.89e+01 1axj b.45.1.1 25747 1mkp 144 4.99e+01 1vhrA c.45.1.1 32654 1jpaA 312 5.03e+01 d.144.1.7 67011 1euwA 152 5.13e+01 1dupA b.85.4.1 28349 1pswA 348 5.13e+01 c.87.1.7 88287 1m8jA 181 5.14e+01 c.26.1.3 84875 1g2hA 61 5.15e+01 1g2hA a.4.1.12 60224 1a79A 171 5.16e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 1zrjA 50 5.16e+01 2as0A 396 5.20e+01 1ccwB 483 5.20e+01 1cb7B c.1.19.2 29646 1vekA 84 5.23e+01 1sixA 174 5.30e+01 b.85.4.1 98892 1ee8A 266 5.35e+01 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1rwzA 245 5.39e+01 d.131.1.2,d.131.1.2 98005,98006 1qb7A 236 5.44e+01 1qb7A c.61.1.1 34087 1xebA 150 5.45e+01 2fi0A 81 5.49e+01 2arsA 262 5.52e+01 1zn8A 180 5.55e+01 1oeyA 83 5.57e+01 d.15.2.2 92800 2ajfA 597 5.61e+01 1sdwA 314 5.62e+01 b.121.1.2,b.121.1.2 98810,98811 1wvqA 167 5.90e+01 1eo6A 117 5.93e+01 1eo6A d.15.1.3 37609 1e79A 510 5.97e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 1rz2A 254 6.10e+01 b.100.1.1 105130 1dpuA 99 6.11e+01 1dpuA a.4.5.16 16150 2a8eA 220 6.20e+01 2pfkA 320 6.24e+01 3pfk c.89.1.1 35577 1xbbA 291 6.28e+01 1id2A 106 6.32e+01 1aac b.6.1.1 62288 1r1qA 100 6.34e+01 d.93.1.1 104763 1zh1A 163 6.42e+01 1nuuA 252 6.42e+01 c.26.1.3 86209 1ifyA 49 6.44e+01 a.5.2.1 71207 1p4oA 322 6.62e+01 d.144.1.7 87775 2aw4Q 117 6.63e+01 1ufkA 254 6.65e+01 c.66.1.39 99340 1z3eA 132 6.68e+01 1p99A 295 6.70e+01 c.94.1.1 94384 1xa1A 255 6.73e+01 e.3.1.1 109529 2b4lA 268 6.74e+01 1p0yA 444 6.74e+01 a.166.1.1,b.85.7.3 87654,87655 1qj2C 285 6.75e+01 1qj2C 1ir3A 306 6.88e+01 1fmk d.144.1.7 41702 2gk4A 232 6.89e+01 1at0 145 6.98e+01 1at0 b.86.1.1 28374 1b8aA 438 7.01e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1ehiA 377 7.02e+01 1iow c.30.1.2,d.142.1.1 31716,41484 1nykA 165 7.05e+01 b.33.1.1 86408 1yf3A 259 7.07e+01 2gu3A 136 7.08e+01 2b18A 164 7.09e+01 1e0gA 48 7.10e+01 1e01A d.7.1.1 37325 1kqqA 139 7.17e+01 a.4.3.1 72885 1rutX 188 7.23e+01 1txvB 440 7.27e+01 1zxiC 288 7.28e+01 1ww7A 160 7.29e+01 1jdpA 441 7.30e+01 c.93.1.1 62906 1i50C 318 7.36e+01 d.74.3.1,d.181.1.1 61756,61757 1u9iA 519 7.39e+01 1uwdA 103 7.41e+01 1q0sA 259 7.45e+01 c.66.1.28 95509 1fo8A 343 7.46e+01 1foaA c.68.1.10 59927 2fsxA 148 7.54e+01 1ryp1 222 7.54e+01 1ryp1 1lba 146 7.55e+01 1lba d.118.1.1 41062 1wdiA 345 7.59e+01 1kgdA 180 7.61e+01 c.37.1.1 68582 1n62C 288 7.66e+01 d.87.2.1,d.145.1.3 80094,80095 1rypK 198 7.68e+01 d.153.1.4 41879 1fr3A 67 7.71e+01 1fr3A b.40.6.1 25436 1x67A 146 7.80e+01 1h8eA 510 7.81e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1b43A 340 7.86e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 1bb9 115 7.92e+01 1bb9 b.34.2.1 24554 1qahA 136 8.02e+01 d.79.1.1 96338 1i7qB 193 8.06e+01 1qdlB c.23.16.1 61902 1wr1B 58 8.06e+01 1kk1A 410 8.07e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 2bwrA 401 8.12e+01 1sknP 92 8.13e+01 1sknP a.37.1.1 17127 1mvwB 145 8.14e+01 i.15.1.1 79524 2f5tX 233 8.17e+01 2g7zA 282 8.18e+01 1ml8A 134 8.18e+01 d.227.1.2 85013 2cmd 312 8.21e+01 2cmd c.2.1.5,d.162.1.1 30135,42102 1n3jA 119 8.26e+01 b.85.7.2 79963 1oi2A 366 8.26e+01 c.119.1.2 103802 1p42A 270 8.28e+01 d.14.1.7,d.14.1.7 87754,87755 2b3oA 532 8.30e+01 1fpzA 212 8.32e+01 1fpzA c.45.1.1 59976 1iukA 140 8.34e+01 c.2.1.8 83712 1oroA 213 8.48e+01 1opr c.61.1.1 34093 1vbwA 68 8.49e+01 1a8p 258 8.50e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1obfO 335 8.50e+01 c.2.1.3,d.81.1.1 86768,86769 1wkvA 389 8.50e+01 1y8oB 128 8.51e+01 1enfA 212 8.52e+01 3seb b.40.2.2,d.15.6.1 25198,37787 1ucaA 190 8.57e+01 d.124.1.1 88462 1rm6B 324 8.60e+01 2bh8A 101 8.67e+01 2csbA 519 8.67e+01 1rypL 212 8.75e+01 d.153.1.4 41880 1a8l 226 8.77e+01 1a8l c.47.1.2,c.47.1.2 32777,32778