# 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 1yr0A 175 2.65e-21 1yvoA 172 2.85e-20 2bl1A 172 4.45e-20 2ge3A 170 7.46e-20 1vhsA 175 9.18e-20 d.108.1.1 100698 2fe7A 166 2.71e-18 1tiqA 180 5.19e-18 d.108.1.1 107010 2ae6A 166 1.41e-17 2beiA 170 2.77e-17 2cy2A 174 1.39e-16 1nslA 184 2.75e-16 d.108.1.1 86137 1z4eA 153 5.83e-16 1wwzA 159 1.44e-15 2b5gA 171 2.92e-15 1s3zA 165 1.14e-14 d.108.1.1 105250 2fckA 181 1.26e-14 1s7kA 182 1.63e-14 1on0A 158 3.09e-14 d.108.1.1 87095 1qsoA 149 3.18e-14 1qsmA d.108.1.1 40812 1qsmA 152 3.24e-14 1qsmA d.108.1.1 40808 1u6mA 199 7.80e-14 1y9kA 157 1.89e-13 1i1dA 161 2.81e-13 1i21A d.108.1.1 61526 1gheA 177 3.03e-13 d.108.1.1 76222 1i12A 160 4.18e-13 1i21A d.108.1.1 61515 2fl4A 149 1.15e-12 1yvkA 163 3.49e-12 1mk4A 157 3.59e-12 d.108.1.1 84979 1yx0A 159 4.06e-12 1yreA 197 5.07e-12 1vkcA 158 6.31e-12 1n71A 180 4.90e-11 d.108.1.1 85370 2a4nA 182 4.96e-11 1b87A 181 7.17e-11 1b87A d.108.1.1 40797 2atrA 138 7.98e-11 2fsrA 195 9.47e-11 1cjwA 166 2.04e-10 1cjwA d.108.1.1 40818 1qstA 160 5.59e-10 1yghA d.108.1.1 40804 1p0hA 318 7.49e-10 d.108.1.1 93866 1q2yA 140 8.42e-10 d.108.1.1 95655 2c27A 315 1.28e-09 1bo4A 168 1.36e-09 1bo4A d.108.1.1 40798 1z4rA 168 1.67e-09 1y9wA 140 3.38e-09 1y7rA 133 4.80e-09 2aj6A 159 5.34e-09 2g3aA 152 8.29e-09 2bswA 146 9.80e-09 1yghA 164 2.66e-08 1yghA d.108.1.1 40802 2ganA 190 8.68e-08 1xebA 150 1.43e-07 1yk3A 210 4.70e-07 1sqhA 312 9.59e-07 d.108.1.5 98966 2d4pA 141 1.34e-06 1m4iA 181 1.83e-06 d.108.1.1 74457 1bob 320 3.12e-05 1bob d.108.1.1 40816 1yleA 342 2.33e-04 1iicA 422 5.41e-03 1nmtA d.108.1.2,d.108.1.2 62422,62423 2givA 295 5.94e-03 1fy7A 278 1.86e-02 1fy7A d.108.1.1 40817 1xmtA 103 3.87e-02 1pbjA 125 7.24e-02 d.37.1.1,d.37.1.1 94414,94415 1o50A 157 7.82e-02 d.37.1.1,d.37.1.1 92478,92479 1svjA 156 8.09e-02 d.220.1.1 106049 1pvmA 184 2.13e-01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1wrdA 103 4.69e-01 1zy9A 564 4.72e-01 1y81A 138 4.93e-01 1lqpA 135 5.44e-01 d.32.1.2 78151 1nkiA 135 6.48e-01 d.32.1.2 91941 1ztuA 341 6.67e-01 1vicA 262 6.75e-01 c.68.1.13 100756 2c3zA 222 6.90e-01 1v2xA 194 7.55e-01 c.116.1.1 100274 1a53 247 9.34e-01 1a53 c.1.2.4 28564 1d3gA 367 9.49e-01 1d3gA c.1.4.1 28600 1igs 248 9.56e-01 1a53 c.1.2.4 28565 1rfmA 344 9.82e-01 c.122.1.1 97385 1j7lA 264 1.00e+00 d.144.1.6 62697 1npk 154 1.00e+00 1npk d.58.6.1 39099 2b0mA 393 1.03e+00 1ne9A 335 1.04e+00 d.108.1.4,d.108.1.4 91839,91840 2f46A 156 1.20e+00 1uiuA 502 1.21e+00 c.94.1.1 99434 1zlqA 502 1.22e+00 2fcjA 119 1.29e+00 1qs0B 338 1.31e+00 1qs0B c.36.1.7,c.48.1.2 31830,33103 1fjgK 129 1.34e+00 1fjfK c.55.4.1 33733 1han 297 1.50e+00 1han d.32.1.3,d.32.1.3 38506,38507 1lkdA 297 1.51e+00 d.32.1.3,d.32.1.3 78059,78060 1pj5A 830 1.68e+00 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1kllA 130 1.78e+00 d.32.1.2 72720 1wr2A 238 2.08e+00 2bkkA 264 2.13e+00 1ss4A 153 2.19e+00 d.32.1.6 105976 1ghhA 81 2.26e+00 1ghhA d.57.1.1 38940 1zo0A 126 2.29e+00 2aboA 136 2.56e+00 1lvmA 229 2.73e+00 b.47.1.3 78243 1pu1A 94 2.90e+00 d.266.1.1 104307 1it2A 146 3.26e+00 a.1.1.2 66365 2gi3A 476 3.41e+00 1vpqA 273 3.52e+00 1dmmA 131 3.65e+00 1opy d.17.4.3 38114 1v7wA 807 3.74e+00 a.102.1.4,b.30.5.3 108411,108412 1j08A 226 3.81e+00 c.47.1.2,c.47.1.2 83855,83856 1d2tA 231 4.01e+00 1d2tA a.111.1.1 19052 1b78A 193 4.07e+00 1b78A c.51.4.1 33221 1ws9A 387 4.10e+00 2cx9A 387 4.18e+00 2b8tA 223 4.33e+00 1y8qA 346 4.52e+00 1hlgA 371 4.59e+00 1hlgA c.69.1.6 34656 1xhdA 173 4.59e+00 1cx4A 305 4.61e+00 b.82.3.2,b.82.3.2 59099,59100 1s57A 153 4.65e+00 1zcoA 262 4.66e+00 1hv9A 456 4.79e+00 1fwyA b.81.1.4,c.68.1.5 28060,34518 1nd4A 264 4.81e+00 d.144.1.6 91815 2fbyA 205 4.85e+00 1qysA 106 4.86e+00 k.41.1.1 96603 2bznA 351 4.92e+00 1pu6A 218 5.00e+00 a.96.1.5 95123 1ecsA 126 5.07e+00 1ecsA d.32.1.2 59407 2czcA 334 5.28e+00 1oaoA 674 5.33e+00 e.26.1.2 86744 2d29A 387 5.33e+00 1shdA 107 5.33e+00 1fmk d.93.1.1 40440 1nv8A 284 5.36e+00 c.66.1.30 86224 1opy 131 5.36e+00 1opy d.17.4.3 38113 1iab 200 5.61e+00 1iae d.92.1.8 40312 1iae 200 5.62e+00 1iae d.92.1.8 40311 1zaiA 363 5.68e+00 1iw8A 231 5.70e+00 a.111.1.1 76866 1oh0A 131 5.75e+00 d.17.4.3 87004 2fyxA 143 5.75e+00 1xfiA 367 5.97e+00 e.50.1.1 109584 1stzA 338 6.01e+00 a.4.5.51,d.110.2.3 106009,106010 2f9zC 159 6.05e+00 1bj4A 470 6.08e+00 1bj4A c.67.1.4 34479 1adoA 363 6.17e+00 1fbaA c.1.10.1 29124 1p4kA 295 6.25e+00 d.153.1.5 87772 1qhfA 240 6.37e+00 1qhfA c.60.1.1 33960 1s2oA 244 6.44e+00 1zmbA 290 6.52e+00 1e58A 249 6.59e+00 1qhfA c.60.1.1 59262 1i5pA 633 6.59e+00 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 1s14A 194 6.64e+00 d.122.1.2 98329 2arhA 203 6.68e+00 1zmaA 118 6.78e+00 1a8l 226 6.80e+00 1a8l c.47.1.2,c.47.1.2 32777,32778 1yueA 427 6.88e+00 1xkfA 133 6.99e+00 1rv3A 483 7.21e+00 c.67.1.4 105101 1ve3A 227 7.37e+00 1j2zA 270 7.38e+00 b.81.1.1 90805 1zfjA 491 7.44e+00 1ak5 c.1.5.1,d.37.1.1,d.37.1.1 28638,38540,38541 1qtnA 164 7.52e+00 1pauA c.17.1.1 30999 2c6qA 351 7.53e+00 1v9nA 360 7.85e+00 1r8oA 96 7.92e+00 b.42.4.1 104852 1zh5A 195 8.03e+00 1i9zA 347 8.06e+00 1i9yA d.151.1.2 62102 1e1aA 314 8.22e+00 1e1aA b.68.6.1 59155 1dxy 333 8.28e+00 1dxy c.2.1.4,c.23.12.1 30094,31354 1zu0A 529 8.30e+00 1st0A 337 8.38e+00 d.13.1.3,d.246.1.1 98979,98980 1cot 129 8.39e+00 1ycc a.3.1.1 15899 2b8eA 273 8.45e+00 1z7dA 433 8.57e+00 1yemA 179 8.62e+00 1f1uA 323 9.03e+00 d.32.1.3,d.32.1.3 83200,83201 8abp 306 9.04e+00 8abp c.93.1.1 35647 1pjxA 314 9.05e+00 b.68.6.1 104167 1wyzA 242 9.13e+00 1vhmA 195 9.15e+00 d.110.2.1 100691 1mgpA 313 9.68e+00 c.119.1.1 79098 1y13A 181 9.70e+00 1y5hA 133 9.74e+00 1tuoA 464 1.00e+01 1kafA 108 1.02e+01 d.199.1.1 68372 1k8qA 377 1.04e+01 c.69.1.6 72177 1nxuA 333 1.05e+01 c.122.1.1 86389 1vmeA 410 1.06e+01 c.23.5.1,d.157.1.3 108893,108894 1oltA 457 1.07e+01 c.1.28.2 93334 1a7tA 232 1.09e+01 1a7tA d.157.1.1 42041 2bh9A 489 1.10e+01 1w8iA 156 1.11e+01 1ucnA 152 1.13e+01 d.58.6.1 99183 1o0sA 605 1.13e+01 c.2.1.7,c.58.1.3 86540,86541 1co6A 107 1.14e+01 1ycc a.3.1.1 15894 1ev7A 317 1.14e+01 1ev7B c.52.1.9 33315 1ohpA 125 1.15e+01 1k3xA 262 1.16e+01 a.156.1.2,b.113.1.1,g.39.1.8 77242,77243,77244 1gefA 123 1.16e+01 1gefA c.52.1.18 60465 1xttA 216 1.17e+01 2b18A 164 1.17e+01 1fxjA 331 1.18e+01 1fwyA b.81.1.4,c.68.1.5 28062,34520 9gafA 295 1.23e+01 1apyA d.153.1.5 42008 1qgxA 357 1.24e+01 1qgxA e.7.1.1 42973 1l3iA 192 1.25e+01 c.66.1.22 77676 1kn6A 90 1.26e+01 d.58.3.3 72770 1r6xA 395 1.26e+01 b.122.1.3,c.26.1.5 97167,97168 1ka1A 357 1.27e+01 e.7.1.1 68369 1o2dA 371 1.28e+01 e.22.1.2 86591 1w4tA 299 1.28e+01 1ml4A 308 1.31e+01 c.78.1.1,c.78.1.1 79255,79256 1xjeA 644 1.32e+01 1apyA 162 1.33e+01 1apyA d.153.1.5 42004 1pea 385 1.33e+01 1pea c.93.1.1 35662 1j8fA 323 1.35e+01 1j8fA c.31.1.5 62738 1ro5A 201 1.36e+01 d.108.1.3 105023 1kw3B 292 1.36e+01 d.32.1.3,d.32.1.3 77549,77550 1wdjA 187 1.37e+01 2cmwA 310 1.37e+01 1g8fA 511 1.38e+01 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 1m6yA 301 1.38e+01 a.60.13.1,c.66.1.23 78716,78717 1xzoA 174 1.38e+01 1pot 325 1.41e+01 1pot c.94.1.1 35807 1d2zB 153 1.41e+01 1d2zB a.77.1.2 18439 2aqjA 538 1.41e+01 2go7A 207 1.46e+01 1o5iA 249 1.46e+01 c.2.1.2 92499 1bmtA 246 1.49e+01 1bmtA a.46.1.1,c.23.6.1 17757,31235 1gk8I 140 1.50e+01 d.73.1.1 65242 1b00A 127 1.51e+01 3chy c.23.1.1 31122 5abp 306 1.53e+01 8abp c.93.1.1 35651 2gcc 70 1.55e+01 2gcc d.10.1.2 37484 1xmrA 243 1.55e+01 1s1hM 132 1.56e+01 i.1.1.1 105165 1lcyA 325 1.57e+01 b.36.1.4,b.47.1.1 73834,73835 1y1uA 585 1.61e+01 2fsxA 148 1.61e+01 1h1dA 221 1.64e+01 c.66.1.1 83452 1ypyA 184 1.64e+01 1t0aA 159 1.65e+01 1a4iA 301 1.67e+01 1a4iA c.2.1.7,c.58.1.2 30278,33926 1tx2A 297 1.67e+01 c.1.21.1 107420 1r5jA 337 1.67e+01 c.77.1.5 97097 1d1gA 168 1.69e+01 1d1gA c.71.1.1 34889 1vlrA 350 1.70e+01 d.13.1.3,d.246.1.1 108860,108861 1cvl 319 1.70e+01 1cvl c.69.1.18 34786 1f1xA 322 1.72e+01 d.32.1.3,d.32.1.3 83208,83209 1go3F 107 1.72e+01 a.60.8.2 65407 2f5gA 133 1.73e+01 1q9iA 571 1.74e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1jjvA 206 1.75e+01 c.37.1.1 71698 1v4pA 157 1.75e+01 1ii5A 233 1.75e+01 c.94.1.1 62412 2gsaA 432 1.77e+01 2gsaA c.67.1.4 34446 2ac4A 309 1.79e+01 1w9gA 104 1.81e+01 1mc0A 368 1.81e+01 d.110.2.1,d.110.2.1 78937,78938 2hbtA 247 1.85e+01 1ga0A 364 1.85e+01 1gceA e.3.1.1 60410 1ygmA 118 1.86e+01 1sflA 238 1.87e+01 1te2A 226 1.87e+01 c.108.1.6 106792 2cybA 323 1.87e+01 1f4lA 551 1.89e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1wv9A 94 1.97e+01 1zesA 125 1.98e+01 1cvrA 435 2.01e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 1o20A 427 2.02e+01 c.82.1.1 86556 1gl4B 98 2.03e+01 b.1.1.4 65288 1gtzA 156 2.03e+01 c.23.13.1 70539 1std 172 2.04e+01 3stdA d.17.4.1 38089 1vpbA 451 2.04e+01 1rro 108 2.05e+01 1a75A a.39.1.4 17195 1p2hA 571 2.06e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1o6dA 163 2.10e+01 c.116.1.3 92567 1shbA 104 2.11e+01 1fmk d.93.1.1 40425 1dozA 309 2.13e+01 1ak1 c.92.1.1 35592 1rypH 205 2.13e+01 d.153.1.4 41876 1sn4A 64 2.16e+01 1aho g.3.7.1 44136 1s4iA 175 2.18e+01 1o4rA 108 2.18e+01 d.93.1.1 92469 1ocvA 125 2.22e+01 d.17.4.3 86810 1h1yA 228 2.26e+01 c.1.2.2 76506 1xuqA 212 2.27e+01 2fomB 185 2.27e+01 2acaA 189 2.29e+01 1vid 221 2.30e+01 1vid c.66.1.1 34178 2b0tA 738 2.30e+01 1hf8A 289 2.31e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1ut1A 148 2.31e+01 b.2.3.6 108014 2h0uA 217 2.32e+01 1cei 94 2.38e+01 1cei a.28.2.1 16939 2as9A 210 2.42e+01 2fsqA 243 2.44e+01 1rgzA 363 2.45e+01 e.3.1.1 97457 1nekA 588 2.46e+01 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 2scpA 174 2.47e+01 2scpA a.39.1.5 17256 1oniA 137 2.49e+01 d.79.1.1 87144 1b5tA 275 2.51e+01 1b5tA c.1.23.1 29676 1zbqA 327 2.54e+01 2bd0A 244 2.56e+01 1c24A 263 2.58e+01 1c24A d.127.1.1 41148 1jqnA 883 2.59e+01 c.1.12.3 77159 2g19A 244 2.60e+01 1pfvA 551 2.61e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1lw6I 64 2.61e+01 d.40.1.1 74294 1z1lA 345 2.63e+01 1lfkA 398 2.65e+01 a.104.1.1 77926 1idpA 172 2.66e+01 d.17.4.1 83685 2a8kA 108 2.68e+01 1t6nA 220 2.70e+01 c.37.1.19 106576 1ohuA 175 2.72e+01 f.1.4.1 93029 1xtlA 175 2.74e+01 1e0cA 271 2.74e+01 1e0cA c.46.1.2,c.46.1.2 32717,32718 2f6kA 307 2.76e+01 1p9oA 313 2.77e+01 c.72.3.1 94397 1y3nA 490 2.77e+01 1d0iA 156 2.77e+01 2dhqA c.23.13.1 31383 1kyhA 276 2.78e+01 c.72.1.4 73222 1dd9A 338 2.81e+01 1dd9A e.13.1.1 43254 1xe7A 203 2.81e+01 1ha1 184 2.82e+01 1ha1 d.58.7.1,d.58.7.1 39147,39148 2dorA 311 2.83e+01 2dorA c.1.4.1 28593 1k6dA 220 2.86e+01 c.124.1.2 72082 1eiwA 111 2.86e+01 1eiwA c.23.3.1 31130 1g61A 228 2.87e+01 1g61A d.126.1.1 41126 1y0pA 571 2.87e+01 1pdo 135 2.88e+01 1pdo c.54.1.1 33376 1q02A 52 2.88e+01 a.5.2.1 95490 1zn6A 227 2.90e+01 1yruA 364 2.91e+01 1uc8A 280 2.93e+01 c.30.1.6,d.142.1.7 99165,99166 1m7jA 484 2.98e+01 b.92.1.6,b.92.1.6,c.1.9.11 78732,78733,78734 2ac2A 309 3.00e+01 1nbfD 76 3.02e+01 d.15.1.1 80390 1yfsA 465 3.02e+01 1vr6A 350 3.06e+01 1l0lA 446 3.07e+01 d.185.1.1,d.185.1.1 84482,84483 2fxuA 375 3.07e+01 1kssA 571 3.09e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1rcwA 231 3.10e+01 a.132.1.4 97299 1cseI 71 3.11e+01 1egpA d.40.1.1 38559 1itwA 741 3.11e+01 c.77.1.2 76793 1wddS 128 3.13e+01 1cpt 412 3.13e+01 1cpt a.104.1.1 18968 1tfzA 424 3.13e+01 d.32.1.3,d.32.1.3 106886,106887 2a2lA 145 3.17e+01 1kw4A 89 3.18e+01 a.60.1.2 73077 1y4tA 322 3.19e+01 1dorA 311 3.20e+01 2dorA c.1.4.1 28595 1lvwA 295 3.20e+01 c.68.1.6 84723 1hr6B 443 3.22e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1xjjA 644 3.22e+01 1hi9A 274 3.23e+01 1hi9A c.99.1.1 61063 1z3eA 132 3.23e+01 1q3iA 214 3.23e+01 d.220.1.1 104524 1m70A 190 3.23e+01 a.3.1.4,a.3.1.4 91200,91201 1f9mA 112 3.24e+01 1erv c.47.1.1 32736 1vr9A 213 3.26e+01 1unkA 87 3.27e+01 1cei a.28.2.1 16935 1vdnA 162 3.27e+01 1is1A 185 3.28e+01 d.67.3.1 83704 1l1jA 239 3.32e+01 b.47.1.1 84516 1yrgA 385 3.32e+01 1yrgA c.10.1.2 30854 2bltA 361 3.33e+01 1gceA e.3.1.1 42739 1ux8A 132 3.35e+01 1vrtA 560 3.35e+01 1rthA c.55.3.1,e.8.1.2 33574,43023 1xgsA 295 3.35e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 2bu3A 254 3.40e+01 1ys1X 320 3.41e+01 1ttzA 87 3.41e+01 c.47.1.1 107309 1wz7A 111 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