# List of top-scoring protein chains for t04-80-60-80-str2+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 2ae0X 345 1.53e-01 1f8fA 371 3.94e-01 b.35.1.2,c.2.1.1 83246,83247 1tx4B 178 5.30e-01 1ctqA c.37.1.8 32045 1ko3A 230 6.23e-01 d.157.1.1 90974 2gw6A 123 6.97e-01 1mrj 247 8.08e-01 1mrj d.165.1.1 42177 2gaeA 346 8.87e-01 1yqzA 438 1.29e+00 1v04A 355 1.53e+00 b.68.6.2 100240 1pq7A 224 1.70e+00 b.47.1.2 95002 2bc2A 227 1.95e+00 1a7tA d.157.1.1 42031 2aeuA 374 1.96e+00 1v25A 541 1.98e+00 e.23.1.1 108275 1s5aA 150 1.99e+00 d.17.4.10 98525 1x3lA 440 2.01e+00 1mrg 263 2.03e+00 1mrj d.165.1.1 42183 1try 224 2.20e+00 5ptp b.47.1.2 26017 1iruK 201 2.37e+00 d.153.1.4 71362 1b0pA 1231 2.40e+00 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 31831,31832,33104,34157,39003 1l6oA 95 2.53e+00 b.36.1.1 84534 1zh5A 195 2.84e+00 1kmqA 184 3.08e+00 c.37.1.8 84412 1s68A 249 3.10e+00 d.142.2.4 98591 1eaxA 241 3.66e+00 b.47.1.2 64889 1x8gA 227 3.72e+00 2govA 195 3.80e+00 1js8A 394 3.93e+00 a.86.1.1,b.112.1.1 67219,67220 2c3mA 1231 3.94e+00 1mfgA 95 4.27e+00 b.36.1.1 79043 2sak 121 4.33e+00 2sak d.15.5.1 37711 1jmcA 246 4.35e+00 1jmcA b.40.4.3,b.40.4.3 25300,25301 1kskA 234 4.36e+00 d.66.1.5,d.265.1.3 72920,90389 1ddgA 374 4.39e+00 1amoA b.43.4.1,c.25.1.4 25671,31559 1g8aA 227 4.51e+00 c.66.1.3 90506 1nrkA 328 4.58e+00 b.44.2.1,d.250.1.1 92089,92090 1vlyA 338 4.59e+00 b.44.2.1,d.250.1.1 108871,108872 1u6dX 308 4.76e+00 2d28C 149 4.77e+00 1zgkA 308 4.92e+00 1kolA 398 5.06e+00 b.35.1.2,c.2.1.1 77474,77475 1fn8A 224 5.14e+00 5ptp b.47.1.2 26012 1mqoA 227 5.16e+00 d.157.1.1 103846 2polA 366 5.24e+00 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 1ja1A 622 5.70e+00 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1x8hA 228 5.84e+00 1kekA 1231 5.85e+00 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 68524,68525,68526,68527,68528 1f3z 161 6.21e+00 1gpr b.84.3.1 28273 1udzA 182 6.25e+00 b.51.1.1 99239 1se8A 301 6.27e+00 b.40.4.3 105448 1wnyA 186 6.27e+00 1vhh 162 6.46e+00 1vhh d.65.1.2 39550 1w15A 153 6.70e+00 b.7.1.2 109041 1yr2A 741 6.80e+00 1aoeA 192 6.83e+00 1aoeA c.71.1.1 34923 3cox 507 6.95e+00 1b8sA c.3.1.2,d.16.1.1 30332,37863 1wi1A 126 7.02e+00 2fibA 269 7.16e+00 3fib d.171.1.1 42457 2fxqA 264 7.20e+00 1azo 232 7.23e+00 1azo c.52.1.14 33329 1gen 218 7.63e+00 1gen b.66.1.1 27536 1yt3A 375 7.84e+00 2ewrA 170 8.42e+00 1vzoA 355 8.58e+00 d.144.1.7 108971 1qwtA 255 8.67e+00 b.26.1.3 96501 2fy6A 143 8.69e+00 1u4bA 580 8.78e+00 c.55.3.5,e.8.1.1 107664,107665 1cewI 108 8.96e+00 1cewI d.17.1.2 37999 1gjwA 637 9.15e+00 b.71.1.1,c.1.8.1 60582,60583 1o0uA 429 9.25e+00 c.118.1.1 80743 2cwaA 263 9.30e+00 1xdnA 277 9.58e+00 1cfzA 162 9.71e+00 1cfzA c.56.1.1 33754 2fhxA 246 9.92e+00 1am2 199 9.96e+00 1am2 b.86.1.2 28381 1lnzA 342 9.98e+00 b.117.1.1,c.37.1.8 78112,78113 1wwrA 171 1.01e+01 1h5zA 455 1.03e+01 a.104.1.1 90622 1vhwA 253 1.06e+01 c.56.2.1 100706 1wk8A 194 1.08e+01 2c12A 439 1.08e+01 1khxA 227 1.09e+01 b.26.1.1 68631 1uufA 369 1.10e+01 b.35.1.2,c.2.1.1 100006,100007 1x8vA 455 1.10e+01 1yr4A 237 1.11e+01 2f91A 237 1.13e+01 3fib 249 1.14e+01 3fib d.171.1.1 42455 2fclA 169 1.17e+01 1h70A 255 1.20e+01 1h70A d.126.1.3 60711 1xw3A 110 1.21e+01 1xtoA 311 1.22e+01 1ryp2 233 1.23e+01 1ryp2 1ile 821 1.24e+01 1ile a.27.1.1,b.51.1.1,c.26.1.1 16924,26889,31591 1roaA 122 1.26e+01 d.17.1.2 105024 1ihjA 98 1.26e+01 1pdr b.36.1.1 62382 1quqB 121 1.28e+01 1quqB b.40.4.3 25305 1shyB 551 1.30e+01 b.69.12.1,g.16.2.1 105565,105566 1yqgA 263 1.31e+01 2a5dA 175 1.31e+01 1br9 194 1.33e+01 1br9 b.40.3.1 25235 1cruA 454 1.33e+01 1c9uA b.68.2.1 27617 2b8nA 429 1.34e+01 1cuk 203 1.34e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1jjtA 228 1.36e+01 1a7tA d.157.1.1 63139 1k9sA 237 1.37e+01 c.56.2.1 68359 1qorA 327 1.39e+01 1qorA b.35.1.2,c.2.1.1 24766,29782 2c2hA 192 1.42e+01 1p0fA 373 1.43e+01 b.35.1.2,c.2.1.1 87642,87643 1vj0A 380 1.50e+01 b.35.1.2,c.2.1.1 100786,100787 1itwA 741 1.54e+01 c.77.1.2 76793 2ohxA 374 1.57e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 1vqwA 457 1.59e+01 1x3zA 335 1.59e+01 1zkpA 268 1.60e+01 1lcyA 325 1.60e+01 b.36.1.4,b.47.1.1 73834,73835 1wosA 364 1.62e+01 b.44.2.1,d.250.1.1 109468,109469 2b0tA 738 1.62e+01 1cm9A 74 1.63e+01 1b3aA d.9.1.1 37405 1g3kA 174 1.67e+01 1nedA d.153.1.4 41989 1agi 125 1.68e+01 7rsa d.5.1.1 37303 1nrzA 164 1.69e+01 c.38.1.1 86131 1rypK 198 1.70e+01 d.153.1.4 41879 1g0uL 241 1.71e+01 d.153.1.4 41894 1u3wA 374 1.72e+01 1rybA 212 1.73e+01 c.56.3.1 98098 1r4aA 165 1.74e+01 c.37.1.8 96986 1ii2A 524 1.75e+01 c.91.1.1,c.109.1.1 66146,66147 1e9xA 455 1.76e+01 1ea1A a.104.1.1 18969 1t2wA 145 1.77e+01 b.100.1.1 106289 1gp6A 356 1.77e+01 b.82.2.1 65441 1n4wA 504 1.77e+01 c.3.1.2,d.16.1.1 91676,91677 1kmvA 186 1.78e+01 c.71.1.1 72757 1gotB 340 1.78e+01 1tbgA b.69.4.1 27648 1qqsA 174 1.78e+01 1nglA b.60.1.1 27143 1qqp2 218 1.79e+01 1qqp2 1a7tA 232 1.84e+01 1a7tA d.157.1.1 42041 1u13A 455 1.85e+01 a.104.1.1 107578 1uptA 171 1.87e+01 c.37.1.8 99767 2c0cA 362 1.90e+01 1ym0A 238 1.91e+01 1h7wA 1025 1.93e+01 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15683,28628,30324,30609,39007 1y10A 407 1.94e+01 1t71A 281 1.94e+01 1gteA 1025 1.94e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70440,70441,70442,70443,70444 1kcqA 104 1.96e+01 d.109.1.1 68449 2chnA 716 1.97e+01 2d0eA 407 1.97e+01 1es7B 89 1.99e+01 1es7B g.7.1.3 44465 1qwrA 319 1.99e+01 b.82.1.3 96491 1jvbA 347 2.01e+01 b.35.1.2,c.2.1.1 77181,77182 2cx7A 130 2.02e+01 1xtqA 177 2.04e+01 2eng 210 2.09e+01 2eng b.52.1.1 26895 1ok7A 366 2.09e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1k8kC 372 2.14e+01 b.69.4.1 68308 1evlA 401 2.26e+01 1qf6A c.51.1.1,d.104.1.1 33202,40751 2cfuA 658 2.28e+01 1qwkA 317 2.28e+01 c.1.7.1 96482 2d1sA 548 2.29e+01 1b4vA 504 2.30e+01 1b8sA c.3.1.2,d.16.1.1 30334,37865 1rzuA 485 2.30e+01 c.87.1.8 105140 1g0sA 209 2.32e+01 1g0sA d.113.1.1 60187 1hetA 374 2.32e+01 2ohxA b.35.1.2,c.2.1.1 60975,60976 1xcbA 211 2.33e+01 a.4.5.38,c.2.1.12 109552,109553 1n9pA 207 2.33e+01 b.1.18.16 80343 2ajgA 196 2.37e+01 1qy6A 274 2.39e+01 b.47.1.1 96574 1l3sA 580 2.40e+01 c.55.3.5,e.8.1.1 84521,84522 1fp2A 352 2.41e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1fmtA 314 2.43e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 1wruA 379 2.46e+01 1wmhB 86 2.49e+01 2ghsA 326 2.53e+01 1i0lA 221 2.54e+01 c.61.1.1 71096 1mxtA 504 2.55e+01 c.3.1.2,d.16.1.1 79671,79672 1lo7A 141 2.55e+01 d.38.1.1 74144 1dv1A 449 2.55e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1izoA 417 2.56e+01 a.104.1.1 83851 2exnA 136 2.61e+01 1n8kA 374 2.66e+01 b.35.1.2,c.2.1.1 80298,80299 1s5uA 138 2.66e+01 d.38.1.1 98573 1x54A 434 2.67e+01 1uc8A 280 2.72e+01 c.30.1.6,d.142.1.7 99165,99166 1h2bA 359 2.77e+01 b.35.1.2,c.2.1.1 90543,90544 1odkA 235 2.81e+01 c.56.2.1 86863 2d09A 407 2.83e+01 1mup 166 2.85e+01 1mup b.60.1.1 27133 1ycyA 71 2.87e+01 1o3yA 166 2.88e+01 c.37.1.8 86618 1jfbA 404 2.89e+01 a.104.1.1 66624 1wkrA 340 2.89e+01 b.50.1.2 109395 1nf2A 268 2.93e+01 c.108.1.10 91849 1v37A 177 2.93e+01 1gpr 162 2.94e+01 1gpr b.84.3.1 28267 1m7bA 184 2.95e+01 c.37.1.8 74572 2bgiA 272 2.95e+01 1l3iA 192 2.99e+01 c.66.1.22 77676 1ecpA 238 3.00e+01 1ecpA c.56.2.1 33775 3mddA 385 3.02e+01 3mdeA a.29.3.1,e.6.1.1 16592,42853 1adjA 421 3.03e+01 1adjA c.51.1.1,d.104.1.1 33188,40737 1s1fA 406 3.04e+01 1rypI 222 3.09e+01 d.153.1.4 41877 2bbhA 269 3.12e+01 1nk4A 580 3.12e+01 c.55.3.5,e.8.1.1 91923,91924 1zxtA 76 3.13e+01 1qy5A 269 3.16e+01 d.122.1.1 96573 1wzlA 585 3.17e+01 1fs0E 138 3.17e+01 1aqt a.2.10.1,b.93.1.1 59997,59998 1htqA 477 3.19e+01 d.15.9.1,d.128.1.1 71035,71036 1jv4A 162 3.21e+01 b.60.1.1 67343 1zndA 174 3.23e+01 1y2tA 142 3.23e+01 1f24A 402 3.24e+01 1rom a.104.1.1 18953 1wmxA 205 3.29e+01 b.18.1.24 109418 1r94A 118 3.30e+01 b.124.1.1 97251 1c3hA 137 3.31e+01 b.22.1.1 90405 1v0wA 506 3.32e+01 d.136.1.2,d.136.1.2 108220,108221 1v3vA 333 3.32e+01 b.35.1.2,c.2.1.1 108345,108346 1bvqA 141 3.32e+01 1bvqA d.38.1.1 38542 1vypX 364 3.33e+01 c.1.4.1 108905 1cjbA 231 3.34e+01 1qk3A c.61.1.1 34079 2cx5A 158 3.36e+01 1oe8A 211 3.36e+01 a.45.1.1,c.47.1.5 86905,86906 1eylA 186 3.40e+01 1wba b.42.4.1 25593 1ni9A 338 3.41e+01 e.7.1.2 85739 1c28A 135 3.44e+01 1c28A b.22.1.1 23857 1q7fA 286 3.46e+01 b.68.9.1 96036 1f20A 435 3.47e+01 b.43.4.1,c.25.1.4 64932,64933 1e4cP 215 3.47e+01 2fua c.74.1.1 34969 1cz4A 185 3.49e+01 1cz4A b.52.2.3,d.31.1.1 26934,38468 1yb3A 175 3.53e+01 1tmxA 293 3.54e+01 1ywmA 200 3.55e+01 1vkdA 338 3.58e+01 b.67.2.4 108644 1i4uA 181 3.59e+01 b.60.1.1 61732 1n26A 325 3.62e+01 b.1.1.4,b.1.2.1,b.1.2.1 79850,79851,79852 1bowA 159 3.65e+01 1bowA d.60.1.1 39528 2er7E 330 3.67e+01 2er7E b.50.1.2 26779 1f5jA 199 3.69e+01 1axkA b.29.1.11 24342 1j0hA 588 3.75e+01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 3pcgA 200 3.75e+01 3pchA b.3.6.1 22647 1mmiA 366 3.83e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1jx4A 352 3.84e+01 d.240.1.1,e.8.1.7 90378,90379 1h9sA 140 3.89e+01 1b9mA b.40.6.2,b.40.6.2 60843,60844 2gefA 217 3.92e+01 1u4cA 349 3.93e+01 b.69.4.2 107666 1i9zA 347 3.94e+01 1i9yA d.151.1.2 62102 2sga 181 3.97e+01 1qq4A b.47.1.1 25808 2f86B 143 3.98e+01 1jofA 365 3.98e+01 b.69.10.1 71775 1jipA 403 3.99e+01 a.104.1.1 66748 2d27A 149 3.99e+01 1eupA 403 4.00e+01 1rom a.104.1.1 18967 1jjeA 222 4.03e+01 1a7tA d.157.1.1 63117 1ep3B 262 4.04e+01 1ep2B b.43.4.2,c.25.1.3 25664,31554 1qtoA 122 4.05e+01 1bylA d.32.1.2 38494 1lqpA 135 4.09e+01 d.32.1.2 78151 1qy1A 174 4.10e+01 b.60.1.1 96568 1rypJ 204 4.12e+01 d.153.1.4 41878 1ukfA 188 4.14e+01 d.3.1.10 99488 1yarH 217 4.16e+01 1dnlA 199 4.16e+01 1ci0A b.45.1.1 25753 2ew0A 192 4.17e+01 1sacA 204 4.19e+01 1sacA b.29.1.5 24237 1vj7A 393 4.21e+01 a.211.1.1,d.218.1.8 100801,100802 1jkeA 145 4.24e+01 c.110.1.1 66791 1nnjA 271 4.30e+01 a.156.1.2,b.113.1.1,g.39.1.8 80669,80670,80671 1s9aA 257 4.34e+01 b.3.6.1 105379 1bk1 184 4.35e+01 1axkA b.29.1.11 24340 1s6lA 212 4.39e+01 7taa 478 4.43e+01 7taa b.71.1.1,c.1.8.1 27778,28765 1opr 213 4.43e+01 1opr c.61.1.1 34091 1xruA 282 4.46e+01 1uesA 191 4.46e+01 a.2.11.1,d.44.1.1 107798,107799 1f86A 115 4.46e+01 1etb1 b.3.4.1 59689 1uedA 406 4.48e+01 a.104.1.1 99256 1di6A 195 4.50e+01 1di6A c.57.1.1 33863 2bcjB 340 4.50e+01 1gvoA 364 4.53e+01 c.1.4.1 76357 1gpuA 680 4.55e+01 c.36.1.10,c.36.1.6,c.48.1.1 65454,65455,65456 1f0iA 504 4.60e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 1g0hA 252 4.63e+01 1dk4A e.7.1.1 60171 1a9xA 1058 4.64e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1azpA 66 4.67e+01 1azpA b.34.13.1 37467 1e5pA 151 4.68e+01 1bj7 b.60.1.1 59272 1vh5A 148 4.69e+01 d.38.1.5 100642 1t1vA 93 4.71e+01 c.47.1.14 106278 1nkiA 135 4.71e+01 d.32.1.2 91941 2bvbA 137 4.73e+01 1wk2A 121 4.73e+01 1jb7B 260 4.75e+01 1otcB b.40.4.3 62839 1oygA 447 4.77e+01 b.67.2.2 93726 2gpzA 111 4.81e+01 1yvvA 336 4.86e+01 1va0A 239 4.94e+01 2gkeA 274 4.97e+01 1e79G 272 4.98e+01 1e79G c.49.2.1 33158 1z8oA 404 4.99e+01 1xhvA 257 5.02e+01 c.52.1.19 109597 1p32A 209 5.04e+01 1p32A d.25.1.1 38379 1v3eA 431 5.04e+01 b.68.1.1 100287 1yemA 179 5.05e+01 1smlA 269 5.09e+01 1smlA d.157.1.1 42053 1fvpA 231 5.10e+01 1nfp c.1.16.2 29556 1cd0A 111 5.14e+01 8fabA b.1.1.1 20559 2atxA 194 5.16e+01 2c6cA 707 5.19e+01 1b8aA 438 5.20e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1lo6A 223 5.21e+01 b.47.1.2 74143 1wguA 136 5.23e+01 1bn7A 294 5.23e+01 1bn6A c.69.1.8 34677 1pjjA 271 5.24e+01 a.156.1.2,b.113.1.1,g.39.1.8 104164,104165,104166 2fcjA 119 5.25e+01 1an9A 340 5.27e+01 1an9A c.4.1.2,d.16.1.3 30617,37904 1nlnA 204 5.27e+01 d.3.1.7 91962 2fe5A 94 5.32e+01 1tdzA 272 5.34e+01 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 1ve2A 235 5.35e+01 1plq 258 5.35e+01 1plq d.131.1.2,d.131.1.2 41388,41389 2phlA 397 5.36e+01 1dgwA b.82.1.2,b.82.1.2 28082,28083 1gxrA 337 5.38e+01 b.69.4.1 70722 1xyiA 66 5.46e+01 1orvA 728 5.46e+01 b.70.3.1,c.69.1.24 87354,87355 2frgP 106 5.50e+01 1hc7A 477 5.54e+01 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 1g79A 218 5.54e+01 1ci0A b.45.1.1 25752 1dosA 358 5.56e+01 1dosA c.1.10.2 29175 1oewA 329 5.57e+01 b.50.1.2 86924 1m3qA 317 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