# List of top-scoring protein chains for t06-80-60-80-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 1.79e-01 1f8fA 371 3.88e-01 b.35.1.2,c.2.1.1 83246,83247 1ko3A 230 6.15e-01 d.157.1.1 90974 2gw6A 123 6.38e-01 1mrj 247 7.71e-01 1mrj d.165.1.1 42177 2gaeA 346 1.02e+00 1yqzA 438 1.18e+00 1v04A 355 1.21e+00 b.68.6.2 100240 1pq7A 224 1.52e+00 b.47.1.2 95002 2aeuA 374 1.75e+00 1x3lA 440 1.77e+00 1mrg 263 1.87e+00 1mrj d.165.1.1 42183 1s5aA 150 1.88e+00 d.17.4.10 98525 1iruK 201 1.90e+00 d.153.1.4 71362 1v25A 541 1.91e+00 e.23.1.1 108275 1zh5A 195 2.45e+00 1s68A 249 2.76e+00 d.142.2.4 98591 1kmqA 184 3.09e+00 c.37.1.8 84412 1x8gA 227 3.10e+00 1eaxA 241 3.14e+00 b.47.1.2 64889 2c3mA 1231 3.28e+00 1js8A 394 3.30e+00 a.86.1.1,b.112.1.1 67219,67220 2sak 121 3.33e+00 2sak d.15.5.1 37711 2govA 195 3.45e+00 1jmcA 246 3.61e+00 1jmcA b.40.4.3,b.40.4.3 25300,25301 1vlyA 338 3.65e+00 b.44.2.1,d.250.1.1 108871,108872 1mfgA 95 3.70e+00 b.36.1.1 79043 2d28C 149 3.86e+00 1g8aA 227 3.92e+00 c.66.1.3 90506 1ddgA 374 3.96e+00 1amoA b.43.4.1,c.25.1.4 25671,31559 1zgkA 308 4.15e+00 1mqoA 227 4.33e+00 d.157.1.1 103846 1kolA 398 4.35e+00 b.35.1.2,c.2.1.1 77474,77475 1ja1A 622 4.61e+00 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1x8hA 228 4.79e+00 1se8A 301 5.36e+00 b.40.4.3 105448 1vhh 162 5.42e+00 1vhh d.65.1.2 39550 1w15A 153 5.63e+00 b.7.1.2 109041 3cox 507 5.64e+00 1b8sA c.3.1.2,d.16.1.1 30332,37863 1udzA 182 5.66e+00 b.51.1.1 99239 1yr2A 741 5.73e+00 1wi1A 126 5.81e+00 1wnyA 186 5.86e+00 1aoeA 192 5.98e+00 1aoeA c.71.1.1 34923 1gen 218 6.12e+00 1gen b.66.1.1 27536 2fxqA 264 6.37e+00 1azo 232 6.43e+00 1azo c.52.1.14 33329 1vzoA 355 7.10e+00 d.144.1.7 108971 2fy6A 143 7.14e+00 1cewI 108 7.39e+00 1cewI d.17.1.2 37999 1yt3A 375 7.48e+00 1u4bA 580 7.53e+00 c.55.3.5,e.8.1.1 107664,107665 1qwtA 255 7.87e+00 b.26.1.3 96501 1gjwA 637 7.98e+00 b.71.1.1,c.1.8.1 60582,60583 1xdnA 277 7.99e+00 1cfzA 162 8.05e+00 1cfzA c.56.1.1 33754 1am2 199 8.36e+00 1am2 b.86.1.2 28381 1wwrA 171 8.53e+00 1vhwA 253 8.59e+00 c.56.2.1 100706 2fhxA 246 8.63e+00 1xw3A 110 8.72e+00 1x8vA 455 8.74e+00 2c12A 439 9.20e+00 2f91A 237 9.28e+00 1khxA 227 9.38e+00 b.26.1.1 68631 2fclA 169 9.45e+00 3fib 249 9.53e+00 3fib d.171.1.1 42455 1h70A 255 9.63e+00 1h70A d.126.1.3 60711 1xtoA 311 9.73e+00 1uufA 369 9.96e+00 b.35.1.2,c.2.1.1 100006,100007 1yqgA 263 1.01e+01 1ryp2 233 1.01e+01 1ryp2 1roaA 122 1.08e+01 d.17.1.2 105024 1quqB 121 1.08e+01 1quqB b.40.4.3 25305 1ihjA 98 1.10e+01 1pdr b.36.1.1 62382 1jjtA 228 1.12e+01 1a7tA d.157.1.1 63139 1cuk 203 1.12e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1br9 194 1.16e+01 1br9 b.40.3.1 25235 1wosA 364 1.18e+01 b.44.2.1,d.250.1.1 109468,109469 1cruA 454 1.18e+01 1c9uA b.68.2.1 27617 2a5dA 175 1.18e+01 2b8nA 429 1.20e+01 1g3kA 174 1.21e+01 1nedA d.153.1.4 41989 1p0fA 373 1.22e+01 b.35.1.2,c.2.1.1 87642,87643 1shyB 551 1.26e+01 b.69.12.1,g.16.2.1 105565,105566 1vj0A 380 1.26e+01 b.35.1.2,c.2.1.1 100786,100787 1nrzA 164 1.33e+01 c.38.1.1 86131 1rypK 198 1.33e+01 d.153.1.4 41879 1gotB 340 1.34e+01 1tbgA b.69.4.1 27648 1lcyA 325 1.38e+01 b.36.1.4,b.47.1.1 73834,73835 1t2wA 145 1.38e+01 b.100.1.1 106289 1u3wA 374 1.39e+01 1zkpA 268 1.39e+01 1n4wA 504 1.40e+01 c.3.1.2,d.16.1.1 91676,91677 1agi 125 1.42e+01 7rsa d.5.1.1 37303 1qwrA 319 1.44e+01 b.82.1.3 96491 2b0tA 738 1.45e+01 1rybA 212 1.48e+01 c.56.3.1 98098 1ym0A 238 1.49e+01 2chnA 716 1.49e+01 1a7tA 232 1.51e+01 1a7tA d.157.1.1 42041 1t71A 281 1.52e+01 1kcqA 104 1.54e+01 d.109.1.1 68449 1gp6A 356 1.58e+01 b.82.2.1 65441 1k8kC 372 1.60e+01 b.69.4.1 68308 1kmvA 186 1.60e+01 c.71.1.1 72757 1qqp2 218 1.61e+01 1qqp2 1gteA 1025 1.61e+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 2cx7A 130 1.63e+01 1ok7A 366 1.64e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1jvbA 347 1.67e+01 b.35.1.2,c.2.1.1 77181,77182 2eng 210 1.68e+01 2eng b.52.1.1 26895 1qwkA 317 1.68e+01 c.1.7.1 96482 1xtqA 177 1.74e+01 2cfuA 658 1.76e+01 1uptA 171 1.82e+01 c.37.1.8 99767 1rzuA 485 1.83e+01 c.87.1.8 105140 1y10A 407 1.83e+01 1g0sA 209 1.84e+01 1g0sA d.113.1.1 60187 1evlA 401 1.84e+01 1qf6A c.51.1.1,d.104.1.1 33202,40751 2ajgA 196 1.89e+01 1dv1A 449 1.89e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 2ghsA 326 1.94e+01 1fmtA 314 1.94e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 2d1sA 548 1.95e+01 1qy6A 274 1.96e+01 b.47.1.1 96574 1wruA 379 1.97e+01 1lo7A 141 1.99e+01 d.38.1.1 74144 1izoA 417 2.01e+01 a.104.1.1 83851 1xcbA 211 2.03e+01 a.4.5.38,c.2.1.12 109552,109553 1fp2A 352 2.04e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1n9pA 207 2.04e+01 b.1.18.16 80343 1wmhB 86 2.05e+01 1i0lA 221 2.05e+01 c.61.1.1 71096 1n8kA 374 2.05e+01 b.35.1.2,c.2.1.1 80298,80299 1nf2A 268 2.09e+01 c.108.1.10 91849 1rypI 222 2.10e+01 d.153.1.4 41877 2exnA 136 2.11e+01 1jfbA 404 2.13e+01 a.104.1.1 66624 1v37A 177 2.18e+01 1x54A 434 2.20e+01 1l3iA 192 2.21e+01 c.66.1.22 77676 1h2bA 359 2.22e+01 b.35.1.2,c.2.1.1 90543,90544 1odkA 235 2.32e+01 c.56.2.1 86863 2bgiA 272 2.32e+01 1uc8A 280 2.35e+01 c.30.1.6,d.142.1.7 99165,99166 1o3yA 166 2.37e+01 c.37.1.8 86618 2bbhA 269 2.38e+01 2cx5A 158 2.38e+01 1s5uA 138 2.41e+01 d.38.1.1 98573 1gpr 162 2.41e+01 1gpr b.84.3.1 28267 1f20A 435 2.43e+01 b.43.4.1,c.25.1.4 64932,64933 1qy5A 269 2.44e+01 d.122.1.1 96573 1s1fA 406 2.45e+01 1vkdA 338 2.47e+01 b.67.2.4 108644 1zxtA 76 2.47e+01 1fs0E 138 2.52e+01 1aqt a.2.10.1,b.93.1.1 59997,59998 1wkrA 340 2.54e+01 b.50.1.2 109395 1v0wA 506 2.54e+01 d.136.1.2,d.136.1.2 108220,108221 1eylA 186 2.60e+01 1wba b.42.4.1 25593 1wmxA 205 2.61e+01 b.18.1.24 109418 1oe8A 211 2.61e+01 a.45.1.1,c.47.1.5 86905,86906 1v3vA 333 2.64e+01 b.35.1.2,c.2.1.1 108345,108346 1wzlA 585 2.65e+01 1m7bA 184 2.66e+01 c.37.1.8 74572 1e4cP 215 2.72e+01 2fua c.74.1.1 34969 1ni9A 338 2.73e+01 e.7.1.2 85739 1ywmA 200 2.74e+01 1cz4A 185 2.76e+01 1cz4A b.52.2.3,d.31.1.1 26934,38468 1zndA 174 2.81e+01 1q7fA 286 2.83e+01 b.68.9.1 96036 1i4uA 181 2.85e+01 b.60.1.1 61732 1j0hA 588 2.89e+01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 1yb3A 175 2.90e+01 1y2tA 142 2.91e+01 1rypJ 204 2.91e+01 d.153.1.4 41878 1n26A 325 2.94e+01 b.1.1.4,b.1.2.1,b.1.2.1 79850,79851,79852 1f5jA 199 2.98e+01 1axkA b.29.1.11 24342 1tmxA 293 2.98e+01 1jofA 365 3.00e+01 b.69.10.1 71775 1di6A 195 3.00e+01 1di6A c.57.1.1 33863 1yarH 217 3.04e+01 2f86B 143 3.05e+01 1ukfA 188 3.05e+01 d.3.1.10 99488 2sga 181 3.13e+01 1qq4A b.47.1.1 25808 3pcgA 200 3.15e+01 3pchA b.3.6.1 22647 1sacA 204 3.15e+01 1sacA b.29.1.5 24237 1vj7A 393 3.23e+01 a.211.1.1,d.218.1.8 100801,100802 2ew0A 192 3.24e+01 1qtoA 122 3.25e+01 1bylA d.32.1.2 38494 1jx4A 352 3.27e+01 d.240.1.1,e.8.1.7 90378,90379 1ep3B 262 3.34e+01 1ep2B b.43.4.2,c.25.1.3 25664,31554 7taa 478 3.35e+01 7taa b.71.1.1,c.1.8.1 27778,28765 1s6lA 212 3.39e+01 1uedA 406 3.39e+01 a.104.1.1 99256 1f86A 115 3.41e+01 1etb1 b.3.4.1 59689 1nkiA 135 3.44e+01 d.32.1.2 91941 1i9zA 347 3.48e+01 1i9yA d.151.1.2 62102 1uesA 191 3.48e+01 a.2.11.1,d.44.1.1 107798,107799 1dnlA 199 3.50e+01 1ci0A b.45.1.1 25753 1qy1A 174 3.53e+01 b.60.1.1 96568 1jkeA 145 3.53e+01 c.110.1.1 66791 1jb7B 260 3.54e+01 1otcB b.40.4.3 62839 1p32A 209 3.58e+01 1p32A d.25.1.1 38379 1xruA 282 3.59e+01 2bcjB 340 3.67e+01 1yemA 179 3.72e+01 1t1vA 93 3.76e+01 c.47.1.14 106278 1va0A 239 3.77e+01 2gpzA 111 3.80e+01 2gkeA 274 3.82e+01 1gpuA 680 3.85e+01 c.36.1.10,c.36.1.6,c.48.1.1 65454,65455,65456 2bvbA 137 3.86e+01 2c6cA 707 3.87e+01 1z8oA 404 3.90e+01 1e5pA 151 3.90e+01 1bj7 b.60.1.1 59272 1pgl1 185 3.91e+01 1bn7A 294 3.92e+01 1bn6A c.69.1.8 34677 1fvpA 231 3.94e+01 1nfp c.1.16.2 29556 1a9xA 1058 3.97e+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 2gefA 217 3.97e+01 2bzvA 181 4.11e+01 1tdzA 272 4.11e+01 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 3bamA 213 4.17e+01 1bam c.52.1.3 33288 1ve2A 235 4.18e+01 2fe5A 94 4.20e+01 1hc7A 477 4.21e+01 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 2fcjA 119 4.23e+01 1lo6A 223 4.27e+01 b.47.1.2 74143 1xyiA 66 4.27e+01 1vh5A 148 4.27e+01 d.38.1.5 100642 1gxrA 337 4.28e+01 b.69.4.1 70722 1oygA 447 4.39e+01 b.67.2.2 93726 1m3qA 317 4.40e+01 a.96.1.3,d.129.1.2 91184,91185 1wk2A 121 4.41e+01 2ddrA 306 4.43e+01 2f4nA 273 4.44e+01 1wguA 136 4.45e+01 1nlnA 204 4.46e+01 d.3.1.7 91962 1pmhX 185 4.50e+01 b.18.1.18 104193 1q7lA 198 4.51e+01 c.56.5.4 96044 1dytA 133 4.51e+01 7rsa d.5.1.1 37288 1jb0D 138 4.52e+01 1jb0D d.187.1.1 62823 2pia 321 4.52e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1dosA 358 4.54e+01 1dosA c.1.10.2 29175 2fneA 117 4.54e+01 1v3eA 431 4.57e+01 b.68.1.1 100287 1tjxA 159 4.58e+01 2a9sA 171 4.60e+01 1g79A 218 4.62e+01 1ci0A b.45.1.1 25752 1b8aA 438 4.63e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1ryp1 222 4.64e+01 1ryp1 1ok8A 394 4.65e+01 b.1.18.4,f.10.1.1 93236,93237 1h65A 270 4.70e+01 c.37.1.8 65640 2f0aA 98 4.71e+01 1rm6B 324 4.73e+01 4dfrA 159 4.74e+01 1vdrA c.71.1.1 34822 1vqoT 120 4.75e+01 1orvA 728 4.75e+01 b.70.3.1,c.69.1.24 87354,87355 1z6nA 167 4.76e+01 2aioA 269 4.77e+01 1fqtA 112 4.77e+01 1fqtA b.33.1.1 24441 2frgP 106 4.78e+01 1p77A 272 4.79e+01 c.2.1.7,c.58.1.5 94214,94215 1oewA 329 4.81e+01 b.50.1.2 86924 1bqbA 301 4.83e+01 1hyt d.92.1.2 58962 1efdN 266 4.83e+01 1efdN c.92.2.1 35597 1c8cA 64 4.89e+01 1azpA b.34.13.1 59084 1fl0A 171 4.92e+01 1eujA b.40.4.4 25315 1whbA 157 4.92e+01 1ijaA 148 4.99e+01 1ijaA b.100.1.1 62484 1h4vB 421 4.99e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 2cxxA 190 5.05e+01 1x31C 206 5.06e+01 1gw5S 142 5.10e+01 d.110.4.2 70633 1ex2A 189 5.13e+01 1ex2A c.51.4.2 33225 8dfr 189 5.15e+01 1aoeA c.71.1.1 34895 1yt8A 539 5.16e+01 2a67A 167 5.21e+01 1r77A 103 5.21e+01 1j48A 110 5.22e+01 b.1.7.1 84112 2cyeA 133 5.24e+01 1mj5A 302 5.29e+01 c.69.1.8 91285 2pth 193 5.29e+01 2pth c.56.3.1 33793 1wdnA 226 5.31e+01 1lst c.94.1.1 35816 1p1jA 533 5.32e+01 c.2.1.3,d.81.1.3 87687,87688 2f46A 156 5.34e+01 1ztcA 221 5.36e+01 1zirA 173 5.36e+01 2ck3A 510 5.37e+01 3gcb 470 5.39e+01 3gcb d.3.1.1 37032 1yp2A 451 5.40e+01 1wmmA 145 5.41e+01 1p35A 299 5.42e+01 1p35A b.28.1.1 23925 1dmhA 311 5.44e+01 1dmhA b.3.6.1 22633 2gimA 106 5.51e+01 1u7nA 336 5.51e+01 c.77.1.4 107726 1yb5A 351 5.54e+01 1nu0A 138 5.60e+01 c.55.3.8 92165 1wqsA 173 5.60e+01 1v0eA 666 5.64e+01 2f51A 118 5.65e+01 1e5rA 290 5.67e+01 1e5rA b.82.2.4 59276 1h8eA 510 5.71e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1q4uA 151 5.73e+01 d.38.1.5 95828 1vdwA 254 5.75e+01 e.7.1.1 100569 1gqzA 274 5.75e+01 d.21.1.1,d.21.1.1 83311,83312 1epuA 591 5.76e+01 1dn1A e.25.1.1 43358 1lh0A 213 5.77e+01 c.61.1.1 73896 1jeoA 180 5.77e+01 c.80.1.3 66611 1oq1A 223 5.77e+01 b.29.1.17 93408 1ckmA 330 5.86e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 1ik9A 213 5.86e+01 b.59.1.1,h.1.11.1 66176,66177 1d2fA 390 5.89e+01 1d2fA c.67.1.3 34411 1ifrA 121 5.93e+01 b.1.16.1 71203 1zc3B 113 5.95e+01 2atpB 115 5.95e+01 1fehA 574 5.96e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 3psg 370 6.01e+01 1smrA b.50.1.2 26841 3pcgM 238 6.01e+01 3pchM b.3.6.1 22742 1zr6A 503 6.05e+01 1n7fA 97 6.06e+01 b.36.1.1 91692 1uteA 313 6.07e+01 1uteA d.159.1.1 42078 1l0bA 229 6.08e+01 c.15.1.3,c.15.1.3 73391,73392 1xocA 520 6.10e+01 1vbwA 68 6.10e+01 1grj 158 6.19e+01 1grj a.2.1.1,d.26.1.2 15691,38433 1zn8A 180 6.20e+01 1kngA 156 6.22e+01 c.47.1.10 72777 1whi 122 6.25e+01 1whi b.39.1.1 24810 1xhnA 184 6.28e+01 1m6yA 301 6.29e+01 a.60.13.1,c.66.1.23 78716,78717 1edqA 540 6.30e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1rwzA 245 6.34e+01 d.131.1.2,d.131.1.2 98005,98006 1mkzA 172 6.34e+01 c.57.1.1 84998 1ujnA 348 6.42e+01 e.22.1.1 99460 1vemA 516 6.42e+01 1x89A 178 6.46e+01 1th7A 81 6.53e+01 1kveB 77 6.54e+01 1kveB 2fywA 267 6.56e+01 2fcr 173 6.60e+01 1rcf c.23.5.1 31151 1gyhA 318 6.60e+01 b.67.2.1 70757 1ivg 388 6.61e+01 2qwc b.68.1.1 27578 1rypH 205 6.62e+01 d.153.1.4 41876 2fimA 276 6.67e+01 1l1qA 186 6.68e+01 c.61.1.1 77653 1gvhA 396 6.70e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1yzsA 121 6.70e+01 1y44A 320 6.72e+01 1cr5A 189 6.86e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 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