# List of top-scoring protein chains for t04-100-30-stride-ebghtl-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 1mk4A 157 3.23e-04 d.108.1.1 84979 1ne9A 335 5.06e-03 d.108.1.4,d.108.1.4 91839,91840 1v93A 296 9.95e-03 c.1.23.1 100532 2d4pA 141 3.94e-02 2fe7A 166 7.11e-02 1z4eA 153 9.22e-02 1sqhA 312 2.44e-01 d.108.1.5 98966 1zu4A 320 2.46e-01 2ge3A 170 3.02e-01 1s3zA 165 3.13e-01 d.108.1.1 105250 2c71A 216 3.45e-01 1vhsA 175 3.46e-01 d.108.1.1 100698 2aj6A 159 4.22e-01 1iicA 422 4.25e-01 1nmtA d.108.1.2,d.108.1.2 62422,62423 2bl1A 172 6.03e-01 1tiqA 180 7.24e-01 d.108.1.1 107010 1dik 874 7.64e-01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 2fl4A 149 8.08e-01 2cy2A 174 8.41e-01 1q0sA 259 1.07e+00 c.66.1.28 95509 1yvoA 172 1.10e+00 2c3zA 222 1.12e+00 1exqA 154 1.12e+00 1b9dA c.55.3.2 33646 1rj9A 304 1.24e+00 a.24.13.1,c.37.1.10 97553,97554 1vqzA 341 1.32e+00 1xtmA 175 1.43e+00 1xtlA 175 1.51e+00 1p0hA 318 1.55e+00 d.108.1.1 93866 1s4iA 175 1.57e+00 1nu5A 370 1.57e+00 c.1.11.2,d.54.1.1 92183,92184 1y9kA 157 1.63e+00 1b0uA 262 1.64e+00 1b0uA c.37.1.12 32370 1yvkA 163 1.66e+00 1a53 247 1.70e+00 1a53 c.1.2.4 28564 1zwwA 256 1.71e+00 1igs 248 1.74e+00 1a53 c.1.2.4 28565 1ho1A 242 1.85e+00 1ho1A c.1.24.1 61097 1zbfA 142 1.86e+00 1xqiA 195 1.87e+00 1yx0A 159 1.94e+00 1u9jA 358 2.05e+00 1u9iA 519 2.25e+00 1lw7A 365 2.38e+00 c.26.1.3,c.37.1.1 74295,74296 1cjwA 166 2.44e+00 1cjwA d.108.1.1 40818 1i1dA 161 2.85e+00 1i21A d.108.1.1 61526 1ecpA 238 2.86e+00 1ecpA c.56.2.1 33775 2c27A 315 2.95e+00 2b67A 204 3.00e+00 1gw5S 142 3.02e+00 d.110.4.2 70633 1m5wA 243 3.03e+00 c.1.24.1 84836 2bllA 345 3.30e+00 1m65A 245 3.41e+00 c.6.3.1 84847 1z7bA 358 3.63e+00 1yx1A 264 3.64e+00 2b5gA 171 3.65e+00 1kblA 873 4.27e+00 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1p1xA 260 4.61e+00 c.1.10.1 104060 2f1rA 171 4.68e+00 2ganA 190 4.70e+00 1wnaA 131 4.83e+00 1i12A 160 5.48e+00 1i21A d.108.1.1 61515 1jclA 260 5.64e+00 c.1.10.1 66501 1n71A 180 5.90e+00 d.108.1.1 85370 1bia 321 5.95e+00 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1e8cA 498 6.09e+00 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1z4rA 168 6.13e+00 1qo7A 394 6.30e+00 1qo7A c.69.1.11 34697 1pq1A 196 6.54e+00 f.1.4.1 94986 1yf3A 259 6.61e+00 1b87A 181 6.73e+00 1b87A d.108.1.1 40797 2a4nA 182 6.78e+00 2dbyA 368 6.88e+00 1o8uA 257 6.97e+00 c.14.1.3 81194 1w0mA 226 7.13e+00 c.1.1.1 109027 1ktaA 365 7.23e+00 e.17.1.1 77533 2atrA 138 7.48e+00 1szoA 257 7.76e+00 c.14.1.3 106164 1gz6A 319 7.85e+00 c.2.1.2 76410 2gtrA 261 7.93e+00 2cxaA 256 8.02e+00 1v7rA 186 8.24e+00 c.51.4.1 100482 1ekfA 365 8.70e+00 1ekfA e.17.1.1 59445 1qlmA 316 9.13e+00 1qlmA d.147.1.1 41765 1ru8A 232 9.44e+00 c.26.2.1 97849 1maz 221 9.60e+00 1maz f.1.4.1 43393 2a1hA 365 1.00e+01 1pgvA 197 1.01e+01 c.10.1.1 88073 1puiA 210 1.02e+01 c.37.1.8 88292 1zy9A 564 1.05e+01 1q2yA 140 1.06e+01 d.108.1.1 95655 1kcxA 518 1.07e+01 b.92.1.3,c.1.9.6 90953,90954 1bl3A 160 1.09e+01 1b9dA c.55.3.2 33655 1cnv 299 1.14e+01 1cnv c.1.8.5 28989 1j0dA 341 1.15e+01 c.79.1.1 83902 1vmeA 410 1.18e+01 c.23.5.1,d.157.1.3 108893,108894 1yirA 408 1.19e+01 1ad2 228 1.19e+01 1ad2 e.24.1.1 43353 1hyvA 166 1.23e+01 1b9dA c.55.3.2 61424 1qjcA 158 1.24e+01 1b6tA c.26.1.3 63328 1qstA 160 1.25e+01 1yghA d.108.1.1 40804 1ad3A 452 1.27e+01 1ad3A c.82.1.1 35335 1cfr 285 1.29e+01 1cfr c.52.1.7 33312 1uxoA 192 1.30e+01 c.69.1.31 108121 1f2dA 341 1.34e+01 1f2dA c.79.1.1 35298 1te6A 439 1.34e+01 c.1.11.1,d.54.1.1 106797,106798 1wfxA 186 1.35e+01 1u46A 291 1.35e+01 d.144.1.7 107656 2cvhA 220 1.45e+01 1kpeA 126 1.47e+01 1kpf d.13.1.1 37508 1k9sA 237 1.53e+01 c.56.2.1 68359 1h09A 338 1.57e+01 b.109.1.1,c.1.8.8 83420,83421 1bo4A 168 1.64e+01 1bo4A d.108.1.1 40798 1wwzA 159 1.68e+01 1yvhA 329 1.68e+01 1u0mA 382 1.73e+01 c.95.1.2,c.95.1.2 107557,107558 2b06A 155 1.76e+01 2cblA 305 1.77e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17380,17774,40528 1tfuA 157 1.81e+01 c.26.1.3 106859 2akzA 439 1.82e+01 1wj5A 120 1.83e+01 2aeuA 374 1.85e+01 1yruA 364 1.86e+01 1mf7A 194 1.92e+01 c.62.1.1 84937 2d13A 227 1.93e+01 1vkcA 158 1.99e+01 1bykA 255 1.99e+01 1bykA c.93.1.1 35706 1kpf 126 2.00e+01 1kpf d.13.1.1 37507 1b5tA 275 2.00e+01 1b5tA c.1.23.1 29676 1ypxA 375 2.01e+01 1h1dA 221 2.01e+01 c.66.1.1 83452 1od6A 160 2.02e+01 c.26.1.3 86836 1h7nA 342 2.04e+01 1b4kA c.1.10.3 60726 1j6zA 376 2.05e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 1ohlA 342 2.05e+01 c.1.10.3 87035 1yemA 179 2.06e+01 1tjyA 316 2.06e+01 c.93.1.1 107062 1usyA 275 2.12e+01 1k6xA 352 2.22e+01 c.2.1.2 68238 1wkyA 464 2.25e+01 7a3hA 303 2.25e+01 7a3hA c.1.8.3 28817 1dkuA 317 2.29e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 4pfk 319 2.31e+01 3pfk c.89.1.1 35582 1u9lA 70 2.37e+01 a.60.4.2 107751 1yghA 164 2.39e+01 1yghA d.108.1.1 40802 1zotA 358 2.40e+01 1wkbA 810 2.43e+01 2reb 352 2.45e+01 2reb c.37.1.11,d.48.1.1 32282,38767 1vid 221 2.51e+01 1vid c.66.1.1 34178 1t1jA 125 2.54e+01 c.137.1.1 106249 1befA 181 2.59e+01 1befA b.47.1.3 26419 2beiA 170 2.65e+01 1nar 290 2.66e+01 1nar c.1.8.5 28988 1e9rA 437 2.69e+01 c.37.1.11 64827 2rslA 140 2.72e+01 2rslA c.53.1.1 33345 1yqyA 523 2.76e+01 2c8vA 288 2.83e+01 1tidB 119 2.83e+01 c.13.2.1 107000 1yr0A 175 2.89e+01 1v9sA 208 2.91e+01 1o04A 500 2.92e+01 c.82.1.1 86508 2ae6A 166 2.92e+01 1gsa 316 2.92e+01 1gsa c.30.1.3,d.142.1.1 31718,41477 1yrtA 364 2.96e+01 1zbqA 327 2.98e+01 2fp8A 322 3.12e+01 1mu5A 471 3.15e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1mb4A 370 3.16e+01 c.2.1.3,d.81.1.1 78908,78909 1jxhA 288 3.19e+01 c.72.1.2 67415 1vr6A 350 3.21e+01 1uh5A 329 3.23e+01 c.2.1.2 107840 1nksA 194 3.24e+01 1nksA c.37.1.1 31886 2a10A 125 3.27e+01 1ockA 412 3.28e+01 c.117.1.1 86802 1wyzA 242 3.29e+01 2fz4A 237 3.31e+01 1q60A 99 3.32e+01 1k8kD 300 3.33e+01 d.198.2.1,d.198.2.1 68309,68310 1pdz 434 3.34e+01 4enl c.1.11.1,d.54.1.1 29215,38859 1e3oC 160 3.34e+01 1au7A a.4.1.1,a.35.1.1 59197,59198 1uok 558 3.39e+01 1uok b.71.1.1,c.1.8.1 27801,28788 1g4wR 383 3.41e+01 1g4uS a.24.11.1,c.45.1.2 16644,32692 1vkyA 347 3.44e+01 e.53.1.1 108696 1itwA 741 3.47e+01 c.77.1.2 76793 1s7hA 200 3.49e+01 d.58.48.2 105349 2fp7B 172 3.49e+01 2bswA 146 3.50e+01 2ck3D 482 3.53e+01 1ha3A 405 3.54e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1kg0C 136 3.54e+01 d.169.1.1 72445 1xp8A 366 3.55e+01 1jzuA 157 3.59e+01 b.60.1.1 84271 1auiB 169 3.62e+01 1auiB a.39.1.5 17325 1je0A 236 3.65e+01 c.56.2.1 66581 1qz5A 375 3.66e+01 c.55.1.1,c.55.1.1 96614,96615 1t6aA 126 3.66e+01 d.129.8.1 106555 1atiA 505 3.67e+01 1atiA c.51.1.1,d.104.1.1 33196,40745 1m7xA 617 3.67e+01 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 1u94A 356 3.70e+01 c.37.1.11,d.48.1.1 107743,107744 1x67A 146 3.72e+01 1gx1A 160 3.76e+01 d.79.5.1 70675 1oh0A 131 3.80e+01 d.17.4.3 87004 1z41A 338 3.81e+01 1laxA 370 3.83e+01 c.94.1.1 84576 1u8zA 168 3.87e+01 1x8hA 228 3.93e+01 1muwA 386 4.01e+01 c.1.15.3 79495 1x8gA 227 4.02e+01 1zxxA 319 4.06e+01 1jljA 189 4.13e+01 c.57.1.1 63169 1ihcA 188 4.13e+01 1di6A c.57.1.1 62379 1qwkA 317 4.17e+01 c.1.7.1 96482 2bodX 286 4.19e+01 2b5dX 528 4.21e+01 1nvmB 312 4.24e+01 c.2.1.3,d.81.1.1 86251,86252 1octC 156 4.26e+01 1au7A a.4.1.1,a.35.1.1 15991,17017 2ew8A 249 4.26e+01 1wo8A 126 4.36e+01 1vhmA 195 4.36e+01 d.110.2.1 100691 1h7sA 365 4.36e+01 d.14.1.3,d.122.1.2 65705,65706 1p7gA 222 4.37e+01 a.2.11.1,d.44.1.1 94223,94224 1xfjA 261 4.44e+01 d.194.1.2 109585 2b8nA 429 4.46e+01 1uf5A 303 4.51e+01 d.160.1.2 107808 1vmaA 306 4.56e+01 a.24.13.1,c.37.1.10 108887,108888 1pwhA 327 4.57e+01 c.79.1.1 95224 1itg 166 4.59e+01 1b9dA c.55.3.2 33661 1vc4A 254 4.60e+01 c.1.2.4 100557 1z5bA 469 4.60e+01 1erzA 303 4.61e+01 1erzA d.160.1.2 59498 1mg7A 417 4.63e+01 d.14.1.6,d.58.26.6 84954,84955 1wz7A 111 4.63e+01 1h8eD 482 4.64e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 1e79D 482 4.64e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18272,26437,32317 1r77A 103 4.64e+01 1ocvA 125 4.66e+01 d.17.4.3 86810 4xis 387 4.66e+01 4xis c.1.15.3 29421 1wuaA 375 4.66e+01 2bg1A 494 4.68e+01 1vypX 364 4.77e+01 c.1.4.1 108905 2fggA 101 4.80e+01 1g5gA 481 4.81e+01 f.12.1.1,h.3.2.1 65155,65156 1p9qC 256 4.81e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1zvdA 380 4.82e+01 1zavA 180 4.82e+01 1ykwA 435 4.83e+01 2coiA 386 4.84e+01 1hrhA 136 4.85e+01 1rthA c.55.3.1 33577 1s99A 200 4.87e+01 1y80A 210 4.88e+01 1k32A 1045 4.90e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1tzzA 392 4.93e+01 1vsrA 136 4.98e+01 1vsrA c.52.1.15 33332 1t9hA 307 5.07e+01 1tr7A 164 5.13e+01 1h2wA 710 5.15e+01 b.69.7.1,c.69.1.4 76596,76597 1pjcA 361 5.16e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 2a1iA 146 5.19e+01 1ls1A 295 5.22e+01 a.24.13.1,c.37.1.10 78170,78171 1wy7A 207 5.26e+01 2gviA 204 5.27e+01 1ohpA 125 5.30e+01 3xis 387 5.33e+01 4xis c.1.15.3 29423 1ej6D 418 5.52e+01 i.7.1.1 45970 1wdnA 226 5.52e+01 1lst c.94.1.1 35816 5nul 138 5.53e+01 5nul c.23.5.1 31191 2b6hA 192 5.55e+01 1crb 134 5.56e+01 1hmt b.60.1.2 27220 1ax4A 467 5.61e+01 1ax4A c.67.1.2 34391 1ukz 203 5.64e+01 1zin c.37.1.1 31840 1onrA 316 5.65e+01 1onrA c.1.10.1 29169 1j7nA 776 5.72e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 2ab5A 269 5.73e+01 1yqdA 366 5.79e+01 1q8dA 108 5.79e+01 a.228.1.1 104554 1kzfA 230 5.81e+01 d.108.1.3 73354 1earA 147 5.82e+01 b.107.1.1,d.58.38.1 64875,64876 1m4iA 181 6.02e+01 d.108.1.1 74457 1nnwA 252 6.02e+01 d.159.1.5 80674 1a79A 171 6.02e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 1j24A 143 6.03e+01 c.52.1.20 84008 2fxuA 375 6.09e+01 1ads 315 6.16e+01 1frb c.1.7.1 28671 1ik9A 213 6.22e+01 b.59.1.1,h.1.11.1 66176,66177 1wxcB 134 6.22e+01 1af3 196 6.24e+01 1maz f.1.4.1 43397 1f9aA 168 6.30e+01 1f9aA c.26.1.3 31602 1nf2A 268 6.33e+01 c.108.1.10 91849 1giqA 413 6.33e+01 d.166.1.1,d.166.1.1 76224,76225 2fbmA 291 6.39e+01 1s7kA 182 6.40e+01 1oi2A 366 6.45e+01 c.119.1.2 103802 2g40A 224 6.45e+01 1tkkA 366 6.50e+01 c.1.11.2,d.54.1.1 107089,107090 1zp4A 304 6.51e+01 2arhA 203 6.52e+01 1sjiA 350 6.53e+01 2a9kA 187 6.53e+01 1jqgA 433 6.55e+01 c.56.5.1,d.58.3.1 71791,71792 4mbp 370 6.56e+01 4mbp c.94.1.1 35777 1g55A 343 6.59e+01 1g55A c.66.1.26 34247 1pwmA 316 6.61e+01 c.1.7.1 95231 2dri 271 6.62e+01 2dri c.93.1.1 35637 1us0A 316 6.63e+01 c.1.7.1 99850 1ubeA 349 6.75e+01 c.37.1.11,d.48.1.1 88412,88413 2pvaA 345 6.75e+01 3pvaA d.153.1.3 41850 2gdzA 267 6.77e+01 1uwfA 158 6.80e+01 1ne2A 200 6.84e+01 c.66.1.32 85586 1u1jA 765 6.86e+01 c.1.22.2,c.1.22.2 107590,107591 2c1gA 431 6.90e+01 1nv8A 284 6.94e+01 c.66.1.30 86224 2co5A 99 6.95e+01 1wmbA 260 7.02e+01 2ar0A 541 7.02e+01 1vdeA 454 7.05e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28378,40581,40582 1cm5A 759 7.10e+01 1cm5A c.7.1.1 30671 1i2oA 316 7.10e+01 1onrA c.1.10.1 61574 1mwpA 96 7.23e+01 1mwpA d.170.2.1 42453 1l2tA 235 7.26e+01 c.37.1.12 73514 1ituA 369 7.26e+01 c.1.9.7 71423 1ki9A 192 7.33e+01 c.37.1.1 84404 1v4pA 157 7.35e+01 1zrn 232 7.36e+01 1qq5A c.108.1.1 43323 2ajrA 331 7.40e+01 1m1zA 513 7.47e+01 c.26.2.1,d.153.1.1 78457,78458 1h49A 512 7.50e+01 c.1.8.4 83477 2gwfA 157 7.57e+01 2fh1A 344 7.58e+01 2cwkA 160 7.59e+01 1gvoA 364 7.62e+01 c.1.4.1 76357 2shpA 525 7.64e+01 2shpA c.45.1.2,d.93.1.1,d.93.1.1 32683,40533,40534 1p8xA 344 7.73e+01 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 1e5mA 416 7.74e+01 1dd8A c.95.1.1,c.95.1.1 58973,58974 1twyA 290 7.78e+01 1e3jA 352 7.79e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 1h61A 364 7.86e+01 1oyc c.1.4.1 60657 1vyrA 364 7.86e+01 c.1.4.1 108906 1yz4A 160 7.87e+01 1zo0A 126 7.88e+01 1tvjA 166 7.88e+01 1vhzA 198 7.90e+01 d.113.1.1 100718 1v0lA 313 7.96e+01 c.1.8.3 108207 2abbA 364 7.99e+01 1spjA 238 8.00e+01 1gggA 226 8.04e+01 1lst c.94.1.1 35817 1jmxA 494 8.09e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66901,66902,66903,66904,66905 2btfA 375 8.16e+01 1yagA c.55.1.1,c.55.1.1 33429,33430 1np6A 174 8.19e+01 c.37.1.10 85954 1wu7A 434 8.26e+01 2agaA 190 8.35e+01 1xmtA 103 8.35e+01 1vrpA 381 8.37e+01 1zarA 282 8.37e+01 1u1hA 765 8.39e+01 c.1.22.2,c.1.22.2 107580,107581 2a61A 145 8.40e+01 2bhuA 602 8.54e+01 1t95A 240 8.54e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1whzA 70 8.59e+01 1dfaA 454 8.63e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28375,40575,40576 1sgjA 284 8.67e+01 c.1.12.5 105535 1y7rA 133 8.68e+01 1n1bA 549 8.72e+01 a.102.4.1,a.128.1.3 79799,79800 1gpmA 525 8.80e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1h8eG 272 8.82e+01 1e79G c.49.2.1 60756 1jflA 228 8.93e+01 c.78.2.1,c.78.2.1 71656,71657 2b0cA 206 8.97e+01 1y7pA 223 8.98e+01