# List of top-scoring protein chains for t2k-100-30-CB_burial_14_7-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.soe.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 2qs7A 144 2.04e-15 1jx7A 117 9.38e-04 c.114.1.1 77195 1l1sA 113 1.18e-03 c.114.1.1 73484 2pd2A 108 1.49e-03 2hy5B 136 1.57e-01 c.114.1.1 136866 3pfk 319 1.17e+00 3pfk 6pfkA 319 1.28e+00 3pfk c.89.1.1 35583 1euhA 475 1.32e+00 1euhA c.82.1.1 35369 3hn0A 283 1.49e+00 2qe0A 475 1.53e+00 1evyA 366 1.74e+00 1evyA a.100.1.6,c.2.1.6 18811,30215 1vbuA 328 1.82e+00 c.1.8.3 119963 1hyqA 263 1.82e+00 1hyqA c.37.1.10 61412 1nw8A 319 1.87e+00 c.66.1.11 86292 1thtA 305 2.18e+00 1thtA c.69.1.13 34711 2fb6A 117 2.31e+00 3fgnA 251 2.37e+00 1xyzA 347 3.09e+00 1taxA c.1.8.3 28804 2hy5C 102 3.33e+00 c.114.1.2 136867 1g0cA 364 3.45e+00 7a3hA c.1.8.3 60165 2hy5A 130 3.55e+00 c.114.1.1 136865 1ass 159 3.62e+00 1a6dA 1assA 159 3.62e+00 c.8.5.2 30818 1f48A 589 3.80e+00 1f48A c.37.1.10,c.37.1.10 32280,32281 1ir6A 424 4.16e+00 c.107.1.2 71342 1irxA 523 4.38e+00 a.97.1.2,c.26.1.1 71378,71379 1ihuA 589 4.46e+00 c.37.1.10,c.37.1.10 62394,62395 1f0kA 364 4.61e+00 1f0kA c.87.1.2 35465 2a1fA 247 4.61e+00 c.73.1.3 125991 2vg1A 228 4.62e+00 2vg0A 227 4.93e+00 1eg2A 319 4.95e+00 1eg2A c.66.1.11 34249 3guvA 167 5.28e+00 1w0mA 226 5.69e+00 c.1.1.1 109027 2d1pB 119 6.03e+00 c.114.1.1 131137 3dhnA 227 6.28e+00 3kcqA 215 6.30e+00 3h7uA 335 6.38e+00 1zxxA 319 6.46e+00 2hi0A 240 6.49e+00 2nyvA 222 6.61e+00 2eq5A 228 6.73e+00 2pfmA 444 6.78e+00 1ybdA 239 7.13e+00 c.73.1.3 122884 1sw2A 275 7.25e+00 c.94.1.1 106064 2h6rA 219 7.32e+00 1wdpA 495 7.37e+00 c.1.8.1 120907 2dbyA 368 7.56e+00 3dfhA 394 8.82e+00 1g94A 448 8.92e+00 b.71.1.1,c.1.8.1 65169,65170 1qfjA 232 8.97e+00 1qfjA b.43.4.2,c.25.1.1 25655,31545 2hp1A 432 9.00e+00 2gsaA 432 9.18e+00 2gsaA c.67.1.4 34446 1ebdA 455 9.24e+00 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 2gmwA 211 9.71e+00 c.108.1.19 147137 3d3aA 612 9.97e+00 3fq8A 427 9.99e+00 1o20A 427 1.00e+01 c.82.1.1 86556 7ceiB 206 1.04e+01 1bxiB d.4.1.1 37134 1z41A 338 1.06e+01 c.1.4.1 124421 1qmyA 167 1.12e+01 1qmyA d.3.1.2 37094 1a6dA 545 1.18e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19488,30819,38936 1m6jA 261 1.21e+01 c.1.1.1 78693 2bneA 241 1.22e+01 c.73.1.3 128824 2wesA 511 1.22e+01 1wjtA 103 1.23e+01 a.48.3.1 114711 1mjnA 179 1.23e+01 c.62.1.1 79210 3draB 390 1.25e+01 2w5vA 375 1.26e+01 1ionA 243 1.28e+01 c.37.1.10 62633 2ywrA 216 1.30e+01 2qu7A 288 1.32e+01 1lfaA 187 1.38e+01 1ido c.62.1.1 34122 1bf6A 291 1.39e+01 1pscA c.1.9.3 29065 1usyC 275 1.50e+01 d.104.1.1 113424 1tk9A 188 1.53e+01 c.80.1.3 107082 1fgs 428 1.53e+01 1fgs 2yvqA 143 1.54e+01 1fiy 883 1.55e+01 1fiy 1phpA 394 1.57e+01 c.86.1.1 35452 1ydgA 211 1.60e+01 c.23.5.8 116614 2qulA 290 1.62e+01 2ioyA 283 1.64e+01 1ssqA 267 1.64e+01 b.81.1.6 105993 1qwgA 251 1.65e+01 c.1.27.1 96473 3beqA 385 1.72e+01 1yzfA 195 1.76e+01 c.23.10.5 124275 1hd2A 161 1.77e+01 c.47.1.10 60962 3cinA 394 1.83e+01 1hmcA 148 1.85e+01 1hmcB a.26.1.2 16867 3fkyA 370 1.86e+01 2krcA 99 1.88e+01 2hc9A 491 1.89e+01 1sw5B 275 1.90e+01 c.94.1.1 106070 1vjpA 394 1.93e+01 c.2.1.3,d.81.1.3 100828,100829 3cyeA 387 1.97e+01 2ct8A 497 1.98e+01 1sw5A 275 2.02e+01 c.94.1.1 106069 2btoA 473 2.02e+01 c.32.1.1,d.79.2.1 145009,145010 2zdsA 340 2.06e+01 1pb7A 292 2.07e+01 c.94.1.1 88025 1sl4A 155 2.12e+01 d.169.1.1 105710 1q74A 303 2.12e+01 c.134.1.1 96019 2pz0A 252 2.18e+01 1v3hA 495 2.19e+01 c.1.8.1 108303 1kq6A 141 2.19e+01 d.189.1.1 91020 3flaA 267 2.20e+01 2wb7A 526 2.21e+01 2gc6A 428 2.23e+01 c.59.1.2,c.72.2.2 134952,134953 2okgA 255 2.24e+01 c.124.1.8 148805 1zclA 180 2.25e+01 2o14A 375 2.27e+01 b.18.1.32,c.23.10.8 148544,148545 2ojwA 384 2.29e+01 1r9gA 216 2.30e+01 c.23.16.1 97258 2r47A 157 2.33e+01 1u7pA 164 2.34e+01 c.108.1.17 113095 3e96A 316 2.43e+01 3b7eA 385 2.43e+01 2qtpA 194 2.46e+01 d.79.9.1 151354 3eafA 391 2.47e+01 1sr2A 116 2.50e+01 a.24.10.4 112109 1x24A 180 2.51e+01 2zcuA 286 2.52e+01 1amoA 615 2.53e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 25669,31210,31557 1yaaA 412 2.53e+01 1ajsA c.67.1.1 34280 2zxrA 666 2.53e+01 3f81A 183 2.56e+01 3m46A 666 2.57e+01 1j31A 262 2.58e+01 d.160.1.2 90808 1v2xA 194 2.62e+01 c.116.1.1 100274 1n82A 331 2.63e+01 c.1.8.3 91703 2yv1A 294 2.63e+01 1gpmA 525 2.65e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 3lxyA 334 2.69e+01 1zzlA 351 2.70e+01 d.144.1.7 125910 1c20A 128 2.74e+01 1c20A a.4.3.1 16079 2q8xA 331 2.78e+01 2pr7A 137 2.88e+01 3fg2P 404 2.92e+01 2nv0A 196 2.93e+01 c.23.16.1 138625 1kshA 186 2.95e+01 c.37.1.8 72914 2hx5A 152 2.98e+01 d.38.1.1 136837 2bekA 257 2.98e+01 2dplA 308 3.00e+01 3losA 543 3.00e+01 1jbwA 428 3.01e+01 c.59.1.2,c.72.2.2 62860,62861 1jqnA 883 3.01e+01 c.1.12.3 77159 3ckzA 385 3.03e+01 1hmcB 148 3.04e+01 1hmcB a.26.1.2 16868 3h4tA 404 3.06e+01 1q5dA 419 3.07e+01 a.104.1.1 95891 2f4dA 184 3.08e+01 3daoA 283 3.10e+01 1frb 315 3.11e+01 1frb 1d3yA 301 3.13e+01 1d3yA e.12.1.1 43252 1t8qA 336 3.19e+01 c.1.18.3 106669 2jkyA 213 3.23e+01 2bfgA 503 3.25e+01 b.71.1.2,c.1.8.3 128423,128424 3c3bA 420 3.28e+01 2witA 566 3.30e+01 1tmyA 120 3.32e+01 c.23.1.1 31083 1vhcA 224 3.33e+01 c.1.10.1 100661 3igsA 232 3.33e+01 3c71A 143 3.34e+01 1q7bA 244 3.38e+01 c.2.1.2 96026 2zueA 629 3.40e+01 1w36B 1180 3.42e+01 c.37.1.19,c.37.1.19,c.52.1.24 114122,114123,114124 2py6A 409 3.42e+01 c.66.1.56 149932 1u0sY 118 3.42e+01 c.23.1.1 107566 2p10A 286 3.47e+01 c.1.12.9 149144 2gasA 307 3.65e+01 1ydyA 356 3.72e+01 c.1.18.3 123006 1mxsA 225 3.77e+01 c.1.10.1 91494 2o7aA 124 3.83e+01 1byb 495 3.84e+01 1byb 3bfvA 271 3.88e+01 2sqcA 631 3.92e+01 2sqcA a.102.4.2,a.102.4.2 18854,18855 3ec1A 369 3.96e+01 2vh3A 113 4.04e+01 1vhrA 184 4.05e+01 1vhrA c.45.1.1 32651 1emsA 440 4.05e+01 1emsA d.13.1.1,d.160.1.1 37520,42086 1gqiA 708 4.08e+01 c.1.8.10,d.92.2.2 76279,76280 2w62A 556 4.09e+01 1s1mA 545 4.13e+01 c.23.16.1,c.37.1.10 105201,105202 2zxiA 637 4.19e+01 3f4wA 211 4.20e+01 1f7uA 607 4.22e+01 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 59673,59674,59675 3dffA 273 4.22e+01 1ps9A 671 4.29e+01 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 2g3fA 421 4.31e+01 b.92.1.10,c.1.9.17 147073,147074 1zckA 154 4.33e+01 1zu4A 320 4.42e+01 2z6iA 332 4.42e+01 1urmA 172 4.42e+01 c.47.1.10 113413 1o94A 729 4.44e+01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 1jdpA 441 4.53e+01 c.93.1.1 62906 2weuA 511 4.56e+01 3e4dA 278 4.59e+01 2r7gA 347 4.66e+01 a.74.1.3,a.74.1.3 151637,151638 2g2cA 167 4.68e+01 c.57.1.1 134535 1iirA 415 4.77e+01 1iirA c.87.1.5 62453 3iplA 501 4.84e+01 1x42A 232 4.90e+01 c.108.1.1 121677 2dfaA 250 4.90e+01 c.6.2.5 131469 1sr9A 644 4.90e+01 a.5.7.1,c.1.10.5,d.270.1.1 105960,105961,105962 2basA 431 4.91e+01 c.1.33.1,d.110.6.2 128244,128245 2va1A 256 4.96e+01 1ejxA 100 4.98e+01 d.8.1.1 83182 3mc1A 226 5.05e+01 2dqwA 294 5.06e+01 1cp2A 269 5.08e+01 1cp2A c.37.1.10 32269 1egzA 291 5.08e+01 7a3hA c.1.8.3 28828 2gqwA 408 5.09e+01 1ir3A 306 5.10e+01 1fmk d.144.1.7 41702 1g3qA 237 5.14e+01 1hyqA c.37.1.10 60237 1gd5A 130 5.18e+01 1gd5A d.189.1.1 60439 1u69A 163 5.25e+01 d.32.1.7 107699 3e58A 214 5.28e+01 1jqoA 970 5.37e+01 c.1.12.3 77160 1jogA 146 5.41e+01 a.24.16.2 77142 1dceB 331 5.43e+01 1dceB a.102.4.3 18872 2tmdA 729 5.44e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28616,30317,30602 1xfcA 384 5.44e+01 1txnA 328 5.51e+01 d.248.1.1 112779 1l0bA 229 5.52e+01 c.15.1.3,c.15.1.3 73391,73392 1z6kA 293 5.54e+01 1ax8 146 5.54e+01 1ax8 1ax8A 146 5.54e+01 a.26.1.1 16844 7a3hA 303 5.56e+01 7a3hA c.1.8.3 28817 1bs2A 607 5.57e+01 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 16930,31597,39563 1o6lA 337 5.57e+01 d.144.1.7 81092 3figA 646 5.58e+01 2avnA 260 5.59e+01 c.66.1.41 127380 2jr7A 89 5.60e+01 3eskA 129 5.64e+01 2hdwA 367 5.72e+01 3a16A 373 5.73e+01 2qg3A 208 5.76e+01 1nf9A 207 5.77e+01 c.33.1.3 85631 2vedA 271 5.78e+01 1djqA 729 5.78e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 2vc6A 292 5.82e+01 1qbqA 333 5.87e+01 1ft1A a.118.6.1 19187 2ha8A 184 5.90e+01 3ffjA 666 5.99e+01 1wcv1 257 6.00e+01 1dgsA 667 6.01e+01 1dgsA a.60.2.2,b.40.4.6,d.142.2.2 17963,25365,41581 2wm8A 187 6.04e+01 1elrA 131 6.05e+01 1a17 a.118.8.1 19209 3bi8A 291 6.11e+01 3ky9A 587 6.15e+01 2h7cA 542 6.16e+01 c.69.1.1 136207 2qvwA 756 6.20e+01 2afhE 289 6.20e+01 c.37.1.10 126683 1xhcA 367 6.27e+01 c.3.1.5,c.3.1.5,d.87.1.1 115292,115293,115294 2ywlA 180 6.35e+01 1wouA 123 6.37e+01 c.47.1.16 109471 1rxdA 159 6.37e+01 c.45.1.1 111959 1h5vA 304 6.38e+01 c.1.8.3 70898 1rvgA 305 6.52e+01 c.1.10.2 97920 1u7zA 226 6.54e+01 c.72.3.1 113107 1vffA 423 6.58e+01 c.1.8.4 120033 3bu3A 306 6.58e+01 d.144.1.7 155590 3jz4A 481 6.59e+01 1s69A 124 6.60e+01 a.1.1.1 105305 2qyxA 238 6.63e+01 1f5qB 252 6.64e+01 1f5qB a.74.1.1,a.74.1.1 18362,18363 3lmzA 257 6.66e+01 3lp8A 442 6.67e+01 3ga7A 326 6.68e+01 1ep3A 311 6.71e+01 2dorA c.1.4.1 28597 2o55A 258 6.71e+01 1tv8A 340 6.74e+01 c.1.28.3 107352 1df0A 700 6.76e+01 1dkvA a.39.1.8,b.14.1.1,d.3.1.3 17375,23674,37106 2gsjA 271 6.79e+01 2bgsA 344 6.85e+01 3bc1A 195 6.91e+01 1st9A 143 6.92e+01 c.47.1.10 98987 1g60A 260 6.93e+01 c.66.1.11 70151 3fbgA 346 6.93e+01 1clqA 903 6.95e+01 1clqA c.55.3.5,e.8.1.1 33717,43006 2tpsA 227 6.96e+01 2tpsA c.1.3.1 28591 3h7eA 237 7.05e+01 2vyoA 254 7.06e+01 1qzmA 94 7.07e+01 c.37.1.20 96651 1d7yA 408 7.11e+01 1d7yA c.3.1.5,c.3.1.5,d.87.1.1 30565,30566,40204 2q2rA 373 7.12e+01 2qc5A 300 7.14e+01 1q16A 1247 7.15e+01 b.52.2.2,c.81.1.1 95546,95547 1be1 137 7.16e+01 1be1 3euvB 427 7.18e+01 1ig9A 903 7.21e+01 1clqA c.55.3.5,e.8.1.1 62367,62368 3egwA 1244 7.22e+01 1cnv 299 7.24e+01 1cnv 1cnvA 299 7.24e+01 c.1.8.5 28989 2p5kA 64 7.25e+01 a.4.5.3 149249 2pmkA 243 7.34e+01 c.37.1.12 149669 2vldA 251 7.39e+01 1d7uA 433 7.42e+01 2dkb c.67.1.4 34439 2zosA 249 7.42e+01 1ur3M 319 7.44e+01 c.1.7.1 99806 2e1vA 454 7.45e+01 1g67A 225 7.48e+01 c.1.3.1 60311 1th8B 116 7.52e+01 c.13.2.1 106909 1u5vA 273 7.52e+01 c.1.12.5 113054 3hzhA 157 7.54e+01 2owbA 335 7.57e+01 1b04A 318 7.60e+01 1b04A d.142.2.2 41579 2e7yA 280 7.64e+01 d.157.1.7 146706 1d8dA 377 7.64e+01 1ft1A a.118.6.1 19185 1mrp 309 7.65e+01 1mrp 1tffA 234 7.67e+01 d.3.1.11 106854 2iucA 375 7.71e+01 1y5iA 1246 7.74e+01 b.52.2.2,c.81.1.1 122639,122640 1jffB 445 7.76e+01 c.32.1.1,d.79.2.1 62934,62935 1tf1A 198 7.76e+01 d.110.2.2 106826 1bteA 97 7.79e+01 1bteA g.7.1.3 44463 3bnjA 485 7.79e+01 1lj1A 571 7.84e+01 a.138.1.3,c.3.1.4,d.168.1.1 78023,78024,78025 2e2zA 100 7.87e+01 2afbA 351 7.89e+01 c.72.1.1 126674 2nytA 190 7.90e+01 2qs8A 418 7.90e+01 b.92.1.9,c.1.9.18 151311,151312 2gfiA 458 7.90e+01 1ih7A 903 7.93e+01 1clqA c.55.3.5,e.8.1.1 62375,62376 3dqzA 258 7.97e+01 1e5dA 402 7.98e+01 1e5dA c.23.5.1,d.157.1.3 31208,42061