# 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.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 1ofgA 381 8.77e-41 1ofgA c.2.1.3,d.81.1.5 30064,39979 1h6dA 433 1.13e-40 c.2.1.3,d.81.1.5 65656,65657 1ydwA 362 6.54e-35 1tltA 319 4.26e-29 c.2.1.3,d.81.1.5 107135,107136 1xeaA 323 4.14e-27 c.2.1.3,d.81.1.5 109572,109573 1gcuA 295 1.17e-19 1gcuA c.2.1.3,d.81.1.4 30063,39978 1lc0A 294 2.71e-19 c.2.1.3,d.81.1.4 73823,73824 1vknA 351 1.32e-05 c.2.1.3,d.81.1.1 108676,108677 1ff9A 450 3.47e-05 1ff9A c.2.1.3,d.81.1.2 30039,39954 1nvmB 312 5.00e-05 c.2.1.3,d.81.1.1 86251,86252 1arzC 273 5.19e-05 1drw c.2.1.3,d.81.1.3 30061,39976 1gd1O 334 6.48e-05 1dssG c.2.1.3,d.81.1.1 29962,39877 1b7gO 340 7.69e-05 1b7gO c.2.1.3,d.81.1.1 29992,39907 2ahrA 259 7.83e-05 2gd1O 334 8.24e-05 1dssG c.2.1.3,d.81.1.1 29978,39893 1ys4A 354 9.37e-05 2czcA 334 1.25e-04 1vpdA 299 4.40e-04 1ldnA 316 6.01e-04 1hyhA c.2.1.5,d.162.1.1 30166,42133 1dih 273 7.47e-04 1drw c.2.1.3,d.81.1.3 30056,39971 1f06A 320 1.12e-03 1dapA c.2.1.3,d.81.1.3 59556,59557 3dapA 320 1.17e-03 1dapA c.2.1.3,d.81.1.3 30051,39966 1ebfA 358 1.45e-03 1ebuA c.2.1.3,d.81.1.2 30033,39948 1dapA 320 1.65e-03 1dapA c.2.1.3,d.81.1.3 30053,39968 1gadO 330 1.66e-03 1dssG c.2.1.3,d.81.1.1 29950,39865 1drw 273 1.79e-03 1drw c.2.1.3,d.81.1.3 30057,39972 2c82A 413 2.62e-03 1cf2O 337 2.98e-03 1b7gO c.2.1.3,d.81.1.1 29994,39909 1nytA 271 4.05e-03 c.2.1.7,c.58.1.5 86417,86418 1a5z 319 4.16e-03 1ceqA c.2.1.5,d.162.1.1 30181,42148 1oi7A 288 4.19e-03 c.2.1.8,c.23.4.1 87049,87050 2g5cA 281 4.21e-03 2d0iA 333 4.64e-03 1xygD 359 5.49e-03 1bg6 359 6.10e-03 1bg6 a.100.1.5,c.2.1.6 18810,30214 1yrlA 491 6.77e-03 1ebuA 358 7.10e-03 1ebuA c.2.1.3,d.81.1.2 30035,39950 1pgjA 478 1.13e-02 2pgd a.100.1.1,c.2.1.6 18783,30195 1wwkA 307 1.24e-02 1hyhA 309 1.26e-02 1hyhA c.2.1.5,d.162.1.1 30150,42117 1gpjA 404 2.24e-02 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1jayA 212 2.29e-02 c.2.1.6 66478 2h78A 302 3.12e-02 2dbqA 334 3.36e-02 2f1kA 279 3.42e-02 1yqgA 263 3.54e-02 1lldA 319 3.57e-02 3ldh c.2.1.5,d.162.1.1 30177,42144 1q0qA 406 4.25e-02 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 2dldA 337 4.27e-02 1dxy c.2.1.4,c.23.12.1 30099,31359 2b4rO 345 4.82e-02 1obbA 480 4.84e-02 c.2.1.5,d.162.1.2 86760,86761 1xdwA 331 5.41e-02 1np3A 338 5.56e-02 a.100.1.2,c.2.1.6 85946,85947 1vm6A 228 5.74e-02 c.2.1.3,d.81.1.3 108876,108877 1k3tA 359 5.83e-02 c.2.1.3,d.81.1.1 72022,72023 1y81A 138 6.11e-02 1gypA 358 7.08e-02 1dssG c.2.1.3,d.81.1.1 30004,39919 2ajrA 331 7.60e-02 1z82A 335 8.56e-02 1vllA 334 8.59e-02 c.2.1.13 108834 2cvzA 289 8.60e-02 1obfO 335 9.03e-02 c.2.1.3,d.81.1.1 86768,86769 1u8fO 335 9.79e-02 1j4aA 333 1.04e-01 c.2.1.4,c.23.12.1 71502,71503 1zejA 293 1.05e-01 1rm4A 337 1.10e-01 c.2.1.3,d.81.1.1 105000,105001 1jvsA 400 1.14e-01 a.69.3.1,c.2.1.3,d.81.1.3 77187,77188,77189 1mldA 314 1.26e-01 2cmd c.2.1.5,d.162.1.1 30122,42089 1vl8A 267 1.32e-01 c.2.1.2 108733 1qp8A 303 1.47e-01 1qp8A c.2.1.4,c.23.12.1 30092,31352 1dpgA 485 1.52e-01 1dpgA c.2.1.3,d.81.1.5 30074,39989 1omoA 322 1.55e-01 c.2.1.13 104017 1i36A 264 1.60e-01 a.100.1.8,c.2.1.6 71108,71109 2pgd 482 1.69e-01 2pgd a.100.1.1,c.2.1.6 18778,30190 2ew2A 316 1.72e-01 1jaxA 212 1.75e-01 c.2.1.6 66476 1pzgA 331 1.86e-01 c.2.1.5,d.162.1.1 95425,95426 1wxdA 263 1.97e-01 1yqdA 366 1.98e-01 2a35A 215 2.00e-01 2gptA 523 2.05e-01 2gn4A 344 2.06e-01 2cy0A 263 2.28e-01 1dliA 402 2.32e-01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18809,30213,31622 2ez3A 302 2.34e-01 1k5hA 398 2.64e-01 a.69.3.1,c.2.1.3,d.81.1.3 68192,68193,68194 1d2fA 390 3.04e-01 1d2fA c.67.1.3 34411 2bh9A 489 3.20e-01 2d5cA 263 3.27e-01 1dssG 333 3.30e-01 1dssG c.2.1.3,d.81.1.1 30022,39937 1r0kA 388 3.66e-01 a.69.3.1,c.2.1.3,d.81.1.3 104723,104724,104725 1dxy 333 3.68e-01 1dxy c.2.1.4,c.23.12.1 30094,31354 1cydA 244 3.78e-01 1cydA c.2.1.2 29825 1evyA 366 3.87e-01 1evyA a.100.1.6,c.2.1.6 18811,30215 1x7dA 350 4.28e-01 1gsoA 431 4.58e-01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 1crwG 333 4.74e-01 1dssG c.2.1.3,d.81.1.1 30026,39941 1p77A 272 5.12e-01 c.2.1.7,c.58.1.5 94214,94215 1v4vA 376 5.67e-01 c.87.1.3 100313 1yixA 265 5.75e-01 2gasA 307 6.78e-01 1b74A 254 7.14e-01 1b74A c.78.2.1,c.78.2.1 35264,35265 1dljA 402 7.15e-01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1ybvA 283 7.58e-01 1ybvA c.2.1.2 29948 1up6A 416 7.92e-01 c.2.1.5,d.162.1.2 107976,107977 2d1yA 256 8.10e-01 1inlA 296 8.29e-01 c.66.1.17 66220 1uirA 314 8.83e-01 c.66.1.17 99429 1up7A 417 9.19e-01 1x1eA 239 9.20e-01 2cdcA 366 9.75e-01 1qydA 313 1.01e+00 c.2.1.2 96583 1hyeA 313 1.01e+00 2cmd c.2.1.5,d.162.1.1 61400,61401 1ldm 329 1.08e+00 3ldh c.2.1.5,d.162.1.1 30160,42127 1y9aA 360 1.09e+00 6ldh 330 1.12e+00 3ldh c.2.1.5,d.162.1.1 30161,42128 1g0oA 283 1.14e+00 1ybvA c.2.1.2 60181 2nadA 393 1.22e+00 2nadA c.2.1.4,c.23.12.1 30090,31350 2dpg 485 1.24e+00 1dpgA c.2.1.3,d.81.1.5 30076,39991 1pjcA 361 1.29e+00 1sayA c.2.1.4,c.23.12.2 30101,31361 2cmd 312 1.31e+00 2cmd c.2.1.5,d.162.1.1 30135,42102 1yizA 429 1.51e+00 1ldg 316 1.57e+00 1ceqA c.2.1.5,d.162.1.1 30165,42132 1pbgA 468 1.57e+00 1e70M c.1.8.4 28946 1jq3A 296 1.58e+00 c.66.1.17 67079 1sayA 361 1.62e+00 1sayA c.2.1.4,c.23.12.2 30102,31362 2bllA 345 1.67e+00 1yiyA 429 1.67e+00 1twiA 434 1.74e+00 b.49.2.3,c.1.6.1 107399,107400 1j0hA 588 1.85e+00 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 3pbgA 468 1.94e+00 1e70M c.1.8.4 28951 1npyA 271 2.01e+00 c.2.1.7,c.58.1.5 85995,85996 2bw0A 329 2.06e+00 1tufA 434 2.10e+00 b.49.2.3,c.1.6.1 107335,107336 1uok 558 2.18e+00 1uok b.71.1.1,c.1.8.1 27801,28788 1ogsA 497 2.29e+00 b.71.1.2,c.1.8.3 86997,86998 1u9jA 358 2.31e+00 1b26A 416 2.32e+00 1hwyA c.2.1.7,c.58.1.1 30232,33880 1t2dA 322 2.33e+00 c.2.1.5,d.162.1.1 99084,99085 1lsuA 147 2.34e+00 c.2.1.9 74250 1z7bA 358 2.35e+00 1l3iA 192 2.38e+00 c.66.1.22 77676 1pjbA 361 2.45e+00 1sayA c.2.1.4,c.23.12.2 30103,31363 1z7aA 308 2.50e+00 1zdzA 302 2.52e+00 1psdA 409 2.65e+00 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1sc6A 404 2.66e+00 1b73A 254 2.75e+00 1b74A c.78.2.1,c.78.2.1 35266,35267 1xuuA 349 2.79e+00 1qycA 308 3.43e+00 c.2.1.2 96581 1b3bA 415 3.52e+00 1hwyA c.2.1.7,c.58.1.1 30244,33892 1khbA 625 3.73e+00 c.91.1.1,c.109.1.1 68606,68607 9ldtA 332 3.96e+00 3ldh c.2.1.5,d.162.1.1 30154,42121 1mx3A 347 3.99e+00 c.2.1.4,c.23.12.1 79638,79639 1o5iA 249 4.01e+00 c.2.1.2 92499 1ceqA 316 4.04e+00 1ceqA c.2.1.5,d.162.1.1 30163,42130 1ymqA 261 4.13e+00 1snyA 267 4.26e+00 c.2.1.2 105833 1ezwA 349 4.32e+00 1ezwA c.1.16.3 29558 1k0fA 277 4.51e+00 c.92.2.2 71974 1guzA 310 5.17e+00 c.2.1.5,d.162.1.1 65586,65587 1kolA 398 5.25e+00 b.35.1.2,c.2.1.1 77474,77475 3ldh 330 5.44e+00 3ldh i.12.1.1 46015 1wy7A 207 5.56e+00 1gm7B 557 5.60e+00 1p5dX 463 5.92e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1gtmA 419 5.93e+00 1hwyA c.2.1.7,c.58.1.1 30223,33871 5ldh 334 5.95e+00 3ldh c.2.1.5,d.162.1.1 30158,42125 1gkfB 557 6.07e+00 1at1A 310 6.12e+00 3csuA c.78.1.1,c.78.1.1 35168,35169 1zcjA 463 6.14e+00 1wzaA 488 6.51e+00 1vjpA 394 6.57e+00 c.2.1.3,d.81.1.3 100828,100829 1sqiA 393 6.74e+00 d.32.1.3,d.32.1.3 105914,105915 1gk9B 557 7.01e+00 1ml4A 308 7.06e+00 c.78.1.1,c.78.1.1 79255,79256 1fsz 372 7.18e+00 1fsz c.32.1.1,d.79.2.1 31750,39802 2a0fA 310 7.19e+00 1e3aB 560 7.20e+00 1ajqB 1s3iA 310 7.21e+00 b.46.1.1,c.65.1.1 98435,98436 1pkn 530 7.30e+00 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27042,29271,33125 1gm9B 557 7.39e+00 1j5pA 253 7.41e+00 d.81.1.3,c.2.1.3 71577,83092 2g1uA 155 7.61e+00 1xgkA 352 7.70e+00 1gegA 256 7.81e+00 1ybvA c.2.1.2 29888 2fflA 756 7.94e+00 1yxmA 303 8.04e+00 1lc5A 364 8.12e+00 c.67.1.1 73827 1zuwA 272 8.14e+00 1scuA 288 8.51e+00 2scuA c.2.1.8,c.23.4.1 30307,31135 2g76A 335 8.65e+00 1jsrA 327 8.76e+00 c.88.1.1 67237 1kf6A 602 8.91e+00 a.7.3.1,c.3.1.4,d.168.1.1 72394,72395,72396 1l2lA 457 9.05e+00 c.72.1.3 77656 1ryc 294 9.10e+00 1ryc a.93.1.1 18601 1o7jA 327 9.14e+00 c.88.1.1 81140 1ve3A 227 9.14e+00 1ee8A 266 9.21e+00 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1qv9A 283 9.37e+00 c.127.1.1 96356 2scuA 288 9.38e+00 2scuA c.2.1.8,c.23.4.1 30303,31131 1jslA 327 9.57e+00 c.88.1.1 67233 1ykfA 352 9.68e+00 1pedA b.35.1.2,c.2.1.1 24757,29773 1e2uA 553 9.82e+00 1e1dA e.26.1.1 43362 8atcA 310 9.83e+00 3csuA c.78.1.1,c.78.1.1 35132,35133 1gntA 553 9.99e+00 e.26.1.1 70290 1g6aA 271 1.00e+01 1btl e.3.1.1 42704 1zzoA 136 1.00e+01 1lkcA 364 1.00e+01 c.67.1.1 73978 1fg7A 356 1.01e+01 1gewA c.67.1.1 59819 1gy8A 397 1.03e+01 c.2.1.2 83376 1q3kA 259 1.06e+01 c.125.1.1 95693 1tqxA 227 1.06e+01 1k2yX 463 1.06e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1ekxA 311 1.07e+01 3csuA c.78.1.1,c.78.1.1 35088,35089 1uxjA 309 1.10e+01 c.2.1.5,d.162.1.1 108112,108113 1xcbA 211 1.10e+01 a.4.5.38,c.2.1.12 109552,109553 1pnkB 557 1.10e+01 1ajqB 1luaA 287 1.11e+01 c.2.1.7,c.58.1.4 78216,78217 1ua7A 422 1.11e+01 b.71.1.1,c.1.8.1 107759,107760 1e4fT 419 1.11e+01 1e4fT c.55.1.1,c.55.1.1 33453,33454 1pjhA 280 1.13e+01 c.14.1.3 94761 1zkdA 387 1.13e+01 2nacA 393 1.13e+01 2nadA c.2.1.4,c.23.12.1 30088,31348 1vqoE 178 1.13e+01 1acmA 310 1.20e+01 3csuA c.78.1.1,c.78.1.1 35180,35181 1ax4A 467 1.20e+01 1ax4A c.67.1.2 34391 1bg4 302 1.20e+01 1taxA c.1.8.3 28806 1jj2E 177 1.21e+01 1ffk1 d.141.1.1,d.141.1.1 63089,63090 2bd0A 244 1.23e+01 1eqjA 511 1.28e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 1s72E 178 1.30e+01 d.141.1.1,d.141.1.1 105323,105324 1jykA 254 1.34e+01 c.68.1.13 67458 1jvbA 347 1.35e+01 b.35.1.2,c.2.1.1 77181,77182 1uufA 369 1.35e+01 b.35.1.2,c.2.1.1 100006,100007 1xxlA 239 1.38e+01 1b31A 302 1.39e+01 1taxA c.1.8.3 28892 1gewA 356 1.41e+01 1gewA c.67.1.1 60470 2c0cA 362 1.43e+01 1dhr 241 1.43e+01 1dhr c.2.1.2 29832 1cbg 490 1.46e+01 1e70M c.1.8.4 28933 1fmtB 314 1.47e+01 1fmtA b.46.1.1,c.65.1.1 25759,34175 1vheA 373 1.47e+01 b.49.3.1,c.56.5.4 100669,100670 1yq2A 1024 1.48e+01 2minB 522 1.48e+01 1qguB c.92.2.3 35610 1bag 425 1.50e+01 1bag b.71.1.1,c.1.8.1 27720,28707 1eucA 311 1.54e+01 2scuA c.2.1.8,c.23.4.1 30311,31139 1m1nB 522 1.55e+01 c.92.2.3 78418 1kevA 351 1.55e+01 1pedA b.35.1.2,c.2.1.1 24749,29765 1hdcA 253 1.58e+01 1e6wA c.2.1.2 29862 2gl5A 410 1.59e+01 2gh1A 301 1.59e+01 1tx2A 297 1.60e+01 c.1.21.1 107420 1g5aA 628 1.60e+01 b.71.1.1,c.1.8.1 65152,65153 1uhvA 500 1.61e+01 b.71.1.2,c.1.8.3 99402,99403 1xewX 182 1.65e+01 1o60A 292 1.68e+01 c.1.10.4 92532 1jcqA 382 1.71e+01 a.118.6.1 66504 1nffA 260 1.72e+01 c.2.1.2 80457 1kay 381 1.72e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1vgvA 384 1.73e+01 c.87.1.3 100608 1o98A 511 1.73e+01 c.105.1.1,c.76.1.3 86684,86685 3minB 522 1.75e+01 1qguB c.92.2.3 35606 1kcxA 518 1.77e+01 b.92.1.3,c.1.9.6 90953,90954 1ld8A 382 1.80e+01 a.118.6.1 73838 1e1dA 553 1.82e+01 1e1dA e.26.1.1 43363 1fmcA 255 1.86e+01 1cydA c.2.1.2 29856 1qh5A 260 1.86e+01 1qh5A d.157.1.2 42057 1eudA 311 1.88e+01 2scuA c.2.1.8,c.23.4.1 30312,31140 1hvyA 288 1.96e+01 1bkpA d.117.1.1 41049 1ejjA 511 1.96e+01 1ejjA c.105.1.1,c.76.1.3 59422,59423 1zowA 313 1.97e+01 1ft1A 377 1.98e+01 1ft1A a.118.6.1 19186 1gc5A 467 2.00e+01 1gc5A c.72.1.3 60429 1ibjA 464 2.00e+01 1ibjA c.67.1.3 62162 1fmtA 314 2.09e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 1hpm 386 2.10e+01 1ba1 c.55.1.1,c.55.1.1 33381,33382 1vlyA 338 2.12e+01 b.44.2.1,d.250.1.1 108871,108872 2hsdA 253 2.13e+01 1e6wA c.2.1.2 29866 1edoA 244 2.14e+01 1ybvA c.2.1.2 29896 1pq4A 291 2.15e+01 c.92.2.2 94995 1l1jA 239 2.16e+01 b.47.1.1 84516 1f83A 425 2.16e+01 1f82A d.92.1.7 40306 1dp4A 435 2.18e+01 1dp4A c.93.1.1 35710 1tn6A 382 2.18e+01 1ow4A 129 2.19e+01 a.39.2.1 93628 2bshA 125 2.22e+01 1qh3A 260 2.23e+01 1qh5A d.157.1.2 42059 1pb7A 292 2.24e+01 c.94.1.1 88025 1f2vA 219 2.27e+01 1f2vA c.23.17.1 59627 1i1hA 219 2.27e+01 1f2vA c.23.17.1 61530 1wcv1 257 2.30e+01 1nrkA 328 2.33e+01 b.44.2.1,d.250.1.1 92089,92090 1te0A 318 2.35e+01 2fji1 399 2.36e+01 1ks9A 291 2.36e+01 a.100.1.7,c.2.1.6 68857,68858 2bhoA 130 2.39e+01 1f5nA 592 2.40e+01 1dg3A a.114.1.1,c.37.1.8 19077,32152 1vliA 385 2.42e+01 b.85.1.1,c.1.10.6 108830,108831 2bgkA 278 2.43e+01 1m2tA 254 2.46e+01 d.165.1.1 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