# List of top-scoring protein chains for t04-100-30-str2-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 2gvkA 317 1.71e-32 1zvdA 380 9.13e-02 1a8y 367 5.71e-01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1t0tV 248 6.98e-01 d.58.4.10 106229 1j7nA 776 7.37e-01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1fj2A 232 1.20e+00 1auoA c.69.1.14 34720 1r8gA 372 1.29e+00 d.128.1.3 104845 2aalA 131 1.62e+00 1dtwB 342 1.81e+00 1qs0B c.36.1.7,c.48.1.2 31828,33102 2cb2A 318 1.98e+00 1tz0A 114 2.09e+00 d.58.4.5 107463 1zdzA 302 2.20e+00 1ys4A 354 2.33e+00 2bklA 695 2.52e+00 1ni4B 341 2.86e+00 c.36.1.7,c.48.1.2 85729,85730 1nbwA 607 3.12e+00 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1v1rB 342 3.22e+00 c.36.1.7,c.48.1.2 108273,108274 1nriA 306 3.26e+00 c.80.1.3 86123 2b34A 199 3.48e+00 1gcb 454 3.52e+00 3gcb d.3.1.1 37034 1jsxA 207 3.55e+00 c.66.1.20 71846 1aoeA 192 3.58e+00 1aoeA c.71.1.1 34923 1x7yB 342 3.64e+00 1hlrA 907 3.77e+00 1vlbA 907 3.79e+00 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 2bfdB 345 3.90e+00 3gcb 470 4.20e+00 3gcb d.3.1.1 37032 1xygD 359 4.87e+00 1l1qA 186 5.05e+00 c.61.1.1 77653 1n7vA 555 5.07e+00 b.126.1.1 85377 1a6q 382 5.26e+00 1a6q a.159.1.1,d.219.1.1 75801,75802 1jyhA 157 5.27e+00 d.60.1.3 71956 1e2kA 331 5.61e+00 1qhiA c.37.1.1 31854 2chnA 716 5.69e+00 1olsB 342 5.72e+00 c.36.1.7,c.48.1.2 93332,93333 2cxnA 557 5.82e+00 1iq4A 179 6.58e+00 1iq4A d.77.1.1 62641 1zkcA 197 6.91e+00 1d4xG 126 6.96e+00 1d0nA d.109.1.1 59109 1jg1A 235 7.19e+00 c.66.1.7 66661 1l3kA 196 7.36e+00 d.58.7.1,d.58.7.1 73539,73540 1nm1G 125 7.61e+00 d.109.1.1 80653 1fmjA 351 7.68e+00 c.37.1.5 59879 1fts 295 8.04e+00 1ng1 a.24.13.1,c.37.1.10 16968,32279 1ha1 184 8.63e+00 1ha1 d.58.7.1,d.58.7.1 39147,39148 1kaeA 434 9.05e+00 c.82.1.2 72247 1jj2H 167 9.10e+00 1ffkF d.41.4.1 63093 1vimA 200 9.67e+00 c.80.1.3 100758 1uxtA 501 9.70e+00 c.82.1.1 108125 8dfr 189 9.76e+00 1aoeA c.71.1.1 34895 1k6xA 352 1.02e+01 c.2.1.2 68238 1fm0E 150 1.08e+01 1fmaE d.41.5.1 38629 1e8cA 498 1.12e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1ayx 492 1.13e+01 1ayx a.102.1.1 18825 1kinA 366 1.14e+01 1zcjA 463 1.17e+01 1y5iA 1246 1.19e+01 1xgkA 352 1.20e+01 1o97D 320 1.23e+01 c.26.2.3,c.31.1.2 81233,81234 1t4hA 290 1.26e+01 d.144.1.7 106420 1v3hA 495 1.26e+01 c.1.8.1 108303 1wpoA 256 1.30e+01 1lay b.57.1.1 27012 1qhiA 366 1.31e+01 1qhiA c.37.1.1 31860 2jdxA 385 1.33e+01 1jdw d.126.1.2 41139 1souA 194 1.33e+01 c.124.1.6 105858 1zx1A 231 1.36e+01 1chmA 401 1.36e+01 1chmA c.55.2.1,d.127.1.1 33545,41142 1yvrA 538 1.39e+01 2exrA 524 1.40e+01 1fuiA 591 1.43e+01 1fuiA b.43.2.1,c.85.1.1 25674,35444 2a6aA 218 1.45e+01 1j27A 102 1.47e+01 d.58.50.1 90778 2bx6A 350 1.50e+01 2fbaA 492 1.51e+01 1ve1A 304 1.55e+01 1y8aA 332 1.57e+01 1hr6B 443 1.57e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1wu7A 434 1.57e+01 1iatA 557 1.60e+01 1dqrA c.80.1.2 62123 1g2oA 268 1.62e+01 1b8oA c.56.2.1 60228 1q2lA 939 1.63e+01 1x7dA 350 1.66e+01 1dysA 348 1.67e+01 1bvwA c.6.1.1 30669 1byb 495 1.68e+01 1byb c.1.8.1 28790 1t5oA 351 1.72e+01 c.124.1.5 106459 1j5xA 342 1.74e+01 c.80.1.1 71591 1qk8A 146 1.74e+01 1ewxA c.47.1.10 33061 1m3sA 186 1.75e+01 c.80.1.3 78573 1ht6A 405 1.76e+01 b.71.1.1,c.1.8.1 83629,83630 1nd7A 374 1.77e+01 d.148.1.1 91817 1uwvA 433 1.78e+01 b.40.4.12,c.66.1.40 100128,100129 2d0oA 610 1.79e+01 1xv5A 401 1.82e+01 1yy7A 213 1.84e+01 1fxlA 167 1.90e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1f1uA 323 1.94e+01 d.32.1.3,d.32.1.3 83200,83201 1tc1A 220 1.99e+01 1tc1A c.61.1.1 34083 2bb6A 414 2.02e+01 2fsjA 346 2.11e+01 1ve5A 311 2.13e+01 1vrmA 325 2.13e+01 1cs1A 386 2.19e+01 1ibjA c.67.1.3 34399 2aeeA 211 2.20e+01 1l9kA 305 2.21e+01 c.66.1.25 84569 1xo7A 166 2.21e+01 1gy8A 397 2.22e+01 c.2.1.2 83376 1p4cA 380 2.22e+01 c.1.4.1 94100 1yr2A 741 2.26e+01 2gasA 307 2.27e+01 1v7cA 351 2.29e+01 c.79.1.1 100446 1omzA 293 2.30e+01 c.68.1.15 87093 1zejA 293 2.33e+01 1b4bA 71 2.36e+01 1b4aA d.74.2.1 39718 1kwgA 645 2.36e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 2fnjB 118 2.38e+01 1q16A 1247 2.39e+01 b.52.2.2,c.81.1.1 95546,95547 1qw9A 502 2.47e+01 b.71.1.2,c.1.8.3 96466,96467 2fytA 340 2.48e+01 2b8eA 273 2.49e+01 1pg4A 652 2.50e+01 e.23.1.1 88067 1vqwA 457 2.52e+01 1tib 269 2.52e+01 3tgl c.69.1.17 34738 1f06A 320 2.53e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 1g8kA 825 2.57e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 1g99A 408 2.58e+01 1g99A c.55.1.2,c.55.1.2 33457,33458 1czaN 917 2.59e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 1fa0A 537 2.60e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 1z0wA 207 2.64e+01 1ckv 141 2.67e+01 1ckv d.137.1.1 41452 1dptA 117 2.78e+01 1dptA d.80.1.3 39862 1zmdA 474 2.79e+01 2bgiA 272 2.79e+01 1jj2B 337 2.83e+01 1ffkB b.43.3.2 63086 1umdB 324 2.85e+01 c.36.1.7,c.48.1.2 99600,99601 1s72B 338 2.86e+01 b.43.3.2 105320 1vj7A 393 2.87e+01 a.211.1.1,d.218.1.8 100801,100802 1ev7A 317 2.89e+01 1ev7B c.52.1.9 33315 1lm8B 118 2.89e+01 d.15.1.1 74033 1sqiA 393 2.94e+01 d.32.1.3,d.32.1.3 105914,105915 1vlpA 441 3.01e+01 d.41.2.2,d.41.2.3 108840,108841 1q6cA 495 3.04e+01 c.1.8.1 95970 1z6kA 293 3.05e+01 1nnhA 294 3.07e+01 d.104.1.1 92005 1ss9A 311 3.07e+01 c.68.1.4 105978 1tk9A 188 3.08e+01 c.80.1.3 107082 5abp 306 3.08e+01 8abp c.93.1.1 35651 2ga9D 469 3.08e+01 1jfrA 262 3.10e+01 1jfrA c.69.1.16 34724 1amp 291 3.13e+01 1amp c.56.5.4 33837 1hgxA 183 3.13e+01 1tc1A c.61.1.1 34027 1fo8A 343 3.15e+01 1foaA c.68.1.10 59927 1nv8A 284 3.16e+01 c.66.1.30 86224 1vcbA 118 3.19e+01 1vcbA d.15.1.1 37603 1wi1A 126 3.19e+01 1vddA 228 3.24e+01 e.49.1.1 108519 1zjcA 418 3.25e+01 1qd1A 325 3.26e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1tr0A 108 3.29e+01 d.58.4.4 107261 1auoA 218 3.30e+01 1auoA c.69.1.14 34716 1ofuX 119 3.31e+01 c.37.1.22 86976 1moq 368 3.39e+01 1moq c.80.1.1 35302 1vknA 351 3.39e+01 c.2.1.3,d.81.1.1 108676,108677 2bj7A 138 3.40e+01 1p9aG 290 3.44e+01 c.10.2.7 87990 1jpzA 473 3.45e+01 a.104.1.1 67069 1opc 110 3.50e+01 1opc a.4.6.1 16231 1sq5A 308 3.54e+01 c.37.1.6 105882 2bkyX 89 3.55e+01 1rwtA 232 3.57e+01 f.43.1.1 97992 2f8lA 344 3.60e+01 1uj6A 227 3.66e+01 c.124.1.4,d.58.40.1 107898,107899 1ow1A 195 3.68e+01 b.131.1.3 93625 1jkeA 145 3.69e+01 c.110.1.1 66791 1ppjA 446 3.71e+01 d.185.1.1,d.185.1.1 104252,104253 1nvmB 312 3.71e+01 c.2.1.3,d.81.1.1 86251,86252 1din 236 3.74e+01 1din c.69.1.9 34682 1wdpA 495 3.76e+01 1nzoA 363 3.76e+01 b.105.1.1,e.3.1.1 92383,92384 1gklA 297 3.81e+01 c.69.1.2 65250 1f3lA 321 3.88e+01 1g6q2 c.66.1.6 59630 1q0uA 219 3.90e+01 c.37.1.19 95512 1kjnA 157 3.90e+01 c.115.1.1 72614 1zk7A 467 3.92e+01 1z9bA 135 3.95e+01 1z3iX 644 3.99e+01 1dciA 275 3.99e+01 1dciA c.14.1.3 30918 1z5oA 242 4.01e+01 1mp9A 198 4.03e+01 d.129.1.1,d.129.1.1 91385,91386 1vdwA 254 4.03e+01 e.7.1.1 100569 1yp2A 451 4.07e+01 1ri7A 171 4.07e+01 a.4.5.32,d.58.4.2 97504,97505 1lokA 291 4.10e+01 c.56.5.4 78122 1cl1A 395 4.14e+01 1cl2A c.67.1.3 34395 1udvA 89 4.15e+01 d.68.6.1 99224 1q4rA 112 4.26e+01 d.58.4.4 95823 1z6fA 363 4.27e+01 1jdw 423 4.31e+01 1jdw d.126.1.2 41129 2gn4A 344 4.31e+01 1uarA 285 4.38e+01 c.46.1.2,c.46.1.2 107762,107763 1t5jA 313 4.51e+01 a.209.1.1 99125 1i1qA 520 4.58e+01 1qdlA d.161.1.1 61543 1vjzA 341 4.64e+01 c.1.8.3 100838 1vbkA 307 4.75e+01 1w6tA 444 4.75e+01 1gt6A 269 4.87e+01 c.69.1.17 76342 2cmuA 342 4.92e+01 1o8xA 146 4.92e+01 c.47.1.10 86681 1wb4A 297 4.92e+01 1esmA 316 4.96e+01 1esmA c.37.1.6 31953 2etvA 346 4.97e+01 1iz0A 302 4.97e+01 b.35.1.2,c.2.1.1 83821,83822 1v7oA 165 4.99e+01 d.67.1.2 100480 2gfhA 260 5.01e+01 1rlhA 173 5.01e+01 d.256.1.1 97646 1uliA 460 5.02e+01 b.33.1.2,d.129.3.3 107921,107922 1rtqA 299 5.04e+01 c.56.5.4 97819 1tfe 145 5.10e+01 1tfe d.43.1.1 38680 1j5uA 136 5.13e+01 d.208.1.1 71584 1k3eA 156 5.14e+01 d.198.1.1 68103 1kb9B 352 5.14e+01 d.185.1.1,d.185.1.1 77313,77314 2aioA 269 5.20e+01 1xrhA 351 5.30e+01 1yirA 408 5.30e+01 1ytlA 174 5.32e+01 1nbaA 264 5.33e+01 1nbaA c.33.1.3 31753 1izoA 417 5.33e+01 a.104.1.1 83851 2gnpA 266 5.41e+01 1pl8A 356 5.43e+01 b.35.1.2,c.2.1.1 94878,94879 1svdA 473 5.44e+01 1gteA 1025 5.47e+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 1s6yA 450 5.50e+01 c.2.1.5,d.162.1.2 105314,105315 1zi8A 236 5.51e+01 1tx4B 178 5.51e+01 1ctqA c.37.1.8 32045 1aocA 175 5.60e+01 1aocA g.17.1.5 44817 1smlA 269 5.64e+01 1smlA d.157.1.1 42053 1vgyA 393 5.67e+01 c.56.5.4,d.58.19.1 100620,100621 1vqoB 338 5.69e+01 1kdoA 227 5.78e+01 c.37.1.1 68478 1wbpA 397 5.80e+01 1db3A 372 5.82e+01 1db3A c.2.1.2 29813 1ga8A 311 5.87e+01 1ga8A c.68.1.4 34516 1ka2A 499 5.88e+01 d.92.1.5 77305 1grj 158 5.89e+01 1grj a.2.1.1,d.26.1.2 15691,38433 1gnxA 479 5.92e+01 c.1.8.4 76241 1e9lA 377 5.93e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 1np6A 174 5.95e+01 c.37.1.10 85954 2bryA 497 6.00e+01 2ckiA 262 6.02e+01 1dyr 206 6.05e+01 1aoeA c.71.1.1 34916 1wteA 272 6.06e+01 1nekA 588 6.07e+01 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 2acaA 189 6.13e+01 1qdeA 224 6.21e+01 1qvaA c.37.1.19 32410 1xdzA 240 6.25e+01 1tkeA 224 6.29e+01 1vkfA 188 6.30e+01 c.1.29.1 108656 1ezvB 352 6.36e+01 1ezvB d.185.1.1,d.185.1.1 59543,59544 1bu7A 455 6.37e+01 1bu7A a.104.1.1 18937 1cliA 345 6.41e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1ovlA 271 6.52e+01 a.123.1.1 87455 1e1oA 504 6.54e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 8abp 306 6.58e+01 8abp c.93.1.1 35647 2btzA 394 6.59e+01 1g97A 459 6.60e+01 1fwyA b.81.1.4,c.68.1.5 60394,60395 1u0tA 307 6.68e+01 e.52.1.1 107567 1cjxA 357 6.70e+01 1cjxA d.32.1.3,d.32.1.3 38516,38517 1gqeA 365 6.71e+01 e.38.1.1 70351 1f0yA 302 6.78e+01 2hdhA a.100.1.3,c.2.1.6 18793,30197 1otfA 62 6.80e+01 1otfA d.80.1.1 39820 2gaiA 633 6.87e+01 1tzfA 259 6.90e+01 c.68.1.13 107476 1f45B 197 6.91e+01 1f45B a.26.1.1 59642 1nnwA 252 6.91e+01 d.159.1.5 80674 1x42A 232 6.94e+01 1jpmA 366 6.97e+01 c.1.11.2,d.54.1.1 67031,67032 1v8dA 235 6.98e+01 c.140.1.1 108425 1l1sA 113 7.04e+01 c.114.1.1 73484 1pv5A 264 7.05e+01 d.251.1.1 95150 1o6uA 403 7.09e+01 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 2bdwA 362 7.15e+01 1qyiA 384 7.16e+01 c.108.1.13 96595 1r6dA 337 7.18e+01 c.2.1.2 97148 1je5A 206 7.19e+01 1je5A b.40.4.7 62909 1x7oA 287 7.24e+01 1w6uA 302 7.24e+01 1rlmA 271 7.24e+01 2b4vA 468 7.28e+01 1kmvA 186 7.33e+01 c.71.1.1 72757 1jnrA 643 7.36e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1pjqA 457 7.36e+01 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 1jv2B 692 7.37e+01 b.1.15.1,c.62.1.1,d.200.1.1,g.3.11.6,g.3.11.6 67338,67339,67340,67341,67342 2cg4A 152 7.37e+01 1qwrA 319 7.38e+01 b.82.1.3 96491 1h3qA 140 7.44e+01 d.110.4.3 76652 1lt8A 406 7.46e+01 c.1.26.1 78186 1f1xA 322 7.48e+01 d.32.1.3,d.32.1.3 83208,83209 1d8cA 723 7.49e+01 1d8cA c.1.13.1 29325 1u0fA 564 7.51e+01 1cf9A 753 7.52e+01 1cf9A c.23.16.3,e.5.1.1 31441,42815 1j7gA 144 7.54e+01 c.110.1.1 84130 1qb7A 236 7.56e+01 1qb7A c.61.1.1 34087 1lopA 164 7.67e+01 2cpl b.62.1.1 27510 1rlmB 271 7.70e+01 1l0lB 439 7.70e+01 d.185.1.1,d.185.1.1 84484,84485 1mo9A 523 7.71e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1cfr 285 7.72e+01 1cfr c.52.1.7 33312 1uxy 340 7.77e+01 2mbr d.145.1.2,d.146.1.1 41748,41761 1d2mA 665 7.80e+01 1d2mA c.37.1.19,c.37.1.19 32417,32418 1nw3A 416 7.83e+01 c.66.1.31 86288 1vdmA 153 7.89e+01 1h7wA 1025 7.93e+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 1f2vA 219 7.95e+01 1f2vA c.23.17.1 59627 1pn0A 665 7.95e+01 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 1ppjB 439 7.96e+01 d.185.1.1,d.185.1.1 104254,104255 1sb8A 352 8.06e+01 c.2.1.2 105410 2b20A 403 8.09e+01 2b7aA 293 8.12e+01 1vf8A 377 8.15e+01 1vp6A 138 8.21e+01 2aynA 404 8.22e+01 2f9dA 125 8.25e+01 1s0yA 76 8.27e+01 d.80.1.1 98314 2bl9A 238 8.28e+01 1olmA 403 8.30e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1kmqA 184 8.31e+01 c.37.1.8 84412 1gqiA 708 8.34e+01 c.1.8.10,d.92.2.2 76279,76280 1dqnA 230 8.35e+01 1dqnA c.61.1.1 34067 1hy7A 173 8.36e+01 d.92.1.11 65957 1iirA 415 8.38e+01 1iirA c.87.1.5 62453 1v64A 108 8.39e+01 a.21.1.1 108392 2blcA 238 8.39e+01 1i19A 561 8.40e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 1mo1A 87 8.41e+01 d.94.1.1 91363 1vjtA 483 8.44e+01 c.2.1.5,d.162.1.2 100833,100834 1y8qB 640 8.46e+01 1hm9A 468 8.51e+01 b.81.1.4,c.68.1.5 65866,65867 2fjbA 643 8.52e+01 1wb0A 445 8.54e+01 1zxxA 319 8.56e+01 1ihp 438 8.57e+01 1ihp c.60.1.2 33993 1v5vA 401 8.58e+01 1r31A 428 8.59e+01 d.58.20.1,d.179.1.1 96897,96898 1yb2A 275 8.59e+01 1hruA 188 8.60e+01 1hruA d.115.1.1 40926 1k1xA 659 8.60e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1tfzA 424 8.60e+01 d.32.1.3,d.32.1.3 106886,106887 1yy5B 513 8.68e+01 1tf4A 605 8.68e+01 1tf4A a.102.1.2,b.2.2.2 18827,22393 1mp8A 281 8.69e+01 d.144.1.7 91384 2fqmA 75 8.72e+01 2bhwA 232 8.72e+01 1ou0A 207 8.79e+01 c.23.17.1 93536 1vmaA 306 8.79e+01 a.24.13.1,c.37.1.10 108887,108888 3ladA 476 8.81e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30573,30574,40208 1wosA 364 8.83e+01 b.44.2.1,d.250.1.1 109468,109469 2ab0A 205 8.84e+01 1ycdA 243 8.86e+01 1vkpA 383 8.86e+01 d.126.1.6 108686 1jysA 242 8.90e+01 c.56.2.1 77216 1phk 298 8.94e+01 1cdkA d.144.1.7 41635