# List of top-scoring protein chains for t06-100-30-bys-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 2.75e-34 1r89A 437 1.96e-01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1t0tV 248 4.67e-01 d.58.4.10 106229 2bklA 695 1.10e+00 1m3sA 186 1.30e+00 c.80.1.3 78573 1moq 368 1.32e+00 1moq c.80.1.1 35302 1q2lA 939 1.53e+00 1fm0E 150 1.64e+00 1fmaE d.41.5.1 38629 1o12A 376 1.94e+00 b.92.1.5,c.1.9.10 80758,80759 2bkyX 89 2.26e+00 1v5vA 401 2.26e+00 1o08A 221 3.14e+00 c.108.1.6 86525 1u8xX 472 3.35e+00 c.2.1.5,d.162.1.2 107741,107742 2cg4A 152 3.39e+00 4ubpC 570 3.42e+00 1ubpC b.92.1.1,c.1.9.2 28431,29053 1fo8A 343 3.74e+00 1foaA c.68.1.10 59927 1epuA 591 3.76e+00 1dn1A e.25.1.1 43358 1omzA 293 3.88e+00 c.68.1.15 87093 1gsa 316 3.92e+00 1gsa c.30.1.3,d.142.1.1 31718,41477 1j1lA 290 4.04e+00 b.82.1.12 90766 1jk7A 323 4.62e+00 1auiA d.159.1.3 63144 1nriA 306 5.05e+00 c.80.1.3 86123 2bkkA 264 5.37e+00 1dciA 275 5.40e+00 1dciA c.14.1.3 30918 1xkrA 206 5.51e+00 2bcgG 453 5.93e+00 1wu4A 396 6.12e+00 1e8cA 498 6.29e+00 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1r8gA 372 6.45e+00 d.128.1.3 104845 1l1sA 113 6.69e+00 c.114.1.1 73484 1rwzA 245 6.81e+00 d.131.1.2,d.131.1.2 98005,98006 1d4xG 126 7.03e+00 1d0nA d.109.1.1 59109 1jeoA 180 7.04e+00 c.80.1.3 66611 1chmA 401 7.35e+00 1chmA c.55.2.1,d.127.1.1 33545,41142 1ow1A 195 7.40e+00 b.131.1.3 93625 1r9jA 673 7.76e+00 1jmsA 381 7.93e+00 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 3gcb 470 8.08e+00 3gcb d.3.1.1 37032 1iirA 415 8.59e+00 1iirA c.87.1.5 62453 1d2mA 665 8.77e+00 1d2mA c.37.1.19,c.37.1.19 32417,32418 1wsrA 375 9.10e+00 1vjqA 79 9.16e+00 k.43.1.1 100830 1uxtA 501 9.45e+00 c.82.1.1 108125 1v9mA 323 9.74e+00 f.40.1.1 100543 1wdjA 187 1.02e+01 2c2aA 258 1.05e+01 2gfhA 260 1.07e+01 1vdwA 254 1.07e+01 e.7.1.1 100569 1esc 306 1.08e+01 1esc c.23.10.1 31334 1up8A 598 1.08e+01 a.111.1.2 99710 1rlhA 173 1.09e+01 d.256.1.1 97646 1opc 110 1.12e+01 1opc a.4.6.1 16231 2bgiA 272 1.15e+01 2dlbA 80 1.18e+01 1x7yB 342 1.26e+01 1kaeA 434 1.26e+01 c.82.1.2 72247 1wz8A 264 1.27e+01 1d1gA 168 1.28e+01 1d1gA c.71.1.1 34889 1t1dA 100 1.28e+01 1t1dA d.42.1.2 38637 2fp8A 322 1.31e+01 1qwrA 319 1.32e+01 b.82.1.3 96491 1mml 265 1.32e+01 1mml e.8.1.2 43015 2f5gA 133 1.34e+01 1qd1A 325 1.34e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1o20A 427 1.35e+01 c.82.1.1 86556 1oe4A 247 1.35e+01 c.18.1.3 86895 1vggA 161 1.36e+01 1a6jA 163 1.36e+01 1a6jA d.112.1.1 40915 1j5uA 136 1.40e+01 d.208.1.1 71584 1qsmA 152 1.44e+01 1qsmA d.108.1.1 40808 1zhxA 438 1.45e+01 1zkcA 197 1.47e+01 2ae6A 166 1.54e+01 1w5fA 353 1.54e+01 1g03A 134 1.57e+01 1qrjB a.73.1.1 60162 1yfsA 465 1.58e+01 1wi1A 126 1.58e+01 2bfdB 345 1.60e+01 2b67A 204 1.60e+01 1jyhA 157 1.66e+01 d.60.1.3 71956 1v3yA 192 1.68e+01 1lopA 164 1.74e+01 2cpl b.62.1.1 27510 1ppjA 446 1.80e+01 d.185.1.1,d.185.1.1 104252,104253 1zdzA 302 1.82e+01 1x1nA 524 1.84e+01 2fug7 129 1.84e+01 1rhs 296 1.89e+01 1rhs c.46.1.2,c.46.1.2 32703,32704 1hbnC 248 1.89e+01 1mroC d.58.31.1 60902 1pch 88 1.89e+01 1ptf d.94.1.1 40564 1bvyF 191 1.95e+01 1bvyF c.23.5.1 31207 1zjcA 418 1.97e+01 1jakA 512 1.97e+01 c.1.8.6,d.92.2.1 66472,66473 1odmA 331 1.98e+01 b.82.2.1 86875 1wosA 364 2.01e+01 b.44.2.1,d.250.1.1 109468,109469 1r8oB 71 2.06e+01 2b34A 199 2.08e+01 1c4oA 664 2.12e+01 1d2mA c.37.1.19,c.37.1.19 32415,32416 1ys4A 354 2.12e+01 2bcgY 206 2.14e+01 1vehA 92 2.21e+01 1rf8B 100 2.22e+01 a.210.1.1 97371 1zj8A 566 2.23e+01 1gnxA 479 2.26e+01 c.1.8.4 76241 1ofuX 119 2.26e+01 c.37.1.22 86976 1wruA 379 2.29e+01 1tl9A 339 2.30e+01 1kmqA 184 2.31e+01 c.37.1.8 84412 1e9rA 437 2.32e+01 c.37.1.11 64827 1p7tA 731 2.36e+01 c.1.13.1 94319 1l1qA 186 2.36e+01 c.61.1.1 77653 1vl2A 421 2.37e+01 c.26.2.1,d.210.1.1 108708,108709 1gbg 214 2.39e+01 1axkA b.29.1.2 24171 1sfe 180 2.41e+01 1sfe a.4.2.1,c.55.7.1 16073,33748 1vimA 200 2.44e+01 c.80.1.3 100758 2a5dA 175 2.46e+01 1ejxC 567 2.48e+01 b.92.1.1,c.1.9.2 83184,83185 1v4pA 157 2.48e+01 1nd4A 264 2.51e+01 d.144.1.6 91815 1p4xA 250 2.53e+01 a.4.5.28,a.4.5.28 87784,87785 2fyxA 143 2.54e+01 1xknA 355 2.55e+01 1ub3A 220 2.55e+01 c.1.10.1 88395 1wvqA 167 2.56e+01 2pgd 482 2.57e+01 2pgd a.100.1.1,c.2.1.6 18778,30190 1id1A 153 2.61e+01 1id1A c.2.1.9 62286 1lm8B 118 2.63e+01 d.15.1.1 74033 1euhA 475 2.63e+01 1euhA c.82.1.1 35369 1nthA 458 2.66e+01 c.1.25.1 80730 1h1nA 305 2.66e+01 c.1.8.3 70855 1yb2A 275 2.69e+01 2d5cA 263 2.75e+01 2fnjB 118 2.77e+01 2cb2A 318 2.80e+01 1jztA 246 2.80e+01 c.104.1.1 63319 1y8aA 332 2.83e+01 1csh 435 2.84e+01 1csh a.103.1.1 18880 1rq2A 382 2.85e+01 c.32.1.1,d.79.2.1 105048,105049 1hgxA 183 2.89e+01 1tc1A c.61.1.1 34027 2bj7A 138 2.90e+01 1t4hA 290 2.92e+01 d.144.1.7 106420 1x42A 232 2.95e+01 1wu7A 434 2.96e+01 1vloA 381 3.04e+01 b.44.2.1,d.250.1.1 108838,108839 2bfwA 200 3.05e+01 1vi2A 300 3.12e+01 c.2.1.7,c.58.1.5 100726,100727 2c7pA 327 3.14e+01 1uzbA 516 3.23e+01 c.82.1.1 100220 2givA 295 3.24e+01 1tt8A 164 3.26e+01 1rr7A 129 3.32e+01 a.4.1.14 105075 1fj2A 232 3.35e+01 1auoA c.69.1.14 34720 2a3nA 355 3.38e+01 1o0xA 262 3.43e+01 d.127.1.1 80755 1nfp 228 3.45e+01 1nfp c.1.16.2 29555 1n83A 270 3.49e+01 a.123.1.1 80276 1hc7A 477 3.49e+01 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 2bhwA 232 3.52e+01 1wr8A 231 3.56e+01 1ss9A 311 3.57e+01 c.68.1.4 105978 1b00A 127 3.59e+01 3chy c.23.1.1 31122 1q1aA 289 3.61e+01 c.31.1.5 95561 1zzmA 259 3.64e+01 1f5jA 199 3.66e+01 1axkA b.29.1.11 24342 2gf6A 135 3.68e+01 1grj 158 3.68e+01 1grj a.2.1.1,d.26.1.2 15691,38433 1n8fA 350 3.69e+01 c.1.10.4 85397 1z0jA 170 3.71e+01 1eu8A 409 3.75e+01 1eu8A c.94.1.1 59502 2ilk 160 3.78e+01 2ilk a.26.1.3 16885 1uzeA 589 3.79e+01 d.92.1.5 108174 1j3aA 142 3.86e+01 c.21.1.1 77070 1ud9A 245 3.86e+01 d.131.1.2,d.131.1.2 107768,107769 1aqcA 172 3.89e+01 1x11A b.55.1.2 26983 1nnhA 294 3.92e+01 d.104.1.1 92005 1iu4A 331 3.92e+01 d.3.1.8 71430 1jg1A 235 3.93e+01 c.66.1.7 66661 2a61A 145 3.94e+01 1yyqA 374 3.95e+01 1eluA 390 3.96e+01 1elqA c.67.1.3 34434 1fvuB 125 4.07e+01 1ixxB d.169.1.1 42346 1ftrA 296 4.07e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1budA 197 4.10e+01 1atlA d.92.1.9 40328 1w6sA 599 4.12e+01 1sc6A 404 4.14e+01 1z3eA 132 4.15e+01 1y0hA 105 4.17e+01 1wdnA 226 4.20e+01 1lst c.94.1.1 35816 1yirA 408 4.23e+01 1g8iA 190 4.28e+01 1rec a.39.1.5 60363 1mp8A 281 4.35e+01 d.144.1.7 91384 1iq4A 179 4.36e+01 1iq4A d.77.1.1 62641 2fmpA 335 4.36e+01 2bjkA 516 4.38e+01 1jysA 242 4.40e+01 c.56.2.1 77216 1su8A 636 4.40e+01 e.26.1.2 98999 1yyaA 250 4.41e+01 1rwtA 232 4.46e+01 f.43.1.1 97992 2cx5A 158 4.47e+01 1hr6A 475 4.50e+01 1hr6A d.185.1.1,d.185.1.1 61164,61165 1ydmA 187 4.51e+01 1jljA 189 4.55e+01 c.57.1.1 63169 1x72A 334 4.64e+01 d.126.1.6 109495 1j27A 102 4.65e+01 d.58.50.1 90778 1xvaA 292 4.66e+01 1xvaA c.66.1.5 34183 1xnaA 183 4.67e+01 1xnaA b.18.1.8 23773 1uc2A 481 4.70e+01 d.261.1.1 99161 1wlzA 105 4.71e+01 1hfuA 503 4.73e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1lm4A 194 4.75e+01 d.167.1.1 84626 2gn4A 344 4.86e+01 1dsxA 87 4.88e+01 1t1dA d.42.1.2 38644 1jpzA 473 4.90e+01 a.104.1.1 67069 1wkaA 147 4.90e+01 1uf2A 1019 4.92e+01 e.28.1.2 99289 1of8A 370 4.98e+01 c.1.10.4 92819 1lzlA 323 5.00e+01 c.69.1.2 78306 1qhfA 240 5.02e+01 1qhfA c.60.1.1 33960 1fy7A 278 5.07e+01 1fy7A d.108.1.1 40817 1io2A 213 5.13e+01 1ekeA c.55.3.1 62612 1xkyA 301 5.14e+01 1kb9B 352 5.17e+01 d.185.1.1,d.185.1.1 77313,77314 1pv5A 264 5.25e+01 d.251.1.1 95150 1vmbA 140 5.27e+01 1no5A 114 5.29e+01 d.218.1.5 92014 1efyA 350 5.34e+01 1a26 a.41.1.1,d.166.1.2 17413,42275 1pvdA 537 5.36e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 1lbvA 252 5.37e+01 e.7.1.1 73813 1p4cA 380 5.37e+01 c.1.4.1 94100 1ufbA 127 5.40e+01 a.24.16.3 99331 8tlnE 316 5.52e+01 1hyt d.92.1.2 59075 1ga8A 311 5.53e+01 1ga8A c.68.1.4 34516 1czaN 917 5.57e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 1zjjA 263 5.61e+01 1ag9A 175 5.71e+01 1rcf c.23.5.1 31178 1vj7A 393 5.72e+01 a.211.1.1,d.218.1.8 100801,100802 1dz3A 130 5.80e+01 1dz3A c.23.1.1 31105 1cjxA 357 5.84e+01 1cjxA d.32.1.3,d.32.1.3 38516,38517 1cs8A 316 5.87e+01 1cs8A d.3.1.1 37065 1q79A 514 5.89e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1q7sA 117 5.95e+01 c.131.1.1 96055 1r0uA 148 5.97e+01 b.60.1.5 96741 2g8lA 299 6.06e+01 1aihA 170 6.12e+01 1aihA d.163.1.1 42149 1ycdA 243 6.13e+01 1ofdA 1520 6.13e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1azo 232 6.14e+01 1azo c.52.1.14 33329 1vpkA 378 6.17e+01 1xkpC 143 6.20e+01 1ht6A 405 6.22e+01 b.71.1.1,c.1.8.1 83629,83630 2govA 195 6.29e+01 1bf5A 545 6.36e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 2c2nA 339 6.36e+01 2aieP 203 6.37e+01 1ckeA 227 6.37e+01 1ckeA c.37.1.1 31846 1yb5A 351 6.40e+01 1l8nA 679 6.45e+01 c.1.8.10,d.92.2.2 84564,84565 1d0qA 103 6.45e+01 1d0qA g.41.3.2 45208 2go7A 207 6.47e+01 1nnwA 252 6.49e+01 d.159.1.5 80674 1mo1A 87 6.49e+01 d.94.1.1 91363 1w2fA 276 6.50e+01 d.143.1.3 109125 2bjqA 345 6.53e+01 1g5hA 454 6.53e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 1yzyA 413 6.56e+01 1f4pA 147 6.56e+01 5nul c.23.5.1 59651 1rlmA 271 6.64e+01 1kq6A 141 6.65e+01 d.189.1.1 91020 1dg6A 191 6.65e+01 1d4vB b.22.1.1 23883 1t5oA 351 6.73e+01 c.124.1.5 106459 1z2iA 358 6.81e+01 2bbeA 108 6.81e+01 1gtvA 214 6.85e+01 c.37.1.1 70537 1rypC 244 6.85e+01 1rypC d.153.1.4 41934 2gnpA 266 6.87e+01 1djxA 624 6.88e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17342,23159,29587 1afwA 393 6.89e+01 1afwA c.95.1.1,c.95.1.1 35900,35901 2cmuA 342 6.90e+01 1nz0A 118 6.95e+01 d.14.1.2 86433 1o4sA 389 7.01e+01 c.67.1.1 86620 1m0wA 491 7.03e+01 c.30.1.4,d.142.1.6 78363,78364 2fuqA 747 7.04e+01 1wddS 128 7.09e+01 1ayx 492 7.12e+01 1ayx a.102.1.1 18825 1bg1A 722 7.19e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17767,22461,40527 1e1oA 504 7.22e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 2dg5B 190 7.30e+01 1avwB 171 7.34e+01 1wba b.42.4.1 25599 1ki1B 352 7.35e+01 a.87.1.1,b.55.1.1 72497,72498 1z54A 132 7.39e+01 2c30A 321 7.39e+01 1vkwA 218 7.44e+01 d.90.1.2 108695 2ga9D 469 7.46e+01 1rypD 241 7.51e+01 1rypD d.153.1.4 41935 2aalA 131 7.52e+01 1bgp 309 7.55e+01 1bgp a.93.1.1 18690 1q4rA 112 7.62e+01 d.58.4.4 95823 1ugpB 226 7.63e+01 b.34.4.4 107832 1qxyA 252 7.64e+01 d.127.1.1 96565 1mtzA 293 7.65e+01 c.69.1.7 79467 1kwgA 645 7.72e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1ml4A 308 7.73e+01 c.78.1.1,c.78.1.1 79255,79256 1h75A 81 7.73e+01 1h75A c.47.1.1 60716 2culA 232 7.75e+01 1ryp1 222 7.78e+01 1ryp1 1yrcA 414 7.82e+01 1j8uA 325 7.84e+01 d.178.1.1 71611 1reqA 727 7.87e+01 1reqA c.1.19.1,c.23.6.1 29620,31247 2bvfA 459 7.93e+01 1tr0A 108 8.05e+01 d.58.4.4 107261 2g6yA 217 8.06e+01 1wyuA 438 8.06e+01 1ffyA 917 8.09e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1vrmA 325 8.18e+01 2b5dX 528 8.18e+01 1je5A 206 8.19e+01 1je5A b.40.4.7 62909 1o97C 264 8.20e+01 c.26.2.3 81232 1o97D 320 8.26e+01 c.26.2.3,c.31.1.2 81233,81234 1qvzA 237 8.27e+01 c.23.16.2 96453 1rcwA 231 8.28e+01 a.132.1.4 97299 1n7vA 555 8.33e+01 b.126.1.1 85377 1ecrA 309 8.34e+01 1ecrA e.2.1.1 42678 1zsqA 528 8.35e+01 1cs1A 386 8.36e+01 1ibjA c.67.1.3 34399 1bkpA 278 8.39e+01 1bkpA d.117.1.1 41029 1eybA 471 8.39e+01 1ey2A b.82.1.4 28115 2fbaA 492 8.42e+01 1a8d 452 8.44e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 2f57A 317 8.48e+01 2av5A 120 8.48e+01 1vybA 238 8.49e+01 d.151.1.1 108897 1hy7A 173 8.49e+01 d.92.1.11 65957 1udxA 416 8.50e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1qhdA 398 8.50e+01 1qhdA a.115.1.2,b.19.1.1 63324,63325 2fkkA 206 8.53e+01 2gaxA 135 8.53e+01 1zd0A 150 8.61e+01 1rypB 250 8.63e+01 1rypB d.153.1.4 41933 2c8mA 262 8.67e+01 2a1vA 144 8.68e+01 1cs6A 382 8.75e+01 1cs6A b.1.1.4,b.1.1.4,b.1.1.4,b.1.1.4 21760,21761,21762,21763 1v4aA 440 8.78e+01 a.24.16.4,d.218.1.9 108350,108351 1p5fA 189 8.79e+01 c.23.16.2 94142 1v4xA 144 8.86e+01 a.1.1.2 108363 1iznB 277 8.86e+01 e.43.1.2 83848 1kjnA 157 8.90e+01 c.115.1.1 72614 2gwhA 298 8.97e+01 1go4A 205 8.98e+01 d.135.1.1 70292