# List of top-scoring protein chains for t04-100-30-dssp-ehl2-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 1v2xA 194 1.83e-22 c.116.1.1 100274 1x7oA 287 2.72e-22 1zjrA 211 1.23e-21 1mxiA 160 1.92e-21 c.116.1.1 79646 1ipaA 274 6.01e-21 c.116.1.1,d.79.3.3 71254,71255 1z85A 234 3.50e-03 1o6dA 163 1.60e-02 c.116.1.3 92567 1v6zA 228 3.66e-02 1p7tA 731 5.89e-02 c.1.13.1 94319 1d8cA 723 6.20e-02 1d8cA c.1.13.1 29325 1k3rA 268 9.42e-02 b.40.4.10,c.116.1.2 72018,72019 1jztA 246 1.14e-01 c.104.1.1 63319 1xewY 172 1.14e-01 1d2nA 272 1.22e-01 1d2nA c.37.1.20 32428 1nsf 273 1.36e-01 1d2nA c.37.1.20 32429 1j2rA 199 1.97e-01 c.33.1.3 90788 1swvA 267 2.95e-01 1rqlA 267 3.75e-01 c.108.1.3 97750 1z7yA 322 5.12e-01 1zxoA 291 5.64e-01 1g38A 393 6.10e-01 2admA c.66.1.27 60235 1vhyA 257 6.37e-01 b.122.1.2,c.116.1.5 100714,100715 1iooA 196 7.35e-01 d.124.1.1 71250 1z7wA 322 7.47e-01 1vbuA 328 9.07e-01 1h1yA 228 9.65e-01 c.1.2.2 76506 1cozA 129 1.09e+00 1cozA c.26.1.2 31598 1nxzA 246 1.12e+00 b.122.1.2,c.116.1.5 86391,86392 1w8sA 263 1.18e+00 1pwxA 254 1.18e+00 c.2.1.2 95262 1zxxA 319 1.37e+00 1ualA 274 1.40e+00 c.116.1.4 88383 1zmtA 254 1.59e+00 1tq8A 163 1.60e+00 c.26.2.4 107204 1ve5A 311 1.67e+00 1ojxA 263 1.75e+00 c.1.10.1 93164 1uufA 369 1.77e+00 b.35.1.2,c.2.1.1 100006,100007 2g76A 335 2.05e+00 1rdfA 267 2.15e+00 c.108.1.3 104884 1ubeA 349 2.49e+00 c.37.1.11,d.48.1.1 88412,88413 1f89A 291 2.58e+00 d.160.1.1 64988 1wl8A 189 2.58e+00 1bmtA 246 2.61e+00 1bmtA a.46.1.1,c.23.6.1 17757,31235 1wm1A 317 2.65e+00 c.69.1.7 109405 1kx5B 102 2.67e+00 a.22.1.1 77594 1hq3D 103 2.75e+00 1aoiB a.22.1.1 16464 1tzyD 103 2.75e+00 a.22.1.1 107533 1vk3A 615 2.80e+00 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 1kkoA 413 2.83e+00 c.1.11.2,d.54.1.1 68675,68676 1rliA 184 2.84e+00 c.23.5.6 97647 1wnfA 328 2.84e+00 1s1pA 331 2.90e+00 c.1.7.1 98350 1tk9A 188 2.95e+00 c.80.1.3 107082 1fts 295 3.28e+00 1ng1 a.24.13.1,c.37.1.10 16968,32279 1wlsA 328 3.33e+00 1ru8A 232 3.44e+00 c.26.2.1 97849 1p3wA 404 3.55e+00 c.67.1.3 87752 1fezA 256 3.63e+00 1fezA c.108.1.3 43343 1kt6A 183 3.67e+00 b.60.1.1 84466 2a2dA 478 3.70e+00 1ir6A 424 3.75e+00 c.107.1.2 71342 1u08A 386 3.77e+00 c.67.1.1 107543 1n2eA 300 3.88e+00 c.26.1.4 85268 2c4nA 250 3.90e+00 2f9lA 199 3.98e+00 1kwgA 645 4.02e+00 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1uwvA 433 4.15e+00 b.40.4.12,c.66.1.40 100128,100129 1js3A 486 4.15e+00 c.67.1.6 67215 1qorA 327 4.16e+00 1qorA b.35.1.2,c.2.1.1 24766,29782 1prxA 224 4.29e+00 1prxA c.47.1.10 33076 1rj9A 304 4.37e+00 a.24.13.1,c.37.1.10 97553,97554 1zm8A 259 4.49e+00 1hbq 183 4.57e+00 1aqb b.60.1.1 27078 1i60A 278 4.64e+00 c.1.15.4 71118 2fr1A 486 4.82e+00 5nul 138 4.88e+00 5nul c.23.5.1 31191 2afbA 351 4.92e+00 1fh9A 312 5.01e+00 1taxA c.1.8.3 28913 1j4aA 333 5.03e+00 c.2.1.4,c.23.12.1 71502,71503 1y9kA 157 5.12e+00 1im5A 180 5.13e+00 c.33.1.3 66211 1mjfA 281 5.32e+00 c.66.1.17 79198 2his 312 5.48e+00 1taxA c.1.8.3 28918 1rlhA 173 5.55e+00 d.256.1.1 97646 1yb5A 351 5.72e+00 1j5vA 351 5.77e+00 c.72.1.1 71585 1tqjA 230 5.77e+00 c.1.2.2 107228 1fhdA 312 5.88e+00 1taxA c.1.8.3 28915 1vkmA 297 5.91e+00 c.138.1.1 108670 1qopA 268 5.94e+00 2tysA c.1.2.4 28570 1kngA 156 5.94e+00 c.47.1.10 72777 1tz9A 367 6.13e+00 c.1.15.6 107466 1rd5A 262 6.19e+00 1f2tB 148 6.22e+00 1f2tB 1q35A 320 6.23e+00 c.94.1.1 95661 1whsB 153 6.30e+00 1whtB 1u6eA 335 6.31e+00 1ns5A 155 6.33e+00 c.116.1.3 80705 1whtB 153 6.36e+00 1whtB 1o4wA 147 6.49e+00 c.120.1.1 86629 1t9kA 347 6.68e+00 c.124.1.5 106721 2czdA 208 6.69e+00 1nowA 507 6.69e+00 c.1.8.6,d.92.2.1 85936,85937 1m3qA 317 6.69e+00 a.96.1.3,d.129.1.2 91184,91185 1e8cA 498 7.01e+00 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 2bg5A 324 7.03e+00 1o5zA 442 7.34e+00 c.59.1.2,c.72.2.2 92530,92531 1qwgA 251 7.49e+00 c.1.27.1 96473 1qtrA 317 7.83e+00 1qtrA c.69.1.7 34660 1nnhA 294 7.86e+00 d.104.1.1 92005 1ebmA 317 7.89e+00 1ebmA a.96.1.3,d.129.1.2 18751,41300 1t9hA 307 7.96e+00 1yx1A 264 7.98e+00 1zbsA 291 8.17e+00 1vizA 240 8.28e+00 c.1.4.1 100784 1xyzA 347 8.30e+00 1taxA c.1.8.3 28804 1hzpA 335 8.43e+00 1hn9A c.95.1.2,c.95.1.2 61455,61456 1uj2A 252 8.49e+00 c.37.1.6 99452 1tqhA 247 8.58e+00 c.69.1.29 107225 2jdxA 385 8.64e+00 1jdw d.126.1.2 41139 2d0iA 333 8.65e+00 2f6uA 234 8.68e+00 1ryaA 160 8.73e+00 d.113.1.5 105122 1tkkA 366 8.84e+00 c.1.11.2,d.54.1.1 107089,107090 1xg5A 279 8.92e+00 1vr6A 350 8.96e+00 2as0A 396 9.07e+00 1othA 321 9.30e+00 1othA c.78.1.1,c.78.1.1 35260,35261 1xg9A 260 9.38e+00 1zghA 260 9.38e+00 1v5xA 203 9.42e+00 c.1.2.4 100377 1bdfA 235 9.50e+00 1bdfA d.74.3.1,d.181.1.1 39727,42602 2aeuA 374 9.52e+00 1qydA 313 9.59e+00 c.2.1.2 96583 1yj1A 76 9.77e+00 1j96A 323 1.00e+01 c.1.7.1 71616 1qv9A 283 1.00e+01 c.127.1.1 96356 2a84A 300 1.00e+01 1efpB 252 1.01e+01 1efvB c.26.2.3 31636 2b25A 336 1.07e+01 1vp8A 201 1.08e+01 2ceyA 306 1.08e+01 1jpmA 366 1.09e+01 c.1.11.2,d.54.1.1 67031,67032 1jae 471 1.09e+01 1smd b.71.1.1,c.1.8.1 27773,28760 1xf1A 926 1.10e+01 1xrtA 467 1.12e+01 1b33N 67 1.13e+01 1b33N d.30.1.1 38459 1atiA 505 1.14e+01 1atiA c.51.1.1,d.104.1.1 33196,40745 1geqA 248 1.17e+01 2tysA c.1.2.4 28589 1jdw 423 1.17e+01 1jdw d.126.1.2 41129 1efvB 255 1.19e+01 1efvB c.26.2.3 31634 1rzmA 338 1.20e+01 c.1.10.4 105137 1r7lA 110 1.22e+01 d.277.1.1 104837 1m2kA 249 1.23e+01 c.31.1.5 84754 2tpt 440 1.23e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17759,31623,38621 1kfcA 268 1.23e+01 c.1.2.4 77371 1xmrA 243 1.24e+01 1tfuA 157 1.25e+01 c.26.1.3 106859 1qj5A 429 1.25e+01 1dtyA c.67.1.4 34493 2ohxA 374 1.26e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 2fdrA 229 1.27e+01 1aqb 183 1.28e+01 1aqb b.60.1.1 27084 1iyxA 432 1.29e+01 c.1.11.1,d.54.1.1 83815,83816 1u9cA 224 1.29e+01 2f4nA 273 1.31e+01 1ezwA 349 1.33e+01 1ezwA c.1.16.3 29558 1js8A 394 1.35e+01 a.86.1.1,b.112.1.1 67219,67220 2frnA 278 1.36e+01 1nf8A 207 1.36e+01 c.33.1.3 85630 1mx3A 347 1.36e+01 c.2.1.4,c.23.12.1 79638,79639 2tysA 268 1.39e+01 2tysA c.1.2.4 28572 1xp8A 366 1.40e+01 1hdoA 206 1.41e+01 1he2A c.2.1.2 60965 1hetA 374 1.41e+01 2ohxA b.35.1.2,c.2.1.1 60975,60976 1iugA 352 1.43e+01 c.67.1.3 90699 1vjrA 271 1.44e+01 c.108.1.14 100832 1nbfD 76 1.45e+01 d.15.1.1 80390 2b8eA 273 1.46e+01 2b0cA 206 1.47e+01 2tpsA 227 1.48e+01 2tpsA c.1.3.1 28591 1jflA 228 1.48e+01 c.78.2.1,c.78.2.1 71656,71657 1wdeA 294 1.49e+01 1gci 269 1.50e+01 1gci c.41.1.1 32503 1vs0A 310 1.51e+01 1s0aA 429 1.52e+01 c.67.1.4 98263 1m65A 245 1.52e+01 c.6.3.1 84847 1sazA 381 1.54e+01 1u94A 356 1.56e+01 c.37.1.11,d.48.1.1 107743,107744 1lwjA 441 1.57e+01 b.71.1.1,c.1.8.1 74303,74304 1k92A 455 1.59e+01 c.26.2.1,d.210.1.1 68325,68326 1wddS 128 1.61e+01 2reb 352 1.62e+01 2reb c.37.1.11,d.48.1.1 32282,38767 1zq6A 359 1.63e+01 1n8kA 374 1.64e+01 b.35.1.2,c.2.1.1 80298,80299 1vb5A 276 1.64e+01 1yh1A 359 1.66e+01 1r9lA 309 1.67e+01 c.94.1.1 97262 1pxvA 183 1.67e+01 d.3.1.1 95301 1vl2A 421 1.70e+01 c.26.2.1,d.210.1.1 108708,108709 1id0A 152 1.70e+01 d.122.1.3 66111 1y4hA 188 1.70e+01 2bbkL 125 1.71e+01 2bbkL g.21.1.1 44882 1yrrA 382 1.72e+01 1xhfA 123 1.72e+01 2fymA 431 1.76e+01 1p0fA 373 1.77e+01 b.35.1.2,c.2.1.1 87642,87643 1ydhA 216 1.80e+01 1r0vA 305 1.81e+01 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 1ldg 316 1.81e+01 1ceqA c.2.1.5,d.162.1.1 30165,42132 1t2dA 322 1.82e+01 c.2.1.5,d.162.1.1 99084,99085 1nq6A 302 1.82e+01 c.1.8.3 92046 1g5aA 628 1.82e+01 b.71.1.1,c.1.8.1 65152,65153 1yqdA 366 1.83e+01 1w5fA 353 1.86e+01 1wviA 257 1.87e+01 2b8tA 223 1.88e+01 1nf9A 207 1.88e+01 c.33.1.3 85631 1oixA 191 1.89e+01 1ka9H 200 1.91e+01 c.23.16.1 77308 1f8fA 371 1.93e+01 b.35.1.2,c.2.1.1 83246,83247 1ars 396 1.93e+01 1ajsA c.67.1.1 34287 1qisA 396 1.94e+01 1ajsA c.67.1.1 34284 1u3wA 374 1.94e+01 1y81A 138 1.96e+01 1k4mA 213 1.97e+01 c.26.1.3 77258 1yixA 265 1.98e+01 1xm3A 264 1.99e+01 1gca 309 1.99e+01 1gca c.93.1.1 35659 2pfkA 320 2.01e+01 3pfk c.89.1.1 35577 1g6sA 427 2.05e+01 1eps d.68.2.2 39584 2bp1A 360 2.08e+01 1icrA 217 2.08e+01 1vfrA d.90.1.1 62274 2hvm 273 2.09e+01 1cnv c.1.8.5 28985 1ykiA 217 2.09e+01 2bmjA 178 2.11e+01 1xuuA 349 2.12e+01 1gcoA 261 2.12e+01 1ybvA c.2.1.2 29884 1v7zA 260 2.12e+01 c.125.1.1 100488 1geeA 261 2.13e+01 c.2.1.2 90509 1tc5A 194 2.13e+01 c.110.1.1 106752 1kbjA 412 2.13e+01 c.1.4.1 72280 1yd7A 395 2.13e+01 1v71A 323 2.14e+01 1li5A 461 2.15e+01 a.27.1.1,c.26.1.1 73912,73913 2gjlA 328 2.17e+01 1rlkA 117 2.18e+01 c.131.1.1 97651 2akzA 439 2.18e+01 2gbp 309 2.19e+01 1gca c.93.1.1 35657 2a2cA 478 2.19e+01 1xklA 273 2.22e+01 1gpmA 525 2.22e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1q9jA 422 2.22e+01 c.43.1.2,c.43.1.2 104590,104591 1zrn 232 2.25e+01 1qq5A c.108.1.1 43323 1xk7A 408 2.27e+01 1esgA 213 2.28e+01 1bam c.52.1.3 33286 1kamA 194 2.31e+01 c.26.1.3 72254 1s0uA 408 2.32e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1b1cA 181 2.33e+01 1amoA c.23.5.2 31212 1xm8A 254 2.35e+01 1v3vA 333 2.36e+01 b.35.1.2,c.2.1.1 108345,108346 1xi3A 215 2.38e+01 c.1.3.1 109601 1ogwA 76 2.38e+01 d.15.1.1 87001 1ubi 76 2.38e+01 1ubi d.15.1.1 37584 1rzuA 485 2.39e+01 c.87.1.8 105140 1zjcA 418 2.41e+01 2gn4A 344 2.41e+01 1yzfA 195 2.42e+01 1tzjA 338 2.44e+01 1ad3A 452 2.45e+01 1ad3A c.82.1.1 35335 1ydnA 295 2.46e+01 1xrjA 261 2.47e+01 1mp4A 292 2.47e+01 c.68.1.6 79376 1wdiA 345 2.49e+01 2b5dX 528 2.50e+01 1m1nB 522 2.50e+01 c.92.2.3 78418 1pfkA 320 2.51e+01 3pfk c.89.1.1 35575 1v5tA 90 2.52e+01 d.15.1.1 108385 1dxeA 256 2.52e+01 1dxeA c.1.12.5 29310 1yumA 242 2.53e+01 1te6A 439 2.54e+01 c.1.11.1,d.54.1.1 106797,106798 1eqjA 511 2.54e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 1ek6A 348 2.54e+01 1xel c.2.1.2 29800 1uc8A 280 2.56e+01 c.30.1.6,d.142.1.7 99165,99166 2fg9A 178 2.56e+01 1uok 558 2.59e+01 1uok b.71.1.1,c.1.8.1 27801,28788 2a14A 263 2.59e+01 1ikoP 178 2.59e+01 b.6.1.5 71243 1nvmA 345 2.63e+01 a.5.7.1,c.1.10.5 86249,86250 1kqzA 273 2.64e+01 c.1.8.5 68844 2dri 271 2.67e+01 2dri c.93.1.1 35637 1g8pA 350 2.68e+01 1g8pA c.37.1.20 60376 1k77A 260 2.68e+01 c.1.15.5 72096 2b8nA 429 2.68e+01 1uumA 372 2.70e+01 c.1.4.1 100010 2g6bA 180 2.70e+01 1o98A 511 2.71e+01 c.105.1.1,c.76.1.3 86684,86685 1nffA 260 2.74e+01 c.2.1.2 80457 1xxlA 239 2.76e+01 1xzoA 174 2.78e+01 1ituA 369 2.82e+01 c.1.9.7 71423 1e87A 118 2.82e+01 1b6e d.169.1.1 42327 1ahxA 396 2.83e+01 1ajsA c.67.1.1 34293 1vliA 385 2.83e+01 b.85.1.1,c.1.10.6 108830,108831 1o08A 221 2.86e+01 c.108.1.6 86525 1r1dA 247 2.87e+01 c.69.1.29 96813 1xwfA 431 2.88e+01 1dxy 333 2.88e+01 1dxy c.2.1.4,c.23.12.1 30094,31354 2amxA 376 2.91e+01 1rz3A 201 3.00e+01 c.37.1.6 98132 1p1xA 260 3.00e+01 c.1.10.1 104060 1cqxA 403 3.01e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1oywA 523 3.01e+01 a.4.5.43,c.37.1.19,c.37.1.19 93760,93761,93762 1o0uA 429 3.02e+01 c.118.1.1 80743 3pmgA 561 3.06e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 1wmdA 434 3.07e+01 b.18.1.20,c.41.1.1 109408,109409 2aeeA 211 3.08e+01 1jclA 260 3.08e+01 c.1.10.1 66501 1wzuA 300 3.08e+01 1j31A 262 3.09e+01 d.160.1.2 90808 1xa3A 437 3.11e+01 1g5bA 221 3.13e+01 1g5bA d.159.1.3 60261 1u8sA 192 3.14e+01 d.58.18.5,d.58.18.5 107737,107738 2bkyA 97 3.19e+01 1t0yA 122 3.19e+01 d.15.1.1 99066 1qnrA 344 3.20e+01 1qnoA c.1.8.3 28834 2acaA 189 3.20e+01 1h5qA 265 3.20e+01 1cydA c.2.1.2 60643 1aihA 170 3.21e+01 1aihA d.163.1.1 42149 1xwyA 264 3.29e+01 1ny1A 240 3.31e+01 c.6.2.3 86395 1uf3A 228 3.33e+01 d.159.1.6 99317 1fcjA 322 3.34e+01 1oasA c.79.1.1 35289 1vhnA 318 3.36e+01 c.1.4.1 100693 1ea9C 583 3.37e+01 b.1.18.2,b.71.1.1,c.1.8.1 70087,70088,70089 1vmeA 410 3.37e+01 c.23.5.1,d.157.1.3 108893,108894 1pg5A 299 3.39e+01 c.78.1.1,c.78.1.1 104146,104147 1nrzA 164 3.40e+01 c.38.1.1 86131 1gox 370 3.41e+01 1gox c.1.4.1 28607 1xwiA 322 3.47e+01 1rvkA 382 3.47e+01 c.1.11.2,d.54.1.1 97928,97929 1pne 140 3.50e+01 1pne d.110.1.1 40866 1ymqA 261 3.51e+01 1xbtA 193 3.52e+01 1r2mA 71 3.53e+01 b.138.1.1 96871 2b97A 71 3.53e+01 1z7dA 433 3.54e+01 1qcwA 410 3.57e+01 1gox c.1.4.1 28622 1rqbA 539 3.57e+01 a.5.7.2,c.1.10.5 105057,105058 1twdA 256 3.64e+01 c.1.30.1 107397 1tg6A 277 3.65e+01 1u9jA 358 3.67e+01 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