# List of top-scoring protein chains for t2k-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 1vjqA 79 8.83e-02 k.43.1.1 100830 1zhvA 134 3.47e-01 1yj7A 171 5.12e-01 1kwmA 402 8.57e-01 c.56.5.1,d.58.3.1 73079,73080 1yioA 208 1.21e+00 2f06A 144 1.54e+00 1dp4A 435 1.88e+00 1dp4A c.93.1.1 35710 1hdoA 206 1.96e+00 1he2A c.2.1.2 60965 1v7rA 186 1.96e+00 c.51.4.1 100482 2gukA 120 2.27e+00 1abe 306 2.46e+00 8abp c.93.1.1 35648 1bap 306 2.51e+00 8abp c.93.1.1 35654 5abp 306 2.51e+00 8abp c.93.1.1 35651 1xppA 115 2.66e+00 2ct8A 497 2.88e+00 1l5jA 865 2.90e+00 a.118.15.1,c.8.2.1,c.83.1.1 73592,73593,73594 8abp 306 3.06e+00 8abp c.93.1.1 35647 2adbA 148 3.10e+00 1dioB 224 3.20e+00 1dioB c.51.3.1 33219 1gh9A 71 3.42e+00 1gh9A g.41.6.1 45266 1ble 163 3.62e+00 1ble c.38.1.1 32475 2c60A 111 3.82e+00 1eexB 224 3.95e+00 1dioB c.51.3.1 33213 2fclA 169 3.95e+00 3chy 128 4.05e+00 3chy c.23.1.1 31038 1ea9C 583 4.14e+00 b.1.18.2,b.71.1.1,c.1.8.1 70087,70088,70089 1he2A 206 4.18e+00 1he2A c.2.1.2 60966 1obpA 159 4.22e+00 1obpA b.60.1.1 27092 1nm2A 317 4.49e+00 c.19.1.1,d.58.23.1 80654,80655 2hhmA 276 4.51e+00 1imbA e.7.1.1 42955 1imbA 277 4.52e+00 1imbA e.7.1.1 42957 2ewrA 170 4.60e+00 1cye 129 4.67e+00 3chy c.23.1.1 31077 1f2tB 148 4.75e+00 1f2tB 1a3yA 149 5.18e+00 1obpA b.60.1.1 27110 1j7xA 302 5.22e+00 c.14.1.2 66425 1hn2A 159 5.67e+00 b.60.1.1 65890 1gt1A 159 5.67e+00 b.60.1.1 90515 1b65A 375 5.69e+00 1b65A d.154.1.1 42020 1s2oA 244 5.79e+00 1mioB 458 5.96e+00 1qguB c.92.2.3 35602 1ezwA 349 5.96e+00 1ezwA c.1.16.3 29558 2bjiA 277 6.00e+00 1dzkA 157 6.01e+00 1obpA b.60.1.1 27096 2b30A 301 6.23e+00 1e69B 322 6.32e+00 1e69B c.37.1.12 32377 1ab5A 125 6.67e+00 3chy c.23.1.1 31056 2cvjA 180 6.97e+00 1ab6A 125 7.44e+00 3chy c.23.1.1 31054 1jfrA 262 7.46e+00 1jfrA c.69.1.16 34724 1jbeA 128 7.61e+00 3chy c.23.1.1 62845 1rv9A 259 7.73e+00 d.194.1.2 105105 1sbyA 254 7.82e+00 1b16A 254 8.09e+00 1b16A c.2.1.2 29875 1bu8A 452 8.15e+00 1gpl b.12.1.2,c.69.1.19 23647,34795 1mejA 223 8.35e+00 c.65.1.1 79029 1a4uA 254 8.36e+00 1b16A c.2.1.2 29878 1xhfA 123 8.46e+00 1ub0A 258 8.55e+00 c.72.1.2 88394 1mkzA 172 8.93e+00 c.57.1.1 84998 1lgtA 297 8.94e+00 d.32.1.3,d.32.1.3 77956,77957 1meoA 209 8.98e+00 c.65.1.1 79035 1han 297 9.01e+00 1han d.32.1.3,d.32.1.3 38506,38507 1lkdA 297 9.01e+00 d.32.1.3,d.32.1.3 78059,78060 1ntr 124 9.22e+00 1dbwA c.23.1.1 31092 1jd1A 129 9.37e+00 1qu9A d.79.1.1 62890 1itxA 419 1.01e+01 c.1.8.5,d.26.3.1 71425,71426 1gnkA 112 1.02e+01 2pii d.58.5.1 39073 1bgj 394 1.04e+01 1pbe c.3.1.2,d.16.1.2 30352,37883 1rz3A 201 1.06e+01 c.37.1.6 98132 1r6dA 337 1.06e+01 c.2.1.2 97148 1omzA 293 1.08e+01 c.68.1.15 87093 2ax4A 198 1.09e+01 1u5tC 202 1.09e+01 a.4.5.54,a.4.5.54 107688,107689 1b9bA 255 1.09e+01 1amk c.1.1.1 28531 1id1A 153 1.12e+01 1id1A c.2.1.9 62286 2fiqA 420 1.16e+01 2b0cA 206 1.16e+01 1x9zA 188 1.16e+01 1cqzA 554 1.18e+01 1cr6B c.69.1.11,c.108.1.2 34689,43339 1tlfA 301 1.28e+01 1tlfA c.93.1.1 35687 1lj9A 144 1.34e+01 a.4.5.28 78035 1jyeA 349 1.36e+01 c.93.1.1 67455 2fqxA 318 1.40e+01 1ykjA 394 1.41e+01 1z3eA 132 1.44e+01 1atlA 202 1.51e+01 1atlA d.92.1.9 40322 1yfnA 118 1.52e+01 1umgA 362 1.53e+01 d.280.1.1 107956 1edg 380 1.58e+01 1edg c.1.8.3 28807 1dthA 203 1.61e+01 1atlA d.92.1.9 40324 1pba 81 1.62e+01 1pytA d.58.3.1 39067 1egzA 291 1.63e+01 7a3hA c.1.8.3 28828 1oo0A 147 1.67e+01 d.232.1.1 87182 1xfiA 367 1.70e+01 e.50.1.1 109584 1ox8A 107 1.70e+01 b.136.1.1 93671 1p27B 106 1.70e+01 d.58.7.1 93908 1xb4A 202 1.73e+01 1pbe 394 1.75e+01 1pbe c.3.1.2,d.16.1.2 30338,37869 1efaA 333 1.76e+01 1tlfA a.35.1.5,c.93.1.1 17106,35691 1wcwA 261 1.76e+01 1k7kA 221 1.78e+01 c.51.4.1 72104 1v6sA 390 1.81e+01 c.86.1.1 100424 1cj3A 392 1.86e+01 1pbe c.3.1.2,d.16.1.2 30347,37878 1xd7A 145 1.86e+01 a.4.5.55 109566 1vpkA 378 1.86e+01 1z3iX 644 1.89e+01 2gd1O 334 1.91e+01 1dssG c.2.1.3,d.81.1.1 29978,39893 1cw0A 155 1.91e+01 1vsrA c.52.1.15 33333 1yrrA 382 1.91e+01 1b1yA 500 1.92e+01 1byb c.1.8.1 28796 2pii 112 1.95e+01 2pii d.58.5.1 39071 2f1kA 279 1.95e+01 1z7lA 276 1.99e+01 1ta3B 303 2.00e+01 c.1.8.3 106732 3grx 82 2.02e+01 1aba c.47.1.1 32769 1oxkB 134 2.03e+01 c.23.1.1 93691 1gmuA 143 2.04e+01 b.107.1.1,d.58.38.1 65335,65336 1j8fA 323 2.05e+01 1j8fA c.31.1.5 62738 1yzbA 182 2.05e+01 1yzyA 413 2.06e+01 1ycdA 243 2.07e+01 2agaA 190 2.09e+01 1zvpA 133 2.13e+01 1pjqA 457 2.14e+01 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 1gmwA 143 2.15e+01 b.107.1.1,d.58.38.1 65347,65348 1ovqA 138 2.17e+01 c.55.3.8 93607 1k0iA 394 2.26e+01 c.3.1.2,d.16.1.2 67942,67943 2f6rA 281 2.28e+01 1nox 205 2.32e+01 1nox d.90.1.1 40242 1yqhA 109 2.34e+01 1y5eA 169 2.37e+01 1v3hA 495 2.38e+01 c.1.8.1 108303 1w8iA 156 2.42e+01 1q6cA 495 2.45e+01 c.1.8.1 95970 1ypqA 135 2.47e+01 1m7xA 617 2.51e+01 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 1fgs 428 2.53e+01 1fgs c.59.1.2,c.72.2.2 33959,34962 1wdpA 495 2.53e+01 1vf8A 377 2.53e+01 1j3mA 129 2.55e+01 d.129.7.1 103836 2cg4A 152 2.56e+01 1ii5A 233 2.64e+01 c.94.1.1 62412 1h75A 81 2.68e+01 1h75A c.47.1.1 60716 1qd9A 124 2.68e+01 1qu9A d.79.1.1 39758 1hzmA 154 2.81e+01 c.46.1.1 65975 2ci1A 275 2.82e+01 2phh 394 2.83e+01 1pbe c.3.1.2,d.16.1.2 30353,37884 1k1xA 659 2.85e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1rybA 212 2.87e+01 c.56.3.1 98098 1dkuA 317 2.88e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1eikA 77 2.93e+01 1eikA d.78.1.1 39751 1iiwA 232 2.94e+01 c.94.1.1 62461 1ewsA 32 2.94e+01 1ewsA g.9.1.1 59534 1kvnA 104 2.97e+01 d.201.1.1 73066 1n71A 180 3.02e+01 d.108.1.1 85370 1yr4A 237 3.03e+01 2f91A 237 3.03e+01 1wi6A 88 3.03e+01 1b87A 181 3.05e+01 1b87A d.108.1.1 40797 1chd 203 3.05e+01 1chd c.40.1.1 32478 1g61A 228 3.06e+01 1g61A d.126.1.1 41126 2gbp 309 3.07e+01 1gca c.93.1.1 35657 1ynfA 458 3.13e+01 1r1qA 100 3.14e+01 d.93.1.1 104763 1gd1O 334 3.14e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 1wexA 104 3.15e+01 1bvoA 175 3.25e+01 1a3qA b.2.5.3 22457 1ho1A 242 3.27e+01 1ho1A c.1.24.1 61097 1h6hA 143 3.30e+01 d.189.1.1 65681 1bsg 266 3.31e+01 1btl e.3.1.1 42729 1uae 419 3.41e+01 1uae d.68.2.2 39574 1cr6B 554 3.41e+01 1cr6B c.69.1.11,c.108.1.2 34688,43338 1g2iA 166 3.43e+01 1g2iA c.23.16.2 31438 2af4C 333 3.46e+01 1gpl 432 3.46e+01 1gpl b.12.1.2,c.69.1.19 23645,34793 1od8A 313 3.47e+01 c.1.8.3 86838 1xriA 151 3.47e+01 1v0lA 313 3.49e+01 c.1.8.3 108207 1e0wA 313 3.49e+01 1taxA c.1.8.3 59150 1ospO 257 3.54e+01 1ospO b.76.1.1 27971 1rf6A 427 3.55e+01 d.68.2.2 97366 1vpqA 273 3.55e+01 1ba9 153 3.57e+01 1mfmA b.1.8.1 22272 3mag 307 3.62e+01 3mag c.66.1.25 34205 1x31C 206 3.65e+01 1v39 322 3.65e+01 3mag c.66.1.25 34206 1vp9 322 3.65e+01 3mag c.66.1.25 34210 1dhy 292 3.80e+01 1han d.32.1.3,d.32.1.3 38504,38505 1vpt 348 3.83e+01 3mag c.66.1.25 34207 1e9lA 377 3.85e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 1afsA 323 3.93e+01 1frb c.1.7.1 28694 1byb 495 3.97e+01 1byb c.1.8.1 28790 1nn5A 215 4.01e+01 c.37.1.1 85892 1e9eA 215 4.01e+01 c.37.1.1 64810 1x6vA 630 4.03e+01 1wzaA 488 4.03e+01 1iqzA 81 4.03e+01 d.58.1.4 66281 1e9cA 215 4.06e+01 c.37.1.1 64808 1oywA 523 4.10e+01 a.4.5.43,c.37.1.19,c.37.1.19 93760,93761,93762 1cz7A 406 4.15e+01 1bg2 c.37.1.9 32194 1kwkA 645 4.21e+01 b.71.1.1,c.1.8.1,c.23.16.5 77565,77566,77567 1rz4A 226 4.26e+01 a.4.5.53,a.118.1.18 105131,105132 1e2gA 215 4.30e+01 3tmkA c.37.1.1 59165 1y81A 138 4.32e+01 1vixA 420 4.35e+01 c.56.5.4,d.58.19.1 100777,100778 2cvlA 124 4.39e+01 1e2fA 215 4.43e+01 3tmkA c.37.1.1 59164 1xn7A 78 4.45e+01 1gca 309 4.50e+01 1gca c.93.1.1 35659 1zk7A 467 4.53e+01 1xp8A 366 4.60e+01 2fiuA 99 4.63e+01 1wy5A 317 4.70e+01 2g76A 335 4.73e+01 3bifA 468 4.76e+01 1bif c.37.1.7,c.60.1.4 31962,34008 1qu9A 128 4.76e+01 1qu9A d.79.1.1 39755 1qu9C 128 4.76e+01 1qu9A d.79.1.1 39757 1pil 112 4.82e+01 2pii d.58.5.1 39072 2a4nA 182 4.84e+01 1qorA 327 4.91e+01 1qorA b.35.1.2,c.2.1.1 24766,29782 2d27A 149 4.94e+01 1oz9A 150 4.95e+01 d.92.1.15 93808 1o2dA 371 4.96e+01 e.22.1.2 86591 1gy8A 397 4.97e+01 c.2.1.2 83376 2eshA 118 4.98e+01 1q9uA 130 5.00e+01 d.129.7.1 96314 1b54 257 5.11e+01 1ct5A c.1.6.2 28664 1m6nA 802 5.16e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 78697,78698,78699,78700 1jbwA 428 5.24e+01 c.59.1.2,c.72.2.2 62860,62861 1mucA 373 5.26e+01 1mucA c.1.11.2,d.54.1.1 29236,38880 1pytA 94 5.27e+01 1pytA d.58.3.1 39064 1bif 469 5.30e+01 1bif c.37.1.7,c.60.1.4 31961,34003 2aeeA 211 5.32e+01 1rlkA 117 5.33e+01 c.131.1.1 97651 1ujcA 161 5.33e+01 1hkkA 364 5.33e+01 c.1.8.5,d.26.3.1 90634,90635 1uv7A 110 5.34e+01 d.67.4.1 100040 1eemA 241 5.36e+01 1eemA a.45.1.1,c.47.1.5 17717,33011 2bifA 469 5.45e+01 1bif c.37.1.7,c.60.1.4 31963,34009 1hh2P 344 5.47e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 65835,65836,65837,65838 1wb0A 445 5.48e+01 1lg2A 365 5.51e+01 c.1.8.5,d.26.3.1 77950,77951 1kw3B 292 5.53e+01 d.32.1.3,d.32.1.3 77549,77550 1k8hA 133 5.59e+01 b.111.1.1 72176 1w30A 201 5.61e+01 1xiyA 182 5.64e+01 1ug8A 87 5.66e+01 d.68.7.1 107825 1d2fA 390 5.67e+01 1d2fA c.67.1.3 34411 1t4bA 367 5.70e+01 c.2.1.3,d.81.1.1 106406,106407 1ga8A 311 5.72e+01 1ga8A c.68.1.4 34516 1dd5A 185 5.73e+01 1dd5A d.67.3.1 39564 1a2n 419 5.82e+01 1uae d.68.2.2 39575 2g0dA 409 5.84e+01 1mixA 206 5.84e+01 a.11.2.1,b.55.1.5 79166,79167 1rp0A 284 5.86e+01 1brmA 367 5.87e+01 1brmA c.2.1.3,d.81.1.1 30030,39945 1xviA 275 5.90e+01 1rkd 309 5.95e+01 1rkd c.72.1.1 34928 1qyrA 252 5.96e+01 c.66.1.24 104657 1p99A 295 6.01e+01 c.94.1.1 94384 1aksA 125 6.01e+01 5ptp b.47.1.2 25969 1n82A 331 6.02e+01 c.1.8.3 91703 1av6A 289 6.04e+01 3mag c.66.1.25 34218 1gz0A 253 6.05e+01 c.116.1.1,d.79.3.3 76391,76392 1t1vA 93 6.11e+01 c.47.1.14 106278 2bkxA 242 6.13e+01 1j8dA 180 6.19e+01 c.108.1.5 66433 1ct5A 256 6.30e+01 1ct5A c.1.6.2 28663 1vhxA 150 6.31e+01 c.55.3.8 100712 1ma3A 253 6.31e+01 c.31.1.5 78883 1w25A 459 6.32e+01 1yqtA 538 6.33e+01 1e12A 253 6.33e+01 1c3wA f.13.1.1 43428 1k1eA 180 6.36e+01 c.108.1.5 67995 1mfmA 153 6.38e+01 1mfmA b.1.8.1 22246 1y1oA 203 6.41e+01 1g10A 102 6.49e+01 1g10A d.137.1.1 60191 1n8nA 212 6.56e+01 c.108.1.12 91706 1o0yA 260 6.61e+01 c.1.10.1 80756 1kwgA 645 6.70e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1auz 116 6.73e+01 1auz c.13.2.1 30883 1iow 306 6.79e+01 1iow c.30.1.2,d.142.1.1 31713,41481 1f1uA 323 6.86e+01 d.32.1.3,d.32.1.3 83200,83201 1v8eA 224 6.86e+01 1lwjA 441 6.93e+01 b.71.1.1,c.1.8.1 74303,74304 1wd7A 261 6.94e+01 1tf5A 844 6.96e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 106834,106835,106836,106837 1vd6A 224 6.97e+01 1bob 320 6.99e+01 1bob d.108.1.1 40816 1fjgP 88 6.99e+01 1emwA d.27.1.1 38444 1ogsA 497 7.01e+01 b.71.1.2,c.1.8.3 86997,86998 1whbA 157 7.05e+01 1dliA 402 7.12e+01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18809,30213,31622 1dljA 402 7.15e+01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1quvA 578 7.26e+01 1quvA e.8.1.4 43119 1ve1A 304 7.32e+01 2fr1A 486 7.32e+01 1w9pA 433 7.34e+01 7taa 478 7.34e+01 7taa b.71.1.1,c.1.8.1 27778,28765 1konA 249 7.36e+01 e.39.1.1 72823 1o6uA 403 7.42e+01 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 1g9rA 311 7.43e+01 1ga8A c.68.1.4 34517 5ptp 223 7.53e+01 5ptp b.47.1.2 25831 2gqrA 237 7.54e+01 1csjA 531 7.54e+01 1quvA e.8.1.4 43120 1pyiA 96 7.56e+01 1pyiA g.38.1.1,h.1.3.1 45079,45512 1hj9A 226 7.59e+01 b.47.1.2 65845 4ptp 223 7.61e+01 2d1uA 104 7.65e+01 1v8fA 276 7.67e+01 c.26.1.4 100503 2f96A 224 7.67e+01 2b82A 211 7.73e+01 1njrA 284 7.74e+01 c.50.1.2 103858 1rmwA 212 7.74e+01 2axpA 173 7.74e+01 1h32B 138 7.78e+01 a.3.1.1 76620 2phy 125 7.78e+01 3pyp d.110.3.1 40901 1tux 301 7.84e+01 1taxA c.1.8.3 28907 1q1aA 289 7.91e+01 c.31.1.5 95561 1zmaA 118 7.96e+01 1xyfA 436 7.99e+01 1taxA b.42.2.1,c.1.8.3 25577,28909 1qstA 160 8.05e+01 1yghA d.108.1.1 40804 1lvaA 258 8.06e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1u11A 182 8.09e+01 c.23.8.1 107576 1imdA 277 8.12e+01 1imbA e.7.1.1 42968 1gx5A 536 8.23e+01 e.8.1.4 70682 1ufkA 254 8.28e+01 c.66.1.39 99340 1dc7A 124 8.32e+01 1dbwA c.23.1.1 31093 1ah2 269 8.33e+01 1gci c.41.1.1 32542 1tin 69 8.41e+01 2sniI d.40.1.1 38580 1mzhA 225 8.42e+01 c.1.10.1 79698 1o4sA 389 8.43e+01 c.67.1.1 86620 1nwzA 125 8.48e+01 d.110.3.1 86370 3pyp 125 8.48e+01 3pyp d.110.3.1 40897 1rp4A 389 8.56e+01 a.227.1.1 105027 1nksA 194 8.56e+01 1nksA c.37.1.1 31886 1g19A 350 8.57e+01 2reb c.37.1.11,d.48.1.1 32284,38770 1iv0A 98 8.57e+01 c.55.3.8 90706 1j0fA 100 8.57e+01 c.47.1.14 90739 1taxA 302 8.58e+01 1taxA 1olmA 403 8.59e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1ss9A 311 8.62e+01 c.68.1.4 105978 1mit 69 8.69e+01 1hymA d.40.1.1 38582 1gadO 330 8.71e+01 1dssG c.2.1.3,d.81.1.1 29950,39865 1efyA 350 8.73e+01 1a26 a.41.1.1,d.166.1.2 17413,42275 1wr8A 231 8.78e+01 1fc6A 388 8.79e+01 1fc6A b.36.1.3,c.14.1.2 64738,64739 1psuA 140 8.85e+01 d.38.1.5 88285 1rch 155 8.88e+01 2rn2 c.55.3.1 33570 1ti6A 875 8.97e+01 b.52.2.2,c.81.1.1 106974,106975