# List of top-scoring protein chains for t2k-100-30-o_sep-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 1itcA 516 3.82e-01 b.3.1.1,c.1.8.1 83705,83706 5bcaA 516 4.49e-01 1b9zA b.3.1.1,c.1.8.1 22529,28799 1b9zA 516 5.08e-01 1b9zA b.3.1.1,c.1.8.1 22528,28798 1vemA 516 5.34e-01 1ggvA 232 5.94e-01 1din c.69.1.9 34683 1din 236 6.19e-01 1din c.69.1.9 34682 1kshA 186 7.66e-01 c.37.1.8 72914 1jdiA 231 7.91e-01 c.74.1.1 66551 1k0wA 231 8.51e-01 c.74.1.1 77220 1nmtA 392 9.95e-01 1nmtA d.108.1.2,d.108.1.2 40823,40824 2agyA 361 1.06e+00 1zi8A 236 1.21e+00 1yyaA 250 1.89e+00 1n0nA 199 2.35e+00 a.2.11.1,d.44.1.1 79750,79751 1pl4A 198 2.55e+00 a.2.11.1,d.44.1.1 94854,94855 1abmA 198 2.65e+00 1avmA 1ap6A 198 2.77e+00 1avmA a.2.11.1,d.44.1.1 15746,38705 1q15A 503 3.40e+00 c.26.2.1,d.153.1.1 95538,95539 1io1A 398 3.59e+00 1io1A e.32.1.1 62611 1nar 290 3.80e+00 1nar c.1.8.5 28988 2gnqA 336 4.20e+00 1nrfA 262 4.27e+00 e.3.1.1 92086 1agx 331 4.35e+00 4pgaA c.88.1.1 35564 1sh0A 510 4.55e+00 e.8.1.4 98876 2a5dA 175 4.65e+00 1nmoA 247 5.01e+00 c.135.1.1 91980 1h49A 512 5.21e+00 c.1.8.4 83477 1iicA 422 5.27e+00 1nmtA d.108.1.2,d.108.1.2 62422,62423 1n1mA 728 5.69e+00 b.70.3.1,c.69.1.24 79815,79816 1sfxA 109 5.97e+00 a.4.5.50 105505 1g65K 211 6.26e+00 d.153.1.4 41907 4icb 76 6.32e+00 4icb a.39.1.1 17145 1ig5A 75 6.56e+00 4icb a.39.1.1 62363 1mr3F 181 6.70e+00 c.37.1.8 79422 1w3jA 468 6.95e+00 c.1.8.4 109156 1wjxA 122 7.19e+00 1q0xH 221 7.45e+00 b.1.1.1,b.1.1.2 95517,95518 2gu3A 136 7.45e+00 1rypL 212 7.51e+00 d.153.1.4 41880 1v02A 565 7.64e+00 c.1.8.4 108194 3icb 75 7.67e+00 4icb a.39.1.1 17147 1wmhA 89 7.74e+00 1hdmA 201 7.80e+00 1iakA b.1.1.2,d.19.1.1 21583,38157 1yadA 221 8.01e+00 1uw4A 91 8.10e+00 d.58.7.4 100071 1e55A 512 8.14e+00 1e70M c.1.8.4 28934 1lci 550 8.23e+00 1lci e.23.1.1 43349 1obdA 306 8.32e+00 d.143.1.1 86767 1garA 212 8.41e+00 2gar c.65.1.1 34162 2cblA 305 8.55e+00 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17380,17774,40528 1g5bA 221 8.68e+00 1g5bA d.159.1.3 60261 1ywnA 316 8.72e+00 1ht9A 76 9.01e+00 4icb a.39.1.1 61252 1m56B 264 9.01e+00 b.6.1.2,f.17.2.1 74472,74473 2cfaA 217 9.07e+00 1zkjA 359 9.37e+00 1rypJ 204 9.41e+00 d.153.1.4 41878 2b30A 301 9.50e+00 1zd9A 188 9.74e+00 1aerA 205 1.01e+01 1aerA d.166.1.1 42249 1dmaA 214 1.01e+01 1aerA d.166.1.1 42251 1bmr 68 1.03e+01 1aho g.3.7.1 44144 2fckA 181 1.05e+01 2acaA 189 1.07e+01 2b43A 526 1.10e+01 1avgL 41 1.13e+01 1ppbL b.47.1.2 26216 1b47A 304 1.14e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17381,17775,40529 2cnqA 306 1.15e+01 1yvhA 329 1.17e+01 1o3yA 166 1.19e+01 c.37.1.8 86618 1ghpA 258 1.21e+01 1btl e.3.1.1 60520 1yumA 242 1.25e+01 2b6hA 192 1.28e+01 2agcA 162 1.28e+01 1f9zA 135 1.29e+01 1qipA d.32.1.1 38484 1a48 306 1.34e+01 1a48 d.143.1.1 41590 1oo0A 147 1.35e+01 d.232.1.1 87182 1hurA 180 1.37e+01 1hurA c.37.1.8 32052 1jlxA 304 1.39e+01 1jlyA b.42.3.1,b.42.3.1 25583,25584 1jkxA 212 1.41e+01 c.65.1.1 66813 2breA 219 1.42e+01 1jlyA 304 1.43e+01 1jlyA b.42.3.1,b.42.3.1 25587,25588 1o50A 157 1.46e+01 d.37.1.1,d.37.1.1 92478,92479 1mg4A 113 1.47e+01 d.15.11.1 84953 1b64 91 1.47e+01 1b64 d.58.12.1 39306 1nvpD 108 1.52e+01 a.32.1.1,b.56.1.1 92213,92214 2fsrA 195 1.54e+01 1gx5A 536 1.60e+01 e.8.1.4 70682 1h4rA 314 1.60e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1j7lA 264 1.61e+01 d.144.1.6 62697 1a4h 230 1.62e+01 1yer d.122.1.1 41099 1q42A 201 1.66e+01 d.17.4.2 95776 1alq 266 1.66e+01 1btl e.3.1.1 42707 1cpzA 68 1.68e+01 1aw0 d.58.17.1 39351 1exbA 332 1.69e+01 1qrqA c.1.7.1 28666 1quvA 578 1.72e+01 1quvA e.8.1.4 43119 1vjeA 166 1.72e+01 d.185.1.2 100807 2cbuA 468 1.72e+01 2bkdN 134 1.75e+01 1zx8A 136 1.75e+01 1bb8 71 1.77e+01 2bb8 d.10.1.1 37478 1a8y 367 1.78e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1aerB 195 1.78e+01 1aerA d.166.1.1 42250 1y1uA 585 1.81e+01 1l6oA 95 1.82e+01 b.36.1.1 84534 1mg7A 417 1.83e+01 d.14.1.6,d.58.26.6 84954,84955 3blm 257 1.83e+01 1btl e.3.1.1 42709 1v5sA 126 1.83e+01 d.129.6.1 108384 1c2pA 576 1.90e+01 1quvA e.8.1.4 43117 1fa8A 135 1.92e+01 1qipA d.32.1.1 38486 2cz1A 206 1.95e+01 1wdyA 285 2.01e+01 1zarA 282 2.01e+01 2fg9A 178 2.04e+01 2f9dA 125 2.04e+01 1qrqA 325 2.05e+01 1qrqA c.1.7.1 28667 1nteA 82 2.07e+01 b.36.1.1 86163 1f6bA 198 2.07e+01 c.37.1.8 64986 1tqmA 282 2.07e+01 a.4.5.56,d.144.1.9 107236,107237 1k0sA 151 2.09e+01 b.40.7.1 67969 2brcA 214 2.13e+01 1amw 214 2.14e+01 1yer d.122.1.1 41093 1xahA 354 2.14e+01 1ab4 477 2.15e+01 1ab4 e.11.1.1 43251 1azo 232 2.16e+01 1azo c.52.1.14 33329 1yh6A 179 2.16e+01 1wwzA 159 2.19e+01 1tw4A 125 2.20e+01 1lm6A 215 2.23e+01 d.167.1.1 84628 1pioA 257 2.25e+01 1btl e.3.1.1 42719 1th0A 226 2.27e+01 d.3.1.7 106903 1cvmA 353 2.28e+01 1qlgA b.68.3.1 27628 1yrvA 169 2.30e+01 1am1 213 2.32e+01 1yer d.122.1.1 41095 1o4rA 108 2.33e+01 d.93.1.1 92469 1b35B 255 2.34e+01 1b35B b.121.4.1 23334 1f35A 162 2.35e+01 1f35A b.94.1.1 59628 1g8yA 279 2.37e+01 1g8yA c.37.1.11 32302 1g2iA 166 2.39e+01 1g2iA c.23.16.2 31438 2basA 431 2.39e+01 2bb8 71 2.39e+01 2bb8 d.10.1.1 37480 1fnmA 691 2.39e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 25709,32144,37546,39302,39303 1fj2A 232 2.40e+01 1auoA c.69.1.14 34720 2a0jA 149 2.41e+01 2b7kA 200 2.42e+01 1shaA 104 2.43e+01 1fmk d.93.1.1 40424 2ajgA 196 2.43e+01 1ikpA 613 2.45e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1r8sA 164 2.49e+01 c.37.1.8 97247 1cojA 212 2.61e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1aotF 106 2.62e+01 1lckA d.93.1.1 40458 1nzjA 298 2.62e+01 c.26.1.1 92377 1l2lA 457 2.64e+01 c.72.1.3 77656 1mml 265 2.65e+01 1mml e.8.1.2 43015 1uswA 260 2.66e+01 c.69.1.17 99895 2fz4A 237 2.68e+01 1zyiA 171 2.69e+01 1r29A 127 2.73e+01 d.42.1.1 96856 1qlgA 355 2.73e+01 1qlgA b.68.3.1 27627 1mil 104 2.76e+01 1d4tA d.93.1.1 40496 1zj6A 187 2.79e+01 1ny9A 143 2.81e+01 a.181.1.1 86401 2bkkA 264 2.81e+01 1xcbA 211 2.82e+01 a.4.5.38,c.2.1.12 109552,109553 2f1kA 279 2.83e+01 1shbA 104 2.86e+01 1fmk d.93.1.1 40425 2ucz 165 2.88e+01 1u9aA d.20.1.1 38330 1j7iA 264 2.89e+01 1j7iA d.144.1.6 62694 1innA 166 2.92e+01 1j98A d.185.1.2 62608 1sxrA 183 2.93e+01 d.118.1.1 106101 1zhvA 134 2.93e+01 1n0qA 93 2.93e+01 k.37.1.1 79754 1h6lA 353 2.93e+01 b.68.3.1 60687 1tib 269 2.94e+01 3tgl c.69.1.17 34738 1uurA 473 2.95e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1th8A 145 2.97e+01 d.122.1.3 106908 1vgwA 231 2.98e+01 c.68.1.13 100612 1ru0A 105 2.99e+01 1uwcA 261 2.99e+01 c.69.1.17 100101 2c1iA 431 3.02e+01 1osdA 72 3.02e+01 d.58.17.1 104022 1wrvA 308 3.04e+01 1yc9A 442 3.06e+01 1ffkP 84 3.07e+01 1ffkP d.12.1.1 37493 1rpyA 114 3.08e+01 d.93.1.1 97718 1f2fA 104 3.09e+01 1fmk d.93.1.1 40455 2aieP 203 3.09e+01 1zsxA 347 3.11e+01 2ftbA 125 3.17e+01 2btvA 901 3.18e+01 2btvA e.28.1.1 43376 2gar 212 3.19e+01 2gar c.65.1.1 34161 1o17A 345 3.20e+01 a.46.2.1,c.27.1.1 80765,80766 1zm8A 259 3.21e+01 1s99A 200 3.21e+01 1j55A 95 3.22e+01 a.39.1.2 77078 1a1aA 107 3.24e+01 1fmk d.93.1.1 40449 1p4kA 295 3.25e+01 d.153.1.5 87772 1ah6 220 3.25e+01 1yer d.122.1.1 41094 2pooA 355 3.27e+01 1qlgA b.68.3.1 27626 1p6pA 125 3.28e+01 b.60.1.2 87839 1v58A 241 3.29e+01 c.47.1.9,d.17.3.1 108371,108372 1jobA 162 3.33e+01 1f35A b.94.1.1 63207 1qd9A 124 3.37e+01 1qu9A d.79.1.1 39758 1m2kA 249 3.37e+01 c.31.1.5 84754 1nrjA 158 3.38e+01 d.110.4.4 86124 1xa1A 255 3.39e+01 e.3.1.1 109529 1ylhA 560 3.42e+01 2aorA 223 3.42e+01 1krs 120 3.43e+01 1krs b.40.4.1 25256 1vmbA 140 3.43e+01 1khiA 176 3.45e+01 b.34.5.2,b.40.4.5 77408,77409 2agaA 190 3.50e+01 1yw4A 341 3.51e+01 1e44B 96 3.51e+01 1e44B b.101.1.1 59220 1btl 263 3.52e+01 1btl e.3.1.1 42691 1qfxA 460 3.54e+01 1qfxA c.60.1.2 33994 1irsA 112 3.54e+01 1qqgA b.55.1.2 26991 1ufwA 95 3.54e+01 d.58.7.1 99358 1ri6A 343 3.58e+01 b.69.11.1 97503 1s7hA 200 3.67e+01 d.58.48.2 105349 1r6jA 82 3.72e+01 b.36.1.1 97151 1fdr 248 3.76e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 1yfnA 118 3.76e+01 2cn3A 737 3.77e+01 1t2jA 116 3.79e+01 1gzqA 300 3.86e+01 b.1.1.2,d.19.1.1 70818,70819 1ew3A 159 3.87e+01 1mup b.60.1.1 27114 2cb2A 318 3.87e+01 1tvoA 368 3.88e+01 1uylA 236 3.89e+01 d.122.1.1 108147 2bkyA 97 3.91e+01 3erk 364 3.92e+01 1hcl d.144.1.7 41654 1yer 228 4.01e+01 1yer d.122.1.1 41101 1vqoS 85 4.04e+01 1zy9A 564 4.04e+01 1sqsA 242 4.05e+01 c.23.5.5 98968 1ih8A 271 4.08e+01 2nsyA c.26.2.1 62377 1xkzA 255 4.08e+01 1htwA 158 4.11e+01 c.37.1.18 71083 2gkpA 167 4.13e+01 1rxdA 159 4.14e+01 1h0xA 100 4.18e+01 d.68.6.1 76451 1i2sA 282 4.18e+01 e.3.1.1 71104 1seiA 130 4.21e+01 1seiA d.140.1.1 41463 1pbgA 468 4.26e+01 1e70M c.1.8.4 28946 1gt6A 269 4.29e+01 c.69.1.17 76342 1efcA 393 4.32e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1dfcA 493 4.34e+01 1dfcA b.42.5.1,b.42.5.1,b.42.5.1,b.42.5.1 25616,25617,25618,25619 2dbsA 90 4.35e+01 2b20A 403 4.36e+01 1nlfA 279 4.36e+01 c.37.1.11 85850 2h17A 181 4.37e+01 1xs1A 193 4.37e+01 1b69A 69 4.39e+01 2bb8 d.10.1.1 37479 1gkxA 388 4.42e+01 a.29.5.1,d.122.1.4 65266,65267 1a4pA 96 4.42e+01 1b4cA a.39.1.2 17176 2bvfA 459 4.42e+01 1wzvA 155 4.42e+01 2c1gA 431 4.42e+01 1hskA 326 4.44e+01 2mbr d.145.1.2,d.146.1.1 61241,61242 1qvjA 292 4.46e+01 d.113.1.1 96431 2f0aA 98 4.47e+01 2ahjC 206 4.47e+01 2ahjA d.149.1.1 41773 1g0uI 205 4.47e+01 d.153.1.4 41891 1zckA 154 4.56e+01 1uz1A 468 4.57e+01 1rcqA 357 4.59e+01 b.49.2.2,c.1.6.1 104882,104883 2ervA 150 4.68e+01 1kveB 77 4.69e+01 1kveB 2gaiA 633 4.71e+01 2b7eA 59 4.81e+01 1etu 394 4.82e+01 1efcA c.37.1.8 64737 1em8A 147 4.83e+01 c.128.1.1 90457 2aexA 346 4.84e+01 1c76A 136 4.87e+01 2sak d.15.5.1 37718 1k2yX 463 4.87e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 3pga1 337 4.87e+01 4pgaA 1y71A 130 4.88e+01 9gafA 295 4.92e+01 1apyA d.153.1.5 42008 1y80A 210 4.95e+01 1e8oA 85 4.96e+01 1914 d.49.1.1 38773 1s5jA 847 4.97e+01 1i3zA 103 4.97e+01 d.93.1.1 83667 2cw8A 537 4.98e+01 1pbv 195 4.99e+01 1pbv a.118.3.1 19179 1as0 353 4.99e+01 1cipA a.66.1.1,c.37.1.8 18212,32095 2atrA 138 4.99e+01 1zt2B 212 4.99e+01 1g2yA 32 5.02e+01 a.34.2.1 17003 2dbnA 461 5.06e+01 1y8qA 346 5.08e+01 1q33A 292 5.08e+01 d.113.1.1 95657 2ahjA 206 5.11e+01 2ahjA d.149.1.1 41772 1nnsA 326 5.12e+01 c.88.1.1 85910 1bmtA 246 5.13e+01 1bmtA a.46.1.1,c.23.6.1 17757,31235 2f57A 317 5.16e+01 1htjF 210 5.18e+01 1htjF a.91.1.1 61254 1rypF 233 5.19e+01 1rypF d.153.1.4 41937 1c5kA 439 5.19e+01 1crzA b.68.4.1,c.51.2.1 27630,33212 2aumA 317 5.22e+01 1jltA 122 5.22e+01 a.133.1.2 66867 1byqA 228 5.23e+01 1yer d.122.1.1 41100 1kolA 398 5.25e+01 b.35.1.2,c.2.1.1 77474,77475 1fnf 368 5.26e+01 1fnf b.1.2.1,b.1.2.1,b.1.2.1,b.1.2.1 21972,21973,21974,21975 1zl0A 311 5.27e+01 1zrsA 317 5.28e+01 1mwwA 128 5.30e+01 d.80.1.4 91483 1sqrA 95 5.30e+01 2fbaA 492 5.31e+01 1g13A 162 5.39e+01 1g13A b.95.1.1 60194 1b1gA 75 5.40e+01 1psrA a.39.1.1 17151 1oa8A 133 5.42e+01 b.145.1.1 92698 1wh8A 111 5.47e+01 2fa8A 105 5.47e+01 2aunA 317 5.48e+01 4blmA 265 5.49e+01 1btl e.3.1.1 42721 1m22A 503 5.50e+01 c.117.1.1 78464 1e69B 322 5.56e+01 1e69B c.37.1.12 32377 1cov3 238 5.57e+01 1aym3 1v04A 355 5.58e+01 b.68.6.2 100240 1gxuA 91 5.59e+01 d.58.10.1 76378 1iz1A 294 5.60e+01 a.4.5.37,c.94.1.1 83823,83824 1vzoA 355 5.61e+01 d.144.1.7 108971 1z57A 339 5.63e+01 1pu5A 164 5.63e+01 b.95.1.1 104310 2chnA 716 5.64e+01 2czrA 226 5.64e+01 1k1aA 241 5.65e+01 d.211.1.1 67992 1cipA 353 5.66e+01 1cipA a.66.1.1,c.37.1.8 18210,32093 2ag9A 164 5.71e+01 1wrjA 156 5.72e+01 1to4A 156 5.78e+01 b.1.8.1 107162 1qmeA 702 5.84e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1txdA 385 5.84e+01 a.87.1.1,b.55.1.1 107422,107423 1m40A 263 5.86e+01 e.3.1.1 74437 1d2eA 397 5.87e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1kvdB 77 5.92e+01 1kveB 1w2fA 276 5.97e+01 d.143.1.3 109125 1dbqA 289 5.99e+01 1qpzA c.93.1.1 35666 1kutA 230 6.02e+01 d.143.1.1 73017 1deuA 277 6.04e+01 1theB d.3.1.1 37085 1xqiA 195 6.07e+01 1bf5A 545 6.07e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 2fswA 107 6.10e+01 1xniA 118 6.17e+01 1ibsA 317 6.19e+01 c.61.1.2,c.61.1.2 66107,66108 1on2A 142 6.21e+01 a.4.5.24,a.76.1.1 87103,87104 1tfzA 424 6.23e+01 d.32.1.3,d.32.1.3 106886,106887 1x0vA 354 6.25e+01 1mbe 53 6.29e+01 1mbe 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