# List of top-scoring protein chains for t06-80-60-80-str2+near-backbone-11-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 1sjyA 159 7.34e-03 d.113.1.1 98900 2b0vA 153 9.34e-02 1lo6A 223 1.12e-01 b.47.1.2 74143 1n08A 163 1.23e-01 b.43.5.1 79730 1w18A 493 1.38e-01 1eaxA 241 1.61e-01 b.47.1.2 64889 1os8A 223 2.19e-01 b.47.1.1 93481 1vcdA 126 3.41e-01 2fkbA 180 4.59e-01 1se8A 301 4.91e-01 b.40.4.3 105448 1shfA 59 5.52e-01 1bbzA b.34.2.1 24462 1y55X 126 5.65e-01 1sawA 225 5.73e-01 1jeyA 609 5.80e-01 1jeqA b.131.1.1,c.62.1.3 90370,90371 1vkyA 347 6.35e-01 e.53.1.1 108696 1vjvA 415 6.60e-01 d.3.1.9 108632 1zd0A 150 7.92e-01 1gtkA 313 8.80e-01 c.94.1.1,d.50.2.1 76346,76347 1vheA 373 9.22e-01 b.49.3.1,c.56.5.4 100669,100670 2cx1A 187 9.29e-01 1j83A 180 1.38e+00 b.18.1.12 66430 1t8tA 271 1.44e+00 c.37.1.5 106685 1kcfA 258 1.50e+00 a.140.2.1,c.55.3.7 68434,68435 1l1dA 152 1.54e+00 b.88.1.3 73452 1twyA 290 1.63e+00 1h8dH 260 1.63e+00 5ptp 1uf2A 1019 1.66e+00 e.28.1.2 99289 1seiA 130 1.67e+00 1seiA d.140.1.1 41463 1aoeA 192 1.68e+00 1aoeA c.71.1.1 34923 1vyoA 128 1.73e+00 3ullA 132 1.83e+00 3ullA b.40.4.3 25282 1wbiA 129 1.84e+00 1l6xA 207 1.99e+00 b.1.1.2,b.1.1.2 73642,73643 1sglA 209 2.06e+00 d.124.1.1 105536 1g2bA 62 2.21e+00 1tud b.34.2.1 24488 1p5vB 147 2.27e+00 b.2.3.2 87814 1jy5A 212 2.49e+00 d.124.1.1 71940 1yt8A 539 2.58e+00 1s3sG 127 2.67e+00 d.15.1.2 98457 1zanH 224 2.74e+00 1m1cA 680 2.78e+00 e.42.1.1 78395 1fonA 240 3.02e+00 5ptp b.47.1.2 26231 2azwA 148 3.10e+00 3pviA 157 3.27e+00 3pviA c.52.1.6 33300 2fvgA 340 3.28e+00 3dfr 162 3.33e+00 3dfr c.71.1.1 34880 1qwnA 1045 3.33e+00 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1vzqH 250 3.34e+00 1vc3B 97 3.36e+00 1w4rA 195 3.50e+00 1cjaA 342 3.69e+00 1cjaA d.144.1.3 41708 1vjfA 180 3.82e+00 d.116.1.1 100809 1jmuB 666 3.82e+00 1qlpA 394 4.20e+00 1ovaA e.1.1.1 42628 1ii7A 333 4.32e+00 1ii7A d.159.1.4 62415 2bbhA 269 4.39e+00 1qhlA 227 4.45e+00 1qhlA c.37.1.12 32382 2a7yA 83 4.59e+00 1x3eA 165 4.90e+00 1k8kA 418 4.95e+00 c.55.1.1,c.55.1.1 68305,68306 1wzoA 246 5.06e+00 1wb4A 297 5.08e+00 2dcnA 311 5.09e+00 1bf2 750 5.15e+00 1bf2 b.1.18.2,b.71.1.1,c.1.8.1 21860,27787,28774 1dleA 298 5.39e+00 1dleA b.47.1.2 26312 1xjvA 294 5.41e+00 1vioA 243 5.47e+00 d.265.1.3,d.66.1.5 100762,100763 1smxA 96 5.57e+00 b.40.4.5 105772 1mi8A 158 5.66e+00 b.86.1.2 91279 1bb9 115 5.72e+00 1bb9 b.34.2.1 24554 1fjgP 88 5.76e+00 1emwA d.27.1.1 38444 1h9mA 145 5.77e+00 1h9jA b.40.6.2,b.40.6.2 60833,60834 1wc3A 219 5.81e+00 1ve1A 304 5.84e+00 1kid 203 5.88e+00 1derA c.8.5.1 30771 2eveA 157 5.92e+00 1lktA 104 6.16e+00 1lktA b.90.1.1 28398 1iu4A 331 6.20e+00 d.3.1.8 71430 1kcvH 217 6.24e+00 b.1.1.1,b.1.1.2 72315,72316 1h9oA 112 6.41e+00 1qadA d.93.1.1 60837 1pht 85 6.41e+00 1ckaA b.34.2.1 24483 1p9bA 442 6.43e+00 c.37.1.10 94385 1qouA 181 6.45e+00 1qouA b.17.1.1 23707 1zvtA 256 6.54e+00 1igqA 62 6.95e+00 b.34.1.3 66130 2fd4A 122 7.15e+00 1ok0A 74 7.22e+00 b.5.1.1 93191 1lvoA 302 7.29e+00 b.47.1.4 74284 1g6gA 127 7.34e+00 1g6gA b.26.1.2 23916 2ey4C 82 7.39e+00 2fsjA 346 7.67e+00 1z52A 470 7.68e+00 2axoA 270 7.79e+00 2arcA 164 7.92e+00 2arcA b.82.4.1 28148 2a1vA 144 7.93e+00 1cghA 224 7.99e+00 1a7s b.47.1.2 26290 1p99A 295 8.02e+00 c.94.1.1 94384 1mqeA 207 8.02e+00 d.113.1.1 91394 1g38A 393 8.07e+00 2admA c.66.1.27 60235 1jhdA 396 8.11e+00 b.122.1.3,c.26.1.5 66712,66713 1vbvA 105 8.26e+00 1gppA 237 8.28e+00 b.86.1.2 76262 1eq9A 222 8.29e+00 5ptp b.47.1.2 26068 1xs5A 241 8.43e+00 1hbnC 248 8.44e+00 1mroC d.58.31.1 60902 1r26A 125 8.56e+00 c.47.1.1 96847 2ahmE 203 8.67e+00 1p32A 209 8.68e+00 1p32A d.25.1.1 38379 2gjgA 248 8.69e+00 1lmq 129 8.69e+00 3lzt d.2.1.2 36588 1dbxA 158 8.75e+00 1dbuA d.116.1.1 40928 1zpsA 138 8.99e+00 1oaoC 729 9.04e+00 e.26.1.3 86746 2g50A 530 9.09e+00 1dynA 125 9.17e+00 1dynA b.55.1.1 26955 1pot 325 9.24e+00 1pot c.94.1.1 35807 1ro2A 216 9.45e+00 d.264.1.2 97665 1gvkB 240 9.79e+00 b.47.1.2 70610 1iwdA 215 9.83e+00 d.3.1.1 83756 1qwtA 255 9.89e+00 b.26.1.3 96501 1bdfA 235 9.99e+00 1bdfA d.74.3.1,d.181.1.1 39727,42602 1neu 124 1.04e+01 1neu b.1.1.1 19704 1ex7A 186 1.06e+01 1gky c.37.1.1 59537 1kkhA 317 1.07e+01 d.14.1.5,d.58.26.3 72645,72646 1mexH 215 1.08e+01 b.1.1.1,b.1.1.2 91257,91258 1wdvA 152 1.10e+01 2bokA 241 1.10e+01 1ykdA 398 1.11e+01 2aegA 268 1.14e+01 2ebn 289 1.16e+01 2ebn c.1.8.5 28990 1a41 234 1.17e+01 1a41 d.163.1.2 42174 1ktbA 405 1.18e+01 b.71.1.1,c.1.8.1 72960,72961 1wznA 252 1.22e+01 1y7mA 164 1.26e+01 1ve2A 235 1.27e+01 1suwA 249 1.28e+01 e.52.1.1 106027 2fgeA 995 1.31e+01 1yloA 348 1.35e+01 1n0lA 224 1.35e+01 b.1.11.1,b.7.2.1 79744,79745 1g31A 111 1.36e+01 1g31A b.35.1.1 24656 1rmwA 212 1.37e+01 2cs3A 93 1.38e+01 1f7lA 121 1.41e+01 1f7lA d.150.1.2 59666 1uthA 315 1.41e+01 c.94.1.1 108032 1ifqA 138 1.42e+01 1ifqA d.110.4.1 62350 1vhrA 184 1.42e+01 1vhrA c.45.1.1 32651 1hyxH 224 1.44e+01 1igtB b.1.1.1,b.1.1.2 20167,21191 1gwmA 153 1.44e+01 b.18.1.19 83348 1elt 236 1.45e+01 5ptp b.47.1.2 26281 1twfI 122 1.46e+01 1ylqA 96 1.48e+01 1ncwH 222 1.51e+01 b.1.1.1,b.1.1.2 85555,85556 1sq9A 397 1.55e+01 b.69.4.1 105889 1ixmA 192 1.56e+01 1ixmA d.123.1.1 41114 1gqzA 274 1.56e+01 d.21.1.1,d.21.1.1 83311,83312 2c0nA 203 1.56e+01 1c8nA 276 1.58e+01 1smvA b.121.4.7 23308 1kk1A 410 1.60e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1uaiA 224 1.62e+01 b.29.1.18 107761 8dfr 189 1.62e+01 1aoeA c.71.1.1 34895 2avyM 117 1.62e+01 1ry9A 145 1.63e+01 d.198.1.1 98094 1wmhA 89 1.64e+01 1xiyA 182 1.64e+01 1gky 187 1.64e+01 1gky c.37.1.1 31839 1zrjA 50 1.65e+01 2fxqA 264 1.65e+01 1olmA 403 1.68e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1rurH 218 1.68e+01 b.1.1.1,b.1.1.2 97879,97880 1u00A 227 1.69e+01 1mai 131 1.72e+01 1mai b.55.1.1 26951 2cvxA 888 1.74e+01 1r8nA 185 1.74e+01 b.42.4.1 104851 2g6tA 306 1.75e+01 1ogaD 215 1.77e+01 b.1.1.1,b.1.1.2 86990,86991 1hztA 190 1.77e+01 1i9aA d.113.1.2 61459 1yw5A 177 1.80e+01 1kmvA 186 1.82e+01 c.71.1.1 72757 1xovA 326 1.82e+01 1pinA 163 1.82e+01 1pinA b.72.1.1,d.26.1.1 27802,38431 1h9dB 134 1.83e+01 2jhbA b.54.1.1 60822 1ir21 140 1.83e+01 1nkiA 135 1.83e+01 d.32.1.2 91941 1uedA 406 1.84e+01 a.104.1.1 99256 1rwjA 82 1.87e+01 a.138.1.1 105114 1t9fA 187 1.88e+01 b.42.6.1 106710 1uc2A 481 1.90e+01 d.261.1.1 99161 1tif 78 1.90e+01 1tif d.15.8.1 37836 2c12A 439 1.90e+01 1fkqA 124 1.92e+01 3lzt d.2.1.2 36601 1sek 378 1.92e+01 1sek e.1.1.1 42675 1l2mA 118 1.94e+01 d.89.1.4 77657 1cpt 412 1.96e+01 1cpt a.104.1.1 18968 1td4A 115 1.97e+01 1gttA 429 1.97e+01 d.177.1.1,d.177.1.1 70529,70530 1qexA 288 1.99e+01 1qexA b.32.1.1 24425 1vemA 516 1.99e+01 1x54A 434 1.99e+01 1vzoA 355 2.00e+01 d.144.1.7 108971 1xezA 721 2.00e+01 1yn8A 59 2.03e+01 1pcfA 66 2.05e+01 1pcfA d.18.1.1 38142 2faoA 309 2.05e+01 1nscA 390 2.07e+01 2qwc b.68.1.1 27591 1j98A 157 2.08e+01 1j98A d.185.1.2 62755 1o1yA 239 2.10e+01 c.23.16.1 86554 1uz8B 212 2.14e+01 b.1.1.1,b.1.1.2 108168,108169 2g09A 297 2.17e+01 1zhrA 238 2.19e+01 1yf2A 425 2.21e+01 1sf8A 126 2.23e+01 d.271.1.1 105472 2ajuH 219 2.24e+01 1vyrA 364 2.24e+01 c.1.4.1 108906 2gaxA 135 2.28e+01 1d4tA 104 2.29e+01 1d4tA d.93.1.1 40537 1a8d 452 2.29e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 1extA 162 2.30e+01 1extA g.24.1.1,g.24.1.1,g.24.1.1 44900,44901,44902 1x52A 124 2.31e+01 1zdrA 164 2.31e+01 1twuA 139 2.31e+01 d.32.1.8 107413 1v9fA 325 2.33e+01 d.265.1.3 108448 1jnyA 435 2.33e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1srqA 341 2.33e+01 e.55.1.1 105967 1xn5A 146 2.33e+01 1yarA 233 2.33e+01 1khdA 345 2.33e+01 a.46.2.1,c.27.1.1 77400,77401 1xcbA 211 2.34e+01 a.4.5.38,c.2.1.12 109552,109553 1yp2A 451 2.37e+01 1k6iA 352 2.38e+01 c.2.1.2 68223 1vkiA 181 2.39e+01 d.116.1.1 108664 1zkoA 136 2.40e+01 2dlbA 80 2.41e+01 1behA 187 2.44e+01 1a44 b.17.1.1 23700 1zhvA 134 2.44e+01 1kw4A 89 2.45e+01 a.60.1.2 73077 1k0iA 394 2.47e+01 c.3.1.2,d.16.1.2 67942,67943 2b82A 211 2.48e+01 1hh1A 143 2.48e+01 1gefA c.52.1.18 61036 1xniA 118 2.50e+01 1fr3A 67 2.50e+01 1fr3A b.40.6.1 25436 1iwlA 182 2.51e+01 b.125.1.1 83757 1jiwI 106 2.58e+01 1smpI b.61.2.1 63078 1g3p 217 2.60e+01 1g3p b.37.1.1,b.37.1.1 24788,24789 2amxA 376 2.61e+01 1r8oA 96 2.62e+01 b.42.4.1 104852 2a6aA 218 2.63e+01 1ro0A 216 2.64e+01 d.264.1.2 97664 1lk9A 448 2.64e+01 c.67.1.1 78057 1g8lA 411 2.65e+01 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1p42A 270 2.69e+01 d.14.1.7,d.14.1.7 87754,87755 1vybA 238 2.70e+01 d.151.1.1 108897 1mugA 168 2.71e+01 1mugA c.18.1.2 31030 1vhsA 175 2.73e+01 d.108.1.1 100698 1xgkA 352 2.76e+01 1xqaA 113 2.78e+01 1ujnA 348 2.80e+01 e.22.1.1 99460 2c78A 405 2.80e+01 2bycA 137 2.81e+01 1o57A 291 2.81e+01 a.4.5.40,c.61.1.1 92483,92484 1fyhB 229 2.82e+01 1jrhI b.1.2.1,b.1.2.1 22055,22056 2bz6H 254 2.86e+01 2essA 248 2.87e+01 1q45A 391 2.90e+01 c.1.4.1 95780 1y4tA 322 2.94e+01 2b4wA 315 2.94e+01 1rwzA 245 2.95e+01 d.131.1.2,d.131.1.2 98005,98006 1xweA 151 2.96e+01 2cb5A 453 2.98e+01 3gcb d.3.1.1 37035 1ll2A 333 2.99e+01 c.68.1.14 74005 1yrcA 414 3.04e+01 1xt5A 135 3.10e+01 1wdiA 345 3.11e+01 1gmxA 108 3.11e+01 c.46.1.3 65355 1tzyD 103 3.12e+01 a.22.1.1 107533 1luqA 127 3.14e+01 b.61.1.1 91128 1zj8A 566 3.16e+01 1wba 175 3.19e+01 1wba b.42.4.1 25591 1x6oA 174 3.20e+01 b.34.5.2,b.40.4.5 109493,109494 1uz5A 402 3.22e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1uv4A 293 3.22e+01 1k3xA 262 3.24e+01 a.156.1.2,b.113.1.1,g.39.1.8 77242,77243,77244 1szwA 379 3.26e+01 d.265.1.4 99047 2ar0A 541 3.26e+01 1jndA 420 3.26e+01 c.1.8.5,d.26.3.1 71757,71758 2c5qA 240 3.26e+01 2f2eA 146 3.27e+01 1b9oA 123 3.27e+01 3lzt d.2.1.2 36597 1f5vA 240 3.30e+01 1bkjA d.90.1.1 40255 1kgcD 206 3.31e+01 b.1.1.1,b.1.1.2 77384,77385 1r3eA 309 3.32e+01 b.122.1.1,d.265.1.2 96907,96908 1i0rA 169 3.33e+01 1i0rA b.45.1.2 61489 1q52A 314 3.37e+01 c.14.1.3 95846 1r6jA 82 3.38e+01 b.36.1.1 97151 1a70 97 3.38e+01 1awd d.15.4.1 37678 1z9lA 128 3.39e+01 1l6wA 220 3.41e+01 c.1.10.1 73632 2bkdN 134 3.42e+01 1u3dA 509 3.42e+01 a.99.1.1,c.28.1.1 107638,107639 1jr2A 286 3.45e+01 c.113.1.1 67111 1yqfA 203 3.47e+01 1gk8I 140 3.48e+01 d.73.1.1 65242 1bkb 136 3.49e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 2agmA 167 3.50e+01 1hm9A 468 3.51e+01 b.81.1.4,c.68.1.5 65866,65867 2bxxA 134 3.52e+01 1rz2A 254 3.52e+01 b.100.1.1 105130 1dkzA 219 3.56e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1tl9A 339 3.56e+01 1tul 108 3.57e+01 1tul b.85.5.1 28373 1l8bA 190 3.58e+01 d.86.1.1 73683 1m93B 245 3.59e+01 1c4eA 35 3.61e+01 1c4eA g.3.4.1 44080 1w1oA 534 3.62e+01 d.58.32.4,d.145.1.1 109071,109072 2c3gA 98 3.62e+01 1bdb 277 3.62e+01 1bdb c.2.1.2 29874 1gutA 68 3.63e+01 b.40.6.1 65576 1cfr 285 3.67e+01 1cfr c.52.1.7 33312 1nz0A 118 3.68e+01 d.14.1.2 86433 2g1lA 104 3.71e+01 1tljA 213 3.73e+01 d.282.1.1 107126 2bgcA 238 3.79e+01 1mzyA 333 3.80e+01 b.6.1.3,b.6.1.3 103848,103849 1z02A 446 3.86e+01 1bg6 359 3.88e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 1xt8A 292 3.90e+01 1mkfA 382 3.91e+01 b.116.1.1 79232 1o7nB 194 3.94e+01 d.17.4.4 81164 1bg2 325 3.97e+01 1bg2 c.37.1.9 32189 1nz6A 101 3.97e+01 a.2.3.1 86441 2b06A 155 3.98e+01 1vqoI 162 3.99e+01 1w7lA 422 4.02e+01 c.67.1.1 109226 1ucdA 190 4.03e+01 d.124.1.1 107767 1dpo 223 4.04e+01 5ptp b.47.1.2 25975 1ej6B 1275 4.04e+01 i.7.1.1 45968 1c7sA 858 4.06e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21812,22408,29011,40410 1w4vA 119 4.08e+01 1qvcA 145 4.09e+01 3ullA b.40.4.3 25284 1fsgA 233 4.10e+01 1qk3A c.61.1.1 34029 1rfkA 98 4.14e+01 1f0xA 571 4.17e+01 1f0xA d.58.32.2,d.145.1.1 39483,41746 1j1nA 492 4.20e+01 c.94.1.1 83978 1hj8A 222 4.22e+01 b.47.1.2 65844 1r44A 202 4.24e+01 d.65.1.4 104787 1w6vA 141 4.26e+01 1mqiA 263 4.28e+01 c.94.1.1 91398 1sg5A 86 4.30e+01 1h8eG 272 4.31e+01 1e79G c.49.2.1 60756 1vlpA 441 4.33e+01 d.41.2.2,d.41.2.3 108840,108841 2fz4A 237 4.34e+01 1y10A 407 4.42e+01 2f4qA 346 4.43e+01 2coaA 125 4.43e+01 1wxrA 1048 4.47e+01 2bgiA 272 4.48e+01 1ktgA 138 4.49e+01 d.113.1.1 72972 2fy7A 287 4.50e+01 1omoA 322 4.53e+01 c.2.1.13 104017 1znf 27 4.56e+01 g.37.1.1 45036 1kjkA 64 4.59e+01 d.10.1.4 72613 1srvA 145 4.61e+01 1derA c.8.5.1 30817 1syxB 86 4.63e+01 1zedA 484 4.64e+01 2an9A 207 4.65e+01 1yt5A 258 4.65e+01 1v8yA 170 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