# List of top-scoring protein chains for t04-100-30-n_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 1v7lA 163 1.22e-04 1nbwA 607 2.66e-02 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 2d0oA 610 1.38e-01 1iz5A 249 1.45e-01 d.131.1.2,d.131.1.2 83834,83835 3cox 507 2.50e-01 1b8sA c.3.1.2,d.16.1.1 30332,37863 1r6xA 395 3.48e-01 b.122.1.3,c.26.1.5 97167,97168 2gp4A 628 3.74e-01 1jztA 246 3.79e-01 c.104.1.1 63319 2ganA 190 4.06e-01 1ln1A 214 4.18e-01 d.129.3.2 74038 1cs1A 386 4.20e-01 1ibjA c.67.1.3 34399 2d13A 227 4.32e-01 1aquA 297 4.48e-01 1aquA c.37.1.5 31942 1jbkA 195 4.68e-01 c.37.1.20 71631 2fe7A 166 4.70e-01 2gupA 292 4.85e-01 2fdrA 229 5.01e-01 2beiA 170 6.93e-01 1g8fA 511 7.33e-01 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 2f9sA 151 7.78e-01 1tlfA 301 7.95e-01 1tlfA c.93.1.1 35687 1f2vA 219 8.24e-01 1f2vA c.23.17.1 59627 2gbp 309 8.38e-01 1gca c.93.1.1 35657 1lldA 319 9.22e-01 3ldh c.2.1.5,d.162.1.1 30177,42144 1qmeA 702 9.54e-01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1yavA 159 1.03e+00 1g2iA 166 1.09e+00 1g2iA c.23.16.2 31438 1u04A 771 1.11e+00 b.34.14.1,c.55.3.10 107539,107540 1jyeA 349 1.18e+00 c.93.1.1 67455 1n0uA 842 1.18e+00 b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 79757,79758,79759,79760,79761 2prd 174 1.18e+00 2prd b.40.5.1 25435 1zymA 258 1.19e+00 1zymA a.60.10.1,c.8.1.2 18110,30705 1yrvA 169 1.21e+00 1nnfA 309 1.23e+00 c.94.1.1 85903 1pxwA 128 1.24e+00 d.79.3.1 95305 1jc4A 148 1.26e+00 1jc4A d.32.1.4 62863 1o58A 303 1.26e+00 c.79.1.1 92491 1uarA 285 1.32e+00 c.46.1.2,c.46.1.2 107762,107763 1wraA 308 1.38e+00 1gr3A 160 1.42e+00 b.22.1.1 65476 1pfkA 320 1.51e+00 3pfk c.89.1.1 35575 1gca 309 1.57e+00 1gca c.93.1.1 35659 1uxtA 501 1.62e+00 c.82.1.1 108125 1amf 233 1.68e+00 1wod c.94.1.1 35833 1j05B 121 1.69e+00 b.1.1.1 90736 1dosA 358 1.84e+00 1dosA c.1.10.2 29175 1uwzA 136 1.87e+00 c.97.1.1 108081 1rxyA 253 1.89e+00 c.56.2.1 98065 1sdsA 117 1.92e+00 d.79.3.1 105439 1vbkA 307 2.01e+00 1yjsA 419 2.02e+00 1ufoA 238 2.07e+00 c.69.1.27 99344 1r6lA 239 2.16e+00 d.14.1.4,d.101.1.1 97153,97154 1ru8A 232 2.18e+00 c.26.2.1 97849 1pmd 675 2.25e+00 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37491,37492,42562,42771 1m1nB 522 2.28e+00 c.92.2.3 78418 1lx7A 253 2.30e+00 c.56.2.1 74329 1xfdA 723 2.31e+00 2gwgA 350 2.31e+00 1o8xA 146 2.34e+00 c.47.1.10 86681 1vi4A 174 2.43e+00 c.8.7.1 100731 1fc6A 388 2.43e+00 1fc6A b.36.1.3,c.14.1.2 64738,64739 1a6wH 120 2.44e+00 1mfa b.1.1.1 20253 1abrA 251 2.49e+00 1mrj d.165.1.1 42196 1li4A 432 2.55e+00 c.2.1.4,c.23.12.3 84616,84617 1xvaA 292 2.55e+00 1xvaA c.66.1.5 34183 1nhkL 144 2.63e+00 1npk d.58.6.1 39142 1vi2A 300 2.70e+00 c.2.1.7,c.58.1.5 100726,100727 1in4A 334 2.74e+00 1hqcA a.4.5.11,c.37.1.20 62597,62598 1nbwB 117 2.80e+00 c.51.3.2 80396 1oaoC 729 2.80e+00 e.26.1.3 86746 2atrA 138 2.82e+00 1xbiA 120 2.93e+00 1gheA 177 2.93e+00 d.108.1.1 76222 1d2oA 187 2.94e+00 1d2oA b.3.5.1,b.3.5.1 22625,22626 1h7mA 102 2.99e+00 d.79.3.1 83485 1kl1A 419 3.00e+00 c.67.1.4 72663 1mrp 309 3.02e+00 1mrp c.94.1.1 35796 1v37A 177 3.04e+00 1i1qA 520 3.09e+00 1qdlA d.161.1.1 61543 1s6yA 450 3.16e+00 c.2.1.5,d.162.1.2 105314,105315 1v8bA 479 3.17e+00 1sheA 103 3.19e+00 d.274.1.1 105551 1ek6A 348 3.22e+00 1xel c.2.1.2 29800 1ls1A 295 3.32e+00 a.24.13.1,c.37.1.10 78170,78171 1k78A 149 3.36e+00 a.4.1.5,a.4.1.5 68255,68256 1zemA 262 3.40e+00 1o08A 221 3.44e+00 c.108.1.6 86525 2aa4A 289 3.47e+00 1jtkA 136 3.49e+00 c.97.1.1 71862 1g57A 217 3.50e+00 1g57A d.115.1.2 60253 3aprE 325 3.52e+00 2er7E b.50.1.2 26820 1wod 233 3.62e+00 1wod c.94.1.1 35832 1xebA 150 3.67e+00 1gp1A 198 3.78e+00 1gp1A c.47.1.10 33059 1p42A 270 3.86e+00 d.14.1.7,d.14.1.7 87754,87755 2cvbA 188 3.93e+00 1vkfA 188 3.96e+00 c.1.29.1 108656 1cjcA 460 4.01e+00 1cjcA c.3.1.1,c.4.1.1 30319,30604 1g0oA 283 4.03e+00 1ybvA c.2.1.2 60181 1mrzA 293 4.06e+00 b.43.5.1,c.26.1.3 91452,91453 1rhs 296 4.07e+00 1rhs c.46.1.2,c.46.1.2 32703,32704 1e44B 96 4.08e+00 1e44B b.101.1.1 59220 1qksA 567 4.10e+00 1qksA a.3.1.2,b.70.2.1 15951,27710 1q0rA 298 4.18e+00 c.69.1.28 95508 2apr 325 4.21e+00 2er7E b.50.1.2 26819 1hw1A 239 4.22e+00 1e2xA a.4.5.6,a.78.1.1 16111,18441 1zbmA 280 4.22e+00 1yqzA 438 4.28e+00 2bibA 547 4.33e+00 2b5gA 171 4.35e+00 1tg6A 277 4.39e+00 1ru3A 732 4.47e+00 e.26.1.3 97835 1st9A 143 4.73e+00 c.47.1.10 98987 1x1iA 752 4.90e+00 2ng1 293 5.05e+00 1ng1 a.24.13.1,c.37.1.10 16962,32273 1oaqH 121 5.10e+00 b.1.1.1 92707 1zsoA 164 5.12e+00 1pwgA 349 5.18e+00 e.3.1.1 104340 1rifA 282 5.22e+00 c.37.1.23 97507 1sdeA 347 5.26e+00 1zbfA 142 5.32e+00 2fvgA 340 5.33e+00 1tksA 204 5.36e+00 d.115.1.2 107114 3pte 349 5.38e+00 3pte e.3.1.1 42687 1syxB 86 5.41e+00 2pfkA 320 5.42e+00 3pfk c.89.1.1 35577 1bxoA 323 5.45e+00 2er7E b.50.1.2 26805 1wwrA 171 5.46e+00 1i7qA 519 5.56e+00 1qdlA d.161.1.1 61901 1mx3A 347 5.58e+00 c.2.1.4,c.23.12.1 79638,79639 1yqsA 349 5.60e+00 1in6A 334 5.60e+00 1hqcA a.4.5.11,c.37.1.20 62601,62602 1w36D 608 5.62e+00 1wq3A 322 5.64e+00 1w99A 558 5.74e+00 1wn5A 130 5.75e+00 2f8aA 208 5.78e+00 1hzpA 335 5.82e+00 1hn9A c.95.1.2,c.95.1.2 61455,61456 1mplA 349 5.97e+00 e.3.1.1 79387 2gasA 307 6.00e+00 1u9cA 224 6.13e+00 1u6eA 335 6.22e+00 1hvbA 349 6.23e+00 3pte e.3.1.1 42686 1mkyA 439 6.28e+00 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1z1dA 103 6.29e+00 1k92A 455 6.43e+00 c.26.2.1,d.210.1.1 68325,68326 2a4dA 160 6.49e+00 1w41A 101 6.52e+00 1uz8B 212 6.65e+00 b.1.1.1,b.1.1.2 108168,108169 1x9pA 523 6.72e+00 1vc3B 97 6.74e+00 1m22A 503 6.92e+00 c.117.1.1 78464 1je0A 236 6.94e+00 c.56.2.1 66581 2gn4A 344 6.97e+00 1egaA 301 6.99e+00 1egaA c.37.1.8,d.52.3.1 32150,38836 1ve5A 311 7.07e+00 2aamA 309 7.08e+00 1w2wB 191 7.16e+00 2cveA 191 7.24e+00 1kb0A 677 7.29e+00 a.3.1.6,b.70.1.1 68378,68379 1o91A 178 7.30e+00 b.22.1.1 92656 1pjxA 314 7.36e+00 b.68.6.1 104167 1gz6A 319 7.39e+00 c.2.1.2 76410 1xn9A 101 7.45e+00 2f06A 144 7.59e+00 1dar 691 7.61e+00 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1 25707,32142,37547,39300 2bjrA 368 7.62e+00 1xwfA 431 7.65e+00 1pwhA 327 7.72e+00 c.79.1.1 95224 1gof 639 7.73e+00 1gof b.1.18.2,b.18.1.1,b.69.1.1 21807,23709,27631 2fy6A 143 7.76e+00 1gvfA 286 7.76e+00 c.1.10.2 70599 1wr7A 41 7.76e+00 2fhzB 108 7.77e+00 1chmA 401 7.77e+00 1chmA c.55.2.1,d.127.1.1 33545,41142 6paxA 133 7.85e+00 6paxA a.4.1.5,a.4.1.5 64758,64759 1evlA 401 7.85e+00 1qf6A c.51.1.1,d.104.1.1 33202,40751 1i12A 160 7.86e+00 1i21A d.108.1.1 61515 1u6dX 308 7.88e+00 1zgkA 308 7.89e+00 1i1dA 161 7.94e+00 1i21A d.108.1.1 61526 1ockA 412 8.02e+00 c.117.1.1 86802 1zatA 250 8.08e+00 1qk8A 146 8.11e+00 1ewxA c.47.1.10 33061 1oniA 137 8.11e+00 d.79.1.1 87144 1x3zA 335 8.18e+00 2fywA 267 8.19e+00 1q40B 219 8.26e+00 d.17.4.2 95771 1sxvA 172 8.30e+00 1mdbA 539 8.31e+00 e.23.1.1 79008 2a8kA 108 8.47e+00 1c1yB 77 8.60e+00 1c1yB d.15.1.5 37618 1ja9A 274 8.61e+00 c.2.1.2 62817 2fp8A 322 8.77e+00 1e1aA 314 8.93e+00 1e1aA b.68.6.1 59155 1ni5A 433 8.93e+00 c.26.2.5,d.229.1.1 80533,80534 1twiA 434 9.04e+00 b.49.2.3,c.1.6.1 107399,107400 1j5xA 342 9.08e+00 c.80.1.1 71591 1xkwA 665 9.20e+00 1vddA 228 9.23e+00 e.49.1.1 108519 1nlbH 218 9.30e+00 b.1.1.1,b.1.1.2 80621,80622 2czlA 272 9.31e+00 1d4fA 431 9.35e+00 1b3rA c.2.1.4,c.23.12.3 30110,31370 1qpcA 279 9.42e+00 1fgkA d.144.1.7 41685 1qahA 136 9.49e+00 d.79.1.1 96338 1okgA 373 9.49e+00 c.46.1.2,c.46.1.2,d.26.1.3 93250,93251,93252 1kid 203 9.56e+00 1derA c.8.5.1 30771 1jpaA 312 9.60e+00 d.144.1.7 67011 1dp4A 435 9.68e+00 1dp4A c.93.1.1 35710 1neu 124 9.74e+00 1neu b.1.1.1 19704 1g3mA 294 9.78e+00 c.37.1.5 83268 1wvfA 520 9.80e+00 2bu3A 254 9.86e+00 1nox 205 9.88e+00 1nox d.90.1.1 40242 1mai 131 9.97e+00 1mai b.55.1.1 26951 1odkA 235 9.98e+00 c.56.2.1 86863 2fhi 147 1.00e+01 1fit d.13.1.1 37505 2pth 193 1.01e+01 2pth c.56.3.1 33793 1j0aA 325 1.01e+01 c.79.1.1 83871 2esrA 177 1.02e+01 1ne2A 200 1.02e+01 c.66.1.32 85586 1vl2A 421 1.02e+01 c.26.2.1,d.210.1.1 108708,108709 1g8yA 279 1.03e+01 1g8yA c.37.1.11 32302 2g64A 140 1.04e+01 1r5tA 142 1.04e+01 c.97.1.1 104812 1ooeA 236 1.05e+01 c.2.1.2 87196 1b66A 140 1.06e+01 1b66A d.96.1.2 40657 1k0wA 231 1.06e+01 c.74.1.1 77220 1u9iA 519 1.06e+01 1uldA 150 1.07e+01 b.29.1.3 99545 1b35A 260 1.07e+01 1b35A b.121.4.1 23333 1wwkA 307 1.08e+01 1s0uA 408 1.08e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1bd3A 243 1.10e+01 1bd3A c.61.1.1 34098 1xf1A 926 1.11e+01 2b33A 140 1.12e+01 1vkyA 347 1.13e+01 e.53.1.1 108696 1ls6A 295 1.13e+01 c.37.1.5 91115 1ujcA 161 1.14e+01 2arkA 188 1.14e+01 2fr1A 486 1.16e+01 1bf6A 291 1.16e+01 1pscA c.1.9.3 29065 1ixcA 294 1.16e+01 a.4.5.37,c.94.1.1 83764,83765 1ycoA 279 1.16e+01 1o5oA 221 1.19e+01 c.61.1.1 92509 2ts1 419 1.19e+01 2ts1 c.26.1.1 31564 1k32A 1045 1.23e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1r3eA 309 1.25e+01 b.122.1.1,d.265.1.2 96907,96908 1wviA 257 1.25e+01 1pk6A 133 1.26e+01 b.22.1.1 94801 1u2cA 246 1.26e+01 b.1.6.2,d.272.1.1 107610,107611 1iy8A 267 1.27e+01 c.2.1.2 83774 1ofdA 1520 1.28e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1q1gA 276 1.28e+01 c.56.2.1 95574 3thiA 371 1.30e+01 2thiA c.94.1.1 35792 1xrtA 467 1.31e+01 1wwzA 159 1.32e+01 1qgdA 662 1.32e+01 c.36.1.6,c.36.1.10,c.48.1.1 88367,88368,88369 1nrfA 262 1.32e+01 e.3.1.1 92086 1k4iA 233 1.32e+01 d.115.1.2 72056 1sffA 426 1.33e+01 c.67.1.4 105482 2cw9A 194 1.33e+01 1nlfA 279 1.33e+01 c.37.1.11 85850 1b7yB 785 1.34e+01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16301,16302,25312,39311,40780,41456 1m4iA 181 1.34e+01 d.108.1.1 74457 1ojrA 274 1.34e+01 c.74.1.1 93147 2es9A 115 1.34e+01 8acn 754 1.35e+01 1amj c.8.2.1,c.83.1.1 30724,35400 1yr0A 175 1.35e+01 1whzA 70 1.35e+01 2b4gA 317 1.35e+01 2gpyA 233 1.37e+01 1ctt 294 1.37e+01 1ctt c.97.1.1,c.97.1.1 36022,36023 1r2mA 71 1.38e+01 b.138.1.1 96871 2b97A 71 1.38e+01 1z5vA 474 1.39e+01 1fmb 104 1.39e+01 1fmb b.50.1.1 26777 1rfeA 162 1.40e+01 1rpnA 335 1.44e+01 c.2.1.2 97708 1s7kA 182 1.45e+01 2bsxA 253 1.46e+01 1jftA 340 1.46e+01 a.35.1.5,c.93.1.1 66652,66653 1kblA 873 1.48e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1w96A 554 1.48e+01 1e4mM 501 1.50e+01 1e70M c.1.8.4 59226 1u53A 196 1.50e+01 1e5mA 416 1.51e+01 1dd8A c.95.1.1,c.95.1.1 58973,58974 1j7dA 145 1.52e+01 1jatB d.20.1.1 62680 1nr0A 611 1.52e+01 b.69.4.1,b.69.4.1 86078,86079 1dpuA 99 1.52e+01 1dpuA a.4.5.16 16150 2cayA 145 1.54e+01 1q7fA 286 1.55e+01 b.68.9.1 96036 1xs5A 241 1.56e+01 1gnxA 479 1.56e+01 c.1.8.4 76241 1byrA 155 1.56e+01 1byrA d.136.1.1 41450 1hf2A 210 1.57e+01 1hf2A b.80.3.1,c.102.1.1 60992,60993 1h4vB 421 1.58e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1ywnA 316 1.59e+01 1lgpA 116 1.60e+01 b.26.1.2 73890 1j8mF 297 1.60e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1xfoA 357 1.60e+01 1fo8A 343 1.62e+01 1foaA c.68.1.10 59927 1hm9A 468 1.62e+01 b.81.1.4,c.68.1.5 65866,65867 1p4cA 380 1.63e+01 c.1.4.1 94100 1m2kA 249 1.63e+01 c.31.1.5 84754 1kpeA 126 1.65e+01 1kpf d.13.1.1 37508 1w9gA 104 1.65e+01 1qznA 173 1.67e+01 b.2.2.2 104669 1wejH 223 1.68e+01 1igtB b.1.1.1,b.1.1.2 20361,21353 2c1gA 431 1.71e+01 1g6uA 48 1.71e+01 1g6uA k.9.1.1 46425 1jcfA 344 1.71e+01 c.55.1.1,c.55.1.1 62878,62879 1b4vA 504 1.71e+01 1b8sA c.3.1.2,d.16.1.1 30334,37865 1zrn 232 1.73e+01 1qq5A c.108.1.1 43323 2c1iA 431 1.73e+01 1dbwA 126 1.74e+01 1dbwA c.23.1.1 31095 1iv3A 152 1.74e+01 d.79.5.1 76828 1tufA 434 1.74e+01 b.49.2.3,c.1.6.1 107335,107336 2a3nA 355 1.75e+01 1npeA 267 1.76e+01 b.68.5.1 92032 2c71A 216 1.77e+01 1mml 265 1.77e+01 1mml e.8.1.2 43015 1wi6A 88 1.78e+01 1q47A 495 1.79e+01 b.69.12.1 104532 2f9fA 177 1.80e+01 1zv9A 172 1.80e+01 1vqoT 120 1.80e+01 1jj2S 119 1.80e+01 1ffkQ b.34.5.1 63104 2fnjA 226 1.81e+01 1m2eA 135 1.82e+01 c.23.1.5 78478 2fp7B 172 1.83e+01 1mxtA 504 1.83e+01 c.3.1.2,d.16.1.1 79671,79672 1n4wA 504 1.84e+01 c.3.1.2,d.16.1.1 91676,91677 1gcoA 261 1.84e+01 1ybvA c.2.1.2 29884 1ujnA 348 1.84e+01 e.22.1.1 99460 2biwA 490 1.84e+01 1e0cA 271 1.85e+01 1e0cA c.46.1.2,c.46.1.2 32717,32718 1ve6A 582 1.86e+01 1e4fT 419 1.87e+01 1e4fT c.55.1.1,c.55.1.1 33453,33454 1xsnA 335 1.89e+01 1vkkA 154 1.90e+01 d.109.1.2 108669 1ptmA 329 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