# List of top-scoring protein chains for t04-100-30-dssp-ebghstl-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 1wqaA 455 2.51e-02 1o2dA 371 1.76e-01 e.22.1.2 86591 2dbbA 151 1.87e-01 1ejeA 192 1.99e-01 1ejeA b.45.1.2 25757 1kv7A 488 2.40e-01 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 1vp4A 425 5.34e-01 1aszB 490 8.11e-01 1b8aA b.40.4.1,d.104.1.1 25241,40762 1e9rA 437 9.08e-01 c.37.1.11 64827 1gegA 256 1.01e+00 1ybvA c.2.1.2 29888 2f5gA 133 1.09e+00 1lc5A 364 1.31e+00 c.67.1.1 73827 1q7zA 566 1.60e+00 c.1.21.2,c.1.26.1 96090,96091 1v04A 355 1.63e+00 b.68.6.2 100240 1aisB 200 1.63e+00 1aisB a.74.1.2,a.74.1.2 18384,18385 1pjqA 457 1.91e+00 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 1sviA 195 1.95e+00 c.37.1.8 106048 1ymqA 261 2.01e+00 1wdiA 345 2.12e+00 1amy 403 2.19e+00 1jdc b.71.1.1,c.1.8.1 27799,28786 1kid 203 2.30e+00 1derA c.8.5.1 30771 2fbiA 142 2.41e+00 1vheA 373 2.60e+00 b.49.3.1,c.56.5.4 100669,100670 1qysA 106 2.68e+00 k.41.1.1 96603 1zpvA 91 2.68e+00 1phk 298 2.74e+00 1cdkA d.144.1.7 41635 2fcr 173 3.01e+00 1rcf c.23.5.1 31151 1wr8A 231 3.20e+00 2akzA 439 3.30e+00 2bynA 227 3.45e+00 1tbd 134 3.59e+00 2tbd d.89.1.1 40240 2d1sA 548 3.68e+00 1avaA 403 3.91e+00 1jdc b.71.1.1,c.1.8.1 27797,28784 1w1wA 430 3.92e+00 1kblA 873 4.41e+00 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 2b3nA 159 4.68e+00 1v60A 123 4.76e+00 2arhA 203 4.91e+00 1lvaA 258 5.06e+00 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 2b0jA 358 5.24e+00 4enl 436 5.70e+00 4enl c.1.11.1,d.54.1.1 29202,38846 2fckA 181 5.76e+00 2a5dA 175 5.95e+00 1qo0D 196 5.98e+00 1qo0D c.23.1.3 31125 1ha3A 405 6.03e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 3chbD 104 6.26e+00 3chbD b.40.2.1 24970 1fjgP 88 6.42e+00 1emwA d.27.1.1 38444 1lvwA 295 6.56e+00 c.68.1.6 84723 1hgxA 183 6.73e+00 1tc1A c.61.1.1 34027 1pvvA 315 6.84e+00 c.78.1.1,c.78.1.1 95190,95191 1wleA 501 6.84e+00 2c78A 405 6.93e+00 2cxxA 190 6.95e+00 2g5cA 281 7.02e+00 1uirA 314 7.10e+00 c.66.1.17 99429 1x7oA 287 7.15e+00 1wwiA 148 7.31e+00 1ww9A 392 7.32e+00 1exmA 405 7.59e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1vjeA 166 7.63e+00 d.185.1.2 100807 1xfoA 357 7.79e+00 1jv2B 692 7.90e+00 b.1.15.1,c.62.1.1,d.200.1.1,g.3.11.6,g.3.11.6 67338,67339,67340,67341,67342 1h70A 255 8.47e+00 1h70A d.126.1.3 60711 1ht6A 405 8.50e+00 b.71.1.1,c.1.8.1 83629,83630 1kafA 108 8.68e+00 d.199.1.1 68372 2al2A 436 8.73e+00 1gveA 327 8.91e+00 c.1.7.1 70597 1te6A 439 9.25e+00 c.1.11.1,d.54.1.1 106797,106798 1ooeA 236 9.29e+00 c.2.1.2 87196 1oneA 436 9.39e+00 4enl c.1.11.1,d.54.1.1 29200,38844 1c7qA 445 9.79e+00 2pgi c.80.1.2 35307 1oj4A 283 9.87e+00 d.14.1.5,d.58.26.5 93083,93084 1k2xB 143 1.01e+01 1tl0D 103 1.02e+01 1iyeA 309 1.03e+01 e.17.1.1 83786 1y89A 238 1.04e+01 1kit 757 1.06e+01 1kit b.29.1.8,b.29.1.8,b.68.1.1 24272,24273,27616 1f2tB 148 1.06e+01 1f2tB 1innA 166 1.08e+01 1j98A d.185.1.2 62608 1e5eA 404 1.11e+01 1ibjA c.67.1.3 59265 1i1kA 309 1.12e+01 1daaA e.17.1.1 61533 1p8kZ 254 1.13e+01 d.95.2.1,d.95.2.1 94361,94362 2al1A 436 1.13e+01 1u1hA 765 1.13e+01 c.1.22.2,c.1.22.2 107580,107581 1jmtA 104 1.14e+01 d.58.7.3 63180 1w0pA 781 1.15e+01 b.29.1.8,b.29.1.8,b.68.1.1 109038,109039,109040 1xn7A 78 1.17e+01 1pdz 434 1.19e+01 4enl c.1.11.1,d.54.1.1 29215,38859 1ow1A 195 1.20e+01 b.131.1.3 93625 2ffuA 501 1.20e+01 3ullA 132 1.27e+01 3ullA b.40.4.3 25282 1zip 217 1.29e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1tqjA 230 1.35e+01 c.1.2.2 107228 1kq3A 376 1.35e+01 e.22.1.2 68790 1j0dA 341 1.36e+01 c.79.1.1 83902 1xbsA 149 1.39e+01 1rz1A 161 1.39e+01 b.45.1.2 98124 1uc8A 280 1.42e+01 c.30.1.6,d.142.1.7 99165,99166 1a6q 382 1.45e+01 1a6q a.159.1.1,d.219.1.1 75801,75802 1o7qA 289 1.46e+01 c.68.1.9 92626 1gx4A 289 1.47e+01 c.68.1.9 83362 1zarA 282 1.49e+01 1ryiA 382 1.52e+01 1gtmA 419 1.55e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1yacA 208 1.55e+01 1yacA c.33.1.3 31757 2aebA 322 1.56e+01 1ng4A 390 1.56e+01 c.3.1.2,d.16.1.3 85666,85667 1tqmA 282 1.56e+01 a.4.5.56,d.144.1.9 107236,107237 1fg7A 356 1.58e+01 1gewA c.67.1.1 59819 1yyvA 131 1.61e+01 1f2dA 341 1.63e+01 1f2dA c.79.1.1 35298 1k32A 1045 1.64e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1u0tA 307 1.64e+01 e.52.1.1 107567 1ursA 402 1.66e+01 c.94.1.1 99833 1o57A 291 1.69e+01 a.4.5.40,c.61.1.1 92483,92484 1p4xA 250 1.76e+01 a.4.5.28,a.4.5.28 87784,87785 1bqk 124 1.78e+01 1bqk b.6.1.1 22889 1xkiA 162 1.83e+01 1zin 217 1.84e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1u7lA 392 1.86e+01 1bykA 255 1.87e+01 1bykA c.93.1.1 35706 1z7dA 433 1.94e+01 1ccwB 483 1.95e+01 1cb7B c.1.19.2 29646 1rkuA 206 1.97e+01 c.108.1.11 97627 1xhbA 472 1.97e+01 1lci 550 2.00e+01 1lci e.23.1.1 43349 1zd3A 555 2.04e+01 1cv8 174 2.04e+01 1cv8 d.3.1.1 37089 1vj5A 555 2.05e+01 c.108.1.2,c.69.1.11 100799,100800 2cw5A 255 2.05e+01 1yovA 537 2.07e+01 1fmcA 255 2.14e+01 1cydA c.2.1.2 29856 1yp2A 451 2.17e+01 1v6tA 255 2.20e+01 1k0eA 453 2.24e+01 d.161.1.1 67938 1j5yA 187 2.26e+01 a.4.5.1,d.94.2.1 71592,71593 1r5tA 142 2.27e+01 c.97.1.1 104812 1m6sA 347 2.27e+01 c.67.1.1 78701 1jg8A 347 2.27e+01 1jg8A c.67.1.1 62946 1vl6A 388 2.27e+01 c.2.1.7,c.58.1.3 108724,108725 1blxA 326 2.32e+01 1hcl d.144.1.7 41596 1xccA 220 2.37e+01 1dc1A 323 2.38e+01 1dc1A c.52.1.11 33321 1nrzA 164 2.39e+01 c.38.1.1 86131 1yavA 159 2.39e+01 1kv8A 216 2.40e+01 c.1.2.3 73054 2bznA 351 2.42e+01 1w6uA 302 2.47e+01 2ethA 154 2.50e+01 1q6oA 216 2.50e+01 c.1.2.3 95986 2bfwA 200 2.50e+01 2atxA 194 2.54e+01 1ipaA 274 2.54e+01 c.116.1.1,d.79.3.3 71254,71255 1gpiA 431 2.61e+01 b.29.1.10 65450 1rm8A 169 2.63e+01 d.92.1.11 97660 1iupA 282 2.63e+01 c.69.1.10 76815 2fuvA 549 2.64e+01 1rpxA 230 2.65e+01 1rpxA c.1.2.2 28536 1zczA 464 2.65e+01 1uk8A 282 2.66e+01 c.69.1.10 107907 2bo4A 397 2.67e+01 1fvgA 199 2.70e+01 1fvaA d.58.28.1 39408 2cuaA 135 2.72e+01 2cuaA b.6.1.2 23039 1b6rA 355 2.75e+01 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28241,31648,41493 1y0nA 78 2.75e+01 1v8gA 329 2.78e+01 a.46.2.1,c.27.1.1 100505,100506 2a1iA 146 2.80e+01 1u3eM 174 2.82e+01 d.4.1.3,d.285.1.1 107640,107641 1w77A 228 2.83e+01 1rq2A 382 2.86e+01 c.32.1.1,d.79.2.1 105048,105049 1srvA 145 2.87e+01 1derA c.8.5.1 30817 1on2A 142 2.88e+01 a.4.5.24,a.76.1.1 87103,87104 1cvrA 435 2.89e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 1wf3A 301 2.92e+01 1t9bA 677 2.93e+01 1t3tA 1303 2.95e+01 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 1dik 874 2.96e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1rfmA 344 2.96e+01 c.122.1.1 97385 1hdr 244 2.97e+01 1dhr c.2.1.2 29837 2f4nA 273 3.01e+01 1yloA 348 3.03e+01 2c0nA 203 3.04e+01 1gewA 356 3.07e+01 1gewA c.67.1.1 60470 2c6qA 351 3.12e+01 2fy7A 287 3.14e+01 2c1cA 312 3.15e+01 1u8sA 192 3.16e+01 d.58.18.5,d.58.18.5 107737,107738 1eudA 311 3.18e+01 2scuA c.2.1.8,c.23.4.1 30312,31140 2ge3A 170 3.20e+01 2c7pA 327 3.23e+01 1qqfA 277 3.24e+01 1c3d a.102.4.4 18875 2bp1A 360 3.24e+01 1zp4A 304 3.25e+01 1bif 469 3.25e+01 1bif c.37.1.7,c.60.1.4 31961,34003 1gs5A 258 3.27e+01 c.73.1.2 70395 1ihjA 98 3.29e+01 1pdr b.36.1.1 62382 1pg4A 652 3.32e+01 e.23.1.1 88067 1r6uA 437 3.35e+01 c.26.1.1 97163 1ri7A 171 3.40e+01 a.4.5.32,d.58.4.2 97504,97505 6mhtA 327 3.44e+01 6mhtA c.66.1.26 34226 2akoA 251 3.48e+01 1xszA 356 3.49e+01 1m7yA 435 3.51e+01 c.67.1.4 78761 2fqxA 318 3.52e+01 1fo8A 343 3.52e+01 1foaA c.68.1.10 59927 1ob8A 135 3.53e+01 1u2wA 122 3.55e+01 1wduA 245 3.55e+01 d.151.1.1 109286 1nwwA 149 3.59e+01 d.17.4.8 86306 1g3qA 237 3.60e+01 1hyqA c.37.1.10 60237 1xrsA 516 3.64e+01 1b5tA 275 3.65e+01 1b5tA c.1.23.1 29676 1prxA 224 3.68e+01 1prxA c.47.1.10 33076 1xnzA 264 3.69e+01 1ko6A 187 3.69e+01 b.119.1.1 77471 1cs1A 386 3.70e+01 1ibjA c.67.1.3 34399 1mml 265 3.71e+01 1mml e.8.1.2 43015 1nt4A 391 3.71e+01 c.60.1.2 92102 2g2cA 167 3.72e+01 1p9qC 256 3.74e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 2d00A 109 3.75e+01 1l8aA 886 3.76e+01 c.36.1.10,c.36.1.6,c.48.1.1 73677,73678,73679 2f46A 156 3.77e+01 2f1fA 164 3.77e+01 1w8sA 263 3.78e+01 1hkfA 122 3.79e+01 b.1.1.1 83553 2ajrA 331 3.82e+01 1gx3A 284 3.84e+01 d.3.1.5 70678 1knwA 425 3.88e+01 b.49.2.3,c.1.6.1 90969,90970 1c24A 263 3.91e+01 1c24A d.127.1.1 41148 1fc6A 388 3.92e+01 1fc6A b.36.1.3,c.14.1.2 64738,64739 2cb2A 318 3.93e+01 1fnlA 175 3.93e+01 2fcbA b.1.1.4,b.1.1.4 21783,21784 2bogX 286 3.94e+01 1fa0A 537 4.01e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 1xtyA 120 4.02e+01 1u2zA 433 4.02e+01 c.66.1.31 107626 1ru3A 732 4.03e+01 e.26.1.3 97835 1kepA 348 4.05e+01 c.2.1.2 68536 1mwvA 714 4.07e+01 a.93.1.3,a.93.1.3 85161,85162 1b25A 619 4.09e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1vljA 407 4.11e+01 e.22.1.2 108832 1yxyA 234 4.13e+01 1tc1A 220 4.23e+01 1tc1A c.61.1.1 34083 1hh2P 344 4.24e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 65835,65836,65837,65838 2bgcA 238 4.24e+01 1g63A 181 4.27e+01 1g5qA c.34.1.1 60299 1wcuA 153 4.27e+01 2ci1A 275 4.28e+01 1hfc 169 4.29e+01 1hfc d.92.1.11 40335 1dhr 241 4.34e+01 1dhr c.2.1.2 29832 1jilA 420 4.35e+01 c.26.1.1 66745 2bhvA 246 4.40e+01 1t0bA 252 4.43e+01 c.23.16.6 106199 1twdA 256 4.52e+01 c.1.30.1 107397 2avnA 260 4.53e+01 2bleA 367 4.53e+01 1r6xA 395 4.54e+01 b.122.1.3,c.26.1.5 97167,97168 1vjuA 309 4.55e+01 d.248.1.1 100835 1yxmA 303 4.56e+01 1srqA 341 4.56e+01 e.55.1.1 105967 1r4wA 226 4.57e+01 c.47.1.13 97050 1lqaA 346 4.57e+01 c.1.7.1 84674 1o66A 275 4.57e+01 c.1.12.8 92547 1ojxA 263 4.58e+01 c.1.10.1 93164 1oc2A 348 4.58e+01 c.2.1.2 92765 1vclA 432 4.59e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 2gcfA 73 4.59e+01 1ve0A 134 4.59e+01 1vzwA 244 4.61e+01 1i0rA 169 4.61e+01 1i0rA b.45.1.2 61489 1i0sA 169 4.61e+01 1i0rA b.45.1.2 61491 1iq8A 582 4.61e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1k20A 310 4.62e+01 c.107.1.1 68027 1o3yA 166 4.63e+01 c.37.1.8 86618 1scuA 288 4.68e+01 2scuA c.2.1.8,c.23.4.1 30307,31135 1j8fA 323 4.74e+01 1j8fA c.31.1.5 62738 1mp8A 281 4.78e+01 d.144.1.7 91384 1g94A 448 4.79e+01 b.71.1.1,c.1.8.1 65169,65170 1o7nA 449 4.85e+01 b.33.1.2,d.129.3.3 81162,81163 1kdoA 227 4.86e+01 c.37.1.1 68478 1ro5A 201 4.87e+01 d.108.1.3 105023 2gf9A 189 4.89e+01 1rhfA 182 4.90e+01 b.1.1.1,b.1.1.4 97469,97470 1qahA 136 4.90e+01 d.79.1.1 96338 1rzsA 61 4.92e+01 a.35.1.2 105139 1r5rA 119 4.93e+01 a.39.2.1 97104 2b4aA 138 4.95e+01 1i2aA 219 4.97e+01 e.24.1.1 90660 1f08A 148 5.02e+01 1f08A d.89.1.2 59564 1dmuA 299 5.04e+01 1dmuA c.52.1.4 33294 1utcA 363 5.04e+01 a.118.1.4,b.69.6.1 99914,99915 1ee4A 423 5.10e+01 1ee4A a.118.1.1 19128 1go4A 205 5.10e+01 d.135.1.1 70292 1g7dA 106 5.12e+01 1g7dA a.71.1.1 18318 1wvnA 82 5.13e+01 1xmxA 385 5.14e+01 1jflA 228 5.16e+01 c.78.2.1,c.78.2.1 71656,71657 1vd6A 224 5.17e+01 1qbjA 81 5.18e+01 1qbjA a.4.5.19 16155 1o5iA 249 5.18e+01 c.2.1.2 92499 1eg9A 449 5.19e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1zejA 293 5.20e+01 1slqA 278 5.22e+01 f.47.1.1 105719 1fp3A 402 5.24e+01 1fp3A a.102.1.3 18842 2av4A 162 5.27e+01 1e8cA 498 5.29e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1y8qA 346 5.32e+01 1f7uA 607 5.40e+01 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 59673,59674,59675 2fiqA 420 5.40e+01 1y0eA 223 5.41e+01 1j08A 226 5.41e+01 c.47.1.2,c.47.1.2 83855,83856 1e6uA 321 5.42e+01 1bsvA c.2.1.2 29805 1bylA 125 5.44e+01 1bylA d.32.1.2 38495 2bryA 497 5.48e+01 1l2tA 235 5.49e+01 c.37.1.12 73514 1wjuA 100 5.51e+01 1pjcA 361 5.54e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 1bkpA 278 5.55e+01 1bkpA d.117.1.1 41029 2a61A 145 5.57e+01 1wi1A 126 5.61e+01 1wkoA 180 5.62e+01 1pysA 350 5.66e+01 1pysA d.104.1.1 40775 1d2eA 397 5.67e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1f52A 468 5.68e+01 1lgr d.15.9.1,d.128.1.1 37839,41169 1pea 385 5.68e+01 1pea c.93.1.1 35662 2acjA 66 5.69e+01 1hv9A 456 5.69e+01 1fwyA b.81.1.4,c.68.1.5 28060,34518 1hwxA 501 5.71e+01 1hwyA c.2.1.7,c.58.1.1 30250,33898 1eceA 358 5.72e+01 1eceA c.1.8.3 28813 1e8gA 560 5.78e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1x1gA 129 5.80e+01 1zbsA 291 5.80e+01 1gcoA 261 5.85e+01 1ybvA c.2.1.2 29884 1kk1A 410 5.85e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1geeA 261 5.85e+01 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