# List of top-scoring protein chains for t04-100-30-str2-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 1.32e-01 1vp4A 425 3.89e-01 1wlsA 328 6.26e-01 1lc5A 364 6.44e-01 c.67.1.1 73827 1ejeA 192 6.62e-01 1ejeA b.45.1.2 25757 1innA 166 7.02e-01 1j98A d.185.1.2 62608 1e9rA 437 7.65e-01 c.37.1.11 64827 1vjeA 166 8.00e-01 d.185.1.2 100807 1f2tB 148 8.12e-01 1f2tB 2f5gA 133 8.33e-01 1wnfA 328 9.78e-01 1rz1A 161 1.49e+00 b.45.1.2 98124 1amy 403 1.54e+00 1jdc b.71.1.1,c.1.8.1 27799,28786 1q7zA 566 1.82e+00 c.1.21.2,c.1.26.1 96090,96091 1w1wA 430 1.89e+00 1avaA 403 2.01e+00 1jdc b.71.1.1,c.1.8.1 27797,28784 1o2dA 371 2.13e+00 e.22.1.2 86591 2fcr 173 2.16e+00 1rcf c.23.5.1 31151 2fbiA 142 2.39e+00 1sviA 195 2.45e+00 c.37.1.8 106048 2b4aA 138 2.62e+00 1fmcA 255 2.75e+00 1cydA c.2.1.2 29856 1t9bA 677 2.75e+00 1tbd 134 2.79e+00 2tbd d.89.1.1 40240 1wtaA 275 2.85e+00 1vheA 373 3.00e+00 b.49.3.1,c.56.5.4 100669,100670 1tqjA 230 3.32e+00 c.1.2.2 107228 1i1kA 309 3.34e+00 1daaA e.17.1.1 61533 1ht6A 405 3.43e+00 b.71.1.1,c.1.8.1 83629,83630 2gnoA 305 3.52e+00 1gegA 256 3.56e+00 1ybvA c.2.1.2 29888 2aebA 322 3.80e+00 1e5eA 404 3.94e+00 1ibjA c.67.1.3 59265 1b8oA 284 3.97e+00 1b8oA c.56.2.1 33762 2bogX 286 4.07e+00 1m7yA 435 4.84e+00 c.67.1.4 78761 1xfsA 178 4.90e+00 d.129.3.5 109589 1iyeA 309 5.30e+00 e.17.1.1 83786 1yyvA 131 5.34e+00 2b3nA 159 5.79e+00 1z5oA 242 5.85e+00 1lp3A 519 5.87e+00 b.121.5.2 74169 1jx6A 342 6.00e+00 c.93.1.1 67406 1gcoA 261 6.04e+00 1ybvA c.2.1.2 29884 1geeA 261 6.04e+00 c.2.1.2 90509 1t64A 377 6.13e+00 c.42.1.2 106543 1fg7A 356 6.17e+00 1gewA c.67.1.1 59819 2bznA 351 6.25e+00 1d3vA 323 6.30e+00 1d3vA c.42.1.1 32559 1yj7A 171 6.66e+00 1knwA 425 6.77e+00 b.49.2.3,c.1.6.1 90969,90970 1g63A 181 6.85e+00 1g5qA c.34.1.1 60299 1pjqA 457 6.97e+00 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 1eceA 358 7.24e+00 1eceA c.1.8.3 28813 1tcvA 287 7.27e+00 1aisB 200 7.29e+00 1aisB a.74.1.2,a.74.1.2 18384,18385 1l7aA 318 7.34e+00 c.69.1.25 77772 1pxwA 128 7.40e+00 d.79.3.1 95305 2b0jA 358 7.59e+00 1pvvA 315 8.05e+00 c.78.1.1,c.78.1.1 95190,95191 1kv7A 488 8.15e+00 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 1rpxA 230 8.30e+00 1rpxA c.1.2.2 28536 1zpvA 91 8.39e+00 1pyoA 167 8.41e+00 c.17.1.1 95370 1wwiA 148 8.57e+00 2dbbA 151 8.57e+00 1jysA 242 8.57e+00 c.56.2.1 77216 1nt4A 391 8.59e+00 c.60.1.2 92102 1vhoA 346 8.59e+00 b.49.3.1,c.56.5.4 100694,100695 2bodX 286 8.78e+00 2cw5A 255 8.84e+00 1xahA 354 8.90e+00 1lvaA 258 8.96e+00 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1xccA 220 9.17e+00 1yacA 208 9.34e+00 1yacA c.33.1.3 31757 2chnA 716 9.39e+00 1yzfA 195 9.50e+00 1r62A 160 9.50e+00 d.122.1.3 104816 1v6tA 255 9.53e+00 1aqm 453 9.59e+00 1smd b.71.1.1,c.1.8.1 27717,28704 1g94A 448 9.66e+00 b.71.1.1,c.1.8.1 65169,65170 1u1hA 765 9.67e+00 c.1.22.2,c.1.22.2 107580,107581 1nrjB 218 9.81e+00 c.37.1.8 86125 1i0rA 169 1.01e+01 1i0rA b.45.1.2 61489 1i0sA 169 1.01e+01 1i0rA b.45.1.2 61491 1ww9A 392 1.01e+01 1rm4A 337 1.05e+01 c.2.1.3,d.81.1.1 105000,105001 1ynuA 473 1.05e+01 1zip 217 1.06e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1oj4A 283 1.07e+01 d.14.1.5,d.58.26.5 93083,93084 1r5lA 262 1.08e+01 a.5.3.1,c.13.1.1 97099,97100 1gewA 356 1.08e+01 1gewA c.67.1.1 60470 1kdoA 227 1.09e+01 c.37.1.1 68478 1yfqA 342 1.10e+01 2akzA 439 1.15e+01 1ks9A 291 1.15e+01 a.100.1.7,c.2.1.6 68857,68858 1twdA 256 1.15e+01 c.1.30.1 107397 2f46A 156 1.16e+01 1aszB 490 1.16e+01 1b8aA b.40.4.1,d.104.1.1 25241,40762 2ae2A 260 1.16e+01 1bdb c.2.1.2 29945 2atxA 194 1.19e+01 1i50K 120 1.19e+01 d.74.3.2 61765 1nwwA 149 1.20e+01 d.17.4.8 86306 1wleA 501 1.20e+01 1zin 217 1.21e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1byb 495 1.21e+01 1byb c.1.8.1 28790 2c6qA 351 1.21e+01 2bynA 227 1.22e+01 1st9A 143 1.24e+01 c.47.1.10 98987 1b8gA 429 1.25e+01 1b8gA c.67.1.4 34499 1jx2B 315 1.26e+01 c.37.1.8 67404 1ojxA 263 1.27e+01 c.1.10.1 93164 6mhtA 327 1.28e+01 6mhtA c.66.1.26 34226 2cbzA 237 1.29e+01 2c7pA 327 1.30e+01 2fm8A 135 1.31e+01 1b5tA 275 1.31e+01 1b5tA c.1.23.1 29676 2c9aA 259 1.32e+01 1xnzA 264 1.34e+01 2c1cA 312 1.35e+01 2ajrA 331 1.36e+01 2b4gA 317 1.37e+01 1kafA 108 1.38e+01 d.199.1.1 68372 1igwA 434 1.41e+01 c.1.12.7 62370 1c24A 263 1.42e+01 1c24A d.127.1.1 41148 1ja9A 274 1.47e+01 c.2.1.2 62817 1gtmA 419 1.49e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 2ew8A 249 1.50e+01 1qwgA 251 1.50e+01 c.1.27.1 96473 1b5pA 385 1.51e+01 c.67.1.1 90403 1cl1A 395 1.51e+01 1cl2A c.67.1.3 34395 2fiqA 420 1.51e+01 1fm0E 150 1.52e+01 1fmaE d.41.5.1 38629 2f9sA 151 1.53e+01 1nrzA 164 1.55e+01 c.38.1.1 86131 1iupA 282 1.55e+01 c.69.1.10 76815 2bgkA 278 1.56e+01 1yavA 159 1.56e+01 4enl 436 1.59e+01 4enl c.1.11.1,d.54.1.1 29202,38846 1wy2A 351 1.61e+01 1wstA 417 1.62e+01 1s2dA 167 1.64e+01 c.23.14.1 98377 2fqxA 318 1.67e+01 1xn7A 78 1.69e+01 1wdpA 495 1.71e+01 1jmtA 104 1.73e+01 d.58.7.3 63180 1iq8A 582 1.73e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1prxA 224 1.74e+01 1prxA c.47.1.10 33076 3chbD 104 1.75e+01 3chbD b.40.2.1 24970 1twfK 120 1.75e+01 2cviA 83 1.76e+01 1te6A 439 1.76e+01 c.1.11.1,d.54.1.1 106797,106798 1u7lA 392 1.76e+01 1u3dA 509 1.79e+01 a.99.1.1,c.28.1.1 107638,107639 1p8kZ 254 1.79e+01 d.95.2.1,d.95.2.1 94361,94362 1k2fA 190 1.81e+01 b.8.1.2 68054 2bleA 367 1.82e+01 1q6cA 495 1.83e+01 c.1.8.1 95970 1o5zA 442 1.85e+01 c.59.1.2,c.72.2.2 92530,92531 2cxxA 190 1.86e+01 2ffmA 91 1.87e+01 1atiA 505 1.89e+01 1atiA c.51.1.1,d.104.1.1 33196,40745 1kicA 339 1.91e+01 c.70.1.1 72510 1jj2F 119 1.91e+01 1ffkE d.79.3.1 63091 1zp4A 304 1.91e+01 2al2A 436 1.92e+01 5abp 306 1.93e+01 8abp c.93.1.1 35651 1kblA 873 1.94e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1uk8A 282 1.94e+01 c.69.1.10 107907 1oneA 436 1.96e+01 4enl c.1.11.1,d.54.1.1 29200,38844 1p4xA 250 1.96e+01 a.4.5.28,a.4.5.28 87784,87785 1hjsA 332 1.96e+01 c.1.8.3 83492 2al1A 436 1.97e+01 2c07A 285 1.97e+01 2cb2A 318 1.98e+01 1bjwA 382 1.98e+01 1bjwA c.67.1.1 34349 2ggcA 263 1.99e+01 1z41A 338 2.00e+01 1w8sA 263 2.01e+01 2cw6A 298 2.03e+01 1z5nA 242 2.05e+01 1xbiA 120 2.08e+01 1wdiA 345 2.09e+01 1onwA 390 2.11e+01 b.92.1.7,c.1.9.13 87172,87173 2bsxA 253 2.11e+01 1srqA 341 2.14e+01 e.55.1.1 105967 1czaN 917 2.17e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 1k0eA 453 2.17e+01 d.161.1.1 67938 1gs5A 258 2.18e+01 c.73.1.2 70395 2ffuA 501 2.19e+01 1gveA 327 2.19e+01 c.1.7.1 70597 1b7gO 340 2.19e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907 1wlgA 299 2.21e+01 1sdsA 117 2.21e+01 d.79.3.1 105439 1dp4A 435 2.23e+01 1dp4A c.93.1.1 35710 1t0hB 224 2.25e+01 c.37.1.1 106208 2cunA 410 2.30e+01 1kid 203 2.33e+01 1derA c.8.5.1 30771 1r6xA 395 2.36e+01 b.122.1.3,c.26.1.5 97167,97168 1wcuA 153 2.36e+01 1mkzA 172 2.37e+01 c.57.1.1 84998 1vcvA 226 2.37e+01 2a1iA 146 2.37e+01 1hfc 169 2.38e+01 1hfc d.92.1.11 40335 2bgzA 299 2.39e+01 2d1sA 548 2.40e+01 2g40A 224 2.42e+01 1u4cA 349 2.44e+01 b.69.4.2 107666 1gd1O 334 2.44e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 2c0nA 203 2.45e+01 2b7kA 200 2.45e+01 2g5cA 281 2.45e+01 2a8yA 270 2.46e+01 1h7mA 102 2.47e+01 d.79.3.1 83485 2bcoA 350 2.47e+01 1yizA 429 2.48e+01 1ohlA 342 2.49e+01 c.1.10.3 87035 1qy5A 269 2.50e+01 d.122.1.1 96573 1kq3A 376 2.51e+01 e.22.1.2 68790 1o9gA 250 2.52e+01 c.66.1.29 86692 1yrgA 385 2.57e+01 1yrgA c.10.1.2 30854 1lci 550 2.61e+01 1lci e.23.1.1 43349 1l8aA 886 2.62e+01 c.36.1.10,c.36.1.6,c.48.1.1 73677,73678,73679 1jcxA 267 2.63e+01 c.1.10.4 66510 1vc4A 254 2.64e+01 c.1.2.4 100557 1rkuA 206 2.66e+01 c.108.1.11 97627 2cxcA 144 2.69e+01 1o1xA 155 2.70e+01 c.121.1.1 86553 1jvnA 555 2.73e+01 c.1.2.1,c.23.16.1 67355,67356 1fp3A 402 2.74e+01 1fp3A a.102.1.3 18842 2f6uA 234 2.75e+01 1vhmA 195 2.76e+01 d.110.2.1 100691 1ox6A 555 2.79e+01 c.1.2.1,c.23.16.1 87505,87506 1rfmA 344 2.81e+01 c.122.1.1 97385 1fnsA 196 2.82e+01 1auq c.62.1.1 34136 2a0mA 316 2.84e+01 1ydnA 295 2.85e+01 1xrsA 516 2.85e+01 1psdA 409 2.86e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1efpB 252 2.86e+01 1efvB c.26.2.3 31636 1g6hA 257 2.90e+01 1gajA c.37.1.12 60318 1w41A 101 2.91e+01 1d3yA 301 2.91e+01 1d3yA e.12.1.1 43252 1k3eA 156 2.93e+01 d.198.1.1 68103 1jilA 420 2.93e+01 c.26.1.1 66745 2akoA 251 2.95e+01 1wmiA 90 2.95e+01 1jhfA 202 2.96e+01 a.4.5.2,b.87.1.1 63057,63058 1v3hA 495 2.97e+01 c.1.8.1 108303 1ywnA 316 2.97e+01 1jmkC 230 3.01e+01 c.69.1.22 71747 2ca6A 386 3.01e+01 1ccwB 483 3.03e+01 1cb7B c.1.19.2 29646 1a05A 358 3.03e+01 1cnzA c.77.1.1 35059 2fa8A 105 3.04e+01 1sgwA 214 3.04e+01 c.37.1.12 105541 1jpaA 312 3.12e+01 d.144.1.7 67011 1qysA 106 3.14e+01 k.41.1.1 96603 1v04A 355 3.15e+01 b.68.6.2 100240 1x8bA 289 3.15e+01 2f1fA 164 3.19e+01 1jnrA 643 3.20e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1bmtA 246 3.22e+01 1bmtA a.46.1.1,c.23.6.1 17757,31235 1dik 874 3.25e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 2b4rO 345 3.25e+01 1ckeA 227 3.25e+01 1ckeA c.37.1.1 31846 1phk 298 3.27e+01 1cdkA d.144.1.7 41635 1h70A 255 3.28e+01 1h70A d.126.1.3 60711 2coiA 386 3.28e+01 1jztA 246 3.31e+01 c.104.1.1 63319 1tuoA 464 3.34e+01 1pjcA 361 3.34e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 1wy7A 207 3.35e+01 1rzsA 61 3.37e+01 a.35.1.2 105139 2gjsA 176 3.37e+01 1zd7A 159 3.38e+01 1v60A 123 3.38e+01 1xrtA 467 3.40e+01 1okgA 373 3.40e+01 c.46.1.2,c.46.1.2,d.26.1.3 93250,93251,93252 1uumA 372 3.46e+01 c.1.4.1 100010 1l2tA 235 3.46e+01 c.37.1.12 73514 1e8cA 498 3.47e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1xknA 355 3.47e+01 1uirA 314 3.48e+01 c.66.1.17 99429 1vhuA 211 3.50e+01 c.50.1.2 100703 1ituA 369 3.51e+01 c.1.9.7 71423 2ct8A 497 3.52e+01 1bqk 124 3.52e+01 1bqk b.6.1.1 22889 1k2xB 143 3.53e+01 2bfwA 200 3.53e+01 2aalA 131 3.53e+01 8abp 306 3.55e+01 8abp c.93.1.1 35647 1cb0A 283 3.57e+01 1cb0A c.56.2.1 33790 1zkpA 268 3.58e+01 1zczA 464 3.58e+01 1j6wA 175 3.61e+01 1j98A d.185.1.2 62663 1zud1 251 3.63e+01 1j9yA 385 3.65e+01 1j9yA c.1.8.3 62791 1bdfA 235 3.66e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 2c3zA 222 3.67e+01 1pdz 434 3.68e+01 4enl c.1.11.1,d.54.1.1 29215,38859 1sc6A 404 3.69e+01 1qqfA 277 3.71e+01 1c3d a.102.4.4 18875 1nmeA 146 3.73e+01 c.17.1.1 85874 1wr8A 231 3.73e+01 1yloA 348 3.75e+01 1dssG 333 3.75e+01 1dssG c.2.1.3,d.81.1.1 30022,39937 2gdjA 264 3.77e+01 1zosA 230 3.78e+01 1f7uA 607 3.78e+01 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 59673,59674,59675 1xt5A 135 3.79e+01 1v0wA 506 3.81e+01 d.136.1.2,d.136.1.2 108220,108221 1mp8A 281 3.86e+01 d.144.1.7 91384 1oxkB 134 3.87e+01 c.23.1.1 93691 2akaB 299 3.87e+01 1dbiA 280 3.88e+01 1gci c.41.1.1 32543 1uozA 315 3.92e+01 7odcA 424 3.94e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 1g66A 207 3.96e+01 1bs9 c.69.1.30 31329 1vzwA 244 3.97e+01 2fckA 181 3.97e+01 1em8B 112 3.97e+01 c.126.1.1 90458 1elqA 390 3.99e+01 1elqA c.67.1.3 34436 1eluA 390 4.00e+01 1elqA c.67.1.3 34434 3ullA 132 4.02e+01 3ullA b.40.4.3 25282 1w77A 228 4.03e+01 1y0eA 223 4.05e+01 1ri7A 171 4.05e+01 a.4.5.32,d.58.4.2 97504,97505 2fjbA 643 4.05e+01 1quqB 121 4.06e+01 1quqB b.40.4.3 25305 1q0uA 219 4.06e+01 c.37.1.19 95512 1wbhA 214 4.06e+01 2c0aA 214 4.06e+01 1omoA 322 4.07e+01 c.2.1.13 104017 1ka9H 200 4.07e+01 c.23.16.1 77308 2asbA 251 4.12e+01 1rhs 296 4.12e+01 1rhs c.46.1.2,c.46.1.2 32703,32704 1ispA 181 4.13e+01 c.69.1.18 76778 1xkrA 206 4.13e+01 1oatA 439 4.16e+01 2dkb c.67.1.4 34461 2cbiA 594 4.18e+01 1jl2A 156 4.18e+01 c.55.3.1 66822 1tl0D 103 4.20e+01 1r7aA 504 4.22e+01 b.71.1.1,c.1.8.1 97192,97193 1g8lA 411 4.24e+01 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1in0A 163 4.25e+01 d.58.49.1,d.58.49.1 83694,83695 1g0cA 364 4.27e+01 7a3hA c.1.8.3 60165 1k0rA 366 4.28e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 67961,67962,67963,67964 1odkA 235 4.29e+01 c.56.2.1 86863 1yb0A 159 4.29e+01 1vkhA 273 4.31e+01 c.69.1.32 108662 1w78A 422 4.31e+01 1iu8A 206 4.31e+01 c.56.4.1 71436 1u2zA 433 4.33e+01 c.66.1.31 107626 2fvgA 340 4.34e+01 1i6wA 181 4.35e+01 1i6wA c.69.1.18 61859 1tp9A 162 4.36e+01 2ethA 154 4.39e+01 2d00A 109 4.40e+01 2g0wA 296 4.42e+01 1o58A 303 4.42e+01 c.79.1.1 92491 1f0iA 504 4.43e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 1cf2O 337 4.44e+01 1b7gO 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