# List of top-scoring protein chains for t2k-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 1ekfA 365 5.13e-01 1ekfA e.17.1.1 59445 2a1hA 365 5.74e-01 1kt8A 365 6.49e-01 e.17.1.1 77531 1vk1A 242 6.55e-01 d.268.1.2 108634 1a8s 273 8.12e-01 1brt c.69.1.12 34710 1sayA 361 8.32e-01 1sayA c.2.1.4,c.23.12.2 30102,31362 1pjcA 361 8.49e-01 1sayA c.2.1.4,c.23.12.2 30101,31361 1pjbA 361 1.36e+00 1sayA c.2.1.4,c.23.12.2 30103,31363 1ktaA 365 1.46e+00 e.17.1.1 77533 1gw5S 142 2.00e+00 d.110.4.2 70633 1va4A 279 3.45e+00 c.69.1.12 108458 1vjeA 166 3.87e+00 d.185.1.2 100807 1id1A 153 4.36e+00 1id1A c.2.1.9 62286 1oj4A 283 4.64e+00 d.14.1.5,d.58.26.5 93083,93084 2coiA 386 5.20e+00 1bl3A 160 5.26e+00 1b9dA c.55.3.2 33655 1q1gA 276 5.77e+00 c.56.2.1 95574 1innA 166 5.79e+00 1j98A d.185.1.2 62608 1hyvA 166 5.87e+00 1b9dA c.55.3.2 61424 1b9dA 163 6.10e+00 1b9dA c.55.3.2 33649 1exqA 154 6.27e+00 1b9dA c.55.3.2 33646 1i1dA 161 7.02e+00 1i21A d.108.1.1 61526 2avnA 260 7.34e+00 1i12A 160 7.92e+00 1i21A d.108.1.1 61515 1mbyA 88 7.96e+00 d.223.1.1 78931 1yt3A 375 8.19e+00 1o89A 345 8.36e+00 b.35.1.2,c.2.1.1 92644,92645 2bsxA 253 8.38e+00 1rxyA 253 8.58e+00 c.56.2.1 98065 1hxhA 253 8.69e+00 c.2.1.2 76725 1lx7A 253 8.93e+00 c.56.2.1 74329 1lssA 140 9.09e+00 c.2.1.9 74246 1a7lA 389 9.17e+00 4mbp c.94.1.1 35787 1v9sA 208 9.18e+00 1z5nA 242 9.39e+00 1ki9A 192 1.01e+01 c.37.1.1 84404 1jysA 242 1.04e+01 c.56.2.1 77216 1pz7A 204 1.05e+01 b.29.1.4 95405 1z5oA 242 1.05e+01 1j24A 143 1.06e+01 c.52.1.20 84008 1vybA 238 1.11e+01 d.151.1.1 108897 1itg 166 1.14e+01 1b9dA c.55.3.2 33661 1hnoA 280 1.16e+01 1hnoA c.14.1.3 61095 1raxA 115 1.17e+01 1lfdA d.15.1.5 37626 1onrA 316 1.21e+01 1onrA c.1.10.1 29169 2a1iA 146 1.21e+01 2fg9A 178 1.23e+01 1nksA 194 1.24e+01 1nksA c.37.1.1 31886 1k3fA 253 1.25e+01 c.56.2.1 68105 1hnuA 280 1.26e+01 1hnoA c.14.1.3 61096 1lw7A 365 1.27e+01 c.26.1.3,c.37.1.1 74295,74296 1vhmA 195 1.31e+01 d.110.2.1 100691 1pjhA 280 1.31e+01 c.14.1.3 94761 1mfa 247 1.32e+01 1mfa b.1.1.1,b.1.1.1 19888,19889 1yvkA 163 1.36e+01 2d4pA 141 1.37e+01 1i2oA 316 1.39e+01 1onrA c.1.10.1 61574 1n6zA 105 1.39e+01 d.263.1.1 85369 1ws6A 171 1.40e+01 1ne2A 200 1.42e+01 c.66.1.32 85586 1b76A 442 1.44e+01 1atiA c.51.1.1,d.104.1.1 33198,40747 1xkqA 280 1.54e+01 2rgf 97 1.57e+01 1lfdA d.15.1.5 37627 1juk 248 1.58e+01 1a53 c.1.2.4 28567 1igs 248 1.60e+01 1a53 c.1.2.4 28565 1zejA 293 1.63e+01 1a0k 131 1.63e+01 3nul d.110.1.1 40892 2c3zA 222 1.75e+01 1khtA 192 1.78e+01 c.37.1.1 84401 3nul 130 1.80e+01 3nul d.110.1.1 40891 1ecpA 238 1.81e+01 1ecpA c.56.2.1 33775 1i21A 159 1.84e+01 1i21A d.108.1.1 61549 1qo7A 394 1.85e+01 1qo7A c.69.1.11 34697 1y1pA 342 1.88e+01 1a53 247 1.93e+01 1a53 c.1.2.4 28564 2fz4A 237 1.94e+01 1m2xA 223 1.97e+01 d.157.1.1 84764 1lxdA 100 1.98e+01 1lfdA d.15.1.5 37624 1xo7A 166 2.02e+01 1wyzA 242 2.08e+01 2bifA 469 2.09e+01 1bif c.37.1.7,c.60.1.4 31963,34009 1cqa 133 2.10e+01 3nul d.110.1.1 40890 1ujmA 342 2.11e+01 2ghpA 292 2.11e+01 1x9zA 188 2.12e+01 1kyhA 276 2.16e+01 c.72.1.4 73222 1qysA 106 2.23e+01 k.41.1.1 96603 1aw5 326 2.25e+01 1b4kA c.1.10.3 29181 1c4oA 664 2.29e+01 1d2mA c.37.1.19,c.37.1.19 32415,32416 1vc1A 110 2.29e+01 c.13.2.1 108493 3bifA 468 2.31e+01 1bif c.37.1.7,c.60.1.4 31962,34008 1vk8A 106 2.32e+01 d.58.48.1 108636 1ef1A 294 2.33e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 1bif 469 2.34e+01 1bif c.37.1.7,c.60.1.4 31961,34003 1sviA 195 2.34e+01 c.37.1.8 106048 1zu4A 320 2.35e+01 1vp8A 201 2.36e+01 2fvx 138 2.42e+01 5nul c.23.5.1 31200 1l6wA 220 2.44e+01 c.1.10.1 73632 1pk9A 237 2.45e+01 c.56.2.1 94823 1ebfA 358 2.46e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1ebuA 358 2.55e+01 1ebuA c.2.1.3,d.81.1.2 30035,39950 1pvgA 418 2.56e+01 d.14.1.3,d.122.1.2 95161,95162 1yruA 364 2.57e+01 1fyvA 161 2.58e+01 1fyvA c.23.2.1 31127 1yqhA 109 2.59e+01 1h6zA 913 2.62e+01 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 1z4rA 168 2.64e+01 2aefA 234 2.65e+01 1lnqA 336 2.67e+01 c.2.1.9,f.14.1.1 74049,74050 1atiB 505 2.68e+01 1atiA c.51.1.1,d.104.1.1 33197,40746 1v37A 177 2.69e+01 1wrvA 308 2.72e+01 2bgkA 278 2.73e+01 1atiA 505 2.76e+01 1atiA c.51.1.1,d.104.1.1 33196,40745 1xiyA 182 2.77e+01 1bdb 277 2.78e+01 1bdb c.2.1.2 29874 2h1nA 567 2.78e+01 1yrtA 364 2.78e+01 1p9rA 418 2.78e+01 c.37.1.11 94399 1zbfA 142 2.79e+01 2reb 352 2.79e+01 2reb c.37.1.11,d.48.1.1 32282,38767 1iy8A 267 2.81e+01 c.2.1.2 83774 1q67A 231 2.98e+01 b.55.1.7 95960 1lsuA 147 2.99e+01 c.2.1.9 74250 2bhuA 602 3.11e+01 2bogX 286 3.13e+01 2f1kA 279 3.15e+01 5gcnA 166 3.22e+01 1yghA d.108.1.1 40807 1khyA 148 3.24e+01 a.174.1.1 77410 1m6yA 301 3.27e+01 a.60.13.1,c.66.1.23 78716,78717 1a41 234 3.29e+01 1a41 d.163.1.2 42174 1v3vA 333 3.29e+01 b.35.1.2,c.2.1.1 108345,108346 1vqtA 213 3.30e+01 1k9sA 237 3.36e+01 c.56.2.1 68359 1914 232 3.38e+01 1914 d.49.1.1,d.49.1.1 83028,83029 3nll 138 3.41e+01 5nul c.23.5.1 31206 1q6zA 528 3.46e+01 1tfuA 157 3.53e+01 c.26.1.3 106859 2bl1A 172 3.54e+01 2cxcA 144 3.56e+01 5nul 138 3.57e+01 5nul c.23.5.1 31191 1bfd 528 3.58e+01 1bfd c.31.1.3,c.36.1.5,c.36.1.9 31745,31801,31802 1iujA 106 3.58e+01 d.58.4.5 90701 1tt7A 330 3.59e+01 2fox 138 3.62e+01 5nul c.23.5.1 31197 1r5jA 337 3.65e+01 c.77.1.5 97097 1fgp 70 3.66e+01 1g3p b.37.1.1 24795 1xhlA 297 3.73e+01 c.2.1.2 109591 1naqA 112 3.73e+01 d.58.5.2 91761 1wy7A 207 3.73e+01 1pkp 150 3.76e+01 1pkp d.14.1.1,d.50.1.2 37551,38787 1dioB 224 3.77e+01 1dioB c.51.3.1 33219 1y7pA 223 3.78e+01 1fyhA 258 3.81e+01 1d9cA a.26.1.3,a.26.1.3 16907,16908 1ockA 412 3.82e+01 c.117.1.1 86802 1rurH 218 3.83e+01 b.1.1.1,b.1.1.2 97879,97880 1fwkA 296 3.84e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1hruA 188 3.85e+01 1hruA d.115.1.1 40926 1zotA 358 3.91e+01 1u94A 356 3.93e+01 c.37.1.11,d.48.1.1 107743,107744 1hw7A 255 3.95e+01 1i7fA d.193.1.1 61297 1w6uA 302 3.95e+01 1z82A 335 3.98e+01 1ve9A 347 4.00e+01 c.4.1.2,d.16.1.3 100571,100572 1m5wA 243 4.00e+01 c.1.24.1 84836 1rz3A 201 4.00e+01 c.37.1.6 98132 1ixcA 294 4.02e+01 a.4.5.37,c.94.1.1 83764,83765 2bodX 286 4.03e+01 1wduA 245 4.08e+01 d.151.1.1 109286 1sbp 310 4.09e+01 1sbp c.94.1.1 35760 1keiA 316 4.15e+01 d.92.1.2 77349 1gqyA 475 4.15e+01 c.5.1.1,c.59.1.1,c.72.2.1 83305,83306,83307 1yemA 179 4.18e+01 1iz1A 294 4.19e+01 a.4.5.37,c.94.1.1 83823,83824 1p3dA 475 4.21e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1h72C 296 4.23e+01 d.14.1.5,d.58.26.1 60712,60713 1u9yA 284 4.24e+01 1vpwA 340 4.26e+01 1qpzA a.35.1.5,c.93.1.1 17087,35680 2bleA 367 4.32e+01 2bmfA 451 4.35e+01 1kdj 102 4.35e+01 1plc b.6.1.1 22864 2c6qA 351 4.35e+01 1h3qA 140 4.35e+01 d.110.4.3 76652 1tvnA 293 4.36e+01 1x8hA 228 4.37e+01 1ho1A 242 4.39e+01 1ho1A c.1.24.1 61097 2es7A 142 4.40e+01 2bznA 351 4.43e+01 1taq 832 4.47e+01 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18082,33352,33698,42991 1u9iA 519 4.48e+01 1eexB 224 4.54e+01 1dioB c.51.3.1 33213 2d1yA 256 4.55e+01 1w0mA 226 4.56e+01 c.1.1.1 109027 1x8gA 227 4.57e+01 1ypfA 336 4.60e+01 1jf8A 131 4.63e+01 c.44.1.1 66621 1mgtA 174 4.65e+01 1mgtA a.4.2.1,c.55.7.1 16078,33753 1aa8A 347 4.68e+01 1an9A 1j98A 157 4.69e+01 1j98A d.185.1.2 62755 1vr5A 547 4.70e+01 1g4uS 383 4.71e+01 1g4uS a.24.11.1,c.45.1.2 16643,32691 1wryA 121 4.72e+01 1tp9A 162 4.72e+01 1ufkA 254 4.74e+01 c.66.1.39 99340 1xp8A 366 4.74e+01 1j6wA 175 4.76e+01 1j98A d.185.1.2 62663 1tidB 119 4.81e+01 c.13.2.1 107000 2itg 163 4.88e+01 1b9dA c.55.3.2 33669 1a3lH 218 4.88e+01 1mfa b.1.1.1,b.1.1.2 20241,21253 1vmeA 410 4.90e+01 c.23.5.1,d.157.1.3 108893,108894 1z5rA 306 4.90e+01 1xm7A 195 5.02e+01 1dbqA 289 5.02e+01 1qpzA c.93.1.1 35666 1fsu 492 5.03e+01 1auk c.76.1.2 35032 1jfvA 131 5.04e+01 c.44.1.1 66654 1cb0A 283 5.06e+01 1cb0A c.56.2.1 33790 1othA 321 5.07e+01 1othA c.78.1.1,c.78.1.1 35260,35261 1on0A 158 5.15e+01 d.108.1.1 87095 1h2bA 359 5.19e+01 b.35.1.2,c.2.1.1 90543,90544 1earA 147 5.20e+01 b.107.1.1,d.58.38.1 64875,64876 1hyt 316 5.21e+01 1hyt d.92.1.2 59005 1lfdA 87 5.21e+01 1lfdA d.15.1.5 37622 1up6A 416 5.22e+01 c.2.1.5,d.162.1.2 107976,107977 1g3p 217 5.26e+01 1g3p b.37.1.1,b.37.1.1 24788,24789 1mgpA 313 5.35e+01 c.119.1.1 79098 1okjA 251 5.35e+01 c.55.1.9,c.55.1.9 103998,103999 1iloA 77 5.38e+01 c.47.1.1 66205 2ex2A 458 5.40e+01 1lopA 164 5.40e+01 2cpl b.62.1.1 27510 1a3h 300 5.41e+01 7a3hA c.1.8.3 28819 7a3hA 303 5.41e+01 7a3hA c.1.8.3 28817 2g5cA 281 5.50e+01 1iieA 75 5.51e+01 1iieA a.109.1.1 19039 1whzA 70 5.52e+01 1y5eA 169 5.55e+01 1e5dA 402 5.56e+01 1e5dA c.23.5.1,d.157.1.3 31208,42061 1ep3A 311 5.57e+01 2dorA c.1.4.1 28597 1nv8A 284 5.61e+01 c.66.1.30 86224 1j5eE 161 5.63e+01 d.14.1.1,d.50.1.2 71547,71548 1fjgE 162 5.65e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 1agdB 99 5.66e+01 1agdB b.1.1.2 20742 1hsbB 99 5.66e+01 1agdB b.1.1.2 20737 1duzB 100 5.67e+01 1agdB b.1.1.2 20671 1i4fB 100 5.68e+01 1agdB b.1.1.2 61689 1duvG 333 5.69e+01 1othA c.78.1.1,c.78.1.1 35228,35229 1hqsA 423 5.70e+01 1iso c.77.1.1 61154 1k5nB 100 5.73e+01 b.1.1.2 77268 8abp 306 5.76e+01 8abp c.93.1.1 35647 1jljA 189 5.79e+01 c.57.1.1 63169 1ihcA 188 5.79e+01 1di6A c.57.1.1 62379 1b3jA 274 5.80e+01 1agdA b.1.1.2,d.19.1.1 20855,38319 1ufhA 180 5.83e+01 d.108.1.1 88485 1chuA 540 5.84e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1a6vH 120 5.85e+01 1mfa b.1.1.1 20257 1hi9A 274 5.98e+01 1hi9A c.99.1.1 61063 2lbp 346 5.98e+01 2liv c.93.1.1 35709 2f46A 156 6.00e+01 1xn7A 78 6.00e+01 1up7A 417 6.04e+01 1kt9A 138 6.07e+01 d.113.1.1 72959 1ktgA 138 6.09e+01 d.113.1.1 72972 1vmaA 306 6.09e+01 a.24.13.1,c.37.1.10 108887,108888 1m2vB 926 6.13e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78497,78498,78499,78500,78501 2tmnE 316 6.13e+01 1hyt d.92.1.2 59055 2bsyA 278 6.15e+01 8tlnE 316 6.15e+01 1hyt d.92.1.2 59075 1v77A 212 6.17e+01 c.6.3.2 108402 1rf6A 427 6.22e+01 d.68.2.2 97366 6tmnE 316 6.23e+01 1hyt d.92.1.2 59071 1pqsA 77 6.24e+01 d.15.2.2 88277 1o8uA 257 6.28e+01 c.14.1.3 81194 1ffa 214 6.29e+01 1cex c.69.1.30 31289 2cxaA 256 6.32e+01 1q0sA 259 6.32e+01 c.66.1.28 95509 1t0qA 498 6.32e+01 a.25.1.2 106220 1yvoA 172 6.33e+01 1nu5A 370 6.34e+01 c.1.11.2,d.54.1.1 92183,92184 1dd6A 228 6.36e+01 1a7tA d.157.1.1 42054 1ejhA 190 6.36e+01 1ejhA d.86.1.1 40147 1u7nA 336 6.38e+01 c.77.1.4 107726 2bh1X 96 6.38e+01 1o54A 277 6.43e+01 c.66.1.13 92482 2gkeA 274 6.50e+01 1jpnA 296 6.50e+01 a.24.13.1,c.37.1.10 67039,67040 1fts 295 6.53e+01 1ng1 a.24.13.1,c.37.1.10 16968,32279 1mh3A 421 6.54e+01 a.4.1.1,c.94.1.1 79112,79113 2az2A 73 6.58e+01 1kbjA 412 6.58e+01 c.1.4.1 72280 2az0A 73 6.60e+01 1gqzA 274 6.65e+01 d.21.1.1,d.21.1.1 83311,83312 1jftA 340 6.66e+01 a.35.1.5,c.93.1.1 66652,66653 1gc5A 467 6.69e+01 1gc5A c.72.1.3 60429 1usgA 346 6.69e+01 c.93.1.1 99864 5abp 306 6.69e+01 8abp c.93.1.1 35651 1abe 306 6.71e+01 8abp c.93.1.1 35648 1khiA 176 6.71e+01 b.34.5.2,b.40.4.5 77408,77409 1y1uA 585 6.73e+01 2a6tA 271 6.73e+01 1oaqH 121 6.76e+01 b.1.1.1 92707 1dvjC 246 6.78e+01 1dvjA c.1.2.3 28548 1cus 200 6.78e+01 1cex c.69.1.30 31287 1t94A 459 6.78e+01 d.240.1.1,e.8.1.7 106701,106702 1dvjA 246 6.78e+01 1dvjA c.1.2.3 28546 1kjvB 100 6.81e+01 b.1.1.2 77423 1gp4A 356 6.82e+01 b.82.2.1 65439 1agy 200 6.83e+01 1cex c.69.1.30 31286 1a14H 120 6.84e+01 1mfa b.1.1.1 20061 1mw7A 240 6.84e+01 e.39.1.1 79557 1kutA 230 6.84e+01 d.143.1.1 73017 1cex 214 6.85e+01 1cex c.69.1.30 31285 1gmxA 108 6.87e+01 c.46.1.3 65355 1yqdA 366 6.88e+01 2cx5A 158 6.90e+01 1qcwA 410 6.93e+01 1gox c.1.4.1 28622 1tqzA 133 6.93e+01 1kllA 130 6.93e+01 d.32.1.2 72720 1gp6A 356 6.97e+01 b.82.2.1 65441 1bap 306 6.99e+01 8abp c.93.1.1 35654 1cliA 345 7.01e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1ng1 294 7.04e+01 1ng1 a.24.13.1,c.37.1.10 16961,32272 1l6rA 227 7.07e+01 c.108.1.10 77768 2nsyA 271 7.08e+01 2nsyA c.26.2.1 31612 1mjuH 227 7.08e+01 b.1.1.1,b.1.1.2 91302,91303 1ih8A 271 7.08e+01 2nsyA c.26.2.1 62377 1gn0A 108 7.10e+01 c.46.1.3 65358 1gg3A 279 7.10e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16372,27007,37615 1huvA 380 7.11e+01 c.1.4.1 61277 1fehA 574 7.11e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1cz3A 168 7.12e+01 1d1gA c.71.1.1 34891 1p4cA 380 7.12e+01 c.1.4.1 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