# List of top-scoring protein chains for t06-100-30-alpha-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 1jsdA 319 2.81e-02 b.19.1.2 63258 1gj7B 253 8.18e-02 1vhsA 175 1.08e-01 d.108.1.1 100698 1ev7A 317 1.10e-01 1ev7B c.52.1.9 33315 1im3D 95 1.46e-01 1im3D b.1.18.5 62568 1p1mA 406 1.55e-01 b.92.1.4,c.1.9.9 87696,87697 1hkyA 86 1.86e-01 g.10.1.3 76714 1vjvA 415 1.93e-01 d.3.1.9 108632 1vrmA 325 2.02e-01 1dgwA 178 2.19e-01 1dgwA b.82.1.2 28090 1wkrA 340 2.24e-01 b.50.1.2 109395 1el6A 219 2.65e-01 1el6B d.182.1.1 42606 1jsmA 325 3.46e-01 b.19.1.2 63264 1iv3A 152 3.89e-01 d.79.5.1 76828 1gvkB 240 4.40e-01 b.47.1.2 70610 1fqtA 112 5.17e-01 1fqtA b.33.1.1 24441 1se8A 301 5.21e-01 b.40.4.3 105448 1whi 122 5.91e-01 1whi b.39.1.1 24810 2mcm 112 6.04e-01 2mcm b.1.7.1 22207 1elt 236 6.82e-01 5ptp b.47.1.2 26281 1pmi 440 6.95e-01 1pmi b.82.1.3 28114 1jb0A 755 7.72e-01 1jb0A f.29.1.1 62820 1eu3A 210 8.84e-01 1an8 b.40.2.2,d.15.6.1 25206,37795 1hq0A 295 9.64e-01 1hzgA d.194.1.1 61122 1ei5A 520 1.14e+00 1ei5A b.61.3.1,b.61.3.1,e.3.1.1 27418,27419,42772 1ro7A 259 1.18e+00 c.130.1.1 97667 1ic6A 279 1.21e+00 1gci c.41.1.1 62257 1ahsA 126 1.22e+00 1ahsA b.19.1.1 23794 1pv5A 264 1.26e+00 d.251.1.1 95150 1ixkA 315 1.28e+00 c.66.1.38 90716 1qjpA 171 1.32e+00 1bxwA f.4.1.1 43742 1v70A 105 1.43e+00 1gnuA 117 1.53e+00 d.15.1.3 65403 1aiw 62 1.56e+00 1aiw b.72.2.1 27808 1a8q 274 1.67e+00 1brt c.69.1.12 34702 1gkpA 458 1.80e+00 b.92.1.3,c.1.9.6 70231,70232 1n62C 288 1.82e+00 d.87.2.1,d.145.1.3 80094,80095 1i7dA 659 1.84e+00 1d6mA e.10.1.1 61886 1bywA 110 1.84e+00 1bywA d.110.3.6 40912 1vp6A 138 2.23e+00 1n7oA 721 2.24e+00 a.102.3.2,b.24.1.1,b.30.5.2 80259,80260,80261 1bec 238 2.34e+00 1bec b.1.1.1,b.1.1.2 20627,21561 1gen 218 2.36e+00 1gen b.66.1.1 27536 1ikpA 613 2.36e+00 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1gttA 429 2.40e+00 d.177.1.1,d.177.1.1 70529,70530 1iyeA 309 2.44e+00 e.17.1.1 83786 1whzA 70 2.45e+00 1ks8A 433 2.58e+00 a.102.1.2 77519 1ecfA 504 2.63e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 1a8y 367 2.75e+00 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1xakA 83 3.02e+00 1v30A 124 3.13e+00 1nnxA 109 3.30e+00 b.40.10.1 92013 1h54A 754 3.53e+00 a.102.1.4,b.30.5.3 60634,60635 1snrA 341 3.54e+00 b.6.1.3,b.6.1.3 105823,105824 1hmt 132 3.59e+00 1hmt b.60.1.2 27169 1gy7A 125 3.66e+00 d.17.4.2 70738 1juvA 193 3.88e+00 c.71.1.1 90912 1ts9A 102 3.93e+00 2g7jA 124 3.99e+00 1bia 321 4.02e+00 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1mhnA 59 4.21e+00 b.34.9.1 84964 1f06A 320 4.30e+00 1dapA c.2.1.3,d.81.1.3 59556,59557 1fjgK 129 4.54e+00 1fjfK c.55.4.1 33733 1ad2 228 4.61e+00 1ad2 e.24.1.1 43353 1hbnC 248 4.99e+00 1mroC d.58.31.1 60902 1d0dA 60 5.32e+00 1kigI g.8.1.2 44566 2fneA 117 5.42e+00 1dykA 394 5.47e+00 1dykA b.29.1.4,b.29.1.4 24223,24224 1b0uA 262 5.47e+00 1b0uA c.37.1.12 32370 1gtzA 156 5.49e+00 c.23.13.1 70539 1ed7A 45 5.49e+00 1ed7A b.72.2.1 27809 1udzA 182 5.64e+00 b.51.1.1 99239 1rm6A 769 5.68e+00 1yb3A 175 5.74e+00 1oruA 195 5.88e+00 b.58.1.2 93464 1nykA 165 5.91e+00 b.33.1.1 86408 1bcpD 110 5.95e+00 1bcpD b.40.2.1 25132 1avwB 171 6.10e+00 1wba b.42.4.1 25599 1dyqA 234 6.11e+00 3seb b.40.2.2,d.15.6.1 59140,59141 1d2sA 170 6.15e+00 1d2sA b.29.1.4 24221 1ga6A 372 6.19e+00 1ga1A c.41.1.2 32556 1i8kA 107 6.29e+00 b.1.1.1 71130 1c8uA 285 6.51e+00 1c8uA d.38.1.3,d.38.1.3 38547,38548 1hw5A 210 6.80e+00 2cgpA a.4.5.4,b.82.3.2 16098,28137 3cla 213 6.89e+00 3cla c.43.1.1 32610 1bb8 71 6.91e+00 2bb8 d.10.1.1 37478 1j96A 323 6.97e+00 c.1.7.1 71616 2arcA 164 7.00e+00 2arcA b.82.4.1 28148 1oxxK 353 7.04e+00 b.40.6.3,c.37.1.12 93715,93716 1go3E 187 7.06e+00 b.40.4.5,d.230.1.1 83054,83055 1l8bA 190 7.17e+00 d.86.1.1 73683 1cr5A 189 7.31e+00 1cr5A b.52.2.3,d.31.1.1 26931,38465 2ci9A 102 7.48e+00 1dkuA 317 7.57e+00 1dkuA c.61.1.2,c.61.1.2 34118,34119 1g7sA 594 7.60e+00 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1p0zA 131 7.62e+00 d.110.6.1 93882 1g4wR 383 7.75e+00 1g4uS a.24.11.1,c.45.1.2 16644,32692 1e0nA 27 7.75e+00 b.72.1.1 27807 3sil 379 7.81e+00 3sil b.68.1.1 27542 1earA 147 7.86e+00 b.107.1.1,d.58.38.1 64875,64876 1ru4A 400 8.28e+00 b.80.1.9 97836 1oflA 481 8.50e+00 b.80.1.4 103934 1gcqC 70 8.58e+00 1gcpA b.34.2.1 60436 1g6hA 257 8.61e+00 1gajA c.37.1.12 60318 1mj5A 302 8.75e+00 c.69.1.8 91285 1gy6A 127 8.80e+00 d.17.4.2 70736 1e9gA 286 8.80e+00 1wgjA b.40.5.1 59393 1fnlA 175 8.88e+00 2fcbA b.1.1.4,b.1.1.4 21783,21784 1jnrA 643 8.98e+00 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1o7iA 119 9.21e+00 b.40.4.3 86642 1f39A 101 9.24e+00 1umuA b.87.1.1 28386 1pvmA 184 9.35e+00 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1ijvA 36 9.46e+00 g.9.1.1 66169 1kv7A 488 9.67e+00 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 1f9zA 135 9.88e+00 1qipA d.32.1.1 38484 1hh8A 213 1.01e+01 1e96B a.118.8.1 61042 1dxgA 36 1.03e+01 1dxgA g.41.5.2 45247 1wdvA 152 1.04e+01 1d4tA 104 1.09e+01 1d4tA d.93.1.1 40537 1jb0D 138 1.11e+01 1jb0D d.187.1.1 62823 1koe 172 1.15e+01 1koe d.169.1.5 42448 1bx7 55 1.16e+01 1bx7 g.3.15.1 44355 1gk9B 557 1.17e+01 1h6tA 291 1.20e+01 b.1.18.15,c.10.2.1 65686,65687 1jmcA 246 1.21e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 1c4rA 182 1.23e+01 1c4rA b.29.1.4 24229 1fehA 574 1.24e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1c9oA 66 1.26e+01 1mjc b.40.4.5 25325 1giqA 413 1.29e+01 d.166.1.1,d.166.1.1 76224,76225 1f0lA 535 1.29e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22377,42239,43382 1fepA 724 1.29e+01 1fepA f.4.3.3 43808 1uuqA 440 1.35e+01 c.1.8.3 100015 1epxA 370 1.36e+01 1fbaA c.1.10.1 29150 1ckeA 227 1.38e+01 1ckeA c.37.1.1 31846 4ubpA 101 1.38e+01 1ubpA d.8.1.1 37352 1xmzA 241 1.38e+01 1b65A 375 1.42e+01 1b65A d.154.1.1 42020 1l9xA 315 1.46e+01 c.23.16.1 73762 1geeA 261 1.46e+01 c.2.1.2 90509 1ee6A 197 1.47e+01 1ee6A b.80.1.1 28024 1fxxA 482 1.47e+01 1fxxA c.55.3.5 33726 1hcnA 92 1.48e+01 1hcnA g.17.1.4 44809 1x82A 190 1.50e+01 2ciaA 102 1.51e+01 1jtdB 273 1.51e+01 b.69.5.2 67265 1nkgA 508 1.52e+01 b.3.1.2,b.18.1.25,b.30.5.10 103859,103860,103861 1l7lA 121 1.54e+01 b.18.1.16 77790 1i0vA 104 1.55e+01 9rnt d.1.1.4 36054 1f2tB 148 1.55e+01 1f2tB 1hic 51 1.56e+01 4htcI g.3.15.2 44371 1hh1A 143 1.57e+01 1gefA c.52.1.18 61036 1dleA 298 1.57e+01 1dleA b.47.1.2 26312 1j5pA 253 1.57e+01 d.81.1.3,c.2.1.3 71577,83092 1e29A 135 1.60e+01 1e29A a.3.1.1 59161 1eaxA 241 1.61e+01 b.47.1.2 64889 1et9A 204 1.63e+01 1an8 b.40.2.2,d.15.6.1 25204,37793 1axh 37 1.65e+01 1axh g.3.6.2 44109 1us0A 316 1.66e+01 c.1.7.1 99850 1j1lA 290 1.66e+01 b.82.1.12 90766 1hf2A 210 1.68e+01 1hf2A b.80.3.1,c.102.1.1 60992,60993 1b9wA 89 1.69e+01 1b9wA g.3.11.4,g.3.11.4 44334,44335 1a8s 273 1.69e+01 1brt c.69.1.12 34710 1jovA 270 1.70e+01 b.30.5.7 84192 1o7nA 449 1.73e+01 b.33.1.2,d.129.3.3 81162,81163 1hdkA 141 1.73e+01 b.29.1.3 65807 1bkzA 135 1.76e+01 1a3k b.29.1.3 24202 1uxy 340 1.76e+01 2mbr d.145.1.2,d.146.1.1 41748,41761 1vmeA 410 1.77e+01 c.23.5.1,d.157.1.3 108893,108894 1rjoA 646 1.77e+01 1ew4A 106 1.78e+01 1ew4A d.82.2.1 40023 1ecsA 126 1.81e+01 1ecsA d.32.1.2 59407 1fjgS 93 1.85e+01 1qkfA d.28.1.1 38451 1ijaA 148 1.87e+01 1ijaA b.100.1.1 62484 1cdcA 99 1.87e+01 1cdcA b.1.1.1 19746 1o7nB 194 1.87e+01 d.17.4.4 81164 1fmhA 33 1.89e+01 1fmhB k.6.1.1 46409 1k7iA 479 1.93e+01 b.80.7.1,d.92.1.6 77281,77282 1yllA 200 1.96e+01 1iukA 140 1.96e+01 c.2.1.8 83712 1sbxA 106 1.99e+01 a.6.1.4 105414 1lvmA 229 1.99e+01 b.47.1.3 78243 1i1wA 303 2.00e+01 c.1.8.3 76732 1d5tA 433 2.00e+01 1gnd c.3.1.3,d.16.1.6 30422,37986 1dtdB 61 2.05e+01 1dtvA g.30.1.1 44962 1i26A 34 2.07e+01 g.3.6.3 65986 1ajj 37 2.09e+01 1ajj g.12.1.1 44609 1mba 147 2.10e+01 2fal a.1.1.2 15149 1tl9A 339 2.11e+01 1e58A 249 2.12e+01 1qhfA c.60.1.1 59262 1enwA 114 2.13e+01 1enwA a.5.4.1 16291 1df7A 159 2.13e+01 3dfr c.71.1.1 34885 1rvkA 382 2.18e+01 c.1.11.2,d.54.1.1 97928,97929 1ir6A 424 2.20e+01 c.107.1.2 71342 1l6rA 227 2.22e+01 c.108.1.10 77768 1bdo 80 2.23e+01 1bdo b.84.1.1 28214 1b2pA 119 2.25e+01 1b2pA b.78.1.1 27998 1go4A 205 2.27e+01 d.135.1.1 70292 1sauA 115 2.30e+01 1vr8A 142 2.31e+01 1o54A 277 2.34e+01 c.66.1.13 92482 1g6gA 127 2.35e+01 1g6gA b.26.1.2 23916 1b77A 228 2.36e+01 1b77A d.131.1.2,d.131.1.2 41362,41363 1y4wA 518 2.38e+01 2evaA 307 2.40e+01 1kqrA 179 2.45e+01 b.29.1.14 72886 1a8d 452 2.46e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 1i4uA 181 2.50e+01 b.60.1.1 61732 1rutX 188 2.50e+01 2evbA 74 2.51e+01 1uaiA 224 2.52e+01 b.29.1.18 107761 3nul 130 2.53e+01 3nul d.110.1.1 40891 1dgwY 93 2.53e+01 1caxB 1n6aA 259 2.53e+01 b.76.2.1,b.85.7.1 80121,80122 1h16A 759 2.54e+01 c.7.1.1 76462 1hj8A 222 2.56e+01 b.47.1.2 65844 1v5vA 401 2.58e+01 1jy4A 35 2.59e+01 k.35.1.1 71938 1vj2A 126 2.59e+01 b.82.1.10 100796 1ff9A 450 2.62e+01 1ff9A c.2.1.3,d.81.1.2 30039,39954 1fd3A 41 2.63e+01 1fd3A g.9.1.1 44572 1iqqA 200 2.65e+01 d.124.1.1 66274 1hdlA 55 2.65e+01 g.68.1.2 65808 1x9iA 302 2.67e+01 1ddgA 374 2.70e+01 1amoA b.43.4.1,c.25.1.4 25671,31559 1odmA 331 2.71e+01 b.82.2.1 86875 1rqpA 299 2.72e+01 b.141.1.1,c.132.1.1 97754,97755 1fyeA 229 2.72e+01 1fyeA c.23.16.4 31477 1hpi 71 2.73e+01 1ckuA g.35.1.1 44995 1vdwA 254 2.78e+01 e.7.1.1 100569 1dekA 241 2.79e+01 1dekA c.37.1.1 31842 1i9gA 280 2.82e+01 c.66.1.13 62090 1xttA 216 2.83e+01 1k2xB 143 2.85e+01 1j58A 385 2.88e+01 b.82.1.2 71531 1b5fB 87 2.88e+01 1b5fB 1khcA 147 2.92e+01 b.34.9.2 68608 1yx1A 264 2.93e+01 1wjxA 122 2.93e+01 1eyqA 222 2.93e+01 1eypA d.36.1.1 38534 1bcpB 199 2.94e+01 1bcpB b.40.2.1,d.169.1.2 25120,42429 1f89A 291 2.97e+01 d.160.1.1 64988 1g7nA 131 3.00e+01 b.60.1.2 83274 1iz6A 138 3.04e+01 b.34.5.2,b.40.4.5 76976,76977 1ogwA 76 3.04e+01 d.15.1.1 87001 1h8eH 146 3.05e+01 1e79H b.93.1.1 60757 1cs6A 382 3.05e+01 1cs6A b.1.1.4,b.1.1.4,b.1.1.4,b.1.1.4 21760,21761,21762,21763 1gpc 218 3.10e+01 1gpc b.40.4.7 25393 1pkoA 139 3.11e+01 b.1.1.1 88147 1ogoX 574 3.17e+01 b.133.1.1,b.80.1.10 92925,92926 1pe9A 361 3.19e+01 b.80.1.1 94595 1gsa 316 3.24e+01 1gsa c.30.1.3,d.142.1.1 31718,41477 1edg 380 3.24e+01 1edg c.1.8.3 28807 1u60A 310 3.32e+01 e.3.1.2 107692 1dec 39 3.33e+01 1dec g.3.15.2 44376 1inlA 296 3.37e+01 c.66.1.17 66220 1kwgA 645 3.39e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1p5dX 463 3.41e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1c8cA 64 3.41e+01 1azpA b.34.13.1 59084 1euwA 152 3.42e+01 1dupA b.85.4.1 28349 1j99A 293 3.45e+01 c.37.1.5 71618 1eu1A 780 3.47e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 1ey4A 149 3.47e+01 1snc b.40.1.1 24815 1ne9A 335 3.55e+01 d.108.1.4,d.108.1.4 91839,91840 1g8aA 227 3.55e+01 c.66.1.3 90506 1bf2 750 3.56e+01 1bf2 b.1.18.2,b.71.1.1,c.1.8.1 21860,27787,28774 1f7lA 121 3.58e+01 1f7lA d.150.1.2 59666 1jb7B 260 3.63e+01 1otcB b.40.4.3 62839 1onwA 390 3.64e+01 b.92.1.7,c.1.9.13 87172,87173 1oewA 329 3.66e+01 b.50.1.2 86924 1eaiC 61 3.68e+01 1eaiC g.22.1.1 44894 1fjgI 128 3.70e+01 1fjfI d.14.1.1 37559 1h7cA 108 3.75e+01 a.7.5.1 70914 1o6vA 466 3.75e+01 b.1.18.15,c.10.2.1 81099,81100 1r6jA 82 3.76e+01 b.36.1.1 97151 1w6sA 599 3.78e+01 1h2bA 359 3.80e+01 b.35.1.2,c.2.1.1 90543,90544 1hfoA 113 3.80e+01 d.80.1.3 61006 1s95A 333 3.81e+01 d.159.1.3 105375 1jihA 531 3.86e+01 d.240.1.1,e.8.1.7 90374,90375 4fiv 113 3.88e+01 1fmb b.50.1.1 26762 1nwwA 149 3.88e+01 d.17.4.8 86306 1t61A 229 3.91e+01 d.169.1.6,d.169.1.6 106529,106530 1f2tA 149 3.91e+01 1f2tA c.37.1.12 32373 1eexA 554 3.95e+01 1dioA c.1.19.3 29650 1pbjA 125 3.95e+01 d.37.1.1,d.37.1.1 94414,94415 1tmxA 293 3.97e+01 1dabA 539 3.97e+01 1dabA b.80.1.7 28049 1juhA 350 3.97e+01 b.82.1.5 71884 1eu8A 409 3.98e+01 1eu8A c.94.1.1 59502 1e6wA 260 3.98e+01 1e6wA c.2.1.2 59326 1iq9A 61 4.01e+01 g.7.1.1 90669 1vr9A 213 4.06e+01 1i8dA 213 4.07e+01 b.43.4.3,b.43.4.3 61953,61954 1gqzA 274 4.07e+01 d.21.1.1,d.21.1.1 83311,83312 1j1iA 296 4.15e+01 c.69.1.10 83977 1senA 164 4.15e+01 c.47.1.1 105465 1o6sB 105 4.17e+01 b.1.6.1 81096 1hxvA 113 4.20e+01 d.26.1.1 71089 1yg9A 330 4.20e+01 1q1fA 151 4.21e+01 a.1.1.2 104476 1qwrA 319 4.22e+01 b.82.1.3 96491 1frb 315 4.25e+01 1frb c.1.7.1 28665 1jhfA 202 4.32e+01 a.4.5.2,b.87.1.1 63057,63058 1b8oA 284 4.35e+01 1b8oA c.56.2.1 33762 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