# List of top-scoring protein chains for t2k-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.soe.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 2jz5A 91 1.98e-17 1u55A 188 8.78e-02 d.278.1.1 107677 2cz8A 69 1.11e-01 2qx2A 344 3.06e-01 1zb9A 143 3.37e-01 2g6yA 217 4.37e-01 2yxyA 115 5.11e-01 1wr2A 238 6.67e-01 1k2yX 463 8.45e-01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 2cy7A 396 1.02e+00 2cstA 411 1.04e+00 1ajsA c.67.1.1 34273 2obdA 476 1.10e+00 2fjlA 150 1.12e+00 b.55.1.1 133611 1fi8A 228 1.13e+00 5ptp b.47.1.2 26374 1p5dX 463 1.26e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 2gagA 965 1.34e+00 1icxA 155 1.47e+00 d.129.3.1 71191 1wteA 272 1.77e+00 c.52.1.29 114876 1in0A 163 2.01e+00 d.58.49.1,d.58.49.1 83694,83695 1gyhA 318 2.15e+00 b.67.2.1 70757 1zpwX 90 2.42e+00 d.58.58.1 125478 1ftrA 296 2.44e+00 1ftrA d.58.33.1,d.58.33.1 39485,39486 1m5sA 297 2.68e+00 d.58.33.1,d.58.33.1 74511,74512 1yb3A 175 2.68e+00 d.296.1.2 122869 1c7nA 399 2.81e+00 1d2fA c.67.1.3 34413 2z1eA 342 2.94e+00 1gydB 315 2.99e+00 b.67.2.1 70751 1f45B 197 3.35e+00 1f45B a.26.1.1 59642 1iujA 106 3.36e+00 d.58.4.5 90701 2i39A 137 3.50e+00 1f9mA 112 3.57e+00 1erv c.47.1.1 32736 1kcgC 178 3.84e+00 d.19.1.1 68440 1iznB 277 3.95e+00 e.43.1.2 83848 1yycA 174 4.11e+00 3b8mA 280 4.53e+00 2gpyA 233 4.54e+00 2b5eA 504 4.57e+00 c.47.1.2,c.47.1.2,c.47.1.2,c.47.1.2 127888,127889,127890,127891 2p10A 286 4.82e+00 1vhiA 142 4.85e+00 1b3tA d.58.8.1 39230 2olnA 397 5.32e+00 1skoB 130 5.34e+00 d.110.7.1 105677 2dtcA 126 5.80e+00 3b49A 211 5.82e+00 2rb9A 334 5.90e+00 1vetB 125 5.95e+00 d.110.7.1 108554 1xkzA 255 6.20e+00 e.3.1.1 115426 1pv9A 348 6.54e+00 c.55.2.1,d.127.1.1 95157,95158 2z0dA 357 6.56e+00 2qyxA 238 6.66e+00 1w0dA 337 6.75e+00 c.77.1.1 114060 1zq1C 633 6.96e+00 a.182.1.2,d.74.4.1,d.128.1.5 125493,125494,125495 1pcaA 95 7.06e+00 d.58.3.1 39063 1upqA 123 7.28e+00 b.55.1.1 113392 2cyyA 151 7.43e+00 a.4.5.32,d.58.4.2 131028,131029 1y4oA 104 7.44e+00 1tkeA 224 7.85e+00 d.15.10.1,d.67.1.1 112470,112471 1irsA 112 7.94e+00 1qqgA b.55.1.2 26991 1jjhA 86 8.07e+00 2bopA d.58.8.1 63119 2hq4A 161 8.16e+00 1uhvA 500 8.37e+00 b.71.1.2,c.1.8.3 99402,99403 2bjdA 101 8.40e+00 1j6uA 469 8.50e+00 c.5.1.1,c.59.1.1,c.72.2.1 77094,77095,77096 1faaA 124 8.86e+00 1erv c.47.1.1 32738 1jl2A 156 8.97e+00 c.55.3.1 66822 1a6zA 275 9.04e+00 1agdA b.1.1.2,d.19.1.1 20781,38280 2i7xA 717 9.11e+00 2jyaA 106 9.39e+00 1b3tA 147 9.44e+00 1b3tA d.58.8.1 39228 1ri7A 171 9.57e+00 a.4.5.32,d.58.4.2 97504,97505 1wy2A 351 9.60e+00 2imjA 166 9.99e+00 1yspA 181 1.04e+01 2e7vA 121 1.04e+01 2hytA 197 1.08e+01 1pjqA 457 1.11e+01 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 1vixA 420 1.13e+01 c.56.5.4,d.58.19.1 100777,100778 2fipA 115 1.13e+01 2pu9C 111 1.15e+01 1mai 131 1.16e+01 1mai 1maiA 131 1.16e+01 b.55.1.1 26951 1nb9A 147 1.23e+01 b.43.5.1 85515 2fb6A 117 1.24e+01 1el5A 389 1.28e+01 1b3mA c.3.1.2,d.16.1.3 30369,37937 1y23A 145 1.28e+01 d.13.1.1 116394 1ylxA 103 1.30e+01 d.82.5.1 123677 1shwB 181 1.31e+01 b.18.1.4 105563 1xo8A 151 1.33e+01 b.1.25.1 115698 1ru0A 105 1.38e+01 d.74.1.1 111937 2pptA 155 1.39e+01 2g3bA 208 1.40e+01 a.4.1.9,a.121.1.1 134558,134559 1t3lA 337 1.42e+01 b.34.2.1,c.37.1.1 106358,106359 1fnoA 417 1.43e+01 d.58.19.1,c.56.5.4 70145,75841 1dq3A 454 1.48e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1jfmA 174 1.49e+01 d.19.1.1 66640 2ftrA 108 1.51e+01 d.58.4.15 134077 2gf3A 389 1.51e+01 c.3.1.2,d.16.1.3 135070,135071 1l9cA 389 1.52e+01 c.3.1.2,d.16.1.3 77815,77816 2pfrA 294 1.55e+01 2h6bA 250 1.56e+01 1w4vA 119 1.56e+01 1qysA 106 1.56e+01 k.41.1.1 96603 1e25A 282 1.56e+01 1e25A e.3.1.1 42731 2uubJ 105 1.58e+01 d.58.15.1 139941 1pyaB 228 1.61e+01 1pyaB 1nukA 183 1.66e+01 1nukA b.18.1.4 23721 1ttwA 138 1.71e+01 d.198.1.1 107308 1drw 273 1.72e+01 1drw 1drwA 273 1.72e+01 c.2.1.3,d.81.1.3 30057,39972 2ys1A 113 1.72e+01 1qqgA 264 1.78e+01 1qqgA b.55.1.2,b.55.1.2 26987,26988 1rm4A 337 1.79e+01 c.2.1.3,d.81.1.1 105000,105001 2dy0A 190 1.81e+01 2hd5A 359 1.81e+01 2q8uA 336 1.83e+01 1tr0A 108 1.84e+01 d.58.4.4 107261 1cg2A 393 1.85e+01 1cg2A c.56.5.4,d.58.19.1 33844,39360 2nlyA 245 1.88e+01 c.6.2.7 138364 2zfzA 79 1.89e+01 1eaf 243 1.91e+01 1eaf 1nswA 105 1.92e+01 c.47.1.1 92097 1aye 401 1.92e+01 1aye 1udsA 255 1.96e+01 d.14.1.4,d.101.1.1 99219,99220 2al6A 375 1.96e+01 a.11.2.1,b.55.1.5,d.15.1.4 126966,126967,126968 2d4rA 147 1.98e+01 d.129.3.6 131256 1iq8A 582 1.99e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1th7A 81 2.06e+01 b.38.1.1 119264 2ichA 335 2.07e+01 1mhxA 65 2.08e+01 d.15.7.1 79134 1p1lA 102 2.08e+01 d.58.5.2 87695 1sf9A 128 2.11e+01 b.34.15.1 98831 2oczA 231 2.16e+01 2ex5A 207 2.21e+01 1t0hA 132 2.26e+01 b.34.2.1 106207 2z1uA 343 2.26e+01 1vq2A 193 2.27e+01 c.97.1.2 114004 1xeeA 91 2.28e+01 1tz0A 114 2.28e+01 d.58.4.5 107463 2uuzA 99 2.31e+01 2ek0A 90 2.34e+01 2hdiA 639 2.36e+01 2ifsA 169 2.38e+01 2op5A 117 2.38e+01 1hqcA 324 2.40e+01 1hqcA a.4.5.11,c.37.1.20 16127,32424 2fp1A 166 2.41e+01 a.130.1.4 133891 1kjvA 284 2.45e+01 b.1.1.2,d.19.1.1 77421,77422 1u58A 253 2.49e+01 2b1pA 355 2.50e+01 d.144.1.7 127672 1nw2A 105 2.53e+01 c.47.1.1 92215 1ib8A 164 2.54e+01 b.38.2.1,d.52.4.1 71168,71169 2g0qA 173 2.54e+01 1kmqA 184 2.57e+01 c.37.1.8 84412 2iv2X 715 2.59e+01 b.52.2.2,c.81.1.1 137714,137715 1kq6A 141 2.61e+01 d.189.1.1 91020 2o66A 135 2.62e+01 1i2hA 168 2.62e+01 b.55.1.4 71103 1r6yA 115 2.67e+01 d.58.4.11 111711 2qndA 144 2.68e+01 1evhA 112 2.70e+01 1evhA b.55.1.4 26997 3biqA 467 2.71e+01 3bn4A 122 2.74e+01 1q5yA 85 2.78e+01 d.58.18.4 95950 2f6lA 166 2.78e+01 a.130.1.4 133049 2ywlA 180 2.79e+01 2aehA 369 2.80e+01 a.11.2.1,b.55.1.5,d.15.1.4 126625,126626,126627 1dpbA 243 2.83e+01 c.43.1.1 32618 1cm7A 363 2.85e+01 1cnzA c.77.1.1 35063 1xkgA 312 2.88e+01 d.3.1.1 122081 1j0dA 341 2.93e+01 c.79.1.1 83902 1l0oA 150 2.93e+01 d.122.1.3 73403 1j7gA 144 2.96e+01 c.110.1.1 84130 1kluD 239 2.97e+01 b.40.2.2,d.15.6.1 72728,72729 2b25A 336 2.99e+01 c.66.1.13 127699 1p3dA 475 3.01e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1v5pA 126 3.01e+01 b.55.1.1 108382 2a4xA 138 3.04e+01 d.32.1.2 126166 2fggA 101 3.05e+01 d.50.5.1 133438 2p5mA 83 3.07e+01 3bueA 79 3.12e+01 1v98A 140 3.15e+01 1uxtA 501 3.17e+01 c.82.1.1 108125 2vobA 652 3.18e+01 1tx4B 178 3.25e+01 1ctqA c.37.1.8 32045 1zx2A 147 3.27e+01 1oyc 400 3.29e+01 1oyc 1oycA 400 3.29e+01 c.1.4.1 28603 2q24A 194 3.29e+01 2od6A 110 3.30e+01 1u5fA 148 3.31e+01 b.55.1.1 119542 1gx5A 536 3.32e+01 e.8.1.4 70682 2fqmA 75 3.36e+01 1q7lA 198 3.38e+01 c.56.5.4 96044 1aisA 182 3.40e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 2je8A 848 3.49e+01 1we0A 187 3.56e+01 c.47.1.10 120930 2f02A 323 3.56e+01 c.72.1.1 132649 3b4tA 262 3.61e+01 1qf6A 642 3.64e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1zo2A 129 3.64e+01 2gcoA 201 3.68e+01 3cj8A 236 3.71e+01 3bevA 274 3.77e+01 1f6dA 376 3.80e+01 1f6dA c.87.1.3 35467 1wwrA 171 3.82e+01 c.97.1.2 121366 1d3uA 181 3.82e+01 1ytbA d.129.1.1,d.129.1.1 41290,41291 1y7rA 133 3.82e+01 d.108.1.1 122716 1kllA 130 3.85e+01 d.32.1.2 72720 1gsoA 431 3.86e+01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 1ko3A 230 3.88e+01 d.157.1.1 90974 1umsA 174 3.90e+01 1hfc d.92.1.11 40368 1sqeA 109 3.92e+01 d.58.4.5 105908 1r9wA 145 3.92e+01 d.89.1.2 97264 2qtpA 194 3.94e+01 2cvjA 180 3.95e+01 2zbcA 83 3.96e+01 2pgcA 207 3.96e+01 2o0uA 364 3.97e+01 d.144.1.7 138868 1umgA 362 4.01e+01 d.280.1.1 107956 2qo4A 126 4.06e+01 1vbkA 307 4.11e+01 c.26.2.6,d.308.1.1 119957,119958 1a3wA 500 4.13e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27060,29288,33142 1fjgJ 105 4.16e+01 1fjfJ d.58.15.1 39330 2cqeA 98 4.17e+01 g.66.1.1,g.66.1.1 130720,130721 3c5oA 157 4.17e+01 2anuA 255 4.21e+01 c.6.3.1 127058 2rn2 155 4.22e+01 2rn2 2amhA 207 4.24e+01 c.51.4.2 127019 2hhiA 204 4.25e+01 2i5uA 83 4.28e+01 2p4mA 219 4.31e+01 2bj0A 203 4.33e+01 1k5nA 276 4.33e+01 b.1.1.2,d.19.1.1 77266,77267 2jraA 67 4.35e+01 2iykA 162 4.36e+01 1b4bA 71 4.40e+01 1b4aA d.74.2.1 39718 1u2bA 138 4.42e+01 b.55.1.1 119474 1kf6A 602 4.42e+01 a.7.3.1,c.3.1.4,d.168.1.1 72394,72395,72396 1pmnA 364 4.44e+01 d.144.1.7 94907 2cw9A 194 4.45e+01 d.17.4.13 130920 1bxnA 485 4.46e+01 1burA c.1.14.1,d.58.9.1 29376,39282 1t00A 112 4.50e+01 2p62A 241 4.51e+01 2haiA 576 4.55e+01 1b4aA 149 4.57e+01 1b4aA a.4.5.3,d.74.2.1 16088,39721 1qgvA 142 4.60e+01 1qgvA c.47.1.8 33056 2oojA 141 4.65e+01 2nrqA 159 4.69e+01 2co1B 20 4.69e+01 1wtjA 343 4.70e+01 1ejbA 168 4.80e+01 1rvv1 c.16.1.1 59417 1an7A 136 4.81e+01 1seiA d.140.1.1 41465 1mkmA 249 4.85e+01 a.4.5.33,d.110.2.2 79242,79243 1j5kA 89 4.86e+01 d.51.1.1 71565 2yx1A 336 4.87e+01 1vjqA 79 4.90e+01 k.43.1.1 100830 1vgvA 384 4.92e+01 c.87.1.3 100608 2abyA 146 4.97e+01 1wl7A 312 4.98e+01 b.67.2.1 120996 2csuA 457 5.02e+01 c.2.1.8,c.23.4.1,c.23.4.1 130781,130782,130783 1t7vA 278 5.12e+01 b.1.1.2,d.19.1.1 112302,112303 1fgyA 127 5.15e+01 1faoA b.55.1.1 26976 1ud9A 245 5.16e+01 d.131.1.2,d.131.1.2 107768,107769 1tcrA 202 5.19e+01 1tcrA b.1.1.1,b.1.1.2 20605,21549 2v7bA 529 5.20e+01 2rfqA 394 5.21e+01 2vfxA 206 5.22e+01 1s9aA 257 5.24e+01 b.3.6.1 105379 2ob5A 153 5.24e+01 1rfmA 344 5.34e+01 c.122.1.1 97385 1dcoA 104 5.36e+01 1dcpA d.74.1.1 39680 1pczA 191 5.37e+01 1ytbA d.129.1.1,d.129.1.1 41292,41293 2ftsA 419 5.38e+01 b.85.6.1,b.103.1.1,c.57.1.2 134079,134080,134081 2pn6A 150 5.43e+01 1r7lA 110 5.44e+01 d.277.1.1 104837 2e0cA 409 5.45e+01 2prvA 153 5.51e+01 1j27A 102 5.53e+01 d.58.50.1 90778 3besR 250 5.58e+01 2cr9A 139 5.62e+01 d.297.1.1 130735 1fjcA 96 5.64e+01 1fjcA d.58.7.1 39212 2f1fA 164 5.66e+01 d.58.18.6,d.58.18.6 132760,132761 1ksyA 154 5.67e+01 d.89.1.2 72948 1vs3A 249 5.68e+01 2r78A 117 5.68e+01 2imlA 199 5.69e+01 2a15A 139 5.69e+01 d.17.4.3 125973 2vjxA 846 5.73e+01 1n35A 1267 5.75e+01 e.8.1.4 79935 2fe3A 145 5.76e+01 2i7cA 283 5.77e+01 2j0vA 212 5.77e+01 1lfoA 127 5.81e+01 b.60.1.2 27223 2o18A 340 5.86e+01 2dx6A 159 5.87e+01 1l2mA 118 5.90e+01 d.89.1.4 77657 2pyyA 228 5.92e+01 2oauA 306 5.93e+01 b.38.1.3,d.58.43.1,f.34.1.1 138978,138979,138980 1txjA 171 5.93e+01 b.88.1.2 107424 2joeA 139 5.94e+01 1n2fA 142 6.01e+01 d.227.1.1 79853 2phcB 225 6.05e+01 1th8A 145 6.11e+01 d.122.1.3 106908 1cnzA 363 6.15e+01 1cnzA c.77.1.1 35061 1tyoA 435 6.17e+01 1u02A 239 6.20e+01 c.108.1.15 107538 1r6lA 239 6.20e+01 d.14.1.4,d.101.1.1 97153,97154 1qwiA 143 6.24e+01 d.227.1.1 96474 1gxuA 91 6.25e+01 d.58.10.1 76378 2bopA 85 6.30e+01 2bopA d.58.8.1 39217 1xodA 118 6.30e+01 b.55.1.4 122202 2q22A 139 6.43e+01 1csmA 256 6.45e+01 5csmA a.130.1.2 19495 1gqnA 252 6.46e+01 c.1.10.1 90514 2nscA 109 6.47e+01 1xkiA 162 6.50e+01 b.60.1.1 115408 1ddvA 111 6.57e+01 1evhA b.55.1.4 27002 1zzkA 82 6.58e+01 d.51.1.1 125909 2gw4B 162 6.59e+01 1vkwA 218 6.59e+01 d.90.1.2 108695 1ddwA 120 6.69e+01 1evhA b.55.1.4 27001 1tuvA 114 6.71e+01 d.58.4.11 112665 2hz5A 106 6.73e+01 2hqkA 219 6.76e+01 1l6pA 125 6.84e+01 b.1.17.1 73626 1c76A 136 6.84e+01 2sak d.15.5.1 37718 2nn6B 249 6.86e+01 2ar9A 278 6.92e+01 2g3mA 693 6.93e+01 1y4iA 398 6.96e+01 c.67.1.3 122619 1q8iA 783 6.98e+01 c.55.3.5,e.8.1.1 96208,96209 1a0p 290 6.99e+01 1a0p 1a0pA 290 6.99e+01 a.60.9.1,d.163.1.1 18105,42165 1t0hB 224 6.99e+01 c.37.1.1 106208 1kgyA 181 7.00e+01 b.18.1.4 72449 2sak 121 7.03e+01 2sak 2sakA 121 7.03e+01 d.15.5.1 37711 1usmA 80 7.08e+01 d.74.1.1 99876 2yutA 207 7.15e+01 1r0pA 312 7.21e+01 d.144.1.7 96734 1ve3A 227 7.27e+01 c.66.1.43 120010 1cxvA 164 7.29e+01 1ck7A d.92.1.11 40404 2eu9A 355 7.31e+01 2axyA 73 7.32e+01 d.51.1.1 127532 1dbdA 100 7.33e+01 2bopA d.58.8.1 39218 2uv0E 175 7.35e+01 1j4wA 174 7.38e+01 d.51.1.1,d.51.1.1 71529,71530 2atzA 180 7.39e+01 d.264.1.3 127317 2c3zA 222 7.50e+01 1vp8A 201 7.50e+01 c.49.1.2 113947 1azvA 153 7.53e+01 1mfmA b.1.8.1 22247 2pvpA 367 7.58e+01 2q79A 93 7.65e+01 2e7xA 150 7.66e+01 2jigA 224 7.68e+01 1zl0A 311 7.75e+01 c.8.10.1,c.23.16.7 125231,125232 2vr4A 846 7.75e+01 1itbB 315 7.75e+01 1itbB b.1.1.4,b.1.1.4,b.1.1.4 21720,21721,21722 1zupA 315 7.80e+01 c.55.3.11 125681 2cvkA 110 7.86e+01 1agdA 276 7.89e+01 1agdA b.1.1.2,d.19.1.1 20741,38260 1aoxA 203 7.91e+01 1aoxA c.62.1.1 34151 3ctvA 110 7.92e+01 1jytA 163 7.93e+01 b.94.1.1 67489 2h8eA 120 7.93e+01 1vlcA 366 7.94e+01 c.77.1.1 108743 1naqA 112 7.98e+01 d.58.5.2 91761