# 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 1htp 131 3.95e-03 1htp 1hpcA 131 7.53e-03 1htp b.84.1.1 28221 1a65A 504 8.72e-03 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 2qnkA 286 1.02e-02 1zkoA 136 1.24e-02 1hfuA 503 1.89e-02 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1us8A 147 2.17e-02 c.37.1.12 99859 1gycA 499 4.07e-02 b.6.1.3,b.6.1.3,b.6.1.3 70748,70749,70750 1brwA 433 4.21e-02 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 2ov0A 105 6.42e-02 1aac 105 7.02e-02 1aac 2dsjA 423 7.09e-02 2idqA 105 7.12e-02 2gbaA 105 7.50e-02 1y8oB 128 7.64e-02 b.84.1.1 122759 1f2tA 149 7.66e-02 1f2tA c.37.1.12 32373 1bdo 80 7.95e-02 1bdo 1bdoA 80 7.95e-02 b.84.1.1 28214 1bxaA 105 7.97e-02 1aac b.6.1.1 22839 1sfdA 105 8.07e-02 b.6.1.1 105480 2g3mA 693 1.02e-01 2cavA 445 1.05e-01 1dgwA b.82.1.2,b.82.1.2 28094,28095 2evbA 74 1.13e-01 1vj2A 126 1.14e-01 b.82.1.10 100796 1yu4A 381 1.50e-01 b.163.1.1,d.169.1.8 124033,124034 1x82A 190 1.57e-01 b.82.1.7 114955 1gjxA 81 1.62e-01 b.84.1.1 65222 1qxrA 189 1.64e-01 b.82.1.7 96552 1dgwA 178 1.82e-01 1dgwA b.82.1.2 28090 2gcuA 245 1.97e-01 1ghj 79 2.08e-01 1ghj 3cnwA 148 2.08e-01 2gaiA 633 2.18e-01 1yu0A 381 2.25e-01 b.163.1.1,d.169.1.8 124025,124026 1cauA 181 2.28e-01 1dgwA b.82.1.2 28102 2i45A 107 2.32e-01 1id2A 106 2.49e-01 1aac b.6.1.1 62288 1tdtA 259 2.82e-01 3tdt b.81.1.2 28055 2eenA 183 3.10e-01 3tdt 274 3.22e-01 3tdt 3tdtA 274 3.22e-01 b.81.1.2 28053 1k8mA 93 3.23e-01 b.84.1.1 68314 1yu1A 381 3.28e-01 b.163.1.1,d.169.1.8 124027,124028 1nr0A 611 3.34e-01 b.69.4.1,b.69.4.1 86078,86079 1v10A 521 3.66e-01 b.6.1.3,b.6.1.3,b.6.1.3 108224,108225,108226 1yu3A 381 3.82e-01 b.163.1.1,d.169.1.8 124031,124032 1cs6A 382 3.91e-01 1cs6A b.1.1.4,b.1.1.4,b.1.1.4,b.1.1.4 21760,21761,21762,21763 1gpr 162 4.04e-01 1gpr 1gprA 162 4.04e-01 b.84.3.1 28267 2gc1A 188 4.07e-01 b.82.1.7 134928 1aozA 552 4.11e-01 1aozA b.6.1.3,b.6.1.3,b.6.1.3 23124,23125,23126 1yu2A 381 4.17e-01 b.163.1.1,d.169.1.8 124029,124030 1seiA 130 4.76e-01 1seiA d.140.1.1 41463 1vdzA 588 4.84e-01 1ej6A 1289 5.35e-01 i.7.1.1 45967 1y7rA 133 5.68e-01 d.108.1.1 122716 1qjoA 80 5.81e-01 1iyu b.84.1.1 28229 1j99A 293 6.02e-01 c.37.1.5 71618 1j1yA 136 6.89e-01 d.38.1.5 90776 2j2zB 173 6.92e-01 1yavA 159 6.94e-01 d.37.1.1,d.37.1.1 116595,116596 2be1A 339 7.01e-01 1kyaA 499 7.16e-01 b.6.1.3,b.6.1.3,b.6.1.3 73203,73204,73205 2p17A 277 7.33e-01 2glwA 92 7.66e-01 1pmyA 123 7.68e-01 b.6.1.1 22888 2a6hC 1119 9.22e-01 e.29.1.1 126264 1v25A 541 9.90e-01 e.23.1.1 108275 1m1hA 248 1.02e+00 b.114.1.1,d.58.42.1 78415,78416 2qt6A 498 1.12e+00 1o4tA 133 1.12e+00 b.82.1.9 86622 1gkuB 1054 1.20e+00 c.37.1.16,c.37.1.16,e.10.1.1 65257,65258,65259 2hrgA 496 1.21e+00 1k82A 268 1.26e+00 a.156.1.2,b.113.1.1,g.39.1.8 75866,75867,75868 1n26A 325 1.27e+00 b.1.1.4,b.1.2.1,b.1.2.1 79850,79851,79852 1k5cA 335 1.45e+00 b.80.1.3 72076 1ds6B 180 1.49e+00 1rhoA b.1.18.8 21898 1fm4A 159 1.50e+00 1bv1 d.129.3.1 76186 1x1oA 286 1.52e+00 1rc6A 261 1.60e+00 b.82.1.11 97287 1v6iA 232 1.62e+00 b.29.1.1 100383 3btxA 204 1.88e+00 1zeqX 84 1.90e+00 2vesA 299 1.93e+00 1mq7A 154 1.96e+00 b.85.4.1 79404 2qm1A 326 1.97e+00 2r15A 212 1.99e+00 3b98A 475 2.01e+00 2qybA 181 2.14e+00 1nkqA 259 2.25e+00 d.177.1.1 103862 1rpxA 230 2.30e+00 1rpxA c.1.2.2 28536 1mzyA 333 2.33e+00 b.6.1.3,b.6.1.3 103848,103849 3b6hA 498 2.35e+00 2p1gA 249 2.43e+00 2e9qA 459 2.52e+00 2dfuA 264 2.55e+00 2sli 679 2.56e+00 2sli 2sliA 679 2.56e+00 b.29.1.9,b.68.1.1 24274,27611 1an7A 136 2.70e+00 1seiA d.140.1.1 41465 2qggA 182 2.74e+00 1qhqA 140 2.76e+00 1qhqA b.6.1.1 63326 1jl0A 334 2.77e+00 1jenA d.156.1.1 63155 2e63A 170 2.81e+00 1pbyA 489 2.94e+00 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 1yx0A 159 2.97e+00 d.108.1.1 124168 1ybyA 215 2.99e+00 2r2cA 183 3.08e+00 2b1yA 104 3.12e+00 b.156.1.1 127684 1hleA 345 3.13e+00 1ovaA e.1.1.1 42618 1vr8A 142 3.20e+00 d.312.1.1 120445 1lmeA 176 3.30e+00 d.167.1.1 84629 2j97A 109 3.33e+00 1sixA 174 3.38e+00 b.85.4.1 98892 2r77A 205 3.40e+00 2eigA 234 3.42e+00 1ru4A 400 3.43e+00 b.80.1.9 97836 1yhfA 115 3.48e+00 b.82.1.9 123176 1ivgA 388 3.53e+00 b.68.1.1 27578 1bteA 97 3.58e+00 1bteA g.7.1.3 44463 2ea7A 434 3.59e+00 2q3uA 383 3.62e+00 d.126.1.6 139809 1vkpA 383 3.63e+00 d.126.1.6 108686 2qcpX 80 3.68e+00 1fqtA 112 3.73e+00 1fqtA b.33.1.1 24441 2aujD 309 3.81e+00 2oziA 98 3.83e+00 2oypA 109 4.14e+00 1bxsA 501 4.21e+00 1bpwA c.82.1.1 35357 1zghA 260 4.24e+00 b.46.1.1,c.65.1.1 125028,125029 1xrkA 124 4.26e+00 d.32.1.2 115881 2dyiA 162 4.32e+00 1wriA 93 4.36e+00 d.15.4.1 114838 1wzcA 249 4.43e+00 c.108.1.10 121491 1pazA 123 4.45e+00 b.6.1.1 22878 2e4qA 109 4.46e+00 1hmt 132 4.50e+00 1hmt 1hmtA 132 4.50e+00 b.60.1.2 27169 2in0A 139 4.56e+00 2yxmA 100 4.59e+00 1oe1A 336 4.63e+00 b.6.1.3,b.6.1.3 86891,86892 1j1lA 290 4.70e+00 b.82.1.12 90766 2gu9A 113 4.77e+00 2b8wA 328 4.85e+00 2zdiC 151 4.89e+00 2p18A 311 4.91e+00 1juhA 350 5.06e+00 b.82.1.5 71884 1gwmA 153 5.17e+00 b.18.1.19 83348 2aq5A 402 5.22e+00 1cseI 71 5.22e+00 1egpA d.40.1.1 38559 2b9uA 176 5.22e+00 1at0 145 5.23e+00 1at0 1at0A 145 5.23e+00 b.86.1.1 28374 1rfmA 344 5.31e+00 c.122.1.1 97385 1y0yA 353 5.35e+00 b.49.3.1,c.56.5.4 122514,122515 1pz7A 204 5.40e+00 b.29.1.4 95405 2gzqA 200 5.44e+00 1zkcA 197 5.55e+00 b.62.1.1 125182 1jenA 267 5.71e+00 1jenA 2vroA 532 5.77e+00 2jenA 261 5.78e+00 1p0iA 529 5.81e+00 c.69.1.1 93867 2g5fA 450 5.81e+00 d.161.1.1 134654 1upiA 225 5.81e+00 b.82.1.1 99757 2btiA 63 5.84e+00 2v24A 208 6.01e+00 3brgC 427 6.15e+00 2iagA 482 6.20e+00 1op3H 225 6.24e+00 b.1.1.1,b.1.1.2 87208,87209 2f41A 121 6.38e+00 d.38.1.5 132904 3csvA 333 6.44e+00 1qqjA 419 6.49e+00 1qcnA b.34.8.1,d.177.1.1 59034,59035 1m6iA 493 6.50e+00 c.3.1.5,c.3.1.5,d.87.1.1 74533,74534,74535 2ys3A 137 6.57e+00 1oj4A 283 6.64e+00 d.14.1.5,d.58.26.5 93083,93084 1f8eA 388 6.66e+00 2qwc b.68.1.1 59694 2axwA 134 6.71e+00 1kafA 108 6.72e+00 d.199.1.1 68372 1qcoA 423 6.77e+00 1qcnA b.34.8.1,d.177.1.1 59021,59022 1u0tA 307 7.04e+00 e.52.1.1 107567 1r75A 141 7.18e+00 b.134.1.1 97189 2qedA 258 7.35e+00 1oi6A 205 7.42e+00 b.82.1.1 103940 1wluA 136 7.44e+00 d.38.1.5 121015 2b2nA 344 7.49e+00 c.37.1.19 127710 1ef8A 261 7.49e+00 1ef8A c.14.1.3 30921 2fl7A 232 7.56e+00 1yfuA 174 7.69e+00 b.82.1.20 123094 1ixlA 131 7.69e+00 d.38.1.5 90717 1e69B 322 7.72e+00 1e69B c.37.1.12 32377 1qpoA 284 7.77e+00 1qpoA c.1.17.1,d.41.2.1 29561,38597 1lktA 104 7.85e+00 1lktA b.90.1.1 28398 2o62A 270 7.98e+00 1nszA 347 8.02e+00 b.30.5.4 80724 1azdA 237 8.08e+00 1nls b.29.1.1 24020 2yu1A 451 8.10e+00 1poiA 317 8.20e+00 1poiA c.124.1.2 34153 1bv1 159 8.24e+00 1bv1 1l8rA 101 8.30e+00 a.6.1.4 73700 2qwc 388 8.31e+00 2qwc 1f5nA 592 8.31e+00 1dg3A a.114.1.1,c.37.1.8 19077,32152 2rmpA 361 8.32e+00 2rmpA b.50.1.2 26825 1rjcA 137 8.40e+00 1v4sA 455 8.48e+00 c.55.1.3,c.55.1.3 100309,100310 2b5iD 217 8.50e+00 g.18.1.1,g.18.1.1 127900,127901 1tu6A 215 8.52e+00 d.3.1.1 107318 2a9gA 418 8.57e+00 d.126.1.4 126435 1xnkA 196 8.67e+00 b.29.1.11 122195 2cghA 268 9.08e+00 1lfkA 398 9.09e+00 a.104.1.1 77926 1xfpA 142 9.11e+00 b.1.1.1 109587 1mdbA 539 9.22e+00 e.23.1.1 79008 2p9oA 169 9.24e+00 1cb8A 678 9.31e+00 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1wzoA 246 9.31e+00 2f4pA 147 9.53e+00 b.82.1.9 132933 2hl0A 143 9.55e+00 1h1aA 191 9.60e+00 b.29.1.11 83450 1ub0A 258 9.62e+00 c.72.1.2 88394 1h9mA 145 9.97e+00 1h9jA b.40.6.2,b.40.6.2 60833,60834 1i52A 236 1.00e+01 1i52A c.68.1.13 61767 1euvA 221 1.01e+01 1euvA d.3.1.7 37133 2obwA 258 1.01e+01 2j73A 103 1.01e+01 1hyoA 421 1.01e+01 1qcnA b.34.8.1,d.177.1.1 59001,59002 1y2qA 143 1.02e+01 2qo4A 126 1.02e+01 1xfoA 357 1.03e+01 b.49.3.1,c.56.5.4 115265,115266 2q30A 110 1.04e+01 2gllA 171 1.05e+01 2b6hA 192 1.05e+01 c.37.1.8 127994 1rhfA 182 1.06e+01 b.1.1.1,b.1.1.4 97469,97470 1moq 368 1.09e+01 1moq 1moqA 368 1.09e+01 c.80.1.1 35302 1s5aA 150 1.11e+01 d.17.4.10 98525 1rxxA 421 1.12e+01 d.126.1.4 98061 1vmeA 410 1.15e+01 c.23.5.1,d.157.1.3 108893,108894 2aukA 190 1.15e+01 1i8kA 107 1.16e+01 b.1.1.1 71130 1v70A 105 1.17e+01 b.82.1.9 113555 1yliA 153 1.18e+01 d.38.1.1 123651 1q5hA 147 1.18e+01 b.85.4.1 95893 1gk7A 39 1.18e+01 h.1.20.1 70212 1whi 122 1.19e+01 1whi 1whiA 122 1.19e+01 b.39.1.1 24810 2bazA 142 1.20e+01 1x8vA 455 1.21e+01 a.104.1.1 114968 2ccmA 191 1.23e+01 1wyuA 438 1.24e+01 c.67.1.7 121452 1xs1A 193 1.25e+01 b.85.4.1 115892 1gyhA 318 1.25e+01 b.67.2.1 70757 1jyhA 157 1.28e+01 d.60.1.3 71956 1o8vA 134 1.29e+01 b.60.1.2 86680 1bihA 395 1.32e+01 1bihA b.1.1.4,b.1.1.4,b.1.1.4,b.1.1.4 21752,21753,21754,21755 2iwkA 642 1.32e+01 1uy4A 145 1.32e+01 b.18.1.10 108131 1zx6A 58 1.32e+01 1i9gA 280 1.34e+01 c.66.1.13 62090 1jrrA 382 1.34e+01 e.1.1.1 63256 2h0bA 184 1.35e+01 2o6pA 161 1.38e+01 1sfnA 246 1.39e+01 b.82.1.11 105496 2adgA 214 1.39e+01 2aioA 269 1.39e+01 d.157.1.1 126829 1mmuA 347 1.40e+01 b.30.5.4 79303 2biwA 490 1.40e+01 1bqk 124 1.43e+01 1bqk 1bqkA 124 1.43e+01 b.6.1.1 22889 1molA 94 1.44e+01 1molA d.17.1.1 37988 1pg4A 652 1.45e+01 e.23.1.1 88067 1mrgA 263 1.46e+01 d.165.1.1 42183 1e30A 155 1.46e+01 1rcy b.6.1.1 23016 1h8gA 95 1.50e+01 b.109.1.1 65735 1tq5A 242 1.51e+01 b.82.1.12 119311 1h70A 255 1.51e+01 1h70A d.126.1.3 60711 1zi0A 307 1.52e+01 2cibA 455 1.52e+01 1wxcB 134 1.53e+01 1cxlA 686 1.55e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21829,22498,27736,28723 1h9jA 145 1.56e+01 1h9jA b.40.6.2,b.40.6.2 60829,60830 1hh1A 143 1.56e+01 1gefA c.52.1.18 61036 2hnxA 136 1.59e+01 b.60.1.2 136633 1ea1A 455 1.59e+01 1ea1A a.104.1.1 18970 1tw4A 125 1.60e+01 b.60.1.2 112690 2v2gA 233 1.61e+01 1juvA 193 1.63e+01 c.71.1.1 90912 2cu2A 337 1.64e+01 1o9gA 250 1.64e+01 c.66.1.29 86692 1wp5A 323 1.65e+01 b.68.10.1 114780 1u0qA 125 1.67e+01 2v6vA 156 1.69e+01 1ciqA 40 1.71e+01 2sniI d.40.1.1 38576 2phlA 397 1.72e+01 1dgwA b.82.1.2,b.82.1.2 28082,28083 2bkyX 89 1.72e+01 d.68.6.1 128717 1u13A 455 1.73e+01 a.104.1.1 107578 2j4hA 193 1.73e+01 1gvmA 136 1.75e+01 b.109.1.1 70612 3c6kA 381 1.76e+01 2obfA 289 1.77e+01 3bjsA 428 1.77e+01 1ibzA 112 1.78e+01 1ibzA b.6.1.4 62237 1d3cA 686 1.79e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21827,22496,27734,28721 2dfbA 190 1.80e+01 b.29.1.11 131470 2ftbA 125 1.81e+01 b.60.1.2 134057 1vrbA 342 1.81e+01 b.82.2.11 120450 2j8gA 339 1.83e+01 2q6kA 283 1.85e+01 1eybA 471 1.86e+01 1ey2A b.82.1.4 28115 1hp1A 516 1.87e+01 d.114.1.1,d.159.1.2 70976,70977 2q78A 153 1.88e+01 1kllA 130 1.89e+01 d.32.1.2 72720 2zb6A 481 1.90e+01 2d5lA 706 1.91e+01 2iimA 62 1.92e+01 b.34.2.1 137434 1jr7A 311 1.93e+01 b.82.2.3 63255 1ss4A 153 1.94e+01 d.32.1.6 105976 1tr8A 102 1.94e+01 2nvaA 372 1.95e+01 3bjkA 153 1.96e+01 1bb9 115 1.96e+01 1bb9 1bb9A 115 1.96e+01 b.34.2.1 24554 2cw8A 537 1.98e+01 1j8mF 297 1.99e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1zud2 66 1.99e+01 2hc8A 113 2.00e+01 2z2nA 299 2.00e+01 1wwrA 171 2.01e+01 c.97.1.2 121366 1pguA 615 2.02e+01 b.69.4.1,b.69.4.1 88069,88070 1xgsA 295 2.02e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1uurA 473 2.04e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1uqxA 113 2.05e+01 b.115.1.1 99801 2r55A 231 2.05e+01 1khiA 176 2.05e+01 b.34.5.2,b.40.4.5 77408,77409 3cjxA 165 2.06e+01 1cqqA 180 2.06e+01 1cqqA b.47.1.4 26422 2o9uX 97 2.06e+01 d.17.1.1 138960 1ri6A 343 2.07e+01 b.69.11.1 97503 1kblA 873 2.10e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 2h0vA 338 2.10e+01 2otnA 308 2.10e+01 1p32A 209 2.11e+01 1p32A d.25.1.1 38379 1b6fA 159 2.12e+01 1bv1 d.129.3.1 41316 2jerA 389 2.12e+01 1tjgH 237 2.13e+01 b.1.1.1,b.1.1.2 112446,112447 1j8yF 297 2.13e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1smlA 269 2.15e+01 1smlA d.157.1.1 42053 1coaI 64 2.15e+01 2sniI d.40.1.1 38574 1zuuA 58 2.15e+01 b.34.2.1 125688 2chhA 114 2.16e+01 b.115.1.1 130471 1xffA 240 2.16e+01 d.153.1.1 109580 2dbqA 334 2.17e+01 1nls 237 2.18e+01 1nls 1rcy 151 2.19e+01 1rcy 1qouA 181 2.20e+01 1qouA b.17.1.1 23707 2pcjA 224 2.20e+01 1zelA 298 2.20e+01 2jbmA 299 2.22e+01 1sv6A 269 2.23e+01 d.177.1.1 106043 2qwvA 208 2.23e+01 2c0cA 362 2.25e+01 1yqeA 282 2.26e+01 c.56.7.1 123879 1ush 550 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