# List of top-scoring protein chains for t2k-100-30-bys-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 3gwfA 540 9.05e-01 2h1tA 188 9.71e-01 b.178.1.1 147215 2wjrA 214 1.31e+00 1cwwA 102 1.51e+00 1cy5A a.77.1.3 18434 3e8tA 220 1.58e+00 1kcgC 178 1.65e+00 d.19.1.1 68440 1q7fA 286 1.65e+00 b.68.9.1 96036 3lzjA 903 1.79e+00 1cy5A 97 1.83e+00 1cy5A a.77.1.3 18430 2ai4A 119 1.85e+00 b.6.1.7 126816 2ox7A 155 1.86e+00 b.172.1.1 149054 2cxxA 190 2.18e+00 c.37.1.8 131013 2j04A 588 2.19e+00 2ygsA 92 2.24e+00 1cy5A a.77.1.3 18431 3f04A 143 2.39e+00 1ih7A 903 2.40e+00 1clqA c.55.3.5,e.8.1.1 62375,62376 1clqA 903 2.45e+00 1clqA c.55.3.5,e.8.1.1 33717,43006 3gkuA 225 2.46e+00 1zarA 282 3.27e+00 a.4.5.56,d.144.1.9 124843,124844 1z2iA 358 3.58e+00 1vbiA 344 3.97e+00 3l8bA 906 3.98e+00 1tqmA 282 4.02e+00 a.4.5.56,d.144.1.9 107236,107237 3h5lA 419 4.02e+00 2pkpA 170 4.06e+00 1wtjA 343 4.27e+00 1nt2A 210 4.33e+00 c.66.1.3 86149 1pbe 394 4.64e+00 1pbe 1pbeA 394 4.64e+00 c.3.1.2,d.16.1.2 30338,37869 1cj3A 392 4.79e+00 1pbe c.3.1.2,d.16.1.2 30347,37878 1i6wA 181 5.52e+00 1i6wA c.69.1.18 61859 1rsy 152 5.65e+00 1rsy 1rsyA 152 5.65e+00 b.7.1.2 23192 2hy7A 406 5.66e+00 1x12A 208 5.72e+00 2bbeA 108 5.80e+00 1ispA 181 5.86e+00 c.69.1.18 76778 1w0pA 781 6.33e+00 b.29.1.8,b.29.1.8,b.68.1.1 109038,109039,109040 1ykjA 394 6.43e+00 c.3.1.2,d.16.1.2 145914,145915 3f85A 463 6.64e+00 2oaaA 249 6.82e+00 1xahA 354 7.18e+00 1u6rA 380 7.36e+00 a.83.1.1,d.128.1.2 119600,119601 1r03A 182 7.48e+00 a.25.1.1 104675 3licA 274 7.93e+00 2wmiA 606 8.57e+00 2v4cA 309 9.16e+00 1k0iA 394 9.59e+00 c.3.1.2,d.16.1.2 67942,67943 2vh1A 220 1.03e+01 3eeyA 197 1.04e+01 3c3yA 237 1.07e+01 3e8vA 82 1.08e+01 2dbnA 461 1.09e+01 2fh1A 344 1.09e+01 d.109.1.1,d.109.1.1,d.109.1.1 133441,133442,133443 1hd2A 161 1.11e+01 c.47.1.10 60962 2dulA 378 1.13e+01 c.66.1.58 146588 3b50A 310 1.16e+01 1cbgA 490 1.22e+01 c.1.8.4 28933 3i3wA 443 1.22e+01 2wmiB 606 1.23e+01 1svdA 473 1.23e+01 c.1.14.1,d.58.9.1 119057,119058 2ceyA 306 1.28e+01 2wmkA 606 1.32e+01 2q4vA 170 1.33e+01 d.108.1.1 139878 1qhaA 917 1.42e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33467,33468,33469,33470 1qstA 160 1.42e+01 1yghA d.108.1.1 40804 1yd9A 193 1.47e+01 c.50.1.2 122976 1v9cA 218 1.54e+01 c.23.17.1 100533 2wozA 318 1.59e+01 2r7hA 177 1.64e+01 1nf5B 286 1.65e+01 c.68.1.2 80454 1nn7A 105 1.67e+01 d.42.1.2 85894 1iyeA 309 1.71e+01 e.17.1.1 83786 1gcuA 295 1.73e+01 1gcuA c.2.1.3,d.81.1.4 30063,39978 1ep1B 261 1.75e+01 1ep2B b.43.4.2,c.25.1.3 25665,31555 1mkyA 439 1.78e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 2zv3A 115 1.88e+01 2rmpA 361 1.89e+01 2rmpA b.50.1.2 26825 2wmfA 581 1.90e+01 1vf1A 229 1.91e+01 1lc0A 294 1.94e+01 c.2.1.3,d.81.1.4 73823,73824 1s1dA 331 1.94e+01 b.67.3.1 98344 1dgkN 917 1.95e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33487,33488,33489,33490 2gzxA 265 1.99e+01 1nmmB 286 2.02e+01 c.68.1.2 80662 1rtwA 220 2.04e+01 a.132.1.3 97823 1ew4A 106 2.04e+01 1ew4A d.82.2.1 40023 2dr3A 247 2.06e+01 1ug8A 87 2.11e+01 d.68.7.1 107825 1xpjA 126 2.13e+01 c.108.1.18 115739 3hihA 223 2.15e+01 1lu4A 136 2.19e+01 c.47.1.10 91124 2fy7A 287 2.20e+01 2j6vA 301 2.24e+01 1qh4A 380 2.26e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 3gwaA 365 2.28e+01 1otkA 249 2.30e+01 a.25.1.2 93521 3cniA 156 2.36e+01 2jf7A 532 2.39e+01 1fgxA 288 2.41e+01 1fgxA c.68.1.2 34508 1qmyA 167 2.41e+01 1qmyA d.3.1.2 37094 1g8aA 227 2.59e+01 c.66.1.3 90506 1k8tA 510 2.60e+01 e.41.1.1 68316 2izpA 303 2.62e+01 a.250.1.1 137826 1urmA 172 2.65e+01 c.47.1.10 113413 1d3uB 201 2.69e+01 1aisB a.74.1.2,a.74.1.2 18386,18387 2w02A 620 2.76e+01 3lhnA 126 2.77e+01 2wmhA 581 2.79e+01 3hhyA 280 2.80e+01 1b56A 135 2.80e+01 b.60.1.2 27183 2bkwA 385 2.84e+01 c.67.1.3 128714 3enbA 222 2.89e+01 c.55.3.14 158189 2wmgA 581 2.97e+01 1lb3A 182 2.97e+01 a.25.1.1 77873 3lfmA 495 2.97e+01 1pztA 286 3.00e+01 c.68.1.2 95470 3h92A 92 3.00e+01 3griA 424 3.01e+01 1wdaA 670 3.03e+01 b.2.9.1,b.6.1.6,d.126.1.5 109243,109244,109245 2cw3A 280 3.05e+01 1yroB 286 3.05e+01 c.68.1.2 123932 2b5gA 171 3.07e+01 d.108.1.1 127892 2w7qA 204 3.09e+01 2q0iA 303 3.11e+01 d.157.1.14 149986 1dk8A 147 3.15e+01 1agrE a.91.1.1 18548 1iu8A 206 3.18e+01 c.56.4.1 71436 3bjoA 103 3.26e+01 2pm7A 399 3.31e+01 3i0yA 140 3.35e+01 1umwA 237 3.38e+01 d.223.1.2,d.223.1.2 99631,99632 2obdA 476 3.38e+01 1zr5A 214 3.44e+01 c.50.1.2 125525 3hikA 237 3.45e+01 2cihA 183 3.45e+01 3fvhA 237 3.50e+01 1ij8A 128 3.55e+01 b.61.1.1 62480 1ig9A 903 3.56e+01 1clqA c.55.3.5,e.8.1.1 62367,62368 1vrpA 381 3.59e+01 a.83.1.1,d.128.1.2 120473,120474 2uxqA 402 3.61e+01 2fha 183 3.65e+01 2fha 1idsA 207 3.66e+01 1avmA a.2.11.1,d.44.1.1 15722,38730 3hxrA 761 3.67e+01 3bn0A 112 3.77e+01 d.27.1.1 155425 2jzbB 74 3.79e+01 2oryA 346 3.80e+01 1nxuA 333 3.81e+01 c.122.1.1 86389 1jmmA 377 3.85e+01 b.30.6.1 71749 3f9sA 146 3.87e+01 1czaN 917 3.92e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 1z5hA 780 3.96e+01 3lacA 215 3.98e+01 2icwG 213 4.02e+01 a.202.1.1 137251 1ep3B 262 4.03e+01 1ep2B b.43.4.2,c.25.1.3 25664,31554 2jkgA 179 4.05e+01 2e2oA 299 4.10e+01 1g60A 260 4.16e+01 c.66.1.11 70151 2ivfB 352 4.16e+01 1at0 145 4.16e+01 1at0 1at0A 145 4.16e+01 b.86.1.1 28374 2r6oA 294 4.25e+01 3cp5A 124 4.26e+01 1kit 757 4.26e+01 1kit 1y55X 126 4.28e+01 1egaA 301 4.30e+01 1egaA c.37.1.8,d.52.3.1 32150,38836 2qg3A 208 4.31e+01 2rdyA 803 4.35e+01 2bneA 241 4.45e+01 c.73.1.3 128824 2bwqA 129 4.50e+01 b.7.1.2 129380 1nqnA 122 4.53e+01 b.61.1.1 86042 3czdA 315 4.54e+01 2o35A 105 4.54e+01 a.293.1.1 148566 2eezA 369 4.57e+01 1ea2A 131 4.58e+01 d.17.4.3 64860 2atrA 138 4.61e+01 d.108.1.1 127305 2w2sA 202 4.71e+01 1xn5A 146 4.72e+01 d.129.3.5 115574 1upvA 257 4.74e+01 a.123.1.1 113398 3bdqA 110 4.79e+01 2z0uA 155 4.81e+01 3g3lA 327 4.85e+01 2qztA 111 4.88e+01 1k9tA 540 4.88e+01 b.1.18.2,c.1.8.5,d.26.3.1 77298,77299,77300 1d8jA 81 5.01e+01 1d8jA a.4.5.18 16153 2dk7A 73 5.03e+01 2bc4B 211 5.13e+01 1tljA 213 5.20e+01 d.282.1.1 107126 2qf3A 243 5.22e+01 b.47.1.1 150724 3d2fA 675 5.23e+01 1opy 131 5.26e+01 1opy 1pb1A 416 5.29e+01 c.77.1.1 88014 1dmmA 131 5.35e+01 1opy d.17.4.3 38114 2wk2A 540 5.40e+01 1gqeA 365 5.41e+01 e.38.1.1 70351 2cxhA 217 5.42e+01 c.51.1.2 131005 2r60A 499 5.45e+01 2k4qA 156 5.46e+01 2p0wA 324 5.50e+01 1edqA 540 5.51e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 2cy2A 174 5.53e+01 d.108.1.1 131016 1vyoA 128 5.57e+01 2wlzA 548 5.57e+01 1hn4A 131 5.59e+01 a.133.1.2 65893 1bd8 156 5.62e+01 1bd8 1bd8A 156 5.62e+01 d.211.1.1 19157 2vqeR 88 5.63e+01 a.4.8.1 153442 1j58A 385 5.71e+01 b.82.1.2 71531 2o7tA 199 5.76e+01 a.4.1.9,a.121.1.1 148670,148671 2oxgA 108 5.78e+01 1xmtA 103 5.80e+01 d.108.1.1 115561 2vdwA 302 5.86e+01 2eeyA 162 5.87e+01 2w5nA 367 5.88e+01 2vk3A 142 5.98e+01 1q2lA 939 6.10e+01 d.185.1.1,d.185.1.1,d.185.1.1,d.185.1.1 118731,118732,118733,118734 3gwqA 426 6.11e+01 3blnA 143 6.11e+01 2qxlA 658 6.17e+01 2w6kA 145 6.21e+01 c.151.1.1 153740 2bsnA 145 6.22e+01 2whqA 548 6.23e+01 1xrhA 351 6.23e+01 c.122.1.1 115871 2carA 196 6.26e+01 c.51.4.1 130161 3lpzA 336 6.26e+01 2wfcA 167 6.36e+01 2uubR 88 6.38e+01 a.4.8.1 139949 3dodA 448 6.41e+01 1wchA 315 6.43e+01 c.45.1.2 114508 2i5hA 205 6.57e+01 e.71.1.1 147513 2fqmA 75 6.59e+01 d.378.1.1 147042 3brcA 156 6.59e+01 2nvmA 126 6.59e+01 d.326.1.1 138631 1dpgA 485 6.62e+01 1dpgA c.2.1.3,d.81.1.5 30074,39989 2gduA 504 6.63e+01 b.71.1.1,c.1.8.1 135032,135033 3dr2A 305 6.64e+01 1xi7A 61 6.67e+01 g.3.6.5 115348 2o1mA 258 6.67e+01 3h8vA 292 6.68e+01 3l57A 299 6.68e+01 3d37A 381 6.70e+01 b.106.1.1,b.106.1.1 157269,157270 3dmcA 134 6.72e+01 d.17.4.10 157805 1ualA 274 6.73e+01 c.116.1.4 88383 1w36C 1122 6.76e+01 c.37.1.19,c.37.1.19,c.52.1.25 114125,114126,114127 3gbxA 420 6.76e+01 1dfoA 417 6.77e+01 1bj4A c.67.1.4 34480 3ygsP 97 6.81e+01 3ygsP a.77.1.3 18435 3by8A 142 6.81e+01 d.110.6.1 155722 1u1sA 82 6.82e+01 b.38.1.2 119451 2a1fA 247 6.89e+01 c.73.1.3 125991 1wbiA 129 7.00e+01 3mtiA 185 7.01e+01 1bob 320 7.01e+01 1bob 1bobA 320 7.01e+01 d.108.1.1 40816 3ipkA 497 7.04e+01 1h9aA 485 7.05e+01 1dpgA c.2.1.3,d.81.1.5 60816,60817 2imfA 203 7.18e+01 1rfmA 344 7.20e+01 c.122.1.1 97385 1hh1A 143 7.24e+01 1gefA c.52.1.18 61036 1uw4B 248 7.29e+01 a.118.1.14 100072 3h1tA 590 7.34e+01 1npeA 267 7.35e+01 b.68.5.1 92032 2r6fA 972 7.49e+01 2zwrA 207 7.53e+01 1nr3A 122 7.58e+01 d.236.1.1 86092 3h51A 156 7.65e+01 1d5rA 324 7.72e+01 1d5rA b.7.1.1,c.45.1.1 23181,32697 2c0gA 248 7.76e+01 a.71.1.1,c.47.1.7 129590,129591 1ctn 540 7.77e+01 1ctn 3dv8A 220 7.90e+01 2ii2A 310 7.97e+01 3ioxA 497 7.98e+01