# 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 1dnlA 199 1.57e-33 1ci0A b.45.1.1 25753 1g79A 218 3.59e-33 1ci0A b.45.1.1 25752 1nrgA 261 1.31e-29 b.45.1.1 80694 1ty9A 222 4.79e-26 1rfeA 162 3.57e-24 2fhqA 141 2.26e-21 2asfA 137 2.31e-19 2arzA 247 6.94e-19 2aq6A 147 4.14e-18 1vl7A 157 1.93e-17 b.45.1.1 108732 2fg9A 178 2.21e-17 1w9aA 147 3.92e-17 2furA 209 3.10e-15 1xhnA 184 4.04e-13 1w3oA 216 7.95e-10 1flmA 122 8.99e-09 1axj b.45.1.1 25747 1ejeA 192 1.55e-04 1ejeA b.45.1.2 25757 1tr8A 102 1.87e-03 1iwmA 186 9.87e-03 b.125.1.2 83758 1pvtA 238 2.38e-02 c.74.1.1 95189 1x82A 190 3.99e-02 1ojrA 274 5.54e-02 c.74.1.1 93147 1q2lA 939 9.36e-02 1ko3A 230 1.24e-01 d.157.1.1 90974 1i0rA 169 1.33e-01 1i0rA b.45.1.2 61489 2cbzA 237 1.68e-01 2d93A 134 2.22e-01 1g8aA 227 2.98e-01 c.66.1.3 90506 1mjfA 281 3.20e-01 c.66.1.17 79198 2cw5A 255 3.67e-01 1snzA 344 3.88e-01 b.30.5.4 98930 1krhA 338 3.95e-01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 1o22A 170 4.10e-01 d.238.1.1 86557 1vs0A 310 4.76e-01 2culA 232 5.39e-01 1a7tA 232 5.56e-01 1a7tA d.157.1.1 42041 1widA 130 6.51e-01 1ooeA 236 6.99e-01 c.2.1.2 87196 2gukA 120 8.38e-01 2cveA 191 8.38e-01 2bbsA 290 8.86e-01 2g7zA 282 9.15e-01 1vkbA 161 9.32e-01 d.269.1.1 108643 1z0nA 96 9.75e-01 2ganA 190 9.95e-01 1vqoE 178 1.01e+00 1s1dA 331 1.04e+00 b.67.3.1 98344 2etjA 250 1.19e+00 1b8aA 438 1.28e+00 1b8aA b.40.4.1,d.104.1.1 25244,40765 1xaoA 121 1.32e+00 1bupA 386 1.33e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 1e3dB 542 1.34e+00 1h2rL e.18.1.1 59189 1llnA 262 1.38e+00 d.165.1.1 84625 2glfA 450 1.42e+00 1y8tA 324 1.55e+00 2a74A 643 1.56e+00 1h7zA 194 1.60e+00 1qhvA b.21.1.1 60733 1a6cA 513 1.61e+00 1a6cA b.121.4.2,b.121.4.2,b.121.4.2 23296,23297,23298 1y4wA 518 1.85e+00 1mkaA 171 1.91e+00 1mkaA d.38.1.2 38543 1fp2A 352 2.08e+00 1fpxA a.4.5.29,c.66.1.12 59941,59942 1jhdA 396 2.22e+00 b.122.1.3,c.26.1.5 66712,66713 2gibA 103 2.30e+00 1j0hA 588 2.37e+00 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 1h9mA 145 2.41e+00 1h9jA b.40.6.2,b.40.6.2 60833,60834 1g291 372 2.42e+00 1g291 2gs8A 317 2.46e+00 1b25A 619 2.52e+00 1b25A a.110.1.1,d.152.1.1 19044,41796 1onwA 390 2.55e+00 b.92.1.7,c.1.9.13 87172,87173 1yloA 348 2.58e+00 1kuuA 202 2.67e+00 d.153.2.1 73019 2cxvA 219 2.69e+00 1e9pA 151 2.78e+00 1mfmA b.1.8.1 22215 2h0bA 184 2.83e+00 1n9lA 109 2.83e+00 d.110.3.6 85468 2bllA 345 2.89e+00 1te0A 318 2.91e+00 1xtmA 175 2.98e+00 1pbuA 162 3.09e+00 d.58.46.1 88030 1i8dA 213 3.16e+00 b.43.4.3,b.43.4.3 61953,61954 2asuB 234 3.20e+00 1wsrA 375 3.24e+00 2gjgA 248 3.31e+00 1r2zA 274 3.32e+00 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1crzA 403 3.34e+00 1crzA b.68.4.1,c.51.2.1 27629,33211 1w6sA 599 3.44e+00 1xsoA 150 3.51e+00 1mfmA b.1.8.1 22273 2bswA 146 3.55e+00 1v84A 253 3.58e+00 c.68.1.7 108419 1q0eA 152 3.62e+00 b.1.8.1 95504 2f15A 96 3.66e+00 1vc1A 110 3.67e+00 c.13.2.1 108493 1a34A 159 3.67e+00 1a34A b.121.7.1 23286 1zt3A 80 3.76e+00 1wy2A 351 3.76e+00 1jkeA 145 4.01e+00 c.110.1.1 66791 1wb4A 297 4.06e+00 1bqbA 301 4.10e+00 1hyt d.92.1.2 58962 2f4iA 197 4.10e+00 1e4cP 215 4.29e+00 2fua c.74.1.1 34969 1xdfA 157 4.40e+00 1ubkL 534 4.47e+00 e.18.1.1 88422 4bcl 366 4.48e+00 4bcl b.75.1.1 27968 1kzlA 208 4.66e+00 b.43.4.3,b.43.4.3 77635,77636 1ylnA 252 4.76e+00 2g1lA 104 4.84e+00 1dgwA 178 4.86e+00 1dgwA b.82.1.2 28090 1x54A 434 5.04e+00 1vzyA 291 5.05e+00 1rl6A 177 5.25e+00 1rl6A d.141.1.1,d.141.1.1 41473,41474 2b4wA 315 5.30e+00 1kxlA 199 5.33e+00 b.40.4.3 73155 1heiA 451 5.41e+00 1heiA c.37.1.14,c.37.1.14 32463,32464 1o54A 277 5.47e+00 c.66.1.13 92482 1yge 839 5.50e+00 1yge a.119.1.1,b.12.1.1 19234,23634 1f2tA 149 5.53e+00 1f2tA c.37.1.12 32373 1wuiL 534 5.58e+00 2fcjA 119 5.62e+00 1vj0A 380 5.64e+00 b.35.1.2,c.2.1.1 100786,100787 1txoA 237 5.78e+00 1gwmA 153 5.78e+00 b.18.1.19 83348 1vq0A 302 5.86e+00 1qmeA 702 5.89e+00 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1r6xA 395 5.90e+00 b.122.1.3,c.26.1.5 97167,97168 1hr0W 71 5.96e+00 1ah9 b.40.4.5 25329 2d13A 227 6.00e+00 2d37A 176 6.05e+00 1uwvA 433 6.23e+00 b.40.4.12,c.66.1.40 100128,100129 1h4gA 207 6.31e+00 b.29.1.11 70863 2bgiA 272 6.33e+00 2aq9A 262 6.33e+00 1gk9B 557 6.45e+00 1ia9A 280 6.59e+00 1ia9A d.144.1.5 62113 1wnyA 186 6.64e+00 2atpB 115 6.77e+00 1hs6A 611 6.79e+00 1hs6A a.118.1.7,b.98.1.1,d.92.1.13 61233,61234,61235 1zd7A 159 6.90e+00 1b0uA 262 6.91e+00 1b0uA c.37.1.12 32370 2f06A 144 7.00e+00 1nxuA 333 7.05e+00 c.122.1.1 86389 2f9dA 125 7.06e+00 1vpkA 378 7.10e+00 2dexX 671 7.22e+00 1m40A 263 7.22e+00 e.3.1.1 74437 1jjtA 228 7.29e+00 1a7tA d.157.1.1 63139 1oa4A 222 7.42e+00 b.29.1.11 86731 1i39A 225 7.45e+00 1ekeA c.55.3.1 61585 2ew2A 316 7.57e+00 1j58A 385 7.65e+00 b.82.1.2 71531 1qx4A 274 7.75e+00 b.43.4.2,c.25.1.1 104624,104625 1avbA 226 7.76e+00 1led b.29.1.1 24158 1g8kB 133 7.79e+00 1g8jB b.33.1.1 24435 1pl8A 356 7.92e+00 b.35.1.2,c.2.1.1 94878,94879 1wlfA 179 7.93e+00 b.52.2.3,d.31.1.1 109396,109397 1h72C 296 8.07e+00 d.14.1.5,d.58.26.1 60712,60713 1v4pA 157 8.08e+00 1yewA 382 8.12e+00 1y7rA 133 8.13e+00 1w8oA 601 8.14e+00 1te5A 257 8.19e+00 d.153.1.1 106795 1z2uA 150 8.31e+00 1yeyA 444 8.57e+00 1udzA 182 8.59e+00 b.51.1.1 99239 1ut7A 171 8.62e+00 b.143.1.1 99906 2cxhA 217 8.69e+00 1z5hA 780 8.87e+00 1am2 199 9.09e+00 1am2 b.86.1.2 28381 2bhuA 602 9.16e+00 1jvbA 347 9.53e+00 b.35.1.2,c.2.1.1 77181,77182 1yb2A 275 9.62e+00 2aukA 190 9.67e+00 1l2tA 235 9.68e+00 c.37.1.12 73514 1q5xA 161 9.70e+00 c.8.7.1 95947 1e6uA 321 9.73e+00 1bsvA c.2.1.2 29805 1k0eA 453 9.77e+00 d.161.1.1 67938 1fqtA 112 9.84e+00 1fqtA b.33.1.1 24441 1r9cA 139 9.91e+00 d.32.1.2 97255 1iz6A 138 9.95e+00 b.34.5.2,b.40.4.5 76976,76977 2fafA 608 1.00e+01 1s4iA 175 1.01e+01 1nd4A 264 1.02e+01 d.144.1.6 91815 2b0vA 153 1.02e+01 1b6a 478 1.02e+01 1bn5 a.4.5.25,d.127.1.1 16223,41160 1b5qA 472 1.02e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 1xiwA 105 1.03e+01 1ss4A 153 1.03e+01 d.32.1.6 105976 1k5cA 335 1.03e+01 b.80.1.3 72076 2fexA 188 1.04e+01 1xkiA 162 1.04e+01 1xr4A 509 1.05e+01 1l1oC 181 1.08e+01 b.40.4.3 73480 1k07A 263 1.08e+01 d.157.1.1 77218 1jkmB 361 1.08e+01 1jkmA c.69.1.2 34634 1xuvA 178 1.09e+01 1kjlA 146 1.11e+01 1cg2A 393 1.12e+01 1cg2A c.56.5.4,d.58.19.1 33844,39360 1ra6A 461 1.12e+01 e.8.1.4 104879 1xqbA 247 1.12e+01 1udxA 416 1.13e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1w0hA 204 1.14e+01 1xv2A 237 1.16e+01 1fo8A 343 1.18e+01 1foaA c.68.1.10 59927 1hg8A 349 1.18e+01 b.80.1.3 65830 1bywA 110 1.18e+01 1bywA d.110.3.6 40912 2ahuA 531 1.21e+01 1yt3A 375 1.21e+01 1yoaA 159 1.22e+01 1ypfA 336 1.22e+01 7fd1A 106 1.24e+01 1a6l d.58.1.2 38953 1h3gA 601 1.24e+01 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1jyoA 130 1.24e+01 d.198.1.1 67483 1umkA 275 1.27e+01 1sqwA 188 1.27e+01 2abqA 306 1.30e+01 1ukgA 252 1.30e+01 b.29.1.1 99489 1kxoA 184 1.33e+01 b.60.1.1 84475 1xyiA 66 1.35e+01 1rg9A 383 1.36e+01 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1mdoA 393 1.37e+01 c.67.1.4 79013 1f6bA 198 1.38e+01 c.37.1.8 64986 1zm8A 259 1.38e+01 1pz7A 204 1.38e+01 b.29.1.4 95405 1dabA 539 1.39e+01 1dabA b.80.1.7 28049 4fiv 113 1.40e+01 1fmb b.50.1.1 26762 2gtqA 867 1.40e+01 1rz1A 161 1.43e+01 b.45.1.2 98124 1rwrA 301 1.44e+01 b.80.1.11 97990 1cqqA 180 1.45e+01 1cqqA b.47.1.4 26422 1ve6A 582 1.45e+01 1zzkA 82 1.46e+01 1o5uA 101 1.47e+01 b.82.1.8 92518 1ut9A 609 1.51e+01 a.102.1.2,b.1.18.2 99912,99913 1qwdA 177 1.53e+01 b.60.1.1 96471 1ssxA 198 1.55e+01 b.47.1.1 98978 3daaA 277 1.56e+01 1daaA e.17.1.1 43272 1l0wA 580 1.57e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1q40B 219 1.59e+01 d.17.4.2 95771 1mhnA 59 1.60e+01 b.34.9.1 84964 1b34B 118 1.61e+01 1b34B b.38.1.1 24797 1v1aA 309 1.62e+01 c.72.1.1 100249 1mkyA 439 1.62e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1ej8A 140 1.63e+01 1qupA b.1.8.1 22300 1ye8A 178 1.64e+01 1h3fA 432 1.66e+01 c.26.1.1,d.66.1.4 76631,76632 1ea5A 537 1.66e+01 2bce c.69.1.1 34592 1zkpA 268 1.66e+01 1zupA 315 1.66e+01 1o7dE 126 1.67e+01 1fehA 574 1.67e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1gj7B 253 1.70e+01 1yrrA 382 1.71e+01 2exrA 524 1.72e+01 1otjA 283 1.72e+01 b.82.2.5 93517 1pbyA 489 1.73e+01 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 1zjkA 403 1.73e+01 1s6lA 212 1.74e+01 1nnxA 109 1.76e+01 b.40.10.1 92013 1vlrA 350 1.77e+01 d.13.1.3,d.246.1.1 108860,108861 1kveB 77 1.78e+01 1kveB 1h54A 754 1.78e+01 a.102.1.4,b.30.5.3 60634,60635 1u79A 129 1.79e+01 d.26.1.1 107714 1winA 143 1.80e+01 2evwX 166 1.80e+01 2cbiA 594 1.81e+01 1rk6A 496 1.81e+01 b.92.1.6,b.92.1.6,c.1.9.11 97599,97600,97601 1zghA 260 1.81e+01 1wj9A 211 1.82e+01 2fe7A 166 1.83e+01 1y1pA 342 1.84e+01 1zbqA 327 1.85e+01 1t77A 414 1.87e+01 2f1rA 171 1.89e+01 1lk2A 274 1.90e+01 b.1.1.2,d.19.1.1 91056,91057 1ta0A 197 1.91e+01 c.108.1.16 106729 1p1jA 533 1.92e+01 c.2.1.3,d.81.1.3 87687,87688 2fvgA 340 1.92e+01 1yb5A 351 1.95e+01 1m1zA 513 1.96e+01 c.26.2.1,d.153.1.1 78457,78458 1ko6A 187 1.96e+01 b.119.1.1 77471 1j24A 143 1.98e+01 c.52.1.20 84008 1zcxA 178 1.99e+01 1b9hA 388 2.00e+01 1b9hA c.67.1.4 34488 1x0pA 143 2.01e+01 1bg1A 722 2.02e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17767,22461,40527 1xebA 150 2.03e+01 2f6rA 281 2.04e+01 2gm6A 208 2.04e+01 1agqA 135 2.05e+01 1agqA g.17.1.2 44789 1gd1O 334 2.05e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 2c4xA 260 2.05e+01 1wy7A 207 2.05e+01 2fswA 107 2.06e+01 1csn 298 2.07e+01 1csn d.144.1.7 41664 1kcqA 104 2.08e+01 d.109.1.1 68449 1ryp1 222 2.08e+01 1ryp1 1ff9A 450 2.11e+01 1ff9A c.2.1.3,d.81.1.2 30039,39954 1twfK 120 2.12e+01 1c7sA 858 2.12e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21812,22408,29011,40410 1yi9A 309 2.13e+01 1jwqA 179 2.14e+01 c.56.5.6 90921 1xipA 388 2.14e+01 1x6mA 196 2.15e+01 2cx7A 130 2.16e+01 2f4eA 180 2.20e+01 1yna 194 2.20e+01 1axkA b.29.1.11 24335 2bjrA 368 2.21e+01 1vh4A 435 2.22e+01 b.80.6.1 100640 1xypA 190 2.22e+01 1axkA b.29.1.11 24327 1oi0A 124 2.23e+01 c.97.3.1 93045 1rocA 155 2.25e+01 b.1.22.1 97673 1umhA 184 2.26e+01 b.18.1.21 99605 1tedA 393 2.27e+01 c.95.1.2 106807 2gk4A 232 2.29e+01 2ai4A 119 2.31e+01 1okiA 210 2.31e+01 b.11.1.1,b.11.1.1 93255,93256 1ms9A 648 2.33e+01 b.29.1.15,b.68.1.1 85088,85089 1qmyA 167 2.34e+01 1qmyA d.3.1.2 37094 2sga 181 2.34e+01 1qq4A b.47.1.1 25808 1b2pA 119 2.35e+01 1b2pA b.78.1.1 27998 1qouA 181 2.35e+01 1qouA b.17.1.1 23707 1wluA 136 2.40e+01 1gzcA 239 2.41e+01 b.29.1.1 70803 1qg8A 255 2.44e+01 1qg8A c.68.1.1 34505 2etvA 346 2.45e+01 3seb 238 2.48e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1puiA 210 2.49e+01 c.37.1.8 88292 1h6dA 433 2.54e+01 c.2.1.3,d.81.1.5 65656,65657 1v8fA 276 2.55e+01 c.26.1.4 100503 2et1A 201 2.56e+01 1io2A 213 2.56e+01 1ekeA c.55.3.1 62612 1f5nA 592 2.58e+01 1dg3A a.114.1.1,c.37.1.8 19077,32152 1rp0A 284 2.59e+01 2pia 321 2.59e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1vzoA 355 2.61e+01 d.144.1.7 108971 1qfjA 232 2.61e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 1i9zA 347 2.62e+01 1i9yA d.151.1.2 62102 1hfoA 113 2.63e+01 d.80.1.3 61006 1p8xA 344 2.63e+01 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 1ur1A 378 2.63e+01 c.1.8.3 99804 1d1gA 168 2.64e+01 1d1gA c.71.1.1 34889 1szoA 257 2.64e+01 c.14.1.3 106164 1ev0A 58 2.67e+01 1ev0A d.71.1.1 39594 2beiA 170 2.67e+01 2gwnA 452 2.69e+01 1fi2A 201 2.69e+01 1fi2A b.82.1.2 59845 2bvfA 459 2.71e+01 1ob8A 135 2.73e+01 1j1yA 136 2.73e+01 d.38.1.5 90776 1wznA 252 2.74e+01 1r75A 141 2.78e+01 b.134.1.1 97189 1or0B 528 2.79e+01 1b8oA 284 2.82e+01 1b8oA c.56.2.1 33762 1k0wA 231 2.83e+01 c.74.1.1 77220 1lurA 339 2.83e+01 b.30.5.4 84717 2ci9A 102 2.84e+01 1rlzA 369 2.84e+01 c.31.1.1 104989 1ta9A 450 2.86e+01 1v7pB 128 2.90e+01 d.169.1.1 108407 1hfuA 503 2.91e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1ff4A 65 2.93e+01 g.7.1.1 83251 1w7jA 795 2.93e+01 1zi8A 236 2.94e+01 1zdzA 302 2.95e+01 1ogiA 303 2.95e+01 b.43.4.2,c.25.1.1 92914,92915 1nlfA 279 2.95e+01 c.37.1.11 85850 1y0yA 353 2.96e+01 1al3 324 2.97e+01 1al3 c.94.1.1 35835 1xnkA 196 2.98e+01 1bkf 107 3.00e+01 1fkj d.26.1.1 38382 1y13A 181 3.01e+01 1s2wA 295 3.02e+01 c.1.12.7 98407 1bdb 277 3.03e+01 1bdb 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