# List of top-scoring protein chains for t06-100-30-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.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 4.58e-33 1ci0A b.45.1.1 25753 1g79A 218 1.15e-32 1ci0A b.45.1.1 25752 1nrgA 261 4.57e-29 b.45.1.1 80694 1ty9A 222 5.18e-25 1rfeA 162 2.68e-23 2fhqA 141 2.73e-20 2asfA 137 1.96e-18 2arzA 247 1.85e-17 2aq6A 147 4.93e-17 1w9aA 147 8.39e-17 1vl7A 157 1.09e-16 b.45.1.1 108732 2fg9A 178 3.94e-16 2furA 209 7.09e-14 1xhnA 184 7.95e-12 1w3oA 216 3.04e-09 1flmA 122 1.83e-07 1axj b.45.1.1 25747 1ejeA 192 1.18e-04 1ejeA b.45.1.2 25757 1i0rA 169 3.94e-02 1i0rA b.45.1.2 61489 1pvtA 238 5.13e-02 c.74.1.1 95189 1jjtA 228 1.12e-01 1a7tA d.157.1.1 63139 2bgiA 272 1.41e-01 1iwmA 186 1.64e-01 b.125.1.2 83758 1bupA 386 1.71e-01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1zd7A 159 1.72e-01 1tr8A 102 2.16e-01 1ojrA 274 3.16e-01 c.74.1.1 93147 1b8aA 438 4.07e-01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1ko3A 230 4.21e-01 d.157.1.1 90974 2etjA 250 5.69e-01 1s1dA 331 8.52e-01 b.67.3.1 98344 1o22A 170 8.57e-01 d.238.1.1 86557 1q2lA 939 8.60e-01 1a7tA 232 9.16e-01 1a7tA d.157.1.1 42041 2gukA 120 1.03e+00 2cbzA 237 1.15e+00 1g8aA 227 1.32e+00 c.66.1.3 90506 2cw5A 255 1.53e+00 1llnA 262 1.55e+00 d.165.1.1 84625 1vs0A 310 1.66e+00 1z5hA 780 1.96e+00 1mkaA 171 2.25e+00 1mkaA d.38.1.2 38543 1hs6A 611 2.38e+00 1hs6A a.118.1.7,b.98.1.1,d.92.1.13 61233,61234,61235 1zt3A 80 2.64e+00 1n9lA 109 2.71e+00 d.110.3.6 85468 1e9pA 151 2.82e+00 1mfmA b.1.8.1 22215 2bswA 146 2.91e+00 1snzA 344 3.12e+00 b.30.5.4 98930 1xv2A 237 3.45e+00 1wsrA 375 3.60e+00 1jyoA 130 3.88e+00 d.198.1.1 67483 1qmeA 702 4.23e+00 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1z0nA 96 4.24e+00 1x54A 434 4.41e+00 1xsoA 150 4.56e+00 1mfmA b.1.8.1 22273 1s2wA 295 4.63e+00 c.1.12.7 98407 1z2iA 358 4.70e+00 1vqoE 178 5.08e+00 2fswA 107 5.19e+00 2f6uA 234 5.24e+00 1i8dA 213 5.28e+00 b.43.4.3,b.43.4.3 61953,61954 2pia 321 5.30e+00 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1ukgA 252 5.33e+00 b.29.1.1 99489 2bmwA 304 5.70e+00 2ck3D 482 5.76e+00 2hlcA 230 5.85e+00 5ptp b.47.1.2 26074 1h7zA 194 5.87e+00 1qhvA b.21.1.1 60733 1ogiA 303 6.29e+00 b.43.4.2,c.25.1.1 92914,92915 2f15A 96 6.61e+00 1rw7A 243 6.62e+00 c.23.16.2 97963 1qmyA 167 6.66e+00 1qmyA d.3.1.2 37094 2cveA 191 6.69e+00 1gk9B 557 6.70e+00 2abqA 306 6.73e+00 2gs8A 317 7.03e+00 1kcqA 104 7.11e+00 d.109.1.1 68449 1rl6A 177 7.71e+00 1rl6A d.141.1.1,d.141.1.1 41473,41474 1m40A 263 7.87e+00 e.3.1.1 74437 1q0eA 152 7.95e+00 b.1.8.1 95504 1ooeA 236 8.41e+00 c.2.1.2 87196 4bcl 366 8.72e+00 4bcl b.75.1.1 27968 1jkeA 145 8.75e+00 c.110.1.1 66791 2f9dA 125 8.83e+00 1aquA 297 8.86e+00 1aquA c.37.1.5 31942 1krhA 338 9.10e+00 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 1yoaA 159 9.15e+00 1e6wA 260 9.19e+00 1e6wA c.2.1.2 59326 1kuuA 202 9.36e+00 d.153.2.1 73019 1g0cA 364 9.43e+00 7a3hA c.1.8.3 60165 1aun 208 9.52e+00 1thv b.25.1.1 23900 1i39A 225 9.61e+00 1ekeA c.55.3.1 61585 1dgwA 178 9.65e+00 1dgwA b.82.1.2 28090 1rypK 198 9.66e+00 d.153.1.4 41879 1l0wA 580 9.82e+00 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 2glfA 450 9.87e+00 1z5yE 149 1.02e+01 2gibA 103 1.04e+01 1qvzA 237 1.05e+01 c.23.16.2 96453 1f6bA 198 1.09e+01 c.37.1.8 64986 2cr9A 139 1.09e+01 1fehA 574 1.09e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 2dexX 671 1.10e+01 1yewA 382 1.13e+01 1t77A 414 1.14e+01 1j0hA 588 1.15e+01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 1e3dB 542 1.16e+01 1h2rL e.18.1.1 59189 1otjA 283 1.18e+01 b.82.2.5 93517 1wb4A 297 1.24e+01 1b25A 619 1.26e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1z0wA 207 1.28e+01 1vr6A 350 1.33e+01 1bqbA 301 1.35e+01 1hyt d.92.1.2 58962 1kxoA 184 1.36e+01 b.60.1.1 84475 1vkbA 161 1.36e+01 d.269.1.1 108643 2bhuA 602 1.37e+01 2fe7A 166 1.40e+01 1wmhA 89 1.40e+01 1tuaA 191 1.40e+01 d.51.1.1,d.51.1.1 107321,107322 1kzlA 208 1.41e+01 b.43.4.3,b.43.4.3 77635,77636 1h6lA 353 1.41e+01 b.68.3.1 60687 1ta9A 450 1.41e+01 2ganA 190 1.43e+01 1b5qA 472 1.44e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 1kgcE 242 1.44e+01 b.1.1.1,b.1.1.2 77386,77387 1yge 839 1.47e+01 1yge a.119.1.1,b.12.1.1 19234,23634 2bjfA 329 1.49e+01 1zymA 258 1.49e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 1nf3C 128 1.51e+01 b.36.1.1 85596 2dpkA 152 1.52e+01 1hrnA 337 1.54e+01 1smrA b.50.1.2 26869 1xdfA 157 1.59e+01 1f00I 282 1.60e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 2ew2A 316 1.60e+01 1vlrA 350 1.61e+01 d.13.1.3,d.246.1.1 108860,108861 1wuiL 534 1.67e+01 1widA 130 1.70e+01 1oewA 329 1.70e+01 b.50.1.2 86924 1fp2A 352 1.72e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 2f69A 261 1.73e+01 1xqbA 247 1.74e+01 1qwdA 177 1.74e+01 b.60.1.1 96471 1yloA 348 1.74e+01 2aq9A 262 1.76e+01 2bbsA 290 1.77e+01 1hh1A 143 1.78e+01 1gefA c.52.1.18 61036 1v6tA 255 1.78e+01 1qmvA 197 1.78e+01 1qq2A c.47.1.10 33066 2gtqA 867 1.80e+01 1k0iA 394 1.87e+01 c.3.1.2,d.16.1.2 67942,67943 1ykjA 394 1.88e+01 1zkoA 136 1.89e+01 1jgsA 138 1.98e+01 a.4.5.28 66683 2fvvA 194 1.99e+01 1ubkL 534 2.01e+01 e.18.1.1 88422 1o54A 277 2.02e+01 c.66.1.13 92482 1ta0A 197 2.02e+01 c.108.1.16 106729 1k8qA 377 2.04e+01 c.69.1.6 72177 1yqdA 366 2.05e+01 1gpc 218 2.06e+01 1gpc b.40.4.7 25393 2atpB 115 2.07e+01 1wy2A 351 2.11e+01 2g6bA 180 2.21e+01 1q0qA 406 2.22e+01 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1ryaA 160 2.23e+01 d.113.1.5 105122 2f6rA 281 2.25e+01 1yzyA 413 2.25e+01 2d93A 134 2.26e+01 1xr4A 509 2.27e+01 1e6uA 321 2.32e+01 1bsvA c.2.1.2 29805 1h3gA 601 2.39e+01 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 2bt6A 108 2.40e+01 1udxA 416 2.43e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1h8eD 482 2.46e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 2fexA 188 2.52e+01 2d13A 227 2.54e+01 1ryp1 222 2.59e+01 1ryp1 1gt1A 159 2.59e+01 b.60.1.1 90515 1t9hA 307 2.60e+01 1vq0A 302 2.64e+01 1p9eA 331 2.66e+01 d.157.1.5 104088 2b4wA 315 2.72e+01 2acaA 189 2.72e+01 1onwA 390 2.74e+01 b.92.1.7,c.1.9.13 87172,87173 1q74A 303 2.76e+01 c.134.1.1 96019 1pl8A 356 2.76e+01 b.35.1.2,c.2.1.1 94878,94879 1wtjA 343 2.83e+01 1ut9A 609 2.85e+01 a.102.1.2,b.1.18.2 99912,99913 1qx4A 274 2.88e+01 b.43.4.2,c.25.1.1 104624,104625 1njhA 119 2.90e+01 b.128.1.1 85787 1c30B 382 2.91e+01 c.8.3.1,c.23.16.1 30736,31413 1vqoS 85 2.92e+01 2et1A 201 2.95e+01 1gefA 123 2.96e+01 1gefA c.52.1.18 60465 1b0uA 262 2.99e+01 1b0uA c.37.1.12 32370 1hfoA 113 3.01e+01 d.80.1.3 61006 1mwmA 320 3.03e+01 c.55.1.1,c.55.1.1 79580,79581 1pvxA 194 3.09e+01 1axkA b.29.1.11 24341 1m6dA 214 3.12e+01 d.3.1.1 84849 1ff9A 450 3.13e+01 1ff9A c.2.1.3,d.81.1.2 30039,39954 1vpsA 289 3.13e+01 1vpsA b.121.6.1 23336 1zbqA 327 3.14e+01 1vflA 356 3.17e+01 1ve6A 582 3.18e+01 1eyqA 222 3.18e+01 1eypA d.36.1.1 38534 1w7jA 795 3.20e+01 1yb2A 275 3.23e+01 1bkb 136 3.23e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 1crzA 403 3.29e+01 1crzA b.68.4.1,c.51.2.1 27629,33211 1tueA 212 3.30e+01 c.37.1.20 107323 1wy7A 207 3.32e+01 1zi8A 236 3.32e+01 2g7zA 282 3.42e+01 1t3yA 141 3.44e+01 1xs0A 136 3.45e+01 1dhn 121 3.48e+01 1dhn d.96.1.3 40663 1a6cA 513 3.52e+01 1a6cA b.121.4.2,b.121.4.2,b.121.4.2 23296,23297,23298 1y8tA 324 3.57e+01 1oapA 109 3.60e+01 d.79.7.1 92706 1yna 194 3.61e+01 1axkA b.29.1.11 24335 2bnuB 241 3.70e+01 1e6yB 433 3.71e+01 1mroB a.89.1.1,d.58.31.2 18535,39453 1k8kB 394 3.72e+01 c.55.1.1 68307 1j58A 385 3.72e+01 b.82.1.2 71531 1din 236 3.73e+01 1din c.69.1.9 34682 1kmqA 184 3.74e+01 c.37.1.8 84412 1pkhA 204 3.82e+01 b.85.4.1 94832 3eipA 84 3.84e+01 3eipA d.26.2.1 38434 1vfgA 390 3.85e+01 a.173.1.1,d.218.1.4 108570,108571 2f4iA 197 3.88e+01 1ykwA 435 3.92e+01 2fgoA 82 3.94e+01 1smoA 119 4.00e+01 b.1.1.1 105764 1fi2A 201 4.00e+01 1fi2A b.82.1.2 59845 1gvp 87 4.07e+01 1gvp b.40.4.7 25369 1htrB 329 4.08e+01 1smrA 1ek6A 348 4.09e+01 1xel c.2.1.2 29800 1y13A 181 4.10e+01 1vzyA 291 4.10e+01 1guqA 348 4.15e+01 1guqA d.13.1.2,d.13.1.2 37522,37523 2evwX 166 4.16e+01 1qg3A 195 4.18e+01 1qg3A b.1.2.1,b.1.2.1 21993,21994 1jcfA 344 4.21e+01 c.55.1.1,c.55.1.1 62878,62879 2a1kA 233 4.25e+01 1at0 145 4.27e+01 1at0 b.86.1.1 28374 1g0sA 209 4.39e+01 1g0sA d.113.1.1 60187 1csn 298 4.45e+01 1csn d.144.1.7 41664 1hkhA 279 4.45e+01 c.69.1.12 90628 1okiA 210 4.48e+01 b.11.1.1,b.11.1.1 93255,93256 1oi2A 366 4.51e+01 c.119.1.2 103802 1ra6A 461 4.52e+01 e.8.1.4 104879 1fgkA 310 4.58e+01 1fgkA d.144.1.7 41693 1qf9A 194 4.62e+01 1zin c.37.1.1 31848 2arpA 116 4.64e+01 2ai4A 119 4.66e+01 2ck3A 510 4.71e+01 2b06A 155 4.71e+01 2ahuA 531 4.71e+01 1h72C 296 4.71e+01 d.14.1.5,d.58.26.1 60712,60713 1ut7A 171 4.73e+01 b.143.1.1 99906 1ignA 246 4.77e+01 1ignA a.4.1.6,a.4.1.6 16048,16049 1umkA 275 4.78e+01 1ad2 228 4.80e+01 1ad2 e.24.1.1 43353 2ew0A 192 4.81e+01 1r8sE 203 4.84e+01 a.118.3.1 97248 1kolA 398 4.84e+01 b.35.1.2,c.2.1.1 77474,77475 2c46A 241 4.84e+01 1zgzA 122 4.86e+01 2fauA 341 4.87e+01 1a9xB 379 4.90e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 1dabA 539 4.95e+01 1dabA b.80.1.7 28049 1hr0W 71 4.97e+01 1ah9 b.40.4.5 25329 1hpcA 131 4.98e+01 1htp b.84.1.1 28221 1zsyA 357 5.03e+01 1n6aA 259 5.03e+01 b.76.2.1,b.85.7.1 80121,80122 2bi7A 384 5.04e+01 1bg2 325 5.06e+01 1bg2 c.37.1.9 32189 1uzmA 247 5.17e+01 1jatA 155 5.17e+01 1u9aA d.20.1.1 62818 1wrmA 165 5.22e+01 2b0vA 153 5.28e+01 1kv7A 488 5.41e+01 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 1qh5A 260 5.45e+01 1qh5A d.157.1.2 42057 1uwvA 433 5.49e+01 b.40.4.12,c.66.1.40 100128,100129 1hcnB 145 5.50e+01 1hcnB g.17.1.4 44810 1wlyA 333 5.50e+01 1zboA 210 5.53e+01 1fqtA 112 5.54e+01 1fqtA b.33.1.1 24441 2biiA 424 5.58e+01 1ry9A 145 5.59e+01 d.198.1.1 98094 1mjfA 281 5.66e+01 c.66.1.17 79198 1u4gA 301 5.67e+01 d.92.1.2 107670 1q8rA 120 5.71e+01 d.79.6.1 96225 1tp9A 162 5.72e+01 2bbdA 350 5.72e+01 1zupA 315 5.73e+01 1yr2A 741 5.79e+01 1vjuA 309 5.82e+01 d.248.1.1 100835 1jvbA 347 5.90e+01 b.35.1.2,c.2.1.1 77181,77182 1xkpC 143 5.91e+01 1b9hA 388 5.92e+01 1b9hA c.67.1.4 34488 1xocA 520 5.92e+01 1k07A 263 5.99e+01 d.157.1.1 77218 1f5nA 592 6.05e+01 1dg3A a.114.1.1,c.37.1.8 19077,32152 1b2pA 119 6.05e+01 1b2pA b.78.1.1 27998 1fo8A 343 6.13e+01 1foaA c.68.1.10 59927 1regX 122 6.19e+01 1regX d.58.27.1 39406 1xm8A 254 6.22e+01 1u7zA 226 6.23e+01 1lc5A 364 6.28e+01 c.67.1.1 73827 1u4bA 580 6.30e+01 c.55.3.5,e.8.1.1 107664,107665 2bllA 345 6.33e+01 2g1lA 104 6.38e+01 1se8A 301 6.39e+01 b.40.4.3 105448 2fo3A 125 6.40e+01 2aexA 346 6.40e+01 1ylnA 252 6.40e+01 2beiA 170 6.42e+01 1jb9A 316 6.44e+01 1fnc b.43.4.2,c.25.1.1 62840,62841 1gwmA 153 6.48e+01 b.18.1.19 83348 1v7pB 128 6.48e+01 d.169.1.1 108407 1n4kA 381 6.57e+01 a.118.22.1,b.42.6.1 79992,79993 2czvC 120 6.59e+01 1gjjA 168 6.62e+01 a.140.1.1,a.140.1.1 83291,83292 2bkaA 242 6.66e+01 1wlfA 179 6.70e+01 b.52.2.3,d.31.1.1 109396,109397 1w6vA 141 6.71e+01 1w0hA 204 6.74e+01 1zkcA 197 6.77e+01 2basA 431 6.78e+01 1rg9A 383 6.78e+01 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1wocA 103 6.79e+01 2c31A 568 6.80e+01 1ss4A 153 6.83e+01 d.32.1.6 105976 1rypB 250 6.88e+01 1rypB d.153.1.4 41933 1edqA 540 6.91e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1cp2A 269 6.91e+01 1cp2A c.37.1.10 32269 1h0hB 214 6.94e+01 d.58.1.5 76437 1k0wA 231 7.03e+01 c.74.1.1 77220 1x8gA 227 7.04e+01 1z57A 339 7.07e+01 1h2eA 207 7.11e+01 c.60.1.1 70857 1ekeA 230 7.16e+01 1ekeA c.55.3.1 33572 1zl0A 311 7.16e+01 1p0fA 373 7.18e+01 b.35.1.2,c.2.1.1 87642,87643 1jkmB 361 7.28e+01 1jkmA c.69.1.2 34634 1sjyA 159 7.28e+01 d.113.1.1 98900 1uufA 369 7.29e+01 b.35.1.2,c.2.1.1 100006,100007 1j24A 143 7.33e+01 c.52.1.20 84008 1lurA 339 7.35e+01 b.30.5.4 84717 1x8hA 228 7.37e+01 1mspA 126 7.37e+01 1mspA b.1.11.2 22333 1vizA 240 7.43e+01 c.1.4.1 100784 1p1jA 533 7.52e+01 c.2.1.3,d.81.1.3 87687,87688 2gm6A 208 7.58e+01 1u79A 129 7.61e+01 d.26.1.1 107714 1h54A 754 7.65e+01 a.102.1.4,b.30.5.3 60634,60635 2fafA 608 7.67e+01 1y1pA 342 7.73e+01 2a74A 643 7.76e+01 1r8gA 372 7.78e+01 d.128.1.3 104845 1vh4A 435 7.80e+01 b.80.6.1 100640 2fymA 431 7.80e+01 1lh0A 213 7.80e+01 c.61.1.1 73896 1xgkA 352 7.85e+01 1bg6 359 7.86e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 1yf2A 425 7.97e+01 1wdjA 187 7.99e+01 2culA 232 7.99e+01 1fmcA 255 8.01e+01 1cydA c.2.1.2 29856 1qfjA 232 8.02e+01 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