# List of top-scoring protein chains for t04-100-40-40-str2+CB_burial_14_7-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 1rlhA 173 5.41e-32 unknown_sccs -10786 1oz9A 150 6.95e-02 unknown_sccs -10588 1fp2A 352 9.34e-02 1fpxA a.4.5.29 59941 c.66.1.12 59942 1ccwA 137 2.39e-01 1be1 c.23.6.1 31238 1l8nA 679 2.43e-01 c.1.8.10 84564 d.92.2.2 84565 1ej0A 180 2.51e-01 1ej0A c.66.1.2 34179 1m3uA 264 2.53e-01 c.1.12.8 84784 1ub3A 220 3.16e-01 c.1.10.1 88395 1jclA 260 3.64e-01 c.1.10.1 66501 1mzbA 136 4.08e-01 unknown_sccs -266 1p1xA 260 4.42e-01 1ttzA 87 4.97e-01 1i1qA 520 4.98e-01 1qdlA d.161.1.1 61543 1uayA 242 5.21e-01 c.2.1.2 88390 1drw 273 8.23e-01 1drw c.2.1.3 30057 d.81.1.3 39972 1ho1A 242 9.20e-01 1ho1A c.1.24.1 61097 1efvA 315 9.37e-01 1efvA c.26.2.3 31633 c.31.1.2 31728 1bn7A 294 9.50e-01 1bn6A c.69.1.8 34677 1l6wA 220 1.03e+00 c.1.10.1 73632 1dmhA 311 1.09e+00 1dmhA b.3.6.1 22633 1i6pA 220 1.21e+00 1ddzA c.53.2.1 61848 1jw9B 249 1.31e+00 c.111.1.1 67377 1oltA 457 1.35e+00 unknown_sccs -5688 1vkfA 188 1.36e+00 1q1oA 98 1.45e+00 d.15.2.2 -9172 1fc4A 401 1.76e+00 1bs0A c.67.1.4 59760 1ff9A 450 1.80e+00 1ff9A c.2.1.3 30039 d.81.1.2 39954 1fwsA 267 1.81e+00 1d9eA c.1.10.4 60063 1q0pA 223 1.81e+00 c.62.1.1 -7979 1hgxA 183 1.85e+00 1tc1A c.61.1.1 34027 1g6hA 257 1.92e+00 1gajA c.37.1.12 60318 1j5pA 253 1.97e+00 c.2.1.3 83092 d.81.1.3 71577 1tikA 213 2.07e+00 1jb9A 316 2.19e+00 1fnc b.43.4.2 62840 c.25.1.1 62841 1vhmA 195 2.20e+00 d.110.2.1 -10828 1uanA 227 2.21e+00 unknown_sccs -8129 1uz5A 402 2.29e+00 b.85.6.1 -5029 b.103.1.1 -5069 c.57.1.2 -7902 1fxqA 267 2.35e+00 1d9eA c.1.10.4 60108 1rxwA 336 2.46e+00 a.60.7.1 -1041 c.120.1.2 -6680 1jcxA 267 2.48e+00 c.1.10.4 66510 1uocA 289 2.49e+00 unknown_sccs -7671 1pe1A 267 2.60e+00 c.1.10.4 -5553 1k1xA 659 2.94e+00 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1o4vA 183 2.97e+00 c.23.8.1 86628 1e3mA 800 3.22e+00 1ewqA a.113.1.1 19075 c.37.1.12 32389 c.55.6.1 33746 d.75.2.1 39747 1id1A 153 3.29e+00 1id1A c.2.1.9 62286 1ry9A 145 3.63e+00 d.198.1.1 -9020 1qdeA 224 3.74e+00 1qvaA c.37.1.19 32410 1uc7A 125 3.75e+00 c.47.1.1 -7414 1dcjA 81 3.76e+00 1dcjA d.68.3.3 59115 1bdmA 327 3.83e+00 1bmdA c.2.1.5 30137 d.162.1.1 42104 1oeyJ 107 4.09e+00 d.15.2.2 -9168 1i7qA 519 4.16e+00 1qdlA d.161.1.1 61901 1burA 475 4.18e+00 1burA 1ujnA 348 4.19e+00 e.22.1.1 -11998 1moq 368 4.20e+00 1moq c.80.1.1 35302 8rucA 475 4.28e+00 1burA c.1.14.1 29339 d.58.9.1 39245 1ewqA 765 4.33e+00 1ewqA a.113.1.1 19069 c.37.1.12 32383 c.55.6.1 33740 d.75.2.1 39743 1gnxA 479 4.36e+00 c.1.8.4 76241 1osdA 72 4.40e+00 1ec7A 446 4.46e+00 1bqg c.1.11.2 29218 d.54.1.1 38862 1mjfA 281 4.56e+00 c.66.1.17 79198 1tz9A 367 4.86e+00 1qczA 169 4.94e+00 1qczA c.23.8.1 31276 1dyr 206 5.26e+00 1aoeA c.71.1.1 34916 1qwgA 251 5.39e+00 unknown_sccs -5678 1jcfA 344 5.45e+00 c.55.1.1 62878 c.55.1.1 62879 1uasA 362 5.54e+00 b.71.1.1 88388 c.1.8.1 88389 1j5vA 351 5.60e+00 c.72.1.1 71585 1dp4A 435 5.91e+00 1dp4A c.93.1.1 35710 1nulA 152 6.07e+00 1nulA c.61.1.1 34011 1m5wA 243 6.21e+00 c.1.24.1 84836 1nm2A 317 6.34e+00 c.19.1.1 80654 d.58.23.1 80655 1r3sA 367 6.40e+00 c.1.22.1 -5648 1r64A 481 6.45e+00 b.18.1.20 -3151 c.41.1.1 -7297 1oc7A 364 6.48e+00 c.6.1.1 86794 1ddgA 374 6.62e+00 1amoA b.43.4.1 25671 c.25.1.4 31559 1im5A 180 6.73e+00 unknown_sccs 66211 1aq0A 306 6.81e+00 1aq0A c.1.8.3 28842 1ka1A 357 6.84e+00 e.7.1.1 68369 1g5cA 170 6.91e+00 1g5cA c.53.2.1 60264 1i06A 180 6.97e+00 1mup b.60.1.1 27131 1dg9A 157 7.08e+00 1dg9A c.44.1.1 32637 1rkqA 282 7.19e+00 c.108.1.10 -6847 1n0wA 243 7.20e+00 c.37.1.11 79772 1nijA 318 7.23e+00 c.37.1.10 85741 d.237.1.1 85742 1hyeA 313 7.35e+00 2cmd c.2.1.5 61400 d.162.1.1 61401 1d7yA 408 7.41e+00 1d7yA c.3.1.5 30565 c.3.1.5 30566 d.87.1.1 40204 1i05A 180 7.42e+00 1mup b.60.1.1 27130 1uroA 367 7.42e+00 1uroA c.1.22.1 29675 1qydA 313 7.58e+00 c.2.1.2 -5786 2prd 174 7.64e+00 2prd b.40.5.1 25435 1gk8A 475 7.77e+00 c.1.14.1 65234 d.58.9.1 65235 1qamA 244 7.86e+00 2ercA c.66.1.24 34220 1mup 166 7.89e+00 1mup b.60.1.1 27133 1pyaB 228 7.89e+00 1pyaB 1cvrA 435 7.91e+00 1cvrA b.1.18.12 21949 c.17.1.2 31006 1jmkC 230 8.00e+00 c.69.1.22 71747 1jv4A 162 8.03e+00 b.60.1.1 67343 1kepA 348 8.04e+00 c.2.1.2 68536 1nrzA 164 8.28e+00 c.38.1.1 86131 1f46A 140 8.75e+00 1f46A d.129.4.1 59643 1va4A 279 9.15e+00 1o54A 277 9.22e+00 c.66.1.13 -8095 1df7A 159 9.32e+00 3dfr c.71.1.1 34885 1k6dA 220 9.36e+00 unknown_sccs 72082 1bj7 156 9.49e+00 1bj7 b.60.1.1 27113 1s6tA 285 9.57e+00 c.37.1.5 -7040 1vkjA 285 9.57e+00 1qycA 308 9.59e+00 c.2.1.2 -5782 1hl9A 449 9.63e+00 unknown_sccs -4694 unknown_sccs -5365 1m0wA 491 9.67e+00 c.30.1.4 78363 d.142.1.6 78364 1r6uA 437 9.72e+00 c.26.1.1 -6594 1r26A 125 9.78e+00 c.47.1.1 -7389 1pdo 135 9.87e+00 1pdo c.54.1.1 33376 1k6xA 352 1.01e+01 c.2.1.2 68238 1qcwA 410 1.01e+01 1gox c.1.4.1 28622 2bvwA 362 1.02e+01 1bvwA c.6.1.1 30666 1knwA 425 1.02e+01 b.49.2.3 -4274 c.1.6.1 -5229 1aoeA 192 1.03e+01 1aoeA c.71.1.1 34923 1qy1A 174 1.05e+01 b.60.1.1 -4445 1kbjA 412 1.06e+01 c.1.4.1 72280 1gky 187 1.08e+01 1gky c.37.1.1 31839 1ig3A 263 1.09e+01 1ig3A b.82.6.1 62358 c.100.1.1 62359 1m7xA 617 1.12e+01 b.1.18.2 78749 b.71.1.1 78750 c.1.8.1 78751 1qgxA 357 1.12e+01 1qgxA e.7.1.1 42973 1rkxA 357 1.13e+01 c.2.1.2 -5770 1fvgA 199 1.16e+01 1fvaA d.58.28.1 39408 1lqtA 456 1.17e+01 c.3.1.1 74198 c.4.1.1 74199 1pjqA 457 1.18e+01 c.2.1.11 -5904 c.90.1.1 -8611 e.37.1.1 -12004 1h7eA 245 1.21e+01 c.68.1.13 60717 1jflA 228 1.22e+01 c.78.2.1 71656 c.78.2.1 71657 1h6kZ 98 1.24e+01 d.58.7.1 60686 1neyA 247 1.25e+01 c.1.1.1 80449 1qhiA 366 1.27e+01 1qhiA c.37.1.1 31860 1vp9 322 1.32e+01 3mag c.66.1.25 34210 6mhtA 327 1.33e+01 6mhtA c.66.1.26 34226 1im8A 244 1.34e+01 c.66.1.14 66212 2ts1 419 1.34e+01 2ts1 c.26.1.1 31564 1vpt 348 1.37e+01 3mag c.66.1.25 34207 1dzkA 157 1.38e+01 1obpA b.60.1.1 27096 1n71A 180 1.39e+01 d.108.1.1 85370 1gvoA 364 1.40e+01 c.1.4.1 76357 1zpdA 568 1.43e+01 1zpdA c.31.1.3 31741 c.36.1.5 31785 c.36.1.9 31786 1c0eA 157 1.45e+01 1dg9A c.44.1.1 32638 1fnnA 389 1.52e+01 1fnnA a.4.5.11 16129 c.37.1.20 32426 1dkuA 317 1.53e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1s96A 219 1.53e+01 c.37.1.1 -6972 1ktbA 405 1.58e+01 b.71.1.1 72960 c.1.8.1 72961 2gar 212 1.60e+01 2gar c.65.1.1 34161 1fts 295 1.61e+01 1ng1 a.24.13.1 16968 c.37.1.10 32279 1adjA 421 1.62e+01 1adjA c.51.1.1 33188 d.104.1.1 40737 1o97C 264 1.63e+01 c.26.2.3 81232 1oc2A 348 1.64e+01 c.2.1.2 -5753 1ex2A 189 1.64e+01 1ex2A c.51.4.2 33225 1qmpA 130 1.70e+01 1dz3A c.23.1.1 31106 1inlA 296 1.72e+01 c.66.1.17 66220 1jakA 512 1.75e+01 c.1.8.6 66472 d.92.2.1 66473 1fbnA 230 1.77e+01 1fbnA c.66.1.3 34181 1gox 370 1.77e+01 1gox c.1.4.1 28607 2ng1 293 1.77e+01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1g8lA 411 1.78e+01 1g8lA b.85.6.1 60365 b.103.1.1 60366 c.57.1.2 60367 1k7jA 206 1.78e+01 d.115.1.1 72103 1ej1A 190 1.80e+01 1ejhA d.86.1.1 40144 1a8y 367 1.81e+01 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1g60A 260 1.82e+01 c.66.1.11 70151 1fsz 372 1.87e+01 1fsz c.32.1.1 31750 d.79.2.1 39802 1souA 194 1.88e+01 1r0wA 286 1.91e+01 c.37.1.12 -7158 1e4mM 501 1.93e+01 1e70M c.1.8.4 59226 3mag 307 1.94e+01 3mag c.66.1.25 34205 1tljA 213 1.97e+01 1h0bA 256 1.98e+01 b.29.1.11 83422 1b78A 193 1.98e+01 1b78A c.51.4.1 33221 1bmdA 327 2.04e+01 1bmdA c.2.1.5 30139 d.162.1.1 42106 1rj9A 304 2.04e+01 a.24.13.1 -631 c.37.1.10 -7129 1r61A 207 2.05e+01 unknown_sccs -6086 1ta3B 303 2.06e+01 1qfeA 252 2.06e+01 1qfeA c.1.10.1 29167 1epxA 370 2.11e+01 1fbaA c.1.10.1 29150 1dhr 241 2.11e+01 1dhr c.2.1.2 29832 1qsgA 265 2.15e+01 1eny c.2.1.2 29935 1ogiA 303 2.20e+01 b.43.4.2 -4042 c.25.1.1 -6587 1v39 322 2.20e+01 3mag c.66.1.25 34206 1tq8A 163 2.20e+01 1k92A 455 2.21e+01 c.26.2.1 68325 d.210.1.1 68326 1o5xA 248 2.21e+01 c.1.1.1 -5157 1kqzA 273 2.21e+01 c.1.8.5 68844 1cjwA 166 2.24e+01 1cjwA d.108.1.1 40818 1iu8A 206 2.24e+01 c.56.4.1 71436 1ls1A 295 2.25e+01 a.24.13.1 78170 c.37.1.10 78171 1o8bA 219 2.25e+01 unknown_sccs 81180 d.58.40.1 81181 1g8sA 230 2.26e+01 c.66.1.3 -8047 1ooeA 236 2.27e+01 c.2.1.2 87196 1dz3A 130 2.30e+01 1dz3A c.23.1.1 31105 1vkmA 297 2.30e+01 1f5aA 513 2.31e+01 1fa0B a.160.1.1 75835 d.218.1.3 75836 d.58.16.1 39337 1yub 245 2.31e+01 2ercA c.66.1.24 34219 1yghA 164 2.31e+01 1yghA d.108.1.1 40802 1que 303 2.33e+01 1fnc b.43.4.2 25647 c.25.1.1 31537 1eny 268 2.33e+01 1eny c.2.1.2 29910 1o0pA 104 2.33e+01 d.58.7.1 86535 1bd0A 388 2.34e+01 1bd0A b.49.2.2 26480 c.1.6.1 28642 1d3yA 301 2.35e+01 1d3yA e.12.1.1 43252 1gqnA 252 2.37e+01 c.1.10.1 -5494 1rt8A 513 2.40e+01 1lhpA 312 2.41e+01 c.72.1.5 77960 7odcA 424 2.41e+01 7odcA b.49.2.3 26488 c.1.6.1 28650 2cmd 312 2.41e+01 2cmd c.2.1.5 30135 d.162.1.1 42102 1o5iA 249 2.42e+01 c.2.1.2 -5833 1vjpA 394 2.44e+01 c.2.1.3 -5897 d.81.1.3 -10480 1p3dA 475 2.48e+01 c.5.1.1 87728 c.59.1.1 87729 c.72.2.1 87730 1i6wA 181 2.51e+01 1i6wA c.69.1.18 61859 1pz1A 333 2.52e+01 c.1.7.1 -5255 1e0wA 313 2.55e+01 1taxA c.1.8.3 59150 1mj5A 302 2.58e+01 c.69.1.8 -8326 2hvm 273 2.59e+01 1cnv c.1.8.5 28985 1jbkA 195 2.60e+01 c.37.1.20 71631 1sftA 388 2.60e+01 1bd0A b.49.2.2 26482 c.1.6.1 28644 1b74A 254 2.62e+01 1b74A c.78.2.1 35264 c.78.2.1 35265 1vknA 351 2.63e+01 1ispA 181 2.65e+01 c.69.1.18 76778 1jj2I 145 2.66e+01 1ffkG c.21.1.1 63094 1fezA 256 2.68e+01 1fezA c.108.1.3 43343 1itcA 516 2.69e+01 b.3.1.1 83705 c.1.8.1 83706 1bf6A 291 2.72e+01 1pscA c.1.9.3 29065 1go2A 304 2.74e+01 b.43.4.2 76243 c.25.1.1 76244 1uqtA 482 2.77e+01 c.87.1.6 -8593 1bcpB 199 2.77e+01 1bcpB b.40.2.1 25120 d.169.1.2 42429 1mvlA 209 2.79e+01 c.34.1.1 85146 1gteA 1025 2.79e+01 a.1.2.2 70440 c.1.4.1 70441 c.3.1.1 70442 c.4.1.1 70443 d.58.1.5 70444 1qstA 160 2.82e+01 1yghA d.108.1.1 40804 2myr 501 2.83e+01 2tmdA 729 2.85e+01 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1g2qA 187 2.86e+01 c.61.1.1 65117 1gntA 553 2.87e+01 e.26.1.1 70290 1gc0A 398 2.87e+01 c.67.1.3 70168 1gqiA 708 2.89e+01 c.1.8.10 76279 d.92.2.2 76280 1m6iA 493 3.02e+01 c.3.1.5 74533 c.3.1.5 74534 d.87.1.1 74535 1e2kA 331 3.06e+01 1qhiA c.37.1.1 31854 1vhyA 257 3.07e+01 b.122.1.2 -5129 c.116.1.5 -6705 1fb6A 105 3.09e+01 1thx c.47.1.1 32739 1r7aA 504 3.10e+01 b.71.1.1 -4664 c.1.8.1 -5283 1i45A 248 3.11e+01 1amk c.1.1.1 61665 1cl1A 395 3.13e+01 1cl2A c.67.1.3 34395 1hp5A 512 3.18e+01 1hp4A c.1.8.6 61113 d.92.2.1 61114 1kid 203 3.20e+01 1derA c.8.5.1 30771 1fc6A 388 3.25e+01 1fc6A b.36.1.3 64738 c.14.1.2 64739 1f9aA 168 3.26e+01 1f9aA c.26.1.3 31602 1gp6A 356 3.26e+01 b.82.2.1 65441 1v8fA 276 3.28e+01 c.26.1.4 -6618 1igs 248 3.30e+01 1a53 c.1.2.4 28565 1j8mF 297 3.31e+01 1ng1 a.24.13.1 62742 c.37.1.10 62743 1cliA 345 3.31e+01 1cliA d.79.4.1 39816 d.139.1.1 41459 1gg4A 452 3.34e+01 1gg4A c.98.1.1 58985 c.59.1.1 33957 c.72.2.1 58986 1j1tA 233 3.34e+01 unknown_sccs -3462 1ru8A 232 3.34e+01 c.26.2.1 -6635 1o17A 345 3.34e+01 a.46.2.1 80765 c.27.1.1 80766 1v4vA 376 3.38e+01 c.87.1.3 -8583 1uteA 313 3.43e+01 1uteA d.159.1.1 42078 1hzyA 332 3.48e+01 1pscA c.1.9.3 61468 1fwkA 296 3.49e+01 1fwkA d.14.1.5 37576 d.58.26.1 39398 1d1qA 161 3.49e+01 1dg9A c.44.1.1 32642 1e20A 209 3.50e+01 1e20A c.34.1.1 31759 1s4qA 228 3.52e+01 c.37.1.1 -6975 1m33A 258 3.53e+01 c.69.1.26 78514 1din 236 3.54e+01 1din c.69.1.9 34682 1h4vB 421 3.54e+01 1adjA c.51.1.1 60624 d.104.1.1 60625 1ldg 316 3.56e+01 1ceqA c.2.1.5 30165 d.162.1.1 42132 1dzfA 215 3.57e+01 1dzfA c.52.3.1 33344 d.78.1.1 39753 1hdr 244 3.58e+01 1dhr c.2.1.2 29837 1ex7A 186 3.60e+01 1gky c.37.1.1 59537 1d1gA 168 3.60e+01 1d1gA c.71.1.1 34889 1d8wA 426 3.69e+01 1de5A c.1.15.2 29394 1nni1 174 3.69e+01 1dqpA 230 3.70e+01 1dqnA c.61.1.1 34069 1j3wA 163 3.71e+01 unknown_sccs -10870 1vi9A 299 3.75e+01 c.72.1.5 -8393 1mzhA 225 3.76e+01 c.1.10.1 79698 1upaA 573 3.78e+01 c.31.1.3 -6745 c.36.1.5 -6903 c.36.1.9 -6943 1i0dA 332 3.82e+01 1pscA c.1.9.3 61487 1q0sA 259 3.83e+01 c.66.1.28 -8110 1ojxA 263 3.85e+01 c.1.10.1 -5445 1h3gA 601 3.86e+01 b.1.18.2 -2725 b.71.1.1 -4653 c.1.8.1 -5277 1kkhA 317 3.87e+01 d.14.1.5 72645 d.58.26.3 72646 1kwmA 402 3.87e+01 c.56.5.1 73079 d.58.3.1 73080 1f8mA 429 3.91e+01 1dquA c.1.12.7 29315 1r89A 437 3.92e+01 unknown_sccs -1147 unknown_sccs -9801 unknown_sccs -10061 1g291 372 3.93e+01 1g291 1qqgA 264 3.99e+01 1qqgA b.55.1.2 26987 b.55.1.2 26988