# List of top-scoring protein chains for t2k-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 1f7sA 139 1.03e-26 1cof d.109.1.2 40857 1v6fA 151 1.96e-26 1cfyA 143 2.01e-25 1cof d.109.1.2 40858 1cnuA 137 3.84e-25 1cof d.109.1.2 40862 1cof 143 4.77e-25 1cof d.109.1.2 40860 1m4jA 142 1.16e-20 d.109.1.2 78602 1ak7 174 6.09e-15 1cof d.109.1.2 40864 1hqz1 141 1.61e-14 1hqz9 141 2.90e-14 1udmA 149 4.16e-10 1svy 114 1.18e-03 1svy d.109.1.1 40831 1svr 114 2.83e-03 1svy d.109.1.1 40833 1svq 114 3.41e-03 1svy d.109.1.1 40832 1yagG 125 3.92e-02 1d0nA d.109.1.1 40846 2vil 126 5.40e-02 2vil d.109.1.1 40830 1d4xG 126 6.05e-02 1d0nA d.109.1.1 59109 1nm1G 125 6.84e-02 d.109.1.1 80653 1qsmA 152 8.74e-02 1qsmA d.108.1.1 40808 2vik 126 1.13e-01 2vil d.109.1.1 40829 1ex2A 189 1.32e-01 1ex2A c.51.4.2 33225 1egaA 301 1.82e-01 1egaA c.37.1.8 32150 d.52.3.1 38836 1kcqA 104 2.14e-01 d.109.1.1 68449 1mml 265 3.05e-01 1mml e.8.1.2 43015 1qsoA 149 3.30e-01 1qsmA d.108.1.1 40812 1oi0A 124 4.06e-01 unknown_sccs -8782 1hw7A 255 9.66e-01 1i7fA d.193.1.1 61297 1vhyA 257 1.05e+00 b.122.1.2 -5129 c.116.1.5 -6705 1nwbA 124 1.06e+00 b.124.1.1 86296 1mai 131 1.19e+00 1mai b.55.1.1 26951 1vkiA 181 1.23e+00 1h6lA 353 1.25e+00 b.68.3.1 60687 8rucI 123 1.28e+00 1rboC d.73.1.1 39629 1pmhX 185 1.30e+00 1rboC 123 1.33e+00 1rboC d.73.1.1 39634 2pooA 355 1.37e+00 1qlgA b.68.3.1 27626 1qlgA 355 1.38e+00 1qlgA b.68.3.1 27627 1d0nA 729 1.72e+00 1d0nA d.109.1.1 40834 d.109.1.1 40835 d.109.1.1 40836 d.109.1.1 40837 d.109.1.1 40838 d.109.1.1 40839 1my6A 199 1.82e+00 a.2.11.1 85232 d.44.1.1 85233 1gv3A 248 1.84e+00 a.2.11.1 70585 d.44.1.1 70586 1hynP 379 1.90e+00 1hynP d.112.1.2 61408 1kkcA 221 1.91e+00 a.2.11.1 68660 d.44.1.1 68661 1n0lA 224 1.94e+00 b.1.11.1 79744 b.7.2.1 79745 1d5nA 205 2.01e+00 1avmA a.2.11.1 15762 d.44.1.1 38687 1cvmA 353 2.09e+00 1qlgA b.68.3.1 27628 1unnC 115 2.16e+00 unknown_sccs -10216 1bsmA 201 2.27e+00 1avmA a.2.11.1 15780 d.44.1.1 38743 1avmA 201 2.48e+00 1avmA a.2.11.1 15782 d.44.1.1 38745 1n6eA 1071 2.54e+00 b.36.1.3 80149 b.68.7.1 80150 b.69.9.1 80151 c.14.1.2 80152 1nmtA 392 2.57e+00 1nmtA d.108.1.2 40823 d.108.1.2 40824 1fjgS 93 2.66e+00 1qkfA d.28.1.1 38451 1qkfA 92 2.72e+00 1qkfA d.28.1.1 38456 1i0hA 205 2.78e+00 1avmA a.2.11.1 15760 d.44.1.1 38685 1nxzA 246 2.83e+00 b.122.1.2 86391 c.116.1.5 86392 1j3wA 163 2.93e+00 unknown_sccs -10870 3dni 260 2.93e+00 3dni d.151.1.1 41791 1dbxA 158 3.53e+00 1dbuA d.116.1.1 40928 1ualA 274 3.56e+00 c.116.1.4 88383 1jofA 365 3.71e+00 b.69.10.1 71775 1mu5A 471 3.81e+00 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1ako 268 3.84e+00 1ako d.151.1.1 41779 1ix9A 205 3.86e+00 a.2.11.1 76899 d.44.1.1 76900 1poiB 260 4.02e+00 1poiB unknown_sccs 34155 1ebfA 358 4.03e+00 1ebuA c.2.1.3 30033 d.81.1.2 39948 1i7fA 292 4.16e+00 1i7fA d.193.1.1 61888 1ge8A 249 4.16e+00 1plq d.131.1.2 41398 d.131.1.2 41399 1dujA 187 4.29e+00 1dujA d.135.1.1 41449 1k32A 1045 4.37e+00 b.36.1.3 68068 b.68.7.1 68069 b.69.9.1 68070 c.14.1.2 68071 1khhA 198 4.39e+00 c.66.1.16 68615 1ihjA 98 4.48e+00 1pdr b.36.1.1 62382 1qavB 115 4.63e+00 1qauA b.36.1.1 24780 1q0pA 223 4.87e+00 c.62.1.1 -7979 1hgxA 183 4.89e+00 1tc1A c.61.1.1 34027 2polA 366 5.01e+00 2polA d.131.1.1 41356 d.131.1.1 41357 d.131.1.1 41358 6pfkA 319 5.24e+00 3pfk c.89.1.1 35583 1eejA 216 5.30e+00 1eejA c.47.1.9 33057 d.17.3.1 38071 1i9zA 347 5.45e+00 1i9yA d.151.1.2 62102 1g8mA 593 5.60e+00 1g8mA c.24.1.3 60371 c.97.2.1 60372 1qppA 218 5.61e+00 1qpxA b.1.11.1 22320 b.7.2.1 23202 1s98A 107 6.02e+00 1dbuA 158 6.10e+00 1dbuA d.116.1.1 40930 1cojA 212 6.22e+00 1avmA a.2.11.1 15737 d.44.1.1 38734 1isaA 192 6.22e+00 1avmA a.2.11.1 15731 d.44.1.1 38724 1vhxA 150 6.23e+00 unknown_sccs -7663 1iscA 192 6.48e+00 1avmA a.2.11.1 15733 d.44.1.1 38726 1btl 263 6.50e+00 1btl e.3.1.1 42691 1m9nA 613 6.62e+00 c.24.1.3 78870 c.97.2.1 78871 1lyxA 248 6.69e+00 c.1.1.1 78304 1p1cA 199 6.71e+00 c.66.1.16 87669 1qpxA 218 6.73e+00 1qpxA b.1.11.1 22318 b.7.2.1 23200 1mmiA 366 6.77e+00 d.131.1.1 -11093 d.131.1.1 -11094 d.131.1.1 -11095 3adk 195 6.92e+00 1zin c.37.1.1 31885 1q98A 165 6.93e+00 c.47.1.10 -7499 1iz5A 249 7.09e+00 d.131.1.2 83834 d.131.1.2 83835 1v04A 355 7.15e+00 unknown_sccs -4592 2dnjA 260 7.25e+00 3dni d.151.1.1 41790 1ksgB 152 7.56e+00 b.1.18.8 72913 1ig8A 486 7.65e+00 2yhx c.55.1.3 64746 c.55.1.3 64747 1v58A 241 7.92e+00 1g1sA 162 8.32e+00 d.169.1.1 65100 g.3.11.1 65101 1go4A 205 8.50e+00 d.135.1.1 70292 1qauA 112 8.98e+00 1qauA b.36.1.1 24779 1r94A 118 9.04e+00 b.124.1.1 -4402 1gtmA 419 9.12e+00 1hwyA c.2.1.7 30223 c.58.1.1 33871 1i9yA 347 9.43e+00 1i9yA d.151.1.2 62101 1qjcA 158 9.64e+00 1b6tA c.26.1.3 63328 1b6tA 159 9.83e+00 1b6tA c.26.1.3 31600 1n9bA 265 9.93e+00 e.3.1.1 85463 1a99A 344 9.98e+00 1pot c.94.1.1 35812 1fw9A 164 1.03e+01 1fw9A d.190.1.1 60059 1ebuA 358 1.05e+01 1ebuA c.2.1.3 30035 d.81.1.2 39950 1pz4A 116 1.05e+01 d.106.1.1 -10780 1r6lA 239 1.06e+01 d.14.1.4 -9057 d.101.1.1 -10747 1jx4A 352 1.11e+01 unknown_sccs -10188 unknown_sccs -11898 1uesA 191 1.11e+01 1a5j 110 1.14e+01 1a5j a.4.1.3 16043 a.4.1.3 16044 1ub4C 85 1.15e+01 b.129.1.1 88401 1gvjA 146 1.16e+01 a.4.5.21 -293 1b06A 210 1.16e+01 1avmA a.2.11.1 15740 d.44.1.1 38737 1am2 199 1.18e+01 1am2 b.86.1.2 28381 1h2xA 710 1.19e+01 b.69.7.1 76598 c.69.1.4 76599 1jyrA 96 1.21e+01 d.93.1.1 71969 1jb0D 138 1.21e+01 1jb0D d.187.1.1 62823 1pv9A 348 1.21e+01 c.55.2.1 -7610 d.127.1.1 -11000 1bix 287 1.26e+01 1bix d.151.1.1 41781 1bg2 325 1.28e+01 1bg2 c.37.1.9 32189 1qnnA 191 1.28e+01 1avmA a.2.11.1 15792 d.44.1.1 38755 1p8xA 344 1.31e+01 d.109.1.1 -10813 d.109.1.1 -10814 d.109.1.1 -10815 4pfk 319 1.33e+01 3pfk c.89.1.1 35582 1qg6A 261 1.40e+01 1eny c.2.1.2 29919 1czaN 917 1.42e+01 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1h40A 71 1.43e+01 1s4kA 120 1.43e+01 1i4wA 353 1.52e+01 c.66.1.24 66028 1dgkN 917 1.52e+01 1qhaA c.55.1.3 33487 c.55.1.3 33488 c.55.1.3 33489 c.55.1.3 33490 1st9A 143 1.52e+01 c.47.1.10 -7503 1qfmA 710 1.55e+01 1qfmA b.69.7.1 27673 c.69.1.4 34641 1qtqA 553 1.55e+01 1gtrA b.53.1.2 26940 c.26.1.1 31579 1bmbA 123 1.57e+01 1griA d.93.1.1 40466 3pfk 319 1.58e+01 3pfk c.89.1.1 35581 1vybA 238 1.58e+01 1oejA 193 1.60e+01 unknown_sccs -4461 1klqA 197 1.60e+01 d.135.1.1 68689 1h2wA 710 1.64e+01 b.69.7.1 76596 c.69.1.4 76597 1b77A 228 1.65e+01 1b77A d.131.1.2 41362 d.131.1.2 41363 1kshB 152 1.66e+01 b.1.18.8 72915 3rubS 123 1.68e+01 1rboC d.73.1.1 39616 1uzcA 71 1.68e+01 a.159.2.1 -339 1fhuA 320 1.72e+01 1fhuA c.1.11.2 29234 d.54.1.1 38878 1gk8I 140 1.78e+01 d.73.1.1 65242 1vk9A 151 1.78e+01 1s2kA 206 1.82e+01 unknown_sccs -3494 1pfkA 320 1.83e+01 3pfk c.89.1.1 35575 1k66A 149 1.87e+01 c.23.1.1 -6406 1iicA 422 1.88e+01 1nmtA d.108.1.2 62422 d.108.1.2 62423 1ijaA 148 1.89e+01 1ijaA b.100.1.1 62484 1f1zA 273 1.91e+01 1f1zA a.4.5.27 16081 c.52.1.16 33334 1psqA 163 1.91e+01 c.47.1.10 88283 1kzhA 555 1.92e+01 c.89.1.1 73361 1plq 258 1.94e+01 1plq d.131.1.2 41388 d.131.1.2 41389 1k8qA 377 1.95e+01 c.69.1.6 72177 1v74A 107 1.99e+01 unknown_sccs -9319 1o5xA 248 2.00e+01 c.1.1.1 -5157 1ua4A 455 2.01e+01 c.72.1.3 -8416 1qhaA 917 2.02e+01 1qhaA c.55.1.3 33467 c.55.1.3 33468 c.55.1.3 33469 c.55.1.3 33470 1eujA 166 2.06e+01 1eujA b.40.4.4 25316 1o6sB 105 2.07e+01 b.1.6.1 81096 1i39A 225 2.09e+01 1ekeA c.55.3.1 61585 1n2zA 245 2.11e+01 c.92.2.2 79865 1bbpA 173 2.12e+01 1bbpA b.60.1.1 27147 1ns5A 155 2.13e+01 c.116.1.3 80705 1gln 468 2.16e+01 1gln a.97.1.1 18752 c.26.1.1 31588 1shuX 182 2.16e+01 c.62.1.1 -7982 1bd3A 243 2.18e+01 1bd3A c.61.1.1 34098 1nrwA 288 2.21e+01 c.108.1.10 86128 1derA 547 2.23e+01 1derA 1mngA 203 2.23e+01 1avmA a.2.11.1 15776 d.44.1.1 38701 1fl0A 171 2.23e+01 1eujA b.40.4.4 25315 1elt 236 2.28e+01 5ptp b.47.1.2 26281 2phlA 397 2.28e+01 1dgwA b.82.1.2 28082 b.82.1.2 28083 1jmcA 246 2.28e+01 1jmcA b.40.4.3 25300 b.40.4.3 25301 1r5tA 142 2.31e+01 1ltqA 301 2.32e+01 c.108.1.9 78208 c.37.1.1 78209 1ltlA 279 2.38e+01 b.40.4.11 84701 1fs0G 230 2.39e+01 1fs0G c.49.2.1 59999 1qsgA 265 2.39e+01 1eny c.2.1.2 29935 1ermA 263 2.41e+01 1btl e.3.1.1 42690 1p9rA 418 2.43e+01 c.37.1.11 -7142 1qk8A 146 2.45e+01 1ewxA c.47.1.10 33061 1thg 544 2.45e+01 1thg c.69.1.17 34763 1vhzA 198 2.52e+01 d.113.1.1 -10897 1eesA 178 2.53e+01 1eesA c.37.1.8 32073 1lu4A 136 2.53e+01 c.47.1.10 -7509 1booA 323 2.57e+01 1booA c.66.1.11 34248 1korA 400 2.58e+01 c.26.2.1 72824 d.210.1.1 72825 1vfrA 218 2.65e+01 1vfrA d.90.1.1 40247 1rkd 309 2.70e+01 1rkd c.72.1.1 34928 1bkjA 240 2.75e+01 1bkjA d.90.1.1 40243 1jr3A 373 2.76e+01 a.80.1.1 63245 c.37.1.20 63246 1p7gA 222 2.76e+01 a.2.11.1 -108 d.44.1.1 -9742 2pfkA 320 2.77e+01 3pfk c.89.1.1 35577 1pjxA 314 2.83e+01 1sq9A 397 2.84e+01 1rgeA 96 2.86e+01 1rgeA d.1.1.2 36028 1j5vA 351 2.88e+01 c.72.1.1 71585 1p0iA 529 2.88e+01 c.69.1.1 -8291 1irxA 523 2.88e+01 a.97.1.2 71378 c.26.1.1 71379 1gen 218 2.91e+01 1gen b.66.1.1 27536 6paxA 133 2.92e+01 6paxA a.4.1.5 64758 a.4.1.5 64759 1e8nA 710 2.93e+01 1qfmA b.69.7.1 27675 c.69.1.4 34643 1qo3C 137 2.96e+01 1qo3C d.169.1.1 42350 1bfi 112 3.00e+01 1qadA d.93.1.1 40499 1edhA 226 3.01e+01 1edhA b.1.6.1 22198 b.1.6.1 22199 1qxhA 167 3.05e+01 c.47.1.10 -7496 1nox 205 3.07e+01 1nox d.90.1.1 40242 1odfA 290 3.10e+01 c.37.1.6 -7045 1o8xA 146 3.13e+01 c.47.1.10 86681 1h9oA 112 3.13e+01 1qadA d.93.1.1 60837 1ly1A 181 3.14e+01 c.37.1.1 74334 1od3A 168 3.14e+01 b.18.1.10 86825 1soxA 466 3.15e+01 1soxA b.1.18.6 21947 d.120.1.1 41090 d.176.1.1 42563 1pl8A 356 3.17e+01 b.35.1.2 -3716 c.2.1.1 -5740 1kngA 156 3.17e+01 c.47.1.10 72777 2kinA 238 3.18e+01 1bg2 c.37.1.9 32190 1iibA 106 3.19e+01 1iibA c.44.2.1 32648 1shcA 195 3.19e+01 1shcA b.55.1.2 26992 1m40A 263 3.22e+01 e.3.1.1 74437 1whtA 256 3.24e+01 1ivyA c.69.1.5 34646 1s4nA 348 3.25e+01 unknown_sccs -8262 1idsA 207 3.26e+01 1avmA a.2.11.1 15722 d.44.1.1 38730 1gky 187 3.30e+01 1gky c.37.1.1 31839 1bcsA 263 3.30e+01 1ivyA c.69.1.5 34647 1ji2A 585 3.30e+01 b.1.18.2 71672 b.71.1.1 71673 c.1.8.1 71674 1nijA 318 3.30e+01 c.37.1.10 85741 d.237.1.1 85742 1pii 452 3.31e+01 1pii c.1.2.4 28559 c.1.2.4 28563 1fy7A 278 3.33e+01 1fy7A d.108.1.1 40817 1pex 207 3.36e+01 1gen b.66.1.1 27540 1qadA 111 3.39e+01 1qadA d.93.1.1 40498 1e1aA 314 3.43e+01 1e1aA b.68.6.1 59155 1914 232 3.49e+01 1914 d.49.1.1 83028 d.49.1.1 83029 1on0A 158 3.50e+01 d.108.1.1 87095 1gdoA 240 3.54e+01 1gdoA d.153.1.1 41804 1chd 203 3.54e+01 1chd c.40.1.1 32478 1ijgA 309 3.60e+01 1fouA e.27.1.1 62493 1eziA 228 3.61e+01 1eyrA c.68.1.13 34512 1whsA 255 3.61e+01 1ivyA c.69.1.5 34649 1i8vA 96 3.66e+01 d.1.1.2 61985 1o1zA 234 3.69e+01 c.1.18.3 86555 1fp2A 352 3.70e+01 1fpxA a.4.5.29 59941 c.66.1.12 59942 1hruA 188 3.70e+01 1hruA d.115.1.1 40926 1grvB 182 3.71e+01 c.61.1.1 76322 2hgsA 474 3.71e+01 2hgsA c.30.1.4 31722 d.142.1.6 75997 1ogpA 393 3.72e+01 b.1.18.6 -2744 d.176.1.1 -11708 1pgvA 197 3.74e+01 c.10.1.1 88073 1cuoA 129 3.75e+01 1nwpA b.6.1.1 23015 1fqgA 263 3.82e+01 1btl e.3.1.1 42699 1nlnA 204 3.83e+01 d.3.1.7 -8897 1gkuB 1054 3.85e+01 c.37.1.16 65257 c.37.1.16 65258 e.10.1.1 65259 1hkbA 917 3.90e+01 1qhaA c.55.1.3 33479 c.55.1.3 33480 c.55.1.3 33481 c.55.1.3 33482 3grx 82 3.91e+01 1aba c.47.1.1 32769 1qlwA 328 3.92e+01 1qlwA c.69.1.15 34722 1skoB 130 3.97e+01