# 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 2ae0X 345 9.36e-01 1v04A 355 9.64e-01 b.68.6.2 100240 2gaeA 346 2.09e+00 1kekA 1231 2.65e+00 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 68524,68525,68526,68527,68528 2c3mA 1231 2.94e+00 1y2tA 142 3.23e+00 1dk4A 252 3.48e+00 1dk4A e.7.1.1 42970 1vdwA 254 3.79e+00 e.7.1.1 100569 1b0pA 1231 3.85e+00 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 31831,31832,33104,34157,39003 1h0cA 392 4.27e+00 c.67.1.3 83424 1qwrA 319 4.28e+00 b.82.1.3 96491 1wucA 250 4.67e+00 1kz8A 337 5.19e+00 e.7.1.1 77633 1g0hA 252 5.34e+00 1dk4A e.7.1.1 60171 1tx4B 178 5.46e+00 1ctqA c.37.1.8 32045 1vj0A 380 5.57e+00 b.35.1.2,c.2.1.1 100786,100787 1a34A 159 6.27e+00 1a34A b.121.7.1 23286 1f8fA 371 6.78e+00 b.35.1.2,c.2.1.1 83246,83247 1kc6A 257 6.78e+00 c.52.1.19 68419 1wi1A 126 7.05e+00 1mrj 247 7.43e+00 1mrj d.165.1.1 42177 1zr6A 503 7.56e+00 1zx5A 300 7.63e+00 1r77A 103 8.66e+00 1ni9A 338 8.77e+00 e.7.1.2 85739 1s5uA 138 8.85e+00 d.38.1.1 98573 1pl8A 356 9.23e+00 b.35.1.2,c.2.1.1 94878,94879 2bgiA 272 9.45e+00 1rdzA 337 1.08e+01 1frpA e.7.1.1 42882 2c0cA 362 1.12e+01 1xhvA 257 1.13e+01 c.52.1.19 109597 1fpkA 335 1.16e+01 1frpA e.7.1.1 42930 5fbpA 335 1.17e+01 1frpA e.7.1.1 42873 1frpA 335 1.19e+01 1frpA e.7.1.1 42875 1dxkA 227 1.26e+01 1a7tA d.157.1.1 42036 1e3jA 352 1.26e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 1js8A 394 1.26e+01 a.86.1.1,b.112.1.1 67219,67220 1dcuA 357 1.31e+01 1frpA e.7.1.1 42943 2a9gA 418 1.34e+01 1e9xA 455 1.39e+01 1ea1A a.104.1.1 18969 1nuyA 337 1.40e+01 e.7.1.1 86213 1lbvA 252 1.47e+01 e.7.1.1 73813 1x3lA 440 1.48e+01 1x8vA 455 1.49e+01 1xezA 721 1.51e+01 2biqA 219 1.51e+01 1u13A 455 1.57e+01 a.104.1.1 107578 1awiA 138 1.58e+01 1pne d.110.1.1 40871 1h5zA 455 1.61e+01 a.104.1.1 90622 2pth 193 1.73e+01 2pth c.56.3.1 33793 1kolA 398 1.75e+01 b.35.1.2,c.2.1.1 77474,77475 1dmhA 311 1.75e+01 1dmhA b.3.6.1 22633 1rxxA 421 1.77e+01 d.126.1.4 98061 1cvjA 190 1.80e+01 1cvjB d.58.7.1,d.58.7.1 39191,39192 3pcgA 200 1.86e+01 3pchA b.3.6.1 22647 1eq6A 189 1.86e+01 1eq6A d.107.1.1 40796 1gnyA 153 1.90e+01 b.18.1.11 65404 1oacA 727 1.94e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24390,38007,38008,40003 1bn7A 294 1.95e+01 1bn6A c.69.1.8 34677 1yqzA 438 1.96e+01 3pcnA 200 2.02e+01 3pchA b.3.6.1 22725 3pchA 200 2.07e+01 3pchA b.3.6.1 22653 1ea1A 455 2.09e+01 1ea1A a.104.1.1 18970 1sz6A 249 2.14e+01 1mqoA 227 2.23e+01 d.157.1.1 103846 2bjiA 277 2.32e+01 1ahc 246 2.34e+01 1mrj d.165.1.1 42184 1v2bA 177 2.36e+01 d.107.1.2 108279 1cqwA 295 2.51e+01 1b6g c.69.1.8 34679 2pcdA 200 2.54e+01 3pchA b.3.6.1 22665 1g79A 218 2.57e+01 1ci0A b.45.1.1 25752 1bn6A 294 2.57e+01 1bn6A c.69.1.8 34678 1kmvA 186 2.68e+01 c.71.1.1 72757 1v3vA 333 2.72e+01 b.35.1.2,c.2.1.1 108345,108346 1mrg 263 2.82e+01 1mrj d.165.1.1 42183 2c1cA 312 2.83e+01 2fibA 269 2.88e+01 3fib d.171.1.1 42457 3cox 507 2.91e+01 1b8sA c.3.1.2,d.16.1.1 30332,37863 1g7jB 116 3.00e+01 1f3rB b.1.1.1 19933 1amoA 615 3.03e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 25669,31210,31557 1vfaB 116 3.03e+01 1gc1H b.1.1.1 19929 2bbhA 269 3.04e+01 1l8fA 207 3.11e+01 b.52.1.1 84537 1cv2A 296 3.12e+01 1bn6A c.69.1.8 34680 1d6zA 727 3.13e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24394,38015,38016,40007 1fil 139 3.15e+01 1pne d.110.1.1 40869 1mj5A 302 3.16e+01 c.69.1.8 91285 1vj1A 363 3.16e+01 b.35.1.2,c.2.1.1 100794,100795 1ja1A 622 3.17e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1qciA 262 3.17e+01 1qi7A d.165.1.1 42201 1a7qH 116 3.19e+01 1gc1H b.1.1.1 19955 1kvdB 77 3.21e+01 1kveB 1miuA 738 3.22e+01 a.170.1.1,a.171.1.1,b.40.4.3,b.40.4.3,b.40.4.3 79153,79154,79155,79156,79157 2ajtA 500 3.23e+01 1dvfD 120 3.34e+01 1mfa b.1.1.1 20107 1va0A 239 3.34e+01 1y10A 407 3.34e+01 1aoeA 192 3.40e+01 1aoeA c.71.1.1 34923 1fdlH 218 3.40e+01 1igtB b.1.1.1,b.1.1.2 19961,21021 2fh7A 595 3.53e+01 1d6aB 262 3.54e+01 1qi7A d.165.1.1 42198 1vqwA 457 3.55e+01 1iz7A 295 3.63e+01 c.69.1.8 76982 1i9yA 347 3.68e+01 1i9yA d.151.1.2 62101 1a8p 258 3.73e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1x54A 434 3.80e+01 1txlA 215 3.81e+01 b.60.1.4 107429 1tsrA 219 3.84e+01 1tupA b.2.5.2 22437 1wqsA 173 3.86e+01 1coy 507 3.93e+01 1b8sA c.3.1.2,d.16.1.1 30333,37864 2cxxA 190 3.95e+01 1spiA 358 4.03e+01 1frpA e.7.1.1 42939 2bc2A 227 4.11e+01 1a7tA d.157.1.1 42031 1nciA 110 4.14e+01 1edhA b.1.6.1 22191 1oe8A 211 4.16e+01 a.45.1.1,c.47.1.5 86905,86906 1s5aA 150 4.16e+01 d.17.4.10 98525 1kveB 77 4.17e+01 1kveB 1sqrA 95 4.18e+01 1sap 66 4.20e+01 1azpA b.34.13.1 37472 1hd5A 213 4.25e+01 2eng b.52.1.1 26896 2gw6A 123 4.29e+01 1h3iA 293 4.32e+01 b.76.2.1,b.85.7.1 76635,76636 1jhsA 188 4.34e+01 d.107.1.1 84172 1ex2A 189 4.41e+01 1ex2A c.51.4.2 33225 1es6A 296 4.45e+01 1es6A b.31.1.1,b.31.1.1 83048,83049 1i9zA 347 4.49e+01 1i9yA d.151.1.2 62102 2cy5A 140 4.54e+01 1v37A 177 4.55e+01 1e5pA 151 4.58e+01 1bj7 b.60.1.1 59272 1utcA 363 4.66e+01 a.118.1.4,b.69.6.1 99914,99915 1a2yB 116 4.71e+01 1gc1H b.1.1.1 19927 1ve2A 235 4.75e+01 2b5oA 402 4.76e+01 1d2fA 390 4.76e+01 1d2fA c.67.1.3 34411 2fnjA 226 4.79e+01 1dnlA 199 4.82e+01 1ci0A b.45.1.1 25753 1tupA 219 4.83e+01 1tupA b.2.5.2 22434 1kf6B 243 4.83e+01 a.1.2.1,d.15.4.2 72397,72398 1dm0A 287 4.87e+01 1dm0A d.165.1.2 42227 1azpA 66 4.91e+01 1azpA b.34.13.1 37467 1uolA 219 4.92e+01 b.2.5.2 99695 1fqgA 263 5.00e+01 1btl e.3.1.1 42699 1t9mA 214 5.08e+01 1yaxA 153 5.10e+01 1uz5A 402 5.10e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1s31A 273 5.12e+01 1s68A 249 5.13e+01 d.142.2.4 98591 8dfr 189 5.14e+01 1aoeA c.71.1.1 34895 1pixA 587 5.18e+01 c.14.1.4 94708 1h2bA 359 5.19e+01 b.35.1.2,c.2.1.1 90543,90544 2eng 210 5.20e+01 2eng b.52.1.1 26895 1f5jA 199 5.21e+01 1axkA b.29.1.11 24342 1g0sA 209 5.27e+01 1g0sA d.113.1.1 60187 1aup 449 5.28e+01 1k89 c.2.1.7,c.58.1.1 30222,33870 1qw2A 102 5.29e+01 d.249.1.1 96456 1ermA 263 5.35e+01 1btl e.3.1.1 42690 1efyA 350 5.35e+01 1a26 a.41.1.1,d.166.1.2 17413,42275 1mkzA 172 5.36e+01 c.57.1.1 84998 1wwrA 171 5.45e+01 1g2qA 187 5.52e+01 c.61.1.1 65117 1m40A 263 5.57e+01 e.3.1.1 74437 1a7oH 116 5.58e+01 1gc1H b.1.1.1 19943 2pcdM 238 5.72e+01 3pchM b.3.6.1 22760 1uk8A 282 5.75e+01 c.69.1.10 107907 1pqhA 143 5.79e+01 b.52.2.1 95017 1azqA 66 5.84e+01 1azpA b.34.13.1 37469 1jvbA 347 5.85e+01 b.35.1.2,c.2.1.1 77181,77182 1k89 449 5.92e+01 1k89 c.2.1.7,c.58.1.1 30218,33866 1spuB 727 6.01e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24399,38025,38026,40012 1jovA 270 6.14e+01 b.30.5.7 84192 1lzlA 323 6.15e+01 c.69.1.2 78306 1iupA 282 6.21e+01 c.69.1.10 76815 2fhxA 246 6.22e+01 1vzoA 355 6.36e+01 d.144.1.7 108971 1uq5A 263 6.39e+01 d.165.1.1 99778 1y5eA 169 6.47e+01 1larA 575 6.51e+01 1larA c.45.1.2,c.45.1.2 32693,32694 1bmc 221 6.52e+01 1a7tA d.157.1.1 42038 1tmxA 293 6.53e+01 1ncg 110 6.57e+01 1edhA b.1.6.1 22193 1qy6A 274 6.60e+01 b.47.1.1 96574 1ftrA 296 6.66e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1u3wA 374 6.70e+01 1mmuA 347 6.77e+01 b.30.5.4 79303 1y791 680 6.80e+01 2bg1A 494 6.86e+01 1n67A 359 6.90e+01 b.2.3.4,b.2.3.4 85354,85355 1l7jB 347 7.01e+01 b.30.5.4 73661 1wejH 223 7.02e+01 1igtB b.1.1.1,b.1.1.2 20361,21353 2aeuA 374 7.02e+01 1hnf 182 7.04e+01 1qa9A b.1.1.1,b.1.1.3 19741,21680 2audA 257 7.09e+01 1cz4A 185 7.11e+01 1cz4A b.52.2.3,d.31.1.1 26934,38468 1ekeA 230 7.11e+01 1ekeA c.55.3.1 33572 1qh0A 295 7.12e+01 b.43.4.2,c.25.1.1 68891,68892 3pcgM 238 7.25e+01 3pchM b.3.6.1 22742 1agnA 373 7.26e+01 2ohxA b.35.1.2,c.2.1.1 24737,29753 1gikA 261 7.32e+01 d.165.1.1 90513 1m2tA 254 7.40e+01 d.165.1.1 84761 1pmd 675 7.53e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37491,37492,42562,42771 1cz7A 406 7.58e+01 1bg2 c.37.1.9 32194 1pt1A 143 7.66e+01 b.52.2.1 95084 1pne 140 7.68e+01 1pne d.110.1.1 40866 1c8zA 265 7.71e+01 1c8zA d.23.1.1 38375 1cliA 345 7.72e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1tcvA 287 7.79e+01 1n6aA 259 7.82e+01 b.76.2.1,b.85.7.1 80121,80122 1vqoA 240 7.83e+01 2sgpE 185 7.90e+01 1qq4A b.47.1.1 25825 1rzuA 485 7.95e+01 c.87.1.8 105140 1zh5A 195 7.98e+01 2f69A 261 8.06e+01 1odkA 235 8.07e+01 c.56.2.1 86863 1jqgA 433 8.08e+01 c.56.5.1,d.58.3.1 71791,71792 1y0bA 197 8.11e+01 1vhh 162 8.23e+01 1vhh d.65.1.2 39550 1lufA 343 8.27e+01 d.144.1.7 78223 1j05B 121 8.28e+01 b.1.1.1 90736 1ng5A 215 8.32e+01 b.100.1.1 91867 1mkeA 152 8.32e+01 b.55.1.4 79231 1jpaA 312 8.33e+01 d.144.1.7 67011 1fiqB 350 8.35e+01 1fiqB d.87.2.1,d.145.1.3 40229,41760 1jmsA 381 8.37e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 2azqA 311 8.41e+01 3pchM 238 8.41e+01 3pchM b.3.6.1 22748 2cb5A 453 8.49e+01 3gcb d.3.1.1 37035 2bc2B 227 8.56e+01 1a7tA d.157.1.1 42032 1o89A 345 8.58e+01 b.35.1.2,c.2.1.1 92644,92645 1yfoA 302 8.66e+01 2shpA c.45.1.2 32681 2booA 247 8.69e+01 1zn8A 180 8.72e+01 1uacL 107 8.82e+01 b.1.1.1 99133 1r4pA 297 8.85e+01 d.165.1.2 97025 1mvuB 121 8.91e+01 b.1.1.1 91475 2fsjA 346 8.91e+01 1yvvA 336 8.92e+01 1ogiA 303 8.93e+01 b.43.4.2,c.25.1.1 92914,92915 1sgjA 284 8.97e+01 c.1.12.5 105535 1a26 361 8.98e+01 1a26 a.41.1.1,d.166.1.2 17412,42274