# 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 1v04A 355 2.65e-01 b.68.6.2 100240 2ae0X 345 1.10e+00 1tx4B 178 1.75e+00 1ctqA c.37.1.8 32045 1mrj 247 2.04e+00 1mrj d.165.1.1 42177 1kekA 1231 2.12e+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 2.15e+00 1wi1A 126 2.26e+00 2gaeA 346 2.53e+00 1g0hA 252 2.54e+00 1dk4A e.7.1.1 60171 1a34A 159 2.57e+00 1a34A b.121.7.1 23286 1b0pA 1231 2.69e+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 1wucA 250 3.06e+00 2gw6A 123 3.18e+00 1frpA 335 3.18e+00 1frpA e.7.1.1 42875 1y2tA 142 4.17e+00 1zx5A 300 4.65e+00 1nuyA 337 4.73e+00 e.7.1.1 86213 1f8fA 371 4.94e+00 b.35.1.2,c.2.1.1 83246,83247 1kc6A 257 5.24e+00 c.52.1.19 68419 1vdwA 254 5.45e+00 e.7.1.1 100569 1r77A 103 6.28e+00 1kmvA 186 6.30e+00 c.71.1.1 72757 1s5uA 138 6.82e+00 d.38.1.1 98573 1eq6A 189 7.13e+00 1eq6A d.107.1.1 40796 1xhvA 257 7.20e+00 c.52.1.19 109597 1bmv1 198 7.22e+00 1bmv1 1ni9A 338 7.52e+00 e.7.1.2 85739 1qwrA 319 8.53e+00 b.82.1.3 96491 2c0cA 362 9.90e+00 1vj0A 380 9.97e+00 b.35.1.2,c.2.1.1 100786,100787 1ja1A 622 1.00e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1sz6A 249 1.10e+01 2c1cA 312 1.18e+01 1v3vA 333 1.19e+01 b.35.1.2,c.2.1.1 108345,108346 2bgiA 272 1.19e+01 1xezA 721 1.25e+01 2pth 193 1.34e+01 2pth c.56.3.1 33793 1yqzA 438 1.34e+01 1jhsA 188 1.38e+01 d.107.1.1 84172 1mrg 263 1.39e+01 1mrj d.165.1.1 42183 1x54A 434 1.41e+01 2bbhA 269 1.43e+01 1dmhA 311 1.44e+01 1dmhA b.3.6.1 22633 1d2fA 390 1.48e+01 1d2fA c.67.1.3 34411 1ftrA 296 1.48e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1l8fA 207 1.66e+01 b.52.1.1 84537 2fibA 269 1.66e+01 3fib d.171.1.1 42457 1kmqA 184 1.67e+01 c.37.1.8 84412 1zr6A 503 1.68e+01 1txlA 215 1.72e+01 b.60.1.4 107429 1h5zA 455 1.74e+01 a.104.1.1 90622 1aoeA 192 1.76e+01 1aoeA c.71.1.1 34923 1js8A 394 1.83e+01 a.86.1.1,b.112.1.1 67219,67220 1vhh 162 1.85e+01 1vhh d.65.1.2 39550 1qorA 327 1.85e+01 1qorA b.35.1.2,c.2.1.1 24766,29782 1a02N 301 1.90e+01 1a02N b.1.18.1,b.2.5.3 21923,22440 1x8vA 455 1.97e+01 1va0A 239 1.97e+01 1e3jA 352 2.00e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 1mqoA 227 2.01e+01 d.157.1.1 103846 1pl8A 356 2.02e+01 b.35.1.2,c.2.1.1 94878,94879 3pcgA 200 2.03e+01 3pchA b.3.6.1 22647 8dfr 189 2.05e+01 1aoeA c.71.1.1 34895 1gnyA 153 2.07e+01 b.18.1.11 65404 1u13A 455 2.25e+01 a.104.1.1 107578 1bn7A 294 2.28e+01 1bn6A c.69.1.8 34677 1e9xA 455 2.31e+01 1ea1A a.104.1.1 18969 1nciA 110 2.35e+01 1edhA b.1.6.1 22191 1lbvA 252 2.35e+01 e.7.1.1 73813 1g79A 218 2.46e+01 1ci0A b.45.1.1 25752 1s31A 273 2.49e+01 1d1gA 168 2.50e+01 1d1gA c.71.1.1 34889 1wmxA 205 2.53e+01 b.18.1.24 109418 3cox 507 2.53e+01 1b8sA c.3.1.2,d.16.1.1 30332,37863 1x3lA 440 2.62e+01 1qciA 262 2.65e+01 1qi7A d.165.1.1 42201 2eng 210 2.69e+01 2eng b.52.1.1 26895 1vj1A 363 2.74e+01 b.35.1.2,c.2.1.1 100794,100795 1utcA 363 2.75e+01 a.118.1.4,b.69.6.1 99914,99915 2bc2A 227 2.78e+01 1a7tA d.157.1.1 42031 1y791 680 2.85e+01 1g0sA 209 2.86e+01 1g0sA d.113.1.1 60187 1efyA 350 2.87e+01 1a26 a.41.1.1,d.166.1.2 17413,42275 1s68A 249 2.92e+01 d.142.2.4 98591 2a9gA 418 2.93e+01 1oe8A 211 2.94e+01 a.45.1.1,c.47.1.5 86905,86906 2fhxA 246 3.02e+01 1njkA 156 3.02e+01 d.38.1.1 85818 2fsxA 148 3.07e+01 1c8zA 265 3.08e+01 1c8zA d.23.1.1 38375 1a8p 258 3.14e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1kveB 77 3.23e+01 1kveB 1pixA 587 3.24e+01 c.14.1.4 94708 1rxxA 421 3.31e+01 d.126.1.4 98061 2ajtA 500 3.36e+01 1oejA 193 3.37e+01 b.60.1.4 92798 1mfgA 95 3.37e+01 b.36.1.1 79043 1qw2A 102 3.43e+01 d.249.1.1 96456 1g7jB 116 3.46e+01 1f3rB b.1.1.1 19933 2cxxA 190 3.47e+01 1dfmA 223 3.48e+01 1d2iA c.52.1.5 33295 2biqA 219 3.52e+01 1mxtA 504 3.55e+01 c.3.1.2,d.16.1.1 79671,79672 1jqgA 433 3.56e+01 c.56.5.1,d.58.3.1 71791,71792 1m2tA 254 3.57e+01 d.165.1.1 84761 1h2bA 359 3.63e+01 b.35.1.2,c.2.1.1 90543,90544 1vqwA 457 3.65e+01 1ixlA 131 3.66e+01 d.38.1.5 90717 1dywA 173 3.80e+01 2cpl b.62.1.1 27505 1n4wA 504 3.82e+01 c.3.1.2,d.16.1.1 91676,91677 1miuA 738 3.83e+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 1y0bA 197 3.87e+01 1e5pA 151 3.95e+01 1bj7 b.60.1.1 59272 1oacA 727 3.99e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24390,38007,38008,40003 1qqgA 264 4.00e+01 1qqgA b.55.1.2,b.55.1.2 26987,26988 1jvbA 347 4.03e+01 b.35.1.2,c.2.1.1 77181,77182 2booA 247 4.20e+01 2fy6A 143 4.22e+01 1rypK 198 4.27e+01 d.153.1.4 41879 1f5jA 199 4.29e+01 1axkA b.29.1.11 24342 1wejH 223 4.45e+01 1igtB b.1.1.1,b.1.1.2 20361,21353 3seb 238 4.48e+01 3seb b.40.2.2,d.15.6.1 25184,37773 2audA 257 4.53e+01 1s5aA 150 4.53e+01 d.17.4.10 98525 2cy5A 140 4.54e+01 1a3k 137 4.55e+01 1a3k b.29.1.3 24218 3bamA 213 4.62e+01 1bam c.52.1.3 33288 1odkA 235 4.64e+01 c.56.2.1 86863 1lzlA 323 4.65e+01 c.69.1.2 78306 1vgyA 393 4.66e+01 c.56.5.4,d.58.19.1 100620,100621 1zn8A 180 4.68e+01 1sglA 209 4.68e+01 d.124.1.1 105536 3fib 249 4.71e+01 3fib d.171.1.1 42455 1kolA 398 4.75e+01 b.35.1.2,c.2.1.1 77474,77475 2bjiA 277 4.77e+01 1qy6A 274 4.83e+01 b.47.1.1 96574 1dnlA 199 4.89e+01 1ci0A b.45.1.1 25753 1ycyA 71 4.89e+01 1g2qA 187 4.94e+01 c.61.1.1 65117 1txnA 328 4.95e+01 1m7bA 184 5.00e+01 c.37.1.8 74572 2fh7A 595 5.02e+01 1zh5A 195 5.02e+01 1ysrA 150 5.07e+01 1cz4A 185 5.08e+01 1cz4A b.52.2.3,d.31.1.1 26934,38468 1at3A 247 5.08e+01 1at3A b.57.1.1 27021 2atpB 115 5.11e+01 1i2aA 219 5.13e+01 e.24.1.1 90660 1widA 130 5.29e+01 1cliA 345 5.36e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 2fnjA 226 5.45e+01 1is3A 135 5.47e+01 b.29.1.3 76773 1zs7A 190 5.50e+01 1fl2A 310 5.51e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1tupA 219 5.53e+01 1tupA b.2.5.2 22434 1i9zA 347 5.53e+01 1i9yA d.151.1.2 62102 1orvA 728 5.55e+01 b.70.3.1,c.69.1.24 87354,87355 1xocA 520 5.69e+01 1uylA 236 5.75e+01 d.122.1.1 108147 1byfA 125 5.77e+01 1byfA d.169.1.1 42419 1yueA 427 5.81e+01 1a2yB 116 5.81e+01 1gc1H b.1.1.1 19927 1sqrA 95 5.84e+01 1rzuA 485 5.85e+01 c.87.1.8 105140 2cx1A 187 5.86e+01 1pmd 675 5.90e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37491,37492,42562,42771 1dyoA 160 5.95e+01 1dyoA b.18.1.7 23771 3pcgM 238 5.96e+01 3pchM b.3.6.1 22742 1azpA 66 6.00e+01 1azpA b.34.13.1 37467 2pia 321 6.04e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1cjbA 231 6.06e+01 1qk3A c.61.1.1 34079 1vzoA 355 6.11e+01 d.144.1.7 108971 1jmcA 246 6.13e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 1mj5A 302 6.14e+01 c.69.1.8 91285 1xx9A 238 6.14e+01 1p7hL 286 6.16e+01 b.1.18.1,b.2.5.3 94271,94272 1hw5A 210 6.16e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 1ko3A 230 6.18e+01 d.157.1.1 90974 1m7xA 617 6.21e+01 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 1es6A 296 6.21e+01 1es6A b.31.1.1,b.31.1.1 83048,83049 2cyeA 133 6.23e+01 1l6oA 95 6.23e+01 b.36.1.1 84534 1try 224 6.38e+01 5ptp b.47.1.2 26017 1l3iA 192 6.41e+01 c.66.1.22 77676 1ekeA 230 6.46e+01 1ekeA c.55.3.1 33572 2a67A 167 6.47e+01 1r6lA 239 6.49e+01 d.14.1.4,d.101.1.1 97153,97154 1gntA 553 6.52e+01 e.26.1.1 70290 1a2vA 655 6.53e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24416,38059,38060 1cv2A 296 6.56e+01 1bn6A c.69.1.8 34680 1qreA 247 6.56e+01 1qreA b.81.1.5 28066 1fn8A 224 6.58e+01 5ptp b.47.1.2 26012 1cfzA 162 6.61e+01 1cfzA c.56.1.1 33754 1pqhA 143 6.62e+01 b.52.2.1 95017 1eonA 245 6.64e+01 1rvaA c.52.1.2 33238 1q6uA 245 6.65e+01 d.26.1.1 95998 1v2bA 177 6.66e+01 d.107.1.2 108279 1xtqA 177 6.71e+01 1kapP 479 6.74e+01 1sat b.80.7.1,d.92.1.6 28012,40298 2fxqA 264 6.80e+01 1vd3A 217 6.81e+01 1sx5A 244 6.88e+01 c.52.1.2 99023 1tp9A 162 6.91e+01 1t2wA 145 6.98e+01 b.100.1.1 106289 1tmxA 293 7.00e+01 1v25A 541 7.00e+01 e.23.1.1 108275 1vhwA 253 7.01e+01 c.56.2.1 100706 2bvbA 137 7.03e+01 1uq5A 263 7.05e+01 d.165.1.1 99778 1yb5A 351 7.08e+01 1uacL 107 7.11e+01 b.1.1.1 99133 1m40A 263 7.11e+01 e.3.1.1 74437 1roaA 122 7.22e+01 d.17.1.2 105024 1b78A 193 7.25e+01 1b78A c.51.4.1 33221 1pgl1 185 7.26e+01 1whi 122 7.26e+01 1whi b.39.1.1 24810 1g7jA 107 7.29e+01 32c2A b.1.1.1 19932 1pne 140 7.31e+01 1pne d.110.1.1 40866 1m5q1 130 7.31e+01 1kwmA 402 7.42e+01 c.56.5.1,d.58.3.1 73079,73080 1deuA 277 7.43e+01 1theB d.3.1.1 37085 1fh0A 221 7.47e+01 1cs8A d.3.1.1 59832 1v37A 177 7.47e+01 1gmyA 261 7.50e+01 d.3.1.1 76236 1bpoA 494 7.61e+01 1bpoA a.118.1.4,b.69.6.1 19143,27670 1y10A 407 7.69e+01 1l0wA 580 7.71e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1ermA 263 7.83e+01 1btl e.3.1.1 42690 1adjA 421 7.86e+01 1adjA c.51.1.1,d.104.1.1 33188,40737 2fsjA 346 7.88e+01 2b5oA 402 7.89e+01 1w6nA 134 7.93e+01 1jnuA 104 7.97e+01 d.110.3.6 71762 1larA 575 7.99e+01 1larA c.45.1.2,c.45.1.2 32693,32694 1e2uA 553 7.99e+01 1e1dA e.26.1.1 43362 1uolA 219 8.06e+01 b.2.5.2 99695 1b4vA 504 8.09e+01 1b8sA c.3.1.2,d.16.1.1 30334,37865 1c4xA 285 8.12e+01 1c4xA c.69.1.10 34684 1cbs 137 8.16e+01 1hmt b.60.1.2 27201 1h8eD 482 8.17e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 1gklA 297 8.17e+01 c.69.1.2 65250 1vqoA 240 8.21e+01 1xcbA 211 8.24e+01 a.4.5.38,c.2.1.12 109552,109553 1ve2A 235 8.30e+01 1lnzA 342 8.31e+01 b.117.1.1,c.37.1.8 78112,78113 1g3kA 174 8.34e+01 1nedA d.153.1.4 41989 1zkpA 268 8.45e+01 1jhjA 171 8.47e+01 b.18.1.9 66714 1ikoP 178 8.54e+01 b.6.1.5 71243 2bsaA 303 8.55e+01 1wb4A 297 8.59e+01 1cr5A 189 8.63e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1qdeA 224 8.65e+01 1qvaA c.37.1.19 32410 1se8A 301 8.68e+01 b.40.4.3 105448 2a8nA 144 8.69e+01 1qmeA 702 8.70e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 2cwzA 141 8.75e+01 1tpfA 250 8.85e+01 1amk c.1.1.1 28467 1iruK 201 8.98e+01 d.153.1.4 71362 2bg1A 494 8.98e+01