# 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 1g7oA 215 4.26e-02 1g7oA a.45.1.1 60332 c.47.1.5 60333 1keyA 235 1.19e-01 a.118.16.1 72389 6gsvA 217 1.34e-01 1b8xA a.45.1.1 17633 c.47.1.5 32925 1io7A 368 1.46e-01 1f4tA a.104.1.1 18971 1phb 414 2.15e-01 1phd a.104.1.1 18906 1f4tA 368 2.51e-01 1f4tA a.104.1.1 18973 1dugA 234 2.53e-01 1b8xA a.45.1.1 17718 c.47.1.5 33012 1jpzA 473 3.04e-01 a.104.1.1 67069 1h6oA 204 3.35e-01 a.146.1.1 60689 1qmqA 414 3.54e-01 1phd a.104.1.1 18907 1phd 414 3.61e-01 1phd a.104.1.1 18913 1qmzB 259 3.69e-01 1vin a.74.1.1 18338 a.74.1.1 18339 1phg 414 4.02e-01 1phd a.104.1.1 18910 1bu7A 455 4.07e-01 1bu7A a.104.1.1 18937 5cpp 414 4.81e-01 1phd a.104.1.1 18935 1mxrA 375 5.12e-01 a.25.1.2 85197 1vin 268 5.13e-01 1vin a.74.1.1 18354 a.74.1.1 18355 1dz4A 414 5.72e-01 1phd a.104.1.1 18903 1m6nA 802 6.19e-01 a.162.1.1 78697 a.172.1.1 78698 c.37.1.19 78699 c.37.1.19 78700 2bmhA 455 6.41e-01 1bu7A a.104.1.1 18941 1h6pA 203 6.45e-01 a.146.1.1 60690 1iv8A 720 6.60e-01 b.71.1.1 76842 c.1.8.1 76843 1jqcA 375 6.68e-01 1xikA a.25.1.2 63229 2gsq 202 6.69e-01 1pd21 a.45.1.1 17715 c.47.1.5 33009 1biqA 375 7.10e-01 1xikA a.25.1.2 16786 1fps 348 7.22e-01 1uby a.128.1.1 19436 1odoA 408 7.35e-01 a.104.1.1 -1463 1n97A 389 7.79e-01 a.104.1.1 80335 1b8xA 280 7.85e-01 1b8xA a.45.1.1 17739 c.47.1.5 33033 1eemA 241 8.29e-01 1eemA a.45.1.1 17717 c.47.1.5 33011 1b4pA 217 8.38e-01 a.45.1.1 83158 c.47.1.5 83159 1uby 367 9.02e-01 1uby a.128.1.1 19435 1tadA 324 9.70e-01 1cipA a.66.1.1 18194 c.37.1.8 32077 1tag 324 1.03e+00 1cipA a.66.1.1 18197 c.37.1.8 32080 1n81A 186 1.17e+00 a.185.1.1 85388 256bA 106 1.22e+00 256bA a.24.3.1 16539 1ribA 375 1.46e+00 1xikA a.25.1.2 16788 1i5nA 146 1.59e+00 1i5nA a.24.10.3 61805 1j1jA 240 1.66e+00 a.118.16.1 -1637 1gjnA 153 1.67e+00 a.1.1.2 70191 1d8vA 263 1.78e+00 1mrj d.165.1.1 42193 1oshA 232 1.80e+00 a.123.1.1 -1697 1xikA 375 2.05e+00 1xikA a.25.1.2 16784 1v4eA 299 2.07e+00 a.128.1.1 -1781 1obbA 480 2.12e+00 c.2.1.5 86760 d.162.1.2 86761 1pd21 199 2.14e+00 1pd21 1i1iP 681 2.15e+00 1i1iP d.92.1.5 40297 1dwtA 153 2.21e+00 1a6m a.1.1.2 15190 1j78A 458 2.58e+00 a.126.1.1 66397 a.126.1.1 66398 a.126.1.1 66399 1d3uB 201 2.98e+00 1aisB a.74.1.2 18386 a.74.1.2 18387 1ie9A 259 3.00e+00 1db1A a.123.1.1 62318 1kxpD 458 3.01e+00 a.126.1.1 73160 a.126.1.1 73161 a.126.1.1 73162 1m0uA 249 3.09e+00 a.45.1.1 78359 c.47.1.5 78360 2ligA 164 3.16e+00 1vls a.24.2.1 16530 1gulA 222 3.23e+00 1pgtA a.45.1.1 17675 c.47.1.5 32969 1di1A 300 3.25e+00 1di1A a.128.1.4 19446 1jmeA 455 3.26e+00 a.104.1.1 66885 1abwA 283 3.35e+00 1abwA a.1.1.2 15288 a.1.1.2 15289 1usuA 260 3.54e+00 unknown_sccs -9045 1h6gA 256 3.61e+00 1h6gA a.24.9.1 60669 a.24.9.1 60670 1elkA 157 3.69e+00 1dvpA a.118.9.2 19217 1gumA 222 3.71e+00 1pgtA a.45.1.1 17683 c.47.1.5 32977 1sctB 151 3.99e+00 3sdhA a.1.1.2 15003 1upkA 341 4.22e+00 unknown_sccs -1565 1prgA 270 4.34e+00 2prgA a.123.1.1 19314 1eb6A 177 4.57e+00 d.92.1.12 64895 1lki 180 5.02e+00 1lki a.26.1.1 16829 1vls 146 5.03e+00 1vls a.24.2.1 16532 1r2fA 319 5.12e+00 1r2fA a.25.1.2 16800 1vjxA 157 5.22e+00 a.25.1.1 -654 1oe8A 211 5.35e+00 a.45.1.1 86905 c.47.1.5 86906 1gw5A 621 5.46e+00 a.118.1.10 70629 1irxA 523 5.71e+00 a.97.1.2 71378 c.26.1.1 71379 1fdyA 297 5.73e+00 1nal3 c.1.10.1 29071 1hl2A 297 5.81e+00 c.1.10.1 83581 1vjtA 483 6.30e+00 c.2.1.5 -5941 d.162.1.2 -11508 1a26 361 6.40e+00 1a26 a.41.1.1 17412 d.166.1.2 42274 7aatA 401 6.44e+00 1ajsA c.67.1.1 34250 1q0sA 259 6.62e+00 c.66.1.28 -8110 1r9dA 787 6.69e+00 1mrj 247 6.79e+00 1mrj d.165.1.1 42177 1s6yA 450 6.92e+00 1nal3 297 6.95e+00 1nal3 1ewqA 765 7.11e+00 1ewqA a.113.1.1 19069 c.37.1.12 32383 c.55.6.1 33740 d.75.2.1 39743 1c3wA 222 7.18e+00 1c3wA f.13.1.1 43405 1fm9D 272 7.21e+00 2prgA a.123.1.1 19313 1n9dA 199 7.33e+00 a.26.1.1 85464 1ha2A 585 7.98e+00 1bj5 a.126.1.1 60866 a.126.1.1 60867 a.126.1.1 60868 1i7gA 287 8.09e+00 a.123.1.1 71121 2e2aA 105 8.23e+00 a.7.2.1 88499 1d6aB 262 8.43e+00 1qi7A d.165.1.1 42198 1fcyA 236 8.59e+00 2lbd a.123.1.1 19282 1bf5A 545 9.13e+00 1bg1A a.47.1.1 17766 b.2.5.5 22460 d.93.1.1 40526 1iyhA 198 9.15e+00 a.45.1.1 83790 c.47.1.5 83791 1nal1 297 9.38e+00 1nal3 1qciA 262 9.46e+00 1qi7A d.165.1.1 42201 1bw0A 416 1.01e+01 1bw0A c.67.1.1 34385 4lbd 267 1.05e+01 2lbd a.123.1.1 19289 1r4vA 171 1.09e+01 unknown_sccs -1221 1mixA 206 1.10e+01 a.11.2.1 79166 b.55.1.5 79167 1ao6A 585 1.10e+01 1bj5 a.126.1.1 19354 a.126.1.1 19355 a.126.1.1 19356 1o04A 500 1.10e+01 c.82.1.1 86508 1fchA 368 1.11e+01 1fchA a.118.8.1 19212 1miwA 404 1.12e+01 a.173.1.1 79162 d.218.1.4 79163 1e2aA 105 1.17e+01 1e2aA a.7.2.1 16322 1v4xA 144 1.17e+01 1a7m 180 1.24e+01 1lki a.26.1.1 16830 1jfbA 404 1.26e+01 a.104.1.1 66624 1q5dA 419 1.27e+01 a.104.1.1 -1454 1f1eA 154 1.30e+01 a.22.1.2 64927 1abrA 251 1.33e+01 1mrj d.165.1.1 42196 1bz4A 144 1.37e+01 1nfn a.24.1.1 16521 1jqiA 388 1.38e+01 a.29.3.1 67087 e.6.1.1 67088 1s9pA 227 1.40e+01 1nubA 229 1.41e+01 1sra a.39.1.3 17191 g.3.11.3 44330 unknown_sccs 44715 1chuA 540 1.41e+01 1chuA a.7.3.1 16325 c.3.1.4 30424 d.168.1.1 42307 1j1qA 261 1.41e+01 d.165.1.1 -11546 1efyA 350 1.46e+01 1a26 a.41.1.1 17413 d.166.1.2 42275 1n3kA 130 1.46e+01 a.77.1.4 79965 1hkxA 147 1.48e+01 d.17.4.7 83567 1a8b 318 1.49e+01 1avc a.65.1.1 18171 1anxA 319 1.50e+01 1avc a.65.1.1 18161 1h0oA 390 1.51e+01 a.25.1.2 70845 1ivhA 394 1.52e+01 3mdeA a.29.3.1 16608 e.6.1.1 42869 1db1A 259 1.52e+01 1db1A a.123.1.1 19329 1ash 150 1.53e+01 1ash a.1.1.2 15622 1h68A 239 1.55e+01 f.13.1.1 60664 1gikA 261 1.60e+01 d.165.1.1 -11545 1lp8A 254 1.62e+01 d.165.1.1 -11551 1ay2 159 1.68e+01 2pil d.24.1.1 38377 1lpe 144 1.71e+01 1nfn a.24.1.1 16524 1v9mA 323 1.72e+01 unknown_sccs -12292 2lbd 267 1.76e+01 2lbd a.123.1.1 19287 1b8dA 164 1.77e+01 1cpcA a.1.1.3 15665 1jgjA 217 1.77e+01 1c3wA f.13.1.1 62952 1myf 153 1.85e+01 1a6m a.1.1.2 15147 1rv3A 483 1.86e+01 1r5zA 323 1.88e+01 unknown_sccs -12289 1n5uA 585 1.88e+01 a.126.1.1 85339 a.126.1.1 85340 a.126.1.1 85341 1m0kA 262 1.90e+01 f.13.1.1 78344 1g8pA 350 1.92e+01 1g8pA c.37.1.20 60376 1colA 204 1.93e+01 1a87 f.1.1.1 43378 1f3aA 222 1.93e+01 1pgtA a.45.1.1 17701 c.47.1.5 32995 1vj7A 393 1.94e+01 unknown_sccs -1265 unknown_sccs -9814 1dghB 498 1.94e+01 1cf9A e.5.1.1 42791 2prgA 271 1.99e+01 2prgA a.123.1.1 19311 3ertA 261 1.99e+01 3erdA a.123.1.1 19292 1fvzA 271 2.06e+01 1fvzA 1l2iA 261 2.10e+01 a.123.1.1 73503 1q5nA 454 2.10e+01 a.127.1.1 -1756 1kaeA 434 2.11e+01 c.82.1.2 72247 1bjz 207 2.17e+01 2tct a.4.1.9 16065 a.121.1.1 19242 1ni4A 365 2.24e+01 c.36.1.7 85728 1spgB 147 2.26e+01 1cg5B a.1.1.2 15588 1aep 161 2.28e+01 1aep a.63.1.1 18139 1f24A 402 2.31e+01 1rom a.104.1.1 18953 1lldA 319 2.32e+01 3ldh c.2.1.5 30177 d.162.1.1 42144 1fewA 184 2.39e+01 1fewA a.7.4.1 16334 1k75A 434 2.40e+01 c.82.1.2 68253 1dowA 205 2.42e+01 1dovA a.24.9.1 16626 1qf9A 194 2.46e+01 1zin c.37.1.1 31848 1lkvX 232 2.50e+01 a.118.14.1 73980 1kgnA 329 2.53e+01 a.25.1.2 68584 1o86A 589 2.57e+01 d.92.1.5 81177 1hqoA 258 2.58e+01 1hqoA a.45.1.1 17749 c.47.1.5 33043 1mqsA 671 2.59e+01 e.25.1.1 79414 1cmnA 402 2.59e+01 1rom a.104.1.1 18958 1i58A 189 2.62e+01 1b3qA d.122.1.3 61773 1mrg 263 2.64e+01 1mrj d.165.1.1 42183 1vi0A 206 2.67e+01 a.4.1.9 -206 a.121.1.1 -1659 1a8a 318 2.72e+01 1avc a.65.1.1 18169 1e7aA 585 2.73e+01 1bj5 a.126.1.1 19360 a.126.1.1 19361 a.126.1.1 19362 1fioA 196 2.74e+01 1fioA a.47.2.1 17773 1oktA 211 2.77e+01 a.45.1.1 -942 c.47.1.5 -7467 1apxA 249 2.78e+01 1ryc a.93.1.1 18669 1ew6B 137 2.79e+01 1ewaA a.1.1.2 15638 5ukdA 194 2.81e+01 1zin c.37.1.1 31851 1rh2F 165 2.81e+01 1rh2F a.26.1.3 16898 1bj5 585 2.83e+01 1bj5 a.126.1.1 19369 a.126.1.1 19370 a.126.1.1 19371 1a41 234 2.99e+01 1a41 d.163.1.2 42174 1g6wA 261 3.01e+01 1hqoA a.45.1.1 17751 c.47.1.5 33045 1k0dA 260 3.03e+01 a.45.1.1 67930 c.47.1.5 67931 1f44A 324 3.09e+01 a.60.9.1 64982 d.163.1.1 64983 1hu4A 288 3.10e+01 1hu4A 1ldg 316 3.11e+01 1ceqA c.2.1.5 30165 d.162.1.1 42132 1n5dA 288 3.11e+01 c.2.1.2 80030 1jr3A 373 3.23e+01 a.80.1.1 63245 c.37.1.20 63246 2pil 159 3.26e+01 2pil d.24.1.1 38376 2ran 316 3.28e+01 1avc a.65.1.1 18170 1jk0A 419 3.30e+01 a.25.1.2 63142 1d2zB 153 3.35e+01 1d2zB a.77.1.2 18439 1jqnA 883 3.39e+01 c.1.12.3 77159 1fnnA 389 3.44e+01 1fnnA a.4.5.11 16129 c.37.1.20 32426 1fm2A 169 3.45e+01 1fm2A d.153.1.2 59877 1iqpA 327 3.47e+01 a.80.1.1 62649 c.37.1.20 62650 1q6aA 107 3.47e+01 unknown_sccs -960 1apa 266 3.49e+01 1qi7A d.165.1.1 42205 1h2sA 225 3.52e+01 f.13.1.1 76578 1l8qA 324 3.53e+01 a.4.12.2 77809 c.37.1.20 77810 1mbd 153 3.54e+01 1a6m a.1.1.2 15033 1lbd 282 3.55e+01 1lbd a.123.1.1 19279 1mtyD 512 3.59e+01 1mhyD a.25.1.2 16742 1cuk 203 3.62e+01 1hjp a.5.1.1 16273 a.60.2.1 17946 b.40.4.2 25265 1j7yA 141 3.62e+01 a.1.1.2 66426 2std 172 3.65e+01 3stdA d.17.4.1 38085 1ew6A 137 3.70e+01 1ewaA a.1.1.2 15637 1ewaA 137 3.70e+01 1ewaA a.1.1.2 15639 1fiuA 286 3.79e+01 1fiuA c.52.1.10 33317 1kgbA 231 3.83e+01 f.13.1.1 68581 1o0sA 605 3.84e+01 c.2.1.7 86540 c.58.1.3 86541 1qq8A 214 3.89e+01 1qq8A 1ffyA 917 3.91e+01 1qu2A a.27.1.1 16926 b.51.1.1 26891 c.26.1.1 31593 1qu2A 917 3.91e+01 1qu2A a.27.1.1 16925 b.51.1.1 26890 c.26.1.1 31592 1hy3A 294 3.91e+01 c.37.1.5 71090 1jboA 162 3.93e+01 a.1.1.3 84150 1budA 197 3.94e+01 1atlA d.92.1.9 40328 1iomA 377 3.95e+01 a.103.1.1 83698