# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7 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 1mhyG 169 1.03e-01 1mtyG a.23.3.1 16518 1rtwA 220 2.40e-01 1l8yA 91 4.90e-01 a.21.1.1 73708 1jigA 146 7.00e-01 a.25.1.1 71685 1vasA 137 8.20e-01 2end a.18.1.1 16404 1fqvD 149 8.93e-01 1fqvD a.157.1.1 19263 d.42.1.1 38667 2pgd 482 1.15e+00 2pgd a.100.1.1 18778 c.2.1.6 30190 1fqvJ 149 1.30e+00 1fqvD a.157.1.1 19266 d.42.1.1 38670 1izcA 339 1.43e+00 c.1.12.5 83838 1xfiA 367 1.51e+00 2end 138 1.78e+00 2end a.18.1.1 16400 1v2yA 105 1.80e+00 1ois 223 1.92e+00 1a36A e.15.1.1 43267 1w53A 84 2.23e+00 1klo 162 2.62e+00 1klo g.3.11.2 44326 g.3.11.2 44327 g.3.11.2 44328 1o4sA 389 2.71e+00 c.67.1.1 86620 1g59A 468 3.01e+00 a.97.1.1 60257 c.26.1.1 60258 1dttA 560 3.47e+00 1rthA c.55.3.1 33611 e.8.1.2 43088 1mtyG 162 3.67e+00 1mtyG a.23.3.1 16498 1riqA 465 3.94e+00 2lefA 86 4.03e+00 2lefA a.21.1.1 16433 1mmoG 162 4.24e+00 1mtyG a.23.3.1 16512 1v95A 130 4.54e+00 1i5nA 146 4.67e+00 1i5nA a.24.10.3 61805 1abv 134 4.88e+00 1abv a.70.1.1 18317 1f4qA 165 5.14e+00 1alvA a.39.1.8 17360 1izlC 473 5.23e+00 i.5.1.1 76996 1rthA 560 5.73e+00 1rthA c.55.3.1 33576 e.8.1.2 43028 1uvqA 197 5.82e+00 1be3D 241 5.84e+00 1be3D a.3.1.3 15955 f.23.11.1 43666 1qgdA 662 5.84e+00 c.36.1.6 88367 c.36.1.10 88368 c.48.1.1 88369 2eiaB 206 6.31e+00 1eia a.28.3.1 16950 a.73.1.1 18330 1v74B 87 6.68e+00 6prcM 323 6.88e+00 6prcM f.26.1.1 43435 1va6A 518 7.55e+00 1e3aA 260 7.63e+00 1ajqA d.153.1.2 41838 1uddA 226 7.64e+00 1r85A 379 7.66e+00 1s9pA 227 7.68e+00 1hiwA 133 7.69e+00 1hiwA a.61.1.1 18122 1axdA 209 7.81e+00 1gnwA a.45.1.1 17730 c.47.1.5 33024 1or7A 194 7.86e+00 a.4.13.2 87332 a.177.1.1 87333 1f5sA 211 7.89e+00 1f5sA c.108.1.4 59656 1ieaA 192 8.07e+00 1iakA b.1.1.2 21631 d.19.1.1 38205 2hmx 133 8.11e+00 1hiwA a.61.1.1 18129 2hmiA 558 8.24e+00 1rthA c.55.3.1 33604 e.8.1.2 43106 1ohuA 175 8.36e+00 1n3gA 113 8.85e+00 d.204.1.1 79962 1csn 298 8.95e+00 1csn d.144.1.7 41664 1ihoA 283 9.02e+00 1ihoA c.26.1.4 62390 1go3F 107 9.07e+00 a.60.8.2 65407 1eemA 241 9.26e+00 1eemA a.45.1.1 17717 c.47.1.5 33011 1hizA 379 9.34e+00 c.1.8.3 65841 1l7mA 211 9.48e+00 c.108.1.4 73664 1iznA 286 9.56e+00 e.43.1.1 83847 1eia 207 1.00e+01 1eia a.28.3.1 16951 a.73.1.1 18331 1dw9A 156 1.00e+01 1dw9A a.35.1.4 17065 d.72.1.1 39596 1colA 204 1.00e+01 1a87 f.1.1.1 43378 1p4dA 330 1.02e+01 1tbmA 326 1.07e+01 1jqjC 343 1.07e+01 a.80.1.1 67097 c.37.1.20 67098 1j97A 211 1.11e+01 1f5sA c.108.1.4 62753 6paxA 133 1.13e+01 6paxA a.4.1.5 64758 a.4.1.5 64759 1fs1B 141 1.15e+01 1vcbB a.157.1.1 19252 d.42.1.1 38664 1lnqA 336 1.17e+01 c.2.1.9 74049 f.14.1.1 74050 1hlvA 131 1.18e+01 a.4.1.7 65854 a.4.1.7 65855 1iu4A 331 1.21e+01 d.3.1.8 71430 1l6nA 289 1.21e+01 a.61.1.1 73624 a.73.1.1 73625 1bccD 241 1.22e+01 1be3D a.3.1.3 15959 f.23.11.1 43698 1pbwA 216 1.22e+01 1pbwA a.116.1.1 19103 1hf8A 289 1.35e+01 1hg5A a.118.10.1 19219 1dwkA 156 1.35e+01 1dw9A a.35.1.4 17075 d.72.1.1 39606 1ig6A 107 1.36e+01 1ig6A a.4.3.1 62364 1ib8A 164 1.37e+01 b.38.2.1 71168 d.52.4.1 71169 1octC 156 1.38e+01 1au7A a.4.1.1 15991 a.35.1.1 17017 1qgtA 149 1.41e+01 1qgtA a.62.1.1 18135 1jchC 551 1.43e+01 b.101.1.1 66495 b.110.1.1 66496 h.4.9.1 66497 1jchA 551 1.43e+01 b.101.1.1 66491 b.110.1.1 66492 h.4.9.1 66493 1t3wA 148 1.45e+01 1bed 181 1.47e+01 1fvkA a.44.1.1 17514 c.47.1.4 32808 1gm7A 209 1.50e+01 d.153.1.2 65302 1okrA 123 1.51e+01 1e3oC 160 1.51e+01 1au7A a.4.1.1 59197 a.35.1.1 59198 1g5yA 238 1.53e+01 1lbd a.123.1.1 60294 1bouA 139 1.54e+01 1bouA a.88.1.1 18521 1fngA 192 1.55e+01 1iakA b.1.1.2 59904 d.19.1.1 59905 1dxrM 323 1.59e+01 6prcM f.26.1.1 43432 1f75A 249 1.59e+01 1f75A c.101.1.1 59662 1iakA 199 1.59e+01 1iakA b.1.1.2 21625 d.19.1.1 38199 1gouA 116 1.59e+01 d.1.1.2 65429 1ckqA 276 1.60e+01 1ckqA c.52.1.1 33229 1f7cA 231 1.60e+01 1f7cA a.116.1.1 19107 1im4A 221 1.60e+01 e.8.1.5 62581 1fneA 192 1.61e+01 1iakA b.1.1.2 59896 d.19.1.1 59897 1cfr 285 1.63e+01 1cfr c.52.1.7 33312 1eysH 259 1.63e+01 6prcH b.41.1.1 25484 f.23.10.1 43517 1k94A 165 1.64e+01 a.39.1.8 68333 1p8kZ 254 1.67e+01 1r7jA 95 1.70e+01 1ko9A 345 1.74e+01 a.96.1.3 68717 d.129.1.2 68718 1ajqA 209 1.75e+01 1ajqA d.153.1.2 41840 1dioA 554 1.77e+01 1dioA c.1.19.3 29656 1ai7A 209 1.77e+01 1ajqA d.153.1.2 41845 1eexA 554 1.83e+01 1dioA c.1.19.3 29650 1l4sA 112 1.90e+01 d.204.1.1 77693 1brnL 110 1.91e+01 1b20A d.1.1.2 36143 1vg0A 650 1.92e+01 1j09A 468 1.96e+01 a.97.1.1 77025 c.26.1.1 77026 1q06A 135 1.97e+01 1k8eA 345 1.99e+01 1o17A 345 1.99e+01 a.46.2.1 80765 c.27.1.1 80766 1us7B 265 2.00e+01 1a2pA 110 2.00e+01 1b20A d.1.1.2 36140 1hg5A 289 2.07e+01 1hg5A a.118.10.1 19221 1deoA 233 2.09e+01 1deoA c.23.10.4 31345 1dipA 78 2.11e+01 1dipA h.1.12.1 45632 1ouvA 273 2.13e+01 1griA 217 2.14e+01 1griA b.34.2.1 24531 b.34.2.1 24532 d.93.1.1 40473 3icb 75 2.14e+01 4icb a.39.1.1 17147 1ki1B 352 2.14e+01 a.87.1.1 72497 b.55.1.1 72498 1eswA 500 2.24e+01 1cwyA c.1.8.1 59500 1n2aA 201 2.24e+01 1b4uA 139 2.24e+01 1bouA a.88.1.1 18523 1gk9A 260 2.26e+01 d.153.1.2 65246 1n45A 233 2.26e+01 a.132.1.1 79981 1bkb 136 2.28e+01 1bkb b.34.5.2 24609 b.40.4.5 25341 1nnlA 225 2.32e+01 c.108.1.4 85906 1imuA 107 2.32e+01 d.204.1.1 66218 1dj8A 89 2.36e+01 1bg8A a.57.1.1 17919 1eriA 276 2.36e+01 1ckqA c.52.1.1 33231 1bnr 110 2.39e+01 1b20A d.1.1.2 36206 1pu6A 218 2.40e+01 1cl8A 276 2.41e+01 1ckqA c.52.1.1 33230 1fseA 74 2.45e+01 1fseA a.4.6.2 60000 1jj2X 240 2.46e+01 1ffkV c.9.2.1 63109 1cwyA 500 2.46e+01 1cwyA c.1.8.1 28789 1rh2F 165 2.47e+01 1rh2F a.26.1.3 16898 1i37A 260 2.48e+01 1a28A a.123.1.1 61583 1vetB 125 2.50e+01 1rnbA 110 2.53e+01 1b20A d.1.1.2 36196 1itf 165 2.56e+01 1b5l a.26.1.3 16899 1je5A 206 2.59e+01 1je5A b.40.4.7 62909 2occF 98 2.60e+01 2occF g.41.5.3 45256 1hs6A 611 2.60e+01 1hs6A a.118.1.7 61233 b.98.1.1 61234 d.92.1.13 61235 1e1hB 174 2.63e+01 1har 216 2.63e+01 1rthA e.8.1.2 43025 1qc9A 276 2.63e+01 1ckqA c.52.1.1 33235 1iuqA 367 2.73e+01 1qgjA 300 2.74e+01 1bgp a.93.1.1 18691 1vj5A 555 2.74e+01 1ljrA 244 2.76e+01 1ljrA a.45.1.1 17707 c.47.1.5 33001 1mlwA 301 2.77e+01 d.178.1.1 79289 1gln 468 2.78e+01 1gln a.97.1.1 18752 c.26.1.1 31588 1jr3A 373 2.81e+01 a.80.1.1 63245 c.37.1.20 63246 1ppjD 241 2.82e+01 1gpjA 404 2.82e+01 a.151.1.1 65451 c.2.1.7 65452 d.58.39.1 65453 1s72Y 241 2.85e+01 1b31A 302 2.89e+01 1taxA c.1.8.3 28892 1s2wA 295 2.90e+01 1g3mA 294 2.93e+01 c.37.1.5 83268 1m8oB 47 2.97e+01 j.60.1.1 78776 1ajqB 557 3.01e+01 1ajqB 1twfF 155 3.07e+01 1ew6A 137 3.11e+01 1ewaA a.1.1.2 15637 1ewaA 137 3.11e+01 1ewaA a.1.1.2 15639 1wmuA 141 3.11e+01 1sxjE 354 3.12e+01 1hqvA 191 3.17e+01 1hqvA a.39.1.8 61160 1dlhB 188 3.19e+01 1iakB b.1.1.2 21598 d.19.1.1 38172 1bd3A 243 3.25e+01 1bd3A c.61.1.1 34098 1je8A 82 3.26e+01 a.4.6.2 77108 1r5qA 102 3.32e+01 1rfzA 168 3.32e+01 1gkxA 388 3.33e+01 a.29.5.1 65266 d.122.1.4 65267 1i50F 155 3.37e+01 d.78.1.2 61760 1wer 334 3.39e+01 1wer a.116.1.2 19108 3chy 128 3.46e+01 3chy c.23.1.1 31038 1rzhL 281 3.47e+01 1eo9A 209 3.49e+01 3pchA b.3.6.1 22731 1jr3D 343 3.52e+01 a.80.1.1 63251 c.37.1.20 63252 1hs7A 97 3.56e+01 1hs7A a.47.2.1 61236 1h99A 224 3.56e+01 a.142.1.1 60814 a.142.1.1 60815 1bg4 302 3.58e+01 1taxA c.1.8.3 28806 1di0A 158 3.62e+01 1di0A c.16.1.1 30957 1eysL 280 3.63e+01 6prcL f.26.1.1 43515 1jbeA 128 3.66e+01 3chy c.23.1.1 62845 1aisA 182 3.67e+01 1ytbA d.129.1.1 41288 d.129.1.1 41289 1np3A 338 3.68e+01 a.100.1.2 85946 c.2.1.6 85947 1otkA 249 3.69e+01 1s6cA 183 3.70e+01 1k7cA 233 3.71e+01 c.23.10.4 68267 1f4kA 122 3.73e+01 1bm9A a.4.5.7 59646 1a17 166 3.79e+01 1a17 a.118.8.1 19206 1k30A 368 3.81e+01 c.112.1.1 68067 1pdnC 128 3.83e+01 6paxA a.4.1.5 16047 1v4xA 144 3.95e+01 1otcB 260 3.95e+01 1otcB b.40.4.3 25310 1ddf 127 3.96e+01 1ddf a.77.1.2 18423 1ib2A 349 3.96e+01 1ib2A a.118.1.8 62141 1tbxA 99 3.97e+01