# List of top-scoring protein chains for t2k-100-30-str2-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 5.88e-02 2gaeA 346 9.90e-02 1b0pA 1231 9.84e-01 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 2c3mA 1231 1.05e+00 1kekA 1231 1.18e+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 2g5dA 422 1.28e+00 1bmv1 198 1.62e+00 1bmv1 1wucA 250 1.93e+00 1v04A 355 2.31e+00 b.68.6.2 100240 1s5uA 138 4.62e+00 d.38.1.1 98573 2ghsA 326 5.38e+00 1cjbA 231 5.50e+00 1qk3A c.61.1.1 34079 1wi1A 126 5.59e+00 3cox 507 7.04e+00 1b8sA c.3.1.2,d.16.1.1 30332,37863 1j6qA 136 7.57e+00 b.40.9.1 77091 1i0lA 221 7.68e+00 c.61.1.1 71096 1vjhA 122 8.03e+00 d.129.3.1 100811 1mrj 247 8.59e+00 1mrj d.165.1.1 42177 1coy 507 1.04e+01 1b8sA c.3.1.2,d.16.1.1 30333,37864 1amoA 615 1.06e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 25669,31210,31557 1pgl1 185 1.06e+01 1n67A 359 1.07e+01 b.2.3.4,b.2.3.4 85354,85355 1tx4B 178 1.10e+01 1ctqA c.37.1.8 32045 1kmvA 186 1.11e+01 c.71.1.1 72757 1d2fA 390 1.12e+01 1d2fA c.67.1.3 34411 1h5zA 455 1.15e+01 a.104.1.1 90622 1x8vA 455 1.16e+01 1miuA 738 1.18e+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 1ea1A 455 1.22e+01 1ea1A a.104.1.1 18970 1ja1A 622 1.22e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1izoA 417 1.23e+01 a.104.1.1 83851 1g0hA 252 1.26e+01 1dk4A e.7.1.1 60171 1a34A 159 1.28e+01 1a34A b.121.7.1 23286 1h0cA 392 1.36e+01 c.67.1.3 83424 1n2fA 142 1.52e+01 d.227.1.1 79853 2cwzA 141 1.54e+01 1g0u1 266 1.75e+01 1ryp2 233 1.75e+01 1ryp2 1ahsA 126 1.81e+01 1ahsA b.19.1.1 23794 1u13A 455 1.87e+01 a.104.1.1 107578 1vclA 432 1.89e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1qy5A 269 1.89e+01 d.122.1.1 96573 1e9xA 455 1.93e+01 1ea1A a.104.1.1 18969 1yemA 179 1.94e+01 1ahc 246 2.03e+01 1mrj d.165.1.1 42184 1mrg 263 2.11e+01 1mrj d.165.1.1 42183 8dfr 189 2.15e+01 1aoeA c.71.1.1 34895 1zkpA 268 2.18e+01 1ok8A 394 2.37e+01 b.1.18.4,f.10.1.1 93236,93237 1kz8A 337 2.38e+01 e.7.1.1 77633 2f86B 143 2.41e+01 1sq9A 397 2.41e+01 b.69.4.1 105889 1vdwA 254 2.52e+01 e.7.1.1 100569 1ixlA 131 2.58e+01 d.38.1.5 90717 1yqzA 438 2.58e+01 1fsgA 233 2.65e+01 1qk3A c.61.1.1 34029 1tc6A 236 2.73e+01 d.122.1.1 106756 1h6yA 170 2.85e+01 b.18.1.7 70904 1e7uA 961 2.93e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1msaA 109 2.97e+01 1b2pA b.78.1.1 27987 1e8xA 961 2.99e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19148,23183,37631,41711 1hxmA 229 3.05e+01 1hxmA b.1.1.1,b.1.1.2 61367,61368 1sqrA 95 3.11e+01 1jpc 109 3.12e+01 1b2pA b.78.1.1 27986 1dyoA 160 3.16e+01 1dyoA b.18.1.7 23771 1zh5A 195 3.18e+01 1qmtA 134 3.29e+01 7rsa d.5.1.1 37290 5bcaA 516 3.44e+01 1b9zA b.3.1.1,c.1.8.1 22529,28799 1n62B 809 3.47e+01 d.41.1.1,d.133.1.1 80092,80093 1itcA 516 3.54e+01 b.3.1.1,c.1.8.1 83705,83706 1vhh 162 3.63e+01 1vhh d.65.1.2 39550 1yueA 427 3.66e+01 1at3A 247 3.72e+01 1at3A b.57.1.1 27021 1udzA 182 3.75e+01 b.51.1.1 99239 1vpjA 192 3.75e+01 1y2tA 142 3.80e+01 1ftrA 296 3.81e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1dk4A 252 3.84e+01 1dk4A e.7.1.1 42970 1b9zA 516 3.85e+01 1b9zA b.3.1.1,c.1.8.1 22528,28798 1qj2B 809 3.86e+01 1qj2B 1e8yA 966 3.87e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1vemA 516 3.97e+01 1zxiB 809 4.02e+01 1agi 125 4.06e+01 7rsa d.5.1.1 37303 1njkA 156 4.09e+01 d.38.1.1 85818 1gm6A 175 4.10e+01 b.60.1.1 70272 2bvbA 137 4.15e+01 1wwrA 171 4.28e+01 1vlyA 338 4.45e+01 b.44.2.1,d.250.1.1 108871,108872 1dytA 133 4.53e+01 7rsa d.5.1.1 37288 1dcs 311 4.54e+01 1dcs b.82.2.1 28124 1a7qH 116 4.55e+01 1gc1H b.1.1.1 19955 1rocA 155 4.56e+01 b.1.22.1 97673 1zk7A 467 4.59e+01 1zs7A 190 4.62e+01 2fibA 269 4.69e+01 3fib d.171.1.1 42457 1ko3A 230 4.71e+01 d.157.1.1 90974 1m98A 317 4.72e+01 a.175.1.1,d.17.4.6 78866,78867 1wnyA 186 4.77e+01 1rdzA 337 4.88e+01 1frpA e.7.1.1 42882 1bn6A 294 4.89e+01 1bn6A c.69.1.8 34678 2gw6A 123 4.89e+01 1cqwA 295 4.98e+01 1b6g c.69.1.8 34679 1bn7A 294 4.98e+01 1bn6A c.69.1.8 34677 1fpkA 335 4.99e+01 1frpA e.7.1.1 42930 1pixA 587 5.04e+01 c.14.1.4 94708 1wmmA 145 5.06e+01 2pcdM 238 5.08e+01 3pchM b.3.6.1 22760 2fdbM 164 5.09e+01 2cx1A 187 5.10e+01 1b0uA 262 5.11e+01 1b0uA c.37.1.12 32370 3pcnA 200 5.16e+01 3pchA b.3.6.1 22725 1a97A 148 5.17e+01 1nulA c.61.1.1 34023 2c3gA 98 5.17e+01 1nuyA 337 5.21e+01 e.7.1.1 86213 3pchA 200 5.21e+01 3pchA b.3.6.1 22653 1y5eA 169 5.22e+01 3pcgA 200 5.22e+01 3pchA b.3.6.1 22647 1n99A 166 5.22e+01 b.36.1.1,b.36.1.1 85459,85460 1kdgA 546 5.25e+01 c.3.1.2,d.16.1.1 77337,77338 1frpA 335 5.45e+01 1frpA e.7.1.1 42875 3aprE 325 5.48e+01 2er7E b.50.1.2 26820 1wk8A 194 5.56e+01 1zd0A 150 5.57e+01 2apr 325 5.70e+01 2er7E b.50.1.2 26819 1b8aA 438 5.74e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1sgjA 284 5.80e+01 c.1.12.5 105535 2polA 366 5.92e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 1nrkA 328 5.96e+01 b.44.2.1,d.250.1.1 92089,92090 1g79A 218 5.98e+01 1ci0A b.45.1.1 25752 5fbpA 335 5.99e+01 1frpA e.7.1.1 42873 1vdmA 153 6.05e+01 1qw2A 102 6.11e+01 d.249.1.1 96456 1uspA 139 6.11e+01 d.227.1.1 99879 1ok7A 366 6.11e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1aoeA 192 6.13e+01 1aoeA c.71.1.1 34923 1ckmA 330 6.34e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 3pcgM 238 6.40e+01 3pchM b.3.6.1 22742 2auaA 224 6.45e+01 1uynX 308 6.53e+01 f.4.5.1 100174 2mjpA 193 6.69e+01 1b78A c.51.4.1 33223 2booA 247 6.70e+01 1h1hA 134 6.72e+01 d.5.1.1 76468 1dcuA 357 6.74e+01 1frpA e.7.1.1 42943 3fib 249 6.77e+01 3fib d.171.1.1 42455 4sli 679 6.80e+01 2sli b.29.1.9,b.68.1.1 24275,27612 2sli 679 6.81e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1ugxA 133 6.92e+01 1nciA 110 6.97e+01 1edhA b.1.6.1 22191 2cyeA 133 7.00e+01 1cfzA 162 7.12e+01 1cfzA c.56.1.1 33754 1cknA 330 7.17e+01 1ckmA b.40.4.6,d.142.2.3 25360,41587 1y0bA 197 7.22e+01 1sgpE 185 7.26e+01 1qq4A b.47.1.1 25816 1fib 269 7.27e+01 3fib d.171.1.1 42456 2pcdA 200 7.35e+01 3pchA b.3.6.1 22665 1uq5A 263 7.39e+01 d.165.1.1 99778 1mj5A 302 7.42e+01 c.69.1.8 91285 1v1qA 134 7.44e+01 1ef1A 294 7.50e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 1bvoA 175 7.51e+01 1a3qA b.2.5.3 22457 1ixmA 192 7.55e+01 1ixmA d.123.1.1 41114 2sgpE 185 7.61e+01 1qq4A b.47.1.1 25825 1rjdA 334 7.63e+01 c.66.1.37 97558 1vqvA 306 7.64e+01 1cqyA 99 7.76e+01 1b9zA b.3.1.1 22527 3pchM 238 7.81e+01 3pchM b.3.6.1 22748 1g2rA 100 7.83e+01 1g2rA d.192.1.1 60231 1cz7A 406 7.92e+01 1bg2 c.37.1.9 32194 1ixmB 192 8.04e+01 1ixmA d.123.1.1 41115 2ai4A 119 8.04e+01 1b8sA 504 8.08e+01 1b8sA c.3.1.2,d.16.1.1 30335,37866 1ncg 110 8.10e+01 1edhA b.1.6.1 22193 1jacA 133 8.17e+01 1jotA 1q8iA 783 8.21e+01 c.55.3.5,e.8.1.1 96208,96209 1ihgA 370 8.24e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 1g0uI 205 8.25e+01 d.153.1.4 41891 1a5v 162 8.33e+01 1cxqA c.55.3.2 33629 1ariA 396 8.41e+01 1ajsA c.67.1.1 34331 1lay 256 8.44e+01 1lay b.57.1.1 27014 1e6oL 212 8.45e+01 32c2A b.1.1.1,b.1.1.2 20494,21452 1xezA 721 8.47e+01 1r77A 103 8.49e+01 1b78A 193 8.65e+01 1b78A c.51.4.1 33221 1obs 267 8.67e+01 1mrj d.165.1.1 42213 2fuqA 747 8.73e+01 1txyA 104 8.80e+01 1h9sA 140 8.82e+01 1b9mA b.40.6.2,b.40.6.2 60843,60844 1sz6A 249 8.85e+01 1b4vA 504 8.92e+01 1b8sA c.3.1.2,d.16.1.1 30334,37865 1ct9A 553 8.94e+01 1ct9A c.26.2.1,d.153.1.1 31616,41834 1jhfA 202 8.94e+01 a.4.5.2,b.87.1.1 63057,63058 3sicI 107 8.96e+01 3ssi d.84.1.1 40028