# List of top-scoring protein chains for t04-100-30-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 2.92e-02 2gaeA 346 4.65e-02 1bmv1 198 6.73e-01 1bmv1 1v04A 355 7.89e-01 b.68.6.2 100240 2g5dA 422 8.77e-01 1b0pA 1231 9.32e-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 9.49e-01 1kekA 1231 1.16e+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 1wucA 250 1.36e+00 1i0lA 221 2.27e+00 c.61.1.1 71096 1cjbA 231 2.46e+00 1qk3A c.61.1.1 34079 1s5uA 138 2.78e+00 d.38.1.1 98573 1kmvA 186 2.80e+00 c.71.1.1 72757 1wi1A 126 2.82e+00 1mrj 247 3.43e+00 1mrj d.165.1.1 42177 1pgl1 185 4.60e+00 3cox 507 4.62e+00 1b8sA c.3.1.2,d.16.1.1 30332,37863 1d2fA 390 4.76e+00 1d2fA c.67.1.3 34411 1ja1A 622 4.82e+00 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1vjhA 122 5.33e+00 d.129.3.1 100811 8dfr 189 5.67e+00 1aoeA c.71.1.1 34895 2ghsA 326 6.11e+00 1a34A 159 6.55e+00 1a34A b.121.7.1 23286 1tx4B 178 7.15e+00 1ctqA c.37.1.8 32045 1n67A 359 7.53e+00 b.2.3.4,b.2.3.4 85354,85355 1j6qA 136 7.79e+00 b.40.9.1 77091 1zs7A 190 8.29e+00 1x8vA 455 8.54e+00 1h5zA 455 8.63e+00 a.104.1.1 90622 2cx1A 187 9.51e+00 1mrg 263 9.90e+00 1mrj d.165.1.1 42183 1ahsA 126 1.19e+01 1ahsA b.19.1.1 23794 1yemA 179 1.22e+01 1ryp2 233 1.27e+01 1ryp2 1dyoA 160 1.30e+01 1dyoA b.18.1.7 23771 1sq9A 397 1.32e+01 b.69.4.1 105889 2cwzA 141 1.36e+01 1jpc 109 1.39e+01 1b2pA b.78.1.1 27986 1u13A 455 1.42e+01 a.104.1.1 107578 1izoA 417 1.46e+01 a.104.1.1 83851 1n2fA 142 1.47e+01 d.227.1.1 79853 1e9xA 455 1.48e+01 1ea1A a.104.1.1 18969 1ixlA 131 1.52e+01 d.38.1.5 90717 1agi 125 1.58e+01 7rsa d.5.1.1 37303 1b0uA 262 1.59e+01 1b0uA c.37.1.12 32370 1udzA 182 1.60e+01 b.51.1.1 99239 1miuA 738 1.66e+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 1ok8A 394 1.67e+01 b.1.18.4,f.10.1.1 93236,93237 1zkpA 268 1.69e+01 1yueA 427 1.69e+01 1fsgA 233 1.71e+01 1qk3A c.61.1.1 34029 1at3A 247 1.75e+01 1at3A b.57.1.1 27021 1qy5A 269 1.77e+01 d.122.1.1 96573 1y0bA 197 1.78e+01 1vclA 432 1.88e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1frpA 335 1.91e+01 1frpA e.7.1.1 42875 1nuyA 337 1.92e+01 e.7.1.1 86213 1yqzA 438 1.97e+01 1ftrA 296 2.04e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1e7uA 961 2.07e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1itcA 516 2.10e+01 b.3.1.1,c.1.8.1 83705,83706 1vhh 162 2.13e+01 1vhh d.65.1.2 39550 1vemA 516 2.15e+01 1aoeA 192 2.19e+01 1aoeA c.71.1.1 34923 1pixA 587 2.19e+01 c.14.1.4 94708 1zh5A 195 2.21e+01 1wnyA 186 2.27e+01 2fdbM 164 2.28e+01 1g0hA 252 2.31e+01 1dk4A e.7.1.1 60171 1m98A 317 2.32e+01 a.175.1.1,d.17.4.6 78866,78867 1y2tA 142 2.40e+01 1nciA 110 2.42e+01 1edhA b.1.6.1 22191 1wk8A 194 2.47e+01 2bvbA 137 2.52e+01 1wwrA 171 2.54e+01 1tc6A 236 2.57e+01 d.122.1.1 106756 1g2rA 100 2.60e+01 1g2rA d.192.1.1 60231 1e8yA 966 2.66e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1vpjA 192 2.70e+01 2c3gA 98 2.75e+01 2f86B 143 2.96e+01 1b8aA 438 3.05e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1wmhB 86 3.07e+01 1sgjA 284 3.14e+01 c.1.12.5 105535 3pcgA 200 3.18e+01 3pchA b.3.6.1 22647 2cyeA 133 3.20e+01 1kdgA 546 3.29e+01 c.3.1.2,d.16.1.1 77337,77338 1njkA 156 3.30e+01 d.38.1.1 85818 1n62B 809 3.30e+01 d.41.1.1,d.133.1.1 80092,80093 1wmmA 145 3.32e+01 1qj2B 809 3.61e+01 1qj2B 1sqrA 95 3.61e+01 2gw6A 123 3.63e+01 1xezA 721 3.66e+01 1zxiB 809 3.74e+01 1i2aA 219 3.78e+01 e.24.1.1 90660 1l2tA 235 3.85e+01 c.37.1.12 73514 2fuqA 747 3.87e+01 1zk7A 467 3.91e+01 1ko3A 230 3.92e+01 d.157.1.1 90974 1vdmA 153 3.98e+01 1vqvA 306 4.01e+01 1uq5A 263 4.05e+01 d.165.1.1 99778 1dytA 133 4.10e+01 7rsa d.5.1.1 37288 3pcgM 238 4.11e+01 3pchM b.3.6.1 22742 1cqyA 99 4.26e+01 1b9zA b.3.1.1 22527 1xocA 520 4.36e+01 1ihgA 370 4.39e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 1bzyA 217 4.39e+01 1qk3A c.61.1.1 34071 1cfzA 162 4.39e+01 1cfzA c.56.1.1 33754 1cwvA 492 4.49e+01 1cwvA b.1.14.1,b.1.14.1,b.1.14.1,b.1.14.1,d.169.1.3 22373,22374,22375,22376,42442 3aprE 325 4.50e+01 2er7E b.50.1.2 26820 1v3eA 431 4.61e+01 b.68.1.1 100287 1vlyA 338 4.63e+01 b.44.2.1,d.250.1.1 108871,108872 1sz6A 249 4.69e+01 2apr 325 4.72e+01 2er7E b.50.1.2 26819 2fibA 269 4.78e+01 3fib d.171.1.1 42457 2polA 366 4.78e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 1zd0A 150 4.79e+01 1qw2A 102 4.79e+01 d.249.1.1 96456 4tmkA 213 4.84e+01 5tmpA c.37.1.1 31930 1wtaA 275 4.88e+01 1ixmA 192 4.94e+01 1ixmA d.123.1.1 41114 1ct9A 553 4.96e+01 1ct9A c.26.2.1,d.153.1.1 31616,41834 1y5eA 169 4.98e+01 2c0cA 362 5.09e+01 1m2tA 254 5.21e+01 d.165.1.1 84761 1h9sA 140 5.39e+01 1b9mA b.40.6.2,b.40.6.2 60843,60844 2fhxA 246 5.50e+01 1dcs 311 5.52e+01 1dcs b.82.2.1 28124 1g79A 218 5.53e+01 1ci0A b.45.1.1 25752 2booA 247 5.53e+01 1ryp1 222 5.56e+01 1ryp1 1jb9A 316 5.58e+01 1fnc b.43.4.2,c.25.1.1 62840,62841 1ef1A 294 5.60e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 1nrkA 328 5.78e+01 b.44.2.1,d.250.1.1 92089,92090 3fib 249 5.79e+01 3fib d.171.1.1 42455 1ok7A 366 5.81e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1ift 263 5.87e+01 1mrj d.165.1.1 42211 3gcb 470 5.92e+01 3gcb d.3.1.1 37032 1rocA 155 5.95e+01 b.1.22.1 97673 1jx4A 352 6.07e+01 d.240.1.1,e.8.1.7 90378,90379 1ckmA 330 6.11e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 1rjdA 334 6.15e+01 c.66.1.37 97558 1uspA 139 6.22e+01 d.227.1.1 99879 1jhfA 202 6.27e+01 a.4.5.2,b.87.1.1 63057,63058 2a9dA 372 6.32e+01 1f8fA 371 6.32e+01 b.35.1.2,c.2.1.1 83246,83247 1i9zA 347 6.35e+01 1i9yA d.151.1.2 62102 1wguA 136 6.35e+01 1jndA 420 6.36e+01 c.1.8.5,d.26.3.1 71757,71758 1soxA 466 6.54e+01 1soxA b.1.18.6,d.120.1.1,d.176.1.1 21947,41090,42563 1azo 232 6.54e+01 1azo c.52.1.14 33329 1sgpE 185 6.54e+01 1qq4A b.47.1.1 25816 2auaA 224 6.56e+01 1g7jB 116 6.57e+01 1f3rB b.1.1.1 19933 1rypL 212 6.64e+01 d.153.1.4 41880 1j48A 110 6.65e+01 b.1.7.1 84112 1l3iA 192 6.65e+01 c.66.1.22 77676 1fa8A 135 6.72e+01 1qipA d.32.1.1 38486 1bvoA 175 6.76e+01 1a3qA b.2.5.3 22457 1dywA 173 6.97e+01 2cpl b.62.1.1 27505 1uf2C 421 7.08e+01 a.115.1.3,b.19.1.1 99291,99292 1lf6A 684 7.13e+01 a.102.1.5,b.30.5.5 77918,77919 1ugxA 133 7.19e+01 1fh0A 221 7.37e+01 1cs8A d.3.1.1 59832 1b4vA 504 7.50e+01 1b8sA c.3.1.2,d.16.1.1 30334,37865 1wk2A 121 7.52e+01 1a2yB 116 7.60e+01 1gc1H b.1.1.1 19927 1qamA 244 7.65e+01 2ercA c.66.1.24 34220 1bn7A 294 7.67e+01 1bn6A c.69.1.8 34677 2ai4A 119 7.67e+01 1g0uL 241 7.77e+01 d.153.1.4 41894 1grj 158 7.81e+01 1grj a.2.1.1,d.26.1.2 15691,38433 1cz4A 185 7.83e+01 1cz4A b.52.2.3,d.31.1.1 26934,38468 1n4wA 504 7.88e+01 c.3.1.2,d.16.1.1 91676,91677 1dmhA 311 7.93e+01 1dmhA b.3.6.1 22633 1tc1A 220 7.94e+01 1tc1A c.61.1.1 34083 1mxtA 504 7.96e+01 c.3.1.2,d.16.1.1 79671,79672 1r77A 103 8.06e+01 2cxxA 190 8.18e+01 1dnlA 199 8.24e+01 1ci0A b.45.1.1 25753 1mc0A 368 8.34e+01 d.110.2.1,d.110.2.1 78937,78938 1mmiA 366 8.37e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1rypJ 204 8.39e+01 d.153.1.4 41878 1n40A 396 8.47e+01 a.104.1.1 79977 1xbrA 184 8.49e+01 1xbrA b.2.5.4 22458 1m4jA 142 8.53e+01 d.109.1.2 78602 1byfA 125 8.71e+01 1byfA d.169.1.1 42419 1txyA 104 8.75e+01 1gnyA 153 8.77e+01 b.18.1.11 65404 2sli 679 8.82e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1vdwA 254 8.82e+01 e.7.1.1 100569 1vsd 152 8.88e+01 1cxqA c.55.3.2 33625 1efdN 266 8.97e+01 1efdN c.92.2.1 35597