# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl 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 8rucI 123 6.33e-02 1rboC d.73.1.1 39629 1rboC 123 6.76e-02 1rboC d.73.1.1 39634 3rubS 123 1.26e-01 1rboC d.73.1.1 39616 1gcyA 527 2.76e-01 1jdc b.71.1.1 27788 c.1.8.1 28775 1u9aA 160 2.85e-01 1u9aA d.20.1.1 38333 1b3jA 274 3.73e-01 1agdA b.1.1.2 20855 d.19.1.1 38319 1agdA 276 4.17e-01 1agdA b.1.1.2 20741 d.19.1.1 38260 1qj4A 257 4.65e-01 1qj4A c.69.1.20 34796 1yasA 257 5.32e-01 1qj4A c.69.1.20 34801 5fbpA 335 5.65e-01 1frpA e.7.1.1 42873 1jdc 429 7.10e-01 1jdc b.71.1.1 27789 c.1.8.1 28776 1frpA 335 8.17e-01 1frpA e.7.1.1 42875 1e3mA 800 1.14e+00 1ewqA a.113.1.1 19075 c.37.1.12 32389 c.55.6.1 33746 d.75.2.1 39747 1rdzA 337 1.29e+00 1frpA e.7.1.1 42882 2ucz 165 1.29e+00 1u9aA d.20.1.1 38330 1go4A 205 1.80e+00 1fpkA 335 1.91e+00 1frpA e.7.1.1 42930 1yghA 164 1.92e+00 1yghA d.108.1.1 40802 1fsz 372 2.40e+00 1fsz c.32.1.1 31750 d.79.2.1 39802 1fzkA 274 2.45e+00 1agdA b.1.1.2 60149 d.19.1.1 60150 1apyB 141 2.55e+00 1apyB 1eylA 186 2.58e+00 1wba b.42.4.1 25593 1a2vA 655 2.69e+00 1a2vA b.30.2.1 24416 d.17.2.1 38059 d.17.2.1 38060 1clqA 903 3.00e+00 1clqA c.55.3.5 33717 e.8.1.1 43006 1f2tB 148 3.18e+00 1f2tB 1fx3B 169 3.39e+00 1fx3B d.33.1.1 38525 1hfc 169 3.40e+00 1hfc d.92.1.11 40335 1gk8I 140 3.67e+00 d.73.1.1 65242 1ig8A 486 3.79e+00 2yhx c.55.1.3 64746 c.55.1.3 64747 1h6rA 236 3.82e+00 d.22.1.1 65683 1inp 400 3.90e+00 1inp e.7.1.1 42972 1kanA 253 4.01e+00 1knyA e.9.1.3 43234 1dkxA 219 4.08e+00 1dkzA e.20.1.1 43315 1fzoA 274 4.47e+00 1agdA b.1.1.2 60155 d.19.1.1 60156 1dqsA 393 4.51e+00 1dqsA e.22.1.1 43347 1jq3A 296 4.51e+00 c.66.1.17 67079 1repC 251 4.62e+00 1repC a.4.5.10 16125 a.4.5.10 16126 1czaN 917 5.44e+00 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1dkzA 219 5.57e+00 1dkzA e.20.1.1 43314 1inlA 296 5.68e+00 c.66.1.17 66220 1ef8A 261 5.83e+00 1ef8A c.14.1.3 30921 1ac5 483 6.01e+00 1ac5 c.69.1.5 34653 1lplA 95 6.10e+00 2ts1 419 6.71e+00 2ts1 c.26.1.1 31564 1dgkN 917 6.74e+00 1qhaA c.55.1.3 33487 c.55.1.3 33488 c.55.1.3 33489 c.55.1.3 33490 1gjuA 637 6.95e+00 b.71.1.1 60580 c.1.8.1 60581 1qcsA 211 7.29e+00 1qcsA b.52.2.3 26927 d.31.1.1 38461 1duzA 275 7.39e+00 1agdA b.1.1.2 20670 d.19.1.1 38224 2bidA 197 7.42e+00 2bidA f.1.4.1 43398 1gjwA 637 7.72e+00 b.71.1.1 60582 c.1.8.1 60583 1boy 219 7.76e+00 1boy b.1.2.1 21955 b.1.2.1 21956 1tiiD 99 8.07e+00 1tiiD b.40.2.1 24965 1ospO 257 8.77e+00 1ospO b.76.1.1 27971 1he1A 135 9.25e+00 1he1A a.24.11.1 16641 1i4fA 275 9.51e+00 1agdA b.1.1.2 61687 d.19.1.1 61688 1qf6A 642 9.60e+00 1qf6A c.51.1.1 33210 d.66.1.1 39551 d.67.1.1 39562 d.104.1.1 40759 1fm0E 150 9.69e+00 1fmaE d.41.5.1 38629 1jenA 267 9.75e+00 1jenA 1f1sA 814 9.80e+00 a.102.3.2 64928 b.1.1.5 64929 b.24.1.1 64930 b.30.3.1 64931 1fmaE 150 1.00e+01 1fmaE d.41.5.1 38630 1g7pA 274 1.00e+01 2hft 218 1.01e+01 1boy b.1.2.1 21951 b.1.2.1 21952 1dcjA 81 1.03e+01 1dcjA d.68.3.1 59115 2btvA 901 1.04e+01 2btvA e.28.1.1 43376 1a5t 334 1.08e+01 1a5t a.80.1.1 18450 c.37.1.13 32423 1jl5A 454 1.15e+01 c.10.2.6 66830 1g9uA 454 1.19e+01 c.10.2.6 65172 1kypA 237 1.19e+01 1csn 298 1.22e+01 1csn d.144.1.1 41664 1e2o 233 1.28e+01 1eaf c.43.1.1 32631 1thv 207 1.32e+01 1thv b.25.1.1 23904 1mwpA 96 1.35e+01 1mwpA d.170.2.1 42453 1d2kA 392 1.35e+01 1d2kA c.1.8.5 29008 d.26.3.1 38442 1spuB 727 1.35e+01 1oacA b.30.2.1 24399 d.17.2.1 38025 d.17.2.1 38026 d.82.1.1 40012 1dupA 152 1.36e+01 1dupA b.85.4.1 28351 1euwA 152 1.36e+01 1dupA b.85.4.1 28349 1gof 639 1.38e+01 1gof b.1.1.5 21807 b.18.1.1 23709 b.69.1.1 27631 1rmvA 157 1.41e+01 1rmvA a.24.5.1 16589 1b87A 181 1.41e+01 1b87A d.108.1.1 40797 1hkcA 917 1.44e+01 1qhaA c.55.1.3 33475 c.55.1.3 33476 c.55.1.3 33477 c.55.1.3 33478 1rypA 243 1.44e+01 1pmaA d.153.1.4 41932 1jatA 155 1.44e+01 1u9aA d.20.1.1 62818 1hi9A 274 1.46e+01 1hi9A c.99.1.1 61063 1b6rA 355 1.48e+01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1c9uA 454 1.49e+01 1c9uA b.68.2.1 27623 1f24A 402 1.54e+01 1rom a.104.1.1 18953 1goh 639 1.54e+01 1gof b.1.1.5 21809 b.18.1.1 23711 b.69.1.1 27633 1pfzA 380 1.57e+01 1smrA b.50.1.2 26881 1thw 207 1.62e+01 1thv b.25.1.1 23903 1g5yA 238 1.62e+01 1lbd a.123.1.1 60294 1jr3E 334 1.65e+01 a.80.1.1 63253 c.37.1.13 63254 1hkbA 917 1.66e+01 1qhaA c.55.1.3 33479 c.55.1.3 33480 c.55.1.3 33481 c.55.1.3 33482 1f4tA 368 1.68e+01 1f4tA a.104.1.1 18973 1rec 201 1.70e+01 1rec a.39.1.5 17326 1i6iA 366 1.71e+01 1bg2 c.37.1.9 61844 1d6zA 727 1.72e+01 1oacA b.30.2.1 24394 d.17.2.1 38015 d.17.2.1 38016 d.82.1.1 40007 1gkxA 388 1.72e+01 a.29.5.1 65266 d.122.1.4 65267 1g8iA 190 1.72e+01 1rec a.39.1.5 60363 1l0oA 150 1.76e+01 1bupA 386 1.78e+01 1ba1 c.55.1.1 33377 c.55.1.1 33378 1ej5A 107 1.79e+01 1ej5A a.68.1.1 18268 1fqiA 147 1.81e+01 1agrE a.91.1.1 18542 1h6zA 913 1.86e+01 1cqxA 403 1.91e+01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1qbiA 454 1.91e+01 1c9uA b.68.2.1 27619 1qsmA 152 1.93e+01 1qsmA d.108.1.1 40808 1bx2B 191 1.93e+01 1iakB b.1.1.2 21610 d.19.1.1 38184 1b77A 228 1.94e+01 1b77A d.131.1.2 41362 d.131.1.2 41363 1mla 309 1.95e+01 1mla c.19.1.1 31031 d.58.23.1 39383 1pprM 312 1.99e+01 1pprM a.131.1.1 19502 a.131.1.1 19503 3cla 213 2.09e+01 3cla c.43.1.1 32610 2scuA 288 2.09e+01 2scuA c.2.1.8 30303 c.23.4.1 31131 1jbbA 153 2.10e+01 1u9aA d.20.1.1 62842 6paxA 133 2.11e+01 6paxA a.4.1.5 64758 a.4.1.5 64759 1kay 381 2.13e+01 1ba1 c.55.1.1 33385 c.55.1.1 33386 1k3iA 656 2.14e+01 b.1.1.5 68113 b.18.1.1 68114 b.69.1.1 68115 1knyA 253 2.19e+01 1knyA e.9.1.3 43232 1qs8A 329 2.19e+01 1smrA b.50.1.2 26887 1rlw 126 2.19e+01 1rlw b.7.1.1 23177 1ba1 386 2.21e+01 1ba1 c.55.1.1 33387 c.55.1.1 33388 1jk3A 158 2.22e+01 d.92.1.11 66790 1scuA 288 2.27e+01 2scuA c.2.1.8 30307 c.23.4.1 31135 1eyhA 144 2.29e+01 1eduA a.118.9.1 19214 1eduA 149 2.30e+01 1eduA a.118.9.1 19215 1e0cA 271 2.32e+01 1e0cA c.46.1.2 32717 c.46.1.2 32718 1p35A 299 2.33e+01 1p35A b.28.1.1 23925 1ema 236 2.34e+01 1ema d.22.1.1 38339 1bag 425 2.37e+01 1bag b.71.1.1 27720 c.1.8.1 28707 2dpmA 284 2.38e+01 2dpmA c.66.1.10 34246 1b6sA 355 2.44e+01 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 1egpA 45 2.46e+01 1egpA d.40.1.1 38561 1lbd 282 2.46e+01 1lbd a.123.1.1 19279 1cruA 454 2.47e+01 1c9uA b.68.2.1 27617 1azwA 313 2.47e+01 1qtrA c.69.1.7 34658 1jrrA 382 2.50e+01 e.1.1.1 63256 1jl0A 334 2.52e+01 1jenA d.156.1.1 63155 1k77A 260 2.56e+01 1e8cA 498 2.59e+01 c.98.1.1 59377 c.59.1.1 59378 c.72.2.1 59379 1bo1A 416 2.61e+01 1bo1A d.143.1.2 41591 1hp1A 516 2.62e+01 1fx3A 169 2.64e+01 1fx3B d.33.1.1 38524 1io7A 368 2.64e+01 1f4tA a.104.1.1 18971 1rypJ 204 2.68e+01 d.153.1.4 41878 1jvwA 167 2.72e+01 1gkzA 388 2.72e+01 a.29.5.1 65268 d.122.1.4 65269 1a2yB 116 2.74e+01 1gc1H b.1.1.1 19927 2kauA 100 2.81e+01 1ubpA d.8.1.1 37335 1jksA 294 2.82e+01 1jykA 254 2.82e+01 c.68.1.13 67458 1c8bA 371 2.89e+01 1c8bA c.56.1.2 59082 7odcA 424 2.93e+01 7odcA b.49.2.1 26488 c.1.6.1 28650 1jfbA 404 2.93e+01 a.104.1.1 66624 1a4mA 349 2.96e+01 1a4mA c.1.9.1 29014 2emo 237 2.98e+01 1ema d.22.1.1 38366 1d7kA 421 2.99e+01 7odcA b.49.2.1 26486 c.1.6.1 28648 1bj8 109 3.03e+01 1bquA b.1.2.1 22070 1qtrA 317 3.05e+01 1qtrA c.69.1.7 34660 1kyoA 430 3.06e+01 1fwcA 100 3.08e+01 1ubpA d.8.1.1 37331 1gmeA 151 3.12e+01 b.15.1.1 65305 3pgk 416 3.13e+01 16pk c.86.1.1 35451 1oacA 727 3.24e+01 1oacA b.30.2.1 24390 d.17.2.1 38007 d.17.2.1 38008 d.82.1.1 40003 1i88A 389 3.28e+01 c.95.1.2 66070 c.95.1.2 66071 1jilA 420 3.28e+01 c.26.1.1 66745 1fuxA 166 3.30e+01 1fjjA b.17.1.2 60034 1fjjA 159 3.32e+01 1fjjA b.17.1.2 59852 4ts1A 319 3.33e+01 2ts1 c.26.1.1 31565 1ush 550 3.35e+01 1ush d.114.1.1 40923 d.159.1.2 42079 1jeqA 609 3.37e+01 1jeqA a.140.2.1 64748 e.31.1.1 64749 1cczA 171 3.42e+01 1cczA b.1.1.1 19758 b.1.1.3 21683 2bb8 71 3.52e+01 2bb8 d.10.1.1 37480 1cr0A 296 3.57e+01 1cr1A c.37.1.11 32287 1cr1A 296 3.58e+01 1cr1A c.37.1.11 32286 1g73A 162 3.58e+01 1fewA a.7.4.1 16332 2cuaA 135 3.60e+01 2cuaA b.6.1.2 23039 2ahjC 206 3.63e+01 2ahjA d.149.1.1 41773 1nhp 447 3.67e+01 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1ikpA 613 3.68e+01 b.29.1.7 66182 d.166.1.1 66183 f.1.5.1 66184 1bb8 71 3.69e+01 2bb8 d.10.1.1 37478 1cseI 71 3.75e+01 1egpA d.40.1.1 38559 1gyfA 62 3.78e+01 1gyfA d.76.1.1 39749 1fokA 568 3.93e+01 2fokA a.4.5.12 16137 a.4.5.12 16138 a.4.5.12 16139 c.52.1.12 33325 1ubpA 101 3.95e+01 1ubpA d.8.1.1 37353