# List of top-scoring protein chains for t2k-100-30-alpha 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 1kkoA 413 1.76e-02 c.1.11.2 68675 d.54.1.1 68676 1qo7A 394 6.63e-01 1qo7A c.69.1.11 34697 1fnoA 417 6.66e-01 1b5tA 275 8.73e-01 1b5tA c.1.23.1 29676 1cr5A 189 9.57e-01 1cr5A b.52.2.3 26931 d.31.1.1 38465 1jksA 294 1.04e+00 1e4cP 215 1.34e+00 2fua c.74.1.1 34969 1k47A 337 1.35e+00 1k32A 1045 1.42e+00 b.36.1.3 68068 b.68.7.1 68069 b.69.9.1 68070 c.14.1.2 68071 1tcrA 202 1.77e+00 1tcrA b.1.1.1 20605 b.1.1.2 21549 1f7cA 231 2.47e+00 1f7cA a.116.1.1 19107 1cewI 108 2.55e+00 1cewI d.17.1.2 37999 1hssA 124 2.70e+00 1bea a.52.1.2 17819 1soxA 466 2.75e+00 1soxA b.1.1.5 21947 d.120.1.1 41090 d.176.1.1 42563 1fua 215 3.10e+00 2fua c.74.1.1 34973 1b3jA 274 3.27e+00 1agdA b.1.1.2 20855 d.19.1.1 38319 2fua 215 3.38e+00 2fua c.74.1.1 34977 1aqb 183 3.82e+00 1aqb b.60.1.1 27084 1fcqA 350 4.01e+00 c.1.8.9 65006 1ky3A 182 4.07e+00 1qhaA 917 4.24e+00 1qhaA c.55.1.3 33467 c.55.1.3 33468 c.55.1.3 33469 c.55.1.3 33470 1obr 326 4.50e+00 1aye c.56.5.2 33828 1eqjA 511 4.94e+00 1ejjA c.105.1.1 59495 c.76.1.3 59496 2dabA 282 4.97e+00 1daaA e.17.1.1 43274 1dk8A 147 5.14e+00 1agrE a.91.1.1 18548 1ejjA 511 5.41e+00 1ejjA c.105.1.1 59422 c.76.1.3 59423 1dgkN 917 5.44e+00 1qhaA c.55.1.3 33487 c.55.1.3 33488 c.55.1.3 33489 c.55.1.3 33490 1fxkB 109 6.09e+00 1fxkA a.2.5.1 15704 1jx4A 352 6.38e+00 e.8.1.5 67405 1gjwA 637 6.40e+00 b.71.1.1 60582 c.1.8.1 60583 1czaN 917 6.55e+00 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1f6vA 91 6.72e+00 1f6vA a.49.1.1 17791 1bmlC 362 6.96e+00 1bmlC d.15.5.1 37729 d.15.5.1 37730 d.15.5.1 37731 1e5eA 404 7.12e+00 1ibjA c.67.1.3 59265 1eps 427 7.18e+00 1eps d.68.2.2 39586 1g5cA 170 7.44e+00 1g5cA c.53.2.1 60264 1vaoA 560 7.67e+00 1qltA d.58.32.1 39461 d.145.1.1 41724 1guzA 310 7.76e+00 c.2.1.5 65586 d.162.1.1 65587 1hkcA 917 7.77e+00 1qhaA c.55.1.3 33475 c.55.1.3 33476 c.55.1.3 33477 c.55.1.3 33478 1e9mA 106 7.81e+00 1ayfA d.15.4.1 59397 1g6sA 427 8.50e+00 1eps d.68.2.2 39584 1hkbA 917 8.67e+00 1qhaA c.55.1.3 33479 c.55.1.3 33480 c.55.1.3 33481 c.55.1.3 33482 1pvdA 537 9.26e+00 1zpdA c.31.1.3 31737 c.36.1.1 31777 c.36.1.1 31778 1qvbA 481 9.84e+00 1qvbA c.1.8.4 28983 1ovaA 386 1.03e+01 1ovaA e.1.1.1 42619 1cliA 345 1.04e+01 1cliA d.79.4.1 39816 d.139.1.1 41459 1g7tA 594 1.04e+01 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1gjuA 637 1.05e+01 b.71.1.1 60580 c.1.8.1 60581 1bg4 302 1.08e+01 1taxA c.1.8.3 28806 1a3c 181 1.09e+01 1a3c c.61.1.1 34095 1d7kA 421 1.09e+01 7odcA b.49.2.1 26486 c.1.6.1 28648 1hwxA 501 1.14e+01 1hwyA c.2.1.7 30250 c.58.1.1 33898 1ryp1 222 1.16e+01 1ryp1 1ipwA 175 1.16e+01 2prd b.40.5.1 25427 1exkA 79 1.17e+01 1exkA g.54.1.1 45384 1eiyB 785 1.18e+01 1pysB a.6.1.1 16305 a.6.1.1 16306 b.40.4.4 25314 d.58.13.1 39313 d.104.1.1 40782 d.138.1.1 41458 1b7yB 785 1.19e+01 1pysB a.6.1.1 16301 a.6.1.1 16302 b.40.4.4 25312 d.58.13.1 39311 d.104.1.1 40780 d.138.1.1 41456 1kijA 390 1.19e+01 1daaA 282 1.25e+01 1daaA e.17.1.1 43270 1as8A 343 1.26e+01 1nif b.6.1.3 23074 b.6.1.3 23075 1aizA 129 1.27e+01 1nwpA b.6.1.1 22903 1a4mA 349 1.27e+01 1a4mA c.1.9.1 29014 1bw0A 416 1.27e+01 1bw0A c.67.1.1 34385 2sas 185 1.28e+01 2sas a.39.1.5 17258 1i3kA 348 1.36e+01 1xel c.2.1.2 61595 1hbq 183 1.37e+01 1aqb b.60.1.1 27078 2azaA 129 1.39e+01 1nwpA b.6.1.1 22901 1eu3A 210 1.39e+01 1an8 b.40.2.2 25206 d.15.6.1 37795 1pysB 785 1.40e+01 1pysB a.6.1.1 16299 a.6.1.1 16300 b.40.4.4 25311 d.58.13.1 39310 d.104.1.1 40779 d.138.1.1 41455 1aw8E 91 1.41e+01 1aw8B 1g5pA 289 1.43e+01 1cp2A c.37.1.10 32253 1dekA 241 1.43e+01 1dekA c.37.1.1 31842 1hwyA 501 1.44e+01 1hwyA c.2.1.7 30262 c.58.1.1 33910 1et7A 341 1.44e+01 1nif b.6.1.3 23070 b.6.1.3 23071 1hmy 327 1.45e+01 6mhtA c.66.1.10 34229 1d1gA 168 1.46e+01 1d1gA c.71.1.1 34889 1eg3A 261 1.46e+01 1eg3A a.39.1.7 17376 a.39.1.7 17377 b.72.1.1 27805 1jj2A 239 1.47e+01 1rl2A b.34.5.3 63084 b.40.4.5 63085 3daaA 277 1.47e+01 1daaA e.17.1.1 43272 1g38A 393 1.54e+01 2admA c.66.1.10 60235 1a8vA 121 1.55e+01 1a62 a.140.3.1 64712 b.40.4.5 64713 1dr9A 201 1.57e+01 1dr9A b.1.1.1 19762 b.1.1.3 21684 1ffyA 917 1.57e+01 1qu2A a.27.1.1 16926 b.51.1.1 26891 c.26.1.1 31593 1qu2A 917 1.57e+01 1qu2A a.27.1.1 16925 b.51.1.1 26890 c.26.1.1 31592 1fxkA 107 1.58e+01 1fxkA a.2.5.1 15703 1lba 146 1.60e+01 1lba d.118.1.1 41062 1rypI 222 1.64e+01 d.153.1.4 41877 1clc 639 1.66e+01 1clc a.102.1.2 18835 b.1.1.5 21872 3mhtA 327 1.68e+01 6mhtA c.66.1.10 34234 1fp6A 289 1.71e+01 1cp2A c.37.1.10 32243 1qmvA 197 1.74e+01 1qq2A c.47.1.10 33066 1kkhA 317 1.77e+01 1kekA 1231 1.79e+01 c.36.1.4 68524 c.36.1.4 68525 c.48.1.3 68526 c.64.1.1 68527 d.58.1.5 68528 1hka 158 1.81e+01 1hka d.58.30.1 39433 1nipA 289 1.82e+01 1cp2A c.37.1.10 32263 1j9qA 341 1.85e+01 1nif b.6.1.3 62765 b.6.1.3 62766 1rbp 182 1.88e+01 1aqb b.60.1.1 27085 6mhtA 327 1.92e+01 6mhtA c.66.1.10 34226 1kk1A 410 1.95e+01 1igrA 478 1.98e+01 1igrA c.10.2.5 30877 c.10.2.5 30878 g.3.9.1 44188 7odcA 424 2.03e+01 7odcA b.49.2.1 26488 c.1.6.1 28650 1ei1A 391 2.05e+01 1aj6 d.14.1.3 37570 d.122.1.2 41104 1add 349 2.08e+01 1a4mA c.1.9.1 29020 1l92 164 2.08e+01 1l92 d.2.1.3 36629 1aw8B 91 2.10e+01 1aw8B 1qagA 226 2.11e+01 1qagA a.40.1.1 17400 a.40.1.1 17401 1efuB 282 2.13e+01 1efuB a.5.2.2 58975 d.43.1.1 58976 d.43.1.1 38677 1kopA 223 2.15e+01 2cba b.74.1.1 27966 1fjgS 93 2.18e+01 1qkfA d.28.1.1 38451 1k4jA 230 2.22e+01 1hbp 183 2.26e+01 1aqb b.60.1.1 27079 1ycqA 107 2.30e+01 1ycqA a.42.1.1 17419 1delA 241 2.34e+01 1dekA c.37.1.1 31844 1l58 164 2.35e+01 1l92 d.2.1.3 36635 1g7rA 594 2.35e+01 1g7rA b.43.3.1 25716 b.43.3.1 25717 c.20.1.1 31034 c.37.1.8 32149 1myo 118 2.35e+01 2myo a.118.2.1 19174 1inlA 296 2.36e+01 c.66.1.17 66220 1dyqA 234 2.38e+01 3seb b.40.2.2 59140 d.15.6.1 59141 1cqwA 295 2.41e+01 1b6g c.69.1.8 34679 1g7sA 594 2.48e+01 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1bn6A 294 2.50e+01 1bn6A c.69.1.8 34678 1kkcA 221 2.54e+01 a.2.11.1 68660 d.44.1.1 68661 1i18A 97 2.56e+01 b.43.4.3 61520 1btl 263 2.59e+01 1btl e.3.1.1 42691 2myo 118 2.70e+01 2myo a.118.2.1 19175 1brt 277 2.71e+01 1brt c.69.1.12 34699 1b0pA 1231 2.72e+01 c.36.1.4 31831 c.36.1.4 31832 c.48.1.3 33104 c.64.1.1 34157 d.58.1.5 39003 2admA 421 2.73e+01 2admA c.66.1.10 34238 1jq3A 296 2.73e+01 c.66.1.17 67079 2plc 274 2.76e+01 2plc c.1.18.2 29614 1nddA 76 2.81e+01 1ubi d.15.1.1 37599 1jq5A 370 2.85e+01 e.22.1.2 67084 1k6iA 352 2.92e+01 c.2.1.2 68223 1llp 343 2.93e+01 1arv a.93.1.1 18578 1bn7A 294 2.98e+01 1bn6A c.69.1.8 34677 1a62 130 3.01e+01 1a62 a.140.3.1 64708 b.40.4.5 64709 1ep0A 185 3.08e+01 1dzrA b.82.1.1 28080 1nfdA 203 3.09e+01 1tcrA b.1.1.1 20612 b.1.1.2 21550 1ckeA 227 3.11e+01 1ckeA c.37.1.1 31846 1aj8A 371 3.11e+01 1aj8A a.103.1.1 18900 3ladA 476 3.19e+01 1lvl c.3.1.5 30573 c.3.1.5 30574 d.87.1.1 40208 1e3dB 542 3.20e+01 1h2rL e.18.1.1 59189 1h7nA 342 3.21e+01 1b4kA c.1.10.3 60726 1fw9A 164 3.22e+01 1fw9A d.190.1.1 60059 1eqoA 158 3.32e+01 1hka d.58.30.1 39432 1mfa 247 3.32e+01 1mfa b.1.1.1 19888 b.1.1.1 19889 1qltA 560 3.37e+01 1qltA d.58.32.1 39457 d.145.1.1 41720 119l 164 3.38e+01 1l92 d.2.1.3 36622 1qpbA 563 3.41e+01 1zpdA c.31.1.3 31739 c.36.1.1 31781 c.36.1.1 31782 1jj2F 119 3.42e+01 1ffkE d.79.3.1 63091 4rhv3 236 3.49e+01 1aym3 8ohm 435 3.50e+01 1heiA c.37.1.14 32469 c.37.1.14 32470 1eg7A 557 3.50e+01 1eg7A c.37.1.10 32241 1g5bA 221 3.51e+01 1g5bA d.159.1.3 60261 1nif 340 3.60e+01 1nif b.6.1.3 23048 b.6.1.3 23049 1rlaA 323 3.61e+01 1d3vA c.42.1.1 32561 1cfr 285 3.62e+01 1cfr c.52.1.7 33312 1ejdA 419 3.63e+01 1uae d.68.2.2 39576 1qhhA 167 3.66e+01 1pjr c.37.1.13 32393 1nddD 76 3.67e+01 1ubi d.15.1.1 37602 1tnrA 144 3.72e+01 2tnfA b.22.1.1 23867 1k0rA 366 3.73e+01 b.40.4.5 67961 d.52.3.1 67962 d.52.3.1 67963 d.202.1.1 67964 1i39A 225 3.74e+01 1ekeA c.55.3.1 61585 1kay 381 3.75e+01 1ba1 c.55.1.1 33385 c.55.1.1 33386 2u1a 88 3.78e+01 2u1a d.58.7.1 39164 1hqkA 154 3.84e+01 c.16.1.1 65902 1d3bB 91 3.84e+01 1d3bB b.38.1.1 24804 1pbwA 216 3.86e+01 1pbwA a.116.1.1 19103 1cseE 274 3.86e+01 1gci c.41.1.1 32481 1d3vA 323 3.87e+01 1d3vA c.42.1.1 32559 1fyvA 161 3.88e+01 1fyvA c.23.2.1 31127 1qjvA 342 3.91e+01 1qjvA b.80.1.5 28035 1qjcA 158 3.94e+01 1b6tA c.26.1.3 63328 1e8gA 560 3.95e+01 1qltA d.58.32.1 39455 d.145.1.1 41718 1ifqA 138 3.99e+01 1ifqA d.110.4.1 62350