# List of top-scoring protein chains for t2k-100-30-alpha-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 1din 236 8.13e-02 1din c.69.1.9 34682 1ggvA 232 8.98e-02 1din c.69.1.9 34683 1zi8A 236 1.13e-01 2cb2A 318 3.13e-01 1yyaA 250 7.14e-01 5bcaA 516 9.36e-01 1b9zA b.3.1.1,c.1.8.1 22529,28799 1b9zA 516 1.01e+00 1b9zA b.3.1.1,c.1.8.1 22528,28798 1vemA 516 1.28e+00 1itcA 516 1.56e+00 b.3.1.1,c.1.8.1 83705,83706 1kshA 186 1.97e+00 c.37.1.8 72914 1o17A 345 2.65e+00 a.46.2.1,c.27.1.1 80765,80766 1nmoA 247 4.89e+00 c.135.1.1 91980 1nmtA 392 4.90e+00 1nmtA d.108.1.2,d.108.1.2 40823,40824 1e55A 512 6.89e+00 1e70M c.1.8.4 28934 1b35B 255 6.97e+00 1b35B b.121.4.1 23334 1h49A 512 7.05e+00 c.1.8.4 83477 1v02A 565 7.50e+00 c.1.8.4 108194 1aotF 106 8.90e+00 1lckA d.93.1.1 40458 1bb8 71 9.12e+00 2bb8 d.10.1.1 37478 1vjeA 166 9.34e+00 d.185.1.2 100807 4icb 76 9.36e+00 4icb a.39.1.1 17145 1o50A 157 9.45e+00 d.37.1.1,d.37.1.1 92478,92479 1dkrA 317 9.57e+00 1dkuA c.61.1.2,c.61.1.2 34114,34115 1hskA 326 9.88e+00 2mbr d.145.1.2,d.146.1.1 61241,61242 1b69A 69 1.08e+01 2bb8 d.10.1.1 37479 1bf5A 545 1.11e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 1g2iA 166 1.15e+01 1g2iA c.23.16.2 31438 1avgL 41 1.17e+01 1ppbL b.47.1.2 26216 3icb 75 1.18e+01 4icb a.39.1.1 17147 1qvbA 481 1.19e+01 1qvbA c.1.8.4 28983 1jr7A 311 1.22e+01 b.82.2.3 63255 2bb8 71 1.27e+01 2bb8 d.10.1.1 37480 1voqa 90 1.29e+01 1y80A 210 1.36e+01 2f1kA 279 1.37e+01 1jfzA 154 1.38e+01 a.149.1.1 66655 1sqsA 242 1.39e+01 c.23.5.5 98968 2cbuA 468 1.44e+01 1l2lA 457 1.44e+01 c.72.1.3 77656 1l4sA 112 1.48e+01 d.204.1.1 77693 1zbpA 273 1.54e+01 1jlxA 304 1.56e+01 1jlyA b.42.3.1,b.42.3.1 25583,25584 1cpzA 68 1.58e+01 1aw0 d.58.17.1 39351 1ig5A 75 1.58e+01 4icb a.39.1.1 62363 1fxiA 96 1.65e+01 1awd d.15.4.1 37664 1jlyA 304 1.68e+01 1jlyA b.42.3.1,b.42.3.1 25587,25588 1innA 166 1.74e+01 1j98A d.185.1.2 62608 2b7eA 59 1.79e+01 1j7lA 264 1.80e+01 d.144.1.6 62697 1x3pA 54 1.80e+01 1oo0A 147 1.85e+01 d.232.1.1 87182 1pbgA 468 1.88e+01 1e70M c.1.8.4 28946 1fy7A 278 1.95e+01 1fy7A d.108.1.1 40817 1ffkP 84 1.95e+01 1ffkP d.12.1.1 37493 1w3jA 468 1.97e+01 c.1.8.4 109156 1i4sA 147 1.98e+01 a.149.1.1 66026 2ucz 165 1.99e+01 1u9aA d.20.1.1 38330 1ht9A 76 1.99e+01 4icb a.39.1.1 61252 1b1gA 75 2.03e+01 1psrA a.39.1.1 17151 1neiA 60 2.08e+01 d.253.1.1 91843 1agx 331 2.10e+01 4pgaA c.88.1.1 35564 1y1uA 585 2.11e+01 1am1 213 2.16e+01 1yer d.122.1.1 41095 1irsA 112 2.20e+01 1qqgA b.55.1.2 26991 1bob 320 2.24e+01 1bob d.108.1.1 40816 1uw4A 91 2.27e+01 d.58.7.4 100071 2brcA 214 2.32e+01 1n1mA 728 2.32e+01 b.70.3.1,c.69.1.24 79815,79816 1q5hA 147 2.32e+01 b.85.4.1 95893 1uv4A 293 2.36e+01 1xahA 354 2.42e+01 2f9dA 125 2.43e+01 1sfxA 109 2.50e+01 a.4.5.50 105505 1j1hA 144 2.52e+01 b.111.1.1 77056 1o7iA 119 2.55e+01 b.40.4.3 86642 1wzvA 155 2.66e+01 1ois 223 2.66e+01 1a36A e.15.1.1 43267 1jmcA 246 2.68e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 1amw 214 2.69e+01 1yer d.122.1.1 41093 1g8yA 279 2.75e+01 1g8yA c.37.1.11 32302 1q15A 503 2.76e+01 c.26.2.1,d.153.1.1 95538,95539 1nlfA 279 2.82e+01 c.37.1.11 85850 1ah6 220 2.83e+01 1yer d.122.1.1 41094 2agyA 361 2.90e+01 1weoA 93 2.91e+01 1ssfA 156 2.93e+01 b.34.9.1,b.34.9.1 105982,105983 1j7iA 264 2.95e+01 1j7iA d.144.1.6 62694 1a4h 230 2.95e+01 1yer d.122.1.1 41099 3pbgA 468 2.99e+01 1e70M c.1.8.4 28951 1flcA 432 3.00e+01 1flcA b.19.1.3,c.23.10.2 23837,31337 1dkuA 317 3.03e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 2breA 219 3.08e+01 1ab2 109 3.16e+01 1lckA d.93.1.1 40506 1htjF 210 3.18e+01 1htjF a.91.1.1 61254 1abmA 198 3.18e+01 1avmA 2acaA 189 3.23e+01 1ibsA 317 3.27e+01 c.61.1.2,c.61.1.2 66107,66108 2d2jA 329 3.28e+01 1bmtA 246 3.30e+01 1bmtA a.46.1.1,c.23.6.1 17757,31235 1azo 232 3.32e+01 1azo c.52.1.14 33329 2aclB 244 3.34e+01 1igqA 62 3.37e+01 b.34.1.3 66130 1mml 265 3.41e+01 1mml e.8.1.2 43015 1zc6A 305 3.53e+01 1gzqA 300 3.65e+01 b.1.1.2,d.19.1.1 70818,70819 1lyxA 248 3.75e+01 c.1.1.1 78304 3pga1 337 3.82e+01 4pgaA 2bkkA 264 3.82e+01 1txgA 335 3.82e+01 1zl0A 311 3.95e+01 1kolA 398 4.08e+01 b.35.1.2,c.2.1.1 77474,77475 2bkyA 97 4.13e+01 2gaiA 633 4.16e+01 1r9fA 136 4.19e+01 d.255.1.1 97257 1h5qA 265 4.23e+01 1cydA c.2.1.2 60643 1z5zA 271 4.24e+01 1xnb 185 4.25e+01 1axkA b.29.1.11 24308 1rypL 212 4.25e+01 d.153.1.4 41880 1iexA 605 4.28e+01 c.1.8.7,c.23.11.1 66127,66128 1aerA 205 4.34e+01 1aerA d.166.1.1 42249 1zfuA 40 4.34e+01 1ykhB 132 4.41e+01 1h0xA 100 4.48e+01 d.68.6.1 76451 2arcB 164 4.49e+01 2arcA b.82.4.1 28149 1ex1A 605 4.50e+01 1ex1A c.1.8.7,c.23.11.1 29013,31347 1cf2O 337 4.53e+01 1b7gO c.2.1.3,d.81.1.1 29994,39909 2aumA 317 4.60e+01 1zrsA 317 4.66e+01 1f32A 149 4.66e+01 1f32A d.62.1.1 39539 1t2jA 116 4.67e+01 2aunA 317 4.70e+01 2ez6A 221 4.76e+01 1x38A 602 4.78e+01 1g5bA 221 4.84e+01 1g5bA d.159.1.3 60261 2bkdN 134 4.89e+01 1uwsA 489 4.93e+01 c.1.8.4 108073 1qqgA 264 5.01e+01 1qqgA b.55.1.2,b.55.1.2 26987,26988 1wwzA 159 5.03e+01 1sxrA 183 5.06e+01 d.118.1.1 106101 1wh8A 111 5.07e+01 1ywhA 313 5.08e+01 1fj2A 232 5.10e+01 1auoA c.69.1.14 34720 1tfzA 424 5.13e+01 d.32.1.3,d.32.1.3 106886,106887 1uurA 473 5.14e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1zd9A 188 5.17e+01 1x47A 98 5.18e+01 1csn 298 5.23e+01 1csn d.144.1.7 41664 1o5xA 248 5.28e+01 c.1.1.1 92528 2cxxA 190 5.30e+01 2fa8A 105 5.32e+01 1wrvA 308 5.34e+01 1iicA 422 5.39e+01 1nmtA d.108.1.2,d.108.1.2 62422,62423 1j55A 95 5.41e+01 a.39.1.2 77078 1g65K 211 5.41e+01 d.153.1.4 41907 1a0hA 159 5.43e+01 1a0hA b.47.1.2,g.14.1.1 26229,44655 1p4kA 295 5.46e+01 d.153.1.5 87772 2jhbA 143 5.52e+01 2jhbA b.54.1.1 26950 2fm8A 135 5.53e+01 1hdmA 201 5.53e+01 1iakA b.1.1.2,d.19.1.1 21583,38157 2dcyA 185 5.56e+01 1i3zA 103 5.59e+01 d.93.1.1 83667 1kveB 77 5.64e+01 1kveB 1mg7A 417 5.65e+01 d.14.1.6,d.58.26.6 84954,84955 2fp7B 172 5.66e+01 1pmaA 233 5.88e+01 1pmaA d.153.1.4 41918 1qd9A 124 5.93e+01 1qu9A d.79.1.1 39758 1awd 94 5.96e+01 1awd d.15.4.1 37673 2bh8A 101 5.96e+01 1n2sA 299 6.04e+01 c.2.1.2 79857 2aacA 177 6.12e+01 2arcA b.82.4.1 28150 1ap6A 198 6.16e+01 1avmA a.2.11.1,d.44.1.1 15746,38705 2ftbA 125 6.17e+01 1tidB 119 6.18e+01 c.13.2.1 107000 1kvdB 77 6.21e+01 1kveB 1rpyA 114 6.22e+01 d.93.1.1 97718 1h1iB 350 6.24e+01 b.82.1.5 76470 1h1iD 350 6.26e+01 b.82.1.5 76472 1jb0D 138 6.30e+01 1jb0D d.187.1.1 62823 1r7lA 110 6.30e+01 d.277.1.1 104837 1ab4 477 6.37e+01 1ab4 e.11.1.1 43251 1h1iC 350 6.38e+01 b.82.1.5 76471 2cfaA 217 6.38e+01 1yadA 221 6.42e+01 1pq9A 253 6.44e+01 a.123.1.1 95004 1uz1A 468 6.44e+01 1xwrA 97 6.45e+01 2ag4A 164 6.53e+01 1xrkA 124 6.57e+01 1kk6A 209 6.58e+01 b.81.1.3 68657 1gowA 489 6.61e+01 1qvbA c.1.8.4 28981 1kx5C 128 6.63e+01 a.22.1.1 77595 1juhA 350 6.65e+01 b.82.1.5 71884 1zy4A 303 6.71e+01 1tw4A 125 6.89e+01 1sk4A 163 6.91e+01 d.118.1.1 105664 2arcA 164 6.94e+01 2arcA b.82.4.1 28148 1nvpD 108 6.96e+01 a.32.1.1,b.56.1.1 92213,92214 1garA 212 6.97e+01 2gar c.65.1.1 34162 1fa8A 135 7.00e+01 1qipA d.32.1.1 38486 1f9zA 135 7.05e+01 1qipA d.32.1.1 38484 2atrA 138 7.05e+01 1ikpA 613 7.06e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1mr7A 209 7.08e+01 b.81.1.3 91430 1thjA 214 7.08e+01 1qreA b.81.1.5 28072 1upvA 257 7.12e+01 1pu5A 164 7.13e+01 b.95.1.1 104310 2fg9A 178 7.16e+01 1t3qB 788 7.21e+01 d.41.1.1,d.133.1.1 106369,106370 1vg5A 73 7.21e+01 1nz0A 118 7.21e+01 d.14.1.2 86433 1jykA 254 7.29e+01 c.68.1.13 67458 1n0nA 199 7.34e+01 a.2.11.1,d.44.1.1 79750,79751 2gqrA 237 7.42e+01 1q0xH 221 7.42e+01 b.1.1.1,b.1.1.2 95517,95518 1yc9A 442 7.45e+01 1pl4A 198 7.49e+01 a.2.11.1,d.44.1.1 94854,94855 1hq3A 129 7.50e+01 1aoiC a.22.1.1 16434 1ub4C 85 7.53e+01 b.129.1.1 88401 2gtrA 261 7.55e+01 1b47A 304 7.57e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17381,17775,40529 1xniA 118 7.66e+01 1jj2R 84 7.69e+01 1ffkP d.12.1.1 63103 1qzgA 187 7.74e+01 b.40.4.3 96643 2agcA 162 7.76e+01 1k51A 72 7.79e+01 d.15.7.1 68147 1sg7A 96 7.85e+01 1dmaA 214 7.88e+01 1aerA d.166.1.1 42251 1tzyA 129 7.90e+01 a.22.1.1 107530 1xxnA 185 7.91e+01 1v5sA 126 7.92e+01 d.129.6.1 108384 1z4eA 153 7.94e+01 1vqoS 85 7.98e+01 1s72S 85 8.07e+01 d.12.1.1 105338 1pv9A 348 8.08e+01 c.55.2.1,d.127.1.1 95157,95158 1w9yA 319 8.11e+01 1qfxA 460 8.11e+01 1qfxA c.60.1.2 33994 1i4yA 114 8.12e+01 2mhr a.24.4.1 61738 1enxA 190 8.14e+01 1axkA b.29.1.11 24325 1gpr 162 8.14e+01 1gpr b.84.3.1 28267 1k7yA 577 8.17e+01 a.46.1.1,c.23.6.1,d.173.1.1 68272,68273,68274 2ag9A 164 8.20e+01 2gdqA 382 8.24e+01 1gydB 315 8.27e+01 b.67.2.1 70751 1ny9A 143 8.33e+01 a.181.1.1 86401 1v93A 296 8.40e+01 c.1.23.1 100532 1qn2A 100 8.42e+01 1ycc a.3.1.1 15882 1usuA 260 8.46e+01 d.14.1.8 99885 1wnaA 131 8.58e+01 1jyoA 130 8.61e+01 d.198.1.1 67483 1nv8A 284 8.67e+01 c.66.1.30 86224 1jkxA 212 8.67e+01 c.65.1.1 66813 1wybA 392 8.68e+01 1xypA 190 8.68e+01 1axkA b.29.1.11 24327 1d8hA 311 8.80e+01 1d8iA d.63.1.1 39544 1zx8A 136 8.81e+01 2a0jA 149 8.83e+01 1rlr 761 8.85e+01 1rlr a.98.1.1,c.7.1.2 18753,30679 1ox8A 107 8.87e+01 b.136.1.1 93671 2f5yA 91 8.87e+01 1bxdA 161 8.88e+01 1bxdA d.122.1.3 41111 2bvcA 486 8.88e+01