# List of top-scoring protein chains for t06-100-30-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 1xqaA 113 1.06e-01 1swvA 267 2.56e-01 1u9aA 160 3.03e-01 1u9aA d.20.1.1 38333 1gd8A 118 3.14e-01 d.188.1.1 60445 2ap1A 327 5.44e-01 2fi9A 128 5.56e-01 2grrA 161 6.11e-01 1exrA 148 6.73e-01 1cll a.39.1.5 17299 1rdfA 267 7.16e-01 c.108.1.3 104884 2a3qA 170 8.71e-01 1eqfA 280 9.15e-01 1eqfA a.29.2.1,a.29.2.1 16972,16973 2aeuA 374 1.30e+00 1h2kA 349 1.35e+00 b.82.2.6 76572 1rypA 243 1.62e+00 1pmaA d.153.1.4 41932 1ggzA 148 1.65e+00 a.39.1.5 70176 1nvvS 481 1.72e+00 a.117.1.1 86279 1uujA 88 1.77e+00 a.221.1.1 108046 1jl5A 454 2.03e+00 c.10.2.6 66830 1hl9A 449 2.18e+00 b.71.1.3,c.1.8.11 90650,90651 1wg8A 285 2.37e+00 2cr9A 139 2.42e+00 1v54E 109 2.53e+00 a.118.11.1 100326 1yirA 408 2.61e+00 1r1qA 100 2.78e+00 d.93.1.1 104763 1jy2O 56 2.99e+00 h.1.8.1 67441 1kr4A 125 3.13e+00 d.58.5.2 72889 1opjA 293 3.14e+00 d.144.1.7 87230 1sziA 247 3.70e+00 a.24.23.1 106159 1wxcB 134 3.83e+00 2cglA 489 3.86e+00 1fseA 74 4.26e+00 1fseA a.4.6.2 60000 1kveB 77 4.31e+00 1kveB 1yf2A 425 4.53e+00 1nepA 130 4.92e+00 b.1.18.7 80440 2ahqA 76 5.07e+00 1i5pA 633 5.09e+00 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 1omrA 201 5.18e+00 a.39.1.5 93349 1a8y 367 5.39e+00 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 2h88C 140 5.62e+00 1z8uA 102 5.94e+00 1sflA 238 5.94e+00 1n82A 331 5.96e+00 c.1.8.3 91703 1lkkA 105 6.53e+00 1lckA d.93.1.1 40412 1aj8A 371 6.92e+00 1aj8A a.103.1.1 18900 1kvkA 395 6.99e+00 d.14.1.5,d.58.26.3 73060,73061 1o0yA 260 7.22e+00 c.1.10.1 80756 1zvaA 77 7.43e+00 2cx1A 187 7.44e+00 1vgmA 378 7.47e+00 2b20A 403 7.61e+00 1uj8A 77 7.65e+00 2f3yA 148 7.75e+00 1wx1A 335 7.96e+00 2db9A 149 9.55e+00 1jyrA 96 9.59e+00 d.93.1.1 71969 1w99A 558 9.59e+00 1ed8A 449 9.59e+00 1b8jA c.76.1.1 34988 1wp5A 323 9.77e+00 1eluA 390 9.84e+00 1elqA c.67.1.3 34434 1uuhA 159 9.91e+00 d.169.1.4 100008 1jggA 60 1.02e+01 2hddA a.4.1.1 62950 1gpjA 404 1.04e+01 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1r85A 379 1.05e+01 c.1.8.3 104839 1t7lA 766 1.06e+01 1dj7A 117 1.07e+01 1dj7A g.36.1.1 44997 1q1vA 70 1.09e+01 a.159.4.1 104479 1na6A 404 1.11e+01 b.142.1.1,c.52.1.22 91748,91749 1xdfA 157 1.11e+01 1k04A 162 1.13e+01 a.24.14.1 67904 1ufiA 64 1.16e+01 a.30.4.1 99336 1w6sB 74 1.17e+01 1vhnA 318 1.20e+01 c.1.4.1 100693 1n2zA 245 1.21e+01 c.92.2.2 79865 1wdtA 665 1.22e+01 1bhdA 118 1.22e+01 1bkrA a.40.1.1 17398 2ajrA 331 1.24e+01 1ov2A 99 1.25e+01 a.13.1.1 93580 1o26A 232 1.25e+01 d.207.1.1 86566 2afdA 88 1.32e+01 1qnrA 344 1.33e+01 1qnoA c.1.8.3 28834 1z5bA 469 1.34e+01 1zczA 464 1.36e+01 1b7yA 350 1.36e+01 1pysA d.104.1.1 40776 1ty0A 211 1.37e+01 b.40.2.2,d.15.6.1 107440,107441 1gu7A 364 1.40e+01 b.35.1.2,c.2.1.1 83321,83322 2ffsA 157 1.43e+01 2dfkA 402 1.45e+01 1m32A 366 1.45e+01 c.67.1.3 78508 2f7fA 494 1.46e+01 2fa8A 105 1.48e+01 1mkfA 382 1.49e+01 b.116.1.1 79232 2f46A 156 1.51e+01 1zgdA 312 1.52e+01 1td6A 306 1.60e+01 1ztpA 251 1.61e+01 2a5lA 200 1.63e+01 1twiA 434 1.64e+01 b.49.2.3,c.1.6.1 107399,107400 1a8d 452 1.64e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 1cg5B 141 1.67e+01 1cg5B a.1.1.2 15585 1g4wR 383 1.69e+01 1g4uS a.24.11.1,c.45.1.2 16644,32692 1dq3A 454 1.71e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 2fjlA 150 1.73e+01 1w77A 228 1.73e+01 1ywzA 175 1.77e+01 2fbwC 141 1.82e+01 1a92A 50 1.83e+01 1a92A h.4.6.1 45791 1rxdA 159 1.83e+01 1yx1A 264 1.84e+01 1akz 223 1.85e+01 3eugA c.18.1.1 31007 1yf9A 171 1.89e+01 1c7gA 456 1.96e+01 c.67.1.2 90415 1wmhA 89 1.98e+01 2fupA 168 1.98e+01 1r8iA 213 2.01e+01 a.8.7.1 97239 1wzvA 155 2.05e+01 1yovA 537 2.09e+01 1sxrA 183 2.12e+01 d.118.1.1 106101 2evaA 307 2.14e+01 1avsA 90 2.16e+01 1cll a.39.1.5 17226 1iomA 377 2.19e+01 a.103.1.1 83698 1h6dA 433 2.19e+01 c.2.1.3,d.81.1.5 65656,65657 1z6oM 191 2.20e+01 1uwcA 261 2.20e+01 c.69.1.17 100101 1qgtA 149 2.21e+01 1qgtA a.62.1.1 18135 1jpzA 473 2.25e+01 a.104.1.1 67069 1wvqA 167 2.26e+01 2gokA 429 2.29e+01 1m3qA 317 2.37e+01 a.96.1.3,d.129.1.2 91184,91185 1neu 124 2.42e+01 1neu b.1.1.1 19704 2cohA 202 2.44e+01 1n4xH 120 2.45e+01 b.1.1.1 85324 1jsdA 319 2.51e+01 b.19.1.2 63258 1sg7A 96 2.52e+01 1gqeA 365 2.52e+01 e.38.1.1 70351 1sjiA 350 2.53e+01 2arhA 203 2.54e+01 1p1lA 102 2.54e+01 d.58.5.2 87695 1e9rA 437 2.55e+01 c.37.1.11 64827 1up8A 598 2.56e+01 a.111.1.2 99710 1sk4A 163 2.57e+01 d.118.1.1 105664 1xg8A 111 2.61e+01 1ars 396 2.63e+01 1ajsA c.67.1.1 34287 2bwfA 77 2.65e+01 1u24A 337 2.67e+01 2bh8A 101 2.68e+01 1k8rB 110 2.69e+01 d.15.1.5 72180 1y44A 320 2.71e+01 1lm8B 118 2.72e+01 d.15.1.1 74033 1z6uA 150 2.81e+01 1gwiA 411 2.83e+01 a.104.1.1 76364 1i76A 163 2.84e+01 1hfc d.92.1.11 61877 1mlwA 301 2.93e+01 d.178.1.1 79289 1jdc 429 2.94e+01 1jdc b.71.1.1,c.1.8.1 27789,28776 1bhe 376 2.95e+01 1bhe b.80.1.3 28030 1p5zB 263 3.03e+01 c.37.1.1 87815 1g8iA 190 3.08e+01 1rec a.39.1.5 60363 1vls 146 3.11e+01 1vls a.24.2.1 16532 1tkeA 224 3.24e+01 1u19A 349 3.26e+01 1kllA 130 3.26e+01 d.32.1.2 72720 1stzA 338 3.29e+01 a.4.5.51,d.110.2.3 106009,106010 1b5pA 385 3.30e+01 c.67.1.1 90403 1s4kA 120 3.30e+01 a.35.1.6 105254 1go4A 205 3.37e+01 d.135.1.1 70292 2fd5A 180 3.38e+01 2fulA 178 3.42e+01 1x3lA 440 3.44e+01 1uyrA 737 3.50e+01 c.14.1.4,c.14.1.4 100188,100189 1upqA 123 3.53e+01 1fi2A 201 3.53e+01 1fi2A b.82.1.2 59845 1wdcC 156 3.69e+01 1wdcC a.39.1.5 17317 1ev0A 58 3.71e+01 1ev0A d.71.1.1 39594 1npeA 267 3.74e+01 b.68.5.1 92032 1tvlA 454 3.74e+01 c.1.16.4 107366 1b3uA 588 3.76e+01 1b3uA a.118.1.2 19135 1no1A 126 3.78e+01 a.179.1.1 85913 1zwwA 256 3.81e+01 1nkpB 83 3.82e+01 a.38.1.1 80574 1xdzA 240 3.84e+01 1v4pA 157 3.86e+01 3nul 130 3.86e+01 3nul d.110.1.1 40891 2et1A 201 3.89e+01 1ub3A 220 3.89e+01 c.1.10.1 88395 2b8nA 429 3.90e+01 1f20A 435 3.92e+01 b.43.4.1,c.25.1.4 64932,64933 2f2lA 167 3.98e+01 1qksA 567 4.02e+01 1qksA a.3.1.2,b.70.2.1 15951,27710 1txjA 171 4.05e+01 b.88.1.2 107424 1p5fA 189 4.05e+01 c.23.16.2 94142 1mvcA 240 4.05e+01 a.123.1.1 79499 1rkbA 173 4.06e+01 1zhcA 76 4.08e+01 1ajsA 412 4.10e+01 1ajsA c.67.1.1 34276 1uxtA 501 4.12e+01 c.82.1.1 108125 1nm8A 616 4.13e+01 c.43.1.3,c.43.1.3 85872,85873 1uzbA 516 4.13e+01 c.82.1.1 100220 1s1qA 145 4.23e+01 d.20.1.2 98351 1l8dA 112 4.28e+01 h.4.12.1 73687 1bf6A 291 4.34e+01 1pscA c.1.9.3 29065 1ldfA 281 4.38e+01 f.19.1.1 73845 1euhA 475 4.39e+01 1euhA c.82.1.1 35369 1pytA 94 4.40e+01 1pytA d.58.3.1 39064 1gttA 429 4.40e+01 d.177.1.1,d.177.1.1 70529,70530 1musA 477 4.40e+01 c.55.3.4 79494 2dbgA 103 4.43e+01 2g8lA 299 4.43e+01 2g0uA 92 4.45e+01 1w32A 348 4.45e+01 1qj4A 257 4.49e+01 1qj4A c.69.1.20 34796 1oxwA 373 4.50e+01 c.19.1.3 87539 2hddA 61 4.51e+01 2hddA a.4.1.1 15971 2bjkA 516 4.54e+01 1guxA 218 4.56e+01 1guxA a.74.1.3 18388 2ga1A 106 4.57e+01 1ail 73 4.72e+01 1ail a.16.1.1 16381 1hn0A 1021 4.73e+01 a.102.3.2,b.18.1.17,b.24.1.1,b.30.5.2 83616,83617,83618,83619 1r62A 160 4.75e+01 d.122.1.3 104816 1zvkA 358 4.80e+01 2bycA 137 4.81e+01 1fus 106 4.81e+01 9rnt d.1.1.4 36050 1m12A 84 4.82e+01 a.64.1.1 84745 2ddrA 306 4.87e+01 1nrjA 158 4.87e+01 d.110.4.4 86124 1k4nA 192 4.93e+01 d.32.1.5 72059 2bpsA 81 5.01e+01 1hs7A 97 5.08e+01 1hs7A a.47.2.1 61236 1s9kD 53 5.20e+01 1e0tA 470 5.23e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1l6pA 125 5.25e+01 b.1.17.1 73626 2gsfA 373 5.28e+01 1ydmA 187 5.36e+01 1ayaA 101 5.37e+01 1qadA d.93.1.1 40460 1d7mA 101 5.41e+01 1d7mA h.1.10.1 45628 2fnjB 118 5.46e+01 1vbiA 344 5.47e+01 1go4E 100 5.47e+01 h.1.22.1 70296 1zd9A 188 5.47e+01 1zo0A 126 5.50e+01 2al6A 375 5.55e+01 1x9iA 302 5.58e+01 1qpcA 279 5.61e+01 1fgkA d.144.1.7 41685 2ex0A 399 5.64e+01 1jnmA 62 5.66e+01 h.1.3.1 84181 1o5kA 306 5.66e+01 c.1.10.1 92504 2b0tA 738 5.79e+01 1t44G 147 5.81e+01 d.109.1.1 106395 2lhb 149 5.81e+01 2fal a.1.1.2 15597 1xttA 216 5.86e+01 1l8nA 679 5.91e+01 c.1.8.10,d.92.2.2 84564,84565 2fqpA 97 5.91e+01 1uvqA 197 5.94e+01 b.1.1.2,d.19.1.1 100062,100063 2d29A 387 5.96e+01 2f5xA 312 5.97e+01 2d7vA 162 5.97e+01 1k24A 253 6.07e+01 f.4.4.2 72002 1ecmA 109 6.07e+01 1ecmA a.130.1.1 19492 1c44A 123 6.07e+01 1qndA d.106.1.1 40795 1ufzA 83 6.07e+01 a.5.9.1 107821 1rgyA 360 6.14e+01 e.3.1.1 97456 2fvhA 120 6.22e+01 2anyA 241 6.28e+01 1yn8A 59 6.28e+01 1vpqA 273 6.31e+01 2fu2A 102 6.35e+01 2bogX 286 6.35e+01 2ah6A 208 6.36e+01 1ul7A 102 6.45e+01 d.129.6.1 99540 1yoeA 322 6.51e+01 1yzmA 51 6.52e+01 1ecrA 309 6.53e+01 1ecrA e.2.1.1 42678 1szoA 257 6.53e+01 c.14.1.3 106164 1v9mA 323 6.55e+01 f.40.1.1 100543 1gtvA 214 6.61e+01 c.37.1.1 70537 1z0kB 69 6.62e+01 1q5zA 177 6.63e+01 a.196.1.1 95954 1vq0A 302 6.67e+01 1p8xA 344 6.73e+01 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 1cjxA 357 6.76e+01 1cjxA d.32.1.3,d.32.1.3 38516,38517 1z08A 170 6.83e+01 1g4iA 123 6.99e+01 1poa a.133.1.2 60241 1dofA 403 7.01e+01 1c3cA a.127.1.1 19429 1uliB 187 7.05e+01 d.17.4.4 107923 1v71A 323 7.08e+01 1ur1A 378 7.11e+01 c.1.8.3 99804 1k1fA 72 7.14e+01 a.147.1.1 68007 1dekA 241 7.18e+01 1dekA c.37.1.1 31842 1pufB 73 7.19e+01 a.4.1.1 95132 1fcyA 236 7.20e+01 2lbd a.123.1.1 19282 1x1rA 178 7.20e+01 2lisA 136 7.24e+01 1lis a.19.1.1 16405 1k7hA 476 7.32e+01 c.76.1.1 72101 1ja9A 274 7.44e+01 c.2.1.2 62817 1op4A 159 7.46e+01 b.1.6.1 93397 1fipA 98 7.47e+01 1fipA a.4.1.12 18980 1ia9A 280 7.53e+01 1ia9A d.144.1.5 62113 1nfp 228 7.54e+01 1nfp c.1.16.2 29555 1u5uA 374 7.57e+01 1eg3A 261 7.66e+01 1eg3A a.39.1.7,a.39.1.7,b.72.1.1 17376,17377,27805 1z2lA 423 7.74e+01 1sauA 115 7.88e+01 1qipA 183 8.07e+01 1qipA d.32.1.1 38470 1rfyA 102 8.12e+01 1adr 76 8.16e+01 1r69 a.35.1.2 17042 1fthA 122 8.19e+01 d.150.1.2 60028 1tazA 365 8.26e+01 a.211.1.2 106734 1u58A 253 8.27e+01 1uv7A 110 8.27e+01 d.67.4.1 100040 1zedA 484 8.29e+01 1ww9A 392 8.34e+01 1aoy 78 8.36e+01 1aoy a.4.5.3 16087 1tdzA 272 8.40e+01 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 1wk2A 121 8.40e+01 1oh0A 131 8.40e+01 d.17.4.3 87004 1d9cA 121 8.41e+01 1d9cA a.26.1.3 16901 1l6kA 77 8.47e+01 h.6.1.1 77724 1w2xA 758 8.47e+01 c.14.1.4,c.14.1.4 109134,109135 1sur 215 8.49e+01 1sur c.26.2.2 31620 2az0A 73 8.50e+01 1wcdJ 441 8.57e+01 2g7uA 257 8.65e+01 1a41 234 8.68e+01 1a41 d.163.1.2 42174 2aegA 268 8.73e+01 1s0yB 71 8.74e+01 d.80.1.1 98315 1lrzA 426 8.77e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1mai 131 8.82e+01 1mai b.55.1.1 26951 1lngA 87 8.82e+01 d.201.1.1 74045 1r0pA 312 8.82e+01 d.144.1.7 96734 1xn5A 146 8.83e+01 1gmjA 84 8.87e+01 h.4.8.1 65310 1sq5A 308 8.91e+01 c.37.1.6 105882 2gmyA 153 8.94e+01 1vknA 351 8.96e+01 c.2.1.3,d.81.1.1 108676,108677