# List of top-scoring protein chains for t04-100-30-bys-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 1xv2A 237 1.42e-06 2al3A 90 7.41e-02 1p5fA 189 1.20e-01 c.23.16.2 94142 1c1yB 77 2.37e-01 1c1yB d.15.1.5 37618 1wm3A 72 2.95e-01 1wrvA 308 3.53e-01 1kv0A 66 4.55e-01 g.3.7.1 91040 1l0gA 358 5.31e-01 e.3.1.1 73400 1pi4A 358 5.90e-01 e.3.1.1 94700 2ffyA 358 6.25e-01 1fsyA 358 6.26e-01 1gceA e.3.1.1 60016 1o51A 114 9.05e-01 d.58.5.4 92480 1i1kA 309 1.01e+00 1daaA e.17.1.1 61533 1iyeA 309 1.26e+00 e.17.1.1 83786 1nwbA 124 1.38e+00 b.124.1.1 86296 2gnxA 365 1.44e+00 1dmhA 311 1.88e+00 1dmhA b.3.6.1 22633 1ys7A 233 1.96e+00 1kgsA 225 2.01e+00 a.4.6.1,c.23.1.1 68596,68597 1euvB 86 2.45e+00 1a5r d.15.1.1 37598 1z4rA 168 2.57e+00 1gskA 513 2.65e+00 b.6.1.3,b.6.1.3,b.6.1.3 83314,83315,83316 1sn4A 64 2.74e+00 1aho g.3.7.1 44136 2eifA 136 3.07e+00 1bkb b.34.5.2,b.40.4.5 24607,25339 1ylxA 103 3.66e+00 1vmjA 151 4.16e+00 1omyA 65 4.30e+00 g.3.7.1 93354 2cvjA 180 4.31e+00 1fukA 165 4.44e+00 1fukA c.37.1.19 32409 1qc5A 192 4.95e+00 1aoxA c.62.1.1 34147 1w2wB 191 5.04e+00 1vpbA 451 5.05e+00 3daaA 277 5.24e+00 1daaA e.17.1.1 43272 1vr6A 350 5.66e+00 1upiA 225 5.71e+00 b.82.1.1 99757 1oa2A 218 5.80e+00 b.29.1.11 86721 1z9lA 128 5.91e+00 1kbjA 412 5.93e+00 c.1.4.1 72280 2axwA 134 5.97e+00 1zjjA 263 5.97e+00 1uv7A 110 6.09e+00 d.67.4.1 100040 2bh8A 101 6.17e+00 1h8vA 218 6.23e+00 2nlrA b.29.1.11 60795 1wcdJ 441 6.50e+00 1rkuA 206 6.64e+00 c.108.1.11 97627 1d4xG 126 6.96e+00 1d0nA d.109.1.1 59109 1dceA 567 7.42e+00 1dceA a.118.6.1,b.7.4.1,c.10.2.2 19191,23218,30867 1usgA 346 7.44e+00 c.93.1.1 99864 2f1rA 171 7.56e+00 1m1hA 248 7.61e+00 b.114.1.1,d.58.42.1 78415,78416 1xeuA 263 7.80e+00 2yhx 457 7.86e+00 2yhx i.12.1.1 46024 1zud1 251 7.97e+00 1qcwA 410 8.20e+00 1gox c.1.4.1 28622 1b56 135 8.75e+00 1hmt b.60.1.2 27183 1k2eA 156 9.21e+00 d.113.1.1 72010 2c6cA 707 9.56e+00 2lbp 346 9.60e+00 2liv c.93.1.1 35709 1vjoA 393 9.92e+00 c.67.1.3 100827 2cpgA 45 1.01e+01 2cpgA a.43.1.3 17455 2b99A 156 1.02e+01 1rgyA 360 1.08e+01 e.3.1.1 97456 1ydyA 356 1.09e+01 1ec7A 446 1.10e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1xsoA 150 1.16e+01 1mfmA b.1.8.1 22273 1lylA 504 1.16e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 1ezwA 349 1.17e+01 1ezwA c.1.16.3 29558 1wmqA 147 1.22e+01 2f96A 224 1.25e+01 1wn2A 121 1.25e+01 1idk 359 1.27e+01 1qcxA b.80.1.2 28025 1wl4A 397 1.28e+01 1jg1A 235 1.29e+01 c.66.1.7 66661 2f91A 237 1.29e+01 1mjc 69 1.29e+01 1mjc b.40.4.5 25319 1wpuA 147 1.31e+01 1ds1A 324 1.32e+01 1drtA b.82.2.2 28127 1t8qA 336 1.37e+01 c.1.18.3 106669 2b0vA 153 1.39e+01 1te5A 257 1.42e+01 d.153.1.1 106795 1vjqA 79 1.44e+01 k.43.1.1 100830 1vizA 240 1.45e+01 c.1.4.1 100784 1ig8A 486 1.47e+01 2yhx c.55.1.3,c.55.1.3 64746,64747 1yrgA 385 1.48e+01 1yrgA c.10.1.2 30854 1zo2A 129 1.49e+01 2fvvA 194 1.49e+01 1hskA 326 1.50e+01 2mbr d.145.1.2,d.146.1.1 61241,61242 2liv 344 1.55e+01 2liv c.93.1.1 35708 1l5pA 93 1.57e+01 d.15.4.1 73598 1vmfA 145 1.57e+01 1sdsA 117 1.61e+01 d.79.3.1 105439 1pm4A 119 1.63e+01 b.135.1.1 94891 1c3mA 147 1.63e+01 1jotA b.77.3.1 27983 1qkkA 155 1.64e+01 1dbwA c.23.1.1 31104 1e1oA 504 1.67e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1oewA 329 1.68e+01 b.50.1.2 86924 1vp4A 425 1.70e+01 1wvcA 259 1.71e+01 1t6kA 278 1.74e+01 1nm1G 125 1.74e+01 d.109.1.1 80653 1wruA 379 1.74e+01 1w8sA 263 1.80e+01 1q7sA 117 1.80e+01 c.131.1.1 96055 1vphA 149 1.81e+01 1ha3A 405 1.83e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1t3qA 168 1.85e+01 a.56.1.1,d.15.4.2 106367,106368 1pt6A 213 1.88e+01 c.62.1.1 95091 1xrtA 467 1.88e+01 1v6fA 151 1.94e+01 d.109.1.2 108395 2ftbA 125 1.94e+01 2cxhA 217 1.99e+01 1yrvA 169 2.00e+01 1gox 370 2.04e+01 1gox c.1.4.1 28607 1xbiA 120 2.06e+01 2bsdA 264 2.06e+01 1z15A 344 2.06e+01 1yr4A 237 2.06e+01 1pvmA 184 2.10e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1ny4A 82 2.11e+01 b.40.4.5 92316 1pmmA 466 2.16e+01 c.67.1.6 94901 1nbfA 353 2.17e+01 d.3.1.9 80387 1pg4A 652 2.19e+01 e.23.1.1 88067 1wfyA 104 2.20e+01 1nxjA 183 2.22e+01 c.8.7.1 86382 1xwtA 405 2.26e+01 1khdA 345 2.26e+01 a.46.2.1,c.27.1.1 77400,77401 1sffA 426 2.27e+01 c.67.1.4 105482 1cs1A 386 2.28e+01 1ibjA c.67.1.3 34399 2ca6A 386 2.33e+01 1vjkA 98 2.34e+01 d.15.3.1 108631 1y8qA 346 2.35e+01 1ysrA 150 2.36e+01 1yioA 208 2.41e+01 1ji1A 637 2.43e+01 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 1uh4A 637 2.44e+01 b.1.18.2,b.71.1.1,c.1.8.1 99391,99392,99393 1e9lA 377 2.46e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 1umgA 362 2.46e+01 d.280.1.1 107956 8prn 289 2.49e+01 3prn f.4.3.1 43767 1vloA 381 2.50e+01 b.44.2.1,d.250.1.1 108838,108839 1iz6A 138 2.50e+01 b.34.5.2,b.40.4.5 76976,76977 1w41A 101 2.55e+01 1gvfA 286 2.56e+01 c.1.10.2 70599 1j3wA 163 2.57e+01 d.110.7.1 90833 1bkb 136 2.57e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 1vl4A 447 2.57e+01 d.283.1.1 108718 1h75A 81 2.62e+01 1h75A c.47.1.1 60716 1ubi 76 2.63e+01 1ubi d.15.1.1 37584 2bzoB 79 2.66e+01 1i12A 160 2.66e+01 1i21A d.108.1.1 61515 1nzaA 103 2.68e+01 d.58.5.2 86444 2er7E 330 2.71e+01 2er7E b.50.1.2 26779 2a0iA 330 2.71e+01 1z6mA 175 2.71e+01 1ktgA 138 2.74e+01 d.113.1.1 72972 1h12A 405 2.76e+01 a.102.1.2 83447 1vcoA 550 2.79e+01 c.23.16.1,c.37.1.10 108508,108509 1d0cA 444 2.81e+01 d.174.1.1 64769 1ng4A 390 2.81e+01 c.3.1.2,d.16.1.3 85666,85667 1xw2A 405 2.85e+01 1rfs 139 2.85e+01 1rfs b.33.1.1 24434 2bkrB 77 2.87e+01 1ounA 127 2.93e+01 1ounA d.17.4.2 38090 1g0oA 283 2.94e+01 1ybvA c.2.1.2 60181 1ygtA 111 2.94e+01 1rlmA 271 2.96e+01 1yloA 348 2.97e+01 1nbcA 155 2.99e+01 1nbcA b.2.2.2 22390 1u1wA 298 3.04e+01 1xjcA 169 3.04e+01 2bjqA 345 3.08e+01 2a2cA 478 3.09e+01 1zruA 264 3.14e+01 1vljA 407 3.15e+01 e.22.1.2 108832 1gwmA 153 3.15e+01 b.18.1.19 83348 3pcgA 200 3.17e+01 3pchA b.3.6.1 22647 1tq8A 163 3.22e+01 c.26.2.4 107204 1r75A 141 3.41e+01 b.134.1.1 97189 2bb6A 414 3.49e+01 1x89A 178 3.55e+01 1vcdA 126 3.56e+01 2a2dA 478 3.58e+01 1m4tA 392 3.59e+01 c.95.1.1,c.95.1.1 78617,78618 1xezA 721 3.60e+01 1i1dA 161 3.61e+01 1i21A d.108.1.1 61526 1ryiA 382 3.62e+01 1m3kA 392 3.63e+01 c.95.1.1,c.95.1.1 78565,78566 2fp7B 172 3.68e+01 1krs 120 3.69e+01 1krs b.40.4.1 25256 1z4xA 532 3.75e+01 1u8sA 192 3.77e+01 d.58.18.5,d.58.18.5 107737,107738 1ydmA 187 3.79e+01 1xubA 298 3.81e+01 1l1jA 239 3.83e+01 b.47.1.1 84516 1naqA 112 3.83e+01 d.58.5.2 91761 1nv8A 284 3.86e+01 c.66.1.30 86224 1n7kA 234 3.86e+01 c.1.10.1 85374 2fp8A 322 3.87e+01 1ogwA 76 3.94e+01 d.15.1.1 87001 1d1vA 444 3.99e+01 1nseA d.174.1.1 59101 1x71A 178 4.02e+01 1t3tA 1303 4.03e+01 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 1wzaA 488 4.09e+01 1kwiA 101 4.11e+01 d.17.1.3 77564 1zq1A 438 4.17e+01 1vhzA 198 4.26e+01 d.113.1.1 100718 2bgcA 238 4.28e+01 2fbeA 201 4.30e+01 1n1tA 641 4.38e+01 b.29.1.15,b.68.1.1 79821,79822 1zpwX 90 4.40e+01 2f6uA 234 4.48e+01 1pcfA 66 4.53e+01 1pcfA d.18.1.1 38142 1zghA 260 4.54e+01 1uk8A 282 4.57e+01 c.69.1.10 107907 2fug1 438 4.57e+01 2c78A 405 4.59e+01 1iupA 282 4.59e+01 c.69.1.10 76815 1xg9A 260 4.66e+01 2be1A 339 4.71e+01 1qflA 389 4.72e+01 1afwA c.95.1.1,c.95.1.1 35908,35909 1ed5A 444 4.74e+01 1nseA d.174.1.1 42530 2g3aA 152 4.76e+01 1fb6A 105 4.77e+01 1thx c.47.1.1 32739 2fsqA 243 4.77e+01 1e25A 282 4.79e+01 1e25A e.3.1.1 42731 2cbiA 594 4.79e+01 1nbfD 76 4.80e+01 d.15.1.1 80390 1gheA 177 4.84e+01 d.108.1.1 76222 1wdaA 670 4.88e+01 b.2.9.1,b.6.1.6,d.126.1.5 109243,109244,109245 1fjgE 162 4.88e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 1v4sA 455 4.89e+01 c.55.1.3,c.55.1.3 100309,100310 1nrwA 288 4.89e+01 c.108.1.10 86128 1vlqA 337 4.90e+01 c.69.1.25 108848 1ohvA 472 4.91e+01 c.67.1.4 93031 1dciA 275 4.93e+01 1dciA c.14.1.3 30918 1w66A 232 4.94e+01 1q42A 201 4.95e+01 d.17.4.2 95776 1lvoA 302 4.99e+01 b.47.1.4 74284 1z4vA 532 5.00e+01 1vhsA 175 5.01e+01 d.108.1.1 100698 2ctc 307 5.02e+01 1aye c.56.5.1 33802 1d3bA 75 5.05e+01 1d3bA b.38.1.1 24798 2basA 431 5.06e+01 3prn 289 5.07e+01 3prn f.4.3.1 43761 1xngA 268 5.08e+01 1gefA 123 5.12e+01 1gefA c.52.1.18 60465 1xebA 150 5.13e+01 1ydwA 362 5.15e+01 1jmvA 141 5.16e+01 c.26.2.4 66897 1wlsA 328 5.18e+01 1o5kA 306 5.20e+01 c.1.10.1 92504 1bag 425 5.31e+01 1bag b.71.1.1,c.1.8.1 27720,28707 1djtA 64 5.32e+01 1aho g.3.7.1 44132 2aukA 190 5.33e+01 1vqzA 341 5.41e+01 1x8hA 228 5.43e+01 1rwhA 757 5.43e+01 a.102.3.2,b.24.1.1,b.30.5.2 97984,97985,97986 1ojxA 263 5.47e+01 c.1.10.1 93164 1uasA 362 5.49e+01 b.71.1.1,c.1.8.1 88388,88389 2ac4A 309 5.54e+01 1egwA 77 5.61e+01 1mnmA d.88.1.1 40234 1j71A 334 5.61e+01 1eagA b.50.1.2 62669 1aym1 285 5.63e+01 1aym1 2bklA 695 5.67e+01 1qqsA 174 5.69e+01 1nglA b.60.1.1 27143 1zkjA 359 5.70e+01 2gfaA 119 5.72e+01 1vf8A 377 5.74e+01 1mpxA 615 5.74e+01 b.18.1.13,c.69.1.21 85041,85042 1dozA 309 5.74e+01 1ak1 c.92.1.1 35592 1vjzA 341 5.81e+01 c.1.8.3 100838 1xwiA 322 5.82e+01 1wdkC 390 5.83e+01 c.95.1.1,c.95.1.1 109258,109259 1i60A 278 5.85e+01 c.1.15.4 71118 1hf2A 210 5.90e+01 1hf2A b.80.3.1,c.102.1.1 60992,60993 1zd3A 555 5.97e+01 1vi4A 174 5.97e+01 c.8.7.1 100731 1bzyA 217 5.97e+01 1qk3A c.61.1.1 34071 1gy6A 127 5.99e+01 d.17.4.2 70736 1yx1A 264 6.01e+01 1pi1A 185 6.02e+01 a.29.7.1 94699 1rkd 309 6.03e+01 1rkd c.72.1.1 34928 1ej0A 180 6.03e+01 1ej0A c.66.1.2 34179 1j31A 262 6.03e+01 d.160.1.2 90808 1exmA 405 6.04e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1l5wA 796 6.09e+01 c.87.1.4 73605 1siqA 392 6.10e+01 a.29.3.1,e.6.1.1 105585,105586 1md6A 154 6.14e+01 b.42.1.2 91242 1g291 372 6.15e+01 1g291 1uqrA 154 6.21e+01 c.23.13.1 99779 1l6rA 227 6.22e+01 c.108.1.10 77768 1ye8A 178 6.28e+01 1m4lA 307 6.30e+01 c.56.5.1 78604 1ekqA 272 6.35e+01 1c3qA c.72.1.2 34941 1zgzA 122 6.39e+01 2cvhA 220 6.41e+01 1bt0A 76 6.51e+01 1ubi d.15.1.1 37607 1et0A 269 6.51e+01 1et0A e.17.1.1 43289 1xruA 282 6.54e+01 2ex5A 207 6.54e+01 1h7mA 102 6.57e+01 d.79.3.1 83485 1zx2A 147 6.59e+01 1kzfA 230 6.62e+01 d.108.1.3 73354 2bltA 361 6.69e+01 1gceA e.3.1.1 42739 1ag6 99 6.69e+01 1plc b.6.1.1 22857 1gs5A 258 6.73e+01 c.73.1.2 70395 1e0gA 48 6.78e+01 1e01A d.7.1.1 37325 1f89A 291 6.86e+01 d.160.1.1 64988 1vrmA 325 6.88e+01 1jj2S 119 6.91e+01 1ffkQ b.34.5.1 63104 1s72T 120 6.92e+01 b.34.5.1 105339 1rlmB 271 6.98e+01 1jmcA 246 7.06e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 1y2qA 143 7.09e+01 1k20A 310 7.10e+01 c.107.1.1 68027 1utyA 187 7.15e+01 b.147.1.1 108036 1lktA 104 7.20e+01 1lktA b.90.1.1 28398 1nddA 76 7.20e+01 1ubi d.15.1.1 37599 1edqA 540 7.22e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1zdrA 164 7.27e+01 1pytA 94 7.34e+01 1pytA d.58.3.1 39064 1c44A 123 7.35e+01 1qndA d.106.1.1 40795 1e9mA 106 7.36e+01 1ayfA d.15.4.1 59397 1rdg 53 7.37e+01 1rb9 g.41.5.1 45221 1qjpA 171 7.38e+01 1bxwA f.4.1.1 43742 1qfhA 212 7.39e+01 1qfhA b.1.18.10,b.1.18.10 21893,21894 1mzbA 136 7.45e+01 a.4.5.42 91497 1o5zA 442 7.47e+01 c.59.1.2,c.72.2.2 92530,92531 1oalA 151 7.51e+01 b.1.8.1 86739 1jbwA 428 7.57e+01 c.59.1.2,c.72.2.2 62860,62861 1ub0A 258 7.61e+01 c.72.1.2 88394 1eudB 396 7.67e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 1dl5A 317 7.67e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 2etgA 296 7.76e+01 2ab0A 205 7.81e+01 1s1qA 145 7.83e+01 d.20.1.2 98351 1qwkA 317 7.92e+01 c.1.7.1 96482 1v5xA 203 7.95e+01 c.1.2.4 100377 1h65A 270 7.97e+01 c.37.1.8 65640 1r77A 103 7.97e+01 1l2lA 457 7.98e+01 c.72.1.3 77656 1m4iA 181 8.01e+01 d.108.1.1 74457 1rqlA 267 8.03e+01 c.108.1.3 97750 1j6zA 376 8.04e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 1hn2A 159 8.13e+01 b.60.1.1 65890 2azqA 311 8.19e+01 1pjpA 226 8.23e+01 5ptp b.47.1.2 26301 1z7gA 217 8.24e+01 1zbtA 371 8.25e+01 2gq1A 332 8.26e+01 1moq 368 8.35e+01 1moq c.80.1.1 35302 1rdfA 267 8.45e+01 c.108.1.3 104884 1jq5A 370 8.46e+01 e.22.1.2 67084 1y9wA 140 8.47e+01 1gt1A 159 8.53e+01 b.60.1.1 90515 2fcjA 119 8.58e+01 1pe9A 361 8.63e+01 b.80.1.1 94595 1tmxA 293 8.64e+01 1tuwA 109 8.66e+01 d.58.4.8 107346 1wzuA 300 8.69e+01 1w94A 156 8.72e+01 1lm4A 194 8.72e+01 d.167.1.1 84626 1je6A 275 8.78e+01 b.1.1.2,d.19.1.1 71638,71639 2bl1A 172 8.78e+01 2tnfA 156 8.79e+01 2tnfA b.22.1.1 23880 1xbsA 149 8.84e+01 1q7lA 198 8.85e+01 c.56.5.4 96044 1nn6A 228 8.95e+01 b.47.1.2 85893 1pz7A 204 8.96e+01 b.29.1.4 95405 1qstA 160 8.96e+01 1yghA d.108.1.1 40804