# 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.soe.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 3flpA 217 1.96e-04 1ms9A 648 4.51e-03 b.29.1.15,b.68.1.1 85088,85089 1n1tA 641 6.12e-03 b.29.1.15,b.68.1.1 79821,79822 3ginA 160 1.93e-02 2ebn 289 3.38e-02 2ebn 2ebnA 289 3.38e-02 c.1.8.5 28990 3hmyA 450 5.85e-02 2dpkA 152 7.17e-02 b.1.27.1 131616 1a8d 452 9.03e-02 1a8d 1a8dA 452 9.03e-02 b.29.1.6,b.42.4.2 24262,25607 2v73A 191 1.52e-01 3g3lA 327 1.92e-01 1z9lA 128 1.92e-01 3cihA 739 2.78e-01 2rr3A 130 3.43e-01 2w08A 204 6.83e-01 1sacA 204 6.84e-01 1sacA b.29.1.5 24237 1sh8A 154 8.58e-01 d.38.1.5 105549 1dypA 271 9.47e-01 1dypA b.29.1.2 24185 3juuA 280 1.23e+00 1gbg 214 1.23e+00 1axkA 1gbgA 214 1.23e+00 b.29.1.2 24171 3e7jA 749 1.34e+00 2fuqA 747 1.39e+00 2vw2A 697 1.43e+00 2ayh 214 1.65e+00 1axkA 2ayhA 214 1.65e+00 b.29.1.2 24172 2p5zX 491 1.66e+00 b.40.8.1,b.106.1.1,b.106.1.1 149263,149264,149265 1d2sA 170 1.80e+00 1d2sA b.29.1.4 24221 1r0mA 375 1.90e+00 c.1.11.2,d.54.1.1 104747,104748 1uaiA 224 2.10e+00 b.29.1.18 107761 2wanA 921 2.25e+00 2qvkA 192 2.27e+00 2oizA 361 2.43e+00 2jkbA 686 2.62e+00 2agyA 361 2.65e+00 3dsmA 328 2.68e+00 3hpyA 309 2.98e+00 1wubA 178 2.98e+00 b.61.6.1 114891 2vxrA 482 3.46e+00 2vu9A 444 3.91e+00 2eabA 899 3.99e+00 1cpnA 208 4.07e+00 b.29.1.2 24175 1f5fA 205 4.23e+00 1d2sA b.29.1.4 24222 1pbyB 337 4.32e+00 b.69.2.2 94422 1smd 496 4.38e+00 1smd 1smdA 496 4.40e+00 b.71.1.1,c.1.8.1 27768,28755 3fg3A 696 4.51e+00 3fdsC 249 4.62e+00 2sli 679 4.76e+00 2sli 2sliA 679 4.76e+00 b.29.1.9,b.68.1.1 24274,27611 3fg1A 696 5.07e+00 1uliB 187 5.17e+00 d.17.4.4 107923 3fg4A 696 5.29e+00 1cs6A 382 5.68e+00 1cs6A b.1.1.4,b.1.1.4,b.1.1.4,b.1.1.4 21760,21761,21762,21763 1epwA 1290 6.18e+00 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 2pltA 98 6.25e+00 b.6.1.1 22862 2wiiA 645 6.28e+00 3guuA 462 6.49e+00 3hxjA 330 6.58e+00 3dhpA 496 6.61e+00 b.71.1.1,c.1.8.1 157725,157726 2zpdA 190 6.79e+00 3g6jA 644 6.83e+00 1us8A 147 7.06e+00 c.37.1.12 99859 2hesX 330 7.20e+00 2veoA 441 7.35e+00 1nhcA 336 7.54e+00 b.80.1.3 91879 1n67A 359 7.91e+00 b.2.3.4,b.2.3.4 85354,85355 1orvA 728 7.91e+00 b.70.3.1,c.69.1.24 87354,87355 1sfp 114 8.03e+00 1sfp 1sfpA 114 8.03e+00 b.23.1.1 23895 2zxqA 1376 8.14e+00 2bibA 547 8.21e+00 b.109.1.1,d.157.1.8 128581,128582 1nwpA 128 8.34e+00 1nwpA b.6.1.1 23011 3ejkA 174 8.58e+00 1h6fA 193 9.27e+00 b.2.5.4 70901 1sfnA 246 9.64e+00 b.82.1.11 105496 1h09A 338 9.67e+00 b.109.1.1,c.1.8.8 83420,83421 3bp5B 202 9.73e+00 1ajkA 214 9.76e+00 1axkA b.29.1.2 24176 1f00I 282 1.03e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1l1nA 183 1.04e+01 b.47.1.4 73476 1gt1A 159 1.04e+01 b.60.1.1 90515 3ilfA 268 1.04e+01 3dcdA 307 1.06e+01 2j8gA 339 1.06e+01 b.109.1.1,c.1.8.8 147915,147916 2r39A 118 1.06e+01 1bkzA 135 1.07e+01 1a3k b.29.1.3 24202 2zb4A 357 1.08e+01 2hmaA 376 1.10e+01 1aohA 147 1.11e+01 1aohA b.2.2.2 22401 3hr9A 241 1.12e+01 1f06A 320 1.14e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 1r8gA 372 1.16e+01 d.128.1.3 104845 3bp6B 202 1.17e+01 2dc4A 165 1.18e+01 1qr4A 186 1.25e+01 1qr4B b.1.2.1,b.1.2.1 21986,21987 2p9wA 334 1.25e+01 1u00A 227 1.26e+01 a.8.4.1,b.130.1.1 112900,112901 1obpA 159 1.26e+01 1obpA b.60.1.1 27092 3ik5A 143 1.27e+01 3f85A 463 1.28e+01 1czfA 362 1.28e+01 1czfA b.80.1.3 28031 2b1xB 172 1.30e+01 d.17.4.4 127677 1t4wA 196 1.31e+01 b.2.5.2 106427 3ij8A 496 1.33e+01 2ix2A 249 1.36e+01 2iaaA 390 1.39e+01 2a15A 139 1.43e+01 d.17.4.3 125973 2jd4A 383 1.43e+01 1tt8A 164 1.45e+01 d.190.1.1 112635 1q7fA 286 1.46e+01 b.68.9.1 96036 2pm7B 297 1.50e+01 2nnuA 205 1.52e+01 b.91.1.1 138401 2gopA 347 1.54e+01 3jz7A 214 1.56e+01 2vngA 180 1.57e+01 b.18.1.33 153335 1s1qA 145 1.58e+01 d.20.1.2 98351 2ntiA 249 1.61e+01 2qzuA 491 1.62e+01 1qu0A 191 1.63e+01 1dykA b.29.1.4 24225 3emhA 318 1.63e+01 2jyaA 106 1.65e+01 2a6zA 222 1.69e+01 b.29.1.13 126319 1r17A 343 1.71e+01 b.2.3.4,b.2.3.4 96796,96797 2qtdA 105 1.74e+01 3h0oA 240 1.75e+01 1behA 187 1.75e+01 1a44 b.17.1.1 23700 2ft6A 124 1.76e+01 3f7xA 151 1.81e+01 2iqyA 190 1.82e+01 2v05A 311 1.84e+01 3l4cA 220 1.88e+01 1v7rA 186 1.96e+01 c.51.4.1 100482 1gu3A 149 1.96e+01 b.18.1.14 76350 2hlvA 160 1.97e+01 3holA 509 1.99e+01 3elqA 571 2.03e+01 2ag4A 164 2.03e+01 b.95.1.1 126717 1qhqA 140 2.05e+01 1qhqA b.6.1.1 63326 2bhoA 130 2.08e+01 1mpxA 615 2.09e+01 b.18.1.13,c.69.1.21 85041,85042 1n9eA 787 2.10e+01 b.30.2.1,d.17.2.1,d.17.2.1 91708,91709,91710 1wlnA 120 2.10e+01 b.26.1.2 121009 1tyjA 170 2.12e+01 b.2.2.2 119390 3immA 201 2.14e+01 1yhfA 115 2.18e+01 b.82.1.9 123176 1l2tA 235 2.19e+01 c.37.1.12 73514 3hx6A 570 2.35e+01 3isyA 120 2.39e+01 3eo6A 106 2.42e+01 3mepA 198 2.44e+01 3fsoA 123 2.46e+01 1p5vA 235 2.48e+01 b.1.11.1,b.7.2.1 87812,87813 1qtfA 246 2.49e+01 1agjA b.47.1.1 25830 1xgyH 219 2.50e+01 b.1.1.2 121985 3i6tA 381 2.50e+01 1icxA 155 2.53e+01 d.129.3.1 71191 2yz1A 120 2.54e+01 2a74A 643 2.55e+01 1ywsA 82 2.57e+01 g.41.17.1 124163 2d7tH 139 2.58e+01 2agcA 162 2.58e+01 1yoxA 250 2.58e+01 b.82.5.2 123789 2ca9A 148 2.58e+01 3ik2A 517 2.59e+01 1mveA 243 2.62e+01 b.29.1.2 85140 3hwjA 172 2.65e+01 1guuA 52 2.65e+01 a.4.1.3 83332 1f2tA 149 2.67e+01 1f2tA c.37.1.12 32373 1nqjA 119 2.81e+01 b.23.2.1 86031 1dueA 242 2.81e+01 b.47.1.1 76140 1epfA 191 2.82e+01 2ncm b.1.1.4,b.1.1.4 21694,21695 1upsA 420 2.83e+01 b.29.1.2,b.42.2.3 113394,113395 1aly 146 2.85e+01 1aly 1alyA 146 2.85e+01 b.22.1.1 23856 3g5bA 405 2.85e+01 2covD 104 2.87e+01 3dtdA 175 2.92e+01 2dvyA 226 2.93e+01 1f3uB 171 2.95e+01 1f3uB b.65.1.1 27525 1lmiA 131 2.96e+01 b.1.19.1 78098 1rl6A 177 2.97e+01 1rl6A d.141.1.1,d.141.1.1 41473,41474 1uwwA 191 2.98e+01 b.18.1.23 108079 2cw8A 537 2.98e+01 2a19A 175 3.02e+01 1hx0A 496 3.03e+01 b.71.1.1,c.1.8.1 61346,61347 2hdiA 639 3.04e+01 2iouG 535 3.05e+01 3cxgA 133 3.06e+01 2d5fA 493 3.08e+01 1g13A 162 3.09e+01 1g13A b.95.1.1 60194 1ew4A 106 3.10e+01 1ew4A d.82.2.1 40023 1zx8A 136 3.11e+01 b.62.1.3 125764 3grdA 134 3.11e+01 3kkfA 105 3.11e+01 3dxpA 359 3.15e+01 3cp3A 148 3.16e+01 2oitA 434 3.21e+01 2vovA 336 3.23e+01 1rsy 152 3.24e+01 1rsy 1rsyA 152 3.24e+01 b.7.1.2 23192 1agjA 242 3.27e+01 1agjA b.47.1.1 25827 1ifrA 121 3.33e+01 b.1.16.1 71203 3dohA 380 3.34e+01 1dboA 506 3.38e+01 1dbgA b.80.1.4 28034 1id2A 106 3.39e+01 1aac b.6.1.1 62288 3ixoA 99 3.42e+01 1dbgA 506 3.49e+01 1dbgA b.80.1.4 28033 2bcmA 165 3.54e+01 3eniA 365 3.54e+01 2o2gA 223 3.55e+01 3lsoA 489 3.58e+01 3llpA 493 3.59e+01 1ledA 243 3.66e+01 b.29.1.1 24039 3hbkA 245 3.66e+01 1od5A 492 3.67e+01 b.82.1.2,b.82.1.2 86832,86833 1led 243 3.70e+01 1led 3es4A 116 3.70e+01 1rjwA 339 3.71e+01 b.35.1.2,c.2.1.1 97582,97583 3eadA 137 3.76e+01 2w7qA 204 3.78e+01 2erfA 209 3.83e+01 b.29.1.4 132287 1pgs 314 3.84e+01 1pgs 1pgsA 314 3.84e+01 b.121.1.1,b.121.1.1 23653,23654 1rwiA 270 3.94e+01 b.68.9.1 97987 2cjtA 131 3.96e+01 b.7.1.1 130549 1deuA 277 3.99e+01 1theB d.3.1.1 37085 3a2sX 355 3.99e+01 1ibyA 112 4.05e+01 1ibzA b.6.1.4 62233 1hmt 132 4.06e+01 1hmt 1hmtA 132 4.06e+01 b.60.1.2 27169 3isrA 293 4.06e+01 3achA 203 4.07e+01 3if6A 266 4.09e+01 1lluA 342 4.17e+01 b.35.1.2,c.2.1.1 91064,91065 3hacA 728 4.19e+01 3cdxA 354 4.22e+01 3gzrA 146 4.22e+01 2wvbA 148 4.25e+01 2b0rA 202 4.27e+01 1xb3A 128 4.28e+01 b.6.1.1 115060 2cclA 158 4.34e+01 b.2.2.2 130248 2wnxA 170 4.35e+01 1ac5 483 4.36e+01 1ac5 1ac5A 483 4.36e+01 c.69.1.5 34653 1xvwA 160 4.38e+01 c.47.1.10 122387 2camA 127 4.42e+01 1swuA b.61.1.1 27407 3jurA 448 4.42e+01 3b9eA 584 4.42e+01 2qc5A 300 4.44e+01 2aanA 139 4.45e+01 3hdpA 133 4.51e+01 2jdaA 145 4.56e+01 3f4fA 167 4.68e+01 1t3uA 104 4.70e+01 d.244.1.1 99120 1ogaE 252 4.71e+01 b.1.1.1,b.1.1.2 86992,86993 1kmoA 774 4.73e+01 f.4.3.3 72753 2og4A 254 4.75e+01 2vhsA 217 4.76e+01 2h14A 317 4.78e+01 1ti6A 875 4.78e+01 b.52.2.2,c.81.1.1 106974,106975 3fvzA 329 4.79e+01 2zv3A 115 4.80e+01 2fhwA 24 4.87e+01 1o4yA 288 4.89e+01 b.29.1.2 92473 1jzgA 128 4.91e+01 b.6.1.1 67855 3bwuD 125 4.92e+01 b.167.1.1 155701 1xgsA 295 4.93e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 2r51A 340 4.95e+01 3kb5A 193 5.02e+01 1mbe 53 5.05e+01 1mbe 2uwaA 274 5.19e+01 1jtdB 273 5.19e+01 b.69.5.2 67265 1n26A 325 5.22e+01 b.1.1.4,b.1.2.1,b.1.2.1 79850,79851,79852 2uu8A 237 5.23e+01 b.29.1.1 152180 2bgzA 299 5.23e+01 1k38A 254 5.27e+01 e.3.1.1 84303 1nls 237 5.28e+01 1nls 1o75A 415 5.29e+01 b.1.20.1,b.1.20.1,b.120.1.1 81117,81118,81119 3bwzA 181 5.30e+01 3ghxA 179 5.30e+01 1a4aA 129 5.31e+01 1nwpA b.6.1.1 22907 3gr0A 197 5.34e+01 1s1dA 331 5.35e+01 b.67.3.1 98344 1goiA 499 5.36e+01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 2dejA 350 5.37e+01 2bpa2 175 5.42e+01 2bpa2 1rznA 205 5.46e+01 c.52.1.28 111981 1w7cA 747 5.56e+01 b.30.2.1,d.17.2.1,d.17.2.1 145814,145815,145816 1cuoA 129 5.62e+01 1nwpA b.6.1.1 23015 1bxoA 323 5.64e+01 2er7E b.50.1.2 26805 2ff7A 247 5.64e+01 c.37.1.12 133377 3fswA 128 5.67e+01 1urmA 172 5.68e+01 c.47.1.10 113413 1h9sA 140 5.68e+01 1b9mA b.40.6.2,b.40.6.2 60843,60844 2kriB 40 5.68e+01 1jyhA 157 5.69e+01 d.60.1.3 71956 1qznA 173 5.74e+01 b.2.2.2 104669 1yu2A 381 5.74e+01 b.163.1.1,d.169.1.8 124029,124030 1kzqA 289 5.81e+01 b.6.2.1,b.6.2.1 73374,73375 2oz4A 265 5.84e+01 b.1.1.3,b.1.1.4,b.1.1.4 149099,149100,149101 1dykA 394 5.86e+01 1dykA b.29.1.4,b.29.1.4 24223,24224 2eh6A 375 5.88e+01 1y43B 173 5.92e+01 2zwnA 339 5.93e+01 1yu1A 381 5.94e+01 b.163.1.1,d.169.1.8 124027,124028 3hbrA 265 5.97e+01 3g0bA 740 5.97e+01 3gm5A 159 6.02e+01 2bsjA 133 6.07e+01 2okmA 147 6.10e+01 2vlmE 244 6.13e+01 b.1.1.1,b.1.1.2 153293,153294 1xe7A 203 6.13e+01 b.82.1.16 115213 3e9tA 114 6.15e+01 2gnqA 336 6.18e+01 2o8lA 274 6.26e+01 b.47.1.1 138932 2wlgA 215 6.29e+01 3hvnA 508 6.31e+01 3lazA 99 6.37e+01 2b59A 187 6.42e+01 b.2.2.2 127879 3griA 424 6.47e+01 1yu4A 381 6.50e+01 b.163.1.1,d.169.1.8 124033,124034 2bshA 125 6.53e+01 3h6eA 482 6.54e+01 1w7jA 795 6.57e+01 b.34.3.1,c.37.1.9 120688,120689 3cuiA 315 6.63e+01 2blcA 238 6.63e+01 2klaA 106 6.63e+01 2ag9A 164 6.64e+01 1oflA 481 6.68e+01 b.80.1.4 103934 3ejjX 289 6.70e+01 1iznA 286 6.70e+01 e.43.1.1 83847 2wjrA 214 6.79e+01 3gh5A 525 6.80e+01 2qy1A 330 6.81e+01 2fwuA 157 6.82e+01 b.1.27.1 134262 3db5A 151 6.83e+01 1x9iA 302 6.86e+01 c.80.1.1 114997 3d01A 165 6.86e+01 1thjA 214 6.96e+01 1qreA b.81.1.5 28072 2pmkA 243 7.00e+01 c.37.1.12 149669 2g1lA 104 7.15e+01 b.26.1.2 134520 1nowA 507 7.18e+01 c.1.8.6,d.92.2.1 85936,85937 3i06A 215 7.19e+01 1mpyA 307 7.24e+01 1mpyA d.32.1.3,d.32.1.3 38508,38509 1w6nA 134 7.26e+01 b.29.1.3 114275 1vrmA 325 7.27e+01 d.96.2.1 120472 1gzwA 134 7.35e+01 b.29.1.3 90535 3jybA 145 7.37e+01 1ze3D 125 7.40e+01 b.167.1.1 124976 1z6bA 154 7.42e+01 d.38.1.6 124510 1o5uA 101 7.43e+01 b.82.1.8 92518 3e0gA 483 7.45e+01 1zv9A 172 7.46e+01 b.2.2.2 125700 1ywkA 289 7.47e+01 b.82.1.13 124155 2pooA 355 7.48e+01 1qlgA b.68.3.1 27626 1nbcA 155 7.48e+01 1nbcA b.2.2.2 22390 1yu3A 381 7.51e+01 b.163.1.1,d.169.1.8 124031,124032 1qd5A 275 7.51e+01 1qd5A f.4.2.1 43748 2hqsA 415 7.59e+01 b.68.4.1,c.51.2.1 136662,136663 2r58A 265 7.59e+01 1ri6A 343 7.59e+01 b.69.11.1 97503 3iutA 221 7.64e+01 1yuwA 554 7.67e+01 b.130.1.1,c.55.1.1,c.55.1.1 124070,124071,124072 3fm8A 124 7.67e+01 1iwlA 182 7.68e+01 b.125.1.1 83757 2a9mH 126 7.68e+01 1v70A 105 7.75e+01 b.82.1.9 113555 2d7eA 105 7.77e+01 1wriA 93 7.77e+01 d.15.4.1 114838 1wlgA 299 7.78e+01 b.152.1.1 114726 3inbA 466 7.78e+01 1fzoA 274 7.83e+01 1agdA b.1.1.2,d.19.1.1 60155,60156 1kn3A 183 7.84e+01 b.17.1.1 72764 2ez2A 456 7.85e+01 1l0qA 391 7.94e+01 b.1.3.1,b.69.2.3 77644,77645 3bx1C 181 7.96e+01 b.42.4.1 155704 1hfoA 113 7.97e+01 d.80.1.3 61006 1msc 129 7.98e+01 1msc 1mscA 129 7.98e+01 d.85.1.1 40039