# List of top-scoring protein chains for t04-100-30-dssp-ehl2-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 1mkmA 249 3.57e-26 a.4.5.33,d.110.2.2 79242,79243 1yspA 181 7.48e-25 2ia2A 265 8.17e-24 1td5A 202 2.20e-23 d.110.2.2 106767 1tf1A 198 2.96e-23 d.110.2.2 106826 2o99A 182 9.16e-23 d.110.2.2 138952 2g7uA 257 1.34e-22 1ysqA 193 2.91e-22 3bjnA 165 1.30e-18 2o0yA 260 5.29e-18 1mc0A 368 2.20e-02 d.110.2.1,d.110.2.1 78937,78938 2o28A 184 3.43e-01 2qybA 181 4.02e-01 2qmlA 198 8.74e-01 2qvpA 275 9.40e-01 2v0uA 146 9.78e-01 2oqrA 230 1.08e+00 1ykdA 398 1.14e+00 1id0A 152 1.15e+00 d.122.1.3 66111 2uv0E 175 1.77e+00 1n9lA 109 1.84e+00 d.110.3.6 85468 1j31A 262 1.99e+00 d.160.1.2 90808 1njrA 284 2.04e+00 c.50.1.2 103858 2ov5A 261 2.90e+00 2odsA 265 2.95e+00 1vs3A 249 3.11e+00 1ihoA 283 3.13e+00 1ihoA c.26.1.4 62390 1mjfA 281 3.27e+00 c.66.1.17 79198 1mx3A 347 3.33e+00 c.2.1.4,c.23.12.1 79638,79639 2a2lA 145 3.73e+00 d.110.9.1 126035 2dgdA 223 3.89e+00 2r00A 336 3.93e+00 2qmjA 870 4.07e+00 1o65A 246 4.18e+00 b.58.1.2 92544 1v5iB 76 4.38e+00 1hw1A 239 4.65e+00 1e2xA a.4.5.6,a.78.1.1 16111,18441 2coiA 386 5.19e+00 2pb2A 420 5.48e+00 1hyeA 313 5.81e+00 2cmd c.2.1.5,d.162.1.1 61400,61401 1j6wA 175 5.94e+00 1j98A d.185.1.2 62663 2z5bB 179 6.30e+00 2j6vA 301 6.51e+00 2oo3A 283 6.73e+00 1rsgA 516 7.42e+00 1f2tB 148 7.83e+00 1f2tB 1dtdA 303 7.97e+00 1aye c.56.5.1 33823 2qubA 615 8.42e+00 1s28A 132 8.52e+00 d.198.1.1 105223 1e0tA 470 8.77e+00 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 2rhmA 193 9.38e+00 1bavA 309 9.55e+00 1aye c.56.5.1 33806 1nxiA 132 9.86e+00 d.58.47.1 86381 2iutA 574 9.93e+00 1te5A 257 1.09e+01 d.153.1.1 106795 1zu0A 529 1.10e+01 2fmlA 273 1.11e+01 a.4.5.68,d.113.1.6 133778,133779 2q3uA 383 1.13e+01 d.126.1.6 139809 2icyA 469 1.14e+01 b.81.1.4,c.68.1.5 137257,137258 1q7lA 198 1.15e+01 c.56.5.4 96044 1vkpA 383 1.16e+01 d.126.1.6 108686 2q09A 416 1.23e+01 1vljA 407 1.23e+01 e.22.1.2 108832 1n4kA 381 1.23e+01 a.118.22.1,b.42.6.1 79992,79993 1f60A 458 1.26e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1louA 101 1.27e+01 1ris d.58.14.1 39323 2pd8A 149 1.27e+01 1ffyA 917 1.29e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 2ctc 307 1.30e+01 1aye 2j5aA 110 1.33e+01 2gb3A 409 1.34e+01 c.67.1.1 134903 1m4lA 307 1.34e+01 c.56.5.1 78604 3c0wA 235 1.34e+01 1r7mA 235 1.35e+01 d.95.2.1,d.95.2.1 111713,111714 2reeA 224 1.36e+01 1xtmA 175 1.40e+01 1pvmA 184 1.43e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 2fv7A 331 1.45e+01 c.72.1.1 134197 1ko7A 314 1.46e+01 c.98.2.1,c.91.1.2 72797,72798 1ve3A 227 1.46e+01 c.66.1.43 120010 1p2fA 220 1.47e+01 a.4.6.1,c.23.1.1 87720,87721 2pdrA 149 1.51e+01 1vfvA 366 1.57e+01 c.37.1.9 108592 1xtlA 175 1.60e+01 1erw 105 1.61e+01 1erv 1erv 105 1.63e+01 1erv 1q2lA 939 1.64e+01 d.185.1.1,d.185.1.1,d.185.1.1,d.185.1.1 118731,118732,118733,118734 2b18A 164 1.66e+01 3c19A 186 1.68e+01 1y9kA 157 1.69e+01 d.108.1.1 122779 1p3dA 475 1.71e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 2o1sA 621 1.73e+01 1gx1A 160 1.74e+01 d.79.5.1 70675 1s4iA 175 1.77e+01 2bjoA 136 1.80e+01 1a8qA 274 1.81e+01 c.69.1.12 34702 3caxA 369 1.82e+01 1yvoA 172 1.83e+01 d.108.1.1 124106 1rscI 111 1.88e+01 d.73.1.1 118620 1i6iA 366 1.93e+01 1bg2 c.37.1.9 61844 1f5mA 180 1.96e+01 1f5mB d.110.2.1 40895 2ae6A 166 1.97e+01 d.108.1.1 126600 2dwcA 433 2.02e+01 3cucA 291 2.02e+01 2r9qA 370 2.02e+01 1vhmA 195 2.04e+01 d.110.2.1 100691 2d4pA 141 2.06e+01 2qdfA 335 2.12e+01 1z90A 469 2.20e+01 b.81.1.4,c.68.1.5 124732,124733 1bsgA 266 2.22e+01 e.3.1.1 42729 1m4yA 171 2.24e+01 d.153.1.4 84802 2cxcA 144 2.24e+01 1aiu 105 2.27e+01 1erv 1q2yA 140 2.27e+01 d.108.1.1 95655 2ffeA 311 2.30e+01 c.143.1.1 133381 2j6gA 266 2.31e+01 2q81A 119 2.33e+01 1ylkA 172 2.33e+01 1tljA 213 2.33e+01 d.282.1.1 107126 2yvyA 278 2.34e+01 2vbuA 136 2.35e+01 2ajrA 331 2.38e+01 c.72.1.1 126892 1o7eA 276 2.41e+01 e.3.1.1 92622 1jc4A 148 2.42e+01 1jc4A d.32.1.4 62863 1iukA 140 2.42e+01 c.2.1.8 83712 2i79A 172 2.44e+01 2dfaA 250 2.51e+01 c.6.2.5 131469 1rfmA 344 2.53e+01 c.122.1.1 97385 2fl4A 149 2.60e+01 d.108.1.1 133706 2z26A 347 2.62e+01 2o0bA 450 2.62e+01 1wwzA 159 2.63e+01 d.108.1.1 121380 2aaoA 166 2.68e+01 2ifqA 105 2.69e+01 c.47.1.1 137343 1y56A 493 2.73e+01 2q66A 525 2.76e+01 1ei5A 520 2.77e+01 1ei5A b.61.3.1,b.61.3.1,e.3.1.1 27418,27419,42772 2bjbA 462 2.78e+01 2absA 383 2.83e+01 c.72.1.1 126534 1yizA 429 2.83e+01 c.67.1.1 123375 2cxaA 256 2.86e+01 d.108.1.6 130993 1pc6A 146 2.87e+01 d.262.1.1 94430 1s3zA 165 2.90e+01 d.108.1.1 105250 2r7hA 177 2.91e+01 1gtmA 419 2.94e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 2dy1A 665 2.96e+01 1wu7A 434 2.96e+01 c.51.1.1,d.104.1.1 121275,121276 2zf5O 497 2.96e+01 2r6uA 148 2.98e+01 2a2cA 478 3.02e+01 2pjhB 193 3.04e+01 1yw5A 177 3.12e+01 1iurA 88 3.12e+01 a.2.3.1 90704 1ufoA 238 3.15e+01 c.69.1.27 99344 2c5sA 413 3.18e+01 c.26.2.6,d.308.1.1 129950,129951 3bh1A 507 3.18e+01 3c6kA 381 3.19e+01 2qfmA 364 3.20e+01 2bo4A 397 3.20e+01 c.68.1.18 128869 2fwtA 125 3.22e+01 2d4eA 515 3.24e+01 1rblI 109 3.28e+01 d.73.1.1 118599 1cliA 345 3.29e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 2atrA 138 3.30e+01 d.108.1.1 127305 2ov9A 216 3.31e+01 1r13A 148 3.31e+01 d.169.1.1,h.1.1.1 96782,96783 1ieaB 228 3.32e+01 1iakB b.1.1.2,d.19.1.1 21632,38206 2e4sA 189 3.39e+01 1jh3A 107 3.40e+01 d.66.1.4 71661 1qtqA 553 3.41e+01 1gtrA b.53.1.2,c.26.1.1 26940,31579 2yrrA 353 3.41e+01 1h1yA 228 3.47e+01 c.1.2.2 76506 2o3bB 136 3.48e+01 d.221.1.1 138902 2qe6A 274 3.49e+01 1vr4A 103 3.51e+01 d.230.5.1 120432 2oo6A 409 3.52e+01 2oqgA 114 3.53e+01 2gx5A 170 3.58e+01 1svdM 110 3.64e+01 d.73.1.1 119059 1t0yA 122 3.66e+01 d.15.1.1 99066 2eg6A 347 3.67e+01 2f6uA 234 3.70e+01 c.1.4.1 133061 8rucI 123 3.74e+01 1rboC d.73.1.1 39629 2burB 241 3.75e+01 b.3.6.1 129228 3cmnA 372 3.75e+01 2j66A 428 3.78e+01 1n00A 321 3.78e+01 a.65.1.1 85241 1cqmA 101 3.82e+01 1ris d.58.14.1 39321 2ckfA 454 3.91e+01 2nwhA 317 3.92e+01 2i5nM 323 3.96e+01 f.26.1.1 137067 1sqiA 393 3.96e+01 d.32.1.3,d.32.1.3 105914,105915 3brqA 296 3.97e+01 1mnmA 100 3.99e+01 1mnmA d.88.1.1 40232 2q2gA 180 3.99e+01 1m7yA 435 4.02e+01 c.67.1.4 78761 2avxA 171 4.03e+01 1v33A 366 4.04e+01 d.264.1.1 100278 1wlxA 129 4.12e+01 2pn0A 141 4.13e+01 2a6hD 1524 4.16e+01 e.29.1.2 126265 2v7pA 310 4.17e+01 1kgdA 180 4.17e+01 c.37.1.1 68582 1ym5A 300 4.21e+01 1qmhA 347 4.23e+01 1qmhA c.47.2.1,d.68.2.1 33082,39568 1auvA 311 4.25e+01 1auvA c.30.1.5,d.142.1.3 31723,41558 1bg2 325 4.25e+01 1bg2 1bg2A 325 4.25e+01 c.37.1.9 32189 2d1hA 109 4.29e+01 a.4.5.50 131125 2ajgA 196 4.31e+01 1r0vA 305 4.31e+01 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 1h12A 405 4.35e+01 a.102.1.2 83447 2oikA 154 4.36e+01 3b8xA 390 4.47e+01 1yvkA 163 4.47e+01 d.108.1.1 124101 3buxB 329 4.51e+01 1vi9A 299 4.52e+01 c.72.1.5 100750 2r6oA 294 4.53e+01 1vizA 240 4.54e+01 c.1.4.1 100784 1v58A 241 4.56e+01 c.47.1.9,d.17.3.1 108371,108372 2ot3A 274 4.57e+01 a.222.1.1 139311 2bvcA 486 4.57e+01 d.15.9.1,d.128.1.1 129243,129244 2cblA 305 4.60e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17380,17774,40528 2d13A 227 4.64e+01 c.26.2.1 131121 1b8gA 429 4.66e+01 1b8gA c.67.1.4 34499 2booA 247 4.68e+01 1fmjA 351 4.68e+01 c.37.1.5 59879 1ynpA 317 4.68e+01 2c5uA 375 4.68e+01 1fa0A 537 4.69e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 2vfjA 366 4.70e+01 3rubS 123 4.72e+01 1rboC d.73.1.1 39616 1ji7A 89 4.73e+01 a.60.1.1 71682 2q0oA 236 4.88e+01 1vchA 175 4.90e+01 c.61.1.1 119980 1xw2A 405 4.92e+01 a.102.1.2 122389 1yvhA 329 4.94e+01 a.39.1.7,a.48.1.1,d.93.1.1 124096,124097,124098 1g71A 347 4.95e+01 1g71A d.264.1.1 43268 1u7bA 261 4.98e+01 d.131.1.2,d.131.1.2 113083,113084 2hgcA 102 4.99e+01 2f57A 317 5.02e+01 1xw8A 252 5.06e+01 c.6.2.5 116111 1k3eA 156 5.06e+01 d.198.1.1 68103 2dplA 308 5.07e+01 1yexA 186 5.08e+01 c.47.1.10 123021 1qgvA 142 5.09e+01 1qgvA c.47.1.8 33056 1q8rA 120 5.10e+01 d.79.6.1 96225 1x4pA 66 5.14e+01 2oynA 146 5.14e+01 2v2gA 233 5.18e+01 2ouxA 286 5.18e+01 2oc6A 124 5.21e+01 1xwtA 405 5.21e+01 a.102.1.2 122410 3ciwA 348 5.22e+01 1r4vA 171 5.22e+01 a.22.1.4 97049 1fbnA 230 5.27e+01 1fbnA c.66.1.3 34181 1xebA 150 5.27e+01 d.108.1.1 115219 2z8xA 617 5.28e+01 2ezhA 75 5.30e+01 a.4.1.2 16029 1g8sA 230 5.31e+01 c.66.1.3 90507 2r1iA 172 5.33e+01 1j7lA 264 5.38e+01 d.144.1.6 62697 1v8fA 276 5.43e+01 c.26.1.4 100503 1yyvA 131 5.49e+01 a.4.5.69 124254 1tbxA 99 5.50e+01 a.4.5.48 106748 1seiA 130 5.52e+01 1seiA d.140.1.1 41463 2oztA 332 5.53e+01 1rj9A 304 5.54e+01 a.24.13.1,c.37.1.10 97553,97554 2v7fA 150 5.55e+01 1poc 134 5.55e+01 1poc 1pocA 134 5.55e+01 a.133.1.1 19513 2j7vA 298 5.58e+01 1iv3A 152 5.59e+01 d.79.5.1 76828 1w5dA 462 5.61e+01 e.3.1.3 120642 1yr0A 175 5.62e+01 d.108.1.1 123905 2hhpA 530 5.65e+01 a.160.1.1,d.218.1.3,d.58.16.1 136503,136504,136505 1j5yA 187 5.68e+01 a.4.5.1,d.94.2.1 71592,71593 1yobA 179 5.73e+01 c.23.5.1 123776 2d0iA 333 5.73e+01 2d59A 144 5.74e+01 c.2.1.8 131266 1vlmA 219 5.75e+01 c.66.1.41 108836 2ob0A 170 5.76e+01 2hp0A 466 5.77e+01 2gruA 368 5.81e+01 1k6zA 141 5.82e+01 d.198.1.1 68247 2qv5A 261 5.83e+01 2byjA 439 5.84e+01 c.67.1.4 129483 2j9oA 298 5.84e+01 2fldA 165 5.86e+01 1gteA 1025 5.87e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70440,70441,70442,70443,70444 1ir21 140 5.87e+01 1t07A 94 5.87e+01 d.279.1.1 106196 2b8tA 223 5.88e+01 c.37.1.24,g.39.1.14 128109,128110 2buwB 241 5.89e+01 1l2tA 235 5.89e+01 c.37.1.12 73514 2a1hA 365 5.95e+01 e.17.1.1 125997 2j0iA 303 5.95e+01 1j79A 347 5.96e+01 1j79A c.1.9.4 62675 1ohtA 215 5.98e+01 d.118.1.1 87036 2euaA 431 6.00e+01 d.161.1.1 132380 1qd1A 325 6.01e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1ttzA 87 6.01e+01 c.47.1.1 107309 1vhoA 346 6.04e+01 b.49.3.1,c.56.5.4 100694,100695 2afrA 231 6.07e+01 2qr6A 393 6.07e+01 1uxjA 309 6.09e+01 c.2.1.5,d.162.1.1 108112,108113 1jyaA 130 6.11e+01 d.198.1.1 67453 1y9uA 323 6.16e+01 c.94.1.1 116594 1lwdA 413 6.21e+01 c.77.1.1 78265 2ebbA 101 6.29e+01 2hpgA 327 6.31e+01 1td2A 287 6.33e+01 c.72.1.5 106765 2p24B 259 6.38e+01 2cy2A 174 6.40e+01 d.108.1.1 131016 1yj7A 171 6.43e+01 2r98A 456 6.45e+01 1k0eA 453 6.46e+01 d.161.1.1 67938 1l1lA 739 6.56e+01 c.7.1.4 73470 2ge3A 170 6.56e+01 d.108.1.1 135044 2j8mA 172 6.58e+01 2bylA 439 6.61e+01 c.67.1.4 129490 1gk8A 475 6.61e+01 c.1.14.1,d.58.9.1 65234,65235 2ddzA 190 6.62e+01 1dp4A 435 6.68e+01 1dp4A c.93.1.1 35710 1z91A 147 6.68e+01 a.4.5.28 124736 2hdwA 367 6.69e+01 1kpf 126 6.70e+01 1kpf 1mxgA 435 6.72e+01 b.71.1.1,c.1.8.1 85193,85194 1kpfA 125 6.74e+01 d.13.1.1 37507 1ehiA 377 6.76e+01 1iow c.30.1.2,d.142.1.1 31716,41484 1ejdA 419 6.80e+01 1uae d.68.2.2 39576 3bczA 293 6.80e+01 2bmoA 447 6.83e+01 b.33.1.2,d.129.3.3 128804,128805 1zotA 358 6.84e+01 1r5jA 337 6.86e+01 c.77.1.5 97097 1ud9A 245 6.88e+01 d.131.1.2,d.131.1.2 107768,107769 2g4rA 160 6.89e+01 1q9uA 130 6.94e+01 d.129.7.1 96314 1jhsA 188 6.97e+01 d.107.1.1 84172 1r1hA 696 6.98e+01 d.92.1.4 104756 1hh1A 143 6.99e+01 1gefA c.52.1.18 61036 1yrtA 364 7.00e+01 1eq6A 189 7.09e+01 1eq6A d.107.1.1 40796 1lml 478 7.10e+01 1lml 1lmlA 478 7.10e+01 d.92.1.3 40295 2fxtA 192 7.14e+01 2iwtA 125 7.16e+01 1dmtA 696 7.21e+01 1dmtA d.92.1.4 40296 1qo8A 566 7.21e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19696,30433,42316 1vhyA 257 7.23e+01 b.122.1.2,c.116.1.5 100714,100715 1e3mA 800 7.23e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19075,32389,33746,39747 1v7pC 200 7.24e+01 c.62.1.1 108408 2cy8A 453 7.28e+01 2hstA 143 7.32e+01 1g8yA 279 7.38e+01 1g8yA c.37.1.11 32302 1fb6A 105 7.41e+01 1thx c.47.1.1 32739 1mvwB 145 7.42e+01 i.15.1.1 79524 1ow1A 195 7.42e+01 b.131.1.3 93625 1zj8A 566 7.43e+01 1rg9A 383 7.45e+01 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1qq9A 284 7.45e+01 1xjo c.56.5.4 33841 1sqhA 312 7.46e+01 d.108.1.5 98966 2zmfA 189 7.47e+01 2d5cA 263 7.62e+01 1mpgA 282 7.63e+01 1mpgA a.96.1.3,d.129.1.2 18747,41296 1x6mA 196 7.66e+01 b.88.1.4 114920 1gk8I 140 7.68e+01 d.73.1.1 65242 1zbsA 291 7.69e+01 c.55.1.5,c.55.1.5 124870,124871 1i1dA 161 7.75e+01 1i21A d.108.1.1 61526 2gauA 232 7.81e+01 a.4.5.4,b.82.3.2 134894,134895 1nlfA 279 7.81e+01 c.37.1.11 85850 1azwA 313 7.82e+01 1qtrA c.69.1.7 34658 2eklA 313 7.84e+01 3cblA 377 7.85e+01 1oz9A 150 7.95e+01 d.92.1.15 93808 1ass 159 7.97e+01 1a6dA 1assA 159 7.97e+01 c.8.5.2 30818