# List of top-scoring protein chains for t06-100-30-str2-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 2f4qA 346 8.37e-02 1lktA 104 5.33e-01 1lktA b.90.1.1 28398 1m93C 41 7.68e-01 2a2pA 129 1.25e+00 1yaxA 153 1.73e+00 2c3vA 102 1.95e+00 1cqyA 99 2.30e+00 1b9zA b.3.1.1 22527 1zkdA 387 2.37e+00 1kllA 130 2.39e+00 d.32.1.2 72720 1tp6A 128 2.61e+00 d.17.4.12 107184 1xfsA 178 2.80e+00 d.129.3.5 109589 1qhoA 686 2.86e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1iscA 192 3.16e+00 1avmA a.2.11.1,d.44.1.1 15733,38726 1vq2A 193 3.76e+00 1p2hA 571 3.88e+00 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 3nul 130 4.10e+00 3nul d.110.1.1 40891 2fa8A 105 4.22e+00 2basA 431 5.03e+00 1qmvA 197 5.18e+00 1qq2A c.47.1.10 33066 1ffyA 917 5.60e+00 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 2gcc 70 5.76e+00 2gcc d.10.1.2 37484 1w9hA 427 5.81e+00 1vjfA 180 5.83e+00 d.116.1.1 100809 1ui0A 205 5.94e+00 c.18.1.2 99411 2fh5A 185 6.38e+00 1dcjA 81 6.45e+00 1dcjA d.68.3.3 59115 1u58A 253 6.45e+00 1l6rA 227 6.49e+00 c.108.1.10 77768 1iow 306 6.62e+00 1iow c.30.1.2,d.142.1.1 31713,41481 2cr5A 109 6.94e+00 3ezmA 101 7.04e+00 3ezmA b.89.1.1 28395 1e2wA 251 7.20e+00 1hcz b.2.6.1,b.84.2.2 22466,28252 2b5nA 323 7.35e+00 1vemA 516 7.49e+00 1vr9A 213 7.54e+00 1v74A 107 7.57e+00 d.243.1.1 100442 1a8q 274 7.67e+00 1brt c.69.1.12 34702 1xc3A 302 8.00e+00 1bywA 110 8.22e+00 1bywA d.110.3.6 40912 1lwdA 413 8.25e+00 c.77.1.1 78265 1h6hA 143 8.31e+00 d.189.1.1 65681 1mtpB 43 8.91e+00 2fq9A 225 8.98e+00 1rewC 135 9.16e+00 g.7.1.3 97336 1q0qA 406 9.82e+00 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1tyv 542 9.84e+00 1tyv b.80.1.6 28038 2ap1A 327 1.00e+01 2dg5B 190 1.01e+01 1uwzA 136 1.01e+01 c.97.1.1 108081 16pk 415 1.03e+01 16pk c.86.1.1 35454 2a25A 193 1.03e+01 1vcdA 126 1.05e+01 1yx1A 264 1.06e+01 1cdq 77 1.07e+01 1cds g.7.1.3 44459 1sqeA 109 1.10e+01 d.58.4.5 105908 1am2 199 1.12e+01 1am2 b.86.1.2 28381 1z0wA 207 1.13e+01 1pm1X 180 1.21e+01 b.60.1.1 104189 1huxA 270 1.23e+01 1huxA c.55.1.5 61278 2be1A 339 1.23e+01 1p6oA 161 1.24e+01 c.97.1.2 94185 1tqzA 133 1.25e+01 1w6sA 599 1.25e+01 1uhvA 500 1.26e+01 b.71.1.2,c.1.8.3 99402,99403 1vjlA 164 1.26e+01 d.257.1.1 100822 1c96A 753 1.30e+01 1amj c.8.2.1,c.83.1.1 30727,35403 1vetA 124 1.34e+01 d.110.7.1 108553 1w4tA 299 1.36e+01 1wrvA 308 1.42e+01 2bf6A 449 1.47e+01 1h9oA 112 1.47e+01 1qadA d.93.1.1 60837 1qauA 112 1.51e+01 1qauA b.36.1.1 24779 1llnA 262 1.52e+01 d.165.1.1 84625 1um5H 217 1.55e+01 1xrkA 124 1.56e+01 1pjxA 314 1.59e+01 b.68.6.1 104167 1rvkA 382 1.60e+01 c.1.11.2,d.54.1.1 97928,97929 1zndA 174 1.61e+01 1pylA 97 1.63e+01 d.1.1.2 104391 2dg5A 366 1.69e+01 1xvqA 175 1.70e+01 1qy1A 174 1.70e+01 b.60.1.1 96568 1bupA 386 1.75e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 2dcnA 311 1.79e+01 2bgiA 272 1.79e+01 1uesA 191 1.80e+01 a.2.11.1,d.44.1.1 107798,107799 1w44A 331 1.80e+01 1nrlA 316 1.81e+01 a.123.1.1 92091 1bu6O 501 1.82e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1voqa 90 1.86e+01 1pvmA 184 1.86e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1txkA 498 1.89e+01 b.1.18.2,b.30.5.9 107425,107426 1bx1A 314 1.89e+01 1fnc b.43.4.2,c.25.1.1 25629,31519 1cv8 174 1.93e+01 1cv8 d.3.1.1 37089 1hjrA 158 1.94e+01 1hjrA c.55.3.6 33727 1hd2A 161 1.95e+01 c.47.1.10 60962 1ri9A 102 1.96e+01 b.34.2.1 97506 1mqeA 207 1.96e+01 d.113.1.1 91394 1vqoS 85 1.96e+01 1xqaA 113 1.98e+01 2gaiA 633 2.00e+01 2a6aA 218 2.01e+01 1fnd 314 2.02e+01 1fnc b.43.4.2,c.25.1.1 25626,31516 1y9wA 140 2.08e+01 1xvsA 126 2.08e+01 2bjfA 329 2.15e+01 1vjvA 415 2.15e+01 d.3.1.9 108632 1xxqA 161 2.20e+01 1p3dA 475 2.31e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1lf6A 684 2.40e+01 a.102.1.5,b.30.5.5 77918,77919 2fv7A 331 2.42e+01 1c44A 123 2.44e+01 1qndA d.106.1.1 40795 1vkcA 158 2.49e+01 1b9wA 89 2.49e+01 1b9wA g.3.11.4,g.3.11.4 44334,44335 1k8kA 418 2.55e+01 c.55.1.1,c.55.1.1 68305,68306 1pufB 73 2.57e+01 a.4.1.1 95132 1y88A 199 2.59e+01 1lfdA 87 2.60e+01 1lfdA d.15.1.5 37622 1lrzA 426 2.62e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 2c2aA 258 2.64e+01 1xkiA 162 2.66e+01 1j79A 347 2.68e+01 1j79A c.1.9.4 62675 1htrB 329 2.69e+01 1smrA 1gpeA 587 2.70e+01 1gpeA c.3.1.2,d.16.1.1 30387,37951 2gfoA 396 2.70e+01 1x6oA 174 2.71e+01 b.34.5.2,b.40.4.5 109493,109494 1k7jA 206 2.73e+01 d.115.1.1 72103 2fhxA 246 2.75e+01 1b8aA 438 2.76e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1lq9A 112 2.80e+01 d.58.4.3 78129 1zbsA 291 2.81e+01 1xniA 118 2.82e+01 1fjgP 88 2.82e+01 1emwA d.27.1.1 38444 1zg2A 107 2.85e+01 1lgpA 116 2.85e+01 b.26.1.2 73890 1u14A 172 2.88e+01 c.51.4.3 107579 2bs3A 656 2.89e+01 1bco 327 2.91e+01 1bco b.48.1.1,c.55.3.3 26431,33676 2a15A 139 2.94e+01 1a9xA 1058 3.01e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1wi1A 126 3.01e+01 1n1tA 641 3.07e+01 b.29.1.15,b.68.1.1 79821,79822 1ttzA 87 3.07e+01 c.47.1.1 107309 1te7A 103 3.09e+01 1cr5A 189 3.11e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1sc6A 404 3.15e+01 1qqp1 213 3.18e+01 1qqp1 2fikA 287 3.19e+01 1ijqA 316 3.20e+01 1ijqA b.68.5.1,g.3.11.1 62506,62507 1z2mA 155 3.21e+01 1zceA 155 3.24e+01 1jofA 365 3.30e+01 b.69.10.1 71775 1r77A 103 3.43e+01 1wdvA 152 3.48e+01 1j5pA 253 3.49e+01 d.81.1.3,c.2.1.3 71577,83092 1s68A 249 3.49e+01 d.142.2.4 98591 2gupA 292 3.51e+01 1ro5A 201 3.56e+01 d.108.1.3 105023 2f9zC 159 3.60e+01 1xkgA 312 3.60e+01 1rk6A 496 3.68e+01 b.92.1.6,b.92.1.6,c.1.9.11 97599,97600,97601 1qveA 126 3.69e+01 d.24.1.1 104594 1wm3A 72 3.70e+01 1v8hA 107 3.70e+01 1o7zA 77 3.70e+01 d.9.1.1 86660 1f00I 282 3.72e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 2cl1A 279 3.85e+01 1sq9A 397 3.87e+01 b.69.4.1 105889 1cs0A 1073 4.01e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1or0B 528 4.02e+01 1qg7A 67 4.04e+01 1a15A d.9.1.1 37449 1n4wA 504 4.05e+01 c.3.1.2,d.16.1.1 91676,91677 2ae5B 528 4.16e+01 1i07A 60 4.23e+01 1aojA b.34.2.1 61477 2a8eA 220 4.24e+01 1kb0A 677 4.27e+01 a.3.1.6,b.70.1.1 68378,68379 1gw5S 142 4.27e+01 d.110.4.2 70633 1sgvA 316 4.30e+01 b.122.1.1,d.265.1.2 98858,98859 2hayA 224 4.39e+01 1vggA 161 4.39e+01 1ecfA 504 4.39e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1ako 268 4.42e+01 1ako d.151.1.1 41779 1uasA 362 4.42e+01 b.71.1.1,c.1.8.1 88388,88389 2dchX 216 4.43e+01 1h3qA 140 4.45e+01 d.110.4.3 76652 1k55A 246 4.45e+01 e.3.1.1 68156 2h3bA 494 4.46e+01 2bynA 227 4.46e+01 1qjpA 171 4.60e+01 1bxwA f.4.1.1 43742 1e0bA 68 4.61e+01 1e0bA b.34.13.2 37476 1e19A 314 4.65e+01 1b7bA c.73.1.1 34967 1s4uX 407 4.69e+01 1qx4A 274 4.70e+01 b.43.4.2,c.25.1.1 104624,104625 1icpA 376 4.73e+01 1oyc c.1.4.1 62270 1h4rA 314 4.81e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 2gk3A 256 4.84e+01 1jb7A 495 4.87e+01 1otcA b.40.4.3,b.40.4.3,b.40.4.3 62836,62837,62838 1pswA 348 4.88e+01 c.87.1.7 88287 1itbB 315 4.90e+01 1itbB b.1.1.4,b.1.1.4,b.1.1.4 21720,21721,21722 1npsA 88 4.91e+01 1prs b.11.1.1 23622 2c82A 413 4.96e+01 2gwnA 452 4.97e+01 1qhtA 775 4.97e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1ka9H 200 4.99e+01 c.23.16.1 77308 1pzxA 289 4.99e+01 c.119.1.1 95484 2a9sA 171 5.05e+01 1eu1A 780 5.05e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 1qhvA 195 5.11e+01 1qhvA b.21.1.1 23842 2he7A 283 5.18e+01 2a5hA 416 5.20e+01 1rkd 309 5.28e+01 1rkd c.72.1.1 34928 1umkA 275 5.33e+01 1qb5D 99 5.34e+01 b.40.2.1 88357 1e25A 282 5.35e+01 1e25A e.3.1.1 42731 1m65A 245 5.36e+01 c.6.3.1 84847 1yqfA 203 5.39e+01 1op3H 225 5.40e+01 b.1.1.1,b.1.1.2 87208,87209 1vecA 206 5.42e+01 c.37.1.19 100575 1hw6A 278 5.43e+01 1frb c.1.7.1 61296 1xf1A 926 5.49e+01 1ny1A 240 5.56e+01 c.6.2.3 86395 1oe8A 211 5.62e+01 a.45.1.1,c.47.1.5 86905,86906 1o12A 376 5.67e+01 b.92.1.5,c.1.9.10 80758,80759 1ln1A 214 5.70e+01 d.129.3.2 74038 2gu3A 136 5.75e+01 2crvA 120 5.76e+01 1epfA 191 5.82e+01 2ncm b.1.1.4,b.1.1.4 21694,21695 1x54A 434 5.86e+01 1ospO 257 5.87e+01 1ospO b.76.1.1 27971 1p57A 114 5.90e+01 d.170.1.2 94125 1ifqA 138 5.91e+01 1ifqA d.110.4.1 62350 1e8gA 560 5.94e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 2aa4A 289 5.97e+01 2ghrA 302 5.97e+01 1ry9A 145 5.99e+01 d.198.1.1 98094 1x0rA 249 5.99e+01 1upsA 420 6.03e+01 1gqzA 274 6.04e+01 d.21.1.1,d.21.1.1 83311,83312 1n13A 52 6.04e+01 d.155.1.2 85248 2b59B 172 6.09e+01 1iwdA 215 6.12e+01 d.3.1.1 83756 1whzA 70 6.17e+01 1g8kA 825 6.17e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 1jcfA 344 6.18e+01 c.55.1.1,c.55.1.1 62878,62879 1iujA 106 6.26e+01 d.58.4.5 90701 1xyiA 66 6.27e+01 2cu3A 64 6.27e+01 2g6fX 59 6.28e+01 1gmyA 261 6.33e+01 d.3.1.1 76236 1brt 277 6.36e+01 1brt c.69.1.12 34699 1s9jA 341 6.42e+01 1kyhA 276 6.43e+01 c.72.1.4 73222 2cw9A 194 6.50e+01 1zm8A 259 6.54e+01 1xuvA 178 6.61e+01 1xuqA 212 6.62e+01 2sli 679 6.69e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1wkqA 164 6.70e+01 c.97.1.2 109393 1gt1A 159 6.80e+01 b.60.1.1 90515 1n9lA 109 6.81e+01 d.110.3.6 85468 2c4xA 260 6.81e+01 1m22A 503 6.94e+01 c.117.1.1 78464 2cwrA 103 6.98e+01 1hw7A 255 6.98e+01 1i7fA d.193.1.1 61297 2bw0A 329 6.99e+01 1xubA 298 7.04e+01 1uvqA 197 7.17e+01 b.1.1.2,d.19.1.1 100062,100063 1sz2A 332 7.20e+01 1q8rA 120 7.25e+01 d.79.6.1 96225 1ayaA 101 7.25e+01 1qadA d.93.1.1 40460 1kyfA 247 7.29e+01 b.1.10.1,d.105.1.1 73220,73221 1p4kA 295 7.33e+01 d.153.1.5 87772 1kngA 156 7.36e+01 c.47.1.10 72777 1o50A 157 7.37e+01 d.37.1.1,d.37.1.1 92478,92479 1xhcA 367 7.40e+01 1d3bA 75 7.42e+01 1d3bA b.38.1.1 24798 2bycA 137 7.46e+01 4ubpC 570 7.47e+01 1ubpC b.92.1.1,c.1.9.2 28431,29053 1qwyA 291 7.49e+01 b.84.3.2 96509 1o7iA 119 7.51e+01 b.40.4.3 86642 2b7kA 200 7.57e+01 2b3yA 888 7.57e+01 1d4tA 104 7.61e+01 1d4tA d.93.1.1 40537 2c7xA 436 7.67e+01 1tt8A 164 7.68e+01 1x8bA 289 7.69e+01 1l6sA 323 7.75e+01 c.1.10.3 73627 1dv1A 449 7.81e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 2fauA 341 7.85e+01 2g6bA 180 7.95e+01 1vbiA 344 7.96e+01 2fnjA 226 7.97e+01 1hynP 379 7.98e+01 1hynP d.112.1.2 61408 1jidA 128 8.08e+01 d.201.1.1 66735 1z4vA 532 8.15e+01 1jatA 155 8.17e+01 1u9aA d.20.1.1 62818 1lkkA 105 8.27e+01 1lckA d.93.1.1 40412 1gtkA 313 8.28e+01 c.94.1.1,d.50.2.1 76346,76347 2f4nA 273 8.33e+01 1h6lA 353 8.42e+01 b.68.3.1 60687 1wwrA 171 8.42e+01 1u7pA 164 8.43e+01 1y8qB 640 8.48e+01 1egwA 77 8.48e+01 1mnmA d.88.1.1 40234 2bt9A 90 8.53e+01 2a46A 238 8.55e+01 1q7fA 286 8.55e+01 b.68.9.1 96036 1n13B 113 8.57e+01 1eajA 126 8.60e+01 1f5wA b.1.1.1 59401 1r9fA 136 8.68e+01 d.255.1.1 97257 1mkiA 330 8.72e+01 e.3.1.2 84994 1wlsA 328 8.76e+01 1f2tB 148 8.76e+01 1f2tB 1bquA 215 8.80e+01 1bquA b.1.2.1,b.1.2.1 22066,22067 1r4pB 70 8.82e+01 b.40.2.1 97026 1sqhA 312 8.84e+01 d.108.1.5 98966 2c6cA 707 8.85e+01 1n8jA 186 8.90e+01 c.47.1.10 85401 1ju2A 536 8.92e+01 c.3.1.2,d.16.1.1 77169,77170 1xkpC 143 8.93e+01