# 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 6.99e-02 1lktA 104 4.09e-01 1lktA b.90.1.1 28398 1m93C 41 6.05e-01 2a2pA 129 6.51e-01 1tp6A 128 1.26e+00 d.17.4.12 107184 1iscA 192 1.33e+00 1avmA a.2.11.1,d.44.1.1 15733,38726 1zkdA 387 1.68e+00 1pm1X 180 1.72e+00 b.60.1.1 104189 2c3vA 102 1.94e+00 1vq2A 193 2.15e+00 1yaxA 153 2.15e+00 1cqyA 99 2.38e+00 1b9zA b.3.1.1 22527 1xvqA 175 2.40e+00 1kllA 130 2.65e+00 d.32.1.2 72720 1w9hA 427 2.76e+00 1iow 306 3.19e+00 1iow c.30.1.2,d.142.1.1 31713,41481 1vr9A 213 3.33e+00 1xfsA 178 3.36e+00 d.129.3.5 109589 2a25A 193 3.49e+00 1qhoA 686 3.78e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1uhvA 500 4.19e+00 b.71.1.2,c.1.8.3 99402,99403 1dcjA 81 4.26e+00 1dcjA d.68.3.3 59115 1zndA 174 4.54e+00 2cr5A 109 4.65e+00 1qy1A 174 4.83e+00 b.60.1.1 96568 3nul 130 4.96e+00 3nul d.110.1.1 40891 3ezmA 101 4.99e+00 3ezmA b.89.1.1 28395 1ffyA 917 5.10e+00 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1v74A 107 5.23e+00 d.243.1.1 100442 1l6rA 227 5.80e+00 c.108.1.10 77768 2h3jA 75 5.83e+00 1xc3A 302 6.11e+00 1p2hA 571 6.58e+00 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1whzA 70 6.73e+00 1lwdA 413 7.02e+00 c.77.1.1 78265 1rewC 135 7.08e+00 g.7.1.3 97336 1h9oA 112 7.26e+00 1qadA d.93.1.1 60837 1txkA 498 7.53e+00 b.1.18.2,b.30.5.9 107425,107426 1yx1A 264 7.88e+00 1ecfA 504 8.27e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 2b5nA 323 8.75e+00 1a8q 274 8.80e+00 1brt c.69.1.12 34702 1bywA 110 8.95e+00 1bywA d.110.3.6 40912 1bupA 386 8.98e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 1am2 199 9.57e+00 1am2 b.86.1.2 28381 1qauA 112 9.69e+00 1qauA b.36.1.1 24779 2basA 431 9.83e+00 2dg5A 366 9.99e+00 1cdq 77 1.01e+01 1cds g.7.1.3 44459 2dg5B 190 1.04e+01 1wrvA 308 1.04e+01 1vqoS 85 1.05e+01 2fq9A 225 1.06e+01 1ui0A 205 1.12e+01 c.18.1.2 99411 1k8kA 418 1.12e+01 c.55.1.1,c.55.1.1 68305,68306 2fa8A 105 1.14e+01 1vemA 516 1.20e+01 1h6hA 143 1.21e+01 d.189.1.1 65681 1xrkA 124 1.21e+01 1qmvA 197 1.22e+01 1qq2A c.47.1.10 33066 1mtpB 43 1.23e+01 1cv8 174 1.24e+01 1cv8 d.3.1.1 37089 1vetA 124 1.26e+01 d.110.7.1 108553 1e2wA 251 1.28e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1cr5A 189 1.29e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1xvsA 126 1.32e+01 16pk 415 1.34e+01 16pk c.86.1.1 35454 2bgiA 272 1.37e+01 2ap1A 327 1.38e+01 1wm3A 72 1.40e+01 1vkcA 158 1.40e+01 1pvmA 184 1.42e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1rvkA 382 1.43e+01 c.1.11.2,d.54.1.1 97928,97929 1p6oA 161 1.47e+01 c.97.1.2 94185 1huxA 270 1.51e+01 1huxA c.55.1.5 61278 1u58A 253 1.51e+01 2be1A 339 1.53e+01 1pylA 97 1.54e+01 d.1.1.2 104391 1sqeA 109 1.59e+01 d.58.4.5 105908 1f00I 282 1.60e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1vjvA 415 1.61e+01 d.3.1.9 108632 1jofA 365 1.64e+01 b.69.10.1 71775 1b9wA 89 1.65e+01 1b9wA g.3.11.4,g.3.11.4 44334,44335 2bryA 497 1.70e+01 1vjlA 164 1.71e+01 d.257.1.1 100822 1vjfA 180 1.73e+01 d.116.1.1 100809 1fjgP 88 1.73e+01 1emwA d.27.1.1 38444 2a15A 139 1.74e+01 1k55A 246 1.74e+01 e.3.1.1 68156 1z0wA 207 1.76e+01 1gpeA 587 1.77e+01 1gpeA c.3.1.2,d.16.1.1 30387,37951 1w6sA 599 1.82e+01 1x8bA 289 1.86e+01 1qqp1 213 1.87e+01 1qqp1 1xkiA 162 1.90e+01 1ijqA 316 1.92e+01 1ijqA b.68.5.1,g.3.11.1 62506,62507 1bu6O 501 1.97e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1m65A 245 1.99e+01 c.6.3.1 84847 1pjxA 314 2.01e+01 b.68.6.1 104167 1zg2A 107 2.04e+01 1hd2A 161 2.05e+01 c.47.1.10 60962 1qjpA 171 2.05e+01 1bxwA f.4.1.1 43742 1hw6A 278 2.06e+01 1frb c.1.7.1 61296 2cu3A 64 2.07e+01 1tyv 542 2.10e+01 1tyv b.80.1.6 28038 1r77A 103 2.14e+01 2bjfA 329 2.18e+01 1w44A 331 2.21e+01 1b24A 188 2.22e+01 1b24A d.95.2.1,d.95.2.1 40573,40574 1iujA 106 2.23e+01 d.58.4.5 90701 1b8aA 438 2.25e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1dv1A 449 2.26e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1gsa 316 2.31e+01 1gsa c.30.1.3,d.142.1.1 31718,41477 1um5H 217 2.34e+01 1atg 231 2.37e+01 1atg c.94.1.1 35834 1q0qA 406 2.37e+01 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 2a8eA 220 2.39e+01 1hjrA 158 2.42e+01 1hjrA c.55.3.6 33727 1lgpA 116 2.44e+01 b.26.1.2 73890 1yirA 408 2.45e+01 1llnA 262 2.45e+01 d.165.1.1 84625 1fnd 314 2.47e+01 1fnc b.43.4.2,c.25.1.1 25626,31516 1bx1A 314 2.52e+01 1fnc b.43.4.2,c.25.1.1 25629,31519 1xniA 118 2.53e+01 1c44A 123 2.56e+01 1qndA d.106.1.1 40795 1ako 268 2.61e+01 1ako d.151.1.1 41779 1ri9A 102 2.64e+01 b.34.2.1 97506 2gcc 70 2.69e+01 2gcc d.10.1.2 37484 1wh5A 80 2.72e+01 2ghrA 302 2.73e+01 1a9xA 1058 2.78e+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 1xkgA 312 2.79e+01 1y8qB 640 2.80e+01 1zbsA 291 2.81e+01 1vcdA 126 2.81e+01 1wn5A 130 2.82e+01 2fh5A 185 2.82e+01 1j79A 347 2.84e+01 1j79A c.1.9.4 62675 1xqaA 113 2.84e+01 1umkA 275 2.89e+01 1x6oA 174 2.90e+01 b.34.5.2,b.40.4.5 109493,109494 1ttzA 87 2.93e+01 c.47.1.1 107309 2gu3A 136 2.95e+01 1htrB 329 2.96e+01 1smrA 1dg9A 157 2.96e+01 1dg9A c.44.1.1 32637 2dcnA 311 2.97e+01 1jcfA 344 2.97e+01 c.55.1.1,c.55.1.1 62878,62879 2sli 679 2.97e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1lf7A 182 3.01e+01 b.60.1.1 73878 2gaiA 633 3.02e+01 1xwwA 157 3.02e+01 2gwnA 452 3.04e+01 1kb0A 677 3.05e+01 a.3.1.6,b.70.1.1 68378,68379 2gfoA 396 3.10e+01 1nrlA 316 3.11e+01 a.123.1.1 92091 1qx4A 274 3.12e+01 b.43.4.2,c.25.1.1 104624,104625 1wlsA 328 3.14e+01 1m22A 503 3.20e+01 c.117.1.1 78464 1c96A 753 3.27e+01 1amj c.8.2.1,c.83.1.1 30727,35403 1kq1A 77 3.27e+01 b.38.1.2 72848 1h6lA 353 3.30e+01 b.68.3.1 60687 2a5hA 416 3.30e+01 2bycA 137 3.33e+01 1xf1A 926 3.34e+01 2f9zC 159 3.35e+01 2bf6A 449 3.37e+01 1zceA 155 3.39e+01 1y9wA 140 3.39e+01 1zbfA 142 3.41e+01 1mqeA 207 3.46e+01 d.113.1.1 91394 2a6aA 218 3.50e+01 1x0rA 249 3.50e+01 2c2aA 258 3.51e+01 4ubpC 570 3.53e+01 1ubpC b.92.1.1,c.1.9.2 28431,29053 1bco 327 3.57e+01 1bco b.48.1.1,c.55.3.3 26431,33676 1sz2A 332 3.58e+01 1cs0A 1073 3.62e+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 1wdvA 152 3.73e+01 1y88A 199 3.74e+01 1jidA 128 3.83e+01 d.201.1.1 66735 1lq9A 112 3.89e+01 d.58.4.3 78129 1xkpC 143 3.91e+01 1j5pA 253 3.94e+01 d.81.1.3,c.2.1.3 71577,83092 1tqzA 133 3.95e+01 1uwzA 136 4.04e+01 c.97.1.1 108081 2bs3A 656 4.14e+01 1gmyA 261 4.21e+01 d.3.1.1 76236 1ju2A 536 4.25e+01 c.3.1.2,d.16.1.1 77169,77170 1i07A 60 4.26e+01 1aojA b.34.2.1 61477 1cq0A 28 4.37e+01 j.6.1.1 46108 1or0B 528 4.38e+01 1ln1A 214 4.39e+01 d.129.3.2 74038 1qveA 126 4.43e+01 d.24.1.1 104594 1z2mA 155 4.48e+01 1yqtA 538 4.51e+01 1ayaA 101 4.53e+01 1qadA d.93.1.1 40460 1ka9H 200 4.56e+01 c.23.16.1 77308 1te7A 103 4.59e+01 2gupA 292 4.59e+01 1lfdA 87 4.65e+01 1lfdA d.15.1.5 37622 1x54A 434 4.82e+01 1ddlA 188 4.83e+01 1auyA b.121.4.6 23317 2fauA 341 4.83e+01 1rk6A 496 4.84e+01 b.92.1.6,b.92.1.6,c.1.9.11 97599,97600,97601 1wfyA 104 4.91e+01 1yb3A 175 4.93e+01 1voqa 90 4.94e+01 2b59B 172 5.03e+01 1pl3A 186 5.03e+01 b.1.9.1 88158 1vggA 161 5.05e+01 2ae5B 528 5.06e+01 1z47A 355 5.12e+01 1o50A 157 5.14e+01 d.37.1.1,d.37.1.1 92478,92479 1npeA 267 5.15e+01 b.68.5.1 92032 1ro5A 201 5.16e+01 d.108.1.3 105023 1fp1D 372 5.18e+01 1fpqA a.4.5.29,c.66.1.12 59939,59940 1lf6A 684 5.25e+01 a.102.1.5,b.30.5.5 77918,77919 1d4tA 104 5.26e+01 1d4tA d.93.1.1 40537 1ospO 257 5.27e+01 1ospO b.76.1.1 27971 1uasA 362 5.28e+01 b.71.1.1,c.1.8.1 88388,88389 1w41A 101 5.31e+01 1u7pA 164 5.45e+01 1wj9A 211 5.52e+01 1xe7A 203 5.63e+01 1oshA 232 5.64e+01 a.123.1.1 93496 1upsA 420 5.65e+01 1e19A 314 5.67e+01 1b7bA c.73.1.1 34967 1epfA 191 5.67e+01 2ncm b.1.1.4,b.1.1.4 21694,21695 1ykjA 394 5.69e+01 1i0rA 169 5.69e+01 1i0rA b.45.1.2 61489 1g8kA 825 5.69e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 2aa4A 289 5.74e+01 1sc6A 404 5.77e+01 1npsA 88 5.81e+01 1prs b.11.1.1 23622 1xxqA 161 5.82e+01 1qg7A 67 5.87e+01 1a15A d.9.1.1 37449 1sgvA 316 5.88e+01 b.122.1.1,d.265.1.2 98858,98859 1xubA 298 5.88e+01 1g8aA 227 5.90e+01 c.66.1.3 90506 1kngA 156 5.94e+01 c.47.1.10 72777 2crvA 120 5.96e+01 1gt1A 159 6.11e+01 b.60.1.1 90515 1k0iA 394 6.12e+01 c.3.1.2,d.16.1.2 67942,67943 1f2tB 148 6.15e+01 1f2tB 1xkzA 255 6.16e+01 1vrbA 342 6.18e+01 2cx5A 158 6.20e+01 2fikA 287 6.22e+01 1h3qA 140 6.32e+01 d.110.4.3 76652 1ne9A 335 6.38e+01 d.108.1.4,d.108.1.4 91839,91840 1u00A 227 6.41e+01 1v8hA 107 6.42e+01 2cwzA 141 6.42e+01 2bgcA 238 6.43e+01 1kfwA 435 6.48e+01 c.1.8.5,d.26.3.1 77376,77377 2fnjA 226 6.49e+01 2cw9A 194 6.52e+01 1gtkA 313 6.54e+01 c.94.1.1,d.50.2.1 76346,76347 1ex0A 731 6.55e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1jatA 155 6.55e+01 1u9aA d.20.1.1 62818 1pswA 348 6.62e+01 c.87.1.7 88287 2aq2B 237 6.63e+01 1aisA 182 6.65e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 2ewcA 126 6.68e+01 1ugiA 84 6.71e+01 1ugiA d.17.5.1 38125 1u14A 172 6.73e+01 c.51.4.3 107579 1gs5A 258 6.76e+01 c.73.1.2 70395 1id0A 152 6.77e+01 d.122.1.3 66111 1iwdA 215 6.79e+01 d.3.1.1 83756 1e25A 282 6.84e+01 1e25A e.3.1.1 42731 1ir21 140 6.92e+01 1khbA 625 6.94e+01 c.91.1.1,c.109.1.1 68606,68607 1n4wA 504 7.03e+01 c.3.1.2,d.16.1.1 91676,91677 1twfK 120 7.05e+01 1qb5D 99 7.07e+01 b.40.2.1 88357 1xm3A 264 7.09e+01 2c4xA 260 7.11e+01 1bxyA 60 7.11e+01 1bxyA d.59.1.1 39525 1q7fA 286 7.11e+01 b.68.9.1 96036 1xebA 150 7.15e+01 1ry9A 145 7.15e+01 d.198.1.1 98094 1xhcA 367 7.19e+01 1gmuA 143 7.21e+01 b.107.1.1,d.58.38.1 65335,65336 1h4rA 314 7.26e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1n13B 113 7.30e+01 1gk8I 140 7.31e+01 d.73.1.1 65242 1brt 277 7.34e+01 1brt c.69.1.12 34699 1p57A 114 7.36e+01 d.170.1.2 94125 1lrzA 426 7.36e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1qgoA 264 7.41e+01 1qgoA c.92.1.2 35596 1n1tA 641 7.45e+01 b.29.1.15,b.68.1.1 79821,79822 1qlwA 328 7.51e+01 1qlwA c.69.1.15 34722 1i88A 389 7.56e+01 c.95.1.2,c.95.1.2 66070,66071 1xksA 450 7.65e+01 1qhtA 775 7.66e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1s9jA 341 7.69e+01 1jtdB 273 7.70e+01 b.69.5.2 67265 1icpA 376 7.73e+01 1oyc c.1.4.1 62270 1h8eG 272 7.76e+01 1e79G c.49.2.1 60756 2gk3A 256 7.78e+01 1nbwA 607 7.81e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1op3H 225 7.82e+01 b.1.1.1,b.1.1.2 87208,87209 1tqxA 227 7.84e+01 1ppjD 241 7.87e+01 a.3.1.3,f.23.11.1 104258,104259 1k7jA 206 7.89e+01 d.115.1.1 72103 1i2kA 269 7.90e+01 e.17.1.1 90661 1o7nA 449 7.93e+01 b.33.1.2,d.129.3.3 81162,81163 2a9sA 171 7.99e+01 2fl7A 232 8.06e+01 2ga9D 469 8.08e+01 1m6iA 493 8.18e+01 c.3.1.5,c.3.1.5,d.87.1.1 74533,74534,74535 1d3bA 75 8.18e+01 1d3bA b.38.1.1 24798 1n8jA 186 8.19e+01 c.47.1.10 85401 1vclA 432 8.21e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1ctt 294 8.24e+01 1ctt c.97.1.1,c.97.1.1 36022,36023 2a46A 238 8.24e+01 1s4iA 175 8.28e+01 1oe8A 211 8.32e+01 a.45.1.1,c.47.1.5 86905,86906 1uok 558 8.35e+01 1uok b.71.1.1,c.1.8.1 27801,28788 1oxxK 353 8.35e+01 b.40.6.3,c.37.1.12 93715,93716 1xezA 721 8.37e+01 1jmxA 494 8.39e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66901,66902,66903,66904,66905 1ca1 370 8.39e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1h9dB 134 8.42e+01 2jhbA b.54.1.1 60822 1gy6A 127 8.42e+01 d.17.4.2 70736 1omhA 293 8.42e+01 d.89.1.5 93348 2g6fX 59 8.50e+01 2d0oA 610 8.52e+01 1w4tA 299 8.57e+01 1uocA 289 8.58e+01 c.55.3.9 99686 1sur 215 8.60e+01 1sur c.26.2.2 31620 1qhvA 195 8.62e+01 1qhvA b.21.1.1 23842 1drw 273 8.64e+01 1drw c.2.1.3,d.81.1.3 30057,39972 1z02A 446 8.64e+01 1zupA 315 8.68e+01 1csn 298 8.69e+01 1csn d.144.1.7 41664 1vjjA 692 8.74e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 1vl2A 421 8.92e+01 c.26.2.1,d.210.1.1 108708,108709 1s68A 249 8.92e+01 d.142.2.4 98591 1o7zA 77 8.92e+01 d.9.1.1 86660 1ifqA 138 8.95e+01 1ifqA d.110.4.1 62350 1wywA 230 9.00e+01