# List of top-scoring protein chains for t04-100-30-stride-ebghtl-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 1.35e-01 2a2pA 129 1.85e-01 1lktA 104 2.45e-01 1lktA b.90.1.1 28398 1yx1A 264 1.01e+00 2c3vA 102 1.69e+00 1tp6A 128 1.89e+00 d.17.4.12 107184 1yaxA 153 2.02e+00 1m93C 41 2.12e+00 1vr9A 213 2.78e+00 1cqyA 99 3.42e+00 1b9zA b.3.1.1 22527 1vqoS 85 3.74e+00 1uh6A 100 3.92e+00 d.15.1.1 99394 1vq2A 193 4.13e+00 1ui0A 205 4.23e+00 c.18.1.2 99411 1hw6A 278 4.27e+00 1frb c.1.7.1 61296 1jj2R 84 4.31e+00 1ffkP d.12.1.1 63103 1s72S 85 4.31e+00 d.12.1.1 105338 1ijqA 316 4.32e+00 1ijqA b.68.5.1,g.3.11.1 62506,62507 1cdq 77 4.38e+00 1cds g.7.1.3 44459 1vetA 124 4.42e+00 d.110.7.1 108553 1h4rA 314 4.53e+00 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1zkdA 387 4.59e+00 1o8uA 257 5.09e+00 c.14.1.3 81194 1wrvA 308 5.60e+00 1byrA 155 5.68e+00 1byrA d.136.1.1 41450 1omiA 248 5.75e+00 b.82.3.3,a.4.5.4 87079,87080 2fhxA 246 5.82e+00 2b59B 172 5.90e+00 1txkA 498 6.20e+00 b.1.18.2,b.30.5.9 107425,107426 2cr5A 109 6.40e+00 1gsa 316 6.62e+00 1gsa c.30.1.3,d.142.1.1 31718,41477 1yb3A 175 7.25e+00 1hw7A 255 7.44e+00 1i7fA d.193.1.1 61297 1xvqA 175 7.68e+00 3ezmA 101 7.87e+00 3ezmA b.89.1.1 28395 1h7mA 102 8.24e+00 d.79.3.1 83485 3nul 130 8.44e+00 3nul d.110.1.1 40891 1a8q 274 8.51e+00 1brt c.69.1.12 34702 1dcjA 81 8.73e+00 1dcjA d.68.3.3 59115 2cvzA 289 8.75e+00 1obr 326 9.01e+00 1aye c.56.5.2 33828 1p6oA 161 9.09e+00 c.97.1.2 94185 1te7A 103 9.73e+00 1wm3A 72 9.73e+00 1m7xA 617 9.78e+00 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 1tqzA 133 1.00e+01 2cu3A 64 1.02e+01 1u0tA 307 1.05e+01 e.52.1.1 107567 1w41A 101 1.08e+01 1pm1X 180 1.09e+01 b.60.1.1 104189 1z0wA 207 1.09e+01 1vjfA 180 1.10e+01 d.116.1.1 100809 1tzaA 134 1.10e+01 b.1.23.1 107468 1e19A 314 1.11e+01 1b7bA c.73.1.1 34967 1mkeA 152 1.13e+01 b.55.1.4 79231 1skoA 143 1.13e+01 d.110.7.1 105676 1qhoA 686 1.14e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1v74A 107 1.19e+01 d.243.1.1 100442 1qauA 112 1.25e+01 1qauA b.36.1.1 24779 1bywA 110 1.26e+01 1bywA d.110.3.6 40912 1ztcA 221 1.30e+01 1r1qA 100 1.34e+01 d.93.1.1 104763 1sqeA 109 1.35e+01 d.58.4.5 105908 2cx5A 158 1.36e+01 1qmvA 197 1.38e+01 1qq2A c.47.1.10 33066 1cv8 174 1.39e+01 1cv8 d.3.1.1 37089 2ghrA 302 1.41e+01 1kllA 130 1.50e+01 d.32.1.2 72720 1l0bA 229 1.57e+01 c.15.1.3,c.15.1.3 73391,73392 2gcc 70 1.63e+01 2gcc d.10.1.2 37484 1dg9A 157 1.65e+01 1dg9A c.44.1.1 32637 1wgoA 123 1.73e+01 1q18A 332 1.77e+01 c.55.1.7,c.55.1.7 104470,104471 1qx4A 274 1.79e+01 b.43.4.2,c.25.1.1 104624,104625 1e39A 571 1.80e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1ffyA 917 1.83e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1kssA 571 1.84e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 2fh5A 185 1.86e+01 1xwwA 157 1.86e+01 1vkiA 181 1.88e+01 d.116.1.1 108664 1szoA 257 1.89e+01 c.14.1.3 106164 1p2hA 571 1.89e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1q9iA 571 1.89e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1ndh 272 1.91e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1y0pA 571 1.92e+01 1zndA 174 1.94e+01 1kfwA 435 1.96e+01 c.1.8.5,d.26.3.1 77376,77377 1f00I 282 2.00e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1i7pA 274 2.00e+01 b.43.4.2,c.25.1.1 66048,66049 1c0eA 157 2.05e+01 1dg9A c.44.1.1 32638 1xc3A 302 2.08e+01 1itcA 516 2.12e+01 b.3.1.1,c.1.8.1 83705,83706 1zu0A 529 2.12e+01 2go8A 122 2.21e+01 1ryaA 160 2.24e+01 d.113.1.5 105122 1qy1A 174 2.25e+01 b.60.1.1 96568 2fbmA 291 2.25e+01 1msc 129 2.29e+01 1msc d.85.1.1 40039 1vemA 516 2.30e+01 1iujA 106 2.33e+01 d.58.4.5 90701 1kq1A 77 2.37e+01 b.38.1.2 72848 1wj9A 211 2.38e+01 1kb0A 677 2.38e+01 a.3.1.6,b.70.1.1 68378,68379 1ttzA 87 2.39e+01 c.47.1.1 107309 1f2tB 148 2.46e+01 1f2tB 1xqaA 113 2.48e+01 1zq7A 207 2.48e+01 1w9hA 427 2.48e+01 1jv4A 162 2.51e+01 b.60.1.1 67343 1x0rA 249 2.56e+01 1ne9A 335 2.61e+01 d.108.1.4,d.108.1.4 91839,91840 1kay 381 2.61e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1xrkA 124 2.62e+01 1wlsA 328 2.65e+01 1bco 327 2.65e+01 1bco b.48.1.1,c.55.3.3 26431,33676 1lgpA 116 2.66e+01 b.26.1.2 73890 2bgcA 238 2.67e+01 1ecfA 504 2.68e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 2gu3A 136 2.68e+01 1sz2A 332 2.70e+01 1bupA 386 2.72e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1xfsA 178 2.72e+01 d.129.3.5 109589 1umkA 275 2.72e+01 2comA 124 2.75e+01 1yqtA 538 2.83e+01 1iscA 192 2.89e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1zhvA 134 2.90e+01 2h3jA 75 2.94e+01 1p57A 114 2.95e+01 d.170.1.2 94125 1i05A 180 2.99e+01 1mup b.60.1.1 27130 1yp2A 451 2.99e+01 1jofA 365 2.99e+01 b.69.10.1 71775 1l6rA 227 3.02e+01 c.108.1.10 77768 1fjgP 88 3.02e+01 1emwA d.27.1.1 38444 2a8eA 220 3.06e+01 2a4hA 126 3.08e+01 1jidA 128 3.08e+01 d.201.1.1 66735 1peeA 180 3.09e+01 b.60.1.1 104126 1a88A 275 3.12e+01 1brt c.69.1.12 34707 2cfuA 658 3.15e+01 1uhvA 500 3.15e+01 b.71.1.2,c.1.8.3 99402,99403 1i06A 180 3.16e+01 1mup b.60.1.1 27131 2basA 431 3.18e+01 1vggA 161 3.21e+01 2pil 159 3.22e+01 2pil d.24.1.1 38376 1uasA 362 3.28e+01 b.71.1.1,c.1.8.1 88388,88389 2ghpA 292 3.39e+01 1sur 215 3.40e+01 1sur c.26.2.2 31620 1wnfA 328 3.40e+01 1pvmA 184 3.40e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1zyeA 220 3.41e+01 1wywA 230 3.42e+01 2evrA 246 3.43e+01 1w6sA 599 3.44e+01 1obpA 159 3.45e+01 1obpA b.60.1.1 27092 1gt1A 159 3.47e+01 b.60.1.1 90515 1xkiA 162 3.47e+01 1hn2A 159 3.51e+01 b.60.1.1 65890 1pufB 73 3.56e+01 a.4.1.1 95132 1b24A 188 3.59e+01 1b24A d.95.2.1,d.95.2.1 40573,40574 1lwdA 413 3.64e+01 c.77.1.1 78265 1aisA 182 3.68e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1vcdA 126 3.69e+01 1k2fA 190 3.70e+01 b.8.1.2 68054 2a25A 193 3.79e+01 2azqA 311 3.86e+01 1euoA 180 3.87e+01 1np1A b.60.1.1 27163 1am2 199 3.91e+01 1am2 b.86.1.2 28381 1daqA 71 3.92e+01 1daqA a.139.1.1 59113 1jtdB 273 3.93e+01 b.69.5.2 67265 1htqA 477 3.94e+01 d.15.9.1,d.128.1.1 71035,71036 1tiiD 99 3.96e+01 1tiiD b.40.2.1 24965 1dmhA 311 3.99e+01 1dmhA b.3.6.1 22633 1z2mA 155 4.04e+01 1lrwA 600 4.07e+01 b.70.1.1 91111 1fa8A 135 4.14e+01 1qipA d.32.1.1 38486 2jdxA 385 4.15e+01 1jdw d.126.1.2 41139 1qb5D 99 4.17e+01 b.40.2.1 88357 2esnA 310 4.17e+01 1m22A 503 4.19e+01 c.117.1.1 78464 1k55A 246 4.21e+01 e.3.1.1 68156 2ciaA 102 4.22e+01 1umuA 116 4.28e+01 1umuA b.87.1.1 28382 2dg5B 190 4.29e+01 1b72B 87 4.30e+01 1akhA a.4.1.1 16001 1i8jA 323 4.31e+01 1b4kA c.1.10.3 61968 1l6sA 323 4.32e+01 c.1.10.3 73627 1htrB 329 4.34e+01 1smrA 1zq1A 438 4.41e+01 1jbbA 153 4.47e+01 1u9aA d.20.1.1 62842 1i0cA 60 4.50e+01 1aojA b.34.2.1 61485 1mup 166 4.51e+01 1mup b.60.1.1 27133 1whnA 128 4.61e+01 1sr8A 298 4.61e+01 e.54.1.1 105959 1gpeA 587 4.65e+01 1gpeA c.3.1.2,d.16.1.1 30387,37951 2aobA 99 4.67e+01 16pk 415 4.67e+01 16pk c.86.1.1 35454 1f9zA 135 4.71e+01 1qipA d.32.1.1 38484 1ef1A 294 4.73e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 2crvA 120 4.75e+01 1uu1A 335 4.78e+01 c.67.1.1 99993 2ewcA 126 4.82e+01 1mtpB 43 4.84e+01 1c44A 123 4.87e+01 1qndA d.106.1.1 40795 1svjA 156 4.91e+01 d.220.1.1 106049 1th8A 145 4.98e+01 d.122.1.3 106908 1cq0A 28 5.02e+01 j.6.1.1 46108 1zbfA 142 5.03e+01 1xxqA 161 5.04e+01 1vbvA 105 5.05e+01 1yarH 217 5.09e+01 1r77A 103 5.12e+01 1ppjD 241 5.14e+01 a.3.1.3,f.23.11.1 104258,104259 1y81A 138 5.17e+01 2grrB 170 5.17e+01 1zxmA 400 5.21e+01 1jdw 423 5.22e+01 1jdw d.126.1.2 41129 1cz6A 25 5.22e+01 j.3.1.3 46072 1vjvA 415 5.23e+01 d.3.1.9 108632 1a79A 171 5.37e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 1cuk 203 5.37e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1huxA 270 5.45e+01 1huxA c.55.1.5 61278 1qhdA 398 5.47e+01 1qhdA a.115.1.2,b.19.1.1 63324,63325 1bhe 376 5.51e+01 1bhe b.80.1.3 28030 1k8kA 418 5.53e+01 c.55.1.1,c.55.1.1 68305,68306 1onqA 283 5.57e+01 b.1.1.2,d.19.1.1 93365,93366 1g5aA 628 5.60e+01 b.71.1.1,c.1.8.1 65152,65153 1ru3A 732 5.68e+01 e.26.1.3 97835 1gmuA 143 5.68e+01 b.107.1.1,d.58.38.1 65335,65336 1b9wA 89 5.75e+01 1b9wA g.3.11.4,g.3.11.4 44334,44335 1zboA 210 5.75e+01 1o50A 157 5.85e+01 d.37.1.1,d.37.1.1 92478,92479 2c4xA 260 5.85e+01 2aa4A 289 5.96e+01 1s4nA 348 6.00e+01 c.68.1.16 98501 1y88A 199 6.01e+01 1m9sA 605 6.05e+01 b.1.18.15,b.34.11.1,b.34.11.1,b.34.11.1,c.10.2.1 78874,78875,78876,78877,78878 1va4A 279 6.10e+01 c.69.1.12 108458 1q7fA 286 6.13e+01 b.68.9.1 96036 1oz7A 131 6.20e+01 d.169.1.1 93806 1j09A 468 6.24e+01 a.97.1.1,c.26.1.1 77025,77026 1ry9A 145 6.25e+01 d.198.1.1 98094 1qjpA 171 6.34e+01 1bxwA f.4.1.1 43742 2bkqA 212 6.35e+01 1kwgA 645 6.39e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1ym5A 300 6.39e+01 1m65A 245 6.43e+01 c.6.3.1 84847 1rewC 135 6.50e+01 g.7.1.3 97336 2db9A 149 6.52e+01 1fzrA 138 6.52e+01 1fzrA c.52.1.17 33336 1y8cA 246 6.54e+01 1m0dA 138 6.59e+01 c.52.1.17 74354 1h0hA 977 6.70e+01 b.52.2.2,c.81.1.1 76435,76436 1h6hA 143 6.73e+01 d.189.1.1 65681 1bu6O 501 6.76e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1xkzA 255 6.77e+01 1iwdA 215 6.80e+01 d.3.1.1 83756 1wdvA 152 6.81e+01 1f1uA 323 6.83e+01 d.32.1.3,d.32.1.3 83200,83201 1i07A 60 6.94e+01 1aojA b.34.2.1 61477 2bvcA 486 6.96e+01 1pcfA 66 7.02e+01 1pcfA d.18.1.1 38142 1oshA 232 7.05e+01 a.123.1.1 93496 1nrlA 316 7.08e+01 a.123.1.1 92091 4tmkA 213 7.10e+01 5tmpA c.37.1.1 31930 1xhcA 367 7.12e+01 1pjxA 314 7.12e+01 b.68.6.1 104167 1ct5A 256 7.27e+01 1ct5A c.1.6.2 28663 1iow 306 7.31e+01 1iow c.30.1.2,d.142.1.1 31713,41481 1j5pA 253 7.34e+01 d.81.1.3,c.2.1.3 71577,83092 1xf1A 926 7.36e+01 1eg9A 449 7.37e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1voqa 90 7.39e+01 1itbB 315 7.43e+01 1itbB b.1.1.4,b.1.1.4,b.1.1.4 21720,21721,21722 1ri9A 102 7.44e+01 b.34.2.1 97506 1mzbA 136 7.47e+01 a.4.5.42 91497 1o7nA 449 7.53e+01 b.33.1.2,d.129.3.3 81162,81163 1g4wR 383 7.62e+01 1g4uS a.24.11.1,c.45.1.2 16644,32692 2ad9A 119 7.67e+01 1m4jA 142 7.73e+01 d.109.1.2 78602 1b8aA 438 7.73e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1d4oA 184 7.75e+01 1d4oA c.31.1.4 31748 1j58A 385 7.76e+01 b.82.1.2 71531 2fdrA 229 7.79e+01 1cr5A 189 7.80e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1pylA 97 7.81e+01 d.1.1.2 104391 2ao9A 155 7.89e+01 1tikA 213 7.91e+01 c.23.5.3 107003 2ga9D 469 7.91e+01 1ugiA 84 8.03e+01 1ugiA d.17.5.1 38125 1n9lA 109 8.03e+01 d.110.3.6 85468 2d2mD 145 8.07e+01 1kpsB 171 8.10e+01 a.118.12.1 68787 1h9oA 112 8.13e+01 1qadA d.93.1.1 60837 1b0uA 262 8.16e+01 1b0uA c.37.1.12 32370 1whzA 70 8.18e+01 1ughI 82 8.19e+01 1ugiA d.17.5.1 38133 1ako 268 8.25e+01 1ako d.151.1.1 41779 1oe8A 211 8.30e+01 a.45.1.1,c.47.1.5 86905,86906 1yirA 408 8.32e+01 1x6oA 174 8.33e+01 b.34.5.2,b.40.4.5 109493,109494 1nzjA 298 8.45e+01 c.26.1.1 92377 2ap1A 327 8.45e+01 1f39A 101 8.45e+01 1umuA b.87.1.1 28386 1c1dA 355 8.46e+01 1bw9A c.2.1.7,c.58.1.1 30270,33918 1jmxA 494 8.49e+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 1ln1A 214 8.53e+01 d.129.3.2 74038 1v1aA 309 8.53e+01 c.72.1.1 100249 1d4tA 104 8.56e+01 1d4tA d.93.1.1 40537 1gtkA 313 8.56e+01 c.94.1.1,d.50.2.1 76346,76347 1xkpC 143 8.61e+01 2agtA 319 8.70e+01 1twuA 139 8.73e+01 d.32.1.8 107413 1nqcA 217 8.73e+01 d.3.1.1 86024 1o1xA 155 8.75e+01 c.121.1.1 86553 1qh5A 260 8.76e+01 1qh5A d.157.1.2 42057 2c26A 260 8.79e+01 1ccwB 483 8.84e+01 1cb7B c.1.19.2 29646 1a8h 500 8.92e+01 1a8h a.27.1.1,c.26.1.1 16922,31589 1g72A 573 8.96e+01 4aahA b.70.1.1 27680 1n3gA 113 8.98e+01 d.204.1.1 79962