# List of top-scoring protein chains for t04-100-40-40-str2+CB_burial_14_7-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 2fe5A 94 3.78e-19 2fneA 117 4.55e-19 1g9oA 91 3.21e-18 1pdr b.36.1.1 60400 1tp5A 119 3.93e-18 1be9A 119 6.82e-18 1pdr b.36.1.1 24774 1qavA 90 7.76e-18 1qauA b.36.1.1 24777 2fcfA 103 1.94e-17 1n7eA 97 7.26e-17 b.36.1.1 91691 1ihjA 98 2.14e-16 1pdr b.36.1.1 62382 2h2bA 107 3.17e-16 1mfgA 95 7.48e-16 b.36.1.1 79043 1n7fA 97 8.79e-16 b.36.1.1 91692 1q3oA 109 1.01e-15 b.36.1.1 95700 2h3lA 103 1.03e-15 1l6oA 95 1.07e-15 b.36.1.1 84534 1nf3C 128 1.40e-14 b.36.1.1 85596 2f0aA 98 1.50e-14 2f5yA 91 1.52e-14 1wf7A 103 3.08e-14 1kwaA 88 3.43e-14 1kwaA b.36.1.1 24772 1qauA 112 1.18e-13 1qauA b.36.1.1 24779 1v5lA 103 4.29e-13 b.36.1.1 108378 1nteA 82 1.14e-12 b.36.1.1 86163 1r6jA 82 2.85e-12 b.36.1.1 97151 1lcyA 325 8.06e-08 b.36.1.4,b.47.1.1 73834,73835 1fc6A 388 1.06e-07 1fc6A b.36.1.3,c.14.1.2 64738,64739 1te0A 318 1.13e-07 1y8tA 324 9.64e-05 1y9wA 140 8.00e-03 1fxlA 167 2.38e-02 1b7fA d.58.7.1,d.58.7.1 39183,39184 1a79A 171 7.41e-02 1a79A c.52.2.1,d.75.1.1 33340,39739 2fe7A 166 8.35e-02 2fl4A 149 1.55e-01 1xebA 150 1.66e-01 1sotA 320 2.01e-01 b.36.1.4,b.47.1.1 105852,105853 1f3z 161 2.44e-01 1gpr b.84.3.1 28273 1bo4A 168 3.82e-01 1bo4A d.108.1.1 40798 2c5qA 240 3.90e-01 1z4eA 153 4.39e-01 1f20A 435 4.84e-01 b.43.4.1,c.25.1.4 64932,64933 1k32A 1045 5.11e-01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1gpr 162 5.14e-01 1gpr b.84.3.1 28267 1tllA 688 5.14e-01 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1r13A 148 5.41e-01 d.169.1.1,h.1.1.1 96782,96783 2bshA 125 8.39e-01 1id0A 152 9.54e-01 d.122.1.3 66111 2bhoA 130 1.08e+00 1vkcA 158 1.36e+00 1a62 130 1.41e+00 1a62 a.140.3.1,b.40.4.5 64708,64709 1luzA 88 1.45e+00 b.40.4.5 74271 2d4pA 141 1.46e+00 1kk1A 410 1.64e+00 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1se8A 301 1.77e+00 b.40.4.3 105448 1r0vA 305 1.83e+00 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 1yb3A 175 2.00e+00 1d4xG 126 2.06e+00 1d0nA d.109.1.1 59109 1uw0A 117 2.49e+00 g.39.1.12 108063 1xk5A 204 2.54e+00 2brfA 110 2.59e+00 1cliA 345 2.72e+00 1cliA d.79.4.1,d.139.1.1 39816,41459 1x6oA 174 2.95e+00 b.34.5.2,b.40.4.5 109493,109494 2awaA 390 2.95e+00 2cy2A 174 3.00e+00 2aefA 234 3.05e+00 1qyaA 307 3.10e+00 d.21.1.2,d.21.1.2 104653,104654 1uheA 97 3.13e+00 1sdjA 310 3.28e+00 d.21.1.2,d.21.1.2 98807,98808 1nm1G 125 3.30e+00 d.109.1.1 80653 2bsjA 133 3.34e+00 1t44G 147 3.40e+00 d.109.1.1 106395 1vzoA 355 3.54e+00 d.144.1.7 108971 1g8aA 227 3.64e+00 c.66.1.3 90506 2avtA 378 3.83e+00 1y7rA 133 3.88e+00 1p7tA 731 3.89e+00 c.1.13.1 94319 1rsy 152 3.95e+00 1rsy b.7.1.2 23192 1vj0A 380 4.02e+00 b.35.1.2,c.2.1.1 100786,100787 8rucI 123 4.14e+00 1rboC d.73.1.1 39629 1ex2A 189 4.14e+00 1ex2A c.51.4.2 33225 1qsmA 152 4.25e+00 1qsmA d.108.1.1 40808 1tiqA 180 4.27e+00 d.108.1.1 107010 1vc3B 97 4.36e+00 1wxaA 116 4.51e+00 1hh1A 143 4.57e+00 1gefA c.52.1.18 61036 1rlhA 173 4.61e+00 d.256.1.1 97646 1jnyA 435 4.66e+00 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1y9kA 157 4.76e+00 2c3gA 98 5.05e+00 1wjuA 100 5.58e+00 1yjmA 110 5.70e+00 1zhhB 242 5.74e+00 2cdqA 510 5.81e+00 1s1qA 145 5.91e+00 d.20.1.2 98351 1k3eA 156 6.00e+00 d.198.1.1 68103 1ti6A 875 6.43e+00 b.52.2.2,c.81.1.1 106974,106975 2bw3A 534 6.54e+00 2bkfA 87 6.56e+00 2dpkA 152 6.75e+00 1yvcA 70 6.98e+00 2g3aA 152 7.05e+00 1nqjA 119 7.25e+00 b.23.2.1 86031 1t9fA 187 7.30e+00 b.42.6.1 106710 1cauB 184 7.41e+00 1caxB b.82.1.2 28103 1s3zA 165 7.48e+00 d.108.1.1 105250 1euwA 152 7.49e+00 1dupA b.85.4.1 28349 1prtF 98 7.60e+00 1prtF b.40.2.1 25140 1eso 154 7.94e+00 1yaiA b.1.8.1 22293 1yvoA 172 8.35e+00 1ema 236 8.58e+00 1ema d.22.1.1 38339 1xkpB 124 8.72e+00 1vheA 373 8.74e+00 b.49.3.1,c.56.5.4 100669,100670 1z4rA 168 9.07e+00 1d8cA 723 9.13e+00 1d8cA c.1.13.1 29325 1r26A 125 9.29e+00 c.47.1.1 96847 1qsoA 149 9.45e+00 1qsmA d.108.1.1 40812 1mjc 69 9.48e+00 1mjc b.40.4.5 25319 2a4nA 182 9.58e+00 1viuA 203 9.62e+00 d.113.1.1 100771 1yvkA 163 9.63e+00 2bl1A 172 9.89e+00 1jeyA 609 1.01e+01 1jeqA b.131.1.1,c.62.1.3 90370,90371 1t3qB 788 1.02e+01 d.41.1.1,d.133.1.1 106369,106370 1xewX 182 1.02e+01 1rwzA 245 1.04e+01 d.131.1.2,d.131.1.2 98005,98006 1k7iA 479 1.06e+01 b.80.7.1,d.92.1.6 77281,77282 1kw4A 89 1.13e+01 a.60.1.2 73077 1pzxA 289 1.14e+01 c.119.1.1 95484 1hw7A 255 1.15e+01 1i7fA d.193.1.1 61297 1qstA 160 1.16e+01 1yghA d.108.1.1 40804 2fl7A 232 1.18e+01 1bmv2 374 1.21e+01 1bmv2 1j1bA 420 1.22e+01 d.144.1.7 90758 1uacL 107 1.22e+01 b.1.1.1 99133 2f9dA 125 1.23e+01 1x65A 89 1.26e+01 1r62A 160 1.26e+01 d.122.1.3 104816 1ifyA 49 1.27e+01 a.5.2.1 71207 2ganA 190 1.28e+01 1ucyH 150 1.29e+01 1ucyH 2f1lA 187 1.32e+01 1t6t1 118 1.34e+01 1yqfA 203 1.35e+01 1eo6A 117 1.35e+01 1eo6A d.15.1.3 37609 1go7P 462 1.36e+01 b.80.7.1,d.92.1.6 76245,76246 1bdfA 235 1.36e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1xwsA 313 1.37e+01 2gw6A 123 1.38e+01 1fl0A 171 1.39e+01 1eujA b.40.4.4 25315 2affA 120 1.40e+01 2f4wA 187 1.41e+01 2a6hA 315 1.41e+01 1ugmA 125 1.43e+01 d.15.1.3 107827 2adcA 229 1.47e+01 1s0uA 408 1.48e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1fxrA 64 1.48e+01 1fxd d.58.1.4 38993 1ha1 184 1.49e+01 1ha1 d.58.7.1,d.58.7.1 39147,39148 1ad3A 452 1.52e+01 1ad3A c.82.1.1 35335 1uscA 178 1.54e+01 b.45.1.2 99860 1b87A 181 1.55e+01 1b87A d.108.1.1 40797 1vkyA 347 1.56e+01 e.53.1.1 108696 1wmhB 86 1.56e+01 1ttwA 138 1.56e+01 d.198.1.1 107308 1ylxA 103 1.59e+01 1gk8I 140 1.59e+01 d.73.1.1 65242 2gs8A 317 1.60e+01 1zn6A 227 1.60e+01 1a8vA 121 1.61e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 1gnuA 117 1.61e+01 d.15.1.3 65403 1zhvA 134 1.64e+01 1o7dE 126 1.64e+01 1smxA 96 1.66e+01 b.40.4.5 105772 1uadC 99 1.67e+01 b.1.18.18 88379 2a19B 284 1.69e+01 1fbnA 230 1.72e+01 1fbnA c.66.1.3 34181 1ppfE 218 1.74e+01 1a7s b.47.1.2 26234 2beiA 170 1.77e+01 1g7sA 594 1.77e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1l7bA 92 1.78e+01 c.15.1.2 91053 1g31A 111 1.79e+01 1g31A b.35.1.1 24656 1db3A 372 1.82e+01 1db3A c.2.1.2 29813 1dazC 99 1.86e+01 1hvc b.50.1.1 26501 1hzdA 272 1.86e+01 c.14.1.3 65969 2b7aA 293 1.87e+01 1pvmA 184 1.89e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1yqbA 100 1.90e+01 1p5vB 147 1.93e+01 b.2.3.2 87814 1p4fA 293 1.95e+01 d.144.1.7 104063 1yloA 348 1.96e+01 2arhA 203 1.97e+01 1qtqA 553 1.99e+01 1gtrA b.53.1.2,c.26.1.1 26940,31579 1n71A 180 2.00e+01 d.108.1.1 85370 1avaC 181 2.02e+01 1avaC b.42.4.1 25604 1ir21 140 2.03e+01 1lvoA 302 2.04e+01 b.47.1.4 74284 1jmuB 666 2.06e+01 1l4iA 206 2.06e+01 b.1.11.1,b.7.2.1 73564,73565 2fhqA 141 2.07e+01 1ze3H 122 2.10e+01 2awkA 228 2.11e+01 1jpaA 312 2.11e+01 d.144.1.7 67011 1xkpC 143 2.16e+01 2ampA 304 2.17e+01 2c2hA 192 2.19e+01 2agcA 162 2.24e+01 2aexA 346 2.26e+01 2gpjA 252 2.29e+01 1z9lA 128 2.32e+01 2d8aA 348 2.33e+01 1kmqA 184 2.33e+01 c.37.1.8 84412 1y0gA 191 2.34e+01 1cq3A 233 2.35e+01 1cq3A b.27.1.1 23923 1g8sA 230 2.35e+01 c.66.1.3 90507 1oo0B 110 2.38e+01 d.58.7.1 87183 1qlaB 239 2.39e+01 1qlaB a.1.2.1,d.15.4.2 15679,37707 1l1dA 152 2.40e+01 b.88.1.3 73452 1fjgQ 105 2.41e+01 1fjfQ b.40.4.5 25352 1cd8 114 2.46e+01 1cd8 b.1.1.1 19714 1yu4A 381 2.49e+01 1hztA 190 2.50e+01 1i9aA d.113.1.2 61459 1v70A 105 2.53e+01 1j8rA 196 2.54e+01 1j8rA b.2.3.3 62745 1eulA 994 2.57e+01 1eulA 2bswA 146 2.57e+01 1ok7A 366 2.58e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1wmhA 89 2.58e+01 1q5xA 161 2.58e+01 c.8.7.1 95947 1dun 134 2.59e+01 1dun b.85.4.1 28371 1vi4A 174 2.59e+01 c.8.7.1 100731 1i1dA 161 2.64e+01 1i21A d.108.1.1 61526 1s29A 92 2.67e+01 a.4.5.46 98373 1uc2A 481 2.68e+01 d.261.1.1 99161 2cqsA 842 2.73e+01 1aw8B 91 2.73e+01 1aw8B 1h6kA 757 2.76e+01 a.118.1.14,a.118.1.14,a.118.1.14 60675,60676,60677 2fvgA 340 2.77e+01 2ad9A 119 2.77e+01 1oalA 151 2.78e+01 b.1.8.1 86739 1io1A 398 2.79e+01 1io1A e.32.1.1 62611 2bikB 313 2.79e+01 1vctA 205 2.81e+01 1rpa 342 2.81e+01 1cviA c.60.1.2 33983 1koe 172 2.82e+01 1koe d.169.1.5 42448 1omyA 65 2.83e+01 g.3.7.1 93354 1sw5A 275 2.84e+01 c.94.1.1 106069 1lw6I 64 2.84e+01 d.40.1.1 74294 2d2eA 250 2.86e+01 1lplA 95 2.87e+01 b.34.10.1 74173 1um0A 365 2.91e+01 d.258.1.1 107942 1gsmA 210 2.93e+01 b.1.1.4,b.1.1.4 65535,65536 1h2kA 349 2.93e+01 b.82.2.6 76572 1v5tA 90 2.94e+01 d.15.1.1 108385 1jjtA 228 2.97e+01 1a7tA d.157.1.1 63139 1nulA 152 2.98e+01 1nulA c.61.1.1 34011 1q52A 314 2.98e+01 c.14.1.3 95846 1i12A 160 2.99e+01 1i21A d.108.1.1 61515 2a6tA 271 3.00e+01 1pgl2 370 3.00e+01 1a2yB 116 3.01e+01 1gc1H b.1.1.1 19927 1wddS 128 3.02e+01 1ifqA 138 3.03e+01 1ifqA d.110.4.1 62350 1q40B 219 3.10e+01 d.17.4.2 95771 1rxwA 336 3.12e+01 a.60.7.1,c.120.1.2 98059,98060 1o50A 157 3.13e+01 d.37.1.1,d.37.1.1 92478,92479 1vr9A 213 3.14e+01 1vs0A 310 3.18e+01 1c1lA 136 3.19e+01 1c1lA b.29.1.3 24219 3vub 101 3.21e+01 3vub b.34.6.1 24613 1m4zA 238 3.24e+01 b.34.12.1 78630 1nd4A 264 3.24e+01 d.144.1.6 91815 2cu1A 103 3.26e+01 1wgrA 100 3.30e+01 2bhvA 246 3.31e+01 1qy5A 269 3.32e+01 d.122.1.1 96573 1u59A 287 3.32e+01 d.144.1.7 107681 1l0wA 580 3.32e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1wlnA 120 3.35e+01 1wjnA 97 3.40e+01 1tw0A 157 3.42e+01 1pht 85 3.44e+01 1ckaA b.34.2.1 24483 1wckA 220 3.55e+01 1lb6A 160 3.55e+01 b.8.1.1 73798 1vqoD 177 3.57e+01 1rypL 212 3.60e+01 d.153.1.4 41880 1fmtA 314 3.61e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 1z96A 40 3.71e+01 1q2yA 140 3.72e+01 d.108.1.1 95655 1lci 550 3.72e+01 1lci e.23.1.1 43349 2f9hA 129 3.72e+01 1m7bA 184 3.73e+01 c.37.1.8 74572 1j08A 226 3.74e+01 c.47.1.2,c.47.1.2 83855,83856 1p7hL 286 3.74e+01 b.1.18.1,b.2.5.3 94271,94272 1jhsA 188 3.74e+01 d.107.1.1 84172 2ewrA 170 3.77e+01 1wvqA 167 3.77e+01 2gsfA 373 3.77e+01 1z7gA 217 3.79e+01 2cvdA 198 3.80e+01 1epwA 1290 3.81e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 2fwhA 134 3.83e+01 1whi 122 3.85e+01 1whi b.39.1.1 24810 1uc7A 125 3.88e+01 c.47.1.1 99163 1yu3A 381 3.89e+01 1i50A 1733 3.91e+01 e.29.1.2 61754 1go3E 187 3.91e+01 b.40.4.5,d.230.1.1 83054,83055 1o8bA 219 3.92e+01 c.124.1.4,d.58.40.1 81180,81181 2glfA 450 3.93e+01 1whmA 92 3.93e+01 1icxA 155 3.96e+01 d.129.3.1 71191 1hvyA 288 3.96e+01 1bkpA d.117.1.1 41049 1wvcA 259 3.97e+01 2hc1A 291 3.98e+01 1mspA 126 4.03e+01 1mspA b.1.11.2 22333 1sfp 114 4.05e+01 1sfp b.23.1.1 23895 1pqhA 143 4.06e+01 b.52.2.1 95017 1ut7A 171 4.09e+01 b.143.1.1 99906 1jksA 294 4.10e+01 d.144.1.7 71710 1kt6A 183 4.12e+01 b.60.1.1 84466 1x71A 178 4.12e+01 1ndh 272 4.17e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1zcbA 362 4.18e+01 1nthA 458 4.22e+01 c.1.25.1 80730 1js8A 394 4.22e+01 a.86.1.1,b.112.1.1 67219,67220 1iyhA 198 4.23e+01 a.45.1.1,c.47.1.5 83790,83791 1tovA 98 4.23e+01 b.34.10.1 107179 1x84A 189 4.24e+01 1qwrA 319 4.27e+01 b.82.1.3 96491 1yr0A 175 4.30e+01 1ppjB 439 4.33e+01 d.185.1.1,d.185.1.1 104254,104255 2cw5A 255 4.33e+01 1jm6A 407 4.43e+01 a.29.5.1,d.122.1.4 66876,66877 1l1oC 181 4.47e+01 b.40.4.3 73480 1sjwA 144 4.48e+01 d.17.4.9 98899 2gs5A 198 4.49e+01 1rutX 188 4.55e+01 1c9oA 66 4.55e+01 1mjc b.40.4.5 25325 2fxqA 264 4.57e+01 1vr3A 191 4.59e+01 1l0lB 439 4.61e+01 d.185.1.1,d.185.1.1 84484,84485 1pvxA 194 4.66e+01 1axkA b.29.1.11 24341 1svy 114 4.69e+01 1svy d.109.1.1 40831 1ppo 216 4.73e+01 1cs8A d.3.1.1 37020 1to2I 64 4.74e+01 1wlfA 179 4.76e+01 b.52.2.3,d.31.1.1 109396,109397 1jhfA 202 4.79e+01 a.4.5.2,b.87.1.1 63057,63058 1jc4A 148 4.79e+01 1jc4A d.32.1.4 62863 1sixA 174 4.81e+01 b.85.4.1 98892 1s6lA 212 4.85e+01 1yezA 68 4.90e+01 1jj2B 337 4.91e+01 1ffkB b.43.3.2 63086 2h03A 291 4.95e+01 1zo0A 126 4.96e+01 1v58A 241 4.99e+01 c.47.1.9,d.17.3.1 108371,108372 1yzbA 182 5.01e+01 1u2cA 246 5.02e+01 b.1.6.2,d.272.1.1 107610,107611 2ghpA 292 5.02e+01 1uzcA 71 5.06e+01 a.159.2.1 100222 1lvaA 258 5.13e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1fs0E 138 5.13e+01 1aqt a.2.10.1,b.93.1.1 59997,59998 1el6A 219 5.14e+01 1el6B d.182.1.1 42606 1ten 90 5.14e+01 1ten b.1.2.1 21990 1j6qA 136 5.19e+01 b.40.9.1 77091 1r0pA 312 5.19e+01 d.144.1.7 96734 1cby 259 5.22e+01 1cby d.103.1.1 40705 1kypA 237 5.30e+01 d.22.1.1 73280 1th8A 145 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