# 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 1g9oA 91 6.63e-26 1pdr b.36.1.1 60400 2fe5A 94 4.10e-24 2fneA 117 2.93e-23 1tp5A 119 3.97e-23 1be9A 119 6.55e-23 1pdr b.36.1.1 24774 1qavA 90 8.25e-23 1qauA b.36.1.1 24777 1n7eA 97 1.52e-22 b.36.1.1 91691 2fcfA 103 2.08e-22 1n7fA 97 2.28e-21 b.36.1.1 91692 1ihjA 98 1.34e-20 1pdr b.36.1.1 62382 2f5yA 91 1.88e-20 1q3oA 109 2.35e-20 b.36.1.1 95700 1wf7A 103 1.62e-19 1nf3C 128 1.72e-19 b.36.1.1 85596 1l6oA 95 1.99e-19 b.36.1.1 84534 1kwaA 88 4.45e-19 1kwaA b.36.1.1 24772 1mfgA 95 5.50e-19 b.36.1.1 79043 1qauA 112 7.09e-19 1qauA b.36.1.1 24779 2f0aA 98 4.73e-18 1nteA 82 5.90e-18 b.36.1.1 86163 1r6jA 82 1.39e-17 b.36.1.1 97151 1v5lA 103 1.99e-17 b.36.1.1 108378 1fc6A 388 1.68e-10 1fc6A b.36.1.3,c.14.1.2 64738,64739 1lcyA 325 1.26e-09 b.36.1.4,b.47.1.1 73834,73835 1te0A 318 2.07e-09 1y8tA 324 1.94e-07 1fxlA 167 3.41e-04 1b7fA d.58.7.1,d.58.7.1 39183,39184 1y9wA 140 1.02e-02 1wjuA 100 4.72e-02 1k32A 1045 8.30e-02 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1sotA 320 1.31e-01 b.36.1.4,b.47.1.1 105852,105853 1r13A 148 2.03e-01 d.169.1.1,h.1.1.1 96782,96783 2bkfA 87 2.28e-01 1a62 130 2.88e-01 1a62 a.140.3.1,b.40.4.5 64708,64709 1xebA 150 2.92e-01 1yloA 348 3.02e-01 1x6oA 174 3.57e-01 b.34.5.2,b.40.4.5 109493,109494 1db3A 372 4.47e-01 1db3A c.2.1.2 29813 2fl4A 149 5.20e-01 1ti6A 875 5.50e-01 b.52.2.2,c.81.1.1 106974,106975 1uheA 97 5.93e-01 2c5qA 240 6.19e-01 2fe7A 166 6.23e-01 1zhhB 242 6.24e-01 1d4xG 126 6.64e-01 1d0nA d.109.1.1 59109 1qfjA 232 6.70e-01 1qfjA b.43.4.2,c.25.1.1 25655,31545 1se8A 301 7.37e-01 b.40.4.3 105448 1luzA 88 7.46e-01 b.40.4.5 74271 1a79A 171 8.12e-01 1a79A c.52.2.1,d.75.1.1 33340,39739 1um0A 365 8.37e-01 d.258.1.1 107942 1ugmA 125 8.79e-01 d.15.1.3 107827 1yqbA 100 9.06e-01 1y7rA 133 9.32e-01 1nm1G 125 9.45e-01 d.109.1.1 80653 1sfp 114 9.63e-01 1sfp b.23.1.1 23895 1g8aA 227 1.02e+00 c.66.1.3 90506 1ha1 184 1.15e+00 1ha1 d.58.7.1,d.58.7.1 39147,39148 1viuA 203 1.22e+00 d.113.1.1 100771 1x65A 89 1.23e+00 1vheA 373 1.32e+00 b.49.3.1,c.56.5.4 100669,100670 1xk5A 204 1.36e+00 1y9kA 157 1.37e+00 1h2kA 349 1.42e+00 b.82.2.6 76572 1vhxA 150 1.45e+00 c.55.3.8 100712 1yb3A 175 1.52e+00 1tllA 688 1.63e+00 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1vc3B 97 1.81e+00 1wjnA 97 1.90e+00 2d4pA 141 2.05e+00 1t0yA 122 2.18e+00 d.15.1.1 99066 1vzoA 355 2.23e+00 d.144.1.7 108971 1ygs 234 2.33e+00 1ygs b.26.1.1 23907 1zhvA 134 2.34e+00 1smxA 96 2.34e+00 b.40.4.5 105772 1a8vA 121 2.37e+00 1a62 a.140.3.1,b.40.4.5 64712,64713 2brfA 110 2.39e+00 2b4aA 138 2.44e+00 1f20A 435 2.45e+00 b.43.4.1,c.25.1.4 64932,64933 1gsmA 210 2.56e+00 b.1.1.4,b.1.1.4 65535,65536 1cq3A 233 2.65e+00 1cq3A b.27.1.1 23923 1uc2A 481 2.78e+00 d.261.1.1 99161 1mspA 126 2.80e+00 1mspA b.1.11.2 22333 1k3eA 156 2.82e+00 d.198.1.1 68103 1t3qB 788 2.87e+00 d.41.1.1,d.133.1.1 106369,106370 1yjmA 110 2.93e+00 1p5vB 147 3.05e+00 b.2.3.2 87814 2ganA 190 3.12e+00 1ema 236 3.14e+00 1ema d.22.1.1 38339 1fl0A 171 3.19e+00 1eujA b.40.4.4 25315 2mspA 126 3.26e+00 1mspA b.1.11.2 22335 1vqoD 177 3.26e+00 1z9lA 128 3.37e+00 1bx4A 345 3.38e+00 1bx4A c.72.1.1 34935 1vs0A 310 3.38e+00 2fvgA 340 3.44e+00 1o50A 157 3.46e+00 d.37.1.1,d.37.1.1 92478,92479 1prtF 98 3.47e+00 1prtF b.40.2.1 25140 1fdr 248 3.49e+00 1fdr b.43.4.2,c.25.1.1 25653,31543 2cy5A 140 3.53e+00 1l0lB 439 3.53e+00 d.185.1.1,d.185.1.1 84484,84485 2prd 174 3.55e+00 2prd b.40.5.1 25435 1j5uA 136 3.55e+00 d.208.1.1 71584 1hh1A 143 3.61e+00 1gefA c.52.1.18 61036 2bshA 125 3.63e+00 1ex2A 189 3.67e+00 1ex2A c.51.4.2 33225 1whi 122 3.75e+00 1whi b.39.1.1 24810 1h3gA 601 3.95e+00 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1cd8 114 4.02e+00 1cd8 b.1.1.1 19714 1pqhA 143 4.18e+00 b.52.2.1 95017 1vd2A 89 4.30e+00 d.15.2.2 108517 1qyaA 307 4.43e+00 d.21.1.2,d.21.1.2 104653,104654 2g8mA 264 4.46e+00 2gw6A 123 4.66e+00 1l3kA 196 4.78e+00 d.58.7.1,d.58.7.1 73539,73540 1ifyA 49 4.79e+00 a.5.2.1 71207 1ad3A 452 4.81e+00 1ad3A c.82.1.1 35335 1shsA 147 4.85e+00 1shsA b.15.1.1 23675 1g31A 111 4.97e+00 1g31A b.35.1.1 24656 2bhoA 130 5.04e+00 1evfA 264 5.16e+00 1bkpA d.117.1.1 40932 2c60A 111 5.17e+00 1nqjA 119 5.18e+00 b.23.2.1 86031 1im3D 95 5.19e+00 1im3D b.1.18.5 62568 1x67A 146 5.22e+00 1wnfA 328 5.23e+00 1ppjB 439 5.45e+00 d.185.1.1,d.185.1.1 104254,104255 1garA 212 5.48e+00 2gar c.65.1.1 34162 1vj0A 380 5.59e+00 b.35.1.2,c.2.1.1 100786,100787 1pzxA 289 5.67e+00 c.119.1.1 95484 2fywA 267 5.73e+00 1wvhA 134 5.91e+00 1klfB 279 5.93e+00 b.2.3.2,b.2.3.2 72684,72685 1bdfA 235 5.96e+00 1bdfA d.74.3.1,d.181.1.1 39727,42602 1g3qA 237 6.04e+00 1hyqA c.37.1.10 60237 1sdjA 310 6.11e+00 d.21.1.2,d.21.1.2 98807,98808 1pvmA 184 6.16e+00 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 2atrA 138 6.19e+00 1mjc 69 6.42e+00 1mjc b.40.4.5 25319 1f00I 282 6.42e+00 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1qlpA 394 6.46e+00 1ovaA e.1.1.1 42628 1bkb 136 6.58e+00 1bkb b.34.5.2,b.40.4.5 24609,25341 1js8A 394 6.61e+00 a.86.1.1,b.112.1.1 67219,67220 1mb3A 124 6.66e+00 c.23.1.1 78907 1qunB 279 6.67e+00 b.2.3.2,b.2.3.2 22411,22412 1ze3H 122 6.88e+00 2awkA 228 6.91e+00 1l7bA 92 6.94e+00 c.15.1.2 91053 2bsjA 133 7.02e+00 1k7iA 479 7.09e+00 b.80.7.1,d.92.1.6 77281,77282 1qqqA 264 7.18e+00 1bkpA d.117.1.1 40931 2aexA 346 7.24e+00 1khxA 227 7.41e+00 b.26.1.1 68631 2f4wA 187 7.43e+00 1rxwA 336 7.47e+00 a.60.7.1,c.120.1.2 98059,98060 1go7P 462 7.57e+00 b.80.7.1,d.92.1.6 76245,76246 2a19B 284 7.74e+00 1b63A 333 7.85e+00 1b63A d.14.1.3,d.122.1.2 37566,41107 1x71A 178 7.88e+00 1xewX 182 7.94e+00 1yphC 131 8.27e+00 1qh7A 207 8.32e+00 1axkA b.29.1.11 24317 1h6kA 757 8.35e+00 a.118.1.14,a.118.1.14,a.118.1.14 60675,60676,60677 1ucyH 150 8.47e+00 1ucyH 1t9fA 187 8.52e+00 b.42.6.1 106710 1f35A 162 8.57e+00 1f35A b.94.1.1 59628 1b43A 340 8.67e+00 1a76 a.60.7.1,c.120.1.2 18092,33362 2a6tA 271 8.67e+00 2c3gA 98 8.85e+00 2b9eA 303 8.91e+00 1v70A 105 8.99e+00 1kw4A 89 9.09e+00 a.60.1.2 73077 1vr9A 213 9.11e+00 1r26A 125 9.14e+00 c.47.1.1 96847 1m4zA 238 9.14e+00 b.34.12.1 78630 1yvkA 163 9.21e+00 1m1sA 116 9.32e+00 b.1.11.2 84747 1nv8A 284 9.45e+00 c.66.1.30 86224 1o8bA 219 9.45e+00 c.124.1.4,d.58.40.1 81180,81181 2g8oA 264 9.68e+00 1s3zA 165 9.80e+00 d.108.1.1 105250 1dun 134 9.97e+00 1dun b.85.4.1 28371 1ixkA 315 1.01e+01 c.66.1.38 90716 1khiA 176 1.02e+01 b.34.5.2,b.40.4.5 77408,77409 2cwaA 263 1.02e+01 1wlsA 328 1.04e+01 1n3jA 119 1.04e+01 b.85.7.2 79963 2bwfA 77 1.07e+01 2f4iA 197 1.09e+01 1cqkA 101 1.10e+01 1cqkA b.1.1.2 21547 1hbq 183 1.12e+01 1aqb b.60.1.1 27078 2f1lA 187 1.13e+01 1xa0A 328 1.14e+01 1qsmA 152 1.15e+01 1qsmA d.108.1.1 40808 1fxrA 64 1.16e+01 1fxd d.58.1.4 38993 1qhlA 227 1.17e+01 1qhlA c.37.1.12 32382 1wckA 220 1.18e+01 1z96A 40 1.18e+01 1uzcA 71 1.20e+01 a.159.2.1 100222 1rxxA 421 1.21e+01 d.126.1.4 98061 1q7hA 153 1.23e+01 b.122.1.1,d.17.6.2 96042,96043 1hzdA 272 1.24e+01 c.14.1.3 65969 1kzlA 208 1.24e+01 b.43.4.3,b.43.4.3 77635,77636 1iyhA 198 1.26e+01 a.45.1.1,c.47.1.5 83790,83791 2bw3A 534 1.26e+01 1fmtA 314 1.29e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 1z7gA 217 1.29e+01 2ghpA 292 1.30e+01 1hvyA 288 1.31e+01 1bkpA d.117.1.1 41049 1h4gA 207 1.33e+01 b.29.1.11 70863 1zsyA 357 1.33e+01 1ip9A 85 1.33e+01 1ip9A d.15.2.2 62638 1kt6A 183 1.40e+01 b.60.1.1 84466 1gvhA 396 1.41e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1p7tA 731 1.43e+01 c.1.13.1 94319 1p7hL 286 1.45e+01 b.1.18.1,b.2.5.3 94271,94272 1qlaB 239 1.45e+01 1qlaB a.1.2.1,d.15.4.2 15679,37707 1vie 62 1.48e+01 1vie b.34.4.1 24592 1vkcA 158 1.49e+01 2atzA 180 1.49e+01 1pyoA 167 1.50e+01 c.17.1.1 95370 1svy 114 1.50e+01 1svy d.109.1.1 40831 1d8cA 723 1.50e+01 1d8cA c.1.13.1 29325 1mk4A 157 1.52e+01 d.108.1.1 84979 2b8nA 429 1.54e+01 1sfjA 238 1.61e+01 1z4rA 168 1.61e+01 1uacL 107 1.64e+01 b.1.1.1 99133 1xv2A 237 1.65e+01 1wmhB 86 1.69e+01 2d2eA 250 1.70e+01 1sjwA 144 1.71e+01 d.17.4.9 98899 1y96A 86 1.73e+01 1usuB 170 1.75e+01 d.83.2.1 99886 1qqcA 773 1.78e+01 1tgoA c.55.3.5,e.8.1.1 33724,43013 1zh1A 163 1.79e+01 1iukA 140 1.80e+01 c.2.1.8 83712 1jb3A 131 1.80e+01 1jc7A b.40.3.2 62833 1ten 90 1.81e+01 1ten b.1.2.1 21990 1rxdA 159 1.81e+01 1o0uA 429 1.84e+01 c.118.1.1 80743 1bqbA 301 1.87e+01 1hyt d.92.1.2 58962 2awaA 390 1.90e+01 1jjtA 228 1.91e+01 1a7tA d.157.1.1 63139 1g7sA 594 1.92e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 2cvdA 198 1.93e+01 1mo1A 87 1.94e+01 d.94.1.1 91363 1gg6B 131 1.97e+01 5ptp 1wmhA 89 1.97e+01 2fxqA 264 1.99e+01 2btzA 394 1.99e+01 1jc4A 148 2.00e+01 1jc4A d.32.1.4 62863 1jmuB 666 2.00e+01 1iarB 207 2.01e+01 1iarB b.1.2.1,b.1.2.1 22037,22038 1aqb 183 2.01e+01 1aqb b.60.1.1 27084 1o7dE 126 2.03e+01 1cyx 205 2.03e+01 1cyx b.6.1.2 23023 1xfoA 357 2.03e+01 1vekA 84 2.05e+01 1vqwA 457 2.05e+01 1ccwB 483 2.06e+01 1cb7B c.1.19.2 29646 1s29A 92 2.07e+01 a.4.5.46 98373 2cw5A 255 2.09e+01 1fr3A 67 2.14e+01 1fr3A b.40.6.1 25436 1llnA 262 2.15e+01 d.165.1.1 84625 2aefA 234 2.17e+01 1krhA 338 2.19e+01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 1l0bA 229 2.20e+01 c.15.1.3,c.15.1.3 73391,73392 1yvoA 172 2.22e+01 1kypA 237 2.24e+01 d.22.1.1 73280 1wl4A 397 2.25e+01 1e3jA 352 2.25e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 2aujD 309 2.26e+01 2a6hA 315 2.28e+01 1eu1A 780 2.31e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 1qorA 327 2.31e+01 1qorA b.35.1.2,c.2.1.1 24766,29782 1hztA 190 2.32e+01 1i9aA d.113.1.2 61459 2b4lA 268 2.33e+01 1vejA 74 2.34e+01 1iz5A 249 2.37e+01 d.131.1.2,d.131.1.2 83834,83835 1xx0A 127 2.37e+01 1x89A 178 2.38e+01 1kssA 571 2.39e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 2ghjA 118 2.41e+01 1lvaA 258 2.44e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1tw0A 157 2.46e+01 1qsoA 149 2.47e+01 1qsmA d.108.1.1 40812 1qmyA 167 2.47e+01 1qmyA d.3.1.2 37094 1lj5A 379 2.47e+01 e.1.1.1 73928 1kkcA 221 2.47e+01 a.2.11.1,d.44.1.1 68660,68661 2ck3A 510 2.49e+01 1l3iA 192 2.50e+01 c.66.1.22 77676 1zckA 154 2.51e+01 2byjA 439 2.51e+01 1ryjA 70 2.57e+01 d.15.3.2 98104 1t6t1 118 2.60e+01 1vkmA 297 2.61e+01 c.138.1.1 108670 1h8eA 510 2.61e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 2cx1A 187 2.63e+01 1q1oA 98 2.63e+01 d.15.2.2 95596 2g3aA 152 2.64e+01 1cqxA 403 2.66e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1qstA 160 2.71e+01 1yghA d.108.1.1 40804 1bo4A 168 2.72e+01 1bo4A d.108.1.1 40798 1y0yA 353 2.73e+01 1widA 130 2.73e+01 1nepA 130 2.76e+01 b.1.18.7 80440 2cu1A 103 2.76e+01 2cqsA 842 2.78e+01 1sflA 238 2.82e+01 1id0A 152 2.83e+01 d.122.1.3 66111 1usuA 260 2.85e+01 d.14.1.8 99885 1e79A 510 2.87e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 1v0aA 178 2.89e+01 1f8fA 371 2.89e+01 b.35.1.2,c.2.1.1 83246,83247 2aukA 190 2.90e+01 1rm6A 769 2.90e+01 1mjhA 162 2.90e+01 1mjhA c.26.2.4 31639 1qw2A 102 2.91e+01 d.249.1.1 96456 1kmvA 186 2.91e+01 c.71.1.1 72757 1f3aA 222 2.93e+01 1pgtA a.45.1.1,c.47.1.5 17701,32995 1pwbA 177 2.94e+01 d.169.1.1,h.1.1.1 95212,95213 2adcA 229 2.94e+01 1yavA 159 2.94e+01 1o6dA 163 2.96e+01 c.116.1.3 92567 1iq8A 582 2.97e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1fjgP 88 3.00e+01 1emwA d.27.1.1 38444 1i8kA 107 3.00e+01 b.1.1.1 71130 1z2mA 155 3.05e+01 1p4fA 293 3.06e+01 d.144.1.7 104063 1j8fA 323 3.08e+01 1j8fA c.31.1.5 62738 1c9oA 66 3.08e+01 1mjc b.40.4.5 25325 2apr 325 3.13e+01 2er7E b.50.1.2 26819 1rl2A 137 3.14e+01 1rl2A b.34.5.3,b.40.4.5 24610,25342 1l7mA 211 3.19e+01 c.108.1.4 73664 1uwkA 557 3.23e+01 e.51.1.1 108065 1g2hA 61 3.24e+01 1g2hA a.4.1.12 60224 2blkA 122 3.25e+01 1kgcE 242 3.25e+01 b.1.1.1,b.1.1.2 77386,77387 3aprE 325 3.27e+01 2er7E b.50.1.2 26820 1zvnA 99 3.27e+01 2cvzA 289 3.28e+01 1tv9A 335 3.29e+01 1ml9A 302 3.30e+01 b.85.7.1 79282 1s8fA 177 3.34e+01 c.37.1.8 105370 1ejfA 125 3.34e+01 1ejfA b.15.1.2 23683 1e7uA 961 3.35e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1v5tA 90 3.35e+01 d.15.1.1 108385 1e39A 571 3.36e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1o4yA 288 3.36e+01 b.29.1.2 92473 1txnA 328 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