# 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 2fneA 117 7.59e-15 2fe5A 94 1.16e-14 1tp5A 119 1.41e-14 1be9A 119 2.70e-14 1pdr b.36.1.1 24774 1qavA 90 5.05e-14 1qauA b.36.1.1 24777 2fcfA 103 5.89e-14 1g9oA 91 9.35e-14 1pdr b.36.1.1 60400 1n7eA 97 3.20e-13 b.36.1.1 91691 1ihjA 98 8.20e-13 1pdr b.36.1.1 62382 2h3lA 103 1.09e-12 2h2bA 107 1.13e-12 1q3oA 109 1.54e-12 b.36.1.1 95700 1nf3C 128 1.59e-12 b.36.1.1 85596 1l6oA 95 1.99e-12 b.36.1.1 84534 1n7fA 97 2.14e-12 b.36.1.1 91692 1mfgA 95 4.74e-12 b.36.1.1 79043 2f0aA 98 2.11e-11 1wf7A 103 2.45e-11 1kwaA 88 2.45e-11 1kwaA b.36.1.1 24772 2f5yA 91 6.51e-11 1qauA 112 9.67e-11 1qauA b.36.1.1 24779 1v5lA 103 3.04e-10 b.36.1.1 108378 1nteA 82 3.79e-10 b.36.1.1 86163 1r6jA 82 6.99e-10 b.36.1.1 97151 1lcyA 325 8.42e-07 b.36.1.4,b.47.1.1 73834,73835 1fc6A 388 2.36e-06 1fc6A b.36.1.3,c.14.1.2 64738,64739 1te0A 318 7.14e-06 1y8tA 324 8.80e-03 1xebA 150 9.10e-02 1y9wA 140 1.06e-01 1fxlA 167 2.48e-01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1wjuA 100 4.69e-01 2fe7A 166 5.96e-01 2bshA 125 7.43e-01 2bsjA 133 7.85e-01 1kk1A 410 8.93e-01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1cq3A 233 9.76e-01 1cq3A b.27.1.1 23923 1a79A 171 1.19e+00 1a79A c.52.2.1,d.75.1.1 33340,39739 1se8A 301 1.38e+00 b.40.4.3 105448 2d4pA 141 1.45e+00 2c5qA 240 1.56e+00 1y9kA 157 1.59e+00 2bhoA 130 1.60e+00 1sotA 320 1.63e+00 b.36.1.4,b.47.1.1 105852,105853 1ucyH 150 1.63e+00 1ucyH 1vkcA 158 1.64e+00 1z4eA 153 1.67e+00 1r13A 148 1.72e+00 d.169.1.1,h.1.1.1 96782,96783 1ti6A 875 1.73e+00 b.52.2.2,c.81.1.1 106974,106975 1on0A 158 1.77e+00 d.108.1.1 87095 2avtA 378 1.83e+00 2cy2A 174 1.83e+00 1eso 154 1.99e+00 1yaiA b.1.8.1 22293 1bo4A 168 2.10e+00 1bo4A d.108.1.1 40798 1qsmA 152 2.86e+00 1qsmA d.108.1.1 40808 2awaA 390 3.10e+00 1z4rA 168 3.36e+00 1vj0A 380 3.46e+00 b.35.1.2,c.2.1.1 100786,100787 1qwrA 319 3.77e+00 b.82.1.3 96491 1ha1 184 4.05e+00 1ha1 d.58.7.1,d.58.7.1 39147,39148 1wi5A 119 4.07e+00 1yqbA 100 5.14e+00 1eo6A 117 5.46e+00 1eo6A d.15.1.3 37609 2fl4A 149 5.48e+00 1avaC 181 5.50e+00 1avaC b.42.4.1 25604 2cu1A 103 5.91e+00 1qsoA 149 6.05e+00 1qsmA d.108.1.1 40812 1yezA 68 6.07e+00 1tiqA 180 6.17e+00 d.108.1.1 107010 1yvkA 163 6.28e+00 1xtlA 175 6.56e+00 1y7rA 133 7.01e+00 1k3eA 156 7.22e+00 d.198.1.1 68103 1p7tA 731 7.26e+00 c.1.13.1 94319 1yb3A 175 7.31e+00 2a6hA 315 7.36e+00 2f4wA 187 7.42e+00 1wjnA 97 7.47e+00 1xtmA 175 7.48e+00 2brfA 110 7.54e+00 1d8cA 723 7.62e+00 1d8cA c.1.13.1 29325 1yvcA 70 7.91e+00 2a6tA 271 8.29e+00 1uyrA 737 8.52e+00 c.14.1.4,c.14.1.4 100188,100189 1f20A 435 8.65e+00 b.43.4.1,c.25.1.4 64932,64933 1tf4A 605 8.70e+00 1tf4A a.102.1.2,b.2.2.2 18827,22393 2bw3A 534 8.77e+00 1luzA 88 8.83e+00 b.40.4.5 74271 1svy 114 8.90e+00 1svy d.109.1.1 40831 1wwzA 159 9.21e+00 1ze3H 122 9.47e+00 1qstA 160 9.72e+00 1yghA d.108.1.1 40804 1w2xA 758 9.73e+00 c.14.1.4,c.14.1.4 109134,109135 1x6oA 174 9.75e+00 b.34.5.2,b.40.4.5 109493,109494 1s0uA 408 9.99e+00 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1rsy 152 1.02e+01 1rsy b.7.1.2 23192 1zn6A 227 1.02e+01 1g2qA 187 1.03e+01 c.61.1.1 65117 1tllA 688 1.03e+01 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1zhhB 242 1.03e+01 1xk5A 204 1.14e+01 1z9lA 128 1.15e+01 1s4iA 175 1.18e+01 1hh1A 143 1.20e+01 1gefA c.52.1.18 61036 1l3kA 196 1.21e+01 d.58.7.1,d.58.7.1 73539,73540 1si6X 282 1.24e+01 1q2yA 140 1.24e+01 d.108.1.1 95655 1d4xG 126 1.31e+01 1d0nA d.109.1.1 59109 1p5vB 147 1.32e+01 b.2.3.2 87814 1bdfA 235 1.32e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1uebA 184 1.34e+01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1cliA 345 1.34e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1jmuB 666 1.36e+01 2btzA 394 1.37e+01 1jnyA 435 1.44e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1f3z 161 1.44e+01 1gpr b.84.3.1 28273 1gnuA 117 1.46e+01 d.15.1.3 65403 1nqjA 119 1.49e+01 b.23.2.1 86031 1wvhA 134 1.64e+01 2fl7A 232 1.65e+01 1bmv2 374 1.66e+01 1bmv2 1t44G 147 1.67e+01 d.109.1.1 106395 1nm1G 125 1.67e+01 d.109.1.1 80653 1yloA 348 1.68e+01 1uc2A 481 1.70e+01 d.261.1.1 99161 2cwaA 263 1.72e+01 1y21A 282 1.73e+01 1oalA 151 1.73e+01 b.1.8.1 86739 2affA 120 1.74e+01 2a4nA 182 1.79e+01 1mk4A 157 1.81e+01 d.108.1.1 84979 1musA 477 1.82e+01 c.55.3.4 79494 2mspA 126 1.84e+01 1mspA b.1.11.2 22335 1k32A 1045 1.91e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1xvsA 126 1.92e+01 1yzbA 182 1.92e+01 1xkpB 124 1.95e+01 1o8bA 219 1.96e+01 c.124.1.4,d.58.40.1 81180,81181 1k7iA 479 2.04e+01 b.80.7.1,d.92.1.6 77281,77282 1yvoA 172 2.08e+01 1cruA 454 2.09e+01 1c9uA b.68.2.1 27617 2ghpA 292 2.10e+01 1a62 130 2.11e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1t6t1 118 2.11e+01 1jndA 420 2.12e+01 c.1.8.5,d.26.3.1 71757,71758 1fjgQ 105 2.12e+01 1fjfQ b.40.4.5 25352 1f3iA 481 2.14e+01 1b7eA 1mspA 126 2.17e+01 1mspA b.1.11.2 22333 1id0A 152 2.19e+01 d.122.1.3 66111 1jm6A 407 2.19e+01 a.29.5.1,d.122.1.4 66876,66877 2cx1A 187 2.20e+01 1qy5A 269 2.21e+01 d.122.1.1 96573 1jc4A 148 2.22e+01 1jc4A d.32.1.4 62863 1uheA 97 2.22e+01 1ifyA 49 2.23e+01 a.5.2.1 71207 1u2cA 246 2.28e+01 b.1.6.2,d.272.1.1 107610,107611 1go7P 462 2.29e+01 b.80.7.1,d.92.1.6 76245,76246 2fxqA 264 2.30e+01 2beiA 170 2.37e+01 1icxA 155 2.37e+01 d.129.3.1 71191 2axwA 134 2.38e+01 2dpkA 152 2.42e+01 2gw6A 123 2.44e+01 1fs0E 138 2.45e+01 1aqt a.2.10.1,b.93.1.1 59997,59998 1kw4A 89 2.49e+01 a.60.1.2 73077 2d8aA 348 2.50e+01 1ten 90 2.50e+01 1ten b.1.2.1 21990 1hw7A 255 2.51e+01 1i7fA d.193.1.1 61297 1zs7A 190 2.59e+01 1gpr 162 2.59e+01 1gpr b.84.3.1 28267 1ml9A 302 2.60e+01 b.85.7.1 79282 1l1dA 152 2.60e+01 b.88.1.3 73452 1ugmA 125 2.60e+01 d.15.1.3 107827 1n71A 180 2.62e+01 d.108.1.1 85370 1h3gA 601 2.72e+01 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1yqzA 438 2.72e+01 1llnA 262 2.72e+01 d.165.1.1 84625 2gnrA 145 2.78e+01 2aegA 268 2.78e+01 1b87A 181 2.82e+01 1b87A d.108.1.1 40797 1wckA 220 2.89e+01 1qtqA 553 2.91e+01 1gtrA b.53.1.2,c.26.1.1 26940,31579 1sfp 114 2.92e+01 1sfp b.23.1.1 23895 2aexA 346 2.93e+01 1fxrA 64 2.98e+01 1fxd d.58.1.4 38993 2as0A 396 2.98e+01 1qfmA 710 3.05e+01 1qfmA b.69.7.1,c.69.1.4 27673,34641 1pgl2 370 3.06e+01 1uadC 99 3.15e+01 b.1.18.18 88379 1rl2A 137 3.19e+01 1rl2A b.34.5.3,b.40.4.5 24610,25342 2aefA 234 3.21e+01 1s3zA 165 3.22e+01 d.108.1.1 105250 1t9fA 187 3.23e+01 b.42.6.1 106710 1zhvA 134 3.24e+01 1a8vA 121 3.26e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 1l1oC 181 3.27e+01 b.40.4.3 73480 1h6kA 757 3.27e+01 a.118.1.14,a.118.1.14,a.118.1.14 60675,60676,60677 1qw2A 102 3.30e+01 d.249.1.1 96456 1go3E 187 3.30e+01 b.40.4.5,d.230.1.1 83054,83055 1wlnA 120 3.30e+01 1f8fA 371 3.34e+01 b.35.1.2,c.2.1.1 83246,83247 1bob 320 3.36e+01 1bob d.108.1.1 40816 2asfA 137 3.36e+01 1yoeA 322 3.36e+01 1obfO 335 3.44e+01 c.2.1.3,d.81.1.1 86768,86769 1ema 236 3.44e+01 1ema d.22.1.1 38339 1vqoB 338 3.46e+01 1yjmA 110 3.54e+01 1l7bA 92 3.58e+01 c.15.1.2 91053 2ew0A 192 3.60e+01 1pzxA 289 3.63e+01 c.119.1.1 95484 1s8fA 177 3.65e+01 c.37.1.8 105370 1yqfA 203 3.65e+01 2f1wA 158 3.69e+01 1yaiA 151 3.74e+01 1yaiA b.1.8.1 22289 2bl1A 172 3.75e+01 1q40B 219 3.76e+01 d.17.4.2 95771 1s29A 92 3.77e+01 a.4.5.46 98373 1p4fA 293 3.78e+01 d.144.1.7 104063 1mpxA 615 3.80e+01 b.18.1.13,c.69.1.21 85041,85042 1vlqA 337 3.83e+01 c.69.1.25 108848 1ygs 234 3.92e+01 1ygs b.26.1.1 23907 1v86A 95 3.93e+01 d.15.1.1 108421 1q3iA 214 4.02e+01 d.220.1.1 104524 1stzA 338 4.04e+01 a.4.5.51,d.110.2.3 106009,106010 2fwhA 134 4.05e+01 2cruA 118 4.13e+01 1lw6I 64 4.14e+01 d.40.1.1 74294 1y791 680 4.23e+01 1mb3A 124 4.24e+01 c.23.1.1 78907 2b5gA 171 4.25e+01 1seiA 130 4.27e+01 1seiA d.140.1.1 41463 1rwzA 245 4.27e+01 d.131.1.2,d.131.1.2 98005,98006 1ik9A 213 4.28e+01 b.59.1.1,h.1.11.1 66176,66177 2f9dA 125 4.32e+01 1l0bA 229 4.32e+01 c.15.1.3,c.15.1.3 73391,73392 2prd 174 4.35e+01 2prd b.40.5.1 25435 1r0uA 148 4.36e+01 b.60.1.5 96741 1s72B 338 4.37e+01 b.43.3.2 105320 1wxaA 116 4.40e+01 2c60A 111 4.42e+01 1kxlA 199 4.44e+01 b.40.4.3 73155 1p7hL 286 4.54e+01 b.1.18.1,b.2.5.3 94271,94272 1w4tA 299 4.56e+01 1o7dE 126 4.57e+01 1gk8I 140 4.57e+01 d.73.1.1 65242 1ip9A 85 4.59e+01 1ip9A d.15.2.2 62638 1z96A 40 4.61e+01 1y0gA 191 4.69e+01 1koe 172 4.71e+01 1koe d.169.1.5 42448 1jj2B 337 4.71e+01 1ffkB b.43.3.2 63086 1r62A 160 4.71e+01 d.122.1.3 104816 1fw9A 164 4.72e+01 1fw9A d.190.1.1 60059 8rucI 123 4.75e+01 1rboC d.73.1.1 39629 1vlmA 219 4.75e+01 c.66.1.41 108836 1um0A 365 4.80e+01 d.258.1.1 107942 1g7sA 594 4.84e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1rxwA 336 4.86e+01 a.60.7.1,c.120.1.2 98059,98060 1l0lB 439 4.87e+01 d.185.1.1,d.185.1.1 84484,84485 1lvaA 258 4.87e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1a6q 382 4.91e+01 1a6q a.159.1.1,d.219.1.1 75801,75802 1feuA 206 4.91e+01 1feuA b.53.1.1 59801 1yzsA 121 4.96e+01 1wxxA 382 4.99e+01 1tzfA 259 4.99e+01 c.68.1.13 107476 1h2wA 710 5.11e+01 b.69.7.1,c.69.1.4 76596,76597 1qfjA 232 5.20e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 2bkfA 87 5.20e+01 1ijgA 309 5.23e+01 1fouA e.27.1.1 62493 2cdqA 510 5.23e+01 1wbiA 129 5.24e+01 2ganA 190 5.25e+01 1rxxA 421 5.25e+01 d.126.1.4 98061 1ha3A 405 5.26e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1sdjA 310 5.49e+01 d.21.1.2,d.21.1.2 98807,98808 1sw5A 275 5.50e+01 c.94.1.1 106069 2rspA 124 5.52e+01 2rspB b.50.1.1 26771 1d7qA 143 5.53e+01 1d7qA b.40.4.5 25331 1srrA 124 5.56e+01 1dz3A c.23.1.1 31110 1vkyA 347 5.57e+01 e.53.1.1 108696 1jjiA 311 5.58e+01 c.69.1.2 66766 1uwkA 557 5.58e+01 e.51.1.1 108065 1pnsC 206 5.59e+01 i.1.1.1 88170 2a10A 125 5.61e+01 1eulA 994 5.61e+01 1eulA 1u6mA 199 5.70e+01 1egiA 147 5.70e+01 1eggA d.169.1.1 42331 1z08A 170 5.73e+01 1wvqA 167 5.73e+01 1k0rA 366 5.75e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 67961,67962,67963,67964 1qipA 183 5.76e+01 1qipA d.32.1.1 38470 2bswA 146 5.76e+01 1l7aA 318 5.78e+01 c.69.1.25 77772 2atzA 180 5.80e+01 1xzoA 174 5.81e+01 1rxdA 159 5.84e+01 1b43A 340 5.84e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 1l0wA 580 5.86e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1zdnA 158 5.87e+01 1sfjA 238 5.92e+01 1oixA 191 5.93e+01 2adcA 229 5.94e+01 1wi1A 126 5.96e+01 1vzoA 355 5.97e+01 d.144.1.7 108971 1qunB 279 5.98e+01 b.2.3.2,b.2.3.2 22411,22412 1e3dA 266 6.00e+01 2frvA e.19.1.1 59188 1tt8A 164 6.02e+01 1fl2A 310 6.03e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1m4zA 238 6.05e+01 b.34.12.1 78630 1fx3A 169 6.06e+01 1fx3B d.33.1.1 38524 1j24A 143 6.11e+01 c.52.1.20 84008 2c78A 405 6.12e+01 1hgxA 183 6.13e+01 1tc1A c.61.1.1 34027 1jksA 294 6.16e+01 d.144.1.7 71710 1g8mA 593 6.18e+01 1g8mA c.24.1.3,c.97.2.1 60371,60372 1x65A 89 6.19e+01 1y8oA 419 6.21e+01 1klfB 279 6.28e+01 b.2.3.2,b.2.3.2 72684,72685 1h5wA 309 6.31e+01 e.27.1.1 65635 1v1qA 134 6.33e+01 1im3D 95 6.37e+01 1im3D b.1.18.5 62568 1l8nA 679 6.41e+01 c.1.8.10,d.92.2.2 84564,84565 1exmA 405 6.42e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1qyaA 307 6.43e+01 d.21.1.2,d.21.1.2 104653,104654 1pne 140 6.43e+01 1pne d.110.1.1 40866 1i7pA 274 6.43e+01 b.43.4.2,c.25.1.1 66048,66049 1v3vA 333 6.44e+01 b.35.1.2,c.2.1.1 108345,108346 1prtF 98 6.49e+01 1prtF b.40.2.1 25140 1inlA 296 6.50e+01 c.66.1.17 66220 1upqA 123 6.52e+01 1vzqH 250 6.55e+01 1zsyA 357 6.56e+01 1o50A 157 6.56e+01 d.37.1.1,d.37.1.1 92478,92479 1xewX 182 6.60e+01 1u3oA 82 6.62e+01 1ndh 272 6.64e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1ypcI 64 6.65e+01 2sniI d.40.1.1 38570 1h8dH 260 6.68e+01 5ptp 1vf7A 369 6.69e+01 f.46.1.1 108557 1to2I 64 6.70e+01 1zclA 180 6.75e+01 1db3A 372 6.75e+01 1db3A c.2.1.2 29813 1i4uA 181 6.76e+01 b.60.1.1 61732 1wvcA 259 6.77e+01 1uw0A 117 6.78e+01 g.39.1.12 108063 1hbq 183 6.79e+01 1aqb b.60.1.1 27078 1vckA 115 6.83e+01 1vc3B 97 6.85e+01 1garA 212 6.89e+01 2gar c.65.1.1 34162 1tt7A 330 6.89e+01 2ai4A 119 6.89e+01 2fvgA 340 6.91e+01 1n0lA 224 6.92e+01 b.1.11.1,b.7.2.1 79744,79745 1uc7A 125 6.93e+01 c.47.1.1 99163 2bsyA 278 6.94e+01 1umkA 275 6.94e+01 1u69A 163 6.96e+01 d.32.1.7 107699 1rutX 188 6.97e+01 2cf8H 257 6.97e+01 1yy6A 155 7.02e+01 1u3wA 374 7.03e+01 2b9eA 303 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