# List of top-scoring protein chains for t06-100-40-40-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 8.05e-17 2fe5A 94 1.48e-16 1g9oA 91 6.18e-16 1pdr b.36.1.1 60400 1tp5A 119 9.86e-16 1qavA 90 2.83e-15 1qauA b.36.1.1 24777 2fcfA 103 6.84e-15 1ihjA 98 9.02e-15 1pdr b.36.1.1 62382 2h2bA 107 1.82e-14 1n7eA 97 2.24e-14 b.36.1.1 91691 1q3oA 109 4.48e-14 b.36.1.1 95700 2h3lA 103 5.74e-14 1mfgA 95 8.81e-14 b.36.1.1 79043 1n7fA 97 1.03e-13 b.36.1.1 91692 1nf3C 128 4.04e-13 b.36.1.1 85596 2f5yA 91 6.03e-13 2f0aA 98 1.10e-12 1qauA 112 1.34e-12 1qauA b.36.1.1 24779 1kwaA 88 1.34e-12 1kwaA b.36.1.1 24772 1wf7A 103 1.53e-12 1r6jA 82 3.21e-11 b.36.1.1 97151 1fc6A 388 5.10e-08 1fc6A b.36.1.3,c.14.1.2 64738,64739 1te0A 318 1.20e-07 1lcyA 325 1.40e-07 b.36.1.4,b.47.1.1 73834,73835 1y8tA 324 4.42e-05 1y9wA 140 3.78e-02 1fxlA 167 1.33e-01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1k32A 1045 1.37e-01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 2fe7A 166 1.61e-01 1f20A 435 2.95e-01 b.43.4.1,c.25.1.4 64932,64933 2c5qA 240 4.10e-01 1xebA 150 4.42e-01 1z4eA 153 5.03e-01 1bo4A 168 6.26e-01 1bo4A d.108.1.1 40798 2fl4A 149 8.31e-01 2d4pA 141 8.78e-01 1id0A 152 8.86e-01 d.122.1.3 66111 2bhoA 130 9.17e-01 2aefA 234 9.50e-01 2bsjA 133 1.04e+00 1y7rA 133 1.38e+00 1a62 130 1.47e+00 1a62 a.140.3.1,b.40.4.5 64708,64709 1d4xG 126 1.64e+00 1d0nA d.109.1.1 59109 1kk1A 410 1.64e+00 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1zhhB 242 1.75e+00 1gpr 162 1.83e+00 1gpr b.84.3.1 28267 1t44G 147 1.88e+00 d.109.1.1 106395 1vkcA 158 1.88e+00 2cy2A 174 1.89e+00 2avtA 378 2.01e+00 1xk5A 204 2.15e+00 1xewX 182 2.15e+00 2gw6A 123 2.18e+00 1se8A 301 2.21e+00 b.40.4.3 105448 1cliA 345 2.39e+00 1cliA d.79.4.1,d.139.1.1 39816,41459 1yb3A 175 2.41e+00 1r0vA 305 2.56e+00 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 1luzA 88 2.71e+00 b.40.4.5 74271 1um0A 365 2.71e+00 d.258.1.1 107942 1x6oA 174 2.77e+00 b.34.5.2,b.40.4.5 109493,109494 1ti6A 875 3.21e+00 b.52.2.2,c.81.1.1 106974,106975 1p7tA 731 3.61e+00 c.1.13.1 94319 1nlqA 108 3.67e+00 b.121.3.1 85853 1rsy 152 3.86e+00 1rsy b.7.1.2 23192 1nqjA 119 3.88e+00 b.23.2.1 86031 2bw3A 534 3.99e+00 1ex2A 189 4.15e+00 1ex2A c.51.4.2 33225 2fhqA 141 4.20e+00 1r26A 125 4.30e+00 c.47.1.1 96847 1ugmA 125 4.31e+00 d.15.1.3 107827 8rucI 123 4.48e+00 1rboC d.73.1.1 39629 2c3gA 98 4.48e+00 1vj0A 380 4.71e+00 b.35.1.2,c.2.1.1 100786,100787 2brfA 110 4.73e+00 1iz5A 249 4.95e+00 d.131.1.2,d.131.1.2 83834,83835 1qsmA 152 4.99e+00 1qsmA d.108.1.1 40808 1qstA 160 5.00e+00 1yghA d.108.1.1 40804 1ok7A 366 5.20e+00 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1uacL 107 5.78e+00 b.1.1.1 99133 2bswA 146 5.96e+00 2bkfA 87 6.36e+00 1c1lA 136 6.40e+00 1c1lA b.29.1.3 24219 1rlhA 173 6.40e+00 d.256.1.1 97646 1hh1A 143 6.91e+00 1gefA c.52.1.18 61036 1s3zA 165 6.95e+00 d.108.1.1 105250 1wgrA 100 6.97e+00 1sdjA 310 7.20e+00 d.21.1.2,d.21.1.2 98807,98808 1yvcA 70 7.21e+00 1yvoA 172 7.21e+00 1sfp 114 7.33e+00 1sfp b.23.1.1 23895 1yloA 348 7.71e+00 1qwrA 319 7.74e+00 b.82.1.3 96491 1z4rA 168 7.83e+00 1wjuA 100 7.94e+00 1oalA 151 8.57e+00 b.1.8.1 86739 2fvgA 340 8.62e+00 1jnyA 435 8.69e+00 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1fjgQ 105 8.80e+00 1fjfQ b.40.4.5 25352 1jeyA 609 9.05e+00 1jeqA b.131.1.1,c.62.1.3 90370,90371 1r62A 160 9.17e+00 d.122.1.3 104816 1lb6A 160 9.29e+00 b.8.1.1 73798 1euwA 152 9.61e+00 1dupA b.85.4.1 28349 1j8rA 196 9.62e+00 1j8rA b.2.3.3 62745 1vpkA 378 9.78e+00 1hw7A 255 9.80e+00 1i7fA d.193.1.1 61297 1uadC 99 1.02e+01 b.1.18.18 88379 2g3aA 152 1.07e+01 1uscA 178 1.11e+01 b.45.1.2 99860 1g6hA 257 1.12e+01 1gajA c.37.1.12 60318 2awkA 228 1.12e+01 1uc2A 481 1.14e+01 d.261.1.1 99161 1io1A 398 1.14e+01 1io1A e.32.1.1 62611 1s29A 92 1.18e+01 a.4.5.46 98373 2b5gA 171 1.20e+01 1upqA 123 1.20e+01 1avaC 181 1.22e+01 1avaC b.42.4.1 25604 1zh1A 163 1.22e+01 1vctA 205 1.23e+01 1kw4A 89 1.23e+01 a.60.1.2 73077 1pzxA 289 1.26e+01 c.119.1.1 95484 1pvmA 184 1.26e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1g31A 111 1.27e+01 1g31A b.35.1.1 24656 1qyaA 307 1.28e+01 d.21.1.2,d.21.1.2 104653,104654 1vheA 373 1.29e+01 b.49.3.1,c.56.5.4 100669,100670 1rwzA 245 1.29e+01 d.131.1.2,d.131.1.2 98005,98006 2f9hA 129 1.30e+01 2dpkA 152 1.31e+01 1t9fA 187 1.32e+01 b.42.6.1 106710 1rypL 212 1.33e+01 d.153.1.4 41880 1wi0A 113 1.35e+01 1qy5A 269 1.36e+01 d.122.1.1 96573 1g7sA 594 1.47e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1zhvA 134 1.47e+01 1ym5A 300 1.47e+01 1xkpB 124 1.50e+01 1x65A 89 1.53e+01 2fl7A 232 1.55e+01 1wmhA 89 1.58e+01 1vr9A 213 1.60e+01 1zn6A 227 1.61e+01 1l0wA 580 1.62e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1t0yA 122 1.63e+01 d.15.1.1 99066 2d2eA 250 1.65e+01 1sixA 174 1.65e+01 b.85.4.1 98892 1kolA 398 1.73e+01 b.35.1.2,c.2.1.1 77474,77475 1eo6A 117 1.74e+01 1eo6A d.15.1.3 37609 1tiqA 180 1.75e+01 d.108.1.1 107010 1dun 134 1.77e+01 1dun b.85.4.1 28371 2beiA 170 1.78e+01 1whi 122 1.79e+01 1whi b.39.1.1 24810 1p4fA 293 1.83e+01 d.144.1.7 104063 2ganA 190 1.84e+01 1pvxA 194 1.84e+01 1axkA b.29.1.11 24341 2f9dA 125 1.86e+01 1jmuB 666 1.86e+01 2gs5A 198 1.90e+01 1g8aA 227 1.90e+01 c.66.1.3 90506 2gs8A 317 1.93e+01 1o50A 157 1.94e+01 d.37.1.1,d.37.1.1 92478,92479 1z9lA 128 1.95e+01 1ten 90 1.95e+01 1ten b.1.2.1 21990 1h2kA 349 1.98e+01 b.82.2.6 76572 1o8bA 219 2.00e+01 c.124.1.4,d.58.40.1 81180,81181 1ylxA 103 2.05e+01 1gnuA 117 2.11e+01 d.15.1.3 65403 1wckA 220 2.11e+01 1yoeA 322 2.11e+01 1t3qB 788 2.12e+01 d.41.1.1,d.133.1.1 106369,106370 1n71A 180 2.12e+01 d.108.1.1 85370 1a2yB 116 2.13e+01 1gc1H b.1.1.1 19927 1j1bA 420 2.13e+01 d.144.1.7 90758 2covD 104 2.22e+01 1wvqA 167 2.22e+01 1q2yA 140 2.25e+01 d.108.1.1 95655 2f1lA 187 2.25e+01 1pk6C 129 2.26e+01 b.22.1.1 94803 1q3iA 214 2.26e+01 d.220.1.1 104524 1vqoD 177 2.29e+01 1lf7A 182 2.32e+01 b.60.1.1 73878 1t6t1 118 2.34e+01 1cq3A 233 2.34e+01 1cq3A b.27.1.1 23923 2bsyA 278 2.36e+01 1j6qA 136 2.37e+01 b.40.9.1 77091 2bikB 313 2.38e+01 1h6kA 757 2.40e+01 a.118.1.14,a.118.1.14,a.118.1.14 60675,60676,60677 1p5vB 147 2.45e+01 b.2.3.2 87814 1a6cA 513 2.47e+01 1a6cA b.121.4.2,b.121.4.2,b.121.4.2 23296,23297,23298 1vggA 161 2.48e+01 1qhlA 227 2.51e+01 1qhlA c.37.1.12 32382 1iqqA 200 2.51e+01 d.124.1.1 66274 2a6tA 271 2.53e+01 1i8kB 124 2.56e+01 b.1.1.1 71131 1f60A 458 2.61e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1bywA 110 2.62e+01 1bywA d.110.3.6 40912 1mspA 126 2.63e+01 1mspA b.1.11.2 22333 1vqoB 338 2.67e+01 2fxqA 264 2.68e+01 1acf 125 2.70e+01 3nul d.110.1.1 40882 1vzoA 355 2.71e+01 d.144.1.7 108971 1jksA 294 2.72e+01 d.144.1.7 71710 1lvoA 302 2.72e+01 b.47.1.4 74284 2gcuA 245 2.73e+01 1rxwA 336 2.73e+01 a.60.7.1,c.120.1.2 98059,98060 1yqfA 203 2.75e+01 2fywA 267 2.77e+01 1usuB 170 2.78e+01 d.83.2.1 99886 1omyA 65 2.82e+01 g.3.7.1 93354 1h2wA 710 2.86e+01 b.69.7.1,c.69.1.4 76596,76597 1l3kA 196 2.87e+01 d.58.7.1,d.58.7.1 73539,73540 2c60A 111 2.96e+01 1q1oA 98 3.00e+01 d.15.2.2 95596 1hzdA 272 3.00e+01 c.14.1.3 65969 1wmhB 86 3.04e+01 1khiA 176 3.06e+01 b.34.5.2,b.40.4.5 77408,77409 2aexA 346 3.08e+01 1nulA 152 3.13e+01 1nulA c.61.1.1 34011 1ppjB 439 3.13e+01 d.185.1.1,d.185.1.1 104254,104255 1ccwB 483 3.14e+01 1cb7B c.1.19.2 29646 1l8nA 679 3.19e+01 c.1.8.10,d.92.2.2 84564,84565 1yqbA 100 3.20e+01 1ttwA 138 3.24e+01 d.198.1.1 107308 1n0qA 93 3.25e+01 k.37.1.1 79754 1v70A 105 3.27e+01 1vkyA 347 3.30e+01 e.53.1.1 108696 1l1dA 152 3.35e+01 b.88.1.3 73452 2hc1A 291 3.36e+01 1iukA 140 3.41e+01 c.2.1.8 83712 2f4wA 187 3.53e+01 1pgl2 370 3.54e+01 1nthA 458 3.55e+01 c.1.25.1 80730 1sw5A 275 3.55e+01 c.94.1.1 106069 1gk8I 140 3.56e+01 d.73.1.1 65242 1vi4A 174 3.59e+01 c.8.7.1 100731 1ppfE 218 3.59e+01 1a7s b.47.1.2 26234 1fmtA 314 3.60e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 1b43A 340 3.61e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 1rxdA 159 3.67e+01 1jpaA 312 3.68e+01 d.144.1.7 67011 1iyhA 198 3.68e+01 a.45.1.1,c.47.1.5 83790,83791 1v3vA 333 3.69e+01 b.35.1.2,c.2.1.1 108345,108346 1oxdA 227 3.75e+01 d.22.1.1 93687 1vlrA 350 3.81e+01 d.13.1.3,d.246.1.1 108860,108861 1qmyA 167 3.82e+01 1qmyA d.3.1.2 37094 1wwzA 159 3.84e+01 2axoA 270 3.87e+01 1zanH 224 3.89e+01 1l6xA 207 3.92e+01 b.1.1.2,b.1.1.2 73642,73643 1zo0A 126 3.92e+01 1ww7A 160 3.93e+01 1mk4A 157 3.94e+01 d.108.1.1 84979 1wl4A 397 4.00e+01 1ud9A 245 4.03e+01 d.131.1.2,d.131.1.2 107768,107769 1oaqH 121 4.05e+01 b.1.1.1 92707 1vc3B 97 4.12e+01 1l2tA 235 4.14e+01 c.37.1.12 73514 1l3iA 192 4.16e+01 c.66.1.22 77676 1fqtA 112 4.17e+01 1fqtA b.33.1.1 24441 1g6gA 127 4.17e+01 1g6gA b.26.1.2 23916 1mw9X 592 4.20e+01 e.10.1.1 91480 2cqsA 842 4.21e+01 1uc7A 125 4.24e+01 c.47.1.1 99163 1cby 259 4.26e+01 1cby d.103.1.1 40705 1wkoA 180 4.28e+01 1i8nA 126 4.28e+01 1i8nA g.10.1.2 61976 3vub 101 4.29e+01 3vub b.34.6.1 24613 1g2hA 61 4.32e+01 1g2hA a.4.1.12 60224 1bdfA 235 4.32e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1q5xA 161 4.34e+01 c.8.7.1 95947 1vs0A 310 4.34e+01 2gpjA 252 4.35e+01 2cvdA 198 4.38e+01 1svy 114 4.38e+01 1svy d.109.1.1 40831 1obfO 335 4.40e+01 c.2.1.3,d.81.1.1 86768,86769 2ex4A 241 4.41e+01 2fwhA 134 4.43e+01 1hztA 190 4.45e+01 1i9aA d.113.1.2 61459 1lvaA 258 4.46e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1wlfA 179 4.53e+01 b.52.2.3,d.31.1.1 109396,109397 1tt8A 164 4.55e+01 1jhfA 202 4.58e+01 a.4.5.2,b.87.1.1 63057,63058 1u09A 476 4.62e+01 e.8.1.4 107545 2cy5A 140 4.63e+01 1k7iA 479 4.65e+01 b.80.7.1,d.92.1.6 77281,77282 1z96A 40 4.66e+01 2bc4A 211 4.70e+01 1gvhA 396 4.73e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1vlpA 441 4.75e+01 d.41.2.2,d.41.2.3 108840,108841 1o4yA 288 4.76e+01 b.29.1.2 92473 1qmvA 197 4.76e+01 1qq2A c.47.1.10 33066 1ir21 140 4.78e+01 1svdM 110 4.80e+01 1vkmA 297 4.87e+01 c.138.1.1 108670 1kxlA 199 4.90e+01 b.40.4.3 73155 1eexA 554 4.91e+01 1dioA c.1.19.3 29650 1wkyA 464 4.93e+01 1sh0A 510 4.95e+01 e.8.1.4 98876 1pne 140 4.96e+01 1pne d.110.1.1 40866 1wxxA 382 4.99e+01 2an3A 289 5.00e+01 1w9yA 319 5.02e+01 2gdjA 264 5.10e+01 1llnA 262 5.10e+01 d.165.1.1 84625 2ghjA 118 5.10e+01 2bhvA 246 5.11e+01 1uheA 97 5.12e+01 1mqkL 120 5.13e+01 b.1.1.1 85054 2ai4A 119 5.15e+01 1kt6A 183 5.19e+01 b.60.1.1 84466 1zsyA 357 5.20e+01 2cdqA 510 5.21e+01 1vmeA 410 5.22e+01 c.23.5.1,d.157.1.3 108893,108894 1pk6A 133 5.25e+01 b.22.1.1 94801 1bqbA 301 5.33e+01 1hyt d.92.1.2 58962 1kmqA 184 5.34e+01 c.37.1.8 84412 2h3bA 494 5.36e+01 1lngA 87 5.39e+01 d.201.1.1 74045 1thtA 305 5.39e+01 1thtA c.69.1.13 34711 1zh5A 195 5.40e+01 1ixkA 315 5.42e+01 c.66.1.38 90716 2fk9A 157 5.47e+01 1a6q 382 5.48e+01 1a6q a.159.1.1,d.219.1.1 75801,75802 1wtaA 275 5.50e+01 1wlgA 299 5.54e+01 1cruA 454 5.56e+01 1c9uA b.68.2.1 27617 2cw5A 255 5.57e+01 2btzA 394 5.60e+01 1w9gA 104 5.63e+01 2asfA 137 5.64e+01 1cd9B 215 5.65e+01 1cto b.1.2.1,b.1.2.1 22041,22042 2f91A 237 5.70e+01 1umkA 275 5.71e+01 1vhxA 150 5.78e+01 c.55.3.8 100712 1a2yA 107 5.79e+01 8fabA b.1.1.1 19926 1umzA 278 5.79e+01 b.29.1.2 99639 1hkfA 122 5.81e+01 b.1.1.1 83553 1trb 320 5.82e+01 1trb c.3.1.5,c.3.1.5 30529,30530 1wwkA 307 5.83e+01 2d8aA 348 5.84e+01 1i60A 278 5.85e+01 c.1.15.4 71118 1jndA 420 5.87e+01 c.1.8.5,d.26.3.1 71757,71758 1y0yA 353 5.89e+01 1sflA 238 5.92e+01 1yu0A 381 5.93e+01 1akz 223 5.93e+01 3eugA c.18.1.1 31007 1u9tA 354 5.93e+01 2b9eA 303 5.94e+01 1xs1A 193 5.95e+01 1c1dA 355 5.98e+01 1bw9A c.2.1.7,c.58.1.1 30270,33918 1v7wA 807 6.01e+01 a.102.1.4,b.30.5.3 108411,108412 2exnA 136 6.01e+01 2gu2A 312 6.03e+01 1qouA 181 6.07e+01 1qouA b.17.1.1 23707 1vk9A 151 6.08e+01 c.139.1.1 108640 1vbvA 105 6.10e+01 1yleA 342 6.14e+01 1n0lA 224 6.15e+01 b.1.11.1,b.7.2.1 79744,79745 1h3gA 601 6.15e+01 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 2glfA 450 6.22e+01 2arhA 203 6.27e+01 1s1qA 145 6.32e+01 d.20.1.2 98351 1olmA 403 6.36e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 2atrA 138 6.37e+01 1k4mA 213 6.38e+01 c.26.1.3 77258 1ngzA 213 6.39e+01 b.1.1.1,b.1.1.2 80500,80501 2a9iA 113 6.40e+01 1cr5A 189 6.40e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1y44A 320 6.41e+01 1xzoA 174 6.42e+01 1a7s 221 6.43e+01 1a7s b.47.1.2 26284 1pdkB 157 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422 8.77e+01 b.29.1.4,b.29.1.4 76604,76605 1uj6A 227 8.77e+01 c.124.1.4,d.58.40.1 107898,107899 1vr3A 191 8.78e+01 1nuuA 252 8.80e+01 c.26.1.3 86209 2fpmA 322 8.80e+01 2b6nA 278 8.82e+01 1wfxA 186 8.83e+01 2bneA 241 8.84e+01 1mh1 186 8.84e+01 1eesA c.37.1.8 32002 1gd0A 122 8.89e+01 1dptA d.80.1.3 39834 2ggcA 263 8.92e+01