# List of top-scoring protein chains for t2k-100-30-near-backbone-11-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 1bg2 325 6.84e-42 1bg2 c.37.1.9 32189 1i5sA 367 1.93e-40 1bg2 c.37.1.9 61822 1i6iA 366 2.30e-39 1bg2 c.37.1.9 61844 1ii6A 368 2.70e-39 1bg2 c.37.1.9 62413 1x88A 359 1.02e-38 1q0bA 367 1.16e-38 c.37.1.9 95502 1vfvA 366 1.87e-38 c.37.1.9 108592 1cz7A 406 2.45e-37 1bg2 c.37.1.9 32194 3kar 346 4.08e-37 1bg2 c.37.1.9 32198 1f9vA 347 1.12e-36 1bg2 c.37.1.9 59745 1ry6A 360 9.63e-35 c.37.1.9 98090 2kinA 238 9.19e-30 1bg2 c.37.1.9 32190 2kinB 100 1.60e-11 3kinB 3kinB 117 3.04e-11 3kinB 1l8qA 324 9.51e-04 a.4.12.2,c.37.1.20 77809,77810 1odfA 290 2.05e-01 c.37.1.6 92782 1d2mA 665 2.87e-01 1d2mA c.37.1.19,c.37.1.19 32417,32418 1p9rA 418 3.31e-01 c.37.1.11 94399 1bouB 302 6.13e-01 1bouB c.56.6.1 33859 1f60A 458 6.38e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1xwiA 322 6.41e-01 1jx2B 315 7.21e-01 c.37.1.8 67404 1jwyB 315 8.72e-01 c.37.1.8 67401 5ukdA 194 1.41e+00 1zin c.37.1.1 31851 1b4uB 302 1.46e+00 1bouB c.56.6.1 33861 1qf9A 194 1.79e+00 1zin c.37.1.1 31848 1g291 372 1.86e+00 1g291 1c4oA 664 2.16e+00 1d2mA c.37.1.19,c.37.1.19 32415,32416 2akaB 299 2.28e+00 1ddzA 496 2.36e+00 1ddzA c.53.2.1,c.53.2.1 33372,33373 1htjF 210 2.44e+00 1htjF a.91.1.1 61254 1xw8A 252 2.56e+00 1g6oA 330 3.13e+00 1g6oA c.37.1.11 32430 1um8A 376 3.75e+00 c.37.1.20 99580 2cdnA 201 3.89e+00 2ghpA 292 4.18e+00 1lv7A 257 4.66e+00 c.37.1.20 78232 3adk 195 5.12e+00 1zin c.37.1.1 31885 1u9iA 519 5.62e+00 1ed1A 135 5.98e+00 1hiwA a.61.1.1 18130 2fx0A 201 6.17e+00 1ihuA 589 6.35e+00 c.37.1.10,c.37.1.10 62394,62395 3bamA 213 6.37e+00 1bam c.52.1.3 33288 1hv8A 367 6.58e+00 1hv8A c.37.1.19,c.37.1.19 32405,32406 1yrbA 262 6.68e+00 1eqfA 280 7.47e+00 1eqfA a.29.2.1,a.29.2.1 16972,16973 1btmA 252 8.20e+00 1amk c.1.1.1 28513 1h6kX 97 8.22e+00 d.58.7.1 60684 1j8mF 297 8.58e+00 1ng1 a.24.13.1,c.37.1.10 62742,62743 1m33A 258 8.72e+00 c.69.1.26 78514 1wmhA 89 9.23e+00 3mag 307 9.62e+00 3mag c.66.1.25 34205 1f48A 589 9.76e+00 1f48A c.37.1.10,c.37.1.10 32280,32281 1h6kZ 98 1.02e+01 d.58.7.1 60686 1z83A 196 1.04e+01 1g8pA 350 1.09e+01 1g8pA c.37.1.20 60376 1vd2A 89 1.10e+01 d.15.2.2 108517 2pfkA 320 1.12e+01 3pfk c.89.1.1 35577 1mr3F 181 1.16e+01 c.37.1.8 79422 1pfkA 320 1.23e+01 3pfk c.89.1.1 35575 2azeA 155 1.25e+01 1vp9 322 1.26e+01 3mag c.66.1.25 34210 1gpjA 404 1.35e+01 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1akr 147 1.35e+01 1rcf c.23.5.1 31152 1h65A 270 1.39e+01 c.37.1.8 65640 1hurA 180 1.40e+01 1hurA c.37.1.8 32052 2bycA 137 1.41e+01 1wi6A 88 1.42e+01 1v39 322 1.42e+01 3mag c.66.1.25 34206 1vf8A 377 1.43e+01 1gvnB 287 1.43e+01 c.37.1.21 76354 1fnnA 389 1.48e+01 1fnnA a.4.5.11,c.37.1.20 16129,32426 1akw 147 1.50e+01 5nul c.23.5.1 31153 2ga9A 297 1.54e+01 1yobA 179 1.60e+01 1bu5A 147 1.62e+01 5nul c.23.5.1 31155 2ng1 293 1.63e+01 1ng1 a.24.13.1,c.37.1.10 16962,32273 1qhlA 227 1.64e+01 1qhlA c.37.1.12 32382 1akt 147 1.66e+01 5nul c.23.5.1 31157 1dmaA 214 1.71e+01 1aerA d.166.1.1 42251 1treA 255 1.72e+01 1amk c.1.1.1 28505 1azl 147 1.72e+01 5nul c.23.5.1 31154 2aq4A 434 1.77e+01 1e9lA 377 1.85e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 3bamB 213 1.93e+01 1bam c.52.1.3 33289 1xizA 159 1.96e+01 1j9eA 147 1.99e+01 c.23.5.1 62756 1z5zA 271 2.03e+01 1jcjA 260 2.06e+01 c.1.10.1 66499 1aerA 205 2.07e+01 1aerA d.166.1.1 42249 1ng1 294 2.07e+01 1ng1 a.24.13.1,c.37.1.10 16961,32272 1fts 295 2.08e+01 1ng1 a.24.13.1,c.37.1.10 16968,32279 2ak3A 226 2.11e+01 1zin c.37.1.1,g.41.2.1 31892,45193 2ccjA 205 2.11e+01 1jclA 260 2.21e+01 c.1.10.1 66501 2fji1 399 2.24e+01 1ad3A 452 2.29e+01 1ad3A c.82.1.1 35335 1yr0A 175 2.32e+01 2bdeA 470 2.32e+01 1t5yA 190 2.33e+01 b.122.1.1,d.17.6.3 106495,106496 1vpt 348 2.40e+01 3mag c.66.1.25 34207 1p27B 106 2.42e+01 d.58.7.1 93908 1dg3A 592 2.45e+01 1dg3A a.114.1.1,c.37.1.8 19078,32153 1p1xA 260 2.45e+01 c.1.10.1 104060 1ls1A 295 2.45e+01 a.24.13.1,c.37.1.10 78170,78171 1w36B 1180 2.47e+01 1eu1A 780 2.60e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 1wmdA 434 2.88e+01 b.18.1.20,c.41.1.1 109408,109409 1ji0A 240 2.88e+01 c.37.1.12 71665 1akq 147 2.89e+01 5nul c.23.5.1 31159 2fx2 147 3.06e+01 1rcf c.23.5.1 31158 1qvaA 223 3.08e+01 1qvaA c.37.1.19 32411 1ffh 294 3.13e+01 1ng1 a.24.13.1,c.37.1.10 16960,32271 1gadO 330 3.15e+01 1dssG c.2.1.3,d.81.1.1 29950,39865 1qdeA 224 3.21e+01 1qvaA c.37.1.19 32410 1oe9A 795 3.28e+01 b.34.3.1,c.37.1.9 92792,92793 1vdxA 184 3.34e+01 1xq6A 253 3.42e+01 1efaA 333 3.43e+01 1tlfA a.35.1.5,c.93.1.1 17106,35691 1jpnA 296 3.44e+01 a.24.13.1,c.37.1.10 67039,67040 2d00A 109 3.49e+01 1r9cA 139 3.49e+01 d.32.1.2 97255 1h2vZ 156 3.57e+01 d.58.7.1 76595 1qfjA 232 3.62e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 1q60A 99 3.64e+01 1k0dA 260 3.66e+01 a.45.1.1,c.47.1.5 67930,67931 1dmhA 311 3.66e+01 1dmhA b.3.6.1 22633 1ukz 203 3.66e+01 1zin c.37.1.1 31840 1kagA 173 3.73e+01 c.37.1.2 72249 2a5yB 549 3.73e+01 1f4pA 147 3.78e+01 5nul c.23.5.1 59651 1ye8A 178 3.90e+01 1r0wA 286 3.97e+01 c.37.1.12 96754 1f6bA 198 3.98e+01 c.37.1.8 64986 1pzgA 331 3.98e+01 c.2.1.5,d.162.1.1 95425,95426 1rypK 198 4.00e+01 d.153.1.4 41879 1bzyA 217 4.01e+01 1qk3A c.61.1.1 34071 1r5jA 337 4.03e+01 c.77.1.5 97097 1ofuA 320 4.05e+01 c.32.1.1,d.79.2.1 86972,86973 2g3bA 208 4.06e+01 1vyiA 112 4.07e+01 2cbzA 237 4.10e+01 1ofhA 310 4.10e+01 c.37.1.20 86948 2polA 366 4.11e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 1bueA 265 4.11e+01 1btl e.3.1.1 42727 2fpmA 322 4.11e+01 1fnuA 221 4.13e+01 3seb b.40.2.2,d.15.6.1 25212,37801 1jlm 192 4.13e+01 1ido c.62.1.1 34140 1vz6A 393 4.17e+01 d.154.1.2 108949 1m2oB 190 4.19e+01 c.37.1.8 78485 1ok7A 366 4.20e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 3aig 202 4.21e+01 1atlA d.92.1.9 40321 1qoxN 449 4.28e+01 1qoxN c.1.8.4 28978 1mmiA 366 4.29e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1yyaA 250 4.30e+01 1o9lA 481 4.33e+01 c.124.1.2,c.124.1.3 81241,81242 1b4kA 337 4.35e+01 1b4kA c.1.10.3 29184 1lyxA 248 4.37e+01 c.1.1.1 78304 1p3jA 217 4.38e+01 c.37.1.1,g.41.2.1 94022,94023 1cwyA 500 4.42e+01 1cwyA c.1.8.1 28789 1uluA 261 4.44e+01 1mv8A 436 4.51e+01 a.100.1.4,c.2.1.6,c.26.3.1 85128,85129,85130 1oyc 400 4.57e+01 1oyc c.1.4.1 28603 1pamA 686 4.57e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21846,22515,27753,28740 1oyb 400 4.58e+01 1oyc c.1.4.1 28602 1ddt 535 4.66e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22379,42241,43384 1jflA 228 4.66e+01 c.78.2.1,c.78.2.1 71656,71657 2ahuA 531 4.79e+01 1tueA 212 4.83e+01 c.37.1.20 107323 1gzgA 337 4.85e+01 c.1.10.3 70805 1ltqA 301 4.85e+01 c.108.1.9,c.37.1.1 78208,78209 1eswA 500 4.88e+01 1cwyA c.1.8.1 59500 1mf7A 194 4.88e+01 c.62.1.1 84937 1xw4X 110 4.92e+01 1rj9A 304 4.94e+01 a.24.13.1,c.37.1.10 97553,97554 1f5nA 592 4.99e+01 1dg3A a.114.1.1,c.37.1.8 19077,32152 1br2A 791 5.04e+01 1lvk b.34.3.1,c.37.1.9 24558,32155 1lkxA 697 5.07e+01 c.37.1.9 73981 1rxr 83 5.07e+01 2nllB g.39.1.2 45114 1oywA 523 5.08e+01 a.4.5.43,c.37.1.19,c.37.1.19 93760,93761,93762 1s7kA 182 5.08e+01 1w9iA 770 5.14e+01 1w5qA 337 5.16e+01 1ooyA 481 5.24e+01 c.124.1.3,c.124.1.2 93388,93389 1oya 400 5.28e+01 1oyc c.1.4.1 28604 1dl5A 317 5.32e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1esgA 213 5.33e+01 1bam c.52.1.3 33286 1e69B 322 5.38e+01 1e69B c.37.1.12 32377 1w5nA 337 5.41e+01 1hqoA 258 5.42e+01 1hqoA a.45.1.1,c.47.1.5 17749,33043 1xkyA 301 5.46e+01 1rkbA 173 5.56e+01 1np3A 338 5.75e+01 a.100.1.2,c.2.1.6 85946,85947 1d2nA 272 5.80e+01 1d2nA c.37.1.20 32428 1o75A 415 5.82e+01 b.1.20.1,b.1.20.1,b.120.1.1 81117,81118,81119 1ny6A 267 5.91e+01 c.37.1.20 92321 2fz4A 237 5.98e+01 2cvhA 220 6.07e+01 1ko7A 314 6.11e+01 c.98.2.1,c.91.1.2 72797,72798 1gcqA 61 6.19e+01 1ckaA b.34.2.1 60434 1xmiA 291 6.21e+01 1cjbA 231 6.23e+01 1qk3A c.61.1.1 34079 1d3cA 686 6.26e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21827,22496,27734,28721 1q5dA 419 6.29e+01 a.104.1.1 95891 1q0uA 219 6.33e+01 c.37.1.19 95512 1by4A 82 6.40e+01 2nllB g.39.1.2 45110 1vnc 609 6.45e+01 1vns a.111.1.3 19065 1wdtA 665 6.55e+01 1fhuA 320 6.58e+01 1fhuA c.1.11.2,d.54.1.1 29234,38878 1oafA 261 6.60e+01 a.93.1.1 86734 1ycdA 243 6.63e+01 1ky3A 182 6.65e+01 c.37.1.8 73193 1adeA 431 6.74e+01 1adeA c.37.1.10 32213 1uptC 170 6.76e+01 c.37.1.8 99769 1kr5A 226 6.78e+01 c.66.1.7 68847 2g03A 194 6.85e+01 1i19A 561 6.89e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 1b1zA 219 6.93e+01 3seb b.40.2.2,d.15.6.1 25216,37805 1fxkC 133 6.93e+01 1fxkC a.2.5.1 15702 1ug6A 431 6.95e+01 c.1.8.4 88490 2ax4A 198 6.96e+01 1ehiA 377 7.04e+01 1iow c.30.1.2,d.142.1.1 31716,41484 1o5xA 248 7.05e+01 c.1.1.1 92528 1e94F 449 7.07e+01 1do0A c.37.1.20 32443 1muhA 481 7.08e+01 c.55.3.4 79485 1i4wA 353 7.15e+01 c.66.1.24 66028 1vgjA 184 7.16e+01 1ot1A 686 7.28e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 87392,87393,87394,87395 1fioA 196 7.39e+01 1fioA a.47.2.1 17773 1ubpB 122 7.40e+01 1ubpB b.85.3.1 28346 1nsf 273 7.48e+01 1d2nA c.37.1.20 32429 1zu4A 320 7.59e+01 2aynA 404 7.68e+01 1k3eA 156 7.83e+01 d.198.1.1 68103 1tlfA 301 7.83e+01 1tlfA c.93.1.1 35687 1v5eA 590 7.88e+01 1sheA 103 7.93e+01 d.274.1.1 105551 1wn2A 121 7.93e+01 1gh6A 114 7.99e+01 a.2.3.1 65191 1w7jA 795 8.01e+01 2bkaA 242 8.02e+01 1mnd 762 8.10e+01 1lvk b.34.3.1,c.37.1.9 24591,32188 1gajA 257 8.13e+01 1gajA c.37.1.12 60416 1v5wA 343 8.13e+01 c.37.1.11 108387 1knqA 175 8.13e+01 c.37.1.17 72786 1z5vA 474 8.16e+01 1dvoA 152 8.19e+01 1dvoA a.136.1.1 19623 1zd8A 227 8.22e+01 1mvwA 840 8.27e+01 i.15.1.1 79523 1m4mA 140 8.38e+01 g.52.1.1 78605 2a4aA 281 8.39e+01 1f42A 306 8.49e+01 1f42A b.1.1.4,b.1.2.1,b.1.2.1 59636,59637,59638 1dszB 85 8.52e+01 2nllB g.39.1.2 45108 1rdfA 267 8.58e+01 c.108.1.3 104884 2irfG 113 8.59e+01 2irfG a.4.5.23 16185 1ceqA 316 8.78e+01 1ceqA c.2.1.5,d.162.1.1 30163,42130 1kafA 108 8.80e+01 d.199.1.1 68372 1rqlA 267 8.85e+01 c.108.1.3 97750 1e9rA 437 8.85e+01 c.37.1.11 64827