# List of top-scoring protein chains for t2k-100-30-dssp-ehl2-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 1eztA 166 4.36e-23 1agrE a.91.1.1 18541 1agrE 205 5.09e-23 1agrE a.91.1.1 18538 1fqiA 147 4.28e-22 1agrE a.91.1.1 18542 2bt2A 161 6.59e-22 2a72A 146 1.71e-21 1agrH 205 1.72e-21 1agrE a.91.1.1 18539 1dk8A 147 5.10e-18 1agrE a.91.1.1 18548 1omwA 689 1.65e-09 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 1htjF 210 2.30e-09 1htjF a.91.1.1 61254 1iapA 211 2.62e-03 a.91.1.1 62119 1lk3A 160 8.53e-01 a.26.1.3 73950 1wixA 164 9.88e-01 1mnaA 298 1.03e+00 c.69.1.22 79322 1io2A 213 1.54e+00 1ekeA c.55.3.1 62612 1p32A 209 1.55e+00 1p32A d.25.1.1 38379 1y3nA 490 1.78e+00 1ilk 151 1.93e+00 2ilk a.26.1.3 16886 2ilk 160 2.09e+00 2ilk a.26.1.3 16885 1il6 185 2.13e+00 1alu a.26.1.1 16827 1jfkA 134 2.68e+00 a.39.1.5 66639 1mq4A 272 2.74e+00 d.144.1.7 91391 1alu 186 3.06e+00 1alu a.26.1.1 16826 1q4mA 221 3.45e+00 a.132.1.3 95805 1ngnA 155 3.48e+00 a.96.1.2 85697 1y6nL 145 3.65e+00 1gkuB 1054 3.94e+00 c.37.1.16,c.37.1.16,e.10.1.1 65257,65258,65259 1p32C 209 3.99e+00 1p32A d.25.1.1 38381 1x3kA 152 4.39e+00 1kobA 387 4.39e+00 1tkiA d.144.1.7 41640 1eljA 381 4.58e+00 4mbp c.94.1.1 35791 1t46A 313 5.17e+00 d.144.1.7 106397 1aw9 216 5.26e+00 1gnwA a.45.1.1,c.47.1.5 17736,33030 1abbA 828 5.64e+00 1a8i c.87.1.4 35536 1bucA 383 6.31e+00 3mdeA a.29.3.1,e.6.1.1 16590,42851 1ao6A 585 6.49e+00 1bj5 a.126.1.1,a.126.1.1,a.126.1.1 19354,19355,19356 2f2gA 221 6.60e+00 1f3aA 222 7.28e+00 1pgtA a.45.1.1,c.47.1.5 17701,32995 1k3lA 221 7.51e+00 a.45.1.1,c.47.1.5 77229,77230 1k3yA 221 7.51e+00 a.45.1.1,c.47.1.5 77245,77246 3pflA 759 7.74e+00 1cm5A c.7.1.1 30673 1eh2 106 7.79e+00 1eh2 a.39.1.6 17339 1wa5B 530 8.13e+00 1n5uA 585 8.22e+00 a.126.1.1,a.126.1.1,a.126.1.1 85339,85340,85341 1gseA 221 8.46e+00 1pgtA a.45.1.1,c.47.1.5 17667,32961 1wvfA 520 8.49e+00 2fw2A 260 8.52e+00 1ir3A 306 8.54e+00 1fmk d.144.1.7 41702 1isiA 265 8.75e+00 e.4.1.1 71394 1lj8A 493 9.07e+00 a.100.1.9,c.2.1.6 90392,90393 2azjA 289 9.14e+00 1bj5 585 9.38e+00 1bj5 a.126.1.1,a.126.1.1,a.126.1.1 19369,19370,19371 1ha2A 585 9.73e+00 1bj5 a.126.1.1,a.126.1.1,a.126.1.1 60866,60867,60868 1ks8A 433 9.87e+00 a.102.1.2 77519 2bxkA 585 9.91e+00 2btzA 394 9.96e+00 1ann 318 1.04e+01 1avc a.65.1.1 18151 2fbmA 291 1.11e+01 1nm2A 317 1.12e+01 c.19.1.1,d.58.23.1 80654,80655 1irk 306 1.17e+01 1fmk d.144.1.7 41703 2b0jA 358 1.17e+01 1aow 309 1.18e+01 1avc a.65.1.1 18152 1cm5A 759 1.24e+01 1cm5A c.7.1.1 30671 1otkA 249 1.25e+01 a.25.1.2 93521 2pflA 759 1.29e+01 1cm5A c.7.1.1 30675 1uor 585 1.29e+01 1bj5 a.126.1.1,a.126.1.1,a.126.1.1 19396,19397,19398 2d29A 387 1.31e+01 2bs3C 256 1.37e+01 1znbA 232 1.42e+01 1a7tA d.157.1.1 42039 1lj2A 110 1.47e+01 h.1.13.2 73926 1qazA 351 1.50e+01 1qazA a.102.3.1 18848 2aw5A 541 1.52e+01 1h16A 759 1.54e+01 c.7.1.1 76462 1e7aA 585 1.58e+01 1bj5 a.126.1.1,a.126.1.1,a.126.1.1 19360,19361,19362 1upkA 341 1.59e+01 a.118.1.15 99758 2bx2L 517 1.62e+01 1qlaC 256 1.62e+01 1qlaC f.21.2.1 43722 1nznA 126 1.69e+01 a.118.8.1 92382 1txuA 273 1.72e+01 a.222.1.1 107439 1eco 136 1.77e+01 1flp a.1.1.2 15208 1k8kG 151 1.85e+01 a.118.13.1 68313 1pgtA 210 1.87e+01 1pgtA a.45.1.1,c.47.1.5 17515,32809 1eca 136 1.87e+01 1flp a.1.1.2 15209 1ecd 136 1.87e+01 1flp a.1.1.2 15211 1k0mA 241 1.88e+01 a.45.1.1,c.47.1.5 67949,67950 1a8a 318 1.94e+01 1avc a.65.1.1 18169 2ran 316 1.96e+01 1avc a.65.1.1 18170 1twfA 1733 1.96e+01 1bc0 319 1.98e+01 1avc a.65.1.1 18174 1k8kB 394 2.00e+01 c.55.1.1 68307 2b3oA 532 2.02e+01 1r5lA 262 2.03e+01 a.5.3.1,c.13.1.1 97099,97100 1m2aA 110 2.05e+01 c.47.1.11 78472 1a8b 318 2.06e+01 1avc a.65.1.1 18171 1m2bA 110 2.09e+01 c.47.1.11 78474 1xc3A 302 2.14e+01 1qlaA 656 2.16e+01 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 16328,30427,42310 1i39A 225 2.17e+01 1ekeA c.55.3.1 61585 1a7tA 232 2.18e+01 1a7tA d.157.1.1 42041 1x6mA 196 2.18e+01 1bc3 319 2.19e+01 1avc a.65.1.1 18175 1b48A 221 2.22e+01 1pgtA a.45.1.1,c.47.1.5 17703,32997 1eg7A 557 2.27e+01 1eg7A c.37.1.10 32241 1ws9A 387 2.35e+01 2bs3A 656 2.35e+01 1d3uB 201 2.38e+01 1aisB a.74.1.2,a.74.1.2 18386,18387 1xg7A 250 2.40e+01 1sa3A 262 2.43e+01 c.52.1.23 105400 1bc1 319 2.56e+01 1avc a.65.1.1 18173 1b25A 619 2.57e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1aqwA 209 2.58e+01 1pgtA a.45.1.1,c.47.1.5 17517,32811 1oniA 137 2.82e+01 d.79.1.1 87144 1gt7A 274 2.84e+01 c.74.1.1 70398 1kgnA 329 2.85e+01 a.25.1.2 68584 1td6A 306 2.88e+01 1qo7A 394 2.89e+01 1qo7A c.69.1.11 34697 1iygA 133 2.90e+01 a.118.8.1 76947 1gq2A 555 2.92e+01 c.2.1.7,c.58.1.3 70308,70309 1c3cA 429 2.94e+01 1c3cA a.127.1.1 19425 1kx9A 112 2.95e+01 a.118.21.1 77602 1ezvC 385 2.97e+01 1be3C f.32.1.1,f.21.1.2 75833,75834 1bq3B 246 2.98e+01 1qhfA c.60.1.1 33979 1z5vA 474 3.04e+01 2c3nA 247 3.05e+01 2bfxA 284 3.06e+01 2fug1 438 3.06e+01 1i50A 1733 3.11e+01 e.29.1.2 61754 18gsA 210 3.18e+01 1pgtA a.45.1.1,c.47.1.5 17528,32822 1kb9C 385 3.21e+01 f.32.1.1,f.21.1.2 77315,77316 1iw7C 1119 3.34e+01 e.29.1.1 71474 1eu8A 409 3.41e+01 1eu8A c.94.1.1 59502 1ojrA 274 3.42e+01 c.74.1.1 93147 1no7A 604 3.42e+01 e.48.1.1 92016 1uetA 437 3.43e+01 a.160.1.3,d.218.1.7,d.58.16.2 99272,99273,99274 1r89A 437 3.43e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1g5hA 454 3.48e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 1zr5A 214 3.51e+01 2a6hC 1119 3.54e+01 2lhb 149 3.55e+01 2fal a.1.1.2 15597 1ct9A 553 3.57e+01 1ct9A c.26.2.1,d.153.1.1 31616,41834 1lbkA 208 3.57e+01 a.45.1.1,c.47.1.5 73809,73810 1kyoC 385 3.57e+01 f.32.1.1,f.21.1.2 75904,75905 1hl2A 297 3.58e+01 c.1.10.1 83581 1a76 326 3.64e+01 1a76 a.60.7.1,c.120.1.2 18091,33361 17gsA 210 3.70e+01 1pgtA a.45.1.1,c.47.1.5 17524,32818 1bk5A 422 3.74e+01 1bk5A a.118.1.1 19130 1a8i 842 3.76e+01 1a8i c.87.1.4 35490 1h5uA 842 3.79e+01 1a8i c.87.1.4 60655 1s96A 219 3.81e+01 c.37.1.1 98740 1fs7A 485 3.86e+01 1qdbA a.138.1.3 19691 1kqfB 294 3.90e+01 d.58.1.5,f.23.22.1 75900,75901 1gpb 842 3.96e+01 1a8i c.87.1.4 35478 1pmzA 86 3.96e+01 a.39.1.10 104195 1c8kA 842 3.97e+01 1a8i c.87.1.4 35491 1ibrB 462 4.01e+01 1qgrA a.118.1.1 19120 1cb1 78 4.06e+01 4icb a.39.1.1 17156 1cd1A 315 4.06e+01 1cd1A b.1.1.2,d.19.1.1 21579,38155 2bg9A 370 4.08e+01 1nal1 297 4.11e+01 1nal3 2an9A 207 4.15e+01 1qahA 136 4.24e+01 d.79.1.1 96338 1m2dA 110 4.27e+01 c.47.1.11 78476 1gaxA 862 4.33e+01 1gaxA b.51.1.1,c.26.1.1,a.2.7.3,a.27.1.1 26893,31595,75842,75843 1gtxA 472 4.39e+01 1gtxA 1p2fA 220 4.41e+01 a.4.6.1,c.23.1.1 87720,87721 1h1yA 228 4.43e+01 c.1.2.2 76506 1oheA 348 4.43e+01 c.45.1.1,c.45.1.1 87013,87014 1fdyA 297 4.45e+01 1nal3 c.1.10.1 29071 1jf4A 147 4.54e+01 a.1.1.2 71643 1k0nA 241 4.59e+01 a.45.1.1,c.47.1.5 67953,67954 1dcfA 136 4.60e+01 1dcfA c.23.1.2 31124 1n8vA 112 4.60e+01 a.118.21.1 85457 1yd9A 193 4.61e+01 1rtwA 220 4.66e+01 a.132.1.3 97823 2akrA 285 4.72e+01 2pviA 157 4.76e+01 3pviA c.52.1.6 33302 1f2dA 341 4.78e+01 1f2dA c.79.1.1 35298 1yyqA 374 4.78e+01 1jm6A 407 4.79e+01 a.29.5.1,d.122.1.4 66876,66877 1h6kA 757 4.81e+01 a.118.1.14,a.118.1.14,a.118.1.14 60675,60676,60677 2evaA 307 5.01e+01 1h2vC 771 5.09e+01 a.118.1.14,a.118.1.14,a.118.1.14 76592,76593,76594 1eueA 86 5.09e+01 1cyo d.120.1.1 59504 2gdnA 267 5.10e+01 1edg 380 5.12e+01 1edg c.1.8.3 28807 1c7qA 445 5.17e+01 2pgi c.80.1.2 35307 3pviA 157 5.20e+01 3pviA c.52.1.6 33300 3icb 75 5.28e+01 4icb a.39.1.1 17147 1bk6A 422 5.33e+01 1bk5A a.118.1.1 19133 1wozA 177 5.36e+01 1szqA 483 5.36e+01 e.44.1.1 99045 1xkpA 246 5.39e+01 1gjsA 65 5.43e+01 1gab a.8.1.2 60578 1wtyA 119 5.43e+01 1u13A 455 5.50e+01 a.104.1.1 107578 8ohm 435 5.51e+01 1heiA c.37.1.14,c.37.1.14 32469,32470 1wy1A 172 5.55e+01 1aisB 200 5.60e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 1eyuA 157 5.63e+01 3pviA c.52.1.6 33304 1f37A 110 5.67e+01 1f37A c.47.1.11 33088 1pvuA 154 5.70e+01 3pviA c.52.1.6 33306 1dxeA 256 5.74e+01 1dxeA c.1.12.5 29310 1bolA 222 5.75e+01 1bolA d.124.1.1 41120 2b7aA 293 5.85e+01 2b33A 140 5.85e+01 1v9sA 208 5.86e+01 1rypD 241 5.89e+01 1rypD d.153.1.4 41935 1b0zA 445 5.93e+01 2pgi c.80.1.2 35309 2pgi 445 5.93e+01 2pgi c.80.1.2 35308 1i1rB 181 5.94e+01 1i1rB a.26.1.1 61548 1l7vA 326 5.97e+01 f.22.1.1 73672 1uyrA 737 5.99e+01 c.14.1.4,c.14.1.4 100188,100189 1l8nA 679 5.99e+01 c.1.8.10,d.92.2.2 84564,84565 1qhfA 240 6.01e+01 1qhfA c.60.1.1 33960 1hekA 131 6.04e+01 a.61.1.5 65818 1chrA 370 6.09e+01 1mucA c.1.11.2,d.54.1.1 29252,38896 1b0nA 111 6.09e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 1xx4A 261 6.12e+01 1ufkA 254 6.13e+01 c.66.1.39 99340 1qguB 519 6.15e+01 1qguB c.92.2.3 35626 2ah5A 210 6.23e+01 1j0dA 341 6.26e+01 c.79.1.1 83902 1qh8B 519 6.30e+01 1qguB c.92.2.3 35634 1ignA 246 6.34e+01 1ignA a.4.1.6,a.4.1.6 16048,16049 1o17A 345 6.36e+01 a.46.2.1,c.27.1.1 80765,80766 1xzpB 150 6.37e+01 1rvgA 305 6.39e+01 c.1.10.2 97920 1pytA 94 6.40e+01 1pytA d.58.3.1 39064 1ez3A 127 6.41e+01 1dn1B a.47.2.1 17768 1ar1A 558 6.44e+01 2occA f.24.1.1 43618 1vreA 147 6.49e+01 2hbg a.1.1.2 15017 1noyA 388 6.56e+01 1clqA c.55.3.5 33713 1zq4A 693 6.56e+01 1vllA 334 6.73e+01 c.2.1.13 108834 1cem 363 6.80e+01 1cem a.102.1.2 18826 1k9dA 679 6.81e+01 c.1.8.10,d.92.2.2 77292,77293 2gtrA 261 6.93e+01 1al6 437 6.95e+01 1csh a.103.1.1 18885 2ex4A 241 7.10e+01 1zpdA 568 7.13e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31741,31785,31786 1amz 435 7.19e+01 1csh a.103.1.1 18884 1qzmA 94 7.19e+01 c.37.1.20 96651 1p99A 295 7.19e+01 c.94.1.1 94384 2fpnA 216 7.21e+01 6cts 433 7.21e+01 1csh a.103.1.1 18891 2c12A 439 7.24e+01 1d9cA 121 7.25e+01 1d9cA a.26.1.3 16901 1csh 435 7.26e+01 1csh a.103.1.1 18880 1csc 433 7.30e+01 1csh a.103.1.1 18886 1h1wA 289 7.45e+01 d.144.1.7 83460 1mp9A 198 7.48e+01 d.129.1.1,d.129.1.1 91385,91386 1geqA 248 7.49e+01 2tysA c.1.2.4 28589 1imbA 277 7.50e+01 1imbA e.7.1.1 42957 1mpxA 615 7.52e+01 b.18.1.13,c.69.1.21 85041,85042 1a48 306 7.54e+01 1a48 d.143.1.1 41590 1vf6A 83 7.58e+01 a.194.1.1 100600 1avhA 320 7.58e+01 1avc a.65.1.1 18159 1uu3A 310 7.62e+01 d.144.1.7 99999 1nal3 297 7.63e+01 1nal3 1omoA 322 7.66e+01 c.2.1.13 104017 1vljA 407 7.67e+01 e.22.1.2 108832 1h3fA 432 7.72e+01 c.26.1.1,d.66.1.4 76631,76632 1obdA 306 7.80e+01 d.143.1.1 86767 1z5lA 285 7.91e+01 1vlgA 176 7.97e+01 a.25.1.1 108816 1ee4A 423 8.01e+01 1ee4A a.118.1.1 19128 1ztdA 133 8.04e+01 1taq 832 8.11e+01 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18082,33352,33698,42991 1kwfA 363 8.11e+01 a.102.1.2 73078 1e6pA 499 8.12e+01 1e15A b.72.2.1,c.1.8.5,d.26.3.1 59314,59315,59316 1yovA 537 8.18e+01 1ltlA 279 8.30e+01 b.40.4.11 84701 1xwmA 217 8.30e+01 1z9hA 290 8.34e+01 1ybhA 590 8.45e+01 2hhmA 276 8.45e+01 1imbA e.7.1.1 42955 1e15A 499 8.48e+01 1e15A b.72.2.1,c.1.8.5,d.26.3.1 27810,29006,38440 1wfxA 186 8.48e+01 1rw6A 210 8.50e+01 a.47.4.1 105113 1u2xA 474 8.54e+01 c.72.1.3 107622 1hmy 327 8.61e+01 6mhtA c.66.1.26 34229 1vdxA 184 8.61e+01 1av1A 201 8.69e+01 1av1A h.5.1.1 45796 1sg6A 393 8.70e+01 e.22.1.1 105522 1uhgA 385 8.72e+01 e.1.1.1 88491 1w8sA 263 8.76e+01 1hvd 319 8.81e+01 1avc a.65.1.1 18154 1z5hA 780 8.84e+01 1lrrA 131 8.86e+01 d.228.1.1 78165 1qgrA 876 8.88e+01 1qgrA a.118.1.1 19119 1anxA 319 8.89e+01 1avc a.65.1.1 18161 1heiA 451 8.93e+01 1heiA c.37.1.14,c.37.1.14 32463,32464