# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl-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 1dq3A 454 3.17e-02 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1xngA 268 5.34e-02 1yhfA 115 4.74e-01 1d2eA 397 6.92e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1llwA 1520 8.64e-01 b.80.4.1,c.1.4.1,d.153.1.1 74017,74018,74019 1n4xH 120 1.02e+00 b.1.1.1 85324 1z0sA 278 1.08e+00 1eylA 186 1.16e+00 1wba b.42.4.1 25593 1nezG 128 1.24e+00 b.1.1.1 85592 1suwA 249 1.25e+00 e.52.1.1 106027 1ofdA 1520 1.30e+00 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1rzfL 213 1.66e+00 b.1.1.1,b.1.1.2 98152,98153 1xzoA 174 1.83e+00 1uypA 432 1.95e+00 b.29.1.19,b.67.2.3 100176,100177 1w2tA 432 1.97e+00 1gg4A 452 2.27e+00 1gg4A c.59.1.1,c.98.1.1,c.72.2.1 33957,58985,58986 1ifrA 121 2.65e+00 b.1.16.1 71203 1cj3A 392 2.67e+00 1pbe c.3.1.2,d.16.1.2 30347,37878 2ait 74 2.69e+00 1hoe b.5.1.1 22837 1ok0A 74 2.76e+00 b.5.1.1 93191 2cokA 113 2.78e+00 1hoe 74 2.91e+00 1hoe b.5.1.1 22833 2a2pA 129 3.54e+00 1zn8A 180 3.98e+00 1bgj 394 4.04e+00 1pbe c.3.1.2,d.16.1.2 30352,37883 1gpmA 525 4.12e+00 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1cgt 684 4.80e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21815,22484,27722,28709 1zvnA 99 4.90e+00 3ait 74 4.99e+00 1hoe b.5.1.1 22835 1zljA 78 5.08e+00 2asi 360 5.19e+00 2rmpA b.50.1.2 26824 1k3iA 656 5.34e+00 b.1.18.2,b.18.1.1,b.69.1.1 68113,68114,68115 1k0iA 394 5.75e+00 c.3.1.2,d.16.1.2 67942,67943 1sb2A 133 5.95e+00 1qmeA 702 5.99e+00 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1aorA 605 6.28e+00 1b25A a.110.1.1,d.152.1.1 19042,41794 1bqhG 129 6.30e+00 1cd8 b.1.1.1 19715 1yu4A 381 6.54e+00 1gof 639 6.77e+00 1gof b.1.18.2,b.18.1.1,b.69.1.1 21807,23709,27631 1xe1A 116 6.78e+00 b.43.3.1 109571 1goh 639 6.98e+00 1gof b.1.18.2,b.18.1.1,b.69.1.1 21809,23711,27633 1rsy 152 7.14e+00 1rsy b.7.1.2 23192 1yu0A 381 7.20e+00 1theB 260 7.48e+00 1theB d.3.1.1 37057 1faoA 126 7.56e+00 1faoA b.55.1.1 26974 1yu1A 381 7.69e+00 1gya 105 7.72e+00 1qa9A b.1.1.1 19745 1z5bA 469 7.82e+00 1theA 260 8.07e+00 1theB d.3.1.1 37056 1yu3A 381 8.22e+00 1pbe 394 8.47e+00 1pbe c.3.1.2,d.16.1.2 30338,37869 1tul 108 8.63e+00 1tul b.85.5.1 28373 1pmzA 86 9.03e+00 a.39.1.10 104195 1yu2A 381 9.55e+00 1iloA 77 9.69e+00 c.47.1.1 66205 1ih8A 271 1.06e+01 2nsyA c.26.2.1 62377 2fs2A 151 1.06e+01 1psuA 140 1.06e+01 d.38.1.5 88285 1a6vL 110 1.12e+01 1mfa b.1.1.1 20256 1h8eD 482 1.13e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 2ck3D 482 1.26e+01 1aoiB 87 1.28e+01 1aoiB a.22.1.1 16470 1id3B 102 1.29e+01 a.22.1.1 66113 1oaqL 120 1.34e+01 b.1.1.1 92708 1e79D 482 1.35e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18272,26437,32317 1kk1A 410 1.46e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1r8nA 185 1.51e+01 b.42.4.1 104851 1gmyA 261 1.53e+01 d.3.1.1 76236 1bynA 128 1.55e+01 1rsy b.7.1.2 23193 1xcbA 211 1.58e+01 a.4.5.38,c.2.1.12 109552,109553 1gotB 340 1.59e+01 1tbgA b.69.4.1 27648 1suh 146 1.64e+01 1edhA b.1.6.1 22206 1hlvA 131 1.65e+01 a.4.1.7,a.4.1.7 65854,65855 1aoiF 87 1.68e+01 1aoiB a.22.1.1 16471 1f89A 291 1.68e+01 d.160.1.1 64988 1hq3D 103 1.74e+01 1aoiB a.22.1.1 16464 1tzyD 103 1.74e+01 a.22.1.1 107533 1tbgA 340 1.77e+01 1tbgA b.69.4.1 27649 1ylnA 252 1.80e+01 1j83A 180 1.81e+01 b.18.1.12 66430 2nsyA 271 1.91e+01 2nsyA c.26.2.1 31612 1sz6B 263 1.92e+01 1kqpA 271 1.92e+01 c.26.2.1 72883 2fhxA 246 1.93e+01 1adqH 225 1.94e+01 1igtB b.1.1.1,b.1.1.2 20273,21273 1kx5B 102 2.03e+01 a.22.1.1 77594 1nsyA 271 2.09e+01 2nsyA c.26.2.1 31614 1b25A 619 2.09e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1ll8A 114 2.11e+01 d.110.3.5 78089 1l1jA 239 2.14e+01 b.47.1.1 84516 1b3mA 389 2.21e+01 1b3mA 2fimA 276 2.23e+01 1mt6A 280 2.23e+01 b.76.2.1,b.85.7.1 79446,79447 1p5dX 463 2.30e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1k2yX 463 2.30e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1ogsA 497 2.32e+01 b.71.1.2,c.1.8.3 86997,86998 2fytA 340 2.32e+01 1mu5A 471 2.32e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1sznA 417 2.33e+01 b.71.1.1,c.1.8.1 106162,106163 2fvgA 340 2.33e+01 2fcbA 173 2.34e+01 2fcbA b.1.1.4,b.1.1.4 21781,21782 1edhA 226 2.37e+01 1edhA b.1.6.1,b.1.6.1 22198,22199 1ykjA 394 2.38e+01 1avwB 171 2.41e+01 1wba b.42.4.1 25599 1wh0A 134 2.43e+01 1czfA 362 2.45e+01 1czfA b.80.1.3 28031 1dg6A 191 2.53e+01 1d4vB b.22.1.1 23883 1aq3A 129 2.56e+01 1msc d.85.1.1 40079 2ghsA 326 2.62e+01 1z6bA 154 2.64e+01 2asuB 234 2.65e+01 1u2fA 90 2.65e+01 1u2fA d.58.7.1 39168 1vqoE 178 2.69e+01 1c14A 262 2.71e+01 1eny c.2.1.2 29927 1qsgA 265 2.75e+01 1eny c.2.1.2 29935 1fnmA 691 2.77e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 25709,32144,37546,39302,39303 1xl3C 92 2.81e+01 1y7mA 164 2.85e+01 1jj2E 177 2.85e+01 1ffk1 d.141.1.1,d.141.1.1 63089,63090 1csbB 205 2.90e+01 1theB 1rwiA 270 2.92e+01 b.68.9.1 97987 1hm2A 700 2.93e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 61083,61084,61085 1hnf 182 2.95e+01 1qa9A b.1.1.1,b.1.1.3 19741,21680 1tnrA 144 2.98e+01 2tnfA b.22.1.1 23867 1m4vA 204 3.10e+01 b.40.2.2,d.15.6.1 74459,74460 1e3aB 560 3.22e+01 1ajqB 1zeqX 84 3.24e+01 1pyaB 228 3.25e+01 1pyaB 1louA 101 3.28e+01 1ris d.58.14.1 39323 1i8nA 126 3.31e+01 1i8nA g.10.1.2 61976 1pnkB 557 3.35e+01 1ajqB 1zkkA 167 3.45e+01 1tif 78 3.47e+01 1tif d.15.8.1 37836 1lkdA 297 3.50e+01 d.32.1.3,d.32.1.3 78059,78060 1yq2A 1024 3.51e+01 1d4vB 163 3.56e+01 1d4vB b.22.1.1 23884 1vj2A 126 3.59e+01 b.82.1.10 100796 1yhpA 212 3.60e+01 1zczA 464 3.63e+01 2ew2A 316 3.63e+01 1wy5A 317 3.70e+01 2ms2A 129 3.78e+01 1msc d.85.1.1 40049 1g1kA 143 3.81e+01 1aohA b.2.2.2 22404 1hfuA 503 3.86e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1qg6A 261 3.87e+01 1eny c.2.1.2 29919 1yt5A 258 3.96e+01 1el5A 389 4.03e+01 1b3mA c.3.1.2,d.16.1.3 30369,37937 2gvaA 87 4.04e+01 1gvp b.40.4.7 25389 1l9fA 389 4.04e+01 c.3.1.2,d.16.1.3 73716,73717 1vr8A 142 4.08e+01 1zp7A 206 4.09e+01 1han 297 4.10e+01 1han d.32.1.3,d.32.1.3 38506,38507 1eal 127 4.17e+01 1hmt b.60.1.2 27227 1zkiA 133 4.20e+01 1h6yA 170 4.21e+01 b.18.1.7 70904 2axwA 134 4.23e+01 1vhzA 198 4.26e+01 d.113.1.1 100718 1s6lA 212 4.27e+01 1o0wA 252 4.33e+01 a.149.1.1,d.50.1.1 80751,80752 1olrA 224 4.34e+01 b.29.1.11 93330 1gd1O 334 4.39e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 1vkiA 181 4.39e+01 d.116.1.1 108664 1ebdC 41 4.40e+01 1ebdC a.9.1.1 16355 1nciA 110 4.43e+01 1edhA b.1.6.1 22191 2aotA 292 4.51e+01 1kb9A 431 4.54e+01 d.185.1.1,d.185.1.1 77311,77312 1ffkQ 119 4.56e+01 1ffkQ b.34.5.1 24605 1ryiA 382 4.58e+01 1gm9B 557 4.62e+01 1scmB 145 4.62e+01 1wdcB a.39.1.5 17304 1jqeA 292 4.63e+01 c.66.1.19 71789 1gkfB 557 4.63e+01 1gk9B 557 4.64e+01 1x0oA 119 4.65e+01 1s72T 120 4.66e+01 b.34.5.1 105339 1jj2S 119 4.66e+01 1ffkQ b.34.5.1 63104 1rznA 205 4.67e+01 1vqoT 120 4.67e+01 1ao7B 100 4.68e+01 1agdB b.1.1.2 20697 1cb8A 678 4.70e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1jjeA 222 4.73e+01 1a7tA d.157.1.1 63117 1atnD 260 4.73e+01 3dni d.151.1.1 41793 1adqL 213 4.74e+01 8fabA b.1.1.1,b.1.1.2 20272,21272 1q9jA 422 4.75e+01 c.43.1.2,c.43.1.2 104590,104591 1gm7B 557 4.79e+01 1ajqB 557 4.79e+01 1ajqB 1xovA 326 5.05e+01 1efcA 393 5.10e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1qtfA 246 5.11e+01 1agjA b.47.1.1 25830 2phh 394 5.11e+01 1pbe c.3.1.2,d.16.1.2 30353,37884 1efuA 385 5.12e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1f3lA 321 5.15e+01 1g6q2 c.66.1.6 59630 2pcdA 200 5.18e+01 3pchA b.3.6.1 22665 1b09A 206 5.22e+01 1sacA b.29.1.5 24247 1mfa 247 5.38e+01 1mfa b.1.1.1,b.1.1.1 19888,19889 2bu3A 254 5.38e+01 1in0A 163 5.45e+01 d.58.49.1,d.58.49.1 83694,83695 2g76A 335 5.52e+01 1z5yE 149 5.53e+01 2b3nA 159 5.54e+01 1y89A 238 5.71e+01 1ojjA 402 5.74e+01 b.29.1.10 93130 1bcpC 199 5.76e+01 1bcpB b.40.2.1,d.169.1.2 25121,42430 1iq6A 134 5.76e+01 d.38.1.4 76755 1wu7A 434 5.76e+01 2gd1O 334 5.85e+01 1dssG c.2.1.3,d.81.1.1 29978,39893 1kppA 145 5.96e+01 d.20.1.2 72846 1ut1A 148 6.02e+01 b.2.3.6 108014 1bb8 71 6.04e+01 2bb8 d.10.1.1 37478 1nkgA 508 6.07e+01 b.3.1.2,b.18.1.25,b.30.5.10 103859,103860,103861 1lvwA 295 6.13e+01 c.68.1.6 84723 1wdcB 156 6.16e+01 1wdcB a.39.1.5 17302 1v70A 105 6.20e+01 1nykA 165 6.26e+01 b.33.1.1 86408 1umhA 184 6.26e+01 b.18.1.21 99605 1f5aA 513 6.31e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39337,75835,75836 1aqt 138 6.32e+01 1aqt a.2.10.1,b.93.1.1 15718,28435 2bb8 71 6.41e+01 2bb8 d.10.1.1 37480 1sh0A 510 6.44e+01 e.8.1.4 98876 1gnhA 206 6.48e+01 1sacA b.29.1.5 24252 1gpwB 201 6.51e+01 c.23.16.1 65461 1ibvB 229 6.52e+01 1bhgA 613 6.56e+01 1bhgA b.1.4.1,b.18.1.5,c.1.8.3 22161,23766,28889 2b43A 526 6.58e+01 1w85I 49 6.59e+01 3pcnA 200 6.61e+01 3pchA b.3.6.1 22725 1de4C 640 6.63e+01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17779,30760,33848 1wwhA 119 6.64e+01 1cd8 114 6.66e+01 1cd8 b.1.1.1 19714 1k9vF 201 6.67e+01 c.23.16.1 68365 1uebA 184 6.67e+01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1kk8B 139 6.68e+01 a.39.1.5 77430 1h54A 754 6.68e+01 a.102.1.4,b.30.5.3 60634,60635 1wruA 379 6.74e+01 1pguA 615 6.75e+01 b.69.4.1,b.69.4.1 88069,88070 1hjrA 158 6.76e+01 1hjrA c.55.3.6 33727 1f6fB 210 6.76e+01 1axiB b.1.2.1,b.1.2.1 22033,22034 1arhA 396 6.83e+01 1ajsA c.67.1.1 34321 3pchA 200 6.85e+01 3pchA b.3.6.1 22653 1ng4A 390 6.92e+01 c.3.1.2,d.16.1.3 85666,85667 1d3cA 686 6.94e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21827,22496,27734,28721 1ws0A 156 6.99e+01 1q79A 514 7.00e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 2g6fX 59 7.02e+01 2d1eA 248 7.09e+01 1e8pA 46 7.17e+01 g.55.1.1 59385 1po5A 476 7.21e+01 a.104.1.1 94963 1ass 159 7.30e+01 1a6dA c.8.5.2 30818 1od5A 492 7.31e+01 b.82.1.2,b.82.1.2 86832,86833 1ni5A 433 7.33e+01 c.26.2.5,d.229.1.1 80533,80534 1ncg 110 7.35e+01 1edhA b.1.6.1 22193 1pz4A 116 7.43e+01 d.106.1.1 95400 1lb2B 84 7.46e+01 a.60.3.1 77871 1io1A 398 7.49e+01 1io1A e.32.1.1 62611 1nn6A 228 7.52e+01 b.47.1.2 85893 1tmxA 293 7.55e+01 1asx 159 7.57e+01 1a6dA c.8.5.2 30821 1ekgA 127 7.59e+01 1dlxA d.82.2.1 40021 1v8hA 107 7.69e+01 1u0tA 307 7.71e+01 e.52.1.1 107567 1rkiA 102 7.72e+01 1xer 103 7.75e+01 1xer d.58.1.3 38990 1m6yA 301 7.83e+01 a.60.13.1,c.66.1.23 78716,78717 2g1lA 104 7.84e+01 1a39 402 7.92e+01 1celA b.29.1.10 24305 1mylA 53 7.98e+01 1bazA a.43.1.1 17427 1cxqA 162 7.99e+01 1cxqA c.55.3.2 33621 2d4qA 257 8.00e+01 1o57A 291 8.06e+01 a.4.5.40,c.61.1.1 92483,92484 2gjgA 248 8.13e+01 1gt1A 159 8.13e+01 b.60.1.1 90515 1qznA 173 8.16e+01 b.2.2.2 104669 1byqA 228 8.17e+01 1yer d.122.1.1 41100 1hn2A 159 8.18e+01 b.60.1.1 65890 1cqxA 403 8.23e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1h54B 754 8.24e+01 a.102.1.4,b.30.5.3 60636,60637 1cojA 212 8.24e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 2cyeA 133 8.29e+01 2rmpA 361 8.31e+01 2rmpA b.50.1.2 26825 1fl9A 161 8.35e+01 c.37.1.18 70137 1m2tB 263 8.41e+01 b.42.2.1,b.42.2.1 84762,84763 1b69A 69 8.42e+01 2bb8 d.10.1.1 37479 1b1iA 123 8.47e+01 7rsa d.5.1.1 37295 1zkpA 268 8.50e+01 1uvzA 119 8.63e+01 1oixA 191 8.67e+01 1yukA 103 8.68e+01 1f60A 458 8.68e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1obpA 159 8.72e+01 1obpA b.60.1.1 27092 1vsd 152 8.82e+01 1cxqA c.55.3.2 33625 1k59A 123 8.82e+01 d.5.1.1 72073 1dymA 402 8.84e+01 1celA b.29.1.10 24304 1d2qA 173 8.89e+01 1d4vB b.22.1.1 23894 1uylA 236 8.90e+01 d.122.1.1 108147 1khbA 625 8.91e+01 c.91.1.1,c.109.1.1 68606,68607 2ak5A 64 8.92e+01 1u24A 337 8.93e+01 1v74B 87 8.93e+01 a.24.20.1 100443 1qw1A 121 8.97e+01 1un3A 123 8.99e+01 d.5.1.1 99646