# List of top-scoring protein chains for T0386.t2k-w0.5 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 2g03A 194 2.27e-18 2f6sA 201 1.27e-17 1d5rA 324 1.71e-01 1d5rA b.7.1.1,c.45.1.1 23181,32697 2cqjA 71 1.13e+00 2gk9A 401 2.58e+00 2fzfA 175 3.50e+00 1tul 108 3.88e+00 1tul b.85.5.1 28373 2cna 237 4.87e+00 1nls b.29.1.1 24010 2bdtA 189 5.32e+00 1fpwA 190 5.57e+00 1rec a.39.1.5 17329 2cyfA 237 1.02e+01 1fvrA 327 1.16e+01 d.144.1.7 60047 2afsA 329 1.37e+01 2d2mB 142 1.37e+01 2afwA 329 1.39e+01 1azdA 237 1.40e+01 1nls b.29.1.1 24020 2afuA 329 1.41e+01 2d0sA 79 1.43e+01 1yp2A 451 1.50e+01 1gnd 447 1.56e+01 1gnd c.3.1.3,d.16.1.6 30423,37987 1lv0A 449 1.57e+01 c.3.1.3,d.16.1.6 91130,91131 1nls 237 1.71e+01 1nls b.29.1.1 23928 1nepA 130 1.89e+01 b.1.18.7 80440 2bgxA 261 1.90e+01 1wuvA 237 1.91e+01 1cqwA 295 2.11e+01 1b6g c.69.1.8 34679 1bn7A 294 2.13e+01 1bn6A c.69.1.8 34677 2cohA 202 2.18e+01 1wfkA 88 2.42e+01 1oazA 123 2.49e+01 c.47.1.1 92741 1k6mA 432 2.54e+01 c.37.1.7,c.60.1.4 77275,77276 1te5A 257 2.56e+01 d.153.1.1 106795 1gaeO 330 2.76e+01 1dssG c.2.1.3,d.81.1.1 29954,39869 1gadO 330 2.79e+01 1dssG c.2.1.3,d.81.1.1 29950,39865 1s7cA 331 2.80e+01 c.2.1.3,d.81.1.1 105346,105347 2gupA 292 2.81e+01 1jymA 183 2.86e+01 d.167.1.1 71957 3cna 237 2.95e+01 1nls b.29.1.1 24017 1njkA 156 3.05e+01 d.38.1.1 85818 1on3A 523 3.13e+01 c.14.1.4,c.14.1.4 87107,87108 1pvrA 349 3.17e+01 a.60.9.1,d.163.1.1 95185,95186 1rqcA 185 3.32e+01 d.167.1.1 97732 1ku9A 152 3.36e+01 a.4.5.36 77544 1y5eA 169 3.52e+01 1t3tA 1303 3.63e+01 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 2e2aA 105 3.67e+01 a.7.2.1 88499 1auyA 189 3.71e+01 1auyA b.121.4.6 23311 1jj2A 239 3.75e+01 1rl2A b.34.5.3,b.40.4.5 63084,63085 1hkvA 453 3.76e+01 b.49.2.3,c.1.6.1 83559,83560 1tb5A 381 3.91e+01 a.211.1.2 106735 1xm6A 398 3.99e+01 1e2aA 105 4.00e+01 1e2aA a.7.2.1 16322 1e97A 131 4.07e+01 d.17.4.3 64803 1zx0A 236 4.13e+01 1nwvA 129 4.14e+01 g.18.1.1,g.18.1.1 86304,86305 1lucA 355 4.16e+01 1lucA c.1.16.1 29547 2fz2A 189 4.22e+01 1gz5A 456 4.23e+01 c.87.1.6 76406 1lfwA 470 4.25e+01 c.56.5.4,d.58.19.1 77942,77943 1pkoA 139 4.38e+01 b.1.1.1 88147 1jtvA 327 4.40e+01 c.2.1.2 84230 1iol 327 4.51e+01 1fds c.2.1.2 29842 1uqtA 482 4.52e+01 c.87.1.6 99794 1crxA 322 4.83e+01 4crxA a.60.9.1,d.163.1.1 18097,42157 1ie0A 157 4.93e+01 d.185.1.2 66120 1xnsA 324 4.98e+01 2c6nA 612 5.12e+01 1nj4A 363 5.23e+01 b.105.1.1,e.3.1.1 80545,80546 1drgA 323 5.30e+01 a.60.9.1,d.163.1.1 64792,64793 2crxA 343 5.31e+01 4crxA a.60.9.1,d.163.1.1 18099,42159 1f44A 324 5.32e+01 a.60.9.1,d.163.1.1 64982,64983 1q3uA 347 5.36e+01 a.60.9.1,d.163.1.1 95752,95753 1gs3A 131 5.39e+01 d.17.4.3 76327 1kbuA 349 5.42e+01 a.60.9.1,d.163.1.1 72284,72285 1f0jA 377 5.77e+01 1f0jA a.211.1.2 19346 1rorA 378 5.78e+01 1v5xA 203 5.89e+01 c.1.2.4 100377 1o12A 376 5.94e+01 b.92.1.5,c.1.9.10 80758,80759 1ly7A 121 5.97e+01 d.82.2.1 74339 5crxA 345 5.98e+01 4crxA a.60.9.1,d.163.1.1 18103,42163 1quqB 121 5.99e+01 1quqB b.40.4.3 25305 1ylfA 149 6.03e+01 2gtxA 261 6.14e+01 1sxjE 354 6.23e+01 a.80.1.1,c.37.1.20 106089,106090 1th8B 116 6.26e+01 c.13.2.1 106909 2gu5A 263 6.28e+01 1z6fA 363 6.32e+01 1whyA 97 6.38e+01 2b3gA 123 6.42e+01 2ggcA 263 6.52e+01 1c24A 263 6.59e+01 1c24A d.127.1.1 41148 1ewiA 114 6.63e+01 1ewiA b.40.4.3 25302 4crxA 322 6.71e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 1xnzA 264 6.82e+01 1rl4A 188 6.86e+01 d.167.1.1 97636 1yvmA 264 6.89e+01 1xo0A 324 6.89e+01 1fds 327 6.90e+01 1fds c.2.1.2 29838 3matA 265 6.90e+01 1c24A d.127.1.1 41149 1gxtA 91 6.96e+01 d.58.10.1 76377 1fdw 327 6.97e+01 1fds c.2.1.2 29845 1fduA 327 6.99e+01 1fds c.2.1.2 29848 4matA 278 7.08e+01 1c24A d.127.1.1 41150 1qqnA 378 7.15e+01 1ba1 c.55.1.1,c.55.1.1 33393,33394 1ba0 386 7.33e+01 1ba1 c.55.1.1,c.55.1.1 33397,33398 3crxA 343 7.35e+01 4crxA a.60.9.1,d.163.1.1 18101,42161 1qqoA 378 7.45e+01 1ba1 c.55.1.1,c.55.1.1 33395,33396 1ngc 386 7.49e+01 1ba1 c.55.1.1,c.55.1.1 33411,33412 1ngf 386 7.58e+01 1ba1 c.55.1.1,c.55.1.1 33405,33406 1qqmA 378 7.59e+01 1ba1 c.55.1.1,c.55.1.1 33391,33392 1ats 386 7.68e+01 1ba1 c.55.1.1,c.55.1.1 33423,33424 1uv5A 350 7.75e+01 d.144.1.7 100029 1ea2A 131 7.86e+01 d.17.4.3 64860 1yclA 156 7.93e+01 1gxuA 91 7.95e+01 d.58.10.1 76378 1sk1A 140 7.97e+01 1c4zD 154 8.03e+01 1u9aA d.20.1.1 38331 1nga 386 8.03e+01 1ba1 c.55.1.1,c.55.1.1 33407,33408 1tidB 119 8.07e+01 c.13.2.1 107000 1r0eA 391 8.08e+01 1nge 386 8.27e+01 1ba1 c.55.1.1,c.55.1.1 33409,33410 1akz 223 8.31e+01 3eugA c.18.1.1 31007 1o9uA 350 8.32e+01 d.144.1.7 92691 1w02A 131 8.33e+01 d.17.4.3 108981 1atr 386 8.42e+01 1ba1 c.55.1.1,c.55.1.1 33421,33422 2sspE 223 8.42e+01 3eugA c.18.1.1 31012 1gngA 378 8.55e+01 d.144.1.7 76239 3crd 100 8.61e+01 3crd a.77.1.3 18429 1ngg 386 8.70e+01 1ba1 c.55.1.1,c.55.1.1 33415,33416 1ngh 386 8.72e+01 1ba1 c.55.1.1,c.55.1.1 33413,33414 1kay 381 8.72e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1kax 381 8.72e+01 1ba1 c.55.1.1,c.55.1.1 33389,33390 1kaz 381 8.72e+01 1ba1 c.55.1.1,c.55.1.1 33383,33384 1bupA 386 8.73e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1ba1 386 8.73e+01 1ba1 c.55.1.1,c.55.1.1 33387,33388 1hpm 386 8.74e+01 1ba1 c.55.1.1,c.55.1.1 33381,33382 2bupA 381 8.82e+01 1ba1 c.55.1.1,c.55.1.1 33379,33380 2pgd 482 8.83e+01 2pgd a.100.1.1,c.2.1.6 18778,30190 1hx1A 400 8.84e+01 1ba1 c.55.1.1,c.55.1.1 61348,61349 1ngd 386 8.85e+01 1ba1 c.55.1.1,c.55.1.1 33417,33418 1h8fB 350 8.88e+01 d.144.1.7 65734 1h8fA 352 8.89e+01 d.144.1.7 65733