# 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 1z54A 132 1.05e-21 1s5uA 138 1.22e-21 d.38.1.1 98573 2cyeA 133 1.50e-19 1lo7A 141 6.87e-19 d.38.1.1 74144 1bvqA 141 1.40e-18 1bvqA d.38.1.1 38542 2gf6A 135 2.30e-18 2av9A 147 1.72e-17 1njkA 156 4.29e-17 d.38.1.1 85818 2aliA 158 8.33e-16 1yliA 153 1.56e-11 1vpmA 169 7.23e-10 2gvhA 288 5.20e-08 2h4uA 145 1.98e-07 2essA 248 1.95e-06 1zkiA 133 4.13e-06 1j1yA 136 5.65e-06 d.38.1.5 90776 1wluA 136 6.57e-06 2b3nA 159 2.18e-05 1u1zA 168 3.62e-05 d.38.1.6 107602 1ixlA 131 1.36e-04 d.38.1.5 90717 2b6eA 146 1.77e-04 1c8uA 285 2.24e-04 1c8uA d.38.1.3,d.38.1.3 38547,38548 1o0iA 138 3.46e-04 d.38.1.5 86532 2fs2A 151 3.65e-04 1psuA 140 3.76e-04 d.38.1.5 88285 2cwzA 141 5.37e-04 1q4uA 151 6.19e-04 d.38.1.5 95828 1iq6A 134 7.85e-03 d.38.1.4 76755 1t82A 155 1.49e-02 d.38.1.5 106639 1vh5A 148 2.36e-02 d.38.1.5 100642 1z6bA 154 3.21e-02 2bi0A 337 6.30e-01 1sh8A 154 7.24e-01 d.38.1.5 105549 2c8mA 262 1.42e+00 1tbuA 118 1.92e+00 2arsA 262 2.03e+00 2bdvA 231 2.05e+00 2bm3A 166 2.55e+00 1f3mA 80 3.57e+00 1f3mA j.66.1.1 46358 1on2A 142 4.26e+00 a.4.5.24,a.76.1.1 87103,87104 2b59A 187 4.64e+00 2a8lA 420 5.17e+00 2a8mA 420 5.42e+00 1hn0A 1021 5.70e+00 a.102.3.2,b.18.1.17,b.24.1.1,b.30.5.2 83616,83617,83618,83619 1m4iA 181 5.79e+00 d.108.1.1 74457 2a8jA 420 6.21e+00 1g7fA 298 7.08e+00 1pty c.45.1.2 60330 2hnp 321 7.08e+00 1pty c.45.1.2 32678 1knwA 425 7.16e+00 b.49.2.3,c.1.6.1 90969,90970 1u04A 771 7.28e+00 b.34.14.1,c.55.3.10 107539,107540 1zyoA 191 7.31e+00 1nkgA 508 7.45e+00 b.3.1.2,b.18.1.25,b.30.5.10 103859,103860,103861 1m3sA 186 8.18e+00 c.80.1.3 78573 2f71A 298 9.34e+00 1aax 321 9.68e+00 1pty c.45.1.2 32657 1w9hA 427 1.03e+01 1f39A 101 1.05e+01 1umuA b.87.1.1 28386 1b76A 442 1.09e+01 1atiA c.51.1.1,d.104.1.1 33198,40747 1pty 321 1.12e+01 1pty c.45.1.2 32656 1ptvA 321 1.13e+01 1pty c.45.1.2 32665 1a5y 330 1.15e+01 1pty c.45.1.2 32673 1u2xA 474 1.16e+01 c.72.1.3 107622 1pa1A 310 1.17e+01 c.45.1.2 94404 1h6uA 308 1.24e+01 b.1.18.15,c.10.2.1 65688,65689 1te2A 226 1.26e+01 c.108.1.6 106792 1tf4A 605 1.27e+01 1tf4A a.102.1.2,b.2.2.2 18827,22393 1l5aA 436 1.40e+01 c.43.1.2,c.43.1.2 75923,75924 1bv1 159 1.41e+01 1bv1 d.129.3.1 41313 1tyjA 170 1.44e+01 1drmA 131 1.55e+01 1drmA d.110.3.2 40908 1yocA 147 1.59e+01 1lswA 131 1.65e+01 d.110.3.2 78181 1drqA 131 1.69e+01 1drmA 1f76A 336 1.69e+01 c.1.4.1 76160 1tlyA 278 1.81e+01 f.4.6.1 107143 1g86A 142 1.92e+01 b.29.1.3 70161 1lcl 142 1.92e+01 1lcl b.29.1.3 24216 1hdkA 141 1.93e+01 b.29.1.3 65807 1h6tA 291 1.94e+01 b.1.18.15,c.10.2.1 65686,65687 1vprA 374 1.96e+01 1hzgA 295 1.96e+01 1hzgA d.194.1.1 61436 1fm4A 159 1.96e+01 1bv1 d.129.3.1 76186 1widA 130 2.00e+01 1xj4A 119 2.04e+01 1u6zA 513 2.04e+01 1mbyA 88 2.22e+01 d.223.1.1 78931 1ao8 162 2.24e+01 3dfr c.71.1.1 34883 1o6vA 466 2.24e+01 b.1.18.15,c.10.2.1 81099,81100 1eeoA 321 2.26e+01 1pty c.45.1.2 32655 1pn2A 280 2.28e+01 d.38.1.4,d.38.1.4 94930,94931 1atiB 505 2.32e+01 1atiA c.51.1.1,d.104.1.1 33197,40746 1jhfA 202 2.32e+01 a.4.5.2,b.87.1.1 63057,63058 1ks2A 219 2.32e+01 c.124.1.4,d.58.40.1 72908,72909 1tw4A 125 2.34e+01 1hq0A 295 2.35e+01 1hzgA d.194.1.1 61122 1rz1A 161 2.37e+01 b.45.1.2 98124 1uisA 231 2.41e+01 d.22.1.1 99431 1ztuA 341 2.48e+01 1o6sA 466 2.48e+01 b.1.18.15,c.10.2.1 81094,81095 1ejeA 192 2.49e+01 1ejeA b.45.1.2 25757 1lshA 1056 2.61e+01 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 2mspA 126 2.62e+01 1mspA b.1.11.2 22335 2h03A 291 2.63e+01 1te5A 257 2.64e+01 d.153.1.1 106795 2bsjA 133 2.66e+01 1zt7A 276 2.73e+01 1zt1A 277 2.75e+01 1v93A 296 2.78e+01 c.1.23.1 100532 1vcaA 202 2.81e+01 1vcaA b.1.1.3,b.1.1.4 21649,21685 1qp2A 70 2.95e+01 1pse b.34.4.2 24596 1mkaA 171 3.00e+01 1mkaA d.38.1.2 38543 2gv8A 447 3.02e+01 1vqwA 457 3.03e+01 1g5hA 454 3.06e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 1pkp 150 3.09e+01 1pkp d.14.1.1,d.50.1.2 37551,38787 1p6pA 125 3.18e+01 b.60.1.2 87839 1tuaA 191 3.37e+01 d.51.1.1,d.51.1.1 107321,107322 1o0wA 252 3.41e+01 a.149.1.1,d.50.1.1 80751,80752 1ftpA 133 3.43e+01 1hmt b.60.1.2 27199 1jvpP 298 3.46e+01 d.144.1.7 67371 1m9sA 605 3.47e+01 b.1.18.15,b.34.11.1,b.34.11.1,b.34.11.1,c.10.2.1 78874,78875,78876,78877,78878 1aipA 405 3.48e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 1dqeA 137 3.49e+01 1dqeA a.39.2.1 17388 2fi1A 190 3.56e+01 1neu 124 3.58e+01 1neu b.1.1.1 19704 2bhoA 130 3.59e+01 1vqzA 341 3.64e+01 3mspA 126 3.66e+01 1mspA b.1.11.2 22343 1gln 468 3.67e+01 1gln a.97.1.1,c.26.1.1 18752,31588 1qmrA 159 3.67e+01 1bv1 d.129.3.1 41314 1b3jA 274 3.73e+01 1agdA b.1.1.2,d.19.1.1 20855,38319 1h54B 754 3.75e+01 a.102.1.4,b.30.5.3 60636,60637 1f1sA 814 3.75e+01 a.102.3.2,b.1.18.2,b.24.1.1,b.30.5.2 64928,64929,64930,64931 1ko9A 345 3.76e+01 a.96.1.3,d.129.1.2 68717,68718 1h54A 754 3.77e+01 a.102.1.4,b.30.5.3 60634,60635 1aipE 405 3.80e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25699,25739,32134 2gtqA 867 3.81e+01 1yveI 524 3.82e+01 1qmgA a.100.1.2,c.2.1.6 18789,30186 1h6lA 353 3.93e+01 b.68.3.1 60687 1mzjA 339 3.98e+01 c.95.1.2,c.95.1.2 79700,79701 1yveJ 524 3.98e+01 1qmgA a.100.1.2,c.2.1.6 18790,30187 1exmA 405 4.01e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1nmtA 392 4.01e+01 1nmtA d.108.1.2,d.108.1.2 40823,40824 1epxA 370 4.08e+01 1fbaA c.1.10.1 29150 2d37A 176 4.09e+01 1lkzA 219 4.10e+01 c.124.1.4,d.58.40.1 73991,73992 1bsjA 168 4.16e+01 1bs4A d.167.1.1 42302 2bh1A 250 4.17e+01 1m93C 41 4.20e+01 1atiA 505 4.25e+01 1atiA c.51.1.1,d.104.1.1 33196,40745 1jf0A 195 4.27e+01 1ej3A a.39.1.5 62926 1pmnA 364 4.28e+01 d.144.1.7 94907 1j5qA 437 4.31e+01 b.121.2.3,b.121.2.3 77084,77085 1rck 106 4.46e+01 9rnt d.1.1.4 36053 1rl4A 188 4.53e+01 d.167.1.1 97636 2breA 219 4.53e+01 1y8qA 346 4.54e+01 1tc5A 194 4.54e+01 c.110.1.1 106752 1zxkA 98 4.54e+01 1wvgA 359 4.57e+01 31bi 153 4.58e+01 2i1b b.42.1.2 25541 1a4h 230 4.59e+01 1yer d.122.1.1 41099 1o2dA 371 4.59e+01 e.22.1.2 86591 1du6A 64 4.64e+01 1akhA a.4.1.1 16002 2f5uA 447 4.66e+01 1wk2A 121 4.68e+01 1m4zA 238 4.69e+01 b.34.12.1 78630 1g59A 468 4.73e+01 a.97.1.1,c.26.1.1 60257,60258 1j09A 468 4.75e+01 a.97.1.1,c.26.1.1 77025,77026 1w66A 232 4.76e+01 1t6cA 315 4.82e+01 c.55.1.8,c.55.1.8 106558,106559 1k78A 149 4.95e+01 a.4.1.5,a.4.1.5 68255,68256 2brcA 214 4.96e+01 1ka8A 100 5.03e+01 a.4.5.20 72241 1mjoA 104 5.04e+01 1cmbA a.43.1.5 17466 1k6zA 141 5.12e+01 d.198.1.1 68247 2bbkL 125 5.27e+01 2bbkL g.21.1.1 44882 1q0bA 367 5.41e+01 c.37.1.9 95502 1efpB 252 5.45e+01 1efvB c.26.2.3 31636 3fib 249 5.48e+01 3fib d.171.1.1 42455 1yf5L 254 5.48e+01 1sur 215 5.48e+01 1sur c.26.2.2 31620 1qmgA 524 5.52e+01 1qmgA a.100.1.2,c.2.1.6 18785,30182 1fib 269 5.57e+01 3fib d.171.1.1 42456 1wn5A 130 5.69e+01 1uscA 178 5.70e+01 b.45.1.2 99860 1g0dA 695 5.70e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 60166,60167,60168,60169 1eg5A 384 5.74e+01 1ecxA c.67.1.3 34429 1ls8A 142 5.74e+01 a.39.2.1 78176 1lwyA 324 5.76e+01 a.96.1.3,d.129.1.2 78285,78286 2fibA 269 5.78e+01 3fib d.171.1.1 42457 1js8A 394 5.81e+01 a.86.1.1,b.112.1.1 67219,67220 1ecxA 384 5.82e+01 1ecxA c.67.1.3 34431 1m3qA 317 5.87e+01 a.96.1.3,d.129.1.2 91184,91185 3dfr 162 5.88e+01 3dfr c.71.1.1 34880 21bi 153 5.89e+01 2i1b b.42.1.2 25542 1m3yA 413 5.91e+01 b.121.2.3,b.121.2.3 78579,78580 2c78A 405 6.05e+01 1zo0A 126 6.09e+01 1g99A 408 6.10e+01 1g99A c.55.1.2,c.55.1.2 33457,33458 1ii6A 368 6.21e+01 1bg2 c.37.1.9 62413 1amw 214 6.22e+01 1yer d.122.1.1 41093 1vr4A 103 6.22e+01 1wxcB 134 6.24e+01 1zw8A 64 6.43e+01 1lylA 504 6.45e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 1xeuA 263 6.46e+01 1xfrA 128 6.50e+01 6paxA 133 6.51e+01 6paxA a.4.1.5,a.4.1.5 64758,64759 2btiA 63 6.55e+01 1yhvA 297 6.67e+01 1ha3A 405 6.68e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 2fupA 168 6.68e+01 2fi9A 128 6.69e+01 2dexX 671 6.76e+01 1cvjB 190 6.83e+01 1cvjB d.58.7.1,d.58.7.1 39193,39194 1k5nA 276 6.84e+01 b.1.1.2,d.19.1.1 77266,77267 1mpgA 282 6.93e+01 1mpgA a.96.1.3,d.129.1.2 18747,41296 1m6nA 802 6.97e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 78697,78698,78699,78700 1kshB 152 6.98e+01 b.1.18.8 72915 1pufB 73 6.98e+01 a.4.1.1 95132 1oglA 283 6.98e+01 a.204.1.1 92922 1t3tA 1303 7.21e+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 1b72B 87 7.22e+01 1akhA a.4.1.1 16001 1jyaA 130 7.27e+01 d.198.1.1 67453 1x88A 359 7.31e+01 1vk6A 269 7.33e+01 d.113.1.4,d.113.1.4 100851,100852 1iqzA 81 7.43e+01 d.58.1.4 66281 1xl7A 612 7.48e+01 1s72N 187 7.48e+01 c.55.4.1 105333 2lfb 100 7.50e+01 1lfb a.4.1.1 15990 2i1b 153 7.58e+01 2i1b b.42.1.2 25538 1bcpC 199 7.62e+01 1bcpB b.40.2.1,d.169.1.2 25121,42430 1n1mA 728 7.65e+01 b.70.3.1,c.69.1.24 79815,79816 1x0gA 112 7.69e+01 1lfo 128 7.70e+01 1hmt b.60.1.2 27223 1gz8A 299 7.74e+01 d.144.1.7 83405 1i1b 153 7.75e+01 2i1b b.42.1.2 25537 1qv1A 195 7.78e+01 a.39.1.5 96347 1v97A 1332 7.78e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 108436,108437,108438,108439,108440,108441 1ah6 220 7.82e+01 1yer d.122.1.1 41094 1pse 69 7.83e+01 1pse b.34.4.2 24595 1blxA 326 7.84e+01 1hcl d.144.1.7 41596 1n9lA 109 7.86e+01 d.110.3.6 85468 2bshA 125 7.93e+01 1b9lA 120 7.93e+01 1b9lA d.96.1.3 40665 1fus 106 8.01e+01 9rnt d.1.1.4 36050 1ijyA 130 8.02e+01 1ijxA a.141.1.1 62517 1hqkA 154 8.06e+01 c.16.1.1 65902 1ax4A 467 8.06e+01 1ax4A c.67.1.2 34391 1lcjA 109 8.09e+01 1qadA d.93.1.1 40414 1ed8A 449 8.15e+01 1b8jA c.76.1.1 34988 1v9yA 167 8.20e+01 d.110.3.2 108454 1avgI 142 8.22e+01 1avgI b.60.1.3 27229 1gg4A 452 8.23e+01 1gg4A c.59.1.1,c.98.1.1,c.72.2.1 33957,58985,58986 2f4lA 297 8.29e+01 2auhB 59 8.35e+01 1aliA 449 8.35e+01 1b8jA c.76.1.1 34996 1anjA 446 8.44e+01 1b8jA c.76.1.1 35008 1k2xB 143 8.47e+01 1e1xA 299 8.47e+01 1hcl d.144.1.7 59157 1mg2B 131 8.50e+01 g.21.1.1 79060 1pdnC 128 8.50e+01 6paxA a.4.1.5 16047 1s1dA 331 8.51e+01 b.67.3.1 98344 1jeoA 180 8.53e+01 c.80.1.3 66611 1xf1A 926 8.54e+01 1ynpA 317 8.55e+01 1wy9A 147 8.63e+01 1wkcA 184 8.67e+01 1vlaA 150 8.82e+01 d.227.1.2 108735 3ssi 113 8.86e+01 3ssi d.84.1.1 40032 1ebdC 41 8.93e+01 1ebdC a.9.1.1 16355 1n67A 359 8.98e+01 b.2.3.4,b.2.3.4 85354,85355 1qznA 173 8.99e+01 b.2.2.2 104669 1czsA 160 8.99e+01 1cztA b.18.1.2 23714 1cztA 160 8.99e+01 1cztA b.18.1.2 23715