# 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 1y2qA 143 3.46e-01 1wqaA 455 4.18e-01 1ufkA 254 6.51e-01 c.66.1.39 99340 2ewtA 71 1.12e+00 1qysA 106 1.29e+00 k.41.1.1 96603 1rz3A 201 1.67e+00 c.37.1.6 98132 1mp9A 198 1.70e+00 d.129.1.1,d.129.1.1 91385,91386 1z4rA 168 2.00e+00 1dlyA 164 2.03e+00 1dlyA a.1.1.1 14983 1wy7A 207 2.29e+00 1pczA 191 2.31e+00 1ytbA d.129.1.1,d.129.1.1 41292,41293 1v6tA 255 2.34e+00 1qb7A 236 2.43e+00 1qb7A c.61.1.1 34087 1vljA 407 2.52e+00 e.22.1.2 108832 2gfgA 193 2.60e+00 1aisA 182 2.79e+00 1ytbA d.129.1.1,d.129.1.1 41288,41289 2fx2 147 2.98e+00 1rcf c.23.5.1 31158 1e1dA 553 3.19e+00 1e1dA e.26.1.1 43363 1akq 147 3.23e+00 5nul c.23.5.1 31159 1vdxA 184 3.32e+00 1usgA 346 3.55e+00 c.93.1.1 99864 1zxmA 400 3.66e+00 1d3uA 181 3.70e+00 1ytbA d.129.1.1,d.129.1.1 41290,41291 1f4pA 147 4.08e+00 5nul c.23.5.1 59651 1vlwA 217 4.18e+00 c.1.10.1 108868 1gesA 450 4.27e+00 3grs c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 1akt 147 4.47e+00 5nul c.23.5.1 31157 1s69A 124 4.50e+00 a.1.1.1 105305 1akr 147 4.60e+00 1rcf c.23.5.1 31152 1akw 147 4.60e+00 5nul c.23.5.1 31153 1gntA 553 4.61e+00 e.26.1.1 70290 1e2uA 553 4.66e+00 1e1dA e.26.1.1 43362 1azl 147 4.70e+00 5nul c.23.5.1 31154 1bu5A 147 4.73e+00 5nul c.23.5.1 31155 1qrdA 273 4.93e+00 1d4aA c.23.5.3 31217 1tqjA 230 5.08e+00 c.1.2.2 107228 1j9eA 147 5.27e+00 c.23.5.1 62756 1gnlA 544 5.28e+00 e.26.1.1 70287 1wa3A 205 5.48e+00 2lbp 346 5.90e+00 2liv c.93.1.1 35709 1fnmA 691 6.00e+00 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 2bcqA 335 6.39e+00 1xqiA 195 6.58e+00 1rtxA 123 6.64e+00 a.1.1.1 97827 1vgjA 184 6.82e+00 1gheA 177 6.94e+00 d.108.1.1 76222 1iyxA 432 7.24e+00 c.1.11.1,d.54.1.1 83815,83816 1tvlA 454 7.71e+00 c.1.16.4 107366 1z15A 344 7.86e+00 1rpjA 288 8.96e+00 2dri c.93.1.1 35656 1pvgA 418 1.04e+01 d.14.1.3,d.122.1.2 95161,95162 2dri 271 1.06e+01 2dri c.93.1.1 35637 1rztA 331 1.09e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 1gefA 123 1.10e+01 1gefA c.52.1.18 60465 1mkyA 439 1.11e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1yx0A 159 1.19e+01 1ituA 369 1.24e+01 c.1.9.7 71423 1o4sA 389 1.29e+01 c.67.1.1 86620 1kmmA 424 1.36e+01 1adjA c.51.1.1,d.104.1.1 33174,40723 1uj2A 252 1.37e+01 c.37.1.6 99452 1gw5A 621 1.40e+01 a.118.1.10 70629 1tde 316 1.48e+01 1trb c.3.1.5,c.3.1.5 30531,30532 1dgjA 907 1.53e+01 1alo a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 17909,37694,38585,41415 1kmnD 424 1.66e+01 1adjA c.51.1.1,d.104.1.1 33185,40734 2liv 344 1.68e+01 2liv c.93.1.1 35708 1vm6A 228 1.74e+01 c.2.1.3,d.81.1.3 108876,108877 1httA 423 1.77e+01 1adjA c.51.1.1,d.104.1.1 33178,40727 1a87 321 1.83e+01 1a87 f.1.1.1 43380 1ipiA 123 1.86e+01 c.52.1.18 66255 1mqsA 671 1.88e+01 e.25.1.1 79414 1vmaA 306 1.89e+01 a.24.13.1,c.37.1.10 108887,108888 1h7mA 102 1.94e+01 d.79.3.1 83485 1q7rA 219 1.95e+01 c.23.16.1 96054 1xgsA 295 1.98e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1uslA 170 2.20e+01 c.121.1.1 99871 1trb 320 2.25e+01 1trb c.3.1.5,c.3.1.5 30529,30530 2blnA 305 2.28e+01 1q5qA 259 2.38e+01 d.153.1.4 95904 1vkmA 297 2.44e+01 c.138.1.1 108670 1xsnA 335 2.44e+01 2f9zC 159 2.45e+01 1l6sA 323 2.49e+01 c.1.10.3 73627 1dliA 402 2.51e+01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18809,30213,31622 1v95A 130 2.56e+01 c.51.1.1 108435 1zesA 125 2.57e+01 1b76A 442 2.59e+01 1atiA c.51.1.1,d.104.1.1 33198,40747 1vlbA 907 2.61e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 1hlrA 907 2.61e+01 1f4kA 122 2.67e+01 1bm9A a.4.5.7 59646 8abp 306 2.72e+01 8abp c.93.1.1 35647 1jg1A 235 2.74e+01 c.66.1.7 66661 1gy7A 125 2.78e+01 d.17.4.2 70738 3ladA 476 2.78e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30573,30574,40208 1dljA 402 2.85e+01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1qhsA 178 3.00e+01 1qhsA c.37.1.3 31938 1bap 306 3.00e+01 8abp c.93.1.1 35654 1geeA 261 3.01e+01 c.2.1.2 90509 2f4nA 273 3.04e+01 1wvcA 259 3.07e+01 1gcoA 261 3.09e+01 1ybvA c.2.1.2 29884 1eucB 396 3.13e+01 2scuB c.23.4.1,d.142.1.4 31149,41570 1zmdA 474 3.14e+01 1gudA 288 3.19e+01 c.93.1.1 83326 2f62A 161 3.30e+01 1n6bA 473 3.32e+01 a.104.1.1 85359 1w85I 49 3.32e+01 1abe 306 3.35e+01 8abp c.93.1.1 35648 1b1cA 181 3.36e+01 1amoA c.23.5.2 31212 1qbgA 272 3.43e+01 1d4aA c.23.5.3 31227 1a8p 258 3.43e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1rl6A 177 3.43e+01 1rl6A d.141.1.1,d.141.1.1 41473,41474 1lvl 458 3.45e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30567,30568,40205 1jnyA 435 3.49e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1s8nA 205 3.57e+01 c.23.1.1 105374 1fc6A 388 3.63e+01 1fc6A b.36.1.3,c.14.1.2 64738,64739 1y8qB 640 3.69e+01 1qhxA 178 3.72e+01 1qhsA c.37.1.3 31936 2abwA 227 3.76e+01 1i8jA 323 3.81e+01 1b4kA c.1.10.3 61968 1ebdC 41 3.84e+01 1ebdC a.9.1.1 16355 1tzfA 259 3.93e+01 c.68.1.13 107476 1mzgA 146 3.94e+01 d.224.1.1 79696 1rp4A 389 3.95e+01 a.227.1.1 105027 1ucnA 152 4.00e+01 d.58.6.1 99183 1cg2A 393 4.02e+01 1cg2A c.56.5.4,d.58.19.1 33844,39360 2f2tA 161 4.03e+01 1y63A 184 4.04e+01 1b4eA 323 4.07e+01 1b4kA c.1.10.3 29186 2a2kA 175 4.08e+01 1vkyA 347 4.09e+01 e.53.1.1 108696 1j8yF 297 4.11e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1kg0C 136 4.16e+01 d.169.1.1 72445 2a0kA 161 4.29e+01 1wf3A 301 4.31e+01 1fmcA 255 4.33e+01 1cydA c.2.1.2 29856 1j34B 123 4.33e+01 d.169.1.1 84049 1i2hA 168 4.38e+01 b.55.1.4 71103 1ub0A 258 4.38e+01 c.72.1.2 88394 1j8mF 297 4.55e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1w25A 459 4.58e+01 1skf 262 4.59e+01 1skf e.3.1.1 42684 1ymkA 175 4.61e+01 1fjgT 106 4.63e+01 1fjfT a.7.6.1 16338 1vmeA 410 4.69e+01 c.23.5.1,d.157.1.3 108893,108894 1ig0A 319 4.70e+01 1ig0A b.82.6.1,c.100.1.1 62354,62355 1r3sA 367 4.74e+01 c.1.22.1 96963 1tc1A 220 4.75e+01 1tc1A c.61.1.1 34083 2cwkA 160 4.89e+01 1b00A 127 4.90e+01 3chy c.23.1.1 31122 2atxA 194 5.05e+01 1is8K 84 5.06e+01 d.205.1.1 66331 1xrjA 261 5.14e+01 1jr3D 343 5.20e+01 a.80.1.1,c.37.1.20 63251,63252 1nx8A 273 5.21e+01 b.82.2.8 86374 1v60A 123 5.24e+01 1v8bA 479 5.28e+01 1ebdA 455 5.28e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 1jkeA 145 5.30e+01 c.110.1.1 66791 1kbqA 273 5.31e+01 c.23.5.3 68391 1d4aA 273 5.39e+01 1d4aA c.23.5.3 31219 1esiA 262 5.40e+01 1skf e.3.1.1 42682 1jg5A 83 5.41e+01 d.205.1.1 66666 1y9aA 360 5.41e+01 1i0lA 221 5.44e+01 c.61.1.1 71096 1nhkL 144 5.48e+01 1npk d.58.6.1 39142 2ax4A 198 5.49e+01 1b3tA 147 5.70e+01 1b3tA d.58.8.1 39228 1kk1A 410 5.74e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1qagA 226 5.87e+01 1qagA a.40.1.1,a.40.1.1 17400,17401 1e79G 272 6.01e+01 1e79G c.49.2.1 33158 1konA 249 6.02e+01 e.39.1.1 72823 1ny6A 267 6.02e+01 c.37.1.20 92321 1uroA 367 6.02e+01 1uroA c.1.22.1 29675 1wvqA 167 6.04e+01 1uetA 437 6.05e+01 a.160.1.3,d.218.1.7,d.58.16.2 99272,99273,99274 1nr6A 473 6.06e+01 a.104.1.1 92085 1r5jA 337 6.10e+01 c.77.1.5 97097 1jv4A 162 6.19e+01 b.60.1.1 67343 2czdA 208 6.22e+01 1es5A 262 6.23e+01 1skf e.3.1.1 42679 1y9kA 157 6.27e+01 1ndk 155 6.32e+01 1npk d.58.6.1 39118 1txjA 171 6.43e+01 b.88.1.2 107424 1npk 154 6.44e+01 1npk d.58.6.1 39099 1zndA 174 6.50e+01 1vhiA 142 6.52e+01 1b3tA d.58.8.1 39230 1tzjA 338 6.58e+01 1t6t1 118 6.62e+01 1rpxA 230 6.63e+01 1rpxA c.1.2.2 28536 1au1A 166 6.66e+01 1ifa a.26.1.3 16889 1l1qA 186 6.72e+01 c.61.1.1 77653 1i06A 180 6.73e+01 1mup b.60.1.1 27131 1yz7A 188 6.74e+01 1oi1A 221 6.76e+01 b.34.9.3,b.34.9.3 87037,87038 2frvA 264 6.82e+01 2frvA e.19.1.1 43303 1o20A 427 6.90e+01 c.82.1.1 86556 1mup 166 6.93e+01 1mup b.60.1.1 27133 1p1lA 102 6.95e+01 d.58.5.2 87695 5abp 306 6.99e+01 8abp c.93.1.1 35651 1oksA 56 7.01e+01 a.8.5.1 93271 2c07A 285 7.08e+01 1l3iA 192 7.18e+01 c.66.1.22 77676 1qy1A 174 7.24e+01 b.60.1.1 96568 1e6yB 433 7.24e+01 1mroB a.89.1.1,d.58.31.2 18535,39453 2b9eA 303 7.28e+01 1hf8A 289 7.28e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1rkd 309 7.42e+01 1rkd c.72.1.1 34928 1eudB 396 7.42e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 1cnt3 187 7.44e+01 1cnt3 1yj7A 171 7.46e+01 1c9bB 180 7.46e+01 1ytbA d.129.1.1,d.129.1.1 41216,41217 1rypH 205 7.52e+01 d.153.1.4 41876 1js3A 486 7.53e+01 c.67.1.6 67215 1r89A 437 7.61e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1b4o 62 7.65e+01 1azpA b.34.13.1 37464 2culA 232 7.65e+01 1f3fA 155 7.67e+01 1npk d.58.6.1 39101 1j6uA 469 7.72e+01 c.5.1.1,c.59.1.1,c.72.2.1 77094,77095,77096 1s2oA 244 7.77e+01 1y9wA 140 7.78e+01 1xqaA 113 7.88e+01 1xt9A 212 7.88e+01 1df3A 162 7.92e+01 1mup b.60.1.1 27134 1wwkA 307 7.94e+01 2pdd 43 7.95e+01 1ebdC a.9.1.1 16358 1fvuB 125 7.96e+01 1ixxB d.169.1.1 42346 2d4pA 141 8.00e+01 1i05A 180 8.00e+01 1mup b.60.1.1 27130 1lu9A 287 8.01e+01 c.2.1.7,c.58.1.4 78210,78211 5lyz 129 8.08e+01 3lzt d.2.1.2 36289 1dj7A 117 8.08e+01 1dj7A g.36.1.1 44997 1xg5A 279 8.08e+01 1ks2A 219 8.10e+01 c.124.1.4,d.58.40.1 72908,72909 1itf 165 8.12e+01 1b5l a.26.1.3 16899 1bm9A 122 8.18e+01 1bm9A a.4.5.7 16116 1duxC 94 8.19e+01 1awcA a.4.5.21 16170 1vzsA 76 8.30e+01 f.45.1.1 108972 1mjhA 162 8.30e+01 1mjhA c.26.2.4 31639 1kwhA 492 8.35e+01 c.94.1.1 68876 1hg2A 289 8.36e+01 1hg5A a.7.8.2,a.118.9.3 90358,90359 1lkzA 219 8.37e+01 c.124.1.4,d.58.40.1 73991,73992 1dqrA 557 8.40e+01 1dqrA c.80.1.2 35305 1qgxA 357 8.40e+01 1qgxA e.7.1.1 42973 1vhoA 346 8.45e+01 b.49.3.1,c.56.5.4 100694,100695 1hg5A 289 8.48e+01 1hg5A a.7.8.2,a.118.9.3 90360,90361 1b7rA 130 8.50e+01 3lzt d.2.1.2 36436 1tikA 213 8.52e+01 c.23.5.3 107003 1wu7A 434 8.54e+01 1iynA 295 8.55e+01 a.93.1.1 90722 1lxjA 104 8.57e+01 d.58.48.1 84736 1r8gA 372 8.60e+01 d.128.1.3 104845 1ka1A 357 8.60e+01 e.7.1.1 68369 1yseA 141 8.66e+01 2bivA 243 8.71e+01 1at6 129 8.74e+01 3lzt d.2.1.2 36333 1wd3A 482 8.75e+01 b.29.1.21,b.42.8.1 109233,109234 133l 130 8.81e+01 3lzt d.2.1.2 36524 1epuA 591 8.85e+01 1dn1A e.25.1.1 43358 2fhxA 246 8.88e+01 1ykfA 352 8.90e+01 1pedA b.35.1.2,c.2.1.1 24757,29773 1luaA 287 8.91e+01 c.2.1.7,c.58.1.4 78216,78217 1nzaA 103 8.94e+01 d.58.5.2 86444 1dxy 333 8.94e+01 1dxy c.2.1.4,c.23.12.1 30094,31354 1b5zA 130 8.95e+01 3lzt d.2.1.2 36567 1ofv 169 8.97e+01 1rcf c.23.5.1 31184 2b0cA 206 8.98e+01 1vheA 373 8.99e+01 b.49.3.1,c.56.5.4 100669,100670