# List of top-scoring protein chains for t2k-100-30-dssp-ehl2 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 1ml8A 134 8.23e-24 d.227.1.2 85013 1qwiA 143 2.14e-12 d.227.1.1 -11183 1ukkA 142 2.85e-12 d.227.1.1 -11206 1n2fA 142 1.27e-10 d.227.1.1 79853 1uspA 139 2.70e-10 d.227.1.1 -11179 1b6fA 159 7.51e-02 1bv1 d.129.3.1 41316 1qm4A 396 7.91e-02 1mxb d.130.1.1 41350 d.130.1.1 41351 d.130.1.1 41352 1bv1 159 1.37e-01 1bv1 d.129.3.1 41313 1qmrA 159 1.74e-01 1bv1 d.129.3.1 41314 1b8aA 438 4.61e-01 1b8aA b.40.4.1 25244 d.104.1.1 40765 1e5pA 151 4.74e-01 1bj7 b.60.1.1 59272 1d1rA 116 4.99e-01 1d1rA d.64.1.1 39548 1eg9A 449 5.18e-01 1ndoA b.33.1.2 24443 d.129.3.3 41322 1ndoA 449 5.21e-01 1ndoA b.33.1.2 24444 d.129.3.3 41323 1ryjA 70 5.26e-01 d.15.3.2 -9179 1otgA 125 5.69e-01 1otgA d.80.1.2 39831 1josA 128 7.18e-01 d.52.7.1 84191 1o7nA 449 7.39e-01 b.33.1.2 81162 d.129.3.3 81163 1phk 298 1.04e+00 1cdkA d.144.1.7 41635 1lldA 319 1.23e+00 3ldh c.2.1.5 30177 d.162.1.1 42144 1dkzA 219 1.25e+00 1dkzA unknown_sccs -445 unknown_sccs -3060 6paxA 133 1.26e+00 6paxA a.4.1.5 64758 a.4.1.5 64759 1dkxA 219 1.35e+00 1dkzA unknown_sccs -446 unknown_sccs -3061 1ekrA 161 1.40e+00 1ekrA d.58.21.1 39380 1vgyA 393 1.51e+00 c.56.5.4 -7882 d.58.19.1 -10106 1hyeA 313 1.73e+00 2cmd c.2.1.5 61400 d.162.1.1 61401 1q4rA 112 1.80e+00 d.58.4.4 -9943 1bpr 191 1.85e+00 1dkzA unknown_sccs 43319 2sak 121 1.88e+00 2sak d.15.5.1 37711 1q53A 112 1.94e+00 d.58.4.4 -9944 1oe4A 247 1.95e+00 c.18.1.3 86895 1meoA 209 2.27e+00 c.65.1.1 79035 1g4wR 383 2.33e+00 1g4uS a.24.11.1 16644 c.45.1.2 32692 1g4uS 383 2.44e+00 1g4uS a.24.11.1 16643 c.45.1.2 32691 1ew3A 159 2.57e+00 1mup b.60.1.1 27114 1bzsA 165 2.58e+00 1hfc d.92.1.11 40348 1fm4A 159 2.62e+00 1bv1 d.129.3.1 76186 1jsbA 73 2.68e+00 1i76A 163 2.76e+00 1hfc d.92.1.11 61877 1mmq 170 2.81e+00 1hfc d.92.1.11 40396 1xyzA 347 2.84e+00 1taxA c.1.8.3 28804 1nepA 130 3.27e+00 b.1.18.7 80440 1dhs 344 3.54e+00 1dhs c.31.1.1 31727 1a8d 452 3.80e+00 1a8d b.29.1.6 24262 b.42.4.2 25607 1v7oA 165 4.12e+00 unknown_sccs -10249 1m56B 264 4.21e+00 b.6.1.2 74472 f.17.2.1 74473 1jeqA 609 4.28e+00 1jeqA a.140.2.1 64748 unknown_sccs -4427 unknown_sccs -7991 1tbaB 180 4.54e+00 1ytbA d.129.1.1 41286 d.129.1.1 41287 1lpuA 332 4.85e+00 d.144.1.7 74177 1m2rA 327 4.86e+00 d.144.1.7 84760 1d0hA 469 5.30e+00 1a8d b.29.1.6 24265 b.42.4.2 25610 1diwA 441 5.35e+00 1a8d b.29.1.6 24264 b.42.4.2 25609 1jeyA 609 5.36e+00 1jeqA unknown_sccs -4426 unknown_sccs -7990 1gm5A 780 5.40e+00 unknown_sccs 65298 b.40.4.9 65299 c.37.1.19 65300 c.37.1.19 65301 1j5eK 129 5.89e+00 c.55.4.1 71554 1hy7A 173 6.02e+00 d.92.1.11 65957 1ytbB 180 6.07e+00 1ytbA d.129.1.1 41278 d.129.1.1 41279 1k3eA 156 6.28e+00 d.198.1.1 68103 1l0bA 229 6.38e+00 c.15.1.3 73391 c.15.1.3 73392 1c76A 136 6.43e+00 2sak d.15.5.1 37718 1jvwA 167 6.43e+00 d.26.1.1 71907 1fgyA 127 6.46e+00 1faoA b.55.1.1 26976 1ma3A 253 6.47e+00 c.31.1.5 78883 1epwA 1290 6.57e+00 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1pzrA 60 6.62e+00 unknown_sccs -815 1r8hA 87 7.08e+00 d.58.8.1 -10041 1jkeA 145 7.16e+00 c.110.1.1 66791 1k78A 149 7.62e+00 a.4.1.5 68255 a.4.1.5 68256 1r6lA 239 7.70e+00 d.14.1.4 -9057 d.101.1.1 -10747 1om1A 332 7.73e+00 d.144.1.7 -11318 1lp4A 332 7.74e+00 d.144.1.7 74170 1pzgA 331 7.97e+00 c.2.1.5 -5931 d.162.1.1 -11498 1ytbA 180 7.97e+00 1ytbA d.129.1.1 41276 d.129.1.1 41277 1vi1A 345 8.21e+00 unknown_sccs -8466 1gvdA 52 8.63e+00 a.4.1.3 83338 1llwA 1520 8.89e+00 b.80.4.1 74017 c.1.4.1 74018 d.153.1.1 74019 1f07A 321 8.98e+00 1ezwA c.1.16.3 59560 1ii7A 333 9.40e+00 1ii7A d.159.1.4 62415 1a0p 290 9.41e+00 1a0p a.60.9.1 18105 d.163.1.1 42165 1nnhA 294 9.51e+00 d.104.1.1 -10772 1v6fA 151 9.72e+00 1mejA 223 9.74e+00 c.65.1.1 79029 2chsA 127 9.89e+00 2chsA d.79.1.2 39764 1tplA 426 1.01e+01 1ax4A c.67.1.2 34387 1hn2A 159 1.02e+01 b.60.1.1 65890 1gt1A 159 1.02e+01 b.60.1.1 -4436 1dgqA 188 1.03e+01 1ido c.62.1.1 34131 1hfs 160 1.07e+01 1hfc d.92.1.11 40370 1fxrA 64 1.07e+01 1fxd d.58.1.4 38993 1s5lH 66 1.08e+01 1qf6A 642 1.09e+01 1qf6A c.51.1.1 33210 d.15.10.1 39551 d.67.1.1 39562 d.104.1.1 40759 1ng4A 390 1.13e+01 c.3.1.2 85666 d.16.1.3 85667 1auq 208 1.18e+01 1auq c.62.1.1 34137 1mjnA 179 1.20e+01 c.62.1.1 79210 1lfaA 187 1.21e+01 1ido c.62.1.1 34122 1ijbA 202 1.22e+01 c.62.1.1 71229 1etb1 127 1.22e+01 1etb1 1ttbA 127 1.24e+01 1etb1 b.3.4.1 22543 1qd5A 275 1.24e+01 1qd5A f.4.2.1 43748 1pdnC 128 1.26e+01 6paxA a.4.1.5 16047 1o7tA 309 1.29e+01 c.94.1.1 86645 1emsA 440 1.30e+01 1emsA d.13.1.1 37520 d.160.1.1 42086 1in0A 163 1.30e+01 d.58.49.1 83694 d.58.49.1 83695 1gtdA 85 1.32e+01 d.58.45.1 76344 1oakA 196 1.33e+01 1auq c.62.1.1 34138 1qrqA 325 1.33e+01 1qrqA c.1.7.1 28667 1dwnA 127 1.33e+01 1dwnA d.85.1.1 40141 1exbA 332 1.33e+01 1qrqA c.1.7.1 28666 1gaxA 862 1.34e+01 1gaxA a.2.7.3 75842 a.27.1.1 75843 b.51.1.1 26893 c.26.1.1 31595 3pmgA 561 1.35e+01 3pmgA c.84.1.1 35408 c.84.1.1 35409 c.84.1.1 35410 d.129.2.1 41301 1glcG 501 1.37e+01 1glcG c.55.1.4 33519 c.55.1.4 33520 1ge9A 184 1.38e+01 1dd5A d.67.3.1 60463 7at1B 154 1.39e+01 8atcB d.58.2.1 39053 g.41.7.1 45305 1obpA 159 1.40e+01 1obpA b.60.1.1 27092 1dbfA 127 1.44e+01 2chsA d.79.1.2 39761 1fs7A 485 1.47e+01 1qdbA a.138.1.3 19691 1jroB 777 1.47e+01 d.41.1.1 67141 d.133.1.1 67142 1qvbA 481 1.48e+01 1qvbA c.1.8.4 28983 1fbaA 361 1.50e+01 1fbaA c.1.10.1 29120 1agnA 373 1.50e+01 2ohxA b.35.1.2 24737 c.2.1.1 29753 1uayA 242 1.50e+01 c.2.1.2 88390 1fnsA 196 1.55e+01 1auq c.62.1.1 34136 1mb4A 370 1.55e+01 c.2.1.3 78908 d.81.1.1 78909 1mjgM 729 1.57e+01 e.26.1.3 79204 1jeqB 565 1.60e+01 1jeqB unknown_sccs -4432 unknown_sccs -7996 1jvr 137 1.64e+01 1jvr a.61.1.2 18132 8rucA 475 1.65e+01 1burA c.1.14.1 29339 d.58.9.1 39245 1itpA 77 1.69e+01 d.58.3.2 66371 1j3wA 163 1.71e+01 unknown_sccs -10870 1oaoC 729 1.71e+01 e.26.1.3 86746 1c0pA 363 1.72e+01 1an9A c.4.1.2 30647 d.16.1.3 37934 1rbp 182 1.75e+01 1aqb b.60.1.1 27085 1qq2A 199 1.82e+01 1qq2A c.47.1.10 33064 1f86A 115 1.86e+01 1etb1 b.3.4.1 59689 1pfkA 320 1.87e+01 3pfk c.89.1.1 35575 1f41A 127 1.88e+01 1etb1 b.3.4.1 22539 1is1A 185 1.89e+01 d.67.3.1 83704 1kk6A 209 1.93e+01 b.81.1.3 68657 1k4wA 252 1.93e+01 a.123.1.1 72068 1l5xA 280 1.93e+01 c.106.1.1 77718 1h1yA 228 1.94e+01 c.1.2.2 76506 1dg3A 592 1.95e+01 1dg3A a.114.1.1 19078 c.37.1.8 32153 1cjxA 357 1.96e+01 1cjxA d.32.1.3 38516 d.32.1.3 38517 1o89A 345 1.99e+01 b.35.1.2 -3703 c.2.1.1 -5727 1fqvJ 149 1.99e+01 1fqvD a.157.1.1 19266 d.42.1.1 38670 1mr7A 209 1.99e+01 b.81.1.3 -4798 1h10A 125 1.99e+01 b.55.1.1 83446 1qd6C 240 2.00e+01 1qd5A 1jlm 192 2.02e+01 1ido c.62.1.1 34140 1bxnA 485 2.05e+01 1burA c.1.14.1 29376 d.58.9.1 39282 1a5j 110 2.10e+01 1a5j a.4.1.3 16043 a.4.1.3 16044 1vjeA 166 2.11e+01 d.185.1.2 -10261 1gm6A 175 2.14e+01 b.60.1.1 70272 1innA 166 2.15e+01 1j98A d.185.1.2 62608 1nq7A 244 2.19e+01 a.123.1.1 -1682 2pfkA 320 2.22e+01 3pfk c.89.1.1 35577 2pabA 127 2.23e+01 1etb1 b.3.4.1 22597 1vizA 240 2.24e+01 c.1.4.1 -5212 1fqvD 149 2.28e+01 1fqvD a.157.1.1 19263 d.42.1.1 38667 1jvnA 555 2.33e+01 c.1.2.1 67355 c.23.16.1 67356 1bj7 156 2.35e+01 1bj7 b.60.1.1 27113 8atcB 154 2.38e+01 8atcB d.58.2.1 39027 g.41.7.1 45279 1euvB 86 2.40e+01 1a5r d.15.1.1 37598 1q1gA 276 2.45e+01 c.56.2.1 -7846 1b3tA 147 2.51e+01 1b3tA d.58.8.1 39228 1e8cA 498 2.51e+01 c.98.1.1 59377 c.59.1.1 59378 c.72.2.1 59379 1qmeA 702 2.59e+01 1pmd d.11.1.1 37487 d.11.1.1 37488 d.175.1.1 42560 e.3.1.1 42769 1eta1 127 2.63e+01 1etb1 1q8yA 373 2.65e+01 d.144.1.7 -11319 1ek8A 185 2.70e+01 1ek8A d.67.3.1 59444 1ftrA 296 2.80e+01 1ftrA d.58.33.1 39485 d.58.33.1 39486 1gx3A 284 2.81e+01 d.3.1.5 70678 2pvaA 345 2.86e+01 3pvaA d.153.1.3 41850 1ur5A 309 2.87e+01 c.2.1.5 -5910 d.162.1.1 -11477 1si7A 369 2.96e+01 unknown_sccs -10163 1mf7A 194 2.99e+01 c.62.1.1 84937 1lqaA 346 2.99e+01 c.1.7.1 84674 1d02A 202 2.99e+01 1d02A c.52.1.8 33313 1liuA 528 3.00e+01 b.58.1.1 77970 c.1.12.1 77971 c.49.1.1 77972 1uf2A 1019 3.03e+01 unknown_sccs -12036 1f60B 94 3.03e+01 1b64 d.58.12.1 39307 1xnaA 183 3.03e+01 1xnaA b.18.1.8 23773 4matA 278 3.06e+01 1c24A d.127.1.1 41150 1fjgK 129 3.07e+01 1fjfK c.55.4.1 33733 1dfd 64 3.11e+01 1fxd d.58.1.4 38995 1c24A 263 3.14e+01 1c24A d.127.1.1 41148 1dax 64 3.14e+01 1fxd d.58.1.4 38996 1j98A 157 3.27e+01 1j98A d.185.1.2 62755 1bu6O 501 3.28e+01 1glcG c.55.1.4 33499 c.55.1.4 33500 1ctt 294 3.36e+01 1ctt c.97.1.1 36022 c.97.1.1 36023 1eijA 80 3.37e+01 1eijA a.5.6.1 16298 1gs5A 258 3.38e+01 c.73.1.2 70395 1nijA 318 3.41e+01 c.37.1.10 85741 d.237.1.1 85742 1j7gA 144 3.43e+01 c.110.1.1 84130 1mkeA 152 3.45e+01 b.55.1.4 79231 1a3yA 149 3.52e+01 1obpA b.60.1.1 27110 1mldA 314 3.57e+01 2cmd c.2.1.5 30122 d.162.1.1 42089 1in4A 334 3.58e+01 1hqcA a.4.5.11 62597 c.37.1.20 62598 1m1lA 236 3.58e+01 unknown_sccs -11674 1aqb 183 3.64e+01 1aqb b.60.1.1 27084 1fmk 452 3.65e+01 1fmk b.34.2.1 24511 d.93.1.1 40436 d.144.1.7 41690 1mkiA 330 3.65e+01 e.3.1.2 84994 1guzA 310 3.66e+01 c.2.1.5 65586 d.162.1.1 65587 1is2A 661 3.66e+01 a.29.3.2 71382 a.29.3.2 71383 e.6.1.2 71384 1m55A 197 3.75e+01 d.89.1.3 74469 1gypA 358 3.77e+01 1dssG c.2.1.3 30004 d.81.1.1 39919 1vimA 200 3.80e+01 c.80.1.3 -8532 1qtrA 317 3.81e+01 1qtrA c.69.1.7 34660 1ofdA 1520 3.82e+01 b.80.4.1 86935 c.1.4.1 86936 d.153.1.1 86937 1jeyB 565 3.83e+01 1jeqB unknown_sccs -4431 unknown_sccs -7995 1r5tA 142 3.84e+01 1k47A 337 3.85e+01 d.14.1.5 72040 d.58.26.4 72041 1rpxA 230 3.89e+01 1rpxA c.1.2.2 28536 1n3yA 198 3.90e+01 c.62.1.1 79976 1s1hM 132 3.90e+01 1kt6A 183 3.92e+01 b.60.1.1 84466 1hbp 183 3.92e+01 1aqb b.60.1.1 27079 1fsz 372 3.93e+01 1fsz c.32.1.1 31750 d.79.2.1 39802 1di2A 69 3.94e+01 1di2A d.50.1.1 38780