# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 8.40e-23 d.227.1.2 85013 1ukkA 142 3.72e-12 d.227.1.1 -11206 1qwiA 143 6.81e-12 d.227.1.1 -11183 1n2fA 142 4.90e-11 d.227.1.1 79853 1uspA 139 2.64e-10 d.227.1.1 -11179 1qm4A 396 1.49e-02 1mxb d.130.1.1 41350 d.130.1.1 41351 d.130.1.1 41352 1b6fA 159 1.01e-01 1bv1 d.129.3.1 41316 1bv1 159 2.27e-01 1bv1 d.129.3.1 41313 1qmrA 159 2.63e-01 1bv1 d.129.3.1 41314 1e5pA 151 2.71e-01 1bj7 b.60.1.1 59272 1vgyA 393 3.08e-01 c.56.5.4 -7882 d.58.19.1 -10106 1b8aA 438 3.91e-01 1b8aA b.40.4.1 25244 d.104.1.1 40765 1d1rA 116 4.19e-01 1d1rA d.64.1.1 39548 1otgA 125 6.05e-01 1otgA d.80.1.2 39831 1pzgA 331 7.86e-01 c.2.1.5 -5931 d.162.1.1 -11498 1ryjA 70 9.40e-01 d.15.3.2 -9179 1ii7A 333 1.36e+00 1ii7A d.159.1.4 62415 1ew3A 159 1.43e+00 1mup b.60.1.1 27114 1q4rA 112 1.44e+00 d.58.4.4 -9943 1q53A 112 1.45e+00 d.58.4.4 -9944 1josA 128 1.56e+00 d.52.7.1 84191 1dkzA 219 1.57e+00 1dkzA unknown_sccs -445 unknown_sccs -3060 1hy7A 173 1.68e+00 d.92.1.11 65957 1dkxA 219 1.95e+00 1dkzA unknown_sccs -446 unknown_sccs -3061 1ekrA 161 2.10e+00 1ekrA d.58.21.1 39380 1dhs 344 2.46e+00 1dhs c.31.1.1 31727 1jeqA 609 2.76e+00 1jeqA a.140.2.1 64748 unknown_sccs -4427 unknown_sccs -7991 1qrqA 325 2.78e+00 1qrqA c.1.7.1 28667 1exbA 332 2.78e+00 1qrqA c.1.7.1 28666 1phk 298 3.04e+00 1cdkA d.144.1.7 41635 6paxA 133 3.09e+00 6paxA a.4.1.5 64758 a.4.1.5 64759 1in0A 163 3.20e+00 d.58.49.1 83694 d.58.49.1 83695 1a8d 452 3.20e+00 1a8d b.29.1.6 24262 b.42.4.2 25607 1jeyA 609 3.31e+00 1jeqA unknown_sccs -4426 unknown_sccs -7990 1r8hA 87 3.51e+00 d.58.8.1 -10041 1fxrA 64 3.53e+00 1fxd d.58.1.4 38993 1c76A 136 3.65e+00 2sak d.15.5.1 37718 1mmq 170 3.68e+00 1hfc d.92.1.11 40396 1mb4A 370 3.87e+00 c.2.1.3 78908 d.81.1.1 78909 1fm4A 159 3.87e+00 1bv1 d.129.3.1 76186 1o7tA 309 4.05e+00 c.94.1.1 86645 1bzsA 165 4.19e+00 1hfc d.92.1.11 40348 2sak 121 4.20e+00 2sak d.15.5.1 37711 1nepA 130 4.56e+00 b.1.18.7 80440 1diwA 441 4.68e+00 1a8d b.29.1.6 24264 b.42.4.2 25609 1xyzA 347 4.69e+00 1taxA c.1.8.3 28804 1dax 64 4.69e+00 1fxd d.58.1.4 38996 1lfaA 187 4.72e+00 1ido c.62.1.1 34122 1tbaB 180 4.75e+00 1ytbA d.129.1.1 41286 d.129.1.1 41287 1ma3A 253 4.78e+00 c.31.1.5 78883 1m56B 264 4.79e+00 b.6.1.2 74472 f.17.2.1 74473 1r6lA 239 4.94e+00 d.14.1.4 -9057 d.101.1.1 -10747 7at1B 154 4.98e+00 8atcB d.58.2.1 39053 g.41.7.1 45305 1epwA 1290 5.01e+00 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1ctt 294 5.05e+00 1ctt c.97.1.1 36022 c.97.1.1 36023 1hfs 160 5.18e+00 1hfc d.92.1.11 40370 1lqaA 346 5.21e+00 c.1.7.1 84674 1lldA 319 5.51e+00 3ldh c.2.1.5 30177 d.162.1.1 42144 8atcB 154 5.60e+00 8atcB d.58.2.1 39027 g.41.7.1 45279 1d0hA 469 6.07e+00 1a8d b.29.1.6 24265 b.42.4.2 25610 1euvB 86 6.15e+00 1a5r d.15.1.1 37598 1mjnA 179 6.74e+00 c.62.1.1 79210 1mejA 223 6.97e+00 c.65.1.1 79029 1emsA 440 7.02e+00 1emsA d.13.1.1 37520 d.160.1.1 42086 1j5eK 129 7.02e+00 c.55.4.1 71554 1mkiA 330 7.23e+00 e.3.1.2 84994 1gs5A 258 7.60e+00 c.73.1.2 70395 1oe4A 247 7.61e+00 c.18.1.3 86895 1mrp 309 7.80e+00 1mrp c.94.1.1 35796 1bpr 191 7.88e+00 1dkzA unknown_sccs 43319 1g4uS 383 8.01e+00 1g4uS a.24.11.1 16643 c.45.1.2 32691 1hyeA 313 8.06e+00 2cmd c.2.1.5 61400 d.162.1.1 61401 1qq2A 199 8.55e+00 1qq2A c.47.1.10 33064 1nnfA 309 8.74e+00 c.94.1.1 85903 1f07A 321 8.86e+00 1ezwA c.1.16.3 59560 1i76A 163 8.94e+00 1hfc d.92.1.11 61877 1g4wR 383 8.97e+00 1g4uS a.24.11.1 16644 c.45.1.2 32692 1o57A 291 8.98e+00 unknown_sccs -249 c.61.1.1 -7960 1p41A 291 8.98e+00 1dgqA 188 9.03e+00 1ido c.62.1.1 34131 1m2rA 327 9.17e+00 d.144.1.7 84760 1j3wA 163 9.46e+00 unknown_sccs -10870 1uayA 242 9.50e+00 c.2.1.2 88390 1s5lH 66 9.60e+00 1om1A 332 9.87e+00 d.144.1.7 -11318 1j9bA 141 9.97e+00 c.47.1.12 66459 1meoA 209 1.01e+01 c.65.1.1 79035 1ah9 71 1.01e+01 1ah9 b.40.4.5 25330 1bu6O 501 1.01e+01 1glcG c.55.1.4 33499 c.55.1.4 33500 1fjgK 129 1.03e+01 1fjfK c.55.4.1 33733 2pfkA 320 1.08e+01 3pfk c.89.1.1 35577 1t15A 214 1.09e+01 c.15.1.3 -6284 c.15.1.3 -6285 1pfkA 320 1.13e+01 3pfk c.89.1.1 35575 1gm6A 175 1.14e+01 b.60.1.1 70272 1etb1 127 1.17e+01 1etb1 1a63 130 1.17e+01 1a62 a.140.3.1 64710 b.40.4.5 64711 1oakA 196 1.21e+01 1auq c.62.1.1 34138 1k3eA 156 1.25e+01 d.198.1.1 68103 1tplA 426 1.25e+01 1ax4A c.67.1.2 34387 1glcG 501 1.26e+01 1glcG c.55.1.4 33519 c.55.1.4 33520 1nnhA 294 1.27e+01 d.104.1.1 -10772 1l0bA 229 1.28e+01 c.15.1.3 73391 c.15.1.3 73392 1kutA 230 1.32e+01 d.143.1.1 73017 1fs7A 485 1.33e+01 1qdbA a.138.1.3 19691 1jkeA 145 1.34e+01 c.110.1.1 66791 1gt1A 159 1.35e+01 b.60.1.1 -4436 1q1gA 276 1.38e+01 c.56.2.1 -7846 1fmk 452 1.38e+01 1fmk b.34.2.1 24511 d.93.1.1 40436 d.144.1.7 41690 1gtdA 85 1.38e+01 d.58.45.1 76344 1bjt 793 1.39e+01 1bjt e.11.1.1 43249 1hn2A 159 1.42e+01 b.60.1.1 65890 1fnsA 196 1.43e+01 1auq c.62.1.1 34136 1bj7 156 1.44e+01 1bj7 b.60.1.1 27113 1c0pA 363 1.44e+01 1an9A c.4.1.2 30647 d.16.1.3 37934 1ttbA 127 1.50e+01 1etb1 b.3.4.1 22543 1jjtA 228 1.50e+01 1a7tA d.157.1.1 63139 1ytbA 180 1.53e+01 1ytbA d.129.1.1 41276 d.129.1.1 41277 1pf5A 131 1.55e+01 d.79.1.1 -10368 1jjeA 222 1.56e+01 1a7tA d.157.1.1 63117 1a0p 290 1.56e+01 1a0p a.60.9.1 18105 d.163.1.1 42165 1vizA 240 1.57e+01 c.1.4.1 -5212 1jroB 777 1.57e+01 d.41.1.1 67141 d.133.1.1 67142 2at2A 300 1.59e+01 3csuA c.78.1.1 35196 c.78.1.1 35197 8rucA 475 1.59e+01 1burA c.1.14.1 29339 d.58.9.1 39245 1vi1A 345 1.59e+01 unknown_sccs -8466 1jsbA 73 1.63e+01 1dfd 64 1.64e+01 1fxd d.58.1.4 38995 1ytbB 180 1.64e+01 1ytbA d.129.1.1 41278 d.129.1.1 41279 1qvbA 481 1.66e+01 1qvbA c.1.8.4 28983 1v6fA 151 1.68e+01 1j26A 112 1.69e+01 2bopA 85 1.71e+01 2bopA d.58.8.1 39217 1itpA 77 1.71e+01 d.58.3.2 66371 1rbp 182 1.72e+01 1aqb b.60.1.1 27085 1gvdA 52 1.76e+01 a.4.1.3 83338 2fhi 147 1.77e+01 1fit d.13.1.1 37505 1a62 130 1.78e+01 1a62 a.140.3.1 64708 b.40.4.5 64709 1xnaA 183 1.87e+01 1xnaA b.18.1.8 23773 1qd6C 240 1.88e+01 1qd5A 1b5eA 246 1.90e+01 1b5eA d.117.1.1 41056 1bxnA 485 1.96e+01 1burA c.1.14.1 29376 d.58.9.1 39282 1ijbA 202 1.99e+01 c.62.1.1 71229 1fjeB 175 2.01e+01 1fj7A d.58.7.1 39210 d.58.7.1 39211 1fit 147 2.01e+01 1fit d.13.1.1 37499 1obpA 159 2.01e+01 1obpA b.60.1.1 27092 2rmcA 182 2.07e+01 2cpl b.62.1.1 27491 1hl9A 449 2.08e+01 unknown_sccs -4694 unknown_sccs -5365 1ng7A 60 2.09e+01 a.178.1.1 85671 1lp4A 332 2.10e+01 d.144.1.7 74170 1j98A 157 2.13e+01 1j98A d.185.1.2 62755 1ido 192 2.14e+01 1ido c.62.1.1 34139 2pabA 127 2.14e+01 1etb1 b.3.4.1 22597 1gx1A 160 2.17e+01 d.79.5.1 70675 1hl8A 449 2.20e+01 unknown_sccs -4690 unknown_sccs -5361 1f86A 115 2.23e+01 1etb1 b.3.4.1 59689 1f41A 127 2.26e+01 1etb1 b.3.4.1 22539 1eta1 127 2.27e+01 1etb1 1jpaA 312 2.31e+01 d.144.1.7 67011 1jlm 192 2.36e+01 1ido c.62.1.1 34140 1auq 208 2.40e+01 1auq c.62.1.1 34137 1ee2A 373 2.41e+01 2ohxA b.35.1.2 24663 c.2.1.1 29679 1fgyA 127 2.42e+01 1faoA b.55.1.1 26976 1m55A 197 2.43e+01 d.89.1.3 74469 1dd6A 228 2.45e+01 1a7tA d.157.1.1 42054 1nxiA 132 2.46e+01 d.58.47.1 86381 1k78A 149 2.46e+01 a.4.1.5 68255 a.4.1.5 68256 1qu9A 128 2.48e+01 1qu9A d.79.1.1 39755 1qu9C 128 2.48e+01 1qu9A d.79.1.1 39757 1l6oA 95 2.49e+01 b.36.1.1 84534 1psdA 409 2.52e+01 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1lyxA 248 2.54e+01 c.1.1.1 78304 1dg3A 592 2.59e+01 1dg3A a.114.1.1 19078 c.37.1.8 32153 1ndoA 449 2.60e+01 1ndoA b.33.1.2 24444 d.129.3.3 41323 1o7nA 449 2.60e+01 b.33.1.2 81162 d.129.3.3 81163 1heuA 374 2.61e+01 2ohxA b.35.1.2 60979 c.2.1.1 60980 1hetA 374 2.61e+01 2ohxA b.35.1.2 60975 c.2.1.1 60976 2ohxA 374 2.62e+01 2ohxA b.35.1.2 24669 c.2.1.1 29685 1eg9A 449 2.62e+01 1ndoA b.33.1.2 24443 d.129.3.3 41322 1l5jA 865 2.63e+01 a.118.15.1 73592 c.8.2.1 73593 c.83.1.1 73594 1v1aA 309 2.63e+01 c.72.1.1 -8400 1qd5A 275 2.65e+01 1qd5A f.4.2.1 43748 1lpuA 332 2.65e+01 d.144.1.7 74177 1g7cB 94 2.69e+01 1b64 d.58.12.1 39308 1ml4A 308 2.70e+01 c.78.1.1 79255 c.78.1.1 79256 1c3gA 170 2.73e+01 1c3gA b.4.1.1 22831 b.4.1.1 22832 1n3yA 198 2.83e+01 c.62.1.1 79976 1pdnC 128 2.87e+01 6paxA a.4.1.5 16047 1pzrA 60 2.87e+01 unknown_sccs -815 1s48A 609 2.88e+01 e.8.1.4 -11955 1p65A 73 2.90e+01 unknown_sccs -10331 1a5j 110 2.95e+01 1a5j a.4.1.3 16043 a.4.1.3 16044 1jvr 137 3.03e+01 1jvr a.61.1.2 18132 1fsz 372 3.03e+01 1fsz c.32.1.1 31750 d.79.2.1 39802 1ssn 136 3.06e+01 2sak d.15.5.1 37720 1o5xA 248 3.07e+01 c.1.1.1 -5157 1pea 385 3.12e+01 1pea c.93.1.1 35662 1g2oA 268 3.13e+01 1b8oA c.56.2.1 60228 1n8kA 374 3.19e+01 b.35.1.2 80298 c.2.1.1 80299 1j6uA 469 3.20e+01 c.5.1.1 77094 c.59.1.1 77095 c.72.2.1 77096 1oeyA 83 3.20e+01 d.15.2.2 -9162 8adh 374 3.21e+01 2ohxA b.35.1.2 24690 c.2.1.1 29706 1innA 166 3.25e+01 1j98A d.185.1.2 62608 1vjeA 166 3.25e+01 d.185.1.2 -10261 1ng4A 390 3.27e+01 c.3.1.2 85666 d.16.1.3 85667 1v5xA 203 3.30e+01 c.1.2.4 -5169 1j8bA 112 3.33e+01 d.222.1.1 77101 1mldA 314 3.35e+01 2cmd c.2.1.5 30122 d.162.1.1 42089 1mzhA 225 3.38e+01 c.1.10.1 79698 1kqqA 139 3.38e+01 a.4.3.1 72885 1vj0A 380 3.40e+01 b.35.1.2 -3697 c.2.1.1 -5721 3pchA 200 3.48e+01 3pchA b.3.6.1 22653 1f60B 94 3.49e+01 1b64 d.58.12.1 39307 1eijA 80 3.53e+01 1eijA a.5.6.1 16298 1vh5A 148 3.53e+01 d.38.1.5 -9677 1dbdA 100 3.56e+01 2bopA d.58.8.1 39218 1mf7A 194 3.57e+01 c.62.1.1 84937 1oz9A 150 3.58e+01 unknown_sccs -10588 1ur5A 309 3.59e+01 c.2.1.5 -5910 d.162.1.1 -11477 1sbp 310 3.63e+01 1sbp c.94.1.1 35760 1mkeA 152 3.77e+01 b.55.1.4 79231 1vhiA 142 3.77e+01 1b3tA d.58.8.1 39230 1k3tA 359 3.80e+01 c.2.1.3 72022 d.81.1.1 72023 1gm5A 780 3.82e+01 unknown_sccs 65298 b.40.4.9 65299 c.37.1.19 65300 c.37.1.19 65301 1mp9A 198 3.86e+01 a.74.1.2 -1127 a.74.1.2 -1128 1v7oA 165 3.88e+01 unknown_sccs -10249 1nkiA 135 3.94e+01 d.32.1.2 -9544 1pysB 785 3.95e+01 1pysB a.6.1.1 16299 a.6.1.1 16300 b.40.4.4 25311 d.58.13.1 39310 d.104.1.1 40779 d.138.1.1 41455 1fqvD 149 3.95e+01 1fqvD a.157.1.1 19263 d.42.1.1 38667 1fqvJ 149 3.98e+01 1fqvD a.157.1.1 19266 d.42.1.1 38670