# 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 1g2qA 187 4.69e-22 c.61.1.1 65117 1o57A 291 6.33e-22 unknown_sccs -249 c.61.1.1 -7960 1p41A 291 6.33e-22 1l1qA 186 3.19e-19 c.61.1.1 77653 1opr 213 2.18e-18 1opr c.61.1.1 34091 1lh0A 213 4.60e-18 c.61.1.1 73896 1qb7A 236 1.33e-17 1qb7A c.61.1.1 34087 1oroA 213 1.95e-17 1opr c.61.1.1 34093 1ecfA 504 5.67e-12 1ecfB c.61.1.1 34053 d.153.1.1 41820 1ecfB 504 2.34e-11 1ecfB c.61.1.1 34054 d.153.1.1 41821 1ao0A 459 5.10e-11 1ecfB c.61.1.1 34049 d.153.1.1 41816 1a3c 181 8.00e-08 1a3c c.61.1.1 34095 1grvB 182 8.48e-08 c.61.1.1 76322 1dkuA 317 1.56e-07 1dkuA c.61.1.2 34118 c.61.1.2 34119 1ibsA 317 2.63e-07 c.61.1.2 66107 c.61.1.2 66108 1bzyA 217 2.73e-07 1qk3A c.61.1.1 34071 1dkrA 317 2.74e-07 1dkuA c.61.1.2 34114 c.61.1.2 34115 1hgxA 183 7.58e-07 1tc1A c.61.1.1 34027 1hmpA 217 9.82e-07 1qk3A c.61.1.1 34075 1nulA 152 1.13e-06 1nulA c.61.1.1 34011 1qk4A 233 7.40e-06 1qk3A c.61.1.1 34037 1cjbA 231 7.75e-06 1qk3A c.61.1.1 34079 1i0lA 221 7.83e-06 c.61.1.1 71096 1fsgA 233 8.93e-06 1qk3A c.61.1.1 34029 1qk3A 233 2.19e-05 1qk3A c.61.1.1 34031 1a98A 152 2.21e-05 1nulA c.61.1.1 34021 1tc1A 220 3.35e-05 1tc1A c.61.1.1 34083 1o5oA 221 5.98e-05 c.61.1.1 -7954 1dqpA 230 5.39e-03 1dqnA c.61.1.1 34069 1dqnA 230 8.07e-03 1dqnA c.61.1.1 34067 1tmy 120 1.67e-01 1dbwA c.23.1.1 31083 1o97C 264 1.85e-01 c.26.2.3 81232 1bd3A 243 2.94e-01 1bd3A c.61.1.1 34098 1h1lA 481 3.18e-01 c.92.2.3 70851 1qguA 478 3.34e-01 1qguA c.92.2.3 35625 1nslA 184 4.23e-01 d.108.1.1 86137 1vi6A 208 4.35e-01 c.23.15.1 -6489 1qh8A 478 5.45e-01 1qguA c.92.2.3 35633 1mk4A 157 5.92e-01 d.108.1.1 84979 1f0kA 364 6.24e-01 1f0kA c.87.1.2 35465 1qv9A 283 1.09e+00 unknown_sccs -6888 1cg2A 393 1.10e+00 1cg2A c.56.5.4 33844 d.58.19.1 39360 1fjgB 256 1.24e+00 1fjfB c.23.15.1 31400 1hh1A 143 1.34e+00 1gefA c.52.1.18 61036 1kq3A 376 1.42e+00 e.22.1.2 68790 1efvB 255 1.51e+00 1efvB c.26.2.3 31634 1pea 385 1.64e+00 1pea c.93.1.1 35662 1i16 130 1.73e+00 1i16 b.36.1.2 24787 1gosA 520 1.77e+00 c.3.1.2 65425 d.16.1.5 65426 1l9gA 192 2.06e+00 c.18.1.2 84568 1nt4A 391 2.22e+00 c.60.1.2 -7942 1p0hA 318 2.29e+00 d.108.1.1 -10802 1iirA 415 2.43e+00 1iirA c.87.1.5 62453 1gzqA 300 2.53e+00 b.1.1.2 70818 d.19.1.1 70819 1cjxA 357 2.60e+00 1cjxA d.32.1.3 38516 d.32.1.3 38517 1rj9A 304 2.67e+00 a.24.13.1 -631 c.37.1.10 -7129 1ml8A 134 2.72e+00 d.227.1.2 85013 3chy 128 2.80e+00 3chy c.23.1.1 31038 1d2nA 272 2.85e+00 1d2nA c.37.1.20 32428 1kl7A 514 3.01e+00 c.79.1.1 72678 1hg3A 225 3.10e+00 1hg3A c.1.1.1 61025 1m1nA 491 3.58e+00 c.92.2.3 78417 1mo2A 294 3.71e+00 c.69.1.22 79331 1oaoA 674 3.74e+00 e.26.1.2 86744 1jbeA 128 3.80e+00 3chy c.23.1.1 62845 1jeoA 180 3.91e+00 c.80.1.3 66611 1p77A 272 3.96e+00 c.2.1.7 -5965 c.58.1.5 -6371 6pfkA 319 4.22e+00 3pfk c.89.1.1 35583 1jjyA 636 4.24e+00 1jjyA 1b06A 210 4.29e+00 1avmA a.2.11.1 15740 d.44.1.1 38737 1mqeA 207 4.36e+00 d.113.1.1 -10884 1s3eA 520 4.66e+00 c.3.1.2 -6022 d.16.1.5 -9242 2pfkA 320 4.69e+00 3pfk c.89.1.1 35577 1pnsB 234 4.75e+00 i.1.1.1 88169 1j5eB 256 4.76e+00 c.23.15.1 71543 1su8A 636 4.78e+00 e.26.1.2 -12015 1ojaA 520 4.81e+00 c.3.1.2 -6000 d.16.1.5 -9220 1p99A 295 4.86e+00 c.94.1.1 -8697 1brt 277 4.87e+00 1brt c.69.1.12 34699 1e6mA 128 4.89e+00 3chy c.23.1.1 31039 1h70A 255 4.92e+00 1h70A d.126.1.3 60711 1pfkA 320 4.93e+00 3pfk c.89.1.1 35575 3pfk 319 5.20e+00 3pfk c.89.1.1 35581 1vkfA 188 5.44e+00 1fsfA 266 5.78e+00 unknown_sccs 65047 1fs5A 266 5.97e+00 unknown_sccs 65044 1us5A 314 5.97e+00 c.94.1.1 -8686 1deaA 266 6.12e+00 1deaA unknown_sccs 31760 1vimA 200 6.26e+00 c.80.1.3 -8532 1fp4A 492 6.27e+00 c.92.2.3 76187 3minC 491 6.31e+00 1qguA c.92.2.3 35607 1dik 874 6.39e+00 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 4pfk 319 6.57e+00 3pfk c.89.1.1 35582 1d4oA 184 6.81e+00 1d4oA c.31.1.4 31748 1mjhA 162 6.87e+00 1mjhA c.26.2.4 31639 1b0uA 262 6.97e+00 1b0uA c.37.1.12 32370 1nsf 273 7.02e+00 1d2nA c.37.1.20 32429 1olsA 400 7.03e+00 c.36.1.11 -6959 1mjhB 162 7.03e+00 1mjhA c.26.2.4 31640 1broA 277 7.19e+00 1brt c.69.1.12 34700 1b5qA 472 7.29e+00 1b37B c.3.1.2 30404 d.16.1.5 37968 1qs0A 407 7.36e+00 1qs0A c.36.1.11 31829 1o97D 320 7.50e+00 c.26.2.3 81233 c.31.1.2 81234 1j6nA 303 7.60e+00 1v1rA 400 7.65e+00 1ku0A 388 7.81e+00 c.69.1.18 72994 1f1xA 322 7.90e+00 d.32.1.3 83208 d.32.1.3 83209 1kblA 873 7.93e+00 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1ffkK 186 8.03e+00 1ffkK c.55.4.1 33731 1b37B 472 8.08e+00 1b37B c.3.1.2 30390 d.16.1.5 37954 1b37A 472 8.16e+00 1b37B c.3.1.2 30389 d.16.1.5 37953 1sesA 421 8.17e+00 1sesA a.2.7.1 15710 d.104.1.1 40710 1ha3A 405 8.32e+00 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1o2dA 371 8.45e+00 e.22.1.2 86591 1j5rA 371 8.46e+00 1uz5A 402 8.74e+00 b.85.6.1 -5029 b.103.1.1 -5069 c.57.1.2 -7902 1exmA 405 9.16e+00 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1m5tA 124 9.65e+00 c.23.1.1 78660 2scuA 288 1.02e+01 2scuA c.2.1.8 30303 c.23.4.1 31131 1c7qA 445 1.07e+01 2pgi c.80.1.2 35307 1hqcA 324 1.08e+01 1hqcA a.4.5.11 16127 c.37.1.20 32424 1f6dA 376 1.09e+01 1f6dA c.87.1.3 35467 1umhA 184 1.11e+01 unknown_sccs -3127 1aw1A 256 1.13e+01 1amk c.1.1.1 28515 1lk5A 229 1.14e+01 unknown_sccs 73960 d.58.40.1 73961 1rpjA 288 1.17e+01 2dri c.93.1.1 35656 1bu5A 147 1.17e+01 5nul c.23.5.1 31155 1jslA 327 1.18e+01 c.88.1.1 67233 1jsrA 327 1.19e+01 c.88.1.1 67237 1hkvA 453 1.20e+01 b.49.2.3 83559 c.1.6.1 83560 1vgvA 384 1.21e+01 c.87.1.3 -8575 1o4vA 183 1.22e+01 c.23.8.1 86628 1o7jA 327 1.25e+01 c.88.1.1 81140 1o58A 303 1.29e+01 c.79.1.1 -8503 1scuA 288 1.30e+01 2scuA c.2.1.8 30307 c.23.4.1 31135 1mb3A 124 1.38e+01 c.23.1.1 78907 2kfnA 605 1.39e+01 1xwl c.55.3.5 33682 e.8.1.1 42975 1reqD 637 1.41e+01 1reqB c.1.19.1 29623 c.23.6.1 31250 1he2A 206 1.42e+01 1he2A c.2.1.2 60966 1reqB 637 1.43e+01 1reqB c.1.19.1 29621 c.23.6.1 31248 1qlwA 328 1.51e+01 1qlwA c.69.1.15 34722 1pg5A 299 1.52e+01 1skyB 502 1.53e+01 1skyB a.69.1.1 18313 b.49.1.1 26478 c.37.1.11 32358 1b0zA 445 1.53e+01 2pgi c.80.1.2 35309 2pgi 445 1.53e+01 2pgi c.80.1.2 35308 1cye 129 1.55e+01 3chy c.23.1.1 31077 2minA 491 1.56e+01 1qguA c.92.2.3 35609 1hdoA 206 1.56e+01 1he2A c.2.1.2 60965 1qysA 106 1.57e+01 unknown_sccs -13432 1m5wA 243 1.62e+01 c.1.24.1 84836 1qmpA 130 1.62e+01 1dz3A c.23.1.1 31106 1qjwA 365 1.62e+01 1bvwA c.6.1.1 30657 1cliA 345 1.64e+01 1cliA d.79.4.1 39816 d.139.1.1 41459 1hskA 326 1.68e+01 2mbr d.145.1.2 61241 d.146.1.1 61242 7reqB 637 1.73e+01 1reqB c.1.19.1 29617 c.23.6.1 31244 1j0aA 325 1.74e+01 c.79.1.1 83871 1uvqA 197 1.77e+01 b.1.1.2 -2649 d.19.1.1 -9336 1n0wA 243 1.83e+01 c.37.1.11 79772 1bib 321 1.86e+01 1bia a.4.5.1 16084 b.34.1.1 24448 d.104.1.2 40788 1pieA 419 1.87e+01 d.14.1.5 -9075 unknown_sccs -10120 1ko3A 230 1.90e+01 d.157.1.1 -11454 1um8A 376 1.91e+01 c.37.1.20 -7251 1nriA 306 1.94e+01 c.80.1.3 86123 1f1uA 323 2.00e+01 d.32.1.3 83200 d.32.1.3 83201 1h6zA 913 2.01e+01 c.1.12.2 70906 c.8.1.1 70907 d.142.1.5 70908 1j9jA 247 2.02e+01 c.106.1.1 62758 3pga1 337 2.03e+01 4pgaA 1on3A 523 2.04e+01 c.14.1.4 87107 c.14.1.4 87108 1b74A 254 2.04e+01 1b74A c.78.2.1 35264 c.78.2.1 35265 1rvaA 244 2.09e+01 1rvaA c.52.1.2 33240 1eonA 245 2.09e+01 1rvaA c.52.1.2 33238 1evlA 401 2.09e+01 1qf6A c.51.1.1 33202 d.104.1.1 40751 1mejA 223 2.09e+01 c.65.1.1 79029 1nytA 271 2.11e+01 c.2.1.7 86417 c.58.1.5 86418 1l2uA 245 2.12e+01 c.1.2.3 73516 1em8A 147 2.13e+01 unknown_sccs -7272 1aj0 282 2.16e+01 1aj2 c.1.21.1 29667 1nv8A 284 2.16e+01 c.66.1.30 86224 1ps9A 671 2.16e+01 c.1.4.1 -5206 1k89 449 2.17e+01 1k89 c.2.1.7 30218 c.58.1.1 33866 1ufkA 254 2.19e+01 unknown_sccs -8103 1byrA 155 2.21e+01 1byrA d.136.1.1 41450 1j9lA 247 2.23e+01 c.106.1.1 62762 1delA 241 2.24e+01 1dekA c.37.1.1 31844 1akr 147 2.26e+01 1rcf c.23.5.1 31152 1d7kA 421 2.27e+01 7odcA b.49.2.3 26486 c.1.6.1 28648 1jq5A 370 2.28e+01 e.22.1.2 67084 1d3vA 323 2.31e+01 1d3vA c.42.1.1 32559 1d2eA 397 2.35e+01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1e5xA 486 2.36e+01 c.79.1.1 59283 1sqhA 312 2.41e+01 unknown_sccs -10812 1gnd 447 2.42e+01 1gnd c.3.1.3 30423 d.16.1.6 37987 1poiA 317 2.45e+01 1poiA unknown_sccs 34153 1oniA 137 2.46e+01 d.79.1.1 87144 1efcA 393 2.46e+01 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 7aatA 401 2.48e+01 1ajsA c.67.1.1 34250 1v4vA 376 2.51e+01 c.87.1.3 -8583 1lkzA 219 2.53e+01 unknown_sccs 73991 d.58.40.1 73992 1llp 343 2.54e+01 1arv a.93.1.1 18578 1hkhA 279 2.57e+01 c.69.1.12 -8342 4pgaA 337 2.58e+01 4pgaA c.88.1.1 35565 1hzgA 295 2.58e+01 1hzgA d.194.1.1 61436 1j9eA 147 2.58e+01 c.23.5.1 62756 1iktA 120 2.58e+01 d.106.1.1 66188 1j7xA 302 2.61e+01 c.14.1.2 66425 1aipE 405 2.62e+01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1s3iA 310 2.63e+01 b.46.1.1 -4111 c.65.1.1 -8042 1rlaA 323 2.64e+01 1d3vA c.42.1.1 32561 1sdoA 203 2.66e+01 unknown_sccs -7558 1gudA 288 2.66e+01 c.93.1.1 83326 2rveA 244 2.67e+01 1rvaA c.52.1.2 33283 1dciA 275 2.69e+01 1dciA c.14.1.3 30918 1fe0A 68 2.70e+01 1cc8A d.58.17.1 39345 1geqA 248 2.75e+01 2tysA c.1.2.4 28589 1ecpA 238 2.80e+01 1ecpA c.56.2.1 33775 1hq0A 295 2.84e+01 1hzgA d.194.1.1 61122 1auoA 218 2.86e+01 1auoA c.69.1.14 34716 1d3cA 686 2.86e+01 1cxlA b.1.18.2 21827 b.3.1.1 22496 b.71.1.1 27734 c.1.8.1 28721 1pwhA 327 2.89e+01 c.79.1.1 -8524 1ptf 88 2.96e+01 1ptf d.94.1.1 40549 1e5dA 402 2.97e+01 1e5dA c.23.5.1 31208 d.157.1.3 42061 1fb6A 105 2.99e+01 1thx c.47.1.1 32739 1jkxA 212 3.01e+01 c.65.1.1 66813 1o5iA 249 3.03e+01 c.2.1.2 -5833 1i1qA 520 3.04e+01 1qdlA d.161.1.1 61543 1usgA 346 3.07e+01 c.93.1.1 -8635 1j5eK 129 3.10e+01 c.55.4.1 71554 1ho1A 242 3.11e+01 1ho1A c.1.24.1 61097 1jx4A 352 3.12e+01 unknown_sccs -10188 unknown_sccs -11898 1ihjA 98 3.12e+01 1pdr b.36.1.1 62382 1k9sA 237 3.12e+01 c.56.2.1 68359 1tk9A 188 3.23e+01 1ks2A 219 3.24e+01 unknown_sccs 72908 d.58.40.1 72909 1n7fA 97 3.25e+01 b.36.1.1 -3746 1asx 159 3.26e+01 1a6dA c.8.5.2 30821 1dekA 241 3.26e+01 1dekA c.37.1.1 31842 1f4pA 147 3.26e+01 5nul c.23.5.1 59651 1ass 159 3.28e+01 1a6dA c.8.5.2 30818 1garA 212 3.29e+01 2gar c.65.1.1 34162 1jqaA 370 3.30e+01 e.22.1.2 67085 1iv3A 152 3.34e+01 d.79.5.1 76828 1aurA 218 3.34e+01 1auoA c.69.1.14 34718 1pvdA 537 3.36e+01 1zpdA c.31.1.3 31737 c.36.1.5 31777 c.36.1.9 31778 1gmxA 108 3.36e+01 c.46.1.3 65355 1a8q 274 3.37e+01 1brt c.69.1.12 34702 1bs4A 168 3.38e+01 1bs4A d.167.1.1 42287 1icjA 168 3.38e+01 1bs4A d.167.1.1 42284 1ayl 541 3.39e+01 1ayl c.91.1.1 64718 c.109.1.1 64719 1s6yA 450 3.43e+01 1onqA 283 3.45e+01 b.1.1.2 -2640 d.19.1.1 -9390 7odcA 424 3.46e+01 7odcA b.49.2.3 26488 c.1.6.1 28650 1mvoA 136 3.47e+01 c.23.1.1 79513 1pmmA 466 3.48e+01 c.67.1.6 -8159 1q8iA 783 3.48e+01 c.55.3.5 -7635 e.8.1.1 -11885 1bia 321 3.50e+01 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 2fx2 147 3.53e+01 1rcf c.23.5.1 31158 1o5zA 442 3.55e+01 c.59.1.2 -7939 c.72.2.2 -8418 1iyeA 309 3.57e+01 e.17.1.1 83786 1gn0A 108 3.57e+01 c.46.1.3 65358 1r2fA 319 3.59e+01 1r2fA a.25.1.2 16800 1g57A 217 3.59e+01 1g57A d.115.1.2 60253 1qvbA 481 3.61e+01 1qvbA c.1.8.4 28983 1vj1A 363 3.65e+01 b.35.1.2 -3728 c.2.1.1 -5752 1mnaA 298 3.65e+01 c.69.1.22 79322 1cb2A 365 3.66e+01 1bvwA c.6.1.1 30661 1aj2 282 3.67e+01 1aj2 c.1.21.1 29665 1qk8A 146 3.70e+01 1ewxA c.47.1.10 33061 1bncB 449 3.71e+01 1bncA b.84.2.1 28237 c.30.1.1 31644 d.142.1.2 41489 1hdmB 193 3.72e+01 1hdmB b.1.1.2 21584 d.19.1.1 38158 1e8gA 560 3.72e+01 1qltA d.58.32.1 39455 d.145.1.1 41718 1sx5A 244 3.73e+01 c.52.1.2 -7551 2minB 522 3.74e+01 1qguB c.92.2.3 35610 1gt8B 1025 3.75e+01 a.1.2.2 70423 c.1.4.1 70424 c.3.1.1 70425 c.4.1.1 70426 d.58.1.5 70427 1o8xA 146 3.76e+01 c.47.1.10 86681 1dbtA 239 3.79e+01 1dbtA c.1.2.3 28539 1ujpA 271 3.79e+01 c.1.2.4 -5177 1j5xA 342 3.80e+01 c.80.1.1 71591 1qjgA 125 3.81e+01 1opy d.17.4.3 38102 1vaoA 560 3.82e+01 1qltA d.58.32.1 39461 d.145.1.1 41724 1h7wD 1025 3.84e+01 a.1.2.2 15686 c.1.4.1 28631 c.3.1.1 30327 c.4.1.1 30612 d.58.1.5 39010 1gthB 1025 3.84e+01 a.1.2.2 70488 c.1.4.1 70489 c.3.1.1 70490 c.4.1.1 70491 d.58.1.5 70492 1gt8A 1025 3.85e+01 a.1.2.2 70418 c.1.4.1 70419 c.3.1.1 70420 c.4.1.1 70421 d.58.1.5 70422 1fcjA 322 3.87e+01 1oasA c.79.1.1 35289 1pk9A 237 3.89e+01 c.56.2.1 -7734 1pjqA 457 3.91e+01 c.2.1.11 -5904 c.90.1.1 -8611 e.37.1.1 -12004 1m1nB 522 3.95e+01 c.92.2.3 78418 2ucz 165 4.00e+01 1u9aA d.20.1.1 38330