# List of top-scoring protein chains for t2k-100-30-stride-ebghtl-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.soe.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 3b93A 133 7.37e-01 1pfo 500 1.11e+00 1pfo 1pfoA 500 1.11e+00 f.9.1.1 43826 1m3iA 471 1.14e+00 f.9.1.1 91178 2iwxA 214 1.61e+00 d.122.1.1 137758 2fxqA 264 1.67e+00 1s3rA 535 2.16e+00 1bnzA 64 2.94e+00 1azpA b.34.13.1 37468 1cruA 454 3.08e+00 1c9uA b.68.2.1 27617 2q1mA 130 3.21e+00 1d5rA 324 3.30e+00 1d5rA b.7.1.1,c.45.1.1 23181,32697 2p9rA 102 3.64e+00 1hd5A 213 3.77e+00 2eng b.52.1.1 26896 2rb6A 61 3.89e+00 2breA 219 3.91e+00 d.122.1.1 128994 1fnhA 271 4.30e+00 1fnhA b.1.2.1,b.1.2.1,b.1.2.1 21976,21977,21978 2q8oA 136 4.42e+00 2v72A 143 4.42e+00 1xyiA 66 4.97e+00 1tdhA 364 5.05e+00 a.156.1.2,b.113.1.1,g.39.1.8 106772,106773,106774 1uldA 150 5.22e+00 b.29.1.3 99545 1bf4A 63 5.22e+00 1azpA b.34.13.1 37461 2frqA 225 5.26e+00 d.3.1.1 133999 1azpA 66 5.28e+00 1azpA b.34.13.1 37467 2f7tA 227 5.94e+00 2o9uX 97 5.96e+00 d.17.1.1 138960 2prdA 174 6.04e+00 b.40.5.1 25435 2f2aB 483 6.19e+00 a.182.1.2,d.128.1.5 132802,132803 3d2lA 243 6.53e+00 1c8cA 64 6.55e+00 1azpA b.34.13.1 59084 2oulA 241 6.80e+00 1c9uA 454 7.30e+00 1c9uA b.68.2.1 27623 1m1sA 116 7.38e+00 b.1.11.2 84747 2oklA 185 7.46e+00 2gu9A 113 7.48e+00 2f4nA 273 7.74e+00 2ra2A 64 8.07e+00 1vdmA 153 8.40e+00 c.61.1.1 119994 2hesX 330 8.52e+00 1nb8A 353 8.69e+00 d.3.1.9 80385 1fepA 724 8.98e+00 1fepA f.4.3.3 43808 1nqcA 217 9.01e+00 d.3.1.1 86024 1suuA 312 9.06e+00 b.68.10.1 99006 2eng 210 9.27e+00 2eng 2engA 210 9.27e+00 b.52.1.1 26895 1zxzA 197 9.32e+00 1jq4A 98 9.41e+00 d.15.4.2 67083 2df7A 458 9.50e+00 b.121.4.9 131449 1yer 228 1.03e+01 1yer 2b0vA 153 1.07e+01 d.113.1.1 127650 2avwA 311 1.12e+01 2gf6A 135 1.13e+01 d.38.1.1 135077 1jmcA 246 1.19e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 2uurA 245 1.19e+01 1fh0A 221 1.20e+01 1cs8A d.3.1.1 59832 2h7jA 220 1.20e+01 d.3.1.1 136216 2qcuA 501 1.22e+01 1dkxA 219 1.25e+01 1dkzA a.8.4.1,b.130.1.1 90339,90340 2nybA 192 1.30e+01 a.2.11.1,d.44.1.1 138804,138805 1iscA 192 1.30e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1molA 94 1.36e+01 1molA d.17.1.1 37988 2c8mA 262 1.36e+01 1bb8 71 1.39e+01 2bb8 1bb8A 71 1.39e+01 d.10.1.1 37478 2fvgA 340 1.39e+01 b.49.3.1,c.56.5.4 134201,134202 3b77A 193 1.39e+01 2vgdA 218 1.41e+01 2hi2A 158 1.44e+01 3bb7A 321 1.44e+01 1dkzA 219 1.45e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1d7cA 190 1.46e+01 1d7bA b.1.9.1 22309 2cohA 202 1.46e+01 a.4.5.4,b.82.3.2 130677,130678 2zcwA 202 1.46e+01 1yqdA 366 1.54e+01 2z3zA 706 1.63e+01 1zc3B 113 1.64e+01 b.55.1.1 124881 1pdr 99 1.65e+01 1pdr 2gu3A 136 1.65e+01 1hw5A 210 1.68e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 1vpmA 169 1.69e+01 d.38.1.1 113967 1b69A 69 1.69e+01 2bb8 d.10.1.1 37479 2dfbA 190 1.69e+01 b.29.1.11 131470 1wcdJ 441 1.70e+01 b.121.4.9 120887 1gyhA 318 1.73e+01 b.67.2.1 70757 1fhgA 154 1.74e+01 1tlk b.1.1.4 21706 1i6xA 209 1.76e+01 a.4.5.4,b.82.3.2 83673,83674 1tlk 154 1.80e+01 1tlk 1i40A 175 1.81e+01 b.40.5.1 66024 2cgpA 210 1.83e+01 2cgpA a.4.5.4,b.82.3.2 16102,28141 2pd8A 149 1.84e+01 2pdrA 149 1.85e+01 1havA 217 1.88e+01 1havA b.47.1.4 26423 1z3qA 200 1.88e+01 2d73A 738 1.89e+01 3pmgA 561 1.99e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 1lm8C 96 2.01e+01 d.42.1.1 74034 2vbkA 514 2.06e+01 1nwpA 128 2.07e+01 1nwpA b.6.1.1 23011 1bd2D 204 2.07e+01 1tcrA b.1.1.1,b.1.1.2 20622,21557 2jozA 135 2.08e+01 3cc6A 281 2.09e+01 2d5lA 706 2.10e+01 1theA 260 2.13e+01 1theB d.3.1.1 37056 1dar 691 2.14e+01 1dar 1dt9A 437 2.14e+01 1dt9A c.55.4.2,d.79.3.2,d.91.1.1 33738,39815,40257 1byqA 228 2.14e+01 1yer d.122.1.1 41100 2bm0A 691 2.15e+01 b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 128748,128749,128750,128751,128752 2au7A 175 2.21e+01 1dg6A 191 2.23e+01 1d4vB b.22.1.1 23883 1viwB 198 2.25e+01 1led b.29.1.1 24170 2okfA 140 2.27e+01 2fnjC 96 2.27e+01 d.42.1.1 133820 2elcA 329 2.29e+01 1qj8A 148 2.30e+01 1qj8A f.4.1.1 43744 1wpxB 220 2.30e+01 2r78A 117 2.32e+01 1be9A 119 2.32e+01 1pdr b.36.1.1 24774 1tp5A 119 2.38e+01 b.36.1.1 119305 1pieA 419 2.43e+01 d.14.1.5,d.58.26.7 94706,94707 2v0uA 146 2.46e+01 1g6nA 210 2.47e+01 2cgpA a.4.5.4,b.82.3.2 16100,28139 1d7bA 186 2.50e+01 1d7bA b.1.9.1 22307 2he2A 102 2.50e+01 2cxvA 219 2.55e+01 b.47.1.4 131012 2rcfA 91 2.56e+01 1udiI 83 2.57e+01 1ugiA d.17.5.1 38124 1ughI 82 2.58e+01 1ugiA d.17.5.1 38133 2ealA 148 2.62e+01 2fp8A 322 2.62e+01 1ospL 214 2.64e+01 32c2A b.1.1.1,b.1.1.2 20116,21146 1qfjA 232 2.67e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 2ih3B 212 2.77e+01 1j6qA 136 2.77e+01 b.40.9.1 77091 1ten 90 2.78e+01 1ten 1tenA 90 2.78e+01 b.1.2.1 21990 1e69B 322 2.80e+01 1e69B c.37.1.12 32377 1fnmA 691 2.82e+01 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 1l8fA 207 2.85e+01 b.52.1.1 84537 2dg5B 190 2.85e+01 1qtrA 317 2.86e+01 1qtrA c.69.1.7 34660 2inbA 140 2.91e+01 1po0A 751 2.95e+01 f.4.3.3 94960 1kb5A 115 2.97e+01 1tvdA b.1.1.1 20611 1h6lA 353 3.00e+01 b.68.3.1 60687 2fk9A 157 3.04e+01 2i1b 153 3.05e+01 2i1b 3bduA 62 3.07e+01 1vkxA 273 3.09e+01 1a3qA b.1.18.1,b.2.5.3 21941,22454 2halA 212 3.10e+01 b.47.1.4 136289 2ft6A 124 3.12e+01 1i2hA 168 3.12e+01 b.55.1.4 71103 3cbjA 266 3.13e+01 1gv3A 248 3.13e+01 a.2.11.1,d.44.1.1 70585,70586 1gmyA 261 3.15e+01 d.3.1.1 76236 2h36X 112 3.19e+01 2apr 325 3.20e+01 2er7E 2aprA 325 3.20e+01 b.50.1.2 26819 1s5pA 235 3.22e+01 c.31.1.5 98569 1gydB 315 3.24e+01 b.67.2.1 70751 1wm1A 317 3.24e+01 c.69.1.7 109405 2yrxA 451 3.25e+01 1uylA 236 3.27e+01 d.122.1.1 108147 2dduA 387 3.28e+01 1lqyA 184 3.30e+01 d.167.1.1 74212 1lla 628 3.32e+01 1lla 1llaA 628 3.32e+01 a.85.1.1,a.86.1.1,b.1.18.3 18485,18496,21861 1dmmA 131 3.32e+01 1opy d.17.4.3 38114 1ddvA 111 3.34e+01 1evhA b.55.1.4 27002 1t17A 148 3.40e+01 d.129.3.6 112215 2fr2A 172 3.42e+01 b.60.1.8 133963 1m2aA 110 3.52e+01 c.47.1.11 78472 2qdxA 257 3.59e+01 1qr4B 186 3.60e+01 1qr4B b.1.2.1,b.1.2.1 21988,21989 1deuA 277 3.61e+01 1theB d.3.1.1 37085 1tu6A 215 3.62e+01 d.3.1.1 107318 1acc 735 3.62e+01 1acc 1accA 735 3.62e+01 f.11.1.1 43828 1n0uA 842 3.64e+01 b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 79757,79758,79759,79760,79761 2h41A 95 3.65e+01 1sfp 114 3.75e+01 1sfp 1sfpA 114 3.75e+01 b.23.1.1 23895 1b8eA 162 3.76e+01 1bebA b.60.1.1 59077 3cbtA 237 3.78e+01 3c2qA 345 3.82e+01 1m2bA 110 3.84e+01 c.47.1.11 78474 1se8A 301 3.84e+01 b.40.4.3 105448 2q7aA 152 3.86e+01 2gq1A 332 3.87e+01 1bbxC 63 3.88e+01 1azpA b.34.13.1 37465 2b1mA 246 3.90e+01 2rb8A 104 3.97e+01 1qftA 175 4.03e+01 1qftA b.60.1.1 27151 3bxtA 257 4.08e+01 2pefA 373 4.10e+01 1p4uA 153 4.14e+01 b.1.10.2 87780 1xoyA 161 4.19e+01 b.18.1.26 115718 1ddwA 120 4.22e+01 1evhA b.55.1.4 27001 2cb5A 453 4.22e+01 3gcb d.3.1.1 37035 1siqA 392 4.22e+01 a.29.3.1,e.6.1.1 105585,105586 1g2rA 100 4.27e+01 1g2rA d.192.1.1 60231 1qr4A 186 4.30e+01 1qr4B b.1.2.1,b.1.2.1 21986,21987 1ea2A 131 4.32e+01 d.17.4.3 64860 1fi8A 228 4.37e+01 5ptp b.47.1.2 26374 3bqxA 150 4.39e+01 1qjoA 80 4.40e+01 1iyu b.84.1.1 28229 1mbyA 88 4.45e+01 d.223.1.1 78931 1d4vB 163 4.47e+01 1d4vB b.22.1.1 23884 2p86A 215 4.48e+01 2covD 104 4.50e+01 1s55A 156 4.52e+01 b.22.1.1 118865 1t61C 227 4.53e+01 d.169.1.6,d.169.1.6 106533,106534 1gjwA 637 4.54e+01 b.71.1.1,c.1.8.1 60582,60583 1keqA 248 4.56e+01 b.74.1.1 72387 2z1cA 75 4.56e+01 1kv9A 668 4.57e+01 a.3.1.6,b.70.1.1 73056,73057 3cloA 258 4.58e+01 2a46A 238 4.61e+01 2p17A 277 4.62e+01 2iufA 688 4.69e+01 1ltqA 301 4.74e+01 c.108.1.9,c.37.1.1 78208,78209 1ll8A 114 4.76e+01 d.110.3.5 78089 1q5fA 156 4.79e+01 d.24.1.1 104536 2nqdB 221 4.90e+01 2gm6A 208 4.90e+01 1jzgA 128 4.92e+01 b.6.1.1 67855 3b5lB 198 4.94e+01 1aznA 128 4.95e+01 1nwpA b.6.1.1 23003 2p4oA 306 4.95e+01 2oexA 351 4.95e+01 2qt5A 200 4.98e+01 3rp2A 224 4.99e+01 1a7s b.47.1.2 26298 3cpxA 321 5.01e+01 1xvsA 126 5.03e+01 b.1.23.1 116095 1nx8A 273 5.04e+01 b.82.2.8 86374 1gpr 162 5.04e+01 1gpr 1gprA 162 5.04e+01 b.84.3.1 28267 1h5yA 253 5.06e+01 c.1.2.1 65638 1aerA 205 5.07e+01 1aerA d.166.1.1 42249 1azrA 128 5.07e+01 1nwpA b.6.1.1 22983 1wgrA 100 5.08e+01 d.15.1.5 114621 1bvzA 585 5.09e+01 1bvzA b.1.18.2,b.71.1.1,c.1.8.1 21856,27783,28770 2vhsA 217 5.10e+01 1mpyA 307 5.12e+01 1mpyA d.32.1.3,d.32.1.3 38508,38509 2gk6A 624 5.16e+01 1h3iA 293 5.16e+01 b.76.2.1,b.85.7.1 76635,76636 1dmaA 214 5.18e+01 1aerA d.166.1.1 42251 2j73A 103 5.19e+01 2in0A 139 5.20e+01 1y08A 323 5.26e+01 d.3.1.12 116280 1pcfA 66 5.29e+01 1pcfA d.18.1.1 38142 1cc3A 130 5.30e+01 1nwpA b.6.1.1 23008 1qfoA 119 5.34e+01 1qfoA b.1.1.1 19708 1xd5A 112 5.41e+01 b.78.1.1 115155 1qg0A 308 5.43e+01 1fnc b.43.4.2,c.25.1.1 25639,31529 1twfC 318 5.52e+01 d.74.3.1,d.181.1.1 112727,112728 1vcaA 202 5.56e+01 1vcaA b.1.1.3,b.1.1.4 21649,21685 1iqaA 160 5.56e+01 b.22.1.1 71274 2aieP 203 5.61e+01 1cj3A 392 5.63e+01 1pbe c.3.1.2,d.16.1.2 30347,37878 2bgcA 238 5.76e+01 a.4.5.4,b.82.3.3 128458,128459 2qfdA 145 5.80e+01 2pbeA 294 5.81e+01 1csbB 205 5.82e+01 1theB 1ouwA 152 5.87e+01 b.77.3.1 93571 1u5fA 148 5.93e+01 b.55.1.1 119542 1te7A 103 6.04e+01 b.122.1.7 112404 2daqA 110 6.07e+01 b.34.9.2 131354 1ag0A 129 6.12e+01 1nwpA b.6.1.1 23001 1br9 194 6.15e+01 1br9 1ywhA 313 6.16e+01 1cs8A 316 6.21e+01 1cs8A d.3.1.1 37065 1noyA 388 6.21e+01 1clqA c.55.3.5 33713 1u06A 62 6.23e+01 b.34.2.1 119404 1lm6A 215 6.24e+01 d.167.1.1 84628 2uwiA 142 6.27e+01 1v5vA 401 6.31e+01 b.44.2.1,d.250.1.1 113539,113540 1l2hA 153 6.31e+01 b.42.1.2 77655 1theB 260 6.33e+01 1theB d.3.1.1 37057 2ds3A 761 6.36e+01 3d3iA 761 6.36e+01 2icuA 229 6.38e+01 1a0qL 212 6.41e+01 8fabA b.1.1.1,b.1.1.2 20286,21278 2gfaA 119 6.41e+01 b.34.9.1,b.34.9.1 135089,135090 1ay1L 210 6.45e+01 8fabA b.1.1.1,b.1.1.2 20242,21254 3bjoA 103 6.49e+01 2oqoA 200 6.52e+01 1tuc 63 6.54e+01 1tuc 2q9vA 90 6.55e+01 3cjxA 165 6.56e+01 2coiA 386 6.58e+01 2h6oA 470 6.58e+01 2jilA 97 6.59e+01 1mjoA 104 6.59e+01 1cmbA a.43.1.5 17466 1uh6A 100 6.60e+01 d.15.1.1 99394 1nciA 110 6.62e+01 1edhA b.1.6.1 22191 2geeA 203 6.63e+01 1svpA 161 6.73e+01 1svpA b.47.1.3 26384 1m2dA 110 6.73e+01 c.47.1.11 78476 1vcbB 112 6.77e+01 1vcbB d.42.1.1 38633 1kmoA 774 6.78e+01 f.4.3.3 72753 1ld4A 264 6.80e+01 i.6.1.1 77886 1jj2A 239 6.81e+01 1rl2A b.34.5.3,b.40.4.5 63084,63085 1djrD 103 6.83e+01 3chbD b.40.2.1 24865 3cewA 125 6.83e+01 1nofA 383 6.84e+01 b.71.1.2,c.1.8.3 92020,92021 2q2bA 179 6.84e+01 1xfdA 723 6.86e+01 b.70.3.1,c.69.1.24 115251,115252 2q20A 109 6.91e+01 1cmbA 104 6.96e+01 1cmbA a.43.1.5 17460 1wwbX 103 7.02e+01 1wwcA b.1.1.4 21777 1sjdA 368 7.04e+01 c.1.11.2,d.54.1.1 105632,105633 2jesA 503 7.10e+01 1b88A 114 7.16e+01 1tcrA b.1.1.1 20608 1hrnA 337 7.18e+01 1smrA b.50.1.2 26869 1x9lA 149 7.19e+01 b.2.10.1 109528 1cqyA 99 7.21e+01 1b9zA b.3.1.1 22527 1ykjA 394 7.23e+01 3bjsA 428 7.24e+01 3bjuA 521 7.24e+01 1u00A 227 7.26e+01 a.8.4.1,b.130.1.1 112900,112901 1yfuA 174 7.32e+01 b.82.1.20 123094 2v17L 214 7.37e+01 1w9aA 147 7.44e+01 b.45.1.1 114408 1k0iA 394 7.47e+01 c.3.1.2,d.16.1.2 67942,67943 1z02A 446 7.49e+01 1xvxA 312 7.50e+01 c.94.1.1 116097 2ipiA 521 7.51e+01 2oq8A 160 7.52e+01 2gllA 171 7.52e+01 1k32A 1045 7.57e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 2pil 159 7.58e+01 2pil 1o7iA 119 7.58e+01 b.40.4.3 86642 1ppoA 216 7.59e+01 d.3.1.1 37020 1f5jA 199 7.64e+01 1axkA b.29.1.11 24342 1ou8A 111 7.65e+01 b.136.1.1 93543 1unfX 238 7.68e+01 a.2.11.1,d.44.1.1 113314,113315 1bebA 162 7.69e+01 1bebA b.60.1.1 27115 1lt5D 103 7.71e+01 3chbD b.40.2.1 24875 2yvlA 248 7.73e+01 3bpuA 88 7.76e+01 1ybyA 215 7.77e+01 1xe1A 116 7.79e+01 b.43.3.1 109571 2por 301 7.81e+01 2por 2porA 301 7.81e+01 f.4.3.1 43759 1yge 839 7.81e+01 1yge 1ygeA 839 7.81e+01 a.119.1.1,b.12.1.1 19234,23634 1b2rA 304 7.91e+01 1fnc b.43.4.2,c.25.1.1 25648,31538