# 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.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 2fcr 173 7.57e-01 1rcf c.23.5.1 31151 1o2dA 371 9.58e-01 e.22.1.2 86591 1oz9A 150 1.04e+00 d.92.1.15 93808 1oi7A 288 1.44e+00 c.2.1.8,c.23.4.1 87049,87050 1g3qA 237 2.33e+00 1hyqA c.37.1.10 60237 1frvB 536 2.35e+00 1h2rL e.18.1.1 43296 1xmxA 385 2.76e+00 1wwiA 148 3.07e+00 1xx6A 191 3.14e+00 1fmcA 255 3.41e+00 1cydA c.2.1.2 29856 1pg4A 652 3.57e+00 e.23.1.1 88067 2cjpA 328 3.76e+00 1geeA 261 4.06e+00 c.2.1.2 90509 1gcoA 261 4.09e+00 1ybvA c.2.1.2 29884 1v98A 140 4.42e+00 1o6uA 403 4.54e+00 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 2fbiA 142 4.84e+00 1rzsA 61 5.02e+00 a.35.1.2 105139 2f96A 224 5.14e+00 1i8tA 367 5.32e+00 c.4.1.3,d.16.1.7 66094,66095 1d3uB 201 5.61e+00 1aisB a.74.1.2,a.74.1.2 18386,18387 1xn7A 78 5.68e+00 1k3eA 156 5.76e+00 d.198.1.1 68103 2fv7A 331 6.16e+00 1zjrA 211 6.42e+00 1olmA 403 7.41e+00 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1ecfA 504 7.49e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 1igwA 434 8.00e+00 c.1.12.7 62370 2anxA 146 8.20e+00 1b6sA 355 8.37e+00 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28242,31649,41494 1b6rA 355 8.39e+00 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28241,31648,41493 1dqnA 230 8.44e+00 1dqnA c.61.1.1 34067 1v8gA 329 8.46e+00 a.46.2.1,c.27.1.1 100505,100506 1dqpA 230 8.58e+00 1dqnA c.61.1.1 34069 1de4C 640 8.59e+00 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17779,30760,33848 1fnmA 691 8.61e+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 1cx8B 639 8.77e+00 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17783,30764,33852 1dzlA 505 9.23e+00 1dzlA b.121.6.1 23586 1aisB 200 9.25e+00 1aisB a.74.1.2,a.74.1.2 18384,18385 1ecfB 504 9.37e+00 1ecfB c.61.1.1,d.153.1.1 34054,41821 1d2eA 397 9.40e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1kid 203 9.43e+00 1derA c.8.5.1 30771 1ionA 243 9.49e+00 c.37.1.10 62633 1yhpA 212 9.76e+00 2fbmA 291 1.00e+01 1cx8A 639 1.10e+01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17782,30763,33851 1d4oA 184 1.13e+01 1d4oA c.31.1.4 31748 1ituA 369 1.21e+01 c.1.9.7 71423 1nkiA 135 1.23e+01 d.32.1.2 91941 1dar 691 1.29e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1 25707,32142,37547,39300 2bgkA 278 1.39e+01 2liv 344 1.39e+01 2liv c.93.1.1 35708 1vclA 432 1.39e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1geqA 248 1.45e+01 2tysA c.1.2.4 28589 1y1oA 203 1.47e+01 2f46A 156 1.49e+01 1fnlA 175 1.53e+01 2fcbA b.1.1.4,b.1.1.4 21783,21784 1auq 208 1.58e+01 1auq c.62.1.1 34137 1yyvA 131 1.66e+01 1y0nA 78 1.69e+01 2fw2A 260 1.73e+01 2bd0A 244 1.73e+01 1qopA 268 1.76e+01 2tysA c.1.2.4 28570 1avyC 74 1.82e+01 1avyB h.1.17.1 45658 1oq9A 363 1.83e+01 a.25.1.2 87257 1j93A 353 1.83e+01 c.1.22.1 66454 1zip 217 1.85e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1qtrA 317 1.88e+01 1qtrA c.69.1.7 34660 1c6vX 81 1.89e+01 1ihvA b.34.7.1 24641 2b69A 343 1.93e+01 1aqm 453 2.01e+01 1smd b.71.1.1,c.1.8.1 27717,28704 2wsyA 268 2.09e+01 2tysA c.1.2.4 28588 1ja9A 274 2.09e+01 c.2.1.2 62817 1g94A 448 2.12e+01 b.71.1.1,c.1.8.1 65169,65170 1o6yA 299 2.14e+01 d.144.1.7 81106 1edoA 244 2.16e+01 1ybvA c.2.1.2 29896 2bx6A 350 2.20e+01 1hmy 327 2.24e+01 6mhtA c.66.1.26 34229 1ybvA 283 2.27e+01 1ybvA c.2.1.2 29948 2feaA 236 2.27e+01 1n67A 359 2.30e+01 b.2.3.4,b.2.3.4 85354,85355 1elvA 333 2.30e+01 5ptp b.47.1.2,g.18.1.1 59454,59455 1jg8A 347 2.38e+01 1jg8A c.67.1.1 62946 1m6sA 347 2.38e+01 c.67.1.1 78701 1yymG 313 2.39e+01 1lqpA 135 2.40e+01 d.32.1.2 78151 1z83A 196 2.51e+01 2bzlA 325 2.54e+01 1g0oA 283 2.54e+01 1ybvA c.2.1.2 60181 1l8aA 886 2.59e+01 c.36.1.10,c.36.1.6,c.48.1.1 73677,73678,73679 1oeyJ 107 2.59e+01 d.15.2.2 92804 1gegA 256 2.61e+01 1ybvA c.2.1.2 29888 2f51A 118 2.62e+01 1zin 217 2.65e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1bksA 268 2.68e+01 2tysA c.1.2.4 28585 1avyB 74 2.69e+01 1avyB h.1.17.1 45657 2d8dA 90 2.69e+01 1kekA 1231 2.69e+01 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 68524,68525,68526,68527,68528 1dvjC 246 2.73e+01 1dvjA c.1.2.3 28548 2tysA 268 2.73e+01 2tysA c.1.2.4 28572 1mixA 206 2.78e+01 a.11.2.1,b.55.1.5 79166,79167 1g4uS 383 2.93e+01 1g4uS a.24.11.1,c.45.1.2 16643,32691 1x1zA 252 2.94e+01 2c3mA 1231 3.02e+01 1ku3A 73 3.02e+01 a.4.13.2 73000 1avyA 74 3.03e+01 1avyB h.1.17.1 45656 1o88A 353 3.03e+01 b.80.1.1 81178 1nvmA 345 3.04e+01 a.5.7.1,c.1.10.5 86249,86250 2bz1A 196 3.13e+01 1yacA 208 3.20e+01 1yacA c.33.1.3 31757 1jhfA 202 3.22e+01 a.4.5.2,b.87.1.1 63057,63058 2gcc 70 3.29e+01 2gcc d.10.1.2 37484 1ijbA 202 3.37e+01 c.62.1.1 71229 1bif 469 3.42e+01 1bif c.37.1.7,c.60.1.4 31961,34003 1wdaA 670 3.46e+01 b.2.9.1,b.6.1.6,d.126.1.5 109243,109244,109245 1km4A 247 3.67e+01 c.1.2.3 72740 2dexX 671 3.68e+01 2bifA 469 3.69e+01 1bif c.37.1.7,c.60.1.4 31963,34009 1rypJ 204 3.73e+01 d.153.1.4 41878 1b0pA 1231 3.73e+01 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 31831,31832,33104,34157,39003 2dri 271 3.75e+01 2dri c.93.1.1 35637 1tf1A 198 3.77e+01 d.110.2.2 106826 1z15A 344 3.83e+01 1w44A 331 3.84e+01 1umdB 324 3.87e+01 c.36.1.7,c.48.1.2 99600,99601 1mpuA 138 3.98e+01 d.169.1.1 85040 2c46A 241 4.01e+01 1gveA 327 4.04e+01 c.1.7.1 70597 1lq9A 112 4.04e+01 d.58.4.3 78129 1ct9A 553 4.12e+01 1ct9A c.26.2.1,d.153.1.1 31616,41834 1z3eA 132 4.14e+01 1xkyA 301 4.14e+01 3bifA 468 4.17e+01 1bif c.37.1.7,c.60.1.4 31962,34008 1k7yA 577 4.19e+01 a.46.1.1,c.23.6.1,d.173.1.1 68272,68273,68274 1hbxG 157 4.21e+01 1awcA a.4.5.21 60934 1fdyA 297 4.22e+01 1nal3 c.1.10.1 29071 1jslA 327 4.24e+01 c.88.1.1 67233 1jsrA 327 4.25e+01 c.88.1.1 67237 1q1hA 110 4.29e+01 a.4.5.41 95580 1ihuA 589 4.35e+01 c.37.1.10,c.37.1.10 62394,62395 1akaA 401 4.35e+01 1ajsA c.67.1.1 34258 1xjjA 644 4.44e+01 2b0mA 393 4.47e+01 1c20A 128 4.47e+01 1c20A a.4.3.1 16079 1q77A 138 4.47e+01 c.26.2.4 96023 1nk4A 580 4.57e+01 c.55.3.5,e.8.1.1 91923,91924 1aa0 113 4.58e+01 1aa0 h.1.17.1 45659 1l3sA 580 4.59e+01 c.55.3.5,e.8.1.1 84521,84522 1khdA 345 4.59e+01 a.46.2.1,c.27.1.1 77400,77401 1eiwA 111 4.60e+01 1eiwA c.23.3.1 31130 1g6nA 210 4.62e+01 2cgpA a.4.5.4,b.82.3.2 16100,28139 1c9bA 207 4.63e+01 1tfb a.74.1.2,a.74.1.2 18372,18373 1rqbA 539 4.67e+01 a.5.7.2,c.1.10.5 105057,105058 1gz0A 253 4.70e+01 c.116.1.1,d.79.3.3 76391,76392 1omoA 322 4.70e+01 c.2.1.13 104017 1lddA 74 4.74e+01 a.4.5.34 73841 1lvaA 258 4.81e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1dvjA 246 4.87e+01 1dvjA c.1.2.3 28546 1u4bA 580 4.91e+01 c.55.3.5,e.8.1.1 107664,107665 1yrbA 262 4.99e+01 2ay1A 394 5.04e+01 1ajsA c.67.1.1 34357 2gtrA 261 5.06e+01 1apxA 249 5.08e+01 1ryc a.93.1.1 18669 1ipaA 274 5.08e+01 c.116.1.1,d.79.3.3 71254,71255 1gs5A 258 5.10e+01 c.73.1.2 70395 1cb7B 483 5.12e+01 1cb7B c.1.19.2 29648 1wyzA 242 5.13e+01 1c1lA 136 5.15e+01 1c1lA b.29.1.3 24219 1zckA 154 5.15e+01 1tvoA 368 5.21e+01 1g7sA 594 5.32e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 7aatA 401 5.35e+01 1ajsA c.67.1.1 34250 1nal1 297 5.37e+01 1nal3 1jbkA 195 5.41e+01 c.37.1.20 71631 1uayA 242 5.42e+01 c.2.1.2 88390 1bpv 112 5.42e+01 1bpv b.1.2.1 22071 1wi9A 72 5.44e+01 1xg9A 260 5.44e+01 1rxdA 159 5.45e+01 1zghA 260 5.45e+01 1d9eA 284 5.51e+01 1d9eA c.1.10.4 29195 1j5kA 89 5.54e+01 d.51.1.1 71565 1gc1G 321 5.54e+01 1gc1G d.172.1.1 42493 1ea0A 1479 5.56e+01 b.80.4.1,c.1.4.1,d.153.1.1 64854,64855,64856 1nfn 191 5.57e+01 1nfn a.24.1.1 16523 1xbtA 193 5.57e+01 2bhvA 246 5.67e+01 1xjeA 644 5.70e+01 1z85A 234 5.82e+01 1nznA 126 5.82e+01 a.118.8.1 92382 1srvA 145 5.84e+01 1derA c.8.5.1 30817 1puc 105 5.89e+01 1puc d.97.1.1 40675 1hl2A 297 5.97e+01 c.1.10.1 83581 1dc1A 323 5.99e+01 1dc1A c.52.1.11 33321 1ccwB 483 6.00e+01 1cb7B c.1.19.2 29646 1i9sA 210 6.09e+01 1i9sA c.45.1.1 62099 1k4iA 233 6.12e+01 d.115.1.2 72056 1ymmE 249 6.19e+01 1iyrA 111 6.21e+01 a.164.1.1 76973 1jdqA 98 6.35e+01 d.68.3.3 66559 1air 353 6.55e+01 1air b.80.1.1 28018 2pec 353 6.55e+01 1air b.80.1.1 28019 1snzA 344 6.65e+01 b.30.5.4 98930 1afrA 345 6.71e+01 1afrA a.25.1.2 16805 2fpoA 202 6.75e+01 1fa0A 537 6.75e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 1zzkA 82 6.76e+01 1fd2 106 6.82e+01 1a6l d.58.1.2 38962 1ss4A 153 6.84e+01 d.32.1.6 105976 1a6l 106 6.87e+01 1a6l d.58.1.2 38966 1vbuA 328 6.91e+01 1d3hA 367 7.01e+01 1d3gA c.1.4.1 28601 2b3nA 159 7.01e+01 2fb0A 94 7.04e+01 1k2xB 143 7.04e+01 1q6oA 216 7.04e+01 c.1.2.3 95986 1lp4A 332 7.15e+01 d.144.1.7 74170 2a6qA 86 7.15e+01 2b0jA 358 7.17e+01 1vc4A 254 7.27e+01 c.1.2.4 100557 1hw5A 210 7.31e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 6mhtA 327 7.35e+01 6mhtA c.66.1.26 34226 1aq6A 253 7.38e+01 1qq5A c.108.1.1 43331 2cgpA 210 7.39e+01 2cgpA a.4.5.4,b.82.3.2 16102,28141 1kv8A 216 7.45e+01 c.1.2.3 73054 2gjgA 248 7.47e+01 2ethA 154 7.49e+01 2awdA 323 7.50e+01 1knwA 425 7.52e+01 b.49.2.3,c.1.6.1 90969,90970 2ghcX 261 7.59e+01 1w4rA 195 7.66e+01 1euhA 475 7.67e+01 1euhA c.82.1.1 35369 1d3uA 181 7.73e+01 1ytbA d.129.1.1,d.129.1.1 41290,41291 1fjxA 327 7.77e+01 6mhtA c.66.1.26 34228 1c7jA 489 7.82e+01 2bce c.69.1.1 34631 1allA 160 7.83e+01 1qgwC a.1.1.3 15647 2gwfB 134 7.85e+01 1jwhA 337 7.86e+01 d.144.1.7 71913 1jflA 228 7.87e+01 c.78.2.1,c.78.2.1 71656,71657 1wm1A 317 7.87e+01 c.69.1.7 109405 1f56A 91 7.94e+01 2cbp b.6.1.1 22896 1uaaA 673 8.01e+01 1pjr c.37.1.19,c.37.1.19 32401,32402 1llwA 1520 8.07e+01 b.80.4.1,c.1.4.1,d.153.1.1 74017,74018,74019 1udxA 416 8.08e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1kijA 390 8.09e+01 d.14.1.3,d.122.1.2 72514,72515 1ofdA 1520 8.11e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1o7jA 327 8.15e+01 c.88.1.1 81140 2bolA 314 8.15e+01 1b65A 375 8.19e+01 1b65A d.154.1.1 42020 1vb3A 428 8.20e+01 1ymiA 334 8.26e+01 1oltA 457 8.26e+01 c.1.28.2 93334 2bnmA 198 8.30e+01 1cem 363 8.37e+01 1cem a.102.1.2 18826 1sz7A 200 8.38e+01 1qtsA 247 8.45e+01 1qtsA b.1.10.1,d.105.1.1 22313,40789 1dpuA 99 8.47e+01 1dpuA a.4.5.16 16150 2bp1A 360 8.50e+01 1bli 483 8.62e+01 1bli b.71.1.1,c.1.8.1 27715,28702 1a8q 274 8.63e+01 1brt c.69.1.12 34702 1rypA 243 8.64e+01 1pmaA d.153.1.4 41932 1xqiA 195 8.68e+01 1eguA 731 8.69e+01 1eguA a.102.3.2,b.24.1.1,b.30.5.2 18850,23899,24423 1vllA 334 8.70e+01 c.2.1.13 108834 1oafA 261 8.77e+01 a.93.1.1 86734 1g0uI 205 8.80e+01 d.153.1.4 41891 1kfcA 268 8.84e+01 c.1.2.4 77371 1qi6A 475 8.91e+01 1euhA c.82.1.1 35373 1vp8A 201 8.96e+01 1wkyA 464 8.97e+01