# List of top-scoring protein chains for t2k-100-30-dssp-ehl2-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 1oz9A 150 4.91e-02 d.92.1.15 93808 1g3qA 237 5.55e-01 1hyqA c.37.1.10 60237 1fmcA 255 5.80e-01 1cydA c.2.1.2 29856 1xx6A 191 6.24e-01 1g94A 448 6.69e-01 b.71.1.1,c.1.8.1 65169,65170 1o2dA 371 8.76e-01 e.22.1.2 86591 1d9eA 284 1.14e+00 1d9eA c.1.10.4 29195 2d00A 109 1.29e+00 1aqm 453 1.29e+00 1smd b.71.1.1,c.1.8.1 27717,28704 1gcoA 261 1.52e+00 1ybvA c.2.1.2 29884 1geeA 261 1.52e+00 c.2.1.2 90509 1qi6A 475 1.69e+00 1euhA c.82.1.1 35373 1euhA 475 1.84e+00 1euhA c.82.1.1 35369 2bx6A 350 1.93e+00 1zjrA 211 2.18e+00 2bgkA 278 2.48e+00 1dqnA 230 2.54e+00 1dqnA c.61.1.1 34067 1ukcA 522 2.81e+00 c.69.1.17 107911 1mpuA 138 2.82e+00 d.169.1.1 85040 1dqpA 230 2.84e+00 1dqnA c.61.1.1 34069 1yymG 313 3.03e+00 1rzsA 61 3.14e+00 a.35.1.2 105139 1xkyA 301 3.39e+00 1wwiA 148 3.61e+00 1v98A 140 3.66e+00 1yacA 208 3.91e+00 1yacA c.33.1.3 31757 2f51A 118 4.14e+00 1aisB 200 4.19e+00 1aisB a.74.1.2,a.74.1.2 18384,18385 1yhpA 212 4.44e+00 1pot 325 4.59e+00 1pot c.94.1.1 35807 1fnlA 175 4.69e+00 2fcbA b.1.1.4,b.1.1.4 21783,21784 2bz1A 196 5.31e+00 1ea0A 1479 5.38e+00 b.80.4.1,c.1.4.1,d.153.1.1 64854,64855,64856 2fbiA 142 5.51e+00 1oq9A 363 5.83e+00 a.25.1.2 87257 2dexX 671 5.97e+00 1wdaA 670 6.04e+00 b.2.9.1,b.6.1.6,d.126.1.5 109243,109244,109245 1nfn 191 6.57e+00 1nfn a.24.1.1 16523 1d3uB 201 6.63e+00 1aisB a.74.1.2,a.74.1.2 18386,18387 1d2eA 397 6.88e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1edoA 244 6.95e+00 1ybvA c.2.1.2 29896 1lvaA 258 7.19e+00 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1ecfB 504 7.33e+00 1ecfB c.61.1.1,d.153.1.1 34054,41821 1ecfA 504 7.39e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 1g9mG 321 7.52e+00 1gc1G d.172.1.1 42492 1twdA 256 7.73e+00 c.1.30.1 107397 1dar 691 7.80e+00 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1 25707,32142,37547,39300 4pgaA 337 7.97e+00 4pgaA c.88.1.1 35565 1v8gA 329 8.21e+00 a.46.2.1,c.27.1.1 100505,100506 1xn7A 78 8.36e+00 1jslA 327 8.40e+00 c.88.1.1 67233 1jsrA 327 8.44e+00 c.88.1.1 67237 2fcr 173 8.46e+00 1rcf c.23.5.1 31151 1hl2A 297 8.90e+00 c.1.10.1 83581 1fdyA 297 9.11e+00 1nal3 c.1.10.1 29071 2fbmA 291 9.24e+00 1ionA 243 9.41e+00 c.37.1.10 62633 1i8tA 367 9.49e+00 c.4.1.3,d.16.1.7 66094,66095 2fw2A 260 9.82e+00 1ymiA 334 9.94e+00 1d4oA 184 1.06e+01 1d4oA c.31.1.4 31748 1nvmA 345 1.08e+01 a.5.7.1,c.1.10.5 86249,86250 1pg4A 652 1.10e+01 e.23.1.1 88067 1pbjA 125 1.11e+01 d.37.1.1,d.37.1.1 94414,94415 1f07A 321 1.13e+01 1ezwA c.1.16.3 59560 1gc1G 321 1.17e+01 1gc1G d.172.1.1 42493 1j93A 353 1.18e+01 c.1.22.1 66454 1o7jA 327 1.23e+01 c.88.1.1 81140 1de4C 640 1.24e+01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17779,30760,33848 1rzjG 321 1.27e+01 d.172.1.1 98200 1q7zA 566 1.29e+01 c.1.21.2,c.1.26.1 96090,96091 1nal1 297 1.31e+01 1nal3 1o60A 292 1.32e+01 c.1.10.4 92532 1ja9A 274 1.35e+01 c.2.1.2 62817 2bolA 314 1.40e+01 1y1oA 203 1.40e+01 1elvA 333 1.43e+01 5ptp b.47.1.2,g.18.1.1 59454,59455 1uayA 242 1.48e+01 c.2.1.2 88390 2bd0A 244 1.55e+01 1ipaA 274 1.58e+01 c.116.1.1,d.79.3.3 71254,71255 2b99A 156 1.61e+01 2bifA 469 1.62e+01 1bif c.37.1.7,c.60.1.4 31963,34009 1y0nA 78 1.67e+01 1xqiA 195 1.74e+01 2gtrA 261 1.75e+01 1k3eA 156 1.76e+01 d.198.1.1 68103 1c6vX 81 1.83e+01 1ihvA b.34.7.1 24641 1v8aA 265 1.84e+01 c.72.1.2 100494 1nal3 297 1.86e+01 1nal3 1kid 203 1.96e+01 1derA c.8.5.1 30771 1jwhA 337 1.98e+01 d.144.1.7 71913 1oi7A 288 1.99e+01 c.2.1.8,c.23.4.1 87049,87050 1vclA 432 2.02e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1c1lA 136 2.14e+01 1c1lA b.29.1.3 24219 1mkmA 249 2.17e+01 a.4.5.33,d.110.2.2 79242,79243 1srvA 145 2.18e+01 1derA c.8.5.1 30817 2d8dA 90 2.22e+01 1xmxA 385 2.23e+01 3bifA 468 2.26e+01 1bif c.37.1.7,c.60.1.4 31962,34008 2wsyA 268 2.28e+01 2tysA c.1.2.4 28588 1jbkA 195 2.30e+01 c.37.1.20 71631 2b3nA 159 2.30e+01 1eiwA 111 2.30e+01 1eiwA c.23.3.1 31130 2bhvA 246 2.33e+01 1rqbA 539 2.36e+01 a.5.7.2,c.1.10.5 105057,105058 1x6vA 630 2.39e+01 1g7vA 284 2.41e+01 1d9eA c.1.10.4 60335 1gegA 256 2.43e+01 1ybvA c.2.1.2 29888 1om1A 332 2.44e+01 d.144.1.7 93347 1lr0A 129 2.45e+01 d.212.1.1 74213 1z2nX 324 2.49e+01 1m2rA 327 2.58e+01 d.144.1.7 84760 1oeyJ 107 2.61e+01 d.15.2.2 92804 1lp4A 332 2.61e+01 d.144.1.7 74170 1sdsA 117 2.63e+01 d.79.3.1 105439 1qtsA 247 2.64e+01 1qtsA b.1.10.1,d.105.1.1 22313,40789 1bq0 103 2.73e+01 1bqz a.2.3.1 15698 1mixA 206 2.76e+01 a.11.2.1,b.55.1.5 79166,79167 1kijA 390 2.77e+01 d.14.1.3,d.122.1.2 72514,72515 1kyfA 247 2.80e+01 b.1.10.1,d.105.1.1 73220,73221 2fv7A 331 2.83e+01 1auq 208 2.85e+01 1auq c.62.1.1 34137 1zip 217 2.87e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1q1hA 110 2.93e+01 a.4.5.41 95580 1w44A 331 2.95e+01 1lddA 74 3.23e+01 a.4.5.34 73841 1o97C 264 3.23e+01 c.26.2.3 81232 1zin 217 3.24e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1zzpA 130 3.25e+01 1nr6A 473 3.32e+01 a.104.1.1 92085 1fjgB 256 3.34e+01 1fjfB c.23.15.1 31400 1y7lA 316 3.35e+01 2rslA 140 3.37e+01 2rslA c.53.1.1 33345 1lap 488 3.37e+01 1lam c.50.1.1,c.56.5.3 33171,33834 2b3hA 329 3.40e+01 1a6o 332 3.42e+01 1a6o 1lpuA 332 3.47e+01 d.144.1.7 74177 1geqA 248 3.49e+01 2tysA c.1.2.4 28589 1p2fA 220 3.53e+01 a.4.6.1,c.23.1.1 87720,87721 1zkdA 387 3.57e+01 1f15B 218 3.62e+01 1f15B b.121.4.5 23321 1a27 289 3.64e+01 1fds c.2.1.2 29839 1ugpA 203 3.65e+01 d.149.1.1 107831 1n93X 375 3.69e+01 a.206.1.1 91707 1g7tA 594 3.71e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25714,25715,31033,32148 1igwA 434 3.85e+01 c.1.12.7 62370 1zynA 202 3.88e+01 1e3sA 261 3.88e+01 1e6wA c.2.1.2 59201 1apxA 249 3.92e+01 1ryc a.93.1.1 18669 1cvrA 435 4.02e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 1hmy 327 4.05e+01 6mhtA c.66.1.26 34229 1fdt 327 4.06e+01 1fds c.2.1.2 29841 1svmA 377 4.07e+01 2bvaA 292 4.07e+01 1b9kA 238 4.10e+01 1qtsA b.1.10.1,d.105.1.1 22315,40791 1pj5A 830 4.12e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1pxwA 128 4.17e+01 d.79.3.1 95305 1prxA 224 4.21e+01 1prxA c.47.1.10 33076 1gveA 327 4.22e+01 c.1.7.1 70597 1kqqA 139 4.23e+01 a.4.3.1 72885 1bllE 488 4.28e+01 1lam c.50.1.1,c.56.5.3 33170,33833 1cx8B 639 4.33e+01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17783,30764,33852 1fnsA 196 4.35e+01 1auq c.62.1.1 34136 1m6sA 347 4.35e+01 c.67.1.1 78701 1jg8A 347 4.36e+01 1jg8A c.67.1.1 62946 1k8kF 168 4.43e+01 d.198.2.1 68312 1oakA 196 4.44e+01 1auq c.62.1.1 34138 1clqA 903 4.51e+01 1clqA c.55.3.5,e.8.1.1 33717,43006 1i5rA 327 4.54e+01 c.2.1.2 83668 1jw2A 72 4.54e+01 a.23.5.1 67372 1cx8A 639 4.61e+01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17782,30763,33851 1n25A 368 4.67e+01 c.37.1.20 85264 1jtvA 327 4.69e+01 c.2.1.2 84230 2feaA 236 4.75e+01 1s58A 554 4.75e+01 b.121.5.2 105262 1olmA 403 4.80e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1ub9A 100 4.88e+01 a.4.5.28 99159 1ihuA 589 4.91e+01 c.37.1.10,c.37.1.10 62394,62395 2gaiA 633 4.92e+01 1qgdA 662 4.93e+01 c.36.1.6,c.36.1.10,c.48.1.1 88367,88368,88369 2gukA 120 4.93e+01 1n6bA 473 4.98e+01 a.104.1.1 85359 1lam 484 4.99e+01 1lam c.50.1.1,c.56.5.3 33166,33829 1tf1A 198 5.02e+01 d.110.2.2 106826 1z15A 344 5.03e+01 2f96A 224 5.07e+01 1j5kA 89 5.10e+01 d.51.1.1 71565 1o6uA 403 5.10e+01 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 1pnsB 234 5.11e+01 i.1.1.1 88169 1ymmE 249 5.11e+01 1qopA 268 5.16e+01 2tysA c.1.2.4 28570 3cla 213 5.20e+01 3cla c.43.1.1 32610 1usgA 346 5.22e+01 c.93.1.1 99864 2liv 344 5.23e+01 2liv c.93.1.1 35708 1xm3A 264 5.28e+01 1ku3A 73 5.29e+01 a.4.13.2 73000 2gdjA 264 5.32e+01 2gcc 70 5.34e+01 2gcc d.10.1.2 37484 2ae2A 260 5.42e+01 1bdb c.2.1.2 29945 1fds 327 5.50e+01 1fds c.2.1.2 29838 2bp1A 360 5.52e+01 1sy7A 715 5.52e+01 1bli 483 5.55e+01 1bli b.71.1.1,c.1.8.1 27715,28702 2bzlA 325 5.56e+01 1thg 544 5.56e+01 1thg c.69.1.17 34763 1on3A 523 5.59e+01 c.14.1.4,c.14.1.4 87107,87108 2d09A 407 5.60e+01 1j5eB 256 5.63e+01 c.23.15.1 71543 1vp4A 425 5.68e+01 1b0pA 1231 5.68e+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 1fnmA 691 5.74e+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 2d0eA 407 5.76e+01 1xbiA 120 5.91e+01 1bksA 268 5.97e+01 2tysA c.1.2.4 28585 2c46A 241 6.02e+01 2dri 271 6.02e+01 2dri c.93.1.1 35637 1jhfA 202 6.03e+01 a.4.5.2,b.87.1.1 63057,63058 1g4uS 383 6.07e+01 1g4uS a.24.11.1,c.45.1.2 16643,32691 1wi9A 72 6.23e+01 1fa0A 537 6.25e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 1hkfA 122 6.26e+01 b.1.1.1 83553 1bif 469 6.27e+01 1bif c.37.1.7,c.60.1.4 31961,34003 2guhA 214 6.36e+01 1t4hA 290 6.41e+01 d.144.1.7 106420 1gs5A 258 6.44e+01 c.73.1.2 70395 1hq1A 105 6.44e+01 1dulA a.36.1.1 17120 1fa0B 537 6.45e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39336,75839,75840 1ijbA 202 6.46e+01 c.62.1.1 71229 3bdpA 580 6.48e+01 1xwl c.55.3.5,e.8.1.1 33711,43004 1sflA 238 6.51e+01 1byb 495 6.54e+01 1byb c.1.8.1 28790 2fyxA 143 6.82e+01 2ethA 154 6.85e+01 2bogX 286 6.86e+01 1wdpA 495 6.88e+01 1x9zA 188 6.89e+01 1llwA 1520 6.92e+01 b.80.4.1,c.1.4.1,d.153.1.1 74017,74018,74019 1lqpA 135 6.95e+01 d.32.1.2 78151 1nkiA 135 6.95e+01 d.32.1.2 91941 1sz9A 144 6.99e+01 a.118.9.4 106139 1pmi 440 7.09e+01 1pmi b.82.1.3 28114 1e6wA 260 7.17e+01 1e6wA c.2.1.2 59326 2ghcX 261 7.35e+01 1fohA 664 7.36e+01 1fohA c.3.1.2,c.47.1.10,d.16.1.2 30381,33078,37900 1f60A 458 7.37e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1y7pA 223 7.39e+01 1z7lA 276 7.43e+01 2c3mA 1231 7.47e+01 1jscA 630 7.48e+01 c.31.1.3,c.36.1.5,c.36.1.9 67224,67225,67226 1xccA 220 7.50e+01 1ofdA 1520 7.55e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1kxpD 458 7.65e+01 a.126.1.1,a.126.1.1,a.126.1.1 73160,73161,73162 1h96A 182 7.68e+01 2fha a.25.1.1 60811 1lb3A 182 7.68e+01 a.25.1.1 77873 1nxuA 333 7.75e+01 c.122.1.1 86389 1y02A 120 7.80e+01 2f46A 156 7.86e+01 1w1wE 121 7.88e+01 2gptA 523 7.90e+01 1nozA 388 7.91e+01 1clqA c.55.3.5 33715 1tqgA 105 7.98e+01 a.24.10.3 107224 1kekA 1231 7.98e+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 1q6cA 495 8.03e+01 c.1.8.1 95970 1afrA 345 8.10e+01 1afrA a.25.1.2 16805 2b7nA 273 8.20e+01 1vdyA 140 8.24e+01 2tysA 268 8.28e+01 2tysA c.1.2.4 28572 2f6uA 234 8.35e+01 2fiyA 309 8.38e+01 1jl2A 156 8.40e+01 c.55.3.1 66822 1hbxG 157 8.47e+01 1awcA a.4.5.21 60934 1l3sA 580 8.53e+01 c.55.3.5,e.8.1.1 84521,84522 1gh9A 71 8.57e+01 1gh9A g.41.6.1 45266 1kuuA 202 8.64e+01 d.153.2.1 73019 1kfcA 268 8.71e+01 c.1.2.4 77371 2d1sA 548 8.72e+01 1bplB 294 8.76e+01 1bli b.71.1.1 27716 2akoA 251 8.79e+01 1b7yB 785 8.83e+01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16301,16302,25312,39311,40780,41456 1c20A 128 8.84e+01 1c20A a.4.3.1 16079 1hgxA 183 8.94e+01 1tc1A c.61.1.1 34027 1ypqA 135 8.97e+01 2anxA 146 8.97e+01