# List of top-scoring protein chains for t04-100-30-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 1o2dA 371 9.83e-03 e.22.1.2 86591 1wwiA 148 1.63e-01 1fmcA 255 2.47e-01 1cydA c.2.1.2 29856 1aqm 453 2.53e-01 1smd b.71.1.1,c.1.8.1 27717,28704 1g94A 448 3.24e-01 b.71.1.1,c.1.8.1 65169,65170 2f46A 156 6.54e-01 1xmxA 385 1.17e+00 1fohA 664 1.33e+00 1fohA c.3.1.2,c.47.1.10,d.16.1.2 30381,33078,37900 1jg8A 347 1.44e+00 1jg8A c.67.1.1 62946 1m6sA 347 1.44e+00 c.67.1.1 78701 1geeA 261 1.47e+00 c.2.1.2 90509 1gcoA 261 1.47e+00 1ybvA c.2.1.2 29884 1ja9A 274 1.50e+00 c.2.1.2 62817 1pn0A 665 2.14e+00 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 2fcr 173 2.41e+00 1rcf c.23.5.1 31151 1ijbA 202 2.53e+00 c.62.1.1 71229 1oi7A 288 2.56e+00 c.2.1.8,c.23.4.1 87049,87050 1dar 691 2.59e+00 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1 25707,32142,37547,39300 1uayA 242 2.59e+00 c.2.1.2 88390 1x1zA 252 2.62e+00 1knwA 425 2.65e+00 b.49.2.3,c.1.6.1 90969,90970 2bgkA 278 2.90e+00 1km4A 247 3.60e+00 c.1.2.3 72740 1yacA 208 3.81e+00 1yacA c.33.1.3 31757 1v98A 140 4.36e+00 1oz9A 150 4.37e+00 d.92.1.15 93808 2fbiA 142 4.41e+00 1zip 217 4.52e+00 1zin c.37.1.1,g.41.2.1 31916,45179 1de4C 640 4.52e+00 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17779,30760,33848 1oaa 259 4.58e+00 1oaa c.2.1.2 29829 2liv 344 4.63e+00 2liv c.93.1.1 35708 1qopA 268 4.83e+00 2tysA c.1.2.4 28570 1usgA 346 4.85e+00 c.93.1.1 99864 1g3qA 237 4.89e+00 1hyqA c.37.1.10 60237 2lbp 346 5.02e+00 2liv c.93.1.1 35709 1dvjA 246 5.16e+00 1dvjA c.1.2.3 28546 1pg4A 652 5.26e+00 e.23.1.1 88067 1elvA 333 5.32e+00 5ptp b.47.1.2,g.18.1.1 59454,59455 2bd0A 244 5.38e+00 2cunA 410 5.39e+00 1xx6A 191 5.41e+00 1g0oA 283 5.64e+00 1ybvA c.2.1.2 60181 2tysA 268 5.66e+00 2tysA c.1.2.4 28572 1hw5A 210 5.80e+00 2cgpA a.4.5.4,b.82.3.2 16098,28137 1ituA 369 5.81e+00 c.1.9.7 71423 1aisB 200 5.87e+00 1aisB a.74.1.2,a.74.1.2 18384,18385 1k2xB 143 6.14e+00 2f51A 118 6.27e+00 2awdA 323 6.31e+00 1sdsA 117 6.32e+00 d.79.3.1 105439 1zjrA 211 6.33e+00 1rzsA 61 6.53e+00 a.35.1.2 105139 2anxA 146 6.56e+00 1fnsA 196 6.56e+00 1auq c.62.1.1 34136 1o6uA 403 6.56e+00 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 1wxiA 275 6.59e+00 1ojxA 263 6.78e+00 c.1.10.1 93164 2f02A 323 7.02e+00 1d2eA 397 7.20e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1zin 217 7.21e+00 1zin c.37.1.1,g.41.2.1 31915,45178 1yavA 159 7.37e+00 1aocA 175 7.46e+00 1aocA g.17.1.5 44817 1gveA 327 7.50e+00 c.1.7.1 70597 6mhtA 327 7.60e+00 6mhtA c.66.1.26 34226 1bif 469 8.32e+00 1bif c.37.1.7,c.60.1.4 31961,34003 1srvA 145 8.86e+00 1derA c.8.5.1 30817 1kid 203 8.94e+00 1derA c.8.5.1 30771 1w44A 331 9.08e+00 1xn7A 78 9.33e+00 1olmA 403 9.42e+00 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 2ae2A 260 9.60e+00 1bdb c.2.1.2 29945 1vk0A 206 9.67e+00 c.55.3.5 100839 1ecfA 504 9.95e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 1ebfA 358 1.03e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 2c7pA 327 1.07e+01 2f96A 224 1.07e+01 2d1sA 548 1.10e+01 1l8aA 886 1.11e+01 c.36.1.10,c.36.1.6,c.48.1.1 73677,73678,73679 2bolA 314 1.11e+01 1kv8A 216 1.13e+01 c.1.2.3 73054 1twdA 256 1.16e+01 c.1.30.1 107397 1q6oA 216 1.16e+01 c.1.2.3 95986 1e6wA 260 1.19e+01 1e6wA c.2.1.2 59326 1rkuA 206 1.24e+01 c.108.1.11 97627 2bx6A 350 1.25e+01 1z15A 344 1.25e+01 1igwA 434 1.30e+01 c.1.12.7 62370 1wdaA 670 1.30e+01 b.2.9.1,b.6.1.6,d.126.1.5 109243,109244,109245 2bz1A 196 1.32e+01 2dexX 671 1.37e+01 1gegA 256 1.38e+01 1ybvA c.2.1.2 29888 1omoA 322 1.39e+01 c.2.1.13 104017 1q6cA 495 1.42e+01 c.1.8.1 95970 1xbiA 120 1.44e+01 1bli 483 1.45e+01 1bli b.71.1.1,c.1.8.1 27715,28702 1rypJ 204 1.59e+01 d.153.1.4 41878 2etvA 346 1.60e+01 2gwfB 134 1.61e+01 1zemA 262 1.62e+01 1vb3A 428 1.66e+01 1i6xA 209 1.73e+01 a.4.5.4,b.82.3.2 83673,83674 2fv7A 331 1.76e+01 1fnlA 175 1.76e+01 2fcbA b.1.1.4,b.1.1.4 21783,21784 1kfcA 268 1.76e+01 c.1.2.4 77371 1rdfA 267 1.78e+01 c.108.1.3 104884 1dzlA 505 1.78e+01 1dzlA b.121.6.1 23586 2amxA 376 1.80e+01 1vc4A 254 1.84e+01 c.1.2.4 100557 1om1A 332 1.97e+01 d.144.1.7 93347 1wqaA 455 2.00e+01 1dc1A 323 2.01e+01 1dc1A c.52.1.11 33321 1qmyA 167 2.03e+01 1qmyA d.3.1.2 37094 1zczA 464 2.05e+01 1k3eA 156 2.05e+01 d.198.1.1 68103 2baa 243 2.12e+01 1cnsA d.2.1.1 36243 1hw7A 255 2.13e+01 1i7fA d.193.1.1 61297 2bynA 227 2.14e+01 1yhuB 144 2.14e+01 2feaA 236 2.14e+01 1ihp 438 2.15e+01 1ihp c.60.1.2 33993 2a6qA 86 2.15e+01 1wmiA 90 2.15e+01 1m2rA 327 2.18e+01 d.144.1.7 84760 1vl8A 267 2.20e+01 c.2.1.2 108733 1ymiA 334 2.23e+01 2dri 271 2.29e+01 2dri c.93.1.1 35637 2aeuA 374 2.30e+01 1ipaA 274 2.33e+01 c.116.1.1,d.79.3.3 71254,71255 1dqnA 230 2.35e+01 1dqnA c.61.1.1 34067 1wdpA 495 2.35e+01 1gwiA 411 2.36e+01 a.104.1.1 76364 1dqpA 230 2.38e+01 1dqnA c.61.1.1 34069 2bryA 497 2.40e+01 1tvoA 368 2.41e+01 1cem 363 2.43e+01 1cem a.102.1.2 18826 2d93A 134 2.43e+01 1byb 495 2.44e+01 1byb c.1.8.1 28790 1bza 262 2.47e+01 1btl e.3.1.1 42701 1yymG 313 2.48e+01 2cjpA 328 2.49e+01 1vllA 334 2.54e+01 c.2.1.13 108834 1yxmA 303 2.55e+01 1oltA 457 2.60e+01 c.1.28.2 93334 2b99A 156 2.64e+01 2d8dA 90 2.68e+01 1l2uA 245 2.72e+01 c.1.2.3 73516 1iioA 84 2.76e+01 a.39.4.1 66150 1vmjA 151 2.77e+01 1g7dA 106 2.78e+01 1g7dA a.71.1.1 18318 1w5rA 278 2.78e+01 1euhA 475 2.78e+01 1euhA c.82.1.1 35369 1v25A 541 2.79e+01 e.23.1.1 108275 1h6zA 913 2.80e+01 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 1bbhA 131 2.83e+01 1bbhA a.24.3.2 16546 1geqA 248 2.88e+01 2tysA c.1.2.4 28589 1nkiA 135 2.89e+01 d.32.1.2 91941 1va4A 279 2.92e+01 c.69.1.12 108458 1pxwA 128 2.93e+01 d.79.3.1 95305 1lj2A 110 2.96e+01 h.1.13.2 73926 1yhpA 212 2.96e+01 1a32 88 2.98e+01 1a32 a.16.1.2 16384 1kuuA 202 3.03e+01 d.153.2.1 73019 1c6vX 81 3.04e+01 1ihvA b.34.7.1 24641 1f7cA 231 3.05e+01 1f7cA a.116.1.1 19107 1cvrA 435 3.07e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 1wmjA 130 3.10e+01 1q1hA 110 3.11e+01 a.4.5.41 95580 1wm5A 208 3.14e+01 2gdjA 264 3.17e+01 1yyvA 131 3.29e+01 2cj4A 150 3.29e+01 1kwfA 363 3.31e+01 a.102.1.2 73078 2bp1A 360 3.32e+01 1v8gA 329 3.39e+01 a.46.2.1,c.27.1.1 100505,100506 1tjyA 316 3.42e+01 c.93.1.1 107062 1vclA 432 3.45e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 2gptA 523 3.45e+01 1jhfA 202 3.46e+01 a.4.5.2,b.87.1.1 63057,63058 1vflA 356 3.50e+01 1x9mA 698 3.54e+01 1d3yA 301 3.56e+01 1d3yA e.12.1.1 43252 1fjgB 256 3.58e+01 1fjfB c.23.15.1 31400 1pmnA 364 3.62e+01 d.144.1.7 94907 1lr0A 129 3.65e+01 d.212.1.1 74213 1q8yA 373 3.67e+01 d.144.1.7 96234 2b0mA 393 3.70e+01 1zckA 154 3.72e+01 1yx1A 264 3.76e+01 1kblA 873 3.80e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1p4xA 250 3.84e+01 a.4.5.28,a.4.5.28 87784,87785 1hh8A 213 3.90e+01 1e96B a.118.8.1 61042 1wi9A 72 3.90e+01 1uehA 253 3.92e+01 c.101.1.1 99259 1nal1 297 3.93e+01 1nal3 1vhcA 224 3.93e+01 c.1.10.1 100661 2utgA 70 3.97e+01 1utg a.101.1.1 18814 1ha3A 405 3.98e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1utg 70 3.98e+01 1utg a.101.1.1 18813 1rrmA 386 3.99e+01 e.22.1.2 105081 1l5jA 865 4.02e+01 a.118.15.1,c.8.2.1,c.83.1.1 73592,73593,73594 1lt8A 406 4.09e+01 c.1.26.1 78186 1gx3A 284 4.09e+01 d.3.1.5 70678 1vp4A 425 4.10e+01 1vljA 407 4.15e+01 e.22.1.2 108832 2c78A 405 4.16e+01 1rxdA 159 4.16e+01 1mucA 373 4.21e+01 1mucA c.1.11.2,d.54.1.1 29236,38880 1exmA 405 4.23e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 2aumA 317 4.23e+01 1thg 544 4.25e+01 1thg c.69.1.17 34763 1b6rA 355 4.26e+01 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28241,31648,41493 1qs0B 338 4.28e+01 1qs0B c.36.1.7,c.48.1.2 31830,33103 1jmkC 230 4.29e+01 c.69.1.22 71747 1o60A 292 4.30e+01 c.1.10.4 92532 1ckeA 227 4.35e+01 1ckeA c.37.1.1 31846 1pfkA 320 4.35e+01 3pfk c.89.1.1 35575 1iw7C 1119 4.41e+01 e.29.1.1 71474 1sjdA 368 4.45e+01 c.1.11.2,d.54.1.1 105632,105633 1or3A 165 4.47e+01 1nfn a.24.1.1 16522 1vp8A 201 4.47e+01 1iqcA 308 4.49e+01 a.3.1.5,a.3.1.5 66266,66267 2fw2A 260 4.51e+01 256bA 106 4.54e+01 256bA a.24.3.1 16539 2pfkA 320 4.56e+01 3pfk c.89.1.1 35577 1ypqA 135 4.59e+01 1tuoA 464 4.67e+01 1mwvA 714 4.71e+01 a.93.1.3,a.93.1.3 85161,85162 1prxA 224 4.71e+01 1prxA c.47.1.10 33076 2fbmA 291 4.72e+01 1k0eA 453 4.73e+01 d.161.1.1 67938 1b7yB 785 4.74e+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 1vr1H 261 4.75e+01 5ptp 1im5A 180 4.83e+01 c.33.1.3 66211 1noyA 388 4.84e+01 1clqA c.55.3.5 33713 1yjsA 419 4.85e+01 1yc5A 246 4.85e+01 1dxjA 242 4.85e+01 1cnsA d.2.1.1 36244 1fds 327 4.85e+01 1fds c.2.1.2 29838 2d0eA 407 4.87e+01 1lvaA 258 4.88e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1gca 309 4.93e+01 1gca c.93.1.1 35659 1kl1A 419 4.95e+01 c.67.1.4 72663 2aunA 317 4.98e+01 1zrsA 317 4.99e+01 1h75A 81 5.03e+01 1h75A c.47.1.1 60716 1t7pA 698 5.12e+01 1t7pA c.55.3.5,e.8.1.1 33712,43005 2cf8H 257 5.14e+01 1uxtA 501 5.14e+01 c.82.1.1 108125 1xkqA 280 5.17e+01 1k8wA 327 5.19e+01 b.122.1.1,d.265.1.2 83094,90388 1hzoA 271 5.20e+01 e.3.1.1 71092 1y02A 120 5.24e+01 1p9oA 313 5.26e+01 c.72.3.1 94397 1lh0A 213 5.34e+01 c.61.1.1 73896 1w1iE 357 5.35e+01 c.1.9.1 109051 1ccwB 483 5.35e+01 1cb7B c.1.19.2 29646 1uz3A 102 5.41e+01 1ofdA 1520 5.50e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1wkyA 464 5.52e+01 1xccA 220 5.52e+01 2azeA 155 5.53e+01 1rxwA 336 5.54e+01 a.60.7.1,c.120.1.2 98059,98060 1iysA 262 5.56e+01 e.3.1.1 90723 1e9rA 437 5.60e+01 c.37.1.11 64827 2bu3A 254 5.64e+01 2d00A 109 5.64e+01 1g7sA 594 5.64e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1hl2A 297 5.68e+01 c.1.10.1 83581 1wgzA 510 5.69e+01 1v3hA 495 5.73e+01 c.1.8.1 108303 2avuE 192 5.81e+01 1uok 558 5.86e+01 1uok b.71.1.1,c.1.8.1 27801,28788 1oj6A 151 5.90e+01 a.1.1.2 93088 1yw3A 208 5.91e+01 1zcjA 463 5.91e+01 1utuA 108 5.93e+01 1xqiA 195 5.95e+01 1sy7A 715 5.99e+01 1puc 105 6.01e+01 1puc d.97.1.1 40675 1ni4B 341 6.10e+01 c.36.1.7,c.48.1.2 85729,85730 1mixA 206 6.11e+01 a.11.2.1,b.55.1.5 79166,79167 1gcb 454 6.13e+01 3gcb d.3.1.1 37034 1xmbA 418 6.13e+01 1y0nA 78 6.15e+01 2fm8A 135 6.16e+01 1w6uA 302 6.25e+01 1wv2A 265 6.39e+01 1ku3A 73 6.39e+01 a.4.13.2 73000 1jvnA 555 6.39e+01 c.1.2.1,c.23.16.1 67355,67356 2cw5A 255 6.50e+01 1v66A 65 6.51e+01 2bzlA 325 6.52e+01 1fehA 574 6.52e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1dosA 358 6.53e+01 1dosA c.1.10.2 29175 1oeyJ 107 6.53e+01 d.15.2.2 92804 2bodX 286 6.57e+01 1vzqH 250 6.62e+01 1dxy 333 6.64e+01 1dxy c.2.1.4,c.23.12.1 30094,31354 1hxhA 253 6.67e+01 c.2.1.2 76725 2c46A 241 6.68e+01 1amuA 563 6.69e+01 1amuA e.23.1.1 43351 1toaA 313 6.71e+01 1toaA c.92.2.2 35598 2ts1 419 6.72e+01 2ts1 c.26.1.1 31564 1i9sA 210 6.77e+01 1i9sA c.45.1.1 62099 1gteA 1025 6.81e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70440,70441,70442,70443,70444 1l3sA 580 6.90e+01 c.55.3.5,e.8.1.1 84521,84522 3gcb 470 6.91e+01 3gcb d.3.1.1 37032 1kdgA 546 6.93e+01 c.3.1.2,d.16.1.1 77337,77338 1nk4A 580 6.98e+01 c.55.3.5,e.8.1.1 91923,91924 2cw6A 298 7.01e+01 1lq9A 112 7.01e+01 d.58.4.3 78129 1opr 213 7.02e+01 1opr c.61.1.1 34091 1rcuA 195 7.03e+01 c.129.1.1 97295 1bt0A 76 7.05e+01 1ubi d.15.1.1 37607 2b3yA 888 7.07e+01 1k8kF 168 7.12e+01 d.198.2.1 68312 1wmaA 276 7.28e+01 1rh5B 74 7.31e+01 f.23.28.1 97465 1tfzA 424 7.34e+01 d.32.1.3,d.32.1.3 106886,106887 1xuuA 349 7.36e+01 1d0vA 356 7.42e+01 1d0vA c.39.1.1 32476 1u4nA 310 7.44e+01 2fb0A 94 7.46e+01 1v93A 296 7.48e+01 c.1.23.1 100532 1l5oA 356 7.49e+01 c.39.1.1 77711 1wstA 417 7.52e+01 1o65A 246 7.53e+01 b.58.1.2 92544 1dik 874 7.56e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1lqpA 135 7.57e+01 d.32.1.2 78151 2ew8A 249 7.57e+01 1o97C 264 7.58e+01 c.26.2.3 81232 1ujkA 147 7.59e+01 a.118.9.2 99457 1ss4A 153 7.65e+01 d.32.1.6 105976 1yz4A 160 7.67e+01 2bhvA 246 7.67e+01 1zq1A 438 7.71e+01 1kdoA 227 7.77e+01 c.37.1.1 68478 1ppjB 439 7.81e+01 d.185.1.1,d.185.1.1 104254,104255 1ax4A 467 7.84e+01 1ax4A c.67.1.2 34391 2bogX 286 7.85e+01 1vi6A 208 7.87e+01 c.23.15.1 100736 1qwgA 251 7.88e+01 c.1.27.1 96473 1e7wA 291 7.88e+01 c.2.1.2 59373 2f6uA 234 7.89e+01 1s8nA 205 7.91e+01 c.23.1.1 105374 2a6hC 1119 7.96e+01 1iyrA 111 7.97e+01 a.164.1.1 76973 1ub9A 100 8.00e+01 a.4.5.28 99159 1yvvA 336 8.00e+01 1vgmA 378 8.02e+01 1j2rA 199 8.05e+01 c.33.1.3 90788 2b69A 343 8.06e+01 1jtvA 327 8.10e+01 c.2.1.2 84230 1lktA 104 8.11e+01 1lktA b.90.1.1 28398 1nsf 273 8.11e+01 1d2nA c.37.1.20 32429 2gbp 309 8.12e+01 1gca c.93.1.1 35657 1y14B 171 8.15e+01 2d09A 407 8.19e+01 1w0mA 226 8.19e+01 c.1.1.1 109027 2fpoA 202 8.24e+01 1u4bA 580 8.35e+01 c.55.3.5,e.8.1.1 107664,107665 2fr1A 486 8.39e+01 1os8A 223 8.41e+01 b.47.1.1 93481 1eiwA 111 8.47e+01 1eiwA c.23.3.1 31130 1sgt 223 8.48e+01 5ptp b.47.1.1 25814 1vqvA 306 8.49e+01 1p2fA 220 8.51e+01 a.4.6.1,c.23.1.1 87720,87721 1snyA 267 8.64e+01 c.2.1.2 105833 1oroA 213 8.81e+01 1opr c.61.1.1 34093 1bkrA 109 8.84e+01 1bkrA a.40.1.1 17394 1xjjA 644 8.88e+01 1eyeA 280 8.88e+01 1aj2 c.1.21.1 29672 1rb9 53 8.95e+01 1rb9 g.41.5.1 45214 1wa3A 205 8.98e+01