# List of top-scoring protein chains for t04-100-40-40-str2+CB_burial_14_7-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 1khdA 345 4.95e-01 a.46.2.1,c.27.1.1 77400,77401 1yhfA 115 5.41e-01 1q8bA 105 7.45e-01 d.58.4.6 96201 1u2cA 246 8.24e-01 b.1.6.2,d.272.1.1 107610,107611 1vphA 149 8.64e-01 1c3hA 137 9.35e-01 b.22.1.1 90405 1vmjA 151 1.03e+00 1nziA 159 1.24e+00 b.23.1.1,g.3.11.1 86449,86450 1ijtA 128 1.25e+00 1bfg b.42.1.1 62510 1tqzA 133 1.27e+00 2fqpA 97 1.33e+00 1dgwA 178 1.46e+00 1dgwA b.82.1.2 28090 1m93B 245 1.53e+00 2b8mA 117 1.69e+00 1eo1A 124 1.94e+00 1eo1A c.55.5.1 33739 1gmmA 133 1.99e+00 b.18.1.10 65314 1vmfA 145 2.06e+00 1xfsA 178 2.06e+00 d.129.3.5 109589 1vquA 374 2.07e+00 2amdA 311 2.07e+00 1w1hA 151 2.51e+00 4enl 436 2.59e+00 4enl c.1.11.1,d.54.1.1 29202,38846 1dq3A 454 2.64e+00 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1ts9A 102 2.69e+00 1lj5A 379 2.76e+00 e.1.1.1 73928 1cojA 212 2.81e+00 1avmA a.2.11.1,d.44.1.1 15737,38734 1h0hB 214 2.82e+00 d.58.1.5 76437 1v0aA 178 2.85e+00 1gr3A 160 2.96e+00 b.22.1.1 65476 1oneA 436 3.03e+00 4enl c.1.11.1,d.54.1.1 29200,38844 2awaA 390 3.05e+00 1f0cA 305 3.07e+00 1c8oA e.1.1.1 42676 1khiA 176 3.20e+00 b.34.5.2,b.40.4.5 77408,77409 2d7nA 93 3.23e+00 1uxxX 133 3.33e+00 b.18.1.10 100169 1o13A 136 3.36e+00 c.55.5.1 80762 2al2A 436 3.37e+00 2al1A 436 3.39e+00 1gmiA 136 3.52e+00 b.7.1.1 65309 1k47A 337 3.63e+00 d.14.1.5,d.58.26.4 72040,72041 1rg9A 383 3.98e+00 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1vqoW 154 4.08e+00 1btl 263 4.09e+00 1btl e.3.1.1 42691 2cbp 96 4.13e+00 2cbp b.6.1.1 22895 2a5kA 307 4.20e+00 1ermA 263 4.20e+00 1btl e.3.1.1 42690 1q2wA 308 4.21e+00 b.47.1.4 88355 1m40A 263 4.47e+00 e.3.1.1 74437 1yfuA 174 4.54e+00 1b87A 181 4.64e+00 1b87A d.108.1.1 40797 2bz8A 58 4.70e+00 1a7cA 379 5.38e+00 1sek e.1.1.1 42660 1svpA 161 5.38e+00 1svpA b.47.1.3 26384 1kwsA 261 5.56e+00 c.68.1.7 73083 1omzA 293 5.61e+00 c.68.1.15 87093 2cy2A 174 5.67e+00 1umgA 362 5.74e+00 d.280.1.1 107956 1d09B 153 5.79e+00 8atcB d.58.2.1,g.41.7.1 39015,45267 1zuxA 224 5.96e+00 1xxqA 161 5.99e+00 1ti6A 875 6.23e+00 b.52.2.2,c.81.1.1 106974,106975 1rzhH 260 6.24e+00 b.41.1.1,f.23.10.1 98162,98163 1sgzA 389 6.36e+00 b.50.1.2 98872 1ji1A 637 6.47e+00 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 1jmxB 349 6.49e+00 b.69.2.2 66906 1jj2V 154 6.65e+00 1ffkT d.59.1.1 63107 1syxB 86 6.72e+00 1j1bA 420 6.72e+00 d.144.1.7 90758 1qovH 260 6.74e+00 6prcH b.41.1.1,f.23.10.1 25464,43457 1s72W 154 6.80e+00 d.59.1.1 105342 2h4vA 320 6.85e+00 1xbfA 140 7.20e+00 d.273.1.1 109538 2ixiA 184 7.29e+00 1u3oA 82 7.29e+00 1ryaA 160 7.36e+00 d.113.1.5 105122 1x31C 206 7.51e+00 1xfoA 357 7.57e+00 1o91A 178 7.72e+00 b.22.1.1 92656 2fk9A 157 7.92e+00 1zndA 174 8.17e+00 1mugA 168 8.18e+00 1mugA c.18.1.2 31030 1w8oA 601 8.26e+00 1gpiA 431 8.61e+00 b.29.1.10 65450 2biwA 490 8.84e+00 1lfdA 87 8.85e+00 1lfdA d.15.1.5 37622 1gcqC 70 8.90e+00 1gcpA b.34.2.1 60436 1usrA 454 8.97e+00 b.68.1.1 99881 1zc3B 113 8.98e+00 1nnwA 252 9.03e+00 d.159.1.5 80674 1g55A 343 9.37e+00 1g55A c.66.1.26 34247 1ve0A 134 9.42e+00 2bhuA 602 9.43e+00 1g9oA 91 9.47e+00 1pdr b.36.1.1 60400 1x82A 190 9.62e+00 2a50B 168 9.71e+00 1qipA 183 9.81e+00 1qipA d.32.1.1 38470 2napA 723 9.94e+00 2napA b.52.2.2,c.81.1.1 26926,35334 1fvuB 125 9.98e+00 1ixxB d.169.1.1 42346 1y0gA 191 1.01e+01 1pbyB 337 1.02e+01 b.69.2.2 94422 1wv3A 238 1.02e+01 1v04A 355 1.03e+01 b.68.6.2 100240 2fbeA 201 1.03e+01 1p6oA 161 1.04e+01 c.97.1.2 94185 1n71A 180 1.07e+01 d.108.1.1 85370 1r26A 125 1.07e+01 c.47.1.1 96847 1d2oA 187 1.08e+01 1d2oA b.3.5.1,b.3.5.1 22625,22626 2a4nA 182 1.12e+01 2avtA 378 1.13e+01 1mpxA 615 1.14e+01 b.18.1.13,c.69.1.21 85041,85042 2bzuA 181 1.14e+01 1soxA 466 1.14e+01 1soxA b.1.18.6,d.120.1.1,d.176.1.1 21947,41090,42563 1df7A 159 1.18e+01 3dfr c.71.1.1 34885 1qy1A 174 1.19e+01 b.60.1.1 96568 2gupA 292 1.20e+01 1umhA 184 1.20e+01 b.18.1.21 99605 2hc1A 291 1.24e+01 1zbsA 291 1.25e+01 2phlA 397 1.26e+01 1dgwA b.82.1.2,b.82.1.2 28082,28083 2h03A 291 1.30e+01 1jmuB 666 1.31e+01 1wkt 88 1.32e+01 1wkt b.11.1.2 23630 2gfaA 119 1.34e+01 1o8xA 146 1.34e+01 c.47.1.10 86681 1sjyA 159 1.35e+01 d.113.1.1 98900 1dxrH 258 1.39e+01 6prcH b.41.1.1,f.23.10.1 25456,43433 1uh4A 637 1.45e+01 b.1.18.2,b.71.1.1,c.1.8.1 99391,99392,99393 1hr6B 443 1.47e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1e8uA 454 1.50e+01 1e8tA b.68.1.1 59389 1o6uA 403 1.53e+01 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 1qk8A 146 1.53e+01 1ewxA c.47.1.10 33061 1wduA 245 1.53e+01 d.151.1.1 109286 1ywfA 296 1.53e+01 1pdz 434 1.54e+01 4enl c.1.11.1,d.54.1.1 29215,38859 1p1mA 406 1.59e+01 b.92.1.4,c.1.9.9 87696,87697 3dfr 162 1.59e+01 3dfr c.71.1.1 34880 1voqa 90 1.60e+01 1epaA 164 1.64e+01 1epaA b.60.1.1 27128 2c9wA 169 1.66e+01 1bywA 110 1.70e+01 1bywA d.110.3.6 40912 1fzvA 132 1.71e+01 1vpfA g.17.1.1 60159 1oqkA 97 1.71e+01 b.137.1.1 93419 1qtrA 317 1.73e+01 1qtrA c.69.1.7 34660 1zzcA 198 1.79e+01 1e79D 482 1.80e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18272,26437,32317 1k0wA 231 1.81e+01 c.74.1.1 77220 1kw3B 292 1.89e+01 d.32.1.3,d.32.1.3 77549,77550 1uovA 159 1.90e+01 b.7.1.2 107974 1wm1A 317 1.91e+01 c.69.1.7 109405 1el4A 195 1.91e+01 1ej3A a.39.1.5 59453 1i9gA 280 1.92e+01 c.66.1.13 62090 1uy4A 145 1.92e+01 b.18.1.10 108131 2fymA 431 1.96e+01 1jf2A 195 1.96e+01 1ej3A a.39.1.5 62930 1ep0A 185 1.97e+01 1dzrA b.82.1.1 28080 2cdcA 366 1.99e+01 1vmhA 144 1.99e+01 1y0yA 353 2.00e+01 1djxA 624 2.00e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17342,23159,29587 1woqA 267 2.01e+01 c.55.1.10,c.55.1.10 109462,109463 1who 96 2.04e+01 1who b.7.3.1 23215 1djxB 624 2.04e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17343,23160,29588 1zn6A 227 2.05e+01 1h7zA 194 2.05e+01 1qhvA b.21.1.1 60733 1i06A 180 2.05e+01 1mup b.60.1.1 27131 1e79H 146 2.09e+01 1e79H a.2.10.1,b.93.1.1 15721,28438 1d4tA 104 2.10e+01 1d4tA d.93.1.1 40537 2cunA 410 2.11e+01 1yuwA 554 2.12e+01 1wwrA 171 2.14e+01 1zvdA 380 2.16e+01 1kyqA 274 2.19e+01 c.2.1.11,e.37.1.1 73281,73282 1wba 175 2.19e+01 1wba b.42.4.1 25591 1pguA 615 2.19e+01 b.69.4.1,b.69.4.1 88069,88070 1lrzA 426 2.20e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1mq7A 154 2.21e+01 b.85.4.1 79404 1ug1A 92 2.24e+01 b.34.2.1 99360 1uoyA 64 2.25e+01 g.3.19.1 99709 1qlwA 328 2.27e+01 1qlwA c.69.1.15 34722 1xtlA 175 2.29e+01 1uq5A 263 2.30e+01 d.165.1.1 99778 1pk6A 133 2.30e+01 b.22.1.1 94801 2et1A 201 2.30e+01 1ift 263 2.33e+01 1mrj d.165.1.1 42211 2bryA 497 2.33e+01 1qv1A 195 2.34e+01 a.39.1.5 96347 1kqfB 294 2.35e+01 d.58.1.5,f.23.22.1 75900,75901 1olzA 663 2.39e+01 b.1.1.4,b.69.12.1,g.16.2.1 93341,93342,93343 2fuqA 747 2.40e+01 2mcm 112 2.40e+01 2mcm b.1.7.1 22207 1vp6A 138 2.42e+01 2fhzB 108 2.43e+01 1j54A 186 2.44e+01 c.55.3.5 77077 1txoA 237 2.45e+01 1hd2A 161 2.46e+01 c.47.1.10 60962 1qxrA 189 2.49e+01 b.82.1.7 96552 2ffsA 157 2.54e+01 1f56A 91 2.56e+01 2cbp b.6.1.1 22896 1v7pB 128 2.57e+01 d.169.1.1 108407 1z0jA 170 2.61e+01 1a2pA 110 2.62e+01 1b20A d.1.1.2 36140 1mkfA 382 2.65e+01 b.116.1.1 79232 1j1qA 261 2.66e+01 d.165.1.1 90768 1hv9A 456 2.70e+01 1fwyA b.81.1.4,c.68.1.5 28060,34518 1vdnA 162 2.72e+01 1vqoB 338 2.73e+01 1tjxA 159 2.73e+01 1wcqA 601 2.74e+01 1t92A 116 2.77e+01 1yr2A 741 2.77e+01 1ex2A 189 2.78e+01 1ex2A c.51.4.2 33225 1han 297 2.80e+01 1han d.32.1.3,d.32.1.3 38506,38507 2cr9A 139 2.86e+01 2al3A 90 2.88e+01 1n4wA 504 2.88e+01 c.3.1.2,d.16.1.1 91676,91677 1mxtA 504 2.91e+01 c.3.1.2,d.16.1.1 79671,79672 2bbdA 350 2.91e+01 1tiyA 164 2.93e+01 c.97.1.2 107012 1pm3A 78 2.98e+01 b.41.1.2 94889 2ae6A 166 3.04e+01 1u6zA 513 3.06e+01 2a46A 238 3.07e+01 1jv4A 162 3.08e+01 b.60.1.1 67343 1uisA 231 3.08e+01 d.22.1.1 99431 2fe7A 166 3.09e+01 1jsxA 207 3.09e+01 c.66.1.20 71846 1omhA 293 3.11e+01 d.89.1.5 93348 1k6wA 426 3.12e+01 b.92.1.2,c.1.9.5 68236,68237 1fi2A 201 3.15e+01 1fi2A b.82.1.2 59845 2bpqA 373 3.17e+01 1yaiA 151 3.17e+01 1yaiA b.1.8.1 22289 1vjtA 483 3.20e+01 c.2.1.5,d.162.1.2 100833,100834 2fnjA 226 3.22e+01 1fxjA 331 3.22e+01 1fwyA b.81.1.4,c.68.1.5 28062,34520 1r6wA 322 3.24e+01 c.1.11.2,d.54.1.1 97165,97166 1olmA 403 3.27e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1w4vA 119 3.28e+01 1zq4A 693 3.29e+01 2ck3D 482 3.30e+01 1o12A 376 3.31e+01 b.92.1.5,c.1.9.10 80758,80759 1ctt 294 3.31e+01 1ctt c.97.1.1,c.97.1.1 36022,36023 2cbzA 237 3.32e+01 1uvzA 119 3.32e+01 1uowA 159 3.37e+01 b.7.1.2 107975 1a2vA 655 3.37e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24416,38059,38060 1a64A 97 3.38e+01 1cdcA b.1.1.1 19750 1f9zA 135 3.39e+01 1qipA d.32.1.1 38484 1j6pA 418 3.40e+01 b.92.1.4,c.1.9.9 77089,77090 2bs6A 90 3.43e+01 1ra0A 430 3.45e+01 1wchA 315 3.46e+01 1s72B 338 3.47e+01 b.43.3.2 105320 1jj2B 337 3.47e+01 1ffkB b.43.3.2 63086 2ftwA 521 3.50e+01 2a9dA 372 3.50e+01 1wkqA 164 3.52e+01 c.97.1.2 109393 2bt9A 90 3.52e+01 1ed5A 444 3.60e+01 1nseA d.174.1.1 42530 1b4vA 504 3.60e+01 1b8sA c.3.1.2,d.16.1.1 30334,37865 1f89A 291 3.61e+01 d.160.1.1 64988 1f15A 218 3.64e+01 1f15B b.121.4.5 23320 2akzA 439 3.64e+01 2ampA 304 3.67e+01 2iv2X 715 3.68e+01 1w50A 411 3.71e+01 b.50.1.2 109173 1ws0A 156 3.71e+01 1xezA 721 3.73e+01 2ak5A 64 3.77e+01 2bnmA 198 3.79e+01 1zhhB 242 3.79e+01 2arcA 164 3.81e+01 2arcA b.82.4.1 28148 1fjgE 162 3.82e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 2bvyA 475 3.83e+01 1wguA 136 3.87e+01 1ywpA 64 3.87e+01 2c2xA 281 3.88e+01 1nt0A 286 3.91e+01 b.23.1.1,b.23.1.1,g.3.11.1 86143,86144,86145 1vavA 222 3.93e+01 b.29.1.18 108472 1wgoA 123 3.94e+01 1ad2 228 3.96e+01 1ad2 e.24.1.1 43353 1uf3A 228 3.96e+01 d.159.1.6 99317 1d1vA 444 3.98e+01 1nseA d.174.1.1 59101 1fltV 98 4.06e+01 1vpfA g.17.1.1 44751 1wnlA 235 4.08e+01 1xtoA 311 4.08e+01 2bitX 165 4.09e+01 1nxmA 197 4.11e+01 b.82.1.1 86385 1sr8A 298 4.11e+01 e.54.1.1 105959 1itcA 516 4.14e+01 b.3.1.1,c.1.8.1 83705,83706 1ra9 159 4.15e+01 1vdrA c.71.1.1 34820 1zybA 232 4.21e+01 2calA 154 4.21e+01 1s4bP 674 4.23e+01 d.92.1.5 105252 1vkcA 158 4.24e+01 1c28A 135 4.25e+01 1c28A b.22.1.1 23857 1yllA 200 4.29e+01 1n7zA 334 4.32e+01 b.127.1.1 85380 1rfs 139 4.34e+01 1rfs b.33.1.1 24434 1ckaA 57 4.34e+01 1ckaA b.34.2.1 24459 1cv8 174 4.35e+01 1cv8 d.3.1.1 37089 2a5jA 191 4.36e+01 1n2fA 142 4.37e+01 d.227.1.1 79853 1d0cA 444 4.40e+01 d.174.1.1 64769 1wqwA 235 4.42e+01 1tzfA 259 4.42e+01 c.68.1.13 107476 2cdpA 160 4.45e+01 1fd3A 41 4.46e+01 1fd3A g.9.1.1 44572 1udxA 416 4.46e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 2bi0A 337 4.48e+01 1gyfA 62 4.51e+01 1gyfA d.76.1.1 39749 1kbeA 49 4.52e+01 g.49.1.1 68380 1qe5A 266 4.52e+01 1b8oA c.56.2.1 33784 2gzqA 200 4.52e+01 1o50A 157 4.53e+01 d.37.1.1,d.37.1.1 92478,92479 2c4bA 143 4.53e+01 1tp6A 128 4.54e+01 d.17.4.12 107184 1yr0A 175 4.54e+01 1i05A 180 4.59e+01 1mup b.60.1.1 27130 1ri6A 343 4.61e+01 b.69.11.1 97503 1y5iA 1246 4.62e+01 1w2wB 191 4.65e+01 1fa8A 135 4.69e+01 1qipA d.32.1.1 38486 1xewY 172 4.73e+01 1k3bA 119 4.73e+01 b.61.5.1 72016 1q5hA 147 4.74e+01 b.85.4.1 95893 2ge3A 170 4.74e+01 1gmuA 143 4.77e+01 b.107.1.1,d.58.38.1 65335,65336 1iarB 207 4.79e+01 1iarB b.1.2.1,b.1.2.1 22037,22038 1di2A 69 4.82e+01 1di2A d.50.1.1 38780 1x1iA 752 4.82e+01 1fxkC 133 4.86e+01 1fxkC a.2.5.1 15702 1zjcA 418 4.86e+01 1fviA 297 4.87e+01 1fviA b.40.4.6,d.142.2.1 25364,41578 2f69A 261 4.88e+01 1g6aA 271 4.89e+01 1btl e.3.1.1 42704 1nw3A 416 4.91e+01 c.66.1.31 86288 2cy5A 140 4.93e+01 1eso 154 4.94e+01 1yaiA b.1.8.1 22293 2fuvA 549 4.94e+01 1u7eB 154 4.95e+01 1pj5A 830 4.96e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 2as0A 396 4.97e+01 1ne6A 283 4.99e+01 b.82.3.2,b.82.3.2 91831,91832 1vemA 516 4.99e+01 1zbfA 142 5.00e+01 1h8eH 146 5.01e+01 1e79H b.93.1.1 60757 1z47A 355 5.06e+01 1eu1A 780 5.13e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 1l4dB 122 5.13e+01 d.15.5.1 77684 2a8kA 108 5.16e+01 1vqqA 646 5.18e+01 1tjyA 316 5.20e+01 c.93.1.1 107062 1te7A 103 5.24e+01 1q16A 1247 5.24e+01 b.52.2.2,c.81.1.1 95546,95547 1xe7A 203 5.29e+01 2cx7A 130 5.33e+01 1te6A 439 5.39e+01 c.1.11.1,d.54.1.1 106797,106798 1w9iA 770 5.42e+01 1kexA 155 5.44e+01 b.18.1.2 77350 1cc1L 498 5.45e+01 1h2rL e.18.1.1 43301 1o97D 320 5.46e+01 c.26.2.3,c.31.1.2 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