# 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 1hr6B 443 2.89e-57 1be3A d.185.1.1,d.185.1.1 61166,61167 1ppjA 446 1.84e-51 d.185.1.1,d.185.1.1 104252,104253 1qcrA 446 4.15e-49 1be3A d.185.1.1,d.185.1.1 59025,59026 1hr6A 475 8.11e-43 1hr6A d.185.1.1,d.185.1.1 61164,61165 1ppjB 439 6.75e-42 d.185.1.1,d.185.1.1 104254,104255 1kb9A 431 3.68e-38 d.185.1.1,d.185.1.1 77311,77312 3cx5A 431 8.32e-38 1ezvA 430 7.21e-37 1be3A d.185.1.1,d.185.1.1 59541,59542 2g47A 990 1.22e-31 1q2lA 939 2.55e-30 d.185.1.1,d.185.1.1,d.185.1.1,d.185.1.1 118731,118732,118733,118734 2fgeA 995 1.15e-24 d.185.1.1,d.185.1.1,d.185.1.1,d.185.1.1 133430,133431,133432,133433 1kb9B 352 7.05e-21 d.185.1.1,d.185.1.1 77313,77314 3cx5B 352 9.68e-21 1ezvB 352 9.82e-20 1ezvB d.185.1.1,d.185.1.1 59543,59544 1k3eA 156 8.15e-02 d.198.1.1 68103 1vaoA 560 1.55e-01 1qltA d.58.32.1,d.145.1.1 39461,41724 1fgs 428 4.69e-01 1fgs 2qruA 274 6.79e-01 1vzyA 291 8.17e-01 d.193.1.1,g.81.1.1 114042,114043 1jbwA 428 8.29e-01 c.59.1.2,c.72.2.2 62860,62861 1vbiA 344 8.44e-01 1w1kA 560 8.74e-01 d.58.32.1,d.145.1.1 109059,109060 2at2A 300 9.03e-01 3csuA c.78.1.1,c.78.1.1 35196,35197 1e8gA 560 9.57e-01 1qltA d.58.32.1,d.145.1.1 39455,41718 1svsA 353 1.05e+00 c.37.1.8 106051 2arhA 203 1.09e+00 d.108.1.9 127197 1qltA 560 1.25e+00 1qltA d.58.32.1,d.145.1.1 39457,41720 2c30A 321 1.27e+00 3cucA 291 1.58e+00 2nogA 173 1.67e+00 1ddfA 127 1.73e+00 a.77.1.2 18423 1zynA 202 2.42e+00 c.47.1.2,c.47.1.2 125838,125839 1hyuA 521 2.56e+00 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 2pceA 386 2.59e+00 1d3uB 201 2.70e+00 1aisB a.74.1.2,a.74.1.2 18386,18387 1pjqA 457 2.72e+00 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 1m5yA 408 2.80e+00 a.223.1.2,d.26.1.1,d.26.1.1 78664,78665,78666 1aisB 200 2.82e+00 1aisB a.74.1.2,a.74.1.2 18384,18385 2hkeA 380 2.93e+00 1zejA 293 3.13e+00 1h2eA 207 3.34e+00 c.60.1.1 70857 2ethA 154 3.46e+00 a.4.5.28 132358 1mp9A 198 3.78e+00 d.129.1.1,d.129.1.1 91385,91386 1xteA 154 3.97e+00 d.189.1.1 116017 1t6cA 315 4.09e+00 c.55.1.8,c.55.1.8 106558,106559 2rexB 197 4.11e+00 1ebbA 202 4.14e+00 c.60.1.1 64900 1cipA 353 4.20e+00 1cipA a.66.1.1,c.37.1.8 18210,32093 2f57A 317 4.28e+00 1kl7A 514 4.31e+00 c.79.1.1 72678 2v75A 104 4.33e+00 3c0iA 351 4.34e+00 1ofcX 304 4.37e+00 a.4.1.3,a.4.1.13,a.187.1.1 92826,92827,92828 1v1aA 309 4.45e+00 c.72.1.1 100249 1omwA 689 4.45e+00 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 1zcjA 463 4.54e+00 1a4rA 191 4.93e+00 1ctqA c.37.1.8 32063 169lA 164 5.07e+00 1l92 d.2.1.3 36963 1kmqA 184 5.15e+00 c.37.1.8 84412 1pczA 191 5.41e+00 1ytbA d.129.1.1,d.129.1.1 41292,41293 1k3sA 113 5.50e+00 d.198.1.1 68120 1m7bA 184 5.84e+00 c.37.1.8 74572 1q1vA 70 6.45e+00 a.159.4.1 104479 2g8yA 385 6.71e+00 1zrzA 364 6.95e+00 2uv0E 175 7.25e+00 2j0iA 303 7.34e+00 104lA 166 7.36e+00 1l92 d.2.1.3 36969 2qddA 378 7.51e+00 2okjA 504 7.68e+00 2vgpA 284 7.85e+00 2qy1A 330 8.14e+00 2bdwA 362 8.21e+00 1paqA 189 8.23e+00 a.118.1.14 94413 2golA 133 8.24e+00 a.61.1.1 135438 2e18A 257 8.27e+00 1sc6A 404 8.75e+00 c.2.1.4,c.23.12.1,d.58.18.1 118932,118933,118934 1a6q 382 8.79e+00 1a6q 1qapA 296 8.92e+00 1qpoA c.1.17.1,d.41.2.1 29559,38595 1sx7A 164 9.14e+00 d.2.1.3 112140 1gdeA 389 9.28e+00 c.67.1.1 60456 2atfA 200 9.39e+00 b.82.1.19 127290 2b5hA 200 9.39e+00 b.82.1.19 127894 1l7mA 211 9.41e+00 c.108.1.4 73664 2g2kA 170 9.44e+00 1f5sA 211 9.77e+00 1f5sA c.108.1.4 59656 1j97A 211 9.77e+00 1f5sA c.108.1.4 62753 2yr5A 721 1.02e+01 1psdA 409 1.05e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1jihA 531 1.08e+01 d.240.1.1,e.8.1.7 90374,90375 2h61A 92 1.09e+01 a.39.1.2 136169 1yirA 408 1.09e+01 c.1.17.2,d.41.2.2 123330,123331 8atcA 310 1.12e+01 3csuA c.78.1.1,c.78.1.1 35132,35133 2b5aA 77 1.13e+01 a.35.1.3 127882 2d4zA 250 1.13e+01 d.37.1.1,d.37.1.1 131260,131261 1volA 204 1.13e+01 1tfb a.74.1.2,a.74.1.2 18370,18371 2yvyA 278 1.15e+01 1h6pA 203 1.19e+01 a.146.1.1 60690 1fjgJ 105 1.19e+01 1fjfJ d.58.15.1 39330 2f5gA 133 1.20e+01 d.58.57.1 132991 1j8fA 323 1.21e+01 1j8fA c.31.1.5 62738 1wn0A 145 1.21e+01 a.24.10.2 121070 1d3uA 181 1.23e+01 1ytbA d.129.1.1,d.129.1.1 41290,41291 1iq8A 582 1.23e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1y74A 57 1.23e+01 a.194.1.1 122679 1squA 155 1.23e+01 d.252.1.1 98971 1e6cA 173 1.24e+01 1shkA c.37.1.2 59296 2btoA 473 1.25e+01 2bvaA 292 1.27e+01 1b6iA 164 1.29e+01 1l92 d.2.1.3 36945 1v9nA 360 1.31e+01 2qrrA 101 1.33e+01 1uehA 253 1.34e+01 c.101.1.1 99259 1p7gA 222 1.36e+01 a.2.11.1,d.44.1.1 94223,94224 1acmA 310 1.41e+01 3csuA c.78.1.1,c.78.1.1 35180,35181 2h5nA 133 1.43e+01 1p9qC 256 1.45e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1sl8A 191 1.46e+01 a.39.1.5 112099 1rliA 184 1.48e+01 c.23.5.6 97647 1s9aA 257 1.48e+01 b.3.6.1 105379 1yfsA 465 1.51e+01 a.203.1.1,d.104.1.1 123088,123089 2bqxA 173 1.52e+01 1jg8A 347 1.54e+01 1jg8A c.67.1.1 62946 1m6sA 347 1.54e+01 c.67.1.1 78701 2a61A 145 1.57e+01 a.4.5.28 126187 1tfb 208 1.59e+01 1tfb 1ln1A 214 1.60e+01 d.129.3.2 74038 1a4pA 96 1.61e+01 1b4cA a.39.1.2 17176 180lA 164 1.62e+01 1l92 d.2.1.3 36867 1uw4B 248 1.65e+01 a.118.1.14 100072 1cfpA 92 1.66e+01 1b4cA a.39.1.2 17172 1tq6A 413 1.66e+01 c.37.1.8 107202 2oryA 346 1.66e+01 2gz4A 207 1.67e+01 1ekxA 311 1.68e+01 3csuA c.78.1.1,c.78.1.1 35088,35089 168lA 164 1.69e+01 1l92 d.2.1.3 36975 1d2fA 390 1.69e+01 1d2fA c.67.1.3 34411 1tn6B 437 1.73e+01 a.102.4.3 112528 175lA 164 1.74e+01 1l92 d.2.1.3 36924 1xi9A 406 1.74e+01 c.67.1.1 115355 1q77A 138 1.75e+01 c.26.2.4 96023 3ch3X 265 1.76e+01 1m0wA 491 1.76e+01 c.30.1.4,d.142.1.6 78363,78364 1ng4A 390 1.78e+01 c.3.1.2,d.16.1.3 85666,85667 2uuuA 584 1.80e+01 1ryiA 382 1.83e+01 c.3.1.2,d.16.1.3 118813,118814 1aisA 182 1.83e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 2g17A 337 1.88e+01 c.2.1.3,d.81.1.1 134512,134513 2cspA 130 1.88e+01 b.1.2.1 130779 1vmkA 277 1.89e+01 c.56.2.1 113680 1gseA 221 1.92e+01 1pgtA a.45.1.1,c.47.1.5 17667,32961 1t95A 240 1.94e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1dmr 823 1.94e+01 1dmr 119l 164 1.95e+01 1l92 3c19A 186 1.97e+01 1wvfA 520 1.97e+01 d.58.32.1,d.145.1.1 121337,121338 1z9zA 60 1.99e+01 1ff9A 450 2.03e+01 1ff9A c.2.1.3,d.81.1.2 30039,39954 1nf3A 195 2.05e+01 c.37.1.8 85594 1u5kA 244 2.05e+01 b.40.4.13,g.45.1.2 113038,113039 1eu1A 780 2.10e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 2nyvA 222 2.12e+01 1wy2A 351 2.13e+01 1lw9A 164 2.15e+01 d.2.1.3 84727 1c3qA 272 2.19e+01 1c3qA c.72.1.2 118436 1nrwA 288 2.21e+01 c.108.1.10 86128 1p36A 164 2.23e+01 d.2.1.3 93978 2dt9A 167 2.24e+01 1qamA 244 2.24e+01 2ercA c.66.1.24 34220 1tx4B 178 2.25e+01 1ctqA c.37.1.8 32045 1z2wA 192 2.25e+01 d.159.1.7 124390 2azeB 106 2.25e+01 e.63.1.2 127606 1tf0B 53 2.29e+01 a.8.1.2 106825 2ig3A 127 2.31e+01 2h6fB 437 2.33e+01 a.102.4.3 136186 1xqiA 195 2.34e+01 d.58.6.1 122237 2vebA 195 2.37e+01 1j98A 157 2.38e+01 1j98A d.185.1.2 62755 2erxA 172 2.39e+01 c.37.1.8 132304 1yozA 116 2.40e+01 a.253.1.1 123796 1vlpA 441 2.40e+01 d.41.2.2,c.1.17.2 108840,108841 2q4uA 272 2.41e+01 2oznB 140 2.41e+01 2oh1A 179 2.42e+01 2onfA 140 2.43e+01 1avqA 228 2.44e+01 1avqA c.52.1.13 33326 1dmtA 696 2.50e+01 1dmtA d.92.1.4 40296 1xp3A 307 2.51e+01 c.1.15.1 122210 1mh1 186 2.52e+01 1eesA 1mh1A 186 2.52e+01 c.37.1.8 32002 1hmt 132 2.53e+01 1hmt 1hmtA 132 2.53e+01 b.60.1.2 27169 2p4fA 299 2.54e+01 2evaA 307 2.57e+01 1ywfA 296 2.57e+01 c.45.1.5 124144 1jyoA 130 2.58e+01 d.198.1.1 67483 1ekqA 272 2.60e+01 1c3qA c.72.1.2 34941 1xjjA 644 2.69e+01 1mtzA 293 2.69e+01 c.69.1.7 79467 3ccyA 203 2.74e+01 2r8jA 554 2.76e+01 2bvcA 486 2.82e+01 d.15.9.1,d.128.1.1 129243,129244 2rh1A 500 2.82e+01 1yptA 305 2.83e+01 1ytw c.45.1.2 32686 2qqhA 334 2.83e+01 2ho1A 252 2.85e+01 2p4bA 295 2.88e+01 1txuA 273 2.91e+01 a.222.1.1 107439 2nuwA 288 2.98e+01 2j1oA 268 3.02e+01 1r8gA 372 3.03e+01 d.128.1.3 104845 2vacA 134 3.05e+01 1x8bA 289 3.06e+01 1gulA 222 3.07e+01 1pgtA a.45.1.1,c.47.1.5 17675,32969 2rdpA 150 3.09e+01 2ia0A 171 3.13e+01 3c1vA 113 3.14e+01 1n1bA 549 3.15e+01 a.102.4.1,a.128.1.3 79799,79800 1i6zA 135 3.20e+01 a.7.7.1 61861 1r5eA 115 3.22e+01 a.8.8.1 111701 2nn4A 72 3.24e+01 1fx4A 231 3.24e+01 1fx2A d.58.29.1 39431 1ljrA 244 3.25e+01 1ljrA a.45.1.1,c.47.1.5 17707,33001 1k3yA 221 3.28e+01 a.45.1.1,c.47.1.5 77245,77246 1m12A 84 3.34e+01 a.64.1.1 84745 1im8A 244 3.35e+01 c.66.1.14 66212 1wgzA 510 3.35e+01 2pv7A 298 3.38e+01 1flp 142 3.38e+01 1flp 2rcyA 262 3.48e+01 1vknA 351 3.49e+01 c.2.1.3,d.81.1.1 108676,108677 3bqpA 80 3.51e+01 1an0A 190 3.53e+01 1ctqA c.37.1.8 32066 2jnkA 140 3.54e+01 2j1pA 293 3.55e+01 1r1hA 696 3.57e+01 d.92.1.4 104756 1bwyA 132 3.62e+01 1hmt b.60.1.2 27172 2ozpA 345 3.62e+01 2atxA 194 3.65e+01 c.37.1.8 127315 1cg2A 393 3.69e+01 1cg2A c.56.5.4,d.58.19.1 33844,39360 2j5yA 61 3.72e+01 1u7lA 392 3.78e+01 e.57.1.1 113093 1wstA 417 3.80e+01 c.67.1.1 121244 1jcrB 437 3.82e+01 a.102.4.3 66507 1dar 691 3.89e+01 1dar 2bfxA 284 3.93e+01 2anrA 178 3.95e+01 174lA 164 3.95e+01 1l92 d.2.1.3 36956 1gu2A 124 3.98e+01 a.3.1.1 76348 1fnmA 691 3.99e+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 1ht9A 76 3.99e+01 4icb a.39.1.1 61252 1zbtA 371 4.00e+01 2fbiA 142 4.03e+01 a.4.5.28 133246 1yhvA 297 4.06e+01 2ftsA 419 4.06e+01 b.85.6.1,b.103.1.1,c.57.1.2 134079,134080,134081 1jhgA 101 4.08e+01 1jhgA a.4.12.1 19009 1fjgB 256 4.09e+01 1fjfB c.23.15.1 31400 2gcoA 201 4.09e+01 1pnsB 234 4.11e+01 i.1.1.1 88169 2q91A 101 4.11e+01 1dlyA 164 4.15e+01 1dlyA a.1.1.1 14983 2z20A 432 4.19e+01 1otgA 125 4.24e+01 1otgA d.80.1.2 39831 167lA 164 4.25e+01 1l92 d.2.1.3 36937 1kyqA 274 4.27e+01 c.2.1.11,e.37.1.1 73281,73282 1xccA 220 4.32e+01 c.47.1.10 115113 1rec 201 4.32e+01 1rec 3b5mA 205 4.36e+01 2bfdA 400 4.37e+01 1tu9A 134 4.38e+01 a.1.1.2 107320 1z08A 170 4.39e+01 c.37.1.8 124303 1c20A 128 4.40e+01 1c20A a.4.3.1 16079 2d9bA 109 4.43e+01 176lA 164 4.44e+01 1l92 d.2.1.3 36942 2ba2A 85 4.44e+01 h.1.30.1 128233 1pb6A 212 4.51e+01 a.4.1.9,a.121.1.1 88017,88018 1qusA 322 4.58e+01 1ltm d.2.1.6 36991 2c71A 216 4.59e+01 c.6.2.3 130017 1ltm 320 4.68e+01 1ltm 1xqwA 293 4.73e+01 1du2A 76 4.75e+01 1du2A a.237.1.1 15701 1lvfA 110 4.76e+01 a.47.2.1 74280 1htqA 477 4.78e+01 d.15.9.1,d.128.1.1 71035,71036 2v79A 135 4.85e+01 3b77A 193 4.87e+01 2imqX 282 4.87e+01 3csuA 310 4.90e+01 3csuA c.78.1.1,c.78.1.1 35094,35095 1zhvA 134 4.93e+01 d.58.18.8,d.58.18.8 125109,125110 1yseA 141 4.96e+01 a.35.1.7 123970 2b0jA 358 4.97e+01 a.100.1.11,c.2.1.6 127639,127640 1p27B 106 4.98e+01 d.58.7.1 93908 1e2xA 243 5.04e+01 1e2xA a.4.5.6,a.78.1.1 16113,18443 1uuyA 167 5.05e+01 c.57.1.1 108059 3bamA 213 5.07e+01 1bam c.52.1.3 33288 137lA 164 5.07e+01 1l92 d.2.1.3 36791 2bivA 243 5.18e+01 b.34.9.3,b.34.9.3 128592,128593 2o4aA 93 5.24e+01 2uubB 256 5.24e+01 c.23.15.1 139932 2hsnA 160 5.25e+01 2bmjA 178 5.27e+01 c.37.1.8 128797 1hnoA 280 5.29e+01 1hnoA c.14.1.3 61095 2adoA 196 5.32e+01 2yufA 142 5.34e+01 2b8wA 328 5.34e+01 2c3gA 98 5.37e+01 2oo4A 234 5.42e+01 2zhgA 154 5.48e+01 1si6X 282 5.52e+01 d.151.1.2 118968 2etxA 209 5.56e+01 2arkA 188 5.57e+01 c.23.5.8 127202 1ut9A 609 5.64e+01 a.102.1.2,b.1.18.2 99912,99913 2d0tA 406 5.67e+01 a.266.1.2 131093 2gp6A 434 5.67e+01 2z0hA 197 5.72e+01 2rckA 225 5.77e+01 2cy8A 453 5.81e+01 3cgvA 397 5.82e+01 2i61A 62 5.82e+01 1w24A 182 5.86e+01 d.159.1.7 120579 3bk2A 562 5.87e+01 1s9jA 341 5.89e+01 d.144.1.7 112049 1ef1C 90 5.99e+01 1ef1C a.137.5.1 19642 1x7yA 400 5.99e+01 c.36.1.11 114944 2op5A 117 6.00e+01 1h8mA 140 6.00e+01 1h8mA d.110.4.1 60782 1vcsA 102 6.05e+01 a.47.2.1 119985 1jq5A 370 6.09e+01 e.22.1.2 67084 2e1bA 216 6.09e+01 1ehaA 558 6.10e+01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21859,27786,28773 2eb0A 307 6.14e+01 2dpoA 319 6.17e+01 3crrA 323 6.20e+01 1vjeA 166 6.20e+01 d.185.1.2 100807 1zp2A 235 6.22e+01 1trrA 107 6.28e+01 1jhgA a.4.12.1 19017 2pq8A 278 6.29e+01 2cxaA 256 6.31e+01 d.108.1.6 130993 2qypA 91 6.33e+01 1e8aA 91 6.35e+01 1b4cA a.39.1.2 17188 3bjaA 139 6.35e+01 2b8nA 429 6.35e+01 c.118.1.1 128093 5eat 548 6.41e+01 5eat 1sz7A 200 6.41e+01 2clqA 295 6.42e+01 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