# List of top-scoring protein chains for t04-100-30-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 1atg 231 2.02e-01 1atg c.94.1.1 35834 1fp1D 372 2.15e-01 1fpqA a.4.5.29,c.66.1.12 59939,59940 1g6oA 330 2.68e-01 1g6oA c.37.1.11 32430 1u0sA 86 4.19e-01 d.58.24.1 107565 2a10A 125 7.59e-01 1xg9A 260 8.98e-01 1zghA 260 8.98e-01 1tib 269 9.66e-01 3tgl c.69.1.17 34738 1t6nA 220 1.02e+00 c.37.1.19 106576 1uarA 285 1.07e+00 c.46.1.2,c.46.1.2 107762,107763 1vjrA 271 1.30e+00 c.108.1.14 100832 2ajrA 331 1.37e+00 1prxA 224 1.67e+00 1prxA c.47.1.10 33076 1gt6A 269 2.62e+00 c.69.1.17 76342 2bvfA 459 2.64e+00 1x9iA 302 2.66e+00 1rg9A 383 2.94e+00 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1tzbA 302 2.99e+00 c.80.1.1 107470 1qtqA 553 3.01e+00 1gtrA b.53.1.2,c.26.1.1 26940,31579 1yqgA 263 3.05e+00 1k87A 669 3.30e+00 a.176.1.1,c.1.23.2 77286,77287 1rcuA 195 3.60e+00 c.129.1.1 97295 1zn6A 227 3.73e+00 1ys7A 233 3.73e+00 1vggA 161 3.88e+00 1v25A 541 4.12e+00 e.23.1.1 108275 1u5tB 169 4.15e+00 a.4.5.54,a.4.5.54 107686,107687 1qwkA 317 4.33e+00 c.1.7.1 96482 1v72A 356 4.73e+00 1i6wA 181 4.76e+00 1i6wA c.69.1.18 61859 1xseA 295 4.76e+00 1ispA 181 4.90e+00 c.69.1.18 76778 1sxgA 280 4.91e+00 2cg4A 152 4.95e+00 2b33A 140 5.19e+00 2cw8A 537 5.50e+00 1xu9A 286 5.56e+00 2g0wA 296 5.70e+00 2f9sA 151 5.76e+00 2a3nA 355 5.86e+00 1wmaA 276 6.07e+00 1k68A 140 6.34e+00 c.23.1.1 90943 1cjwA 166 6.53e+00 1cjwA d.108.1.1 40818 1luaA 287 6.71e+00 c.2.1.7,c.58.1.4 78216,78217 1zavA 180 7.15e+00 1whvA 100 7.27e+00 1r5jA 337 7.62e+00 c.77.1.5 97097 1cydA 244 8.25e+00 1cydA c.2.1.2 29825 1i3cA 149 8.40e+00 c.23.1.1 71112 1xkqA 280 8.54e+00 2g6tA 306 8.56e+00 1mzhA 225 8.60e+00 c.1.10.1 79698 1o4sA 389 8.69e+00 c.67.1.1 86620 1c7gA 456 8.90e+00 c.67.1.2 90415 1wekA 217 8.98e+00 1k9uA 78 9.28e+00 a.39.1.10 84348 1ywqA 200 9.35e+00 1edzA 320 9.63e+00 1ee9A c.2.1.7,c.58.1.2 30287,33935 1ogsA 497 9.81e+00 b.71.1.2,c.1.8.3 86997,86998 1zzmA 259 9.85e+00 1elqA 390 1.03e+01 1elqA c.67.1.3 34436 1eluA 390 1.03e+01 1elqA c.67.1.3 34434 1st9A 143 1.05e+01 c.47.1.10 98987 1xocA 520 1.06e+01 1j5xA 342 1.07e+01 c.80.1.1 71591 1oi7A 288 1.08e+01 c.2.1.8,c.23.4.1 87049,87050 1xccA 220 1.09e+01 1lssA 140 1.13e+01 c.2.1.9 74246 1io2A 213 1.14e+01 1ekeA c.55.3.1 62612 1wod 233 1.17e+01 1wod c.94.1.1 35832 2f4iA 197 1.21e+01 1amf 233 1.23e+01 1wod c.94.1.1 35833 1spxA 278 1.32e+01 c.2.1.2 98958 1w3iA 293 1.34e+01 c.1.10.1 109152 1hu4A 288 1.36e+01 1hu4A 1n5dA 288 1.36e+01 c.2.1.2 80030 1wohA 305 1.38e+01 c.42.1.1 109446 1l3kA 196 1.39e+01 d.58.7.1,d.58.7.1 73539,73540 2bkkA 264 1.40e+01 1obbA 480 1.42e+01 c.2.1.5,d.162.1.2 86760,86761 1vk9A 151 1.43e+01 c.139.1.1 108640 1ha1 184 1.44e+01 1ha1 d.58.7.1,d.58.7.1 39147,39148 2a2fX 325 1.50e+01 1tk1A 260 1.56e+01 d.248.1.1 107066 1sd4A 126 1.57e+01 a.4.5.39 105428 1ccwA 137 1.60e+01 1be1 c.23.6.1 31238 1rwxA 178 1.62e+01 1y1pA 342 1.62e+01 1uxtA 501 1.69e+01 c.82.1.1 108125 1o60A 292 1.71e+01 c.1.10.4 92532 1yt8A 539 1.74e+01 1p9qC 256 1.75e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 2atzA 180 1.76e+01 1j1uA 306 1.79e+01 c.26.1.1 83980 1w9hA 427 1.82e+01 1fcjA 322 1.84e+01 1oasA c.79.1.1 35289 1sc3A 178 1.84e+01 c.17.1.1 105416 1el5A 389 1.88e+01 1b3mA c.3.1.2,d.16.1.3 30369,37937 1wdjA 187 1.89e+01 1sheA 103 1.90e+01 d.274.1.1 105551 1qu9A 128 1.90e+01 1qu9A d.79.1.1 39755 1qd9A 124 1.98e+01 1qu9A d.79.1.1 39758 1v4pA 157 2.02e+01 1zjkA 403 2.02e+01 1ei6A 406 2.06e+01 c.76.1.4 90443 1u02A 239 2.14e+01 c.108.1.15 107538 1j5pA 253 2.15e+01 d.81.1.3,c.2.1.3 71577,83092 1i19A 561 2.17e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 1m45A 148 2.17e+01 a.39.1.5 78598 2awaA 390 2.18e+01 1ecsA 126 2.19e+01 1ecsA d.32.1.2 59407 1vj1A 363 2.22e+01 b.35.1.2,c.2.1.1 100794,100795 1gca 309 2.22e+01 1gca c.93.1.1 35659 1j79A 347 2.25e+01 1j79A c.1.9.4 62675 1w7jB 151 2.28e+01 1t5hX 504 2.28e+01 e.23.1.1 106449 1nox 205 2.30e+01 1nox d.90.1.1 40242 2gdjA 264 2.31e+01 1lvaA 258 2.35e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1mho 88 2.37e+01 1b4cA a.39.1.2 17171 1mvoA 136 2.41e+01 c.23.1.1 79513 2g0dA 409 2.43e+01 1vecA 206 2.47e+01 c.37.1.19 100575 1u6mA 199 2.50e+01 1s95A 333 2.54e+01 d.159.1.3 105375 1kvkA 395 2.55e+01 d.14.1.5,d.58.26.3 73060,73061 1jh6A 189 2.55e+01 d.61.1.1 66707 2cvdA 198 2.55e+01 1b7gO 340 2.55e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907 1xhlA 297 2.61e+01 c.2.1.2 109591 1jetA 517 2.63e+01 1jevA c.94.1.1 35718 1h4vB 421 2.65e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1qpoA 284 2.65e+01 1qpoA c.1.17.1,d.41.2.1 29561,38597 1pdo 135 2.66e+01 1pdo c.54.1.1 33376 2f1fA 164 2.67e+01 1hdoA 206 2.69e+01 1he2A c.2.1.2 60965 1x0pA 143 2.70e+01 1z6aA 500 2.71e+01 1ujmA 342 2.73e+01 1lfpA 249 2.79e+01 e.39.1.1 73885 1z63A 500 2.79e+01 1s4nA 348 2.97e+01 c.68.1.16 98501 1kqfB 294 2.98e+01 d.58.1.5,f.23.22.1 75900,75901 1exrA 148 2.99e+01 1cll a.39.1.5 17299 1fxlA 167 2.99e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1d5yA 292 3.01e+01 1d5yA a.4.1.8,a.4.1.8,d.60.1.2 16055,16056,39532 1v5xA 203 3.01e+01 c.1.2.4 100377 2olbA 517 3.01e+01 1jevA c.94.1.1 35721 1aisA 182 3.02e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1iugA 352 3.03e+01 c.67.1.3 90699 1t6aA 126 3.14e+01 d.129.8.1 106555 1wlsA 328 3.16e+01 1txnA 328 3.21e+01 1dcfA 136 3.21e+01 1dcfA c.23.1.2 31124 2glzA 153 3.21e+01 1q35A 320 3.24e+01 c.94.1.1 95661 1oniA 137 3.24e+01 d.79.1.1 87144 1zsyA 357 3.29e+01 1iyhA 198 3.31e+01 a.45.1.1,c.47.1.5 83790,83791 2c3zA 222 3.31e+01 1ws6A 171 3.33e+01 1kk8B 139 3.33e+01 a.39.1.5 77430 1fxjA 331 3.38e+01 1fwyA b.81.1.4,c.68.1.5 28062,34520 1vj0A 380 3.40e+01 b.35.1.2,c.2.1.1 100786,100787 1z5zA 271 3.41e+01 1vddA 228 3.41e+01 e.49.1.1 108519 1z2aA 168 3.45e+01 1aq0A 306 3.51e+01 1aq0A c.1.8.3 28842 1szoA 257 3.54e+01 c.14.1.3 106164 5abp 306 3.56e+01 8abp c.93.1.1 35651 1iwmA 186 3.56e+01 b.125.1.2 83758 1ad1A 266 3.59e+01 1aj2 c.1.21.1 29668 1wy9A 147 3.59e+01 1t95A 240 3.61e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1hwxA 501 3.62e+01 1hwyA c.2.1.7,c.58.1.1 30250,33898 1v3vA 333 3.64e+01 b.35.1.2,c.2.1.1 108345,108346 1fsiA 189 3.67e+01 1fsiA d.61.1.1 39536 1ad4A 266 3.74e+01 1aj2 c.1.21.1 29670 1z5oA 242 3.76e+01 1x1oA 286 3.78e+01 1o8uA 257 3.79e+01 c.14.1.3 81194 1ixkA 315 3.85e+01 c.66.1.38 90716 1jysA 242 3.87e+01 c.56.2.1 77216 1vicA 262 3.92e+01 c.68.1.13 100756 1jq5A 370 3.94e+01 e.22.1.2 67084 1x6mA 196 3.95e+01 1v7oA 165 3.98e+01 d.67.1.2 100480 1tqyB 415 4.00e+01 c.95.1.1,c.95.1.1 107247,107248 1ur3M 319 4.12e+01 c.1.7.1 99806 2bl0B 145 4.12e+01 1k20A 310 4.21e+01 c.107.1.1 68027 1rkqA 282 4.23e+01 c.108.1.10 97621 1ble 163 4.25e+01 1ble c.38.1.1 32475 1jd1A 129 4.27e+01 1qu9A d.79.1.1 62890 2a5yB 549 4.31e+01 1w6vA 141 4.39e+01 1eybA 471 4.40e+01 1ey2A b.82.1.4 28115 1rkuA 206 4.41e+01 c.108.1.11 97627 2fkiA 126 4.41e+01 1y5mA 276 4.44e+01 1y4jA 284 4.44e+01 1y9uA 323 4.46e+01 1z5nA 242 4.46e+01 1lm6A 215 4.48e+01 d.167.1.1 84628 1ylhA 560 4.50e+01 1adjA 421 4.57e+01 1adjA c.51.1.1,d.104.1.1 33188,40737 1gnlA 544 4.59e+01 e.26.1.1 70287 1yw3A 208 4.59e+01 1fxkB 109 4.64e+01 1fxkA a.2.5.1 15704 1vknA 351 4.64e+01 c.2.1.3,d.81.1.1 108676,108677 2fb1A 226 4.68e+01 1o20A 427 4.72e+01 c.82.1.1 86556 1f4qA 165 4.84e+01 1alvA a.39.1.8 17360 1ga8A 311 4.85e+01 1ga8A c.68.1.4 34516 1xo3A 101 4.85e+01 1st0A 337 4.86e+01 d.13.1.3,d.246.1.1 98979,98980 1mvwB 145 4.87e+01 i.15.1.1 79524 1k0fA 277 4.89e+01 c.92.2.2 71974 1neeA 138 4.93e+01 d.241.1.1,g.59.1.1 91841,91842 1yh1A 359 5.01e+01 1uu1A 335 5.01e+01 c.67.1.1 99993 2af4C 333 5.02e+01 1uc7A 125 5.04e+01 c.47.1.1 99163 1jf2A 195 5.05e+01 1ej3A a.39.1.5 62930 1dd9A 338 5.06e+01 1dd9A e.13.1.1 43254 1odfA 290 5.06e+01 c.37.1.6 92782 1mo9A 523 5.09e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 2dcnA 311 5.11e+01 1hrdA 449 5.11e+01 1k89 c.2.1.7,c.58.1.1 30219,33867 3pmgA 561 5.12e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 1vjvA 415 5.16e+01 d.3.1.9 108632 1zdrA 164 5.17e+01 2au3A 407 5.19e+01 1o4uA 285 5.21e+01 c.1.17.1,d.41.2.1 86624,86625 1iz0A 302 5.25e+01 b.35.1.2,c.2.1.1 83821,83822 1xfkA 336 5.25e+01 1pjhA 280 5.29e+01 c.14.1.3 94761 1tbxA 99 5.31e+01 a.4.5.48 106748 1xznA 179 5.42e+01 1i12A 160 5.44e+01 1i21A d.108.1.1 61515 1ss9A 311 5.46e+01 c.68.1.4 105978 1e79D 482 5.50e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18272,26437,32317 1vlwA 217 5.53e+01 c.1.10.1 108868 8abp 306 5.55e+01 8abp c.93.1.1 35647 1g57A 217 5.58e+01 1g57A d.115.1.2 60253 1wryA 121 5.68e+01 1lyvA 306 5.68e+01 c.45.1.2 74348 1qahA 136 5.75e+01 d.79.1.1 96338 1j6zA 376 5.77e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 1vmbA 140 5.78e+01 2b9hA 353 5.82e+01 1tca 317 5.84e+01 1tca c.69.1.17 34726 1itwA 741 5.85e+01 c.77.1.2 76793 2bjnA 160 5.86e+01 1kkhA 317 5.91e+01 d.14.1.5,d.58.26.3 72645,72646 1j55A 95 5.93e+01 a.39.1.2 77078 1x7dA 350 5.97e+01 1ykhB 132 5.97e+01 1y7lA 316 6.07e+01 2fokA 579 6.09e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16131,16132,16133,33323 1ub3A 220 6.13e+01 c.1.10.1 88395 1khbA 625 6.15e+01 c.91.1.1,c.109.1.1 68606,68607 1bmqA 167 6.18e+01 1pauA c.17.1.1 30998 1pyoA 167 6.21e+01 c.17.1.1 95370 1xcbA 211 6.25e+01 a.4.5.38,c.2.1.12 109552,109553 1ytw 306 6.26e+01 1ytw c.45.1.2 32689 1om1A 332 6.27e+01 d.144.1.7 93347 1bkpA 278 6.29e+01 1bkpA d.117.1.1 41029 2a9fA 398 6.35e+01 1orvA 728 6.35e+01 b.70.3.1,c.69.1.24 87354,87355 1wqaA 455 6.36e+01 1wr8A 231 6.36e+01 1inp 400 6.37e+01 1inp e.7.1.1 42972 1bgvA 449 6.37e+01 1k89 c.2.1.7,c.58.1.1 30217,33865 2mnr 357 6.37e+01 2mnr c.1.11.2,d.54.1.1 29245,38889 1me8A 503 6.41e+01 c.1.5.1 79028 2g9iA 249 6.46e+01 1qm4A 396 6.51e+01 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41350,41351,41352 1h2eA 207 6.52e+01 c.60.1.1 70857 1pvtA 238 6.58e+01 c.74.1.1 95189 2ck3D 482 6.62e+01 1euhA 475 6.64e+01 1euhA c.82.1.1 35369 1mdl 359 6.66e+01 2mnr c.1.11.2,d.54.1.1 29247,38891 1rzrA 332 6.66e+01 1a4sA 503 6.71e+01 1bpwA c.82.1.1 35361 1hv9A 456 6.72e+01 1fwyA b.81.1.4,c.68.1.5 28060,34518 1b5tA 275 6.78e+01 1b5tA c.1.23.1 29676 1dgaA 375 6.79e+01 1yagA 1xg5A 279 6.82e+01 1o4vA 183 6.86e+01 c.23.8.1 86628 2ct9A 208 6.91e+01 1vjtA 483 6.92e+01 c.2.1.5,d.162.1.2 100833,100834 1wdcB 156 6.93e+01 1wdcB a.39.1.5 17302 1h8eD 482 6.97e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 1vhh 162 7.00e+01 1vhh d.65.1.2 39550 2d1sA 548 7.02e+01 1wnaA 131 7.03e+01 1qx2A 76 7.08e+01 a.39.1.1 104622 1onrA 316 7.10e+01 1onrA c.1.10.1 29169 1eljA 381 7.12e+01 4mbp c.94.1.1 35791 1o57A 291 7.21e+01 a.4.5.40,c.61.1.1 92483,92484 2aotA 292 7.35e+01 1nonA 179 7.40e+01 c.61.1.1 103868 2bwrA 401 7.44e+01 1j05A 111 7.49e+01 b.1.1.1 90735 1el4A 195 7.49e+01 1ej3A a.39.1.5 59453 1qv1A 195 7.49e+01 a.39.1.5 96347 1m2rA 327 7.49e+01 d.144.1.7 84760 2bkaA 242 7.51e+01 2bnjA 303 7.51e+01 1bvyF 191 7.52e+01 1bvyF c.23.5.1 31207 1cqmA 101 7.56e+01 1ris d.58.14.1 39321 1fus 106 7.57e+01 9rnt d.1.1.4 36050 1yzfA 195 7.64e+01 1i2oA 316 7.68e+01 1onrA c.1.10.1 61574 2g0qA 173 7.69e+01 1w30A 201 7.70e+01 1ve1A 304 7.72e+01 1k0hA 117 7.73e+01 b.106.1.2 71975 1u6tA 121 7.73e+01 2gbp 309 7.73e+01 1gca c.93.1.1 35657 2bh1X 96 7.74e+01 1o04A 500 7.75e+01 c.82.1.1 86508 1o12A 376 7.80e+01 b.92.1.5,c.1.9.10 80758,80759 1ycyA 71 7.83e+01 1ylqA 96 7.92e+01 1mngA 203 8.00e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 2arhA 203 8.03e+01 2g40A 224 8.04e+01 1s48A 609 8.06e+01 e.8.1.4 98475 1us0A 316 8.08e+01 c.1.7.1 99850 1mb3A 124 8.16e+01 c.23.1.1 78907 2cveA 191 8.16e+01 1zupA 315 8.18e+01 1u5tA 233 8.26e+01 a.4.5.54,a.4.5.54 107684,107685 1kllA 130 8.27e+01 d.32.1.2 72720 1dkiA 371 8.28e+01 1dkiA d.3.1.1 37090 1wxxA 382 8.29e+01 1zx8A 136 8.31e+01 2c2xA 281 8.34e+01 2aieP 203 8.43e+01 1nxzA 246 8.44e+01 b.122.1.2,c.116.1.5 86391,86392 1jkvA 266 8.46e+01 a.25.1.3 71719 1a53 247 8.47e+01 1a53 c.1.2.4 28564 1o9iA 266 8.47e+01 a.25.1.3 92671 1ggzA 148 8.47e+01 a.39.1.5 70176 2cxcA 144 8.58e+01 1i1dA 161 8.58e+01 1i21A d.108.1.1 61526 1e6yC 247 8.62e+01 1mroC d.58.31.1 39441 1suwA 249 8.64e+01 e.52.1.1 106027 1gyxA 76 8.69e+01 d.80.1.1 76387 1j7lA 264 8.71e+01 d.144.1.6 62697 1hgxA 183 8.72e+01 1tc1A c.61.1.1 34027 1pjzA 203 8.81e+01 c.66.1.36 94794 1gdeA 389 8.84e+01 c.67.1.1 60456 1e2uA 553 8.85e+01 1e1dA e.26.1.1 43362 1gntA 553 8.85e+01 e.26.1.1 70290 1ia9A 280 8.90e+01 1ia9A d.144.1.5 62113 1brwA 433 8.90e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1v6zA 228 8.91e+01 2avtA 378 8.96e+01