# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl-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 1c1yB 77 3.66e-01 1c1yB d.15.1.5 37618 2al3A 90 4.85e-01 1guaB 81 5.70e-01 1c1yB d.15.1.5 37619 1b59A 370 2.92e+00 1bn5 a.4.5.25,d.127.1.1 16225,41162 1wrvA 308 3.53e+00 2g7jA 124 3.59e+00 1kv0A 66 3.59e+00 g.3.7.1 91040 1xv2A 237 3.70e+00 1bn5 478 3.91e+00 1bn5 a.4.5.25,d.127.1.1 16224,41161 1b6a 478 3.96e+00 1bn5 a.4.5.25,d.127.1.1 16223,41160 1ys7A 233 3.98e+00 1wm3A 72 5.41e+00 1rfa 79 5.49e+00 1c1yB d.15.1.5 37620 1wvhA 134 5.71e+00 1djtA 64 6.06e+00 1aho g.3.7.1 44132 1sn4A 64 7.26e+00 1aho g.3.7.1 44136 1vjoA 393 7.41e+00 c.67.1.3 100827 1wn2A 121 7.67e+00 2cvjA 180 7.83e+00 1iyeA 309 7.88e+00 e.17.1.1 83786 1euvB 86 7.89e+00 1a5r d.15.1.1 37598 1bkb 136 8.03e+00 1bkb b.34.5.2,b.40.4.5 24609,25341 1dgmA 363 8.22e+00 1bx4A c.72.1.1 34936 1rybA 212 8.35e+00 c.56.3.1 98098 1a3gA 308 8.92e+00 1daaA e.17.1.1 43286 3hhrB 203 9.71e+00 1axiB b.1.2.1,b.1.2.1 22005,22006 1i1kA 309 1.09e+01 1daaA e.17.1.1 61533 2cxhA 217 1.28e+01 1gzqA 300 1.31e+01 b.1.1.2,d.19.1.1 70818,70819 1vmjA 151 1.35e+01 1b1yA 500 1.35e+01 1byb c.1.8.1 28796 1nwbA 124 1.46e+01 b.124.1.1 86296 1zud1 251 1.48e+01 1qstA 160 1.50e+01 1yghA d.108.1.1 40804 2absA 383 1.51e+01 1j3kA 280 1.55e+01 c.71.1.1 84070 1iz6A 138 1.57e+01 b.34.5.2,b.40.4.5 76976,76977 1t4wA 196 1.58e+01 b.2.5.2 106427 1vcoA 550 1.66e+01 c.23.16.1,c.37.1.10 108508,108509 1zncA 266 1.67e+01 2cba b.74.1.1 27955 1jkfA 533 1.74e+01 c.2.1.3,d.81.1.3 71700,71701 2aliA 158 1.75e+01 1so7A 382 1.77e+01 2blsA 358 1.91e+01 1gceA e.3.1.1 42747 1qcwA 410 1.98e+01 1gox c.1.4.1 28622 2yhx 457 1.99e+01 2yhx i.12.1.1 46024 1c3mA 147 2.00e+01 1jotA b.77.3.1 27983 1jg1A 235 2.05e+01 c.66.1.7 66661 1c3kA 147 2.06e+01 1jotA b.77.3.1 27984 1h1wA 289 2.09e+01 d.144.1.7 83460 1fsyA 358 2.17e+01 1gceA e.3.1.1 60016 1kvlA 358 2.18e+01 e.3.1.1 73062 2awgA 118 2.22e+01 2ffyA 358 2.23e+01 1l0gA 358 2.25e+01 e.3.1.1 73400 1pi4A 358 2.34e+01 e.3.1.1 94700 1fcbA 511 2.36e+01 1gox c.1.4.1,d.120.1.1 28620,41087 1umgA 362 2.37e+01 d.280.1.1 107956 2gnxA 365 2.45e+01 1n71A 180 2.49e+01 d.108.1.1 85370 2bzoB 79 2.56e+01 2eifA 136 2.70e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1r6fA 310 2.74e+01 e.46.1.1 97149 1b78A 193 2.77e+01 1b78A c.51.4.1 33221 1gsa 316 2.87e+01 1gsa c.30.1.3,d.142.1.1 31718,41477 1liiA 363 3.00e+01 c.72.1.1 73921 1lay 256 3.01e+01 1lay b.57.1.1 27014 1vizA 240 3.03e+01 c.1.4.1 100784 1uu3A 310 3.06e+01 d.144.1.7 99999 1q42A 201 3.07e+01 d.17.4.2 95776 1swuA 127 3.08e+01 1swuA b.61.1.1 27230 1wddS 128 3.18e+01 1gqoL 143 3.24e+01 c.23.13.1 76306 1t4hA 290 3.24e+01 d.144.1.7 106420 1k26A 156 3.25e+01 d.113.1.1 72003 1yh6A 179 3.28e+01 1gqoS 143 3.29e+01 c.23.13.1 76313 1b96A 244 3.30e+01 1rvaA c.52.1.2 33268 1y8qA 346 3.31e+01 1qkkA 155 3.32e+01 1dbwA c.23.1.1 31104 1gqoJ 143 3.33e+01 c.23.13.1 76304 1gqoG 143 3.33e+01 c.23.13.1 76301 1v8yA 170 3.33e+01 1gqoC 143 3.34e+01 c.23.13.1 76297 1gqoY 143 3.35e+01 c.23.13.1 76318 1gqoM 143 3.36e+01 c.23.13.1 76307 1gqoQ 143 3.36e+01 c.23.13.1 76311 1gqoV 143 3.37e+01 c.23.13.1 76316 1gqoF 143 3.37e+01 c.23.13.1 76300 1gqoE 143 3.38e+01 c.23.13.1 76299 1gqoR 143 3.39e+01 c.23.13.1 76312 2bgcA 238 3.41e+01 1gqoK 143 3.41e+01 c.23.13.1 76305 1gqoX 143 3.44e+01 c.23.13.1 76317 1gqoO 143 3.45e+01 c.23.13.1 76309 1gqoI 143 3.46e+01 c.23.13.1 76303 1gqoB 143 3.48e+01 c.23.13.1 76296 1gqoP 143 3.51e+01 c.23.13.1 76310 2c6cA 707 3.58e+01 1r3nA 462 3.59e+01 c.56.5.4,d.58.19.1 96945,96946 1bco 327 3.62e+01 1bco b.48.1.1,c.55.3.3 26431,33676 1kgsA 225 3.63e+01 a.4.6.1,c.23.1.1 68596,68597 1vdxA 184 3.66e+01 1l5zA 155 3.67e+01 c.23.1.1 77722 1gwmA 153 3.71e+01 b.18.1.19 83348 1sriA 121 3.75e+01 1swuA b.61.1.1 27276 1daaA 282 3.75e+01 1daaA e.17.1.1 43270 1o51A 114 3.80e+01 d.58.5.4 92480 1d8cA 723 3.81e+01 1d8cA c.1.13.1 29325 1enxA 190 3.89e+01 1axkA b.29.1.11 24325 1b87A 181 3.90e+01 1b87A d.108.1.1 40797 2izhB 123 3.91e+01 1swuA b.61.1.1 27234 1kbjA 412 3.97e+01 c.1.4.1 72280 1l3aA 228 4.02e+01 d.18.1.2 73531 1pv9A 348 4.06e+01 c.55.2.1,d.127.1.1 95157,95158 1i8dA 213 4.09e+01 b.43.4.3,b.43.4.3 61953,61954 1p7tA 731 4.12e+01 c.1.13.1 94319 3daaA 277 4.17e+01 1daaA e.17.1.1 43272 2a5kA 307 4.19e+01 2b0vA 153 4.21e+01 1gqoT 143 4.25e+01 c.23.13.1 76314 1cov3 238 4.25e+01 1aym3 1axiB 236 4.32e+01 1axiB b.1.2.1,b.1.2.1 21997,21998 1b56 135 4.36e+01 1hmt b.60.1.2 27183 1qgvA 142 4.41e+01 1qgvA c.47.1.8 33056 1gqoH 143 4.41e+01 c.23.13.1 76302 1zjjA 263 4.43e+01 1k2eA 156 4.44e+01 d.113.1.1 72010 1l7jA 347 4.45e+01 b.30.5.4 73660 1edqA 540 4.46e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 2tdt 274 4.51e+01 3tdt b.81.1.2 28054 1vjqA 79 4.52e+01 k.43.1.1 100830 1tz9A 367 4.56e+01 c.1.15.6 107466 1a9eA 277 4.57e+01 1agdA b.1.1.2,d.19.1.1 20757,38268 2coaA 125 4.60e+01 1a22B 238 4.63e+01 1axiB b.1.2.1,b.1.2.1 22003,22004 1eejA 216 4.64e+01 1eejA c.47.1.9,d.17.3.1 33057,38071 1dl5A 317 4.68e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1a0gA 282 4.69e+01 1daaA e.17.1.1 43276 1ctn 540 4.71e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21876,29005,38439 1ysrA 150 4.72e+01 1gskA 513 4.73e+01 b.6.1.3,b.6.1.3,b.6.1.3 83314,83315,83316 1e01A 48 4.73e+01 1e01A 5gcnA 166 4.85e+01 1yghA d.108.1.1 40807 1b01A 45 4.85e+01 2cpgA a.43.1.3 17458 1fwyA 331 4.87e+01 1fwyA b.81.1.4,c.68.1.5 28064,34522 1qh8B 519 4.89e+01 1qguB c.92.2.3 35634 1qguB 519 4.93e+01 1qguB c.92.2.3 35626 1wpoA 256 4.95e+01 1lay b.57.1.1 27012 1glv 303 4.99e+01 1gsa c.30.1.3,d.142.1.1 31721,41480 2dabA 282 5.01e+01 1daaA e.17.1.1 43274 1zrzA 364 5.04e+01 2mjpA 193 5.11e+01 1b78A c.51.4.1 33223 3tdt 274 5.11e+01 3tdt b.81.1.2 28053 1ltdA 506 5.12e+01 1gox c.1.4.1,d.120.1.1 28618,41086 1fxjA 331 5.13e+01 1fwyA b.81.1.4,c.68.1.5 28062,34520 1h1yA 228 5.18e+01 c.1.2.2 76506 1h8eD 482 5.22e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 1zmdA 474 5.26e+01 1rj8A 164 5.27e+01 b.22.1.1 97547 1914 232 5.33e+01 1914 d.49.1.1,d.49.1.1 83028,83029 1a1nA 276 5.35e+01 1agdA b.1.1.2,d.19.1.1 20755,38267 2c0zA 216 5.43e+01 1k92A 455 5.45e+01 c.26.2.1,d.210.1.1 68325,68326 1zd7A 159 5.52e+01 1zesA 125 5.52e+01 1yqzA 438 5.53e+01 1j71A 334 5.57e+01 1eagA b.50.1.2 62669 1jrkA 156 5.57e+01 d.113.1.1 71827 1b1a 137 5.62e+01 1be1 c.23.6.1 31242 1a1oA 276 5.69e+01 1agdA b.1.1.2,d.19.1.1 20751,38265 2f01A 127 5.70e+01 1faoA 126 5.72e+01 1faoA b.55.1.1 26974 1xnzA 264 5.77e+01 1vl5A 260 5.78e+01 c.66.1.41 108720 1l3lA 234 5.79e+01 a.4.6.2,d.110.5.1 73541,73542 2izgB 123 5.86e+01 1swuA b.61.1.1 27236 1q2wA 308 5.88e+01 b.47.1.4 88355 1k9tA 540 5.88e+01 b.1.18.2,c.1.8.5,d.26.3.1 77298,77299,77300 2a2dA 478 5.89e+01 2a3nA 355 5.89e+01 2amdA 311 5.92e+01 1mmuA 347 5.96e+01 b.30.5.4 79303 2a2cA 478 5.96e+01 1l7jB 347 5.98e+01 b.30.5.4 73661 1gqoD 143 6.00e+01 c.23.13.1 76298 1jjiA 311 6.02e+01 c.69.1.2 66766 1mat 264 6.06e+01 1c24A d.127.1.1 41152 1gqoU 143 6.08e+01 c.23.13.1 76315 1vq0A 302 6.22e+01 1luqA 127 6.25e+01 b.61.1.1 91128 1gqoN 143 6.25e+01 c.23.13.1 76308 1b00A 127 6.25e+01 3chy c.23.1.1 31122 1o5zA 442 6.30e+01 c.59.1.2,c.72.2.2 92530,92531 1jkxA 212 6.30e+01 c.65.1.1 66813 1sc6A 404 6.35e+01 2cpgA 45 6.35e+01 2cpgA a.43.1.3 17455 1mioB 458 6.37e+01 1qguB c.92.2.3 35602 1v6fA 151 6.50e+01 d.109.1.2 108395 1yx1A 264 6.51e+01 1a1mA 278 6.57e+01 1agdA b.1.1.2,d.19.1.1 20753,38266 1mvfA 135 6.65e+01 b.1.1.1 85141 1uv7A 110 6.66e+01 d.67.4.1 100040 1sesA 421 6.69e+01 1sesA a.2.7.1,d.104.1.1 15710,40710 1tdtA 259 6.70e+01 3tdt b.81.1.2 28055 1qvjA 292 6.73e+01 d.113.1.1 96431 1jj2R 84 6.75e+01 1ffkP d.12.1.1 63103 2a4nA 182 6.77e+01 1wn4A 28 6.83e+01 j.113.1.1 109426 1s72S 85 6.84e+01 d.12.1.1 105338 2afbA 351 6.86e+01 1hv9A 456 6.91e+01 1fwyA b.81.1.4,c.68.1.5 28060,34518 1vphA 149 6.95e+01 1h8uA 117 7.00e+01 1h8uA d.169.1.1 60793 1xh3A 276 7.04e+01 1c24A 263 7.05e+01 1c24A d.127.1.1 41148 2cab 261 7.08e+01 2cba b.74.1.1 27906 1q33A 292 7.09e+01 d.113.1.1 95657 1kmtA 141 7.10e+01 b.1.18.8 77442 1pcfA 66 7.10e+01 1pcfA d.18.1.1 38142 1xypA 190 7.12e+01 1axkA b.29.1.11 24327 1fj7A 101 7.16e+01 1fj7A d.58.7.1 39209 3lriA 83 7.23e+01 1zeiA g.1.1.1 43995 1gxrA 337 7.26e+01 b.69.4.1 70722 1sffA 426 7.36e+01 c.67.1.4 105482 2etgA 296 7.36e+01 1jwiA 131 7.43e+01 d.169.1.1 67383 1ajw 145 7.46e+01 1rhoA b.1.18.8 21905 2gh1A 301 7.52e+01 1nra 63 7.54e+01 1aho g.3.7.1 44126 1e0gA 48 7.55e+01 1e01A d.7.1.1 37325 1wdkC 390 7.61e+01 c.95.1.1,c.95.1.1 109258,109259 1pytA 94 7.65e+01 1pytA d.58.3.1 39064 1wthD 391 7.67e+01 1vgjA 184 7.68e+01 1hpgA 187 7.73e+01 1qq4A b.47.1.1 25813 1ib8A 164 7.73e+01 b.38.2.1,d.52.4.1 71168,71169 1wy2A 351 7.76e+01 1frrA 95 7.77e+01 1awd d.15.4.1 37674 1hcb 260 7.82e+01 2cba b.74.1.1 27814 1kgqA 274 7.95e+01 b.81.1.2 72447 2matA 264 7.98e+01 1c24A d.127.1.1 41146 1yduA 170 8.06e+01 1ipiA 123 8.14e+01 c.52.1.18 66255 1g291 372 8.15e+01 1g291 4matA 278 8.15e+01 1c24A d.127.1.1 41150 1rxyA 253 8.22e+01 c.56.2.1 98065 1jqnA 883 8.22e+01 c.1.12.3 77159 1lx7A 253 8.30e+01 c.56.2.1 74329 2ccvA 101 8.36e+01 1qb4A 883 8.40e+01 c.1.12.3 74640 1k32A 1045 8.44e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1w66A 232 8.45e+01 1b47A 304 8.46e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17381,17775,40529 1omyA 65 8.48e+01 g.3.7.1 93354 1xrtA 467 8.56e+01 1sdsA 117 8.65e+01 d.79.3.1 105439 2f4mA 295 8.66e+01 1gjwA 637 8.67e+01 b.71.1.1,c.1.8.1 60582,60583 1m0qA 433 8.67e+01 c.67.1.4 78350 1b6sA 355 8.68e+01 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28242,31649,41494 1njkA 156 8.70e+01 d.38.1.1 85818 1yna 194 8.77e+01 1axkA b.29.1.11 24335 2f06A 144 8.84e+01 2gf1 70 8.88e+01 2gf1 g.1.1.1 43990 1j5vA 351 8.89e+01 c.72.1.1 71585 1wbiA 129 8.98e+01