# List of top-scoring protein chains for t04-80-60-80-str2+near-backbone-11-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 1a58 177 8.53e-16 2cpl b.62.1.1 27495 2rmcA 182 8.18e-15 2cpl b.62.1.1 27491 1ihgA 370 9.47e-15 2cpl a.118.8.1,b.62.1.1 62380,62381 1dywA 173 9.77e-15 2cpl b.62.1.1 27505 1awsA 164 1.06e-14 2cpl b.62.1.1 27431 1yndA 165 1.23e-14 2cpl 165 1.24e-14 2cpl b.62.1.1 27420 1xo7A 166 1.46e-14 1qoiA 177 1.67e-14 2cpl b.62.1.1 27490 2bitX 165 1.83e-14 1zcxA 178 2.34e-14 1awqA 164 2.70e-14 2cpl b.62.1.1 27461 2cfeA 162 4.49e-14 2a2nA 176 4.53e-14 1vdnA 162 9.29e-14 1h0pA 182 9.47e-14 b.62.1.1 76450 1zkcA 197 9.88e-14 2fu0A 160 2.01e-13 2b71A 196 6.23e-13 1xwnA 174 8.67e-13 1j2aA 166 1.99e-11 b.62.1.1 90779 1v9tA 166 3.03e-11 b.62.1.1 108451 1lopA 164 1.87e-10 2cpl b.62.1.1 27510 1zx8A 136 5.76e-01 1i8dA 213 8.51e-01 b.43.4.3,b.43.4.3 61953,61954 1ja1A 622 1.75e+00 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 2b25A 336 2.46e+00 1wsrA 375 2.67e+00 1juvA 193 3.45e+00 c.71.1.1 90912 1mdbA 539 4.20e+00 e.23.1.1 79008 1jyaA 130 4.76e+00 d.198.1.1 67453 1sxvA 172 4.90e+00 1m1hA 248 5.05e+00 b.114.1.1,d.58.42.1 78415,78416 1kzlA 208 5.59e+00 b.43.4.3,b.43.4.3 77635,77636 1xnb 185 5.77e+00 1axkA b.29.1.11 24308 1em2A 229 6.04e+00 1em2A d.129.3.2 41321 2cy7A 396 6.16e+00 1fr7A 260 6.93e+00 2cba b.74.1.1 27828 1x8qA 184 7.45e+00 1fvuB 125 8.22e+00 1ixxB d.169.1.1 42346 1zoxA 113 8.24e+00 1paz 123 9.19e+00 1bqk b.6.1.1 22878 1h1aA 191 9.29e+00 b.29.1.11 83450 1mh1 186 9.76e+00 1eesA c.37.1.8 32002 1yoeA 322 9.82e+00 1bqk 124 9.86e+00 1bqk b.6.1.1 22889 1yna 194 9.88e+00 1axkA b.29.1.11 24335 1vr0A 247 9.99e+00 2dcyA 185 1.01e+01 1dg9A 157 1.01e+01 1dg9A c.44.1.1 32637 1pmy 123 1.01e+01 1bqk b.6.1.1 22888 1xhkA 187 1.05e+01 1c0eA 157 1.05e+01 1dg9A c.44.1.1 32638 2gf9A 189 1.10e+01 1jssA 224 1.13e+01 d.129.3.2 71844 1x31C 206 1.15e+01 2b49A 287 1.18e+01 1yo1A 260 1.21e+01 1xxnA 185 1.22e+01 1vr8A 142 1.25e+01 2apoA 357 1.29e+01 2cba 260 1.29e+01 2cba b.74.1.1 27821 1xnkA 196 1.29e+01 1aisA 182 1.31e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1uowA 159 1.38e+01 b.7.1.2 107975 1k8kD 300 1.40e+01 d.198.2.1,d.198.2.1 68309,68310 1t3qB 788 1.40e+01 d.41.1.1,d.133.1.1 106369,106370 1fl1A 230 1.41e+01 1at3A b.57.1.1 27023 1s72E 178 1.44e+01 d.141.1.1,d.141.1.1 105323,105324 1wchA 315 1.45e+01 1h9mA 145 1.46e+01 1h9jA b.40.6.2,b.40.6.2 60833,60834 1t4wA 196 1.46e+01 b.2.5.2 106427 1xtaA 221 1.47e+01 1f1zA 273 1.48e+01 1f1zA a.4.5.27,c.52.1.16 16081,33334 1ad3A 452 1.50e+01 1ad3A c.82.1.1 35335 1erxA 184 1.52e+01 1np1A b.60.1.1 27164 1wosA 364 1.54e+01 b.44.2.1,d.250.1.1 109468,109469 1tjxA 159 1.55e+01 1jj2E 177 1.56e+01 1ffk1 d.141.1.1,d.141.1.1 63089,63090 1sy3A 184 1.57e+01 b.60.1.1 106110 2gcuA 245 1.59e+01 1htwA 158 1.60e+01 c.37.1.18 71083 2b8mA 117 1.61e+01 1brwA 433 1.62e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 2eu9A 355 1.63e+01 1dzkA 157 1.67e+01 1obpA b.60.1.1 27096 1wf3A 301 1.69e+01 1f8fA 371 1.73e+01 b.35.1.2,c.2.1.1 83246,83247 1yy5B 513 1.74e+01 1fjgQ 105 1.77e+01 1fjfQ b.40.4.5 25352 1v9nA 360 1.78e+01 1hcb 260 1.81e+01 2cba b.74.1.1 27814 1k07A 263 1.82e+01 d.157.1.1 77218 1in0A 163 1.87e+01 d.58.49.1,d.58.49.1 83694,83695 1jhsA 188 1.87e+01 d.107.1.1 84172 1nf3A 195 1.91e+01 c.37.1.8 85594 1pm1X 180 1.92e+01 b.60.1.1 104189 1mixA 206 1.92e+01 a.11.2.1,b.55.1.5 79166,79167 1lugA 259 1.96e+01 b.74.1.1 91127 1wvhA 134 1.97e+01 1tkiA 321 1.98e+01 1tkiA d.144.1.7 41638 1kdj 102 2.02e+01 1plc b.6.1.1 22864 1rkiA 102 2.05e+01 1jetA 517 2.09e+01 1jevA c.94.1.1 35718 2bw2A 140 2.10e+01 2foyA 260 2.13e+01 3nul 130 2.15e+01 3nul d.110.1.1 40891 1n0lA 224 2.16e+01 b.1.11.1,b.7.2.1 79744,79745 1xypA 190 2.17e+01 1axkA b.29.1.11 24327 1qj5A 429 2.17e+01 1dtyA c.67.1.4 34493 1lzlA 323 2.18e+01 c.69.1.2 78306 1dkuA 317 2.22e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1xgsA 295 2.29e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1mw7A 240 2.29e+01 e.39.1.1 79557 1uovA 159 2.31e+01 b.7.1.2 107974 1v72A 356 2.34e+01 1vioA 243 2.35e+01 d.265.1.3,d.66.1.5 100762,100763 1pbyA 489 2.38e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 1o8bA 219 2.39e+01 c.124.1.4,d.58.40.1 81180,81181 2olbA 517 2.39e+01 1jevA c.94.1.1 35721 1rhs 296 2.44e+01 1rhs c.46.1.2,c.46.1.2 32703,32704 1wu7A 434 2.45e+01 1n9bA 265 2.46e+01 e.3.1.1 85463 1rc9A 221 2.47e+01 1s0aA 429 2.52e+01 c.67.1.4 98263 1o94A 729 2.52e+01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 1bdfA 235 2.53e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1yb3A 175 2.57e+01 2bzlA 325 2.60e+01 1q5fA 156 2.62e+01 d.24.1.1 104536 1zd9A 188 2.63e+01 3cox 507 2.63e+01 1b8sA c.3.1.2,d.16.1.1 30332,37863 1l9vA 317 2.65e+01 d.13.2.1,d.216.1.1 73760,73761 1koiA 184 2.65e+01 b.60.1.1 68725 2fuvA 549 2.66e+01 1hn2A 159 2.66e+01 b.60.1.1 65890 1ej8A 140 2.66e+01 1qupA b.1.8.1 22300 1xfjA 261 2.68e+01 d.194.1.2 109585 1gt1A 159 2.69e+01 b.60.1.1 90515 1mqoA 227 2.70e+01 d.157.1.1 103846 1bebA 162 2.72e+01 1bebA b.60.1.1 27115 2bc2A 227 2.74e+01 1a7tA d.157.1.1 42031 1vloA 381 2.80e+01 b.44.2.1,d.250.1.1 108838,108839 1sq2N 113 2.80e+01 b.1.1.1 105881 1uiuA 502 2.82e+01 c.94.1.1 99434 1pvxA 194 2.82e+01 1axkA b.29.1.11 24341 2napA 723 2.91e+01 2napA b.52.2.2,c.81.1.1 26926,35334 1g0sA 209 2.94e+01 1g0sA d.113.1.1 60187 1kmqA 184 2.95e+01 c.37.1.8 84412 1vfjA 116 2.95e+01 2bkxA 242 2.96e+01 1j7lA 264 2.97e+01 d.144.1.6 62697 1xwwA 157 2.99e+01 1v5iB 76 2.99e+01 1faaA 124 3.01e+01 1erv c.47.1.1 32738 2coqA 108 3.06e+01 1h4vB 421 3.08e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1eq6A 189 3.09e+01 1eq6A d.107.1.1 40796 2sli 679 3.10e+01 2sli b.29.1.9,b.68.1.1 24274,27611 2aynA 404 3.11e+01 1peeA 180 3.12e+01 b.60.1.1 104126 1smlA 269 3.14e+01 1smlA d.157.1.1 42053 2b3yA 888 3.14e+01 1egaA 301 3.17e+01 1egaA c.37.1.8,d.52.3.1 32150,38836 1vknA 351 3.18e+01 c.2.1.3,d.81.1.1 108676,108677 1qqsA 174 3.21e+01 1nglA b.60.1.1 27143 1tq4A 413 3.24e+01 c.37.1.8 107201 1uc2A 481 3.24e+01 d.261.1.1 99161 2c30A 321 3.25e+01 16pk 415 3.27e+01 16pk c.86.1.1 35454 1fxxA 482 3.29e+01 1fxxA c.55.3.5 33726 1jykA 254 3.31e+01 c.68.1.13 67458 1y89A 238 3.34e+01 1qy1A 174 3.37e+01 b.60.1.1 96568 1kaeA 434 3.37e+01 c.82.1.2 72247 1u7lA 392 3.38e+01 1xocA 520 3.40e+01 1p8kZ 254 3.42e+01 d.95.2.1,d.95.2.1 94361,94362 1xb2B 291 3.43e+01 1gpc 218 3.44e+01 1gpc b.40.4.7 25393 1euoA 180 3.45e+01 1np1A b.60.1.1 27163 1oixA 191 3.49e+01 1agjA 242 3.49e+01 1agjA b.47.1.1 25827 1pa1A 310 3.50e+01 c.45.1.2 94404 1djnA 729 3.51e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 1e5pA 151 3.52e+01 1bj7 b.60.1.1 59272 1itwA 741 3.54e+01 c.77.1.2 76793 1y60A 169 3.55e+01 1xipA 388 3.57e+01 2fk9A 157 3.57e+01 1z94A 147 3.61e+01 3cla 213 3.63e+01 3cla c.43.1.1 32610 1vqoE 178 3.63e+01 2bjkA 516 3.66e+01 2f71A 298 3.69e+01 2bcgY 206 3.71e+01 1vjyA 303 3.73e+01 d.144.1.7 108633 1f9mA 112 3.74e+01 1erv c.47.1.1 32736 1xn5A 146 3.74e+01 1ikoP 178 3.74e+01 b.6.1.5 71243 1o04A 500 3.75e+01 c.82.1.1 86508 1djqA 729 3.79e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 1o7iA 119 3.80e+01 b.40.4.3 86642 1uouA 474 3.83e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 1wb0A 445 3.85e+01 1v3rA 116 3.87e+01 1uzbA 516 3.89e+01 c.82.1.1 100220 1fljA 260 3.93e+01 2cba b.74.1.1 27954 1fsgA 233 3.93e+01 1qk3A c.61.1.1 34029 1nslA 184 3.94e+01 d.108.1.1 86137 1v0wA 506 3.94e+01 d.136.1.2,d.136.1.2 108220,108221 1obpA 159 3.97e+01 1obpA b.60.1.1 27092 1h6tA 291 3.97e+01 b.1.18.15,c.10.2.1 65686,65687 1qg3A 195 4.00e+01 1qg3A b.1.2.1,b.1.2.1 21993,21994 1iseA 185 4.04e+01 d.67.3.1 90691 1zlqA 502 4.05e+01 1qpxA 218 4.06e+01 1qpxA b.1.11.1,b.7.2.1 22318,23200 2fhxA 246 4.06e+01 1euhA 475 4.07e+01 1euhA c.82.1.1 35369 1t0fA 276 4.08e+01 1gmiA 136 4.11e+01 b.7.1.1 65309 1kypA 237 4.11e+01 d.22.1.1 73280 1xk7A 408 4.12e+01 2fxqA 264 4.12e+01 1dar 691 4.13e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1 25707,32142,37547,39300 1foeA 377 4.14e+01 1foeA a.87.1.1,b.55.1.1 18517,26969 1mp9A 198 4.16e+01 d.129.1.1,d.129.1.1 91385,91386 1bj7 156 4.20e+01 1bj7 b.60.1.1 27113 1louA 101 4.22e+01 1ris d.58.14.1 39323 1ptvA 321 4.22e+01 1pty c.45.1.2 32665 1zd7A 159 4.23e+01 2pii 112 4.27e+01 2pii d.58.5.1 39071 2cxxA 190 4.27e+01 1pyaB 228 4.29e+01 1pyaB 1xr4A 509 4.30e+01 1qczA 169 4.32e+01 1qczA c.23.8.1 31276 1c0pA 363 4.32e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1bylA 125 4.35e+01 1bylA d.32.1.2 38495 2a1kA 233 4.36e+01 1cjxA 357 4.40e+01 1cjxA d.32.1.3,d.32.1.3 38516,38517 2bikB 313 4.43e+01 1z9lA 128 4.47e+01 1nkiA 135 4.49e+01 d.32.1.2 91941 2tmdA 729 4.50e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28616,30317,30602 1tz0A 114 4.52e+01 d.58.4.5 107463 2ajrA 331 4.54e+01 1ema 236 4.54e+01 1ema d.22.1.1 38339 1xtzA 264 4.60e+01 1jc4A 148 4.61e+01 1jc4A d.32.1.4 62863 2bsjA 133 4.61e+01 1rsgA 516 4.63e+01 1xa3A 437 4.64e+01 1djxB 624 4.64e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17343,23160,29588 2g8oA 264 4.65e+01 3proC 166 4.68e+01 3proC d.52.1.1,d.52.1.1 38812,38813 1lqpA 135 4.69e+01 d.32.1.2 78151 1xn9A 101 4.69e+01 1vhrA 184 4.69e+01 1vhrA c.45.1.1 32651 1va0A 239 4.70e+01 1qh3A 260 4.71e+01 1qh5A d.157.1.2 42059 1hkkA 364 4.71e+01 c.1.8.5,d.26.3.1 90634,90635 2aioA 269 4.72e+01 1dkmA 410 4.74e+01 1dklA c.60.1.2 34000 2bf6A 449 4.74e+01 1xppA 115 4.75e+01 1sqwA 188 4.76e+01 1jh6A 189 4.80e+01 d.61.1.1 66707 1u2pA 163 4.81e+01 2b9wA 424 4.90e+01 1je0A 236 4.91e+01 c.56.2.1 66581 2fctA 313 4.92e+01 1btl 263 4.97e+01 1btl e.3.1.1 42691 1wgbA 159 5.05e+01 1vziA 126 5.06e+01 b.1.13.1,g.41.5.2 108967,108968 1uu3A 310 5.09e+01 d.144.1.7 99999 1aszB 490 5.10e+01 1b8aA b.40.4.1,d.104.1.1 25241,40762 1hetA 374 5.11e+01 2ohxA b.35.1.2,c.2.1.1 60975,60976 1xffA 240 5.12e+01 d.153.1.1 109580 1t6gC 184 5.13e+01 b.29.1.11 106569 1sb2A 133 5.22e+01 1zndA 174 5.22e+01 1ze3C 205 5.23e+01 1fonA 240 5.23e+01 5ptp b.47.1.2 26231 1cjaA 342 5.25e+01 1cjaA d.144.1.3 41708 1x8gA 227 5.27e+01 1i4uA 181 5.27e+01 b.60.1.1 61732 1txlA 215 5.28e+01 b.60.1.4 107429 1hvyA 288 5.28e+01 1bkpA d.117.1.1 41049 1f1xA 322 5.29e+01 d.32.1.3,d.32.1.3 83208,83209 2awkA 228 5.31e+01 2b8eA 273 5.33e+01 1gpmA 525 5.34e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 2cr9A 139 5.34e+01 1tuwA 109 5.34e+01 d.58.4.8 107346 2cb2A 318 5.35e+01 2ajgA 196 5.38e+01 1bkpA 278 5.38e+01 1bkpA d.117.1.1 41029 1ve2A 235 5.39e+01 1p3dA 475 5.42e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1is1A 185 5.46e+01 d.67.3.1 83704 1tyjA 170 5.47e+01 1pcxA 810 5.49e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 94497,94498,94499,94500,94501 1oxdA 227 5.53e+01 d.22.1.1 93687 2a8eA 220 5.53e+01 1wv3A 238 5.54e+01 1v5vA 401 5.55e+01 1z47A 355 5.56e+01 1wndA 495 5.56e+01 1l3aA 228 5.56e+01 d.18.1.2 73531 1o6vA 466 5.57e+01 b.1.18.15,c.10.2.1 81099,81100 1idpA 172 5.61e+01 d.17.4.1 83685 2g8mA 264 5.61e+01 1koqA 253 5.63e+01 2cba b.74.1.1 27964 1u8sA 192 5.67e+01 d.58.18.5,d.58.18.5 107737,107738 1gnkA 112 5.70e+01 2pii d.58.5.1 39073 1vj0A 380 5.74e+01 b.35.1.2,c.2.1.1 100786,100787 1lg7A 182 5.75e+01 d.213.1.1 73888 1mp4A 292 5.75e+01 c.68.1.6 79376 1mr3F 181 5.77e+01 c.37.1.8 79422 2f9lA 199 5.77e+01 2bh9A 489 5.77e+01 2dg5B 190 5.78e+01 1ej1A 190 5.79e+01 1ejhA d.86.1.1 40144 1jv4A 162 5.87e+01 b.60.1.1 67343 1lfpA 249 5.91e+01 e.39.1.1 73885 1kskA 234 6.01e+01 d.66.1.5,d.265.1.3 72920,90389 1vr5A 547 6.09e+01 1hq8A 123 6.11e+01 1b6e d.169.1.1 61127 1oejA 193 6.12e+01 b.60.1.4 92798 2glzA 153 6.14e+01 2bkkA 264 6.18e+01 3rabA 169 6.20e+01 1ctqA c.37.1.8 32018 2g6yA 217 6.22e+01 1p15A 253 6.23e+01 c.45.1.2 93894 1cyx 205 6.25e+01 1cyx b.6.1.2 23023 1uv0A 149 6.25e+01 d.169.1.1 100028 1ec7A 446 6.25e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 2a6aA 218 6.25e+01 1b5eA 246 6.26e+01 1b5eA d.117.1.1 41056 2aexA 346 6.30e+01 1m2xA 223 6.31e+01 d.157.1.1 84764 1dytA 133 6.33e+01 7rsa d.5.1.1 37288 1dnlA 199 6.34e+01 1ci0A b.45.1.1 25753 1pne 140 6.36e+01 1pne d.110.1.1 40866 1mup 166 6.37e+01 1mup b.60.1.1 27133 1g8lA 411 6.41e+01 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1xm7A 195 6.42e+01 1f1uA 323 6.44e+01 d.32.1.3,d.32.1.3 83200,83201 1h8eD 482 6.44e+01 1skyE 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