# 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 1mdl 359 1.13e-01 2mnr c.1.11.2,d.54.1.1 29247,38891 1mucA 373 1.64e-01 1mucA c.1.11.2,d.54.1.1 29236,38880 2mnr 357 2.15e-01 2mnr c.1.11.2,d.54.1.1 29245,38889 1r6wA 322 2.76e-01 c.1.11.2,d.54.1.1 97165,97166 1z7yA 322 4.13e-01 2gl5A 410 4.50e-01 2aa4A 289 7.55e-01 1nu5A 370 8.22e-01 c.1.11.2,d.54.1.1 92183,92184 1a12A 413 8.83e-01 1a12A b.69.5.1 27663 1jtdB 273 9.08e-01 b.69.5.2 67265 1sjdA 368 9.31e-01 c.1.11.2,d.54.1.1 105632,105633 1nnwA 252 1.10e+00 d.159.1.5 80674 2gshA 414 1.30e+00 1g66A 207 1.36e+00 1bs9 c.69.1.30 31329 1tkkA 366 1.44e+00 c.1.11.2,d.54.1.1 107089,107090 1jpmA 366 1.45e+00 c.1.11.2,d.54.1.1 67031,67032 1ec7A 446 1.46e+00 1bqg c.1.11.2,d.54.1.1 29218,38862 1fhuA 320 1.48e+00 1fhuA c.1.11.2,d.54.1.1 29234,38878 1r0mA 375 1.49e+00 c.1.11.2,d.54.1.1 104747,104748 1rvkA 382 1.61e+00 c.1.11.2,d.54.1.1 97928,97929 1z7wA 322 1.64e+00 1jbbA 153 1.72e+00 1u9aA d.20.1.1 62842 2a6hA 315 1.85e+00 1w6tA 444 1.89e+00 2d1sA 548 1.93e+00 1sazA 381 1.99e+00 2dcnA 311 2.04e+00 1g99A 408 2.10e+00 1g99A c.55.1.2,c.55.1.2 33457,33458 2fyxA 143 2.19e+00 1qo7A 394 2.22e+00 1qo7A c.69.1.11 34697 1ng0A 253 2.26e+00 b.121.4.7 80475 2gdqA 382 2.59e+00 1my6A 199 2.60e+00 a.2.11.1,d.44.1.1 85232,85233 3tgl 269 2.87e+00 3tgl c.69.1.17 34733 1tzzA 392 2.90e+00 1isiA 265 3.22e+00 e.4.1.1 71394 1q0rA 298 3.50e+00 c.69.1.28 95508 1lci 550 3.52e+00 1lci e.23.1.1 43349 1xuqA 212 3.58e+00 1eceA 358 3.59e+00 1eceA c.1.8.3 28813 1jatA 155 3.65e+00 1u9aA d.20.1.1 62818 1yeyA 444 4.04e+00 1j5pA 253 4.09e+00 d.81.1.3,c.2.1.3 71577,83092 1apyB 141 4.14e+00 1apyB 1mv8A 436 4.25e+00 a.100.1.4,c.2.1.6,c.26.3.1 85128,85129,85130 1ehiA 377 4.28e+00 1iow c.30.1.2,d.142.1.1 31716,41484 1u9aA 160 4.32e+00 1u9aA d.20.1.1 38333 1o17A 345 4.45e+00 a.46.2.1,c.27.1.1 80765,80766 1eudA 311 4.48e+00 2scuA c.2.1.8,c.23.4.1 30312,31140 1ryp1 222 4.53e+00 1ryp1 1ng2A 193 4.57e+00 b.34.2.1,b.34.2.1 85660,85661 1iyxA 432 4.62e+00 c.1.11.1,d.54.1.1 83815,83816 1jfuA 186 5.02e+00 c.47.1.10 62940 1u9yA 284 5.14e+00 1hufA 140 5.24e+00 1hufA d.195.1.1 61272 1h9oA 112 5.38e+00 1qadA d.93.1.1 60837 1i7qB 193 5.49e+00 1qdlB c.23.16.1 61902 1rypJ 204 5.60e+00 d.153.1.4 41878 2gx9A 129 5.72e+00 1rsgA 516 5.80e+00 2anuA 255 5.81e+00 1h0hB 214 5.93e+00 d.58.1.5 76437 1w1iE 357 5.99e+00 c.1.9.1 109051 1u24A 337 6.16e+00 1ayaA 101 6.24e+00 1qadA d.93.1.1 40460 1yqeA 282 6.28e+00 1uxy 340 6.29e+00 2mbr d.145.1.2,d.146.1.1 41748,41761 1pl4A 198 6.33e+00 a.2.11.1,d.44.1.1 94854,94855 1x3mA 415 6.36e+00 1dkuA 317 6.89e+00 1dkuA c.61.1.2,c.61.1.2 34118,34119 1fviA 297 6.91e+00 1fviA b.40.4.6,d.142.2.1 25364,41578 1llp 343 7.00e+00 1arv a.93.1.1 18578 1jykA 254 7.02e+00 c.68.1.13 67458 1to6A 371 7.29e+00 c.141.1.1 107170 1mgtA 174 7.46e+00 1mgtA a.4.2.1,c.55.7.1 16078,33753 2grrA 161 7.49e+00 2bbhA 269 7.60e+00 1q0qA 406 7.70e+00 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1rypH 205 7.71e+00 d.153.1.4 41876 1cfr 285 7.71e+00 1cfr c.52.1.7 33312 1xjdA 345 7.73e+00 1fcjA 322 7.74e+00 1oasA c.79.1.1 35289 1wn5A 130 7.98e+00 1q0pA 223 8.02e+00 c.62.1.1 95507 1f1uA 323 8.13e+00 d.32.1.3,d.32.1.3 83200,83201 1xk5A 204 8.13e+00 1oo4A 111 8.20e+00 d.93.1.1 87185 2fymA 431 8.21e+00 1fkx 349 8.30e+00 1a4mA c.1.9.1 29018 2cqsA 842 8.38e+00 1f9yA 158 8.48e+00 d.58.30.1 83249 1y37A 304 8.60e+00 1x23A 155 8.71e+00 1ehyA 294 8.80e+00 1ehyA c.69.1.11 34693 1uwzA 136 8.85e+00 c.97.1.1 108081 1jtkA 136 8.90e+00 c.97.1.1 71862 1azwA 313 9.11e+00 1qtrA c.69.1.7 34658 1iscA 192 9.16e+00 1avmA a.2.11.1,d.44.1.1 15733,38726 1o50A 157 9.32e+00 d.37.1.1,d.37.1.1 92478,92479 1rzhH 260 9.33e+00 b.41.1.1,f.23.10.1 98162,98163 1c4xA 285 9.96e+00 1c4xA c.69.1.10 34684 1dxrH 258 1.00e+01 6prcH b.41.1.1,f.23.10.1 25456,43433 1ew6A 137 1.02e+01 1ewaA a.1.1.2 15637 1a4mA 349 1.03e+01 1a4mA c.1.9.1 29014 1qovH 260 1.04e+01 6prcH b.41.1.1,f.23.10.1 25464,43457 1gv3A 248 1.04e+01 a.2.11.1,d.44.1.1 70585,70586 2abqA 306 1.06e+01 153l 185 1.07e+01 153l d.2.1.5 36984 1vr9A 213 1.07e+01 1tufA 434 1.11e+01 b.49.2.3,c.1.6.1 107335,107336 1i4jA 110 1.12e+01 d.55.1.1 76734 1fo4A 1332 1.12e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 17910,37695,38586,40227,41416,41758 2b61A 377 1.12e+01 1ac5 483 1.13e+01 1ac5 c.69.1.5 34653 1ve1A 304 1.14e+01 1hgxA 183 1.16e+01 1tc1A c.61.1.1 34027 1ycdA 243 1.16e+01 2f4wA 187 1.17e+01 1uteA 313 1.17e+01 1uteA d.159.1.1 42078 1xbsA 149 1.18e+01 2ayvA 166 1.20e+01 1c25 161 1.21e+01 1c25 c.46.1.1 32698 2c9wA 169 1.22e+01 1v7rA 186 1.23e+01 c.51.4.1 100482 1ir21 140 1.23e+01 2boqA 331 1.24e+01 1fn9A 365 1.25e+01 1fn9A d.196.1.1 59894 1s72S 85 1.25e+01 d.12.1.1 105338 1jj2R 84 1.25e+01 1ffkP d.12.1.1 63103 1td6A 306 1.25e+01 1jvsA 400 1.26e+01 a.69.3.1,c.2.1.3,d.81.1.3 77187,77188,77189 1t77A 414 1.26e+01 1gbs 185 1.26e+01 153l d.2.1.5 36986 1xreA 217 1.26e+01 1unnC 115 1.27e+01 d.240.1.1 99680 1y7lA 316 1.27e+01 1uk8A 282 1.29e+01 c.69.1.10 107907 1ap6A 198 1.30e+01 1avmA a.2.11.1,d.44.1.1 15746,38705 1u2xA 474 1.31e+01 c.72.1.3 107622 2h1tA 188 1.33e+01 1o58A 303 1.33e+01 c.79.1.1 92491 1qc5A 192 1.35e+01 1aoxA c.62.1.1 34147 2fr1A 486 1.35e+01 1eh8A 207 1.36e+01 1sfe a.4.2.1,c.55.7.1 16077,33752 1bdfA 235 1.36e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1dtdA 303 1.39e+01 1aye c.56.5.1 33823 1j3wA 163 1.41e+01 d.110.7.1 90833 1tdzA 272 1.41e+01 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 1yy5B 513 1.43e+01 1bxeA 113 1.43e+01 1bxeA d.55.1.1 38898 1n0nA 199 1.44e+01 a.2.11.1,d.44.1.1 79750,79751 1ro7A 259 1.45e+01 c.130.1.1 97667 2ew8A 249 1.45e+01 2fo3A 125 1.49e+01 1ve2A 235 1.49e+01 1ptmA 329 1.50e+01 c.77.1.3 95104 1ihnA 113 1.50e+01 1ihnA c.103.1.1 62388 1qntA 176 1.50e+01 1sfe a.4.2.1,c.55.7.1 16074,33749 1sur 215 1.51e+01 1sur c.26.2.2 31620 1rzuA 485 1.51e+01 c.87.1.8 105140 1lbeA 258 1.53e+01 1lbeA e.4.1.1 42773 1r6dA 337 1.53e+01 c.2.1.2 97148 2ciaA 102 1.54e+01 1y6lA 149 1.54e+01 1jh6A 189 1.55e+01 d.61.1.1 66707 2a6mA 155 1.57e+01 1pfo 500 1.59e+01 1pfo f.9.1.1 43826 1p99A 295 1.60e+01 c.94.1.1 94384 1ufyA 122 1.61e+01 d.79.1.2 88489 1t5hX 504 1.62e+01 e.23.1.1 106449 1voqa 90 1.62e+01 2pth 193 1.63e+01 2pth c.56.3.1 33793 1wkoA 180 1.65e+01 1jpaA 312 1.66e+01 d.144.1.7 67011 1pvmA 184 1.67e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1yavA 159 1.67e+01 1oatA 439 1.69e+01 2dkb c.67.1.4 34461 1kcfA 258 1.72e+01 a.140.2.1,c.55.3.7 68434,68435 1v9sA 208 1.77e+01 1i1iP 681 1.77e+01 1i1iP d.92.1.5 40297 1v93A 296 1.78e+01 c.1.23.1 100532 1yumA 242 1.78e+01 1vflA 356 1.79e+01 1n8fA 350 1.79e+01 c.1.10.4 85397 1xeeA 91 1.83e+01 1us5A 314 1.84e+01 c.94.1.1 99856 2ap1A 327 1.84e+01 1uayA 242 1.84e+01 c.2.1.2 88390 1g0uL 241 1.85e+01 d.153.1.4 41894 1uesA 191 1.85e+01 a.2.11.1,d.44.1.1 107798,107799 2arhA 203 1.86e+01 1wod 233 1.88e+01 1wod c.94.1.1 35832 1rypG 244 1.88e+01 d.153.1.4 41938 1rypE 242 1.88e+01 1rypE d.153.1.4 41936 1o6dA 163 1.89e+01 c.116.1.3 92567 1ql0A 241 1.90e+01 1qaeA d.4.1.2 37139 1zkiA 133 1.90e+01 1zrzA 364 1.90e+01 1mgpA 313 1.91e+01 c.119.1.1 79098 1zesA 125 1.93e+01 1ebfA 358 1.94e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1r1mA 164 1.95e+01 d.79.7.1 96820 1ab8A 220 1.95e+01 1azsA d.58.29.1 39414 1fa0A 537 1.95e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 1ix9A 205 1.96e+01 a.2.11.1,d.44.1.1 76899,76900 2g84A 197 1.97e+01 2aehA 369 1.97e+01 1twiA 434 1.98e+01 b.49.2.3,c.1.6.1 107399,107400 1r77A 103 2.01e+01 2f02A 323 2.02e+01 1z7gA 217 2.02e+01 1eh6A 207 2.03e+01 1sfe a.4.2.1,c.55.7.1 16076,33751 1s1qA 145 2.07e+01 d.20.1.2 98351 1gc5A 467 2.10e+01 1gc5A c.72.1.3 60429 2f7fA 494 2.10e+01 1ww9A 392 2.12e+01 1qqcA 773 2.14e+01 1tgoA c.55.3.5,e.8.1.1 33724,43013 1rttA 193 2.15e+01 c.23.5.4 105098 1yw5A 177 2.16e+01 2fl7A 232 2.18e+01 1w0hA 204 2.19e+01 1o1xA 155 2.21e+01 c.121.1.1 86553 1blxA 326 2.21e+01 1hcl d.144.1.7 41596 1rypI 222 2.21e+01 d.153.1.4 41877 1yydA 357 2.22e+01 2f4nA 273 2.23e+01 1lycA 343 2.24e+01 a.93.1.1 74344 1xkyA 301 2.25e+01 1qs0A 407 2.25e+01 1qs0A c.36.1.11 31829 1whbA 157 2.28e+01 1m98A 317 2.28e+01 a.175.1.1,d.17.4.6 78866,78867 2bkrA 212 2.28e+01 1dljA 402 2.29e+01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1w4xA 542 2.29e+01 c.3.1.5,c.3.1.5 109171,109172 2aq2B 237 2.31e+01 1t0bA 252 2.31e+01 c.23.16.6 106199 1ep3B 262 2.32e+01 1ep2B b.43.4.2,c.25.1.3 25664,31554 1iupA 282 2.34e+01 c.69.1.10 76815 2c4nA 250 2.35e+01 2a5hA 416 2.36e+01 1z7dA 433 2.38e+01 1qhxA 178 2.39e+01 1qhsA c.37.1.3 31936 1xuuA 349 2.43e+01 2evaA 307 2.43e+01 1ii5A 233 2.44e+01 c.94.1.1 62412 1vqoS 85 2.46e+01 1f8rA 498 2.46e+01 1f8rA c.3.1.2,d.16.1.5 30410,37974 1mdbA 539 2.48e+01 e.23.1.1 79008 1zfpE 98 2.48e+01 1griA d.93.1.1 40465 1za7A 165 2.50e+01 1yioA 208 2.51e+01 1zbmA 280 2.56e+01 1qpaA 345 2.56e+01 1arv a.93.1.1 18585 1zq9A 285 2.57e+01 1vdc 333 2.57e+01 1trb c.3.1.5,c.3.1.5 30545,30546 1j1iA 296 2.57e+01 c.69.1.10 83977 1d4tA 104 2.58e+01 1d4tA d.93.1.1 40537 1vgjA 184 2.59e+01 1qwzA 235 2.61e+01 b.100.1.1 96510 1amf 233 2.61e+01 1wod c.94.1.1 35833 1aru 344 2.62e+01 1arv a.93.1.1 18589 1yarH 217 2.63e+01 1y0eA 223 2.63e+01 1wm1A 317 2.63e+01 c.69.1.7 109405 1j6wA 175 2.65e+01 1j98A d.185.1.2 62663 1f5aA 513 2.67e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39337,75835,75836 1z2uA 150 2.70e+01 2bfxA 284 2.71e+01 1p0zA 131 2.71e+01 d.110.6.1 93882 1chd 203 2.72e+01 1chd c.40.1.1 32478 1ax4A 467 2.72e+01 1ax4A c.67.1.2 34391 1iqqA 200 2.74e+01 d.124.1.1 66274 1scuA 288 2.75e+01 2scuA c.2.1.8,c.23.4.1 30307,31135 1bn7A 294 2.75e+01 1bn6A c.69.1.8 34677 1yh3A 256 2.76e+01 2al6A 375 2.77e+01 1fm0E 150 2.77e+01 1fmaE d.41.5.1 38629 1vj0A 380 2.78e+01 b.35.1.2,c.2.1.1 100786,100787 1te6A 439 2.78e+01 c.1.11.1,d.54.1.1 106797,106798 1hbnB 442 2.79e+01 1mroB a.89.1.1,d.58.31.2 60900,60901 1ydnA 295 2.80e+01 1k68A 140 2.81e+01 c.23.1.1 90943 1pu1A 94 2.84e+01 d.266.1.1 104307 1nb9A 147 2.85e+01 b.43.5.1 85515 1zm8A 259 2.88e+01 1v8eA 224 2.89e+01 1a44 185 2.91e+01 1a44 b.17.1.1 23704 1zdnA 158 2.91e+01 2cfqA 417 2.93e+01 1wzcA 249 2.94e+01 1xqoA 256 2.97e+01 1yj7A 171 2.98e+01 1v97A 1332 2.99e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 108436,108437,108438,108439,108440,108441 2fywA 267 3.02e+01 2a7mA 250 3.02e+01 1nwaA 203 3.02e+01 d.58.28.1 86295 1azsB 212 3.03e+01 1azsA d.58.29.1 39423 7atjA 308 3.03e+01 1bgp a.93.1.1 18673 1vjlA 164 3.04e+01 d.257.1.1 100822 1frb 315 3.05e+01 1frb c.1.7.1 28665 1ae9A 179 3.05e+01 1ae9A d.163.1.1 42153 1wg8A 285 3.06e+01 1xppA 115 3.06e+01 1xklA 273 3.08e+01 1f0iA 504 3.13e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 1yge 839 3.14e+01 1yge a.119.1.1,b.12.1.1 19234,23634 1x6vA 630 3.15e+01 1eny 268 3.16e+01 1eny c.2.1.2 29910 1u59A 287 3.17e+01 d.144.1.7 107681 1v0wA 506 3.17e+01 d.136.1.2,d.136.1.2 108220,108221 1i0hA 205 3.17e+01 1avmA a.2.11.1,d.44.1.1 15760,38685 1hekA 131 3.18e+01 a.61.1.5 65818 1qb0A 211 3.20e+01 1c25 c.46.1.1 32699 1n8jA 186 3.21e+01 c.47.1.10 85401 1pz1A 333 3.23e+01 c.1.7.1 95390 2fa1A 160 3.24e+01 1dhn 121 3.24e+01 1dhn d.96.1.3 40663 1pjjA 271 3.25e+01 a.156.1.2,b.113.1.1,g.39.1.8 104164,104165,104166 1zkjA 359 3.26e+01 1wzvA 155 3.26e+01 2fcr 173 3.27e+01 1rcf c.23.5.1 31151 1w5tA 412 3.28e+01 1qo2A 241 3.28e+01 1qo2A c.1.2.1 28533 1mroB 442 3.31e+01 1mroB a.89.1.1,d.58.31.2 18531,39449 1s9jA 341 3.33e+01 1qmhA 347 3.34e+01 1qmhA c.47.2.1,d.68.2.1 33082,39568 1r1qA 100 3.35e+01 d.93.1.1 104763 1hjsA 332 3.35e+01 c.1.8.3 83492 2azpA 318 3.36e+01 1shdA 107 3.36e+01 1fmk d.93.1.1 40440 1vhnA 318 3.39e+01 c.1.4.1 100693 1vd6A 224 3.40e+01 1s3eA 520 3.41e+01 c.3.1.2,d.16.1.5 98426,98427 1obr 326 3.48e+01 1aye c.56.5.2 33828 1dysA 348 3.49e+01 1bvwA c.6.1.1 30669 1nnjA 271 3.51e+01 a.156.1.2,b.113.1.1,g.39.1.8 80669,80670,80671 1pg4A 652 3.52e+01 e.23.1.1 88067 2awpA 198 3.54e+01 1sviA 195 3.55e+01 c.37.1.8 106048 2cxaA 256 3.55e+01 1xc3A 302 3.56e+01 2g9iA 249 3.58e+01 2kinA 238 3.59e+01 1bg2 c.37.1.9 32190 1n3gA 113 3.60e+01 d.204.1.1 79962 1mngA 203 3.61e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 2d0oA 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