# List of top-scoring protein chains for t04-100-30-alpha 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 1rxxA 421 5.82e-06 1jdw 423 7.62e-04 1jdw d.126.1.2 41129 1s9rA 410 2.45e-02 1h70A 255 9.91e-02 1h70A d.126.1.3 60711 1nxjA 183 1.14e-01 c.8.7.1 86382 1id0A 152 1.41e-01 d.122.1.3 66111 1m0dA 138 2.19e-01 c.52.1.17 74354 1nnlA 225 2.24e-01 c.108.1.4 85906 1ctn 540 3.80e-01 1ctn b.1.18.2 21876 c.1.8.5 29005 d.26.3.1 38439 1fzrA 138 5.06e-01 1fzrA c.52.1.17 33336 1bs0A 384 5.21e-01 1bs0A c.67.1.4 34490 1h2eA 207 6.27e-01 c.60.1.1 70857 1heiA 451 6.48e-01 1heiA c.37.1.14 32463 c.37.1.14 32464 1e19A 314 6.55e-01 1b7bA c.73.1.1 34967 1vhwA 253 6.61e-01 1f74A 293 7.43e-01 1nal3 c.1.10.1 29079 1edqA 540 9.30e-01 1ctn b.1.18.2 21873 c.1.8.5 29002 d.26.3.1 38436 1pbgA 468 9.62e-01 1e70M c.1.8.4 28946 1mwpA 96 1.20e+00 1mwpA d.170.2.1 42453 1id1A 153 1.23e+00 1id1A c.2.1.9 62286 1f6dA 376 1.27e+00 1f6dA c.87.1.3 35467 3bamA 213 1.56e+00 1bam c.52.1.3 33288 1hlrA 907 1.58e+00 a.56.1.1 65850 d.15.4.2 65851 d.41.1.1 65852 d.133.1.1 65853 1gmlA 178 1.63e+00 c.8.5.2 70273 1o5zA 442 1.93e+00 1jb7B 260 2.10e+00 1otcB b.40.4.3 62839 1o5oA 221 2.16e+00 1diiC 80 2.30e+00 1diiC a.3.1.1 15925 1dqaA 467 2.30e+00 1dqaA d.58.20.1 39364 d.179.1.1 42585 1j08A 226 2.48e+00 c.47.1.2 83855 c.47.1.2 83856 1hc7A 477 2.59e+00 1hc7A c.51.1.1 60938 d.68.5.1 60940 d.104.1.1 60939 1uc2A 481 2.67e+00 1bcpB 199 2.79e+00 1bcpB b.40.2.1 25120 d.169.1.2 42429 1g61A 228 2.84e+00 1g61A d.126.1.1 41126 1kte 105 2.87e+00 1kte c.47.1.1 32771 1pg6A 243 2.96e+00 1alo 907 3.14e+00 1alo 1cl1A 395 3.22e+00 1cl2A c.67.1.3 34395 1g6oA 330 3.24e+00 1g6oA c.37.1.11 32430 1bif 469 3.24e+00 1bif c.37.1.7 31961 c.60.1.4 34003 1esgA 213 3.30e+00 1bam c.52.1.3 33286 1lox 662 3.44e+00 1lox a.119.1.2 19238 b.12.1.1 23638 1dozA 309 3.64e+00 1ak1 c.92.1.1 35592 1j1nA 492 3.65e+00 c.94.1.1 83978 1bzyA 217 3.69e+00 1qk3A c.61.1.1 34071 1vjqA 79 3.72e+00 1sviA 195 3.74e+00 4bcl 366 3.75e+00 4bcl b.75.1.1 27968 1dkiA 371 3.76e+00 1dkiA d.3.1.1 37090 1dekA 241 3.77e+00 1dekA c.37.1.1 31842 1l9xA 315 3.91e+00 c.23.16.1 73762 1szwA 379 3.97e+00 1i60A 278 4.05e+00 c.1.15.4 71118 2rslA 140 4.35e+00 2rslA c.53.1.1 33345 1k9sA 237 4.41e+00 c.56.2.1 68359 1kutA 230 4.45e+00 d.143.1.1 73017 1fs0E 138 4.50e+00 1aqt a.2.10.1 59997 b.93.1.1 59998 1o8bA 219 4.52e+00 c.35.1.2 81180 d.58.40.1 81181 1ehiA 377 4.63e+00 1iow c.30.1.2 31716 d.142.1.1 41484 1ecpA 238 4.70e+00 1ecpA c.56.2.1 33775 1h09A 338 4.81e+00 b.109.1.1 83420 c.1.8.8 83421 1lw6I 64 4.87e+00 d.40.1.1 74294 1b1cA 181 4.91e+00 1amoA c.23.5.2 31212 1gci 269 4.93e+00 1gci c.41.1.1 32503 1b8bA 605 4.96e+00 1b8bA 1iqrA 420 5.56e+00 a.99.1.1 66275 c.28.1.1 66276 1hr6A 475 5.81e+00 1hr6A d.185.1.1 61164 d.185.1.1 61165 1ji8A 111 5.82e+00 d.203.1.1 66733 1ypcI 64 6.03e+00 2sniI d.40.1.1 38570 1fnsA 196 6.30e+00 1auq c.62.1.1 34136 1uxoA 192 6.30e+00 1qgvA 142 6.31e+00 1qgvA c.47.1.8 33056 1qlwA 328 6.45e+00 1qlwA c.69.1.15 34722 1o6dA 163 6.46e+00 2fha 183 6.78e+00 2fha a.25.1.1 16674 1pmi 440 6.80e+00 1pmi b.82.1.3 28114 1qj4A 257 6.83e+00 1qj4A c.69.1.20 34796 1a8l 226 6.88e+00 1a8l c.47.1.2 32777 c.47.1.2 32778 1ivg 388 6.93e+00 2qwc b.68.1.1 27578 1yasA 257 6.95e+00 1qj4A c.69.1.20 34801 1ijbA 202 6.96e+00 c.62.1.1 71229 1qgxA 357 7.10e+00 1qgxA e.7.1.1 42973 1oaa 259 7.21e+00 1oaa c.2.1.2 29829 1ogqA 313 7.23e+00 c.10.2.8 86996 1o8xA 146 7.28e+00 c.47.1.10 86681 1g66A 207 7.36e+00 1bs9 c.23.9.1 31329 1s0uA 408 7.47e+00 1kafA 108 7.48e+00 d.199.1.1 68372 1b5qA 472 7.57e+00 1b37B c.3.1.2 30404 d.16.1.5 37968 1eemA 241 7.71e+00 1eemA a.45.1.1 17717 c.47.1.5 33011 1dosA 358 7.84e+00 1dosA c.1.10.2 29175 1i1qB 192 7.91e+00 1qdlB c.23.16.1 61544 1e5dA 402 7.96e+00 1e5dA c.23.5.1 31208 d.157.1.3 42061 1i5gA 144 8.01e+00 1ewxA c.47.1.10 61784 1hfoA 113 8.12e+00 d.80.1.3 61006 1qk8A 146 8.14e+00 1ewxA c.47.1.10 33061 1goiA 499 8.15e+00 b.72.2.1 65413 c.1.8.5 65414 d.26.3.1 65415 1e6pA 499 8.25e+00 1e15A b.72.2.1 59314 c.1.8.5 59315 d.26.3.1 59316 1ea7A 310 8.37e+00 c.41.1.1 70086 1ka1A 357 8.63e+00 e.7.1.1 68369 1cf9A 753 8.80e+00 1cf9A c.23.16.3 31441 e.5.1.1 42815 1nh9A 87 8.90e+00 1v93A 296 8.94e+00 1k77A 260 9.22e+00 c.1.15.5 72096 1pg4A 652 9.23e+00 e.23.1.1 88067 1k47A 337 9.32e+00 d.14.1.5 72040 d.58.26.4 72041 1n7hA 381 9.59e+00 c.2.1.2 80250 1m6yA 301 9.92e+00 a.60.13.1 78716 c.66.1.23 78717 1nx8A 273 1.00e+01 b.82.2.8 86374 1vp9 322 1.05e+01 3mag c.66.1.25 34210 1onxA 390 1.07e+01 b.92.1.7 87176 c.1.9.13 87177 1jjiA 311 1.07e+01 c.69.1.2 66766 1o57A 291 1.07e+01 1m6dA 214 1.08e+01 d.3.1.1 84849 1v39 322 1.08e+01 3mag c.66.1.25 34206 1bolA 222 1.10e+01 1bolA d.124.1.1 41120 1gp1A 198 1.11e+01 1gp1A c.47.1.10 33059 1s4qA 228 1.11e+01 1ujnA 348 1.14e+01 1gzgA 337 1.15e+01 c.1.10.3 70805 1no5A 114 1.18e+01 1hv9A 456 1.19e+01 1fwyA b.81.1.4 28060 c.68.1.5 34518 1v7oA 165 1.22e+01 1qy6A 274 1.23e+01 1i4wA 353 1.24e+01 c.66.1.24 66028 1mzhA 225 1.26e+01 c.1.10.1 79698 1iugA 352 1.28e+01 1srvA 145 1.30e+01 1derA c.8.5.1 30817 1vhuA 211 1.31e+01 1d5tA 433 1.35e+01 1gnd c.3.1.3 30422 d.16.1.6 37986 1g8aA 227 1.36e+01 1nnwA 252 1.37e+01 d.159.1.5 80674 1khdA 345 1.38e+01 a.46.2.1 77400 c.27.1.1 77401 1jbwA 428 1.40e+01 c.59.1.2 62860 c.72.2.2 62861 1qjcA 158 1.41e+01 1b6tA c.26.1.3 63328 2hhmA 276 1.41e+01 1imbA e.7.1.1 42955 1pz1A 333 1.43e+01 1poiB 260 1.44e+01 1poiB c.63.1.3 34155 1j0aA 325 1.45e+01 c.79.1.1 83871 1dd9A 338 1.46e+01 1dd9A e.13.1.1 43254 1pkhA 204 1.47e+01 1d4aA 273 1.48e+01 1d4aA c.23.5.3 31219 1fyeA 229 1.52e+01 1fyeA c.23.16.4 31477 1st9A 143 1.52e+01 1e0tA 470 1.53e+01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1vi2A 300 1.54e+01 1dpgA 485 1.56e+01 1dpgA c.2.1.3 30074 d.81.1.5 39989 1l6rA 227 1.58e+01 c.108.1.10 77768 1cseI 71 1.58e+01 1egpA d.40.1.1 38559 1hgxA 183 1.59e+01 1tc1A c.61.1.1 34027 1ja1A 622 1.60e+01 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1q0rA 298 1.60e+01 1lvwA 295 1.63e+01 c.68.1.6 84723 1hl9A 449 1.64e+01 1nmoA 247 1.66e+01 1iv8A 720 1.66e+01 b.71.1.1 76842 c.1.8.1 76843 1p9qC 256 1.67e+01 1vhxA 150 1.67e+01 1uanA 227 1.68e+01 1o58A 303 1.69e+01 1i76A 163 1.70e+01 1hfc d.92.1.11 61877 1onwA 390 1.75e+01 b.92.1.7 87172 c.1.9.13 87173 1p80A 753 1.78e+01 1e5rA 290 1.81e+01 1e5rA b.82.2.4 59276 1dat 174 1.82e+01 2fha a.25.1.1 16677 1euvA 221 1.90e+01 1euvA d.3.1.7 37133 1rwiA 270 1.92e+01 1b4kA 337 1.93e+01 1b4kA c.1.10.3 29184 1hjzA 192 1.95e+01 c.50.1.2 83520 1tfr 305 1.97e+01 1tfr a.60.7.1 18081 c.120.1.2 33351 1f8yA 157 1.99e+01 1f8xA c.23.14.1 31395 3mag 307 1.99e+01 3mag c.66.1.25 34205 1ji7A 89 2.00e+01 a.60.1.1 71682 1rcd 173 2.00e+01 2fha a.25.1.1 16687 1gnd 447 2.01e+01 1gnd c.3.1.3 30423 d.16.1.6 37987 1f2rI 100 2.03e+01 1c9fA d.15.2.1 37641 1n2eA 300 2.05e+01 c.26.1.4 85268 5reqA 727 2.05e+01 1reqA c.1.19.1 29632 c.23.6.1 31259 1ilr1 152 2.06e+01 1irp 1l7mA 211 2.08e+01 c.108.1.4 73664 1v6sA 390 2.17e+01 1f8eA 388 2.20e+01 2qwc b.68.1.1 59694 1reqA 727 2.20e+01 1reqA c.1.19.1 29620 c.23.6.1 31247 8abp 306 2.20e+01 8abp c.93.1.1 35647 1ag9A 175 2.21e+01 1rcf c.23.5.1 31178 1h8dH 260 2.25e+01 5ptp 1fcqA 350 2.26e+01 c.1.8.9 65006 1q45A 391 2.27e+01 1iz0A 302 2.29e+01 b.35.1.2 83821 c.2.1.1 83822 1ogdA 131 2.30e+01 1i7qB 193 2.35e+01 1qdlB c.23.16.1 61902 1jx4A 352 2.35e+01 e.8.1.5 67405 1g2qA 187 2.39e+01 c.61.1.1 65117 1htqA 477 2.40e+01 d.15.9.1 71035 d.128.1.1 71036 1t2aA 375 2.40e+01 1k5cA 335 2.42e+01 b.80.1.3 72076 1fc4A 401 2.45e+01 1bs0A c.67.1.4 59760 1o4vA 183 2.45e+01 c.23.8.1 86628 1iw7C 1119 2.45e+01 e.29.1.1 71474 1rkd 309 2.47e+01 1rkd c.72.1.1 34928 1obfO 335 2.51e+01 c.2.1.3 86768 d.81.1.1 86769 1kekA 1231 2.53e+01 c.36.1.8 68524 c.36.1.12 68525 c.48.1.3 68526 c.64.1.1 68527 d.58.1.5 68528 1ijgA 309 2.54e+01 1fouA e.27.1.1 62493 1r2rA 248 2.58e+01 1p2fA 220 2.59e+01 a.4.6.1 87720 c.23.1.1 87721 1jmxA 494 2.62e+01 a.3.1.7 66901 a.3.1.7 66902 b.1.18.14 66903 b.1.18.14 66904 b.61.4.1 66905 1imbA 277 2.62e+01 1imbA e.7.1.1 42957 1nddA 76 2.64e+01 1ubi d.15.1.1 37599 1j97A 211 2.64e+01 1f5sA c.108.1.4 62753 1i1wA 303 2.64e+01 c.1.8.3 76732 12asA 330 2.67e+01 12asA d.104.1.1 40783 1kyhA 276 2.69e+01 c.72.1.4 73222 1kpgA 287 2.70e+01 c.66.1.18 68735 1o70A 324 2.72e+01 b.118.1.1 81115 b.118.1.1 81116 1jndA 420 2.73e+01 c.1.8.5 71757 d.26.3.1 71758 1bwzA 274 2.73e+01 1bwzA d.21.1.1 38337 d.21.1.1 38338 1n2aA 201 2.73e+01 1i2kA 269 2.73e+01 1jeyA 609 2.81e+01 1jeqA e.31.1.1 62924 1fnnA 389 2.81e+01 1fnnA a.4.5.11 16129 c.37.1.20 32426 1k4mA 213 2.82e+01 c.26.1.3 77258 1pz4A 116 2.85e+01 1ualA 274 2.87e+01 c.116.1.4 88383 1byqA 228 2.88e+01 1yer d.122.1.1 41100 1f4pA 147 2.90e+01 5nul c.23.5.1 59651 1msc 129 2.92e+01 1msc d.85.1.1 40039 1gadO 330 2.94e+01 1dssG c.2.1.3 29950 d.81.1.1 39865 7a3hA 303 2.98e+01 7a3hA c.1.8.3 28817 1bmv1 198 2.98e+01 1bmv1 1l6xB 34 2.99e+01 k.13.1.1 73644 1burS 123 3.01e+01 1rboC 1by2 119 3.02e+01 1by2 d.170.1.1 42452 1io2A 213 3.04e+01 1ekeA c.55.3.1 62612 2nacA 393 3.08e+01 2nadA c.2.1.4 30088 c.23.12.1 31348 1k7jA 206 3.11e+01 d.115.1.1 72103 1v4vA 376 3.11e+01 1v33A 366 3.15e+01 2hgsA 474 3.16e+01 2hgsA c.30.1.4 31722 d.142.1.6 75997 1pgl1 185 3.17e+01 1qz5A 375 3.19e+01 1t15A 214 3.24e+01 1knmA 130 3.27e+01 b.42.2.1 72781 1g5tA 196 3.28e+01 1g5rA c.37.1.11 32366 1m4jA 142 3.30e+01 d.109.1.2 78602 1r6dA 337 3.30e+01 1kmqA 184 3.30e+01 c.37.1.8 84412 1jqeA 292 3.34e+01 c.66.1.19 71789 1vpt 348 3.34e+01 3mag c.66.1.25 34207 1hdiA 413 3.35e+01 16pk c.86.1.1 60964 1qhfA 240 3.37e+01 1qhfA c.60.1.1 33960 1vjoA 393 3.37e+01 1jl0A 334 3.38e+01 1jenA d.156.1.1 63155 1ezm 301 3.39e+01 1hyt d.92.1.2 58980 1n7vA 555 3.39e+01 b.126.1.1 85377 1oi1A 221 3.41e+01 b.34.9.3 87037 b.34.9.3 87038 1lbvA 252 3.41e+01 e.7.1.1 73813 1k2xB 143 3.42e+01 1prtF 98 3.43e+01 1prtF b.40.2.1 25140 1ip9A 85 3.44e+01 1ip9A d.15.2.2 62638 1gppA 237 3.44e+01 b.86.1.2 76262 1gt91 357 3.46e+01 1f08A 148 3.48e+01 1f08A d.89.1.2 59564 1i45A 248 3.52e+01 1amk c.1.1.1 61665 1kzlA 208 3.54e+01 b.43.4.3 77635 b.43.4.3 77636 2gsaA 432 3.54e+01 2gsaA c.67.1.4 34446 1ofuA 320 3.56e+01 c.32.1.1 86972 d.79.2.1 86973 1js1X 324 3.56e+01 c.78.1.1 71834 c.78.1.1 71835 1j2rA 199 3.56e+01 1a88A 275 3.60e+01 1brt c.69.1.12 34707 1qrrA 394 3.61e+01 1qrrA c.2.1.2 29824 1sdjA 310 3.61e+01 1b0pA 1231 3.66e+01 c.36.1.8 31831 c.36.1.12 31832 c.48.1.3 33104 c.64.1.1 34157 d.58.1.5 39003 1v32A 101 3.67e+01 1qauA 112 3.75e+01 1qauA b.36.1.1 24779 1uocA 289 3.75e+01 1f3aA 222 3.75e+01 1pgtA a.45.1.1 17701 c.47.1.5 32995 1gqzA 274 3.77e+01 d.21.1.1 83311 d.21.1.1 83312 1a05A 358 3.79e+01 1cnzA c.77.1.1 35059 1neyA 247 3.80e+01 c.1.1.1 80449 1kn6A 90 3.81e+01 d.58.3.3 72770 1jbiA 100 3.81e+01 d.209.1.1 66481 1d8wA 426 3.82e+01 1de5A c.1.15.2 29394 1o5iA 249 3.82e+01 1itxA 419 3.87e+01 c.1.8.5 71425 d.26.3.1 71426 1qd1A 325 3.88e+01 1qd1A d.58.34.1 39493 d.58.34.1 39494 1nr4A 71 3.89e+01 1erzA 303 3.90e+01 1erzA d.160.1.2 59498 1amp 291 3.90e+01 1amp c.56.5.4 33837 1a8q 274 3.90e+01 1brt c.69.1.12 34702 1kid 203 3.91e+01 1derA c.8.5.1 30771 1a3c 181 3.93e+01 1a3c c.61.1.1 34095 1p35A 299 3.96e+01 1p35A b.28.1.1 23925 1xo1A 291 3.96e+01 1exnA a.60.7.1 18086 c.120.1.2 33356 1mgtA 174 3.96e+01 1mgtA a.4.2.1 16078 c.55.7.1 33753 1q0pA 223 3.98e+01 1j5xA 342 3.99e+01 c.80.1.1 71591