# List of top-scoring protein chains for t2k-w0.5 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 1c96A 753 5.26e-01 1amj c.8.2.1 30727 c.83.1.1 35403 1c97A 753 5.97e-01 1amj c.8.2.1 30731 c.83.1.1 35407 1b0mA 753 6.01e-01 1amj c.8.2.1 30722 c.83.1.1 35398 1b0jA 754 6.06e-01 1amj c.8.2.1 30719 c.83.1.1 35395 6acn 754 6.08e-01 1amj c.8.2.1 30721 c.83.1.1 35397 1ejiA 478 6.70e-01 1bj4A c.67.1.4 34475 1bjx 110 9.69e-01 1bjx c.47.1.2 32774 2bjxA 110 9.69e-01 1bjx c.47.1.2 32776 1cliA 345 9.75e-01 1cliA d.79.4.1 39816 d.139.1.1 41459 1kpsB 171 1.10e+00 a.118.12.1 68787 1e3jA 352 1.13e+00 1e3jA b.35.1.2 24765 c.2.1.1 29781 1bj4A 470 1.35e+00 1bj4A c.67.1.4 34479 1smaA 588 1.47e+00 1bvzA b.1.1.5 21854 b.71.1.1 27781 c.1.8.1 28768 1amj 754 1.50e+00 1amj c.8.2.1 30725 c.83.1.1 35401 8acn 754 1.50e+00 1amj c.8.2.1 30724 c.83.1.1 35400 1nis 754 1.53e+00 1amj c.8.2.1 30730 c.83.1.1 35406 1cj0A 470 1.67e+00 1bj4A c.67.1.4 34473 1jtrH 275 1.92e+00 1be1 137 2.22e+00 1be1 c.23.6.1 31237 1vpe 398 2.41e+00 16pk c.86.1.1 35453 1fkx 349 2.83e+00 1a4mA c.1.9.1 29018 1b1yA 500 2.87e+00 1byb c.1.8.2 28796 1a4mA 349 2.92e+00 1a4mA c.1.9.1 29014 1add 349 2.92e+00 1a4mA c.1.9.1 29020 2ada 352 2.93e+00 1a4mA c.1.9.1 29027 1fkw 349 3.27e+00 1a4mA c.1.9.1 29019 1c3pA 375 3.33e+00 1c3pA c.42.1.2 32606 1c3rA 375 3.33e+00 1c3pA c.42.1.2 32607 1kuuA 202 3.44e+00 1kj2I 277 3.63e+00 1kj3H 279 3.69e+00 1oszA 274 3.70e+00 1agdA b.1.1.2 20795 d.19.1.1 38287 1fo0H 276 3.76e+00 1agdA b.1.1.2 20797 d.19.1.1 38288 2mhaA 270 3.81e+00 1agdA b.1.1.2 20803 d.19.1.1 38291 1uip 349 3.91e+00 1a4mA c.1.9.1 29022 1d2zA 108 3.97e+00 1d2zA a.77.1.1 18437 1uio 349 4.05e+00 1a4mA c.1.9.1 29021 1qleA 538 4.33e+00 2occA f.2.1.3 43620 1fzoA 274 4.50e+00 1agdA b.1.1.2 60155 d.19.1.1 60156 1ar1A 558 4.54e+00 2occA f.2.1.3 43618 1dp4A 435 4.76e+00 1dp4A c.93.1.1 35710 1rblA 467 5.44e+00 1burA c.1.14.1 29380 d.58.9.1 39286 1f3tB 425 5.59e+00 7odcA b.49.2.1 26494 c.1.6.1 28656 2todA 425 5.64e+00 7odcA b.49.2.1 26489 c.1.6.1 28651 1rscA 472 5.69e+00 1burA c.1.14.1 29381 d.58.9.1 39287 1e9yB 569 5.82e+00 b.92.1.1 64848 c.1.9.2 64849 1fzkA 274 5.91e+00 1agdA b.1.1.2 60149 d.19.1.1 60150 1f07A 321 5.99e+00 1ezwA c.1.16.3 59560 1jdfB 442 6.04e+00 c.1.11.2 62899 d.54.1.1 62900 1e9zB 569 6.35e+00 b.92.1.1 64852 c.1.9.2 64853 1ezwA 349 6.87e+00 1ezwA c.1.16.3 29558 1ee6A 197 7.01e+00 1ee6A b.80.1.1 28024 1g67A 225 7.02e+00 c.1.3.1 60311 1g4sA 226 7.07e+00 c.1.3.1 60247 1g6cB 227 7.09e+00 c.1.3.1 60316 2tpsA 227 7.11e+00 2tpsA c.1.3.1 28591 1hz4A 373 7.11e+00 a.118.8.2 65960 1g69B 228 7.12e+00 c.1.3.1 60314 1jdfD 442 7.14e+00 c.1.11.2 62903 d.54.1.1 62904 1g20B 523 7.65e+00 1qguB c.92.2.3 35614 2minB 522 7.66e+00 1qguB c.92.2.3 35610 3minB 522 7.66e+00 1qguB c.92.2.3 35606 1jdfC 442 8.26e+00 c.1.11.2 62901 d.54.1.1 62902 1llqA 605 9.09e+00 1jdfA 442 1.00e+01 c.1.11.2 62897 d.54.1.1 62898 1edg 380 1.06e+01 1edg c.1.8.3 28807 1ibgH 217 1.06e+01 1igtB b.1.1.1 20049 b.1.1.2 21091 1gkh 87 1.14e+01 1gvp b.40.4.7 25371 1vqj 87 1.15e+01 1gvp b.40.4.7 25374 1b3bA 415 1.21e+01 1hwyA c.2.1.7 30244 c.58.1.1 33892 1ae3 86 1.22e+01 1gvp b.40.4.7 25381 1gvp 87 1.23e+01 1gvp b.40.4.7 25369 2gn5 87 1.23e+01 1gvp b.40.4.7 25386 1vqb 87 1.23e+01 1gvp b.40.4.7 25370 1mgtA 174 1.26e+01 1mgtA a.4.2.1 16078 c.55.7.1 33753 2tmgA 415 1.27e+01 1hwyA c.2.1.7 30238 c.58.1.1 33886 1gdhA 320 1.30e+01 1gdhA c.2.1.4 30095 c.23.12.1 31355 1i21A 159 1.31e+01 1i21A d.108.1.1 61549 1b26A 416 1.31e+01 1hwyA c.2.1.7 30232 c.58.1.1 33880 1ec7A 446 1.42e+01 1bqg c.1.11.2 29218 d.54.1.1 38862 1e58A 249 1.45e+01 1qhfA c.60.1.1 59262 1pviA 157 1.45e+01 3pviA c.52.1.6 33310 1dfoA 417 1.46e+01 1bj4A c.67.1.4 34480 1vqf 87 1.47e+01 1gvp b.40.4.7 25372 1fts 295 1.48e+01 1ng1 a.24.13.1 16968 c.37.1.10 32279 1vqi 87 1.56e+01 1gvp b.40.4.7 25373 1vqe 87 1.56e+01 1gvp b.40.4.7 25380 1i12A 160 1.61e+01 1i21A d.108.1.1 61515 1i1dA 161 1.61e+01 1i21A d.108.1.1 61526 1eqbB 417 1.63e+01 1bj4A c.67.1.4 34485 1vqh 87 1.68e+01 1gvp b.40.4.7 25379 1yhb 87 1.74e+01 1gvp b.40.4.7 25383 1i9cA 137 1.77e+01 1i5qB 358 1.80e+01 e.3.1.1 61821 1vqc 87 1.82e+01 1gvp b.40.4.7 25378 1eceA 358 1.83e+01 1eceA c.1.8.3 28813 1vqa 87 1.90e+01 1gvp b.40.4.7 25377 1c0dA 358 1.91e+01 1eceA c.1.8.3 28815 1vqd 87 1.92e+01 1gvp b.40.4.7 25375 1kafA 108 1.94e+01 d.199.1.1 68372 1bxnA 485 1.94e+01 1burA c.1.14.1 29376 d.58.9.1 39282 2blsA 358 1.95e+01 1gceA e.3.1.1 42747 1fsyA 358 1.95e+01 1gceA e.3.1.1 60016 1jxaA 608 1.95e+01 c.80.1.1 67407 d.153.1.1 67408 1avaA 403 1.96e+01 1jdc b.71.1.1 27797 c.1.8.1 28784 1ccwA 137 1.97e+01 1be1 c.23.6.1 31238 1kvlA 358 2.00e+01 1b1a 137 2.01e+01 1be1 c.23.6.1 31242 1hqtA 326 2.04e+01 1frb c.1.7.1 61156 1cwn 324 2.05e+01 1frb c.1.7.1 28686 1ae4 325 2.05e+01 1frb c.1.7.1 28689 1ryt 190 2.06e+01 1ryt a.25.1.1 16646 g.41.5.1 45245 1b71A 191 2.07e+01 1ryt a.25.1.1 16647 g.41.5.1 45246 1dvbA 191 2.07e+01 1ryt a.25.1.1 16645 g.41.5.1 45244 1jecA 510 2.09e+01 b.58.1.2 66595 c.26.1.5 66596 c.37.1.15 66597 1vqg 87 2.09e+01 1gvp b.40.4.7 25376 1jctA 446 2.12e+01 c.1.11.2 62882 d.54.1.1 62883 1i2rA 316 2.18e+01 1onrA c.1.10.1 61580 1jtdB 273 2.20e+01 b.69.5.2 67265 1bic 260 2.20e+01 2cba b.74.1.1 27854 1g8fA 511 2.28e+01 1g8fA b.58.1.2 60348 c.26.1.5 60349 c.37.1.15 60350 2pviA 157 2.30e+01 3pviA c.52.1.6 33302 1gaxA 862 2.32e+01 1gaxA a.27.1.1 16928 b.51.1.1 26893 c.26.1.1 31595 1earA 147 2.33e+01 b.107.1.1 64875 d.58.38.1 64876 1b0aA 288 2.40e+01 1a4iA c.2.1.7 30286 c.58.1.2 33934 1i1iP 681 2.43e+01 1i1iP d.92.1.5 40297 1dtn 359 2.44e+01 2mnr c.1.11.2 29249 d.54.1.1 38893 1kgsA 225 2.49e+01 a.4.6.1 68596 c.23.1.1 68597 1bymA 97 2.52e+01 1bi0 b.34.1.2 24458 1nfp 228 2.52e+01 1nfp c.1.16.2 29555 1tpwA 247 2.57e+01 1amk c.1.1.1 28449 1al7 359 2.58e+01 1gox c.1.4.1 28609 1tpc1 247 2.59e+01 1amk 1fcnB 358 2.62e+01 1gceA e.3.1.1 42752 1k8kC 372 2.62e+01 b.69.4.1 68308 3pviA 157 2.63e+01 3pviA c.52.1.6 33300 1g5cA 170 2.64e+01 1g5cA c.53.2.1 60264 1gox 369 2.65e+01 1gox c.1.4.1 28607 1mdl 359 2.66e+01 2mnr c.1.11.2 29247 d.54.1.1 38891 1gylA 369 2.66e+01 1gox c.1.4.1 28610 2mnr 357 2.75e+01 2mnr c.1.11.2 29245 d.54.1.1 38889 1mdr 359 2.76e+01 2mnr c.1.11.2 29248 d.54.1.1 38892 1pgjA 478 2.77e+01 2pgd a.100.1.1 18783 c.2.1.6 30195 1e19A 314 2.79e+01 1b7bA c.73.1.1 34967 3adk 195 2.80e+01 1zin c.37.1.1 31885 1bwkA 399 2.81e+01 1oyc c.1.4.1 28605 1i58A 189 2.86e+01 1b3qA d.122.1.3 61773 1bwvA 493 2.88e+01 1burA c.1.14.1 29372 d.58.9.1 39278 1bwlA 399 2.92e+01 1oyc c.1.4.1 28606 1i5dA 191 2.93e+01 1b3qA d.122.1.3 61783 1jehB 478 2.94e+01 c.3.1.5 62915 c.3.1.5 62916 d.87.1.1 62917 2hrvA 142 2.95e+01 2hrvA b.47.1.4 26429 1nal1 297 2.96e+01 1nal3 1nal3 297 2.96e+01 1nal3 1qnxA 209 3.01e+01 1qnxA d.111.1.1 40914 1fziA 527 3.09e+01 1mhyD a.25.1.2 60140 1fdyA 297 3.10e+01 1nal3 c.1.10.1 29071 1k03A 399 3.11e+01 c.1.4.1 63322 1dkrA 317 3.18e+01 1dkuA c.61.1.2 34114 c.61.1.2 34115 1dkuA 317 3.18e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1qh8A 478 3.27e+01 1qguA c.92.2.3 35633 1qguA 478 3.27e+01 1qguA c.92.2.3 35625 1i2nA 316 3.29e+01 1onrA c.1.10.1 61572 1efuA 385 3.29e+01 1efcA b.43.3.1 25682 b.44.1.1 25722 c.37.1.8 32115 1i2pA 316 3.30e+01 1onrA c.1.10.1 61576 1mtyD 512 3.33e+01 1mhyD a.25.1.2 16742 1mmoD 512 3.33e+01 1mhyD a.25.1.2 16770 1i2oA 316 3.33e+01 1onrA c.1.10.1 61574 1oya 400 3.35e+01 1oyc c.1.4.1 28604 1oyc 400 3.35e+01 1oyc c.1.4.1 28603 1oaa 259 3.36e+01 1oaa c.2.1.2 29829 1emsA 440 3.37e+01 1emsA d.13.1.1 37520 d.160.1.1 42086 1sep 261 3.38e+01 1oaa c.2.1.2 29830 1onrA 316 3.41e+01 1onrA c.1.10.1 29169 1cd31 152 3.46e+01 1cd31 1ecmA 109 3.46e+01 1ecmA a.130.1.1 19492 1ucwA 317 3.47e+01 1onrA c.1.10.1 29171 1li5A 461 3.49e+01 1c16A 260 3.49e+01 1agdA b.1.1.2 20856 d.19.1.1 38320 1efcA 393 3.51e+01 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1d8tA 393 3.52e+01 1efcA b.43.3.1 25686 b.44.1.1 25726 c.37.1.8 32119 1dg1G 394 3.57e+01 1efcA b.43.3.1 25684 b.44.1.1 25724 c.37.1.8 32117 1moq 368 3.64e+01 1moq c.80.1.1 35302 1pymA 295 3.73e+01 1pymA c.1.12.4 29308 1g8mA 593 3.73e+01 1g8mA c.24.1.3 60371 c.97.2.1 60372 1pvuA 154 3.76e+01 3pviA c.52.1.6 33306 1huvA 380 3.82e+01 c.1.4.1 61277 1aiv 686 3.86e+01 1nnt c.94.1.2 35885 c.94.1.2 35886 1eqjA 511 3.98e+01 1ejjA c.105.1.1 59495 c.76.1.3 59496 1ejjA 511 3.98e+01 1ejjA c.105.1.1 59422 c.76.1.3 59423