# List of top-scoring protein chains for t2k-100-30-near-backbone-11 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 1prxA 224 1.40e-04 1prxA c.47.1.10 33076 1prxB 224 6.91e-04 1prxA c.47.1.10 33077 1v3wA 173 2.34e-02 b.81.1.5 -4815 1qmvA 197 4.14e-02 1qq2A c.47.1.10 33066 1ex7A 186 5.38e-02 1gky c.37.1.1 59537 1gky 187 8.56e-02 1gky c.37.1.1 31839 1itpA 77 1.06e-01 d.58.3.2 66371 1qubA 319 4.45e-01 1qubA g.18.1.1 44863 g.18.1.1 44864 g.18.1.1 44865 g.18.1.1 44866 g.18.1.1 44867 1cqmA 101 4.54e-01 1ris d.58.14.1 39321 1n9lA 109 4.65e-01 d.110.3.6 85468 1ads 315 4.67e-01 1frb c.1.7.1 28671 1g5pA 289 4.96e-01 1cp2A c.37.1.10 32253 1fp6A 289 6.05e-01 1cp2A c.37.1.10 32243 1m6sA 347 6.47e-01 c.67.1.1 78701 1jg8A 347 8.17e-01 1jg8A c.67.1.1 62946 1louA 101 8.82e-01 1ris d.58.14.1 39323 1aye 401 9.66e-01 1aye c.56.5.1 33824 d.58.3.1 39065 2acr 315 9.73e-01 1frb c.1.7.1 28674 1ris 101 9.77e-01 1ris d.58.14.1 39314 1p5jA 372 1.04e+00 1gw5S 142 1.08e+00 d.110.4.2 70633 1guuA 52 1.09e+00 a.4.1.3 83332 1sknP 92 1.13e+00 1sknP a.37.1.1 17127 1vhcA 224 1.13e+00 c.1.10.1 -5488 1cds 77 1.22e+00 1cds g.7.1.3 44461 1nipA 289 1.40e+00 1cp2A c.37.1.10 32263 1pwmA 316 1.45e+00 c.1.7.1 -5232 1us0A 316 1.61e+00 c.1.7.1 -5233 1a3yA 149 1.93e+00 1obpA b.60.1.1 27110 1mqsA 671 2.01e+00 e.25.1.1 79414 1iomA 377 2.21e+00 a.103.1.1 83698 1wdcC 156 2.21e+00 1wdcC a.39.1.5 17317 1vkeA 133 2.27e+00 1kyoA 430 2.30e+00 d.185.1.1 73249 d.185.1.1 73250 1v7oA 165 2.30e+00 unknown_sccs -10249 1mbe 53 2.43e+00 1mbe a.4.1.3 16038 1faoA 126 2.59e+00 1faoA b.55.1.1 26974 1gzqA 300 2.64e+00 b.1.1.2 70818 d.19.1.1 70819 1p8cA 145 2.77e+00 unknown_sccs -1927 1el3A 316 2.88e+00 1frb c.1.7.1 28672 1kb9A 431 2.90e+00 d.185.1.1 77311 d.185.1.1 77312 1wdcB 156 2.95e+00 1wdcB a.39.1.5 17302 1eso 154 3.17e+00 1yaiA b.1.8.1 22293 1a8d 452 3.18e+00 1a8d b.29.1.6 24262 b.42.4.2 25607 1g61A 228 3.35e+00 1g61A d.126.1.1 41126 1s4qA 228 3.58e+00 c.37.1.1 -6975 1ezvA 430 3.70e+00 1be3A d.185.1.1 59541 d.185.1.1 59542 1diwA 441 3.70e+00 1a8d b.29.1.6 24264 b.42.4.2 25609 1eulA 994 3.71e+00 1eulA 1frb 315 3.80e+00 1frb c.1.7.1 28665 1dzkA 157 3.93e+00 1obpA b.60.1.1 27096 2abk 211 3.96e+00 2abk a.96.1.1 18743 1is1A 185 4.08e+00 d.67.3.1 83704 1fxrA 64 4.19e+00 1fxd d.58.1.4 38993 1m12A 84 4.36e+00 a.64.1.1 84745 1cdq 77 4.39e+00 1cds g.7.1.3 44459 5nseA 444 4.40e+00 d.174.1.1 74644 1pz1A 333 4.53e+00 c.1.7.1 -5255 1rh6A 55 4.64e+00 1a80 277 4.92e+00 1frb c.1.7.1 28700 1d0hA 469 4.93e+00 1a8d b.29.1.6 24265 b.42.4.2 25610 1okrA 123 5.00e+00 unknown_sccs -235 1kigI 60 5.01e+00 1kigI g.8.1.2 44567 1qwkA 317 5.03e+00 c.1.7.1 -5237 1lw6I 64 5.08e+00 d.40.1.1 74294 1ed5A 444 5.23e+00 1nseA d.174.1.1 42530 1pvaA 110 5.27e+00 1a75A a.39.1.4 17207 1qo7A 394 5.52e+00 1qo7A c.69.1.11 34697 1kqaA 203 5.63e+00 b.81.1.3 72868 1krrA 203 5.65e+00 b.81.1.3 72899 1t6aA 126 5.70e+00 1d1vA 444 5.71e+00 1nseA d.174.1.1 59101 1fjgM 126 5.86e+00 1fjfM a.156.1.1 16293 1i4jA 110 5.87e+00 d.55.1.1 76734 1p3jA 217 6.01e+00 c.37.1.1 -6996 g.41.2.1 -12769 1rpl 251 6.09e+00 1bpyA a.60.12.1 75933 d.218.1.2 75934 1dax 64 6.12e+00 1fxd d.58.1.4 38996 2afpA 129 6.22e+00 2afpA d.169.1.1 42349 1sedA 117 6.65e+00 1nseA 444 6.80e+00 1nseA d.174.1.1 42534 1gw5A 621 6.96e+00 a.118.1.10 70629 1hfx 123 7.03e+00 3lzt d.2.1.2 36600 1su4A 994 7.11e+00 b.82.7.1 -4927 c.108.1.7 -6854 d.220.1.1 -11668 f.33.1.1 -12333 1d0cA 444 7.41e+00 d.174.1.1 64769 1qhqA 140 7.55e+00 1qhqA b.6.1.1 63326 1gvdA 52 7.68e+00 a.4.1.3 83338 1hw6A 278 8.00e+00 1frb c.1.7.1 61296 1myn 44 8.18e+00 1gpt g.3.7.4 44172 1eudA 311 8.39e+00 2scuA c.2.1.8 30312 c.23.4.1 31140 1pm6A 72 8.42e+00 a.6.1.7 -386 1cseI 71 8.53e+00 1egpA d.40.1.1 38559 1jnuA 104 8.56e+00 d.110.3.6 71762 2sniI 83 8.85e+00 2sniI d.40.1.1 38573 1s96A 219 8.87e+00 c.37.1.1 -6972 1cdp 109 9.28e+00 1a75A a.39.1.4 17197 1uxc 65 9.31e+00 1uxc a.35.1.5 17119 1o7xD 377 9.76e+00 a.103.1.1 81174 1q53A 112 1.03e+01 d.58.4.4 -9944 1gr8A 412 1.04e+01 1bpb 248 1.05e+01 1bpyA a.60.12.1 75811 d.218.1.2 75812 1bd8 156 1.07e+01 1bd8 d.211.1.1 19157 1lddA 74 1.07e+01 a.4.5.34 73841 1ockA 412 1.07e+01 c.117.1.1 86802 1sro 76 1.11e+01 1sro b.40.4.5 25327 1jqaA 370 1.12e+01 e.22.1.2 67085 1bxeA 113 1.14e+01 1bxeA d.55.1.1 38898 1ibrB 462 1.15e+01 1qgrA a.118.1.1 19120 1l6oA 95 1.16e+01 b.36.1.1 84534 1adeA 431 1.18e+01 1adeA c.37.1.10 32213 1qf5A 431 1.18e+01 1adeA c.37.1.10 32212 1om4A 422 1.20e+01 d.174.1.1 87067 1jnyA 435 1.21e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1gks 78 1.22e+01 1cc5 a.3.1.1 15909 1pbjA 125 1.24e+01 d.37.1.1 -9608 d.37.1.1 -9609 1d0dA 60 1.29e+01 1kigI g.8.1.2 44566 1v2bA 177 1.33e+01 1b9oA 123 1.36e+01 3lzt d.2.1.2 36597 1egpA 45 1.37e+01 1egpA d.40.1.1 38561 1j93A 353 1.38e+01 c.1.22.1 66454 1ktbA 405 1.39e+01 b.71.1.1 72960 c.1.8.1 72961 1zin 217 1.39e+01 1zin c.37.1.1 31915 g.41.2.1 45178 1q4rA 112 1.46e+01 d.58.4.4 -9943 1coaI 64 1.48e+01 2sniI d.40.1.1 38574 1bpyA 335 1.52e+01 1bpyA a.60.6.1 17980 a.60.12.1 75819 d.218.1.2 75820 1gqiA 708 1.52e+01 c.1.8.10 76279 d.92.2.2 76280 1gxjA 186 1.55e+01 d.215.1.1 70707 1dfd 64 1.56e+01 1fxd d.58.1.4 38995 1hruA 188 1.57e+01 1hruA d.115.1.1 40926 1m3yA 413 1.61e+01 b.121.2.3 78579 b.121.2.3 78580 1aoiB 87 1.62e+01 1aoiB a.22.1.1 16470 1lx8A 55 1.62e+01 a.6.1.7 84734 1p35A 299 1.63e+01 1p35A b.28.1.1 23925 1nb9A 147 1.66e+01 b.43.5.1 85515 1ek8A 185 1.70e+01 1ek8A d.67.3.1 59444 1lliA 92 1.71e+01 1lmb3 a.35.1.2 17025 1hml 142 1.72e+01 3lzt d.2.1.2 36598 1nom 248 1.73e+01 1bpyA a.60.12.1 75929 d.218.1.2 75930 1n81A 186 1.75e+01 a.185.1.1 85388 1aoiF 87 1.75e+01 1aoiB a.22.1.1 16471 1oi1A 221 1.76e+01 b.34.9.3 87037 b.34.9.3 87038 1ed1A 135 1.79e+01 1hiwA a.61.1.1 18130 1tfe 145 1.79e+01 1tfe d.43.1.1 38680 1ls6A 295 1.80e+01 c.37.1.5 -7026 1k3lA 221 1.81e+01 a.45.1.1 77229 c.47.1.5 77230 1tap 60 1.82e+01 1kigI g.8.1.2 44569 1r1bA 59 1.83e+01 1r1bA a.16.1.3 16396 1o7bT 98 1.84e+01 d.169.1.4 -11647 1ocyA 198 1.87e+01 d.231.1.1 86817 1kx5B 102 1.90e+01 a.22.1.1 77594 1br1B 150 1.99e+01 1wdcC a.39.1.5 17309 1ksyA 154 2.04e+01 d.89.1.2 72948 1ghhA 81 2.07e+01 1ghhA d.57.1.1 38940 1uxd 65 2.08e+01 1uxc a.35.1.5 17118 2xat 212 2.11e+01 2xat b.81.1.3 28058 1dlyA 164 2.13e+01 1dlyA a.1.1.1 14983 1k3yA 221 2.15e+01 a.45.1.1 77245 c.47.1.5 77246 1l0wA 580 2.16e+01 b.40.4.1 73426 d.74.4.1 73427 d.104.1.1 73428 1o7xB 377 2.17e+01 a.103.1.1 81172 1ggzA 148 2.20e+01 a.39.1.5 70176 1jqnA 883 2.20e+01 c.1.12.3 77159 1ctf 74 2.21e+01 1ctf d.45.1.1 38759 4ts1A 319 2.24e+01 2ts1 c.26.1.1 31565 1r9wA 145 2.24e+01 d.89.1.2 -10511 1f3aA 222 2.24e+01 1pgtA a.45.1.1 17701 c.47.1.5 32995 1ndbA 596 2.25e+01 c.43.1.3 80411 c.43.1.3 80412 1o7xC 377 2.27e+01 a.103.1.1 81173 1pyfA 312 2.30e+01 c.1.7.1 -5251 1fshA 105 2.32e+01 1fshA a.4.5.31 60006 1cch 82 2.33e+01 451c a.3.1.1 15902 1b43A 340 2.40e+01 1a76 a.60.7.1 18092 c.120.1.2 33362 1ppjA 446 2.41e+01 1fc2C 58 2.42e+01 1fc2C a.8.1.1 16345 1a5j 110 2.45e+01 1a5j a.4.1.3 16043 a.4.1.3 16044 1r4gA 53 2.47e+01 unknown_sccs -428 1gdvA 85 2.48e+01 1ctj a.3.1.1 60458 1fo1A 271 2.50e+01 1fo1A c.10.2.3 30869 d.58.7.2 39213 1e9gA 286 2.51e+01 1wgjA b.40.5.1 59393 1top 162 2.51e+01 1ncx a.39.1.5 17223 1avsA 90 2.53e+01 1cll a.39.1.5 17226 1wgjA 286 2.56e+01 1wgjA b.40.5.1 25397 1hcrA 52 2.56e+01 1hcrA a.4.1.2 16020 1hn0A 1021 2.58e+01 a.102.3.2 83616 b.18.1.17 83617 b.24.1.1 83618 b.30.5.2 83619 2gmfA 127 2.58e+01 2gmfA a.26.1.2 16849 1gxlA 213 2.62e+01 d.215.1.1 70713 1j09A 468 2.72e+01 a.97.1.1 77025 c.26.1.1 77026 1oyjA 231 2.73e+01 a.45.1.1 87597 c.47.1.5 87598 1eljA 381 2.73e+01 4mbp c.94.1.1 35791 1v3vA 333 2.75e+01 1iuqA 367 2.78e+01 c.112.1.1 -8440 1fe6C 52 2.81e+01 1fe6C h.1.19.1 45664 1qb4A 883 2.81e+01 c.1.12.3 74640 1pmt 203 2.82e+01 1a0fA a.45.1.1 17740 c.47.1.5 33034 1fmjA 351 2.85e+01 c.37.1.5 59879 1onqA 283 2.90e+01 b.1.1.2 -2640 d.19.1.1 -9390 1bxvA 91 2.91e+01 1aac b.6.1.1 22875 1ilr1 152 2.93e+01 1irp 1d2tA 231 2.93e+01 1d2tA a.111.1.1 19052 1fiy 883 2.94e+01 1fiy c.1.12.3 29307 1iweA 457 2.95e+01 c.37.1.10 71486 1k3eA 156 3.04e+01 d.198.1.1 68103 1hgxA 183 3.05e+01 1tc1A c.61.1.1 34027 1euaA 213 3.18e+01 1fwrA c.1.10.1 29155 1uuhA 159 3.18e+01 d.169.1.4 -11651 1o6lA 337 3.18e+01 d.144.1.7 81092 1qwdA 177 3.20e+01 b.60.1.1 -4455 1ncx 162 3.21e+01 1ncx a.39.1.5 17222 8prkA 287 3.26e+01 1wgjA b.40.5.1 25395 1bjoA 360 3.28e+01 1bjnA c.67.1.4 34471 1g33A 73 3.32e+01 a.39.1.4 65121 1jj2O 148 3.41e+01 1ffkM a.94.1.1 63100 1j5qA 437 3.49e+01 b.121.2.3 77084 b.121.2.3 77085 1f08A 148 3.49e+01 1f08A d.89.1.2 59564 1iraX 152 3.49e+01 1irp b.42.1.2 25556 1faeA 629 3.50e+01 1fce a.102.1.2 18837 1obfO 335 3.51e+01 c.2.1.3 86768 d.81.1.1 86769 1fce 629 3.52e+01 1fce a.102.1.2 18836 1eexG 173 3.53e+01 1dioG a.23.2.1 16490 4cpv 109 3.53e+01 1a75A a.39.1.4 17198 1ljrA 244 3.57e+01 1ljrA a.45.1.1 17707 c.47.1.5 33001 1g9gA 629 3.60e+01 a.102.1.2 83279 1llp 343 3.61e+01 1arv a.93.1.1 18578 1fq0A 213 3.62e+01 1fwrA c.1.10.1 29161 1eucA 311 3.70e+01 2scuA c.2.1.8 30311 c.23.4.1 31139 1xat 212 3.73e+01 2xat b.81.1.3 28059 1nofA 383 3.78e+01 b.71.1.2 -4668 c.1.8.3 -5339 1gvnA 90 3.80e+01 a.8.2.1 76353 1s72P 149 3.88e+01 1booA 323 3.92e+01 1booA c.66.1.11 34248 1ofuA 320 3.95e+01 c.32.1.1 86972 d.79.2.1 86973 1aquA 297 3.97e+01 1aquA c.37.1.5 31942