# List of top-scoring protein chains for t2k-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 1i9yA 347 4.29e-65 1i9yA d.151.1.2 62101 1i9zA 347 5.07e-65 1i9yA d.151.1.2 62102 1ako 268 6.80e-08 1ako d.151.1.1 41779 1hd7A 318 3.56e-05 1bix d.151.1.1 41780 1bix 287 8.93e-05 1bix d.151.1.1 41781 3dni 260 1.73e-04 3dni d.151.1.1 41791 2dnjA 260 4.12e-04 3dni d.151.1.1 41790 1qmuA 380 2.40e-01 1qmuA b.3.2.1 22534 c.56.5.1 33827 1bhjA 292 4.85e-01 1xvaA c.66.1.5 34189 1jnyA 435 6.40e-01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1xvaA 292 6.49e-01 1xvaA c.66.1.5 34183 1g6aA 271 6.50e-01 1btl e.3.1.1 42704 1ppo 216 9.31e-01 1cs8A d.3.1.1 37020 1ckmA 330 9.38e-01 1ckmA b.40.4.6 25358 d.142.2.3 41585 2cb5A 453 9.97e-01 3gcb d.3.1.1 37035 1cknA 330 1.08e+00 1ckmA b.40.4.6 25360 d.142.2.3 41587 8acn 754 1.41e+00 1amj c.8.2.1 30724 c.83.1.1 35400 1hurA 180 1.58e+00 1hurA c.37.1.8 32052 1qapA 296 1.65e+00 1qpoA c.1.17.1 29559 d.41.2.1 38595 1jenA 267 1.69e+00 1jenA 1pbe 394 1.70e+00 1pbe c.3.1.2 30338 d.16.1.2 37869 1jk7A 323 1.77e+00 1auiA d.159.1.3 63144 1amj 754 1.80e+00 1amj c.8.2.1 30725 c.83.1.1 35401 1memA 215 2.06e+00 1cs8A d.3.1.1 37069 1h6tA 291 2.44e+00 b.1.1.6 65686 c.10.2.1 65687 1kk1A 410 2.63e+00 1an8 208 2.83e+00 1an8 b.40.2.2 25202 d.15.6.1 37791 2phh 394 2.92e+00 1pbe c.3.1.2 30353 d.16.1.2 37884 1jl0A 334 3.12e+00 1jenA d.156.1.1 63155 2fcr 173 3.27e+00 1rcf c.23.5.1 31151 1gqpA 221 3.43e+00 1jmxA 494 3.49e+00 a.3.1.7 66901 a.3.1.7 66902 b.1.1.6 66903 b.1.1.6 66904 b.61.4.1 66905 1cb8A 678 3.77e+00 1cb8A a.102.3.2 18849 b.24.1.1 23898 b.30.3.1 24422 1k0iA 394 4.19e+00 c.3.1.2 67942 d.16.1.2 67943 1ej6A 1289 4.21e+00 i.7.1.1 45967 7acn 754 4.37e+00 1amj c.8.2.1 30717 c.83.1.1 35393 1fjmA 330 4.48e+00 1auiA d.159.1.3 42082 1bhe 376 4.67e+00 1bhe b.80.1.3 28030 1qhdA 398 4.78e+00 1qhdA a.115.1.2 63324 b.19.1.1 63325 1c96A 753 4.92e+00 1amj c.8.2.1 30727 c.83.1.1 35403 1bgj 394 4.93e+00 1pbe c.3.1.2 30352 d.16.1.2 37883 6acn 754 5.20e+00 1amj c.8.2.1 30721 c.83.1.1 35397 1ofv 169 5.26e+00 1rcf c.23.5.1 31184 1ei5A 520 5.39e+00 1ei5A b.61.3.1 27418 b.61.3.1 27419 e.3.1.1 42772 1gv9A 260 5.55e+00 1bueA 265 5.73e+00 1btl e.3.1.1 42727 1jg1A 235 5.92e+00 c.66.1.7 66661 1pjr 724 5.98e+00 1pjr c.37.1.13 32391 c.37.1.13 32392 2fox 138 6.40e+00 5nul c.23.5.1 31197 1brnL 110 6.61e+00 1b20A d.1.1.1 36143 1cznA 169 6.82e+00 1rcf c.23.5.1 31181 2bpa1 426 6.83e+00 2bpa1 1bolA 222 7.14e+00 1bolA d.124.1.1 41120 1gkuB 1054 7.22e+00 c.37.1.16 65257 c.37.1.16 65258 e.10.1.1 65259 1j9jA 247 7.23e+00 c.106.1.1 62758 1gp4A 356 7.27e+00 b.82.2.1 65439 1gp6A 356 7.39e+00 b.82.2.1 65441 1b0jA 754 7.42e+00 1amj c.8.2.1 30719 c.83.1.1 35395 1c24A 263 7.55e+00 1c24A d.127.1.1 41148 1cs8A 316 7.68e+00 1cs8A d.3.1.1 37065 1ex2A 189 7.76e+00 1ex2A c.51.4.2 33225 1f0lA 535 7.83e+00 1ddt b.2.1.1 22377 d.166.1.1 42239 f.1.2.1 43382 1mat 264 8.02e+00 1c24A d.127.1.1 41152 1fo0A 116 8.12e+00 1tvdA b.1.1.1 20610 1jyhA 157 8.49e+00 1ppfE 218 9.02e+00 1a7s b.47.1.2 26234 1b3qA 379 9.18e+00 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1l1nA 183 9.31e+00 1a2pA 110 9.95e+00 1b20A d.1.1.1 36140 1mpyA 307 1.02e+01 1mpyA d.32.1.3 38508 d.32.1.3 38509 3pgk 416 1.04e+01 16pk c.86.1.1 35451 1d2eA 397 1.04e+01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1gnd 447 1.05e+01 1gnd c.3.1.3 30423 d.16.1.6 37987 1k0eA 453 1.07e+01 d.161.1.1 67938 1djxB 624 1.08e+01 1djxB a.39.1.7 17343 b.7.1.1 23160 c.1.18.1 29588 1ddt 535 1.10e+01 1ddt b.2.1.1 22379 d.166.1.1 42241 f.1.2.1 43384 1ayyA 151 1.12e+01 1apyA d.153.1.5 42016 2matA 264 1.13e+01 1c24A d.127.1.1 41146 1arzC 273 1.15e+01 1drw c.2.1.3 30061 d.81.1.3 39976 1bzyA 217 1.15e+01 1qk3A c.61.1.1 34071 1eq6A 189 1.16e+01 1eq6A d.107.1.1 40796 1aogA 485 1.16e+01 3grs c.3.1.5 30517 c.3.1.5 30518 d.87.1.1 40190 1nfiC 301 1.17e+01 b.1.1.5 21943 b.2.5.1 22456 1efcA 393 1.17e+01 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1d5tA 433 1.17e+01 1gnd c.3.1.3 30422 d.16.1.6 37986 1fecA 490 1.20e+01 3grs c.3.1.5 30489 c.3.1.5 30490 d.87.1.1 40176 1rypH 205 1.20e+01 d.153.1.4 41876 1b06A 210 1.20e+01 1avmA a.2.11.1 15740 d.44.1.1 38737 1cipA 353 1.21e+01 1cipA a.66.1.1 18210 c.37.1.8 32093 1j8wB 273 1.21e+01 c.68.1.2 66441 1kafA 108 1.21e+01 d.199.1.1 68372 1nfiA 301 1.24e+01 1a3qA b.1.1.5 21942 b.2.5.1 22455 1l7uA 263 1.31e+01 1m40A 263 1.31e+01 1kfiA 572 1.32e+01 c.84.1.1 68555 c.84.1.1 68556 c.84.1.1 68557 d.129.2.1 68558 1aipE 405 1.32e+01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1djxA 624 1.33e+01 1djxB a.39.1.7 17342 b.7.1.1 23159 c.1.18.1 29587 1i7oA 429 1.35e+01 1i7oA d.177.1.1 61893 d.177.1.1 61894 1jjvA 206 1.37e+01 1reqD 637 1.39e+01 1reqB c.1.19.1 29623 c.23.6.1 31250 1fwxA 595 1.39e+01 b.6.1.4 60069 b.69.3.1 60070 1i7qA 519 1.39e+01 1qdlA d.161.1.1 61901 1aqzA 149 1.45e+01 1aqzA d.1.1.1 36238 1jrrA 382 1.46e+01 e.1.1.1 63256 1rnbA 110 1.47e+01 1b20A d.1.1.1 36196 1qqjA 419 1.49e+01 1qcnA b.34.8.1 59034 d.177.1.1 59035 1drw 273 1.49e+01 1drw c.2.1.3 30057 d.81.1.3 39972 5nul 138 1.53e+01 5nul c.23.5.1 31191 1f6bA 198 1.53e+01 c.37.1.8 64986 1al0F 426 1.53e+01 2bpa1 b.10.1.1 23274 1bvyF 191 1.56e+01 1bvyF c.23.5.1 31207 1qhoA 686 1.58e+01 1cxlA b.1.1.5 21844 b.3.1.1 22513 b.71.1.1 27751 c.1.8.1 28738 1cr0A 296 1.58e+01 1cr1A c.37.1.11 32287 1cd1A 315 1.60e+01 1cd1A b.1.1.2 21579 d.19.1.1 38155 1apa 266 1.61e+01 1qi7A d.165.1.1 42205 1b20A 110 1.62e+01 1b20A d.1.1.1 36207 1btl 263 1.62e+01 1btl e.3.1.1 42691 1b9lA 120 1.64e+01 1b9lA d.96.1.3 40665 1ermA 263 1.65e+01 1btl e.3.1.1 42690 1reqB 637 1.70e+01 1reqB c.1.19.1 29621 c.23.6.1 31248 1f60A 458 1.71e+01 1efcA b.43.3.1 25705 b.44.1.1 25745 c.37.1.8 32140 1ha3A 405 1.72e+01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1ddgA 374 1.72e+01 1amoA b.43.4.1 25671 c.25.1.4 31559 1bjwA 382 1.72e+01 1bjwA c.67.1.1 34349 1kas 412 1.76e+01 1dd8A c.95.1.1 35964 c.95.1.1 35965 1crzA 403 1.79e+01 1crzA b.68.4.1 27629 c.51.2.1 33211 1dpgA 485 1.80e+01 1dpgA c.2.1.3 30074 d.81.1.5 39989 1amk 251 1.81e+01 1amk c.1.1.1 28503 1inp 400 1.85e+01 1inp e.7.1.1 42972 3timA 250 1.86e+01 1amk c.1.1.1 28483 1yal 218 1.88e+01 1cs8A d.3.1.1 37025 1irqA 71 1.91e+01 a.43.1.2 66297 1jjrA 151 1.92e+01 a.140.2.1 66772 1ush 550 1.93e+01 1ush d.114.1.1 40923 d.159.1.2 42079 1rpjA 288 1.97e+01 2dri c.93.1.1 35656 1at1A 310 2.04e+01 3csuA c.78.1.1 35168 c.78.1.1 35169 1jn5A 140 2.04e+01 d.17.4.2 66921 1j9lA 247 2.04e+01 c.106.1.1 62762 1g1tA 157 2.06e+01 d.169.1.1 65104 g.3.11.1 65105 2act 220 2.09e+01 1cs8A d.3.1.1 37002 1eguA 731 2.10e+01 1eguA a.102.3.2 18850 b.24.1.1 23899 b.30.3.1 24423 1cqzA 554 2.10e+01 1cr6B c.108.1.2 43339 c.69.1.11 34689 1fo8A 343 2.12e+01 1foaA c.68.1.10 59927 1exmA 405 2.14e+01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1ek1A 554 2.15e+01 1cr6B c.108.1.2 43335 c.69.1.11 34685 1qfcA 306 2.15e+01 1uteA d.159.1.1 42077 1e54A 332 2.16e+01 1e54A f.4.3.1 59258 1qcnA 421 2.18e+01 1qcnA b.34.8.1 59017 d.177.1.1 59018 1fgxA 288 2.21e+01 1fgxA c.68.1.2 34508 1dih 273 2.22e+01 1drw c.2.1.3 30056 d.81.1.3 39971 1fzqA 181 2.22e+01 1hurA c.37.1.8 32060 1elyA 449 2.22e+01 1b8jA c.76.1.1 35028 1byqA 228 2.24e+01 1yer d.122.1.1 41100 1hyoA 421 2.25e+01 1qcnA b.34.8.1 59001 d.177.1.1 59002 1ed8A 449 2.26e+01 1b8jA c.76.1.1 34988 1fqgA 263 2.32e+01 1btl e.3.1.1 42699 1cyj 90 2.33e+01 1ctj a.3.1.1 15805 1cyi 90 2.37e+01 1ctj a.3.1.1 15804 1krs 120 2.37e+01 1krs b.40.4.1 25256 1aa6 715 2.39e+01 2napA b.52.2.2 26916 c.81.1.1 35324 1qexA 288 2.39e+01 1qexA b.32.1.1 24425 1j6wA 175 2.39e+01 1j98A d.185.1.2 62663 3csuA 310 2.42e+01 3csuA c.78.1.1 35094 c.78.1.1 35095 1fhdA 312 2.44e+01 1taxA c.1.8.3 28915 1b8jA 449 2.49e+01 1b8jA c.76.1.1 34992 1jjuA 489 2.50e+01 a.3.1.7 66774 a.3.1.7 66775 b.1.1.6 66776 b.1.1.6 66777 b.61.4.1 66778 7pcy 98 2.52e+01 1plc b.6.1.1 22863 1a3z 155 2.54e+01 1rcy b.6.1.1 23019 1jdpA 441 2.55e+01 c.93.1.1 62906 3nll 138 2.56e+01 5nul c.23.5.1 31206 1rcf 169 2.59e+01 1rcf c.23.5.1 31170 1ht9A 76 2.60e+01 4icb a.39.1.1 61252 1k0gA 453 2.60e+01 d.161.1.1 67940 2hgsA 474 2.62e+01 2hgsA c.30.1.4 31722 d.142.1.6 41575 d.142.1.6 41576 1g97A 459 2.62e+01 1fwyA b.81.1.4 60394 c.68.1.5 60395 1jjoC 261 2.62e+01 1fc6A 388 2.65e+01 1fc6A b.36.1.3 64738 c.14.1.2 64739 1aqzB 149 2.67e+01 1aqzA d.1.1.1 36239 1dp4A 435 2.74e+01 1dp4A c.93.1.1 35710 1qfxA 460 2.75e+01 1qfxA c.60.1.3 33994 1ahjB 212 2.80e+01 2ahjB b.34.4.4 24601 1b3nA 412 2.81e+01 1dd8A c.95.1.1 35966 c.95.1.1 35967 1deuA 277 2.83e+01 1theB d.3.1.1 37085 1i5pA 633 2.89e+01 1i5pA b.18.1.3 61817 b.77.2.1 61818 f.1.3.1 61819 1gdeA 389 2.90e+01 c.67.1.1 60456 1iuz 98 2.93e+01 1plc b.6.1.1 22861 1e30A 155 3.00e+01 1rcy b.6.1.1 23016 1qniA 581 3.04e+01 1qniA b.6.1.4 23042 b.69.3.1 27642 2gd1O 334 3.09e+01 1dssG c.2.1.3 29978 d.81.1.1 39893 1i1nA 226 3.10e+01 1mntA 76 3.12e+01 1bazA a.43.1.1 17453 1dfmA 223 3.12e+01 1d2iA c.52.1.5 33295 1fh9A 312 3.13e+01 1taxA c.1.8.3 28913 1dd3C 32 3.14e+01 1dd3C a.108.1.1 19033 1cgt 684 3.15e+01 1cxlA b.1.1.5 21815 b.3.1.1 22484 b.71.1.1 27722 c.1.8.1 28709 1f2aA 215 3.18e+01 1cs8A d.3.1.1 37040 1gceA 364 3.23e+01 1gceA e.3.1.1 42738 1id0A 152 3.25e+01 d.122.1.3 66111 1alkA 449 3.28e+01 1b8jA c.76.1.1 34994 1go3E 187 3.31e+01 b.40.4.5 65406 2mtaC 147 3.33e+01 2mtaC a.3.1.1 15908 1qatB 622 3.38e+01 1djxB a.39.1.7 17355 b.7.1.1 23172 c.1.18.1 29600 1icpA 376 3.41e+01 1oyc c.1.4.1 62270 1hm9A 468 3.41e+01 b.81.1.4 65866 c.68.1.5 65867 1han 297 3.42e+01 1han d.32.1.3 38506 d.32.1.3 38507 1ovaA 386 3.42e+01 1ovaA e.1.1.1 42619 1i58A 189 3.47e+01 1b3qA d.122.1.3 61773 1tpfA 250 3.48e+01 1amk c.1.1.1 28467 2fvx 138 3.53e+01 5nul c.23.5.1 31200 1fviA 297 3.59e+01 1fviA b.40.4.6 25364 d.142.2.1 41578 1d2iA 223 3.61e+01 1d2iA c.52.1.5 33297 1cr6B 554 3.61e+01 1cr6B c.108.1.2 43338 c.69.1.11 34688 1jkgA 140 3.74e+01 d.17.4.2 66795 1cseE 274 3.75e+01 1gci c.41.1.1 32481 1gpl 432 3.79e+01 1gpl b.12.1.2 23645 c.69.1.19 34793 1i6iA 366 3.88e+01 1bg2 c.37.1.9 61844 1kh5A 449 3.89e+01 2anhA 446 3.89e+01 1b8jA c.76.1.1 35004 1bouB 302 3.94e+01 1bouB c.56.6.1 33859 1dlc 584 3.98e+01 1ciy b.18.1.3 23719 b.77.2.1 27976 f.1.3.1 43391 1qpsA 261 3.98e+01 1ckqA c.52.1.1 33234 1knvA 293 3.99e+01 c.52.1.7 68707