# 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 1dciA 275 2.03e-02 1dciA c.14.1.3 30918 1mioB 458 2.32e-02 1qguB c.92.2.3 35602 1ef8A 261 2.47e-02 1ef8A c.14.1.3 30921 1hzdA 272 7.38e-02 c.14.1.3 65969 1ey3A 258 2.53e-01 c.14.1.3 64911 2dubE 261 2.54e-01 1nzyA c.14.1.3 30916 1bvuA 418 4.29e-01 1hwyA c.2.1.7 30226 c.58.1.1 33874 1eqjA 511 5.91e-01 1ejjA c.105.1.1 59495 c.76.1.3 59496 1ejjA 511 5.91e-01 1ejjA c.105.1.1 59422 c.76.1.3 59423 1rpxA 230 9.88e-01 1rpxA c.1.2.2 28536 1thfD 253 1.85e+00 1thfD c.1.2.1 28535 1csbB 205 1.96e+00 1theB 1gpwC 253 2.19e+00 c.1.2.1 65462 1d2eA 397 2.34e+00 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1mpp 361 2.73e+00 2rmpA b.50.1.2 26856 1qdqA 253 3.00e+00 1theB d.3.1.1 37064 1mirA 322 3.20e+00 1theB d.3.1.1 37062 1k3fA 253 3.72e+00 c.56.2.1 68105 1lx7A 253 3.82e+00 1kk0A 410 3.94e+00 1nzyB 269 3.94e+00 1nzyA c.14.1.3 30904 1cteB 254 4.11e+00 1theB d.3.1.1 37059 2csn 297 4.19e+00 1csn d.144.1.1 41665 1csn 298 4.23e+00 1csn d.144.1.1 41664 1theB 260 4.26e+00 1theB d.3.1.1 37057 1theA 260 4.26e+00 1theB d.3.1.1 37056 1jdbF 382 4.44e+00 c.8.3.1 30757 c.23.16.1 31434 1kk3A 410 4.58e+00 1c3oB 382 4.75e+00 1c3oB c.8.3.1 30744 c.23.16.1 31421 1cs0B 382 4.75e+00 1c3oB c.8.3.1 30740 c.23.16.1 31417 1gtmA 419 4.78e+00 1hwyA c.2.1.7 30223 c.58.1.1 33871 1a9xB 379 4.99e+00 1c3oB c.8.3.1 30732 c.23.16.1 31409 1k4iA 233 5.26e+00 2fgwH 232 5.27e+00 1gc1H b.1.1.1 19855 b.1.1.2 20957 1seiA 130 5.28e+00 1seiA d.140.1.1 41463 1kk1A 410 5.52e+00 1dtwA 400 5.55e+00 1qs0A c.36.1.3 31827 1hv8A 367 5.98e+00 1hv8A c.37.1.13 32405 c.37.1.13 32406 3dbvO 334 6.19e+00 1dssG c.2.1.3 29982 d.81.1.1 39897 1ftaA 337 6.48e+00 1frpA e.7.1.1 42934 1b4wA 122 6.93e+00 1poa a.133.1.2 19536 1efm 393 7.35e+00 1efcA c.37.1.8 64732 1etu 394 7.55e+00 1efcA c.37.1.8 64737 1bfd 528 7.80e+00 1bfd c.31.1.3 31745 c.36.1.1 31801 c.36.1.1 31802 1dtyA 429 8.11e+00 1dtyA c.67.1.4 34495 1qj5A 429 8.17e+00 1dtyA c.67.1.4 34493 1lgyA 269 8.26e+00 3tgl c.69.1.17 34758 1fchA 368 8.53e+00 1fchA a.118.8.1 19212 1efcA 393 8.60e+00 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1d8tA 393 8.60e+00 1efcA b.43.3.1 25686 b.44.1.1 25726 c.37.1.8 32119 1dg1G 394 8.60e+00 1efcA b.43.3.1 25684 b.44.1.1 25724 c.37.1.8 32117 1efuA 385 8.63e+00 1efcA b.43.3.1 25682 b.44.1.1 25722 c.37.1.8 32115 1hnuA 280 8.66e+00 1hnoA c.14.1.3 61096 1hnoA 280 8.66e+00 1hnoA c.14.1.3 61095 1othA 321 8.87e+00 1othA c.78.1.1 35260 c.78.1.1 35261 1b23P 405 8.95e+00 1efcA b.43.3.1 25689 b.44.1.1 25729 c.37.1.8 32124 3cox 507 9.16e+00 1b8sA c.3.1.2 30332 d.16.1.1 37863 1jxzB 269 9.29e+00 c.14.1.3 67436 1exmA 405 9.46e+00 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1ha3A 405 9.46e+00 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1aipE 405 9.48e+00 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1nzyA 269 1.02e+01 1nzyA c.14.1.3 30903 1qgc2 218 1.02e+01 1qqp2 1eft 405 1.03e+01 1efcA b.43.3.1 25688 b.44.1.1 25728 c.37.1.8 32123 1ex7A 186 1.03e+01 1gky c.37.1.1 59537 1gky 187 1.03e+01 1gky c.37.1.1 31839 1qqp2 218 1.06e+01 1qqp2 1ekqA 272 1.08e+01 1c3qA c.72.1.2 34941 1dbp 271 1.09e+01 2dri c.93.1.1 35639 1c3qA 272 1.10e+01 1c3qA c.72.1.2 34948 1esjA 284 1.17e+01 1c3qA c.72.1.2 34943 1k3bB 164 1.19e+01 1cf7B 95 1.22e+01 1cf7B a.4.5.17 16152 1gjyA 167 1.26e+01 3pbh 317 1.26e+01 1theB d.3.1.1 37053 1g3qA 237 1.26e+01 1hyqA c.37.1.10 60237 1dysA 348 1.28e+01 1bvwA c.6.1.1 30669 1dosA 358 1.28e+01 1dosA c.1.10.2 29175 1srvA 145 1.29e+01 1derA c.8.5.1 30817 1b57A 358 1.33e+01 1dosA c.1.10.2 29177 1gs5A 258 1.34e+01 1gbnA 402 1.35e+01 2dkb c.67.1.4 34455 2oatA 439 1.37e+01 2dkb c.67.1.4 34452 1oatA 439 1.37e+01 2dkb c.67.1.4 34461 1lmhA 184 1.42e+01 8pchA 220 1.52e+01 1cs8A d.3.1.1 37084 1dz4A 414 1.54e+01 1phd a.104.1.1 18903 1euzE 419 1.55e+01 1k89 c.2.1.7 59521 c.58.1.1 59522 3hadA 308 1.55e+01 2hdhA a.100.1.3 18799 c.2.1.6 30203 7odcA 424 1.61e+01 7odcA b.49.2.1 26488 c.1.6.1 28650 1d7kA 421 1.62e+01 7odcA b.49.2.1 26486 c.1.6.1 28648 1juoB 198 1.62e+01 a.39.1.8 67313 1j51A 414 1.64e+01 a.104.1.1 66393 1il0A 302 1.65e+01 a.100.1.3 66189 c.2.1.6 66190 1f0yA 302 1.67e+01 2hdhA a.100.1.3 18793 c.2.1.6 30197 1id0A 152 1.68e+01 d.122.1.3 66111 1cknB 330 1.69e+01 1ckmA b.40.4.6 25361 d.142.2.3 41588 1cknA 330 1.70e+01 1ckmA b.40.4.6 25360 d.142.2.3 41587 1ckmA 330 1.70e+01 1ckmA b.40.4.6 25358 d.142.2.3 41585 1qmqA 414 1.72e+01 1phd a.104.1.1 18907 1kk6B 209 1.73e+01 b.81.1.3 68658 1jah 166 1.75e+01 1ctqA c.37.1.8 31972 1drk 271 1.75e+01 2dri c.93.1.1 35638 2dri 271 1.78e+01 2dri c.93.1.1 35637 1phb 414 1.78e+01 1phd a.104.1.1 18906 1phd 414 1.78e+01 1phd a.104.1.1 18913 1phg 414 1.78e+01 1phd a.104.1.1 18910 5cpp 414 1.78e+01 1phd a.104.1.1 18935 1drj 271 1.78e+01 2dri c.93.1.1 35642 1iwiA 415 1.78e+01 1iwkA 415 1.79e+01 1c8jA 414 1.80e+01 1phd a.104.1.1 59085 1bkdS 439 1.81e+01 1bkdS a.117.1.1 19111 1npsA 88 1.83e+01 1prs b.11.1.1 23622 1iwjA 415 1.84e+01 1ar72 272 1.84e+01 1aym2 1aop 497 1.87e+01 2aop d.58.36.1 39501 d.58.36.1 39502 d.134.1.1 41425 d.134.1.1 41426 2aop 497 1.87e+01 2aop d.58.36.1 39503 d.58.36.1 39504 d.134.1.1 41427 d.134.1.1 41428 1j4wA 174 1.87e+01 1ihmA 530 1.90e+01 1ihmA b.10.1.4 62385 1gof 639 1.91e+01 1gof b.1.1.5 21807 b.18.1.1 23709 b.69.1.1 27631 1goh 639 1.91e+01 1gof b.1.1.5 21809 b.18.1.1 23711 b.69.1.1 27633 1egeA 396 1.92e+01 3mdeA a.29.3.1 16604 e.6.1.1 42865 1dp4A 435 1.93e+01 1dp4A c.93.1.1 35710 1qksA 567 1.94e+01 1qksA a.3.1.2 15951 b.70.2.1 27710 1aoqA 567 1.94e+01 1qksA a.3.1.2 15934 b.70.2.1 27692 1aomA 567 1.94e+01 1qksA b.70.2.1 27694 1gebA 415 1.95e+01 1phd a.104.1.1 18932 1k3iA 656 1.95e+01 b.1.1.5 68113 b.18.1.1 68114 b.69.1.1 68115 1yna 194 1.98e+01 1axkA b.29.1.11 24335 1dw9A 156 2.00e+01 1dw9A a.35.1.4 17065 d.72.1.1 39596 1dwkA 156 2.00e+01 1dw9A a.35.1.4 17075 d.72.1.1 39606 1egdA 396 2.00e+01 3mdeA a.29.3.1 16596 e.6.1.1 42857 721p 166 2.02e+01 1ctqA c.37.1.8 31975 1cp3A 277 2.04e+01 1pauA c.17.1.1 30992 1f17A 310 2.04e+01 2hdhA a.100.1.3 18797 c.2.1.6 30201 1eah2 271 2.08e+01 1aym2 1ie7C 570 2.09e+01 1ubpC b.92.1.1 62315 c.1.9.2 62316 4ubpC 570 2.09e+01 1ubpC b.92.1.1 28431 c.1.9.2 29053 1ubpC 570 2.09e+01 1ubpC b.92.1.1 28432 c.1.9.2 29054 1gsjA 258 2.16e+01 1l8pA 436 2.21e+01 1oneA 436 2.24e+01 4enl c.1.11.1 29200 d.54.1.1 38844 2oneA 436 2.24e+01 4enl c.1.11.1 29203 d.54.1.1 38847 4enl 436 2.24e+01 4enl c.1.11.1 29202 d.54.1.1 38846 521p 166 2.26e+01 1ctqA c.37.1.8 31992 1gi8B 245 2.27e+01 1gi7B 245 2.27e+01 1hxs2 272 2.32e+01 1dgi2 268 2.32e+01 1hzgA 295 2.35e+01 1hzgA d.194.1.1 61436 1ba2A 271 2.36e+01 2dri c.93.1.1 35640 1gj7B 253 2.37e+01 1c5yB 253 2.37e+01 5ptp 221p 166 2.41e+01 1ctqA c.37.1.8 31987 1lmwB 253 2.42e+01 5ptp 1hq0A 295 2.42e+01 1hzgA d.194.1.1 61122 1pov0 341 2.43e+01 2hdhA 293 2.46e+01 2hdhA a.100.1.3 18795 c.2.1.6 30199 1fv9A 245 2.46e+01 5ptp b.47.1.2 26283 821p 166 2.47e+01 1ctqA c.37.1.8 31969 2cp4 414 2.47e+01 1phd a.104.1.1 18933 421p 166 2.51e+01 1ctqA c.37.1.8 31983 1d3e2 252 2.54e+01 1e2rB 567 2.55e+01 1qksA a.3.1.2 15954 b.70.2.1 27713 1he8B 166 2.56e+01 1ctqA c.37.1.8 31995 2q21 171 2.56e+01 1ctqA c.37.1.8 31986 1gpmA 525 2.58e+01 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 1igwA 434 2.60e+01 c.1.12.6 62370 1agp 166 2.62e+01 1ctqA c.37.1.8 31985 3hdhA 302 2.67e+01 2hdhA a.100.1.3 18805 c.2.1.6 30209 1ecxA 384 2.87e+01 1ecxA c.67.1.3 34431 1udh 244 2.90e+01 3eugA c.18.1.1 31015 1udg 244 2.90e+01 3eugA c.18.1.1 31016 1b25A 619 3.01e+01 1b25A a.110.1.1 19044 d.152.1.1 41796 1c8m2 252 3.03e+01 1aym2 1aym2 261 3.10e+01 1aym2 1imhC 281 3.11e+01 b.1.1.5 66214 b.2.5.1 66215 1fcqA 350 3.11e+01 c.1.8.9 65006 1fokA 568 3.14e+01 2fokA a.4.5.12 16137 a.4.5.12 16138 a.4.5.12 16139 c.52.1.12 33325 621p 166 3.20e+01 1ctqA c.37.1.8 31988 1j58A 385 3.27e+01 1ordA 730 3.31e+01 1ordA c.23.7.1 31274 c.67.1.5 34503 d.125.1.1 41124 1c4kA 730 3.43e+01 1ordA c.23.7.1 31273 c.67.1.5 34502 d.125.1.1 41123 1g6eA 87 3.43e+01 1g6eA b.11.1.6 60317 2bvvA 185 3.45e+01 1axkA b.29.1.11 24309 1qo2A 241 3.51e+01 1qo2A c.1.2.1 28533 3mdeA 385 3.58e+01 3mdeA a.29.3.1 16594 e.6.1.1 42855 3mddA 385 3.58e+01 3mdeA a.29.3.1 16592 e.6.1.1 42853 6q21A 171 3.67e+01 1ctqA c.37.1.8 31979 1ctqA 166 3.68e+01 1ctqA c.37.1.8 31965 5p21 166 3.68e+01 1ctqA c.37.1.8 31966 1hybA 181 3.68e+01 1f9aA c.26.1.3 61399 1ej2A 181 3.69e+01 1f9aA c.26.1.3 59414 1a48 306 3.70e+01 1a48 d.143.1.1 41590 1bq3B 246 3.74e+01 1qhfA c.60.1.1 33979 1qhfA 240 3.76e+01 1qhfA c.60.1.1 33960 4q21 189 3.80e+01 1ctqA c.37.1.8 31978 1iaqC 166 3.88e+01 c.37.1.8 62122 7adh 374 3.93e+01 b.35.1.2 24708 c.2.1.1 29724 1e1aA 314 3.98e+01 1e1aA b.68.6.1 59155 1befA 181 3.99e+01 1befA b.47.1.3 26419