# 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 1rgs 288 1.59e-01 1rgs b.82.3.2 28146 b.82.3.2 28147 1hbnB 442 5.45e-01 1mroB a.89.1.1 60900 d.58.31.2 60901 1mroB 442 5.45e-01 1mroB a.89.1.1 18531 d.58.31.2 39449 1jmxA 494 5.57e-01 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 1srvA 145 1.03e+00 1derA c.8.5.1 30817 1jgtA 513 1.13e+00 c.26.2.1 66684 d.153.1.1 66685 3ullA 132 1.29e+00 3ullA b.40.4.3 25282 1oelA 547 1.94e+00 1derA a.129.1.1 19452 c.8.5.1 30781 d.56.1.1 38900 1grl 548 2.08e+00 1derA a.129.1.1 19487 c.8.5.1 30816 d.56.1.1 38935 1b63A 333 2.27e+00 1b63A d.14.1.3 37566 d.122.1.2 41107 1bknA 352 2.37e+00 1b63A d.14.1.3 37568 d.122.1.2 41109 1b62A 349 2.45e+00 1b63A d.14.1.3 37567 d.122.1.2 41108 1hh2P 344 3.97e+00 b.40.4.5 65835 d.52.3.1 65836 d.52.3.1 65837 d.202.1.1 65838 1fvsA 72 4.16e+00 1aw0 d.58.17.1 60049 1f4tA 368 4.18e+00 1f4tA a.104.1.1 18973 1io7A 368 4.18e+00 1f4tA a.104.1.1 18971 1io8A 368 4.18e+00 1f4tA a.104.1.1 62618 1gruA 547 4.45e+00 i.16.1.1 65508 1derA 547 4.50e+00 1derA a.129.1.1 19459 c.8.5.1 30788 d.56.1.1 38907 1gr5A 547 4.50e+00 i.16.1.1 65478 1m6hA 373 4.82e+00 1jp5A 247 4.87e+00 b.1.1.1 67001 b.1.1.1 67002 1ii8B 174 5.17e+00 1f2tB 1je0A 236 5.45e+00 c.56.2.1 66581 2cevA 299 5.62e+00 1d3vA c.42.1.1 32576 1hneE 218 6.11e+00 1a7s b.47.1.2 26235 2dfpA 534 6.24e+00 2bce c.69.1.1 34597 1b8qA 127 6.48e+00 1qauA b.36.1.1 24781 1ppgE 218 6.59e+00 1a7s b.47.1.2 26236 1ppfE 218 6.59e+00 1a7s b.47.1.2 26234 1fy9A 193 7.57e+00 1derA c.8.5.1 30779 1fyaA 193 8.00e+00 1derA c.8.5.1 30774 1f6dA 376 8.33e+00 1f6dA c.87.1.3 35467 1dywA 173 9.15e+00 2cpl b.62.1.1 27505 1b0fA 218 9.43e+00 1a7s b.47.1.2 26237 2pia 321 9.95e+00 2pia b.43.4.2 25663 c.25.1.2 31553 d.15.4.2 37704 1f2tB 148 9.98e+00 1f2tB 1dk7A 146 1.02e+01 1derA c.8.5.1 30772 1fn7A 317 1.02e+01 1ebmA a.96.1.3 59892 d.129.1.2 59893 1ebmA 317 1.03e+01 1ebmA a.96.1.3 18751 d.129.1.2 41300 1qoxN 449 1.06e+01 1qoxN c.1.8.4 28978 1jon 155 1.08e+01 1derA c.8.5.1 30780 1ex2A 189 1.11e+01 1ex2A c.51.4.2 33225 1bcj1 154 1.12e+01 1rtm1 1afb1 154 1.13e+01 1rtm1 1fihA 154 1.15e+01 1rtm1 d.169.1.1 42396 h.1.1.1 45404 1i12A 160 1.17e+01 1i21A d.108.1.1 61515 1i1dA 161 1.18e+01 1i21A d.108.1.1 61526 1gsjA 258 1.21e+01 1ko9A 345 1.22e+01 a.96.1.3 68717 d.129.1.2 68718 3nul 130 1.23e+01 3nul d.110.1.1 40891 1kid 203 1.24e+01 1derA c.8.5.1 30771 1la1A 192 1.27e+01 1i45A 248 1.29e+01 1amk c.1.1.1 61665 1l5jA 865 1.30e+01 1f4pA 147 1.32e+01 5nul c.23.5.1 59651 1fx1 148 1.32e+01 1rcf c.23.5.1 31169 2fx2 147 1.32e+01 1rcf c.23.5.1 31158 1bu5A 147 1.32e+01 5nul c.23.5.1 31155 1akr 147 1.33e+01 1rcf c.23.5.1 31152 1j9eA 147 1.34e+01 c.23.5.1 62756 1i1oA 147 1.34e+01 5nul c.23.5.1 61542 1akt 147 1.36e+01 5nul c.23.5.1 31157 1j9gA 147 1.37e+01 c.23.5.1 62757 1c7fA 147 1.39e+01 5nul c.23.5.1 31163 1lnrP 100 1.39e+01 1aku 147 1.43e+01 5nul c.23.5.1 31161 1hyeA 313 1.45e+01 2cmd c.2.1.5 61400 d.162.1.1 61401 1qmcA 52 1.46e+01 1ihvA b.34.7.1 24633 1ihvA 52 1.53e+01 1ihvA b.34.7.1 24629 1azl 147 1.55e+01 5nul c.23.5.1 31154 1a0k 131 1.55e+01 3nul d.110.1.1 40892 1akw 147 1.56e+01 5nul c.23.5.1 31153 1cmiA 85 1.57e+01 1cmiA d.39.1.1 38551 1fpqA 372 1.58e+01 1fpqA a.4.5.29 59947 c.66.1.12 59948 1e3lA 376 1.58e+01 2ohxA b.35.1.2 24745 c.2.1.1 29761 1bch1 154 1.59e+01 1rtm1 1e2tA 284 1.61e+01 1e2tA d.3.1.5 37121 1io2A 213 1.62e+01 1ekeA c.55.3.1 62612 1qavB 115 1.63e+01 1qauA b.36.1.1 24780 1c2oA 539 1.66e+01 2bce c.69.1.1 34610 1c2bA 540 1.67e+01 2bce c.69.1.1 34614 7timA 247 1.68e+01 1amk c.1.1.1 28457 1f95A 89 1.68e+01 1cmiA d.39.1.1 38555 1k8kB 394 1.69e+01 c.55.1.1 68307 1gs5A 258 1.71e+01 3ypiA 247 1.72e+01 1amk c.1.1.1 28463 1mahA 543 1.76e+01 2bce c.69.1.1 34619 1maaD 547 1.77e+01 2bce c.69.1.1 34618 1qauA 112 1.77e+01 1qauA b.36.1.1 24779 1jjbA 532 1.77e+01 1eeaA 534 1.78e+01 2bce c.69.1.1 34609 1acl 537 1.78e+01 2bce c.69.1.1 34590 1vxrA 537 1.78e+01 2bce c.69.1.1 34595 1qidA 537 1.78e+01 2bce c.69.1.1 34593 1ea5A 537 1.78e+01 2bce c.69.1.1 34592 1amn 532 1.79e+01 2bce c.69.1.1 34587 1bmtA 246 1.79e+01 1bmtA a.46.1.1 17757 c.23.6.1 31235 1eve 543 1.81e+01 2bce c.69.1.1 34585 1lmkA 238 1.91e+01 1mfa b.1.1.1 20034 b.1.1.1 20035 1e3iA 376 1.91e+01 2ohxA b.35.1.2 24741 c.2.1.1 29757 1mkp 144 1.94e+01 1vhrA c.45.1.1 32654 2bifA 469 2.02e+01 1bif c.37.1.7 31963 c.60.1.4 34009 1i21A 159 2.15e+01 1i21A d.108.1.1 61549 1jilA 420 2.27e+01 c.26.1.1 66745 1ml1A 242 2.31e+01 1amk c.1.1.1 28489 1qk9A 92 2.40e+01 1qk9A d.10.1.3 37485 1zbdB 134 2.41e+01 1zbdB g.50.1.1 45359 1i1rA 303 2.42e+01 1bquA b.1.2.1 61545 b.1.2.1 61546 b.1.2.1 61547 1fuiA 591 2.50e+01 1fuiA b.43.2.1 25674 c.85.1.1 35444 1fyc 106 2.50e+01 1fyc b.84.1.1 28230 2nadA 393 2.57e+01 2nadA c.2.1.4 30090 c.23.12.1 31350 2nacA 393 2.57e+01 2nadA c.2.1.4 30088 c.23.12.1 31348 1a58 177 2.59e+01 2cpl b.62.1.1 27495 1an9A 340 2.64e+01 1an9A c.4.1.2 30617 d.16.1.3 37904 1aa8A 347 2.65e+01 1an9A c.4.1.2 30619 d.16.1.3 37906 1d5yA 292 2.66e+01 1d5yA a.4.1.8 16055 a.4.1.8 16056 d.60.1.2 39532 1fp1D 372 2.68e+01 1fpqA a.4.5.29 59939 c.66.1.12 59940 1qdsA 251 2.76e+01 1amk c.1.1.1 28504 1ckv 141 2.84e+01 1ckv d.137.1.1 41452 1cynA 178 2.90e+01 2cpl b.62.1.1 27489 1eudA 311 2.93e+01 2scuA c.2.1.8 30312 c.23.4.1 31140 1amk 251 2.93e+01 1amk c.1.1.1 28503 1edzA 320 2.96e+01 1ee9A c.2.1.7 30287 c.58.1.2 33935 1ee9A 320 2.96e+01 1ee9A c.2.1.7 30288 c.58.1.2 33936 1dcjA 81 2.97e+01 1dcjA d.68.3.1 59115 1gt91 357 3.15e+01 1c7qA 445 3.15e+01 2pgi c.80.1.2 35307 2pgi 445 3.15e+01 2pgi c.80.1.2 35308 1eucA 311 3.21e+01 2scuA c.2.1.8 30311 c.23.4.1 31139 1dekA 241 3.25e+01 1dekA c.37.1.1 31842 1delA 241 3.25e+01 1dekA c.37.1.1 31844 1qfxA 460 3.26e+01 1qfxA c.60.1.3 33994 1gq2A 555 3.27e+01 1b59A 370 3.30e+01 1bn5 a.4.5.25 16225 d.127.1.1 41162 1fjgI 128 3.37e+01 1fjfI d.14.1.1 37559 1pbv 195 3.39e+01 1pbv a.118.3.1 19179 1f2jA 370 3.41e+01 1fbaA c.1.10.1 29154 1cx4A 305 3.47e+01 b.82.3.2 59099 b.82.3.2 59100 1h4jA 599 3.51e+01 4aahA b.70.1.1 60590 1h4iA 599 3.52e+01 4aahA b.70.1.1 60586 1bn5 478 3.57e+01 1bn5 a.4.5.25 16224 d.127.1.1 41161 1qngA 170 3.64e+01 2cpl b.62.1.1 27507 1tri 243 3.65e+01 1amk c.1.1.1 28479 1qbjA 81 3.74e+01 1qbjA a.4.5.19 16155 1glv 303 3.74e+01 1gsa c.30.1.3 31721 d.142.1.1 41480 1k7yA 577 3.76e+01 a.46.1.1 68272 c.23.6.1 68273 d.173.1.1 68274 1dk5A 322 3.78e+01 1dk5A a.65.1.1 18192 1qnhA 170 3.79e+01 2cpl b.62.1.1 27508 1qgpA 77 3.80e+01 1qbjA a.4.5.19 16158 1azwA 313 3.89e+01 1qtrA c.69.1.7 34658 1fhuA 320 3.93e+01 1fhuA c.1.11.2 29234 d.54.1.1 38878 1qokA 282 3.94e+01 1f3rB b.1.1.1 20492 b.1.1.1 20493 1fhvA 323 3.94e+01 1fhuA c.1.11.2 29235 d.54.1.1 38879 1mssA 243 3.97e+01 1amk c.1.1.1 28480 1f32A 149 3.97e+01 1f32A d.62.1.1 39539