# List of top-scoring protein chains for t2k-100-30-bys 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 1dptA 117 4.40e-03 1dptA d.80.1.3 39862 1hfoA 113 9.24e-03 d.80.1.3 61006 1gyxA 76 1.04e-02 d.80.1.1 76387 9gafA 295 2.39e-02 1apyA d.153.1.5 42008 1p4kA 295 2.72e-02 d.153.1.5 87772 1s0yA 76 5.82e-02 d.80.1.1 -10434 1mfiA 114 1.05e-01 1dptA d.80.1.3 39856 1otfA 62 1.05e-01 1otfA d.80.1.1 39820 1otgA 125 4.36e-01 1otgA d.80.1.2 39831 1qysA 106 5.16e-01 unknown_sccs -13432 1iv3A 152 1.00e+00 d.79.5.1 76828 1hnuA 280 1.52e+00 1hnoA c.14.1.3 61096 1uvqB 198 1.81e+00 b.1.1.2 -2659 d.19.1.1 -9348 1b3qA 379 1.95e+00 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1i60A 278 2.12e+00 c.1.15.4 71118 1gd0A 122 2.17e+00 1dptA d.80.1.3 39834 1hnoA 280 2.46e+00 1hnoA c.14.1.3 61095 1fzyA 149 2.72e+00 d.20.1.1 65072 1fjgJ 105 2.91e+00 1fjfJ d.58.15.1 39330 1nrhX 472 2.96e+00 c.2.1.5 -5944 d.162.1.2 -11511 1m4jA 142 3.05e+00 d.109.1.2 78602 1ihfA 99 3.36e+00 1huuA a.55.1.1 17893 1mml 265 3.54e+00 1mml e.8.1.2 43015 1pjhA 280 3.73e+00 c.14.1.3 -6229 1npdA 288 3.90e+00 c.2.1.7 80681 c.58.1.5 80682 1ow1A 195 4.33e+00 unknown_sccs -4422 1pwhA 327 4.54e+00 c.79.1.1 -8524 1ex2A 189 4.58e+00 1ex2A c.51.4.2 33225 1brsD 89 4.69e+00 1ay7B c.9.1.1 30825 1jtaA 361 4.81e+00 b.80.1.1 71859 1rypI 222 5.55e+00 d.153.1.4 41877 1ii7A 333 5.72e+00 1ii7A d.159.1.4 62415 1iicA 422 5.75e+00 1nmtA d.108.1.2 62422 d.108.1.2 62423 1owfA 99 6.05e+00 a.55.1.1 87487 1i58A 189 6.24e+00 1b3qA d.122.1.3 61773 1k6xA 352 6.34e+00 c.2.1.2 68238 1k6iA 352 6.51e+00 c.2.1.2 68223 1mwwA 128 6.72e+00 unknown_sccs -10451 1r2rA 248 6.83e+00 c.1.1.1 -5147 1bif 469 6.83e+00 1bif c.37.1.7 31961 c.60.1.4 34003 1s0aA 429 6.89e+00 c.67.1.4 -8201 1pieA 419 6.92e+00 d.14.1.5 -9075 unknown_sccs -10120 1qj5A 429 7.17e+00 1dtyA c.67.1.4 34493 1vi2A 300 7.54e+00 c.2.1.7 -5960 c.58.1.5 -6366 1b2rA 304 7.89e+00 1fnc b.43.4.2 25648 c.25.1.1 31538 1d4xG 126 7.92e+00 1d0nA d.109.1.1 59109 1ortA 335 7.99e+00 1othA c.78.1.1 35204 c.78.1.1 35205 1mo0A 275 8.34e+00 c.1.1.1 79329 1ogiA 303 8.38e+00 b.43.4.2 -4042 c.25.1.1 -6587 1hqsA 423 8.46e+00 1iso c.77.1.1 61154 1udc 338 8.69e+00 1xel c.2.1.2 29785 1hnnA 282 8.76e+00 c.66.1.15 65895 1ffkI 194 9.18e+00 1ffkI d.12.1.2 37494 1oneA 436 9.22e+00 4enl c.1.11.1 29200 d.54.1.1 38844 1mnmA 100 9.29e+00 1mnmA d.88.1.1 40232 1yagG 125 9.36e+00 1d0nA d.109.1.1 40846 1h5vA 304 9.38e+00 c.1.8.3 70898 1xel 338 9.47e+00 1xel c.2.1.2 29786 1go2A 304 9.78e+00 b.43.4.2 76243 c.25.1.1 76244 1qh0A 295 9.88e+00 b.43.4.2 68891 c.25.1.1 68892 1dtyA 429 9.93e+00 1dtyA c.67.1.4 34495 1que 303 1.03e+01 1fnc b.43.4.2 25647 c.25.1.1 31537 2udpA 338 1.04e+01 1xel c.2.1.2 29791 1bam 213 1.05e+01 1bam c.52.1.3 33285 1pysA 350 1.08e+01 1pysA d.104.1.1 40775 1jwqA 179 1.13e+01 unknown_sccs -7897 1p5jA 372 1.13e+01 1sdoA 203 1.19e+01 unknown_sccs -7558 1nm1G 125 1.20e+01 d.109.1.1 80653 1qqrA 138 1.23e+01 1bmlC d.15.5.1 37721 1l0oA 150 1.25e+01 d.122.1.3 73403 1v2zA 111 1.26e+01 1kvs 338 1.29e+01 1xel c.2.1.2 29799 1id0A 152 1.31e+01 d.122.1.3 66111 3bamA 213 1.35e+01 1bam c.52.1.3 33288 1nkxA 348 1.37e+01 c.94.1.2 -8704 1kb0A 677 1.39e+01 a.3.1.6 68378 b.70.1.1 68379 1kvlA 358 1.42e+01 e.3.1.1 73062 1evlA 401 1.43e+01 1qf6A c.51.1.1 33202 d.104.1.1 40751 1ae1A 273 1.43e+01 1bdb c.2.1.2 29943 1udb 338 1.48e+01 1xel c.2.1.2 29787 1esgA 213 1.50e+01 1bam c.52.1.3 33286 1ur1A 378 1.51e+01 c.1.8.3 -5311 1gskA 513 1.51e+01 b.6.1.3 83314 b.6.1.3 83315 b.6.1.3 83316 1nmoA 247 1.53e+01 unknown_sccs -8746 1e6qM 501 1.60e+01 1e70M c.1.8.4 28920 1th8A 145 1.63e+01 1l0gA 358 1.65e+01 e.3.1.1 73400 4enl 436 1.67e+01 4enl c.1.11.1 29202 d.54.1.1 38846 1dkrA 317 1.67e+01 1dkuA c.61.1.2 34114 c.61.1.2 34115 1b7yA 350 1.70e+01 1pysA d.104.1.1 40776 1o5xA 248 1.72e+01 c.1.1.1 -5157 1eluA 390 1.77e+01 1elqA c.67.1.3 34434 1cwpA 190 1.77e+01 1cwpA b.121.4.5 23305 1pi4A 358 1.78e+01 e.3.1.1 -11774 1btkB 169 1.78e+01 1btkA b.55.1.1 26960 1uiuA 502 1.78e+01 c.94.1.1 -8674 1im3D 95 1.80e+01 1im3D b.1.18.5 62568 7a3hA 303 1.82e+01 7a3hA c.1.8.3 28817 1fsyA 358 1.89e+01 1gceA e.3.1.1 60016 1exbA 332 1.90e+01 1qrqA c.1.7.1 28666 3bamB 213 1.91e+01 1bam c.52.1.3 33289 1a3h 300 1.91e+01 7a3hA c.1.8.3 28819 1eluB 390 1.94e+01 1elqA c.67.1.3 34435 1uuqA 440 1.99e+01 c.1.8.3 -5321 1ui0A 205 2.00e+01 c.18.1.2 -6328 1ldjA 760 2.02e+01 a.4.5.34 73847 a.118.17.1 73848 e.40.1.1 73849 1d5mB 192 2.05e+01 1iakB b.1.1.2 21618 d.19.1.1 38192 1elqA 390 2.07e+01 1elqA c.67.1.3 34436 1bjnA 360 2.09e+01 1bjnA c.67.1.4 34469 1fxtA 149 2.10e+01 d.20.1.1 65055 1rypD 241 2.11e+01 1rypD d.153.1.4 41935 1ukkA 142 2.14e+01 d.227.1.1 -11206 1lyxA 248 2.14e+01 c.1.1.1 78304 1uunA 184 2.15e+01 unknown_sccs -12370 3pnp 289 2.17e+01 1b8oA c.56.2.1 33763 1howA 373 2.19e+01 1hcl d.144.1.7 41679 1ni4A 365 2.21e+01 c.36.1.7 85728 1spvA 184 2.22e+01 c.50.1.2 -7937 1e4mM 501 2.22e+01 1e70M c.1.8.4 59226 1cmiA 85 2.24e+01 1cmiA d.39.1.1 38551 1tph1 247 2.26e+01 1amk 1fr1A 361 2.27e+01 1gceA e.3.1.1 42734 1btkA 169 2.27e+01 1btkA b.55.1.1 26959 2bifA 469 2.35e+01 1bif c.37.1.7 31963 c.60.1.4 34009 1k20A 310 2.39e+01 c.107.1.1 68027 1p8xA 344 2.41e+01 d.109.1.1 -10813 d.109.1.1 -10814 d.109.1.1 -10815 1go4A 205 2.41e+01 d.135.1.1 70292 1dkuA 317 2.46e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1ihnA 113 2.47e+01 1ihnA c.103.1.1 62388 1gw9A 388 2.52e+01 c.1.15.3 70658 1mijA 152 2.54e+01 a.4.1.1 79150 1pzrA 60 2.56e+01 unknown_sccs -815 1gefA 123 2.59e+01 1gefA c.52.1.18 60465 1konA 249 2.61e+01 e.39.1.1 72823 1rgyA 360 2.62e+01 e.3.1.1 -11768 2bltA 361 2.63e+01 1gceA e.3.1.1 42739 1e70M 501 2.67e+01 1e70M c.1.8.4 28926 1dctA 324 2.69e+01 6mhtA c.66.1.26 34244 1mj5A 302 2.70e+01 c.69.1.8 -8326 1f2tB 148 2.78e+01 1f2tB 1dbfA 127 2.79e+01 2chsA d.79.1.2 39761 1e9iA 431 2.80e+01 c.1.11.1 64818 d.54.1.1 64819 1jkxA 212 2.83e+01 c.65.1.1 66813 1ipiA 123 2.85e+01 c.52.1.18 66255 2ptd 298 2.89e+01 2plc c.1.18.2 29605 1jp3A 253 2.92e+01 1f75A c.101.1.1 63221 1bjoA 360 2.95e+01 1bjnA c.67.1.4 34471 2pth 193 2.96e+01 2pth c.56.3.1 33793 1b2sD 90 3.01e+01 1ay7B c.9.1.1 30837 1eqnA 321 3.02e+01 1dd9A e.13.1.1 43256 1o4tA 133 3.03e+01 b.82.1.9 86622 1ay7B 89 3.03e+01 1ay7B c.9.1.1 30836 1kkoA 413 3.05e+01 c.1.11.2 68675 d.54.1.1 68676 1pe9A 361 3.14e+01 b.80.1.1 -4765 1nz0A 118 3.14e+01 d.14.1.2 86433 1q8yA 373 3.14e+01 d.144.1.7 -11319 1bzyA 217 3.15e+01 1qk3A c.61.1.1 34071 1n0wA 243 3.15e+01 c.37.1.11 79772 1d2rB 326 3.17e+01 1d2rB c.26.1.1 31573 1hmpA 217 3.25e+01 1qk3A c.61.1.1 34075 1d2rA 326 3.26e+01 1d2rB c.26.1.1 31572 3bifA 468 3.27e+01 1bif c.37.1.7 31962 c.60.1.4 34008 1k1xA 659 3.31e+01 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1iz7A 295 3.35e+01 c.69.1.8 76982 1iyhA 198 3.38e+01 a.45.1.1 83790 c.47.1.5 83791 1lfaA 187 3.44e+01 1ido c.62.1.1 34122 2chsA 127 3.45e+01 2chsA d.79.1.2 39764 1lmb3 92 3.46e+01 1lmb3 1enp 312 3.46e+01 1enp c.2.1.2 29906 2blsA 358 3.47e+01 1gceA e.3.1.1 42747 1nni1 174 3.59e+01 1i7kA 179 3.61e+01 1u9aA d.20.1.1 61889 1lliA 92 3.65e+01 1lmb3 a.35.1.2 17025 1rboC 123 3.65e+01 1rboC d.73.1.1 39634 1oshA 232 3.69e+01 a.123.1.1 -1697 1t3cA 421 3.71e+01 1dmhA 311 3.72e+01 1dmhA b.3.6.1 22633 1p7tA 731 3.75e+01 c.1.13.1 -5600 1r5lA 262 3.90e+01 a.5.3.1 -360 c.13.1.1 -6215 1j7nB 776 3.95e+01 d.92.1.14 66412 d.92.1.14 66413 d.166.1.1 66414 1q7hA 153 3.95e+01 b.122.1.1 -5124 unknown_sccs -9313 1h8eD 482 3.97e+01 1skyE a.69.1.1 60747 b.49.1.1 60748 c.37.1.11 60749