# List of top-scoring protein chains for t2k-100-30-str 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 1dk0A 188 1.46e-03 1b2vA d.35.1.1 38530 1b2vA 188 1.46e-03 1b2vA d.35.1.1 38532 1g59A 468 1.38e-01 a.97.1.1 60257 c.26.1.1 60258 3pte 349 1.77e-01 3pte e.3.1.1 42687 1hvbA 349 1.90e-01 3pte e.3.1.1 42686 2baa 243 2.12e-01 1cnsA d.2.1.1 36243 1gln 468 3.44e-01 1gln a.97.1.1 18752 c.26.1.1 31588 1dxjA 242 4.25e-01 1cnsA d.2.1.1 36244 1qisA 396 5.87e-01 1ajsA c.67.1.1 34284 2ucz 165 6.95e-01 1u9aA d.20.1.1 38330 1bea 127 7.98e-01 1bea a.52.1.2 17826 1skyE 473 1.09e+00 1skyE a.69.1.1 18314 b.49.1.1 26479 c.37.1.11 32359 1cnsA 243 1.33e+00 1cnsA d.2.1.1 36241 1fyhA 258 1.40e+00 1d9cA a.26.1.3 16907 a.26.1.3 16908 1coo 98 1.49e+00 1coo a.60.3.1 17967 1igd 61 1.71e+00 2igd d.15.7.1 37822 2igd 61 1.71e+00 2igd d.15.7.1 37821 1anxA 319 1.76e+00 1avc a.65.1.1 18161 1agrH 205 1.78e+00 1agrE a.91.1.1 18539 1ahxA 396 1.81e+00 1ajsA c.67.1.1 34293 1a8i 842 1.84e+00 1a8i c.87.1.4 35490 1gwcA 230 1.87e+00 1art 396 1.90e+00 1ajsA c.67.1.1 34285 1dmhA 311 1.92e+00 1dmhA b.3.6.1 22633 1jrjA 39 2.05e+00 j.6.1.1 67135 1phr 157 2.40e+00 1dg9A c.44.1.1 32635 1spa 396 2.50e+00 1ajsA c.67.1.1 34291 1jr5A 90 2.62e+00 a.150.1.1 67113 1dg9A 157 2.64e+00 1dg9A c.44.1.1 32637 1aua 296 2.64e+00 1aua a.5.3.1 16290 c.13.1.1 30882 1qhhA 167 2.69e+00 1pjr c.37.1.13 32393 1t7pA 698 2.72e+00 1t7pA c.55.3.5 33712 e.8.1.1 43005 1b78A 193 2.93e+00 1b78A c.51.4.1 33221 1g24A 211 3.04e+00 1g24A d.166.1.1 42270 1bjnA 360 3.16e+00 1bjnA c.67.1.4 34469 1brfA 53 3.27e+00 1rb9 g.41.5.1 45236 1fiqC 763 3.29e+00 1fiqC d.41.1.1 38588 d.133.1.1 41418 2mjpA 193 3.56e+00 1b78A c.51.4.1 33223 1is8A 230 3.56e+00 d.96.1.1 66321 1mpb 370 3.66e+00 4mbp c.94.1.1 35780 1omp 370 3.92e+00 4mbp c.94.1.1 35778 1g0cA 364 3.97e+00 7a3hA c.1.8.3 60165 1cec 343 3.98e+00 1ceo c.1.8.3 28809 1bjoA 360 4.08e+00 1bjnA c.67.1.4 34471 1gefA 123 4.26e+00 1gefA c.52.1.18 60465 1j7lA 264 4.26e+00 d.144.1.6 62697 1uaaA 673 4.33e+00 1pjr c.37.1.13 32401 c.37.1.13 32402 2aat 396 4.49e+00 1ajsA c.67.1.1 34348 1ceo 343 4.56e+00 1ceo c.1.8.3 28808 1jyhA 157 4.57e+00 1bqbA 301 5.03e+00 1hyt d.92.1.2 58962 1agrE 205 5.20e+00 1agrE a.91.1.1 18538 1aa8A 347 5.35e+00 1an9A c.4.1.2 30619 d.16.1.3 37906 1jetA 517 5.71e+00 1jevA c.94.1.1 35718 1c8kA 842 5.71e+00 1a8i c.87.1.4 35491 2ran 316 5.99e+00 1avc a.65.1.1 18170 1a8b 318 6.04e+00 1avc a.65.1.1 18171 1kzhA 555 6.26e+00 1h5uA 842 6.33e+00 1a8i c.87.1.4 60655 2bvwA 362 6.62e+00 1bvwA c.6.1.1 30666 1ars 396 6.78e+00 1ajsA c.67.1.1 34287 1yagA 375 6.95e+00 1yagA c.55.1.1 33449 c.55.1.1 33450 1an9A 340 7.08e+00 1an9A c.4.1.2 30617 d.16.1.3 37904 1bal 51 7.26e+00 1bbl a.9.1.1 16357 1ecl 597 7.44e+00 1ecl e.10.1.1 43238 1bvwA 360 7.48e+00 1bvwA c.6.1.1 30668 1ltzA 297 7.59e+00 1lucB 324 7.67e+00 1lucA c.1.16.1 29548 1cfzA 162 7.67e+00 1cfzA c.56.1.1 33754 4mbp 370 7.73e+00 4mbp c.94.1.1 35777 1jevA 517 7.84e+00 1jevA c.94.1.1 35720 1bbl 51 8.03e+00 1bbl a.9.1.1 16356 1jqlB 140 8.04e+00 c.37.1.13 63234 1mat 264 8.30e+00 1c24A d.127.1.1 41152 1hvd 319 8.76e+00 1avc a.65.1.1 18154 1amuA 563 8.99e+00 1amuA e.23.1.1 43351 1b6sA 355 9.00e+00 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 1dguA 183 9.15e+00 1dguA a.39.1.5 17333 1avc 673 9.40e+00 1avc a.65.1.1 18178 a.65.1.1 18179 1jnyA 435 9.41e+00 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1vls 146 9.55e+00 1vls a.24.2.1 16532 1dgsA 667 9.86e+00 1dgsA a.60.2.2 17963 b.40.4.6 25365 d.142.2.2 41581 8rxnA 52 1.02e+01 1rb9 g.41.5.1 45215 1jj2Q 154 1.03e+01 1ffkO d.55.1.1 63102 1rb9 53 1.03e+01 1rb9 g.41.5.1 45214 2scuA 288 1.04e+01 2scuA c.2.1.8 30303 c.23.4.1 31131 1qd9A 124 1.04e+01 1qu9A d.79.1.1 39758 3crxA 343 1.08e+01 4crxA a.60.9.1 18101 d.163.1.1 42161 1l6xB 34 1.09e+01 1ffkO 154 1.09e+01 1ffkO d.55.1.1 38899 2tct 207 1.10e+01 2tct a.4.1.9 16063 a.121.1.1 19240 1i50B 1224 1.10e+01 e.29.1.2 61755 1cuk 203 1.13e+01 1hjp a.5.1.1 16273 a.60.2.1 17946 b.40.4.2 25265 2ligA 164 1.17e+01 1vls a.24.2.1 16530 1g8oA 310 1.20e+01 1g8oA c.68.1.9 60375 1ka8A 100 1.22e+01 1bkjA 240 1.24e+01 1bkjA d.90.1.1 40243 1gw5S 142 1.24e+01 1pd21 199 1.26e+01 1pd21 1brlB 324 1.26e+01 1lucA c.1.16.1 29554 1djxB 624 1.28e+01 1djxB a.39.1.7 17343 b.7.1.1 23160 c.1.18.1 29588 1k4vA 289 1.28e+01 1aisA 182 1.32e+01 1ytbA d.129.1.1 41288 d.129.1.1 41289 1jraA 117 1.34e+01 a.24.15.1 67117 1j77A 209 1.34e+01 1j77A a.132.1.2 62674 1adjA 421 1.34e+01 1adjA c.51.1.1 33188 d.104.1.1 40737 1gkuB 1054 1.34e+01 c.37.1.16 65257 c.37.1.16 65258 e.10.1.1 65259 1iro 54 1.35e+01 1rb9 g.41.5.1 45223 1it2A 146 1.35e+01 a.1.1.2 66365 1knzA 164 1.36e+01 e.34.1.1 68709 2matA 264 1.38e+01 1c24A d.127.1.1 41146 1jkfA 533 1.44e+01 1ci4A 89 1.50e+01 1qckA a.60.5.1 17970 1d4xA 375 1.51e+01 1yagA c.55.1.1 59107 c.55.1.1 59108 1hjp 203 1.52e+01 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1bax 94 1.53e+01 1bax a.61.1.3 18133 1f5xA 208 1.55e+01 1f5xA a.87.1.1 18516 1b6rA 355 1.56e+01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1mhyD 521 1.57e+01 1mhyD a.25.1.2 16780 1gryA 290 1.58e+01 1h4vB 421 1.58e+01 1adjA c.51.1.1 60624 d.104.1.1 60625 1jg1A 235 1.60e+01 c.66.1.7 66661 1ka3A 90 1.61e+01 1mdyA 68 1.63e+01 1mdyA a.38.1.1 17132 1jgtA 513 1.66e+01 c.26.2.1 66684 d.153.1.1 66685 2olbA 517 1.67e+01 1jevA c.94.1.1 35721 1ih8A 271 1.69e+01 2nsyA c.26.2.1 62377 1a1z 91 1.69e+01 1a1z a.77.1.1 18427 1qckA 89 1.69e+01 1qckA a.60.5.1 17976 2ezxA 89 1.69e+01 1qckA a.60.5.1 17978 1c24A 263 1.70e+01 1c24A d.127.1.1 41148 1pyiA 96 1.70e+01 1pyiA g.38.1.1 45079 h.1.3.1 45512 2nsyA 271 1.71e+01 2nsyA c.26.2.1 31612 1fc3A 120 1.71e+01 1fc3A a.4.6.3 16237 1l5wA 796 1.75e+01 1aisB 200 1.76e+01 1aisB a.74.1.2 18384 a.74.1.2 18385 4rxn 54 1.77e+01 1rb9 g.41.5.1 45226 1mup 166 1.78e+01 1mup b.60.1.1 27133 1hx1B 114 1.78e+01 1hx1B a.7.7.1 61350 1a1w 91 1.81e+01 1a1z a.77.1.1 18425 1cf9A 753 1.81e+01 1cf9A c.23.16.3 31441 e.5.1.1 42815 1rdg 53 1.82e+01 1rb9 g.41.5.1 45221 1ffkM 148 1.82e+01 1ffkM a.94.1.1 18740 1gpb 842 1.82e+01 1a8i c.87.1.4 35478 1e96B 203 1.83e+01 1e96B a.118.8.1 19211 1ahpA 797 1.85e+01 1a8i c.87.1.4 35544 1jj2O 148 1.86e+01 1ffkM a.94.1.1 63100 1iqcA 308 1.91e+01 a.3.1.5 66266 a.3.1.5 66267 1j6zA 376 1.91e+01 1yagA c.55.1.1 62667 c.55.1.1 62668 1g61A 228 1.91e+01 1g61A d.126.1.1 41126 1hh8A 213 1.91e+01 1e96B a.118.8.1 61042 1iqrA 420 1.95e+01 a.99.1.1 66275 c.28.1.1 66276 1k1gA 131 2.03e+01 d.51.1.1 68015 1scuA 288 2.04e+01 2scuA c.2.1.8 30307 c.23.4.1 31135 1f0jA 377 2.09e+01 1f0jA a.125.1.1 19346 1cmbA 104 2.09e+01 1cmbA a.43.1.2 17460 3pvaA 335 2.09e+01 3pvaA d.153.1.3 41854 1eudA 311 2.11e+01 2scuA c.2.1.8 30312 c.23.4.1 31140 1h8eD 482 2.14e+01 1skyE a.69.1.1 60747 b.49.1.1 60748 c.37.1.11 60749 1ew3A 159 2.20e+01 1mup b.60.1.1 27114 1gosA 520 2.21e+01 c.3.1.2 65425 d.16.1.5 65426 1rpxA 230 2.21e+01 1rpxA c.1.2.2 28536 1jr8A 117 2.26e+01 a.24.15.1 67115 1i7kA 179 2.28e+01 1u9aA d.20.1.1 61889 1jm7B 117 2.30e+01 g.44.1.1 66881 1tml 286 2.32e+01 1tml c.6.1.1 30656 1hi0P 664 2.35e+01 1hi0P e.8.1.6 61051 1eq2A 310 2.37e+01 1eq2A c.2.1.2 29814 1kafA 108 2.38e+01 d.199.1.1 68372 1j8mF 297 2.48e+01 1ng1 a.24.13.1 62742 c.37.1.10 62743 1anf 370 2.51e+01 4mbp c.94.1.1 35776 1ek8A 185 2.53e+01 1ek8A d.67.3.1 59444 1hekA 131 2.53e+01 a.61.1.5 65818 1e79D 482 2.54e+01 1skyE a.69.1.1 18272 b.49.1.1 26437 c.37.1.11 32317 1guxA 218 2.54e+01 1guxA a.74.1.3 18388 1hn2A 159 2.59e+01 b.60.1.1 65890 1obpA 159 2.59e+01 1obpA b.60.1.1 27092 1kqpA 271 2.59e+01 1nsyA 271 2.61e+01 2nsyA c.26.2.1 31614 1zymA 258 2.68e+01 1zymA a.60.10.1 18110 c.8.1.2 30705 2btfA 375 2.70e+01 1yagA c.55.1.1 33429 c.55.1.1 33430 1fo4A 1332 2.73e+01 a.56.1.1 17910 d.15.4.2 37695 d.41.1.1 38586 d.87.2.1 40227 d.133.1.1 41416 d.145.1.3 41758 1h54A 754 2.80e+01 a.102.1.4 60634 b.30.4.1 60635 1e55A 512 2.85e+01 1e70M c.1.8.4 28934 1h67A 108 2.85e+01 a.40.1.1 65643 1l5aA 436 2.97e+01 1bvoA 175 2.97e+01 1a3qA b.2.5.1 22457 1kv8A 216 3.01e+01 1j7iA 264 3.03e+01 1j7iA d.144.1.6 62694 1oakA 196 3.10e+01 1auq c.62.1.1 34138 1c8bA 371 3.20e+01 1c8bA c.56.1.2 59082 2ahjB 212 3.24e+01 2ahjB b.34.4.4 24599 2pvaA 345 3.28e+01 3pvaA d.153.1.3 41850 1jd1A 129 3.31e+01 1qu9A d.79.1.1 62890 2ms2A 129 3.38e+01 1msc d.85.1.1 40049 1u9aA 160 3.42e+01 1u9aA d.20.1.1 38333 1aoy 78 3.46e+01 1aoy a.4.5.3 16087 1brwA 433 3.47e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1gox 370 3.48e+01 1gox c.1.4.1 28607 1hhsA 664 3.48e+01 1hi0P e.8.1.6 61045 1cmcA 104 3.48e+01 1cmbA a.43.1.2 17462 2shpA 525 3.50e+01 2shpA c.45.1.2 32683 d.93.1.1 40533 d.93.1.1 40534 1ej2A 181 3.54e+01 1f9aA c.26.1.3 59414 1dlyA 164 3.58e+01 1dlyA a.1.1.1 14983 1rypH 205 3.59e+01 d.153.1.4 41876 2tdt 274 3.64e+01 3tdt b.81.1.2 28054 1k8kD 300 3.69e+01 d.198.2.1 68309 d.198.2.1 68310 1udh 244 3.69e+01 3eugA c.18.1.1 31015 1dgaA 375 3.70e+01 1yagA c.55.1.1 33441 c.55.1.1 33442 1xsm 390 3.73e+01 1xsm a.25.1.2 16804 1qh4A 380 3.79e+01 1qh4A a.83.1.1 18462 d.128.1.2 41197 1ahjB 212 3.85e+01 2ahjB b.34.4.4 24601 1ig6A 107 3.90e+01 1ig6A a.4.3.2 62364 1e4iA 447 3.97e+01 1e70M c.1.8.4 59225