# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl 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 1.71e-03 1b2vA d.35.1.1 38530 1b2vA 188 1.71e-03 1b2vA d.35.1.1 38532 2baa 243 2.85e-02 1cnsA d.2.1.1 36243 1dxjA 242 3.67e-02 1cnsA d.2.1.1 36244 1g59A 468 6.54e-02 a.97.1.1 60257 c.26.1.1 60258 1gln 468 1.28e-01 1gln a.97.1.1 18752 c.26.1.1 31588 1cnsA 243 1.44e-01 1cnsA d.2.1.1 36241 1skyE 473 1.62e-01 1skyE a.69.1.1 18314 b.49.1.1 26479 c.37.1.11 32359 2ucz 165 1.66e-01 1u9aA d.20.1.1 38330 1hvbA 349 3.35e-01 3pte e.3.1.1 42686 1anxA 319 3.47e-01 1avc a.65.1.1 18161 3pte 349 3.73e-01 3pte e.3.1.1 42687 1uaaA 673 5.71e-01 1pjr c.37.1.13 32401 c.37.1.13 32402 1aua 296 6.39e-01 1aua a.5.3.1 16290 c.13.1.1 30882 1qisA 396 7.63e-01 1ajsA c.67.1.1 34284 1j7lA 264 7.86e-01 d.144.1.6 62697 1ahxA 396 8.37e-01 1ajsA c.67.1.1 34293 1qhhA 167 9.89e-01 1pjr c.37.1.13 32393 1phr 157 1.09e+00 1dg9A c.44.1.1 32635 1mpb 370 1.10e+00 4mbp c.94.1.1 35780 1omp 370 1.11e+00 4mbp c.94.1.1 35778 1pd21 199 1.16e+00 1pd21 1dg9A 157 1.18e+00 1dg9A c.44.1.1 32637 2mjpA 193 1.30e+00 1b78A c.51.4.1 33223 1igd 61 1.30e+00 2igd d.15.7.1 37822 2igd 61 1.30e+00 2igd d.15.7.1 37821 1bea 127 1.30e+00 1bea a.52.1.2 17826 1b78A 193 1.34e+00 1b78A c.51.4.1 33221 1jrjA 39 1.34e+00 j.6.1.1 67135 1art 396 1.39e+00 1ajsA c.67.1.1 34285 2ran 316 1.39e+00 1avc a.65.1.1 18170 1a8b 318 1.44e+00 1avc a.65.1.1 18171 1coo 98 1.69e+00 1coo a.60.3.1 17967 1bjnA 360 1.78e+00 1bjnA c.67.1.4 34469 1avc 673 1.79e+00 1avc a.65.1.1 18178 a.65.1.1 18179 1g24A 211 1.81e+00 1g24A d.166.1.1 42270 4mbp 370 1.82e+00 4mbp c.94.1.1 35777 1jqlB 140 1.83e+00 c.37.1.13 63234 1is8A 230 2.00e+00 d.96.1.1 66321 2aat 396 2.04e+00 1ajsA c.67.1.1 34348 1a8i 842 2.05e+00 1a8i c.87.1.4 35490 1bjoA 360 2.15e+00 1bjnA c.67.1.4 34471 1fiqC 763 2.28e+00 1fiqC d.41.1.1 38588 d.133.1.1 41418 1agrH 205 2.65e+00 1agrE a.91.1.1 18539 1f0jA 377 2.89e+00 1f0jA a.125.1.1 19346 1ecl 597 3.24e+00 1ecl e.10.1.1 43238 1jr5A 90 3.28e+00 a.150.1.1 67113 1t7pA 698 3.32e+00 1t7pA c.55.3.5 33712 e.8.1.1 43005 1jetA 517 3.36e+00 1jevA c.94.1.1 35718 1gefA 123 3.48e+00 1gefA c.52.1.18 60465 1fyhA 258 3.58e+00 1d9cA a.26.1.3 16907 a.26.1.3 16908 1ltzA 297 3.69e+00 1jyhA 157 3.70e+00 1spa 396 3.70e+00 1ajsA c.67.1.1 34291 1jevA 517 3.90e+00 1jevA c.94.1.1 35720 1mat 264 3.95e+00 1c24A d.127.1.1 41152 1gpb 842 4.09e+00 1a8i c.87.1.4 35478 2scuA 288 4.20e+00 2scuA c.2.1.8 30303 c.23.4.1 31131 1yagA 375 4.46e+00 1yagA c.55.1.1 33449 c.55.1.1 33450 1i50B 1224 4.52e+00 e.29.1.2 61755 2olbA 517 4.57e+00 1jevA c.94.1.1 35721 1qh4A 380 4.60e+00 1qh4A a.83.1.1 18462 d.128.1.2 41197 1bqbA 301 4.99e+00 1hyt d.92.1.2 58962 1cfzA 162 5.02e+00 1cfzA c.56.1.1 33754 1jg1A 235 5.08e+00 c.66.1.7 66661 1a1w 91 5.38e+00 1a1z a.77.1.1 18425 1iqrA 420 5.51e+00 a.99.1.1 66275 c.28.1.1 66276 2shpA 525 5.61e+00 2shpA c.45.1.2 32683 d.93.1.1 40533 d.93.1.1 40534 1bkjA 240 5.63e+00 1bkjA d.90.1.1 40243 1aa8A 347 5.65e+00 1an9A c.4.1.2 30619 d.16.1.3 37906 1amuA 563 5.65e+00 1amuA e.23.1.1 43351 2bvwA 362 5.71e+00 1bvwA c.6.1.1 30666 1vls 146 6.03e+00 1vls a.24.2.1 16532 1ars 396 6.08e+00 1ajsA c.67.1.1 34287 1hvd 319 6.15e+00 1avc a.65.1.1 18154 1d4xA 375 6.23e+00 1yagA c.55.1.1 59107 c.55.1.1 59108 1kzhA 555 6.24e+00 1iqcA 308 6.27e+00 a.3.1.5 66266 a.3.1.5 66267 1lucB 324 6.36e+00 1lucA c.1.16.1 29548 1bal 51 6.42e+00 1bbl a.9.1.1 16357 1bbl 51 6.54e+00 1bbl a.9.1.1 16356 1quqB 121 6.59e+00 1quqB b.40.4.3 25305 1jnyA 435 6.62e+00 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1an9A 340 6.64e+00 1an9A c.4.1.2 30617 d.16.1.3 37904 1dmhA 311 6.79e+00 1dmhA b.3.6.1 22633 1scuA 288 6.87e+00 2scuA c.2.1.8 30307 c.23.4.1 31135 1gryA 290 6.90e+00 1l6xB 34 7.17e+00 2ligA 164 7.23e+00 1vls a.24.2.1 16530 1brfA 53 7.30e+00 1rb9 g.41.5.1 45236 1j6zA 376 7.45e+00 1yagA c.55.1.1 62667 c.55.1.1 62668 1c3d 294 7.59e+00 1c3d a.102.4.4 18874 2matA 264 7.64e+00 1c24A d.127.1.1 41146 1a1z 91 7.81e+00 1a1z a.77.1.1 18427 1h8eD 482 7.99e+00 1skyE a.69.1.1 60747 b.49.1.1 60748 c.37.1.11 60749 1eudA 311 8.04e+00 2scuA c.2.1.8 30312 c.23.4.1 31140 1bvwA 360 8.52e+00 1bvwA c.6.1.1 30668 1cec 343 8.99e+00 1ceo c.1.8.3 28809 2ms2A 129 9.05e+00 1msc d.85.1.1 40049 1bax 94 9.26e+00 1bax a.61.1.3 18133 1jkfA 533 9.31e+00 1jj2Q 154 9.38e+00 1ffkO d.55.1.1 63102 1dgaA 375 9.55e+00 1yagA c.55.1.1 33441 c.55.1.1 33442 1ffkO 154 9.65e+00 1ffkO d.55.1.1 38899 1brlB 324 9.68e+00 1lucA c.1.16.1 29554 1bvh 157 9.76e+00 1dg9A c.44.1.1 32640 1j7iA 264 1.00e+01 1j7iA d.144.1.6 62694 1cf9A 753 1.00e+01 1cf9A c.23.16.3 31441 e.5.1.1 42815 1gwcA 230 1.01e+01 1hjp 203 1.02e+01 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1e79D 482 1.02e+01 1skyE a.69.1.1 18272 b.49.1.1 26437 c.37.1.11 32317 1ceo 343 1.03e+01 1ceo c.1.8.3 28808 1ka8A 100 1.04e+01 1msc 129 1.06e+01 1msc d.85.1.1 40039 1i7kA 179 1.09e+01 1u9aA d.20.1.1 61889 1qqfA 277 1.09e+01 1c3d a.102.4.4 18875 1k1gA 131 1.13e+01 d.51.1.1 68015 1a41 234 1.15e+01 1a41 d.163.1.2 42174 1ih8A 271 1.16e+01 2nsyA c.26.2.1 62377 2nsyA 271 1.16e+01 2nsyA c.26.2.1 31612 1jm7B 117 1.18e+01 g.44.1.1 66881 1h4vB 421 1.25e+01 1adjA c.51.1.1 60624 d.104.1.1 60625 1g0cA 364 1.25e+01 7a3hA c.1.8.3 60165 1adjA 421 1.29e+01 1adjA c.51.1.1 33188 d.104.1.1 40737 2btfA 375 1.31e+01 1yagA c.55.1.1 33429 c.55.1.1 33430 1aisA 182 1.34e+01 1ytbA d.129.1.1 41288 d.129.1.1 41289 1u9aA 160 1.39e+01 1u9aA d.20.1.1 38333 1gw5S 142 1.40e+01 1mhyD 521 1.41e+01 1mhyD a.25.1.2 16780 1hi0P 664 1.41e+01 1hi0P e.8.1.6 61051 1knzA 164 1.43e+01 e.34.1.1 68709 1c24A 263 1.44e+01 1c24A d.127.1.1 41148 1cuk 203 1.45e+01 1hjp a.5.1.1 16273 a.60.2.1 17946 b.40.4.2 25265 1jraA 117 1.49e+01 a.24.15.1 67117 1qd9A 124 1.52e+01 1qu9A d.79.1.1 39758 1l3lA 234 1.59e+01 1agrE 205 1.63e+01 1agrE a.91.1.1 18538 1jkw 323 1.63e+01 1jkw a.74.1.1 18356 a.74.1.1 18357 1cmbA 104 1.65e+01 1cmbA a.43.1.2 17460 1fo4A 1332 1.66e+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 1qc5A 192 1.67e+01 1aoxA c.62.1.1 34147 1it2A 146 1.68e+01 a.1.1.2 66365 1hekA 131 1.70e+01 a.61.1.5 65818 1ahpA 797 1.70e+01 1a8i c.87.1.4 35544 1ponB 36 1.70e+01 1ponB 1kafA 108 1.70e+01 d.199.1.1 68372 1kxrA 339 1.74e+01 1pyiA 96 1.75e+01 1pyiA g.38.1.1 45079 h.1.3.1 45512 1auq 208 1.75e+01 1auq c.62.1.1 34137 1eq2A 310 1.76e+01 1eq2A c.2.1.2 29814 1oakA 196 1.80e+01 1auq c.62.1.1 34138 1ijbA 202 1.85e+01 1j77A 209 1.86e+01 1j77A a.132.1.2 62674 1gox 370 1.91e+01 1gox c.1.4.1 28607 1h54A 754 1.92e+01 a.102.1.4 60634 b.30.4.1 60635 1g71A 347 1.95e+01 1g71A e.16.1.1 43268 1iro 54 1.96e+01 1rb9 g.41.5.1 45223 1co6A 107 1.97e+01 1ycc a.3.1.1 15894 1g61A 228 1.98e+01 1g61A d.126.1.1 41126 1scfA 273 1.99e+01 1exzA a.26.1.2 16873 1dguA 183 2.00e+01 1dguA a.39.1.5 17333 1e2fA 215 2.03e+01 3tmkA c.37.1.1 59164 1aoy 78 2.04e+01 1aoy a.4.5.3 16087 1fnsA 196 2.05e+01 1auq c.62.1.1 34136 1hhsA 664 2.05e+01 1hi0P e.8.1.6 61045 1e9eA 215 2.06e+01 c.37.1.1 64810 1egdA 396 2.08e+01 3mdeA a.29.3.1 16596 e.6.1.1 42857 1mup 166 2.12e+01 1mup b.60.1.1 27133 1ffkM 148 2.13e+01 1ffkM a.94.1.1 18740 1guxA 218 2.14e+01 1guxA a.74.1.3 18388 1jr8A 117 2.17e+01 a.24.15.1 67115 1jgtA 513 2.18e+01 c.26.2.1 66684 d.153.1.1 66685 1ordA 730 2.21e+01 1ordA c.23.7.1 31274 c.67.1.5 34503 d.125.1.1 41124 1e2gA 215 2.22e+01 3tmkA c.37.1.1 59165 1djxB 624 2.23e+01 1djxB a.39.1.7 17343 b.7.1.1 23160 c.1.18.1 29588 1tdtA 259 2.26e+01 3tdt b.81.1.2 28055 8rxnA 52 2.26e+01 1rb9 g.41.5.1 45215 1mdyA 68 2.29e+01 1mdyA a.38.1.1 17132 1rb9 53 2.29e+01 1rb9 g.41.5.1 45214 1c8kA 842 2.31e+01 1a8i c.87.1.4 35491 3pvaA 335 2.33e+01 3pvaA d.153.1.3 41854 1ek8A 185 2.33e+01 1ek8A d.67.3.1 59444 4rxn 54 2.36e+01 1rb9 g.41.5.1 45226 1kv8A 216 2.39e+01 1colA 204 2.43e+01 1a87 f.1.1.1 43378 1jj2O 148 2.46e+01 1ffkM a.94.1.1 63100 1h5uA 842 2.57e+01 1a8i c.87.1.4 60655 2tdt 274 2.59e+01 3tdt b.81.1.2 28054 1dqnA 230 2.60e+01 1dqnA c.61.1.1 34067 1l5wA 796 2.60e+01 1cmcA 104 2.64e+01 1cmbA a.43.1.2 17462 1c8bA 371 2.64e+01 1c8bA c.56.1.2 59082 1hn2A 159 2.68e+01 b.60.1.1 65890 1obpA 159 2.71e+01 1obpA b.60.1.1 27092 1fc3A 120 2.74e+01 1fc3A a.4.6.3 16237 1dgsA 667 2.76e+01 1dgsA a.60.2.2 17963 b.40.4.6 25365 d.142.2.2 41581 1b4cA 92 2.76e+01 1b4cA a.39.1.2 17169 1efnB 152 2.77e+01 1efnB d.102.1.1 40699 1rgs 288 2.78e+01 1rgs b.82.3.2 28146 b.82.3.2 28147 1ka3A 90 2.79e+01 1bt3A 345 2.80e+01 1bt3A a.86.1.2 18507 3crxA 343 2.80e+01 4crxA a.60.9.1 18101 d.163.1.1 42161 1ii7A 333 2.83e+01 1ii7A d.159.1.4 62415 1httA 423 2.83e+01 1adjA c.51.1.1 33178 d.104.1.1 40727 1rdg 53 2.84e+01 1rb9 g.41.5.1 45221 1dqpA 230 2.84e+01 1dqnA c.61.1.1 34069 1eokA 290 2.88e+01 1eokA c.1.8.5 28991 1oasA 322 2.91e+01 1oasA c.79.1.1 35293 1tbgE 68 2.92e+01 1tbgE a.137.3.1 19630 1f7lA 121 2.99e+01 1f7lA d.150.1.2 59666 1fmjA 351 2.99e+01 c.37.1.5 59879 1ad1A 266 3.04e+01 1aj2 c.1.21.1 29668 1i50J 70 3.05e+01 a.4.11.1 61764 1k8kD 300 3.06e+01 d.198.2.1 68309 d.198.2.1 68310 1a8q 274 3.07e+01 1brt c.69.1.12 34702 1fcjA 322 3.09e+01 1oasA c.79.1.1 35289 2pvaA 345 3.14e+01 3pvaA d.153.1.3 41850 3tdt 274 3.16e+01 3tdt b.81.1.2 28053 1qcwA 410 3.22e+01 1gox c.1.4.1 28622 1jljA 189 3.23e+01 c.57.1.1 63169 1def 147 3.24e+01 1bs4A d.167.1.1 42306 1zymA 258 3.24e+01 1zymA a.60.10.1 18110 c.8.1.2 30705 1fjgM 126 3.26e+01 1fjfM a.5.5.1 16293 1k8kA 418 3.27e+01 c.55.1.1 68305 c.55.1.1 68306 1ihcA 188 3.27e+01 1di6A c.57.1.1 62379 2tmkA 216 3.28e+01 3tmkA c.37.1.1 31928 1ej2A 181 3.37e+01 1f9aA c.26.1.3 59414 1f0cA 305 3.37e+01 1c8oA e.1.1.1 42676 1rypH 205 3.37e+01 d.153.1.4 41876 1beo 98 3.42e+01 1bxm a.134.1.1 19619 1maz 221 3.45e+01 1maz f.1.4.1 43393 1k3kA 158 3.47e+01 1xsm 390 3.47e+01 1xsm a.25.1.2 16804 1mbe 53 3.48e+01 1mbe a.4.1.3 16038 1g2yA 32 3.51e+01 a.34.1.1 17003 1dlyA 164 3.56e+01 1dlyA a.1.1.1 14983 1gqvA 135 3.57e+01 1hi2A 135 3.57e+01 7rsa d.5.1.1 61057 1kqpA 271 3.58e+01 1ly1A 181 3.58e+01 1nsyA 271 3.61e+01 2nsyA c.26.2.1 31614 1ig3A 263 3.64e+01 1ig3A b.82.6.1 62358 c.100.1.1 62359 1mba 147 3.64e+01 2fal a.1.1.2 15149 1bix 287 3.66e+01 1bix d.151.1.1 41781 1anf 370 3.67e+01 4mbp c.94.1.1 35776 1hx1B 114 3.69e+01 1hx1B a.7.7.1 61350 1nfiC 301 3.73e+01 b.1.1.5 21943 b.2.5.1 22456 1pme 380 3.74e+01 1hcl d.144.1.1 41653 1jscA 630 3.77e+01 c.31.1.3 67224 c.36.1.1 67225 c.36.1.1 67226 1epbA 164 3.85e+01 1epaA b.60.1.1 27126 1amk 251 3.86e+01 1amk c.1.1.1 28503 1epaA 164 3.87e+01 1epaA b.60.1.1 27128 1aisB 200 3.92e+01 1aisB a.74.1.2 18384 a.74.1.2 18385 1jqjC 343 3.96e+01 a.80.1.1 67097 c.37.1.13 67098 1bcpB 199 3.98e+01 1bcpB b.40.2.1 25120 d.169.1.2 42429 1rpxA 230 3.98e+01 1rpxA c.1.2.2 28536 1hyqA 263 3.98e+01 1hyqA c.37.1.10 61412 1brwA 433 4.00e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626