# List of top-scoring protein chains for t2k-100-30-alpha 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 1bvqA 141 3.31e-04 1bvqA d.38.1.1 38542 1lo7A 141 4.77e-04 1c8uA 285 1.56e-03 1c8uA d.38.1.3 38547 d.38.1.3 38548 1iq0A 592 5.60e-02 a.27.1.1 66257 c.26.1.1 66258 d.67.2.1 66259 1whi 122 2.85e-01 1whi b.39.1.1 24810 1koqA 253 4.25e-01 2cba b.74.1.1 27964 1nfiA 301 6.83e-01 1a3qA b.1.1.5 21942 b.2.5.1 22455 3pcnA 200 8.32e-01 3pchA b.3.6.1 22725 1hf2A 210 9.39e-01 1hf2A b.80.3.1 60992 c.102.1.1 60993 3pcgA 200 9.72e-01 3pchA b.3.6.1 22647 1kopA 223 9.77e-01 2cba b.74.1.1 27966 2pcdA 200 9.87e-01 3pchA b.3.6.1 22665 3pchA 200 1.07e+00 3pchA b.3.6.1 22653 1eo9B 241 1.15e+00 3pchM b.3.6.1 22826 3pcgM 238 1.17e+00 3pchM b.3.6.1 22742 1bzyA 217 1.23e+00 1qk3A c.61.1.1 34071 2pia 321 1.24e+00 2pia b.43.4.2 25663 c.25.1.2 31553 d.15.4.2 37704 3pchM 238 1.27e+00 3pchM b.3.6.1 22748 1tf4A 605 1.27e+00 1tf4A a.102.1.2 18827 b.2.2.2 22393 1fil 139 1.43e+00 1pne d.110.1.1 40869 1az9 457 1.64e+00 1az9 c.55.2.1 33547 d.127.1.1 41164 2bpa1 426 1.65e+00 2bpa1 1ihkA 174 1.71e+00 1bfg b.42.1.1 62384 1jjyA 636 1.74e+00 1jjyA e.26.1.2 63141 1ffyA 917 1.83e+00 1qu2A a.27.1.1 16926 b.51.1.1 26891 c.26.1.1 31593 1qu2A 917 1.83e+00 1qu2A a.27.1.1 16925 b.51.1.1 26890 c.26.1.1 31592 1b65A 375 1.89e+00 1b65A d.154.1.1 42020 1pne 140 2.35e+00 1pne d.110.1.1 40866 1al0F 426 2.56e+00 2bpa1 b.10.1.1 23274 1ca1 370 2.64e+00 1ca1 a.124.1.1 19340 b.12.1.3 23648 2pcdM 238 2.67e+00 3pchM b.3.6.1 22760 1gaxA 862 2.79e+00 1gaxA a.27.1.1 16928 b.51.1.1 26893 c.26.1.1 31595 1dboA 506 2.91e+00 1dbgA b.80.1.4 28034 1gtrA 553 3.08e+00 1gtrA b.53.1.2 26939 c.26.1.1 31578 2scuB 388 3.35e+00 2scuB c.23.4.1 31141 d.142.1.4 41562 1hnoA 280 3.59e+00 1hnoA c.14.1.3 61095 1qhvA 195 3.72e+00 1qhvA b.21.1.1 23842 1krs 120 3.72e+00 1krs b.40.4.1 25256 1cvsC 225 3.78e+00 1cvsC b.1.1.4 21726 b.1.1.4 21727 1hnuA 280 4.00e+00 1hnoA c.14.1.3 61096 1svb 395 4.16e+00 1svb b.1.1.5 21814 f.10.1.1 43827 1qtqA 553 4.20e+00 1gtrA b.53.1.2 26940 c.26.1.1 31579 1qqtA 551 4.49e+00 1qqtA a.27.1.1 16923 c.26.1.1 31590 g.41.1.1 45175 1cne 270 4.67e+00 1ndh b.43.4.2 25661 c.25.1.1 31551 1dqeA 137 4.85e+00 1dqeA a.39.2.1 17388 1cskA 71 4.98e+00 1ckaA b.34.2.1 24513 1g7sA 594 4.99e+00 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1pcfA 66 5.00e+00 1pcfA d.18.1.1 38142 1dbgA 506 5.00e+00 1dbgA b.80.1.4 28033 1g7tA 594 5.01e+00 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1ibcB 88 5.07e+00 1pauB 1pvc2 271 5.10e+00 1aym2 1bmqB 88 5.32e+00 1pauB 1cor 82 5.38e+00 451c a.3.1.1 15903 1ayyA 151 6.17e+00 1apyA d.153.1.5 42016 1f4lA 551 6.27e+00 1qqtA a.27.1.1 59648 c.26.1.1 59649 g.41.1.1 59650 1lylA 504 6.59e+00 1lylA b.40.4.1 25261 d.104.1.1 40717 2bb8 71 6.78e+00 2bb8 d.10.1.1 37480 1acc 735 6.94e+00 1acc f.11.1.1 43828 1vcaA 202 6.96e+00 1vcaA b.1.1.3 21649 b.1.1.4 21685 1ckaA 57 6.96e+00 1ckaA b.34.2.1 24459 2gwxA 267 6.98e+00 2prgA a.123.1.1 19323 2ae2A 260 7.21e+00 1bdb c.2.1.2 29945 1hmpA 217 7.28e+00 1qk3A c.61.1.1 34075 1e1oA 504 7.55e+00 1lylA b.40.4.1 25258 d.104.1.1 40714 1aw8E 91 7.65e+00 1aw8B 1ospH 218 7.75e+00 1igtB b.1.1.1 20117 b.1.1.2 21147 1dceA 567 7.81e+00 1dceA a.118.6.1 19191 b.7.4.1 23218 c.10.2.2 30867 1dabA 539 7.82e+00 1dabA b.80.1.7 28049 1vkxA 273 8.10e+00 1a3qA b.1.1.5 21941 b.2.5.1 22454 1ecfA 504 8.22e+00 1ecfB c.61.1.1 34053 d.153.1.1 41820 2gdm 153 8.29e+00 2gdm a.1.1.2 15212 1l0wA 580 8.33e+00 1bb8 71 8.38e+00 2bb8 d.10.1.1 37478 1qg3A 195 9.20e+00 1qg3A b.1.2.1 21993 b.1.2.1 21994 1cd8 114 9.37e+00 1cd8 b.1.1.1 19714 1hmt 132 9.72e+00 1hmt b.60.1.2 27169 1je5A 206 1.00e+01 1je5A b.40.4.7 62909 1p32A 209 1.08e+01 1p32A d.25.1.1 38379 1fm0D 81 1.08e+01 1fmaD d.15.3.1 37642 1g7rA 594 1.14e+01 1g7rA b.43.3.1 25716 b.43.3.1 25717 c.20.1.1 31034 c.37.1.8 32149 1cwvA 492 1.14e+01 1cwvA b.1.14.1 22373 b.1.14.1 22374 b.1.14.1 22375 b.1.14.1 22376 d.169.1.3 42442 1mkaA 171 1.14e+01 1mkaA d.38.1.2 38543 1gm6A 175 1.15e+01 1lh1 153 1.16e+01 2gdm a.1.1.2 15222 1fmaD 81 1.16e+01 1fmaD d.15.3.1 37643 1fuiA 591 1.18e+01 1fuiA b.43.2.1 25674 c.85.1.1 35444 1gcvA 140 1.23e+01 1cg5B a.1.1.2 15410 1h5uA 842 1.24e+01 1a8i c.87.1.4 60655 9gafA 295 1.27e+01 1apyA d.153.1.5 42008 1eo1A 124 1.32e+01 1eo1A c.55.5.1 33739 2ms2A 129 1.37e+01 1msc d.85.1.1 40049 1c3mA 147 1.40e+01 1jotA b.77.3.1 27983 1aw8B 91 1.41e+01 1aw8B 3ullA 132 1.42e+01 3ullA b.40.4.3 25282 1np4A 184 1.43e+01 1np1A b.60.1.1 27166 1xypA 190 1.43e+01 1axkA b.29.1.11 24327 1lcl 142 1.46e+01 1lcl b.29.1.3 24216 1j9qA 341 1.46e+01 1nif b.6.1.3 62765 b.6.1.3 62766 1ecfB 504 1.47e+01 1ecfB c.61.1.1 34054 d.153.1.1 41821 3mhtA 327 1.48e+01 6mhtA c.66.1.10 34234 1hdkA 141 1.51e+01 b.29.1.3 65807 1chmA 401 1.56e+01 1chmA c.55.2.1 33545 d.127.1.1 41142 1erxA 184 1.58e+01 1np1A b.60.1.1 27164 1dmzA 158 1.63e+01 1qu5A b.26.1.2 23921 1ha3A 405 1.63e+01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1a28A 256 1.64e+01 1a28A a.123.1.1 19290 1ekqA 272 1.68e+01 1c3qA c.72.1.2 34941 1plr 258 1.72e+01 1plq d.131.1.2 41390 d.131.1.2 41391 1vcc 77 1.74e+01 1vcc d.121.1.1 41092 1ijgA 309 1.74e+01 1fouA e.27.1.1 62493 1h5wA 309 1.75e+01 e.27.1.1 65635 1jmcA 246 1.76e+01 1jmcA b.40.4.3 25300 b.40.4.3 25301 1as8A 343 1.76e+01 1nif b.6.1.3 23074 b.6.1.3 23075 1hms 132 1.79e+01 1hmt b.60.1.2 27168 1lox 662 1.79e+01 1lox a.119.1.2 19238 b.12.1.1 23638 2lh2 153 1.80e+01 2gdm a.1.1.2 15220 1ghqB 134 1.81e+01 1ghqB g.18.1.1 60522 g.18.1.1 60523 1ris 101 1.83e+01 1ris d.58.14.1 39314 1cx4A 305 1.91e+01 b.82.3.2 59099 b.82.3.2 59100 1jj2N 115 1.91e+01 1ffkL c.12.1.1 63099 1louA 101 1.95e+01 1ris d.58.14.1 39323 1fts 295 1.97e+01 1ng1 a.24.13.1 16968 c.37.1.10 32279 1aop 497 1.97e+01 2aop d.58.36.1 39501 d.58.36.1 39502 d.134.1.1 41425 d.134.1.1 41426 1qq8A 214 2.00e+01 1qq8A a.132.1.1 19508 1cr1A 296 2.01e+01 1cr1A c.37.1.11 32286 1pls 113 2.05e+01 1pls b.55.1.1 26965 1lm8V 160 2.06e+01 1c7qA 445 2.06e+01 2pgi c.80.1.2 35307 2apr 325 2.09e+01 2er7E b.50.1.2 26819 1f02T 66 2.09e+01 1f02T j.67.1.1 46360 1mn1 357 2.09e+01 1arv a.93.1.1 18667 2cb5A 453 2.10e+01 3gcb d.3.1.1 37035 2mjpA 193 2.11e+01 1b78A c.51.4.1 33223 830cA 168 2.11e+01 1ck7A d.92.1.11 40400 1ea2A 131 2.12e+01 d.17.4.3 64860 3aprE 325 2.14e+01 2er7E b.50.1.2 26820 1icjA 168 2.15e+01 1bs4A d.167.1.1 42284 1bwwA 109 2.16e+01 8fabA b.1.1.1 20518 1bywA 110 2.17e+01 1bywA d.110.3.3 40912 1plq 258 2.17e+01 1plq d.131.1.2 41388 d.131.1.2 41389 1b78A 193 2.21e+01 1b78A c.51.4.1 33221 1np1A 184 2.22e+01 1np1A b.60.1.1 27155 1fjgK 129 2.24e+01 1fjfK c.55.4.1 33733 1i5pA 633 2.27e+01 1i5pA b.18.1.3 61817 b.77.2.1 61818 f.1.3.1 61819 1p32C 209 2.29e+01 1p32A d.25.1.1 38381 1cqmA 101 2.29e+01 1ris d.58.14.1 39321 1i31A 314 2.30e+01 1bw8A b.2.7.1 22481 1an9A 340 2.31e+01 1an9A c.4.1.2 30617 d.16.1.3 37904 1kxgA 152 2.36e+01 1fwyA 331 2.36e+01 1fwyA b.81.1.4 28064 c.68.1.5 34522 2pgi 445 2.38e+01 2pgi c.80.1.2 35308 1et7A 341 2.42e+01 1nif b.6.1.3 23070 b.6.1.3 23071 1xgsA 295 2.43e+01 1bn5 a.4.5.25 16216 d.127.1.1 41153 2reb 352 2.44e+01 2reb c.37.1.11 32282 d.48.1.1 38767 1ble 163 2.51e+01 1ble c.38.1.1 32475 1dmmA 131 2.53e+01 1opy d.17.4.3 38114 1scs 237 2.59e+01 1nls b.29.1.1 23930 1ez1A 392 2.60e+01 1ez1A b.84.2.1 28248 c.30.1.1 31655 d.142.1.2 41500 1hxs2 272 2.60e+01 1fxjA 331 2.63e+01 1fwyA b.81.1.4 28062 c.68.1.5 34520 1eyzA 392 2.65e+01 1ez1A b.84.2.1 28246 c.30.1.1 31653 d.142.1.2 41498 1ddzA 496 2.67e+01 1ddzA c.53.2.1 33372 c.53.2.1 33373 1bwzA 274 2.69e+01 1bwzA d.21.1.1 38337 d.21.1.1 38338 1kk1A 410 2.70e+01 1xat 212 2.73e+01 2xat b.81.1.3 28059 1b64 91 2.79e+01 1b64 d.58.12.1 39306 1msc 129 2.79e+01 1msc d.85.1.1 40039 1bbzA 58 2.80e+01 1bbzA b.34.2.1 24477 1ijtA 128 2.83e+01 1bfg b.42.1.1 62510 1lepA 99 2.86e+01 1lepA b.35.1.1 24649 1koiA 184 2.87e+01 b.60.1.1 68725 1aa8A 347 2.90e+01 1an9A c.4.1.2 30619 d.16.1.3 37906 1iazA 179 2.93e+01 1iazA b.97.1.1 62131 1quqB 121 3.07e+01 1quqB b.40.4.3 25305 1g2oA 268 3.07e+01 1b8oA c.56.2.1 60228 1rrpB 134 3.07e+01 1rrpB b.55.1.3 26995 1qlyA 58 3.08e+01 1bbzA b.34.2.1 24530 1hnnA 282 3.12e+01 c.66.1.15 65895 1stfI 98 3.15e+01 1stfI d.17.1.2 38006 1vcbC 160 3.16e+01 1vcbC b.3.3.1 22535 1bs4A 168 3.19e+01 1bs4A d.167.1.1 42287 1e3mA 800 3.22e+01 1ewqA a.113.1.1 19075 c.37.1.12 32389 c.55.6.1 33746 d.75.2.1 39747 1nukA 183 3.23e+01 1nukA b.18.1.4 23721 1g7jA 107 3.28e+01 32c2A b.1.1.1 19932 1cauA 181 3.29e+01 1dgwA b.82.1.2 28102 1cr0A 296 3.29e+01 1cr1A c.37.1.11 32287 1bsjA 168 3.31e+01 1bs4A d.167.1.1 42302 1pa2A 306 3.31e+01 1bgp a.93.1.1 18693 1ca4A 168 3.32e+01 1d0aB b.8.1.1 23238 h.1.2.1 45445 1dj7B 75 3.34e+01 1dj7B b.34.4.3 24598 1opy 131 3.34e+01 1opy d.17.4.3 38113 1k4wA 252 3.34e+01 1gqpA 221 3.35e+01 1hmy 327 3.36e+01 6mhtA c.66.1.10 34229 1quqA 129 3.41e+01 1quqA b.40.4.3 25303 1b35A 260 3.42e+01 1b35A b.10.1.3 23333 1azu 128 3.43e+01 1nwpA b.6.1.1 23007 1ezvI 55 3.45e+01 1be3J f.2.1.8 59553 1f5mB 180 3.46e+01 1f5mB d.110.2.1 40896 1czyC 168 3.48e+01 1d0aB b.8.1.1 23222 h.1.2.1 45429 1jzgA 128 3.49e+01 b.6.1.1 67855 1i8fA 81 3.52e+01 1i8fA b.38.1.1 61959 1mdc 133 3.57e+01 1hmt b.60.1.2 27198 1ca9A 192 3.60e+01 1d0aB b.8.1.1 23244 h.1.2.1 45451 1i7gA 287 3.61e+01 1aipE 405 3.61e+01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 2rn2 155 3.64e+01 2rn2 c.55.3.1 33551 1cxvA 164 3.73e+01 1ck7A d.92.1.11 40404 1f5mA 180 3.74e+01 1f5mB d.110.2.1 40895 1hw5A 210 3.74e+01 2cgpA a.4.5.4 16098 b.82.3.2 28137 1f0lA 535 3.79e+01 1ddt b.2.1.1 22377 d.166.1.1 42239 f.1.2.1 43382 1fyhA 258 3.81e+01 1d9cA a.26.1.3 16907 a.26.1.3 16908 1mnmC 87 3.81e+01 1akhB a.4.1.1 15983 2aop 497 3.81e+01 2aop d.58.36.1 39503 d.58.36.1 39504 d.134.1.1 41427 d.134.1.1 41428 1a79A 171 3.82e+01 1a79A c.52.2.1 33340 d.75.1.1 39739 1djnA 729 3.85e+01 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 6mhtA 327 3.86e+01 6mhtA c.66.1.10 34226 1je0A 236 3.87e+01 c.56.2.1 66581 1vfbA 107 3.91e+01 8fabA b.1.1.1 19930 1smlA 269 3.93e+01 1smlA d.157.1.1 42053 2cuaA 135 3.94e+01 2cuaA b.6.1.2 23039 1gcb 454 3.96e+01 3gcb d.3.1.1 37034