# 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 1lo7A 141 6.30e-07 1bvqA 141 1.33e-06 1bvqA d.38.1.1 38542 1c8uA 285 4.36e-05 1c8uA d.38.1.3 38547 d.38.1.3 38548 1hnuA 280 6.09e-02 1hnoA c.14.1.3 61096 1hnoA 280 6.82e-02 1hnoA c.14.1.3 61095 1lylA 504 4.25e-01 1lylA b.40.4.1 25261 d.104.1.1 40717 1mkaA 171 7.69e-01 1mkaA d.38.1.2 38543 1whi 122 1.05e+00 1whi b.39.1.1 24810 1iq0A 592 1.06e+00 a.27.1.1 66257 c.26.1.1 66258 d.67.2.1 66259 1jjyA 636 1.43e+00 1jjyA e.26.1.2 63141 1xypA 190 1.93e+00 1axkA b.29.1.11 24327 2bpa1 426 2.66e+00 2bpa1 1f4lA 551 3.74e+00 1qqtA a.27.1.1 59648 c.26.1.1 59649 g.41.1.1 59650 1f8yA 157 3.80e+00 1f8xA c.23.14.1 31395 1cskA 71 4.00e+00 1ckaA b.34.2.1 24513 1c1lA 136 4.01e+00 1c1lA b.29.1.3 24219 1f8xA 157 4.19e+00 1f8xA c.23.14.1 31397 1qg3A 195 4.59e+00 1qg3A b.1.2.1 21993 b.1.2.1 21994 1e1oA 504 4.60e+00 1lylA b.40.4.1 25258 d.104.1.1 40714 1qqtA 551 4.76e+00 1qqtA a.27.1.1 16923 c.26.1.1 31590 g.41.1.1 45175 1ckaA 57 5.37e+00 1ckaA b.34.2.1 24459 1jeqA 609 5.68e+00 1jeqA a.140.2.1 64748 e.31.1.1 64749 1jeyA 609 5.73e+00 1jeqA e.31.1.1 62924 1d5mB 192 5.84e+00 1iakB b.1.1.2 21618 d.19.1.1 38192 1i0rA 169 5.89e+00 1i0rA b.45.1.2 61489 1i0sA 169 5.89e+00 1i0rA b.45.1.2 61491 1bsjA 168 6.28e+00 1bs4A d.167.1.1 42302 1dciA 275 6.30e+00 1dciA c.14.1.3 30918 1kk1A 410 6.42e+00 1mdc 133 7.31e+00 1hmt b.60.1.2 27198 1ibcB 88 7.79e+00 1pauB 1dqeA 137 8.20e+00 1dqeA a.39.2.1 17388 1b35A 260 8.29e+00 1b35A b.10.1.3 23333 1bmqB 88 8.34e+00 1pauB 1cor 82 8.64e+00 451c a.3.1.1 15903 1aw8B 91 8.65e+00 1aw8B 1fzoA 274 8.79e+00 1agdA b.1.1.2 60155 d.19.1.1 60156 1b65A 375 8.89e+00 1b65A d.154.1.1 42020 1hmpA 217 9.13e+00 1qk3A c.61.1.1 34075 1hdkA 141 9.19e+00 b.29.1.3 65807 1lcl 142 9.27e+00 1lcl b.29.1.3 24216 1aw8E 91 9.51e+00 1aw8B 1sltA 134 9.58e+00 1c1lA b.29.1.3 24186 1koqA 253 9.78e+00 2cba b.74.1.1 27964 1ifc 132 1.01e+01 b.60.1.2 27173 1qupA 222 1.02e+01 1qupA b.1.8.1 22301 d.58.17.1 39352 1e32A 458 1.03e+01 1e32A b.52.2.3 59183 c.37.1.13 59184 d.31.1.1 59185 1pcfA 66 1.04e+01 1pcfA d.18.1.1 38142 1qk3A 233 1.08e+01 1qk3A c.61.1.1 34031 2stv 195 1.12e+01 2stv b.10.1.2 23287 1qtsA 247 1.16e+01 1qtsA b.1.10.1 22313 d.105.1.1 40789 1gqvA 135 1.30e+01 1fzkA 274 1.34e+01 1agdA b.1.1.2 60149 d.19.1.1 60150 1bzyA 217 1.40e+01 1qk3A c.61.1.1 34071 1kyfA 247 1.40e+01 3hhrB 203 1.40e+01 1axiB b.1.2.1 22005 b.1.2.1 22006 1tf4A 605 1.40e+01 1tf4A a.102.1.2 18827 b.2.2.2 22393 1lla 628 1.44e+01 1lla a.85.1.1 18485 a.86.1.1 18496 b.1.1.5 21861 2gdm 153 1.44e+01 2gdm a.1.1.2 15212 1lh1 153 1.44e+01 2gdm a.1.1.2 15222 2lh2 153 1.44e+01 2gdm a.1.1.2 15220 1agdA 276 1.45e+01 1agdA b.1.1.2 20741 d.19.1.1 38260 1ezvI 55 1.52e+01 1be3J f.2.1.8 59553 1h5wA 309 1.58e+01 e.27.1.1 65635 1b9kA 238 1.66e+01 1qtsA b.1.10.1 22315 d.105.1.1 40791 1hi2A 135 1.66e+01 7rsa d.5.1.1 61057 1gaxA 862 1.67e+01 1gaxA a.27.1.1 16928 b.51.1.1 26893 c.26.1.1 31595 1gcvA 140 1.74e+01 1cg5B a.1.1.2 15410 1cd8 114 1.78e+01 1cd8 b.1.1.1 19714 1l9mA 692 1.82e+01 830cA 168 1.87e+01 1ck7A d.92.1.11 40400 1b9zA 516 1.91e+01 1b9zA b.3.1.1 22528 c.1.8.2 28798 1qhvA 195 1.92e+01 1qhvA b.21.1.1 23842 1ej8A 140 1.98e+01 1qupA b.1.8.1 22300 2ae2A 260 2.00e+01 1bdb c.2.1.2 29945 1hms 132 2.11e+01 1hmt b.60.1.2 27168 1hmt 132 2.11e+01 1hmt b.60.1.2 27169 1fjgQ 105 2.12e+01 1fjfQ b.40.4.5 25352 1i4fA 275 2.23e+01 1agdA b.1.1.2 61687 d.19.1.1 61688 1sltB 134 2.26e+01 1c1lA b.29.1.3 24187 1duzA 275 2.26e+01 1agdA b.1.1.2 20670 d.19.1.1 38224 1nfiA 301 2.27e+01 1a3qA b.1.1.5 21942 b.2.5.1 22455 1a79A 171 2.36e+01 1a79A c.52.2.1 33340 d.75.1.1 39739 1ndh 272 2.39e+01 1ndh b.43.4.2 25662 c.25.1.1 31552 2fibA 269 2.43e+01 3fib d.171.1.1 42457 1hbyA 123 2.43e+01 7rsa d.5.1.1 60936 2pia 321 2.43e+01 2pia b.43.4.2 25663 c.25.1.2 31553 d.15.4.2 37704 1ll1 590 2.44e+01 1lla a.85.1.1 18488 a.86.1.1 18499 b.1.1.5 21864 1b8aA 438 2.47e+01 1b8aA b.40.4.1 25244 d.104.1.1 40765 1g4mA 393 2.51e+01 b.1.1.5 65143 b.1.1.5 65144 1a4yB 123 2.55e+01 7rsa d.5.1.1 37296 1pyaB 228 2.58e+01 1pyaB 1a78A 134 2.59e+01 1c1lA b.29.1.3 24212 1gmmA 133 2.66e+01 b.18.1.10 65314 1e54A 332 2.68e+01 1e54A f.4.3.1 59258 1egnA 434 2.68e+01 1celA b.29.1.10 59411 6cel 434 2.68e+01 1celA b.29.1.10 24279 1f46A 140 2.70e+01 1f46A d.129.4.1 59643 1az9 457 2.74e+01 1az9 c.55.2.1 33547 d.127.1.1 41164 1hzgA 295 2.76e+01 1hzgA d.194.1.1 61436 1celA 434 2.76e+01 1celA b.29.1.10 24280 1hq0A 295 2.79e+01 1hzgA d.194.1.1 61122 3fib 249 2.89e+01 3fib d.171.1.1 42455 1slaA 134 3.02e+01 1c1lA b.29.1.3 24196 1qq8A 214 3.06e+01 1qq8A a.132.1.1 19508 1ifqA 138 3.14e+01 1ifqA d.110.4.1 62350 1cxvA 164 3.16e+01 1ck7A d.92.1.11 40404 1fib 269 3.16e+01 3fib d.171.1.1 42456 1ffyA 917 3.18e+01 1qu2A a.27.1.1 16926 b.51.1.1 26891 c.26.1.1 31593 1qu2A 917 3.18e+01 1qu2A a.27.1.1 16925 b.51.1.1 26890 c.26.1.1 31592 1sftA 388 3.28e+01 1bd0A b.49.2.1 26482 c.1.6.1 28644 1fsgA 233 3.30e+01 1qk3A c.61.1.1 34029 1gefA 123 3.32e+01 1gefA c.52.1.18 60465 1ijgA 309 3.41e+01 1fouA e.27.1.1 62493 1vcaA 202 3.41e+01 1vcaA b.1.1.3 21649 b.1.1.4 21685 1l0wA 580 3.43e+01 1ecfB 504 3.45e+01 1ecfB c.61.1.1 34054 d.153.1.1 41821 1bd0A 388 3.47e+01 1bd0A b.49.2.1 26480 c.1.6.1 28642 1k59A 123 3.52e+01 1deuA 277 3.65e+01 1theB d.3.1.1 37085 1g7tA 594 3.72e+01 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1hqsA 423 3.72e+01 1iso c.77.1.1 61154 1i31A 314 3.77e+01 1bw8A b.2.7.1 22481 1cewI 108 3.77e+01 1cewI d.17.1.2 37999 1plq 258 3.99e+01 1plq d.131.1.2 41388 d.131.1.2 41389