# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-scores 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 1szwA 379 1.71e-01 unknown_sccs -10164 1s4bP 674 5.16e-01 1shwA 138 5.78e-01 1je5A 206 7.07e-01 1je5A b.40.4.7 62909 1n9lA 109 8.53e-01 d.110.3.6 85468 1egiA 147 1.31e+00 1eggA d.169.1.1 42331 2hft 218 1.31e+00 1boy b.1.2.1 21951 b.1.2.1 21952 1tul 108 1.35e+00 1tul b.85.5.1 28373 1eggA 147 1.37e+00 1eggA d.169.1.1 42333 1shbA 104 1.37e+00 1fmk d.93.1.1 40425 1shaA 104 1.43e+00 1fmk d.93.1.1 40424 1op4A 159 1.47e+00 b.1.6.1 -2794 1vavA 222 1.69e+00 1mjc 69 1.70e+00 1mjc b.40.4.5 25319 1lckA 175 1.71e+00 1lckA b.34.2.1 24552 d.93.1.1 40421 1bftA 101 1.87e+00 1a3qA b.1.18.1 21934 1o4rA 108 1.90e+00 d.93.1.1 -10624 1eluB 390 2.12e+00 1elqA c.67.1.3 34435 1danU 121 2.14e+00 1boy b.1.2.1 21954 1bj8 109 2.34e+00 1bquA b.1.2.1 22070 1eza 259 2.61e+00 1zymA a.60.10.1 18113 c.8.1.2 30708 1s0uA 408 2.73e+00 b.43.3.1 -4053 b.44.1.1 -4061 c.37.1.8 -7096 1f2fA 104 3.07e+00 1fmk d.93.1.1 40455 1c8pA 102 3.13e+00 1c8pA b.1.2.1 22040 1f7tA 122 3.48e+00 1f7lA d.150.1.2 59667 1bquA 215 3.50e+00 1bquA b.1.2.1 22066 b.1.2.1 22067 1pyaB 228 3.51e+00 1pyaB 1eluA 390 3.53e+00 1elqA c.67.1.3 34434 1ibvB 229 3.64e+00 1elqA 390 3.70e+00 1elqA c.67.1.3 34436 1q6hA 224 3.75e+00 d.26.1.1 -9487 1jsxA 207 3.86e+00 c.66.1.20 71846 1hyhA 309 3.90e+00 1hyhA c.2.1.5 30150 d.162.1.1 42117 1boy 219 4.10e+00 1boy b.1.2.1 21955 b.1.2.1 21956 1mh9A 197 4.24e+00 c.108.1.8 79118 1ts3A 194 4.41e+00 1aw7A b.40.2.2 25168 d.15.6.1 37757 1csp 67 4.68e+00 1mjc b.40.4.5 25321 1grwA 126 4.72e+00 b.1.11.2 70391 1vheA 373 4.81e+00 unknown_sccs -4280 c.56.5.4 -7890 1m4jA 142 5.13e+00 d.109.1.2 78602 1guiA 155 5.29e+00 b.18.1.14 76351 1ncg 110 5.34e+00 1edhA b.1.6.1 22193 1ois 223 5.49e+00 1a36A e.15.1.1 43267 1aw7A 194 5.52e+00 1aw7A b.40.2.2 25164 d.15.6.1 37753 1si7A 369 5.74e+00 unknown_sccs -10163 1bp3B 211 5.97e+00 1axiB b.1.2.1 22031 b.1.2.1 22032 1iz6A 138 6.08e+00 b.34.5.2 76976 b.40.4.5 76977 2eifA 136 6.13e+00 1bkb b.34.5.2 24607 b.40.4.5 25339 1jzgA 128 6.24e+00 b.6.1.1 67855 1lqtA 456 6.48e+00 c.3.1.1 74198 c.4.1.1 74199 1shdA 107 6.71e+00 1fmk d.93.1.1 40440 1vddA 228 6.72e+00 1oyeA 1049 6.88e+00 d.58.44.1 87587 d.58.44.1 87588 d.58.44.1 87589 d.58.44.1 87590 d.225.1.1 87591 d.225.1.1 87592 f.35.1.1 87593 f.35.1.1 87594 1r0kA 388 7.00e+00 1f15A 218 7.02e+00 1f15B b.121.4.5 23320 1i1iP 681 7.04e+00 1i1iP d.92.1.5 40297 1draA 159 7.16e+00 1vdrA c.71.1.1 34831 1g1sA 162 7.21e+00 d.169.1.1 65100 g.3.11.1 65101 1qr0A 228 7.34e+00 1qr0A d.150.1.1 59038 d.150.1.1 59039 1jkmB 361 7.46e+00 1jkmA c.69.1.2 34634 1mfa 247 7.52e+00 1mfa b.1.1.1 19888 b.1.1.1 19889 1jr8A 117 7.87e+00 a.24.15.1 67115 1jraA 117 7.96e+00 a.24.15.1 67117 1q4rA 112 8.11e+00 d.58.4.4 -9943 1g5aA 628 8.32e+00 b.71.1.1 65152 c.1.8.1 65153 1gu3A 149 8.43e+00 b.18.1.14 76350 1ib8A 164 8.69e+00 b.38.2.1 71168 d.52.4.1 71169 1efcA 393 8.96e+00 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1cc3A 130 9.13e+00 1nwpA b.6.1.1 23008 3tss 194 9.29e+00 1aw7A b.40.2.2 25160 d.15.6.1 37749 1jkmA 358 9.36e+00 1jkmA c.69.1.2 34633 1q92A 197 9.37e+00 c.108.1.8 -6819 1gl4B 98 9.39e+00 b.1.1.4 65288 1jsdA 319 9.58e+00 b.19.1.2 63258 8prkA 287 9.62e+00 1wgjA b.40.5.1 25395 1txb 73 9.69e+00 1txb g.7.1.1 44455 1e0tA 470 9.70e+00 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1fmk 452 9.76e+00 1fmk b.34.2.1 24511 d.93.1.1 40436 d.144.1.7 41690 1nciA 110 1.00e+01 1edhA b.1.6.1 22191 1ia9A 280 1.01e+01 1ia9A d.144.1.5 62113 1pkn 530 1.02e+01 1a49A b.58.1.1 27042 c.1.12.1 29271 c.49.1.1 33125 7taa 478 1.05e+01 7taa b.71.1.1 27778 c.1.8.1 28765 1c9oA 66 1.05e+01 1mjc b.40.4.5 25325 1on0A 158 1.07e+01 d.108.1.1 87095 1mjgM 729 1.09e+01 e.26.1.3 79204 1jn5A 140 1.09e+01 d.17.4.2 66921 1f7lA 121 1.10e+01 1f7lA d.150.1.2 59666 1n3oA 252 1.10e+01 b.29.1.1 79967 1a3qA 285 1.11e+01 1a3qA b.1.18.1 21932 b.2.5.3 22447 1ten 90 1.13e+01 1ten b.1.2.1 21990 1fokA 568 1.19e+01 2fokA a.4.5.12 16137 a.4.5.12 16138 a.4.5.12 16139 c.52.1.12 33325 1fxoA 293 1.19e+01 1g0rA c.68.1.6 34524 1r8oA 96 1.20e+01 1f6fB 210 1.20e+01 1axiB b.1.2.1 22033 b.1.2.1 22034 1bywA 110 1.23e+01 1bywA d.110.3.6 40912 1jj2I 145 1.24e+01 1ffkG c.21.1.1 63094 1avgI 142 1.25e+01 1avgI b.60.1.3 27229 1iqrA 420 1.25e+01 a.99.1.1 66275 c.28.1.1 66276 1f15B 218 1.30e+01 1f15B b.121.4.5 23321 1fnf 368 1.31e+01 1fnf b.1.2.1 21972 b.1.2.1 21973 b.1.2.1 21974 b.1.2.1 21975 1s72Q 96 1.33e+01 1ln1A 214 1.33e+01 d.129.3.2 74038 6dfr 159 1.33e+01 1vdrA c.71.1.1 34874 1a3k 137 1.35e+01 1a3k b.29.1.3 24218 1pz1A 333 1.36e+01 c.1.7.1 -5255 1fnhA 271 1.37e+01 1fnhA b.1.2.1 21976 b.1.2.1 21977 b.1.2.1 21978 1e6yB 433 1.38e+01 1mroB a.89.1.1 18535 d.58.31.2 39453 1vixA 420 1.39e+01 c.56.5.4 -7866 d.58.19.1 -10090 1my7A 114 1.41e+01 b.1.18.1 79675 1wgjA 286 1.42e+01 1wgjA b.40.5.1 25397 1lwdA 413 1.43e+01 c.77.1.1 78265 1h95A 79 1.45e+01 b.40.4.5 65742 1ukgA 252 1.45e+01 b.29.1.1 -3390 1g0rA 293 1.47e+01 1g0rA c.68.1.6 34532 1cdi 179 1.48e+01 1cdy b.1.1.1 19727 b.1.1.3 21666 1kewA 361 1.53e+01 c.2.1.2 68544 1hyeA 313 1.58e+01 2cmd c.2.1.5 61400 d.162.1.1 61401 1id2A 106 1.60e+01 1aac b.6.1.1 62288 1fy7A 278 1.61e+01 1fy7A d.108.1.1 40817 1uf6A 178 1.63e+01 unknown_sccs -4533 1ur5A 309 1.63e+01 c.2.1.5 -5910 d.162.1.1 -11477 1ufhA 180 1.64e+01 d.108.1.1 88485 1oaoC 729 1.71e+01 e.26.1.3 86746 1my5A 114 1.71e+01 b.1.18.1 79673 1rowA 109 1.73e+01 b.1.11.2 -2851 1pxvA 183 1.75e+01 d.3.1.1 -8881 1sb0A 87 1.75e+01 a.12.1.1 -455 1jkgA 140 1.76e+01 d.17.4.2 66795 1j8yF 297 1.77e+01 1ng1 a.24.13.1 62747 c.37.1.10 62748 2hdhA 293 1.79e+01 2hdhA a.100.1.3 18795 c.2.1.6 30199 32c2A 217 1.79e+01 32c2A b.1.1.1 20438 b.1.1.2 21404 1fna 93 1.83e+01 1fnf b.1.2.1 21971 1nkqA 259 1.84e+01 1c1lA 136 1.84e+01 1c1lA b.29.1.3 24219 1feuA 206 1.87e+01 1feuA b.53.1.1 59801 1r3eA 309 1.88e+01 b.122.1.1 -5118 unknown_sccs -10146 1aizA 129 1.91e+01 1nwpA b.6.1.1 22903 1ir6A 424 1.92e+01 c.107.1.2 71342 1jh2A 99 1.96e+01 1mspA 126 1.97e+01 1mspA b.1.11.2 22333 1o6zA 303 1.99e+01 c.2.1.5 81107 d.162.1.1 81108 1j8mF 297 1.99e+01 1ng1 a.24.13.1 62742 c.37.1.10 62743 1mw9X 592 2.00e+01 e.10.1.1 -11986 1mfn 185 2.01e+01 1qr4B b.1.2.1 21984 b.1.2.1 21985 1nfiA 301 2.03e+01 1a3qA b.1.18.1 21942 b.2.5.3 22455 1ftrA 296 2.06e+01 1ftrA d.58.33.1 39485 d.58.33.1 39486 1ksr 100 2.07e+01 1qfhA b.1.18.10 21897 1nwpA 128 2.07e+01 1nwpA b.6.1.1 23011 1sltA 134 2.07e+01 1c1lA b.29.1.3 24186 1ntyA 311 2.11e+01 1e9gA 286 2.12e+01 1wgjA b.40.5.1 59393 1e9gB 286 2.15e+01 1wgjA b.40.5.1 59394 1sltB 134 2.15e+01 1c1lA b.29.1.3 24187 1iwgA 1053 2.17e+01 d.58.44.1 76874 d.58.44.1 76875 d.58.44.1 76876 d.58.44.1 76877 d.225.1.1 76878 d.225.1.1 76879 f.35.1.1 76880 f.35.1.1 76881 1f3rB 257 2.19e+01 1f3rB b.1.1.1 20417 b.1.1.1 20416 1mqvA 125 2.20e+01 a.24.3.2 79415 2mspA 126 2.21e+01 1mspA b.1.11.2 22335 1h5rA 293 2.24e+01 c.68.1.6 65623 1ipd 345 2.26e+01 1cnzA c.77.1.1 35038 1hdkA 141 2.26e+01 b.29.1.3 65807 1q53A 112 2.30e+01 d.58.4.4 -9944 1a81A 254 2.32e+01 1a81A d.93.1.1 40507 d.93.1.1 40508 3mefA 69 2.32e+01 1mjc b.40.4.5 25320 1lkkA 105 2.32e+01 1lckA d.93.1.1 40412 1ffkG 145 2.35e+01 1ffkG c.21.1.1 31035 1miuA 738 2.36e+01 a.170.1.1 79153 a.171.1.1 79154 b.40.4.3 79155 b.40.4.3 79156 b.40.4.3 79157 1qg3A 195 2.39e+01 1qg3A b.1.2.1 21993 b.1.2.1 21994 1jj2P 95 2.40e+01 1ffkN b.34.5.1 63101 1acc 735 2.42e+01 1acc f.11.1.1 43828 1cy9A 264 2.44e+01 1ecl e.10.1.1 43236 1eaf 243 2.44e+01 1eaf c.43.1.1 32617 1lcl 142 2.45e+01 1lcl b.29.1.3 24216 1nw3A 416 2.52e+01 c.66.1.31 86288 1fnoA 417 2.53e+01 c.56.5.4 75841 d.58.19.1 70145 2fnbA 95 2.53e+01 2fnbA b.1.2.1 21979 1n3yA 198 2.54e+01 c.62.1.1 79976 1k0rA 366 2.54e+01 b.40.4.5 67961 d.52.3.1 67962 d.52.3.1 67963 d.202.1.1 67964 1tsrA 219 2.55e+01 1tupA b.2.5.2 22437 1l5aA 436 2.68e+01 c.43.1.2 75923 c.43.1.2 75924 1h9sA 140 2.69e+01 1b9mA b.40.6.2 60843 b.40.6.2 60844 1dpb 243 2.70e+01 1eaf c.43.1.1 32618 1mp9A 198 2.71e+01 a.74.1.2 -1127 a.74.1.2 -1128 1a4uA 254 2.71e+01 1b16A c.2.1.2 29878 1avwB 171 2.74e+01 1wba b.42.4.1 25599 1kk1A 410 2.82e+01 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 1f5nA 592 2.84e+01 1dg3A a.114.1.1 19077 c.37.1.8 32152 1a7s 221 2.84e+01 1a7s b.47.1.2 26284 1tupA 219 2.86e+01 1tupA b.2.5.2 22434 1b16A 254 2.88e+01 1b16A c.2.1.2 29875 1mvfA 135 2.90e+01 b.1.1.1 85141 1p5hA 428 2.91e+01 c.123.1.1 87802 8prkB 287 2.92e+01 1wgjA b.40.5.1 25396 1q9jA 422 2.93e+01 1dr8B 344 2.93e+01 1cnzA c.77.1.1 35052 1a8vA 121 2.95e+01 1a62 a.140.3.1 64712 b.40.4.5 64713 1jc7A 131 2.95e+01 1jc7A b.40.3.2 62873 1gzwA 134 2.96e+01 b.29.1.3 -3412 1bkzA 135 2.96e+01 1a3k b.29.1.3 24202 1b6rA 355 2.99e+01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1g0xA 197 3.00e+01 1nkr b.1.1.4 21805 b.1.1.4 21806 1e3sA 261 3.03e+01 1e6wA c.2.1.2 59201 1g86A 142 3.04e+01 b.29.1.3 70161 1nfiC 301 3.05e+01 b.1.18.1 21943 b.2.5.3 22456 1a49A 530 3.08e+01 1a49A b.58.1.1 27026 c.1.12.1 29255 c.49.1.1 33109 1bpv 112 3.11e+01 1bpv b.1.2.1 22071 1ci3M 249 3.15e+01 1hcz b.2.6.1 22480 b.84.2.2 28266 1esl 162 3.21e+01 1esl d.169.1.1 42353 g.3.11.1 44225 1c5cH 215 3.21e+01 1igtB b.1.1.1 20475 b.1.1.2 21439 3ullA 132 3.22e+01 3ullA b.40.4.3 25282 1i7qA 519 3.23e+01 1qdlA d.161.1.1 61901 1kdxA 81 3.23e+01 1kdxA a.12.1.1 16375 1lldA 319 3.24e+01 3ldh c.2.1.5 30177 d.162.1.1 42144 1ov3A 138 3.27e+01 b.34.2.1 87451 b.34.2.1 87452 1nhp 447 3.27e+01 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1avaC 181 3.30e+01 1avaC b.42.4.1 25604 1go3E 187 3.30e+01 b.40.4.5 83054 d.230.1.1 83055 1bdyA 123 3.32e+01 1bdyA b.7.1.1 23190 1noa 113 3.39e+01 2mcm b.1.7.1 22208 1ekjB 221 3.43e+01 1ekjB c.53.2.1 33365 1uyrA 737 3.46e+01 c.14.1.4 -6258 c.14.1.4 -6259 1cr6B 554 3.51e+01 1cr6B c.108.1.2 43338 c.69.1.11 34688 1nhs 447 3.52e+01 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1k2fA 190 3.54e+01 b.8.1.2 68054 1ris 101 3.54e+01 1ris d.58.14.1 39314 1bio 228 3.58e+01 5ptp b.47.1.2 26314 1jlm 192 3.58e+01 1ido c.62.1.1 34140 1fftB 315 3.63e+01 1cyx b.6.1.2 23025 f.17.2.1 43628 1a62 130 3.63e+01 1a62 a.140.3.1 64708 b.40.4.5 64709 1fx3A 169 3.65e+01 1fx3B d.33.1.1 38524 1a7vA 125 3.66e+01 1cpq a.24.3.2 16562 1bxkA 355 3.66e+01 1bxkA c.2.1.2 29803 1ycsA 199 3.68e+01 1tupA b.2.5.2 22433 1bk1 184 3.68e+01 1axkA b.29.1.11 24340 1cc1S 283 3.70e+01 2frvA e.19.1.1 43313 1cp3A 277 3.73e+01 1pauA c.17.1.1 30992 1adn 92 3.74e+01 1adn g.48.1.1 45348 1cbs 137 3.74e+01 1hmt b.60.1.2 27201 1kwiA 101 3.76e+01 d.17.1.3 77564 1jp4A 308 3.81e+01 1jp4A e.7.1.1 63223 1b7eA 420 3.84e+01 1b7eA c.55.3.4 33680 7acn 754 3.85e+01 1amj c.8.2.1 30717 c.83.1.1 35393 1pwt 61 3.85e+01 1tud b.34.2.1 24490 2azaA 129 3.87e+01 1nwpA b.6.1.1 22901 1yna 194 3.87e+01 1axkA b.29.1.11 24335 1zymA 258 3.88e+01 1zymA a.60.10.1 18110 c.8.1.2 30705 1azu 128 3.92e+01 1nwpA b.6.1.1 23007 1h6yA 170 3.92e+01 b.18.1.7 70904 1vgyA 393 3.93e+01 c.56.5.4 -7882 d.58.19.1 -10106 1v3vA 333 3.95e+01 1b9kA 238 3.96e+01 1qtsA b.1.10.1 22315 d.105.1.1 40791 1musA 477 3.98e+01 c.55.3.4 79494 1c96A 753 4.00e+01 1amj c.8.2.1 30727 c.83.1.1 35403