# List of top-scoring protein chains for t04-100-40-40-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 1q9uA 130 4.13e-05 unknown_sccs -11025 1j3mA 129 4.77e-03 1ihoA 283 3.54e-02 1ihoA c.26.1.4 62390 1qtoA 122 9.96e-02 1bylA d.32.1.2 38494 1cx4A 305 2.58e-01 b.82.3.2 59099 b.82.3.2 59100 1lfpA 249 2.84e-01 e.39.1.1 73885 1ecsA 126 2.84e-01 1ecsA d.32.1.2 59407 1nxiA 132 3.39e-01 d.58.47.1 86381 1bazA 53 4.55e-01 1bazA a.43.1.1 17421 1hw5A 210 4.60e-01 2cgpA a.4.5.4 16098 b.82.3.2 28137 1pp7U 131 7.92e-01 unknown_sccs -304 1uf6A 178 1.07e+00 unknown_sccs -4533 1i9bA 217 1.11e+00 1i9bA b.96.1.1 62084 1qhlA 227 1.15e+00 1qhlA c.37.1.12 32382 1ufkA 254 1.21e+00 unknown_sccs -8103 1h7eA 245 1.29e+00 c.68.1.13 60717 1vjqA 79 1.33e+00 unknown_sccs -13478 1o6aA 96 1.37e+00 unknown_sccs -4101 1trb 320 1.43e+00 1trb c.3.1.5 30529 c.3.1.5 30530 1vrtA 560 1.71e+00 1rthA c.55.3.1 33574 e.8.1.2 43023 1m6iA 493 1.98e+00 c.3.1.5 74533 c.3.1.5 74534 d.87.1.1 74535 1fjgP 88 1.98e+00 1emwA d.27.1.1 38444 1ew0A 130 2.04e+00 1drmA d.110.3.2 40905 1j6qA 136 2.21e+00 b.40.9.1 77091 1gmuA 143 2.53e+00 b.107.1.1 65335 d.58.38.1 65336 1vjfA 180 2.54e+00 d.116.1.1 -10941 1hh1A 143 2.74e+00 1gefA c.52.1.18 61036 1sczA 233 2.78e+00 c.43.1.1 -7326 1cl1A 395 2.95e+00 1cl2A c.67.1.3 34395 1molA 94 2.99e+00 1molA d.17.1.1 37988 1tu1A 148 3.14e+00 1o8bA 219 3.14e+00 unknown_sccs 81180 d.58.40.1 81181 1t82A 155 3.26e+00 1h9dB 134 3.64e+00 2jhbA b.54.1.1 60822 1e3aB 560 3.64e+00 1ajqB 1gz8A 299 3.91e+00 d.144.1.7 83405 1mml 265 4.01e+00 1mml e.8.1.2 43015 1ne6A 283 4.16e+00 b.82.3.2 -4918 b.82.3.2 -4919 1s72H 171 4.21e+00 1gk9B 557 4.27e+00 1v9yA 167 4.32e+00 1p97A 114 4.43e+00 unknown_sccs -10844 1tuhA 156 4.57e+00 1i50F 155 4.70e+00 d.78.1.2 61760 1mo9A 523 4.71e+00 c.3.1.5 79341 c.3.1.5 79342 d.87.1.1 79343 1a7cA 379 4.75e+00 1sek e.1.1.1 42660 1nfp 228 4.80e+00 1nfp c.1.16.2 29555 1uw6A 211 4.93e+00 b.96.1.1 -3077 1e19A 314 4.95e+00 1b7bA c.73.1.1 34967 1eonA 245 4.99e+00 1rvaA c.52.1.2 33238 1ss4A 153 5.09e+00 1e7lA 157 5.29e+00 1en7A a.140.4.1 64728 d.4.1.5 64729 1hm9A 468 5.36e+00 b.81.1.4 65866 c.68.1.5 65867 1ci3M 249 5.47e+00 1hcz b.2.6.1 22480 b.84.2.2 28266 1jyoA 130 5.58e+00 d.198.1.1 67483 1l6rA 227 5.91e+00 c.108.1.10 77768 1nhp 447 5.92e+00 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1rlkA 117 6.26e+00 unknown_sccs -7526 1gefA 123 6.34e+00 1gefA c.52.1.18 60465 1oh0A 131 6.43e+00 d.17.4.3 87004 1nhs 447 6.51e+00 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1rvaA 244 6.72e+00 1rvaA c.52.1.2 33240 1fxlA 167 6.83e+00 1b7fA d.58.7.1 39183 d.58.7.1 39184 1i52A 236 6.97e+00 1i52A c.68.1.13 61767 1jhdA 396 7.08e+00 b.122.1.3 66712 c.26.1.5 66713 1rthA 560 7.40e+00 1rthA c.55.3.1 33576 e.8.1.2 43028 1or0B 528 7.59e+00 1iso 416 7.61e+00 1iso c.77.1.1 35065 1i3zA 103 7.72e+00 d.93.1.1 83667 1go4A 205 7.87e+00 d.135.1.1 70292 1hc7A 477 8.29e+00 1hc7A c.51.1.1 60938 d.68.5.1 60940 d.104.1.1 60939 1jyrA 96 8.57e+00 d.93.1.1 71969 1nrwA 288 8.63e+00 c.108.1.10 86128 1g8sA 230 9.14e+00 c.66.1.3 -8047 1q7hA 153 9.39e+00 b.122.1.1 -5124 unknown_sccs -9313 1ly1A 181 9.40e+00 c.37.1.1 74334 1pb1A 416 9.54e+00 c.77.1.1 88014 1iz0A 302 9.62e+00 b.35.1.2 83821 c.2.1.1 83822 1fbnA 230 9.69e+00 1fbnA c.66.1.3 34181 1fm2B 520 9.79e+00 1fm2B 1v8cA 168 9.98e+00 d.15.3.1 -9175 unknown_sccs -11012 1e4fT 419 1.01e+01 1e4fT c.55.1.1 33453 c.55.1.1 33454 1rg9A 383 1.02e+01 d.130.1.1 -11057 d.130.1.1 -11058 d.130.1.1 -11059 1t1vA 93 1.02e+01 1pvmA 184 1.02e+01 d.37.1.1 -9612 d.37.1.1 -9613 unknown_sccs -12799 1usuB 170 1.08e+01 unknown_sccs -10492 2cpgA 45 1.14e+01 2cpgA unknown_sccs 17455 1dx5I 118 1.15e+01 1dx5I g.3.11.1 44302 g.3.11.1 44303 g.3.11.1 44304 1sx5A 244 1.19e+01 c.52.1.2 -7551 1npk 154 1.21e+01 1npk d.58.6.1 39099 1havA 217 1.23e+01 1havA b.47.1.4 26423 1azo 232 1.27e+01 1azo c.52.1.14 33329 1nrgA 261 1.28e+01 b.45.1.1 80694 1zfpE 98 1.31e+01 1griA d.93.1.1 40465 1g97A 459 1.32e+01 1fwyA b.81.1.4 60394 c.68.1.5 60395 1eaf 243 1.33e+01 1eaf c.43.1.1 32617 1d8cA 723 1.34e+01 1d8cA c.1.13.1 29325 1fvrA 327 1.34e+01 d.144.1.7 60047 1uw1A 80 1.35e+01 unknown_sccs -13438 1p7tA 731 1.36e+01 c.1.13.1 -5600 3nul 130 1.36e+01 3nul d.110.1.1 40891 1itwA 741 1.40e+01 c.77.1.2 76793 1mwpA 96 1.43e+01 1mwpA d.170.2.1 42453 1thx 115 1.46e+01 1thx c.47.1.1 32732 1r0pA 312 1.51e+01 d.144.1.7 -11377 1gd8A 118 1.54e+01 d.188.1.1 60445 1i50A 1733 1.55e+01 e.29.1.2 61754 1c9oA 66 1.56e+01 1mjc b.40.4.5 25325 1nrlA 316 1.63e+01 a.123.1.1 -1668 1lj5A 379 1.63e+01 e.1.1.1 73928 1se8A 301 1.64e+01 1uc8A 280 1.64e+01 unknown_sccs -6718 unknown_sccs -11230 1sgvA 316 1.65e+01 b.122.1.1 -5120 unknown_sccs -10148 1lci 550 1.66e+01 1lci e.23.1.1 43349 1tiqA 180 1.66e+01 1kafA 108 1.66e+01 d.199.1.1 68372 1v25A 541 1.67e+01 1sh8A 154 1.72e+01 1uc7A 125 1.72e+01 c.47.1.1 -7414 1o0pA 104 1.74e+01 d.58.7.1 86535 1vhzA 198 1.76e+01 d.113.1.1 -10897 1h75A 81 1.76e+01 1h75A c.47.1.1 60716 1htyA 1015 1.78e+01 a.8.3.1 83064 b.30.5.6 83065 c.6.2.1 83066 1fjlA 81 1.79e+01 2hddA a.4.1.1 16017 1a8vA 121 1.81e+01 1a62 a.140.3.1 64712 b.40.4.5 64713 1hcl 298 1.82e+01 1hcl d.144.1.7 41593 1buoA 121 1.82e+01 1buoA d.42.1.1 38631 1nz6A 101 1.86e+01 a.2.3.1 86441 1opy 131 1.89e+01 1opy d.17.4.3 38113 1nijA 318 1.92e+01 c.37.1.10 85741 d.237.1.1 85742 1ul7A 102 1.93e+01 unknown_sccs -11020 1qjcA 158 1.96e+01 1b6tA c.26.1.3 63328 1od6A 160 2.01e+01 c.26.1.3 86836 1tif 78 2.03e+01 1tif d.15.8.1 37836 1omiA 248 2.03e+01 a.4.5.4 87079 b.82.3.3 87080 1g7sA 594 2.03e+01 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1nnvA 110 2.08e+01 unknown_sccs -9309 1udxA 416 2.10e+01 b.117.1.1 -3546 c.37.1.8 -7101 unknown_sccs -9009 1ikoP 178 2.12e+01 b.6.1.5 71243 1mjhA 162 2.13e+01 1mjhA c.26.2.4 31639 1mq4A 272 2.19e+01 d.144.1.7 -11349 1ukkA 142 2.22e+01 d.227.1.1 -11206 1pz4A 116 2.25e+01 d.106.1.1 -10780 1f3uA 118 2.29e+01 1f3uA b.65.1.1 27521 1l2mA 118 2.31e+01 d.89.1.4 77657 1s4qA 228 2.34e+01 c.37.1.1 -6975 1i12A 160 2.38e+01 1i21A d.108.1.1 61515 1h6qA 168 2.39e+01 1h6qA b.88.1.2 60692 1ytc 112 2.43e+01 1ycc a.3.1.1 15835 1ygs 234 2.44e+01 1ygs b.26.1.1 23907 1sur 215 2.44e+01 1sur c.26.2.2 31620 1qwiA 143 2.45e+01 d.227.1.1 -11183 1fw9A 164 2.45e+01 1fw9A d.190.1.1 60059 1s72T 120 2.49e+01 1jj2S 119 2.49e+01 1ffkQ b.34.5.1 63104 1korA 400 2.49e+01 c.26.2.1 72824 d.210.1.1 72825 1vhsA 175 2.52e+01 d.108.1.1 -10794 1ko6A 187 2.53e+01 b.119.1.1 77471 1bm9A 122 2.56e+01 1bm9A a.4.5.7 16116 1dcoA 104 2.63e+01 1dcpA d.74.1.1 39680 1mw7A 240 2.63e+01 e.39.1.1 79557 1o57A 291 2.64e+01 unknown_sccs -249 c.61.1.1 -7960 1i1dA 161 2.64e+01 1i21A d.108.1.1 61526 1dmmA 131 2.64e+01 1opy d.17.4.3 38114 1qy5A 269 2.67e+01 d.122.1.1 -10958 1jiwI 106 2.81e+01 1smpI b.61.2.1 63078 1eaxA 241 2.81e+01 b.47.1.2 64889 1bkb 136 2.85e+01 1bkb b.34.5.2 24609 b.40.4.5 25341 1tn3 137 2.86e+01 1htn d.169.1.1 42423 1o6sB 105 2.87e+01 b.1.6.1 81096 1kv0A 66 2.90e+01 g.3.7.1 -12437 1edzA 320 2.94e+01 1ee9A c.2.1.7 30287 c.58.1.2 33935 1sjyA 159 2.94e+01 d.113.1.1 -10908 1go3E 187 2.95e+01 b.40.4.5 83054 d.230.1.1 83055 1cqmA 101 2.99e+01 1ris d.58.14.1 39321 1qwnA 1045 3.00e+01 a.8.3.1 -414 b.30.5.6 -3517 c.6.2.1 -6058 1m2rA 327 3.07e+01 d.144.1.7 84760 1j1tA 233 3.10e+01 unknown_sccs -3462 1mswD 883 3.13e+01 e.8.1.3 79427 1ne9A 335 3.16e+01 d.108.1.4 -10805 d.108.1.4 -10806 1aiu 105 3.30e+01 1erv c.47.1.1 32746 1f60B 94 3.34e+01 1b64 d.58.12.1 39307 1on2A 142 3.34e+01 a.4.5.24 87103 a.76.1.1 87104 1b0uA 262 3.36e+01 1b0uA c.37.1.12 32370 1fx3A 169 3.40e+01 1fx3B d.33.1.1 38524 1uv7A 110 3.41e+01 unknown_sccs -10256 1d3bA 75 3.41e+01 1d3bA b.38.1.1 24798 1h05A 146 3.41e+01 c.23.13.1 76433 1fvgA 199 3.43e+01 1fvaA d.58.28.1 39408 1mjc 69 3.46e+01 1mjc b.40.4.5 25319 1qovH 260 3.47e+01 6prcH b.41.1.1 25464 f.23.10.1 43457 1mszA 86 3.51e+01 d.68.7.1 79428 1dceB 331 3.52e+01 1dceB a.102.4.3 18872 1n97A 389 3.53e+01 a.104.1.1 80335 1f4qA 165 3.56e+01 1alvA a.39.1.8 17360 1owxA 121 3.60e+01 d.58.7.1 87494 1gsmA 210 3.64e+01 b.1.1.4 65535 b.1.1.4 65536 1h6hA 143 3.68e+01 d.189.1.1 65681 1g4fA 86 3.69e+01 1qubA g.18.1.1 44873 1a6o 332 3.75e+01 1a6o 1ru8A 232 3.79e+01 c.26.2.1 -6635 1om1A 332 3.81e+01 d.144.1.7 -11318 1vpsA 289 3.82e+01 1vpsA b.121.6.1 23336 1q7sA 117 3.85e+01 unknown_sccs -7522 2dhqA 146 3.85e+01 2dhqA c.23.13.1 31382 1lswA 131 3.86e+01 d.110.3.2 78181 1ospH 218 3.97e+01 1igtB b.1.1.1 20117 b.1.1.2 21147 1dkgA 197 3.99e+01 1dkgA b.73.1.1 27812 h.1.9.1 45626