# List of top-scoring protein chains for t2k-100-30-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 1jnyA 435 1.90e-01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1p4wA 99 5.94e-01 a.4.6.2 87783 1dgnA 89 1.79e+00 1dgnA a.77.1.3 18436 1ulyA 192 1.83e+00 2bk9A 153 1.94e+00 1urvA 190 1.97e+00 1ut0A 190 1.97e+00 a.1.1.2 108012 1tq4A 413 2.03e+00 c.37.1.8 107201 1sedA 117 2.19e+00 a.219.1.1 105449 2amlA 373 2.35e+00 2dc3A 193 2.49e+00 1xouB 95 2.58e+00 1jk0A 419 3.03e+00 a.25.1.2 63142 2aaoA 166 3.21e+00 1pixA 587 3.32e+00 c.14.1.4 94708 1gx5A 536 3.71e+00 e.8.1.4 70682 1dd3A 128 3.74e+00 1dd3C a.108.1.1,d.45.1.1 19031,38760 2ct9A 208 4.14e+00 1csjA 531 4.32e+00 1quvA e.8.1.4 43120 1ezfA 340 5.10e+00 1ezfA a.128.1.2 19440 1zkrA 153 6.08e+00 2arpF 152 6.64e+00 1fnnA 389 7.19e+00 1fnnA a.4.5.11,c.37.1.20 16129,32426 1pvaA 110 7.19e+00 1a75A a.39.1.4 17207 1a2xA 159 7.23e+00 1ncx a.39.1.5 17251 1io2A 213 7.27e+00 1ekeA c.55.3.1 62612 1eupA 403 7.27e+00 1rom a.104.1.1 18967 2ax8A 256 7.97e+00 2ab5A 269 7.98e+00 1pv9A 348 8.24e+00 c.55.2.1,d.127.1.1 95157,95158 1eljA 381 8.27e+00 4mbp c.94.1.1 35791 1tr1A 447 8.42e+00 1e70M c.1.8.4 28957 1kl9A 182 8.65e+00 b.40.4.5 72681 1rfmA 344 8.77e+00 c.122.1.1 97385 1a2s 89 8.97e+00 1ctj a.3.1.1 15800 2ax6A 256 9.16e+00 1z8sA 146 9.29e+00 1w85A 368 9.96e+00 1oe0A 230 1.02e+01 c.37.1.1 92788 1smtA 122 1.07e+01 1smtA a.4.5.5 16109 1i4jA 110 1.08e+01 d.55.1.1 76734 1jipA 403 1.08e+01 a.104.1.1 66748 1udiI 83 1.09e+01 1ugiA d.17.5.1 38124 1h8bA 75 1.11e+01 a.39.1.7 60736 1puoA 170 1.12e+01 a.101.1.1,a.101.1.1 95134,95135 2ax9A 256 1.12e+01 1ctj 89 1.14e+01 1ctj a.3.1.1 15798 1dmwA 307 1.14e+01 4pah d.178.1.1 42580 1jkgB 250 1.15e+01 d.17.4.2 66796 1smtB 122 1.15e+01 1smtA a.4.5.5 16110 3nul 130 1.15e+01 3nul d.110.1.1 40891 1ughI 82 1.16e+01 1ugiA d.17.5.1 38133 4pah 308 1.16e+01 4pah d.178.1.1 42576 1a0k 131 1.17e+01 3nul d.110.1.1 40892 1z8oA 404 1.19e+01 1j1bA 420 1.20e+01 d.144.1.7 90758 1zchA 255 1.20e+01 1j8uA 325 1.23e+01 d.178.1.1 71611 1jvpP 298 1.25e+01 d.144.1.7 67371 1e4iA 447 1.30e+01 1e70M c.1.8.4 59225 1hcl 298 1.31e+01 1hcl d.144.1.7 41593 1j90A 230 1.33e+01 c.37.1.1 66448 2bidA 197 1.36e+01 2bidA f.1.4.1 43398 1pah 308 1.38e+01 4pah d.178.1.1 42578 1jn5B 250 1.40e+01 d.17.4.2 66922 1gz8A 299 1.42e+01 d.144.1.7 83405 1s6cA 183 1.43e+01 a.39.1.5 98594 1b5sA 242 1.45e+01 1eaf c.43.1.1 32626 1bo9A 73 1.48e+01 1bo9A a.65.1.1 18146 1aj4 161 1.52e+01 1ncx a.39.1.5 17244 2mysB 166 1.55e+01 1wdcB a.39.1.5 17308 1w9rA 119 1.56e+01 1oxa 403 1.58e+01 1f4tA a.104.1.1 18965 1ak1 310 1.58e+01 1ak1 c.92.1.1 35594 1ltqA 301 1.59e+01 c.108.1.9,c.37.1.1 78208,78209 1t7rA 269 1.63e+01 a.123.1.1 106635 2cruA 118 1.63e+01 1yovA 537 1.67e+01 1ugiA 84 1.68e+01 1ugiA d.17.5.1 38125 1br2A 791 1.68e+01 1lvk b.34.3.1,c.37.1.9 24558,32155 1r1tA 122 1.71e+01 a.4.5.5 104769 1dn1B 267 1.72e+01 1dn1B a.47.2.1 17771 1itkA 731 1.74e+01 a.93.1.3,a.93.1.3 71417,71418 4ubpA 101 1.77e+01 1ubpA d.8.1.1 37352 1lr7A 74 1.80e+01 g.3.11.3,g.68.1.1 84679,84680 1rxxA 421 1.83e+01 d.126.1.4 98061 1hx1B 114 1.84e+01 1hx1B a.7.7.1 61350 2a9gA 418 1.84e+01 2ac4A 309 1.85e+01 1dozA 309 1.90e+01 1ak1 c.92.1.1 35592 1v9vA 114 1.93e+01 1b8aA 438 1.95e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1e1xA 299 1.95e+01 1hcl d.144.1.7 59157 1ubpA 101 1.96e+01 1ubpA d.8.1.1 37353 1ptmA 329 1.97e+01 c.77.1.3 95104 1derA 547 1.98e+01 1derA 1l8qA 324 1.99e+01 a.4.12.2,c.37.1.20 77809,77810 1vqoI 162 2.02e+01 2ccmA 191 2.11e+01 1cqmA 101 2.15e+01 1ris d.58.14.1 39321 1s72I 162 2.17e+01 a.4.7.1 105328 1oksA 56 2.20e+01 a.8.5.1 93271 1j7nB 776 2.23e+01 d.92.1.14,d.92.1.14,d.166.1.1 66412,66413,66414 2fkcA 247 2.26e+01 2if1 126 2.32e+01 2if1 d.64.1.1 39547 1ly1A 181 2.35e+01 c.37.1.1 74334 1vl4A 447 2.37e+01 d.283.1.1 108718 1qusA 322 2.39e+01 1ltm d.2.1.6 36991 1nynA 131 2.41e+01 d.235.1.1 86410 1eg3A 261 2.42e+01 1eg3A a.39.1.7,a.39.1.7,b.72.1.1 17376,17377,27805 2ac2A 309 2.46e+01 1cxqA 162 2.47e+01 1cxqA c.55.3.2 33621 1mlwA 301 2.47e+01 d.178.1.1 79289 1daqA 71 2.49e+01 1daqA a.139.1.1 59113 1bdc 60 2.51e+01 1fc2C a.8.1.1 16350 1apa 266 2.53e+01 1qi7A d.165.1.1 42205 1tn4 159 2.61e+01 1ncx a.39.1.5 17248 1vajA 214 2.64e+01 1a5v 162 2.66e+01 1cxqA c.55.3.2 33629 1lf7A 182 2.71e+01 b.60.1.1 73878 1i37A 260 2.73e+01 1a28A a.123.1.1 61583 1o97D 320 2.75e+01 c.26.2.3,c.31.1.2 81233,81234 1ynmA 247 2.76e+01 1ncx 162 2.79e+01 1ncx a.39.1.5 17222 1v7nV 163 2.83e+01 a.26.1.2 100476 2kauA 100 2.84e+01 1ubpA d.8.1.1 37335 1ohzB 60 2.87e+01 a.139.1.1 93044 1pmi 440 2.88e+01 1pmi b.82.1.3 28114 1rro 108 2.90e+01 1a75A a.39.1.4 17195 1fwcA 100 2.92e+01 1ubpA d.8.1.1 37331 1lkcA 364 2.94e+01 c.67.1.1 73978 2b0uC 288 2.97e+01 1j7qA 86 2.99e+01 1j7rA a.39.1.5 62700 1qgpA 77 3.01e+01 1qbjA a.4.5.19 16158 1pch 88 3.05e+01 1ptf d.94.1.1 40564 2fkiA 126 3.05e+01 1top 162 3.10e+01 1ncx a.39.1.5 17223 1ovaA 386 3.17e+01 1ovaA e.1.1.1 42619 1y10A 407 3.24e+01 1zm7A 230 3.25e+01 1vsd 152 3.28e+01 1cxqA c.55.3.2 33625 1bxeA 113 3.31e+01 1bxeA d.55.1.1 38898 1t98A 287 3.38e+01 1ejxA 100 3.44e+01 d.8.1.1 83182 2govA 195 3.45e+01 1iw2A 182 3.48e+01 b.60.1.1 71468 1bkjA 240 3.55e+01 1bkjA d.90.1.1 40243 1g61A 228 3.57e+01 1g61A d.126.1.1 41126 1yzfA 195 3.60e+01 1gzqA 300 3.61e+01 b.1.1.2,d.19.1.1 70818,70819 1rloA 271 3.62e+01 1ufyA 122 3.63e+01 d.79.1.2 88489 2fbmA 291 3.67e+01 1grwA 126 3.83e+01 b.1.11.2 70391 2ao0A 324 3.85e+01 2bmoB 194 3.86e+01 1j7rA 86 3.95e+01 1j7rA a.39.1.5 62701 1vpbA 451 3.96e+01 2a5lA 200 3.97e+01 2sas 185 3.97e+01 2sas a.39.1.5 17258 2ex4A 241 3.98e+01 1ltm 320 4.03e+01 1ltm d.2.1.6 36992 1yqyA 523 4.04e+01 1snlA 103 4.04e+01 a.39.1.7 105820 1b79A 119 4.07e+01 1b79A a.81.1.1 18451 1rwzA 245 4.07e+01 d.131.1.2,d.131.1.2 98005,98006 1xmkA 79 4.08e+01 1zbmA 280 4.11e+01 1aoa 275 4.13e+01 1aoa a.40.1.1,a.40.1.1 17396,17397 1gr5A 547 4.14e+01 i.16.1.1 65478 1zroA 602 4.16e+01 1fp6A 289 4.30e+01 1cp2A c.37.1.10 32243 1b24A 188 4.32e+01 1b24A d.95.2.1,d.95.2.1 40573,40574 1ny1A 240 4.39e+01 c.6.2.3 86395 2b5aA 77 4.43e+01 1foaA 348 4.44e+01 1foaA c.68.1.10 59929 1y1xA 191 4.46e+01 1s1eA 224 4.52e+01 1dpgA 485 4.58e+01 1dpgA c.2.1.3,d.81.1.5 30074,39989 1cyj 90 4.60e+01 1ctj a.3.1.1 15805 1wehA 171 4.61e+01 1kp8A 547 4.64e+01 a.129.1.1,c.8.5.1,d.56.1.1 84414,84415,84416 1x6mA 196 4.65e+01 1uz3A 102 4.65e+01 1mvwB 145 4.68e+01 i.15.1.1 79524 1quvA 578 4.70e+01 1quvA e.8.1.4 43119 2dpg 485 4.71e+01 1dpgA c.2.1.3,d.81.1.5 30076,39991 1louA 101 4.72e+01 1ris d.58.14.1 39323 1qtfA 246 4.73e+01 1agjA b.47.1.1 25830 2frnA 278 4.77e+01 2a3dA 73 4.81e+01 2a3dA k.9.1.1 46424 1i5nA 146 4.86e+01 1i5nA a.24.10.3 61805 1asu 162 4.87e+01 1cxqA c.55.3.2 33626 2fw2A 260 4.88e+01 1bj7 156 4.90e+01 1bj7 b.60.1.1 27113 1vq0A 302 5.03e+01 1gosA 520 5.09e+01 c.3.1.2,d.16.1.5 65425,65426 1ne8A 117 5.16e+01 b.34.6.2 80424 1iq3A 110 5.23e+01 1iq3A a.39.1.6 62640 1emvA 86 5.24e+01 1cei a.28.2.1 16944 1ktpA 162 5.24e+01 a.1.1.3 72990 1j54A 186 5.25e+01 c.55.3.5 77077 1scmB 145 5.26e+01 1wdcB a.39.1.5 17304 1yw5A 177 5.30e+01 1dlyA 164 5.42e+01 1dlyA a.1.1.1 14983 1z3eA 132 5.48e+01 1wh5A 80 5.63e+01 1utuA 108 5.64e+01 1bf5A 545 5.67e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 1g8iA 190 5.74e+01 1rec a.39.1.5 60363 1xn8A 131 5.81e+01 2scpA 174 5.83e+01 2scpA a.39.1.5 17256 1a79A 171 5.84e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 1mfiA 114 5.86e+01 1dptA d.80.1.3 39856 1uzxA 169 5.87e+01 d.20.1.2 100238 1cp2A 269 5.90e+01 1cp2A c.37.1.10 32269 2bl0B 145 5.92e+01 1jaxA 212 5.96e+01 c.2.1.6 66476 1odeA 122 5.98e+01 d.79.1.2 86846 1jboA 162 5.99e+01 a.1.1.3 84150 1jweA 114 6.10e+01 1b79A a.81.1.1 18455 1ayg 80 6.15e+01 451c a.3.1.1 15831 1b88A 114 6.25e+01 1tcrA b.1.1.1 20608 1uhnA 189 6.28e+01 a.39.1.5 99399 1w4xA 542 6.29e+01 c.3.1.5,c.3.1.5 109171,109172 1dtyA 429 6.32e+01 1dtyA c.67.1.4 34495 1v7wA 807 6.32e+01 a.102.1.4,b.30.5.3 108411,108412 2fwtA 125 6.38e+01 1zxzA 197 6.44e+01 1ehyA 294 6.59e+01 1ehyA c.69.1.11 34693 1nksA 194 6.60e+01 1nksA c.37.1.1 31886 1xd8A 289 6.62e+01 1wdcB 156 6.63e+01 1wdcB a.39.1.5 17302 1xuuA 349 6.72e+01 1fo8A 343 6.81e+01 1foaA c.68.1.10 59927 1u04A 771 6.85e+01 b.34.14.1,c.55.3.10 107539,107540 1n5uA 585 6.90e+01 a.126.1.1,a.126.1.1,a.126.1.1 85339,85340,85341 1jayA 212 6.90e+01 c.2.1.6 66478 1umnA 165 6.97e+01 a.25.1.1 99607 1t5eA 360 6.97e+01 f.46.1.1 106436 1osa 148 6.99e+01 1cll a.39.1.5 17300 1fi4A 416 7.03e+01 1fi4A d.14.1.5,d.58.26.2 59847,59848 1e5pA 151 7.04e+01 1bj7 b.60.1.1 59272 1dgsA 667 7.08e+01 1dgsA a.60.2.2,b.40.4.6,d.142.2.2 17963,25365,41581 1u7eB 154 7.11e+01 1cyi 90 7.17e+01 1ctj a.3.1.1 15804 1uc7A 125 7.21e+01 c.47.1.1 99163 1cby 259 7.26e+01 1cby d.103.1.1 40705 1khtA 192 7.26e+01 c.37.1.1 84401 1zac 90 7.31e+01 1ncx a.39.1.5 17236 1v9nA 360 7.31e+01 2bjrA 368 7.34e+01 1lk3A 160 7.35e+01 a.26.1.3 73950 1jfkA 134 7.41e+01 a.39.1.5 66639 1xdnA 277 7.46e+01 1x54A 434 7.49e+01 1jhfA 202 7.52e+01 a.4.5.2,b.87.1.1 63057,63058 1nogA 177 7.54e+01 a.25.2.2 85923 1cei 94 7.57e+01 1cei a.28.2.1 16939 1lc5A 364 7.60e+01 c.67.1.1 73827 1cmiA 85 7.62e+01 1cmiA d.39.1.1 38551 1fr2A 86 7.62e+01 a.28.2.1 83256 2a8eA 220 7.64e+01 1io7A 368 7.68e+01 1f4tA a.104.1.1 18971 1dvh 79 7.82e+01 1c53 a.3.1.1 15802 2afdA 88 7.84e+01 1f4tA 368 7.87e+01 1f4tA a.104.1.1 18973 1exrA 148 7.89e+01 1cll a.39.1.5 17299 1fexA 59 7.92e+01 a.4.1.3 59803 1xfxO 149 7.93e+01 1qb2A 109 7.97e+01 1qb2A a.36.1.1 17125 1gzgA 337 7.97e+01 c.1.10.3 70805 1lswA 131 8.02e+01 d.110.3.2 78181 2bifA 469 8.07e+01 1bif c.37.1.7,c.60.1.4 31963,34009 1ug7A 128 8.09e+01 a.24.24.1 107824 1vm8A 534 8.13e+01 1t4hA 290 8.14e+01 d.144.1.7 106420 1j8rA 196 8.18e+01 1j8rA b.2.3.3 62745 1bea 127 8.19e+01 1bea a.52.1.2 17826 1fo9A 348 8.25e+01 1foaA c.68.1.10 59928 1zejA 293 8.29e+01 1x46A 150 8.32e+01 1uhgA 385 8.33e+01 e.1.1.1 88491 1o7nB 194 8.39e+01 d.17.4.4 81164 1nddD 76 8.40e+01 1ubi d.15.1.1 37602 1h5yA 253 8.45e+01 c.1.2.1 65638 1nddA 76 8.49e+01 1ubi d.15.1.1 37599 1lliA 92 8.51e+01 1lmb3 a.35.1.2 17025 1u9yA 284 8.52e+01 1g5pA 289 8.64e+01 1cp2A c.37.1.10 32253 2aalA 131 8.68e+01 1zy1B 197 8.69e+01 2blfA 373 8.71e+01 1wveC 80 8.83e+01 1w5nA 337 8.83e+01 1a6o 332 8.84e+01 1a6o 3bifA 468 8.91e+01 1bif c.37.1.7,c.60.1.4 31962,34008 1w5qA 337 8.95e+01 1ojaA 520 8.97e+01 c.3.1.2,d.16.1.5 93096,93097 1qhhA 167 8.98e+01 1pjr c.37.1.19 32393