# 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 1eni 138 3.35e-01 2end a.18.1.1 16403 1enj 138 3.44e-01 2end a.18.1.1 16401 1jpaA 312 5.22e-01 d.144.1.7 67011 1enk 138 8.24e-01 2end a.18.1.1 16402 1e6iA 121 9.12e-01 1b91A a.29.2.1 16969 1vasA 137 1.27e+00 2end a.18.1.1 16404 1efuA 385 1.36e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1trrA 107 1.39e+00 1jhgA a.4.12.1 19017 2end 138 1.42e+00 2end a.18.1.1 16400 1efcA 393 1.69e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 2furA 209 1.72e+00 1tbmA 326 1.82e+00 a.211.1.2 106744 2wrpR 107 1.87e+00 1jhgA a.4.12.1 19010 2ctoA 93 2.39e+00 1ggzA 148 2.72e+00 a.39.1.5 70176 1ahr 146 3.01e+00 1cll a.39.1.5 17287 1zv1A 65 3.14e+00 2bl0C 142 3.59e+00 3cln 148 3.79e+00 1cll a.39.1.5 17286 1ig6A 107 4.28e+00 1ig6A a.4.3.1 62364 1u7lA 392 4.37e+00 1n3gA 113 4.61e+00 d.204.1.1 79962 1zd3A 555 4.66e+00 1qhhA 167 4.78e+00 1pjr c.37.1.19 32393 1n3kA 130 5.07e+00 a.77.1.4 79965 1u59A 287 5.57e+00 d.144.1.7 107681 1vj5A 555 5.65e+00 c.108.1.2,c.69.1.11 100799,100800 1cll 148 5.65e+00 1cll a.39.1.5 17263 2a2fX 325 5.75e+00 1eumA 165 6.34e+00 1eumA a.25.1.1 59507 2bbrA 195 6.96e+00 1wdcC 156 6.96e+00 1wdcC a.39.1.5 17317 1m48A 133 7.02e+00 a.26.1.2 74443 1b4pA 217 7.41e+00 a.45.1.1,c.47.1.5 83158,83159 1w0bA 102 7.53e+00 a.7.11.1 108985 1x6vA 630 7.97e+00 1gqeA 365 8.02e+00 e.38.1.1 70351 1ugpA 203 8.48e+00 d.149.1.1 107831 1cr6B 554 8.89e+00 1cr6B c.69.1.11,c.108.1.2 34688,43338 3crxA 343 8.94e+00 4crxA a.60.9.1,d.163.1.1 18101,42161 1tn4 159 8.95e+00 1ncx a.39.1.5 17248 1ireA 204 9.31e+00 d.149.1.1 76769 2esnA 310 9.34e+00 1jhgA 101 9.60e+00 1jhgA a.4.12.1 19009 1zboA 210 9.97e+00 1m6kA 251 1.07e+01 e.3.1.1 78695 1etu 394 1.08e+01 1efcA c.37.1.8 64737 2lefA 86 1.11e+01 2lefA a.21.1.1 16433 1kbuA 349 1.13e+01 a.60.9.1,d.163.1.1 72284,72285 6gsvA 217 1.16e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 2c5rA 67 1.16e+01 1xw5A 217 1.20e+01 1pveA 72 1.24e+01 a.189.1.1 104322 2c4jA 218 1.25e+01 1wjtA 103 1.26e+01 1rcsA 105 1.28e+01 1jhgA a.4.12.1 19025 1eemA 241 1.30e+01 1eemA a.45.1.1,c.47.1.5 17717,33011 1lwbA 122 1.30e+01 a.133.1.3 84728 1vkmA 297 1.33e+01 c.138.1.1 108670 1o9rA 162 1.41e+01 a.25.1.1 86706 1gewA 356 1.42e+01 1gewA c.67.1.1 60470 1yurA 98 1.52e+01 1q16C 225 1.54e+01 f.21.3.1 95549 1hx1B 114 1.57e+01 1hx1B a.7.7.1 61350 2f3yA 148 1.65e+01 1qo7A 394 1.74e+01 1qo7A c.69.1.11 34697 2fj6A 82 1.77e+01 1xo0A 324 1.82e+01 1dg3A 592 1.92e+01 1dg3A a.114.1.1,c.37.1.8 19078,32153 1kk8B 139 1.94e+01 a.39.1.5 77430 1vjrA 271 1.94e+01 c.108.1.14 100832 1irl 133 1.97e+01 3inkC a.26.1.2 16883 2a6cA 83 2.05e+01 2gsfA 373 2.08e+01 1crxA 322 2.10e+01 4crxA a.60.9.1,d.163.1.1 18097,42157 1jhdA 396 2.13e+01 b.122.1.3,c.26.1.5 66712,66713 1xn7A 78 2.13e+01 2bnkA 67 2.17e+01 1aua 296 2.18e+01 1aua a.5.3.1,c.13.1.1 16290,30882 1b72B 87 2.19e+01 1akhA a.4.1.1 16001 1opjA 293 2.20e+01 d.144.1.7 87230 1c7nA 399 2.20e+01 1d2fA c.67.1.3 34413 1mw5A 187 2.20e+01 d.259.1.1 91477 1eia 207 2.21e+01 1eia a.28.3.1,a.73.1.1 16951,18331 1br1B 150 2.22e+01 1wdcC a.39.1.5 17309 1fazA 122 2.23e+01 1fazA a.133.1.3 59757 2f1sA 186 2.24e+01 1rcd 173 2.26e+01 2fha a.25.1.1 16687 1osa 148 2.27e+01 1cll a.39.1.5 17300 1v9dA 340 2.31e+01 a.207.1.1 100535 1b8aA 438 2.35e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1eu8A 409 2.45e+01 1eu8A c.94.1.1 59502 1m9xC 146 2.45e+01 a.73.1.1 84907 1ggwA 140 2.47e+01 1ggwA a.39.1.5 60490 1yviA 149 2.49e+01 1l4sA 112 2.51e+01 d.204.1.1 77693 2b1eA 564 2.52e+01 1y5iC 225 2.55e+01 1jr3E 334 2.57e+01 a.80.1.1,c.37.1.20 63253,63254 1f5nA 592 2.59e+01 1dg3A a.114.1.1,c.37.1.8 19077,32152 1mv8A 436 2.64e+01 a.100.1.4,c.2.1.6,c.26.3.1 85128,85129,85130 1y01A 102 2.67e+01 1pp7U 131 2.67e+01 a.4.5.44 94973 2myo 118 2.67e+01 2myo d.211.1.1 19175 1ttzA 87 2.68e+01 c.47.1.1 107309 1z8uA 102 2.75e+01 1y88A 199 2.81e+01 1zs3A 182 2.82e+01 1sedA 117 2.95e+01 a.219.1.1 105449 1qgtA 149 2.98e+01 1qgtA a.62.1.1 18135 1g4yR 148 2.98e+01 1cll a.39.1.5 60252 1wwuA 99 2.99e+01 1efdN 266 3.01e+01 1efdN c.92.2.1 35597 2occH 85 3.05e+01 2occH a.51.1.1 17796 1b35A 260 3.06e+01 1b35A b.121.4.1 23333 1kdxA 81 3.06e+01 1kdxA a.12.1.1 16375 1w7jB 151 3.11e+01 2ethA 154 3.13e+01 1y82A 157 3.15e+01 1umgA 362 3.15e+01 d.280.1.1 107956 1s6lA 212 3.21e+01 1exrA 148 3.21e+01 1cll a.39.1.5 17299 2ew2A 316 3.32e+01 1s5dA 240 3.36e+01 d.166.1.1 98541 2a1dD 329 3.38e+01 1p4dA 330 3.40e+01 d.89.1.5 94101 1rxqA 178 3.42e+01 a.213.1.1 105118 1b79A 119 3.54e+01 1b79A a.81.1.1 18451 1jogA 146 3.59e+01 a.24.16.2 77142 1aihA 170 3.61e+01 1aihA d.163.1.1 42149 1bku 33 3.63e+01 1bku j.6.1.1 46104 1iieA 75 3.67e+01 1iieA a.109.1.1 19039 1ej2A 181 3.68e+01 1f9aA c.26.1.3 59414 1a6q 382 3.71e+01 1a6q a.159.1.1,d.219.1.1 75801,75802 1xwl 580 3.77e+01 1xwl c.55.3.5,e.8.1.1 33708,43001 1sknP 92 3.77e+01 1sknP a.37.1.1 17127 2d2eA 250 3.80e+01 1t0qA 498 3.88e+01 a.25.1.2 106220 1jeyB 565 3.95e+01 1jeqB b.131.1.2,c.62.1.4 90372,90373 2ccmA 191 3.96e+01 1ylmA 144 3.99e+01 1dqaC 467 3.99e+01 1dqaA d.58.20.1,d.179.1.1 39366,42587 1zbfA 142 4.02e+01 1b48A 221 4.06e+01 1pgtA a.45.1.1,c.47.1.5 17703,32997 1fhuA 320 4.06e+01 1fhuA c.1.11.2,d.54.1.1 29234,38878 1xfxO 149 4.09e+01 1i6zA 135 4.10e+01 a.7.7.1 61861 1ftt 68 4.10e+01 2hddA a.4.1.1 15997 1myo 118 4.12e+01 2myo d.211.1.1 19174 1p9bA 442 4.20e+01 c.37.1.10 94385 1m8jA 181 4.22e+01 c.26.1.3 84875 1dqaA 467 4.24e+01 1dqaA d.58.20.1,d.179.1.1 39364,42585 1n45A 233 4.28e+01 a.132.1.1 79981 2fu4A 83 4.33e+01 1d5wC 126 4.35e+01 1dbwA c.23.1.1 31101 1ykhB 132 4.35e+01 1pauB 102 4.40e+01 1pauB 1mvwB 145 4.40e+01 i.15.1.1 79524 4crxA 322 4.41e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 1x1fA 149 4.45e+01 1ak8 76 4.45e+01 1cll a.39.1.5 17281 3bdpA 580 4.47e+01 1xwl c.55.3.5,e.8.1.1 33711,43004 1ak4C 145 4.53e+01 1ak4C a.73.1.1 18321 1hwyA 501 4.54e+01 1hwyA c.2.1.7,c.58.1.1 30262,33910 1afvA 151 4.54e+01 1ak4C a.73.1.1 18324 1hw8A 467 4.66e+01 1dqaA d.58.20.1,d.179.1.1 61298,61299 2es4D 332 4.67e+01 1nk4A 580 4.69e+01 c.55.3.5,e.8.1.1 91923,91924 1v54H 85 4.73e+01 a.51.1.1 100329 1a1w 91 4.75e+01 1a1z a.77.1.4 18425 2f9dP 43 4.86e+01 1n1cA 217 4.88e+01 a.184.1.1 85254 1u4bA 580 4.89e+01 c.55.3.5,e.8.1.1 107664,107665 1hnoA 280 4.98e+01 1hnoA c.14.1.3 61095 1v54G 85 4.99e+01 f.23.2.1 100328 1a41 234 5.01e+01 1a41 d.163.1.2 42174 1vekA 84 5.07e+01 2b0jA 358 5.14e+01 1b4cA 92 5.14e+01 1b4cA a.39.1.2 17169 1ux5A 411 5.19e+01 a.207.1.1 100144 1scmB 145 5.21e+01 1wdcB a.39.1.5 17304 1top 162 5.22e+01 1ncx a.39.1.5 17223 2beiA 170 5.24e+01 1q5nA 454 5.27e+01 a.127.1.1 95901 2gpjA 252 5.31e+01 1musA 477 5.32e+01 c.55.3.4 79494 1fgkA 310 5.34e+01 1fgkA d.144.1.7 41693 1tns 76 5.35e+01 1qpmA a.6.1.7 16228 1pyiA 96 5.36e+01 1pyiA g.38.1.1,h.1.3.1 45079,45512 1llmC 88 5.41e+01 g.37.1.1,g.37.1.1 91059,91060 2bdpA 580 5.43e+01 1xwl c.55.3.5,e.8.1.1 33709,43002 1ds1A 324 5.47e+01 1drtA b.82.2.2 28127 1n4kA 381 5.48e+01 a.118.22.1,b.42.6.1 79992,79993 1o8rA 94 5.53e+01 d.234.1.1 86677 1kqfB 294 5.53e+01 d.58.1.5,f.23.22.1 75900,75901 1yewA 382 5.55e+01 1x74A 360 5.74e+01 1k6iA 352 5.75e+01 c.2.1.2 68223 1nmeB 92 5.79e+01 1i1gA 141 5.81e+01 a.4.5.32,d.58.4.2 65982,65983 1f7uA 607 5.82e+01 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 59673,59674,59675 1b47A 304 5.92e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17381,17775,40529 1f3iA 481 5.93e+01 1b7eA 5csmA 256 5.95e+01 5csmA a.130.1.2 19494 1cnpA 90 5.98e+01 4icb a.39.1.2 17161 1p4xA 250 6.02e+01 a.4.5.28,a.4.5.28 87784,87785 2aheA 267 6.03e+01 2b1xA 470 6.03e+01 1vyiA 112 6.04e+01 1ncx 162 6.05e+01 1ncx a.39.1.5 17222 1ockA 412 6.12e+01 c.117.1.1 86802 1rijA 25 6.12e+01 k.32.1.1 104951 1wdcB 156 6.21e+01 1wdcB a.39.1.5 17302 1jm4B 118 6.24e+01 a.29.2.1 71746 1fjlA 81 6.28e+01 2hddA a.4.1.1 16017 1im5A 180 6.32e+01 c.33.1.3 66211 1hwxA 501 6.40e+01 1hwyA c.2.1.7,c.58.1.1 30250,33898 1i0aA 466 6.45e+01 1auwA a.127.1.1 61479 1hniB 427 6.61e+01 1rthA e.8.1.2 43045 1qczA 169 6.65e+01 1qczA c.23.8.1 31276 2ajfA 597 6.75e+01 1bd8 156 6.76e+01 1bd8 d.211.1.1 19157 1h2vC 771 6.79e+01 a.118.1.14,a.118.1.14,a.118.1.14 76592,76593,76594 2cblA 305 6.83e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17380,17774,40528 1csmA 256 6.86e+01 5csmA a.130.1.2 19495 1w2wA 211 6.91e+01 c.124.1.5 109130 1l3sA 580 6.91e+01 c.55.3.5,e.8.1.1 84521,84522 1w2fA 276 6.93e+01 d.143.1.3 109125 1muhA 481 7.01e+01 c.55.3.4 79485 1mp8A 281 7.01e+01 d.144.1.7 91384 2occE 109 7.03e+01 2occE a.118.11.1 19224 1h3fA 432 7.04e+01 c.26.1.1,d.66.1.4 76631,76632 1i5jA 79 7.06e+01 1i5jA j.39.1.1 61788 1e39A 571 7.09e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1sheA 103 7.12e+01 d.274.1.1 105551 1bw0A 416 7.13e+01 1bw0A c.67.1.1 34385 2mev2 256 7.17e+01 1aym2 1a2xA 159 7.31e+01 1ncx a.39.1.5 17251 1pufB 73 7.33e+01 a.4.1.1 95132 1tqnA 486 7.35e+01 a.104.1.1 107238 1wtyA 119 7.36e+01 2occG 84 7.41e+01 2occG f.23.2.1 43522 2af8 86 7.50e+01 2af8 a.28.1.1 16933 1cfr 285 7.50e+01 1cfr c.52.1.7 33312 1jchC 551 7.68e+01 b.101.1.1,b.110.1.1,h.4.9.1 66495,66496,66497 1jchA 551 7.68e+01 b.101.1.1,b.110.1.1,h.4.9.1 66491,66492,66493 2iu5A 195 7.70e+01 1pjhA 280 7.74e+01 c.14.1.3 94761 1l6nA 289 7.84e+01 a.61.1.1,a.73.1.1 73624,73625 1hdiA 413 7.87e+01 16pk c.86.1.1 60964 1sb0A 87 7.91e+01 a.12.1.1 98789 2dp5A 332 7.93e+01 1guxA 218 7.96e+01 1guxA a.74.1.3 18388 1p2hA 571 7.98e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1yw0A 276 8.03e+01 1a1z 91 8.13e+01 1a1z a.77.1.4 18427 1dckA 126 8.14e+01 1dbwA c.23.1.1 31097 1dryA 324 8.28e+01 1drtA b.82.2.2 28128 1vgmA 378 8.28e+01 2avuE 192 8.28e+01 1v37A 177 8.33e+01 1ei1A 391 8.37e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 1xgkA 352 8.48e+01 1j55A 95 8.50e+01 a.39.1.2 77078 1yozA 116 8.50e+01 1c20A 128 8.56e+01 1c20A a.4.3.1 16079 1e08A 371 8.58e+01 i.4.1.1 45914 1x91A 153 8.62e+01 1dmhA 311 8.66e+01 1dmhA b.3.6.1 22633 1w5fA 353 8.80e+01 1x3zA 335 8.83e+01 1u6rA 380 8.88e+01 2gfhA 260 8.92e+01 1fg7A 356 8.95e+01 1gewA c.67.1.1 59819 1zjjA 263 8.95e+01 1k6kA 143 8.98e+01 a.174.1.1 77274