# 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 2d1uA 104 4.72e-01 1tzaA 134 6.01e-01 b.1.23.1 107468 1wmhB 86 1.62e+00 1souA 194 1.68e+00 c.124.1.6 105858 2ifeA 100 2.51e+00 1tig d.68.1.1 39567 1pqxA 91 2.67e+00 d.267.1.1 104296 1fr3A 67 4.19e+00 1fr3A b.40.6.1 25436 2a2pA 129 4.40e+00 1hyuA 521 4.43e+00 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1hqz9 141 5.58e+00 1h2cA 140 5.75e+00 b.31.1.1 83462 1gutA 68 6.31e+00 b.40.6.1 65576 1qvcA 145 6.38e+00 3ullA b.40.4.3 25284 1y96B 85 6.56e+00 1oiaA 95 7.67e+00 d.58.7.1 87051 1cx0A 95 7.80e+00 1urnA d.58.7.1 39158 1xn5A 146 8.34e+00 1nxiA 132 9.13e+00 d.58.47.1 86381 1mkaA 171 9.68e+00 1mkaA d.38.1.2 38543 1hqz1 141 1.01e+01 1urnA 97 1.05e+01 1urnA d.58.7.1 39153 1ka6A 128 1.13e+01 d.93.1.1 68370 1m5oC 100 1.16e+01 d.58.7.1 78654 1q59A 172 1.18e+01 f.1.4.1 95881 1v5tA 90 1.21e+01 d.15.1.1 108385 1oeyJ 107 1.24e+01 d.15.2.2 92804 1agnA 373 1.30e+01 2ohxA b.35.1.2,c.2.1.1 24737,29753 1fhgA 154 1.33e+01 1tlk b.1.1.4 21706 1ddf 127 1.34e+01 1ddf a.77.1.2 18423 1tlk 154 1.36e+01 1tlk b.1.1.4 21707 1xewY 172 1.38e+01 1zynA 202 1.44e+01 1xkrA 206 1.45e+01 2dfkA 402 1.47e+01 1ov3A 138 1.47e+01 b.34.2.1,b.34.2.1 87451,87452 1repC 251 1.51e+01 1repC a.4.5.10,a.4.5.10 16125,16126 1vhxA 150 1.56e+01 c.55.3.8 100712 1o0pA 104 1.57e+01 d.58.7.1 86535 1gg6B 131 1.63e+01 5ptp 2aefA 234 1.69e+01 1wmhA 89 1.72e+01 2bw2A 140 1.75e+01 1q38A 89 1.75e+01 b.1.2.1 95663 1ny4A 82 1.76e+01 b.40.4.5 92316 1audA 101 1.80e+01 1urnA d.58.7.1 39156 1o9iA 266 1.85e+01 a.25.1.3 92671 1q87A 221 1.88e+01 e.47.1.1 96192 2aioA 269 1.92e+01 1jkvA 266 1.98e+01 a.25.1.3 71719 2f4mA 295 2.00e+01 1lqtA 456 2.03e+01 c.3.1.1,c.4.1.1 74198,74199 1ma3A 253 2.08e+01 c.31.1.5 78883 1a0rP 245 2.12e+01 1b9yC c.47.1.6 33054 1rfeA 162 2.19e+01 2etxA 209 2.19e+01 1keoA 154 2.27e+01 b.64.1.1 68534 1toaA 313 2.29e+01 1toaA c.92.2.2 35598 1sqsA 242 2.35e+01 c.23.5.5 98968 1uheA 97 2.36e+01 2g0uA 92 2.45e+01 1vddA 228 2.55e+01 e.49.1.1 108519 1tbrR 103 2.57e+01 1tbrR g.68.1.1,g.68.1.1 44707,44708 1gnf 46 2.67e+01 1gatA g.39.1.1 45107 1wgvA 124 2.79e+01 1xyiA 66 2.79e+01 1smlA 269 2.81e+01 1smlA d.157.1.1 42053 1q18A 332 2.82e+01 c.55.1.7,c.55.1.7 104470,104471 2cunA 410 2.83e+01 1kal 29 2.86e+01 g.3.3.1 44077 1o7kA 131 2.86e+01 d.189.1.1 81144 1f7sA 139 2.87e+01 1cof d.109.1.2 40857 1jic 62 2.87e+01 1azpA b.34.13.1 37462 2adoA 196 2.89e+01 1bc4 111 2.89e+01 1onc d.5.1.1 37279 1pnsC 206 2.90e+01 i.1.1.1 88170 1nteA 82 2.94e+01 b.36.1.1 86163 1fw9A 164 2.95e+01 1fw9A d.190.1.1 60059 1xtoA 311 2.97e+01 1ft5A 211 2.97e+01 1bvb a.138.1.3 19681 1omzA 293 2.97e+01 c.68.1.15 87093 1j5eC 239 2.98e+01 d.52.3.1,d.53.1.1 71544,71545 2d9rA 104 2.99e+01 2f9dA 125 3.05e+01 1yg6A 193 3.06e+01 1af8 86 3.07e+01 2af8 a.28.1.1 16932 1r6jA 82 3.09e+01 b.36.1.1 97151 1yphC 131 3.15e+01 2culA 232 3.20e+01 2axwA 134 3.22e+01 1pbjA 125 3.24e+01 d.37.1.1,d.37.1.1 94414,94415 1d4tA 104 3.25e+01 1d4tA d.93.1.1 40537 1fjgC 239 3.27e+01 1fjfC d.52.3.1,d.53.1.1 38831,38839 1yaxA 153 3.32e+01 1zkdA 387 3.32e+01 1nu4A 97 3.36e+01 d.58.7.1 80731 1bvb 211 3.38e+01 1bvb a.138.1.3 19683 1sap 66 3.39e+01 1azpA b.34.13.1 37472 1bxlA 181 3.43e+01 1maz f.1.4.1 43396 1m93A 55 3.44e+01 e.1.1.1 91235 1gpmA 525 3.44e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1vp2A 208 3.45e+01 2af8 86 3.46e+01 2af8 a.28.1.1 16933 2bg5A 324 3.52e+01 1b1yA 500 3.63e+01 1byb c.1.8.1 28796 1bby 69 3.67e+01 2bby a.4.5.15 16149 1bnzA 64 3.68e+01 1azpA b.34.13.1 37468 1qwnA 1045 3.72e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 2gmqA 118 3.73e+01 1tt8A 164 3.73e+01 1hwwA 1015 3.76e+01 a.8.3.1,b.30.5.6,c.6.2.1 83067,83068,83069 2bkfA 87 3.79e+01 1hxkA 1015 3.80e+01 a.8.3.1,b.30.5.6,c.6.2.1 83070,83071,83072 1al0F 426 3.86e+01 2bpa1 b.121.5.1 23274 2bpa1 426 3.90e+01 2bpa1 1cc1S 283 3.96e+01 2frvA e.19.1.1 43313 1k8mA 93 4.07e+01 b.84.1.1 68314 1ej0A 180 4.09e+01 1ej0A c.66.1.2 34179 2bsdA 264 4.10e+01 1bj4A 470 4.10e+01 1bj4A c.67.1.4 34479 1ylqA 96 4.14e+01 1htyA 1015 4.17e+01 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 1m07A 111 4.20e+01 d.5.1.1 78328 2fvtA 135 4.21e+01 1yqcA 170 4.27e+01 1b7fA 168 4.28e+01 1b7fA d.58.7.1,d.58.7.1 39169,39170 2wsyB 396 4.29e+01 2tysB c.79.1.1 35288 2cu6A 103 4.34e+01 1pxeA 63 4.39e+01 g.73.1.1 95286 1wouA 123 4.41e+01 c.47.1.16 109471 1tr0A 108 4.42e+01 d.58.4.4 107261 1s4nA 348 4.49e+01 c.68.1.16 98501 1eziA 228 4.60e+01 1eyrA c.68.1.13 34512 1t0hA 132 4.63e+01 b.34.2.1 106207 1vr4A 103 4.66e+01 1azqA 66 4.69e+01 1azpA b.34.13.1 37469 1nwwA 149 4.75e+01 d.17.4.8 86306 1dyqA 234 4.78e+01 3seb b.40.2.2,d.15.6.1 59140,59141 1yv4A 104 4.89e+01 1gm9B 557 4.97e+01 1quqB 121 5.02e+01 1quqB b.40.4.3 25305 1hbxA 92 5.05e+01 1mnmA d.88.1.1 60930 1ri5A 298 5.09e+01 c.66.1.34 97502 1uwdA 103 5.11e+01 1kebA 108 5.11e+01 c.47.1.1 77341 1vr7A 142 5.14e+01 1yc5A 246 5.15e+01 1xedA 117 5.20e+01 1e3aB 560 5.24e+01 1ajqB 1qh0A 295 5.28e+01 b.43.4.2,c.25.1.1 68891,68892 1lv3A 68 5.32e+01 g.39.1.9 78231 1ayrB 363 5.37e+01 1cf1A b.1.18.11,b.1.18.11 21917,21918 2gh1A 301 5.37e+01 1wrjA 156 5.49e+01 1whbA 157 5.55e+01 1rm6A 769 5.60e+01 1he2A 206 5.60e+01 1he2A c.2.1.2 60966 1gkfB 557 5.67e+01 1v30A 124 5.68e+01 1ztsA 139 5.69e+01 1rwiA 270 5.73e+01 b.68.9.1 97987 1w34A 304 5.74e+01 1zruA 264 5.79e+01 1gm7B 557 5.80e+01 1sb2A 133 5.85e+01 1c5eA 95 5.86e+01 1c5eA b.85.2.1 28317 2axpA 173 5.86e+01 1vfsA 386 5.90e+01 b.49.2.2,c.1.6.1 108584,108585 1vbvA 105 5.90e+01 1gk9B 557 5.94e+01 1h9jA 145 6.05e+01 1h9jA b.40.6.2,b.40.6.2 60829,60830 1hdoA 206 6.08e+01 1he2A c.2.1.2 60965 1wjnA 97 6.08e+01 2bwfA 77 6.13e+01 2fj6A 82 6.20e+01 1esfA 233 6.21e+01 3seb b.40.2.2,d.15.6.1 25146,37735 1rwzA 245 6.22e+01 d.131.1.2,d.131.1.2 98005,98006 1id0A 152 6.26e+01 d.122.1.3 66111 1go3E 187 6.28e+01 b.40.4.5,d.230.1.1 83054,83055 2cu3A 64 6.32e+01 1mxb 383 6.34e+01 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41329,41330,41331 1aj6 219 6.41e+01 1aj6 d.122.1.2 41106 1oj4A 283 6.42e+01 d.14.1.5,d.58.26.5 93083,93084 1e25A 282 6.46e+01 1e25A e.3.1.1 42731 2bby 69 6.52e+01 2bby a.4.5.15 16148 1wh0A 134 6.67e+01 1h9mA 145 6.67e+01 1h9jA b.40.6.2,b.40.6.2 60833,60834 2ak5A 64 6.78e+01 1kzlA 208 6.87e+01 b.43.4.3,b.43.4.3 77635,77636 1azpA 66 6.89e+01 1azpA b.34.13.1 37467 1x74A 360 6.93e+01 1kmdA 117 6.93e+01 d.189.1.1 72744 2frnA 278 6.96e+01 1sz2A 332 6.98e+01 1ztcA 221 7.04e+01 2aj6A 159 7.04e+01 1mwwA 128 7.08e+01 d.80.1.4 91483 1r1qA 100 7.08e+01 d.93.1.1 104763 2g64A 140 7.19e+01 2gaiA 633 7.32e+01 1cf1A 404 7.41e+01 1cf1A b.1.18.11,b.1.18.11 21907,21908 1aho 64 7.46e+01 1aho g.3.7.1 44127 2fz4A 237 7.49e+01 1kz7A 353 7.60e+01 a.87.1.1,b.55.1.1 73333,73334 1g6gA 127 7.60e+01 1g6gA b.26.1.2 23916 2gw6A 123 7.60e+01 1azeA 56 7.62e+01 b.34.2.1 24536 1nu0A 138 7.67e+01 c.55.3.8 92165 2rslA 140 7.67e+01 2rslA c.53.1.1 33345 1tikA 213 7.69e+01 c.23.5.3 107003 1ftpA 133 7.70e+01 1hmt b.60.1.2 27199 1np7A 489 7.72e+01 a.99.1.1,c.28.1.1 80677,80678 2cq2A 114 7.75e+01 1b2rA 304 7.77e+01 1fnc b.43.4.2,c.25.1.1 25648,31538 1wf3A 301 7.80e+01 1zlhB 75 7.88e+01 1o1zA 234 8.00e+01 c.1.18.3 86555 1wyxA 69 8.01e+01 1mxa 383 8.02e+01 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41326,41327,41328 1tif 78 8.05e+01 1tif d.15.8.1 37836 2ewrA 170 8.06e+01 1ajqB 557 8.07e+01 1ajqB 1njhA 119 8.07e+01 b.128.1.1 85787 1go2A 304 8.11e+01 b.43.4.2,c.25.1.1 76243,76244 2agmA 167 8.12e+01 1fht 116 8.13e+01 1urnA d.58.7.1 39157 1segA 64 8.19e+01 g.3.7.1 105453 1cor 82 8.19e+01 451c a.3.1.1 15903 1uurA 473 8.23e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 2amyA 246 8.36e+01 1kv0A 66 8.36e+01 g.3.7.1 91040 1nrlA 316 8.38e+01 a.123.1.1 92091 1db3A 372 8.45e+01 1db3A c.2.1.2 29813 1wggA 96 8.56e+01 1sso 62 8.59e+01 1azpA b.34.13.1 37463 1no5A 114 8.65e+01 d.218.1.5 92014 1bia 321 8.68e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1juvA 193 8.84e+01 c.71.1.1 90912 2tysB 397 8.87e+01 2tysB c.79.1.1 35272