# 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 1y96B 85 2.33e-01 1wmhB 86 1.39e+00 2ifeA 100 1.60e+00 1tig d.68.1.1 39567 1xewY 172 1.70e+00 1hyuA 521 1.83e+00 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1cx0A 95 1.91e+00 1urnA d.58.7.1 39158 1keoA 154 2.11e+00 b.64.1.1 68534 1urnA 97 2.48e+00 1urnA d.58.7.1 39153 1m5oC 100 3.03e+00 d.58.7.1 78654 1hqz9 141 3.39e+00 1fr3A 67 3.76e+00 1fr3A b.40.6.1 25436 1u24A 337 3.78e+00 1oiaA 95 4.23e+00 d.58.7.1 87051 1repC 251 4.45e+00 1repC a.4.5.10,a.4.5.10 16125,16126 1xn5A 146 4.73e+00 1vr7A 142 5.03e+00 2cunA 410 5.71e+00 1o0pA 104 5.79e+00 d.58.7.1 86535 1audA 101 5.85e+00 1urnA d.58.7.1 39156 1kjwA 295 6.34e+00 b.34.2.1,c.37.1.1 68643,68644 2etxA 209 6.63e+00 1h2cA 140 6.87e+00 b.31.1.1 83462 2wsyB 396 7.50e+00 2tysB c.79.1.1 35288 1hqz1 141 7.94e+00 2adoA 196 8.61e+00 1vp2A 208 9.05e+00 1nu4A 97 9.13e+00 d.58.7.1 80731 1gutA 68 9.38e+00 b.40.6.1 65576 1oeyJ 107 9.48e+00 d.15.2.2 92804 1gm9B 557 9.82e+00 2frnA 278 1.01e+01 1agnA 373 1.02e+01 2ohxA b.35.1.2,c.2.1.1 24737,29753 1qwlA 505 1.04e+01 e.5.1.1 96483 1nrlA 316 1.05e+01 a.123.1.1 92091 2tysB 397 1.07e+01 2tysB c.79.1.1 35272 1pnsC 206 1.07e+01 i.1.1.1 88170 1zynA 202 1.09e+01 1wkqA 164 1.10e+01 c.97.1.2 109393 1j5eC 239 1.11e+01 d.52.3.1,d.53.1.1 71544,71545 1e3aB 560 1.12e+01 1ajqB 1ml8A 134 1.16e+01 d.227.1.2 85013 1sqsA 242 1.16e+01 c.23.5.5 98968 2g64A 140 1.17e+01 1rfeA 162 1.19e+01 1iw7C 1119 1.20e+01 e.29.1.1 71474 1gnf 46 1.23e+01 1gatA g.39.1.1 45107 1tluA 130 1.25e+01 d.156.1.2 107139 1gkfB 557 1.29e+01 1gk9B 557 1.34e+01 1gm7B 557 1.35e+01 2gmqA 118 1.38e+01 1s12A 94 1.39e+01 1dyqA 234 1.42e+01 3seb b.40.2.2,d.15.6.1 59140,59141 8rucI 123 1.44e+01 1rboC d.73.1.1 39629 1vhxA 150 1.46e+01 c.55.3.8 100712 1tiyA 164 1.48e+01 c.97.1.2 107012 1rboC 123 1.51e+01 1rboC d.73.1.1 39634 1a50B 396 1.52e+01 2tysB c.79.1.1 35280 1jxmA 301 1.52e+01 b.34.2.1,c.37.1.1 67420,67421 1uurA 473 1.55e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1xtoA 311 1.56e+01 1k8yB 396 1.56e+01 c.79.1.1 72184 1bksB 397 1.58e+01 2tysB c.79.1.1 35285 1aho 64 1.63e+01 1aho g.3.7.1 44127 1tbrR 103 1.65e+01 1tbrR g.68.1.1,g.68.1.1 44707,44708 1kzlA 208 1.68e+01 b.43.4.3,b.43.4.3 77635,77636 1s4nA 348 1.69e+01 c.68.1.16 98501 1ka6A 128 1.73e+01 d.93.1.1 68370 2dfkA 402 1.74e+01 2d9rA 104 1.76e+01 1jjgA 102 1.78e+01 b.40.4.5 71696 1qopB 396 1.81e+01 2tysB c.79.1.1 35270 1ajqB 557 1.83e+01 1ajqB 1toaA 313 1.90e+01 1toaA c.92.2.2 35598 2bkfA 87 1.92e+01 2amyA 246 1.93e+01 2ewrA 170 2.00e+01 1fw9A 164 2.01e+01 1fw9A d.190.1.1 60059 1d4tA 104 2.02e+01 1d4tA d.93.1.1 40537 1xsrA 168 2.06e+01 1w2iA 91 2.10e+01 d.58.10.1 109127 1zpvA 91 2.11e+01 1pms 136 2.13e+01 1awe b.55.1.1 26966 1tlk 154 2.14e+01 1tlk b.1.1.4 21707 1yqcA 170 2.16e+01 1x74A 360 2.20e+01 1c52 131 2.29e+01 1c52 a.3.1.1 15810 1fjgC 239 2.32e+01 1fjfC d.52.3.1,d.53.1.1 38831,38839 1fhgA 154 2.34e+01 1tlk b.1.1.4 21706 1ylqA 96 2.35e+01 1esfA 233 2.36e+01 3seb b.40.2.2,d.15.6.1 25146,37735 1tt8A 164 2.37e+01 2gw6A 123 2.38e+01 1nteA 82 2.40e+01 b.36.1.1 86163 1t0hA 132 2.43e+01 b.34.2.1 106207 1hh2P 344 2.44e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 65835,65836,65837,65838 1gtqA 140 2.49e+01 1b66A d.96.1.2 40661 1wyxA 69 2.52e+01 1r6jA 82 2.55e+01 b.36.1.1 97151 1omzA 293 2.61e+01 c.68.1.15 87093 2cu6A 103 2.63e+01 1quqB 121 2.76e+01 1quqB b.40.4.3 25305 2ak5A 64 2.80e+01 1a0rP 245 2.81e+01 1b9yC c.47.1.6 33054 1f7sA 139 2.85e+01 1cof d.109.1.2 40857 1b66A 140 2.87e+01 1b66A d.96.1.2 40657 1div 149 2.90e+01 1div d.99.1.1,d.100.1.1 40692,40693 1ycyA 71 2.96e+01 1vr4A 103 3.00e+01 2fclA 169 3.08e+01 1aj6 219 3.15e+01 1aj6 d.122.1.2 41106 1luzA 88 3.15e+01 b.40.4.5 74271 1pnkB 557 3.20e+01 1ajqB 2aj6A 159 3.20e+01 1hbxA 92 3.24e+01 1mnmA d.88.1.1 60930 1fht 116 3.27e+01 1urnA d.58.7.1 39157 1m5q1 130 3.29e+01 1vbvA 105 3.32e+01 1n99A 166 3.32e+01 b.36.1.1,b.36.1.1 85459,85460 1xsqA 168 3.33e+01 1c9oA 66 3.37e+01 1mjc b.40.4.5 25325 1x8dA 104 3.42e+01 1ip9A 85 3.52e+01 1ip9A d.15.2.2 62638 1z52A 470 3.58e+01 1al0F 426 3.59e+01 2bpa1 b.121.5.1 23274 1yukB 120 3.69e+01 1m13A 316 3.73e+01 a.123.1.1 84746 1wrjA 156 3.79e+01 1juvA 193 3.81e+01 c.71.1.1 90912 1yg6A 193 3.82e+01 1segA 64 3.97e+01 g.3.7.1 105453 1ayrB 363 4.00e+01 1cf1A b.1.18.11,b.1.18.11 21917,21918 2ewcA 126 4.02e+01 1dqiA 124 4.03e+01 1do6A b.1.13.1 22357 1z6gA 218 4.06e+01 1i7pA 274 4.14e+01 b.43.4.2,c.25.1.1 66048,66049 1bc4 111 4.16e+01 1onc d.5.1.1 37279 2g6fX 59 4.22e+01 1bia 321 4.23e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1a9nB 96 4.29e+01 1urnA d.58.7.1 39165 1sro 76 4.32e+01 1sro b.40.4.5 25327 1preB 470 4.32e+01 1preA d.169.1.2,f.8.1.1 42438,43825 1cf1A 404 4.40e+01 1cf1A b.1.18.11,b.1.18.11 21907,21908 1cf7A 76 4.40e+01 1cf7B a.4.5.17 16151 1oj4A 283 4.42e+01 d.14.1.5,d.58.26.5 93083,93084 1bxdA 161 4.44e+01 1bxdA d.122.1.3 41111 2fhzB 108 4.44e+01 1smxA 96 4.47e+01 b.40.4.5 105772 1ft5A 211 4.51e+01 1bvb a.138.1.3 19681 1fk9A 543 4.54e+01 1rthA c.55.3.1,e.8.1.2 33607,43080 2bby 69 4.55e+01 2bby a.4.5.15 16148 1gpmA 525 4.56e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1ujrA 110 4.57e+01 1uwdA 103 4.58e+01 1wh0A 134 4.67e+01 1m07A 111 4.77e+01 d.5.1.1 78328 2fueA 262 4.78e+01 1di2A 69 4.82e+01 1di2A d.50.1.1 38780 1bvb 211 4.84e+01 1bvb a.138.1.3 19683 1focA 132 4.86e+01 1c52 a.3.1.1 15812 1wspA 84 4.87e+01 1sn4A 64 4.88e+01 1aho g.3.7.1 44136 1tig 94 4.94e+01 1tig d.68.1.1 39566 2b25A 336 4.95e+01 1kz7A 353 4.96e+01 a.87.1.1,b.55.1.1 73333,73334 1u46A 291 4.99e+01 d.144.1.7 107656 1pbjA 125 4.99e+01 d.37.1.1,d.37.1.1 94414,94415 1kzhA 555 4.99e+01 c.89.1.1 73361 1mnmA 100 4.99e+01 1mnmA d.88.1.1 40232 1eziA 228 5.01e+01 1eyrA c.68.1.13 34512 1gh8A 89 5.06e+01 1gh8A d.58.12.1 39309 1qysA 106 5.06e+01 k.41.1.1 96603 2a6aA 218 5.07e+01 1bib 321 5.09e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16084,24448,40788 1wz7A 111 5.11e+01 1jx2B 315 5.20e+01 c.37.1.8 67404 1vkuA 100 5.28e+01 a.28.1.1 108690 1azeA 56 5.29e+01 b.34.2.1 24536 2culA 232 5.30e+01 1p27B 106 5.33e+01 d.58.7.1 93908 1wojA 214 5.34e+01 1psuA 140 5.50e+01 d.38.1.5 88285 1kv0A 66 5.51e+01 g.3.7.1 91040 1pz1A 333 5.55e+01 c.1.7.1 95390 1b1yA 500 5.63e+01 1byb c.1.8.1 28796 1icxA 155 5.66e+01 d.129.3.1 71191 1k38A 254 5.73e+01 e.3.1.1 84303 2c7hA 86 5.75e+01 1mo9A 523 5.77e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1m93A 55 5.84e+01 e.1.1.1 91235 2gh1A 301 5.86e+01 1ztcA 221 5.89e+01 1yv4A 104 5.95e+01 1jenB 67 5.99e+01 1jenB d.156.1.1 42029 1preA 470 6.03e+01 1preA d.169.1.2,f.8.1.1 42437,43824 1d1gA 168 6.06e+01 1d1gA c.71.1.1 34889 1e25A 282 6.08e+01 1e25A e.3.1.1 42731 1lq9A 112 6.21e+01 d.58.4.3 78129 1njhA 119 6.22e+01 b.128.1.1 85787 1nhyA 219 6.26e+01 a.45.1.1,c.47.1.5 80520,80521 1zc1A 208 6.28e+01 1u6bA 98 6.34e+01 d.58.7.1 107703 1fd8A 73 6.41e+01 1cc8A d.58.17.1 59770 1mnmC 87 6.45e+01 1akhB a.4.1.1 15983 1vi7A 217 6.49e+01 d.14.1.11,d.58.11.2 100740,100741 1do6A 124 6.51e+01 1do6A b.1.13.1 22361 1b76A 442 6.52e+01 1atiA c.51.1.1,d.104.1.1 33198,40747 1cf7B 95 6.53e+01 1cf7B a.4.5.17 16152 1nt2A 210 6.54e+01 c.66.1.3 86149 1f2tB 148 6.54e+01 1f2tB 1b33N 67 6.70e+01 1b33N d.30.1.1 38459 2eulA 156 6.72e+01 2fs2A 151 6.78e+01 1zud1 251 6.85e+01 2a4dA 160 6.87e+01 1vddA 228 7.14e+01 e.49.1.1 108519 2myr 501 7.14e+01 1wmhA 89 7.17e+01 1gouA 116 7.22e+01 d.1.1.2 65429 1qb2A 109 7.22e+01 1qb2A a.36.1.1 17125 2gi9A 56 7.24e+01 1y8oB 128 7.24e+01 1mwwA 128 7.28e+01 d.80.1.4 91483 2fneA 117 7.29e+01 1uheA 97 7.30e+01 1k0fA 277 7.35e+01 c.92.2.2 71974 1pgx 83 7.43e+01 2igd d.15.7.1 37823 2gaiA 633 7.46e+01 1v9jA 113 7.54e+01 d.52.6.1 100542 1jic 62 7.58e+01 1azpA b.34.13.1 37462 1zvpA 133 7.67e+01 1qayA 428 7.70e+01 1qaxA d.58.20.1,d.179.1.1 39378,42599 1bby 69 7.74e+01 2bby a.4.5.15 16149 2cxcA 144 7.74e+01 2hrvA 142 7.74e+01 2hrvA b.47.1.4 26429 1wznA 252 7.77e+01 1d6mA 653 7.78e+01 1d6mA e.10.1.1 43248 1cz3A 168 7.80e+01 1d1gA c.71.1.1 34891 1ma3A 253 7.81e+01 c.31.1.5 78883 2f9dA 125 7.86e+01 1uzcA 71 7.88e+01 a.159.2.1 100222 1whi 122 7.89e+01 1whi b.39.1.1 24810 1id0A 152 7.96e+01 d.122.1.3 66111 1r1qA 100 8.13e+01 d.93.1.1 104763 1l3iA 192 8.24e+01 c.66.1.22 77676 2c6yA 111 8.30e+01 1mkaA 171 8.35e+01 1mkaA d.38.1.2 38543 1v5tA 90 8.41e+01 d.15.1.1 108385 1w2lA 99 8.41e+01 1hfoA 113 8.43e+01 d.80.1.3 61006 1q68A 38 8.45e+01 j.48.1.1 95962 1i8fA 81 8.45e+01 1i8fA b.38.1.1 61959 1fo5A 85 8.57e+01 1fo5A c.47.1.1 59922 1ri5A 298 8.57e+01 c.66.1.34 97502 1jhsA 188 8.58e+01 d.107.1.1 84172 1ri7A 171 8.59e+01 a.4.5.32,d.58.4.2 97504,97505 1vyqA 173 8.62e+01 1z02A 446 8.69e+01 1j1yA 136 8.69e+01 d.38.1.5 90776 1gyxA 76 8.71e+01 d.80.1.1 76387 1djtA 64 8.72e+01 1aho g.3.7.1 44132 2rslA 140 8.78e+01 2rslA c.53.1.1 33345 1j7dA 145 8.85e+01 1jatB d.20.1.1 62680 1mu7A 485 8.93e+01 d.136.1.3,d.136.1.3 79475,79476 1e4mM 501 8.94e+01 1e70M c.1.8.4 59226