# 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 2.28e-01 1xewY 172 8.02e-01 1wmhB 86 8.23e-01 1keoA 154 1.64e+00 b.64.1.1 68534 1hyuA 521 1.77e+00 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1cx0A 95 1.80e+00 1urnA d.58.7.1 39158 1urnA 97 2.37e+00 1urnA d.58.7.1 39153 1vr7A 142 2.61e+00 1m5oC 100 2.96e+00 d.58.7.1 78654 1hqz9 141 3.06e+00 1fr3A 67 3.57e+00 1fr3A b.40.6.1 25436 1repC 251 3.84e+00 1repC a.4.5.10,a.4.5.10 16125,16126 2ifeA 100 4.03e+00 1tig d.68.1.1 39567 1gm9B 557 4.09e+00 1ip9A 85 4.12e+00 1ip9A d.15.2.2 62638 1oiaA 95 4.13e+00 d.58.7.1 87051 2g64A 140 4.17e+00 1xn5A 146 4.19e+00 2cunA 410 4.31e+00 1kjwA 295 4.99e+00 b.34.2.1,c.37.1.1 68643,68644 1e3aB 560 5.20e+00 1ajqB 1h2cA 140 5.47e+00 b.31.1.1 83462 1gk9B 557 5.56e+00 2etxA 209 5.61e+00 1gkfB 557 5.66e+00 1audA 101 5.81e+00 1urnA d.58.7.1 39156 1gm7B 557 5.83e+00 1u24A 337 6.11e+00 2adoA 196 6.56e+00 1qwlA 505 6.57e+00 e.5.1.1 96483 1hqz1 141 6.99e+00 1vp2A 208 7.37e+00 2wsyB 396 7.53e+00 2tysB c.79.1.1 35288 1ajqB 557 7.92e+00 1ajqB 1gutA 68 8.23e+00 b.40.6.1 65576 1nu4A 97 8.24e+00 d.58.7.1 80731 1agnA 373 8.70e+00 2ohxA b.35.1.2,c.2.1.1 24737,29753 1nrlA 316 9.13e+00 a.123.1.1 92091 1zpvA 91 9.54e+00 1tluA 130 9.55e+00 d.156.1.2 107139 1gnf 46 9.82e+00 1gatA g.39.1.1 45107 1pnsC 206 1.01e+01 i.1.1.1 88170 2tysB 397 1.02e+01 2tysB c.79.1.1 35272 1j5eC 239 1.03e+01 d.52.3.1,d.53.1.1 71544,71545 1s12A 94 1.09e+01 1zynA 202 1.16e+01 1r6jA 82 1.18e+01 b.36.1.1 97151 1oeyJ 107 1.19e+01 d.15.2.2 92804 1jxmA 301 1.19e+01 b.34.2.1,c.37.1.1 67420,67421 1vhxA 150 1.23e+01 c.55.3.8 100712 1jjgA 102 1.25e+01 b.40.4.5 71696 2frnA 278 1.26e+01 1nteA 82 1.26e+01 b.36.1.1 86163 1sro 76 1.31e+01 1sro b.40.4.5 25327 1pnkB 557 1.47e+01 1ajqB 1ml8A 134 1.47e+01 d.227.1.2 85013 1a50B 396 1.48e+01 2tysB c.79.1.1 35280 1dyqA 234 1.49e+01 3seb b.40.2.2,d.15.6.1 59140,59141 2dfkA 402 1.49e+01 1iw7C 1119 1.50e+01 e.29.1.1 71474 1bksB 397 1.51e+01 2tysB c.79.1.1 35285 1s4nA 348 1.51e+01 c.68.1.16 98501 1di2A 69 1.51e+01 1di2A d.50.1.1 38780 1k8yB 396 1.54e+01 c.79.1.1 72184 2d9rA 104 1.59e+01 1fw9A 164 1.61e+01 1fw9A d.190.1.1 60059 1sqsA 242 1.62e+01 c.23.5.5 98968 1x74A 360 1.67e+01 1qopB 396 1.68e+01 2tysB c.79.1.1 35270 8rucI 123 1.72e+01 1rboC d.73.1.1 39629 1toaA 313 1.74e+01 1toaA c.92.2.2 35598 1hbxA 92 1.74e+01 1mnmA d.88.1.1 60930 1d4tA 104 1.75e+01 1d4tA d.93.1.1 40537 1yqcA 170 1.76e+01 1xsrA 168 1.81e+01 1hh2P 344 1.81e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 65835,65836,65837,65838 2amyA 246 1.82e+01 1rboC 123 1.82e+01 1rboC d.73.1.1 39634 2fhzB 108 1.84e+01 2cu6A 103 1.85e+01 2c7hA 86 1.88e+01 1ylqA 96 1.91e+01 1pms 136 1.92e+01 1awe b.55.1.1 26966 1c52 131 1.93e+01 1c52 a.3.1.1 15810 1z52A 470 1.96e+01 1wkqA 164 1.96e+01 c.97.1.2 109393 1xtoA 311 1.97e+01 2bkfA 87 1.98e+01 1tt8A 164 1.98e+01 2ewrA 170 2.01e+01 1ka6A 128 2.01e+01 d.93.1.1 68370 1omzA 293 2.05e+01 c.68.1.15 87093 1tbrR 103 2.06e+01 1tbrR g.68.1.1,g.68.1.1 44707,44708 2gmqA 118 2.09e+01 1tlk 154 2.12e+01 1tlk b.1.1.4 21707 2ewcA 126 2.13e+01 1fjgC 239 2.21e+01 1fjfC d.52.3.1,d.53.1.1 38831,38839 1tiyA 164 2.27e+01 c.97.1.2 107012 1preB 470 2.30e+01 1preA d.169.1.2,f.8.1.1 42438,43825 1wyxA 69 2.32e+01 1esfA 233 2.37e+01 3seb b.40.2.2,d.15.6.1 25146,37735 1b33N 67 2.37e+01 1b33N d.30.1.1 38459 1fhgA 154 2.42e+01 1tlk b.1.1.4 21706 1vr4A 103 2.48e+01 1fht 116 2.54e+01 1urnA d.58.7.1 39157 2gw6A 123 2.56e+01 2ak5A 64 2.57e+01 1focA 132 2.62e+01 1c52 a.3.1.1 15812 1z6gA 218 2.63e+01 1gtqA 140 2.63e+01 1b66A d.96.1.2 40661 1m5q1 130 2.67e+01 1uurA 473 2.71e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1xsqA 168 2.73e+01 1gh8A 89 2.84e+01 1gh8A d.58.12.1 39309 1b66A 140 2.87e+01 1b66A d.96.1.2 40657 1ycyA 71 2.88e+01 1aho 64 2.89e+01 1aho g.3.7.1 44127 1a0rP 245 2.92e+01 1b9yC c.47.1.6 33054 1preA 470 3.01e+01 1preA d.169.1.2,f.8.1.1 42437,43824 1x8dA 104 3.05e+01 1i8fA 81 3.09e+01 1i8fA b.38.1.1 61959 1uwdA 103 3.14e+01 1f7sA 139 3.14e+01 1cof d.109.1.2 40857 1aj6 219 3.15e+01 1aj6 d.122.1.2 41106 1smxA 96 3.16e+01 b.40.4.5 105772 1luzA 88 3.20e+01 b.40.4.5 74271 2aj6A 159 3.25e+01 2fclA 169 3.26e+01 1quqB 121 3.29e+01 1quqB b.40.4.3 25305 1rfeA 162 3.31e+01 1t0hA 132 3.39e+01 b.34.2.1 106207 1yg6A 193 3.44e+01 2g6fX 59 3.59e+01 1c9oA 66 3.60e+01 1mjc b.40.4.5 25325 1yukB 120 3.64e+01 1lq9A 112 3.65e+01 d.58.4.3 78129 1juvA 193 3.80e+01 c.71.1.1 90912 1cf7A 76 3.82e+01 1cf7B a.4.5.17 16151 1ri7A 171 3.90e+01 a.4.5.32,d.58.4.2 97504,97505 1gh6A 114 3.91e+01 a.2.3.1 65191 1icxA 155 3.92e+01 d.129.3.1 71191 2fiuA 99 3.94e+01 1o0pA 104 3.97e+01 d.58.7.1 86535 1bia 321 3.98e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1kz7A 353 4.00e+01 a.87.1.1,b.55.1.1 73333,73334 2c6yA 111 4.12e+01 1vi7A 217 4.19e+01 d.14.1.11,d.58.11.2 100740,100741 1y8oB 128 4.20e+01 2cxcA 144 4.21e+01 1u46A 291 4.28e+01 d.144.1.7 107656 1eziA 228 4.28e+01 1eyrA c.68.1.13 34512 1tig 94 4.29e+01 1tig d.68.1.1 39566 2bby 69 4.30e+01 2bby a.4.5.15 16148 1gouA 116 4.30e+01 d.1.1.2 65429 1fk9A 543 4.34e+01 1rthA c.55.3.1,e.8.1.2 33607,43080 1mhxA 65 4.37e+01 d.15.7.1 79134 1n99A 166 4.38e+01 b.36.1.1,b.36.1.1 85459,85460 1a9nB 96 4.42e+01 1urnA d.58.7.1 39165 1bib 321 4.45e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16084,24448,40788 1segA 64 4.50e+01 g.3.7.1 105453 1kzhA 555 4.53e+01 c.89.1.1 73361 1p27B 106 4.53e+01 d.58.7.1 93908 1dqiA 124 4.61e+01 1do6A b.1.13.1 22357 1zc1A 208 4.62e+01 1gpmA 525 4.64e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 2fueA 262 4.65e+01 1wrjA 156 4.66e+01 1hfoA 113 4.68e+01 d.80.1.3 61006 1ft5A 211 4.71e+01 1bvb a.138.1.3 19681 1ayrB 363 4.75e+01 1cf1A b.1.18.11,b.1.18.11 21917,21918 1mo9A 523 4.82e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 2b25A 336 4.86e+01 1div 149 4.86e+01 1div d.99.1.1,d.100.1.1 40692,40693 1pbjA 125 4.94e+01 d.37.1.1,d.37.1.1 94414,94415 1bvb 211 4.96e+01 1bvb a.138.1.3 19683 1v9jA 113 5.01e+01 d.52.6.1 100542 2a6aA 218 5.01e+01 1oj4A 283 5.01e+01 d.14.1.5,d.58.26.5 93083,93084 2fneA 117 5.01e+01 1wz7A 111 5.15e+01 1v5tA 90 5.18e+01 d.15.1.1 108385 1mnmC 87 5.20e+01 1akhB a.4.1.1 15983 1psuA 140 5.21e+01 d.38.1.5 88285 1jx2B 315 5.23e+01 c.37.1.8 67404 1m93A 55 5.25e+01 e.1.1.1 91235 1cf7B 95 5.29e+01 1cf7B a.4.5.17 16152 1wojA 214 5.32e+01 1z02A 446 5.38e+01 1qysA 106 5.48e+01 k.41.1.1 96603 1n7eA 97 5.52e+01 b.36.1.1 91691 1m13A 316 5.58e+01 a.123.1.1 84746 1k38A 254 5.58e+01 e.3.1.1 84303 1fd8A 73 5.75e+01 1cc8A d.58.17.1 59770 1njhA 119 5.78e+01 b.128.1.1 85787 1azeA 56 5.79e+01 b.34.2.1 24536 1nhyA 219 5.80e+01 a.45.1.1,c.47.1.5 80520,80521 2culA 232 5.81e+01 1u6bA 98 5.82e+01 d.58.7.1 107703 1ujrA 110 5.87e+01 1sn4A 64 5.89e+01 1aho g.3.7.1 44136 1wspA 84 5.96e+01 1cf1A 404 5.98e+01 1cf1A b.1.18.11,b.1.18.11 21907,21908 2a4dA 160 5.99e+01 1d1gA 168 6.10e+01 1d1gA c.71.1.1 34889 1kzlA 208 6.13e+01 b.43.4.3,b.43.4.3 77635,77636 1e25A 282 6.18e+01 1e25A e.3.1.1 42731 1vbvA 105 6.23e+01 1bmlC 362 6.23e+01 1bmlC d.15.5.1,d.15.5.1,d.15.5.1 37729,37730,37731 1f2tB 148 6.24e+01 1f2tB 1jenB 67 6.28e+01 1jenB d.156.1.1 42029 2f9dA 125 6.28e+01 1b76A 442 6.29e+01 1atiA c.51.1.1,d.104.1.1 33198,40747 1vkuA 100 6.29e+01 a.28.1.1 108690 1zvpA 133 6.31e+01 1al0F 426 6.35e+01 2bpa1 b.121.5.1 23274 2fs2A 151 6.40e+01 1mnmA 100 6.43e+01 1mnmA d.88.1.1 40232 2gh1A 301 6.57e+01 1d6mA 653 6.60e+01 1d6mA e.10.1.1 43248 1ztcA 221 6.61e+01 2gi9A 56 6.63e+01 2u2fA 85 6.66e+01 2u2fA d.58.7.1 39167 1wmhA 89 6.68e+01 1gyxA 76 6.72e+01 d.80.1.1 76387 1wznA 252 6.79e+01 1i7pA 274 6.82e+01 b.43.4.2,c.25.1.1 66048,66049 1nt2A 210 6.93e+01 c.66.1.3 86149 2myr 501 6.95e+01 1no5A 114 7.07e+01 d.218.1.5 92014 1qb2A 109 7.10e+01 1qb2A a.36.1.1 17125 1pgx 83 7.12e+01 2igd d.15.7.1 37823 1do6A 124 7.15e+01 1do6A b.1.13.1 22361 1r1qA 100 7.18e+01 d.93.1.1 104763 1neiA 60 7.24e+01 d.253.1.1 91843 1ma3A 253 7.25e+01 c.31.1.5 78883 2eulA 156 7.29e+01 1go3E 187 7.33e+01 b.40.4.5,d.230.1.1 83054,83055 1whi 122 7.37e+01 1whi b.39.1.1 24810 2coqA 108 7.41e+01 1rwsA 77 7.44e+01 d.15.3.2 97991 1qayA 428 7.47e+01 1qaxA d.58.20.1,d.179.1.1 39378,42599 1coo 98 7.56e+01 1coo a.60.3.1 17967 1hymA 45 7.57e+01 1hymA d.40.1.1 38581 1x1gA 129 7.59e+01 1cz3A 168 7.61e+01 1d1gA c.71.1.1 34891 1nwwA 149 7.67e+01 d.17.4.8 86306 2a5hA 416 7.67e+01 1kv0A 66 7.71e+01 g.3.7.1 91040 1uzcA 71 7.77e+01 a.159.2.1 100222 1bby 69 7.90e+01 2bby a.4.5.15 16149 2g6tA 306 7.94e+01 1j7dA 145 8.10e+01 1jatB d.20.1.1 62680 1tq8A 163 8.28e+01 c.26.2.4 107204 2gaiA 633 8.32e+01 1vm6A 228 8.38e+01 c.2.1.3,d.81.1.3 108876,108877 1wkaA 147 8.42e+01 2ab5A 269 8.46e+01 1vl6A 388 8.48e+01 c.2.1.7,c.58.1.3 108724,108725 2hrvA 142 8.49e+01 2hrvA b.47.1.4 26429 1kebA 108 8.50e+01 c.47.1.1 77341 1pp0A 199 8.53e+01 d.103.1.1 104211 1l4wB 25 8.54e+01 1qaxA 428 8.58e+01 1qaxA d.58.20.1,d.179.1.1 39376,42597 1m07A 111 8.60e+01 d.5.1.1 78328 1whbA 157 8.61e+01 1mu7A 485 8.65e+01 d.136.1.3,d.136.1.3 79475,79476 1gppA 237 8.69e+01 b.86.1.2 76262 1e4mM 501 8.71e+01 1e70M c.1.8.4 59226 2aw42 46 8.76e+01 1pqzA 238 8.77e+01 b.1.1.2,d.19.1.1 104297,104298 1qvaA 223 8.81e+01 1qvaA c.37.1.19 32411 1q68A 38 8.81e+01 j.48.1.1 95962 1rec 201 8.87e+01 1rec a.39.1.5 17326 1mwsA 646 8.92e+01 d.17.4.5,d.175.1.1,e.3.1.1 79592,79593,79594 1mykA 53 8.93e+01 1bazA a.43.1.1 17425 1mylA 53 8.94e+01 1bazA a.43.1.1 17427 2g3aA 152 8.95e+01 1xdfA 157 8.97e+01 1a5fL 220 8.99e+01 8fabA b.1.1.1,b.1.1.2 20302,21294