# 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 1ebfA 358 3.37e-02 1ebuA c.2.1.3,d.81.1.2 30033,39948 1ebuA 358 2.34e-01 1ebuA c.2.1.3,d.81.1.2 30035,39950 2cyeA 133 3.84e-01 1kum 108 5.37e-01 1kum b.3.1.1 22525 1y6hA 177 9.64e-01 3pchA 200 1.26e+00 3pchA b.3.6.1 22653 3pcgA 200 1.26e+00 3pchA b.3.6.1 22647 1e19A 314 1.65e+00 1b7bA c.73.1.1 34967 1h2wA 710 2.23e+00 b.69.7.1,c.69.1.4 76596,76597 3pcnA 200 2.29e+00 3pchA b.3.6.1 22725 1tu1A 148 2.31e+00 d.107.1.3 107316 1b4aA 149 2.37e+00 1b4aA a.4.5.3,d.74.2.1 16088,39721 2achA 360 2.64e+00 1c8oA e.1.1.1 42626 1zpvA 91 2.83e+00 2pcdA 200 2.99e+00 3pchA b.3.6.1 22665 1qfmA 710 3.05e+00 1qfmA b.69.7.1,c.69.1.4 27673,34641 1e8nA 710 3.28e+00 1qfmA b.69.7.1,c.69.1.4 27675,34643 2b18A 164 3.37e+00 1d8iA 311 3.38e+00 1d8iA d.63.1.1 39541 2bjuA 453 3.57e+00 1h2xA 710 3.62e+00 b.69.7.1,c.69.1.4 76598,76599 1g2aA 168 4.24e+00 d.167.1.1 65109 1v8fA 276 4.40e+00 c.26.1.4 100503 2b20A 403 4.67e+00 1as4A 341 6.16e+00 1sek e.1.1.1 42623 2c52B 59 6.17e+00 1g55A 343 6.27e+00 1g55A c.66.1.26 34247 3proC 166 6.28e+00 3proC d.52.1.1,d.52.1.1 38812,38813 1f15B 218 6.44e+00 1f15B b.121.4.5 23321 1jyhA 157 6.52e+00 d.60.1.3 71956 1kao 167 6.54e+00 1ctqA c.37.1.8 32014 1bs4A 168 6.55e+00 1bs4A d.167.1.1 42287 1tiqA 180 6.85e+00 d.108.1.1 107010 3proD 166 7.13e+00 3proC d.52.1.1,d.52.1.1 38814,38815 1icjA 168 7.36e+00 1bs4A d.167.1.1 42284 1v3yA 192 7.43e+00 1ecrA 309 7.53e+00 1ecrA e.2.1.1 42678 2apr 325 7.90e+00 2er7E b.50.1.2 26819 1lqwA 183 7.95e+00 d.167.1.1 74210 3aprE 325 8.26e+00 2er7E b.50.1.2 26820 1d8hA 311 8.28e+00 1d8iA d.63.1.1 39544 6prcH 258 8.37e+00 6prcH b.41.1.1,f.23.10.1 25457,43436 1xeoA 168 8.47e+00 2basA 431 8.82e+00 1lf2A 331 8.99e+00 b.50.1.2 77914 1dxrH 258 9.78e+00 6prcH b.41.1.1,f.23.10.1 25456,43433 1t5yA 190 1.03e+01 b.122.1.1,d.17.6.3 106495,106496 1o0iA 138 1.08e+01 d.38.1.5 86532 2as0A 396 1.14e+01 1a31A 538 1.15e+01 1a36A d.163.1.2,e.15.1.1 42170,43263 1jxcA 68 1.17e+01 g.3.7.5 77201 1bkjA 240 1.23e+01 1bkjA d.90.1.1 40243 2cttA 104 1.25e+01 1dfmA 223 1.26e+01 1d2iA c.52.1.5 33295 1lmhA 184 1.34e+01 d.167.1.1 74036 1n5nA 180 1.38e+01 d.167.1.1 85336 1dw9A 156 1.42e+01 1dw9A a.35.1.4,d.72.1.1 17065,39596 1d2iA 223 1.50e+01 1d2iA c.52.1.5 33297 1ibvB 229 1.51e+01 1ds6B 180 1.52e+01 1rhoA b.1.18.8 21898 1pyaB 228 1.65e+01 1pyaB 1dwkA 156 1.66e+01 1dw9A a.35.1.4,d.72.1.1 17075,39606 1iuhA 198 1.68e+01 d.61.1.2 83711 2f1lA 187 1.69e+01 1vr3A 191 1.74e+01 1dbhA 354 1.75e+01 1awe a.87.1.1,b.55.1.1 18514,26967 1b7bA 310 1.76e+01 1b7bA c.73.1.1 34963 1sqwA 188 1.84e+01 1rgxA 114 1.84e+01 g.77.1.1 104932 2c5uA 375 1.85e+01 1o6aA 96 1.85e+01 b.139.1.1 92562 1c0aA 585 1.85e+01 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1xakA 83 1.85e+01 2occG 84 1.91e+01 2occG f.23.2.1 43522 2c3gA 98 1.93e+01 1ygtA 111 1.98e+01 1mli 96 1.98e+01 1mli d.58.4.1 39070 1a35A 538 2.04e+01 1a36A d.163.1.2,e.15.1.1 42171,43264 1x99A 145 2.11e+01 1f13A 731 2.24e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21877,22163,22164,37107 6mhtA 327 2.28e+01 6mhtA c.66.1.26 34226 1lg7A 182 2.33e+01 d.213.1.1 73888 1sesA 421 2.37e+01 1sesA a.2.7.1,d.104.1.1 15710,40710 2bukA 196 2.42e+01 2stv 195 2.42e+01 2stv b.121.7.1 23287 1bsjA 168 2.50e+01 1bs4A d.167.1.1 42302 1miqA 375 2.55e+01 b.50.1.2 79151 1rz2A 254 2.57e+01 b.100.1.1 105130 1kgqA 274 2.58e+01 b.81.1.2 72447 1vm6A 228 2.60e+01 c.2.1.3,d.81.1.3 108876,108877 1a7cA 379 2.64e+01 1sek e.1.1.1 42660 1a36A 592 2.64e+01 1a36A a.2.8.1,d.163.1.2,e.15.1.1 15715,42173,43266 2axyA 73 2.66e+01 1jae 471 2.69e+01 1smd b.71.1.1,c.1.8.1 27773,28760 1smeA 329 2.70e+01 1smrA b.50.1.2 26885 1dixA 208 2.70e+01 1bk7A d.124.1.1 41122 1v6zA 228 2.73e+01 1c05A 159 2.73e+01 1c05A d.66.1.2 39559 1g6oA 330 2.76e+01 1g6oA c.37.1.11 32430 1v8cA 168 2.79e+01 d.15.3.1,d.129.5.1 100495,100496 1ois 223 2.86e+01 1a36A e.15.1.1 43267 1jltB 122 2.86e+01 a.133.1.2 66868 1dpjA 329 2.87e+01 1smrA b.50.1.2 26828 1i1gA 141 2.92e+01 a.4.5.32,d.58.4.2 65982,65983 1qrkA 731 2.93e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21889,22187,22188,37119 1ej9A 563 3.04e+01 1a36A d.163.1.2,e.15.1.1 42172,43265 1awe 130 3.06e+01 1awe b.55.1.1 26968 1twuA 139 3.06e+01 d.32.1.8 107413 1ystH 260 3.06e+01 6prcH b.41.1.1,f.23.10.1 25482,43511 1qrjB 199 3.07e+01 1qrjB a.28.3.1 16952 1smd 496 3.07e+01 1smd b.71.1.1,c.1.8.1 27768,28755 1jwiA 131 3.17e+01 d.169.1.1 67383 1gcqC 70 3.19e+01 1gcpA b.34.2.1 60436 1h59B 54 3.25e+01 g.3.9.1 70881 2atvA 196 3.28e+01 1ohpA 125 3.33e+01 1t6aA 126 3.34e+01 d.129.8.1 106555 1dj0A 264 3.36e+01 1dj0A d.265.1.1 90337 1ki0A 253 3.37e+01 g.14.1.1,g.14.1.1,g.14.1.1 72493,72494,72495 1ex0A 731 3.41e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 2tdt 274 3.41e+01 3tdt b.81.1.2 28054 1ifrA 121 3.43e+01 b.1.16.1 71203 1ocxA 182 3.46e+01 b.81.1.3 86814 1a7j 290 3.48e+01 1a7j c.37.1.6 31952 1xxbA 78 3.50e+01 1xxaA d.74.2.1 39706 3tdt 274 3.50e+01 3tdt b.81.1.2 28053 2a73B 991 3.54e+01 1jj2H 167 3.54e+01 1ffkF d.41.4.1 63093 1f15A 218 3.60e+01 1f15B b.121.4.5 23320 2bzuA 181 3.64e+01 1v54G 85 3.66e+01 f.23.2.1 100328 8cho 125 3.71e+01 1opy d.17.4.3 38108 1ckmA 330 3.79e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 1qjgA 125 3.79e+01 1opy d.17.4.3 38102 1k1zA 78 3.81e+01 b.34.2.1 68026 1imvA 398 3.89e+01 e.1.1.1 62591 1luzA 88 3.90e+01 b.40.4.5 74271 1nqzA 194 3.94e+01 d.113.1.1 86077 1f5mA 180 3.98e+01 1f5mB d.110.2.1 40895 1sh8A 154 3.99e+01 d.38.1.5 105549 1wfuA 120 3.99e+01 1xtmA 175 4.01e+01 1ocvA 125 4.03e+01 d.17.4.3 86810 1boeA 47 4.06e+01 1boeA g.3.9.1 44187 1ve6A 582 4.07e+01 1aokB 122 4.11e+01 1poa a.133.1.2 19561 1pfzA 380 4.13e+01 1smrA b.50.1.2 26881 1m7vA 363 4.14e+01 d.174.1.1 78748 1bb9 115 4.18e+01 1bb9 b.34.2.1 24554 1gcpA 70 4.22e+01 1gcpA b.34.2.1 60430 1vdeA 454 4.25e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28378,40581,40582 1iybA 208 4.26e+01 d.124.1.1 90720 1evuA 731 4.27e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1ll1 590 4.27e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18488,18499,21864 1yuiA 54 4.29e+01 1yuiA g.37.1.1 45073 821p 166 4.40e+01 1ctqA c.37.1.8 31969 1eybA 471 4.43e+01 1ey2A b.82.1.4 28115 5p21 166 4.48e+01 1ctqA c.37.1.8 31966 1dokA 77 4.49e+01 1dokA d.9.1.1 37420 1vj2A 126 4.53e+01 b.82.1.10 100796 1gg3A 279 4.53e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16372,27007,37615 1dkgA 197 4.56e+01 1dkgA b.73.1.1,h.1.9.1 27812,45626 1skoA 143 4.62e+01 d.110.7.1 105676 1gguA 731 4.64e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21885,22179,22180,37115 1pms 136 4.66e+01 1awe b.55.1.1 26966 1occG 84 4.69e+01 2occG f.23.2.1 43562 1jmoA 480 4.75e+01 e.1.1.1 77138 1jkmA 358 4.75e+01 1jkmA c.69.1.2 34633 9apiA 347 4.80e+01 1ovaA e.1.1.1 42630 1xtlA 175 4.81e+01 1bcpC 199 4.82e+01 1bcpB b.40.2.1,d.169.1.2 25121,42430 1kdj 102 4.88e+01 1plc b.6.1.1 22864 1tdtA 259 4.94e+01 3tdt b.81.1.2 28055 1xl3C 92 5.06e+01 1r5pA 108 5.06e+01 c.47.1.15 97101 1cmxA 236 5.11e+01 1uch d.3.1.6 37130 1k4tA 592 5.32e+01 a.2.8.1,d.163.1.2,e.15.1.1 77263,77264,77265 1ey2A 471 5.52e+01 1ey2A b.82.1.4 28116 1dmhA 311 5.53e+01 1dmhA b.3.6.1 22633 1lj5A 379 5.54e+01 e.1.1.1 73928 1agi 125 5.64e+01 7rsa d.5.1.1 37303 2bzvA 181 5.69e+01 3mhtA 327 5.70e+01 6mhtA c.66.1.26 34234 1rtfB 252 5.73e+01 5ptp 1sbp 310 5.75e+01 1sbp c.94.1.1 35760 1ret 43 5.82e+01 1ret a.4.1.2 16024 1qs8A 329 5.86e+01 1smrA b.50.1.2 26887 1ounA 127 5.98e+01 1ounA d.17.4.2 38090 1wwjA 105 6.00e+01 1vetA 124 6.06e+01 d.110.7.1 108553 1jrhI 108 6.11e+01 1jrhI b.1.2.1 22059 2cfxA 144 6.11e+01 1xk7A 408 6.13e+01 1jsuC 84 6.18e+01 1jsuC j.55.1.1 46339 1v8hA 107 6.19e+01 1ppt 36 6.24e+01 1ppt j.6.1.1 46089 1uw4A 91 6.26e+01 d.58.7.4 100071 1epaA 164 6.31e+01 1epaA b.60.1.1 27128 1m13A 316 6.46e+01 a.123.1.1 84746 2gkpA 167 6.54e+01 1epbA 164 6.55e+01 1epaA b.60.1.1 27126 1res 43 6.61e+01 1ret a.4.1.2 16023 1sskA 158 6.62e+01 b.148.1.1 105986 1xneA 113 6.70e+01 1p0zA 131 6.74e+01 d.110.6.1 93882 1bcpD 110 6.78e+01 1bcpD b.40.2.1 25132 1rzhH 260 6.79e+01 b.41.1.1,f.23.10.1 98162,98163 2czsA 80 6.83e+01 1o1yA 239 6.85e+01 c.23.16.1 86554 2gf6A 135 6.86e+01 1prtD 110 6.89e+01 1bcpD b.40.2.1 25128 1ga3A 113 6.90e+01 1ga3A a.26.1.2 60411 1ar0A 127 6.91e+01 1ounA d.17.4.2 38092 1ggtB 731 6.93e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21882,22173,22174,37112 1konA 249 7.00e+01 e.39.1.1 72823 1x9gA 200 7.01e+01 c.33.1.3 109527 1df7A 159 7.03e+01 3dfr c.71.1.1 34885 1w2lA 99 7.11e+01 1ctqA 166 7.13e+01 1ctqA c.37.1.8 31965 1lybA 97 7.17e+01 1smrA b.50.1.2 26857 2fua 215 7.18e+01 2fua c.74.1.1 34977 1db2A 377 7.20e+01 1sek e.1.1.1 42672 1qr0A 228 7.22e+01 1qr0A d.150.1.1,d.150.1.1 59038,59039 1w2xA 758 7.29e+01 c.14.1.4,c.14.1.4 109134,109135 2bmjA 178 7.30e+01 2er7E 330 7.33e+01 2er7E b.50.1.2 26779 1v25A 541 7.40e+01 e.23.1.1 108275 2b6eA 146 7.53e+01 1lmeA 176 7.55e+01 d.167.1.1 84629 1acz 108 7.56e+01 1kum b.3.1.1 22524 1bj7 156 7.60e+01 1bj7 b.60.1.1 27113 1c3hA 137 7.70e+01 b.22.1.1 90405 1ghtA 105 7.74e+01 2rslA c.53.1.1 60526 1gdtA 183 7.77e+01 2rslA a.4.1.2,c.53.1.1 16021,33348 1iwmA 186 7.82e+01 b.125.1.2 83758 1s4iA 175 7.83e+01 2azeA 155 7.93e+01 1t46A 313 7.94e+01 d.144.1.7 106397 1k8hA 133 7.99e+01 b.111.1.1 72176 1jkmB 361 8.00e+01 1jkmA c.69.1.2 34634 1g87A 614 8.08e+01 a.102.1.2,b.2.2.2 83275,83276 1a15A 67 8.09e+01 1a15A d.9.1.1 37451 1q9jA 422 8.11e+01 c.43.1.2,c.43.1.2 104590,104591 1x1rA 178 8.14e+01 1pvc3 238 8.17e+01 1aym3 1ffkF 157 8.17e+01 1ffkF d.41.4.1 38628 1gvuA 329 8.17e+01 b.50.1.2 70619 1sek 378 8.35e+01 1sek e.1.1.1 42675 1gmiA 136 8.35e+01 b.7.1.1 65309 2f6hX 419 8.35e+01 1qxrA 189 8.51e+01 b.82.1.7 96552 1rip 81 8.53e+01 1rip b.40.4.5 25357 1n13A 52 8.54e+01 d.155.1.2 85248 1qj5A 429 8.57e+01 1dtyA c.67.1.4 34493 2a90A 240 8.67e+01 1epnE 330 8.67e+01 2er7E b.50.1.2 26780 1cknA 330 8.70e+01 1ckmA b.40.4.6,d.142.2.3 25360,41587 1wgkA 114 8.70e+01 1f5mB 180 8.72e+01 1f5mB d.110.2.1 40896 1m93B 245 8.73e+01 1wruA 379 8.75e+01 2nmbA 160 8.77e+01 2nmbA b.55.1.2 26994 1zq4A 693 8.83e+01 2sttA 96 8.85e+01 1awcA a.4.5.21 16163 1j9bA 141 8.85e+01 c.47.1.12 66459 2bf9A 36 8.90e+01 1vk0A 206 8.93e+01 c.55.3.5 100839 1x82A 190 9.00e+01