# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl-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.soe.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 1gefA 123 1.03e-04 1gefA c.52.1.18 60465 2eo0A 147 2.43e-04 1hh1A 143 1.07e-03 1gefA c.52.1.18 61036 1ob8A 135 4.54e-03 c.52.1.18 111627 1y88A 199 2.27e-02 a.60.4.3,c.52.1.30 116560,116561 1cliA 345 3.54e-02 1cliA d.79.4.1,d.139.1.1 39816,41459 1sw2A 275 9.36e-02 c.94.1.1 106064 2nw5A 360 1.27e-01 2ganA 190 2.18e-01 d.108.1.1 134889 1zmdA 474 2.98e-01 1j3nA 408 5.30e-01 c.95.1.1,c.95.1.1 84074,84075 1dctA 324 5.63e-01 6mhtA c.66.1.26 34244 2j5vA 367 6.60e-01 1e4eA 343 6.60e-01 1iow c.30.1.2,d.142.1.1 59221,59222 1o0pA 104 7.16e-01 d.58.7.1 86535 1zthA 258 7.34e-01 2nu8B 388 7.53e-01 2scuB 388 7.88e-01 2scuB c.23.4.1,d.142.1.4 31141,41562 2i2qA 137 8.05e-01 2abyA 146 8.34e-01 1tz9A 367 8.46e-01 c.1.15.6 107466 1ky9A 448 8.76e-01 b.36.1.4,b.47.1.1 73198,73199 2c5uA 375 9.44e-01 1dosA 358 9.77e-01 1dosA c.1.10.2 29175 1sw5B 275 1.03e+00 c.94.1.1 106070 1hqz1 141 1.07e+00 1sw5A 275 1.15e+00 c.94.1.1 106069 2pbxA 203 1.18e+00 1dv2A 452 1.18e+00 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28238,31645,41490 2ostA 151 1.18e+00 1iow 306 1.26e+00 1iow 1iowA 306 1.26e+00 c.30.1.2,d.142.1.1 31713,41481 1j7nA 776 1.33e+00 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 2btuA 346 1.49e+00 1nz0A 118 1.56e+00 d.14.1.2 86433 1bssA 244 1.61e+00 1rvaA c.52.1.2 33256 2v79A 135 1.68e+00 1pv9A 348 1.79e+00 c.55.2.1,d.127.1.1 95157,95158 1fp1D 372 1.81e+00 1fpqA a.4.5.29,c.66.1.12 59939,59940 1fpqA 372 1.90e+00 1fpqA a.4.5.29,c.66.1.12 59947,59948 1dv1A 449 1.90e+00 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1o12A 376 1.95e+00 b.92.1.5,c.1.9.10 80758,80759 1whzA 70 1.98e+00 d.50.3.2 114656 2ex4A 241 1.99e+00 c.66.1.42 132516 2dgmA 466 2.01e+00 c.67.1.6 131508 1l1jA 239 2.07e+00 b.47.1.1 84516 1pmmA 466 2.07e+00 c.67.1.6 94901 1qxoA 388 2.11e+00 d.258.1.1 96539 1qb5D 99 2.26e+00 b.40.2.1 88357 1ka9H 200 2.39e+00 c.23.16.1 77308 1tiiD 99 2.41e+00 1tiiD b.40.2.1 24965 1b96A 244 2.42e+00 1rvaA c.52.1.2 33268 3cc6A 281 2.57e+00 2yzkA 178 2.62e+00 3bqxA 150 2.63e+00 1sx5A 244 2.63e+00 c.52.1.2 99023 1lvwA 295 2.73e+00 c.68.1.6 84723 1yqyA 523 2.74e+00 d.92.1.14,d.166.1.1 123903,123904 1vf8A 377 2.88e+00 c.1.8.5,d.26.3.1 120029,120030 1b94A 244 3.03e+00 1rvaA c.52.1.2 33250 1eonA 245 3.07e+00 1rvaA c.52.1.2 33238 1an7A 136 3.09e+00 1seiA d.140.1.1 41465 2pziA 681 3.10e+00 2yydA 345 3.13e+00 2zodA 345 3.13e+00 1xtoA 311 3.74e+00 d.157.1.6 116030 1b97A 244 3.78e+00 1rvaA c.52.1.2 33252 2icgA 160 3.78e+00 2fomB 185 3.98e+00 b.47.1.3 133884 1q7fA 286 4.20e+00 b.68.9.1 96036 1iukA 140 4.27e+00 c.2.1.8 83712 1kshA 186 4.36e+00 c.37.1.8 72914 1seiA 130 4.40e+00 1seiA d.140.1.1 41463 1t15A 214 4.47e+00 c.15.1.3,c.15.1.3 99067,99068 1wfwA 74 4.62e+00 b.34.2.1 114595 1vr8A 142 4.67e+00 d.312.1.1 120445 1y4oA 104 4.89e+00 1nv8A 284 4.94e+00 c.66.1.30 86224 2avxA 171 5.12e+00 1gsa 316 5.20e+00 1gsa 1gsaA 316 5.20e+00 c.30.1.3,d.142.1.1 31718,41477 1jq4A 98 5.27e+00 d.15.4.2 67083 2b2nA 344 5.59e+00 c.37.1.19 127710 1e9lA 377 5.60e+00 1e9lA c.1.8.5,d.26.3.1 59395,59396 1suuA 312 6.01e+00 b.68.10.1 99006 1u2cA 246 6.03e+00 b.1.6.2,d.272.1.1 107610,107611 2cxnA 557 6.03e+00 2f9zC 159 6.05e+00 1oroA 213 6.09e+00 1opr c.61.1.1 34093 1gvfA 286 6.09e+00 c.1.10.2 70599 2okfA 140 6.17e+00 1qwoA 442 6.53e+00 c.60.1.2 104620 2evbA 74 6.78e+00 1jj2M 186 6.99e+00 1ffkK c.55.4.1 63098 1yr0A 175 7.12e+00 d.108.1.1 123905 2fe7A 166 7.33e+00 d.108.1.1 133325 1h7sA 365 7.35e+00 d.14.1.3,d.122.1.2 65705,65706 2pezA 179 7.62e+00 2oikA 154 7.65e+00 2j7uA 635 7.80e+00 2dgkA 452 7.92e+00 2bo9A 308 8.15e+00 c.56.5.1 128897 3bs2A 148 8.28e+00 1u0fA 564 8.49e+00 c.80.1.2 112912 1wkyA 464 8.52e+00 b.18.1.31,c.1.8.3 120992,120993 2iruA 303 8.63e+00 1kllA 130 8.68e+00 d.32.1.2 72720 1ceo 343 8.81e+00 1ceo 1ceoA 343 8.81e+00 c.1.8.3 28808 6rxnA 45 8.90e+00 g.41.5.1 45222 2fp4B 395 8.95e+00 c.23.4.1,d.142.1.4 133897,133898 1fjgD 209 9.02e+00 1c05A d.66.1.2 39553 2inpE 118 9.07e+00 1f9zA 135 9.10e+00 1qipA d.32.1.1 38484 2je6A 277 9.28e+00 2pbeA 294 9.37e+00 2inbA 140 9.50e+00 1s1qA 145 9.64e+00 d.20.1.2 98351 1ukgA 252 9.64e+00 b.29.1.1 99489 2iy2A 72 9.82e+00 2ax4A 198 9.96e+00 2q8zA 342 9.97e+00 1wy7A 207 1.00e+01 c.66.1.32 121433 3cxjA 165 1.00e+01 1vqoN 187 1.01e+01 c.55.4.1 120375 1booA 323 1.03e+01 1booA c.66.1.11 34248 2yvyA 278 1.05e+01 1lh0A 213 1.06e+01 c.61.1.1 73896 1ml8A 134 1.07e+01 d.227.1.2 85013 1yemA 179 1.07e+01 d.63.1.2 116646 2z2nA 299 1.09e+01 2rauA 354 1.09e+01 2oodA 475 1.14e+01 2a2lA 145 1.14e+01 d.110.9.1 126035 1eokA 290 1.17e+01 1eokA c.1.8.5 28991 1opr 213 1.21e+01 1opr 2o3bB 136 1.23e+01 d.221.1.1 138902 1z15A 344 1.25e+01 1g0uG 252 1.25e+01 d.153.1.4 41952 1rypA 243 1.26e+01 1pmaA d.153.1.4 41932 1brfA 53 1.28e+01 1rb9 g.41.5.1 45236 1vffA 423 1.29e+01 c.1.8.4 120033 1bq8A 54 1.30e+01 1rb9 g.41.5.1 45237 1bq9A 54 1.30e+01 1rb9 g.41.5.1 45238 2r76A 152 1.31e+01 1xvsA 126 1.31e+01 b.1.23.1 116095 1wtaA 275 1.32e+01 2i6cA 160 1.35e+01 d.108.1.1 137095 1twfF 155 1.36e+01 a.143.1.2 112731 2q7eA 291 1.36e+01 2pvxA 54 1.39e+01 2qz7A 194 1.40e+01 3clkA 290 1.43e+01 1ohvA 472 1.45e+01 c.67.1.4 93031 1mtzA 293 1.46e+01 c.69.1.7 79467 3c8uA 208 1.47e+01 1te5A 257 1.47e+01 d.153.1.1 106795 2liv 344 1.48e+01 2liv 2e5vA 472 1.48e+01 2v1yA 108 1.52e+01 1lj5A 379 1.53e+01 e.1.1.1 73928 2uubD 209 1.54e+01 d.66.1.2 139935 1mp4A 292 1.59e+01 c.68.1.6 79376 1b34B 118 1.60e+01 1b34B b.38.1.1 24797 1irxA 523 1.62e+01 a.97.1.2,c.26.1.1 71378,71379 2o88A 58 1.64e+01 1bbzA 58 1.64e+01 1bbzA b.34.2.1 24477 1iicA 422 1.64e+01 1nmtA d.108.1.2,d.108.1.2 62422,62423 2absA 383 1.66e+01 c.72.1.1 126534 1lt4A 247 1.66e+01 1lt3A d.166.1.1 42231 1aboA 62 1.66e+01 1bbzA b.34.2.1 24474 1jj2R 84 1.67e+01 1ffkP d.12.1.1 63103 1n8fA 350 1.68e+01 c.1.10.4 85397 2b95A 106 1.68e+01 1gg1A 350 1.69e+01 1qr7A c.1.10.4 29187 2hz5A 106 1.69e+01 1mo9A 523 1.70e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 2vqeD 209 1.71e+01 2idrA 177 1.73e+01 1ijyA 130 1.73e+01 1ijxA a.141.1.1 62517 1lenA 181 1.75e+01 1led b.29.1.1 24032 1a9cA 221 1.76e+01 1a8rA d.96.1.1 40602 1uxtA 501 1.77e+01 c.82.1.1 108125 1eg9A 449 1.77e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1xqwA 293 1.78e+01 1skoA 143 1.79e+01 d.110.7.1 105676 2jesA 503 1.83e+01 1gulA 222 1.83e+01 1pgtA a.45.1.1,c.47.1.5 17675,32969 1a7cA 379 1.85e+01 1sek e.1.1.1 42660 1l2lA 457 1.85e+01 c.72.1.3 77656 1k0iA 394 1.85e+01 c.3.1.2,d.16.1.2 67942,67943 2iz6A 176 1.86e+01 1ndoA 449 1.86e+01 1ndoA b.33.1.2,d.129.3.3 24444,41323 1a9xA 1058 1.87e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1yk4A 52 1.89e+01 1x6vA 630 2.01e+01 b.122.1.3,c.26.1.5,c.37.1.4 121755,121756,121757 2dsxA 52 2.02e+01 g.41.5.1 131699 1v74A 107 2.02e+01 d.243.1.1 100442 2oz8A 389 2.03e+01 1f75A 249 2.05e+01 1f75A c.101.1.1 59662 2jc5A 259 2.06e+01 1pbyB 337 2.08e+01 b.69.2.2 94422 1vetA 124 2.14e+01 d.110.7.1 108553 1jqiA 388 2.14e+01 a.29.3.1,e.6.1.1 67087,67088 1eudB 396 2.14e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 1yrrA 382 2.15e+01 b.92.1.5,c.1.9.10 123935,123936 1h5rA 293 2.15e+01 c.68.1.6 65623 1oh0A 131 2.15e+01 d.17.4.3 87004 2ggoA 401 2.17e+01 1m5yA 408 2.18e+01 a.223.1.2,d.26.1.1,d.26.1.1 78664,78665,78666 1ykjA 394 2.19e+01 2imqX 282 2.19e+01 1usgA 346 2.22e+01 c.93.1.1 99864 1qr7A 350 2.25e+01 1qr7A c.1.10.4 29191 1to3A 304 2.26e+01 c.1.10.1 107161 2fvhA 120 2.27e+01 2a4xA 138 2.29e+01 d.32.1.2 126166 3bhwA 209 2.30e+01 1o7nA 449 2.32e+01 b.33.1.2,d.129.3.3 81162,81163 2es9A 115 2.35e+01 a.247.1.1 132318 1fa8A 135 2.36e+01 1qipA d.32.1.1 38486 1rvgA 305 2.36e+01 c.1.10.2 97920 5croA 66 2.40e+01 1orc a.35.1.2 17044 2fqpA 97 2.41e+01 2r60A 499 2.42e+01 1u8sA 192 2.46e+01 d.58.18.5,d.58.18.5 107737,107738 2e52A 300 2.47e+01 1f8fA 371 2.49e+01 b.35.1.2,c.2.1.1 83246,83247 1lml 478 2.49e+01 1lml 1lmlA 478 2.49e+01 d.92.1.3 40295 2pveA 54 2.49e+01 2fiaA 162 2.51e+01 d.108.1.1 133514 1kit 757 2.53e+01 1kit 1t1iA 364 2.55e+01 c.41.1.2 106248 1i6uA 130 2.59e+01 d.140.1.1 61850 1zmyA 142 2.60e+01 2o1sA 621 2.62e+01 1a8rA 221 2.62e+01 1a8rA d.96.1.1 40587 1b2jA 54 2.63e+01 1rb9 g.41.5.1 45231 1iroA 54 2.63e+01 g.41.5.1 45223 2pl5A 366 2.63e+01 1b2oA 54 2.65e+01 1rb9 g.41.5.1 45233 1vajA 214 2.66e+01 d.309.1.1 119907 1adjA 421 2.66e+01 1adjA c.51.1.1,d.104.1.1 33188,40737 2fl4A 149 2.67e+01 d.108.1.1 133706 2zceA 291 2.70e+01 2hq6A 185 2.71e+01 1si6X 282 2.72e+01 d.151.1.2 118968 1kjnA 157 2.78e+01 c.115.1.1 72614 1yspA 181 2.79e+01 1a9nB 96 2.83e+01 1urnA d.58.7.1 39165 1b13A 54 2.84e+01 1rb9 g.41.5.1 45227 2jerA 389 2.84e+01 1mzuA 129 2.85e+01 d.110.3.1 79714 1orc 71 2.86e+01 1orc 1orcA 71 2.86e+01 a.35.1.2 17054 1rl6A 177 2.86e+01 1rl6A d.141.1.1,d.141.1.1 41473,41474 1o7fA 469 2.92e+01 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 2ebeA 106 2.94e+01 2ovgA 66 2.99e+01 2dc4A 165 3.03e+01 1wwtA 88 3.05e+01 1wj5A 120 3.10e+01 a.4.5.59 114692 1sq5A 308 3.11e+01 c.37.1.6 105882 1moq 368 3.13e+01 1moq 1moqA 368 3.13e+01 c.80.1.1 35302 2pajA 492 3.13e+01 1uc8A 280 3.16e+01 c.30.1.6,d.142.1.7 99165,99166 1vqoS 85 3.16e+01 d.12.1.1 120380 1prn 289 3.19e+01 3prn 1tljA 213 3.23e+01 d.282.1.1 107126 1yprA 125 3.27e+01 3nul d.110.1.1 40888 2pljA 419 3.28e+01 1mnmA 100 3.32e+01 1mnmA d.88.1.1 40232 2anuA 255 3.32e+01 c.6.3.1 127058 2hs3A 603 3.33e+01 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 136712,136713,136714,136715 1s1dA 331 3.33e+01 b.67.3.1 98344 2h4uA 145 3.35e+01 d.38.1.5 136082 1fxoA 293 3.36e+01 1g0rA c.68.1.6 34524 1bli 483 3.40e+01 1bli 2ct8A 497 3.41e+01 1xmxA 385 3.42e+01 c.52.1.26 115568 1sjiA 350 3.42e+01 2pb2A 420 3.44e+01 3caiA 406 3.44e+01 1zq7A 207 3.45e+01 d.309.1.1 125501 2dvkA 188 3.46e+01 1fzdA 201 3.46e+01 3fib d.171.1.1 42484 1dxkA 227 3.47e+01 1a7tA d.157.1.1 42036 1zkcA 197 3.49e+01 b.62.1.1 125182 1w8sA 263 3.50e+01 c.1.10.1 120744 1nd4A 264 3.53e+01 d.144.1.6 91815 2vupA 190 3.57e+01 1wosA 364 3.57e+01 b.44.2.1,d.250.1.1 109468,109469 2buwB 241 3.59e+01 1lt3A 240 3.61e+01 1lt3A d.166.1.1 42230 1g0rA 293 3.61e+01 1g0rA c.68.1.6 34532 2gzqA 200 3.61e+01 1j3wA 163 3.63e+01 d.110.7.1 90833 1db2A 377 3.63e+01 1sek e.1.1.1 42672 2go8A 122 3.65e+01 2burB 241 3.65e+01 b.3.6.1 129228 2uv4A 152 3.71e+01 1acf 125 3.72e+01 3nul 1acfA 125 3.72e+01 d.110.1.1 40882 1a8y 367 3.78e+01 1a8y 1a8yA 367 3.78e+01 c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 2p4hX 322 3.80e+01 1sg7A 96 3.82e+01 a.239.1.1 118961 1jeqB 565 3.91e+01 1jeqB b.131.1.2,c.62.1.4 90368,90369 2qmlA 198 3.94e+01 1y08A 323 3.96e+01 d.3.1.12 116280 2fjrA 189 4.01e+01 3rubS 123 4.02e+01 1rboC d.73.1.1 39616 1k1fA 72 4.03e+01 a.147.1.1 68007 1wyuA 438 4.08e+01 c.67.1.7 121452 1sskA 158 4.08e+01 b.148.1.1 105986 1h6vA 499 4.10e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 60693,60694,60695 2hl0A 143 4.12e+01 2jroA 78 4.15e+01 1y81A 138 4.21e+01 c.2.1.8 122731 1y2qA 143 4.22e+01 2q2gA 180 4.23e+01 1qmvA 197 4.24e+01 1qq2A c.47.1.10 33066 2dc3A 193 4.25e+01 1umqA 81 4.26e+01 a.4.1.12 99625 2j3wA 142 4.26e+01 d.110.4.3 137981 2p7oA 133 4.27e+01 1h49A 512 4.29e+01 c.1.8.4 83477 1df7A 159 4.31e+01 3dfr c.71.1.1 34885 1rb9A 52 4.32e+01 g.41.5.1 45214 1icxA 155 4.33e+01 d.129.3.1 71191 1ylnA 252 4.35e+01 b.45.2.1,b.45.2.2 123657,123658 1rb9 53 4.37e+01 1rb9 1dgmA 363 4.39e+01 1bx4A c.72.1.1 34936 1opy 131 4.40e+01 1opy 1ea2A 131 4.40e+01 d.17.4.3 64860 1dmmA 131 4.42e+01 1opy d.17.4.3 38114 1c4kA 730 4.49e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 2j4jA 226 4.56e+01 2iswA 323 4.61e+01 1ryp1 222 4.68e+01 1ryp1 2ejaA 338 4.69e+01 2bzeA 153 4.71e+01 3ladA 476 4.71e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30573,30574,40208 1xesA 413 4.74e+01 1s3zA 165 4.76e+01 d.108.1.1 105250 1j2mA 99 4.82e+01 a.165.1.1 84018 2dgxA 96 4.82e+01 d.58.7.1 131515 1xwjB 26 4.85e+01 2basA 431 4.86e+01 c.1.33.1,d.110.6.2 128244,128245 1gowA 489 4.87e+01 1qvbA c.1.8.4 28981 2g8cO 251 4.89e+01 2fh1A 344 4.94e+01 d.109.1.1,d.109.1.1,d.109.1.1 133441,133442,133443 2yvuA 186 4.95e+01 2pcjA 224 4.96e+01 1wxxA 382 4.99e+01 b.122.1.9,c.66.1.51 121418,121419 1vcvA 226 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