# List of top-scoring protein chains for T0298.t2k-w0.5 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 1mb4A 370 4.20e-30 c.2.1.3,d.81.1.1 78908,78909 1ys4A 354 6.58e-30 1nwcA 371 7.06e-30 c.2.1.3,d.81.1.1 92229,92230 1t4bA 367 1.13e-29 c.2.1.3,d.81.1.1 106406,106407 1brmA 367 1.13e-29 1brmA c.2.1.3,d.81.1.1 30030,39945 1pr3A 371 1.16e-29 c.2.1.3,d.81.1.1 104300,104301 1ps8A 371 1.22e-29 c.2.1.3,d.81.1.1 104304,104305 1pquA 371 1.59e-29 c.2.1.3,d.81.1.1 104288,104289 1ozaA 371 1.83e-29 c.2.1.3,d.81.1.1 104045,104046 1nwhA 371 2.09e-29 c.2.1.3,d.81.1.1 92233,92234 1pqpA 371 2.35e-29 c.2.1.3,d.81.1.1 104286,104287 1pu2A 371 2.81e-29 c.2.1.3,d.81.1.1 104308,104309 1q2xA 371 3.46e-29 c.2.1.3,d.81.1.1 104503,104504 1xygA 359 2.70e-26 2cvoA 366 2.90e-26 1vknA 351 8.24e-26 c.2.1.3,d.81.1.1 108676,108677 2g17A 337 1.18e-21 1hdgO 332 4.00e-07 1dssG c.2.1.3,d.81.1.1 29990,39905 1vc2A 331 6.81e-07 c.2.1.3,d.81.1.1 100555,100556 1cf2O 337 1.10e-06 1b7gO c.2.1.3,d.81.1.1 29994,39909 1cerA 331 1.51e-06 1obfO 335 3.29e-06 c.2.1.3,d.81.1.1 86768,86769 3gpdG 334 3.88e-06 1dssG c.2.1.3,d.81.1.1 30029,39944 4gpd1 333 4.37e-06 1dssG 1gpdG 334 4.40e-06 1dssG c.2.1.3,d.81.1.1 30020,39935 1crwG 333 4.45e-06 1dssG c.2.1.3,d.81.1.1 30026,39941 1ihxA 333 4.53e-06 c.2.1.3,d.81.1.1 71211,71212 1u8fO 335 5.25e-06 1znqO 338 5.28e-06 1j0xO 332 6.41e-06 c.2.1.3,d.81.1.1 90750,90751 1gd1O 334 1.79e-05 1dssG c.2.1.3,d.81.1.1 29962,39877 2dbvO 334 1.88e-05 1dssG c.2.1.3,d.81.1.1 29970,39885 3dbvO 334 2.06e-05 1dssG c.2.1.3,d.81.1.1 29982,39897 1dssG 333 2.46e-05 1dssG c.2.1.3,d.81.1.1 30022,39937 1rm4A 337 8.33e-05 c.2.1.3,d.81.1.1 105000,105001 1rm5A 337 8.89e-05 c.2.1.3,d.81.1.1 105006,105007 1ywgO 337 8.94e-05 2b4rO 345 8.96e-05 1nptO 334 9.27e-05 c.2.1.3,d.81.1.1 85987,85988 2czcA 334 9.30e-05 1rm3A 337 1.04e-04 c.2.1.3,d.81.1.1 104994,104995 1nqoA 334 1.07e-04 c.2.1.3,d.81.1.1 86044,86045 1s7cA 331 1.54e-04 c.2.1.3,d.81.1.1 105346,105347 1gadO 330 1.56e-04 1dssG c.2.1.3,d.81.1.1 29950,39865 1gaeO 330 1.88e-04 1dssG c.2.1.3,d.81.1.1 29954,39869 1jn0A 335 2.86e-04 c.2.1.3,d.81.1.1 66915,66916 1i32A 360 2.27e-03 c.2.1.3,d.81.1.1 65993,65994 1gypA 358 2.27e-03 1dssG c.2.1.3,d.81.1.1 30004,39919 1nvmB 312 2.89e-03 c.2.1.3,d.81.1.1 86251,86252 1b7gO 340 3.79e-03 1b7gO c.2.1.3,d.81.1.1 29992,39907 1k3tA 359 9.35e-03 c.2.1.3,d.81.1.1 72022,72023 1ggaA 358 2.18e-02 1dssG c.2.1.3,d.81.1.1 30002,39917 2fmuA 248 4.30e-02 1hyeA 313 4.57e-02 2cmd c.2.1.5,d.162.1.1 61400,61401 2bkaA 242 5.59e-02 1qydA 313 1.44e-01 c.2.1.2 96583 1jayA 212 1.54e-01 c.2.1.6 66478 2fr1A 486 2.62e-01 2a35A 215 4.87e-01 1bwsA 321 5.59e-01 1bsvA c.2.1.2 29812 1bsvA 321 5.61e-01 1bsvA c.2.1.2 29809 1e6uA 321 6.33e-01 1bsvA c.2.1.2 29805 1j49A 333 6.59e-01 c.2.1.4,c.23.12.1 71498,71499 2dfdA 342 6.84e-01 1j4aA 333 6.87e-01 c.2.1.4,c.23.12.1 71502,71503 1e7rA 321 7.61e-01 1bsvA c.2.1.2 29808 1e7sA 321 7.71e-01 1bsvA c.2.1.2 29806 1qniA 581 8.06e-01 1qniA b.6.1.4,b.69.3.1 23042,27642 1e7qA 321 8.56e-01 1bsvA c.2.1.2 29807 2gn4A 344 1.02e+00 1drw 273 1.07e+00 1drw c.2.1.3,d.81.1.3 30057,39972 1p77A 272 1.28e+00 c.2.1.7,c.58.1.5 94214,94215 1p9lA 245 1.29e+00 c.2.1.3,d.81.1.3 94393,94394 1yl5A 247 1.32e+00 1mldA 314 1.47e+00 2cmd c.2.1.5,d.162.1.1 30122,42089 1yl7A 245 1.50e+00 2cbiA 594 1.66e+00 1f06A 320 1.76e+00 1dapA c.2.1.3,d.81.1.3 59556,59557 1xq6A 253 4.22e+00 1r0kA 388 4.97e+00 a.69.3.1,c.2.1.3,d.81.1.3 104723,104724,104725 1wzeA 327 5.60e+00 1z7bA 358 6.01e+00 1vp5A 298 6.06e+00 1z74A 358 6.06e+00 1ooeA 236 6.08e+00 c.2.1.2 87196 1u9jA 358 6.14e+00 1z75A 358 6.22e+00 1qycA 308 6.26e+00 c.2.1.2 96581 1z73A 358 6.45e+00 1o6zA 303 6.98e+00 c.2.1.5,d.162.1.1 81107,81108 2dldA 337 7.01e+00 1dxy c.2.1.4,c.23.12.1 30099,31359 1hdr 244 7.44e+00 1dhr c.2.1.2 29837 1d3aA 303 7.46e+00 1ceqA c.2.1.5,d.162.1.1 30143,42110 1z7eA 660 8.09e+00 2hlpA 303 8.11e+00 1ceqA c.2.1.5,d.162.1.1 30141,42108 1vdc 333 8.32e+00 1trb c.3.1.5,c.3.1.5 30545,30546 1smkA 326 9.10e+00 1sevA 362 9.11e+00 2bllA 345 9.40e+00 1vm6A 228 9.56e+00 c.2.1.3,d.81.1.3 108876,108877 1y81A 138 9.69e+00 1dhr 241 9.73e+00 1dhr c.2.1.2 29832 1nytA 271 1.05e+01 c.2.1.7,c.58.1.5 86417,86418 1yaaA 412 1.07e+01 1ajsA c.67.1.1 34280 1cvrA 435 1.10e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 1v77A 212 1.17e+01 c.6.3.2 108402 1w93A 553 1.22e+01 1w96A 554 1.22e+01 1udxA 416 1.24e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1xgkA 352 1.29e+01 1vl0A 292 1.31e+01 c.2.1.2 108704 1ldnA 316 1.39e+01 1hyhA c.2.1.5,d.162.1.1 30166,42133 1ldbA 317 1.39e+01 1aqdA 192 1.44e+01 1iakA b.1.1.2,d.19.1.1 21585,38159 1ymmA 191 1.45e+01 1m4mA 140 1.46e+01 g.52.1.1 78605 1wxxA 382 1.50e+01 1kluA 179 1.52e+01 b.1.1.2,d.19.1.1 72724,72725 1sjhA 180 1.53e+01 b.1.1.2,d.19.1.1 105648,105649 1t5xA 181 1.55e+01 b.1.1.2,d.19.1.1 106489,106490 2pviA 157 1.55e+01 3pviA c.52.1.6 33302 1pywA 182 1.56e+01 b.1.1.2,d.19.1.1 95377,95378 1t5wA 180 1.57e+01 b.1.1.2,d.19.1.1 106481,106482 1a6aA 176 1.57e+01 1iakA b.1.1.2,d.19.1.1 21615,38189 1klgA 177 1.58e+01 b.1.1.2,d.19.1.1 72714,72715 1fv1A 181 1.58e+01 1iakA b.1.1.2,d.19.1.1 21605,38179 1bdmA 327 1.58e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 1bmdA 327 1.58e+01 1bmdA c.2.1.5,d.162.1.1 30139,42106 3pviA 157 1.64e+01 3pviA c.52.1.6 33300 1eq2A 310 1.64e+01 1eq2A c.2.1.2 29814 1xoxA 117 1.71e+01 1k0zA 156 1.84e+01 c.52.1.6 84273 1e31A 142 1.84e+01 1f3hA g.52.1.1 45379 1eyuA 157 1.85e+01 3pviA c.52.1.6 33304 1cfzA 162 1.86e+01 1cfzA c.56.1.1 33754 1op8A 234 1.87e+01 b.47.1.2 87224 1ni0A 159 1.89e+01 c.52.1.6 80522 1qfjA 232 1.93e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 1z6bA 154 1.96e+01 1i36A 264 1.98e+01 a.100.1.8,c.2.1.6 71108,71109 1gcuA 295 1.99e+01 1gcuA c.2.1.3,d.81.1.4 30063,39978 1ib6A 312 2.09e+01 c.2.1.5,d.162.1.1 62146,62147 2kinA 238 2.09e+01 1bg2 c.37.1.9 32190 1y5eA 169 2.11e+01 2fcfA 103 2.12e+01 1ah0 316 2.12e+01 1frb c.1.7.1 28685 1f3hA 142 2.13e+01 1f3hA g.52.1.1 45381 1ah4 315 2.13e+01 1frb c.1.7.1 28684 1dlaA 314 2.14e+01 1frb c.1.7.1 28690 1f3oA 235 2.16e+01 1b0uA c.37.1.12 59631 1lc0A 294 2.19e+01 c.2.1.3,d.81.1.4 73823,73824 1y7tA 327 2.31e+01 2cxxA 190 2.34e+01 2cmd 312 2.40e+01 2cmd c.2.1.5,d.162.1.1 30135,42102 1hdoA 206 2.47e+01 1he2A c.2.1.2 60965 2gqdA 437 2.49e+01 1l2tA 235 2.53e+01 c.37.1.12 73514 1pz1A 333 2.57e+01 c.1.7.1 95390 1ziwA 680 2.65e+01 1z3nA 319 2.68e+01 2agtA 319 2.69e+01 1el3A 316 2.69e+01 1frb c.1.7.1 28672 1us0A 316 2.70e+01 c.1.7.1 99850 1ads 315 2.70e+01 1frb c.1.7.1 28671 1xgdA 315 2.70e+01 2a0zA 705 2.70e+01 1abn 315 2.71e+01 1frb c.1.7.1 28683 1az1 315 2.75e+01 1frb c.1.7.1 28677 1no4A 97 2.91e+01 h.1.24.1 85918 1kvt 338 2.93e+01 1xel c.2.1.2 29798 1e6bA 221 2.98e+01 1e6bA a.45.1.1,c.47.1.5 59294,59295 1kvs 338 2.99e+01 1xel c.2.1.2 29799 1q4rA 112 3.00e+01 d.58.4.4 95823 1fp2A 352 3.00e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1udb 338 3.01e+01 1xel c.2.1.2 29787 1lrkA 338 3.01e+01 c.2.1.2 74225 1wu2A 396 3.02e+01 1kvq 338 3.07e+01 1xel c.2.1.2 29797 1a9z 338 3.10e+01 1xel c.2.1.2 29795 1udc 338 3.11e+01 1xel c.2.1.2 29785 1sc6A 404 3.12e+01 1kvu 338 3.15e+01 1xel c.2.1.2 29794 1kvr 338 3.16e+01 1xel c.2.1.2 29793 1tkbA 678 3.19e+01 1trkA c.36.1.10,c.36.1.6,c.48.1.1 31807,31808,33092 1gpuA 680 3.19e+01 c.36.1.10,c.36.1.6,c.48.1.1 65454,65455,65456 1a9y 338 3.20e+01 1xel c.2.1.2 29789 1ea6A 364 3.30e+01 d.14.1.3,d.122.1.2 64871,64872 1h7sA 365 3.31e+01 d.14.1.3,d.122.1.2 65705,65706 1l3iA 192 3.38e+01 c.66.1.22 77676 2acu 315 3.43e+01 1frb c.1.7.1 28676 1psdA 409 3.52e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1ybaA 410 3.53e+01 1dlgA 419 3.62e+01 1uae d.68.2.2 39580 1vpdA 299 3.63e+01 1e3wA 261 3.67e+01 1e6wA c.2.1.2 59207 1e3sA 261 3.70e+01 1e6wA c.2.1.2 59201 1e6wA 260 3.76e+01 1e6wA c.2.1.2 59326 2a92A 321 3.79e+01 1n2sA 299 3.80e+01 c.2.1.2 79857 1orfA 234 3.82e+01 b.47.1.2 87338 1xknA 355 3.86e+01 1qg4A 216 3.91e+01 1byuA c.37.1.8 32035 1yqcA 170 3.92e+01 2d7vA 162 3.92e+01 1a4iA 301 3.95e+01 1a4iA c.2.1.7,c.58.1.2 30278,33926 1digA 306 3.97e+01 1a4iA c.2.1.7,c.58.1.2 30282,33930 1d6nA 214 3.97e+01 1qk3A c.61.1.1 34077 1xsrA 168 4.01e+01 1z95A 246 4.02e+01 1xowA 249 4.03e+01 1gs4A 248 4.06e+01 a.123.1.1 76328 1t65A 251 4.08e+01 1byuA 216 4.08e+01 1byuA c.37.1.8 32032 1wa3A 205 4.11e+01 1xsqA 168 4.13e+01 1i2mA 216 4.13e+01 1byuA c.37.1.8 61568 2ax9A 256 4.14e+01 1xj7A 257 4.15e+01 2ax8A 256 4.16e+01 1ay0A 680 4.16e+01 1trkA c.36.1.10,c.36.1.6,c.48.1.1 31823,31824,33100 1qg2A 216 4.16e+01 1byuA c.37.1.8 32034 1i37A 260 4.19e+01 1a28A a.123.1.1 61583 1z7gA 217 4.21e+01 1e3gA 263 4.22e+01 1a28A a.123.1.1 59192 2ax6A 256 4.22e+01 1vlwA 217 4.24e+01 c.1.10.1 108868 1bnkA 216 4.25e+01 1bnkA b.46.1.2 25765 1piwA 360 4.27e+01 b.35.1.2,c.2.1.1 104156,104157 1i38A 260 4.27e+01 1a28A a.123.1.1 61584 3ranA 216 4.37e+01 1byuA c.37.1.8 32028 1z82A 335 4.46e+01 1t7rA 269 4.46e+01 a.123.1.1 106635 2gswA 182 4.48e+01 2gl5A 410 4.49e+01 1nni1 174 4.50e+01 1sqeA 109 4.55e+01 d.58.4.5 105908 1xklA 273 4.74e+01 1y7iA 268 4.80e+01 1wxqA 397 4.84e+01 1jeyB 565 4.98e+01 1jeqB b.131.1.2,c.62.1.4 90372,90373 1vizA 240 4.99e+01 c.1.4.1 100784 1t2eA 322 5.09e+01 c.2.1.5,d.162.1.1 99086,99087 1p0kA 349 5.11e+01 c.1.4.1 87648 1z6gA 218 5.12e+01 1t2dA 322 5.20e+01 c.2.1.5,d.162.1.1 99084,99085 1csh 435 5.32e+01 1csh a.103.1.1 18880 1al6 437 5.33e+01 1csh a.103.1.1 18885 1oc4A 322 5.45e+01 c.2.1.5,d.162.1.1 92770,92771 1ydxA 406 5.58e+01 1auvA 311 5.71e+01 1auvA c.30.1.5,d.142.1.3 31723,41558 1xzpA 482 5.81e+01 1bebA 162 5.85e+01 1bebA b.60.1.1 27115 1zvuA 716 5.96e+01 1q20A 299 6.00e+01 c.37.1.5 95616 1ceqA 316 6.07e+01 1ceqA c.2.1.5,d.162.1.1 30163,42130 2fp3A 316 6.13e+01 1qg5A 162 6.18e+01 1bebA b.60.1.1 63323 1cj5A 162 6.18e+01 1bebA b.60.1.1 27124 1ldg 316 6.21e+01 1ceqA c.2.1.5,d.162.1.1 30165,42132 1adn 92 6.21e+01 1adn g.48.1.1 45348 1i7bA 267 6.26e+01 1jenA 1pmd 675 6.28e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37491,37492,42562,42771 1b8eA 162 6.30e+01 1bebA b.60.1.1 59077 1qnxA 209 6.34e+01 1qnxA d.111.1.1 40914 1pyyA 702 6.34e+01 d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 95385,95386,95387,95388 1qmeA 702 6.38e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1bwuA 106 6.44e+01 1b2pA b.78.1.1 27993 1msvA 354 6.45e+01 d.156.1.1 85094 1uz2X 162 6.45e+01 b.60.1.1 108149 1rp5A 702 6.48e+01 d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 97694,97695,97696,97697 1jenA 267 6.50e+01 1jenA 1x9qA 268 6.66e+01 1xtlA 175 6.72e+01 1qvvA 237 6.73e+01 c.23.16.2 96442 1rw7A 243 6.74e+01 c.23.16.2 97963 1yupA 162 6.76e+01 1q1qA 350 6.78e+01 c.37.1.5 95599 1f91A 406 6.78e+01 1dd8A c.95.1.1,c.95.1.1 59713,59714 2gnnA 127 6.82e+01 1xtmA 175 6.90e+01 1s4iA 175 6.97e+01 1ek4A 418 7.00e+01 1dd8A c.95.1.1,c.95.1.1 59436,59437 1kqwA 134 7.02e+01 b.60.1.2 72887 2gasA 307 7.07e+01 1nyaA 176 7.10e+01 a.39.1.5 92335 1es9A 232 7.10e+01 1wab c.23.10.3 31340 1z5zA 271 7.12e+01 2f1kA 279 7.17e+01 1htrB 329 7.26e+01 1smrA 2c5eA 379 7.27e+01 2czgA 433 7.30e+01 1rpnA 335 7.34e+01 c.2.1.2 97708 1pk8A 422 7.40e+01 c.30.1.5,d.142.1.3 94807,94808 2c54A 379 7.42e+01 2c5aA 379 7.43e+01 2c59A 379 7.46e+01 1ispA 181 7.49e+01 c.69.1.18 76778 1tikA 213 7.54e+01 c.23.5.3 107003 1xcbA 211 7.57e+01 a.4.5.38,c.2.1.12 109552,109553 2ahoB 266 7.57e+01 1v4bA 200 7.59e+01 2fcr 173 7.67e+01 1rcf c.23.5.1 31151 1cb0A 283 7.78e+01 1cb0A c.56.2.1 33790 1gtzA 156 7.79e+01 c.23.13.1 70539 1hukA 281 7.83e+01 1wgjA b.40.5.1 25405 1hujA 281 7.85e+01 1wgjA b.40.5.1 25403 1e9gA 286 7.88e+01 1wgjA b.40.5.1 59393 1m38A 287 7.88e+01 b.40.5.1 78531 1sbzA 197 7.89e+01 1em1A 198 7.96e+01 1avmA a.2.11.1,d.44.1.1 15752,38711 2fgcA 193 7.98e+01 1mi3A 322 8.02e+01 c.1.7.1 91274 2bz3A 418 8.06e+01 1jvbA 347 8.10e+01 b.35.1.2,c.2.1.1 77181,77182 1z9aA 321 8.11e+01 2bz4A 418 8.12e+01 1gu1A 156 8.14e+01 c.23.13.1 70563 2bt4A 157 8.18e+01 1tueA 212 8.19e+01 c.37.1.20 107323 1h4fA 406 8.21e+01 c.95.1.1,c.95.1.1 90609,90610 2buhA 406 8.23e+01 1dd8A 406 8.25e+01 1dd8A c.95.1.1,c.95.1.1 35932,35933 1ye6A 322 8.32e+01 1hdmA 201 8.39e+01 1iakA b.1.1.2,d.19.1.1 21583,38157 2bywA 418 8.43e+01 1r85A 379 8.47e+01 c.1.8.3 104839 1e9gB 286 8.49e+01 1wgjA b.40.5.1 59394 1nawA 419 8.55e+01 1uae d.68.2.2 39582 1t4mA 181 8.56e+01 1n32D 208 8.57e+01 d.66.1.2 79872 1sm9A 322 8.57e+01 1xmqD 209 8.58e+01 1i8nA 126 8.60e+01 1i8nA g.10.1.2 61976 1fjgD 209 8.71e+01 1c05A d.66.1.2 39553 1nn4A 162 8.75e+01 c.121.1.1 85888 1t2nA 181 8.77e+01 1rrpA 204 8.82e+01 1byuA c.37.1.8 32042 1wpkA 146 8.91e+01 1zsvA 349 8.92e+01 2d0iA 333 8.98e+01 1vb5A 276 8.98e+01