# List of top-scoring protein chains for t2k-100-30-bys-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 1zkoA 136 5.18e-02 1hpcA 131 6.31e-02 1htp b.84.1.1 28221 1htp 131 7.91e-02 1htp 1y8oB 128 1.60e-01 b.84.1.1 122759 1brwA 433 6.25e-01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1tdtA 259 7.49e-01 3tdt b.81.1.2 28055 2rmpA 361 9.58e-01 2rmpA b.50.1.2 26825 2evbA 74 1.00e+00 3tdt 274 1.33e+00 3tdt 3tdtA 274 1.33e+00 b.81.1.2 28053 2qm1A 326 1.67e+00 2sli 679 1.84e+00 2sli 2sliA 679 1.84e+00 b.29.1.9,b.68.1.1 24274,27611 1v6iA 232 2.20e+00 b.29.1.1 100383 2qnkA 286 2.52e+00 2eenA 183 2.59e+00 3cnwA 148 2.91e+00 1gjxA 81 3.09e+00 b.84.1.1 65222 1vdzA 588 3.35e+00 1hdhA 536 3.59e+00 c.76.1.2 65805 2e4qA 109 3.91e+00 1gycA 499 4.14e+00 b.6.1.3,b.6.1.3,b.6.1.3 70748,70749,70750 1mppA 361 4.25e+00 b.50.1.2 26856 1x1oA 286 4.53e+00 1j99A 293 4.62e+00 c.37.1.5 71618 1p0iA 529 4.83e+00 c.69.1.1 93867 1yu2A 381 4.90e+00 b.163.1.1,d.169.1.8 124029,124030 1aozA 552 5.04e+00 1aozA b.6.1.3,b.6.1.3,b.6.1.3 23124,23125,23126 1qjoA 80 5.06e+00 1iyu b.84.1.1 28229 1ghj 79 5.08e+00 1ghj 1gpr 162 5.09e+00 1gpr 1gprA 162 5.09e+00 b.84.3.1 28267 2vesA 299 5.40e+00 1yu3A 381 5.52e+00 b.163.1.1,d.169.1.8 124031,124032 1rpxA 230 5.69e+00 1rpxA c.1.2.2 28536 2phnA 254 5.71e+00 d.340.1.1 139696 1v25A 541 5.82e+00 e.23.1.1 108275 2bwrA 401 5.86e+00 2eigA 234 6.13e+00 1yu0A 381 6.26e+00 b.163.1.1,d.169.1.8 124025,124026 1pmyA 123 6.28e+00 b.6.1.1 22888 1an7A 136 6.75e+00 1seiA d.140.1.1 41465 2gcuA 245 6.94e+00 1uy4A 145 7.72e+00 b.18.1.10 108131 1y7rA 133 8.18e+00 d.108.1.1 122716 1yu1A 381 8.31e+00 b.163.1.1,d.169.1.8 124027,124028 2g9iA 249 8.87e+00 d.340.1.1 134806 2gaiA 633 8.93e+00 2j97A 109 9.29e+00 2gc1A 188 9.40e+00 b.82.1.7 134928 1seiA 130 9.61e+00 1seiA d.140.1.1 41463 2r77A 205 1.10e+01 2in0A 139 1.12e+01 1k5cA 335 1.13e+01 b.80.1.3 72076 2bh8A 101 1.16e+01 2breA 219 1.16e+01 d.122.1.1 128994 1pg4A 652 1.23e+01 e.23.1.1 88067 2j2zB 173 1.24e+01 2g0qA 173 1.25e+01 1vhmA 195 1.29e+01 d.110.2.1 100691 2ok3A 161 1.32e+01 2vroA 532 1.32e+01 2e3hA 90 1.33e+01 1jyhA 157 1.37e+01 d.60.1.3 71956 1oj4A 283 1.37e+01 d.14.1.5,d.58.26.5 93083,93084 1qxrA 189 1.39e+01 b.82.1.7 96552 2f4wA 187 1.40e+01 d.20.1.1 132958 1yx0A 159 1.46e+01 d.108.1.1 124168 2qedA 258 1.48e+01 1kyhA 276 1.49e+01 c.72.1.4 73222 1xviA 275 1.49e+01 c.108.1.10 116088 1yu4A 381 1.52e+01 b.163.1.1,d.169.1.8 124033,124034 2c0cA 362 1.58e+01 1vqoM 195 1.60e+01 d.12.1.2 120374 2o6pA 161 1.61e+01 1lmeA 176 1.62e+01 d.167.1.1 84629 2ftbA 125 1.72e+01 b.60.1.2 134057 1v10A 521 1.73e+01 b.6.1.3,b.6.1.3,b.6.1.3 108224,108225,108226 2oziA 98 1.74e+01 2iwxA 214 1.86e+01 d.122.1.1 137758 2v2gA 233 1.88e+01 2cobA 70 1.92e+01 a.4.1.15 130673 1hrnA 337 1.93e+01 1smrA b.50.1.2 26869 1qhqA 140 1.94e+01 1qhqA b.6.1.1 63326 1poiA 317 2.01e+01 1poiA c.124.1.2 34153 1x82A 190 2.03e+01 b.82.1.7 114955 1ejxA 100 2.06e+01 d.8.1.1 83182 2arrA 382 2.12e+01 2ijrA 300 2.15e+01 1euvA 221 2.21e+01 1euvA d.3.1.7 37133 1bdo 80 2.26e+01 1bdo 1bdoA 80 2.26e+01 b.84.1.1 28214 1cqqA 180 2.29e+01 1cqqA b.47.1.4 26422 1cauA 181 2.29e+01 1dgwA b.82.1.2 28102 1nr0A 611 2.30e+01 b.69.4.1,b.69.4.1 86078,86079 1mdbA 539 2.32e+01 e.23.1.1 79008 1py0A 125 2.33e+01 b.6.1.1 111645 2cw8A 537 2.36e+01 2cavA 445 2.40e+01 1dgwA b.82.1.2,b.82.1.2 28094,28095 1molA 94 2.41e+01 1molA d.17.1.1 37988 2obwA 258 2.58e+01 1xnkA 196 2.65e+01 b.29.1.11 122195 1u5kA 244 2.67e+01 b.40.4.13,g.45.1.2 113038,113039 1ixlA 131 2.70e+01 d.38.1.5 90717 1h1aA 191 2.70e+01 b.29.1.11 83450 1hleA 345 2.73e+01 1ovaA e.1.1.1 42618 1u0tA 307 2.74e+01 e.52.1.1 107567 1qy5A 269 2.75e+01 d.122.1.1 96573 1u13A 455 2.78e+01 a.104.1.1 107578 1zkcA 197 2.78e+01 b.62.1.1 125182 2gj3A 120 2.84e+01 1x8vA 455 2.93e+01 a.104.1.1 114968 2cibA 455 2.93e+01 1xvwA 160 2.95e+01 c.47.1.10 122387 1ss4A 153 2.99e+01 d.32.1.6 105976 1yizA 429 3.00e+01 c.67.1.1 123375 1yqeA 282 3.01e+01 c.56.7.1 123879 2v24A 208 3.03e+01 1ag7A 34 3.04e+01 g.3.6.1 44086 1a7cA 379 3.05e+01 1sek e.1.1.1 42660 1p4kA 295 3.07e+01 d.153.1.5 87772 1ej6A 1289 3.23e+01 i.7.1.1 45967 1wzcA 249 3.24e+01 c.108.1.10 121491 1rjoA 646 3.25e+01 b.30.2.1,d.17.2.1,d.17.2.1 111832,111833,111834 2dfbA 190 3.30e+01 b.29.1.11 131470 1k8mA 93 3.33e+01 b.84.1.1 68314 1ea1A 455 3.35e+01 1ea1A a.104.1.1 18970 2g8sA 353 3.35e+01 1vf8A 377 3.39e+01 c.1.8.5,d.26.3.1 120029,120030 1kllA 130 3.39e+01 d.32.1.2 72720 1gvmA 136 3.39e+01 b.109.1.1 70612 1h5zA 455 3.41e+01 a.104.1.1 90622 1d0dA 60 3.46e+01 1kigI g.8.1.2 44566 1h70A 255 3.48e+01 1h70A d.126.1.3 60711 2o9uX 97 3.48e+01 d.17.1.1 138960 1i9gA 280 3.58e+01 c.66.1.13 62090 2hqsA 415 3.59e+01 b.68.4.1,c.51.2.1 136662,136663 1pazA 123 3.64e+01 b.6.1.1 22878 1dik 874 3.66e+01 1dik 2qggA 182 3.70e+01 1t3bA 211 3.71e+01 c.47.1.9,d.17.3.1 106341,106342 2durA 253 3.75e+01 2i8dA 123 3.75e+01 2ayvA 166 3.76e+01 d.20.1.1 127572 1yliA 153 3.77e+01 d.38.1.1 123651 1crzA 403 3.80e+01 1crzA b.68.4.1,c.51.2.1 27629,33211 2o3hA 285 3.84e+01 1ub0A 258 3.90e+01 c.72.1.2 88394 1i52A 236 3.91e+01 1i52A c.68.1.13 61767 1kblA 873 3.96e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 2oa2A 148 3.97e+01 1q5hA 147 4.05e+01 b.85.4.1 95893 2d1wA 638 4.13e+01 b.30.2.1,d.17.2.1,d.17.2.1 131145,131146,131147 1bv4A 118 4.18e+01 1rtm1 d.169.1.1 42380 1j8yF 297 4.20e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1us8A 147 4.20e+01 c.37.1.12 99859 1gk7A 39 4.22e+01 h.1.20.1 70212 1wriA 93 4.24e+01 d.15.4.1 114838 1w6gA 646 4.24e+01 b.30.2.1,d.17.2.1,d.17.2.1 120660,120661,120662 1e30A 155 4.26e+01 1rcy b.6.1.1 23016 2cghA 268 4.26e+01 2aanA 139 4.37e+01 1bix 287 4.47e+01 1bix 9gafA 295 4.49e+01 1apyA d.153.1.5 42008 1bteA 97 4.53e+01 1bteA g.7.1.3 44463 1zghA 260 4.57e+01 b.46.1.1,c.65.1.1 125028,125029 1q7fA 286 4.57e+01 b.68.9.1 96036 2ftwA 521 4.61e+01 b.92.1.3,c.1.9.6 134083,134084 1jrrA 382 4.69e+01 e.1.1.1 63256 2p18A 311 4.75e+01 1ylhA 560 4.76e+01 1nb9A 147 4.86e+01 b.43.5.1 85515 1fqtA 112 4.96e+01 1fqtA b.33.1.1 24441 1ui8A 638 4.98e+01 b.30.2.1,d.17.2.1,d.17.2.1 99419,99420,99421 2a4xA 138 5.00e+01 d.32.1.2 126166 1oi0A 124 5.00e+01 c.97.3.1 93045 1dgwA 178 5.02e+01 1dgwA b.82.1.2 28090 2b2nA 344 5.15e+01 c.37.1.19 127710 1ayl 541 5.15e+01 1ayl 2ccmA 191 5.18e+01 2r55A 231 5.24e+01 1euwA 152 5.31e+01 1dupA b.85.4.1 28349 1tw4A 125 5.40e+01 b.60.1.2 112690 1xqaA 113 5.51e+01 d.32.1.2 115837 2qmlA 198 5.52e+01 1l8rA 101 5.52e+01 a.6.1.4 73700 1iqyA 638 5.63e+01 b.30.2.1,d.17.2.1,d.17.2.1 76763,76764,76765 1cs6A 382 5.67e+01 1cs6A b.1.1.4,b.1.1.4,b.1.1.4,b.1.1.4 21760,21761,21762,21763 2o2iA 300 5.71e+01 2gbaA 105 5.72e+01 1eokA 290 5.82e+01 1eokA c.1.8.5 28991 2qvbA 297 5.86e+01 1y0bA 197 5.87e+01 c.61.1.1 122476 2aujD 309 5.88e+01 2b6hA 192 5.88e+01 c.37.1.8 127994 2z14A 133 5.88e+01 2r2cA 183 5.90e+01 1pm4A 119 5.95e+01 b.135.1.1 94891 1bxaA 105 6.00e+01 1aac b.6.1.1 22839 1tovA 98 6.08e+01 b.34.10.1 107179 1k9uA 78 6.10e+01 a.39.1.10 84348 1qi7A 253 6.13e+01 1qi7A d.165.1.1 42210 2calA 154 6.15e+01 2or4A 709 6.15e+01 a.48.2.1,c.8.4.1,c.56.5.5 139258,139259,139260 1lj5A 379 6.31e+01 e.1.1.1 73928 1uyrA 737 6.33e+01 c.14.1.4,c.14.1.4 100188,100189 2a1hA 365 6.34e+01 e.17.1.1 125997 3bh7B 352 6.37e+01 1ciqA 40 6.37e+01 2sniI d.40.1.1 38576 1e9lA 377 6.43e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 1uylA 236 6.44e+01 d.122.1.1 108147 1jr7A 311 6.46e+01 b.82.2.3 63255 1ui7A 638 6.52e+01 b.30.2.1,d.17.2.1,d.17.2.1 99413,99414,99415 2bh9A 489 6.54e+01 3b98A 475 6.56e+01 1mxgA 435 6.60e+01 b.71.1.1,c.1.8.1 85193,85194 1nzjA 298 6.63e+01 c.26.1.1 92377 1qtnA 164 6.65e+01 1pauA c.17.1.1 30999 2iwkA 642 6.69e+01 3c2qA 345 6.71e+01 1yavA 159 6.75e+01 d.37.1.1,d.37.1.1 116595,116596 1ogoX 574 6.78e+01 b.133.1.1,b.80.1.10 92925,92926 1wluA 136 6.83e+01 d.38.1.5 121015 1b33B 161 6.85e+01 1qgwC a.1.1.3 15650 1jboB 172 6.90e+01 a.1.1.3 84151 1yrzA 528 6.96e+01 b.29.1.23,b.67.2.1 123948,123949 1lb6A 160 6.96e+01 b.8.1.1 73798 1wyuA 438 7.11e+01 c.67.1.7 121452 2fyxA 143 7.12e+01 d.58.57.1 134411 1s4iA 175 7.14e+01 1zvfA 176 7.21e+01 3cbtA 237 7.25e+01 1b04A 318 7.33e+01 1b04A d.142.2.2 41579 3bixA 574 7.37e+01 1fd9A 213 7.43e+01 1fd9A d.26.1.1 59771 1aquA 297 7.45e+01 1aquA c.37.1.5 31942 1jlyA 304 7.47e+01 1jlyA b.42.3.1,b.42.3.1 25587,25588 1fwxA 595 7.47e+01 b.6.1.4,b.69.3.1 60069,60070 1t0hA 132 7.58e+01 b.34.2.1 106207 1mfqC 129 7.60e+01 a.36.1.1 79046 1smlA 269 7.61e+01 1smlA d.157.1.1 42053 1vqoA 240 7.62e+01 b.34.5.3,b.40.4.5 120361,120362 2awgA 118 7.63e+01 1fzvA 132 7.65e+01 1vpfA g.17.1.1 60159 1gyhA 318 7.65e+01 b.67.2.1 70757 1jvwA 167 7.66e+01 d.26.1.1 71907 1aac 105 7.73e+01 1aac 1p90A 145 7.74e+01 c.55.5.2 94377 1ds6B 180 7.76e+01 1rhoA b.1.18.8 21898 2dsjA 423 7.79e+01 1rznA 205 7.82e+01 c.52.1.28 111981 1yer 228 7.85e+01 1yer 2qklA 127 7.96e+01