# List of top-scoring protein chains for t04-80-60-80-str2+near-backbone-11-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 1e54A 332 1.22e-11 1e54A f.4.3.1 59258 2j1nA 346 1.32e-11 2omf 340 1.48e-11 2omf 1hxxA 340 1.65e-11 2omf f.4.3.1 61385 2fgqX 332 3.90e-11 f.4.3.1 133439 2porA 301 1.17e-04 f.4.3.1 43759 2por 301 1.50e-04 2por 3prnA 289 5.22e-03 f.4.3.1 43761 3prn 289 5.48e-03 3prn 1prn 289 9.19e-03 3prn 1wcdJ 441 5.25e-01 b.121.4.9 120887 2bbdA 350 7.88e-01 2df7A 458 1.23e+00 b.121.4.9 131449 1gl4A 285 1.62e+00 d.22.1.2,g.3.11.5 65286,65287 2o4vA 411 1.64e+00 1oe1A 336 2.14e+00 b.6.1.3,b.6.1.3 86891,86892 1kw3B 292 2.32e+00 d.32.1.3,d.32.1.3 77549,77550 1q2lA 939 2.54e+00 d.185.1.1,d.185.1.1,d.185.1.1,d.185.1.1 118731,118732,118733,118734 2fauA 341 2.71e+00 1zlqA 502 2.83e+00 c.94.1.1 125253 2grvA 621 3.27e+00 2i4lA 458 3.68e+00 2cqsA 842 3.82e+00 2axtO 247 3.93e+00 1ju3A 583 4.40e+00 b.18.1.13,c.69.1.21 67300,67301 2hdiA 639 4.42e+00 1ex0A 731 4.47e+00 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1nif 340 4.97e+00 1nif 1xocA 520 5.08e+00 c.94.1.1 122201 2nooA 502 5.23e+00 1kcbA 340 5.55e+00 b.6.1.3,b.6.1.3 90951,90952 1uiuA 502 5.90e+00 c.94.1.1 99434 2bw4A 340 5.98e+00 b.6.1.3,b.6.1.3 129320,129321 1jovA 270 6.29e+00 b.30.5.7 84192 1r17A 343 6.48e+00 b.2.3.4,b.2.3.4 96796,96797 2pgzA 230 6.63e+00 1z02A 446 7.33e+00 1uv6A 210 7.54e+00 b.96.1.1 100030 1hfuA 503 7.87e+00 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 2bj0A 203 8.11e+00 1y55X 126 8.35e+00 2i6qA 517 8.66e+00 1a65A 504 8.74e+00 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 1hleA 345 8.77e+00 1ovaA e.1.1.1 42618 1vjjA 692 8.97e+00 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 1v10A 521 9.03e+00 b.6.1.3,b.6.1.3,b.6.1.3 108224,108225,108226 1uw6A 211 9.04e+00 b.96.1.1 100079 1k1xA 659 9.08e+00 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1ynaA 194 9.51e+00 b.29.1.11 24335 1g8sA 230 9.87e+00 c.66.1.3 90507 1ux2A 212 1.04e+01 b.96.1.1 100132 2q7nA 488 1.06e+01 1vclA 432 1.07e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1hr6B 443 1.10e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 2ehzA 302 1.12e+01 3psgA 370 1.17e+01 b.50.1.2 26841 2e3nA 255 1.19e+01 1evuA 731 1.21e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1h2wA 710 1.29e+01 b.69.7.1,c.69.1.4 76596,76597 1mppA 361 1.29e+01 b.50.1.2 26856 1t3qB 788 1.33e+01 d.41.1.1,d.133.1.1 106369,106370 1xcrA 316 1.41e+01 d.290.1.2 121860 1lurA 339 1.41e+01 b.30.5.4 84717 1lkdA 297 1.45e+01 d.32.1.3,d.32.1.3 78059,78060 2ih8A 559 1.47e+01 b.6.1.3,b.6.1.3,b.6.1.3 137407,137408,137409 1c4kA 730 1.47e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 1t16A 427 1.48e+01 f.4.3.4 106242 1vprA 374 1.48e+01 b.60.1.7 120066 2odpA 509 1.49e+01 1han 297 1.55e+01 1han 1vyoA 128 1.55e+01 2qt6A 498 1.59e+01 2e26A 725 1.60e+01 2in5A 207 1.62e+01 1j5wA 298 1.64e+01 d.104.1.1 71589 1jv2A 957 1.73e+01 b.1.15.1,b.1.15.1,b.1.15.1,b.69.8.1 67334,67335,67336,67337 1a7cA 379 1.74e+01 1sek e.1.1.1 42660 1snrA 341 1.75e+01 b.6.1.3,b.6.1.3 105823,105824 1j83A 180 1.83e+01 b.18.1.12 66430 1i9bA 217 1.83e+01 1i9bA b.96.1.1 62084 2q9oA 559 1.86e+01 2bynA 227 1.92e+01 1ttuA 477 1.92e+01 b.1.18.1,b.2.5.8,b.42.7.1 107305,107306,107307 1yfsA 465 1.93e+01 a.203.1.1,d.104.1.1 123088,123089 2ppeA 343 1.94e+01 1n67A 359 1.94e+01 b.2.3.4,b.2.3.4 85354,85355 1r6lA 239 1.98e+01 d.14.1.4,d.101.1.1 97153,97154 1gadO 330 2.01e+01 1dssG c.2.1.3,d.81.1.1 29950,39865 2r5rA 271 2.04e+01 2oz4A 265 2.12e+01 2de6A 392 2.12e+01 b.33.1.2,d.129.3.3 131415,131416 1qfmA 710 2.15e+01 1qfmA b.69.7.1,c.69.1.4 27673,34641 1j9qA 341 2.15e+01 1nif b.6.1.3,b.6.1.3 62765,62766 1kypA 237 2.17e+01 d.22.1.1 73280 1cb8A 678 2.17e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 2vovA 336 2.20e+01 1fbnA 230 2.26e+01 1fbnA c.66.1.3 34181 2o7iA 592 2.27e+01 1zdsA 336 2.27e+01 b.6.1.3,b.6.1.3 124952,124953 1hx6A 394 2.28e+01 1cjdA b.121.2.1,b.121.2.1 58995,58996 2idbA 505 2.37e+01 b.45.1.3,d.333.1.1 137270,137271 1mkfA 382 2.46e+01 b.116.1.1 79232 1g5hA 454 2.48e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 1qdlA 422 2.51e+01 1qdlA d.161.1.1 42088 3cmsA 323 2.52e+01 b.50.1.2 26865 1xeaA 323 2.57e+01 c.2.1.3,d.81.1.5 109572,109573 2f4lA 297 2.59e+01 b.23.3.1 132927 1mzyA 333 2.60e+01 b.6.1.3,b.6.1.3 103848,103849 1olrA 224 2.62e+01 b.29.1.11 93330 2q86B 254 2.64e+01 2ej9A 237 2.65e+01 1p4tA 155 2.68e+01 f.4.1.1 87779 1h4uA 265 2.68e+01 1h4uA d.22.1.2,g.3.11.5 60622,60623 1dssG 333 2.70e+01 1dssG c.2.1.3,d.81.1.1 30022,39937 1g8aA 227 2.73e+01 c.66.1.3 90506 1ezvB 352 2.76e+01 1ezvB d.185.1.1,d.185.1.1 59543,59544 1ema 236 2.80e+01 1ema 2jisA 515 2.81e+01 1pg4A 652 2.81e+01 e.23.1.1 88067 2psoA 237 2.84e+01 2o62A 270 2.84e+01 1lfwA 470 2.84e+01 c.56.5.4,d.58.19.1 77942,77943 1ravA 127 2.89e+01 1swuA b.61.1.1 27409 2qn6A 414 2.90e+01 2awkA 228 3.01e+01 1lj5A 379 3.06e+01 e.1.1.1 73928 1rm4A 337 3.10e+01 c.2.1.3,d.81.1.1 105000,105001 1dleA 298 3.11e+01 1dleA b.47.1.2 26312 2z79A 185 3.12e+01 1nr0A 611 3.18e+01 b.69.4.1,b.69.4.1 86078,86079 1e3dB 542 3.20e+01 1h2rL e.18.1.1 59189 1vrmA 325 3.24e+01 d.96.2.1 120472 1xdiA 499 3.26e+01 c.3.1.5,d.87.1.1 115160,115161 1zk7A 467 3.29e+01 1fx5A 242 3.36e+01 1led b.29.1.1 24135 1txnA 328 3.36e+01 d.248.1.1 112779 2h5uA 499 3.38e+01 1u8fO 335 3.39e+01 c.2.1.3,d.81.1.1 119626,119627 1wbiA 129 3.40e+01 3b5qA 482 3.44e+01 1h0hA 977 3.48e+01 b.52.2.2,c.81.1.1 76435,76436 1e42A 258 3.55e+01 1e42A b.1.10.1,d.105.1.1 22316,40792 2oitA 434 3.58e+01 1s1dA 331 3.64e+01 b.67.3.1 98344 2hykA 245 3.82e+01 1avgI 142 3.84e+01 1avgI b.60.1.3 27229 2camA 127 3.87e+01 1swuA b.61.1.1 27407 1vgyA 393 3.99e+01 c.56.5.4,d.58.19.1 100620,100621 2p52A 196 4.04e+01 2uuuA 584 4.04e+01 3bi7A 212 4.06e+01 2cduA 452 4.09e+01 2drwA 363 4.17e+01 e.3.1.1 131674 1bd0A 388 4.19e+01 1bd0A b.49.2.2,c.1.6.1 26480,28642 2cirA 297 4.19e+01 1b7yB 785 4.20e+01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,b.153.1.1 16301,16302,25312,39311,40780,41456 2oxaA 600 4.20e+01 2hrgA 496 4.21e+01 1atiA 505 4.22e+01 1atiA c.51.1.1,d.104.1.1 33196,40745 2qsvA 220 4.23e+01 2arrA 382 4.23e+01 1oa2A 218 4.24e+01 b.29.1.11 86721 1h8vA 218 4.26e+01 2nlrA b.29.1.11 60795 2cy9A 140 4.30e+01 d.38.1.5 131019 2madH 373 4.30e+01 2bbkH b.69.2.1 27639 1c30B 382 4.45e+01 c.8.3.1,c.23.16.1 30736,31413 9gafA 295 4.48e+01 1apyA d.153.1.5 42008 2bypA 214 4.59e+01 3bmzA 199 4.86e+01 2aqmA 154 4.88e+01 2q3zA 687 4.93e+01 2vesA 299 5.02e+01 1h6vA 499 5.22e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 60693,60694,60695 2ayh 214 5.25e+01 1axkA 1wuiL 534 5.32e+01 e.18.1.1 121289 1a9xB 379 5.32e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 1ppjA 446 5.35e+01 d.185.1.1,d.185.1.1 104252,104253 1bvoA 175 5.41e+01 1a3qA b.2.5.3 22457 1io1A 398 5.44e+01 1io1A e.32.1.1 62611 1dmuA 299 5.47e+01 1dmuA c.52.1.4 33294 2rb8A 104 5.51e+01 2uwaA 274 5.52e+01 2obeA 932 5.53e+01 2ayhA 214 5.56e+01 b.29.1.2 24172 2rhsB 800 5.56e+01 1v0eA 666 5.57e+01 b.68.1.2,b.108.1.3 113466,113467 1bquA 215 5.59e+01 1bquA b.1.2.1,b.1.2.1 22066,22067 2vfrA 422 5.60e+01 2je6B 250 5.61e+01 2g30A 258 5.65e+01 b.1.10.1,d.105.1.1 134546,134547 2okjA 504 5.72e+01 1uhvA 500 5.72e+01 b.71.1.2,c.1.8.3 99402,99403 2v5mA 388 5.74e+01 2co7B 221 5.74e+01 2j58A 359 5.80e+01 2b79A 144 5.85e+01 1v7wA 807 5.88e+01 a.102.1.4,b.30.5.3 108411,108412 1vq0A 302 5.89e+01 d.193.1.1,g.81.1.1 114000,114001 1p5vA 235 5.92e+01 b.1.11.1,b.7.2.1 87812,87813 1b7gO 340 5.98e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907 2d4gA 171 6.00e+01 2i51A 195 6.11e+01 1omhA 293 6.17e+01 d.89.1.5 93348 1oq1A 223 6.19e+01 b.29.1.17 93408 1xnb 185 6.20e+01 1axkA 2p0wA 324 6.25e+01 1fsoA 139 6.36e+01 1rhoA b.1.18.8 60007 1b5qA 472 6.38e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 1o6gA 710 6.45e+01 b.69.7.1,c.69.1.4 81087,81088 1nqnA 122 6.51e+01 b.61.1.1 86042 2dd7A 216 6.53e+01 1wu7A 434 6.63e+01 c.51.1.1,d.104.1.1 121275,121276 2d1cA 496 6.68e+01 1w50A 411 6.75e+01 b.50.1.2 109173 3b3fA 341 6.77e+01 1ten 90 6.93e+01 1ten 2fctA 313 6.93e+01 b.82.2.9 133282 1mpyA 307 6.95e+01 1mpyA d.32.1.3,d.32.1.3 38508,38509 1c0pA 363 6.96e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 2rghA 571 6.99e+01 1sx5A 244 7.08e+01 c.52.1.2 99023 1tenA 90 7.15e+01 b.1.2.1 21990 1yuwA 554 7.21e+01 b.130.1.1,c.55.1.1,c.55.1.1 124070,124071,124072 2d5wA 603 7.25e+01 1hq0A 295 7.33e+01 1hzgA d.194.1.1 61122 1bkzA 135 7.36e+01 1a3k b.29.1.3 24202 1qexA 288 7.39e+01 1qexA b.32.1.1 24425 1nhpA 447 7.41e+01 c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 2re9A 181 7.43e+01 2tbvA 387 7.45e+01 2tbvA b.121.4.7 23302 1lwjA 441 7.47e+01 b.71.1.1,c.1.8.1 74303,74304 1amy 403 7.48e+01 1jdc 2bqxA 173 7.48e+01 1u2xA 474 7.51e+01 c.72.1.3 107622 1wthD 391 7.55e+01 b.106.1.1,b.106.1.1 121268,121269 1w1oA 534 7.56e+01 d.58.32.4,d.145.1.1 109071,109072 2hyxA 352 7.60e+01 1korA 400 7.63e+01 c.26.2.1,d.210.1.1 72824,72825 1nhsA 447 7.72e+01 c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 1aol 228 7.80e+01 1aol 1aolA 228 7.80e+01 b.20.1.1 23840 1bia 321 7.81e+01 1bia 1biaA 321 7.81e+01 a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 2fgeA 995 7.82e+01 d.185.1.1,d.185.1.1,d.185.1.1,d.185.1.1 133430,133431,133432,133433 2ipiA 521 7.83e+01 1dg6A 191 7.83e+01 1d4vB b.22.1.1 23883 2gjgA 248 7.86e+01 2h4pA 394 7.89e+01 1uy4A 145 7.94e+01 b.18.1.10 108131 2c1sA 126 7.98e+01 1c3mA 147 7.99e+01 1jotA b.77.3.1 27983