# List of top-scoring protein chains for t2k-100-30-str2 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 1f7sA 139 3.29e-19 1cof d.109.1.2 40857 1v6fA 151 1.99e-18 1cfyA 143 1.08e-17 1cof d.109.1.2 40858 1cof 143 1.77e-17 1cof d.109.1.2 40860 1cnuA 137 4.99e-17 1cof d.109.1.2 40862 1m4jA 142 8.89e-15 d.109.1.2 78602 1ak7 174 1.63e-14 1cof d.109.1.2 40864 1hqz1 141 1.02e-08 1hqz9 141 1.41e-08 1udmA 149 1.65e-06 1svr 114 2.24e-01 1svy d.109.1.1 40833 1svq 114 4.05e-01 1svy d.109.1.1 40832 1svy 114 4.77e-01 1svy d.109.1.1 40831 2vil 126 7.27e-01 2vil d.109.1.1 40830 2vik 126 7.43e-01 2vil d.109.1.1 40829 1mai 131 1.67e+00 1mai b.55.1.1 26951 1o6sB 105 2.73e+00 b.1.6.1 81096 1p1cA 199 2.76e+00 c.66.1.16 87669 1khhA 198 2.94e+00 c.66.1.16 68615 1gtmA 419 3.09e+00 1hwyA c.2.1.7 30223 c.58.1.1 33871 1p8xA 344 3.18e+00 d.109.1.1 -10813 d.109.1.1 -10814 d.109.1.1 -10815 1pvgA 418 3.21e+00 d.14.1.3 -9032 d.122.1.2 -10965 1qk8A 146 3.49e+00 1ewxA c.47.1.10 33061 1ecfA 504 3.61e+00 1ecfB c.61.1.1 34053 d.153.1.1 41820 1ex2A 189 3.82e+00 1ex2A c.51.4.2 33225 1ecfB 504 3.83e+00 1ecfB c.61.1.1 34054 d.153.1.1 41821 1mml 265 3.83e+00 1mml e.8.1.2 43015 1aj6 219 4.19e+00 1aj6 d.122.1.2 41106 1jb0D 138 4.96e+00 1jb0D d.187.1.1 62823 1l0oA 150 5.23e+00 d.122.1.3 73403 1j7iA 264 5.55e+00 1j7iA d.144.1.6 62694 1d4xG 126 5.60e+00 1d0nA d.109.1.1 59109 1o8xA 146 5.68e+00 c.47.1.10 86681 1qy5A 269 5.81e+00 d.122.1.1 -10958 1h2xA 710 5.90e+00 b.69.7.1 76598 c.69.1.4 76599 1poiB 260 6.14e+00 1poiB unknown_sccs 34155 1yagG 125 6.28e+00 1d0nA d.109.1.1 40846 1nm1G 125 6.63e+00 d.109.1.1 80653 1cp3A 277 7.05e+00 1pauA c.17.1.1 30992 1ewxA 146 7.10e+00 1ewxA c.47.1.10 33062 1i4wA 353 7.23e+00 c.66.1.24 66028 1suh 146 7.23e+00 1edhA b.1.6.1 22206 1e8nA 710 7.53e+00 1qfmA b.69.7.1 27675 c.69.1.4 34643 1d0nA 729 7.54e+00 1d0nA d.109.1.1 40834 d.109.1.1 40835 d.109.1.1 40836 d.109.1.1 40837 d.109.1.1 40838 d.109.1.1 40839 1qfmA 710 7.78e+00 1qfmA b.69.7.1 27673 c.69.1.4 34641 1a99A 344 7.90e+00 1pot c.94.1.1 35812 1h2wA 710 7.91e+00 b.69.7.1 76596 c.69.1.4 76597 1dssG 333 8.62e+00 1dssG c.2.1.3 30022 d.81.1.1 39937 1gqyA 475 8.76e+00 c.5.1.1 83305 c.59.1.1 83306 c.72.2.1 83307 1k32A 1045 8.81e+00 b.36.1.3 68068 b.68.7.1 68069 b.69.9.1 68070 c.14.1.2 68071 1pmhX 185 9.37e+00 1mu5A 471 9.52e+00 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1qxhA 167 1.02e+01 c.47.1.10 -7496 1a9xA 1058 1.04e+01 a.92.1.1 18550 c.24.1.1 31479 c.30.1.1 31657 c.30.1.1 31658 d.142.1.2 41502 d.142.1.2 41503 1c3oE 1073 1.04e+01 a.92.1.1 18564 c.24.1.1 31493 c.30.1.1 31685 c.30.1.1 31686 d.142.1.2 41530 d.142.1.2 41531 1bxrA 1073 1.07e+01 a.92.1.1 18570 c.24.1.1 31499 c.30.1.1 31697 c.30.1.1 31698 d.142.1.2 41542 d.142.1.2 41543 1c3oC 1073 1.07e+01 a.92.1.1 18563 c.24.1.1 31492 c.30.1.1 31683 c.30.1.1 31684 d.142.1.2 41528 d.142.1.2 41529 1ei1A 391 1.11e+01 1aj6 d.14.1.3 37570 d.122.1.2 41104 1crwG 333 1.13e+01 1dssG c.2.1.3 30026 d.81.1.1 39941 1cs0C 1073 1.17e+01 a.92.1.1 18559 c.24.1.1 31488 c.30.1.1 31675 c.30.1.1 31676 d.142.1.2 41520 d.142.1.2 41521 1keeC 1073 1.18e+01 a.92.1.1 68500 c.24.1.1 68501 c.30.1.1 68502 c.30.1.1 68503 d.142.1.2 68504 d.142.1.2 68505 2nmbA 160 1.19e+01 2nmbA b.55.1.2 26994 1jn5A 140 1.21e+01 d.17.4.2 66921 1kzhA 555 1.21e+01 c.89.1.1 73361 1keeE 1073 1.22e+01 a.92.1.1 68508 c.24.1.1 68509 c.30.1.1 68510 c.30.1.1 68511 d.142.1.2 68512 d.142.1.2 68513 1jdbB 1073 1.24e+01 a.92.1.1 18574 c.24.1.1 31503 c.30.1.1 31705 c.30.1.1 31706 d.142.1.2 41550 d.142.1.2 41551 1keeA 1073 1.27e+01 a.92.1.1 68492 c.24.1.1 68493 c.30.1.1 68494 c.30.1.1 68495 d.142.1.2 68496 d.142.1.2 68497 1mdbA 539 1.32e+01 e.23.1.1 79008 1q98A 165 1.36e+01 c.47.1.10 -7499 1fwyA 331 1.39e+01 1fwyA b.81.1.4 28064 c.68.1.5 34522 1qo3C 137 1.40e+01 1qo3C d.169.1.1 42350 1hv9A 456 1.41e+01 1fwyA b.81.1.4 28060 c.68.1.5 34518 1n6eA 1071 1.42e+01 b.36.1.3 80149 b.68.7.1 80150 b.69.9.1 80151 c.14.1.2 80152 1keeG 1073 1.43e+01 a.92.1.1 68516 c.24.1.1 68517 c.30.1.1 68518 c.30.1.1 68519 d.142.1.2 68520 d.142.1.2 68521 1nwbA 124 1.43e+01 b.124.1.1 86296 1j7lA 264 1.46e+01 d.144.1.6 62697 1j8bA 112 1.47e+01 d.222.1.1 77101 1jkgA 140 1.52e+01 d.17.4.2 66795 1nb9A 147 1.52e+01 b.43.5.1 85515 1c3oG 1073 1.56e+01 a.92.1.1 18565 c.24.1.1 31494 c.30.1.1 31687 c.30.1.1 31688 d.142.1.2 41532 d.142.1.2 41533 1gv3A 248 1.58e+01 a.2.11.1 70585 d.44.1.1 70586 1vsd 152 1.58e+01 1cxqA c.55.3.2 33625 1edhA 226 1.59e+01 1edhA b.1.6.1 22198 b.1.6.1 22199 1i0hA 205 1.59e+01 1avmA a.2.11.1 15760 d.44.1.1 38685 1g5bA 221 1.60e+01 1g5bA d.159.1.3 60261 1cxqA 162 1.60e+01 1cxqA c.55.3.2 33621 1fxjA 331 1.61e+01 1fwyA b.81.1.4 28062 c.68.1.5 34520 1asu 162 1.67e+01 1cxqA c.55.3.2 33626 1ehiA 377 1.67e+01 1iow c.30.1.2 31716 d.142.1.1 41484 1c3oA 1073 1.68e+01 1c3oA a.92.1.1 18562 c.24.1.1 31491 c.30.1.1 31681 c.30.1.1 31682 d.142.1.2 41526 d.142.1.2 41527 1guaB 81 1.72e+01 1c1yB d.15.1.5 37619 1unnC 115 1.84e+01 unknown_sccs -10216 1f0xA 571 1.90e+01 1f0xA d.58.32.2 39483 d.145.1.1 41746 1elt 236 1.92e+01 5ptp b.47.1.2 26281 1nmeA 146 1.94e+01 c.17.1.1 85874 1ub4C 85 1.95e+01 b.129.1.1 88401 1ix9A 205 1.97e+01 a.2.11.1 76899 d.44.1.1 76900 1d5nA 205 1.97e+01 1avmA a.2.11.1 15762 d.44.1.1 38687 1p3dA 475 2.00e+01 c.5.1.1 87728 c.59.1.1 87729 c.72.2.1 87730 1lw3A 657 2.00e+01 unknown_sccs -4378 unknown_sccs -7358 1n5nA 180 2.02e+01 d.167.1.1 85336 1hnnA 282 2.07e+01 c.66.1.15 65895 3dni 260 2.11e+01 3dni d.151.1.1 41791 1vjrA 271 2.16e+01 unknown_sccs -6853 1o58A 303 2.19e+01 c.79.1.1 -8503 1hw7A 255 2.31e+01 1i7fA d.193.1.1 61297 1rkd 309 2.34e+01 1rkd c.72.1.1 34928 1j6nA 303 2.34e+01 1gw1A 376 2.36e+01 c.1.8.3 76361 1jd0A 263 2.37e+01 2cba b.74.1.1 62888 1fpxA 352 2.43e+01 1fpxA a.4.5.29 59950 c.66.1.12 59951 1n0lA 224 2.55e+01 b.1.11.1 79744 b.7.2.1 79745 1afwA 393 2.59e+01 1afwA c.95.1.1 35900 c.95.1.1 35901 1hwwA 1015 2.64e+01 a.8.3.1 83067 b.30.5.6 83068 c.6.2.1 83069 1qcxA 359 2.65e+01 1qcxA b.80.1.2 28028 1nnmA 652 2.79e+01 1pg4A 652 2.79e+01 e.23.1.1 88067 1pauA 147 2.79e+01 1pauA c.17.1.1 30994 1c1yB 77 2.84e+01 1c1yB d.15.1.5 37618 1iqoA 88 2.85e+01 d.214.1.1 71277 1dik 874 2.87e+01 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 1hxkA 1015 2.88e+01 a.8.3.1 83070 b.30.5.6 83071 c.6.2.1 83072 1htyA 1015 2.89e+01 a.8.3.1 83064 b.30.5.6 83065 c.6.2.1 83066 1lgpA 116 2.94e+01 b.26.1.2 73890 1uch 230 2.94e+01 1uch d.3.1.6 37129 1qwnA 1045 2.94e+01 a.8.3.1 -414 b.30.5.6 -3517 c.6.2.1 -6058 1kblA 873 3.09e+01 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1lnzA 342 3.12e+01 b.117.1.1 78112 c.37.1.8 78113 1i7fA 292 3.15e+01 1i7fA d.193.1.1 61888 1pxtB 390 3.15e+01 1afwA c.95.1.1 35906 c.95.1.1 35907 1h12A 405 3.22e+01 a.102.1.2 83447 1pmt 203 3.27e+01 1a0fA a.45.1.1 17740 c.47.1.5 33034 2hgsA 474 3.29e+01 2hgsA c.30.1.4 31722 d.142.1.6 75997 1fp2A 352 3.36e+01 1fpxA a.4.5.29 59941 c.66.1.12 59942 5croA 66 3.47e+01 1orc a.35.1.2 17044 1mmiA 366 3.47e+01 d.131.1.1 -11093 d.131.1.1 -11094 d.131.1.1 -11095 1fe0A 68 3.50e+01 1cc8A d.58.17.1 39345 1gikA 261 3.54e+01 d.165.1.1 -11545 1nox 205 3.55e+01 1nox d.90.1.1 40242 1h9oA 112 3.57e+01 1qadA d.93.1.1 60837 1e4yA 214 3.64e+01 1zin c.37.1.1 31901 g.41.2.1 45181 1odfA 290 3.65e+01 c.37.1.6 -7045 2dnjA 260 3.73e+01 3dni d.151.1.1 41790 1rypH 205 3.73e+01 d.153.1.4 41876 1kl9A 182 3.78e+01 b.40.4.5 72681 1qqp2 218 3.78e+01 1qqp2 1g5vA 88 3.79e+01 1g5vA b.34.9.1 60292 1j9yA 385 3.79e+01 1j9yA c.1.8.3 62791 1cc8A 73 3.81e+01 1cc8A d.58.17.1 39343 1hjrA 158 3.85e+01 1hjrA c.55.3.6 33727 2polA 366 3.88e+01 2polA d.131.1.1 41356 d.131.1.1 41357 d.131.1.1 41358 1d3hA 367 3.89e+01 1d3gA c.1.4.1 28601 1jbeA 128 3.94e+01 3chy c.23.1.1 62845 1cpn 208 3.94e+01 1axkA b.29.1.2 24175 1bsg 266 3.97e+01 1btl e.3.1.1 42729 1se8A 301 3.98e+01 3pte 349 4.00e+01 3pte e.3.1.1 42687