# List of top-scoring protein chains for t2k-100-30-alpha 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 1mp1A 111 5.49e-01 a.188.1.1 91382 1m6yA 301 6.29e-01 a.60.13.1 78716 c.66.1.23 78717 1wa5C 960 1.20e+00 1vr3A 191 1.64e+00 1zb1A 392 1.70e+00 1fgs 428 1.79e+00 1fgs c.59.1.2 33959 c.72.2.2 34962 1zkiA 133 1.92e+00 1v6sA 390 1.98e+00 c.86.1.1 100424 1jbwA 428 2.06e+00 c.59.1.2 62860 c.72.2.2 62861 2d7vA 162 2.13e+00 1lzlA 323 2.53e+00 c.69.1.2 78306 1e4mM 501 2.81e+00 1e70M c.1.8.4 59226 1e70M 501 2.83e+00 1e70M c.1.8.4 28926 1uuqA 440 3.12e+00 c.1.8.3 100015 1e5rA 290 3.15e+00 1e5rA b.82.2.4 59276 1e6qM 501 3.28e+00 1e70M c.1.8.4 28920 1evsA 187 3.50e+00 1evsA a.26.1.1 16845 1lkcA 364 3.80e+00 c.67.1.1 73978 2f02A 323 3.82e+00 2az4A 429 3.85e+00 1gmlA 178 4.07e+00 c.8.5.2 70273 2awdA 323 4.10e+00 1w23A 360 4.35e+00 1kutA 230 4.54e+00 d.143.1.1 73017 1u9yA 284 4.80e+00 1keiA 316 5.07e+00 d.92.1.2 77349 1u7iA 136 5.23e+00 d.32.1.7 107724 1bg4 302 5.24e+00 1taxA c.1.8.3 28806 1fqvA 336 5.38e+00 1fqvA a.158.1.1 19254 c.10.1.3 30856 1xyfA 436 5.44e+00 1taxA b.42.2.1 25577 c.1.8.3 28909 1f6dA 376 5.72e+00 1f6dA c.87.1.3 35467 1hyt 316 5.75e+00 1hyt d.92.1.2 59005 1vi0A 206 5.79e+00 a.4.1.9 100720 a.121.1.1 100721 1vgvA 384 5.83e+00 c.87.1.3 100608 6tmnE 316 5.87e+00 1hyt d.92.1.2 59071 1tmxA 293 5.91e+00 8tlnE 316 5.98e+00 1hyt d.92.1.2 59075 1b31A 302 6.14e+00 1taxA c.1.8.3 28892 1ntyA 311 6.33e+00 a.87.1.1 103873 b.55.1.1 103874 2tmnE 316 6.39e+00 1hyt d.92.1.2 59055 2ts1 419 6.49e+00 2ts1 c.26.1.1 31564 1lc5A 364 6.75e+00 c.67.1.1 73827 1vlmA 219 6.78e+00 c.66.1.41 108836 1w32A 348 6.87e+00 2myr 501 7.41e+00 1clxA 347 7.86e+00 1taxA c.1.8.3 28899 1uruA 244 7.95e+00 h.4.14.1 99835 2bneA 241 7.98e+00 2bkaA 242 8.78e+00 2b8tA 223 8.89e+00 1ynmA 247 8.95e+00 2bvwA 362 9.37e+00 1bvwA c.6.1.1 30666 1drw 273 9.52e+00 1drw c.2.1.3 30057 d.81.1.3 39972 2bexA 460 9.53e+00 1gvfA 286 9.67e+00 c.1.10.2 70599 1dih 273 9.68e+00 1drw c.2.1.3 30056 d.81.1.3 39971 1a4yA 460 9.75e+00 1a4yA c.10.1.1 30852 1ev0A 58 1.01e+01 1ev0A d.71.1.1 39594 1kfwA 435 1.02e+01 c.1.8.5 77376 d.26.3.1 77377 1hl8A 449 1.02e+01 b.71.1.3 90646 c.1.8.11 90647 1b9hA 388 1.03e+01 1b9hA c.67.1.4 34488 1ydiA 263 1.04e+01 1y07A 128 1.04e+01 2d1eA 248 1.08e+01 1fy2A 229 1.12e+01 1fyeA c.23.16.4 31478 1bvwA 360 1.12e+01 1bvwA c.6.1.1 30668 1qgrA 876 1.14e+01 1qgrA a.118.1.1 19119 1rkeA 262 1.14e+01 a.24.9.1 97608 a.24.9.1 97609 1fyeA 229 1.15e+01 1fyeA c.23.16.4 31477 2ao9A 155 1.18e+01 1ocnA 362 1.19e+01 c.6.1.1 86808 1evlA 401 1.19e+01 1qf6A c.51.1.1 33202 d.104.1.1 40751 1cb8A 678 1.23e+01 1cb8A a.102.3.2 18849 b.24.1.1 23898 b.30.5.2 24422 1lqvA 193 1.23e+01 d.19.1.1 74206 1gm5A 780 1.24e+01 a.24.21.1 65298 b.40.4.9 65299 c.37.1.19 65300 c.37.1.19 65301 1arzC 273 1.26e+01 1drw c.2.1.3 30061 d.81.1.3 39976 1z7xW 461 1.33e+01 1t01A 255 1.37e+01 a.24.9.1 106188 a.24.9.1 106189 2bidA 197 1.38e+01 2bidA f.1.4.1 43398 1zvzA 279 1.39e+01 1rcuA 195 1.40e+01 c.129.1.1 97295 1vkfA 188 1.41e+01 c.1.29.1 108656 1oc7A 364 1.42e+01 c.6.1.1 86794 1l8qA 324 1.43e+01 a.4.12.2 77809 c.37.1.20 77810 1lmzA 187 1.43e+01 a.96.1.4 74037 2fkcA 247 1.47e+01 1xhkA 187 1.49e+01 1ebdA 455 1.50e+01 1lvl c.3.1.5 30577 c.3.1.5 30578 d.87.1.1 40210 1x8yA 86 1.52e+01 1jeoA 180 1.55e+01 c.80.1.3 66611 2eiaB 206 1.57e+01 1eia a.28.3.1 16950 a.73.1.1 18330 1lwjA 441 1.58e+01 b.71.1.1 74303 c.1.8.1 74304 1vz6A 393 1.58e+01 d.154.1.2 108949 2dorA 311 1.61e+01 2dorA c.1.4.1 28593 1xxqA 161 1.68e+01 1pbwA 216 1.69e+01 1pbwA a.116.1.1 19103 1nq6A 302 1.70e+01 c.1.8.3 92046 1ofcX 304 1.82e+01 a.4.1.3 92826 a.4.1.13 92827 a.187.1.1 92828 1nscA 390 1.83e+01 2qwc b.68.1.1 27591 2b34A 199 1.84e+01 1pjhA 280 1.84e+01 c.14.1.3 94761 2arcA 164 1.85e+01 2arcA b.82.4.1 28148 1sfkA 76 1.92e+01 a.190.1.1 105488 1hnnA 282 1.99e+01 c.66.1.15 65895 2arcB 164 2.00e+01 2arcA b.82.4.1 28149 2cq2A 114 2.01e+01 1ywfA 296 2.01e+01 1eia 207 2.02e+01 1eia a.28.3.1 16951 a.73.1.1 18331 1h1oA 183 2.02e+01 a.3.1.4 83454 a.3.1.4 83455 1vloA 381 2.02e+01 b.44.2.1 108838 d.250.1.1 108839 1h3gA 601 2.03e+01 b.1.18.2 90594 b.71.1.1 90595 c.1.8.1 90596 1dorA 311 2.04e+01 2dorA c.1.4.1 28595 1to2I 64 2.04e+01 1sjyA 159 2.07e+01 d.113.1.1 98900 1dqaC 467 2.08e+01 1dqaA d.58.20.1 39366 d.179.1.1 42587 1o9rA 162 2.10e+01 a.25.1.1 86706 1u6rA 380 2.10e+01 1qvzA 237 2.12e+01 c.23.16.2 96453 1in0A 163 2.15e+01 d.58.49.1 83694 d.58.49.1 83695 1htyA 1015 2.17e+01 a.8.3.1 83064 b.30.5.6 83065 c.6.2.1 83066 1v9dA 340 2.17e+01 a.207.1.1 100535 1qf6A 642 2.20e+01 1qf6A c.51.1.1 33210 d.15.10.1 39551 d.67.1.1 39562 d.104.1.1 40759 1hxkA 1015 2.22e+01 a.8.3.1 83070 b.30.5.6 83071 c.6.2.1 83072 1qhbA 596 2.27e+01 1qhbA a.111.1.2 19055 1cd9B 215 2.27e+01 1cto b.1.2.1 22041 b.1.2.1 22042 2cvxA 888 2.27e+01 1g8mA 593 2.28e+01 1g8mA c.24.1.3 60371 c.97.2.1 60372 1neu 124 2.31e+01 1neu b.1.1.1 19704 1m7sA 484 2.34e+01 e.5.1.1 74574 1ekeA 230 2.35e+01 1ekeA c.55.3.1 33572 1hm2A 700 2.36e+01 1cb8A a.102.3.2 61083 b.24.1.1 61084 b.30.5.2 61085 1hw8A 467 2.42e+01 1dqaA d.58.20.1 61298 d.179.1.1 61299 1kiuB 279 2.45e+01 b.2.3.2 72525 b.2.3.2 72526 1qwnA 1045 2.46e+01 a.8.3.1 96487 b.30.5.6 96488 c.6.2.1 96489 1bmlC 362 2.46e+01 1bmlC d.15.5.1 37729 d.15.5.1 37730 d.15.5.1 37731 1pxtB 390 2.55e+01 1afwA c.95.1.1 35906 c.95.1.1 35907 1pcxA 810 2.59e+01 a.71.2.1 94497 b.2.8.1 94498 c.62.1.2 94499 d.109.2.1 94500 g.41.10.1 94501 1faeA 629 2.65e+01 1fce a.102.1.2 18837 1isaA 192 2.66e+01 1avmA a.2.11.1 15731 d.44.1.1 38724 1jt7A 146 2.68e+01 b.42.1.1 67255 2bb3A 221 2.68e+01 1coaI 64 2.68e+01 2sniI d.40.1.1 38574 1ypcI 64 2.74e+01 2sniI d.40.1.1 38570 1zotA 358 2.75e+01 1pgjA 478 2.77e+01 2pgd a.100.1.1 18783 c.2.1.6 30195 1fce 629 2.78e+01 1fce a.102.1.2 18836 3ldh 330 2.79e+01 3ldh i.12.1.1 46015 2basA 431 2.79e+01 1m9nA 613 2.81e+01 c.24.1.3 78870 c.97.2.1 78871 1ku1A 230 2.82e+01 a.118.3.1 72996 1g9gA 629 2.84e+01 a.102.1.2 83279 2aq5A 402 2.86e+01 1hwwA 1015 2.87e+01 a.8.3.1 83067 b.30.5.6 83068 c.6.2.1 83069 1ucpA 91 2.90e+01 a.77.1.5 99186 1dqaA 467 2.92e+01 1dqaA d.58.20.1 39364 d.179.1.1 42585 1eq2A 310 2.94e+01 1eq2A c.2.1.2 29814 1zd0A 150 2.96e+01 2aynA 404 2.96e+01 1rw7A 243 3.04e+01 c.23.16.2 97963 1u8xX 472 3.06e+01 c.2.1.5 107741 d.162.1.2 107742 1jubA 311 3.07e+01 c.1.4.1 90908 1jqzA 146 3.14e+01 b.42.1.1 67109 2apjA 260 3.14e+01 1pa7A 130 3.14e+01 a.40.1.1 94410 1b1yA 500 3.15e+01 1byb c.1.8.1 28796 1axj 122 3.15e+01 1axj b.45.1.1 25749 1m2vB 926 3.16e+01 a.71.2.1 78497 b.2.8.1 78498 c.62.1.2 78499 d.109.2.1 78500 g.41.10.1 78501 2fflA 756 3.17e+01 1od8A 313 3.17e+01 c.1.8.3 86838 2c1iA 431 3.18e+01 1u9iA 519 3.19e+01 1b9vA 390 3.19e+01 2qwc b.68.1.1 27603 1z23A 163 3.27e+01 1smd 496 3.30e+01 1smd b.71.1.1 27768 c.1.8.1 28755 1j0hA 588 3.34e+01 b.1.18.2 77027 b.71.1.1 77028 c.1.8.1 77029 1iscA 192 3.34e+01 1avmA a.2.11.1 15733 d.44.1.1 38726 1nxhA 126 3.35e+01 a.200.1.1 92300 1dbxA 158 3.36e+01 1dbuA d.116.1.1 40928 1yruA 364 3.37e+01 1qhoA 686 3.38e+01 1cxlA b.1.18.2 21844 b.3.1.1 22513 b.71.1.1 27751 c.1.8.1 28738 1jgcA 161 3.40e+01 a.25.1.1 66673 1lw6I 64 3.41e+01 d.40.1.1 74294 1wrvA 308 3.42e+01 1gw5S 142 3.43e+01 d.110.4.2 70633 2czcA 334 3.43e+01 1dmtA 696 3.47e+01 1dmtA d.92.1.4 40296 1yrtA 364 3.54e+01 1zh5A 195 3.57e+01 1bob 320 3.63e+01 1bob d.108.1.1 40816 2aacA 177 3.64e+01 2arcA b.82.4.1 28150 1ik9A 213 3.70e+01 b.59.1.1 66176 h.1.11.1 66177 1s7bA 110 3.73e+01 f.39.1.1 98634 1j6uA 469 3.73e+01 c.5.1.1 77094 c.59.1.1 77095 c.72.2.1 77096 1gl2B 65 3.75e+01 h.1.15.1 65279 1d8cA 723 3.76e+01 1d8cA c.1.13.1 29325 1r1hA 696 3.76e+01 d.92.1.4 104756 1rlaA 323 3.83e+01 1d3vA c.42.1.1 32561 1v0lA 313 3.85e+01 c.1.8.3 108207 1hpcA 131 3.88e+01 1htp b.84.1.1 28221 1at1A 310 3.88e+01 3csuA c.78.1.1 35168 c.78.1.1 35169 1gqyA 475 3.92e+01 c.5.1.1 83305 c.59.1.1 83306 c.72.2.1 83307