# List of top-scoring protein chains for t2k-100-30-n_notor2-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.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 2fs2A 151 3.60e-11 1psuA 140 3.80e-11 d.38.1.5 88285 1wluA 136 9.25e-11 1j1yA 136 9.74e-11 d.38.1.5 90776 1zkiA 133 1.56e-10 1vh5A 148 1.89e-08 d.38.1.5 100642 1yliA 153 2.91e-08 1vpmA 169 3.77e-08 1o0iA 138 9.09e-08 d.38.1.5 86532 2b6eA 146 9.62e-08 1q4uA 151 2.12e-07 d.38.1.5 95828 1ixlA 131 3.15e-07 d.38.1.5 90717 2gvhA 288 2.27e-05 2cwzA 141 5.70e-04 1yocA 147 2.19e-03 1z54A 132 1.54e-02 2cyeA 133 1.98e-02 1s5uA 138 2.18e-02 d.38.1.1 98573 1iq6A 134 2.28e-02 d.38.1.4 76755 1sh8A 154 3.27e-02 d.38.1.5 105549 1njkA 156 4.81e-02 d.38.1.1 85818 2b3nA 159 5.35e-02 1mkaA 171 8.70e-02 1mkaA d.38.1.2 38543 2av9A 147 1.08e-01 1c8uA 285 1.15e-01 1c8uA d.38.1.3,d.38.1.3 38547,38548 1t82A 155 1.38e-01 d.38.1.5 106639 1tltA 319 4.78e-01 c.2.1.3,d.81.1.5 107135,107136 1u1zA 168 5.29e-01 d.38.1.6 107602 2gf6A 135 6.99e-01 1z6bA 154 7.89e-01 1tbuA 118 1.04e+00 2fflA 756 1.09e+00 1fxlA 167 1.44e+00 1b7fA d.58.7.1,d.58.7.1 39183,39184 1drtA 324 1.55e+00 1drtA b.82.2.2 28130 1su8A 636 2.11e+00 e.26.1.2 98999 1lo7A 141 2.15e+00 d.38.1.1 74144 2ch4A 320 2.30e+00 2blnA 305 2.58e+00 1n4oA 276 3.70e+00 e.3.1.1 91621 1g8kA 825 4.04e+00 1g8jA b.52.2.2,c.81.1.1 26920,35328 1qwgA 251 4.16e+00 c.1.27.1 96473 1ve3A 227 4.71e+00 7acn 754 5.01e+00 1amj c.8.2.1,c.83.1.1 30717,35393 2azqA 311 5.21e+00 1heiA 451 5.49e+00 1heiA c.37.1.14,c.37.1.14 32463,32464 2cfeA 162 5.52e+00 1a54A 321 5.69e+00 1ixh c.94.1.1 35763 1h8lA 380 5.82e+00 b.3.2.1,c.56.5.1 65737,65738 2bi0A 337 6.02e+00 1ixh 321 6.06e+00 1ixh c.94.1.1 35761 2aliA 158 6.18e+00 1ecfA 504 6.21e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 1d8dB 437 6.49e+00 1ft1B a.102.4.3 18866 1zy9A 564 6.56e+00 1gxjA 186 7.23e+00 d.215.1.1 70707 1bsjA 168 7.37e+00 1bs4A d.167.1.1 42302 1pamA 686 7.47e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21846,22515,27753,28740 2ghpA 292 7.51e+00 2biwA 490 7.98e+00 2gdnA 267 8.03e+00 1amj 754 8.10e+00 1amj c.8.2.1,c.83.1.1 30725,35401 1jihA 531 8.13e+00 d.240.1.1,e.8.1.7 90374,90375 8acn 754 8.70e+00 1amj c.8.2.1,c.83.1.1 30724,35400 6acn 754 8.88e+00 1amj c.8.2.1,c.83.1.1 30721,35397 1cwoA 165 9.31e+00 2cpl b.62.1.1 27445 1se8A 301 9.49e+00 b.40.4.3 105448 1ebuA 358 9.50e+00 1ebuA c.2.1.3,d.81.1.2 30035,39950 1qhdA 398 9.57e+00 1qhdA a.115.1.2,b.19.1.1 63324,63325 1bvqA 141 9.76e+00 1bvqA d.38.1.1 38542 1qhoA 686 9.85e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1a3qA 285 9.89e+00 1a3qA b.1.18.1,b.2.5.3 21932,22447 1gthD 1025 9.92e+00 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70498,70499,70500,70501,70502 1b63A 333 9.98e+00 1b63A d.14.1.3,d.122.1.2 37566,41107 2essA 248 1.02e+01 1xeoA 168 1.05e+01 1b5qA 472 1.12e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 2d0oA 610 1.13e+01 1g8jA 825 1.14e+01 1g8jA b.52.2.2,c.81.1.1 26924,35332 1xf1A 926 1.15e+01 1gthB 1025 1.17e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70488,70489,70490,70491,70492 2ffcA 353 1.17e+01 1k7gA 479 1.21e+01 b.80.7.1,d.92.1.6 77279,77280 1px5A 349 1.22e+01 a.160.1.2,d.218.1.6 95277,95278 1yndA 165 1.24e+01 1xovA 326 1.25e+01 1rerA 391 1.30e+01 b.1.18.4,f.10.1.1 97327,97328 1ux6A 350 1.31e+01 b.29.1.16,g.75.1.1 100145,100146 1pg4A 652 1.33e+01 e.23.1.1 88067 1qhfA 240 1.33e+01 1qhfA c.60.1.1 33960 2bdvA 231 1.37e+01 1bpe 335 1.42e+01 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 18076,75815,75816 1ojjA 402 1.47e+01 b.29.1.10 93130 1ogsA 497 1.50e+01 b.71.1.2,c.1.8.3 86997,86998 2cvhA 220 1.57e+01 1te5A 257 1.57e+01 d.153.1.1 106795 1sotA 320 1.60e+01 b.36.1.4,b.47.1.1 105852,105853 1c96A 753 1.62e+01 1amj c.8.2.1,c.83.1.1 30727,35403 1hlrA 907 1.62e+01 1vlbA 907 1.63e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 1poiA 317 1.69e+01 1poiA c.124.1.2 34153 1p35A 299 1.70e+01 1p35A b.28.1.1 23925 1uylA 236 1.76e+01 d.122.1.1 108147 1p3dA 475 1.76e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1hm9A 468 1.76e+01 b.81.1.4,c.68.1.5 65866,65867 1jpzA 473 1.79e+01 a.104.1.1 67069 2ahxA 617 1.81e+01 2bmhA 455 1.83e+01 1bu7A a.104.1.1 18941 1yymG 313 1.83e+01 1w61A 414 1.84e+01 1g2aA 168 1.87e+01 d.167.1.1 65109 1e6qM 501 1.91e+01 1e70M c.1.8.4 28920 1cb0A 283 1.92e+01 1cb0A c.56.2.1 33790 1e4mM 501 1.93e+01 1e70M c.1.8.4 59226 1w9hA 427 1.94e+01 1qksA 567 1.95e+01 1qksA a.3.1.2,b.70.2.1 15951,27710 1svcP 365 1.98e+01 1a3qA b.1.18.1,b.2.5.3 21924,22443 1qwzA 235 1.98e+01 b.100.1.1 96510 1ga6A 372 2.00e+01 1ga1A c.41.1.2 32556 1crkA 380 2.01e+01 1qh4A a.83.1.1,d.128.1.2 18458,41193 1aoqA 567 2.02e+01 1qksA a.3.1.2,b.70.2.1 15934,27692 1hzoA 271 2.07e+01 e.3.1.1 71092 1qwnA 1045 2.10e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 2fp4B 395 2.10e+01 1k77A 260 2.11e+01 c.1.15.5 72096 1nnjA 271 2.13e+01 a.156.1.2,b.113.1.1,g.39.1.8 80669,80670,80671 1su4A 994 2.14e+01 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 98993,98994,98995,98996 1ooyA 481 2.16e+01 c.124.1.3,c.124.1.2 93388,93389 2bitX 165 2.21e+01 2aaa 484 2.22e+01 7taa b.71.1.1,c.1.8.1 27777,28764 2bx6A 350 2.24e+01 1jmeA 455 2.29e+01 a.104.1.1 66885 1ve4A 206 2.31e+01 1gguA 731 2.33e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21885,22179,22180,37115 1zxiC 288 2.39e+01 1vzyA 291 2.43e+01 3cox 507 2.45e+01 1b8sA c.3.1.2,d.16.1.1 30332,37863 1askA 127 2.45e+01 1ounA d.17.4.2 38094 1mxgA 435 2.49e+01 b.71.1.1,c.1.8.1 85193,85194 1rwhA 757 2.55e+01 a.102.3.2,b.24.1.1,b.30.5.2 97984,97985,97986 1xd3A 230 2.57e+01 1icjA 168 2.62e+01 1bs4A d.167.1.1 42284 1hxkA 1015 2.66e+01 a.8.3.1,b.30.5.6,c.6.2.1 83070,83071,83072 1by5A 714 2.69e+01 1by5A f.4.3.3 43800 1rlmB 271 2.72e+01 1jr7A 311 2.78e+01 b.82.2.3 63255 2ew0A 192 2.78e+01 1ikpA 613 2.79e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1te0A 318 2.79e+01 1pioA 257 2.87e+01 1btl e.3.1.1 42719 1ga1A 372 2.89e+01 1ga1A c.41.1.2 32557 2bvfA 459 2.90e+01 1u94A 356 2.91e+01 c.37.1.11,d.48.1.1 107743,107744 2auaA 224 2.95e+01 1jroB 777 2.96e+01 d.41.1.1,d.133.1.1 67141,67142 1llp 343 2.97e+01 1arv a.93.1.1 18578 1jtaA 361 3.03e+01 b.80.1.1 71859 2biqA 219 3.06e+01 1bs4A 168 3.07e+01 1bs4A d.167.1.1 42287 1l1lA 739 3.08e+01 c.7.1.4 73470 2avnA 260 3.15e+01 1coy 507 3.16e+01 1b8sA c.3.1.2,d.16.1.1 30333,37864 2cqsA 842 3.26e+01 1wbiA 129 3.29e+01 1jndA 420 3.29e+01 c.1.8.5,d.26.3.1 71757,71758 1at0 145 3.34e+01 1at0 b.86.1.1 28374 1qxoA 388 3.37e+01 d.258.1.1 96539 2cpl 165 3.38e+01 2cpl b.62.1.1 27420 1hwxA 501 3.38e+01 1hwyA c.2.1.7,c.58.1.1 30250,33898 1gqyA 475 3.42e+01 c.5.1.1,c.59.1.1,c.72.2.1 83305,83306,83307 1e70M 501 3.46e+01 1e70M c.1.8.4 28926 1suuA 312 3.54e+01 b.68.10.1 99006 3minC 491 3.64e+01 1qguA c.92.2.3 35607 1t3tA 1303 3.68e+01 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 1hl9A 449 3.69e+01 b.71.1.3,c.1.8.11 90650,90651 1ct9A 553 3.70e+01 1ct9A c.26.2.1,d.153.1.1 31616,41834 1ax0 239 3.70e+01 1led b.29.1.1 24042 1nnxA 109 3.75e+01 b.40.10.1 92013 1xkpC 143 3.79e+01 1gc0A 398 3.80e+01 c.67.1.3 70168 1h7xB 1025 3.85e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15688,28633,30329,30614,39012 1bsg 266 3.86e+01 1btl e.3.1.1 42729 1w99A 558 3.88e+01 1cpn 208 3.89e+01 1axkA b.29.1.2 24175 1r2jA 366 3.94e+01 a.29.3.1,e.6.1.1 96869,96870 2a6hA 315 3.99e+01 1lucB 324 4.01e+01 1lucA c.1.16.1 29548 1ynmA 247 4.02e+01 2gn4A 344 4.03e+01 1b54 257 4.09e+01 1ct5A c.1.6.2 28664 2bllA 345 4.09e+01 1sr8A 298 4.09e+01 e.54.1.1 105959 1sxgA 280 4.10e+01 1yq2A 1024 4.12e+01 1ji0A 240 4.14e+01 c.37.1.12 71665 1zxiF 288 4.16e+01 1qh4A 380 4.19e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 1sz6A 249 4.23e+01 1m98A 317 4.30e+01 a.175.1.1,d.17.4.6 78866,78867 1mj5A 302 4.35e+01 c.69.1.8 91285 1ti6A 875 4.36e+01 b.52.2.2,c.81.1.1 106974,106975 1otcA 495 4.36e+01 1otcA b.40.4.3,b.40.4.3,b.40.4.3 25307,25308,25309 2bklA 695 4.36e+01 1bf6A 291 4.39e+01 1pscA c.1.9.3 29065 1ef1A 294 4.39e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 1edzA 320 4.40e+01 1ee9A c.2.1.7,c.58.1.2 30287,33935 7ceiB 206 4.45e+01 1bxiB d.4.1.1 37134 1d0cA 444 4.45e+01 d.174.1.1 64769 1mhyD 521 4.46e+01 1mhyD a.25.1.2 16780 2aamA 309 4.47e+01 1c7sA 858 4.55e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21812,22408,29011,40410 1s0aA 429 4.56e+01 c.67.1.4 98263 1h7xA 1025 4.56e+01 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15687,28632,30328,30613,39011 1sc3A 178 4.59e+01 c.17.1.1 105416 1y21A 282 4.60e+01 1bh3 289 4.62e+01 3prn f.4.3.1 43766 1dgsA 667 4.62e+01 1dgsA a.60.2.2,b.40.4.6,d.142.2.2 17963,25365,41581 7reqB 637 4.64e+01 1reqB c.1.19.1,c.23.6.1 29617,31244 1y9qA 192 4.65e+01 2fauA 341 4.67e+01 2be1A 339 4.68e+01 1itwA 741 4.69e+01 c.77.1.2 76793 1sh7A 284 4.78e+01 1g94A 448 4.86e+01 b.71.1.1,c.1.8.1 65169,65170 1gthC 1025 4.91e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70493,70494,70495,70496,70497 1eft 405 4.92e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1ao0A 459 4.95e+01 1ecfB c.61.1.1,d.153.1.1 34049,41816 1p0zA 131 4.96e+01 d.110.6.1 93882 2fdsA 352 5.02e+01 1h09A 338 5.02e+01 b.109.1.1,c.1.8.8 83420,83421 1cv2A 296 5.05e+01 1bn6A c.69.1.8 34680 1ubeA 349 5.09e+01 c.37.1.11,d.48.1.1 88412,88413 1a8rA 221 5.10e+01 1a8rA d.96.1.1 40587 1l2qA 458 5.14e+01 c.1.25.1 73510 1ayrB 363 5.20e+01 1cf1A b.1.18.11,b.1.18.11 21917,21918 1vnc 609 5.21e+01 1vns a.111.1.3 19065 1go8P 462 5.25e+01 b.80.7.1,d.92.1.6 76247,76248 1cfb 205 5.31e+01 1cfb b.1.2.1,b.1.2.1 21991,21992 1ng5A 215 5.31e+01 b.100.1.1 91867 1ve5A 311 5.33e+01 2ez3A 302 5.37e+01 1wgzA 510 5.39e+01 1bn8A 420 5.41e+01 1pcl b.80.1.1 28022 1g7tA 594 5.42e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25714,25715,31033,32148 1cs6A 382 5.44e+01 1cs6A b.1.1.4,b.1.1.4,b.1.1.4,b.1.1.4 21760,21761,21762,21763 1nthA 458 5.47e+01 c.1.25.1 80730 1eagA 342 5.51e+01 1eagA b.50.1.2 26826 1yf3A 259 5.60e+01 1b02A 279 5.60e+01 1bkpA d.117.1.1 41035 2b6nA 278 5.64e+01 1jcrB 437 5.67e+01 a.102.4.3 66507 2avyC 232 5.67e+01 1bn6A 294 5.76e+01 1bn6A c.69.1.8 34678 3pvaA 335 5.77e+01 3pvaA d.153.1.3 41854 1si6X 282 5.90e+01 1bykA 255 5.95e+01 1bykA c.93.1.1 35706 1fwxA 595 6.03e+01 b.6.1.4,b.69.3.1 60069,60070 2ddfA 257 6.04e+01 1i1b 153 6.18e+01 2i1b b.42.1.2 25537 1bu7A 455 6.19e+01 1bu7A a.104.1.1 18937 1a5mC 566 6.20e+01 1ubpC b.92.1.1,c.1.9.2 28423,29045 1j1nA 492 6.22e+01 c.94.1.1 83978 1amy 403 6.24e+01 1jdc b.71.1.1,c.1.8.1 27799,28786 1k7qA 479 6.34e+01 b.80.7.1,d.92.1.6 77283,77284 1t1uA 639 6.36e+01 2d1eA 248 6.37e+01 1b2wH 220 6.38e+01 1igtB b.1.1.1,b.1.1.2 20307,21299 2c30A 321 6.42e+01 1l8aA 886 6.49e+01 c.36.1.10,c.36.1.6,c.48.1.1 73677,73678,73679 1ymtA 246 6.53e+01 1qpaA 345 6.66e+01 1arv a.93.1.1 18585 2giyA 191 6.69e+01 1upaA 573 6.69e+01 c.31.1.3,c.36.1.5,c.36.1.9 99714,99715,99716 1cgt 684 6.75e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21815,22484,27722,28709 1qydA 313 6.79e+01 c.2.1.2 96583 1ox0A 430 6.82e+01 c.95.1.1,c.95.1.1 87495,87496 1f3eA 386 6.94e+01 1pud c.1.20.1 29661 1rlmA 271 7.03e+01 1mnp 357 7.17e+01 1arv a.93.1.1 18668 1w5qA 337 7.19e+01 1vkdA 338 7.23e+01 b.67.2.4 108644 1zzmA 259 7.26e+01 1yydA 357 7.26e+01 1d3cA 686 7.29e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21827,22496,27734,28721 2aorA 223 7.36e+01 1rdr 461 7.38e+01 1rdr e.8.1.4 43116 1lv7A 257 7.39e+01 c.37.1.20 78232 1xqwA 293 7.42e+01 1sw5B 275 7.49e+01 c.94.1.1 106070 1i78A 297 7.50e+01 f.4.4.1 66046 1b0pA 1231 7.51e+01 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 31831,31832,33104,34157,39003 1o0uA 429 7.52e+01 c.118.1.1 80743 1bunA 120 7.56e+01 1poa a.133.1.2 19614 2gu3A 136 7.59e+01 1hfuA 503 7.78e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1xksA 450 7.81e+01 1htqA 477 7.87e+01 d.15.9.1,d.128.1.1 71035,71036 1yloA 348 7.91e+01 1qg6A 261 7.92e+01 1eny c.2.1.2 29919 1ry6A 360 7.93e+01 c.37.1.9 98090 1y42X 392 8.00e+01 1wqaA 455 8.01e+01 1ihoA 283 8.08e+01 1ihoA c.26.1.4 62390 2fomB 185 8.12e+01 1qrkA 731 8.17e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21889,22187,22188,37119 1ntfA 282 8.21e+01 d.151.1.2 92104 2av4A 162 8.22e+01 1hl8A 449 8.23e+01 b.71.1.3,c.1.8.11 90646,90647 2fr1A 486 8.24e+01 1gthA 1025 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