# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1qmvA 197 9.06e-34 1qq2A c.47.1.10 33066 1prxB 224 1.73e-31 1prxA c.47.1.10 33077 1prxA 224 1.83e-31 1prxA c.47.1.10 33076 1qq2A 199 3.38e-31 1qq2A c.47.1.10 33064 1n8jA 186 8.62e-21 c.47.1.10 85401 1hd2A 161 3.11e-19 c.47.1.10 60962 1psqA 163 8.10e-18 c.47.1.10 88283 1st9A 143 6.17e-16 c.47.1.10 -7503 1qxhA 167 1.17e-13 c.47.1.10 -7496 1q98A 165 1.80e-12 c.47.1.10 -7499 1kngA 156 4.06e-10 c.47.1.10 72777 1jfuA 186 7.30e-10 c.47.1.10 62940 1lu4A 136 2.27e-09 c.47.1.10 -7509 1ewxA 146 1.15e-04 1ewxA c.47.1.10 33062 1qk8A 146 1.63e-04 1ewxA c.47.1.10 33061 1o8xA 146 2.81e-03 c.47.1.10 86681 1o6jA 150 4.17e-03 c.47.1.10 81089 1mek 120 7.19e-03 1erv c.47.1.2 32775 1faaA 124 9.61e-03 1erv c.47.1.1 32738 1f9mA 112 1.97e-02 1erv c.47.1.1 32736 2trxA 108 2.27e-02 1thx c.47.1.1 32719 1nw2A 105 2.37e-02 c.47.1.1 -7380 1i5gA 144 4.65e-02 1ewxA c.47.1.10 61784 1f5sA 211 5.58e-02 1f5sA c.108.1.4 59656 1j97A 211 5.58e-02 1f5sA c.108.1.4 62753 1kebA 108 6.80e-02 c.47.1.1 77341 1l7mA 211 7.28e-02 c.108.1.4 73664 1a8y 367 1.48e-01 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1gp1A 198 1.56e-01 1gp1A c.47.1.10 33059 1thx 115 1.60e-01 1thx c.47.1.1 32732 1es9A 232 1.64e-01 1wab c.23.10.3 31340 1l6rA 227 1.64e-01 c.108.1.10 77768 1uz5A 402 2.43e-01 b.85.6.1 -5029 b.103.1.1 -5069 c.57.1.2 -7902 1qhtA 775 2.89e-01 1tgoA c.55.3.5 33722 e.8.1.1 43011 1wab 232 3.45e-01 1wab c.23.10.3 31341 1erv 105 3.54e-01 1erv c.47.1.1 32743 1a6dA 545 3.85e-01 1a6dA a.129.1.2 19488 c.8.5.2 30819 d.56.1.2 38936 1fb6A 105 6.86e-01 1thx c.47.1.1 32739 1ak5 503 7.48e-01 1ak5 c.1.5.1 28639 1j6oA 268 9.86e-01 c.1.9.12 77088 1gt91 357 1.13e+00 1gqyA 475 1.15e+00 c.5.1.1 83305 c.59.1.1 83306 c.72.2.1 83307 1dkxA 219 1.34e+00 1dkzA unknown_sccs -446 unknown_sccs -3061 1zrn 232 1.35e+00 1qq5A c.108.1.1 43323 1dkzA 219 1.39e+00 1dkzA unknown_sccs -445 unknown_sccs -3060 1k1eA 180 1.59e+00 c.108.1.5 67995 1d7kA 421 1.62e+00 7odcA b.49.2.3 26486 c.1.6.1 28648 1senA 164 1.65e+00 1f0xA 571 1.82e+00 1f0xA d.58.32.2 39483 d.145.1.1 41746 1r26A 125 1.88e+00 c.47.1.1 -7389 1ccwA 137 2.29e+00 1be1 c.23.6.1 31238 1i1qB 192 2.31e+00 1qdlB c.23.16.1 61544 1o1zA 234 2.37e+00 c.1.18.3 86555 1atg 231 2.50e+00 1atg c.94.1.1 35834 1ohtA 215 2.67e+00 d.118.1.1 87036 1k7yA 577 2.98e+00 a.46.1.1 68272 c.23.6.1 68273 d.173.1.1 68274 1tmy 120 3.32e+00 1dbwA c.23.1.1 31083 1me8A 503 3.36e+00 c.1.5.1 79028 1nrwA 288 3.37e+00 c.108.1.10 86128 1bjx 110 3.56e+00 1bjx c.47.1.2 32774 2bjxA 110 3.56e+00 1bjx c.47.1.2 32776 1p3dA 475 3.64e+00 c.5.1.1 87728 c.59.1.1 87729 c.72.2.1 87730 1vheA 373 3.65e+00 unknown_sccs -4280 c.56.5.4 -7890 1o63A 219 3.89e+00 c.94.1.1 -8691 7odcA 424 3.99e+00 7odcA b.49.2.3 26488 c.1.6.1 28650 2dhqA 146 4.08e+00 2dhqA c.23.13.1 31382 1kid 203 4.24e+00 1derA c.8.5.1 30771 1h05A 146 4.39e+00 c.23.13.1 76433 1bmtA 246 4.64e+00 1bmtA a.46.1.1 17757 c.23.6.1 31235 1g0oA 283 4.96e+00 1ybvA c.2.1.2 60181 1id1A 153 5.00e+00 1id1A c.2.1.9 62286 1vdwA 254 5.09e+00 e.7.1.1 -11868 1bh5A 183 5.14e+00 1qipA d.32.1.1 38476 2ae2A 260 5.36e+00 1bdb c.2.1.2 29945 1j8dA 180 5.86e+00 c.108.1.5 66433 1ecfB 504 5.94e+00 1ecfB c.61.1.1 34054 d.153.1.1 41821 1geqA 248 6.17e+00 2tysA c.1.2.4 28589 1tgoA 773 6.41e+00 1tgoA c.55.3.5 33721 e.8.1.1 43010 1dymA 402 6.68e+00 1celA b.29.1.10 24304 1ojjA 402 6.69e+00 b.29.1.10 -3473 1ybvA 283 6.91e+00 1ybvA c.2.1.2 29948 1gz6A 319 7.30e+00 c.2.1.2 76410 1ba1 386 7.39e+00 1ba1 c.55.1.1 33387 c.55.1.1 33388 1bupA 386 7.39e+00 1ba1 c.55.1.1 33377 c.55.1.1 33378 1kay 381 7.45e+00 1ba1 c.55.1.1 33385 c.55.1.1 33386 1f75A 249 7.52e+00 1f75A c.101.1.1 59662 1j1nA 492 7.61e+00 c.94.1.1 83978 1nijA 318 7.86e+00 c.37.1.10 85741 d.237.1.1 85742 1nozA 388 7.96e+00 1clqA c.55.3.5 33715 1jl1A 155 8.09e+00 c.55.3.1 66821 1h7mA 102 8.09e+00 d.79.3.1 83485 1kt8A 365 8.12e+00 e.17.1.1 77531 1tof 112 8.47e+00 1erv c.47.1.1 32733 1ae1A 273 8.94e+00 1bdb c.2.1.2 29943 1hyhA 309 9.19e+00 1hyhA c.2.1.5 30150 d.162.1.1 42117 1bpr 191 9.32e+00 1dkzA unknown_sccs 43319 1gsoA 431 9.41e+00 1gsoA b.84.2.1 28240 c.30.1.1 31647 d.142.1.2 41492 1qycA 308 9.88e+00 c.2.1.2 -5782 1e6iA 121 1.00e+01 1b91A a.29.2.1 16969 1nvmA 345 1.03e+01 a.5.7.1 86249 c.1.10.5 86250 1m0wA 491 1.04e+01 c.30.1.4 78363 d.142.1.6 78364 1hgxA 183 1.12e+01 1tc1A c.61.1.1 34027 1pzxA 289 1.14e+01 c.119.1.1 -8623 1qipA 183 1.14e+01 1qipA d.32.1.1 38470 1su4A 994 1.16e+01 b.82.7.1 -4927 c.108.1.7 -6854 d.220.1.1 -11668 f.33.1.1 -12333 1qh8A 478 1.21e+01 1qguA c.92.2.3 35633 1fl0A 171 1.22e+01 1eujA b.40.4.4 25315 1eulA 994 1.24e+01 1eulA 1qguA 478 1.27e+01 1qguA c.92.2.3 35625 1rhcA 330 1.34e+01 c.1.16.3 -5606 1f6dA 376 1.35e+01 1f6dA c.87.1.3 35467 1aiu 105 1.37e+01 1erv c.47.1.1 32746 1e8uA 454 1.38e+01 1e8tA b.68.1.1 59389 1qksA 567 1.39e+01 1qksA a.3.1.2 15951 b.70.2.1 27710 1kwhA 492 1.39e+01 c.94.1.1 68876 1dkuA 317 1.41e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1h75A 81 1.41e+01 1h75A c.47.1.1 60716 1ji2A 585 1.42e+01 b.1.18.2 71672 b.71.1.1 71673 c.1.8.1 71674 1k9dA 679 1.43e+01 c.1.8.10 77292 d.92.2.2 77293 1dkrA 317 1.44e+01 1dkuA c.61.1.2 34114 c.61.1.2 34115 1eujA 166 1.46e+01 1eujA b.40.4.4 25316 1b73A 254 1.48e+01 1b74A c.78.2.1 35266 c.78.2.1 35267 1oe8A 211 1.49e+01 a.45.1.1 86905 c.47.1.5 86906 1c0pA 363 1.53e+01 1an9A c.4.1.2 30647 d.16.1.3 37934 1ecfA 504 1.54e+01 1ecfB c.61.1.1 34053 d.153.1.1 41820 1ttzA 87 1.58e+01 1sk4A 163 1.58e+01 1vgvA 384 1.61e+01 c.87.1.3 -8575 1j6qA 136 1.66e+01 b.40.9.1 77091 1ibsA 317 1.67e+01 c.61.1.2 66107 c.61.1.2 66108 1mrzA 293 1.72e+01 b.43.5.1 -4048 c.26.1.3 -6616 1h1lA 481 1.73e+01 c.92.2.3 70851 1ktaA 365 1.74e+01 e.17.1.1 77533 1uc7A 125 1.74e+01 c.47.1.1 -7414 1ehyA 294 1.75e+01 1ehyA c.69.1.11 34693 1f21A 155 1.76e+01 2rn2 c.55.3.1 33550 1m32A 366 1.77e+01 c.67.1.3 78508 1b74A 254 1.82e+01 1b74A c.78.2.1 35264 c.78.2.1 35265 1ovnA 248 1.84e+01 a.71.1.1 -1096 c.47.1.7 -7477 1ktbA 405 1.86e+01 b.71.1.1 72960 c.1.8.1 72961 1k66A 149 1.88e+01 c.23.1.1 -6406 1iwgA 1053 1.88e+01 d.58.44.1 76874 d.58.44.1 76875 d.58.44.1 76876 d.58.44.1 76877 d.225.1.1 76878 d.225.1.1 76879 f.35.1.1 76880 f.35.1.1 76881 1ekfA 365 1.91e+01 1ekfA e.17.1.1 59445 1e8tA 454 1.93e+01 1e8tA b.68.1.1 59387 1b91A 118 1.95e+01 1b91A 1i7qB 193 1.97e+01 1qdlB c.23.16.1 61902 1aoqA 567 2.02e+01 1qksA a.3.1.2 15934 b.70.2.1 27692 1gw5M 435 2.10e+01 b.2.7.1 70631 d.110.4.2 70632 1dad 224 2.16e+01 1byi c.37.1.10 32204 8ohm 435 2.17e+01 1heiA c.37.1.14 32469 c.37.1.14 32470 1d4fA 431 2.18e+01 1b3rA c.2.1.4 30110 c.23.12.3 31370 1b3rA 431 2.21e+01 1b3rA c.2.1.4 30106 c.23.12.3 31366 1bvzA 585 2.27e+01 1bvzA b.1.18.2 21856 b.71.1.1 27783 c.1.8.1 28770 1j1uA 306 2.30e+01 c.26.1.1 83980 1a8l 226 2.32e+01 1a8l c.47.1.2 32777 c.47.1.2 32778 1fm5A 199 2.35e+01 1fm5A d.169.1.1 42330 1q4rA 112 2.36e+01 d.58.4.4 -9943 1dbs 224 2.39e+01 1byi c.37.1.10 32209 1k0eA 453 2.40e+01 d.161.1.1 67938 1m1nB 522 2.42e+01 c.92.2.3 78418 1gw5S 142 2.44e+01 d.110.4.2 70633 1ecsA 126 2.45e+01 1ecsA d.32.1.2 59407 1q7bA 244 2.46e+01 c.2.1.2 -5826 1udsA 255 2.49e+01 d.14.1.4 -9055 d.101.1.1 -10745 2rn2 155 2.51e+01 2rn2 c.55.3.1 33551 1rch 155 2.51e+01 2rn2 c.55.3.1 33570 1lssA 140 2.52e+01 c.2.1.9 74246 3minB 522 2.52e+01 1qguB c.92.2.3 35606 1ek6A 348 2.54e+01 1xel c.2.1.2 29800 1aerA 205 2.57e+01 1aerA d.166.1.1 42249 1li4A 432 2.60e+01 c.2.1.4 84616 c.23.12.3 84617 2tpsA 227 2.60e+01 2tpsA c.1.3.1 28591 1jflA 228 2.60e+01 c.78.2.1 71656 c.78.2.1 71657 1ja9A 274 2.61e+01 c.2.1.2 62817 1eejA 216 2.62e+01 1eejA c.47.1.9 33057 d.17.3.1 38071 2minB 522 2.63e+01 1qguB c.92.2.3 35610 1s8fA 177 2.63e+01 1liuA 528 2.68e+01 b.58.1.1 77970 c.1.12.1 77971 c.49.1.1 77972 1gg4A 452 2.68e+01 1gg4A c.98.1.1 58985 c.59.1.1 33957 c.72.2.1 58986 1lqaA 346 2.69e+01 c.1.7.1 84674 1l1jA 239 2.71e+01 b.47.1.1 84516 1jmcA 246 2.71e+01 1jmcA b.40.4.3 25300 b.40.4.3 25301 1a7aA 432 2.78e+01 1b3rA c.2.1.4 30104 c.23.12.3 31364 1df9A 191 2.80e+01 1befA b.47.1.3 26420 2ebn 289 2.81e+01 2ebn c.1.8.5 28990 1q53A 112 2.91e+01 d.58.4.4 -9944 1fs1B 141 2.92e+01 1vcbB a.157.1.1 19252 d.42.1.1 38664 1j5sA 463 2.93e+01 c.1.9.8 71580 1dts 221 2.94e+01 1byi c.37.1.10 32200 1j3wA 163 3.00e+01 unknown_sccs -10870 1sqsA 242 3.01e+01 unknown_sccs -6433 2mbr 340 3.01e+01 2mbr d.145.1.2 41749 d.146.1.1 41762 1gmuA 143 3.04e+01 b.107.1.1 65335 d.58.38.1 65336 1uxy 340 3.06e+01 2mbr d.145.1.2 41748 d.146.1.1 41761 1nnlA 225 3.11e+01 c.108.1.4 85906 1byi 224 3.14e+01 1byi c.37.1.10 32199 1nykA 165 3.14e+01 b.33.1.1 86408 1mkiA 330 3.18e+01 e.3.1.2 84994 1g6q2 328 3.21e+01 1g6q2 1i4wA 353 3.21e+01 c.66.1.24 66028 1ass 159 3.21e+01 1a6dA c.8.5.2 30818 1k28D 391 3.24e+01 b.106.1.1 68052 b.106.1.1 68053 1eh9A 558 3.26e+01 1ehaA b.1.18.2 21858 b.71.1.1 27785 c.1.8.1 28772 3minC 491 3.27e+01 1qguA c.92.2.3 35607 1o0uA 429 3.27e+01 c.118.1.1 80743 1g01A 364 3.28e+01 7a3hA c.1.8.3 60161 1uf5A 303 3.31e+01 1onxA 390 3.33e+01 b.92.1.7 87176 c.1.9.13 87177 1erzA 303 3.34e+01 1erzA d.160.1.2 59498 1un8A 552 3.35e+01 unknown_sccs -1942 c.32.1.2 -6792 d.79.2.2 -10401 1ilyA 90 3.36e+01 c.55.4.1 71245 1qwgA 251 3.42e+01 unknown_sccs -5678 1ewjA 126 3.44e+01 1ecsA d.32.1.2 59526 1o6aA 96 3.47e+01 unknown_sccs -4101 1fjhA 257 3.60e+01 1fjhB c.2.1.2 29870 1qn2A 100 3.60e+01 1ycc a.3.1.1 15882 1g0cA 364 3.63e+01 7a3hA c.1.8.3 60165 1n67A 359 3.64e+01 b.2.3.4 85354 b.2.3.4 85355 1m3uA 264 3.64e+01 c.1.12.8 84784 1uok 558 3.66e+01 1uok b.71.1.1 27801 c.1.8.1 28788 1fgqA 839 3.68e+01 1yge a.119.1.1 59826 b.12.1.1 59827 1f8nA 839 3.73e+01 1yge a.119.1.1 59703 b.12.1.1 59704 1fgyA 127 3.74e+01 1faoA b.55.1.1 26976 2acr 315 3.79e+01 1frb c.1.7.1 28674 1yge 839 3.81e+01 1yge a.119.1.1 19234 b.12.1.1 23634 1ltzA 297 3.83e+01 d.178.1.1 74254 1mhyD 521 3.86e+01 1mhyD a.25.1.2 16780 1bymA 97 3.88e+01 1bi0 b.34.1.2 24458 1eo1A 124 3.91e+01 1eo1A c.55.5.1 33739 1k0gA 453 3.94e+01 d.161.1.1 67940 1emsA 440 3.97e+01 1emsA d.13.1.1 37520 d.160.1.1 42086