# List of top-scoring protein chains for t2k-100-30-bys 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 1kfuS 184 7.22e-02 a.39.1.8 68574 1j3mA 129 1.24e-01 1alvA 173 2.50e-01 1alvA a.39.1.8 17370 1xgsA 295 3.22e-01 1bn5 a.4.5.25 16216 d.127.1.1 41153 1jdfA 447 3.49e-01 c.1.11.2 62897 d.54.1.1 62898 1thtA 305 3.73e-01 1thtA c.69.1.13 34711 1bouB 302 5.99e-01 1bouB c.56.6.1 33859 1b4uB 302 6.07e-01 1bouB c.56.6.1 33861 3fruA 269 6.09e-01 1agdA b.1.1.2 20657 d.19.1.1 38150 1h7wD 1025 8.56e-01 a.1.2.2 15686 c.1.4.1 28631 c.3.1.1 30327 c.4.1.1 30612 d.58.1.5 39010 1h7xD 1025 8.65e-01 a.1.2.2 15690 c.1.4.1 28635 c.3.1.1 30331 c.4.1.1 30616 d.58.1.5 39014 1h7xC 1025 8.66e-01 a.1.2.2 15689 c.1.4.1 28634 c.3.1.1 30330 c.4.1.1 30615 d.58.1.5 39013 1gteD 1025 8.89e-01 a.1.2.2 70455 c.1.4.1 70456 c.3.1.1 70457 c.4.1.1 70458 d.58.1.5 70459 1gthD 1025 8.91e-01 a.1.2.2 70498 c.1.4.1 70499 c.3.1.1 70500 c.4.1.1 70501 d.58.1.5 70502 1h7xB 1025 8.95e-01 a.1.2.2 15688 c.1.4.1 28633 c.3.1.1 30329 c.4.1.1 30614 d.58.1.5 39012 1h7wA 1025 9.10e-01 1h7wA a.1.2.2 15683 c.1.4.1 28628 c.3.1.1 30324 c.4.1.1 30609 d.58.1.5 39007 1gthA 1025 9.29e-01 a.1.2.2 70483 c.1.4.1 70484 c.3.1.1 70485 c.4.1.1 70486 d.58.1.5 70487 1h7wB 1025 9.37e-01 a.1.2.2 15684 c.1.4.1 28629 c.3.1.1 30325 c.4.1.1 30610 d.58.1.5 39008 1h7xA 1025 9.37e-01 1h7wA a.1.2.2 15687 c.1.4.1 28632 c.3.1.1 30328 c.4.1.1 30613 d.58.1.5 39011 1gthC 1025 9.49e-01 a.1.2.2 70493 c.1.4.1 70494 c.3.1.1 70495 c.4.1.1 70496 d.58.1.5 70497 1dgsA 667 9.65e-01 1dgsA a.60.2.2 17963 b.40.4.6 25365 d.142.2.2 41581 1gt8B 1025 1.04e+00 a.1.2.2 70423 c.1.4.1 70424 c.3.1.1 70425 c.4.1.1 70426 d.58.1.5 70427 1gthB 1025 1.05e+00 a.1.2.2 70488 c.1.4.1 70489 c.3.1.1 70490 c.4.1.1 70491 d.58.1.5 70492 1gt8A 1025 1.07e+00 a.1.2.2 70418 c.1.4.1 70419 c.3.1.1 70420 c.4.1.1 70421 d.58.1.5 70422 1gteA 1025 1.08e+00 a.1.2.2 70440 c.1.4.1 70441 c.3.1.1 70442 c.4.1.1 70443 d.58.1.5 70444 1gt8D 1025 1.11e+00 a.1.2.2 70433 c.1.4.1 70434 c.3.1.1 70435 c.4.1.1 70436 d.58.1.5 70437 1bupA 386 1.24e+00 1ba1 c.55.1.1 33377 c.55.1.1 33378 1q4uA 151 1.41e+00 d.38.1.5 -9701 1agdB 99 1.46e+00 1agdB b.1.1.2 20742 1gt8C 1025 1.47e+00 a.1.2.2 70428 c.1.4.1 70429 c.3.1.1 70430 c.4.1.1 70431 d.58.1.5 70432 1kay 381 1.55e+00 1ba1 c.55.1.1 33385 c.55.1.1 33386 1ba1 386 1.69e+00 1ba1 c.55.1.1 33387 c.55.1.1 33388 1un8A 552 1.70e+00 unknown_sccs -1942 c.32.1.2 -6792 d.79.2.2 -10401 1q7lA 198 1.72e+00 c.56.5.4 -7886 1bueA 265 1.76e+00 1btl e.3.1.1 42727 1nffA 260 2.09e+00 c.2.1.2 80457 1fo5A 85 2.12e+00 1fo5A c.47.1.1 59922 2hdhA 293 2.12e+00 2hdhA a.100.1.3 18795 c.2.1.6 30199 1oivA 191 2.49e+00 c.37.1.8 -7074 1i4fB 100 2.50e+00 1agdB b.1.1.2 61689 1v4vA 376 2.56e+00 c.87.1.3 -8583 1que 303 2.58e+00 1fnc b.43.4.2 25647 c.25.1.1 31537 1k5nB 100 2.66e+00 b.1.1.2 77268 1duzB 100 2.68e+00 1agdB b.1.1.2 20671 1ogiA 303 2.71e+00 b.43.4.2 -4042 c.25.1.1 -6587 1hsbB 99 2.72e+00 1agdB b.1.1.2 20737 1ecsA 126 3.16e+00 1ecsA d.32.1.2 59407 1qh0A 295 3.20e+00 b.43.4.2 68891 c.25.1.1 68892 1go2A 304 3.26e+00 b.43.4.2 76243 c.25.1.1 76244 1b2rA 304 3.31e+00 1fnc b.43.4.2 25648 c.25.1.1 31538 1edhA 226 3.36e+00 1edhA b.1.6.1 22198 b.1.6.1 22199 1ufoA 238 3.57e+00 unknown_sccs -8303 1h6kA 757 3.81e+00 unknown_sccs 60675 unknown_sccs 60676 unknown_sccs 60677 2rslA 140 4.00e+00 2rslA c.53.1.1 33345 1h1yA 228 4.00e+00 c.1.2.2 76506 1lddA 74 4.50e+00 a.4.5.34 73841 1o6jA 150 4.63e+00 c.47.1.10 81089 1t7pA 698 4.72e+00 1t7pA c.55.3.5 33712 e.8.1.1 43005 1suh 146 4.87e+00 1edhA b.1.6.1 22206 1trkA 680 5.23e+00 1trkA c.36.1.6 31804 c.36.1.10 31803 c.48.1.1 33090 1ewjA 126 5.37e+00 1ecsA d.32.1.2 59526 2polA 366 5.66e+00 2polA d.131.1.1 41356 d.131.1.1 41357 d.131.1.1 41358 1kjvB 100 5.80e+00 b.1.1.2 77423 1krhA 338 5.94e+00 b.43.4.2 72891 c.25.1.2 72892 d.15.4.2 72893 153l 185 5.95e+00 153l d.2.1.5 36984 1ga8A 311 5.98e+00 1ga8A c.68.1.4 34516 1ohvA 472 5.98e+00 c.67.1.4 -8181 1n9lA 109 6.11e+00 d.110.3.6 85468 1g9rA 311 6.37e+00 1ga8A c.68.1.4 34517 1top 162 6.73e+00 1ncx a.39.1.5 17223 1f0yA 302 7.01e+00 2hdhA a.100.1.3 18793 c.2.1.6 30197 1tkaA 678 7.02e+00 1trkA c.36.1.6 31816 c.36.1.10 31815 c.48.1.1 33096 2trxA 108 7.02e+00 1thx c.47.1.1 32719 1zac 90 7.08e+00 1ncx a.39.1.5 17236 1ei9A 279 7.30e+00 1ei9A c.69.1.13 34713 1gtxA 472 7.33e+00 1gtxA 1gpuA 680 7.34e+00 c.36.1.6 65455 c.36.1.10 65454 c.48.1.1 65456 1o12A 376 7.38e+00 b.92.1.5 80758 c.1.9.10 80759 1kkuA 279 7.54e+00 c.26.1.3 72661 1d7kA 421 7.59e+00 7odcA b.49.2.3 26486 c.1.6.1 28648 1q6oA 216 7.70e+00 c.1.2.3 -5162 1trb 320 7.93e+00 1trb c.3.1.5 30529 c.3.1.5 30530 2pta 35 7.99e+00 2pta g.3.7.2 44168 487dH 224 8.07e+00 1ad2 i.1.1.2 45835 1ad2 228 8.36e+00 1ad2 e.24.1.1 43353 1nr3A 122 8.66e+00 d.236.1.1 86092 1mmiA 366 8.66e+00 d.131.1.1 -11093 d.131.1.1 -11094 d.131.1.1 -11095 1sjdA 368 8.68e+00 1lhpA 312 8.73e+00 c.72.1.5 77960 1q40B 219 8.81e+00 d.17.4.2 -9287 1cfzA 162 9.04e+00 1cfzA c.56.1.1 33754 1kv8A 216 9.36e+00 c.1.2.3 73054 1f5nA 592 9.50e+00 1dg3A a.114.1.1 19077 c.37.1.8 32152 1e3yA 104 9.68e+00 1fadA a.77.1.2 18426 1op0A 234 9.73e+00 1o9yA 84 9.85e+00 unknown_sccs -4105 1peqA 714 1.01e+01 1a7vA 125 1.06e+01 1cpq a.24.3.2 16562 1s1pA 331 1.07e+01 c.1.7.1 -5240 1ec7A 446 1.09e+01 1bqg c.1.11.2 29218 d.54.1.1 38862 1g291 372 1.10e+01 1g291 1dg3A 592 1.11e+01 1dg3A a.114.1.1 19078 c.37.1.8 32153 1kebA 108 1.18e+01 c.47.1.1 77341 1sddA 306 1.19e+01 1im8A 244 1.19e+01 c.66.1.14 66212 1db3A 372 1.22e+01 1db3A c.2.1.2 29813 1a7tA 232 1.24e+01 1a7tA d.157.1.1 42041 1muhA 481 1.26e+01 c.55.3.4 79485 1ghtA 105 1.27e+01 2rslA c.53.1.1 60526 1n7hA 381 1.27e+01 c.2.1.2 80250 1gdtA 183 1.28e+01 2rslA a.4.1.2 16021 c.53.1.1 33348 1mqvA 125 1.28e+01 a.24.3.2 79415 1auz 116 1.28e+01 1auz c.13.2.1 30883 1ln1A 214 1.30e+01 d.129.3.2 74038 1d2oA 187 1.30e+01 1d2oA b.3.5.1 22625 b.3.5.1 22626 1us0A 316 1.31e+01 c.1.7.1 -5233 1b9dA 163 1.32e+01 1b9dA c.55.3.2 33649 1mogA 67 1.37e+01 d.230.2.1 85034 1v8gA 329 1.37e+01 a.46.2.1 -953 c.27.1.1 -6644 1ki1B 352 1.39e+01 a.87.1.1 72497 b.55.1.1 72498 1pwmA 316 1.40e+01 c.1.7.1 -5232 1i5gA 144 1.41e+01 1ewxA c.47.1.10 61784 1q98A 165 1.42e+01 c.47.1.10 -7499 1j96A 323 1.42e+01 c.1.7.1 71616 1mml 265 1.44e+01 1mml e.8.1.2 43015 1jvr 137 1.45e+01 1jvr a.61.1.2 18132 1f5vA 240 1.46e+01 1bkjA d.90.1.1 40255 1c49A 35 1.49e+01 2pta g.3.7.2 44169 1gbs 185 1.50e+01 153l d.2.1.5 36986 1jy5A 212 1.50e+01 d.124.1.1 71940 1i0sA 169 1.52e+01 1i0rA b.45.1.2 61491 1mzhA 225 1.53e+01 c.1.10.1 79698 1afrA 345 1.55e+01 1afrA a.25.1.2 16805 2cmd 312 1.59e+01 2cmd c.2.1.5 30135 d.162.1.1 42102 1iy8A 267 1.67e+01 c.2.1.2 83774 1goiA 499 1.68e+01 b.72.2.1 65413 c.1.8.5 65414 d.26.3.1 65415 1i7dA 659 1.69e+01 1d6mA e.10.1.1 61886 1jcfA 344 1.69e+01 c.55.1.1 62878 c.55.1.1 62879 1d2pA 373 1.70e+01 1d2oA b.3.5.1 22629 b.3.5.1 22630 b.3.5.1 22631 b.3.5.1 22632 1dozA 309 1.71e+01 1ak1 c.92.1.1 35592 1e15A 499 1.72e+01 1e15A b.72.2.1 27810 c.1.8.5 29006 d.26.3.1 38440 1hgxA 183 1.73e+01 1tc1A c.61.1.1 34027 1i0rA 169 1.73e+01 1i0rA b.45.1.2 61489 1rl4A 188 1.79e+01 d.167.1.1 -11593 1ak1 310 1.83e+01 1ak1 c.92.1.1 35594 1n8nA 212 1.85e+01 unknown_sccs -6830 1go4A 205 1.89e+01 d.135.1.1 70292 1v93A 296 1.90e+01 c.1.23.1 -5654 1bowA 159 1.91e+01 1bowA d.60.1.1 39528 1jceA 344 1.91e+01 c.55.1.1 62876 c.55.1.1 62877 1gqzA 274 1.95e+01 d.21.1.1 83311 d.21.1.1 83312 1lmiA 131 1.96e+01 b.1.19.1 78098 1a79A 171 1.97e+01 1a79A c.52.2.1 33340 d.75.1.1 39739 1te5A 257 1.99e+01 1p5jA 372 2.00e+01 1o6sB 105 2.01e+01 b.1.6.1 81096 1et0A 269 2.08e+01 1et0A e.17.1.1 43289 1eo6A 117 2.15e+01 1eo6A d.15.1.3 37609 1aho 64 2.17e+01 1aho g.3.7.1 44127 1jj2I 145 2.20e+01 1ffkG c.21.1.1 63094 1hmpA 217 2.23e+01 1qk3A c.61.1.1 34075 1ns5A 155 2.25e+01 c.116.1.3 80705 1nznA 126 2.25e+01 a.118.8.1 -1616 1f3iA 481 2.27e+01 1b7eA 1lkoA 191 2.28e+01 a.25.1.1 78063 g.41.5.1 78064 1i2kA 269 2.28e+01 e.17.1.1 -11995 2acr 315 2.29e+01 1frb c.1.7.1 28674 1ads 315 2.31e+01 1frb c.1.7.1 28671 1lo6A 223 2.35e+01 b.47.1.2 74143 1b71A 191 2.40e+01 1ryt a.25.1.1 16647 g.41.5.1 45246 1stfI 98 2.41e+01 1stfI d.17.1.2 38006 1f1mA 164 2.41e+01 1ggqA a.24.12.1 59598 1iibA 106 2.47e+01 1iibA c.44.2.1 32648 1bwzA 274 2.48e+01 1bwzA d.21.1.1 38337 d.21.1.1 38338 1wdcC 156 2.49e+01 1wdcC a.39.1.5 17317 1pq1A 196 2.53e+01 f.1.4.1 -12055 1qnoA 344 2.57e+01 1qnoA c.1.8.3 28838 1ncx 162 2.60e+01 1ncx a.39.1.5 17222 1el3A 316 2.60e+01 1frb c.1.7.1 28672 1bli 483 2.62e+01 1bli b.71.1.1 27715 c.1.8.1 28702 1nkpA 88 2.62e+01 a.38.1.1 80573 1e2b 106 2.64e+01 1iibA c.44.2.1 32650 1huqA 164 2.64e+01 1byuA c.37.1.8 32020 1avsA 90 2.65e+01 1cll a.39.1.5 17226 1qnrA 344 2.66e+01 1qnoA c.1.8.3 28834 1eucB 396 2.67e+01 2scuB c.23.4.1 31149 d.142.1.4 41570 1i40A 175 2.69e+01 b.40.5.1 66024 2ae2A 260 2.71e+01 1bdb c.2.1.2 29945 1rboC 123 2.75e+01 1rboC d.73.1.1 39634 1evxA 162 2.77e+01 1a73A d.4.1.3 37149 8rucI 123 2.86e+01 1rboC d.73.1.1 39629 1q7zA 566 2.94e+01 c.1.21.2 -5638 c.1.26.1 -5666 1wod 233 3.00e+01 1wod c.94.1.1 35832 1ryt 190 3.02e+01 1ryt a.25.1.1 16646 g.41.5.1 45245 1fj2A 232 3.07e+01 1auoA c.69.1.14 34720 1hta 69 3.08e+01 1a7w a.22.1.2 16476 1kyoG 126 3.08e+01 f.27.1.1 73259 1amf 233 3.09e+01 1wod c.94.1.1 35833 1ugmA 125 3.11e+01 1dvbA 191 3.14e+01 1ryt a.25.1.1 16645 g.41.5.1 45244 1m4mA 140 3.16e+01 g.52.1.1 78605 1gsa 316 3.17e+01 1gsa c.30.1.3 31718 d.142.1.1 41477 1bcg 77 3.19e+01 1aho g.3.7.1 44130 1obwA 175 3.19e+01 2prd b.40.5.1 25416 1zfjA 491 3.22e+01 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1zin 217 3.29e+01 1zin c.37.1.1 31915 g.41.2.1 45178 1pvyA 227 3.31e+01 d.115.1.2 -10937 1r2jA 366 3.36e+01 a.29.3.1 -748 e.6.1.1 -11864 1b3jA 274 3.38e+01 1agdA b.1.1.2 20855 d.19.1.1 38319 1ipwA 175 3.41e+01 2prd b.40.5.1 25427 1mwmA 320 3.42e+01 c.55.1.1 79580 c.55.1.1 79581 1hqvA 191 3.46e+01 1hqvA a.39.1.8 61160 1glv 303 3.48e+01 1gsa c.30.1.3 31721 d.142.1.1 41480 1af3 196 3.51e+01 1maz f.1.4.1 43397 1r1dA 247 3.55e+01 unknown_sccs -8335 1kb9G 125 3.57e+01 f.27.1.1 77322 1l3eB 101 3.57e+01 g.53.1.1 73536 1k6kA 143 3.60e+01 a.174.1.1 77274 1kotA 119 3.60e+01 d.15.1.3 68732 1fo1A 271 3.61e+01 1fo1A c.10.2.3 30869 d.58.7.2 39213 1oq9A 363 3.63e+01 a.25.1.2 87257 1atg 231 3.70e+01 1atg c.94.1.1 35834 1cvl 319 3.75e+01 1cvl c.69.1.18 34786 1ewnA 219 3.76e+01 1bnkA b.46.1.2 25762 1a87 321 3.77e+01 1a87 f.1.1.1 43380 1fecA 490 3.78e+01 3grs c.3.1.5 30489 c.3.1.5 30490 d.87.1.1 40176 1uch 230 3.78e+01 1uch d.3.1.6 37129 1jkvA 266 3.81e+01 unknown_sccs 71719 1maz 221 3.81e+01 1maz f.1.4.1 43393 1gnuA 117 3.92e+01 d.15.1.3 65403 1ee9A 320 3.93e+01 1ee9A c.2.1.7 30288 c.58.1.2 33936 1vjs 483 3.96e+01 1bli b.71.1.1 27714 c.1.8.1 28701 1musA 477 3.98e+01 c.55.3.4 79494