# 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 1v7zA 260 1.38e+00 unknown_sccs -6353 1svr 114 2.09e+00 1svy d.109.1.1 40833 1bquA 215 2.21e+00 1bquA b.1.2.1 22066 b.1.2.1 22067 1svq 114 2.38e+00 1svy d.109.1.1 40832 1e19A 314 2.75e+00 1b7bA c.73.1.1 34967 1k8wA 327 2.95e+00 b.122.1.1 83094 unknown_sccs -10143 1cs1C 386 3.80e+00 1ibjA c.67.1.3 34401 1nykA 165 3.87e+00 b.33.1.1 86408 1g7tA 594 4.29e+00 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1cs1A 386 5.12e+00 1ibjA c.67.1.3 34399 1gv4A 528 5.36e+00 c.3.1.5 70589 c.3.1.5 70590 d.87.1.1 70591 1tif 78 5.48e+00 1tif d.15.8.1 37836 1g86A 142 6.42e+00 b.29.1.3 70161 1hdkA 141 6.78e+00 b.29.1.3 65807 1m6iA 493 6.83e+00 c.3.1.5 74533 c.3.1.5 74534 d.87.1.1 74535 1q3kA 259 7.11e+00 unknown_sccs -6335 1m6sA 347 7.17e+00 c.67.1.1 78701 1jg8A 347 7.18e+00 1jg8A c.67.1.1 62946 1j0hA 588 7.43e+00 b.1.18.2 77027 b.71.1.1 77028 c.1.8.1 77029 1mo9A 523 7.59e+00 c.3.1.5 79341 c.3.1.5 79342 d.87.1.1 79343 1ux6A 350 7.61e+00 unknown_sccs -3451 unknown_sccs -12886 1q9uA 130 7.63e+00 unknown_sccs -11025 1bj8 109 7.65e+00 1bquA b.1.2.1 22070 1fit 147 8.34e+00 1fit d.13.1.1 37499 1dyoA 160 8.54e+00 1dyoA b.18.1.7 23771 1keeA 1073 8.59e+00 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 1htrB 329 8.75e+00 1smrA 1h6yA 170 8.95e+00 b.18.1.7 70904 1c3oC 1073 8.98e+00 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 1lmzA 187 9.39e+00 a.96.1.4 74037 1bxrA 1073 9.78e+00 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 1danU 121 9.82e+00 1boy b.1.2.1 21954 1jaxA 212 1.01e+01 c.2.1.6 66476 1r6xA 395 1.04e+01 b.122.1.3 -5125 c.26.1.5 -6620 1eonA 245 1.07e+01 1rvaA c.52.1.2 33238 1dmaA 214 1.08e+01 1aerA d.166.1.1 42251 1ejrC 567 1.08e+01 1ubpC b.92.1.1 28420 c.1.9.2 29042 1lcl 142 1.14e+01 1lcl b.29.1.3 24216 1je5A 206 1.15e+01 1je5A b.40.4.7 62909 1ejxC 567 1.18e+01 b.92.1.1 83184 c.1.9.2 83185 1pxvA 183 1.18e+01 d.3.1.1 -8881 1fwcC 567 1.19e+01 1ubpC b.92.1.1 28410 c.1.9.2 29032 1od5A 492 1.23e+01 b.82.1.2 86832 b.82.1.2 86833 1an9A 340 1.23e+01 1an9A c.4.1.2 30617 d.16.1.3 37904 1vjqA 79 1.24e+01 unknown_sccs -13478 1c3oA 1073 1.24e+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 1jayA 212 1.26e+01 c.2.1.6 66478 1m1cA 680 1.26e+01 e.42.1.1 78395 1cj3A 392 1.27e+01 1pbe c.3.1.2 30347 d.16.1.2 37878 1i1nA 226 1.29e+01 c.66.1.7 71102 3tss 194 1.30e+01 1aw7A b.40.2.2 25160 d.15.6.1 37749 2tgi 112 1.35e+01 2tgi g.17.1.2 44777 1ha3A 405 1.38e+01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1ts3A 194 1.38e+01 1aw7A b.40.2.2 25168 d.15.6.1 37757 1fq0A 213 1.40e+01 1fwrA c.1.10.1 29161 1exmA 405 1.41e+01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1h3fA 432 1.44e+01 c.26.1.1 76631 d.66.1.4 76632 1e5eA 404 1.49e+01 1ibjA c.67.1.3 59265 1m4jA 142 1.53e+01 d.109.1.2 78602 1ql1A 46 1.55e+01 1ql1A h.1.4.1 45564 1kr5A 226 1.57e+01 c.66.1.7 68847 1tlk 154 1.62e+01 1tlk b.1.1.4 21707 1th8A 145 1.62e+01 1g7sA 594 1.63e+01 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1sx5A 244 1.64e+01 c.52.1.2 -7551 1gd5A 130 1.67e+01 1gd5A d.189.1.1 60439 1igwA 434 1.69e+01 c.1.12.7 62370 1mzbA 136 1.70e+01 unknown_sccs -266 1avaC 181 1.70e+01 1avaC b.42.4.1 25604 1keeC 1073 1.73e+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 1vhoA 346 1.76e+01 unknown_sccs -4283 c.56.5.4 -7893 1ve9A 347 1.78e+01 c.4.1.2 -6056 d.16.1.3 -9214 1qtoA 122 1.89e+01 1bylA d.32.1.2 38494 1c9oA 66 1.90e+01 1mjc b.40.4.5 25325 1a9xA 1058 1.93e+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 1tqyB 415 1.94e+01 1cs0C 1073 1.94e+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 1mejA 223 2.04e+01 c.65.1.1 79029 1qwtA 255 2.04e+01 unknown_sccs -3329 1csp 67 2.05e+01 1mjc b.40.4.5 25321 1keeE 1073 2.07e+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 1tfg 112 2.11e+01 2tgi g.17.1.2 44778 1aw7A 194 2.11e+01 1aw7A b.40.2.2 25164 d.15.6.1 37753 1evuA 731 2.18e+01 1f13A b.1.18.9 21883 b.1.5.1 22175 b.1.5.1 22176 d.3.1.4 37113 1pbgA 468 2.23e+01 1e70M c.1.8.4 28946 1f32A 149 2.26e+01 1f32A d.62.1.1 39539 1p4dA 330 2.28e+01 unknown_sccs -10522 1k0wA 231 2.33e+01 c.74.1.1 77220 1kdxA 81 2.35e+01 1kdxA a.12.1.1 16375 1f6yA 262 2.35e+01 1f6yA c.1.21.2 29673 1c3oG 1073 2.43e+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 1wba 175 2.44e+01 1wba b.42.4.1 25591 1jdiA 231 2.44e+01 c.74.1.1 66551 1euaA 213 2.45e+01 1fwrA c.1.10.1 29155 1ex0A 731 2.46e+01 b.1.18.9 -2754 b.1.5.1 -2778 b.1.5.1 -2779 d.3.1.4 -8889 1igd 61 2.47e+01 2igd d.15.7.1 37822 1p9uA 302 2.48e+01 b.47.1.4 88001 1e0tA 470 2.48e+01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1djnA 729 2.48e+01 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 1g8fA 511 2.50e+01 1g8fA b.122.1.3 60348 c.26.1.5 60349 c.37.1.15 60350 2tmdA 729 2.52e+01 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1sb0A 87 2.55e+01 a.12.1.1 -455 1mzhA 225 2.60e+01 c.1.10.1 79698 1o7kA 131 2.63e+01 d.189.1.1 81144 1nb8A 353 2.64e+01 d.3.1.9 80385 1aa8A 347 2.66e+01 1an9A 1kq6A 141 2.69e+01 d.189.1.1 -9926 1iqpA 327 2.74e+01 a.80.1.1 62649 c.37.1.20 62650 1tqnA 486 2.80e+01 1fwrA 213 2.86e+01 1fwrA c.1.10.1 29164 1c3oE 1073 2.89e+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 1k0iA 394 2.89e+01 c.3.1.2 67942 d.16.1.2 67943 1kjqA 391 2.93e+01 b.84.2.1 72616 c.30.1.1 72617 d.142.1.2 72618 1devC 196 2.93e+01 1ygs b.26.1.1 23915 1c24A 263 2.96e+01 1c24A d.127.1.1 41148 1tplA 426 2.98e+01 1ax4A c.67.1.2 34387 1ko7A 314 2.98e+01 c.98.2.1 72797 c.91.1.2 72798 1ohuA 175 3.01e+01 f.1.4.1 -12058 2igd 61 3.02e+01 2igd d.15.7.1 37821 1res 43 3.05e+01 1ret a.4.1.2 16023 1nf1A 333 3.06e+01 1nf1A a.116.1.2 19110 1j05A 111 3.08e+01 b.1.1.1 -2114 1uvjA 664 3.10e+01 e.8.1.6 -11964 1c7gA 456 3.15e+01 c.67.1.2 -8153 1gp1A 198 3.16e+01 1gp1A c.47.1.10 33059 1jdbB 1073 3.16e+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 1ne9A 335 3.17e+01 d.108.1.4 -10805 d.108.1.4 -10806 1mdoA 393 3.19e+01 c.67.1.4 79013 1mjc 69 3.19e+01 1mjc b.40.4.5 25319 1rcd 173 3.22e+01 2fha a.25.1.1 16687 1bw0A 416 3.23e+01 1bw0A c.67.1.1 34385 1ftrA 296 3.23e+01 1ftrA d.58.33.1 39485 d.58.33.1 39486 1dkuA 317 3.26e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1qwdA 177 3.28e+01 b.60.1.1 -4455 1ex2A 189 3.32e+01 1ex2A c.51.4.2 33225 1mvfD 82 3.32e+01 b.129.1.1 85143 1hhsA 664 3.32e+01 1hi0P e.8.1.6 61045 1f13A 731 3.39e+01 1f13A b.1.18.9 21877 b.1.5.1 22163 b.1.5.1 22164 d.3.1.4 37107 1giqA 413 3.39e+01 d.166.1.1 76224 d.166.1.1 76225 1lfb 99 3.39e+01 1lfb a.4.1.1 15989 1tvdA 116 3.42e+01 1tvdA b.1.1.1 20650 7icd 416 3.45e+01 1iso c.77.1.1 35072 1hyp 80 3.52e+01 1hyp a.52.1.1 17806 1fcjA 322 3.54e+01 1oasA c.79.1.1 35289 1rvaA 244 3.54e+01 1rvaA c.52.1.2 33240 1pb1A 416 3.55e+01 c.77.1.1 88014 1dkrA 317 3.58e+01 1dkuA c.61.1.2 34114 c.61.1.2 34115 1aogA 485 3.59e+01 3grs c.3.1.5 30517 c.3.1.5 30518 d.87.1.1 40190 1b8gA 429 3.63e+01 1b8gA c.67.1.4 34499 1pkn 530 3.64e+01 1a49A b.58.1.1 27042 c.1.12.1 29271 c.49.1.1 33125 1dleA 298 3.70e+01 1dleA b.47.1.2 26312 1o1zA 234 3.70e+01 c.1.18.3 86555 1oniA 137 3.72e+01 d.79.1.1 87144 1o94A 729 3.74e+01 c.1.4.1 81200 c.3.1.1 81201 c.4.1.1 81202 1khxA 227 3.76e+01 b.26.1.1 68631 1rfmA 344 3.79e+01 c.122.1.1 -8032 1eyeA 280 3.82e+01 1aj2 c.1.21.1 29672 2matA 264 3.82e+01 1c24A d.127.1.1 41146 1keeG 1073 3.82e+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 1d3bA 75 3.83e+01 1d3bA b.38.1.1 24798 1svy 114 3.84e+01 1svy d.109.1.1 40831 1hi0P 664 3.86e+01 1hi0P e.8.1.6 61051 1nr3A 122 3.87e+01 d.236.1.1 86092 8ohm 435 3.87e+01 1heiA c.37.1.14 32469 c.37.1.14 32470 1lvmA 229 3.91e+01 b.47.1.3 78243 1eyzA 392 3.99e+01 1ez1A b.84.2.1 28246 c.30.1.1 31653 d.142.1.2 41498