# 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 1od5A 492 3.11e-02 b.82.1.2 86832 b.82.1.2 86833 1mdoA 393 6.41e-01 c.67.1.4 79013 1hdkA 141 6.83e-01 b.29.1.3 65807 1mjgM 729 8.66e-01 e.26.1.3 79204 1svy 114 1.35e+00 1svy d.109.1.1 40831 1lcl 142 1.47e+00 1lcl b.29.1.3 24216 1boy 219 1.47e+00 1boy b.1.2.1 21955 b.1.2.1 21956 1g86A 142 1.64e+00 b.29.1.3 70161 1jeyA 609 1.75e+00 1jeqA unknown_sccs -4426 unknown_sccs -7990 1v7zA 260 1.77e+00 unknown_sccs -6353 1ne9A 335 2.22e+00 d.108.1.4 -10805 d.108.1.4 -10806 1a3k 137 2.28e+00 1a3k b.29.1.3 24218 1k8wA 327 2.41e+00 b.122.1.1 83094 unknown_sccs -10143 1gp1A 198 2.87e+00 1gp1A c.47.1.10 33059 1tqnA 486 2.89e+00 1oaoC 729 2.94e+00 e.26.1.3 86746 1ru3A 732 2.98e+00 e.26.1.3 -12021 1f20A 435 2.98e+00 b.43.4.1 64932 c.25.1.4 64933 1ekfA 365 3.09e+00 1ekfA e.17.1.1 59445 1bpv 112 3.12e+00 1bpv b.1.2.1 22071 1vhoA 346 3.32e+00 unknown_sccs -4283 c.56.5.4 -7893 1bc8C 93 3.39e+00 1awcA a.4.5.21 16168 1e7uA 961 3.42e+00 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1aogA 485 3.45e+00 3grs c.3.1.5 30517 c.3.1.5 30518 d.87.1.1 40190 1a3yA 149 3.46e+00 1obpA b.60.1.1 27110 1svr 114 3.54e+00 1svy d.109.1.1 40833 1m1cA 680 3.60e+00 e.42.1.1 78395 2hft 218 3.74e+00 1boy b.1.2.1 21951 b.1.2.1 21952 1e0tA 470 3.84e+00 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1l2tA 235 3.91e+00 c.37.1.12 73514 1bj8 109 4.11e+00 1bquA b.1.2.1 22070 1dzkA 157 4.13e+00 1obpA b.60.1.1 27096 1hn2A 159 4.17e+00 b.60.1.1 65890 1jeqA 609 4.29e+00 1jeqA a.140.2.1 64748 unknown_sccs -4427 unknown_sccs -7991 1a65A 504 4.42e+00 1a65A b.6.1.3 23148 b.6.1.3 23149 b.6.1.3 23150 4rnpA 883 4.51e+00 1cezA e.8.1.3 43113 1danU 121 4.53e+00 1boy b.1.2.1 21954 1mo9A 523 4.75e+00 c.3.1.5 79341 c.3.1.5 79342 d.87.1.1 79343 2dpmA 284 4.76e+00 2dpmA c.66.1.28 34246 1hfuA 503 4.86e+00 b.6.1.3 65827 b.6.1.3 65828 b.6.1.3 65829 1kt9A 138 4.99e+00 d.113.1.1 72959 1uwwA 191 5.03e+00 8ohm 435 5.06e+00 1heiA c.37.1.14 32469 c.37.1.14 32470 1qr4A 186 5.20e+00 1qr4B b.1.2.1 21986 b.1.2.1 21987 1bquA 215 5.22e+00 1bquA b.1.2.1 22066 b.1.2.1 22067 1tlk 154 5.31e+00 1tlk b.1.1.4 21707 1jhnA 424 5.68e+00 b.29.1.12 70060 b.104.1.1 66722 1dmaA 214 5.93e+00 1aerA d.166.1.1 42251 1hm9A 468 6.00e+00 b.81.1.4 65866 c.68.1.5 65867 1on0A 158 6.09e+00 d.108.1.1 87095 1lvoA 302 6.14e+00 b.47.1.4 74284 1q3kA 259 6.15e+00 unknown_sccs -6335 1k42A 168 6.30e+00 b.18.1.14 72032 1th8A 145 6.52e+00 1obpA 159 6.63e+00 1obpA b.60.1.1 27092 1l0oA 150 6.70e+00 d.122.1.3 73403 1gt1A 159 7.13e+00 b.60.1.1 -4436 1ktgA 138 7.18e+00 d.113.1.1 72972 1uvjA 664 7.30e+00 e.8.1.6 -11964 1aa8A 347 7.50e+00 1an9A 1rie 129 7.50e+00 1rie b.33.1.1 24427 1j1uA 306 7.64e+00 c.26.1.1 83980 1hhsA 664 7.65e+00 1hi0P e.8.1.6 61045 1an9A 340 7.79e+00 1an9A c.4.1.2 30617 d.16.1.3 37904 1e19A 314 7.81e+00 1b7bA c.73.1.1 34967 1b9kA 238 7.82e+00 1qtsA b.1.10.1 22315 d.105.1.1 40791 1ve9A 347 7.82e+00 c.4.1.2 -6056 d.16.1.3 -9214 1bxrA 1073 7.93e+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 1mkaA 171 8.00e+00 1mkaA d.38.1.2 38543 1bgj 394 8.08e+00 1pbe c.3.1.2 30352 d.16.1.2 37883 1p5vA 235 8.14e+00 b.1.11.1 87812 b.7.2.1 87813 1kt8A 365 8.55e+00 e.17.1.1 77531 1g97A 459 8.72e+00 1fwyA b.81.1.4 60394 c.68.1.5 60395 1p9uA 302 8.72e+00 b.47.1.4 88001 1qr4B 186 8.79e+00 1qr4B b.1.2.1 21988 b.1.2.1 21989 1k0wA 231 9.12e+00 c.74.1.1 77220 1ktaA 365 9.12e+00 e.17.1.1 77533 1qwtA 255 9.24e+00 unknown_sccs -3329 1o94A 729 9.27e+00 c.1.4.1 81200 c.3.1.1 81201 c.4.1.1 81202 1qtsA 247 9.48e+00 1qtsA b.1.10.1 22313 d.105.1.1 40789 1jdiA 231 9.66e+00 c.74.1.1 66551 1ipwA 175 9.67e+00 2prd b.40.5.1 25427 1a49A 530 9.67e+00 1a49A b.58.1.1 27026 c.1.12.1 29255 c.49.1.1 33109 1xgsA 295 9.72e+00 1bn5 a.4.5.25 16216 d.127.1.1 41153 1tif 78 9.85e+00 1tif d.15.8.1 37836 1gu7A 364 9.87e+00 b.35.1.2 83321 c.2.1.1 83322 1e3jA 352 9.89e+00 1e3jA b.35.1.2 24765 c.2.1.1 29781 1lmzA 187 9.90e+00 a.96.1.4 74037 1q8iA 783 1.01e+01 c.55.3.5 -7635 e.8.1.1 -11885 1i05A 180 1.03e+01 1mup b.60.1.1 27130 1o0wA 252 1.03e+01 a.149.1.1 80751 d.50.1.1 80752 1sty 150 1.05e+01 1snc b.40.1.1 24812 1l4iA 206 1.05e+01 b.1.11.1 73564 b.7.2.1 73565 1sb0A 87 1.07e+01 a.12.1.1 -455 1j0hA 588 1.10e+01 b.1.18.2 77027 b.71.1.1 77028 c.1.8.1 77029 1ebaA 215 1.11e+01 1eerB b.1.2.1 22015 b.1.2.1 22016 1cj3A 392 1.14e+01 1pbe c.3.1.2 30347 d.16.1.2 37878 1kq6A 141 1.15e+01 d.189.1.1 -9926 1cknA 330 1.17e+01 1ckmA b.40.4.6 25360 d.142.2.3 41587 1gpiA 431 1.20e+01 b.29.1.10 65450 1kngA 156 1.20e+01 c.47.1.10 72777 1kyfA 247 1.21e+01 b.1.10.1 73220 d.105.1.1 73221 1keeC 1073 1.23e+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 1p4uA 153 1.23e+01 b.1.10.2 87780 1ey4A 149 1.24e+01 1snc b.40.1.1 24815 1i50B 1224 1.24e+01 e.29.1.1 61755 1pxvA 183 1.29e+01 d.3.1.1 -8881 1gd5A 130 1.30e+01 1gd5A d.189.1.1 60439 1c24A 263 1.30e+01 1c24A d.127.1.1 41148 1pbgA 468 1.32e+01 1e70M c.1.8.4 28946 1cs0C 1073 1.33e+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 1c3oC 1073 1.39e+01 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 1fhgA 154 1.40e+01 1tlk b.1.1.4 21706 1jkxA 212 1.40e+01 c.65.1.1 66813 2matA 264 1.42e+01 1c24A d.127.1.1 41146 1o7kA 131 1.43e+01 d.189.1.1 81144 2tmdA 729 1.44e+01 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1keeE 1073 1.45e+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 1a9xA 1058 1.46e+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 1f15A 218 1.47e+01 1f15B b.121.4.5 23320 1svq 114 1.48e+01 1svy d.109.1.1 40832 1ckmA 330 1.49e+01 1ckmA b.40.4.6 25358 d.142.2.3 41585 1hi0P 664 1.49e+01 1hi0P e.8.1.6 61051 1qreA 247 1.50e+01 1qreA b.81.1.5 28066 3bamA 213 1.51e+01 1bam c.52.1.3 33288 1dq3A 454 1.52e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1fxzA 476 1.55e+01 b.82.1.2 65059 b.82.1.2 65060 1f15B 218 1.56e+01 1f15B b.121.4.5 23321 1jkgA 140 1.57e+01 d.17.4.2 66795 1ux6A 350 1.62e+01 unknown_sccs -3451 unknown_sccs -12886 1ejrC 567 1.64e+01 1ubpC b.92.1.1 28420 c.1.9.2 29042 1c9oA 66 1.64e+01 1mjc b.40.4.5 25325 1fwcC 567 1.66e+01 1ubpC b.92.1.1 28410 c.1.9.2 29032 1gl4B 98 1.67e+01 b.1.1.4 65288 1i06A 180 1.73e+01 1mup b.60.1.1 27131 1k8hA 133 1.76e+01 b.111.1.1 72176 1djnA 729 1.77e+01 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 1n0uA 842 1.78e+01 b.43.3.1 79757 c.37.1.8 79758 d.14.1.1 79759 d.58.11.1 79760 d.58.11.1 79761 1p7hL 286 1.80e+01 b.1.18.1 -2700 b.2.5.3 -2894 1rx0A 393 1.80e+01 a.29.3.1 -742 e.6.1.1 -11858 1kdxA 81 1.83e+01 1kdxA a.12.1.1 16375 1ej6D 418 1.84e+01 i.7.1.1 45970 1cyx 205 1.84e+01 1cyx b.6.1.2 23023 1g3kA 174 1.85e+01 1nedA d.153.1.4 41989 1r94A 118 1.86e+01 b.124.1.1 -4402 1odkA 235 1.88e+01 c.56.2.1 86863 1c3oA 1073 1.90e+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 3bamB 213 1.91e+01 1bam c.52.1.3 33289 1glv 303 1.91e+01 1gsa c.30.1.3 31721 d.142.1.1 41480 1dg6A 191 1.93e+01 1d4vB b.22.1.1 23883 1cd8 114 1.95e+01 1cd8 b.1.1.1 19714 1gv4A 528 1.96e+01 c.3.1.5 70589 c.3.1.5 70590 d.87.1.1 70591 1hyp 80 1.98e+01 1hyp a.52.1.1 17806 1c3oE 1073 2.01e+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 1keeA 1073 2.01e+01 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 1csp 67 2.02e+01 1mjc b.40.4.5 25321 1iw7C 1119 2.05e+01 e.29.1.1 71474 1pkn 530 2.10e+01 1a49A b.58.1.1 27042 c.1.12.1 29271 c.49.1.1 33125 2tgi 112 2.13e+01 2tgi g.17.1.2 44777 1aerA 205 2.14e+01 1aerA d.166.1.1 42249 1vjqA 79 2.17e+01 unknown_sccs -13478 1mjc 69 2.20e+01 1mjc b.40.4.5 25319 1kcw 1046 2.25e+01 1kcw b.6.1.3 23151 b.6.1.3 23152 b.6.1.3 23153 b.6.1.3 23154 b.6.1.3 23155 b.6.1.3 23156 1fdr 248 2.25e+01 1fdr b.43.4.2 25653 c.25.1.1 31543 1jdbB 1073 2.27e+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 1c8pA 102 2.28e+01 1c8pA b.1.2.1 22040 1jn5A 140 2.32e+01 d.17.4.2 66921 1nfiA 301 2.33e+01 1a3qA b.1.18.1 21942 b.2.5.3 22455 1n0lA 224 2.36e+01 b.1.11.1 79744 b.7.2.1 79745 1l7lA 121 2.37e+01 b.18.1.16 77790 1ebpA 211 2.39e+01 1eerB b.1.2.1 22023 b.1.2.1 22024 1k0iA 394 2.40e+01 c.3.1.2 67942 d.16.1.2 67943 1pl8A 356 2.40e+01 b.35.1.2 -3716 c.2.1.1 -5740 1keeG 1073 2.44e+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 1c3oG 1073 2.48e+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 1tm0A 350 2.48e+01 1a8p 258 2.49e+01 1fdr b.43.4.2 25654 c.25.1.1 31544 1nfiC 301 2.50e+01 b.1.18.1 21943 b.2.5.3 22456 1k8kC 372 2.50e+01 b.69.4.1 68308 1nslA 184 2.50e+01 d.108.1.1 86137 1e42A 258 2.51e+01 1e42A b.1.10.1 22316 d.105.1.1 40792 1pbe 394 2.52e+01 1pbe c.3.1.2 30338 d.16.1.2 37869 1ufhA 180 2.53e+01 d.108.1.1 88485 1iarB 207 2.55e+01 1iarB b.1.2.1 22037 b.1.2.1 22038 1g1cA 99 2.57e+01 b.1.1.4 65078 1m4jA 142 2.60e+01 d.109.1.2 78602 1oh0A 131 2.65e+01 d.17.4.3 87004 4bcl 366 2.65e+01 4bcl b.75.1.1 27968 1ejxC 567 2.66e+01 b.92.1.1 83184 c.1.9.2 83185 1qy1A 174 2.67e+01 b.60.1.1 -4445 1knwA 425 2.69e+01 b.49.2.3 -4274 c.1.6.1 -5229 1twdA 256 2.72e+01 1m7vA 363 2.72e+01 d.174.1.1 78748 1d4vB 163 2.73e+01 1d4vB b.22.1.1 23884 1ihuA 589 2.73e+01 c.37.1.10 62394 c.37.1.10 62395 4matA 278 2.74e+01 1c24A d.127.1.1 41150 1i8kA 107 2.76e+01 b.1.1.1 71130 1m6iA 493 2.77e+01 c.3.1.5 74533 c.3.1.5 74534 d.87.1.1 74535 1b7bA 310 2.79e+01 1b7bA c.73.1.1 34963 1ffkU 91 2.81e+01 1ffkU d.29.1.1 38458 1g13A 162 2.84e+01 1g13A b.95.1.1 60194 1q0uA 219 2.85e+01 c.37.1.19 -7205 1fna 93 2.91e+01 1fnf b.1.2.1 21971 4ubpC 570 2.92e+01 1ubpC b.92.1.1 28431 c.1.9.2 29053 1jvwA 167 2.94e+01 d.26.1.1 71907 1l2mA 118 2.97e+01 d.89.1.4 77657 1g7tA 594 2.98e+01 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1aipE 405 3.00e+01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1ie7C 570 3.01e+01 1ubpC b.92.1.1 62315 c.1.9.2 62316 1i50C 318 3.02e+01 d.74.3.1 61756 d.181.1.1 61757 1gdtA 183 3.12e+01 2rslA a.4.1.2 16021 c.53.1.1 33348 1pfiA 46 3.15e+01 1pfiA h.1.4.1 45558 1q0sA 259 3.21e+01 c.66.1.28 -8110 1bo1A 416 3.21e+01 1bo1A d.143.1.2 41591 1mx3A 347 3.27e+01 c.2.1.4 79638 c.23.12.1 79639 1b5pA 385 3.28e+01 c.67.1.1 -8133 1jayA 212 3.28e+01 c.2.1.6 66478 1bp3B 211 3.29e+01 1axiB b.1.2.1 22031 b.1.2.1 22032 1h61A 364 3.29e+01 1oyc c.1.4.1 60657 1jg8A 347 3.30e+01 1jg8A c.67.1.1 62946 1qtoA 122 3.31e+01 1bylA d.32.1.2 38494 1q9uA 130 3.41e+01 unknown_sccs -11025 1ubpC 570 3.42e+01 1ubpC b.92.1.1 28432 c.1.9.2 29054 1avaC 181 3.43e+01 1avaC b.42.4.1 25604 1qg0A 308 3.44e+01 1fnc b.43.4.2 25639 c.25.1.1 31529 1louA 101 3.44e+01 1ris d.58.14.1 39323 1liuA 528 3.44e+01 b.58.1.1 77970 c.1.12.1 77971 c.49.1.1 77972 1fdo 715 3.49e+01 2napA b.52.2.2 26917 c.81.1.1 35325 1si7A 369 3.49e+01 unknown_sccs -10163 1a9v 129 3.52e+01 1a9v b.1.18.7 21946 1fo1A 271 3.56e+01 1fo1A c.10.2.3 30869 d.58.7.2 39213 1h6yA 170 3.58e+01 b.18.1.7 70904 1uc8A 280 3.58e+01 unknown_sccs -6718 unknown_sccs -11230 1g4fA 86 3.58e+01 1qubA g.18.1.1 44873 1r26A 125 3.59e+01 c.47.1.1 -7389 1gnwA 211 3.61e+01 1gnwA a.45.1.1 17727 c.47.1.5 33021 1jmcA 246 3.62e+01 1jmcA b.40.4.3 25300 b.40.4.3 25301 1q15A 503 3.68e+01 c.26.2.1 -6625 d.153.1.1 -11400 1tfg 112 3.68e+01 2tgi g.17.1.2 44778 1eudA 311 3.72e+01 2scuA c.2.1.8 30312 c.23.4.1 31140 1ts3A 194 3.72e+01 1aw7A b.40.2.2 25168 d.15.6.1 37757 1m6sA 347 3.73e+01 c.67.1.1 78701 1pba 81 3.75e+01 1pytA d.58.3.1 39067 1fc1A 224 3.76e+01 1igtB b.1.1.2 21520 b.1.1.2 21521 1nykA 165 3.80e+01 b.33.1.1 86408 1c1lA 136 3.81e+01 1c1lA b.29.1.3 24219 1vavA 222 3.82e+01 2scuA 288 3.82e+01 2scuA c.2.1.8 30303 c.23.4.1 31131 1kezA 300 3.85e+01 c.69.1.22 68546 1i4wA 353 3.88e+01 c.66.1.24 66028 1vyrA 364 3.90e+01 1ns5A 155 3.96e+01 c.116.1.3 80705 3cd4 182 3.97e+01 1cdy b.1.1.1 19720 b.1.1.3 21659 1feuA 206 3.97e+01 1feuA b.53.1.1 59801 1cdy 178 3.98e+01 1cdy b.1.1.1 19719 b.1.1.3 21658 1vypX 364 3.99e+01