# 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 1nb8A 353 1.77e-46 d.3.1.9 80385 1ubi 76 3.27e-03 1ubi d.15.1.1 37584 1ogwA 76 2.16e-02 d.15.1.1 87001 1d3zA 76 2.42e-02 1ubi d.15.1.1 37592 1ubq 76 2.84e-02 1ubi d.15.1.1 37585 1c8gA 548 1.61e-01 2cas b.121.5.2 23380 1nddA 76 2.81e-01 1ubi d.15.1.1 37599 1vcbA 118 3.79e-01 1vcbA d.15.1.1 37603 1kfuS 184 3.95e-01 a.39.1.8 68574 1nddD 76 4.21e-01 1ubi d.15.1.1 37602 1hkfA 122 5.19e-01 b.1.1.1 83553 1lm8B 118 6.99e-01 d.15.1.1 74033 2cas 548 7.85e-01 2cas b.121.5.2 23376 1hleA 345 8.76e-01 1ovaA e.1.1.1 42618 1mdaH 368 9.64e-01 2bbkH b.69.2.1 27637 1qb4A 883 9.83e-01 c.1.12.3 74640 1ng7A 60 1.02e+00 a.178.1.1 85671 1fiy 883 1.10e+00 1fiy c.1.12.3 29307 4dpvZ 584 1.12e+00 2cas b.121.5.2 23377 1jqnA 883 1.13e+00 c.1.12.3 77159 1bt0A 76 1.14e+00 1ubi d.15.1.1 37607 1ih7A 903 1.25e+00 1clqA c.55.3.5 62375 e.8.1.1 62376 1ed5A 444 1.52e+00 1nseA d.174.1.1 42530 1d1vA 444 1.61e+00 1nseA d.174.1.1 59101 1d0cA 444 1.73e+00 d.174.1.1 64769 1osa 148 1.77e+00 1cll a.39.1.5 17300 1alvA 173 1.91e+00 1alvA a.39.1.8 17370 1exrA 148 2.11e+00 1cll a.39.1.5 17299 1nseA 444 2.14e+00 1nseA d.174.1.1 42534 1clqA 903 2.19e+00 1clqA c.55.3.5 33717 e.8.1.1 43006 1rdg 53 2.21e+00 1rb9 g.41.5.1 45221 1a0p 290 2.26e+00 1a0p a.60.9.1 18105 d.163.1.1 42165 5nseA 444 2.39e+00 d.174.1.1 74644 1vh4A 435 2.52e+00 unknown_sccs -4794 1k6kA 143 2.59e+00 a.174.1.1 77274 1uurA 473 2.64e+00 a.47.1.1 -968 b.2.5.5 -2904 d.93.1.1 -10632 1q1aA 289 2.86e+00 c.31.1.5 -6781 1fvuB 125 3.73e+00 1ixxB d.169.1.1 42346 1eg3A 261 4.09e+00 1eg3A a.39.1.7 17376 a.39.1.7 17377 b.72.1.1 27805 1ni3A 392 4.65e+00 c.37.1.8 80531 d.15.10.2 80532 1gnc 178 4.68e+00 1bgc a.26.1.1 16821 1itbB 315 4.91e+00 1itbB b.1.1.4 21720 b.1.1.4 21721 b.1.1.4 21722 1brfA 53 5.01e+00 1rb9 g.41.5.1 45236 1bq9A 54 5.23e+00 1rb9 g.41.5.1 45238 1bq8A 54 5.66e+00 1rb9 g.41.5.1 45237 1mjhB 162 5.93e+00 1mjhA c.26.2.4 31640 1gm5A 780 6.52e+00 unknown_sccs 65298 b.40.4.9 65299 c.37.1.19 65300 c.37.1.19 65301 1hc7A 477 6.92e+00 1hc7A c.51.1.1 60938 d.68.5.1 60940 d.104.1.1 60939 1kt8A 365 7.83e+00 e.17.1.1 77531 1qxfA 66 8.20e+00 g.41.8.4 -12822 1sqgA 429 8.56e+00 1mjhA 162 8.57e+00 1mjhA c.26.2.4 31639 1hcxA 127 8.67e+00 b.109.1.1 65800 1gvmA 136 8.84e+00 b.109.1.1 70612 1psrA 100 9.12e+00 1psrA a.39.1.2 17180 1l1oC 181 9.20e+00 b.40.4.3 73480 1ekfA 365 9.50e+00 1ekfA e.17.1.1 59445 1b4cA 92 1.06e+01 1b4cA a.39.1.2 17169 1meyC 87 1.08e+01 2gliA k.12.1.1 46430 1ktaA 365 1.26e+01 e.17.1.1 77533 1onqA 283 1.28e+01 b.1.1.2 -2640 d.19.1.1 -9390 1tfi 50 1.29e+01 1tfi g.41.3.1 45204 1b06A 210 1.31e+01 1avmA a.2.11.1 15740 d.44.1.1 38737 1exzA 141 1.31e+01 1exzA a.26.1.2 16877 1k8kC 372 1.31e+01 b.69.4.1 68308 1gvhA 396 1.32e+01 a.1.1.2 70601 b.43.4.2 70602 c.25.1.5 70603 1mtpA 323 1.33e+01 e.1.1.1 85107 3aig 202 1.41e+01 1atlA d.92.1.9 40321 1jeqB 565 1.41e+01 1jeqB unknown_sccs -4432 unknown_sccs -7996 1r89A 437 1.46e+01 unknown_sccs -1147 unknown_sccs -9801 unknown_sccs -10061 1qbqA 333 1.47e+01 1ft1A a.118.6.1 19187 1uetA 437 1.54e+01 unknown_sccs -1144 unknown_sccs -9798 unknown_sccs -10058 1mijA 152 1.56e+01 a.4.1.1 79150 1qmpA 130 1.56e+01 1dz3A c.23.1.1 31106 1czaN 917 1.57e+01 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1ba1 386 1.63e+01 1ba1 c.55.1.1 33387 c.55.1.1 33388 9apiA 347 1.65e+01 1ovaA e.1.1.1 42630 1kf6A 602 1.68e+01 a.7.3.1 72394 c.3.1.4 72395 d.168.1.1 72396 1qk8A 146 1.70e+01 1ewxA c.47.1.10 33061 1lshA 1056 1.74e+01 a.118.4.1 74242 f.7.1.1 74243 f.7.1.1 74244 1dx8A 70 1.78e+01 1rb9 g.41.5.1 45243 1ncx 162 1.78e+01 1ncx a.39.1.5 17222 1duzA 275 1.79e+01 1agdA b.1.1.2 20670 d.19.1.1 38224 1hkbA 917 1.80e+01 1qhaA c.55.1.3 33479 c.55.1.3 33480 c.55.1.3 33481 c.55.1.3 33482 1ash 150 1.82e+01 1ash a.1.1.2 15622 1i4fA 275 1.84e+01 1agdA b.1.1.2 61687 d.19.1.1 61688 1cd9C 175 1.92e+01 1bgc a.26.1.1 16816 1o8xA 146 1.96e+01 c.47.1.10 86681 1rms 105 1.98e+01 9rnt d.1.1.4 36235 1jjoC 261 2.01e+01 1dz3A 130 2.05e+01 1dz3A c.23.1.1 31105 1rds 105 2.07e+01 9rnt d.1.1.4 36236 1q8iA 783 2.11e+01 c.55.3.5 -7635 e.8.1.1 -11885 1bupA 386 2.14e+01 1ba1 c.55.1.1 33377 c.55.1.1 33378 1sjwA 144 2.15e+01 unknown_sccs -9296 1j55A 95 2.16e+01 a.39.1.2 77078 1cll 148 2.16e+01 1cll a.39.1.5 17263 1nkr 201 2.19e+01 1nkr b.1.1.4 21799 b.1.1.4 21800 1kay 381 2.20e+01 1ba1 c.55.1.1 33385 c.55.1.1 33386 1dgkN 917 2.20e+01 1qhaA c.55.1.3 33487 c.55.1.3 33488 c.55.1.3 33489 c.55.1.3 33490 1lkvX 232 2.21e+01 a.118.14.1 73980 1l3kA 196 2.23e+01 d.58.7.1 73539 d.58.7.1 73540 1avsA 90 2.23e+01 1cll a.39.1.5 17226 1ithA 141 2.28e+01 1ithA a.1.1.2 15623 1g2fC 90 2.30e+01 k.12.1.1 60222 1ggzA 148 2.31e+01 a.39.1.5 70176 1f82A 424 2.37e+01 1f82A d.92.1.7 40307 1jp3A 253 2.41e+01 1f75A c.101.1.1 63221 1bgp 309 2.45e+01 1bgp a.93.1.1 18690 1kmiZ 214 2.46e+01 h.4.11.1 72752 6rxn 46 2.53e+01 1rb9 g.41.5.1 45222 1pb6A 212 2.58e+01 a.4.1.9 88017 a.121.1.1 88018 1cqxA 403 2.59e+01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1r13A 148 2.60e+01 d.169.1.1 -11646 h.1.1.1 -12895 1fnnA 389 2.61e+01 1fnnA a.4.5.11 16129 c.37.1.20 32426 1faq 52 2.67e+01 1far g.49.1.1 45352 6prcL 273 2.68e+01 6prcL f.26.1.1 43434 1as4A 341 2.69e+01 1sek e.1.1.1 42623 1hr6A 475 2.72e+01 1hr6A d.185.1.1 61164 d.185.1.1 61165 1k5nA 276 2.74e+01 b.1.1.2 77266 d.19.1.1 77267 1sr7A 259 2.74e+01 1ewxA 146 2.80e+01 1ewxA c.47.1.10 33062 1i37A 260 2.81e+01 1a28A a.123.1.1 61583 1kmvA 186 2.85e+01 c.71.1.1 72757 1far 52 2.85e+01 1far g.49.1.1 45351 1sctB 151 2.86e+01 3sdhA a.1.1.2 15003 1rb9 53 2.88e+01 1rb9 g.41.5.1 45214 3rnt 104 2.88e+01 9rnt d.1.1.4 36069 1r75A 141 2.89e+01 unknown_sccs -3243 1top 162 2.92e+01 1ncx a.39.1.5 17223 8rxnA 52 2.96e+01 1rb9 g.41.5.1 45215 1i0vA 104 2.97e+01 9rnt d.1.1.4 36054 1mhyB 395 3.04e+01 1mtyB a.25.1.2 16781 1qlpA 394 3.05e+01 1ovaA e.1.1.1 42628 1jr7A 311 3.06e+01 b.82.2.3 63255 1jeyB 565 3.11e+01 1jeqB unknown_sccs -4431 unknown_sccs -7995 3nodB 423 3.15e+01 1nseA d.174.1.1 42513 1dzoA 123 3.16e+01 1dzoA d.24.1.1 38378 1a28A 256 3.31e+01 1a28A a.123.1.1 19290 1hkcA 917 3.34e+01 1qhaA c.55.1.3 33475 c.55.1.3 33476 c.55.1.3 33477 c.55.1.3 33478 1f83A 425 3.35e+01 1f82A d.92.1.7 40306 1sbp 310 3.37e+01 1sbp c.94.1.1 35760 1ozjA 144 3.38e+01 d.164.1.1 -11537 3cln 148 3.40e+01 1cll a.39.1.5 17286 1v9kA 228 3.41e+01 1jmxA 494 3.47e+01 a.3.1.7 66901 a.3.1.7 66902 b.1.18.14 66903 b.1.18.14 66904 b.61.4.1 66905 1dxrL 273 3.52e+01 6prcL f.26.1.1 43431 1bgeB 175 3.52e+01 1bgc a.26.1.1 16824 1k94A 165 3.57e+01 a.39.1.8 68333 1qc7A 101 3.64e+01 1qc7A a.118.14.1 18456 1fipA 98 3.69e+01 1fipA unknown_sccs 18980 2cpl 165 3.81e+01 2cpl b.62.1.1 27420 1d0nA 729 3.81e+01 1d0nA d.109.1.1 40834 d.109.1.1 40835 d.109.1.1 40836 d.109.1.1 40837 d.109.1.1 40838 d.109.1.1 40839 1dbhA 354 3.82e+01 1awe a.87.1.1 18514 b.55.1.1 26967 1uehA 253 3.91e+01 c.101.1.1 -6879