# 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 1nb8A 353 3.59e-53 d.3.1.9 80385 1hleA 345 2.96e-02 1ovaA e.1.1.1 42618 1d1vA 444 3.89e-02 1nseA d.174.1.1 59101 1ed5A 444 4.18e-02 1nseA d.174.1.1 42530 1nseA 444 4.41e-02 1nseA d.174.1.1 42534 5nseA 444 5.57e-02 d.174.1.1 74644 1d0cA 444 5.63e-02 d.174.1.1 64769 1as4A 341 5.97e-02 1sek e.1.1.1 42623 1ogwA 76 1.25e-01 d.15.1.1 87001 1ubi 76 1.29e-01 1ubi d.15.1.1 37584 1ubq 76 1.29e-01 1ubi d.15.1.1 37585 1d3zA 76 1.48e-01 1ubi d.15.1.1 37592 1lm8B 118 1.54e-01 d.15.1.1 74033 1vcbA 118 1.80e-01 1vcbA d.15.1.1 37603 1fiy 883 4.00e-01 1fiy c.1.12.3 29307 1ksfX 758 4.41e-01 a.174.1.1 77522 c.37.1.20 77523 c.37.1.20 77524 1mdaH 368 5.35e-01 2bbkH b.69.2.1 27637 1dbhA 354 5.55e-01 1awe a.87.1.1 18514 b.55.1.1 26967 1gnc 178 6.66e-01 1bgc a.26.1.1 16821 2cas 548 6.75e-01 2cas b.121.5.2 23376 1jqnA 883 7.95e-01 c.1.12.3 77159 1qb4A 883 8.17e-01 c.1.12.3 74640 1dlc 584 9.24e-01 1ciy b.18.1.3 23719 b.77.2.1 27976 f.1.3.1 43391 1gvhA 396 1.03e+00 a.1.1.2 70601 b.43.4.2 70602 c.25.1.5 70603 1l5wA 796 1.13e+00 c.87.1.4 73605 1c8gA 548 1.14e+00 2cas b.121.5.2 23380 1uhgA 385 1.18e+00 e.1.1.1 88491 1k6kA 143 1.55e+00 a.174.1.1 77274 1gm5A 780 1.58e+00 unknown_sccs 65298 b.40.4.9 65299 c.37.1.19 65300 c.37.1.19 65301 1ovaA 386 1.59e+00 1ovaA e.1.1.1 42619 1q1aA 289 1.65e+00 c.31.1.5 -6781 9apiA 347 1.82e+00 1ovaA e.1.1.1 42630 1ih7A 903 1.87e+00 1clqA c.55.3.5 62375 e.8.1.1 62376 1fnnA 389 1.87e+00 1fnnA a.4.5.11 16129 c.37.1.20 32426 1clqA 903 2.29e+00 1clqA c.55.3.5 33717 e.8.1.1 43006 1kfuS 184 2.42e+00 a.39.1.8 68574 1ahpA 797 2.73e+00 1a8i c.87.1.4 35544 1b9rA 105 2.95e+00 1ayfA d.15.4.1 37683 1hc7A 477 3.05e+00 1hc7A c.51.1.1 60938 d.68.5.1 60940 d.104.1.1 60939 1e1oA 504 3.11e+00 1lylA b.40.4.1 25258 d.104.1.1 40714 4dpvZ 584 3.63e+00 2cas b.121.5.2 23377 1cqxA 403 3.66e+00 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1cd9C 175 3.73e+00 1bgc a.26.1.1 16816 1jrrA 382 3.84e+00 e.1.1.1 63256 1alvA 173 3.88e+00 1alvA a.39.1.8 17370 1hkfA 122 3.93e+00 b.1.1.1 83553 1f82A 424 4.31e+00 1f82A d.92.1.7 40307 1nddA 76 4.39e+00 1ubi d.15.1.1 37599 1nddD 76 4.53e+00 1ubi d.15.1.1 37602 1eg3A 261 5.00e+00 1eg3A a.39.1.7 17376 a.39.1.7 17377 b.72.1.1 27805 1lylA 504 5.14e+00 1lylA b.40.4.1 25261 d.104.1.1 40717 1mtpA 323 5.42e+00 e.1.1.1 85107 1rpa 342 5.78e+00 1cviA c.60.1.2 33983 1jjoC 261 6.10e+00 1ts3A 194 6.25e+00 1aw7A b.40.2.2 25168 d.15.6.1 37757 1osa 148 6.26e+00 1cll a.39.1.5 17300 1f0cA 305 6.36e+00 1c8oA e.1.1.1 42676 1bmlC 362 6.52e+00 1bmlC d.15.5.1 37729 d.15.5.1 37730 d.15.5.1 37731 1a81A 254 6.63e+00 1a81A d.93.1.1 40507 d.93.1.1 40508 1ki1B 352 6.76e+00 a.87.1.1 72497 b.55.1.1 72498 1f2eA 201 7.10e+00 1a0fA a.45.1.1 17745 c.47.1.5 33039 1b4cA 92 7.36e+00 1b4cA a.39.1.2 17169 1uurA 473 8.38e+00 a.47.1.1 -968 b.2.5.5 -2904 d.93.1.1 -10632 1b47A 304 8.91e+00 2cblA a.39.1.7 17381 a.48.1.1 17775 d.93.1.1 40529 1hjp 203 9.04e+00 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1exrA 148 9.24e+00 1cll a.39.1.5 17299 1qlpA 394 9.31e+00 1ovaA e.1.1.1 42628 2cblA 305 9.96e+00 2cblA a.39.1.7 17380 a.48.1.1 17774 d.93.1.1 40528 1mi1A 414 1.05e+01 a.169.1.1 79137 b.55.1.6 79138 1lt3A 240 1.05e+01 1lt3A d.166.1.1 42230 1avsA 90 1.06e+01 1cll a.39.1.5 17226 1nzjA 298 1.07e+01 c.26.1.1 -6600 1sek 378 1.12e+01 1sek e.1.1.1 42675 1gc1H 229 1.13e+01 1gc1H b.1.1.1 20265 b.1.1.2 21265 1bt0A 76 1.16e+01 1ubi d.15.1.1 37607 1lkoA 191 1.20e+01 a.25.1.1 78063 g.41.5.1 78064 1jeyB 565 1.21e+01 1jeqB unknown_sccs -4431 unknown_sccs -7995 1ng7A 60 1.25e+01 a.178.1.1 85671 1mho 88 1.26e+01 1b4cA a.39.1.2 17171 1ej2A 181 1.30e+01 1f9aA c.26.1.3 59414 1f83A 425 1.32e+01 1f82A d.92.1.7 40306 2masA 314 1.34e+01 2masA c.70.1.1 34810 1b5pA 385 1.34e+01 c.67.1.1 -8133 1qxyA 252 1.36e+01 d.127.1.1 -10993 1sqgA 429 1.37e+01 1ryt 190 1.38e+01 1ryt a.25.1.1 16646 g.41.5.1 45245 1a8i 842 1.47e+01 1a8i c.87.1.4 35490 1vh4A 435 1.48e+01 unknown_sccs -4794 1dvbA 191 1.55e+01 1ryt a.25.1.1 16645 g.41.5.1 45244 1mijA 152 1.57e+01 a.4.1.1 79150 1lla 628 1.57e+01 1lla a.85.1.1 18485 a.86.1.1 18496 b.1.18.3 21861 1a8h 500 1.68e+01 1a8h a.27.1.1 16922 c.26.1.1 31589 1nofA 383 1.74e+01 b.71.1.2 -4668 c.1.8.3 -5339 1kxrA 339 1.76e+01 d.3.1.3 73175 2dvh 79 1.79e+01 1c53 a.3.1.1 15803 1qhhA 167 1.82e+01 1pjr c.37.1.19 32393 1b71A 191 1.85e+01 1ryt a.25.1.1 16647 g.41.5.1 45246 1mugA 168 1.85e+01 1mugA c.18.1.2 31030 1fgqA 839 1.87e+01 1yge a.119.1.1 59826 b.12.1.1 59827 1nb5I 98 1.88e+01 d.17.1.2 80381 1bq9A 54 1.92e+01 1rb9 g.41.5.1 45238 1bgeB 175 1.95e+01 1bgc a.26.1.1 16824 1sjwA 144 2.01e+01 unknown_sccs -9296 1l1oC 181 2.02e+01 b.40.4.3 73480 1a7cA 379 2.04e+01 1sek e.1.1.1 42660 1gdoB 240 2.05e+01 1gdoA d.153.1.1 41805 1bq8A 54 2.11e+01 1rb9 g.41.5.1 45237 1rdg 53 2.13e+01 1rb9 g.41.5.1 45221 1h5uA 842 2.15e+01 1a8i c.87.1.4 60655 1qwyA 291 2.19e+01 unknown_sccs -5023 1brfA 53 2.20e+01 1rb9 g.41.5.1 45236 1jeqB 565 2.21e+01 1jeqB unknown_sccs -4432 unknown_sccs -7996 1cuk 203 2.23e+01 1hjp a.5.1.1 16273 a.60.2.1 17946 b.40.4.2 25265 1ggzA 148 2.26e+01 a.39.1.5 70176 1uetA 437 2.28e+01 unknown_sccs -1144 unknown_sccs -9798 unknown_sccs -10058 1vjoA 393 2.31e+01 c.67.1.3 -8173 1guaB 81 2.33e+01 1c1yB d.15.1.5 37619 1mjhB 162 2.35e+01 1mjhA c.26.2.4 31640 1ly7A 121 2.38e+01 d.82.2.1 74339 1fpzA 212 2.47e+01 1fpzA c.45.1.1 59976 1hybA 181 2.51e+01 1f9aA c.26.1.3 61399 1oxxK 353 2.51e+01 b.40.6.3 -3969 c.37.1.12 -7187 1ipiA 123 2.52e+01 c.52.1.18 66255 1lj5A 379 2.59e+01 e.1.1.1 73928 1vhzA 198 2.67e+01 d.113.1.1 -10897 1itg 166 2.69e+01 1b9dA c.55.3.2 33661 1b0zA 445 2.72e+01 2pgi c.80.1.2 35309 2pgi 445 2.72e+01 2pgi c.80.1.2 35308 1kk1A 410 2.80e+01 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 1uwoA 92 2.81e+01 4icb a.39.1.2 17174 1c1yB 77 2.81e+01 1c1yB d.15.1.5 37618 3rnt 104 2.83e+01 9rnt d.1.1.4 36069 1om4A 422 2.86e+01 d.174.1.1 87067 1sva1 361 2.89e+01 1vpsA 1eijA 80 2.90e+01 1eijA a.5.6.1 16298 1i0vA 104 2.93e+01 9rnt d.1.1.4 36054 1l0wA 580 2.94e+01 b.40.4.1 73426 d.74.4.1 73427 d.104.1.1 73428 2pia 321 2.95e+01 2pia b.43.4.2 25663 c.25.1.2 31553 d.15.4.2 37704 9rnt 104 3.01e+01 9rnt d.1.1.4 36055 1jnyA 435 3.02e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1o5zA 442 3.03e+01 c.59.1.2 -7939 c.72.2.2 -8418 1op3H 225 3.05e+01 b.1.1.1 87208 b.1.1.2 87209 1r89A 437 3.09e+01 unknown_sccs -1147 unknown_sccs -9801 unknown_sccs -10061 1nvhA 66 3.18e+01 1j55A 95 3.20e+01 a.39.1.2 77078 1jmxA 494 3.21e+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 1ohuA 175 3.21e+01 f.1.4.1 -12058 1raxA 115 3.25e+01 1lfdA d.15.1.5 37626 1lxdA 100 3.28e+01 1lfdA d.15.1.5 37624 1pa7A 130 3.34e+01 a.40.1.1 -896 1izcA 339 3.40e+01 c.1.12.5 83838 1qxfA 66 3.41e+01 g.41.8.4 -12822 1bjwA 382 3.41e+01 1bjwA c.67.1.1 34349 1euvB 86 3.50e+01 1a5r d.15.1.1 37598 1top 162 3.50e+01 1ncx a.39.1.5 17223 1a28A 256 3.52e+01 1a28A a.123.1.1 19290 1a5r 103 3.52e+01 1a5r d.15.1.1 37597 1oxsC 353 3.54e+01 b.40.6.3 87519 c.37.1.12 87520 1c8kA 842 3.54e+01 1a8i c.87.1.4 35491 1ekgA 127 3.59e+01 1dlxA d.82.2.1 40021 1odfA 290 3.60e+01 c.37.1.6 -7045 1szqA 483 3.60e+01 unknown_sccs -11791 1qj2A 166 3.62e+01 1qj2A 1n62A 166 3.65e+01 a.56.1.1 80090 d.15.4.2 80091 1r6fA 310 3.65e+01 unknown_sccs -11804 1mjhA 162 3.77e+01 1mjhA c.26.2.4 31639 1gajA 257 3.85e+01 1gajA c.37.1.12 60416 1nijA 318 3.85e+01 c.37.1.10 85741 d.237.1.1 85742 1nd7A 374 3.96e+01 d.148.1.1 -11394