# List of top-scoring protein chains for t2k-100-30-str2 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 2.89e-01 a.39.1.8 68574 3fruA 269 4.32e-01 1agdA b.1.1.2 20657 d.19.1.1 38150 1alvA 173 7.48e-01 1alvA a.39.1.8 17370 1q7lA 198 1.16e+00 1bupA 386 2.22e+00 1ba1 c.55.1.1 33377 c.55.1.1 33378 1ln1A 214 2.38e+00 d.129.3.2 74038 1ba1 386 2.44e+00 1ba1 c.55.1.1 33387 c.55.1.1 33388 1kay 381 2.59e+00 1ba1 c.55.1.1 33385 c.55.1.1 33386 1op0A 234 3.12e+00 1taq 832 3.42e+00 1taq a.60.7.1 18082 c.120.1.2 33352 c.55.3.5 33698 e.8.1.1 42991 1psdA 409 4.91e+00 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1un8A 552 5.06e+00 1mmiA 366 5.34e+00 1nffA 260 6.69e+00 c.2.1.2 80457 1suh 146 6.87e+00 1edhA b.1.6.1 22206 3bamA 213 7.44e+00 1bam c.52.1.3 33288 1ewjA 126 7.45e+00 1ecsA d.32.1.2 59526 1ecsA 126 7.60e+00 1ecsA d.32.1.2 59407 1q4uA 151 7.63e+00 1edhA 226 9.21e+00 1edhA b.1.6.1 22198 b.1.6.1 22199 1i0rA 169 9.33e+00 1i0rA b.45.1.2 61489 1i0sA 169 9.33e+00 1i0rA b.45.1.2 61491 1h7xC 1025 1.07e+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 1h7xB 1025 1.08e+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 1h7xD 1025 1.09e+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 1h7xA 1025 1.09e+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 1h7wA 1025 1.10e+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 1h7wB 1025 1.10e+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 1h7wD 1025 1.10e+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 1gteD 1025 1.11e+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 1gthA 1025 1.12e+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 1gt8A 1025 1.13e+01 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 1qh0A 295 1.14e+01 b.43.4.2 68891 c.25.1.1 68892 1ogiA 303 1.16e+01 1gthD 1025 1.18e+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 1que 303 1.18e+01 1fnc b.43.4.2 25647 c.25.1.1 31537 1b2rA 304 1.19e+01 1fnc b.43.4.2 25648 c.25.1.1 31538 1go2A 304 1.19e+01 b.43.4.2 76243 c.25.1.1 76244 1gthC 1025 1.20e+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 1gteA 1025 1.21e+01 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 1.22e+01 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 1h6kA 757 1.26e+01 a.118.1.2 60675 a.118.1.2 60676 a.118.1.2 60677 1gthB 1025 1.28e+01 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 1ohvA 472 1.30e+01 1gt8B 1025 1.32e+01 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 1t8hA 277 1.32e+01 1o12A 376 1.35e+01 b.92.1.5 80758 c.1.9.10 80759 2polA 366 1.35e+01 2polA d.131.1.1 41356 d.131.1.1 41357 d.131.1.1 41358 1gt8C 1025 1.40e+01 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 1mw7A 240 1.41e+01 e.39.1.1 79557 1jvr 137 1.55e+01 1jvr a.61.1.2 18132 1thtA 305 1.59e+01 1thtA c.69.1.13 34711 1stfI 98 1.62e+01 1stfI d.17.1.2 38006 1mwmA 320 1.77e+01 c.55.1.1 79580 c.55.1.1 79581 1dgsA 667 1.78e+01 1dgsA a.60.2.2 17963 b.40.4.6 25365 d.142.2.2 41581 1rwzA 245 1.81e+01 1fo5A 85 1.90e+01 1fo5A c.47.1.1 59922 1mogA 67 1.94e+01 d.230.2.1 85034 1spbP 78 1.95e+01 1scjB d.58.3.2 39068 1lhpA 312 1.97e+01 c.72.1.5 77960 1xgsA 295 2.00e+01 1bn5 a.4.5.25 16216 d.127.1.1 41153 1ufoA 238 2.05e+01 1nw1A 429 2.14e+01 d.144.1.8 86286 1obwA 175 2.14e+01 2prd b.40.5.1 25416 1qnrA 344 2.15e+01 1qnoA c.1.8.3 28834 1qnoA 344 2.17e+01 1qnoA c.1.8.3 28838 1ayaA 101 2.19e+01 1qadA d.93.1.1 40460 1i40A 175 2.23e+01 b.40.5.1 66024 1ako 268 2.31e+01 1ako d.151.1.1 41779 1j27A 102 2.40e+01 1gtxA 472 2.41e+01 1gtxA c.67.1.4 34464 1fj2A 232 2.53e+01 1auoA c.69.1.14 34720 1scjB 71 2.54e+01 1scjB d.58.3.2 39069 1zac 90 2.55e+01 1ncx a.39.1.5 17236 1n13B 113 2.63e+01 1o6sB 105 2.67e+01 b.1.6.1 81096 1i7dA 659 2.77e+01 1d6mA e.10.1.1 61886 1b54 257 2.84e+01 1ct5A c.1.6.2 28664 1r5pA 108 2.85e+01 1e3yA 104 2.88e+01 1fadA a.77.1.2 18426 1top 162 2.97e+01 1ncx a.39.1.5 17223 1ncx 162 2.97e+01 1ncx a.39.1.5 17222 1lo6A 223 2.99e+01 b.47.1.2 74143 1bueA 265 3.05e+01 1btl e.3.1.1 42727 1edzA 320 3.41e+01 1ee9A c.2.1.7 30287 c.58.1.2 33935 1muhA 481 3.42e+01 c.55.3.4 79485 1bfeA 119 3.52e+01 1pdr b.36.1.1 24775 1auz 116 3.53e+01 1auz c.13.2.1 30883 1ipwA 175 3.57e+01 2prd b.40.5.1 25427 1ltqA 301 3.75e+01 c.108.1.9 78208 c.37.1.1 78209 1ee9A 320 3.82e+01 1ee9A c.2.1.7 30288 c.58.1.2 33936 1f5vA 240 3.92e+01 1bkjA d.90.1.1 40255 1j3mA 129 3.92e+01 1o6jA 150 3.95e+01 c.47.1.10 81089 1esgA 213 3.98e+01 1bam c.52.1.3 33286