# List of top-scoring protein chains for t2k-w0.5 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 1lba 146 1.57e-23 1lba d.118.1.1 41062 1aroL 151 1.59e-23 1lba d.118.1.1 41063 1ku1A 230 1.00e-01 1bdfA 235 2.97e-01 1bdfA d.74.3.1 39727 d.181.1.1 42602 1eq9A 222 8.04e-01 5ptp b.47.1.2 26068 1vne 609 8.29e-01 1vns a.111.1.3 19063 1vnh 609 9.67e-01 1vns a.111.1.3 19062 1vns 609 9.80e-01 1vns a.111.1.3 19061 1vnc 609 9.80e-01 1vns a.111.1.3 19065 1iduA 609 1.02e+00 1vns a.111.1.3 62303 1b9vA 390 1.07e+00 2qwc b.68.1.1 27603 1vnf 609 1.08e+00 1vns a.111.1.3 19067 1inf 390 1.08e+00 2qwc b.68.1.1 27602 1b74A 254 1.48e+00 1b74A c.78.2.1 35264 c.78.2.1 35265 1b73A 254 1.48e+00 1b74A c.78.2.1 35266 c.78.2.1 35267 1tlk 154 1.76e+00 1tlk b.1.1.4 21707 1nscA 390 1.80e+00 2qwc b.68.1.1 27591 1fhgA 154 1.80e+00 1tlk b.1.1.4 21706 1k30A 368 2.10e+00 c.112.1.1 68067 1jeoA 180 2.21e+00 c.80.1.3 66611 1jf8A 131 2.76e+00 c.44.1.1 66621 2mcm 112 2.76e+00 2mcm b.1.7.1 22207 1i6lA 328 2.85e+00 c.26.1.1 66041 1jfvA 131 3.07e+00 c.44.1.1 66654 1d2rA 326 3.47e+00 1d2rB c.26.1.1 31572 1d2rB 326 3.47e+00 1d2rB c.26.1.1 31573 1i6mA 328 3.75e+00 c.26.1.1 66042 1jf9A 408 3.99e+00 1c0nA c.67.1.3 62931 1kmjA 406 4.04e+00 c.67.1.3 68695 1djqA 729 4.26e+00 2tmdA c.1.4.1 28614 c.3.1.1 30315 c.4.1.1 30600 1jsdB 176 4.26e+00 h.3.1.1 63259 1djnA 729 4.36e+00 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 2tmdA 729 4.36e+00 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1f2fA 104 4.50e+00 1fmk d.93.1.1 40455 2sli 679 4.87e+00 2sli b.29.1.9 24274 b.68.1.1 27611 4sli 679 4.87e+00 2sli b.29.1.9 24275 b.68.1.1 27612 1rypB 250 5.01e+00 1rypB d.153.1.4 41933 1b8gA 429 5.04e+00 1b8gA c.67.1.4 34499 1hrhA 136 5.20e+00 1rthA c.55.3.1 33577 1rdhA 146 5.50e+00 1rthA c.55.3.1 33588 1lbeA 258 5.84e+00 1lbeA e.4.1.1 42773 1isiA 265 5.85e+00 2dldA 337 6.15e+00 1dxy c.2.1.4 30099 c.23.12.1 31359 1jj2F 119 6.73e+00 1ffkE d.79.3.1 63091 1ffkE 119 6.73e+00 1ffkE d.79.3.1 39812 1jv2B 692 7.79e+00 b.1.15.1 67338 c.62.1.1 67339 d.200.1.1 67340 g.3.11.6 67341 g.3.11.6 67342 1ktgA 138 7.96e+00 1vng 609 8.68e+00 1vns a.111.1.3 19066 1c0nA 406 8.77e+00 1c0nA c.67.1.3 34433 1k7xB 396 9.19e+00 1chkA 238 9.34e+00 1chkA d.2.1.7 36999 1e5dA 402 9.97e+00 1e5dA c.23.5.1 31208 d.157.1.3 42061 1fu5A 111 1.02e+01 1qadA d.93.1.1 40505 1lxa 262 1.06e+01 1lxa b.81.1.1 28052 1qoqB 396 1.07e+01 2tysB c.79.1.1 35271 1jmuB 666 1.08e+01 1qopB 396 1.08e+01 2tysB c.79.1.1 35270 1beuB 397 1.09e+01 2tysB c.79.1.1 35274 2wsyB 396 1.09e+01 2tysB c.79.1.1 35288 1ubsB 397 1.09e+01 2tysB c.79.1.1 35273 2tysB 397 1.10e+01 2tysB c.79.1.1 35272 1bksB 397 1.10e+01 2tysB c.79.1.1 35285 1csyA 112 1.15e+01 1lckA d.93.1.1 40519 1fuyB 396 1.17e+01 2tysB c.79.1.1 35279 1a9cA 221 1.24e+01 1a8rA d.96.1.1 40602 1c8bA 371 1.29e+01 1c8bA c.56.1.2 59082 1fiwA 290 1.34e+01 5ptp 2frvA 264 1.37e+01 2frvA e.19.1.1 43303 1bvaA 294 1.42e+01 1ryc a.93.1.1 18604 1c3pA 375 1.42e+01 1c3pA c.42.1.2 32606 1c3rA 375 1.43e+01 1c3pA c.42.1.2 32607 1qi5A 429 1.44e+01 1jdc b.71.1.1 27792 c.1.8.1 28779 1fnoA 417 1.60e+01 1mup 166 1.63e+01 1mup b.60.1.1 27133 1b65A 375 1.64e+01 1b65A d.154.1.1 42020 1jv4A 162 1.68e+01 b.60.1.1 67343 1i06A 180 1.71e+01 1mup b.60.1.1 27131 1i05A 180 1.71e+01 1mup b.60.1.1 27130 1earA 147 1.72e+01 b.107.1.1 64875 d.58.38.1 64876 1qpkA 418 1.79e+01 1jdc b.71.1.1 27793 c.1.8.1 28780 1chd 203 1.79e+01 1chd c.40.1.1 32478 1qi3A 429 1.80e+01 1jdc b.71.1.1 27794 c.1.8.1 28781 1qi4A 429 1.80e+01 1jdc b.71.1.1 27791 c.1.8.1 28778 1jdc 429 1.81e+01 1jdc b.71.1.1 27789 c.1.8.1 28776 1azzA 226 1.81e+01 5ptp b.47.1.2 26072 2amg 415 1.81e+01 1jdc b.71.1.1 27796 c.1.8.1 28783 1shdA 107 1.85e+01 1fmk d.93.1.1 40440 1kyaA 499 1.92e+01 1eqyS 125 1.95e+01 1d0nA d.109.1.1 40853 1c0gS 127 2.00e+01 1d0nA d.109.1.1 40848 1gcyA 527 2.02e+01 1jdc b.71.1.1 27788 c.1.8.1 28775 1b3oB 514 2.07e+01 1ak5 c.1.5.1 28641 d.37.1.1 38538 d.37.1.1 38539 1a1aA 107 2.12e+01 1fmk d.93.1.1 40449 1frvA 264 2.18e+01 2frvA e.19.1.1 43308 1hfoA 113 2.21e+01 d.80.1.3 61006 1gm6A 175 2.22e+01 1jr1A 514 2.24e+01 c.1.5.1 63241 d.37.1.1 63242 d.37.1.1 63243 1qvbA 481 2.26e+01 1qvbA c.1.8.4 28983 5pal 109 2.41e+01 1a75A a.39.1.4 17215 1dot 686 2.44e+01 1nnt c.94.1.2 35876 c.94.1.2 35877 1lqc 56 2.44e+01 1pru a.35.1.5 17109 1gmlA 178 2.44e+01 1isuA 62 2.52e+01 1isuA g.35.1.1 44978 1a2oA 349 2.56e+01 1chd c.23.1.1 31120 c.40.1.1 32479 1skj 113 2.56e+01 1fmk d.93.1.1 40427 1lccA 51 2.59e+01 1pru a.35.1.5 17110 1lcdA 51 2.59e+01 1pru a.35.1.5 17111 1a91 79 2.63e+01 1a91 f.2.1.4 43635 1c0vA 79 2.63e+01 1a91 f.2.1.4 43634 1ijpA 79 2.64e+01 1a06 332 2.65e+01 1tkiA d.144.1.1 41634 1jhdA 396 2.67e+01 b.58.1.2 66712 c.26.1.5 66713 1bhgA 613 2.70e+01 1bhgA b.1.4.1 22161 b.18.1.5 23766 c.1.8.3 28889 1cjgA 62 2.71e+01 1pru a.35.1.5 17112 1ilvB 247 2.82e+01 c.106.1.1 66207 1a05A 358 2.82e+01 1cnzA c.77.1.1 35059 1is0B 106 2.87e+01 d.93.1.1 66300 1ekjB 221 2.89e+01 1ekjB c.53.2.1 33365 1ekjA 221 2.89e+01 1ekjB c.53.2.1 33364 1ehyA 294 2.91e+01 1ehyA c.69.1.11 34693 1gmxA 108 2.97e+01 c.46.1.3 65355 1cgn 127 2.98e+01 1bbhA a.24.3.2 16548 1fljA 260 2.99e+01 2cba b.74.1.1 27954 1nnt 328 3.01e+01 1nnt c.94.1.2 35884 1l1mA 62 3.03e+01 1i5uA 82 3.04e+01 1cyo d.120.1.1 61824 1dn2E 14 3.05e+01 1nea 61 3.08e+01 3ebx g.7.1.1 44452 1qdlB 195 3.12e+01 1qdlB c.23.16.1 31437 1shaA 104 3.17e+01 1fmk d.93.1.1 40424 1shbA 104 3.17e+01 1fmk d.93.1.1 40425 1fxuA 289 3.24e+01 1b8oA c.56.2.1 33772 2a2uA 181 3.24e+01 1mup b.60.1.1 27135 1a9p 289 3.30e+01 1b8oA c.56.2.1 33774 1pbn 289 3.30e+01 1b8oA c.56.2.1 33771 3pnp 289 3.30e+01 1b8oA c.56.2.1 33763 3pdzA 96 3.31e+01 1pdr b.36.1.1 24782 1hqgA 323 3.31e+01 1d3vA c.42.1.1 61136 1ivhA 394 3.33e+01 3mdeA a.29.3.1 16608 e.6.1.1 42869 1f03A 82 3.35e+01 1cyo d.120.1.1 41068 1poc 134 3.35e+01 1poc a.133.1.1 19513 1ebeA 294 3.41e+01 1ryc a.93.1.1 59406 1dgsA 667 3.44e+01 1dgsA a.60.2.2 17963 b.40.4.6 25365 d.142.2.2 41581 1f3uA 118 3.45e+01 1f3uA b.65.1.1 27521 1f95A 89 3.50e+01 1cmiA d.39.1.1 38555 1aty 79 3.53e+01 1aty j.35.1.1 46259 2cyp 294 3.55e+01 1ryc a.93.1.1 18600 1es1A 82 3.55e+01 1cyo d.120.1.1 41067 1krjA 294 3.63e+01 a.93.1.1 68852 1jciA 294 3.64e+01 1jdrA 294 3.68e+01 1ryc a.93.1.1 62908 1dd5A 185 3.72e+01 1dd5A d.67.3.1 39564 1cgo 127 3.73e+01 1cpq a.24.3.2 16550 1hqxA 323 3.78e+01 1d3vA c.42.1.1 61161 1rlaA 323 3.78e+01 1d3vA c.42.1.1 32561 1d3vA 323 3.78e+01 1d3vA c.42.1.1 32559 2rlaA 323 3.78e+01 1d3vA c.42.1.1 32573 1ehbA 82 3.80e+01 1cyo d.120.1.1 41066 1b0nA 111 3.81e+01 1b0nA a.34.1.1 17001 a.35.1.3 17064 1qoxN 449 3.83e+01 1qoxN c.1.8.4 28978 3rlaA 323 3.89e+01 1d3vA c.42.1.1 32564 1gmiA 136 3.90e+01 b.7.1.1 65309 1mifA 115 3.92e+01 1dptA d.80.1.3 39852 1hzhL 215 3.93e+01 32c2A b.1.1.1 61445 b.1.1.2 61446 1cyo 93 3.94e+01 1cyo d.120.1.1 41065