# 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.soe.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 2fgqX 332 1.57e-38 f.4.3.1 133439 1e54A 332 1.57e-38 1e54A f.4.3.1 59258 2fgrA 332 2.59e-38 f.4.3.1 133440 1hxuA 340 3.09e-21 2omf f.4.3.1 61384 2omfA 340 4.27e-21 f.4.3.1 43749 1hxxA 340 4.82e-21 2omf f.4.3.1 61385 1bt9A 340 5.40e-21 2omf f.4.3.1 43756 1mpfA 340 5.48e-21 f.4.3.1 43752 1gfoA 340 1.01e-20 f.4.3.1 43753 1phoA 330 1.03e-20 f.4.3.1 43758 1gfmA 340 1.20e-20 f.4.3.1 43755 1gfpA 340 1.22e-20 f.4.3.1 43750 2ixwA 343 1.26e-20 1osmA 342 2.76e-20 2omf f.4.3.1 43769 1gfqA 340 3.35e-20 f.4.3.1 43751 2j1nA 346 4.71e-20 1gfnA 334 7.77e-20 f.4.3.1 43754 2ixxA 354 4.77e-19 1hxtA 340 8.26e-19 2omf f.4.3.1 61383 2porA 301 5.22e-06 f.4.3.1 43759 2prnA 289 3.51e-01 f.4.3.1 43763 1f74A 293 5.32e-01 1nal3 c.1.10.1 29079 1mmaA 762 5.65e-01 b.34.3.1 24587 c.37.1.9 32184 1w9kA 770 5.92e-01 1d0yA 761 6.03e-01 1lvk b.34.3.1 24581 c.37.1.9 32178 1yv3A 762 6.08e-01 2akaA 776 6.23e-01 1jx2A 776 6.25e-01 b.34.3.1 67402 c.37.1.9 67403 1w9lA 770 6.28e-01 1w9iA 770 6.39e-01 1w9jA 770 6.70e-01 2odjA 428 7.08e-01 1prnA 289 7.42e-01 f.4.3.1 43762 6prnA 289 7.51e-01 f.4.3.1 43765 5prnA 289 7.56e-01 f.4.3.1 43764 1mmnA 762 7.66e-01 b.34.3.1 24582 c.37.1.9 32179 3prnA 289 8.88e-01 f.4.3.1 43761 7prnA 289 9.07e-01 f.4.3.1 43768 8prnA 289 9.14e-01 f.4.3.1 43767 1fmvA 761 9.55e-01 1lvk b.34.3.1 24580 c.37.1.9 32177 1vomA 762 9.59e-01 b.34.3.1 24577 c.37.1.9 32174 1lvkA 762 9.85e-01 b.34.3.1 24576 c.37.1.9 32173 1bh3A 289 1.01e+00 f.4.3.1 43766 1g8xA 1010 1.12e+00 1lvk k.1.1.1 46378 1qd6C 240 1.34e+00 1qd5A 2iciA 227 1.35e+00 1p4tA 155 1.43e+00 f.4.1.1 87779 2d6oX 159 1.63e+00 1fw3A 275 1.70e+00 1qd5A f.4.2.1 60054 1qd5A 275 1.70e+00 1qd5A f.4.2.1 43748 2d6mA 159 1.84e+00 2dj0A 137 2.15e+00 1ilzA 275 2.22e+00 f.4.2.1 66209 1mmgA 762 2.70e+00 b.34.3.1 24579 c.37.1.9 32176 1i78A 297 2.96e+00 f.4.4.1 66046 1zkaA 110 3.66e+00 1tk1A 260 3.96e+00 d.248.1.1 107066 1nhcA 336 3.97e+00 b.80.1.3 91879 2qdrA 303 4.04e+00 2c58A 537 4.76e+00 c.69.1.1 129891 1txkA 498 4.88e+00 b.1.18.2 107425 b.30.5.9 107426 1zoyB 252 5.44e+00 1eeaA 534 5.75e+00 2bce c.69.1.1 34609 2cekA 535 5.76e+00 c.69.1.1 130347 1gqrA 532 5.76e+00 c.69.1.1 70374 2dfpA 534 5.76e+00 2bce c.69.1.1 34597 1ea5A 537 5.77e+00 2bce c.69.1.1 34592 1ut6A 537 5.77e+00 c.69.1.1 119698 1w6rA 543 5.80e+00 c.69.1.1 114283 1h6s1 307 5.90e+00 1txnA 328 6.35e+00 d.248.1.1 112779 1tklA 326 6.39e+00 d.248.1.1 107105 1m93B 245 6.49e+00 2b3rA 134 6.76e+00 2z3oA 233 7.00e+00 2f1cX 286 7.13e+00 2dpsA 254 7.19e+00 1wiwA 290 7.42e+00 c.80.1.1 114681 2rcyA 262 7.56e+00 2cxaA 256 8.50e+00 d.108.1.6 130993 1c8oA 300 8.52e+00 1c8oA e.1.1.1 42677 2jqyA 280 9.25e+00 2iwvA 281 9.41e+00 2h88B 252 9.43e+00 2fbwB 252 9.43e+00 2dpyA 438 1.00e+01 1f0cA 305 1.06e+01 1c8oA e.1.1.1 42676 1nqfA 594 1.11e+01 f.4.3.3 86028 1mqsA 671 1.13e+01 e.25.1.1 79414 1vb3A 428 1.20e+01 c.79.1.1 119942 1rhi3 236 1.32e+01 1aym3 1tiyA 164 1.36e+01 c.97.1.2 107012 1mjcA 69 1.38e+01 b.40.4.5 25319 1uxvA 501 1.39e+01 c.82.1.1 108127 2gufA 594 1.45e+01 f.4.3.3 135736 1nqeA 594 1.45e+01 f.4.3.3 86027 2gskA 590 1.45e+01 f.4.3.3 135587 1uxtA 501 1.48e+01 c.82.1.1 108125 1h5rA 293 1.50e+01 c.68.1.6 65623 1h5sA 293 1.54e+01 c.68.1.6 65627 1h5sD 293 1.60e+01 c.68.1.6 65630 2g7cA 255 1.63e+01 1h5rB 293 1.66e+01 c.68.1.6 65624 2nyyA 1295 1.68e+01 2gt4A 160 1.74e+01 2agkA 260 1.75e+01 1iinA 292 1.76e+01 1g0rA c.68.1.6 62447 1wkqA 164 1.78e+01 c.97.1.2 109393 1dbhA 354 1.78e+01 1awe a.87.1.1 18514 b.55.1.1 26967 2p51A 333 1.79e+01 2ozuA 284 1.88e+01 d.108.1.1 139451 1mp5A 292 1.94e+01 c.68.1.6 79378 1t16A 427 1.98e+01 f.4.3.4 106242 2gf3A 389 1.98e+01 c.3.1.2 135070 d.16.1.3 135071 1el5A 389 1.98e+01 1b3mA c.3.1.2 30369 d.16.1.3 37937 1nxuA 333 2.02e+01 c.122.1.1 86389 1ryaA 160 2.04e+01 d.113.1.5 105122 3bhkA 390 2.06e+01 1s20A 340 2.08e+01 c.122.1.1 98356 1mp4A 292 2.15e+01 c.68.1.6 79376 1ncqC 236 2.17e+01 b.121.4.1 91804 2abrA 418 2.25e+01 d.126.1.4 126530 2a9gA 418 2.51e+01 d.126.1.4 126435 2aafA 418 2.55e+01 d.126.1.4 126471 1rxxA 421 2.56e+01 d.126.1.4 98061 1g9xA 257 2.70e+01 c.37.1.12 76219 1bunA 120 2.72e+01 1poa a.133.1.2 19614 1zk9A 110 2.87e+01 2fp8A 322 2.92e+01 2aciA 418 2.94e+01 d.126.1.4 126551 1jawA 440 2.97e+01 c.55.2.1 33549 d.127.1.1 41166 3cihA 739 3.00e+01 1qwlA 505 3.06e+01 e.5.1.1 96483 1po0A 751 3.10e+01 f.4.3.3 94960 2ovjA 201 3.14e+01 2qntA 141 3.14e+01 2hfcA 239 3.16e+01 1qfxA 460 3.17e+01 1qfxA c.60.1.2 33994 2okxA 956 3.18e+01 1kmoA 774 3.19e+01 f.4.3.3 72753 2uz9A 476 3.23e+01 2o3oA 254 3.28e+01 1xahA 354 3.33e+01 1nekB 238 3.43e+01 a.1.2.1 80429 d.15.4.2 80430 1l9cA 389 3.44e+01 c.3.1.2 77815 d.16.1.3 77816 2pggA 774 3.54e+01 1qy3A 229 3.55e+01 d.22.1.1 96570 1qxtA 230 3.55e+01 d.22.1.1 96562 2b2aA 199 3.57e+01 2pusA 852 3.63e+01 1tlyA 278 3.83e+01 f.4.6.1 107143 1uf0A 116 3.88e+01 d.15.11.1 99287 1gajA 257 3.93e+01 1gajA c.37.1.12 60416 1z7s1 298 3.94e+01 1y5lC 225 3.97e+01