# 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 1ucsA 64 1.74e-02 b.85.1.1 88466 1msi 70 3.97e-02 1msi b.85.1.1 28281 1c89A 134 7.53e-02 1msi b.85.1.1 28314 b.85.1.1 28315 1hg7A 66 1.01e-01 1msi b.85.1.1 28280 1innA 166 1.82e+00 1j98A d.185.1.2 62608 1vjeA 166 1.83e+00 d.185.1.2 -10261 1b87A 181 1.96e+00 1b87A d.108.1.1 40797 1n71A 180 2.04e+00 d.108.1.1 85370 1qc9A 276 2.89e+00 1ckqA c.52.1.1 33235 1fiuA 286 3.01e+00 1fiuA c.52.1.10 33317 1fr2B 134 3.02e+00 d.4.1.1 83257 1oahA 519 3.10e+00 a.138.1.3 86736 1bxiB 134 3.33e+00 1bxiB d.4.1.1 37136 1emvB 134 3.99e+00 1bxiB d.4.1.1 37135 1qpsA 261 4.10e+00 1ckqA c.52.1.1 33234 1cl8A 276 4.38e+00 1ckqA c.52.1.1 33230 1ckqA 276 4.39e+00 1ckqA c.52.1.1 33229 1eriA 276 5.39e+00 1ckqA c.52.1.1 33231 1ao0A 459 5.40e+00 1ecfB c.61.1.1 34049 d.153.1.1 41816 1a7cA 379 6.44e+00 1sek e.1.1.1 42660 1f1xA 322 6.47e+00 d.32.1.3 83208 d.32.1.3 83209 1dujA 187 7.14e+00 1dujA d.135.1.1 41449 1gjxA 81 7.44e+00 b.84.1.1 65222 1lj5A 379 7.44e+00 e.1.1.1 73928 1ml9A 302 7.63e+00 b.85.7.1 79282 1f1uA 323 8.44e+00 d.32.1.3 83200 d.32.1.3 83201 1k5dC 386 8.88e+00 c.10.1.2 68170 2rusB 490 9.24e+00 1burA c.1.14.1 29385 d.58.9.1 39291 1rusA 490 1.01e+01 1burA c.1.14.1 29388 d.58.9.1 39294 1go4A 205 1.06e+01 d.135.1.1 70292 1lizA 136 1.08e+01 3tgl 269 1.28e+01 3tgl c.69.1.17 34733 1yrgB 385 1.34e+01 1yrgA c.10.1.2 30855 5rubA 490 1.36e+01 1burA c.1.14.1 29382 d.58.9.1 39288 1l7dA 384 1.36e+01 c.2.1.4 77774 c.23.12.2 77775 1f8gA 384 1.37e+01 1sayA c.2.1.4 59695 c.23.12.2 59696 1pne 140 1.42e+01 1pne d.110.1.1 40866 1im5A 180 1.43e+01 unknown_sccs 66211 1klqA 197 1.50e+01 d.135.1.1 68689 1jqlB 140 1.51e+01 c.37.1.20 63234 1g1eB 89 1.54e+01 1g1eB a.59.1.1 17931 1lrwA 600 1.60e+01 b.70.1.1 -4629 1yrgA 385 1.61e+01 1yrgA c.10.1.2 30854 1aym3 238 1.63e+01 1aym3 1lgyA 269 1.69e+01 3tgl c.69.1.17 34758 1fil 139 1.71e+01 1pne d.110.1.1 40869 1mhyD 521 1.71e+01 1mhyD a.25.1.2 16780 1griA 217 1.78e+01 1griA b.34.2.1 24531 b.34.2.1 24532 d.93.1.1 40473 4rhv3 236 1.86e+01 1aym3 1v5xA 203 2.04e+01 c.1.2.4 -5169 1nnt 328 2.04e+01 1nnt c.94.1.2 35884 1smrA 335 2.07e+01 1smrA b.50.1.2 26878 1p5hA 428 2.22e+01 c.123.1.1 87802 2phh 394 2.27e+01 1pbe c.3.1.2 30353 d.16.1.2 37884 1qdlB 195 2.33e+01 1qdlB c.23.16.1 31437 1ihmA 530 2.38e+01 1ihmA b.121.4.3 62385 1pfl 139 2.47e+01 1pne d.110.1.1 40877 1a8h 500 2.64e+01 1a8h a.27.1.1 16922 c.26.1.1 31589 1nj4A 363 2.74e+01 b.105.1.1 80545 e.3.1.1 80546 1qm4A 396 2.78e+01 1mxb d.130.1.1 41350 d.130.1.1 41351 d.130.1.1 41352 1rhi3 236 2.88e+01 1aym3 1udzA 182 3.08e+01 b.51.1.1 -4307 1nd4A 264 3.08e+01 d.144.1.6 -11381 1j6wA 175 3.10e+01 1j98A d.185.1.2 62663 1g3fA 117 3.11e+01 1g3fA g.52.1.1 45378 1gzwA 134 3.14e+01 b.29.1.3 -3412 1ljoA 77 3.23e+01 b.38.1.1 73941 1nftA 329 3.34e+01 1nnt c.94.1.2 35881 1k0iA 394 3.36e+01 c.3.1.2 67942 d.16.1.2 67943 1jdpA 441 3.36e+01 c.93.1.1 62906 1mai 131 3.38e+01 1mai b.55.1.1 26951 1tfaA 329 3.38e+01 1nnt c.94.1.2 35880 1pbe 394 3.39e+01 1pbe c.3.1.2 30338 d.16.1.2 37869 1fuxA 166 3.61e+01 1fjjA b.17.1.2 60034 1cj3A 392 3.65e+01 1pbe c.3.1.2 30347 d.16.1.2 37878 1k0hA 117 3.84e+01 b.106.1.2 71975 1gehA 444 3.96e+01 c.1.14.1 65181 d.58.9.1 65182 1f37A 110 3.98e+01 1f37A c.47.1.11 33088