# List of top-scoring protein chains for T0222.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 1ops 64 1.58e-01 1msi b.85.1.1 28302 3nla 74 2.92e-01 1msi b.85.1.1 28316 1ucsA 64 4.11e-01 b.85.1.1 88466 1c89A 134 4.77e-01 1msi b.85.1.1 28314 b.85.1.1 28315 1fiuA 286 5.51e-01 1fiuA c.52.1.10 33317 9ameA 66 8.24e-01 1msi b.85.1.1 28294 1nnt 328 1.45e+00 1nnt c.94.1.2 35884 1iejA 332 1.46e+00 1nnt c.94.1.2 62328 1tfaA 329 1.65e+00 1nnt c.94.1.2 35880 1ovb 159 2.21e+00 1nnt c.94.1.2 35875 1gvcA 157 2.51e+00 c.94.1.2 65607 1gv8A 159 2.51e+00 c.94.1.2 65606 1ovt 686 3.06e+00 1nnt c.94.1.2 35882 c.94.1.2 35883 1b7jA 66 3.66e+00 1msi b.85.1.1 28283 1nzoA 363 3.75e+00 b.105.1.1 -2933 e.3.1.1 -11784 1dot 686 3.77e+00 1nnt c.94.1.2 35876 c.94.1.2 35877 1nj4A 363 3.85e+00 b.105.1.1 80545 e.3.1.1 80546 1eklA 66 4.13e+00 1msi b.85.1.1 28289 7msi 66 4.15e+00 1msi b.85.1.1 28290 2msi 66 4.16e+00 1msi b.85.1.1 28297 2jiaA 66 4.36e+00 1msi b.85.1.1 28286 1msi 70 4.69e+00 1msi b.85.1.1 28281 5msi 66 4.78e+00 1msi b.85.1.1 28293 6msi 66 5.11e+00 1msi b.85.1.1 28296 3msi 66 5.27e+00 1msi b.85.1.1 28282 1ml9A 302 5.32e+00 b.85.7.1 79282 1kde 70 5.43e+00 1msi b.85.1.1 28310 4msi 66 5.65e+00 1msi b.85.1.1 28292 2msjA 66 5.76e+00 1msi b.85.1.1 28303 9msiA 66 5.84e+00 1msi b.85.1.1 28307 1b7iA 66 6.02e+00 1msi b.85.1.1 28288 1ame 67 6.04e+00 1msi b.85.1.1 28285 1hg7A 66 6.13e+00 1msi b.85.1.1 28280 1gzi 65 6.39e+00 1msi b.85.1.1 28295 1lcuA 371 6.61e+00 c.55.1.1 73830 c.55.1.1 73831 1atnA 373 6.85e+00 1yagA c.55.1.1 33437 c.55.1.1 33438 1qz5A 375 6.86e+00 c.55.1.1 -7590 c.55.1.1 -7591 1j6zA 376 6.90e+00 1yagA c.55.1.1 62667 c.55.1.1 62668 1esvA 377 6.94e+00 1yagA c.55.1.1 33433 c.55.1.1 33434 1ma9B 376 6.98e+00 c.55.1.1 78890 c.55.1.1 78891 1d4xA 375 7.12e+00 1yagA c.55.1.1 59107 c.55.1.1 59108 1t0bA 252 7.18e+00 3ameA 66 7.18e+00 1msi b.85.1.1 28304 1ejiA 478 7.25e+00 1bj4A c.67.1.4 34475 1jabA 66 7.36e+00 1msi b.85.1.1 28284 2spgA 66 7.39e+00 1msi b.85.1.1 28291 2btfA 375 7.41e+00 1yagA c.55.1.1 33429 c.55.1.1 33430 1p8sA 314 8.02e+00 c.42.1.1 87979 8msiA 66 8.19e+00 1msi b.85.1.1 28308 1p8nA 314 8.25e+00 c.42.1.1 87965 8ameA 66 8.25e+00 1msi b.85.1.1 28301 6ameA 66 8.47e+00 1msi b.85.1.1 28299 1p8qA 314 8.54e+00 c.42.1.1 87974 2rlaA 323 8.59e+00 1d3vA c.42.1.1 32573 7ameA 66 8.94e+00 1msi b.85.1.1 28287 1p8oA 314 9.11e+00 c.42.1.1 87968 1p8mA 314 9.12e+00 c.42.1.1 87962 1p8pA 314 9.15e+00 c.42.1.1 87971 1p8rA 308 9.21e+00 c.42.1.1 87977 1hqgA 323 9.26e+00 1d3vA c.42.1.1 61136 2ameA 66 9.29e+00 1msi b.85.1.1 28300 1hqxA 323 9.30e+00 1d3vA c.42.1.1 61161 1d3vA 323 9.32e+00 1d3vA c.42.1.1 32559 3rlaA 323 9.33e+00 1d3vA c.42.1.1 32564 1f1uA 323 9.35e+00 d.32.1.3 83200 d.32.1.3 83201 1vjeA 166 9.37e+00 d.185.1.2 -10261 1msjA 66 1.01e+01 1msi b.85.1.1 28305 1yvnA 375 1.07e+01 1yagA c.55.1.1 33451 c.55.1.1 33452 4ameA 66 1.09e+01 1msi b.85.1.1 28298 1yagA 375 1.09e+01 1yagA c.55.1.1 33449 c.55.1.1 33450 1bev3 242 1.10e+01 1aym3 1v13A 134 1.33e+01 1kv9A 668 1.45e+01 a.3.1.6 73056 b.70.1.1 73057 1r21A 128 1.48e+01 b.26.1.2 -3322 1b7kA 66 1.55e+01 1msi b.85.1.1 28306 1sr3A 136 1.64e+01 b.40.9.1 -3894 1k1dA 460 1.65e+01 b.92.1.3 71979 c.1.9.6 71980 1k28D 391 1.67e+01 b.106.1.1 68052 b.106.1.1 68053 1qrhA 261 1.93e+01 1ckqA c.52.1.1 33232 1qriA 261 1.93e+01 1ckqA c.52.1.1 33233 1qpsA 261 1.93e+01 1ckqA c.52.1.1 33234 1q27A 171 1.99e+01 d.113.1.2 -10932 1cl8A 276 1.99e+01 1ckqA c.52.1.1 33230 1rkd 309 2.06e+01 1rkd c.72.1.1 34928 1ithA 141 2.14e+01 1ithA a.1.1.2 15623 1nkwS 115 2.16e+01 i.1.1.2 80604 1oxwA 373 2.29e+01 c.19.1.3 87539 1d6sA 322 2.40e+01 1oasA c.79.1.1 35295 1fcjA 322 2.46e+01 1oasA c.79.1.1 35289 1esvS 125 2.49e+01 1d0nA d.109.1.1 40852 1c0gS 127 2.60e+01 1d0nA d.109.1.1 40848 1m1zA 513 2.65e+01 c.26.2.1 78457 d.153.1.1 78458 1fr2B 134 2.67e+01 d.4.1.1 83257 1sctA 150 2.69e+01 3sdhA a.1.1.2 15002 1a6tA 210 2.72e+01 8fabA b.1.1.1 20248 b.1.1.2 21258 1gp1A 198 3.02e+01 1gp1A c.47.1.10 33059 1pnuS 113 3.03e+01 i.1.1.1 88216 1uwjA 276 3.12e+01 d.144.1.7 -11357 1uwhA 276 3.22e+01 d.144.1.7 -11355 1rl1A 114 3.30e+01 unknown_sccs -3054 1m5sA 297 3.31e+01 d.58.33.1 74511 d.58.33.1 74512 1d0qA 103 3.41e+01 1d0qA g.41.3.2 45208 1c0gA 375 3.56e+01 1yagA c.55.1.1 33443 c.55.1.1 33444 1fr1A 361 3.63e+01 1gceA e.3.1.1 42734 1mpgA 282 3.67e+01 1mpgA a.96.1.3 18747 d.129.1.2 41296 1n62C 288 3.68e+01 d.87.2.1 80094 d.145.1.3 80095 1lci 550 3.68e+01 1lci e.23.1.1 43349 1f1xA 322 3.78e+01 d.32.1.3 83208 d.32.1.3 83209 1jpaA 312 3.83e+01 d.144.1.7 67011 1im5A 180 3.90e+01 unknown_sccs 66211 1rgiG 346 3.93e+01 1amx 180 3.96e+01 1amx b.2.3.1 22410 1cm8A 367 3.97e+01 1hcl d.144.1.7 41651 1q0cA 365 3.99e+01 d.32.1.3 88343 d.32.1.3 88344