# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7 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 1yo8A 634 8.95e-03 1p30A 952 5.65e-01 b.121.2.2 93964 b.121.2.2 93965 1ehkB 168 6.38e-01 2cuaA b.6.1.2 23041 f.17.2.1 43625 1dhx 967 1.19e+00 1dhx 1ospO 257 3.25e+00 1ospO b.76.1.1 27971 2aujD 309 3.48e+00 1p2zA 968 4.12e+00 b.121.2.2 93962 b.121.2.2 93963 1o6lA 337 4.57e+00 d.144.1.7 81092 2fflA 756 4.63e+00 1gg6B 131 4.81e+00 5ptp 1ruxA 951 4.99e+00 1dhx 2cavA 445 5.50e+00 1dgwA b.82.1.2 28094 b.82.1.2 28095 1ib8A 164 5.82e+00 b.38.2.1 71168 d.52.4.1 71169 1s4cA 155 6.10e+00 1dkgA 197 6.12e+00 1dkgA b.73.1.1 27812 h.1.9.1 45626 2cas 548 7.04e+00 2cas b.121.5.2 23376 1w9zA 283 7.06e+00 1vgyA 393 7.17e+00 c.56.5.4 100620 d.58.19.1 100621 1yphC 131 7.24e+00 2bvcA 486 8.75e+00 1w99A 558 8.84e+00 4dpvZ 584 9.05e+00 2cas b.121.5.2 23377 1jopA 155 9.11e+00 b.82.2.7 84187 1dmuA 299 9.31e+00 1dmuA c.52.1.4 33294 1ezvE 185 9.65e+00 1rie b.33.1.1 59548 f.23.12.1 59549 1b9mA 265 1.00e+01 1b9mA a.4.5.8 16118 b.40.6.2 58938 b.40.6.2 58939 1div 149 1.00e+01 1div d.99.1.1 40692 d.100.1.1 40693 1lrzA 426 1.03e+01 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 2azeB 106 1.07e+01 1yarO 237 1.10e+01 1d8iA 311 1.10e+01 1d8iA d.63.1.1 39541 1l9mA 692 1.15e+01 b.1.18.9 73732 b.1.5.1 73733 b.1.5.1 73734 d.3.1.4 73735 1dih 273 1.16e+01 1drw c.2.1.3 30056 d.81.1.3 39971 1t5eA 360 1.24e+01 f.46.1.1 106436 1bsmA 201 1.25e+01 1avmA a.2.11.1 15780 d.44.1.1 38743 1bqhG 129 1.31e+01 1cd8 b.1.1.1 19715 1x82A 190 1.32e+01 2f86B 143 1.34e+01 1avmA 201 1.38e+01 1avmA a.2.11.1 15782 d.44.1.1 38745 1bccE 196 1.38e+01 1rie b.33.1.1 24431 f.23.12.1 43699 1dkgB 197 1.40e+01 1dkgA b.73.1.1 27813 h.1.9.1 45627 2bvyA 475 1.42e+01 1occG 84 1.51e+01 2occG f.23.2.1 43562 1jn5B 250 1.53e+01 d.17.4.2 66922 1vjjA 692 1.54e+01 b.1.18.9 100814 b.1.5.1 100815 b.1.5.1 100816 d.3.1.4 100817 1p7gA 222 1.57e+01 a.2.11.1 94223 d.44.1.1 94224 1jk7A 323 1.69e+01 1auiA d.159.1.3 63144 2f1fA 164 1.69e+01 1h4vB 421 1.81e+01 1adjA c.51.1.1 60624 d.104.1.1 60625 1nnvA 110 1.85e+01 d.17.7.1 92012 1v25A 541 1.97e+01 e.23.1.1 108275 1vqoB 338 2.02e+01 1s72B 338 2.10e+01 b.43.3.2 105320 2eifA 136 2.13e+01 1bkb b.34.5.2 24607 b.40.4.5 25339 1fd9A 213 2.15e+01 1fd9A d.26.1.1 59771 1a6cA 513 2.16e+01 1a6cA b.121.4.2 23296 b.121.4.2 23297 b.121.4.2 23298 2ffuA 501 2.23e+01 1jj2B 337 2.30e+01 1ffkB b.43.3.2 63086 1jkgB 250 2.37e+01 d.17.4.2 66796 2occG 84 2.39e+01 2occG f.23.2.1 43522 1azsA 220 2.41e+01 1azsA d.58.29.1 39416 1v87A 114 2.49e+01 g.44.1.1 108422 1drw 273 2.58e+01 1drw c.2.1.3 30057 d.81.1.3 39972 1vqoX 92 2.60e+01 1kgyA 181 2.64e+01 b.18.1.4 72449 1vf7A 369 2.64e+01 f.46.1.1 108557 1culA 217 2.67e+01 1azsA d.58.29.1 39417 1k28A 584 2.73e+01 b.40.8.1 68049 b.108.1.2 68050 d.2.1.3 68051 1iuhA 198 2.78e+01 d.61.1.2 83711 1cgo 127 2.89e+01 1cpq a.24.3.2 16550 1qvcA 145 2.90e+01 3ullA b.40.4.3 25284 1o4yA 288 2.92e+01 b.29.1.2 92473 1jj2L 194 2.94e+01 1ffkI d.12.1.2 63097 1u32A 293 2.96e+01 d.159.1.3 107631 1p4cA 380 2.97e+01 c.1.4.1 94100 1k24A 253 2.98e+01 f.4.4.2 72002 1o7nB 194 3.04e+01 d.17.4.4 81164 1fzdA 201 3.11e+01 3fib d.171.1.1 42484 1sva1 361 3.16e+01 1vpsA 1l6rA 227 3.20e+01 c.108.1.10 77768 1hkxA 147 3.22e+01 d.17.4.7 83567 1q40B 219 3.26e+01 d.17.4.2 95771 1q42A 201 3.29e+01 d.17.4.2 95776 1pf4A 582 3.29e+01 c.37.1.12 88052 f.37.1.1 88053 1gm5A 780 3.32e+01 a.24.21.1 65298 b.40.4.9 65299 c.37.1.19 65300 c.37.1.19 65301 1v54G 85 3.33e+01 f.23.2.1 100328 1odeA 122 3.35e+01 d.79.1.2 86846 2bydA 323 3.52e+01 2atfA 200 3.56e+01 2occB 227 3.56e+01 2occB b.6.1.2 23027 f.17.2.1 43519 1fouA 309 3.57e+01 1fouA e.27.1.1 43364 1yx1A 264 3.57e+01 2cvhA 220 3.58e+01 1smvA 260 3.64e+01 1smvA b.121.4.7 23288 1g3gA 164 3.64e+01 1g6gA b.26.1.2 23918 1uldA 150 3.65e+01 b.29.1.3 99545 2fmlA 273 3.68e+01 1g87A 614 3.70e+01 a.102.1.2 83275 b.2.2.2 83276 1ndoB 194 3.76e+01 1ndoB d.17.4.4 38121 2a6hE 99 3.87e+01 1psuA 140 3.88e+01 d.38.1.5 88285 1gbg 214 3.90e+01 1axkA b.29.1.2 24171 1v54B 227 3.99e+01 b.6.1.2 100322 f.17.2.1 100323 2cr5A 109 3.99e+01