# List of top-scoring protein chains for T0301.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 2b3nA 159 9.24e-01 1uf2K 506 1.87e+00 1b1cA 181 2.20e+00 1amoA c.23.5.2 31212 1kkoA 413 2.57e+00 c.1.11.2,d.54.1.1 68675,68676 1ygs 234 3.43e+00 1ygs b.26.1.1 23907 1mr1A 235 3.46e+00 b.26.1.1 79418 1u7vB 236 3.51e+00 b.26.1.1 107730 1u7fB 239 3.57e+00 b.26.1.1 107721 1g88A 268 3.60e+00 1ygs b.26.1.1 23911 1dd1A 268 3.74e+00 b.26.1.1 23908 1tm0A 350 5.97e+00 d.21.1.3 107147 2fug3 783 6.14e+00 2ftsA 419 7.17e+00 1t3eA 421 7.18e+00 b.85.6.1,b.103.1.1,c.57.1.2 106348,106349,106350 1shzC 233 7.42e+00 1o9jA 501 7.54e+00 c.82.1.1 86694 1re5A 450 7.88e+00 a.127.1.1 104911 1wchA 315 7.92e+00 2gkeA 274 8.44e+00 1ja1A 622 9.03e+00 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1j9zA 622 9.10e+00 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62792,62793,62794 1ja0A 620 9.10e+00 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62798,62799,62800 1amoA 615 9.10e+00 1amoA b.43.4.1,c.23.5.2,c.25.1.4 25669,31210,31557 1bwzA 274 1.08e+01 1bwzA d.21.1.1,d.21.1.1 38337,38338 1yeeL 219 1.27e+01 32c2A b.1.1.1,b.1.1.2 20156,21186 1zo1I 501 1.36e+01 2deoA 230 1.37e+01 1yedA 219 1.47e+01 32c2A b.1.1.1,b.1.1.2 20150,21180 1yejL 219 1.48e+01 8fabA b.1.1.1,b.1.1.2 20140,21170 1ewrA 649 1.59e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1 19073,32387,33744 1ewqA 765 1.68e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1fw6A 768 1.70e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19071,32385,33742,39745 1d4dA 572 2.01e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19702,30439,42322 1b1xA 689 2.03e+01 1cb6A c.94.1.2,c.94.1.2 35865,35866 1f9bA 695 2.04e+01 1cb6A c.94.1.2,c.94.1.2 35869,35870 1moq 368 2.07e+01 1moq c.80.1.1 35302 2c1pA 218 2.24e+01 1jazA 326 2.27e+01 c.88.1.1 90883 1ho3A 326 2.28e+01 4pgaA c.88.1.1 61101 1nnsA 326 2.31e+01 c.88.1.1 85910 1xi6A 262 2.31e+01 1c7qA 445 2.32e+01 2pgi c.80.1.2 35307 4ecaA 326 2.35e+01 4pgaA c.88.1.1 35550 1lm6A 215 2.43e+01 d.167.1.1 84628 1d4cA 572 2.48e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19698,30435,42318 1yecL 219 2.49e+01 8fabA b.1.1.1,b.1.1.2 20144,21174 1o0pA 104 2.55e+01 d.58.7.1 86535 1z8wA 208 2.60e+01 2c1oA 254 2.61e+01 1z8xA 208 2.61e+01 1x10A 208 2.63e+01 1z8tA 208 2.63e+01 1x12A 208 2.63e+01 1ioiA 208 2.63e+01 1a2zA c.56.4.1 62629 2a5vA 213 2.64e+01 1ym3A 215 2.66e+01 1iofA 208 2.69e+01 1a2zA c.56.4.1 62625 1viuA 203 2.94e+01 d.113.1.1 100771 2biwA 490 2.98e+01 1mxmA 254 3.03e+01 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1n1jB 97 3.09e+01 a.22.1.3 79814 2gsq 202 3.19e+01 1pd21 a.45.1.1,c.47.1.5 17715,33009 1pgjA 478 3.21e+01 2pgd a.100.1.1,c.2.1.6 18783,30195 2aiaA 203 3.29e+01 2aieP 203 3.39e+01 2b94A 267 3.44e+01 1miqA 375 3.66e+01 b.50.1.2 79151 1w78A 422 3.68e+01 1nkpA 88 3.92e+01 a.38.1.1 80573 1xhkA 187 3.98e+01 1prxA 224 4.25e+01 1prxA c.47.1.10 33076 1cauB 184 4.32e+01 1caxB b.82.1.2 28103 1pprM 312 4.48e+01 1pprM a.131.1.1,a.131.1.1 19502,19503 1tqbC 219 4.57e+01 b.1.1.1,b.1.1.2 107215,107216 2a8nA 144 4.62e+01 1kxjA 205 4.69e+01 c.23.16.1 73153 1ncwL 219 4.71e+01 b.1.1.1,b.1.1.2 85557,85558 2f3oA 776 4.75e+01 1rumL 219 4.76e+01 b.1.1.1,b.1.1.2 97869,97870 1hl9A 449 4.81e+01 b.71.1.3,c.1.8.11 90650,90651 1k9vF 201 4.92e+01 c.23.16.1 68365 2d85A 124 4.98e+01 1seiA 130 5.05e+01 1seiA d.140.1.1 41463 1f5vA 240 5.08e+01 1bkjA d.90.1.1 40255 2d7uA 339 5.12e+01 1ci0A 228 5.32e+01 1ci0A b.45.1.1 25750 1gc9A 345 5.35e+01 1cnzA c.77.1.1 35037 1oi4A 193 5.39e+01 c.23.16.2 87047 1oe4A 247 5.60e+01 c.18.1.3 86895 1ikfL 214 5.76e+01 32c2A b.1.1.1,b.1.1.2 20032,21086 1q90M 39 5.77e+01 f.23.25.1 96246 1kvkA 395 5.91e+01 d.14.1.5,d.58.26.3 73060,73061 1wjoA 124 5.98e+01 1cm0A 168 5.99e+01 1yghA d.108.1.1 40800 1cr9L 219 6.03e+01 8fabA b.1.1.1,b.1.1.2 20430,21400 1tetL 216 6.11e+01 32c2A b.1.1.1,b.1.1.2 19902,20996 1zeaL 216 6.13e+01 1b4rA 80 6.16e+01 1b4rA b.1.3.1 22072 1jscA 630 6.23e+01 c.31.1.3,c.36.1.5,c.36.1.9 67224,67225,67226 2bsxA 253 6.28e+01 1souA 194 6.28e+01 c.124.1.6 105858 1nldL 219 6.32e+01 8fabA b.1.1.1,b.1.1.2 20110,21140 1t9bA 677 6.36e+01 1q1gA 276 6.36e+01 c.56.2.1 95574 1sq6A 253 6.48e+01 c.56.2.1 98964 2bplA 608 6.52e+01 1zivA 339 6.58e+01 2bpjA 608 6.59e+01 1l7tL 219 6.62e+01 b.1.1.1,b.1.1.2 77801,77802 1plgL 215 6.74e+01 8fabA b.1.1.1,b.1.1.2 20080,21112 2f4lA 297 6.98e+01 4ubpC 570 7.01e+01 1ubpC b.92.1.1,c.1.9.2 28431,29053 1f8tL 219 7.01e+01 32c2A b.1.1.1,b.1.1.2 59707,59708 1v1cA 71 7.05e+01 1ie7C 570 7.09e+01 1ubpC b.92.1.1,c.1.9.2 62315,62316 1ji8A 111 7.21e+01 d.203.1.1 66733 2a1wL 216 7.33e+01 2ai0L 217 7.34e+01 2d03L 217 7.49e+01 2a77L 216 7.67e+01 2ajuL 216 7.72e+01 1t2qL 217 8.01e+01 1nksA 194 8.10e+01 1nksA c.37.1.1 31886 1yioA 208 8.14e+01 1xttA 216 8.20e+01 2crzA 110 8.31e+01 1v9cA 218 8.34e+01 c.23.17.1 100533 1ub6B 213 8.40e+01 b.1.1.1,b.1.1.2 99153,99154 1fl3B 214 8.41e+01 32c2A b.1.1.1,b.1.1.2 20487,21451 1udeA 195 8.43e+01 b.40.5.1 99208 1vplA 256 8.48e+01 1rlgA 119 8.61e+01 d.79.3.1 104981 1vqoF 120 8.66e+01 1mr4A 47 8.86e+01 g.3.7.5 91429 1bx4A 345 8.91e+01 1bx4A c.72.1.1 34935 1kl7A 514 8.93e+01 c.79.1.1 72678 1xc3A 302 8.93e+01 1vhxA 150 8.93e+01 c.55.3.8 100712 1fh5L 213 8.94e+01 32c2A b.1.1.1,b.1.1.2 20464,21428