# 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.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 1b1cA 181 7.78e-01 1amoA c.23.5.2 31212 1fp1D 372 9.46e-01 1fpqA a.4.5.29 59939 c.66.1.12 59940 1ex2A 189 1.01e+00 1ex2A c.51.4.2 33225 1fpqA 372 1.11e+00 1fpqA a.4.5.29 59947 c.66.1.12 59948 1jmxA 494 1.55e+00 a.3.1.7 66901 a.3.1.7 66902 b.1.1.6 66903 b.1.1.6 66904 b.61.4.1 66905 1xlmA 394 1.71e+00 4xis c.1.15.3 29441 1xlaA 394 1.74e+00 4xis c.1.15.3 29445 4xiaA 393 1.75e+00 4xis c.1.15.3 29439 1gowA 489 1.83e+00 1qvbA c.1.8.4 28981 1ja0A 620 2.00e+00 1amoA b.43.4.1 62798 c.23.5.2 62799 c.25.1.4 62800 1j9zA 622 2.00e+00 1amoA b.43.4.1 62792 c.23.5.2 62793 c.25.1.4 62794 1amoA 615 2.01e+00 1amoA b.43.4.1 25669 c.23.5.2 31210 c.25.1.4 31557 1ja1A 622 2.01e+00 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1dctA 324 2.11e+00 6mhtA c.66.1.10 34244 1edsA 31 2.40e+00 1edsA j.35.1.1 46240 1qnlA 385 2.60e+00 1pea c.93.1.1 35665 1pdz 434 3.45e+00 4enl c.1.11.1 29215 d.54.1.1 38859 1i94L 131 3.82e+00 1fjfL b.40.4.5 62003 1fjgL 135 4.08e+00 1fjfL b.40.4.5 25346 1d1jD 139 4.09e+00 1pne d.110.1.1 40881 1bjwA 382 4.25e+00 1bjwA c.67.1.1 34349 1bkgA 385 4.27e+00 1bjwA c.67.1.1 34351 1gckA 385 4.36e+00 c.67.1.1 65177 1gc3A 385 4.38e+00 c.67.1.1 60417 1f51F 119 5.07e+00 1dz3A c.23.1.1 31115 2fsp 124 5.13e+00 1dz3A c.23.1.1 31119 1srrA 124 5.21e+00 1dz3A c.23.1.1 31110 1f2eA 201 5.45e+00 1a0fA a.45.1.1 17745 c.47.1.5 33039 1hyeA 313 5.64e+00 2cmd c.2.1.5 61400 d.162.1.1 61401 2btfP 139 7.01e+00 1pne d.110.1.1 40867 1pne 140 7.04e+00 1pne d.110.1.1 40866 3cox 507 7.23e+00 1b8sA c.3.1.2 30332 d.16.1.1 37863 1db0B 331 7.31e+00 1d0nA d.109.1.1 40854 d.109.1.1 40855 d.109.1.1 40856 1awiA 138 7.41e+00 1pne d.110.1.1 40871 1fil 139 7.44e+00 1pne d.110.1.1 40869 1lqsL 157 7.58e+00 1rgs 288 8.54e+00 1rgs b.82.3.2 28146 b.82.3.2 28147 2rlaA 323 9.31e+00 1d3vA c.42.1.1 32573 1hqxA 323 9.42e+00 1d3vA c.42.1.1 61161 1rlaA 323 9.42e+00 1d3vA c.42.1.1 32561 1d3vA 323 9.42e+00 1d3vA c.42.1.1 32559 1hqgA 323 9.66e+00 1d3vA c.42.1.1 61136 3rlaA 323 9.80e+00 1d3vA c.42.1.1 32564 1b62A 349 9.93e+00 1b63A d.14.1.3 37567 d.122.1.2 41108 1b63A 333 9.98e+00 1b63A d.14.1.3 37566 d.122.1.2 41107 1ak9 275 1.01e+01 1gci c.41.1.1 32517 1bknA 352 1.01e+01 1b63A d.14.1.3 37568 d.122.1.2 41109 1je0A 236 1.01e+01 c.56.2.1 66581 1a2q 275 1.02e+01 1gci c.41.1.1 32512 1aqn 275 1.03e+01 1gci c.41.1.1 32514 1sbh 275 1.04e+01 1gci c.41.1.1 32518 1s01 275 1.04e+01 1gci c.41.1.1 32511 1sbi 275 1.04e+01 1gci c.41.1.1 32533 1hey 128 1.07e+01 3chy c.23.1.1 31061 1pea 385 1.15e+01 1pea c.93.1.1 35662 1fkvA 124 1.19e+01 3lzt d.2.1.2 36602 1qagA 226 1.27e+01 1qagA a.40.1.1 17400 a.40.1.1 17401 1fkqA 124 1.27e+01 3lzt d.2.1.2 36601 1g2nA 264 1.40e+01 1lbd a.123.1.1 60227 1k3fA 253 1.40e+01 c.56.2.1 68105 1m1jA 491 1.41e+01 1lx7A 253 1.41e+01 1b4kA 337 1.41e+01 1b4kA c.1.10.3 29184 1xymA 386 1.44e+01 4xis c.1.15.3 29415 1xyaA 386 1.46e+01 4xis c.1.15.3 29411 1a5cA 368 1.47e+01 1fbaA c.1.10.1 29148 1s02 275 1.66e+01 1gci c.41.1.1 32525 1sup 275 1.66e+01 1gci c.41.1.1 32510 1sub 275 1.66e+01 1gci c.41.1.1 32513 2sniE 275 1.66e+01 1gci c.41.1.1 32529 1sud 275 1.67e+01 1gci c.41.1.1 32526 1ubnA 275 1.69e+01 1gci c.41.1.1 32535 1duiA 266 1.71e+01 1gci c.41.1.1 32530 1gnsA 263 1.72e+01 1hmkA 124 1.72e+01 3lzt d.2.1.2 36603 1hfyA 123 1.73e+01 3lzt d.2.1.2 36604 1spbS 266 1.74e+01 1gci c.41.1.1 32532 1sue 266 1.75e+01 1gci c.41.1.1 32520 1suaA 266 1.77e+01 1gci c.41.1.1 32531 1gnvA 266 1.77e+01 1mioA 525 1.78e+01 1qguA c.92.2.3 35601 1mioC 533 1.81e+01 1qguA c.92.2.3 35603 1suc 266 1.82e+01 1gci c.41.1.1 32521 1fjgI 128 1.98e+01 1fjfI d.14.1.1 37559 1eh8A 207 1.98e+01 1sfe a.4.2.1 16077 c.55.7.1 33752 1eh7A 207 1.98e+01 1sfe a.4.2.1 16075 c.55.7.1 33750 1k6cA 99 2.01e+01 b.50.1.1 68215 1f2tB 148 2.03e+01 1f2tB 1akt 147 2.13e+01 5nul c.23.5.1 31157 1hdoA 206 2.21e+01 1he2A c.2.1.2 60965 1he2A 206 2.21e+01 1he2A c.2.1.2 60966 1ymv 129 2.27e+01 3chy c.23.1.1 31045 1d5yA 292 2.28e+01 1d5yA a.4.1.8 16055 a.4.1.8 16056 d.60.1.2 39532 1afcA 140 2.28e+01 1bfg b.42.1.1 25506 1ii8B 174 2.36e+01 1f2tB 1fx1 148 2.37e+01 1rcf c.23.5.1 31169 1ln6A 348 2.38e+01 1l9hA 349 2.39e+01 1hzxA 349 2.39e+01 1f88A f.2.1.1 61466 1f88A 348 2.40e+01 1f88A f.2.1.1 43429 1barB 140 2.40e+01 1bfg b.42.1.1 25505 1npsA 88 2.46e+01 1prs b.11.1.1 23622 1bu5A 147 2.60e+01 5nul c.23.5.1 31155 2fx2 147 2.64e+01 1rcf c.23.5.1 31158 1eh6A 207 2.75e+01 1sfe a.4.2.1 16076 c.55.7.1 33751 1igmH 129 2.78e+01 1igtB b.1.1.1 19827 1xaa 345 2.82e+01 1cnzA c.77.1.1 35033 1c7fA 147 2.84e+01 5nul c.23.5.1 31163 1g2uA 345 2.85e+01 1cnzA c.77.1.1 35036 1gc8A 345 2.85e+01 1cnzA c.77.1.1 35042 1dr0A 346 2.86e+01 1cnzA c.77.1.1 35045 1osjA 345 2.86e+01 1cnzA c.77.1.1 35039 1walA 345 2.87e+01 1cnzA c.77.1.1 35041 1dr8B 344 2.87e+01 1cnzA c.77.1.1 35052 1h6gA 256 2.88e+01 1h6gA a.24.9.1 60669 a.24.9.1 60670 1c7mA 100 2.89e+01 1ycc a.3.1.1 15830 1ipd 345 2.89e+01 1cnzA c.77.1.1 35038 1gc9A 345 2.89e+01 1cnzA c.77.1.1 35037 1ql3A 99 2.89e+01 1ycc a.3.1.1 15822 1dpzA 349 2.90e+01 1cnzA c.77.1.1 35053 1j9eA 147 2.92e+01 c.23.5.1 62756 1qn0A 112 2.93e+01 3cyr a.138.1.1 19659 1jnpA 116 3.04e+01 b.63.1.1 66964 1f4pA 147 3.07e+01 5nul c.23.5.1 59651 1l7cA 269 3.10e+01 1ihvA 52 3.16e+01 1ihvA b.34.7.1 24629 1itpA 77 3.19e+01 d.58.3.2 66371 1dfbH 229 3.21e+01 1igtB b.1.1.1 19811 b.1.1.2 20921 1xac 345 3.31e+01 1cnzA c.77.1.1 35056 1hfzD 124 3.33e+01 3lzt d.2.1.2 36621 1qhtA 775 3.36e+01 1tgoA c.55.3.5 33722 e.8.1.1 43011 1f6rA 123 3.39e+01 3lzt d.2.1.2 36606 1aku 147 3.43e+01 5nul c.23.5.1 31161 1dywA 173 3.57e+01 2cpl b.62.1.1 27505 1dzdA 127 3.59e+01 1bfg b.42.1.1 25532 1dfx 125 3.61e+01 1dfx b.1.13.1 22367 g.41.5.2 45255 1gsjA 258 3.63e+01 1eyxA 164 3.72e+01 1cpcA a.1.1.3 15669 1tipA 191 3.80e+01 1bif c.60.1.4 34006 1ep7A 112 3.80e+01 c.47.1.1 64905 1ep8A 112 3.81e+01 c.47.1.1 64907 1qmcA 52 3.84e+01 1ihvA b.34.7.1 24633 1auiA 521 3.93e+01 1auiA d.159.1.3 42085 1gs5A 258 3.99e+01 1dzcA 131 3.99e+01 1bfg b.42.1.1 25531