# 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 1opgH 227 3.11e-01 1igtB b.1.1.1 20069 b.1.1.2 21101 1bfvH 119 1.10e+00 1igtB b.1.1.1 20163 1dfbH 229 1.21e+00 1igtB b.1.1.1 19811 b.1.1.2 20921 1adqH 225 1.26e+00 1igtB b.1.1.1 20273 b.1.1.2 21273 1knoB 220 1.43e+00 1igtB b.1.1.1 20009 b.1.1.2 21063 2gfbB 219 1.60e+00 b.1.1.1 19993 b.1.1.2 21047 1aozA 552 1.69e+00 1aozA b.6.1.3 23124 b.6.1.3 23125 b.6.1.3 23126 1h3pH 219 1.81e+00 1lnrE 185 1.83e+00 1vfe 333 1.97e+00 1cb6A c.94.1.2 35854 1dsn 333 1.98e+00 1cb6A c.94.1.2 35837 1lct 333 2.00e+00 1cb6A c.94.1.2 35836 1hse 333 2.02e+00 1cb6A c.94.1.2 35849 1eh3A 334 2.02e+00 1nnt c.94.1.2 35842 1ji0A 240 2.09e+00 1vfd 330 2.13e+00 1cb6A c.94.1.2 35855 2mobA 138 2.14e+00 1ckv d.137.1.1 41453 1l5tA 332 2.14e+00 1ucbH 219 2.24e+00 1igtB b.1.1.1 20101 b.1.1.2 21133 1ezm 301 2.38e+00 1hyt d.92.1.2 58980 1mmn 762 2.40e+00 1lvk b.34.3.1 24582 c.37.1.9 32179 1mmg 762 2.49e+00 1lvk b.34.3.1 24579 c.37.1.9 32176 1lvk 762 2.66e+00 1lvk b.34.3.1 24576 c.37.1.9 32173 1clzH 218 2.83e+00 1igtB b.1.1.1 20105 b.1.1.2 21137 1hezD 224 2.92e+00 b.1.1.1 60989 b.1.1.2 60990 1vom 762 2.99e+00 1lvk b.34.3.1 24577 c.37.1.9 32174 1mnd 762 2.99e+00 1lvk b.34.3.1 24591 c.37.1.9 32188 1b0lA 691 3.05e+00 1cb6A c.94.1.2 35847 c.94.1.2 35848 1fckA 692 3.05e+00 1cb6A c.94.1.2 35843 c.94.1.2 35844 1cb6A 691 3.05e+00 1cb6A c.94.1.2 35840 c.94.1.2 35841 1lfi 691 3.07e+00 1cb6A c.94.1.2 35850 c.94.1.2 35851 1lfg 691 3.18e+00 1cb6A c.94.1.2 35845 c.94.1.2 35846 1lcf 691 3.19e+00 1cb6A c.94.1.2 35838 c.94.1.2 35839 1lfh 691 3.20e+00 1cb6A c.94.1.2 35856 c.94.1.2 35857 1jn3A 251 3.35e+00 1bpyA e.9.1.1 63183 1nom 248 3.71e+00 1bpyA e.9.1.1 43220 1bpb 248 3.71e+00 1bpyA e.9.1.1 43215 1rpl 251 3.74e+00 1bpyA e.9.1.1 43212 2fbjH 220 3.90e+00 1igtB b.1.1.1 19851 b.1.1.2 20955 8fabB 224 4.08e+00 1igtB b.1.1.1 19773 b.1.1.2 20883 2fb4H 229 4.29e+00 1igtB b.1.1.1 19847 b.1.1.2 20951 1blnB 218 4.41e+00 1igtB b.1.1.1 20331 b.1.1.2 21323 1huoA 335 5.04e+00 1bpyA a.60.6.1 61273 e.9.1.1 61274 1bpe 335 5.12e+00 1bpyA a.60.6.1 18076 e.9.1.1 43228 1dqlH 123 5.89e+00 1igtB b.1.1.1 19829 1igcH 222 5.89e+00 1igtB b.1.1.1 20047 b.1.1.2 21089 1bz7B 217 6.11e+00 1igtB b.1.1.1 20403 b.1.1.2 21375 1ejoH 220 6.13e+00 1igtB b.1.1.1 20429 b.1.1.2 21399 2ig2H 455 6.14e+00 1igtB b.1.1.1 19849 b.1.1.2 20953 1rlbE 174 6.19e+00 1aqb b.60.1.1 27090 1aqkH 226 6.36e+00 1igtB b.1.1.1 20193 b.1.1.2 21209 1deeB 223 6.43e+00 1igtB b.1.1.1 20443 b.1.1.2 21409 1kcuH 217 6.57e+00 1l1dA 152 6.86e+00 4fabH 216 7.12e+00 1igtB b.1.1.1 19907 b.1.1.2 21001 1flrH 219 7.15e+00 1igtB b.1.1.1 19905 b.1.1.2 20999 1r24B 217 7.16e+00 1igtB b.1.1.1 20405 b.1.1.2 21377 1g8xA 1010 7.39e+00 1lvk k.1.1.1 46378 1lox 662 7.49e+00 1lox a.119.1.2 19238 b.12.1.1 23638 1sm3H 218 8.61e+00 1igtB b.1.1.1 20369 b.1.1.2 21361 1qkzH 219 8.99e+00 1igtB b.1.1.1 20137 b.1.1.2 21167 1hbq 183 9.76e+00 1aqb b.60.1.1 27078 1hbp 183 9.90e+00 1aqb b.60.1.1 27079 1m5bA 263 1.06e+01 1lbcA 263 1.08e+01 1hdhA 536 1.12e+01 c.76.1.2 65805 1lbbA 263 1.15e+01 1m5dA 263 1.15e+01 1ivhA 394 1.16e+01 3mdeA a.29.3.1 16608 e.6.1.1 42869 1htiA 248 1.30e+01 1amk c.1.1.1 28455 1kenH 221 1.32e+01 1sbsH 222 1.32e+01 1igtB b.1.1.1 20367 b.1.1.2 21359 1aqb 183 1.37e+01 1aqb b.60.1.1 27084 1qleH 119 1.45e+01 1igtB b.1.1.1 20209 1ar1C 127 1.47e+01 1igtB b.1.1.1 20207 1c12B 220 1.47e+01 1igtB b.1.1.1 20381 b.1.1.2 21373 1b3oB 514 1.50e+01 1ak5 c.1.5.1 28641 d.37.1.1 38538 d.37.1.1 38539 32c2B 218 1.50e+01 1igtB b.1.1.1 20439 b.1.1.2 21405 1kb9J 127 1.51e+01 1b6rA 355 1.55e+01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1b6sA 355 1.55e+01 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 1f9bA 695 1.55e+01 1cb6A c.94.1.2 35869 c.94.1.2 35870 1jjgA 102 1.72e+01 1bafH 217 1.74e+01 1igtB b.1.1.1 19779 b.1.1.2 20889 1hfh 120 1.78e+01 1hfh g.18.1.1 44821 g.18.1.1 44822 1ireA 204 1.78e+01 1e5pA 151 1.79e+01 1bj7 b.60.1.1 59272 1lb8A 263 1.90e+01 1fv3A 472 1.91e+01 b.29.1.6 60038 b.42.4.2 60039 1go4A 205 1.94e+01 1fe8A 196 2.02e+01 1atzA c.62.1.1 59783 1fmvA 761 2.05e+01 1lvk b.34.3.1 24580 c.37.1.9 32177 1a8d 452 2.08e+01 1a8d b.29.1.6 24262 b.42.4.2 25607 1d0hA 469 2.15e+01 1a8d b.29.1.6 24265 b.42.4.2 25610 1hilB 220 2.24e+01 1igtB b.1.1.1 19787 b.1.1.2 20897 1duwA 292 2.31e+01 19hcA a.138.1.1 59138 1nsnH 210 2.35e+01 1igtB b.1.1.1 20071 b.1.1.2 21103 1rvfH 119 2.36e+01 1mfa b.1.1.1 19991 1axtH 218 2.52e+01 1igtB b.1.1.1 20305 b.1.1.2 21297 1dfqA 444 2.55e+01 1a8d b.29.1.6 24267 b.42.4.2 25612 1ecxA 384 2.59e+01 1ecxA c.67.1.3 34431 1g5jA 175 2.59e+01 1maz f.1.4.1 43394 1ao3A 187 2.61e+01 1atzA c.62.1.1 34134 1atzB 189 2.63e+01 1atzA c.62.1.1 34133 1atzA 189 2.63e+01 1atzA c.62.1.1 34132 1bxlA 181 2.64e+01 1maz f.1.4.1 43396 1frgH 220 2.76e+01 1igtB b.1.1.1 19925 b.1.1.2 21019 1mngA 203 2.77e+01 1avmA a.2.11.1 15776 d.44.1.1 38701 1a8y 367 2.91e+01 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1ts4A 194 2.97e+01 1aw7A b.40.2.2 25182 d.15.6.1 37771 1eg5A 384 2.99e+01 1ecxA c.67.1.3 34429 1d0yA 761 3.01e+01 1lvk b.34.3.1 24581 c.37.1.9 32178 1dllA 441 3.03e+01 1a8d b.29.1.6 24263 b.42.4.2 25608 1diwA 441 3.03e+01 1a8d b.29.1.6 24264 b.42.4.2 25609 1aw7A 194 3.04e+01 1aw7A b.40.2.2 25164 d.15.6.1 37753 1mma 762 3.08e+01 1lvk b.34.3.1 24587 c.37.1.9 32184 1f8tH 220 3.13e+01 1igtB b.1.1.1 59705 b.1.1.2 59706 1kcvH 217 3.15e+01 1fiwA 290 3.15e+01 5ptp 1d8lA 149 3.24e+01 1hjp a.60.2.1 17948 b.40.4.2 25267 1yrgA 385 3.46e+01 1yrgA c.10.1.2 30854 1yrgB 385 3.46e+01 1yrgA c.10.1.2 30855 1k5dC 386 3.47e+01 c.10.1.2 68170 1gjhA 166 3.50e+01 1maz f.1.4.1 60575 1gc1G 321 3.53e+01 1gc1G d.172.1.1 42493 1g9mG 321 3.54e+01 1gc1G d.172.1.1 42492 2tssA 194 3.64e+01 1aw7A b.40.2.2 25161 d.15.6.1 37750 1g5mA 166 3.66e+01 1maz f.1.4.1 60286 1yuiA 54 3.66e+01 1yuiA g.37.1.1 45073 1b2wH 220 3.67e+01 1igtB b.1.1.1 20307 b.1.1.2 21299 1fh5H 198 3.78e+01 1igtB b.1.1.1 20465 b.1.1.2 21429 3tss 194 3.82e+01 1aw7A b.40.2.2 25160 d.15.6.1 37749 2nef 136 3.83e+01 1efnB d.102.1.1 40704 1hjp 203 3.86e+01 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1pvxA 194 3.87e+01 1axkA b.29.1.11 24341 1qjhA 101 3.87e+01 1ris d.58.14.1 39326 1jw3A 140 3.89e+01 d.208.1.1 67373 1b0wA 108 3.90e+01 8fabA b.1.1.1 20532 1cuk 203 3.91e+01 1hjp a.5.1.1 16273 a.60.2.1 17946 b.40.4.2 25265 1igtB 444 3.91e+01 1igtB b.1.1.1 19765 b.1.1.2 20867 b.1.1.2 20868 b.1.1.2 20869 1igtD 444 3.91e+01 1igtB b.1.1.1 19767 b.1.1.2 20871 b.1.1.2 20872 b.1.1.2 20873 1qp1A 107 3.94e+01 8fabA b.1.1.1 20535 1eg0C 97 3.96e+01 1ris i.1.1.1 45809 1bpyA 335 3.98e+01 1bpyA a.60.6.1 17980 e.9.1.1 43122