# 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.soe.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 2frzA 414 1.12e+00 a.104.1.1 134001 1c8jA 414 1.15e+00 1phd a.104.1.1 59085 1y6dA 120 1.45e+00 a.24.10.5 116504 2qbmA 421 1.62e+00 1iwkA 415 1.65e+00 a.104.1.1 71490 2qbnA 421 1.66e+00 2a1nA 415 1.67e+00 2a1oA 415 1.69e+00 2a1mA 415 1.69e+00 a.104.1.1 126003 2zawA 415 1.69e+00 1rf9A 417 1.70e+00 a.104.1.1 111795 2fe6A 421 1.70e+00 a.104.1.1 133324 1gebA 415 1.73e+00 1phd a.104.1.1 18932 6cp4A 414 1.74e+00 a.104.1.1 18924 1qmqA 414 1.77e+00 1phd a.104.1.1 18907 1yrcA 414 1.77e+00 a.104.1.1 123917 2cp4A 414 1.77e+00 a.104.1.1 18933 2h7rA 414 1.78e+00 1t85A 414 1.78e+00 a.104.1.1 106650 1p2yA 420 1.78e+00 a.104.1.1 93961 2gqxA 405 1.79e+00 1dz4A 414 1.80e+00 1phd a.104.1.1 18903 1iwjA 415 1.81e+00 a.104.1.1 71489 1tp9A 162 1.95e+00 c.47.1.10 119306 2ckfB 174 2.43e+00 1v2aA 210 2.78e+00 a.45.1.1 100263 c.47.1.5 100264 2ferA 411 2.85e+00 a.104.1.1 133350 2ocgA 254 2.85e+00 2ockA 254 3.29e+00 2oclA 254 3.77e+00 3c0iA 351 4.12e+00 1z21A 112 4.95e+00 a.243.1.2 124367 1nkrA 201 5.76e+00 b.1.1.4 21799 b.1.1.4 21800 1im9D 225 6.01e+00 1nkr b.1.1.4 62585 b.1.1.4 62586 2quqA 562 7.41e+00 2veqA 565 7.42e+00 1umwA 237 8.21e+00 d.223.1.2 99631 d.223.1.2 99632 2ogqA 239 8.28e+00 d.223.1.2 139063 d.223.1.2 139064 1q4kA 259 8.62e+00 d.223.1.2 95797 d.223.1.2 95798 2dkaA 544 9.98e+00 1umnA 165 1.19e+01 a.25.1.1 99607 2ux1A 165 1.19e+01 1jvaA 475 1.40e+01 b.86.1.2 77175 d.95.2.2 77176 d.95.2.2 77177 1ef0A 462 1.46e+01 1vdeA b.86.1.2 28376 d.95.2.2 40577 d.95.2.2 40578 1um2A 454 1.56e+01 b.86.1.2 107946 d.95.2.2 107947 d.95.2.2 107948 1dfaA 454 1.58e+01 1vdeA b.86.1.2 28375 d.95.2.2 40575 d.95.2.2 40576 1vdeA 454 1.58e+01 1vdeA b.86.1.2 28378 d.95.2.2 40581 d.95.2.2 40582 1ygsA 234 1.63e+01 b.26.1.1 23907 1mr1A 235 1.69e+01 b.26.1.1 79418 1u7vB 236 1.72e+01 b.26.1.1 107730 1u7fB 239 1.74e+01 b.26.1.1 107721 1vl7A 157 1.91e+01 b.45.1.1 108732 3csvA 333 1.96e+01 1u6gC 1230 2.03e+01 a.118.1.2 113066 3cs3A 277 2.05e+01 2r2oA 138 2.20e+01 3ckdA 312 2.23e+01 2rexA 121 2.29e+01 1dd1A 268 2.35e+01 b.26.1.1 23908 2o71A 115 2.41e+01 1g88A 268 2.46e+01 1ygs b.26.1.1 23911 1tqyA 424 2.68e+01 c.95.1.1 107245 c.95.1.1 107246 2ouxA 286 2.82e+01 1dxyA 333 2.83e+01 c.2.1.4 30094 c.23.12.1 31354 1nu0A 138 2.87e+01 c.55.3.8 92165 2pkgA 580 2.99e+01 a.118.1.2 139708 2du8A 347 2.99e+01 2ie4A 589 3.00e+01 a.118.1.2 137291 1b3uA 588 3.00e+01 1b3uA a.118.1.2 19135 2nymA 582 3.00e+01 a.118.1.2 138821 1usrA 454 3.02e+01 b.68.1.1 99881 1e8tA 454 3.02e+01 1e8tA b.68.1.1 59387 2eguA 308 3.15e+01 2ftsA 419 3.16e+01 b.85.6.1 134079 b.103.1.1 134080 c.57.1.2 134081 1nmnA 138 3.17e+01 c.55.3.8 91978 2pf4A 589 3.23e+01 1t3eA 421 3.27e+01 b.85.6.1 106348 b.103.1.1 106349 c.57.1.2 106350 1bccE 196 3.31e+01 1rie b.33.1.1 24431 f.23.12.1 43699 2vpzC 253 3.35e+01 1ykbA 142 3.40e+01 a.26.1.3 123503 1m4rA 151 3.45e+01 a.26.1.3 84799 1ppjE 196 3.61e+01 b.33.1.1 104260 f.23.12.1 104261 1bgyE 196 3.61e+01 1bgyE f.23.12.1 43683 1ifkA 51 3.73e+01 h.1.4.1 45565 2tsrA 307 3.77e+01 1bkpA d.117.1.1 41043 1pu6A 218 3.78e+01 a.96.1.5 95123