# List of top-scoring protein chains for T0478.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 2.19e+00 a.104.1.1 134001 1c8jA 414 2.24e+00 1phd a.104.1.1 59085 1y6dA 120 2.83e+00 a.24.10.5 116504 2qbmA 421 3.16e+00 1iwkA 415 3.23e+00 a.104.1.1 71490 2qbnA 421 3.25e+00 2a1nA 415 3.26e+00 2a1oA 415 3.31e+00 2a1mA 415 3.32e+00 a.104.1.1 126003 2zawA 415 3.32e+00 1rf9A 417 3.33e+00 a.104.1.1 111795 2fe6A 421 3.33e+00 a.104.1.1 133324 1gebA 415 3.39e+00 1phd a.104.1.1 18932 6cp4A 414 3.41e+00 a.104.1.1 18924 1qmqA 414 3.47e+00 1phd a.104.1.1 18907 1yrcA 414 3.47e+00 a.104.1.1 123917 2cp4A 414 3.47e+00 a.104.1.1 18933 2h7rA 414 3.48e+00 1t85A 414 3.48e+00 a.104.1.1 106650 1p2yA 420 3.49e+00 a.104.1.1 93961 2gqxA 405 3.51e+00 1dz4A 414 3.52e+00 1phd a.104.1.1 18903 1iwjA 415 3.55e+00 a.104.1.1 71489 1tp9A 162 3.83e+00 c.47.1.10 119306 2ckfB 174 4.77e+00 1v2aA 210 5.47e+00 a.45.1.1,c.47.1.5 100263,100264 2ferA 411 5.59e+00 a.104.1.1 133350 2ocgA 254 5.60e+00 2ockA 254 6.48e+00 2oclA 254 7.43e+00 3c0iA 351 8.12e+00 1z21A 112 9.77e+00 a.243.1.2 124367 1nkrA 201 1.14e+01 b.1.1.4,b.1.1.4 21799,21800 1im9D 225 1.19e+01 1nkr b.1.1.4,b.1.1.4 62585,62586 2quqA 562 1.47e+01 2veqA 565 1.47e+01 1umwA 237 1.63e+01 d.223.1.2,d.223.1.2 99631,99632 2ogqA 239 1.64e+01 d.223.1.2,d.223.1.2 139063,139064 1q4kA 259 1.71e+01 d.223.1.2,d.223.1.2 95797,95798 2dkaA 544 1.98e+01 1umnA 165 2.36e+01 a.25.1.1 99607 2ux1A 165 2.36e+01 1jvaA 475 2.78e+01 b.86.1.2,d.95.2.2,d.95.2.2 77175,77176,77177 1ef0A 462 2.90e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28376,40577,40578 1um2A 454 3.10e+01 b.86.1.2,d.95.2.2,d.95.2.2 107946,107947,107948 1dfaA 454 3.15e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28375,40575,40576 1ygsA 234 3.25e+01 b.26.1.1 23907 1mr1A 235 3.35e+01 b.26.1.1 79418 1u7vB 236 3.42e+01 b.26.1.1 107730 1u7fB 239 3.46e+01 b.26.1.1 107721 1vl7A 157 3.80e+01 b.45.1.1 108732 3csvA 333 3.90e+01 1u6gC 1230 4.04e+01 a.118.1.2 113066 3cs3A 277 4.08e+01 2r2oA 138 4.37e+01 3ckdA 312 4.43e+01 2rexA 121 4.56e+01 1dd1A 268 4.69e+01 b.26.1.1 23908 2o71A 115 4.79e+01 1g88A 268 4.90e+01 1ygs b.26.1.1 23911 1tqyA 424 5.34e+01 c.95.1.1,c.95.1.1 107245,107246 2ouxA 286 5.63e+01 1dxyA 333 5.66e+01 c.2.1.4,c.23.12.1 30094,31354 1nu0A 138 5.73e+01 c.55.3.8 92165 2pkgA 580 5.97e+01 a.118.1.2 139708 2du8A 347 5.97e+01 2ie4A 589 5.98e+01 a.118.1.2 137291 1b3uA 588 5.98e+01 1b3uA a.118.1.2 19135 2nymA 582 5.99e+01 a.118.1.2 138821 1usrA 454 6.03e+01 b.68.1.1 99881 2eguA 308 6.28e+01 2ftsA 419 6.31e+01 b.85.6.1,b.103.1.1,c.57.1.2 134079,134080,134081 1nmnA 138 6.33e+01 c.55.3.8 91978 2pf4A 589 6.45e+01 1t3eA 421 6.53e+01 b.85.6.1,b.103.1.1,c.57.1.2 106348,106349,106350 1bccE 196 6.62e+01 1rie b.33.1.1,f.23.12.1 24431,43699 2vpzC 253 6.68e+01 1ykbA 142 6.79e+01 a.26.1.3 123503 1m4rA 151 6.90e+01 a.26.1.3 84799 1ppjE 196 7.21e+01 b.33.1.1,f.23.12.1 104260,104261 1ifkA 51 7.46e+01 h.1.4.1 45565 2tsrA 307 7.53e+01 1bkpA d.117.1.1 41043 1pu6A 218 7.56e+01 a.96.1.5 95123