# 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 1d0cA 444 1.68e+00 d.174.1.1 64769 1ed5A 444 1.68e+00 1nseA d.174.1.1 42530 1nseA 444 1.68e+00 1nseA d.174.1.1 42534 1d1vA 444 1.68e+00 1nseA d.174.1.1 59101 1bkcI 256 2.75e+00 1bkcA d.92.1.10 40334 1bkcA 255 2.77e+00 1bkcA d.92.1.10 40331 1bkcC 254 2.77e+00 1bkcA d.92.1.10 40332 1bkcE 256 2.85e+00 1bkcA d.92.1.10 40333 1lt4A 247 3.70e+00 1lt3A d.166.1.1 42231 3bifA 468 4.05e+00 1bif c.37.1.7 31962 c.60.1.4 34008 1bif 469 4.05e+00 1bif c.37.1.7 31961 c.60.1.4 34003 3nosA 427 4.30e+00 1nseA d.174.1.1 42520 2bifA 469 5.31e+00 1bif c.37.1.7 31963 c.60.1.4 34009 2prd 174 5.52e+00 2prd b.40.5.1 25435 1lmq 129 7.13e+00 3lzt d.2.1.2 36588 1i83A 444 9.08e+00 d.174.1.1 61938 1nocA 388 9.18e+00 1nseA d.174.1.1 42505 1dd7A 389 9.21e+00 1nseA d.174.1.1 42497 1bhgA 613 9.42e+00 1bhgA b.1.4.1 22161 b.18.1.5 23766 c.1.8.3 28889 1dwvA 420 9.63e+00 1nseA d.174.1.1 42501 3nodB 423 9.66e+00 1nseA d.174.1.1 42513 1qomA 440 9.83e+00 1nseA d.174.1.1 42514 1jwkA 434 9.84e+00 d.174.1.1 67387 1jwjA 433 1.00e+01 d.174.1.1 67385 1srvA 145 1.14e+01 1derA c.8.5.1 30817 1hcp 76 1.15e+01 2nllB g.39.1.2 45121 1hcqA 84 1.29e+01 2nllB g.39.1.2 45117 1b0aA 288 1.57e+01 1a4iA c.2.1.7 30286 c.58.1.2 33934 1ltaA 188 1.66e+01 1lt3A d.166.1.1 42232 1ltiA 192 1.66e+01 1lt3A d.166.1.1 42233 1ltgA 191 1.66e+01 1lt3A d.166.1.1 42235 1kyfA 247 1.83e+01 1qtsA 247 1.83e+01 1qtsA b.1.10.1 22313 d.105.1.1 40789 1ao0A 459 1.99e+01 1ecfB c.61.1.1 34049 d.153.1.1 41816 2semB 60 2.03e+01 1ckaA b.34.2.1 24547 1smlA 269 2.04e+01 1smlA d.157.1.1 42053 1ethA 448 2.10e+01 1gpl b.12.1.2 23641 c.69.1.19 34789 1ltsA 185 2.18e+01 1lt3A d.166.1.1 42229 3lck 271 2.26e+01 1fmk d.144.1.2 41686 1acx 108 2.26e+01 2mcm b.1.7.1 22211 1gph1 465 2.27e+01 1ecfB 1semA 58 2.27e+01 1ckaA b.34.2.1 24544 1pdo 135 2.29e+01 1pdo c.54.1.1 33376 1k32A 1045 2.29e+01 b.36.1.3 68068 b.68.7.1 68069 b.69.9.1 68070 c.14.1.2 68071 1qpcA 279 2.29e+01 1fgkA d.144.1.2 41685 1tvdA 116 2.33e+01 1tvdA b.1.1.1 20650 1htlA 191 2.33e+01 1lt3A d.166.1.1 42237 1bmsA 129 2.34e+01 1msc d.85.1.1 40082 1emrA 159 2.35e+01 1lki a.26.1.1 59456 1gtzA 156 2.37e+01 1d0iA 156 2.39e+01 2dhqA c.23.13.1 31383 1fpn2 261 2.42e+01 1aym2 1b9kA 238 2.44e+01 1qtsA b.1.10.1 22315 d.105.1.1 40791 1ijaA 148 2.45e+01 1ijaA b.100.1.1 62484 1kfvA 271 2.47e+01 1dm0A 287 2.54e+01 1dm0A d.165.1.2 42227 1nsiA 431 2.63e+01 1nseA d.174.1.1 42522 4nosA 427 2.65e+01 1nseA d.174.1.1 42516 1fzyA 149 2.73e+01 d.20.1.1 65072 1jwiB 125 3.05e+01 d.169.1.1 67384 3pgk 416 3.11e+01 16pk c.86.1.1 35451 1gwjA 377 3.12e+01 1qtpA 247 3.29e+01 1qtsA b.1.10.1 22314 d.105.1.1 40790 1gav! 129 3.32e+01 1hyeA 313 3.36e+01 2cmd c.2.1.5 61400 d.162.1.1 61401 3fib 249 3.62e+01 3fib d.171.1.1 42455 1kcyA 75 3.63e+01 a.39.1.1 68450 1koa 491 3.64e+01 1tkiA b.1.1.4 21712 d.144.1.1 41642 1unaA 129 3.68e+01 1msc d.85.1.1 40094 2fibA 269 3.76e+01 3fib d.171.1.1 42457 1fib 269 3.76e+01 3fib d.171.1.1 42456 1cvsC 225 3.84e+01 1cvsC b.1.1.4 21726 b.1.1.4 21727 1qpdA 279 3.88e+01 1fmk d.144.1.2 41687 1ce7A 241 3.95e+01 1mrj d.165.1.1 42194 1evtD 225 3.97e+01 1cvsC b.1.1.4 21732 b.1.1.4 21733 3cms 323 3.98e+01 1smrA b.50.1.2 26865