# 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 1i1dA 161 1.33e-03 1i21A d.108.1.1 61526 1i12A 160 1.35e-03 1i21A d.108.1.1 61515 1i21A 159 1.60e-03 1i21A d.108.1.1 61549 1ib1E 200 8.42e-02 1cjwA d.108.1.1 62137 1kuxA 207 1.03e-01 1d3yA 301 1.17e-01 1d3yA e.12.1.1 43252 1b6bA 174 4.33e-01 1cjwA d.108.1.1 40819 1cjwA 166 4.42e-01 1cjwA d.108.1.1 40818 1qsoA 149 5.52e-01 1qsmA d.108.1.1 40812 1fl5B 219 5.53e-01 b.1.1.1 65017 b.1.1.2 65018 1qsmA 152 5.84e-01 1qsmA d.108.1.1 40808 1drmA 131 2.73e+00 1drmA d.110.3.2 40908 1drqA 131 2.73e+00 1drmA d.110.3.2 40910 1jjiA 311 3.32e+00 c.69.1.2 66766 1a1s 314 4.34e+00 1othA c.78.1.1 35258 c.78.1.1 35259 1sra 151 5.16e+00 1sra a.39.1.3 17190 1kelH 218 5.54e+00 1igtB b.1.1.1 20113 b.1.1.2 21143 1c9rB 430 5.89e+00 1rthA e.8.1.2 43109 1bfoB 216 6.54e+00 1igtB b.1.1.1 20311 b.1.1.2 21303 1nubA 229 7.36e+00 1sra a.39.1.3 17191 g.3.11.3 44330 g.15.1.1 44715 1xyn 178 7.36e+00 1axkA b.29.1.11 24322 1bmoA 233 7.43e+00 1sra a.39.1.3 17193 g.3.11.3 44332 g.15.1.1 44717 1jlgA 560 7.56e+00 c.55.3.1 66848 e.8.1.2 66849 1xtcD 103 8.97e+00 3chbD b.40.2.1 25005 1kewA 361 9.18e+00 c.2.1.2 68544 1qg3A 195 9.39e+00 1qg3A b.1.2.1 21993 b.1.2.1 21994 1mamH 217 1.06e+01 1igtB b.1.1.1 19887 b.1.1.2 20983 1jleB 440 1.10e+01 e.8.1.2 66844 1hniB 427 1.12e+01 1rthA e.8.1.2 43045 1rt3B 440 1.12e+01 1rthA e.8.1.2 43053 1cm0A 168 1.13e+01 1yghA d.108.1.1 40800 1rtjB 440 1.17e+01 1rthA e.8.1.2 43035 1fkpB 440 1.19e+01 1rthA e.8.1.2 43099 1rt3A 560 1.20e+01 1rthA c.55.3.1 33590 e.8.1.2 43052 1jlfA 560 1.26e+01 c.55.3.1 66845 e.8.1.2 66846 1rtdA 554 1.28e+01 1rthA c.55.3.1 33591 e.8.1.2 43048 2cb5A 453 1.28e+01 3gcb d.3.1.1 37035 1har 216 1.30e+01 1rthA e.8.1.2 43025 1fk9A 543 1.31e+01 1rthA c.55.3.1 33607 e.8.1.2 43080 1rthA 560 1.32e+01 1rthA c.55.3.1 33576 e.8.1.2 43028 1vrtA 560 1.32e+01 1rthA c.55.3.1 33574 e.8.1.2 43023 1dttA 560 1.34e+01 1rthA c.55.3.1 33611 e.8.1.2 43088 1fkoA 543 1.34e+01 1rthA c.55.3.1 33612 e.8.1.2 43094 1qe1B 427 1.38e+01 1rthA e.8.1.2 43055 1bqnB 430 1.43e+01 1rthA e.8.1.2 43065 1igrA 478 1.44e+01 1igrA c.10.2.5 30877 c.10.2.5 30878 g.3.9.1 44188 1iruF 263 1.48e+01 1qo7A 394 1.57e+01 1qo7A c.69.1.11 34697 1qe1A 558 1.61e+01 1rthA c.55.3.1 33593 e.8.1.2 43054 1bx2B 191 1.63e+01 1iakB b.1.1.2 21610 d.19.1.1 38184 1brsD 89 1.66e+01 1ay7B c.9.1.1 30825 1b27D 90 1.66e+01 1ay7B c.9.1.1 30840 1qq2A 199 1.67e+01 1qq2A c.47.1.10 33064 1ew3A 159 1.69e+01 1mup b.60.1.1 27114 1jlaB 440 1.80e+01 e.8.1.2 66835 1b3sD 90 1.86e+01 1ay7B c.9.1.1 30846 1bqnA 558 1.87e+01 1rthA c.55.3.1 33599 e.8.1.2 43064 1b2uD 90 1.87e+01 1ay7B c.9.1.1 30843 1bob 320 1.90e+01 1bob d.108.1.1 40816 1ay7B 89 1.91e+01 1ay7B c.9.1.1 30836 1a19A 90 1.95e+01 1ay7B c.9.1.1 30831 1hvuB 423 2.01e+01 1rthA e.8.1.2 43069 1hysB 425 2.02e+01 1rthA e.8.1.2 61419 1hnvB 427 2.03e+01 1rthA e.8.1.2 43057 1ikwB 427 2.04e+01 e.8.1.2 62532 1bqmB 430 2.04e+01 1rthA e.8.1.2 43061 1cb5A 453 2.04e+01 3gcb d.3.1.1 37037 1ikxB 427 2.07e+01 e.8.1.2 62535 1jkhA 560 2.07e+01 c.55.3.1 66797 e.8.1.2 66798 1hquB 430 2.07e+01 1rthA e.8.1.2 61159 1c1bB 440 2.10e+01 1rthA e.8.1.2 43077 1hmvB 440 2.10e+01 1rthA e.8.1.2 43047 1jl5A 454 2.24e+01 c.10.2.6 66830 1g9uA 454 2.24e+01 c.10.2.6 65172 1qmvA 197 2.29e+01 1qq2A c.47.1.10 33066 1bl0A 129 2.29e+01 1d5yA a.4.1.8 16053 a.4.1.8 16054 1glv 303 2.33e+01 1gsa c.30.1.3 31721 d.142.1.1 41480 1hysA 553 2.37e+01 1rthA c.55.3.1 61417 e.8.1.2 61418 1dloA 556 2.37e+01 1rthA c.55.3.1 33584 e.8.1.2 43040 2hmiA 558 2.37e+01 1rthA c.55.3.1 33604 e.8.1.2 43106 1hvuA 554 2.38e+01 1rthA c.55.3.1 33600 e.8.1.2 43068 3hvtA 556 2.39e+01 1rthA c.55.3.1 33598 e.8.1.2 43066 1eetA 557 2.39e+01 1rthA c.55.3.1 33608 e.8.1.2 43078 1ikwA 560 2.39e+01 1rthA c.55.3.1 62530 e.8.1.2 62531 1hmvA 560 2.39e+01 1rthA c.55.3.1 33587 e.8.1.2 43046 1qitA 396 2.40e+01 1ajsA c.67.1.1 34286 1hquA 560 2.42e+01 1rthA c.55.3.1 61157 e.8.1.2 61158 1ikxA 560 2.43e+01 1rthA c.55.3.1 62533 e.8.1.2 62534 1ibrB 462 2.49e+01 1qgrA a.118.1.1 19120 1iaoB 222 2.54e+01 1iakB b.1.1.2 21642 d.19.1.1 38216 3hvtB 398 2.65e+01 1rthA e.8.1.2 43067 1ktdB 215 2.69e+01 1eg3A 261 2.78e+01 1eg3A a.39.1.7 17376 a.39.1.7 17377 b.72.1.1 27805 1j7lA 264 2.84e+01 d.144.1.6 62697 1j7iA 264 2.84e+01 1j7iA d.144.1.6 62694 1a6aB 187 2.90e+01 1iakB b.1.1.2 21616 d.19.1.1 38190 2iadB 205 2.90e+01 1iakB b.1.1.2 21640 d.19.1.1 38214 1kt2B 213 2.96e+01 1qhoA 686 2.99e+01 1cxlA b.1.1.5 21844 b.3.1.1 22513 b.71.1.1 27751 c.1.8.1 28738 1iebB 227 3.03e+01 1iakB b.1.1.2 21636 d.19.1.1 38210 1uwbB 427 3.14e+01 1rthA e.8.1.2 43063 1dj7B 75 3.14e+01 1dj7B b.34.4.3 24598 1d06A 130 3.19e+01 1drmA d.110.3.2 40906 1ew0A 130 3.19e+01 1drmA d.110.3.2 40905 1b2sD 90 3.20e+01 1ay7B c.9.1.1 30837 1kk6B 209 3.20e+01 b.81.1.3 68658 1hixB 190 3.21e+01 b.29.1.11 65840 1fneB 224 3.61e+01 1iakB b.1.1.2 59898 d.19.1.1 59899 1uwbA 558 3.69e+01 1rthA c.55.3.1 33596 e.8.1.2 43062 1e12A 253 3.71e+01 1c3wA f.2.1.1 43428 1chpD 103 3.87e+01 3chbD b.40.2.1 24980 1g8zD 103 3.90e+01 3chbD b.40.2.1 60383