# List of top-scoring protein chains for t2k-100-30-alpha 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 1bet 107 1.81e-02 1bndA g.17.1.3 44801 1cviA 342 2.14e-02 1cviA c.60.1.2 33989 2hpaA 342 4.51e-02 1cviA c.60.1.2 33985 1rpa 342 7.97e-02 1cviA c.60.1.2 33983 1hs6A 611 2.71e-01 1hs6A a.118.1.7 61233 b.98.1.1 61234 d.92.1.13 61235 1pcp 106 8.55e-01 2pspA g.16.1.1 44742 g.16.1.1 44743 1quqB 121 9.11e-01 1quqB b.40.4.3 25305 1bjx 110 1.02e+00 1bjx c.47.1.2 32774 2bjxA 110 1.02e+00 1bjx c.47.1.2 32776 2pspA 106 1.17e+00 2pspA g.16.1.1 44730 g.16.1.1 44731 1bolA 222 1.18e+00 1bolA d.124.1.1 41120 1uok 558 1.46e+00 1uok b.71.1.1 27801 c.1.8.1 28788 1d2kA 392 1.80e+00 1d2kA c.1.8.5 29008 d.26.3.1 38442 1ji2A 585 1.94e+00 1gyxA 76 2.19e+00 1a6wL 109 2.26e+00 1mfa b.1.1.1 20252 1ecxA 384 2.30e+00 1ecxA c.67.1.3 34431 1g0uI 205 2.31e+00 d.153.1.4 41891 487dL 133 2.70e+00 1mmsA i.1.1.2 45839 1bvzA 585 2.83e+00 1bvzA b.1.1.5 21856 b.71.1.1 27783 c.1.8.1 28770 1rypJ 204 2.90e+00 d.153.1.4 41878 1eg5A 384 3.11e+00 1ecxA c.67.1.3 34429 1a6uL 108 3.40e+00 1mfa b.1.1.1 20254 1dynA 125 3.46e+00 1dynA b.55.1.1 26955 1hcl 298 3.74e+00 1hcl d.144.1.1 41593 1i50B 1224 3.90e+00 e.29.1.2 61755 1e1xA 299 4.25e+00 1hcl d.144.1.1 59157 1gatA 60 4.67e+00 1gatA g.39.1.1 45106 1kamA 194 4.86e+00 1mmsA 140 5.00e+00 1mmsA a.4.7.1 16247 d.47.1.1 38766 1jvpP 298 5.06e+00 d.144.1.1 67371 1irqA 71 5.24e+00 a.43.1.2 66297 3gatA 66 6.96e+00 1gatA g.39.1.1 45103 1fzvA 132 8.40e+00 1vpfA g.17.1.1 60159 2pldA 105 8.52e+00 1qadA d.93.1.1 40521 1apa 266 8.67e+00 1qi7A d.165.1.1 42205 1dcnD 436 8.75e+00 1auwA a.127.1.1 19423 1d0nA 729 8.97e+00 1d0nA d.109.1.1 40834 d.109.1.1 40835 d.109.1.1 40836 d.109.1.1 40837 d.109.1.1 40838 d.109.1.1 40839 1a6jA 163 9.56e+00 1a6jA d.112.1.1 40915 2gatA 66 9.71e+00 1gatA g.39.1.1 45102 1cczA 171 1.02e+01 1cczA b.1.1.1 19758 b.1.1.3 21683 1rec 201 1.06e+01 1rec a.39.1.5 17326 1hxs1 302 1.07e+01 1g0rA 293 1.10e+01 1g0rA c.68.1.6 34532 1j7dA 145 1.12e+01 1jatB d.20.1.1 62680 1qp8A 303 1.14e+01 1qp8A c.2.1.4 30092 c.23.12.1 31352 1ej6A 1289 1.15e+01 i.7.1.1 45967 1k7wA 468 1.18e+01 1a8p 258 1.23e+01 1fdr b.43.4.2 25654 c.25.1.1 31544 2pleA 105 1.26e+01 1qadA d.93.1.1 40522 1fxoA 293 1.27e+01 1g0rA c.68.1.6 34524 1fhoA 119 1.31e+01 1fhoA b.55.1.1 26982 1gm6A 175 1.35e+01 1cz4A 185 1.40e+01 1cz4A b.52.2.3 26934 d.31.1.1 38468 1ew4A 106 1.49e+01 1ew4A d.82.2.1 40023 1e4mM 501 1.62e+01 1e70M c.1.8.4 59226 1otgA 125 1.63e+01 1otgA d.80.1.2 39831 1c8bA 371 1.64e+01 1c8bA c.56.1.2 59082 1bia 321 1.78e+01 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1e6qM 501 1.82e+01 1e70M c.1.8.4 28920 1rmg 422 1.83e+01 1rmg b.80.1.3 28029 1e42A 258 1.92e+01 1e42A b.1.10.1 22316 d.105.1.1 40792 1bag 425 1.93e+01 1bag b.71.1.1 27720 c.1.8.1 28707 1ds6B 180 1.97e+01 1rhoA b.1.1.5 21898 1lox 662 2.00e+01 1lox a.119.1.2 19238 b.12.1.1 23638 1e70M 501 2.02e+01 1e70M c.1.8.4 28926 1f3uB 171 2.05e+01 1f3uB b.65.1.1 27525 1j7iA 264 2.05e+01 1j7iA d.144.1.6 62694 1dm5A 315 2.06e+01 1avc a.65.1.1 18186 2pooA 355 2.16e+01 1qlgA b.68.3.1 27626 1bftA 101 2.16e+01 1a3qA b.1.1.5 21934 1fpzA 212 2.16e+01 1fpzA c.45.1.1 59976 1cs6A 382 2.18e+01 1cs6A b.1.1.4 21760 b.1.1.4 21761 b.1.1.4 21762 b.1.1.4 21763 1irxA 523 2.18e+01 12asA 330 2.31e+01 12asA d.104.1.1 40783 1qlgA 355 2.31e+01 1qlgA b.68.3.1 27627 1jjfA 268 2.33e+01 c.69.1.2 66765 2rslA 140 2.33e+01 2rslA c.53.1.1 33345 1d4xG 126 2.35e+01 1d0nA d.109.1.1 59109 1tit 98 2.37e+01 1tit b.1.1.4 21716 1a8s 273 2.38e+01 1brt c.69.1.12 34710 1bib 321 2.43e+01 1bia a.4.5.1 16084 b.34.1.1 24448 d.104.1.2 40788 1dzrA 183 2.54e+01 1dzrA b.82.1.1 28076 1bk1 184 2.54e+01 1axkA b.29.1.11 24340 1hnoA 280 2.54e+01 1hnoA c.14.1.3 61095 1bhjA 292 2.54e+01 1xvaA c.66.1.5 34189 1hqvA 191 2.57e+01 1hqvA a.39.1.8 61160 1qfoC 119 2.63e+01 1qfoA b.1.1.1 19710 2dynA 122 2.66e+01 1dynA b.55.1.1 26957 1daqA 71 2.92e+01 1daqA a.139.1.1 59113 1ah6 220 2.96e+01 1yer d.122.1.1 41094 1g2qA 187 2.97e+01 c.61.1.1 65117 1a28A 256 2.98e+01 1a28A a.123.1.1 19290 1hnuA 280 3.03e+01 1hnoA c.14.1.3 61096 1auwA 468 3.03e+01 1auwA a.127.1.1 19416 1pov1 302 3.06e+01 1pov1 1itvA 195 3.11e+01 1ecfA 504 3.22e+01 1ecfB c.61.1.1 34053 d.153.1.1 41820 1cx8A 639 3.22e+01 1cx8B a.48.2.1 17782 c.8.4.1 30763 c.56.5.5 33851 1dpb 243 3.31e+01 1eaf c.43.1.1 32618 1dcnA 424 3.31e+01 1auwA a.127.1.1 19420 1xvaA 292 3.44e+01 1xvaA c.66.1.5 34183 1cx8B 639 3.62e+01 1cx8B a.48.2.1 17783 c.8.4.1 30764 c.56.5.5 33852 1f46A 140 3.70e+01 1f46A d.129.4.1 59643 1iyjA 70 3.73e+01 1jl3A 139 3.74e+01 c.44.1.1 66826 1cvmA 353 3.90e+01 1qlgA b.68.3.1 27628 1bxdA 161 3.95e+01 1bxdA d.122.1.3 41111