# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7 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 1eni 138 2.57e-02 2end a.18.1.1 16403 1enk 138 3.05e-02 2end a.18.1.1 16402 1vasA 137 3.50e-02 2end a.18.1.1 16404 1enj 138 8.26e-02 2end a.18.1.1 16401 2end 138 1.27e-01 2end a.18.1.1 16400 1yx4A 132 4.71e-01 1urqA 63 6.52e-01 h.1.15.1 107994 1su4A 994 9.14e-01 b.82.7.1 98993 c.108.1.7 98994 d.220.1.1 98995 f.33.1.1 98996 1mml 265 1.10e+00 1mml e.8.1.2 43015 1ny9A 143 1.63e+00 a.181.1.1 86401 1ufbA 127 1.65e+00 a.24.16.3 99331 1b43A 340 1.73e+00 1a76 a.60.7.1 18092 c.120.1.2 33362 2hfh 109 1.99e+00 2hfh a.4.5.14 16145 1ijyA 130 2.02e+00 1ijxA a.141.1.1 62517 1rwtA 232 2.59e+00 f.43.1.1 97992 1im4A 221 2.83e+00 e.8.1.7 62581 1mroC 247 2.89e+00 1mroC d.58.31.1 39437 1ovnA 248 2.91e+00 a.71.1.1 93602 c.47.1.7 93603 1hbnC 248 3.12e+00 1mroC d.58.31.1 60902 1jb0D 138 3.24e+00 1jb0D d.187.1.1 62823 1ijxA 127 3.33e+00 1ijxA a.141.1.1 62511 1f07A 321 3.45e+00 1ezwA c.1.16.3 59560 1cokA 68 3.76e+00 1cokA a.60.1.2 17945 1w6uA 302 4.16e+00 1zsxA 347 4.18e+00 1r5zA 323 4.27e+00 f.40.1.1 97135 1bpe 335 4.31e+00 1bpyA a.60.6.1 18076 a.60.12.1 75815 d.218.1.2 75816 1iyjB 817 4.31e+00 a.170.1.1 76948 a.171.1.1 76949 b.40.4.3 76950 b.40.4.3 76951 b.40.4.3 76952 1qs0A 407 4.51e+00 1qs0A c.36.1.11 31829 1nt4A 391 4.78e+00 c.60.1.2 92102 1a8rA 221 4.89e+00 1a8rA d.96.1.1 40587 1sfkA 76 4.91e+00 a.190.1.1 105488 1unlD 208 5.28e+00 1h4lD 147 5.37e+00 a.74.1.1 70873 1x9mA 698 5.66e+00 1o51A 114 5.68e+00 d.58.5.4 92480 1v1rA 400 5.82e+00 c.36.1.11 108272 1x7yA 400 6.55e+00 1wwpA 119 6.61e+00 2astA 159 7.19e+00 1fqvJ 149 7.22e+00 1fqvD a.157.1.1 19266 d.42.1.1 38670 1t7pA 698 7.42e+00 1t7pA c.55.3.5 33712 e.8.1.1 43005 1qb2A 109 7.78e+00 1qb2A a.36.1.1 17125 2fpmA 322 7.82e+00 1uelB 48 8.18e+00 j.105.1.1 99266 1yewB 247 8.32e+00 1tv9A 335 8.40e+00 1e0fI 57 8.44e+00 1e0fI g.3.15.2 44377 1olsA 400 8.60e+00 c.36.1.11 93331 1v9mA 323 8.66e+00 f.40.1.1 100543 1exbA 332 8.97e+00 1qrqA c.1.7.1 28666 1ztsA 139 9.49e+00 1xo3A 101 1.00e+01 1fqvD 149 1.03e+01 1fqvD a.157.1.1 19263 d.42.1.1 38667 1g8eA 116 1.06e+01 1g8eA a.145.1.1 60346 1gfsA 321 1.08e+01 c.2.1.2 29811 1bsvA 321 1.09e+01 1bsvA c.2.1.2 29809 1vk9A 151 1.09e+01 c.139.1.1 108640 1aa7A 158 1.10e+01 1aa7A a.95.1.1 18741 1yaxA 153 1.10e+01 1m5yA 408 1.12e+01 a.167.1.1 78664 d.26.1.1 78665 d.26.1.1 78666 1umgA 362 1.15e+01 d.280.1.1 107956 1jgsA 138 1.20e+01 a.4.5.28 66683 1alvA 173 1.21e+01 1alvA a.39.1.8 17370 1cfi 47 1.22e+01 1cfi g.32.1.1 44971 1t4gA 322 1.31e+01 a.60.4.1 106418 c.37.1.11 106419 1xfxO 149 1.33e+01 1bpyA 335 1.38e+01 1bpyA a.60.6.1 17980 a.60.12.1 75819 d.218.1.2 75820 1sk4A 163 1.48e+01 d.118.1.1 105664 1or7A 194 1.48e+01 a.4.13.2 87332 a.177.1.1 87333 1w7jB 151 1.53e+01 2beqD 48 1.54e+01 1a00B 146 1.54e+01 1abwA a.1.1.2 15469 1zsyA 357 1.54e+01 1ubi 76 1.56e+01 1ubi d.15.1.1 37584 1wywA 230 1.58e+01 1h7sA 365 1.61e+01 d.14.1.3 65705 d.122.1.2 65706 1ubq 76 1.62e+01 1ubi d.15.1.1 37585 1ea3A 164 1.63e+01 1aa7A a.95.1.1 59398 1p9cA 45 1.75e+01 j.105.1.1 94386 2aalA 131 1.77e+01 1xn8A 131 1.77e+01 2c43A 323 1.78e+01 1aj5A 173 1.78e+01 1alvA a.39.1.8 17367 1cg5B 141 1.78e+01 1cg5B a.1.1.2 15585 1vl2A 421 1.79e+01 c.26.2.1 108708 d.210.1.1 108709 1ogwA 76 1.82e+01 d.15.1.1 87001 1jj2L 194 1.84e+01 1ffkI d.12.1.2 63097 1b4cA 92 1.85e+01 1b4cA a.39.1.2 17169 1l8cA 95 1.90e+01 g.53.1.1 73685 1h6oA 204 1.90e+01 a.146.1.1 60689 2a4hA 126 1.92e+01 2lbp 346 1.97e+01 2liv c.93.1.1 35709 1oj6A 151 1.98e+01 a.1.1.2 93088 2au3A 407 2.06e+01 1af7 274 2.06e+01 1af7 a.58.1.1 17928 c.66.1.8 34203 1qbgA 272 2.09e+01 1d4aA c.23.5.3 31227 1h32B 138 2.10e+01 a.3.1.1 76620 1ash 150 2.10e+01 1ash a.1.1.2 15622 1hbyA 123 2.13e+01 7rsa d.5.1.1 60936 1q1fA 151 2.17e+01 a.1.1.2 104476 1tbrR 103 2.19e+01 1tbrR g.68.1.1 44707 g.68.1.1 44708 1to6A 371 2.24e+01 c.141.1.1 107170 1ajyA 71 2.29e+01 1zmeC g.38.1.1 45083 h.1.3.1 45516 1e7rA 321 2.29e+01 1bsvA c.2.1.2 29808 1d4aA 273 2.29e+01 1d4aA c.23.5.3 31219 1d3zA 76 2.30e+01 1ubi d.15.1.1 37592 1whtA 256 2.32e+01 1ivyA c.69.1.5 34646 1wpgA 994 2.35e+01 1fdyA 297 2.35e+01 1nal3 c.1.10.1 29071 1nbfD 76 2.35e+01 d.15.1.1 80390 1a79A 171 2.36e+01 1a79A c.52.2.1 33340 d.75.1.1 39739 1wehA 171 2.36e+01 1b1eA 123 2.39e+01 7rsa d.5.1.1 37300 1m2eA 135 2.39e+01 c.23.1.5 78478 1whsA 255 2.41e+01 1ivyA c.69.1.5 34649 1bwsA 321 2.44e+01 1bsvA c.2.1.2 29812 1abmA 198 2.44e+01 1avmA 2fe7A 166 2.50e+01 1a17 166 2.52e+01 1a17 a.118.8.1 19206 1nal1 297 2.53e+01 1nal3 1qhdA 398 2.53e+01 1qhdA a.115.1.2 63324 b.19.1.1 63325 1njkA 156 2.54e+01 d.38.1.1 85818 1qrqA 325 2.56e+01 1qrqA c.1.7.1 28667 4rxn 54 2.58e+01 1rb9 g.41.5.1 45226 1hgeB 175 2.59e+01 1hgeB h.3.1.1 45680 2viuB 175 2.66e+01 1hgeB h.3.1.1 45676 1u5kA 244 2.66e+01 1zzaA 90 2.66e+01 3hmgB 175 2.68e+01 1hgeB h.3.1.1 45704 1ezjA 115 2.69e+01 1ezjA h.1.14.1 45638 1pv6A 417 2.70e+01 f.38.1.2 95151 5rxn 54 2.72e+01 1rb9 g.41.5.1 45225 1k8tA 510 2.73e+01 e.41.1.1 68316 1vflA 356 2.77e+01 1yruB 74 2.78e+01 1e6uA 321 2.80e+01 1bsvA c.2.1.2 29805 1kbqA 273 2.81e+01 c.23.5.3 68391 1nal3 297 2.81e+01 1nal3 1vqsA 116 2.82e+01 1r1mA 164 2.84e+01 d.79.7.1 96820 1wolA 122 2.93e+01 1sfxA 109 2.94e+01 a.4.5.50 105505 1b1iA 123 2.96e+01 7rsa d.5.1.1 37295 1jy3P 48 2.99e+01 h.1.8.1 67448 1avgL 41 3.02e+01 1ppbL b.47.1.2 26216 1uf5A 303 3.03e+01 d.160.1.2 107808 1ap6A 198 3.07e+01 1avmA a.2.11.1 15746 d.44.1.1 38705 1wu3I 161 3.17e+01 2a73B 991 3.18e+01 1s4bP 674 3.28e+01 d.92.1.5 105252 1u9lA 70 3.32e+01 a.60.4.2 107751 1kekA 1231 3.36e+01 c.36.1.8 68524 c.36.1.12 68525 c.48.1.3 68526 c.64.1.1 68527 d.58.1.5 68528 1n0nA 199 3.37e+01 a.2.11.1 79750 d.44.1.1 79751 1aipC 196 3.38e+01 1tfe a.5.2.2 58930 d.43.1.1 58931 2aamA 309 3.44e+01 1on2A 142 3.45e+01 a.4.5.24 87103 a.76.1.1 87104 1mqeA 207 3.46e+01 d.113.1.1 91394 1wspA 84 3.48e+01 1k59A 123 3.53e+01 d.5.1.1 72073 1kxqE 120 3.58e+01 b.1.1.1 73171 2b9hA 353 3.60e+01 1erzA 303 3.60e+01 1erzA d.160.1.2 59498 1g72B 69 3.61e+01 4aahB a.137.2.1 19627 1bc5A 269 3.65e+01 1af7 a.58.1.1 17929 c.66.1.8 34204 2ae6A 166 3.66e+01 1llp 343 3.66e+01 1arv a.93.1.1 18578 1zmbA 290 3.68e+01 1vicA 262 3.68e+01 c.68.1.13 100756 1yydA 357 3.70e+01 1hcc 59 3.75e+01 1hfh g.18.1.1 44820 1b2jA 54 3.77e+01 1rb9 g.41.5.1 45231 1ru4A 400 3.79e+01 b.80.1.9 97836 1f0mA 82 3.84e+01 1b4fA a.60.1.2 17942 1mn1 357 3.85e+01 1arv a.93.1.1 18667 1pl4A 198 3.90e+01 a.2.11.1 94854 d.44.1.1 94855 1j34C 46 3.96e+01 g.32.1.1 84050 2fb6A 117 3.97e+01