# List of top-scoring protein chains for t2k-80-60-80-str2+near-backbone-11-scores 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 1theA 260 1.50e+00 1theB d.3.1.1 37056 1k8kA 418 1.59e+00 c.55.1.1,c.55.1.1 68305,68306 1m1fA 110 1.64e+00 b.34.6.2 78401 2bkaA 242 1.81e+00 1gv4A 528 3.94e+00 c.3.1.5,c.3.1.5,d.87.1.1 70589,70590,70591 1zowA 313 4.13e+00 1qq2A 199 4.15e+00 1qq2A c.47.1.10 33064 1imoA 88 4.76e+00 1imoA c.15.1.2 62590 1k7hA 476 6.53e+00 c.76.1.1 72101 2c1dA 264 7.42e+00 1kdj 102 8.02e+00 1plc b.6.1.1 22864 1ne8A 117 8.13e+00 b.34.6.2 80424 1jmoA 480 8.97e+00 e.1.1.1 77138 1sj1A 66 9.69e+00 d.58.1.4 105595 1ugnA 198 1.02e+01 b.1.1.4,b.1.1.4 107828,107829 1dleA 298 1.03e+01 1dleA b.47.1.2 26312 1theB 260 1.21e+01 1theB d.3.1.1 37057 1dnpA 471 1.36e+01 1qnf a.99.1.1,c.28.1.1 18775,31630 1bw0A 416 1.37e+01 1bw0A c.67.1.1 34385 2bh1A 250 1.37e+01 1yiyA 429 1.38e+01 2ar0A 541 1.39e+01 1m5dA 263 1.48e+01 c.94.1.1 78641 1h32A 261 1.50e+01 a.3.1.8,a.3.1.8 76618,76619 1jr3E 334 1.55e+01 a.80.1.1,c.37.1.20 63253,63254 1vhsA 175 1.61e+01 d.108.1.1 100698 1g0xA 197 1.72e+01 1nkr b.1.1.4,b.1.1.4 21805,21806 1mqdA 261 1.77e+01 c.94.1.1 85049 1m5eA 263 1.78e+01 c.94.1.1 78642 1nwbA 124 2.10e+01 b.124.1.1 86296 1pbp 321 2.19e+01 1ixh c.94.1.1 35768 1h91A 180 2.32e+01 b.60.1.1 60805 1cztA 160 2.35e+01 1cztA b.18.1.2 23715 2cb4A 291 2.35e+01 1mqiA 263 2.39e+01 c.94.1.1 91398 1a40 321 2.61e+01 1ixh c.94.1.1 35767 2atrA 138 2.65e+01 1w4tA 299 2.68e+01 2ihl 129 2.73e+01 3lzt d.2.1.2 36408 1oh0A 131 2.76e+01 d.17.4.3 87004 1yizA 429 2.82e+01 1wstA 417 2.84e+01 1c8nA 276 2.85e+01 1smvA b.121.4.7 23308 1evlA 401 2.88e+01 1qf6A c.51.1.1,d.104.1.1 33202,40751 1czsA 160 2.89e+01 1cztA b.18.1.2 23714 1mr1C 99 2.94e+01 d.217.1.2 79420 1gph1 465 3.03e+01 1ecfB 1ab3 88 3.03e+01 1a32 a.16.1.2 16395 1qnf 484 3.24e+01 1qnf a.99.1.1,c.28.1.1 18777,31632 1ixh 321 3.37e+01 1ixh c.94.1.1 35761 1a8uA 277 3.40e+01 1brt c.69.1.12 34703 1sy3A 184 3.55e+01 b.60.1.1 106110 2cvxA 888 3.55e+01 1pc3A 350 3.61e+01 c.94.1.1 104102 1broA 277 3.61e+01 1brt c.69.1.12 34700 1a54A 321 3.65e+01 1ixh c.94.1.1 35763 1mfa 247 3.73e+01 1mfa b.1.1.1,b.1.1.1 19888,19889 1f15A 218 3.76e+01 1f15B b.121.4.5 23320 1brt 277 3.77e+01 1brt c.69.1.12 34699 1twyA 290 3.80e+01 1x8qA 184 3.92e+01 1nfdA 203 4.06e+01 1tcrA b.1.1.1,b.1.1.2 20612,21550 1x35A 268 4.19e+01 1s3rA 535 4.20e+01 2bg5A 324 4.23e+01 1owlA 484 4.25e+01 a.99.1.1,c.28.1.1 93647,93648 1y8oB 128 4.26e+01 1s72H 171 4.29e+01 d.41.4.1 105327 1b59A 370 4.33e+01 1bn5 a.4.5.25,d.127.1.1 16225,41162 1uch 230 4.36e+01 1uch d.3.1.6 37129 1puc 105 4.37e+01 1puc d.97.1.1 40675 1uj8A 77 4.40e+01 1i6kA 328 4.40e+01 c.26.1.1 66040 1xd3A 230 4.41e+01 1e5uI 187 4.42e+01 1f00I b.1.14.1,d.169.1.3 22372,42441 1eft 405 4.42e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1vasA 137 4.45e+01 2end a.18.1.1 16404 1exmA 405 4.50e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1cjaA 342 4.52e+01 1cjaA d.144.1.3 41708 1rybA 212 4.60e+01 c.56.3.1 98098 1b55A 169 4.61e+01 1btkA b.55.1.1 26963 193l 129 4.63e+01 3lzt d.2.1.2 36247 2end 138 4.64e+01 2end a.18.1.1 16400 1axtH 218 4.64e+01 1igtB b.1.1.1,b.1.1.2 20305,21297 102l 165 4.67e+01 1l92 d.2.1.3 36724 1koiA 184 4.70e+01 b.60.1.1 68725 1zwxA 301 4.71e+01 1upqA 123 4.72e+01 1q0pA 223 4.75e+01 c.62.1.1 95507 1gydB 315 4.78e+01 b.67.2.1 70751 1jk0A 419 4.88e+01 a.25.1.2 63142 1q33A 292 4.89e+01 d.113.1.1 95657 1w9gA 104 4.90e+01 3eipA 84 4.91e+01 3eipA d.26.2.1 38434 1jm1A 204 4.92e+01 b.33.1.1 71745 1bpb 248 4.93e+01 1bpyA a.60.12.1,d.218.1.2 75811,75812 1cpt 412 5.07e+01 1cpt a.104.1.1 18968 1m2oA 768 5.11e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78480,78481,78482,78483,78484 1o4sA 389 5.20e+01 c.67.1.1 86620 1i6lA 328 5.32e+01 c.26.1.1 66041 1qvjA 292 5.32e+01 d.113.1.1 96431 2fz4A 237 5.42e+01 1uv4A 293 5.44e+01 1d2rA 326 5.49e+01 1d2rB c.26.1.1 31572 1z3iX 644 5.52e+01 1yf5L 254 5.54e+01 1efcA 393 5.56e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1g6gA 127 5.56e+01 1g6gA b.26.1.2 23916 1cghA 224 5.59e+01 1a7s b.47.1.2 26290 1gtkA 313 5.60e+01 c.94.1.1,d.50.2.1 76346,76347 1bdb 277 5.63e+01 1bdb c.2.1.2 29874 1at6 129 5.70e+01 3lzt d.2.1.2 36333 1fi8A 228 5.70e+01 5ptp b.47.1.2 26374 1u7kA 131 5.70e+01 3ullA 132 5.74e+01 3ullA b.40.4.3 25282 2grrA 161 5.76e+01 1v1hA 103 5.85e+01 b.83.1.1,h.1.17.1 108243,108244 1enj 138 5.86e+01 2end a.18.1.1 16401 1x3eA 165 6.01e+01 1ll2A 333 6.09e+01 c.68.1.14 74005 1ej6B 1275 6.10e+01 i.7.1.1 45968 2bjfA 329 6.11e+01 1rfs 139 6.11e+01 1rfs b.33.1.1 24434 1lm8B 118 6.13e+01 d.15.1.1 74033 5lyz 129 6.25e+01 3lzt d.2.1.2 36289 1urrA 102 6.36e+01 d.58.10.1 107998 1njrA 284 6.44e+01 c.50.1.2 103858 1wrjA 156 6.50e+01 1tcrA 202 6.66e+01 1tcrA b.1.1.1,b.1.1.2 20605,21549 1vqoH 171 6.67e+01 2gnxA 365 6.74e+01 1f15B 218 6.75e+01 1f15B b.121.4.5 23321 1d2rB 326 6.90e+01 1d2rB c.26.1.1 31573 2b5eA 504 6.95e+01 1b91A 118 6.96e+01 1b91A 1w68A 390 6.98e+01 a.25.1.2 109216 1ihkA 174 6.99e+01 1bfg b.42.1.1 62384 1y71A 130 7.05e+01 2acaA 189 7.05e+01 1t3bA 211 7.06e+01 c.47.1.9,d.17.3.1 106341,106342 1w07A 659 7.07e+01 1dmmA 131 7.16e+01 1opy d.17.4.3 38114 1r4xA 275 7.24e+01 b.1.10.3,d.105.1.2 97054,97055 1ha3A 405 7.25e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1vlgA 176 7.25e+01 a.25.1.1 108816 1ue1A 164 7.26e+01 b.40.4.3 99243 1kuuA 202 7.28e+01 d.153.2.1 73019 1a5t 334 7.38e+01 1a5t a.80.1.1,c.37.1.20 18450,32423 1l0wA 580 7.53e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1em8B 112 7.57e+01 c.126.1.1 90458 1anf 370 7.58e+01 4mbp c.94.1.1 35776 176lA 164 7.59e+01 1l92 d.2.1.3 36942 1mz4A 137 7.63e+01 a.3.1.1 91496 1gmyA 261 7.75e+01 d.3.1.1 76236 2bbkL 125 7.83e+01 2bbkL g.21.1.1 44882 1mgpA 313 7.88e+01 c.119.1.1 79098 1erxA 184 7.90e+01 1np1A b.60.1.1 27164 1zh5A 195 7.93e+01 1cjwA 166 7.96e+01 1cjwA d.108.1.1 40818 1mzbA 136 7.97e+01 a.4.5.42 91497 1qk4A 233 7.99e+01 1qk3A c.61.1.1 34037 1nwaA 203 8.05e+01 d.58.28.1 86295 1mgtA 174 8.06e+01 1mgtA a.4.2.1,c.55.7.1 16078,33753 1xewY 172 8.07e+01 1e42A 258 8.16e+01 1e42A b.1.10.1,d.105.1.1 22316,40792 1ng2A 193 8.21e+01 b.34.2.1,b.34.2.1 85660,85661 1jffB 445 8.22e+01 c.32.1.1,d.79.2.1 62934,62935 1w7lA 422 8.30e+01 c.67.1.1 109226 1mb1 130 8.34e+01 1bm8 d.34.1.1 38529 1drw 273 8.35e+01 1drw c.2.1.3,d.81.1.3 30057,39972 1zjkA 403 8.36e+01 2fkcA 247 8.39e+01 1hh1A 143 8.43e+01 1gefA c.52.1.18 61036 1mg2B 131 8.68e+01 g.21.1.1 79060 1wr8A 231 8.88e+01 1jse 129 8.94e+01 3lzt d.2.1.2 36387 1ko9A 345 8.95e+01 a.96.1.3,d.129.1.2 68717,68718 1pjpA 226 8.96e+01 5ptp b.47.1.2 26301 2fmpA 335 8.96e+01