# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 2acaA 189 7.57e-01 1zi8A 236 1.44e+00 1ggvA 232 2.63e+00 1din c.69.1.9 34683 1n0uA 842 3.46e+00 b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 79757,79758,79759,79760,79761 1din 236 3.68e+00 1din c.69.1.9 34682 1knwA 425 4.55e+00 b.49.2.3,c.1.6.1 90969,90970 1wpoB 256 4.57e+00 1lay b.57.1.1 27013 2fsrA 195 5.14e+00 1p65A 73 5.39e+00 d.254.1.1 94156 1obdA 306 6.60e+00 d.143.1.1 86767 1kshA 186 7.25e+00 c.37.1.8 72914 1mg4A 113 7.26e+00 d.15.11.1 84953 1zarA 282 8.04e+00 2bvfA 459 8.93e+00 1g8kA 825 9.16e+00 1g8jA b.52.2.2,c.81.1.1 26920,35328 2cfaA 217 9.44e+00 1a48 306 9.50e+00 1a48 d.143.1.1 41590 1ii2A 524 9.69e+00 c.91.1.1,c.109.1.1 66146,66147 2ftbA 125 9.73e+00 1tw4A 125 1.02e+01 1tqmA 282 1.03e+01 a.4.5.56,d.144.1.9 107236,107237 1p6pA 125 1.04e+01 b.60.1.2 87839 1si6X 282 1.05e+01 1a5mC 566 1.15e+01 1ubpC b.92.1.1,c.1.9.2 28423,29045 1at0 145 1.27e+01 1at0 b.86.1.1 28374 2c1gA 431 1.32e+01 1yzbA 182 1.37e+01 2d2jA 329 1.42e+01 1uocA 289 1.46e+01 c.55.3.9 99686 1y1uA 585 1.52e+01 1y21A 282 1.57e+01 1krs 120 1.58e+01 1krs b.40.4.1 25256 2fe7A 166 1.66e+01 1xs1A 193 1.68e+01 1wwzA 159 1.70e+01 1yspA 181 1.86e+01 1g8jA 825 1.90e+01 1g8jA b.52.2.2,c.81.1.1 26924,35332 1mml 265 1.93e+01 1mml e.8.1.2 43015 1ejxC 567 1.96e+01 b.92.1.1,c.1.9.2 83184,83185 1mm4A 170 1.98e+01 f.4.1.2 79294 1i16 130 2.00e+01 1i16 b.36.1.2 24787 1tt7A 330 2.17e+01 1rmvA 157 2.20e+01 1rmvA a.24.5.1 16589 2avnA 260 2.24e+01 1scy 32 2.25e+01 1pnh g.3.7.2 44155 2c1iA 431 2.27e+01 1xpkC 388 2.33e+01 1jenB 67 2.37e+01 1jenB d.156.1.1 42029 1suuA 312 2.41e+01 b.68.10.1 99006 1gyfA 62 2.42e+01 1gyfA d.76.1.1 39749 1ve9A 347 2.45e+01 c.4.1.2,d.16.1.3 100571,100572 1yadA 221 2.47e+01 1itcA 516 2.52e+01 b.3.1.1,c.1.8.1 83705,83706 2gfsA 372 2.53e+01 1b35B 255 2.62e+01 1b35B b.121.4.1 23334 2bszA 278 2.65e+01 1azwA 313 2.67e+01 1qtrA c.69.1.7 34658 1mw7A 240 2.68e+01 e.39.1.1 79557 2akzA 439 2.69e+01 1hleB 31 2.70e+01 1hleB 1te6A 439 2.70e+01 c.1.11.1,d.54.1.1 106797,106798 1xpmA 396 2.90e+01 1s99A 200 2.94e+01 1s7hA 200 2.97e+01 d.58.48.2 105349 1pnh 31 2.98e+01 1pnh g.3.7.2 44162 1ntfA 282 3.06e+01 d.151.1.2 92104 1ejhA 190 3.10e+01 1ejhA d.86.1.1 40147 1oz7A 131 3.12e+01 d.169.1.1 93806 1a8y 367 3.15e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 2f4mA 295 3.20e+01 1j58A 385 3.24e+01 b.82.1.2 71531 1vemA 516 3.27e+01 1nmoA 247 3.35e+01 c.135.1.1 91980 1repC 251 3.42e+01 1repC a.4.5.10,a.4.5.10 16125,16126 1a7aA 432 3.54e+01 1b3rA c.2.1.4,c.23.12.3 30104,31364 1azo 232 3.55e+01 1azo c.52.1.14 33329 1tc6A 236 3.56e+01 d.122.1.1 106756 1fwcC 567 3.57e+01 1ubpC b.92.1.1,c.1.9.2 28410,29032 1u24A 337 3.62e+01 1tvzA 388 3.63e+01 c.95.1.2,c.95.1.2 107367,107368 1mixA 206 3.63e+01 a.11.2.1,b.55.1.5 79166,79167 2azeB 106 3.74e+01 1l8bA 190 3.77e+01 d.86.1.1 73683 1b5fA 239 3.87e+01 1smrA b.50.1.2 26836 1hdmA 201 3.87e+01 1iakA b.1.1.2,d.19.1.1 21583,38157 2aorA 223 3.88e+01 1a5kC 566 3.93e+01 1ubpC b.92.1.1,c.1.9.2 28425,29047 1k9sA 237 4.02e+01 c.56.2.1 68359 1i0dA 332 4.33e+01 1pscA c.1.9.3 61487 1hzyA 332 4.38e+01 1pscA c.1.9.3 61468 1fxzA 476 4.39e+01 b.82.1.2,b.82.1.2 65059,65060 1o6eA 235 4.52e+01 b.57.1.1 81083 2b5iC 199 4.52e+01 1q5hA 147 4.53e+01 b.85.4.1 95893 1jlyA 304 4.55e+01 1jlyA b.42.3.1,b.42.3.1 25587,25588 1jo0A 98 4.55e+01 d.68.4.1 77140 1dmtA 696 4.60e+01 1dmtA d.92.1.4 40296 1pscA 365 4.63e+01 1pscA c.1.9.3 29058 1wtaA 275 4.67e+01 1cjaA 342 4.69e+01 1cjaA d.144.1.3 41708 1pjvA 32 4.69e+01 g.3.7.2 94792 1pta 318 4.71e+01 1pscA c.1.9.3 29064 1vkiA 181 4.71e+01 d.116.1.1 108664 4icb 76 4.78e+01 4icb a.39.1.1 17145 1ht9A 76 4.88e+01 4icb a.39.1.1 61252 1eywA 331 4.91e+01 1pscA c.1.9.3 29057 1zbxB 141 5.11e+01 4pep 326 5.15e+01 1smrA b.50.1.2 26843 1wbsA 360 5.16e+01 1xm7A 195 5.16e+01 2ax4A 198 5.27e+01 1l6rA 227 5.29e+01 c.108.1.10 77768 1zthA 258 5.38e+01 3fruA 269 5.44e+01 1agdA b.1.1.2,d.19.1.1 20657,38150 1go4A 205 5.47e+01 d.135.1.1 70292 1b6g 310 5.50e+01 1b6g c.69.1.8 34661 1s0yA 76 5.59e+01 d.80.1.1 98314 1o7nA 449 5.66e+01 b.33.1.2,d.129.3.3 81162,81163 1h8eI 50 5.72e+01 1e79I a.137.8.1 60758 1oh0A 131 5.81e+01 d.17.4.3 87004 2c5qA 240 5.84e+01 1z4rA 168 5.93e+01 1gpr 162 5.93e+01 1gpr b.84.3.1 28267 1jyhA 157 6.02e+01 d.60.1.3 71956 1aa8A 347 6.14e+01 1an9A 3bdpA 580 6.25e+01 1xwl c.55.3.5,e.8.1.1 33711,43004 1r8sA 164 6.27e+01 c.37.1.8 97247 8tfvA 21 6.39e+01 j.3.1.2 46071 2c0cA 362 6.52e+01 1bmr 68 6.58e+01 1aho g.3.7.1 44144 1f6bA 198 6.62e+01 c.37.1.8 64986 1php 394 6.63e+01 16pk c.86.1.1 35452 2djkA 133 6.64e+01 1ejrC 567 6.64e+01 1ubpC b.92.1.1,c.1.9.2 28420,29042 1pk9A 237 6.74e+01 c.56.2.1 94823 1fggA 261 6.75e+01 1fggA c.68.1.7 34576 1qr0A 228 6.78e+01 1qr0A d.150.1.1,d.150.1.1 59038,59039 1ax4A 467 6.88e+01 1ax4A c.67.1.2 34391 1b9zA 516 7.01e+01 1b9zA b.3.1.1,c.1.8.1 22528,28798 1nk4A 580 7.02e+01 c.55.3.5,e.8.1.1 91923,91924 1a8uA 277 7.04e+01 1brt c.69.1.12 34703 1hrnA 337 7.12e+01 1smrA b.50.1.2 26869 1eg9A 449 7.14e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1mr3F 181 7.17e+01 c.37.1.8 79422 1v6sA 390 7.19e+01 c.86.1.1 100424 2bgkA 278 7.20e+01 1rhs 296 7.31e+01 1rhs c.46.1.2,c.46.1.2 32703,32704 1l3sA 580 7.34e+01 c.55.3.5,e.8.1.1 84521,84522 1ndoA 449 7.36e+01 1ndoA b.33.1.2,d.129.3.3 24444,41323 1ecpA 238 7.49e+01 1ecpA c.56.2.1 33775 1u4bA 580 7.66e+01 c.55.3.5,e.8.1.1 107664,107665 1vajA 214 7.68e+01 1rypE 242 7.80e+01 1rypE d.153.1.4 41936 3hhrB 203 7.81e+01 1axiB b.1.2.1,b.1.2.1 22005,22006 1i3zA 103 7.82e+01 d.93.1.1 83667 1iezA 217 7.91e+01 d.115.1.2 66129 1kxrA 339 7.96e+01 d.3.1.3 73175 1fit 147 8.02e+01 1fit d.13.1.1 37499 1bjt 793 8.04e+01 1bjt e.11.1.1 43249 16pk 415 8.04e+01 16pk c.86.1.1 35454 1dmmA 131 8.15e+01 1opy d.17.4.3 38114 1kwsA 261 8.18e+01 c.68.1.7 73083 1deuA 277 8.20e+01 1theB d.3.1.1 37085 1q0rA 298 8.21e+01 c.69.1.28 95508 1g8mA 593 8.29e+01 1g8mA c.24.1.3,c.97.2.1 60371,60372 1zzlA 351 8.34e+01 1oo0A 147 8.35e+01 d.232.1.1 87182 1oygA 447 8.36e+01 b.67.2.2 93726 1ex7A 186 8.38e+01 1gky c.37.1.1 59537 1ro2A 216 8.45e+01 d.264.1.2 97665 1v52A 133 8.46e+01 1g57A 217 8.51e+01 1g57A d.115.1.2 60253 1vloA 381 8.52e+01 b.44.2.1,d.250.1.1 108838,108839 2prgC 88 8.58e+01 2prgC j.112.1.1 19644 1aerB 195 8.62e+01 1aerA d.166.1.1 42250 1fg7A 356 8.65e+01 1gewA c.67.1.1 59819 1ycdA 243 8.68e+01 1mdl 359 8.68e+01 2mnr c.1.11.2,d.54.1.1 29247,38891 1vj5A 555 8.69e+01 c.108.1.2,c.69.1.11 100799,100800 1ehxA 94 8.74e+01 1ehxA b.1.18.13 21950 1qrqA 325 8.75e+01 1qrqA c.1.7.1 28667 1yw5A 177 8.86e+01 2faoA 309 8.92e+01 1g2iA 166 8.93e+01 1g2iA c.23.16.2 31438 1cnpA 90 8.93e+01 4icb a.39.1.2 17161 1zw8A 64 8.94e+01 2evrA 246 8.94e+01 1k4fA 248 8.98e+01 e.3.1.1 68138 1ej1A 190 8.98e+01 1ejhA d.86.1.1 40144