# List of top-scoring protein chains for t04-100-40-40-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 1z2lA 423 8.89e-03 2aa4A 289 1.12e-02 2f5tX 233 2.73e-02 1ig8A 486 6.12e-02 2yhx c.55.1.3,c.55.1.3 64746,64747 1bu6O 501 6.18e-02 1glcG c.55.1.4,c.55.1.4 33499,33500 1c9kA 180 6.34e-02 1c9kB c.37.1.11 32363 1xc3A 302 1.07e-01 1z47A 355 1.18e-01 2ap1A 327 1.85e-01 1cnzA 363 2.73e-01 1cnzA c.77.1.1 35061 1e4fT 419 2.97e-01 1e4fT c.55.1.1,c.55.1.1 33453,33454 1glcG 501 3.13e-01 1glcG c.55.1.4,c.55.1.4 33519,33520 1s72H 171 3.20e-01 d.41.4.1 105327 1yvoA 172 3.69e-01 1k9sA 237 3.88e-01 c.56.2.1 68359 1nu0A 138 4.20e-01 c.55.3.8 92165 1gheA 177 4.70e-01 d.108.1.1 76222 2anuA 255 4.93e-01 1q18A 332 5.01e-01 c.55.1.7,c.55.1.7 104470,104471 1lnsA 763 5.29e-01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1n0wA 243 5.87e-01 c.37.1.11 79772 1sz2A 332 6.02e-01 2bl1A 172 6.08e-01 1vqoH 171 6.29e-01 1m6iA 493 6.89e-01 c.3.1.5,c.3.1.5,d.87.1.1 74533,74534,74535 1y9kA 157 6.97e-01 1i39A 225 7.11e-01 1ekeA c.55.3.1 61585 1hv9A 456 7.66e-01 1fwyA b.81.1.4,c.68.1.5 28060,34518 1fl2A 310 7.85e-01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1eo1A 124 8.32e-01 1eo1A c.55.5.1 33739 1k77A 260 8.99e-01 c.1.15.5 72096 1huxA 270 9.17e-01 1huxA c.55.1.5 61278 1l2tA 235 9.60e-01 c.37.1.12 73514 1jg1A 235 9.72e-01 c.66.1.7 66661 1phk 298 9.92e-01 1cdkA d.144.1.7 41635 1g7sA 594 1.12e+00 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1gs5A 258 1.12e+00 c.73.1.2 70395 1srrA 124 1.15e+00 1dz3A c.23.1.1 31110 1z2wA 192 1.21e+00 1vk9A 151 1.25e+00 c.139.1.1 108640 1mb3A 124 1.26e+00 c.23.1.1 78907 1yvkA 163 1.27e+00 1z4eA 153 1.28e+00 1ecpA 238 1.31e+00 1ecpA c.56.2.1 33775 1t6cA 315 1.35e+00 c.55.1.8,c.55.1.8 106558,106559 2g9iA 249 1.38e+00 1y5iA 1246 1.43e+00 1wraA 308 1.51e+00 1hh1A 143 1.53e+00 1gefA c.52.1.18 61036 1ws0A 156 1.54e+00 1q16A 1247 1.56e+00 b.52.2.2,c.81.1.1 95546,95547 7odcA 424 1.56e+00 7odcA b.49.2.3,c.1.6.1 26488,28650 2reb 352 1.71e+00 2reb c.37.1.11,d.48.1.1 32282,38767 2b99A 156 1.72e+00 1i24A 404 1.77e+00 c.2.1.2 83663 1io2A 213 1.81e+00 1ekeA c.55.3.1 62612 1fxjA 331 1.83e+00 1fwyA b.81.1.4,c.68.1.5 28062,34520 1pfkA 320 1.84e+00 3pfk c.89.1.1 35575 1jkxA 212 1.90e+00 c.65.1.1 66813 2pfkA 320 1.96e+00 3pfk c.89.1.1 35577 1qrrA 394 1.99e+00 1qrrA c.2.1.2 29824 1e19A 314 2.04e+00 1b7bA c.73.1.1 34967 1y43B 173 2.07e+00 1xfoA 357 2.08e+00 1woqA 267 2.16e+00 c.55.1.10,c.55.1.10 109462,109463 1o0iA 138 2.17e+00 d.38.1.5 86532 1hjrA 158 2.23e+00 1hjrA c.55.3.6 33727 1vypX 364 2.23e+00 c.1.4.1 108905 1kcfA 258 2.28e+00 a.140.2.1,c.55.3.7 68434,68435 2cvhA 220 2.34e+00 1tfr 305 2.38e+00 1tfr a.60.7.1,c.120.1.2 18081,33351 1vhxA 150 2.38e+00 c.55.3.8 100712 1g291 372 2.43e+00 1g291 1vp2A 208 2.48e+00 1t0fA 276 2.50e+00 1on0A 158 2.53e+00 d.108.1.1 87095 2f4nA 273 2.69e+00 1gvoA 364 2.71e+00 c.1.4.1 76357 2bibA 547 2.99e+00 1g0hA 252 3.10e+00 1dk4A e.7.1.1 60171 1wab 232 3.11e+00 1wab c.23.10.3 31341 1x13A 401 3.13e+00 1fobA 334 3.13e+00 c.1.8.3 83255 1hyuA 521 3.14e+00 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1ko7A 314 3.22e+00 c.98.2.1,c.91.1.2 72797,72798 2fe7A 166 3.23e+00 1u6mA 199 3.26e+00 1obdA 306 3.34e+00 d.143.1.1 86767 1h61A 364 3.59e+00 1oyc c.1.4.1 60657 1k1eA 180 3.62e+00 c.108.1.5 67995 2b6eA 146 3.63e+00 1lc0A 294 3.82e+00 c.2.1.3,d.81.1.4 73823,73824 1jf8A 131 3.86e+00 c.44.1.1 66621 1a48 306 3.89e+00 1a48 d.143.1.1 41590 2gshA 414 3.97e+00 1vp8A 201 4.01e+00 1ykdA 398 4.05e+00 1vr3A 191 4.07e+00 1ghhA 81 4.09e+00 1ghhA d.57.1.1 38940 1e0tA 470 4.10e+00 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1es9A 232 4.16e+00 1wab c.23.10.3 31340 1f1zA 273 4.34e+00 1f1zA a.4.5.27,c.52.1.16 16081,33334 1xwiA 322 4.43e+00 1itwA 741 4.68e+00 c.77.1.2 76793 1u04A 771 4.71e+00 b.34.14.1,c.55.3.10 107539,107540 1tp9A 162 4.72e+00 2abbA 364 4.86e+00 1ccwA 137 5.05e+00 1be1 c.23.6.1 31238 1kngA 156 5.09e+00 c.47.1.10 72777 1w24A 182 5.20e+00 1wl8A 189 5.23e+00 1x4rA 99 5.27e+00 1f9aA 168 5.31e+00 1f9aA c.26.1.3 31602 1vyrA 364 5.31e+00 c.1.4.1 108906 1fvuB 125 5.43e+00 1ixxB d.169.1.1 42346 1tmy 120 5.47e+00 1dbwA c.23.1.1 31083 1gmmA 133 5.47e+00 b.18.1.10 65314 4pfk 319 5.53e+00 3pfk c.89.1.1 35582 1j54A 186 5.60e+00 c.55.3.5 77077 2gupA 292 5.67e+00 2cy2A 174 5.89e+00 2a67A 167 5.92e+00 1uxxX 133 5.95e+00 b.18.1.10 100169 1jx2B 315 5.96e+00 c.37.1.8 67404 1o97D 320 6.00e+00 c.26.2.3,c.31.1.2 81233,81234 2cw5A 255 6.01e+00 1j8yF 297 6.19e+00 1ng1 a.24.13.1,c.37.1.10 62747,62748 1dkiA 371 6.24e+00 1dkiA d.3.1.1 37090 1gcuA 295 6.25e+00 1gcuA c.2.1.3,d.81.1.4 30063,39978 3sil 379 6.53e+00 3sil b.68.1.1 27542 1u0sY 118 6.61e+00 c.23.1.1 107566 1o5uA 101 6.74e+00 b.82.1.8 92518 1pj5A 830 7.00e+00 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1c3hA 137 7.04e+00 b.22.1.1 90405 1b0uA 262 7.10e+00 1b0uA c.37.1.12 32370 2acaA 189 7.21e+00 1m2kA 249 7.44e+00 c.31.1.5 84754 1qipA 183 7.50e+00 1qipA d.32.1.1 38470 1rvgA 305 7.62e+00 c.1.10.2 97920 1f8gA 384 7.76e+00 1sayA c.2.1.4,c.23.12.2 59695,59696 1ualA 274 7.80e+00 c.116.1.4 88383 1vrmA 325 7.81e+00 2avtA 378 7.84e+00 1f3iA 481 8.17e+00 1b7eA 2fexA 188 8.70e+00 1y0yA 353 8.87e+00 1d1gA 168 8.92e+00 1d1gA c.71.1.1 34889 1sg4A 260 8.94e+00 2d4pA 141 8.99e+00 1yr0A 175 9.09e+00 1ih8A 271 9.11e+00 2nsyA c.26.2.1 62377 1l7mA 211 9.13e+00 c.108.1.4 73664 1xx6A 191 9.21e+00 1orrA 347 9.28e+00 c.2.1.2 93460 1v9wA 130 9.48e+00 c.47.1.16 108453 1s5aA 150 9.57e+00 d.17.4.10 98525 1j97A 211 9.93e+00 1f5sA c.108.1.4 62753 1q6oA 216 1.01e+01 c.1.2.3 95986 2fuqA 747 1.02e+01 2ge3A 170 1.02e+01 1i12A 160 1.05e+01 1i21A d.108.1.1 61515 1fthA 122 1.05e+01 d.150.1.2 60028 1qwgA 251 1.05e+01 c.1.27.1 96473 2cunA 410 1.05e+01 1kqpA 271 1.06e+01 c.26.2.1 72883 1vm0A 130 1.08e+01 d.68.6.2 108873 1u7zA 226 1.11e+01 1w8iA 156 1.11e+01 1d2oA 187 1.12e+01 1d2oA b.3.5.1,b.3.5.1 22625,22626 1p90A 145 1.12e+01 c.55.5.2 94377 2gar 212 1.12e+01 2gar c.65.1.1 34161 2b5gA 171 1.14e+01 1hdoA 206 1.16e+01 1he2A c.2.1.2 60965 1rxyA 253 1.17e+01 c.56.2.1 98065 1f2tA 149 1.17e+01 1f2tA c.37.1.12 32373 1umhA 184 1.18e+01 b.18.1.21 99605 1v71A 323 1.18e+01 1p9oA 313 1.19e+01 c.72.3.1 94397 2cdcA 366 1.22e+01 1ye8A 178 1.23e+01 1u94A 356 1.26e+01 c.37.1.11,d.48.1.1 107743,107744 1jndA 420 1.28e+01 c.1.8.5,d.26.3.1 71757,71758 1wyzA 242 1.32e+01 1kv8A 216 1.32e+01 c.1.2.3 73054 1j8mF 297 1.33e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1qo2A 241 1.33e+01 1qo2A c.1.2.1 28533 1xp8A 366 1.36e+01 1chuA 540 1.38e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1w2xA 758 1.38e+01 c.14.1.4,c.14.1.4 109134,109135 1t6kA 278 1.41e+01 1ivnA 190 1.42e+01 c.23.10.5 83719 2c46A 241 1.43e+01 1n2sA 299 1.44e+01 c.2.1.2 79857 1vfvA 366 1.45e+01 c.37.1.9 108592 1uox 296 1.45e+01 1uox 1uliB 187 1.47e+01 d.17.4.4 107923 1nrfA 262 1.48e+01 e.3.1.1 92086 2a6aA 218 1.48e+01 1u1wA 298 1.49e+01 1dciA 275 1.49e+01 1dciA c.14.1.3 30918 1zmaA 118 1.50e+01 1vhwA 253 1.51e+01 c.56.2.1 100706 1c0pA 363 1.52e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1ckmA 330 1.53e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 2bvpA 276 1.54e+01 2tmdA 729 1.54e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28616,30317,30602 1t5bA 201 1.54e+01 c.23.5.3 106433 1ush 550 1.55e+01 1ush d.114.1.1,d.159.1.2 40923,42079 1djqA 729 1.56e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 2a4nA 182 1.57e+01 1rg9A 383 1.60e+01 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1jx7A 117 1.60e+01 c.114.1.1 77195 1djnA 729 1.63e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 2b0tA 738 1.64e+01 1uf3A 228 1.65e+01 d.159.1.6 99317 1h2eA 207 1.67e+01 c.60.1.1 70857 2gqrA 237 1.68e+01 2basA 431 1.71e+01 1musA 477 1.71e+01 c.55.3.4 79494 1khdA 345 1.73e+01 a.46.2.1,c.27.1.1 77400,77401 1meoA 209 1.74e+01 c.65.1.1 79035 1whtB 153 1.74e+01 1whtB 2g9zA 348 1.74e+01 1xubA 298 1.75e+01 1hqsA 423 1.76e+01 1iso c.77.1.1 61154 1i1dA 161 1.76e+01 1i21A d.108.1.1 61526 1uoyA 64 1.76e+01 g.3.19.1 99709 1jmxB 349 1.78e+01 b.69.2.2 66906 1bupA 386 1.78e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1whsB 153 1.78e+01 1whtB 1o91A 178 1.80e+01 b.22.1.1 92656 2d0oA 610 1.82e+01 1pvdA 537 1.82e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 1bs4A 168 1.84e+01 1bs4A d.167.1.1 42287 1iz5A 249 1.84e+01 d.131.1.2,d.131.1.2 83834,83835 1rlhA 173 1.84e+01 d.256.1.1 97646 2a1rA 430 1.85e+01 1r4uA 301 1.85e+01 d.96.1.4,d.96.1.4 97047,97048 2ae6A 166 1.86e+01 1jmvA 141 1.90e+01 c.26.2.4 66897 1zx1A 231 1.91e+01 1l7dA 384 1.93e+01 c.2.1.4,c.23.12.2 77774,77775 1augA 215 1.94e+01 1a2zA c.56.4.1 33798 1i6iA 366 1.95e+01 1bg2 c.37.1.9 61844 1yd7A 395 1.95e+01 1n71A 180 1.95e+01 d.108.1.1 85370 2bkfA 87 1.96e+01 1m2oA 768 2.00e+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 1ve5A 311 2.03e+01 1qo7A 394 2.03e+01 1qo7A c.69.1.11 34697 1sg0A 230 2.03e+01 1itvA 195 2.04e+01 b.66.1.1 76791 2bhvA 246 2.05e+01 1xm7A 195 2.06e+01 1j7xA 302 2.07e+01 c.14.1.2 66425 1bdb 277 2.10e+01 1bdb c.2.1.2 29874 1garA 212 2.11e+01 2gar c.65.1.1 34162 1nzoA 363 2.13e+01 b.105.1.1,e.3.1.1 92383,92384 1ek1A 554 2.13e+01 1cr6B c.69.1.11,c.108.1.2 34685,43335 1us8A 147 2.17e+01 c.37.1.12 99859 1kay 381 2.18e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 2gm3A 175 2.18e+01 1mjhA 162 2.20e+01 1mjhA c.26.2.4 31639 2ac2A 309 2.20e+01 2b49A 287 2.21e+01 1v4vA 376 2.23e+01 c.87.1.3 100313 2cw9A 194 2.23e+01 1v8fA 276 2.24e+01 c.26.1.4 100503 2amdA 311 2.25e+01 1vplA 256 2.26e+01 1tq8A 163 2.26e+01 c.26.2.4 107204 1xeoA 168 2.29e+01 1i9sA 210 2.30e+01 1i9sA c.45.1.1 62099 1w3jA 468 2.31e+01 c.1.8.4 109156 1a04A 215 2.37e+01 1a04A a.4.6.2,c.23.1.1 16234,31089 1ebfA 358 2.37e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1szoA 257 2.41e+01 c.14.1.3 106164 1ng4A 390 2.45e+01 c.3.1.2,d.16.1.3 85666,85667 2ajrA 331 2.46e+01 1wrrA 301 2.46e+01 1b74A 254 2.47e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1gr3A 160 2.48e+01 b.22.1.1 65476 1tyjA 170 2.49e+01 1ma3A 253 2.51e+01 c.31.1.5 78883 2b8mA 117 2.51e+01 1l8nA 679 2.53e+01 c.1.8.10,d.92.2.2 84564,84565 2aioA 269 2.54e+01 1sqsA 242 2.56e+01 c.23.5.5 98968 1qv9A 283 2.56e+01 c.127.1.1 96356 2ct8A 497 2.56e+01 1dbiA 280 2.57e+01 1gci c.41.1.1 32543 1vhsA 175 2.57e+01 d.108.1.1 100698 1s2dA 167 2.62e+01 c.23.14.1 98377 1q4uA 151 2.62e+01 d.38.1.5 95828 1g2aA 168 2.65e+01 d.167.1.1 65109 1z6bA 154 2.65e+01 1qmyA 167 2.67e+01 1qmyA d.3.1.2 37094 1ve4A 206 2.67e+01 1b87A 181 2.68e+01 1b87A d.108.1.1 40797 2etvA 346 2.69e+01 1ako 268 2.69e+01 1ako d.151.1.1 41779 1v5wA 343 2.70e+01 c.37.1.11 108387 2a1fA 247 2.70e+01 1vl6A 388 2.72e+01 c.2.1.7,c.58.1.3 108724,108725 2cohA 202 2.72e+01 1nnwA 252 2.73e+01 d.159.1.5 80674 1dozA 309 2.73e+01 1ak1 c.92.1.1 35592 1kwsA 261 2.75e+01 c.68.1.7 73083 1o97C 264 2.75e+01 c.26.2.3 81232 1h0hB 214 2.75e+01 d.58.1.5 76437 2ac4A 309 2.79e+01 1g5hA 454 2.82e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 1q77A 138 2.86e+01 c.26.2.4 96023 2b7oA 464 2.86e+01 2av4A 162 2.87e+01 1vpqA 273 2.87e+01 1a05A 358 2.91e+01 1cnzA c.77.1.1 35059 1uyrA 737 2.93e+01 c.14.1.4,c.14.1.4 100188,100189 2bfdA 400 2.94e+01 1uebA 184 2.95e+01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1y0gA 191 2.96e+01 2ethA 154 2.96e+01 1yhfA 115 2.96e+01 1r62A 160 2.97e+01 d.122.1.3 104816 2sak 121 2.97e+01 2sak d.15.5.1 37711 1ek0A 170 2.98e+01 1ctqA c.37.1.8 32076 1svfB 38 3.01e+01 1svfB h.3.2.1 45764 1ybdA 239 3.02e+01 1n7kA 234 3.07e+01 c.1.10.1 85374 1g6hA 257 3.07e+01 1gajA c.37.1.12 60318 1smlA 269 3.07e+01 1smlA d.157.1.1 42053 1jksA 294 3.08e+01 d.144.1.7 71710 1cr1A 296 3.08e+01 1cr1A c.37.1.11 32286 1w9gA 104 3.08e+01 1q1oA 98 3.12e+01 d.15.2.2 95596 1hp1A 516 3.13e+01 d.114.1.1,d.159.1.2 70976,70977 1bo4A 168 3.13e+01 1bo4A d.108.1.1 40798 2bswA 146 3.15e+01 1zc6A 305 3.16e+01 1hzdA 272 3.16e+01 c.14.1.3 65969 1iukA 140 3.20e+01 c.2.1.8 83712 1w96A 554 3.22e+01 1ujcA 161 3.22e+01 1n8jA 186 3.22e+01 c.47.1.10 85401 1yuwA 554 3.24e+01 1v1rA 400 3.24e+01 c.36.1.11 108272 1y8tA 324 3.25e+01 1wz7A 111 3.25e+01 1fa8A 135 3.29e+01 1qipA d.32.1.1 38486 1iq6A 134 3.29e+01 d.38.1.4 76755 2c31A 568 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