# 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 3.51e-03 1ig8A 486 3.06e-02 2yhx c.55.1.3,c.55.1.3 64746,64747 1c9kA 180 4.19e-02 1c9kB c.37.1.11 32363 1bu6O 501 5.86e-02 1glcG c.55.1.4,c.55.1.4 33499,33500 2aa4A 289 1.00e-01 1nu0A 138 2.45e-01 c.55.3.8 92165 1cnzA 363 2.51e-01 1cnzA c.77.1.1 35061 2anuA 255 2.90e-01 1glcG 501 3.36e-01 1glcG c.55.1.4,c.55.1.4 33519,33520 1k9sA 237 4.28e-01 c.56.2.1 68359 2ap1A 327 4.67e-01 1z47A 355 5.37e-01 1gheA 177 5.71e-01 d.108.1.1 76222 1vk9A 151 7.17e-01 c.139.1.1 108640 1z4eA 153 7.58e-01 2f9zC 159 7.82e-01 1k77A 260 7.88e-01 c.1.15.5 72096 1i39A 225 8.99e-01 1ekeA c.55.3.1 61585 2g9iA 249 9.82e-01 1y9kA 157 1.02e+00 1tfr 305 1.03e+00 1tfr a.60.7.1,c.120.1.2 18081,33351 1yvkA 163 1.10e+00 1lwdA 413 1.11e+00 c.77.1.1 78265 1eo1A 124 1.11e+00 1eo1A c.55.5.1 33739 1hh1A 143 1.18e+00 1gefA c.52.1.18 61036 1gs5A 258 1.22e+00 c.73.1.2 70395 1dkiA 371 1.24e+00 1dkiA d.3.1.1 37090 1mb3A 124 1.25e+00 c.23.1.1 78907 2b5gA 171 1.26e+00 1srrA 124 1.28e+00 1dz3A c.23.1.1 31110 1phk 298 1.30e+00 1cdkA d.144.1.7 41635 1hjrA 158 1.32e+00 1hjrA c.55.3.6 33727 1t0fA 276 1.41e+00 1vp8A 201 1.51e+00 1vhxA 150 1.51e+00 c.55.3.8 100712 1i24A 404 1.60e+00 c.2.1.2 83663 2b99A 156 1.67e+00 2fe7A 166 1.70e+00 2f4nA 273 1.73e+00 1xewX 182 1.75e+00 1qrrA 394 1.83e+00 1qrrA c.2.1.2 29824 1io2A 213 1.83e+00 1ekeA c.55.3.1 62612 1fobA 334 1.99e+00 c.1.8.3 83255 1ecpA 238 2.06e+00 1ecpA c.56.2.1 33775 1zzgA 415 2.07e+00 1vypX 364 2.15e+00 c.1.4.1 108905 1kcfA 258 2.22e+00 a.140.2.1,c.55.3.7 68434,68435 1gvoA 364 2.66e+00 c.1.4.1 76357 1on0A 158 2.66e+00 d.108.1.1 87095 1yvoA 172 2.68e+00 1g291 372 2.77e+00 1g291 1jf8A 131 2.81e+00 c.44.1.1 66621 2gshA 414 2.84e+00 1f1zA 273 2.88e+00 1f1zA a.4.5.27,c.52.1.16 16081,33334 1n0wA 243 2.92e+00 c.37.1.11 79772 1wab 232 3.01e+00 1wab c.23.10.3 31341 1jx2B 315 3.14e+00 c.37.1.8 67404 1itwA 741 3.39e+00 c.77.1.2 76793 1ghhA 81 3.45e+00 1ghhA d.57.1.1 38940 1h61A 364 3.63e+00 1oyc c.1.4.1 60657 2bl1A 172 3.69e+00 2a67A 167 3.76e+00 1m2kA 249 3.86e+00 c.31.1.5 84754 1ccwA 137 3.86e+00 1be1 c.23.6.1 31238 2sak 121 3.89e+00 2sak d.15.5.1 37711 1k1eA 180 3.90e+00 c.108.1.5 67995 1c0pA 363 4.11e+00 1an9A c.4.1.2,d.16.1.3 30647,37934 1xc3A 302 4.12e+00 1xwiA 322 4.21e+00 1es9A 232 4.29e+00 1wab c.23.10.3 31340 1f9aA 168 4.32e+00 1f9aA c.26.1.3 31602 1sz2A 332 4.38e+00 2d4pA 141 4.73e+00 1xx6A 191 4.89e+00 2abbA 364 4.93e+00 1ih8A 271 5.02e+00 2nsyA c.26.2.1 62377 1q6oA 216 5.17e+00 c.1.2.3 95986 1vyrA 364 5.36e+00 c.1.4.1 108906 2tmdA 729 5.61e+00 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28616,30317,30602 1tmy 120 5.67e+00 1dbwA c.23.1.1 31083 2gm5A 139 5.76e+00 1j54A 186 6.11e+00 c.55.3.5 77077 1u0sY 118 6.21e+00 c.23.1.1 107566 1djqA 729 6.38e+00 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 1q18A 332 6.41e+00 c.55.1.7,c.55.1.7 104470,104471 1bupA 386 6.43e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 1kqpA 271 6.44e+00 c.26.2.1 72883 1kay 381 6.49e+00 1ba1 c.55.1.1,c.55.1.1 33385,33386 2fexA 188 6.54e+00 1djnA 729 6.72e+00 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 1rvgA 305 7.02e+00 c.1.10.2 97920 7odcA 424 7.11e+00 7odcA b.49.2.3,c.1.6.1 26488,28650 1vp2A 208 8.02e+00 2cglA 489 8.25e+00 1s72H 171 8.63e+00 d.41.4.1 105327 1ualA 274 8.69e+00 c.116.1.4 88383 1kv8A 216 8.84e+00 c.1.2.3 73054 1e4fT 419 9.08e+00 1e4fT c.55.1.1,c.55.1.1 33453,33454 1sg4A 260 9.12e+00 1bdb 277 9.13e+00 1bdb c.2.1.2 29874 1u04A 771 9.52e+00 b.34.14.1,c.55.3.10 107539,107540 1bo4A 168 9.70e+00 1bo4A d.108.1.1 40798 1qwgA 251 9.81e+00 c.1.27.1 96473 1orrA 347 9.86e+00 c.2.1.2 93460 1w8iA 156 9.94e+00 1zy9A 564 1.01e+01 1mjhA 162 1.03e+01 1mjhA c.26.2.4 31639 1p90A 145 1.05e+01 c.55.5.2 94377 2a4nA 182 1.05e+01 1v9wA 130 1.07e+01 c.47.1.16 108453 2basA 431 1.08e+01 2ajrA 331 1.08e+01 1l2tA 235 1.08e+01 c.37.1.12 73514 1rxyA 253 1.09e+01 c.56.2.1 98065 1n71A 180 1.10e+01 d.108.1.1 85370 1s2dA 167 1.12e+01 c.23.14.1 98377 1u7bA 261 1.13e+01 1i12A 160 1.15e+01 1i21A d.108.1.1 61515 1chuA 540 1.16e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1lnsA 763 1.16e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1h2eA 207 1.17e+01 c.60.1.1 70857 2gm3A 175 1.17e+01 1j8yF 297 1.21e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1qo7A 394 1.22e+01 1qo7A c.69.1.11 34697 2cohA 202 1.24e+01 1m2oA 768 1.25e+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 2c46A 241 1.25e+01 2gupA 292 1.25e+01 1zx1A 231 1.29e+01 1jndA 420 1.30e+01 c.1.8.5,d.26.3.1 71757,71758 2ge3A 170 1.32e+01 2bkfA 87 1.35e+01 1hqsA 423 1.36e+01 1iso c.77.1.1 61154 1sg0A 230 1.37e+01 1woqA 267 1.40e+01 c.55.1.10,c.55.1.10 109462,109463 1w2xA 758 1.42e+01 c.14.1.4,c.14.1.4 109134,109135 1jmvA 141 1.42e+01 c.26.2.4 66897 1hdoA 206 1.46e+01 1he2A c.2.1.2 60965 1jx7A 117 1.46e+01 c.114.1.1 77195 1vqoH 171 1.48e+01 1pfkA 320 1.48e+01 3pfk c.89.1.1 35575 1dciA 275 1.48e+01 1dciA c.14.1.3 30918 1i1dA 161 1.50e+01 1i21A d.108.1.1 61526 1v71A 323 1.51e+01 2b49A 287 1.52e+01 1ye8A 178 1.53e+01 2b0tA 738 1.53e+01 1t5bA 201 1.58e+01 c.23.5.3 106433 2bswA 146 1.59e+01 1q77A 138 1.61e+01 c.26.2.4 96023 1p9oA 313 1.61e+01 c.72.3.1 94397 1hv9A 456 1.62e+01 1fwyA b.81.1.4,c.68.1.5 28060,34518 2pfkA 320 1.62e+01 3pfk c.89.1.1 35577 1ek0A 170 1.63e+01 1ctqA c.37.1.8 32076 2cvhA 220 1.64e+01 1t6cA 315 1.68e+01 c.55.1.8,c.55.1.8 106558,106559 2av4A 162 1.71e+01 2aioA 269 1.74e+01 1n2sA 299 1.76e+01 c.2.1.2 79857 1j8mF 297 1.76e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1r6xA 395 1.76e+01 b.122.1.3,c.26.1.5 97167,97168 1a05A 358 1.78e+01 1cnzA c.77.1.1 35059 1mzbA 136 1.78e+01 a.4.5.42 91497 1vpqA 273 1.80e+01 2gptA 523 1.80e+01 1a04A 215 1.80e+01 1a04A a.4.6.2,c.23.1.1 16234,31089 1qo2A 241 1.81e+01 1qo2A c.1.2.1 28533 2avtA 378 1.84e+01 1t6kA 278 1.85e+01 1wraA 308 1.85e+01 1wb0A 445 1.87e+01 1ooeA 236 1.88e+01 c.2.1.2 87196 1augA 215 1.89e+01 1a2zA c.56.4.1 33798 1zhvA 134 1.94e+01 1eswA 500 1.94e+01 1cwyA c.1.8.1 59500 1vhwA 253 1.96e+01 c.56.2.1 100706 1ivnA 190 1.97e+01 c.23.10.5 83719 1v4vA 376 1.98e+01 c.87.1.3 100313 1v58A 241 2.02e+01 c.47.1.9,d.17.3.1 108371,108372 1b87A 181 2.05e+01 1b87A d.108.1.1 40797 1mveA 243 2.06e+01 b.29.1.2 85140 2akaB 299 2.06e+01 1i9sA 210 2.06e+01 1i9sA c.45.1.1 62099 1o94A 729 2.10e+01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 2ethA 154 2.12e+01 1smlA 269 2.14e+01 1smlA d.157.1.1 42053 1v8fA 276 2.20e+01 c.26.1.4 100503 2ai4A 119 2.20e+01 1ek1A 554 2.23e+01 1cr6B c.69.1.11,c.108.1.2 34685,43335 2ae6A 166 2.26e+01 1meoA 209 2.28e+01 c.65.1.1 79035 1wyzA 242 2.30e+01 1f8gA 384 2.31e+01 1sayA c.2.1.4,c.23.12.2 59695,59696 1szoA 257 2.31e+01 c.14.1.3 106164 1jksA 294 2.32e+01 d.144.1.7 71710 1u9yA 284 2.33e+01 1ve4A 206 2.33e+01 1w3jA 468 2.37e+01 c.1.8.4 109156 1czaN 917 2.37e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 1yr0A 175 2.39e+01 1cb0A 283 2.40e+01 1cb0A c.56.2.1 33790 1sqsA 242 2.42e+01 c.23.5.5 98968 1ve5A 311 2.43e+01 2cw5A 255 2.44e+01 2beiA 170 2.44e+01 1x1nA 524 2.44e+01 1wbsA 360 2.45e+01 1tq8A 163 2.48e+01 c.26.2.4 107204 1b0uA 262 2.50e+01 1b0uA c.37.1.12 32370 2hf9A 226 2.50e+01 2bibA 547 2.50e+01 1xdnA 277 2.52e+01 1tyjA 170 2.52e+01 1q1oA 98 2.54e+01 d.15.2.2 95596 1qv9A 283 2.56e+01 c.127.1.1 96356 2f5tX 233 2.57e+01 2ftxB 64 2.58e+01 2fuvA 549 2.59e+01 1svfB 38 2.60e+01 1svfB h.3.2.1 45764 2ac2A 309 2.61e+01 1ma3A 253 2.64e+01 c.31.1.5 78883 1hkkA 364 2.65e+01 c.1.8.5,d.26.3.1 90634,90635 1a0i 348 2.65e+01 1a0i b.40.4.6,d.142.2.1 25363,41577 1r94A 118 2.66e+01 b.124.1.1 97251 1xubA 298 2.70e+01 2d0oA 610 2.70e+01 1vl6A 388 2.71e+01 c.2.1.7,c.58.1.3 108724,108725 1uyrA 737 2.72e+01 c.14.1.4,c.14.1.4 100188,100189 1xniA 118 2.77e+01 1smpI 101 2.78e+01 1smpI b.61.2.1 27417 1amx 180 2.79e+01 1amx b.2.3.1 22410 1xmtA 103 2.83e+01 1t8tA 271 2.84e+01 c.37.1.5 106685 1hp1A 516 2.85e+01 d.114.1.1,d.159.1.2 70976,70977 1fl2A 310 2.90e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 2bfdA 400 2.91e+01 1vplA 256 2.92e+01 1w9gA 104 2.93e+01 1p4fA 293 2.94e+01 d.144.1.7 104063 1hyvA 166 3.01e+01 1b9dA c.55.3.2 61424 1u1wA 298 3.03e+01 2reb 352 3.06e+01 2reb c.37.1.11,d.48.1.1 32282,38767 2ac4A 309 3.07e+01 1exqA 154 3.12e+01 1b9dA c.55.3.2 33646 1u6mA 199 3.16e+01 1a8q 274 3.17e+01 1brt c.69.1.12 34702 1w0dA 337 3.18e+01 2b7oA 464 3.19e+01 1yd7A 395 3.19e+01 1wz7A 111 3.20e+01 1v1rA 400 3.22e+01 c.36.1.11 108272 1x13A 401 3.23e+01 1l8nA 679 3.25e+01 c.1.8.10,d.92.2.2 84564,84565 1n7kA 234 3.26e+01 c.1.10.1 85374 1uqrA 154 3.28e+01 c.23.13.1 99779 1dozA 309 3.30e+01 1ak1 c.92.1.1 35592 1nbwA 607 3.35e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 2d28C 149 3.35e+01 1ush 550 3.36e+01 1ush d.114.1.1,d.159.1.2 40923,42079 1vcsA 102 3.37e+01 1m8jA 181 3.45e+01 c.26.1.3 84875 1k07A 263 3.46e+01 d.157.1.1 77218 2a9sA 171 3.47e+01 1ig3A 263 3.47e+01 1ig3A b.82.6.1,c.100.1.1 62358,62359 1j7xA 302 3.47e+01 c.14.1.2 66425 1hjsA 332 3.47e+01 c.1.8.3 83492 1vetA 124 3.48e+01 d.110.7.1 108553 2eu9A 355 3.49e+01 1e19A 314 3.51e+01 1b7bA c.73.1.1 34967 1shsA 147 3.52e+01 1shsA b.15.1.1 23675 1x7yA 400 3.53e+01 1xx4A 261 3.55e+01 1pvdA 537 3.56e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 1l7dA 384 3.60e+01 c.2.1.4,c.23.12.2 77774,77775 1e9lA 377 3.63e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 1iukA 140 3.65e+01 c.2.1.8 83712 1r2qA 170 3.68e+01 c.37.1.8 96874 1pe1A 267 3.69e+01 c.1.10.4 94591 1k3rA 268 3.71e+01 b.40.4.10,c.116.1.2 72018,72019 2g9zA 348 3.73e+01 1xwnA 174 3.73e+01 1m3uA 264 3.74e+01 c.1.12.8 84784 2a1fA 247 3.75e+01 1yacA 208 3.75e+01 1yacA c.33.1.3 31757 1wwzA 159 3.77e+01 1zuhA 168 3.78e+01 1lx7A 253 3.80e+01 c.56.2.1 74329 1zz2A 360 3.82e+01 1e6uA 321 3.84e+01 1bsvA c.2.1.2 29805 1ybdA 239 3.85e+01 2di4A 238 3.85e+01 1o66A 275 3.88e+01 c.1.12.8 92547 1huqA 164 3.89e+01 1byuA c.37.1.8 32020 1ec7A 446 3.91e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 2a10A 125 3.92e+01 1j6oA 268 3.93e+01 c.1.9.12 77088 2etvA 346 3.95e+01 1yuwA 554 3.95e+01 1pkoA 139 3.97e+01 b.1.1.1 88147 1evlA 401 3.97e+01 1qf6A c.51.1.1,d.104.1.1 33202,40751 2a8yA 270 4.00e+01 2eshA 118 4.02e+01 1vliA 385 4.05e+01 b.85.1.1,c.1.10.6 108830,108831 2f9lA 199 4.05e+01 1nslA 184 4.08e+01 d.108.1.1 86137 2citA 282 4.10e+01 4pfk 319 4.11e+01 3pfk c.89.1.1 35582 1qcwA 410 4.11e+01 1gox c.1.4.1 28622 2etjA 250 4.17e+01 1u94A 356 4.23e+01 c.37.1.11,d.48.1.1 107743,107744 1w5qA 337 4.23e+01 1wc3A 219 4.25e+01 1ywrA 360 4.27e+01 1nni1 174 4.28e+01 2co5A 99 4.29e+01 1dbiA 280 4.32e+01 1gci c.41.1.1 32543 2a1rA 430 4.34e+01 1b74A 254 4.34e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1hrkA 359 4.36e+01 1hrkA c.92.1.1 61228 1m93B 245 4.37e+01 2fbiA 142 4.38e+01 1ekeA 230 4.48e+01 1ekeA c.55.3.1 33572 1qipA 183 4.51e+01 1qipA d.32.1.1 38470 1u7zA 226 4.52e+01 1tikA 213 4.53e+01 c.23.5.3 107003 1kkeA 210 4.54e+01 b.21.1.2,b.83.1.2 68669,68670 1har 216 4.54e+01 1rthA e.8.1.2 43025 1xb4A 202 4.55e+01 1d4xG 126 4.57e+01 1d0nA d.109.1.1 59109 1bl3A 160 4.57e+01 1b9dA c.55.3.2 33655 1nhkL 144 4.59e+01 1npk d.58.6.1 39142 1t8xA 267 4.67e+01 1xm7A 195 4.67e+01 1amuA 563 4.69e+01 1amuA e.23.1.1 43351 1rxxA 421 4.70e+01 d.126.1.4 98061 1y1oA 203 4.74e+01 1uwvA 433 4.76e+01 b.40.4.12,c.66.1.40 100128,100129 1eajA 126 4.76e+01 1f5wA b.1.1.1 59401 1zbfA 142 4.78e+01 1hzdA 272 4.79e+01 c.14.1.3 65969 1i05A 180 4.84e+01 1mup b.60.1.1 27130 1vicA 262 4.84e+01 c.68.1.13 100756 1o8uA 257 4.85e+01 c.14.1.3 81194 1mkp 144 4.86e+01 1vhrA c.45.1.1 32654 1y0eA 223 4.88e+01 1r3cA 366 4.89e+01 d.144.1.7 96906 1e7rA 321 4.94e+01 1bsvA c.2.1.2 29808 2rslA 140 4.98e+01 2rslA c.53.1.1 33345 2gqrA 237 5.02e+01 1i06A 180 5.03e+01 1mup b.60.1.1 27131 1zhaA 267 5.08e+01 2a5sA 284 5.10e+01 1s3zA 165 5.13e+01 d.108.1.1 105250 1yn9A 169 5.14e+01 1fwsA 267 5.18e+01 1d9eA c.1.10.4 60063 2dhqA 146 5.20e+01 2dhqA c.23.13.1 31382 1ho1A 242 5.21e+01 1ho1A c.1.24.1 61097 1c3jA 351 5.23e+01 1c3jA c.87.1.1 35459 1xp8A 366 5.24e+01 1r3eA 309 5.24e+01 b.122.1.1,d.265.1.2 96907,96908 1nm1G 125 5.24e+01 d.109.1.1 80653 1olsA 400 5.25e+01 c.36.1.11 93331 1g7sA 594 5.29e+01 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