# List of top-scoring protein chains for t04-100-30-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 1v6tA 255 5.16e-03 1xm8A 254 6.00e-02 1lwjA 441 8.13e-02 b.71.1.1,c.1.8.1 74303,74304 2blnA 305 8.58e-02 1wd5A 208 8.63e-02 1mi3A 322 9.49e-02 c.1.7.1 91274 1td2A 287 9.74e-02 c.72.1.5 106765 2ah5A 210 9.76e-02 1vl4A 447 1.28e-01 d.283.1.1 108718 1xw8A 252 1.44e-01 1gca 309 1.51e-01 1gca c.93.1.1 35659 1ny1A 240 1.58e-01 c.6.2.3 86395 2c71A 216 1.70e-01 1vi9A 299 1.85e-01 c.72.1.5 100750 2gbp 309 2.79e-01 1gca c.93.1.1 35657 1wr2A 238 2.86e-01 1yzfA 195 2.91e-01 1qwkA 317 3.90e-01 c.1.7.1 96482 1louA 101 4.19e-01 1ris d.58.14.1 39323 2b0jA 358 4.50e-01 1ffyA 917 4.54e-01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1cqmA 101 5.21e-01 1ris d.58.14.1 39321 1vk3A 615 5.67e-01 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 1vjzA 341 6.89e-01 c.1.8.3 100838 2c3zA 222 7.92e-01 1sc6A 404 8.51e-01 2bbrA 195 8.64e-01 1f8rA 498 9.86e-01 1f8rA c.3.1.2,d.16.1.5 30410,37974 1jmvA 141 1.03e+00 c.26.2.4 66897 1tv8A 340 1.14e+00 c.1.28.3 107352 2f1sA 186 1.23e+00 1i2aA 219 1.25e+00 e.24.1.1 90660 1ws6A 171 1.25e+00 1knqA 175 1.27e+00 c.37.1.17 72786 2f5xA 312 1.29e+00 1j7xA 302 1.29e+00 c.14.1.2 66425 1w0hA 204 1.31e+00 1psdA 409 1.33e+00 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1wa3A 205 1.36e+00 1mroA 548 1.37e+00 1mroA a.89.1.1,d.58.31.2 18525,39443 1reoA 486 1.37e+00 c.3.1.2,d.16.1.5 97325,97326 1bw0A 416 1.45e+00 1bw0A c.67.1.1 34385 1hbnA 549 1.48e+00 1mroA a.89.1.1,d.58.31.2 60898,60899 1ebmA 317 1.50e+00 1ebmA a.96.1.3,d.129.1.2 18751,41300 2ng1 293 1.53e+00 1ng1 a.24.13.1,c.37.1.10 16962,32273 4tmkA 213 1.54e+00 5tmpA c.37.1.1 31930 1umdA 367 1.58e+00 c.36.1.11 99599 1wyuA 438 1.60e+00 1m3qA 317 1.60e+00 a.96.1.3,d.129.1.2 91184,91185 1t7lA 766 1.67e+00 1wzuA 300 1.70e+00 1fnoA 417 1.71e+00 d.58.19.1,c.56.5.4 70145,75841 1vixA 420 1.72e+00 c.56.5.4,d.58.19.1 100777,100778 1gzgA 337 2.04e+00 c.1.10.3 70805 1w5nA 337 2.05e+00 1ls1A 295 2.07e+00 a.24.13.1,c.37.1.10 78170,78171 1a4iA 301 2.08e+00 1a4iA c.2.1.7,c.58.1.2 30278,33926 1igs 248 2.11e+00 1a53 c.1.2.4 28565 1h4pA 408 2.22e+00 c.1.8.3 90617 1cb0A 283 2.30e+00 1cb0A c.56.2.1 33790 2aaa 484 2.49e+00 7taa b.71.1.1,c.1.8.1 27777,28764 1km4A 247 2.52e+00 c.1.2.3 72740 1dvjA 246 2.52e+00 1dvjA c.1.2.3 28546 1vlmA 219 2.65e+00 c.66.1.41 108836 1x1zA 252 2.68e+00 1vlwA 217 2.70e+00 c.1.10.1 108868 1uehA 253 2.93e+00 c.101.1.1 99259 1vc4A 254 3.02e+00 c.1.2.4 100557 1a53 247 3.05e+00 1a53 c.1.2.4 28564 1s0aA 429 3.08e+00 c.67.1.4 98263 1sh0A 510 3.08e+00 e.8.1.4 98876 1b4kA 337 3.14e+00 1b4kA c.1.10.3 29184 1qzzA 374 3.17e+00 a.4.5.29,c.66.1.12 96719,96720 1d2fA 390 3.20e+00 1d2fA c.67.1.3 34411 1z63A 500 3.21e+00 1ituA 369 3.22e+00 c.1.9.7 71423 1wraA 308 3.23e+00 1rlmB 271 3.26e+00 1iukA 140 3.26e+00 c.2.1.8 83712 1khyA 148 3.32e+00 a.174.1.1 77410 2amxA 376 3.34e+00 1i7pA 274 3.42e+00 b.43.4.2,c.25.1.1 66048,66049 1zzmA 259 3.42e+00 1e6yA 569 3.43e+00 1mroA a.89.1.1,d.58.31.2 18529,39447 1uarA 285 3.46e+00 c.46.1.2,c.46.1.2 107762,107763 1umkA 275 3.47e+00 1vljA 407 3.54e+00 e.22.1.2 108832 1hx0A 496 3.57e+00 b.71.1.1,c.1.8.1 61346,61347 1z6aA 500 3.68e+00 2c1gA 431 3.70e+00 2g7lA 243 3.72e+00 1px5A 349 3.77e+00 a.160.1.2,d.218.1.6 95277,95278 1c4kA 730 3.78e+00 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 1vr6A 350 3.81e+00 1rpxA 230 3.82e+00 1rpxA c.1.2.2 28536 1fc6A 388 3.83e+00 1fc6A b.36.1.3,c.14.1.2 64738,64739 1sffA 426 3.85e+00 c.67.1.4 105482 1v7rA 186 3.93e+00 c.51.4.1 100482 1s2oA 244 4.08e+00 2b43A 526 4.19e+00 2f9sA 151 4.32e+00 1smd 496 4.41e+00 1smd b.71.1.1,c.1.8.1 27768,28755 1imjA 210 4.44e+00 c.69.1.23 71246 1l9vA 317 4.52e+00 d.13.2.1,d.216.1.1 73760,73761 1zckA 154 4.88e+00 1us0A 316 4.97e+00 c.1.7.1 99850 2aucA 126 5.07e+00 2c1iA 431 5.41e+00 1rlmA 271 5.50e+00 1e7lA 157 5.55e+00 1en7A a.140.4.1,d.4.1.5 64728,64729 1zhaA 267 5.73e+00 1rxdA 159 5.73e+00 1vkmA 297 5.85e+00 c.138.1.1 108670 1pwmA 316 5.86e+00 c.1.7.1 95231 1qj5A 429 5.92e+00 1dtyA c.67.1.4 34493 1w5qA 337 6.03e+00 2agtA 319 6.05e+00 1x24A 180 6.22e+00 1st9A 143 6.35e+00 c.47.1.10 98987 2f9lA 199 6.48e+00 1k4iA 233 6.55e+00 d.115.1.2 72056 1rzmA 338 6.57e+00 c.1.10.4 105137 1cjxA 357 6.60e+00 1cjxA d.32.1.3,d.32.1.3 38516,38517 1z6oM 191 6.66e+00 1oixA 191 7.01e+00 1eluA 390 7.19e+00 1elqA c.67.1.3 34434 1udzA 182 7.39e+00 b.51.1.1 99239 1af3 196 7.43e+00 1maz f.1.4.1 43397 3nul 130 7.49e+00 3nul d.110.1.1 40891 2cw8A 537 7.60e+00 1meoA 209 7.67e+00 c.65.1.1 79035 1qrrA 394 7.78e+00 1qrrA c.2.1.2 29824 1qusA 322 7.99e+00 1ltm d.2.1.6 36991 1pe1A 267 8.01e+00 c.1.10.4 94591 1eceA 358 8.04e+00 1eceA c.1.8.3 28813 1z3iX 644 8.32e+00 1svdM 110 8.38e+00 1s1pA 331 8.40e+00 c.1.7.1 98350 1ob8A 135 8.42e+00 1wznA 252 8.43e+00 1dl5A 317 8.58e+00 1dl5A c.66.1.7,d.197.1.1 64720,64721 2pii 112 8.72e+00 2pii d.58.5.1 39071 1q7zA 566 8.85e+00 c.1.21.2,c.1.26.1 96090,96091 2f3yA 148 8.89e+00 1i24A 404 8.99e+00 c.2.1.2 83663 1t0bA 252 9.10e+00 c.23.16.6 106199 2madH 373 9.19e+00 2bbkH b.69.2.1 27639 1sdoA 203 9.20e+00 c.52.1.21 98809 1hh1A 143 9.37e+00 1gefA c.52.1.18 61036 1t8xA 267 9.40e+00 1wnyA 186 9.46e+00 1rd5A 262 9.60e+00 2an1A 292 9.62e+00 1h6gA 256 9.72e+00 1h6gA a.24.9.1,a.24.9.1 60669,60670 1vm7A 311 9.83e+00 c.72.1.1 108884 1epuA 591 1.01e+01 1dn1A e.25.1.1 43358 1j4aA 333 1.02e+01 c.2.1.4,c.23.12.1 71502,71503 1x7oA 287 1.04e+01 1wbeA 209 1.05e+01 1mdoA 393 1.05e+01 c.67.1.4 79013 1rzrA 332 1.08e+01 1wk8A 194 1.08e+01 1r9lA 309 1.08e+01 c.94.1.1 97262 1zoyB 252 1.08e+01 1j31A 262 1.10e+01 d.160.1.2 90808 1nar 290 1.10e+01 1nar c.1.8.5 28988 1k7jA 206 1.11e+01 d.115.1.1 72103 1bf6A 291 1.13e+01 1pscA c.1.9.3 29065 1pysA 350 1.13e+01 1pysA d.104.1.1 40775 1ads 315 1.13e+01 1frb c.1.7.1 28671 1ov2A 99 1.14e+01 a.13.1.1 93580 1pq1A 196 1.16e+01 f.1.4.1 94986 1ig8A 486 1.17e+01 2yhx c.55.1.3,c.55.1.3 64746,64747 2faoA 309 1.18e+01 1j96A 323 1.19e+01 c.1.7.1 71616 1bgp 309 1.21e+01 1bgp a.93.1.1 18690 1o98A 511 1.21e+01 c.105.1.1,c.76.1.3 86684,86685 2d13A 227 1.22e+01 1zclA 180 1.22e+01 1eqjA 511 1.23e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 1vecA 206 1.25e+01 c.37.1.19 100575 1us5A 314 1.27e+01 c.94.1.1 99856 1vsd 152 1.31e+01 1cxqA c.55.3.2 33625 1ngr 85 1.31e+01 1ngr a.77.1.2 18422 2ae8A 221 1.32e+01 1fwsA 267 1.33e+01 1d9eA c.1.10.4 60063 1o60A 292 1.33e+01 c.1.10.4 92532 1fds 327 1.33e+01 1fds c.2.1.2 29838 1fb6A 105 1.34e+01 1thx c.47.1.1 32739 1ygs 234 1.36e+01 1ygs b.26.1.1 23907 1u1hA 765 1.37e+01 c.1.22.2,c.1.22.2 107580,107581 1yruB 74 1.39e+01 2pfkA 320 1.41e+01 3pfk c.89.1.1 35577 1a70 97 1.41e+01 1awd d.15.4.1 37678 2akoA 251 1.42e+01 1sxgA 280 1.42e+01 2dpmA 284 1.44e+01 2dpmA c.66.1.28 34246 1t8sA 484 1.45e+01 c.56.2.1 106679 1j8mF 297 1.48e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1uv7A 110 1.48e+01 d.67.4.1 100040 1h2bA 359 1.49e+01 b.35.1.2,c.2.1.1 90543,90544 1w66A 232 1.50e+01 1div 149 1.51e+01 1div d.99.1.1,d.100.1.1 40692,40693 2blkA 122 1.51e+01 1o0yA 260 1.54e+01 c.1.10.1 80756 1ua4A 455 1.54e+01 c.72.1.3 99128 1p1xA 260 1.55e+01 c.1.10.1 104060 1eyhA 144 1.55e+01 1eduA a.118.9.1 19214 1jcxA 267 1.57e+01 c.1.10.4 66510 1pfkA 320 1.58e+01 3pfk c.89.1.1 35575 1uj6A 227 1.58e+01 c.124.1.4,d.58.40.1 107898,107899 1u1jA 765 1.58e+01 c.1.22.2,c.1.22.2 107590,107591 1maz 221 1.60e+01 1maz f.1.4.1 43393 1jxhA 288 1.62e+01 c.72.1.2 67415 1rz4A 226 1.63e+01 a.4.5.53,a.118.1.18 105131,105132 1in6A 334 1.63e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 1elqA 390 1.63e+01 1elqA c.67.1.3 34436 1pbuA 162 1.64e+01 d.58.46.1 88030 1j8yF 297 1.65e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1qx4A 274 1.66e+01 b.43.4.2,c.25.1.1 104624,104625 1b7yA 350 1.67e+01 1pysA d.104.1.1 40776 1ckeA 227 1.68e+01 1ckeA c.37.1.1 31846 2akaB 299 1.69e+01 1fxqA 267 1.69e+01 1d9eA c.1.10.4 60108 1whzA 70 1.70e+01 1o4uA 285 1.71e+01 c.1.17.1,d.41.2.1 86624,86625 1frb 315 1.71e+01 1frb c.1.7.1 28665 1tu5A 746 1.73e+01 1jtvA 327 1.74e+01 c.2.1.2 84230 1oivA 191 1.75e+01 c.37.1.8 93076 1io2A 213 1.77e+01 1ekeA c.55.3.1 62612 1jclA 260 1.77e+01 c.1.10.1 66501 2b99A 156 1.77e+01 1i1kA 309 1.79e+01 1daaA e.17.1.1 61533 1xg5A 279 1.80e+01 1n2zA 245 1.81e+01 c.92.2.2 79865 1n3gA 113 1.83e+01 d.204.1.1 79962 2aqjA 538 1.87e+01 1iyeA 309 1.87e+01 e.17.1.1 83786 1nnhA 294 1.87e+01 d.104.1.1 92005 1fpzA 212 1.90e+01 1fpzA c.45.1.1 59976 2fbwB 252 1.91e+01 1u8sA 192 1.93e+01 d.58.18.5,d.58.18.5 107737,107738 1zip 217 1.93e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1ecfA 504 1.93e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1rm6A 769 1.94e+01 1nsj 205 1.97e+01 1nsj c.1.2.4 28560 1z5yE 149 1.97e+01 2go7A 207 1.99e+01 1z00B 84 1.99e+01 1qo0D 196 2.00e+01 1qo0D c.23.1.3 31125 1vqoS 85 2.02e+01 1xewX 182 2.03e+01 1e5rA 290 2.04e+01 1e5rA b.82.2.4 59276 1cxqA 162 2.04e+01 1cxqA c.55.3.2 33621 1tlfA 301 2.05e+01 1tlfA c.93.1.1 35687 1ir21 140 2.05e+01 1jjvA 206 2.06e+01 c.37.1.1 71698 1smlA 269 2.07e+01 1smlA d.157.1.1 42053 1s4kA 120 2.08e+01 a.35.1.6 105254 1s72S 85 2.09e+01 d.12.1.1 105338 2cvbA 188 2.11e+01 1fkx 349 2.13e+01 1a4mA c.1.9.1 29018 1sftA 388 2.14e+01 1bd0A b.49.2.2,c.1.6.1 26482,28644 1fgs 428 2.16e+01 1fgs c.59.1.2,c.72.2.2 33959,34962 1jj2R 84 2.17e+01 1ffkP d.12.1.1 63103 1e2wA 251 2.19e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1yyaA 250 2.19e+01 1yqhA 109 2.21e+01 1g57A 217 2.22e+01 1g57A d.115.1.2 60253 1fmjA 351 2.22e+01 c.37.1.5 59879 2bmaA 470 2.23e+01 1exrA 148 2.25e+01 1cll a.39.1.5 17299 2anuA 255 2.27e+01 1lre 81 2.29e+01 1lre a.13.1.1 16376 1c0pA 363 2.29e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 7aatA 401 2.29e+01 1ajsA c.67.1.1 34250 1riqA 465 2.30e+01 a.203.1.1,d.104.1.1 97516,97517 1r13A 148 2.30e+01 d.169.1.1,h.1.1.1 96782,96783 1aop 497 2.31e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39501,39502,41425,41426 1xjjA 644 2.33e+01 1gk8I 140 2.38e+01 d.73.1.1 65242 2aotA 292 2.39e+01 1yb3A 175 2.39e+01 1ifyA 49 2.39e+01 a.5.2.1 71207 1ycdA 243 2.40e+01 2gokA 429 2.42e+01 1oltA 457 2.46e+01 c.1.28.2 93334 1vkyA 347 2.46e+01 e.53.1.1 108696 1q35A 320 2.48e+01 c.94.1.1 95661 1vhrA 184 2.49e+01 1vhrA c.45.1.1 32651 1zin 217 2.49e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1tfjA 219 2.49e+01 1ng0A 253 2.49e+01 b.121.4.7 80475 1mk4A 157 2.50e+01 d.108.1.1 84979 1xs1A 193 2.53e+01 1w3iA 293 2.54e+01 c.1.10.1 109152 1c52 131 2.55e+01 1c52 a.3.1.1 15810 1knwA 425 2.56e+01 b.49.2.3,c.1.6.1 90969,90970 1zmaA 118 2.58e+01 1vjgA 218 2.58e+01 c.23.10.6 100810 1xfkA 336 2.59e+01 1octC 156 2.62e+01 1au7A a.4.1.1,a.35.1.1 15991,17017 1guqA 348 2.63e+01 1guqA d.13.1.2,d.13.1.2 37522,37523 2aioA 269 2.64e+01 1xpjA 126 2.64e+01 1jftA 340 2.68e+01 a.35.1.5,c.93.1.1 66652,66653 1p0fA 373 2.68e+01 b.35.1.2,c.2.1.1 87642,87643 1yfsA 465 2.68e+01 1aocA 175 2.71e+01 1aocA g.17.1.5 44817 1fmcA 255 2.76e+01 1cydA c.2.1.2 29856 1y3nA 490 2.79e+01 1jbwA 428 2.80e+01 c.59.1.2,c.72.2.2 62860,62861 1v98A 140 2.80e+01 1x42A 232 2.81e+01 2jdxA 385 2.81e+01 1jdw d.126.1.2 41139 1twyA 290 2.82e+01 1byrA 155 2.83e+01 1byrA d.136.1.1 41450 1sgwA 214 2.83e+01 c.37.1.12 105541 1vp8A 201 2.84e+01 2gupA 292 2.85e+01 1vdkA 466 2.86e+01 a.127.1.1 100561 1ksiA 642 2.92e+01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24408,38043,38044 1xfuA 747 2.93e+01 1v37A 177 2.93e+01 1vhcA 224 2.94e+01 c.1.10.1 100661 1wbhA 214 2.96e+01 2c0aA 214 2.96e+01 1zgdA 312 2.97e+01 1rkbA 173 2.97e+01 1ysjA 404 2.97e+01 1lt8A 406 2.98e+01 c.1.26.1 78186 7taa 478 2.99e+01 7taa b.71.1.1,c.1.8.1 27778,28765 1qh3A 260 3.00e+01 1qh5A d.157.1.2 42059 2ao0A 324 3.02e+01 1scuA 288 3.03e+01 2scuA c.2.1.8,c.23.4.1 30307,31135 1yx1A 264 3.03e+01 1kafA 108 3.04e+01 d.199.1.1 68372 1dbxA 158 3.04e+01 1dbuA d.116.1.1 40928 1xriA 151 3.05e+01 1xxlA 239 3.06e+01 1tia 279 3.06e+01 3tgl c.69.1.17 34737 1ryoA 327 3.06e+01 c.94.1.2 98108 1v4vA 376 3.07e+01 c.87.1.3 100313 1tbxA 99 3.07e+01 a.4.5.48 106748 1dzfA 215 3.09e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1ykwA 435 3.10e+01 1vj1A 363 3.10e+01 b.35.1.2,c.2.1.1 100794,100795 1gnkA 112 3.14e+01 2pii d.58.5.1 39073 1sflA 238 3.14e+01 1u4nA 310 3.16e+01 1j0aA 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