# List of top-scoring protein chains for t04-100-30-stride-ebghtl-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 1u8fO 335 3.12e-39 1gd1O 334 8.32e-39 1dssG c.2.1.3,d.81.1.1 29962,39877 1dssG 333 1.65e-38 1dssG c.2.1.3,d.81.1.1 30022,39937 1gadO 330 2.50e-38 1dssG c.2.1.3,d.81.1.1 29950,39865 2b4rO 345 8.89e-38 1obfO 335 3.28e-36 c.2.1.3,d.81.1.1 86768,86769 1rm4A 337 5.33e-36 c.2.1.3,d.81.1.1 105000,105001 1k3tA 359 5.30e-35 c.2.1.3,d.81.1.1 72022,72023 1gypA 358 2.34e-34 1dssG c.2.1.3,d.81.1.1 30004,39919 1mb4A 370 8.43e-32 c.2.1.3,d.81.1.1 78908,78909 1t4bA 367 9.38e-31 c.2.1.3,d.81.1.1 106406,106407 1ys4A 354 1.53e-30 1brmA 367 3.67e-29 1brmA c.2.1.3,d.81.1.1 30030,39945 1xygD 359 1.02e-28 1vknA 351 2.52e-27 c.2.1.3,d.81.1.1 108676,108677 1cf2O 337 4.74e-13 1b7gO c.2.1.3,d.81.1.1 29994,39909 2czcA 334 1.56e-11 1b7gO 340 1.90e-10 1b7gO c.2.1.3,d.81.1.1 29992,39907 1nvmB 312 6.92e-06 c.2.1.3,d.81.1.1 86251,86252 1h6dA 433 3.34e-05 c.2.1.3,d.81.1.5 65656,65657 1ofgA 381 1.35e-04 1ofgA c.2.1.3,d.81.1.5 30064,39979 1f06A 320 2.93e-04 1dapA c.2.1.3,d.81.1.3 59556,59557 2g5cA 281 4.45e-04 2bkaA 242 7.14e-04 1mldA 314 1.26e-03 2cmd c.2.1.5,d.162.1.1 30122,42089 1t2dA 322 1.41e-03 c.2.1.5,d.162.1.1 99084,99085 2f1kA 279 1.49e-03 1hyeA 313 1.63e-03 2cmd c.2.1.5,d.162.1.1 61400,61401 1qydA 313 2.08e-03 c.2.1.2 96583 1drw 273 2.56e-03 1drw c.2.1.3,d.81.1.3 30057,39972 1ldg 316 4.07e-03 1ceqA c.2.1.5,d.162.1.1 30165,42132 1w5fA 353 4.45e-03 1z82A 335 4.78e-03 1xcbA 211 8.29e-03 a.4.5.38,c.2.1.12 109552,109553 1xq6A 253 9.37e-03 1fsz 372 1.02e-02 1fsz c.32.1.1,d.79.2.1 31750,39802 2bllA 345 1.10e-02 1y81A 138 1.15e-02 1xgkA 352 1.23e-02 1j5pA 253 1.54e-02 d.81.1.3,c.2.1.3 71577,83092 1vm6A 228 1.58e-02 c.2.1.3,d.81.1.3 108876,108877 2gasA 307 1.62e-02 1oc2A 348 2.01e-02 c.2.1.2 92765 1u9jA 358 2.20e-02 1xeaA 323 2.21e-02 c.2.1.3,d.81.1.5 109572,109573 1j4aA 333 2.21e-02 c.2.1.4,c.23.12.1 71502,71503 2ew2A 316 2.22e-02 1kepA 348 2.52e-02 c.2.1.2 68536 1zejA 293 2.54e-02 1lc0A 294 2.67e-02 c.2.1.3,d.81.1.4 73823,73824 2cmd 312 2.84e-02 2cmd c.2.1.5,d.162.1.1 30135,42102 1uxjA 309 2.86e-02 c.2.1.5,d.162.1.1 108112,108113 1hyhA 309 2.94e-02 1hyhA c.2.1.5,d.162.1.1 30150,42117 1ebfA 358 3.00e-02 1ebuA c.2.1.3,d.81.1.2 30033,39948 1ur5A 309 3.35e-02 c.2.1.5,d.162.1.1 99807,99808 1dljA 402 3.42e-02 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1z7bA 358 3.44e-02 1gcuA 295 3.95e-02 1gcuA c.2.1.3,d.81.1.4 30063,39978 1gy8A 397 4.37e-02 c.2.1.2 83376 2ahrA 259 4.64e-02 1y8qB 640 7.35e-02 1mv8A 436 7.71e-02 a.100.1.4,c.2.1.6,c.26.3.1 85128,85129,85130 1c0pA 363 8.45e-02 1an9A c.4.1.2,d.16.1.3 30647,37934 1ydwA 362 8.53e-02 1xhcA 367 9.07e-02 1qycA 308 1.01e-01 c.2.1.2 96581 1bxkA 355 1.03e-01 1bxkA c.2.1.2 29803 1gteA 1025 1.04e-01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70440,70441,70442,70443,70444 1rq2A 382 1.09e-01 c.32.1.1,d.79.2.1 105048,105049 4uagA 437 1.10e-01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1h7wA 1025 1.27e-01 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15683,28628,30324,30609,39007 2ez9A 603 1.29e-01 1poxA 585 1.48e-01 1poxA c.31.1.3,c.36.1.5,c.36.1.9 31731,31793,31794 1x0vA 354 1.72e-01 1vqwA 457 1.73e-01 1g3qA 237 1.74e-01 1hyqA c.37.1.10 60237 2d0iA 333 1.76e-01 2b69A 343 1.78e-01 2cvzA 289 1.79e-01 1rpnA 335 1.88e-01 c.2.1.2 97708 1pzgA 331 1.89e-01 c.2.1.5,d.162.1.1 95425,95426 1lsuA 147 1.97e-01 c.2.1.9 74250 2bi7A 384 2.03e-01 2gn4A 344 2.16e-01 1hdoA 206 2.21e-01 1he2A c.2.1.2 60965 2a35A 215 2.27e-01 1lssA 140 2.33e-01 c.2.1.9 74246 2g76A 335 2.34e-01 1pjqA 457 2.57e-01 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 1t2aA 375 2.58e-01 c.2.1.2 99078 1gdhA 320 2.64e-01 1gdhA c.2.1.4,c.23.12.1 30095,31355 1b74A 254 2.79e-01 1b74A c.78.2.1,c.78.2.1 35264,35265 1sbyA 254 2.88e-01 1i36A 264 2.97e-01 a.100.1.8,c.2.1.6 71108,71109 1b16A 254 3.06e-01 1b16A c.2.1.2 29875 2bw0A 329 3.10e-01 1gdeA 389 3.14e-01 c.67.1.1 60456 1m1nA 491 3.16e-01 c.92.2.3 78417 1ac5 483 3.26e-01 1ac5 c.69.1.5 34653 1ryiA 382 3.32e-01 6ldh 330 3.55e-01 3ldh c.2.1.5,d.162.1.1 30161,42128 1e94F 449 3.70e-01 1do0A c.37.1.20 32443 1kewA 361 4.31e-01 c.2.1.2 68544 1wwkA 307 4.34e-01 1pz1A 333 4.67e-01 c.1.7.1 95390 1oi7A 288 4.70e-01 c.2.1.8,c.23.4.1 87049,87050 2b0jA 358 4.72e-01 1eq2A 310 4.80e-01 1eq2A c.2.1.2 29814 1kv8A 216 5.22e-01 c.1.2.3 73054 1gtmA 419 5.85e-01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1guzA 310 6.18e-01 c.2.1.5,d.162.1.1 65586,65587 1p77A 272 6.21e-01 c.2.1.7,c.58.1.5 94214,94215 1e6uA 321 6.26e-01 1bsvA c.2.1.2 29805 1xel 338 6.73e-01 1xel c.2.1.2 29786 1txgA 335 6.88e-01 1e7rA 321 6.89e-01 1bsvA c.2.1.2 29808 1v5xA 203 7.14e-01 c.1.2.4 100377 1g0oA 283 7.28e-01 1ybvA c.2.1.2 60181 1udc 338 7.33e-01 1xel c.2.1.2 29785 1q0qA 406 7.52e-01 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 2bmaA 470 7.63e-01 1q6oA 216 7.77e-01 c.1.2.3 95986 1ng4A 390 7.88e-01 c.3.1.2,d.16.1.3 85666,85667 1nijA 318 8.02e-01 c.37.1.10,d.237.1.1 85741,85742 1e5xA 486 8.54e-01 c.79.1.1 59283 1xrjA 261 8.81e-01 1jffA 451 8.83e-01 c.32.1.1,d.79.2.1 62932,62933 1lldA 319 9.07e-01 3ldh c.2.1.5,d.162.1.1 30177,42144 1g5cA 170 9.24e-01 1g5cA c.53.2.1 60264 1qvzA 237 9.25e-01 c.23.16.2 96453 1p0kA 349 9.43e-01 c.1.4.1 87648 1an9A 340 1.06e+00 1an9A c.4.1.2,d.16.1.3 30617,37904 1tltA 319 1.09e+00 c.2.1.3,d.81.1.5 107135,107136 1ek6A 348 1.10e+00 1xel c.2.1.2 29800 1c1dA 355 1.10e+00 1bw9A c.2.1.7,c.58.1.1 30270,33918 1jqbA 351 1.11e+00 b.35.1.2,c.2.1.1 77151,77152 1bmdA 327 1.13e+00 1bmdA c.2.1.5,d.162.1.1 30139,42106 1vl6A 388 1.16e+00 c.2.1.7,c.58.1.3 108724,108725 1uj2A 252 1.19e+00 c.37.1.6 99452 1zcjA 463 1.20e+00 1cv8 174 1.22e+00 1cv8 d.3.1.1 37089 1tg7A 971 1.22e+00 1s3iA 310 1.22e+00 b.46.1.1,c.65.1.1 98435,98436 1o12A 376 1.30e+00 b.92.1.5,c.1.9.10 80758,80759 1jvsA 400 1.30e+00 a.69.3.1,c.2.1.3,d.81.1.3 77187,77188,77189 1y7tA 327 1.32e+00 1p99A 295 1.33e+00 c.94.1.1 94384 2liv 344 1.33e+00 2liv c.93.1.1 35708 1jayA 212 1.37e+00 c.2.1.6 66478 1gr0A 367 1.37e+00 c.2.1.3,d.81.1.3 70379,70380 1kyqA 274 1.39e+00 c.2.1.11,e.37.1.1 73281,73282 1kevA 351 1.40e+00 1pedA b.35.1.2,c.2.1.1 24749,29765 1gesA 450 1.40e+00 3grs c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 1db3A 372 1.44e+00 1db3A c.2.1.2 29813 1bgvA 449 1.45e+00 1k89 c.2.1.7,c.58.1.1 30217,33865 1f0kA 364 1.46e+00 1f0kA c.87.1.2 35465 2ax3A 502 1.46e+00 1bdmA 327 1.49e+00 1bmdA c.2.1.5,d.162.1.1 30137,42104 1cydA 244 1.52e+00 1cydA c.2.1.2 29825 1usgA 346 1.61e+00 c.93.1.1 99864 1ff9A 450 1.63e+00 1ff9A c.2.1.3,d.81.1.2 30039,39954 1aa8A 347 1.63e+00 1an9A 1hrdA 449 1.63e+00 1k89 c.2.1.7,c.58.1.1 30219,33867 1k2yX 463 1.64e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1ykjA 394 1.69e+00 1sb8A 352 1.70e+00 c.2.1.2 105410 1o6zA 303 1.73e+00 c.2.1.5,d.162.1.1 81107,81108 1tv8A 340 1.77e+00 c.1.28.3 107352 2bmfA 451 1.78e+00 1sc6A 404 1.82e+00 1k0iA 394 1.89e+00 c.3.1.2,d.16.1.2 67942,67943 1cnzA 363 1.91e+00 1cnzA c.77.1.1 35061 1k6xA 352 1.92e+00 c.2.1.2 68238 1pbe 394 1.92e+00 1pbe c.3.1.2,d.16.1.2 30338,37869 1iukA 140 1.92e+00 c.2.1.8 83712 1ofuA 320 2.04e+00 c.32.1.1,d.79.2.1 86972,86973 1z3iX 644 2.08e+00 2nacA 393 2.10e+00 2nadA c.2.1.4,c.23.12.1 30088,31348 1tufA 434 2.21e+00 b.49.2.3,c.1.6.1 107335,107336 1nhp 447 2.25e+00 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 1v7oA 165 2.29e+00 d.67.1.2 100480 1p5dX 463 2.34e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1qh8A 478 2.35e+00 1qguA c.92.2.3 35633 2ao0A 324 2.37e+00 1nytA 271 2.38e+00 c.2.1.7,c.58.1.5 86417,86418 1pyfA 312 2.41e+00 c.1.7.1 95334 1xdwA 331 2.49e+00 1cl1A 395 2.51e+00 1cl2A c.67.1.3 34395 2lbp 346 2.52e+00 2liv c.93.1.1 35709 1pot 325 2.58e+00 1pot c.94.1.1 35807 1o5kA 306 2.62e+00 c.1.10.1 92504 1l2lA 457 2.67e+00 c.72.1.3 77656 1tr0A 108 2.69e+00 d.58.4.4 107261 1vjpA 394 2.69e+00 c.2.1.3,d.81.1.3 100828,100829 1m98A 317 2.70e+00 a.175.1.1,d.17.4.6 78866,78867 1rw7A 243 2.81e+00 c.23.16.2 97963 1nf3A 195 2.82e+00 c.37.1.8 85594 2g9zA 348 2.83e+00 1r6dA 337 2.83e+00 c.2.1.2 97148 1up7A 417 2.95e+00 1wchA 315 2.96e+00 1yqzA 438 2.97e+00 1ps9A 671 3.07e+00 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 1bg6 359 3.07e+00 1bg6 a.100.1.5,c.2.1.6 18810,30214 1wcv1 257 3.10e+00 1mh1 186 3.11e+00 1eesA c.37.1.8 32002 1cs1A 386 3.12e+00 1ibjA c.67.1.3 34399 1fmcA 255 3.19e+00 1cydA c.2.1.2 29856 1q7bA 244 3.23e+00 c.2.1.2 96026 1r0kA 388 3.37e+00 a.69.3.1,c.2.1.3,d.81.1.3 104723,104724,104725 1su8A 636 3.45e+00 e.26.1.2 98999 1vl2A 421 3.55e+00 c.26.2.1,d.210.1.1 108708,108709 1vi6A 208 3.59e+00 c.23.15.1 100736 1j1nA 492 3.72e+00 c.94.1.1 83978 2fr1A 486 3.75e+00 1np3A 338 3.77e+00 a.100.1.2,c.2.1.6 85946,85947 1i24A 404 3.78e+00 c.2.1.2 83663 1jjyA 636 3.79e+00 1jjyA 1t71A 281 3.83e+00 1ww8A 439 3.96e+00 1psdA 409 3.96e+00 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1qrrA 394 4.00e+00 1qrrA c.2.1.2 29824 1wviA 257 4.09e+00 1pgjA 478 4.12e+00 2pgd a.100.1.1,c.2.1.6 18783,30195 1yqgA 263 4.12e+00 1ek4A 418 4.12e+00 1dd8A c.95.1.1,c.95.1.1 59436,59437 1k68A 140 4.12e+00 c.23.1.1 90943 1ecfA 504 4.13e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 1tt7A 330 4.24e+00 1o4uA 285 4.25e+00 c.1.17.1,d.41.2.1 86624,86625 1lba 146 4.33e+00 1lba d.118.1.1 41062 1zx5A 300 4.43e+00 3nul 130 4.49e+00 3nul d.110.1.1 40891 1vjoA 393 4.52e+00 c.67.1.3 100827 1kmqA 184 4.54e+00 c.37.1.8 84412 1ivyA 452 4.62e+00 1ivyA c.69.1.5 34654 1jeoA 180 4.66e+00 c.80.1.3 66611 1ea5A 537 4.72e+00 2bce c.69.1.1 34592 2bkkA 264 4.72e+00 1xccA 220 4.75e+00 1xg5A 279 4.77e+00 1gnd 447 4.77e+00 1gnd c.3.1.3,d.16.1.6 30423,37987 1gpjA 404 4.84e+00 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1vpdA 299 4.89e+00 1l5jA 865 4.97e+00 a.118.15.1,c.8.2.1,c.83.1.1 73592,73593,73594 1nhs 447 5.00e+00 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 1z15A 344 5.01e+00 1zfjA 491 5.18e+00 1ak5 c.1.5.1,d.37.1.1,d.37.1.1 28638,38540,38541 3pmgA 561 5.20e+00 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 1pxvA 183 5.28e+00 d.3.1.1 95301 1vhcA 224 5.40e+00 c.1.10.1 100661 1ede 310 5.45e+00 1b6g c.69.1.8 34662 1fmtA 314 5.54e+00 1fmtA b.46.1.1,c.65.1.1 25758,34174 1ig0A 319 5.58e+00 1ig0A b.82.6.1,c.100.1.1 62354,62355 1zjjA 263 5.61e+00 1t15A 214 5.71e+00 c.15.1.3,c.15.1.3 99067,99068 1b6g 310 5.88e+00 1b6g c.69.1.8 34661 1wlsA 328 5.92e+00 1ks9A 291 5.93e+00 a.100.1.7,c.2.1.6 68857,68858 1x88A 359 5.95e+00 1vhvA 268 6.08e+00 c.90.1.1 100704 1ads 315 6.13e+00 1frb c.1.7.1 28671 2fokA 579 6.19e+00 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16131,16132,16133,33323 1mx3A 347 6.20e+00 c.2.1.4,c.23.12.1 79638,79639 1zemA 262 6.25e+00 1f8gA 384 6.32e+00 1sayA c.2.1.4,c.23.12.2 59695,59696 2anuA 255 6.43e+00 2c2hA 192 6.50e+00 1p0fA 373 6.51e+00 b.35.1.2,c.2.1.1 87642,87643 1jx6A 342 6.63e+00 c.93.1.1 67406 1oaoA 674 6.69e+00 e.26.1.2 86744 1jdw 423 6.74e+00 1jdw d.126.1.2 41129 1bd3A 243 6.75e+00 1bd3A c.61.1.1 34098 2c07A 285 6.76e+00 1kao 167 6.79e+00 1ctqA c.37.1.8 32014 2d9rA 104 6.81e+00 1p3dA 475 6.81e+00 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1ve9A 347 6.89e+00 c.4.1.2,d.16.1.3 100571,100572 1l7dA 384 6.90e+00 c.2.1.4,c.23.12.2 77774,77775 1frb 315 6.98e+00 1frb c.1.7.1 28665 1vimA 200 6.99e+00 c.80.1.3 100758 2agtA 319 6.99e+00 2aqjA 538 7.08e+00 1qo0D 196 7.16e+00 1qo0D c.23.1.3 31125 2bcgG 453 7.22e+00 1ukvG 453 7.28e+00 c.3.1.3,c.3.1.3,d.16.1.6 107915,107916,107917 1jflA 228 7.28e+00 c.78.2.1,c.78.2.1 71656,71657 1zq1A 438 7.48e+00 1wnfA 328 7.76e+00 1f60A 458 7.82e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1itcA 516 7.90e+00 b.3.1.1,c.1.8.1 83705,83706 1jnyA 435 7.91e+00 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1jw9B 249 7.97e+00 c.111.1.1 67377 1i6pA 220 8.18e+00 1ddzA c.53.2.1 61848 1t4gA 322 8.20e+00 a.60.4.1,c.37.1.11 106418,106419 1cjcA 460 8.35e+00 1cjcA c.3.1.1,c.4.1.1 30319,30604 1wstA 417 8.36e+00 1q0bA 367 8.58e+00 c.37.1.9 95502 1w4xA 542 8.64e+00 c.3.1.5,c.3.1.5 109171,109172 1r9jA 673 8.71e+00 1us0A 316 8.82e+00 c.1.7.1 99850 1yb5A 351 8.86e+00 1uufA 369 8.89e+00 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