# List of top-scoring protein chains for t04-100-30-str2-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 1bg2 325 4.68e-45 1bg2 c.37.1.9 32189 1i6iA 366 5.20e-43 1bg2 c.37.1.9 61844 1x88A 359 4.45e-42 1q0bA 367 5.33e-42 c.37.1.9 95502 1vfvA 366 1.10e-41 c.37.1.9 108592 1f9vA 347 3.45e-40 1bg2 c.37.1.9 59745 1ry6A 360 1.80e-36 c.37.1.9 98090 2kinA 238 6.84e-34 1bg2 c.37.1.9 32190 2kinB 100 6.26e-12 3kinB 1jx4A 352 2.06e-01 d.240.1.1,e.8.1.7 90378,90379 1ex2A 189 2.70e-01 1ex2A c.51.4.2 33225 1zxiB 809 5.88e-01 1wf3A 301 6.86e-01 1qj2B 809 7.20e-01 1qj2B 1n62B 809 7.36e-01 d.41.1.1,d.133.1.1 80092,80093 2ghpA 292 9.20e-01 1go4A 205 1.10e+00 d.135.1.1 70292 1htjF 210 1.28e+00 1htjF a.91.1.1 61254 2aq4A 434 1.43e+00 1odfA 290 1.44e+00 c.37.1.6 92782 2b67A 204 1.51e+00 1w7jA 795 1.67e+00 1d2mA 665 1.95e+00 1d2mA c.37.1.19,c.37.1.19 32417,32418 1gvnB 287 2.03e+00 c.37.1.21 76354 2napA 723 2.21e+00 2napA b.52.2.2,c.81.1.1 26926,35334 1nm1G 125 2.23e+00 d.109.1.1 80653 1lvk 762 2.28e+00 1lvk b.34.3.1,c.37.1.9 24576,32173 2ng1 293 2.61e+00 1ng1 a.24.13.1,c.37.1.10 16962,32273 1c4oA 664 2.67e+00 1d2mA c.37.1.19,c.37.1.19 32415,32416 1d4xG 126 2.69e+00 1d0nA d.109.1.1 59109 1rypJ 204 2.85e+00 d.153.1.4 41878 1o54A 277 3.08e+00 c.66.1.13 92482 1pzgA 331 3.24e+00 c.2.1.5,d.162.1.1 95425,95426 1t3qB 788 3.32e+00 d.41.1.1,d.133.1.1 106369,106370 1f7sA 139 3.33e+00 1cof d.109.1.2 40857 1of5A 221 3.36e+00 d.17.4.2 86933 1ls1A 295 3.42e+00 a.24.13.1,c.37.1.10 78170,78171 1ofuA 320 3.71e+00 c.32.1.1,d.79.2.1 86972,86973 1d0yA 761 3.84e+00 1lvk b.34.3.1,c.37.1.9 24581,32178 1ukkA 142 4.13e+00 d.227.1.1 99491 1t2dA 322 4.31e+00 c.2.1.5,d.162.1.1 99084,99085 1mvwA 840 4.48e+00 i.15.1.1 79523 1q5qA 259 5.72e+00 d.153.1.4 95904 1oe9A 795 5.82e+00 b.34.3.1,c.37.1.9 92792,92793 1wn5A 130 5.93e+00 1k7kA 221 6.21e+00 c.51.4.1 72104 1esgA 213 6.46e+00 1bam c.52.1.3 33286 1v6fA 151 6.76e+00 d.109.1.2 108395 1q5dA 419 6.97e+00 a.104.1.1 95891 2bycA 137 7.07e+00 1tljA 213 7.23e+00 d.282.1.1 107126 1unnC 115 7.25e+00 d.240.1.1 99680 1yewA 382 7.25e+00 2azeA 155 7.32e+00 1ihuA 589 7.48e+00 c.37.1.10,c.37.1.10 62394,62395 1vom 762 7.54e+00 1lvk b.34.3.1,c.37.1.9 24577,32174 1lwjA 441 7.75e+00 b.71.1.1,c.1.8.1 74303,74304 1h6kZ 98 8.12e+00 d.58.7.1 60686 1qwiA 143 9.44e+00 d.227.1.1 96474 1txvB 440 9.62e+00 2atrA 138 9.65e+00 1qm4A 396 1.01e+01 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41350,41351,41352 1tvjA 166 1.03e+01 2ap1A 327 1.04e+01 1ryp2 233 1.09e+01 1ryp2 2cdnA 201 1.10e+01 1vjjA 692 1.10e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 1inlA 296 1.12e+01 c.66.1.17 66220 3pmgA 561 1.12e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 1ei1A 391 1.17e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 1ldg 316 1.20e+01 1ceqA c.2.1.5,d.162.1.1 30165,42132 1r4xA 275 1.21e+01 b.1.10.3,d.105.1.2 97054,97055 1vj5A 555 1.25e+01 c.108.1.2,c.69.1.11 100799,100800 1vkkA 154 1.28e+01 d.109.1.2 108669 1zd3A 555 1.30e+01 1xvaA 292 1.31e+01 1xvaA c.66.1.5 34183 2por 301 1.32e+01 2por f.4.3.1 43759 2azqA 311 1.34e+01 2bzuA 181 1.35e+01 1y14A 187 1.37e+01 1lv7A 257 1.42e+01 c.37.1.20 78232 1n2fA 142 1.43e+01 d.227.1.1 79853 1c0pA 363 1.43e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1cqmA 101 1.46e+01 1ris d.58.14.1 39321 1tc6A 236 1.46e+01 d.122.1.1 106756 1az9 457 1.47e+01 1az9 c.55.2.1,d.127.1.1 33547,41164 1nd4A 264 1.49e+01 d.144.1.6 91815 1wi6A 88 1.52e+01 1yr0A 175 1.53e+01 1ush 550 1.60e+01 1ush d.114.1.1,d.159.1.2 40923,42079 1wddS 128 1.60e+01 2akaA 776 1.62e+01 1vfrA 218 1.68e+01 1vfrA d.90.1.1 40247 2faoA 309 1.70e+01 1p4tA 155 1.71e+01 f.4.1.1 87779 1hrdA 449 1.73e+01 1k89 c.2.1.7,c.58.1.1 30219,33867 1k2eA 156 1.76e+01 d.113.1.1 72010 1z2mA 155 1.76e+01 1rsy 152 1.78e+01 1rsy b.7.1.2 23192 1ji0A 240 1.81e+01 c.37.1.12 71665 1bgvA 449 1.84e+01 1k89 c.2.1.7,c.58.1.1 30217,33865 2bwvA 440 1.87e+01 2fsjA 346 1.87e+01 1ymmA 191 1.90e+01 1j8mF 297 1.91e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1g8kA 825 1.93e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 2fggA 101 1.93e+01 1vraB 215 1.96e+01 1vz6A 393 1.96e+01 d.154.1.2 108949 1jeyA 609 2.01e+01 1jeqA b.131.1.1,c.62.1.3 90370,90371 1xkrA 206 2.01e+01 2gk4A 232 2.04e+01 1hjxA 362 2.04e+01 c.1.8.5,d.26.3.1 83512,83513 1rypH 205 2.09e+01 d.153.1.4 41876 1hlrA 907 2.11e+01 1vlbA 907 2.11e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 1qf5A 431 2.12e+01 1adeA c.37.1.10 32212 2a5yB 549 2.16e+01 1nfkA 325 2.16e+01 1a3qA b.1.18.1,b.2.5.3 21929,22444 1tjyA 316 2.17e+01 c.93.1.1 107062 1r9cA 139 2.18e+01 d.32.1.2 97255 1wl9A 440 2.20e+01 1fg7A 356 2.20e+01 1gewA c.67.1.1 59819 1m1zA 513 2.23e+01 c.26.2.1,d.153.1.1 78457,78458 1ooyA 481 2.24e+01 c.124.1.3,c.124.1.2 93388,93389 1gewA 356 2.25e+01 1gewA c.67.1.1 60470 1p8xA 344 2.26e+01 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 1jb7B 260 2.27e+01 1otcB b.40.4.3 62839 1hdiA 413 2.28e+01 16pk c.86.1.1 60964 2av4A 162 2.29e+01 1jihA 531 2.30e+01 d.240.1.1,e.8.1.7 90374,90375 1g291 372 2.31e+01 1g291 1auiA 521 2.33e+01 1auiA d.159.1.3 42085 2f5tX 233 2.33e+01 1owqA 361 2.34e+01 c.1.8.5,d.26.3.1 104041,104042 2akaB 299 2.38e+01 1g8pA 350 2.48e+01 1g8pA c.37.1.20 60376 2cunA 410 2.48e+01 1t71A 281 2.49e+01 1ne9A 335 2.52e+01 d.108.1.4,d.108.1.4 91839,91840 1sa3A 262 2.54e+01 c.52.1.23 105400 1ujnA 348 2.58e+01 e.22.1.1 99460 2cx7A 130 2.58e+01 1xmrA 243 2.64e+01 1cliA 345 2.65e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 5ukdA 194 2.65e+01 1zin c.37.1.1 31851 2adcA 229 2.66e+01 2fsrA 195 2.69e+01 1j1iA 296 2.70e+01 c.69.1.10 83977 1sheA 103 2.79e+01 d.274.1.1 105551 16pk 415 2.80e+01 16pk c.86.1.1 35454 1k2yX 463 2.80e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1m4jA 142 2.82e+01 d.109.1.2 78602 1dar 691 2.85e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1 25707,32142,37547,39300 3rubS 123 2.90e+01 1rboC d.73.1.1 39616 1v7rA 186 2.91e+01 c.51.4.1 100482 1x74A 360 2.91e+01 1rypG 244 2.92e+01 d.153.1.4 41938 1hdoA 206 2.93e+01 1he2A c.2.1.2 60965 1xdpA 687 2.94e+01 1ti6A 875 2.98e+01 b.52.2.2,c.81.1.1 106974,106975 2b1xB 172 3.02e+01 1dhn 121 3.07e+01 1dhn d.96.1.3 40663 1w9iA 770 3.09e+01 1qf9A 194 3.10e+01 1zin c.37.1.1 31848 1lk2A 274 3.11e+01 b.1.1.2,d.19.1.1 91056,91057 1pvyA 227 3.14e+01 d.115.1.2 95195 1snnA 227 3.14e+01 d.115.1.2 105821 1amuA 563 3.24e+01 1amuA e.23.1.1 43351 1q7zA 566 3.26e+01 c.1.21.2,c.1.26.1 96090,96091 1p5dX 463 3.26e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1t94A 459 3.28e+01 d.240.1.1,e.8.1.7 106701,106702 1ur4A 399 3.36e+01 1yuwA 554 3.43e+01 1gr0A 367 3.45e+01 c.2.1.3,d.81.1.3 70379,70380 1fzoA 274 3.53e+01 1agdA b.1.1.2,d.19.1.1 60155,60156 1vp2A 208 3.54e+01 2aiqA 231 3.60e+01 1dmgA 225 3.60e+01 1dmgA c.22.1.1 31036 1i88A 389 3.62e+01 c.95.1.2,c.95.1.2 66070,66071 1fxlA 167 3.69e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1hp1A 516 3.69e+01 d.114.1.1,d.159.1.2 70976,70977 1yb2A 275 3.76e+01 1e8gA 560 3.78e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1vk1A 242 3.82e+01 d.268.1.2 108634 1dxy 333 3.83e+01 1dxy c.2.1.4,c.23.12.1 30094,31354 1vg0A 650 3.85e+01 c.3.1.3,d.16.1.6 108596,108597 1h12A 405 3.87e+01 a.102.1.2 83447 1v30A 124 3.90e+01 1xhlA 297 3.91e+01 c.2.1.2 109591 2fnaA 357 3.95e+01 2bzlA 325 4.00e+01 1lw9A 164 4.04e+01 d.2.1.3 84727 2fpmA 322 4.04e+01 1ryp1 222 4.07e+01 1ryp1 1wohA 305 4.13e+01 c.42.1.1 109446 1ltqA 301 4.18e+01 c.108.1.9,c.37.1.1 78208,78209 1uzxA 169 4.21e+01 d.20.1.2 100238 1cbf 285 4.24e+01 1cbf c.90.1.1 35587 1xs0A 136 4.25e+01 1wruA 379 4.26e+01 1yqtA 538 4.26e+01 2bf6A 449 4.27e+01 1f3iA 481 4.28e+01 1b7eA 8rucI 123 4.28e+01 1rboC d.73.1.1 39629 1swyA 164 4.31e+01 1sx7A 164 4.31e+01 1ukvG 453 4.31e+01 c.3.1.3,c.3.1.3,d.16.1.6 107915,107916,107917 1wv2A 265 4.36e+01 1l7aA 318 4.38e+01 c.69.1.25 77772 1g2rA 100 4.38e+01 1g2rA d.192.1.1 60231 1h4uA 265 4.38e+01 1h4uA d.22.1.2,g.3.11.5 60622,60623 1zhhB 242 4.43e+01 1xizA 159 4.48e+01 1g0uL 241 4.49e+01 d.153.1.4 41894 119l 164 4.52e+01 1l92 d.2.1.3 36622 2bl1A 172 4.55e+01 1qf6A 642 4.55e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1p36A 164 4.67e+01 d.2.1.3 93978 1wqaA 455 4.70e+01 1cs0A 1073 4.72e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1vmeA 410 4.78e+01 c.23.5.1,d.157.1.3 108893,108894 1z6nA 167 4.79e+01 1nnlA 225 4.83e+01 c.108.1.4 85906 1bo4A 168 4.83e+01 1bo4A d.108.1.1 40798 1vd2A 89 4.85e+01 d.15.2.2 108517 1dpe 507 4.92e+01 1dpe c.94.1.1 35799 1vicA 262 4.93e+01 c.68.1.13 100756 1tjxA 159 4.98e+01 1qg3A 195 4.99e+01 1qg3A b.1.2.1,b.1.2.1 21993,21994 1x3sA 195 5.03e+01 1fmtA 314 5.04e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 1dljA 402 5.05e+01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1m48A 133 5.05e+01 a.26.1.2 74443 1p42A 270 5.08e+01 d.14.1.7,d.14.1.7 87754,87755 2fqxA 318 5.08e+01 1m33A 258 5.12e+01 c.69.1.26 78514 1e58A 249 5.18e+01 1qhfA c.60.1.1 59262 1qdeA 224 5.19e+01 1qvaA c.37.1.19 32410 1ukvY 206 5.22e+01 c.37.1.8 107918 1u9iA 519 5.24e+01 1uluA 261 5.24e+01 1q77A 138 5.26e+01 c.26.2.4 96023 1jx2B 315 5.29e+01 c.37.1.8 67404 1w1kA 560 5.34e+01 d.58.32.1,d.145.1.1 109059,109060 1tmxA 293 5.38e+01 1u2eA 289 5.40e+01 1qgxA 357 5.41e+01 1qgxA e.7.1.1 42973 1tfzA 424 5.42e+01 d.32.1.3,d.32.1.3 106886,106887 1ybdA 239 5.44e+01 1xx1A 285 5.44e+01 1dekA 241 5.47e+01 1dekA c.37.1.1 31842 1lehA 364 5.48e+01 1bw9A c.2.1.7,c.58.1.1 30268,33916 1yvoA 172 5.48e+01 1ytfB 53 5.55e+01 1ytfB a.32.1.1 16997 1xwiA 322 5.59e+01 1tp9A 162 5.59e+01 1v25A 541 5.60e+01 e.23.1.1 108275 1rl6A 177 5.66e+01 1rl6A d.141.1.1,d.141.1.1 41473,41474 1qy5A 269 5.71e+01 d.122.1.1 96573 2g8lA 299 5.76e+01 1mzyA 333 5.77e+01 b.6.1.3,b.6.1.3 103848,103849 1n9lA 109 5.86e+01 d.110.3.6 85468 2axtI 38 5.87e+01 1ej2A 181 5.92e+01 1f9aA c.26.1.3 59414 1rkuA 206 5.98e+01 c.108.1.11 97627 1nox 205 5.99e+01 1nox d.90.1.1 40242 2fpeA 62 6.00e+01 1yobA 179 6.02e+01 1ka1A 357 6.05e+01 e.7.1.1 68369 1vpsA 289 6.05e+01 1vpsA b.121.6.1 23336 1spxA 278 6.11e+01 c.2.1.2 98958 1i19A 561 6.13e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 1s7kA 182 6.15e+01 1ieaA 192 6.19e+01 1iakA b.1.1.2,d.19.1.1 21631,38205 2pia 321 6.21e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1yz4A 160 6.24e+01 1tt7A 330 6.26e+01 1woqA 267 6.28e+01 c.55.1.10,c.55.1.10 109462,109463 1cfzA 162 6.31e+01 1cfzA c.56.1.1 33754 2czrA 226 6.37e+01 1nh2B 53 6.40e+01 a.32.1.1 91874 1jssA 224 6.42e+01 d.129.3.2 71844 1z0jA 170 6.44e+01 1jz8A 1023 6.53e+01 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 67830,67831,67832,67833,67834 1vypX 364 6.54e+01 c.1.4.1 108905 1uxzA 131 6.67e+01 b.18.1.10 100170 1qx4A 274 6.70e+01 b.43.4.2,c.25.1.1 104624,104625 1v6tA 255 6.70e+01 1m8jA 181 6.70e+01 c.26.1.3 84875 1xewY 172 6.73e+01 1jvwA 167 6.75e+01 d.26.1.1 71907 2ew0A 192 6.77e+01 1w85A 368 6.80e+01 1g6oA 330 6.82e+01 1g6oA c.37.1.11 32430 1j24A 143 6.83e+01 c.52.1.20 84008 1nv8A 284 6.83e+01 c.66.1.30 86224 1z1zA 131 6.87e+01 1wdtA 665 6.94e+01 1zclA 180 6.99e+01 1yruA 364 7.00e+01 1gvoA 364 7.03e+01 c.1.4.1 76357 1h61A 364 7.07e+01 1oyc c.1.4.1 60657 1ltlA 279 7.07e+01 b.40.4.11 84701 1dq3A 454 7.09e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1z06A 189 7.10e+01 1mrzA 293 7.17e+01 b.43.5.1,c.26.1.3 91452,91453 1e19A 314 7.19e+01 1b7bA c.73.1.1 34967 1ivyA 452 7.20e+01 1ivyA c.69.1.5 34654 2ahqA 76 7.22e+01 1ro5A 201 7.25e+01 d.108.1.3 105023 1svvA 359 7.26e+01 c.67.1.1 106054 2bd0A 244 7.30e+01 1cr5A 189 7.35e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1usyA 275 7.39e+01 1e9rA 437 7.43e+01 c.37.1.11 64827 2bcgY 206 7.43e+01 2cy7A 396 7.48e+01 1r6wA 322 7.58e+01 c.1.11.2,d.54.1.1 97165,97166 2c07A 285 7.59e+01 1in4A 334 7.60e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 2abbA 364 7.61e+01 1wlsA 328 7.63e+01 1vyrA 364 7.66e+01 c.1.4.1 108906 1mtzA 293 7.71e+01 c.69.1.7 79467 2bllA 345 7.79e+01 1tu5A 746 7.82e+01 1u69A 163 7.83e+01 d.32.1.7 107699 1u04A 771 7.85e+01 b.34.14.1,c.55.3.10 107539,107540 3inkC 133 7.85e+01 3inkC a.26.1.2 16881 1w0hA 204 7.87e+01 1p1mA 406 7.89e+01 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