# List of top-scoring protein chains for t04-80-60-80-str2+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 2b6eA 146 2.77e-15 1zkiA 133 6.19e-15 1o0iA 138 7.36e-15 d.38.1.5 86532 1vh5A 148 9.25e-15 d.38.1.5 100642 1u1zA 168 2.47e-14 d.38.1.6 107602 1psuA 140 3.40e-14 d.38.1.5 88285 1wluA 136 3.57e-14 1j1yA 136 3.76e-14 d.38.1.5 90776 2fs2A 151 5.08e-14 1q4uA 151 6.56e-13 d.38.1.5 95828 1yliA 153 1.06e-12 1ixlA 131 1.06e-12 d.38.1.5 90717 1vpmA 169 3.50e-12 1yocA 147 5.69e-12 2cyeA 133 9.50e-12 1z6bA 154 1.19e-11 1t82A 155 2.21e-11 d.38.1.5 106639 1s5uA 138 3.54e-11 d.38.1.1 98573 1njkA 156 6.01e-11 d.38.1.1 85818 1sh8A 154 9.80e-11 d.38.1.5 105549 2gvhA 288 1.31e-10 2av9A 147 2.58e-10 1z54A 132 5.02e-10 2essA 248 1.54e-09 2gf6A 135 3.35e-09 2cwzA 141 3.05e-08 1c8uA 285 3.72e-08 1c8uA d.38.1.3,d.38.1.3 38547,38548 1lo7A 141 6.30e-08 d.38.1.1 74144 2b3nA 159 9.27e-08 2aliA 158 1.29e-07 1bvqA 141 1.99e-07 1bvqA d.38.1.1 38542 1mkaA 171 2.99e-07 1mkaA d.38.1.2 38543 1tbuA 118 1.03e-05 1iq6A 134 7.31e-05 d.38.1.4 76755 2bi0A 337 7.39e-05 1pn2A 280 8.05e-02 d.38.1.4,d.38.1.4 94930,94931 1yqzA 438 2.03e-01 1ydwA 362 2.65e-01 1te5A 257 2.93e-01 d.153.1.1 106795 1pn0A 665 3.41e-01 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 1sr8A 298 3.97e-01 e.54.1.1 105959 2g8yA 385 5.67e-01 1wmdA 434 5.78e-01 b.18.1.20,c.41.1.1 109408,109409 1fohA 664 6.20e-01 1fohA c.3.1.2,c.47.1.10,d.16.1.2 30381,33078,37900 1i40A 175 9.06e-01 b.40.5.1 66024 2b59A 187 1.02e+00 1oruA 195 1.16e+00 b.58.1.2 93464 1iq4A 179 1.16e+00 1iq4A d.77.1.1 62641 1y8oA 419 1.20e+00 1w66A 232 1.20e+00 1gl4A 285 1.24e+00 d.22.1.2,g.3.11.5 65286,65287 1obpA 159 1.33e+00 1obpA b.60.1.1 27092 1vjhA 122 1.40e+00 d.129.3.1 100811 1hw7A 255 1.46e+00 1i7fA d.193.1.1 61297 1avgI 142 1.48e+00 1avgI b.60.1.3 27229 2covD 104 1.60e+00 1cr5A 189 1.75e+00 1cr5A b.52.2.3,d.31.1.1 26931,38465 1zk7A 467 1.76e+00 1nxuA 333 1.77e+00 c.122.1.1 86389 2btzA 394 1.85e+00 1sdjA 310 1.91e+00 d.21.1.2,d.21.1.2 98807,98808 1vgyA 393 2.05e+00 c.56.5.4,d.58.19.1 100620,100621 1ab8A 220 2.06e+00 1azsA d.58.29.1 39414 2bm3A 166 2.18e+00 1sz7A 200 2.30e+00 2f5tX 233 2.58e+00 1gesA 450 2.67e+00 3grs c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 2a9kB 223 2.84e+00 1fmtA 314 3.01e+00 1fmtA b.46.1.1,c.65.1.1 25758,34174 1v9nA 360 3.06e+00 1h2kA 349 3.17e+00 b.82.2.6 76572 1vrmA 325 3.51e+00 1vr5A 547 3.54e+00 1pkhA 204 3.58e+00 b.85.4.1 94832 1z9lA 128 3.58e+00 1qqp3 220 3.64e+00 1qqp3 1gqeA 365 3.79e+00 e.38.1.1 70351 1lfwA 470 4.03e+00 c.56.5.4,d.58.19.1 77942,77943 1a34A 159 4.10e+00 1a34A b.121.7.1 23286 1qyaA 307 4.26e+00 d.21.1.2,d.21.1.2 104653,104654 1o97C 264 4.26e+00 c.26.2.3 81232 1jnyA 435 4.35e+00 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1xkrA 206 4.61e+00 1gt1A 159 4.64e+00 b.60.1.1 90515 1obwA 175 4.73e+00 2prd b.40.5.1 25416 1efpB 252 4.97e+00 1efvB c.26.2.3 31636 1stmA 157 5.13e+00 1stmA b.121.7.1 23281 1uolA 219 5.15e+00 b.2.5.2 99695 2ch9A 131 5.17e+00 1rj8A 164 5.23e+00 b.22.1.1 97547 1slqA 278 5.36e+00 f.47.1.1 105719 1snzA 344 5.53e+00 b.30.5.4 98930 1wvqA 167 5.57e+00 1fnoA 417 5.64e+00 d.58.19.1,c.56.5.4 70145,75841 2hgsA 474 5.67e+00 2hgsA c.30.1.4,d.142.1.6 31722,75997 1hskA 326 5.75e+00 2mbr d.145.1.2,d.146.1.1 61241,61242 1hn2A 159 5.82e+00 b.60.1.1 65890 1kutA 230 5.91e+00 d.143.1.1 73017 1mdwA 328 5.94e+00 d.3.1.3 84934 1ha3A 405 5.96e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1pmmA 466 6.28e+00 c.67.1.6 94901 1j83A 180 6.39e+00 b.18.1.12 66430 1hn4A 131 6.53e+00 a.133.1.2 65893 2bolA 314 6.61e+00 1widA 130 6.77e+00 1id0A 152 6.84e+00 d.122.1.3 66111 2cuaA 135 6.88e+00 2cuaA b.6.1.2 23039 1h5uA 842 6.89e+00 1a8i c.87.1.4 60655 2d42A 249 7.07e+00 1brwA 433 7.36e+00 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1xgkA 352 7.42e+00 1jm6A 407 7.57e+00 a.29.5.1,d.122.1.4 66876,66877 1smvA 260 7.62e+00 1smvA b.121.4.7 23288 1hbq 183 7.86e+00 1aqb b.60.1.1 27078 1dun 134 7.91e+00 1dun b.85.4.1 28371 1x36A 237 8.16e+00 1qg3A 195 8.18e+00 1qg3A b.1.2.1,b.1.2.1 21993,21994 1i8aA 189 8.24e+00 1i82A b.1.9.2 61951 1vixA 420 8.25e+00 c.56.5.4,d.58.19.1 100777,100778 1p5vA 235 8.48e+00 b.1.11.1,b.7.2.1 87812,87813 1vqvA 306 8.49e+00 1cvrA 435 8.73e+00 1cvrA b.1.18.12,c.17.1.2 21949,31006 1pxvA 183 8.73e+00 d.3.1.1 95301 1f15A 218 8.73e+00 1f15B b.121.4.5 23320 1k6xA 352 8.84e+00 c.2.1.2 68238 1jhfA 202 8.98e+00 a.4.5.2,b.87.1.1 63057,63058 1bbt3 220 9.16e+00 1qqp3 1je0A 236 9.21e+00 c.56.2.1 66581 1rfmA 344 9.21e+00 c.122.1.1 97385 1z94A 147 9.24e+00 1x33A 268 9.49e+00 1mo9A 523 9.52e+00 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1y08A 323 9.53e+00 1gp6A 356 9.64e+00 b.82.2.1 65441 1tm0A 350 9.67e+00 d.21.1.3 107147 1g24A 211 9.68e+00 1g24A d.166.1.1 42270 1u0kA 288 9.71e+00 d.21.1.2,d.21.1.2 107547,107548 1upsA 420 9.75e+00 1pvgA 418 9.86e+00 d.14.1.3,d.122.1.2 95161,95162 1g7sA 594 9.91e+00 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1qflA 389 1.00e+01 1afwA c.95.1.1,c.95.1.1 35908,35909 1vbiA 344 1.00e+01 1npyA 271 1.01e+01 c.2.1.7,c.58.1.5 85995,85996 1wtjA 343 1.02e+01 1gydB 315 1.02e+01 b.67.2.1 70751 1xubA 298 1.03e+01 1ufkA 254 1.03e+01 c.66.1.39 99340 1bdfA 235 1.04e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1f0lA 535 1.04e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22377,42239,43382 1vpgA 192 1.05e+01 1g87A 614 1.05e+01 a.102.1.2,b.2.2.2 83275,83276 1cbs 137 1.06e+01 1hmt b.60.1.2 27201 1bv1 159 1.06e+01 1bv1 d.129.3.1 41313 2f2hA 773 1.08e+01 1rz1A 161 1.12e+01 b.45.1.2 98124 1mdc 133 1.14e+01 1hmt b.60.1.2 27198 1wnhA 225 1.17e+01 1zy1B 197 1.17e+01 1y4hA 188 1.19e+01 1xkiA 162 1.20e+01 1nnhA 294 1.21e+01 d.104.1.1 92005 1xypA 190 1.21e+01 1axkA b.29.1.11 24327 1a8i 842 1.23e+01 1a8i c.87.1.4 35490 1j5uA 136 1.24e+01 d.208.1.1 71584 1tupA 219 1.24e+01 1tupA b.2.5.2 22434 2b49A 287 1.25e+01 1u55A 188 1.25e+01 d.278.1.1 107677 1fxlA 167 1.26e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1yuwA 554 1.29e+01 1wvhA 134 1.30e+01 1t4aA 84 1.31e+01 d.284.1.1 106404 1yspA 181 1.31e+01 2b4hA 254 1.31e+01 1svb 395 1.33e+01 1svb b.1.18.4,f.10.1.1 21814,43827 1bowA 159 1.33e+01 1bowA d.60.1.1 39528 1ewkA 490 1.33e+01 1ewkA c.93.1.1 35712 1aisA 182 1.35e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1u1wA 298 1.35e+01 1ciy 590 1.36e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1itcA 516 1.38e+01 b.3.1.1,c.1.8.1 83705,83706 1vemA 516 1.39e+01 1g7nA 131 1.39e+01 b.60.1.2 83274 1s72H 171 1.41e+01 d.41.4.1 105327 1agjA 242 1.42e+01 1agjA b.47.1.1 25827 1d2eA 397 1.43e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1mml 265 1.45e+01 1mml e.8.1.2 43015 1olmA 403 1.46e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1xrhA 351 1.47e+01 2d27A 149 1.47e+01 1g38A 393 1.47e+01 2admA c.66.1.27 60235 2bj0A 203 1.48e+01 1vb3A 428 1.49e+01 1xsjA 778 1.52e+01 1rg9A 383 1.53e+01 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1bjt 793 1.54e+01 1bjt e.11.1.1 43249 1h4uA 265 1.55e+01 1h4uA d.22.1.2,g.3.11.5 60622,60623 1fsu 492 1.56e+01 1auk c.76.1.2 35032 1fm4A 159 1.57e+01 1bv1 d.129.3.1 76186 1vgjA 184 1.57e+01 1zo2A 129 1.59e+01 2bl1A 172 1.60e+01 1cb0A 283 1.60e+01 1cb0A c.56.2.1 33790 1f4lA 551 1.60e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1wcdJ 441 1.64e+01 2et1A 201 1.69e+01 1cliA 345 1.74e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1se8A 301 1.74e+01 b.40.4.3 105448 1o6uA 403 1.76e+01 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 2ffsA 157 1.78e+01 1vr8A 142 1.80e+01 1hq0A 295 1.80e+01 1hzgA d.194.1.1 61122 1b5eA 246 1.82e+01 1b5eA d.117.1.1 41056 2d0eA 407 1.83e+01 1iznA 286 1.83e+01 e.43.1.1 83847 2ajtA 500 1.84e+01 1kskA 234 1.85e+01 d.66.1.5,d.265.1.3 72920,90389 1th5A 74 1.86e+01 1nziA 159 1.86e+01 b.23.1.1,g.3.11.1 86449,86450 1itvA 195 1.87e+01 b.66.1.1 76791 1tltA 319 1.87e+01 c.2.1.3,d.81.1.5 107135,107136 1bu8A 452 1.87e+01 1gpl b.12.1.2,c.69.1.19 23647,34795 1xmbA 418 1.87e+01 1n0lA 224 1.87e+01 b.1.11.1,b.7.2.1 79744,79745 1x8qA 184 1.87e+01 1pfvA 551 1.88e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1vi2A 300 1.88e+01 c.2.1.7,c.58.1.5 100726,100727 1i8dA 213 1.89e+01 b.43.4.3,b.43.4.3 61953,61954 1qznA 173 1.91e+01 b.2.2.2 104669 1ysjA 404 1.93e+01 1ej1A 190 1.94e+01 1ejhA d.86.1.1 40144 1p49A 562 1.94e+01 c.76.1.2 94089 1o0wA 252 1.95e+01 a.149.1.1,d.50.1.1 80751,80752 1yfqA 342 1.95e+01 1gyhA 318 1.97e+01 b.67.2.1 70757 1ef1A 294 2.01e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 1r45A 204 2.04e+01 1t6kA 278 2.05e+01 1j98A 157 2.07e+01 1j98A d.185.1.2 62755 1q1rA 431 2.08e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 2biqA 219 2.08e+01 1tcvA 287 2.11e+01 1ah6 220 2.12e+01 1yer d.122.1.1 41094 1u6mA 199 2.12e+01 1fi2A 201 2.14e+01 1fi2A b.82.1.2 59845 1wgvA 124 2.16e+01 2gzqA 200 2.16e+01 1squA 155 2.16e+01 d.252.1.1 98971 1tyjA 170 2.17e+01 1hh2P 344 2.17e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 65835,65836,65837,65838 1auk 489 2.17e+01 1auk c.76.1.2 35030 1za7A 165 2.18e+01 1nrgA 261 2.20e+01 b.45.1.1 80694 1pm1X 180 2.23e+01 b.60.1.1 104189 1pg6A 243 2.24e+01 b.82.5.2 94673 1g2oA 268 2.24e+01 1b8oA c.56.2.1 60228 2f4mA 295 2.25e+01 1nhp 447 2.26e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 1rthA 560 2.27e+01 1rthA c.55.3.1,e.8.1.2 33576,43028 2c1lA 358 2.28e+01 1wthD 391 2.29e+01 1od3A 168 2.30e+01 b.18.1.10 86825 1efvB 255 2.30e+01 1efvB c.26.2.3 31634 1ww7A 160 2.33e+01 1rlmA 271 2.33e+01 1twfK 120 2.34e+01 1e8cA 498 2.35e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1rf6A 427 2.37e+01 d.68.2.2 97366 1tljA 213 2.38e+01 d.282.1.1 107126 1vzyA 291 2.41e+01 1whi 122 2.48e+01 1whi b.39.1.1 24810 1f5mA 180 2.48e+01 1f5mB d.110.2.1 40895 2gcuA 245 2.48e+01 2brcA 214 2.49e+01 1wz8A 264 2.50e+01 1nszA 347 2.50e+01 b.30.5.4 80724 1w5rA 278 2.50e+01 1zkkA 167 2.51e+01 1erxA 184 2.52e+01 1np1A b.60.1.1 27164 1azsB 212 2.52e+01 1azsA d.58.29.1 39423 2c78A 405 2.52e+01 2bv4A 113 2.53e+01 1jihA 531 2.55e+01 d.240.1.1,e.8.1.7 90374,90375 1tw0A 157 2.55e+01 1g4wR 383 2.56e+01 1g4uS a.24.11.1,c.45.1.2 16644,32692 1wdpA 495 2.56e+01 1nhs 447 2.56e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 1twjA 84 2.59e+01 d.284.1.1 107407 2bh9A 489 2.60e+01 1zmdA 474 2.60e+01 2dkaA 544 2.61e+01 1exg 110 2.62e+01 1exg b.2.2.1 22387 1xhcA 367 2.64e+01 1nbwA 607 2.65e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1hnuA 280 2.66e+01 1hnoA c.14.1.3 61096 1jhjA 171 2.68e+01 b.18.1.9 66714 1gwmA 153 2.68e+01 b.18.1.19 83348 1zosA 230 2.68e+01 1vq0A 302 2.68e+01 3ladA 476 2.70e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30573,30574,40208 1rlmB 271 2.70e+01 1senA 164 2.72e+01 c.47.1.1 105465 1wteA 272 2.72e+01 1in0A 163 2.73e+01 d.58.49.1,d.58.49.1 83694,83695 1r8eA 278 2.75e+01 a.6.1.3,d.60.1.1 104843,104844 1gk8A 475 2.75e+01 c.1.14.1,d.58.9.1 65234,65235 1guiA 155 2.75e+01 b.18.1.14 76351 1l5jA 865 2.76e+01 a.118.15.1,c.8.2.1,c.83.1.1 73592,73593,73594 1koiA 184 2.77e+01 b.60.1.1 68725 2fw2A 260 2.79e+01 1wqaA 455 2.81e+01 1s1fA 406 2.82e+01 1quqB 121 2.84e+01 1quqB b.40.4.3 25305 2gtrA 261 2.85e+01 1xhvA 257 2.86e+01 c.52.1.19 109597 1jenA 267 2.87e+01 1jenA 1un7A 400 2.88e+01 b.92.1.5,c.1.9.10 99657,99658 1gx3A 284 2.89e+01 d.3.1.5 70678 1jj2Q 154 2.90e+01 1ffkO d.55.1.1 63102 1h4rA 314 2.92e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1dpe 507 2.93e+01 1dpe c.94.1.1 35799 1aohA 147 2.94e+01 1aohA b.2.2.2 22401 1eaf 243 2.94e+01 1eaf c.43.1.1 32617 1qqrA 138 2.95e+01 1bmlC d.15.5.1 37721 1zhxA 438 2.96e+01 1wosA 364 2.97e+01 b.44.2.1,d.250.1.1 109468,109469 1n67A 359 2.98e+01 b.2.3.4,b.2.3.4 85354,85355 1l1qA 186 2.99e+01 c.61.1.1 77653 1t3iA 420 3.01e+01 c.67.1.3 106354 1x1oA 286 3.01e+01 1vkyA 347 3.01e+01 e.53.1.1 108696 1zuxA 224 3.03e+01 1o12A 376 3.03e+01 b.92.1.5,c.1.9.10 80758,80759 1f3lA 321 3.03e+01 1g6q2 c.66.1.6 59630 2blnA 305 3.03e+01 1t71A 281 3.04e+01 1t17A 148 3.06e+01 1uyjA 296 3.07e+01 f.8.1.2 108143 1mw7A 240 3.10e+01 e.39.1.1 79557 1q8rA 120 3.11e+01 d.79.6.1 96225 1c2pA 576 3.15e+01 1quvA e.8.1.4 43117 1f60A 458 3.19e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1cb8A 678 3.20e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1uspA 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