# List of top-scoring protein chains for t06-100-30-bys-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 1s5uA 138 6.50e-16 d.38.1.1 98573 2cyeA 133 1.11e-15 1z54A 132 6.10e-15 2aliA 158 3.13e-13 1vpmA 169 5.95e-13 2gf6A 135 1.36e-12 1lo7A 141 1.42e-12 d.38.1.1 74144 1yliA 153 2.66e-12 2essA 248 6.38e-11 2gvhA 288 4.51e-10 2h4uA 145 1.19e-08 1wluA 136 8.32e-08 2fs2A 151 9.28e-08 1j1yA 136 1.24e-07 d.38.1.5 90776 1zkiA 133 4.98e-07 1ixlA 131 1.23e-06 d.38.1.5 90717 1o0iA 138 6.72e-06 d.38.1.5 86532 2cwzA 141 7.24e-06 2b3nA 159 1.14e-05 1q4uA 151 3.27e-05 d.38.1.5 95828 1iq6A 134 3.34e-05 d.38.1.4 76755 1c8uA 285 2.08e-04 1c8uA d.38.1.3,d.38.1.3 38547,38548 1vh5A 148 3.27e-04 d.38.1.5 100642 1t82A 155 3.47e-04 d.38.1.5 106639 1sh8A 154 6.31e-04 d.38.1.5 105549 1z6bA 154 1.28e-03 1tbuA 118 1.49e-02 1yocA 147 3.71e-02 2bi0A 337 5.36e-02 1pn2A 280 4.38e-01 d.38.1.4,d.38.1.4 94930,94931 1l0wA 580 7.73e-01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1mdc 133 9.68e-01 1hmt b.60.1.2 27198 1jeoA 180 1.80e+00 c.80.1.3 66611 1fm0D 81 1.82e+00 1fmaD d.15.3.1 37642 1j09A 468 1.99e+00 a.97.1.1,c.26.1.1 77025,77026 2bm3A 166 1.99e+00 2b7uA 257 2.14e+00 1jyaA 130 2.23e+00 d.198.1.1 67453 1m3sA 186 2.36e+00 c.80.1.3 78573 1j5uA 136 2.39e+00 d.208.1.1 71584 1dnlA 199 2.42e+00 1ci0A b.45.1.1 25753 1vcaA 202 2.45e+00 1vcaA b.1.1.3,b.1.1.4 21649,21685 1e8yA 966 2.98e+00 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1g87A 614 3.14e+00 a.102.1.2,b.2.2.2 83275,83276 2bdvA 231 3.17e+00 1k4nA 192 3.25e+00 d.32.1.5 72059 1b8aA 438 3.39e+00 1b8aA b.40.4.1,d.104.1.1 25244,40765 1hn0A 1021 3.85e+00 a.102.3.2,b.18.1.17,b.24.1.1,b.30.5.2 83616,83617,83618,83619 1vzyA 291 3.95e+00 1e25A 282 3.97e+00 1e25A e.3.1.1 42731 2cu3A 64 4.08e+00 1tyjA 170 4.38e+00 1yqgA 263 4.44e+00 1v93A 296 4.65e+00 c.1.23.1 100532 1nxuA 333 4.88e+00 c.122.1.1 86389 1kt6A 183 4.98e+00 b.60.1.1 84466 1vjzA 341 5.11e+00 c.1.8.3 100838 2c8mA 262 5.17e+00 1r4xA 275 5.26e+00 b.1.10.3,d.105.1.2 97054,97055 1jbeA 128 5.33e+00 3chy c.23.1.1 62845 2as0A 396 5.45e+00 1qfoA 119 6.35e+00 1qfoA b.1.1.1 19708 1j1bA 420 6.40e+00 d.144.1.7 90758 1nzjA 298 6.83e+00 c.26.1.1 92377 2a90A 240 6.90e+00 1g79A 218 6.94e+00 1ci0A b.45.1.1 25752 1zanL 214 7.13e+00 1k78A 149 7.28e+00 a.4.1.5,a.4.1.5 68255,68256 1n67A 359 7.52e+00 b.2.3.4,b.2.3.4 85354,85355 1bwwA 109 7.53e+00 8fabA b.1.1.1 20518 1qxyA 252 7.88e+00 d.127.1.1 96565 1a2yA 107 7.95e+00 8fabA b.1.1.1 19926 1ox0A 430 8.37e+00 c.95.1.1,c.95.1.1 87495,87496 1xc3A 302 8.42e+00 1qusA 322 8.65e+00 1ltm d.2.1.6 36991 1mjuL 219 8.70e+00 b.1.1.1,b.1.1.2 91304,91305 1w66A 232 8.87e+00 1vyfA 135 8.96e+00 b.60.1.2 108902 1mqkL 120 9.04e+00 b.1.1.1 85054 1txqA 93 9.13e+00 1lshA 1056 9.34e+00 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 1ifc 132 9.51e+00 b.60.1.2 27173 2afbA 351 1.02e+01 1te5A 257 1.04e+01 d.153.1.1 106795 2as9A 210 1.07e+01 1akz 223 1.08e+01 3eugA c.18.1.1 31007 1f3mA 80 1.09e+01 1f3mA j.66.1.1 46358 1yqvL 211 1.14e+01 1ikoP 178 1.19e+01 b.6.1.5 71243 1g7nA 131 1.20e+01 b.60.1.2 83274 1t4wA 196 1.23e+01 b.2.5.2 106427 1on2A 142 1.24e+01 a.4.5.24,a.76.1.1 87103,87104 1z7lA 276 1.25e+01 1dqeA 137 1.25e+01 1dqeA a.39.2.1 17388 2a74A 643 1.26e+01 1wkbA 810 1.32e+01 1lrzA 426 1.33e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1x67A 146 1.37e+01 2f96A 224 1.42e+01 2booA 247 1.42e+01 2eifA 136 1.44e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1y8qA 346 1.51e+01 1hkfA 122 1.51e+01 b.1.1.1 83553 2fi9A 128 1.51e+01 3fib 249 1.52e+01 3fib d.171.1.1 42455 1hw7A 255 1.55e+01 1i7fA d.193.1.1 61297 1ylxA 103 1.56e+01 1o4yA 288 1.57e+01 b.29.1.2 92473 2ftbA 125 1.57e+01 2gfgA 193 1.60e+01 1um5L 219 1.61e+01 2bhoA 130 1.62e+01 1oruA 195 1.63e+01 b.58.1.2 93464 1r0mA 375 1.66e+01 c.1.11.2,d.54.1.1 104747,104748 2aalA 131 1.67e+01 1se8A 301 1.68e+01 b.40.4.3 105448 1o6aA 96 1.69e+01 b.139.1.1 92562 2auhB 59 1.69e+01 1lkdA 297 1.70e+01 d.32.1.3,d.32.1.3 78059,78060 1v4sA 455 1.72e+01 c.55.1.3,c.55.1.3 100309,100310 1zwyA 185 1.75e+01 1lk2A 274 1.75e+01 b.1.1.2,d.19.1.1 91056,91057 1um5H 217 1.78e+01 1q7lA 198 1.78e+01 c.56.5.4 96044 1oe4A 247 1.95e+01 c.18.1.3 86895 1nlbH 218 1.95e+01 b.1.1.1,b.1.1.2 80621,80622 1b56 135 1.96e+01 1hmt b.60.1.2 27183 1ngzA 213 2.02e+01 b.1.1.1,b.1.1.2 80500,80501 1yoaA 159 2.07e+01 1yemA 179 2.10e+01 1r9hA 135 2.12e+01 d.26.1.1 97260 2btiA 63 2.13e+01 1wmaA 276 2.14e+01 1te2A 226 2.15e+01 c.108.1.6 106792 1y8aA 332 2.15e+01 1xfrA 128 2.16e+01 1y0yA 353 2.17e+01 1bu8A 452 2.22e+01 1gpl b.12.1.2,c.69.1.19 23647,34795 1vr5A 547 2.24e+01 1b3aA 67 2.24e+01 1b3aA d.9.1.1 37410 1hkhA 279 2.24e+01 c.69.1.12 90628 1nkqA 259 2.24e+01 d.177.1.1 103862 2fimA 276 2.24e+01 1yq2A 1024 2.25e+01 1e19A 314 2.26e+01 1b7bA c.73.1.1 34967 1ttwA 138 2.30e+01 d.198.1.1 107308 1mkmA 249 2.34e+01 a.4.5.33,d.110.2.2 79242,79243 2gqrA 237 2.36e+01 2bc4A 211 2.38e+01 1kzfA 230 2.38e+01 d.108.1.3 73354 1npsA 88 2.38e+01 1prs b.11.1.1 23622 1w9hA 427 2.40e+01 1b65A 375 2.40e+01 1b65A d.154.1.1 42020 1ww7A 160 2.42e+01 1lyvA 306 2.42e+01 c.45.1.2 74348 1bf6A 291 2.43e+01 1pscA c.1.9.3 29065 1k6iA 352 2.45e+01 c.2.1.2 68223 1pmnA 364 2.47e+01 d.144.1.7 94907 2ajuL 216 2.48e+01 1rurL 217 2.49e+01 b.1.1.1,b.1.1.2 97881,97882 1ny4A 82 2.50e+01 b.40.4.5 92316 1wk2A 121 2.52e+01 3eipA 84 2.58e+01 3eipA d.26.2.1 38434 1xfcA 384 2.60e+01 2bh1A 250 2.60e+01 1oaqH 121 2.62e+01 b.1.1.1 92707 1n4xH 120 2.65e+01 b.1.1.1 85324 1eu3A 210 2.69e+01 1an8 b.40.2.2,d.15.6.1 25206,37795 830cA 168 2.70e+01 1ck7A d.92.1.11 40400 1n0wA 243 2.70e+01 c.37.1.11 79772 1mla 309 2.71e+01 1mla c.19.1.1,d.58.23.1 31031,39383 1i1jA 108 2.74e+01 1i1jA b.34.2.1 61531 1z4vA 532 2.76e+01 2fpnA 216 2.79e+01 1owfB 94 2.82e+01 a.55.1.1 87488 1nezG 128 2.84e+01 b.1.1.1 85592 1oxxK 353 2.87e+01 b.40.6.3,c.37.1.12 93715,93716 1cbs 137 2.93e+01 1hmt b.60.1.2 27201 1xpjA 126 2.94e+01 2gtqA 867 2.94e+01 1s4kA 120 2.95e+01 a.35.1.6 105254 1sc3B 88 2.97e+01 1f5mA 180 2.98e+01 1f5mB d.110.2.1 40895 1tqyA 424 3.00e+01 c.95.1.1,c.95.1.1 107245,107246 1z2lA 423 3.00e+01 1kcvL 214 3.01e+01 b.1.1.1,b.1.1.2 72317,72318 4bcl 366 3.03e+01 4bcl b.75.1.1 27968 1tc3C 51 3.04e+01 1tc3C a.4.1.2 16025 1xpkC 388 3.06e+01 1tuoA 464 3.07e+01 1u69A 163 3.10e+01 d.32.1.7 107699 1iam 185 3.11e+01 1zxq b.1.1.3,b.1.1.4 21653,21689 1i12A 160 3.15e+01 1i21A d.108.1.1 61515 1rm6A 769 3.16e+01 1r77A 103 3.25e+01 1rhcA 330 3.26e+01 c.1.16.3 97468 1hf2A 210 3.33e+01 1hf2A b.80.3.1,c.102.1.1 60992,60993 1q79A 514 3.36e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1ka8A 100 3.39e+01 a.4.5.20 72241 1ulrA 88 3.40e+01 1pufB 73 3.41e+01 a.4.1.1 95132 1erjA 393 3.43e+01 1erjA b.69.4.1 27660 1pcfA 66 3.44e+01 1pcfA d.18.1.1 38142 1u14A 172 3.45e+01 c.51.4.3 107579 1js1X 324 3.46e+01 c.78.1.1,c.78.1.1 71834,71835 1nm2A 317 3.48e+01 c.19.1.1,d.58.23.1 80654,80655 1q77A 138 3.48e+01 c.26.2.4 96023 1wdeA 294 3.50e+01 1ztsA 139 3.50e+01 1u2hA 99 3.53e+01 1mkaA 171 3.54e+01 1mkaA d.38.1.2 38543 1xpmA 396 3.55e+01 1wznA 252 3.55e+01 1su8A 636 3.55e+01 e.26.1.2 98999 1q3iA 214 3.57e+01 d.220.1.1 104524 2pgd 482 3.65e+01 2pgd a.100.1.1,c.2.1.6 18778,30190 1euwA 152 3.66e+01 1dupA b.85.4.1 28349 1jkoC 52 3.67e+01 a.4.1.2 66809 1exrA 148 3.72e+01 1cll a.39.1.5 17299 1q8rA 120 3.78e+01 d.79.6.1 96225 1mexL 213 3.79e+01 b.1.1.1,b.1.1.2 91259,91260 1vk3A 615 3.82e+01 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 1knwA 425 3.83e+01 b.49.2.3,c.1.6.1 90969,90970 1tuaA 191 3.84e+01 d.51.1.1,d.51.1.1 107321,107322 1k2xB 143 3.86e+01 2aboA 136 3.86e+01 1wdyA 285 3.88e+01 2dcnA 311 3.90e+01 1y96A 86 3.97e+01 1j6oA 268 3.98e+01 c.1.9.12 77088 1k77A 260 4.01e+01 c.1.15.5 72096 1kpf 126 4.02e+01 1kpf d.13.1.1 37507 1oo0A 147 4.02e+01 d.232.1.1 87182 1oj4A 283 4.05e+01 d.14.1.5,d.58.26.5 93083,93084 2gfaA 119 4.05e+01 1wj9A 211 4.06e+01 1zv9A 172 4.07e+01 2a8jA 420 4.08e+01 1wg8A 285 4.08e+01 1i0dA 332 4.08e+01 1pscA c.1.9.3 61487 1rlmA 271 4.09e+01 1vl4A 447 4.10e+01 d.283.1.1 108718 1otvA 259 4.11e+01 a.132.1.4 93526 1uujA 88 4.11e+01 a.221.1.1 108046 1qhxA 178 4.13e+01 1qhsA c.37.1.3 31936 1ejbA 168 4.24e+01 1rvv1 c.16.1.1 59417 1v6tA 255 4.30e+01 1uacL 107 4.31e+01 b.1.1.1 99133 1psrA 100 4.32e+01 1psrA a.39.1.2 17180 1w68A 390 4.33e+01 a.25.1.2 109216 1n0wB 35 4.33e+01 j.97.1.1 79773 1xrtA 467 4.36e+01 1wmwA 330 4.41e+01 1aohA 147 4.42e+01 1aohA b.2.2.2 22401 1ggzA 148 4.43e+01 a.39.1.5 70176 1qznA 173 4.46e+01 b.2.2.2 104669 1pm1X 180 4.50e+01 b.60.1.1 104189 1ecsA 126 4.52e+01 1ecsA d.32.1.2 59407 1yp5A 58 4.55e+01 1cb0A 283 4.59e+01 1cb0A c.56.2.1 33790 1lf7A 182 4.60e+01 b.60.1.1 73878 1qrvA 73 4.64e+01 1cktA a.21.1.1 16425 1pzsA 208 4.70e+01 b.1.8.1 104397 1b5pA 385 4.70e+01 c.67.1.1 90403 1tc5A 194 4.70e+01 c.110.1.1 106752 1f8vA 355 4.78e+01 2bbvA b.121.4.4 23329 2erbA 125 4.79e+01 1umhA 184 4.79e+01 b.18.1.21 99605 1vq2A 193 4.81e+01 1m1hA 248 4.86e+01 b.114.1.1,d.58.42.1 78415,78416 2ccvA 101 4.89e+01 1yc7A 124 4.91e+01 1ug3A 339 4.92e+01 1wmmA 145 4.94e+01 1bs0A 384 4.96e+01 1bs0A c.67.1.4 34490 1cmcA 104 4.97e+01 1cmbA a.43.1.5 17462 1fqtA 112 4.98e+01 1fqtA b.33.1.1 24441 2b06A 155 5.01e+01 1n0qA 93 5.01e+01 k.37.1.1 79754 2cuaA 135 5.02e+01 2cuaA b.6.1.2 23039 1kxoA 184 5.05e+01 b.60.1.1 84475 1qg7A 67 5.06e+01 1a15A d.9.1.1 37449 1nnxA 109 5.08e+01 b.40.10.1 92013 1wbiA 129 5.10e+01 1gttA 429 5.10e+01 d.177.1.1,d.177.1.1 70529,70530 1xgkA 352 5.15e+01 1iy8A 267 5.19e+01 c.2.1.2 83774 1ga3A 113 5.22e+01 1ga3A a.26.1.2 60411 1xkpB 124 5.24e+01 1vq0A 302 5.24e+01 1y43B 173 5.25e+01 1a62 130 5.26e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1vjqA 79 5.26e+01 k.43.1.1 100830 1puc 105 5.26e+01 1puc d.97.1.1 40675 1mvuA 114 5.27e+01 b.1.1.1 91474 2bmeA 186 5.28e+01 2b0vA 153 5.29e+01 1yqhA 109 5.29e+01 1js8A 394 5.34e+01 a.86.1.1,b.112.1.1 67219,67220 1vqvA 306 5.40e+01 2b1yA 104 5.41e+01 1w7lA 422 5.43e+01 c.67.1.1 109226 2ap1A 327 5.44e+01 1vlbA 907 5.49e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 1vc3B 97 5.53e+01 1j05A 111 5.53e+01 b.1.1.1 90735 1jmtA 104 5.53e+01 d.58.7.3 63180 1rr7A 129 5.54e+01 a.4.1.14 105075 1yu0A 381 5.54e+01 1i8kA 107 5.56e+01 b.1.1.1 71130 1vhyA 257 5.56e+01 b.122.1.2,c.116.1.5 100714,100715 1iynA 295 5.59e+01 a.93.1.1 90722 1ktbA 405 5.61e+01 b.71.1.1,c.1.8.1 72960,72961 1gqeA 365 5.61e+01 e.38.1.1 70351 1rzhM 307 5.61e+01 f.26.1.1 98165 1vhoA 346 5.63e+01 b.49.3.1,c.56.5.4 100694,100695 1gl4B 98 5.65e+01 b.1.1.4 65288 1v54K 56 5.65e+01 f.23.5.1 100332 1f02T 66 5.67e+01 1f02T j.67.1.1 46360 1nnwA 252 5.69e+01 d.159.1.5 80674 1vdnA 162 5.70e+01 1xjvA 294 5.73e+01 1kzlA 208 5.75e+01 b.43.4.3,b.43.4.3 77635,77636 2cs8A 108 5.75e+01 2bsfA 176 5.77e+01 1clc 639 5.83e+01 1clc a.102.1.2,b.1.18.2 18835,21872 1jsdA 319 5.83e+01 b.19.1.2 63258 1ollA 188 5.83e+01 b.1.1.4,b.1.1.4 93313,93314 1j6qA 136 5.91e+01 b.40.9.1 77091 1nd4A 264 5.91e+01 d.144.1.6 91815 1wwjA 105 5.95e+01 1vqoX 92 6.02e+01 1ed8A 449 6.02e+01 1b8jA c.76.1.1 34988 1fmcA 255 6.06e+01 1cydA c.2.1.2 29856 1ytaA 180 6.06e+01 1uj6A 227 6.07e+01 c.124.1.4,d.58.40.1 107898,107899 4sgbI 51 6.07e+01 4sgbI g.69.1.1 44724 2ahrA 259 6.07e+01 1em9A 154 6.14e+01 1d1dA a.73.1.1 18333 1ztuA 341 6.14e+01 1r8gA 372 6.14e+01 d.128.1.3 104845 1odzA 386 6.15e+01 c.1.8.3 86889 1gk9B 557 6.17e+01 1hdkA 141 6.20e+01 b.29.1.3 65807 1h5uA 842 6.23e+01 1a8i c.87.1.4 60655 2a6cA 83 6.24e+01 2au3A 407 6.27e+01 1im3D 95 6.27e+01 1im3D b.1.18.5 62568 1obbA 480 6.28e+01 c.2.1.5,d.162.1.2 86760,86761 1xvsA 126 6.30e+01 1xx6A 191 6.34e+01 1ogaD 215 6.37e+01 b.1.1.1,b.1.1.2 86990,86991 3il8 72 6.39e+01 1tvxA d.9.1.1 37356 1lmzA 187 6.40e+01 a.96.1.4 74037 2fp7A 54 6.41e+01 3pcgM 238 6.41e+01 3pchM b.3.6.1 22742 1ka2A 499 6.44e+01 d.92.1.5 77305 1irqA 71 6.46e+01 a.43.1.4 66297 1atg 231 6.53e+01 1atg c.94.1.1 35834 1sw6A 327 6.54e+01 1sw6A d.211.1.1 19176 1vr4A 103 6.54e+01 2cw9A 194 6.55e+01 1uu1A 335 6.64e+01 c.67.1.1 99993 1kv7A 488 6.65e+01 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 2tpsA 227 6.66e+01 2tpsA c.1.3.1 28591 2c5uA 375 6.67e+01 1pht 85 6.68e+01 1ckaA b.34.2.1 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