# List of top-scoring protein chains for t06-100-30-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 1xb4A 202 1.09e-01 1y0nA 78 1.13e+00 1e7wA 291 2.27e+00 c.2.1.2 59373 1pv5A 264 2.35e+00 d.251.1.1 95150 1ne7A 289 2.45e+00 c.124.1.1 91833 1oe4A 247 2.51e+00 c.18.1.3 86895 2bivA 243 3.31e+00 2cvxA 888 3.51e+00 1zs9A 261 3.55e+00 1o20A 427 3.88e+00 c.82.1.1 86556 1yyqA 374 3.91e+00 1exqA 154 4.05e+00 1b9dA c.55.3.2 33646 2fwhA 134 4.11e+00 1uc7A 125 4.15e+00 c.47.1.1 99163 1zvtA 256 4.30e+00 1w85A 368 4.62e+00 1xvxA 312 4.63e+00 1zz1A 369 4.65e+00 1jsf 130 4.75e+00 3lzt d.2.1.2 36410 1st9A 143 4.90e+00 c.47.1.10 98987 2fdbM 164 5.61e+00 1wkaA 147 5.85e+00 1z15A 344 5.89e+00 1oz2A 331 6.22e+00 b.34.9.3,b.34.9.3,b.34.9.3 93781,93782,93783 1iwmA 186 6.26e+00 b.125.1.2 83758 2f9sA 151 6.95e+00 1npiA 61 7.21e+00 g.3.7.1 80685 1eceA 358 7.57e+00 1eceA c.1.8.3 28813 1yewC 289 7.69e+00 1gqvA 135 7.73e+00 d.5.1.1 70376 1ignA 246 9.29e+00 1ignA a.4.1.6,a.4.1.6 16048,16049 1a6m 151 9.44e+00 1a6m a.1.1.2 15018 2ew8A 249 1.07e+01 2b49A 287 1.08e+01 2bbrA 195 1.12e+01 1zv9A 172 1.12e+01 1ro2A 216 1.17e+01 d.264.1.2 97665 1ro0A 216 1.19e+01 d.264.1.2 97664 1nnhA 294 1.20e+01 d.104.1.1 92005 1wp5A 323 1.22e+01 1z0kB 69 1.22e+01 1za0A 275 1.26e+01 1obdA 306 1.28e+01 d.143.1.1 86767 1h5uA 842 1.29e+01 1a8i c.87.1.4 60655 1b4pA 217 1.31e+01 a.45.1.1,c.47.1.5 83158,83159 2cnqA 306 1.36e+01 1whzA 70 1.39e+01 1qznA 173 1.40e+01 b.2.2.2 104669 2bn5A 33 1.40e+01 1iybA 208 1.40e+01 d.124.1.1 90720 1wtaA 275 1.42e+01 1fmcA 255 1.45e+01 1cydA c.2.1.2 29856 2ftwA 521 1.47e+01 1ff9A 450 1.62e+01 1ff9A c.2.1.3,d.81.1.2 30039,39954 1ltqA 301 1.66e+01 c.108.1.9,c.37.1.1 78208,78209 1h0pA 182 1.68e+01 b.62.1.1 76450 2a65A 519 1.76e+01 1ly1A 181 1.81e+01 c.37.1.1 74334 1uvjA 664 1.85e+01 e.8.1.6 100045 2al3A 90 1.88e+01 1bea 127 1.89e+01 1bea a.52.1.2 17826 1uw4A 91 1.92e+01 d.58.7.4 100071 1gjnA 153 1.95e+01 a.1.1.2 70191 1x6oA 174 1.96e+01 b.34.5.2,b.40.4.5 109493,109494 2gs5A 198 2.00e+01 2f3yA 148 2.06e+01 2erfA 209 2.08e+01 2frfA 153 2.09e+01 2f6eA 127 2.11e+01 1augA 215 2.13e+01 1a2zA c.56.4.1 33798 1lmzA 187 2.19e+01 a.96.1.4 74037 1dmgA 225 2.25e+01 1dmgA c.22.1.1 31036 1xzoA 174 2.25e+01 1bjt 793 2.27e+01 1bjt e.11.1.1 43249 2ch0A 133 2.31e+01 1wn5A 130 2.32e+01 1l4dB 122 2.36e+01 d.15.5.1 77684 1vyrA 364 2.40e+01 c.1.4.1 108906 1tueA 212 2.41e+01 c.37.1.20 107323 2d1yA 256 2.45e+01 1ucnA 152 2.48e+01 d.58.6.1 99183 1v3vA 333 2.54e+01 b.35.1.2,c.2.1.1 108345,108346 1xu9A 286 2.56e+01 1zelA 298 2.56e+01 1ihkA 174 2.61e+01 1bfg b.42.1.1 62384 1np7A 489 2.61e+01 a.99.1.1,c.28.1.1 80677,80678 1gqzA 274 2.67e+01 d.21.1.1,d.21.1.1 83311,83312 1zrn 232 2.68e+01 1qq5A c.108.1.1 43323 1jdlA 121 2.69e+01 a.3.1.1 66557 1htrP 43 2.73e+01 1htrP b.50.1.2 26852 1bif 469 2.73e+01 1bif c.37.1.7,c.60.1.4 31961,34003 1jpzA 473 2.76e+01 a.104.1.1 67069 1unlD 208 2.81e+01 1tc5A 194 2.82e+01 c.110.1.1 106752 1bzkA 43 2.83e+01 1bzkA j.35.1.1 46250 1s2oA 244 2.95e+01 1ja9A 274 2.98e+01 c.2.1.2 62817 1cydA 244 3.05e+01 1cydA c.2.1.2 29825 1eaiC 61 3.08e+01 1eaiC g.22.1.1 44894 2bl0B 145 3.10e+01 1fr2B 134 3.10e+01 d.4.1.1 83257 1q1uA 144 3.17e+01 b.42.1.1 95608 1pylA 97 3.19e+01 d.1.1.2 104391 1vqoA 240 3.19e+01 1mlwA 301 3.22e+01 d.178.1.1 79289 1orsC 132 3.25e+01 f.14.1.1 87353 1anf 370 3.30e+01 4mbp c.94.1.1 35776 1exrA 148 3.30e+01 1cll a.39.1.5 17299 2g5dA 422 3.31e+01 2c4jA 218 3.35e+01 1lktA 104 3.40e+01 1lktA b.90.1.1 28398 2f9zC 159 3.41e+01 1v58A 241 3.43e+01 c.47.1.9,d.17.3.1 108371,108372 2gsfA 373 3.43e+01 1tfzA 424 3.47e+01 d.32.1.3,d.32.1.3 106886,106887 1gegA 256 3.50e+01 1ybvA c.2.1.2 29888 1ug7A 128 3.55e+01 a.24.24.1 107824 3htsB 102 3.62e+01 2hts a.4.5.22 16175 2aa1B 146 3.62e+01 1h1yA 228 3.67e+01 c.1.2.2 76506 1yj7A 171 3.71e+01 1m65A 245 3.71e+01 c.6.3.1 84847 1k6iA 352 3.73e+01 c.2.1.2 68223 2dfkA 402 3.77e+01 2cmwA 310 3.78e+01 2gviA 204 3.80e+01 1yw5A 177 3.85e+01 1iqzA 81 3.85e+01 d.58.1.4 66281 2fhfA 1083 3.87e+01 1xgkA 352 3.87e+01 1j99A 293 3.90e+01 c.37.1.5 71618 1r0pA 312 3.93e+01 d.144.1.7 96734 1dptA 117 3.94e+01 1dptA d.80.1.3 39862 2gkeA 274 3.95e+01 1b0nA 111 3.96e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 1hywA 68 4.00e+01 1hywA d.186.1.1 61425 2g0uA 92 4.03e+01 1kb0A 677 4.06e+01 a.3.1.6,b.70.1.1 68378,68379 1x0rA 249 4.06e+01 1apyA 162 4.07e+01 1apyA d.153.1.5 42004 1jmxA 494 4.07e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66901,66902,66903,66904,66905 1wi9A 72 4.16e+01 1y81A 138 4.19e+01 1qi9A 556 4.25e+01 1qhbA a.111.1.2 19053 1sv0C 82 4.29e+01 a.60.1.1 106037 1qh8A 478 4.32e+01 1qguA c.92.2.3 35633 1xkpB 124 4.33e+01 1seiA 130 4.33e+01 1seiA d.140.1.1 41463 1ustA 93 4.36e+01 a.4.5.13 99884 1pn0A 665 4.37e+01 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 2b0tA 738 4.37e+01 1dk8A 147 4.38e+01 1agrE a.91.1.1 18548 1vr5A 547 4.39e+01 1u5tA 233 4.40e+01 a.4.5.54,a.4.5.54 107684,107685 1sk7A 198 4.43e+01 a.132.1.2 105671 1ijtA 128 4.44e+01 1bfg b.42.1.1 62510 1fjhA 257 4.51e+01 1fjhB c.2.1.2 29870 1x54A 434 4.52e+01 1u3eM 174 4.53e+01 d.4.1.3,d.285.1.1 107640,107641 1r3jC 124 4.55e+01 f.14.1.1 96932 1vf8A 377 4.58e+01 1px5A 349 4.65e+01 a.160.1.2,d.218.1.6 95277,95278 1pii 452 4.75e+01 1pii c.1.2.4,c.1.2.4 28559,28563 1dzkA 157 4.78e+01 1obpA b.60.1.1 27096 1sauA 115 4.81e+01 2f62A 161 4.81e+01 2c1iA 431 4.84e+01 1urjA 1136 4.85e+01 1w9iA 770 4.87e+01 2es7A 142 4.93e+01 1fd3A 41 4.94e+01 1fd3A g.9.1.1 44572 2a2pA 129 4.95e+01 1gt1A 159 4.98e+01 b.60.1.1 90515 1fc4A 401 4.99e+01 1bs0A c.67.1.4 59760 1xyiA 66 5.06e+01 1ui5A 215 5.06e+01 a.4.1.9,a.121.1.1 107856,107857 2h1tA 188 5.12e+01 1nw1A 429 5.15e+01 d.144.1.8 86286 1nzjA 298 5.15e+01 c.26.1.1 92377 2a6sA 84 5.18e+01 1z2lA 423 5.21e+01 2bcqA 335 5.22e+01 1nuuA 252 5.32e+01 c.26.1.3 86209 1x7yA 400 5.33e+01 2fj6A 82 5.34e+01 1wkqA 164 5.34e+01 c.97.1.2 109393 2afbA 351 5.35e+01 1wvfA 520 5.35e+01 1vj1A 363 5.40e+01 b.35.1.2,c.2.1.1 100794,100795 1t4wA 196 5.45e+01 b.2.5.2 106427 1psrA 100 5.45e+01 1psrA a.39.1.2 17180 2g09A 297 5.46e+01 1vcc 77 5.48e+01 1vcc d.121.1.1 41092 1zklA 353 5.49e+01 1tn6A 382 5.54e+01 6rxn 46 5.54e+01 1rb9 g.41.5.1 45222 1yfbA 59 5.57e+01 1ob8A 135 5.60e+01 1e8gA 560 5.61e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1chuA 540 5.64e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1gpr 162 5.66e+01 1gpr b.84.3.1 28267 1mgrA 99 5.66e+01 d.1.1.2 79106 1iujA 106 5.68e+01 d.58.4.5 90701 1kxvC 121 5.70e+01 b.1.1.1 73190 1wy9A 147 5.72e+01 2ex0A 399 5.73e+01 1wzoA 246 5.75e+01 1ju2A 536 5.75e+01 c.3.1.2,d.16.1.1 77169,77170 1vflA 356 5.77e+01 2czrA 226 5.79e+01 1xc0A 33 5.84e+01 j.6.1.1 109542 1lngA 87 5.87e+01 d.201.1.1 74045 2b95A 106 5.87e+01 1nvvS 481 5.91e+01 a.117.1.1 86279 1ywfA 296 5.92e+01 1m70A 190 5.95e+01 a.3.1.4,a.3.1.4 91200,91201 2bs3A 656 5.97e+01 1ry6A 360 5.98e+01 c.37.1.9 98090 1x9mA 698 6.05e+01 1tdhA 364 6.06e+01 a.156.1.2,b.113.1.1,g.39.1.8 106772,106773,106774 1y4tA 322 6.06e+01 3thiA 371 6.08e+01 2thiA c.94.1.1 35792 1ucdA 190 6.08e+01 d.124.1.1 107767 2cvbA 188 6.11e+01 2a8yA 270 6.19e+01 1wrjA 156 6.25e+01 2bfdA 400 6.31e+01 2an3A 289 6.32e+01 1ituA 369 6.32e+01 c.1.9.7 71423 2f6rA 281 6.39e+01 1i60A 278 6.41e+01 c.1.15.4 71118 1lwdA 413 6.51e+01 c.77.1.1 78265 1snrA 341 6.52e+01 b.6.1.3,b.6.1.3 105823,105824 1ylkA 172 6.55e+01 2h1rA 299 6.61e+01 1ub1A 133 6.61e+01 d.10.1.3 99140 2b7kA 200 6.68e+01 1x3aA 100 6.69e+01 1p0zA 131 6.71e+01 d.110.6.1 93882 2bm3A 166 6.71e+01 1m0wA 491 6.77e+01 c.30.1.4,d.142.1.6 78363,78364 1to6A 371 6.78e+01 c.141.1.1 107170 1gnlA 544 6.79e+01 e.26.1.1 70287 1hfeL 421 6.82e+01 1fehA c.96.1.1,d.58.1.5 36018,39001 1xjjA 644 6.93e+01 1un7A 400 6.94e+01 b.92.1.5,c.1.9.10 99657,99658 1k8qA 377 6.95e+01 c.69.1.6 72177 1geeA 261 6.96e+01 c.2.1.2 90509 1ib2A 349 6.99e+01 1ib2A a.118.1.8 62141 2bzvA 181 7.01e+01 1x88A 359 7.02e+01 1w6uA 302 7.02e+01 1p9kA 79 7.06e+01 d.66.1.6 94392 1u60A 310 7.07e+01 e.3.1.2 107692 1rypL 212 7.11e+01 d.153.1.4 41880 1v25A 541 7.15e+01 e.23.1.1 108275 1l5aA 436 7.20e+01 c.43.1.2,c.43.1.2 75923,75924 2d2eA 250 7.21e+01 1gmeA 151 7.21e+01 b.15.1.1 65305 1avsA 90 7.25e+01 1cll a.39.1.5 17226 1dxsA 80 7.26e+01 1cokA a.60.1.2 17944 1i7nA 309 7.26e+01 c.30.1.5,d.142.1.3 83681,83682 1gkmA 509 7.27e+01 a.127.1.2 70228 1flmA 122 7.27e+01 1axj b.45.1.1 25747 1vemA 516 7.33e+01 2ahqA 76 7.36e+01 2gh1A 301 7.40e+01 1yuzA 202 7.45e+01 1mw9X 592 7.52e+01 e.10.1.1 91480 1krs 120 7.55e+01 1krs b.40.4.1 25256 1mngA 203 7.57e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 2f96A 224 7.61e+01 1e5mA 416 7.62e+01 1dd8A c.95.1.1,c.95.1.1 58973,58974 1a99A 344 7.62e+01 1pot c.94.1.1 35812 1s9uA 207 7.66e+01 a.184.1.1 105390 1fjgK 129 7.66e+01 1fjfK c.55.4.1 33733 2gz4A 207 7.68e+01 2fafA 608 7.69e+01 1a2zA 220 7.71e+01 1a2zA c.56.4.1 33794 1yrcA 414 7.71e+01 1lniA 96 7.71e+01 d.1.1.2 74046 1qrvA 73 7.75e+01 1cktA a.21.1.1 16425 1f02T 66 7.75e+01 1f02T j.67.1.1 46360 2bjfA 329 7.80e+01 1zpdA 568 7.84e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31741,31785,31786 2eutA 294 7.89e+01 1d7oA 297 7.89e+01 1enp c.2.1.2 29907 1n40A 396 7.90e+01 a.104.1.1 79977 2f06A 144 8.02e+01 1vpmA 169 8.03e+01 1wzzA 334 8.05e+01 1us0A 316 8.13e+01 c.1.7.1 99850 1g4wR 383 8.17e+01 1g4uS a.24.11.1,c.45.1.2 16644,32692 2a4dA 160 8.19e+01 1oshA 232 8.21e+01 a.123.1.1 93496 1vyiA 112 8.29e+01 1s1pA 331 8.32e+01 c.1.7.1 98350 1brfA 53 8.35e+01 1rb9 g.41.5.1 45236 1o2dA 371 8.37e+01 e.22.1.2 86591 1regX 122 8.37e+01 1regX d.58.27.1 39406 1z64A 26 8.40e+01 1i0dA 332 8.41e+01 1pscA c.1.9.3 61487 1wzcA 249 8.44e+01 1rypJ 204 8.52e+01 d.153.1.4 41878 2pspA 106 8.56e+01 2pspA g.16.1.1,g.16.1.1 44730,44731 1qstA 160 8.58e+01 1yghA d.108.1.1 40804 1qipA 183 8.58e+01 1qipA d.32.1.1 38470 2abqA 306 8.61e+01 1dp4A 435 8.68e+01 1dp4A c.93.1.1 35710 1ksoA 101 8.71e+01 a.39.1.2 72926 1zxfA 155 8.74e+01 1yqgA 263 8.77e+01 1gwiA 411 8.79e+01 a.104.1.1 76364 1iqvA 218 8.82e+01 1rss a.75.1.1 62661 2aukA 190 8.84e+01 2btdA 210 8.85e+01 1xrtA 467 8.87e+01 1yk4A 52 8.88e+01 1ash 150 8.91e+01 1ash a.1.1.2 15622 2f6hX 419 8.92e+01 2ae0X 345 8.93e+01 2ae2A 260 8.98e+01 1bdb c.2.1.2 29945