# 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 1yfbA 59 9.59e-01 1ne7A 289 2.00e+00 c.124.1.1 91833 1xb4A 202 2.12e+00 1cydA 244 2.24e+00 1cydA c.2.1.2 29825 1sk7A 198 2.32e+00 a.132.1.2 105671 1oe4A 247 2.56e+00 c.18.1.3 86895 1eceA 358 2.90e+00 1eceA c.1.8.3 28813 1yyqA 374 2.94e+00 1zs9A 261 3.00e+00 1exrA 148 3.00e+00 1cll a.39.1.5 17299 1iwmA 186 3.76e+00 b.125.1.2 83758 1z0kB 69 3.85e+00 1pv5A 264 3.95e+00 d.251.1.1 95150 1yw5A 177 4.33e+00 2bivA 243 4.44e+00 1gqvA 135 4.45e+00 d.5.1.1 70376 1h6fA 193 4.81e+00 b.2.5.4 70901 1exqA 154 5.56e+00 1b9dA c.55.3.2 33646 1qipA 183 5.57e+00 1qipA d.32.1.1 38470 1utcA 363 6.12e+00 a.118.1.4,b.69.6.1 99914,99915 1zz1A 369 6.16e+00 1za0A 275 6.32e+00 1i0dA 332 6.39e+00 1pscA c.1.9.3 61487 1nnhA 294 6.55e+00 d.104.1.1 92005 1oz2A 331 6.84e+00 b.34.9.3,b.34.9.3,b.34.9.3 93781,93782,93783 1jdlA 121 7.10e+00 a.3.1.1 66557 2ew8A 249 7.35e+00 1jmxA 494 7.78e+00 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 1pmzA 86 8.21e+00 a.39.1.10 104195 2fhfA 1083 8.43e+00 1lmzA 187 8.80e+00 a.96.1.4 74037 2f3yA 148 8.81e+00 1agi 125 9.09e+00 7rsa d.5.1.1 37303 1mkmA 249 9.48e+00 a.4.5.33,d.110.2.2 79242,79243 1x0rA 249 9.93e+00 1f02T 66 1.01e+01 1f02T j.67.1.1 46360 1xw8A 252 1.01e+01 1jpzA 473 1.03e+01 a.104.1.1 67069 1npiA 61 1.07e+01 g.3.7.1 80685 1tueA 212 1.09e+01 c.37.1.20 107323 2b7kA 200 1.09e+01 2jdxA 385 1.11e+01 1jdw d.126.1.2 41139 1ignA 246 1.11e+01 1ignA a.4.1.6,a.4.1.6 16048,16049 1tfzA 424 1.12e+01 d.32.1.3,d.32.1.3 106886,106887 1hdoA 206 1.12e+01 1he2A c.2.1.2 60965 1wy9A 147 1.12e+01 1ovlA 271 1.14e+01 a.123.1.1 87455 2bbrA 195 1.15e+01 2g0uA 92 1.16e+01 1k9uA 78 1.17e+01 a.39.1.10 84348 1orsC 132 1.24e+01 f.14.1.1 87353 2bn5A 33 1.27e+01 1vyrA 364 1.27e+01 c.1.4.1 108906 1gppA 237 1.31e+01 b.86.1.2 76262 2f6eA 127 1.32e+01 1lrzA 426 1.37e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1qkkA 155 1.38e+01 1dbwA c.23.1.1 31104 1mpp 361 1.38e+01 2rmpA b.50.1.2 26856 1o2dA 371 1.39e+01 e.22.1.2 86591 1ywfA 296 1.41e+01 1y0nA 78 1.47e+01 1ylkA 172 1.47e+01 1ggzA 148 1.49e+01 a.39.1.5 70176 1jdw 423 1.50e+01 1jdw d.126.1.2 41129 2f6hX 419 1.51e+01 1wkaA 147 1.51e+01 1o6dA 163 1.60e+01 c.116.1.3 92567 1jsf 130 1.61e+01 3lzt d.2.1.2 36410 1ob8A 135 1.61e+01 2erfA 209 1.63e+01 1geqA 248 1.64e+01 2tysA c.1.2.4 28589 1inlA 296 1.65e+01 c.66.1.17 66220 3thiA 371 1.65e+01 2thiA c.94.1.1 35792 1wdpA 495 1.67e+01 1x3aA 100 1.80e+01 3htsB 102 1.84e+01 2hts a.4.5.22 16175 1u7pA 164 1.84e+01 2abqA 306 1.89e+01 1v58A 241 1.91e+01 c.47.1.9,d.17.3.1 108371,108372 1lq9A 112 1.91e+01 d.58.4.3 78129 1cojA 212 1.93e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1fcyA 236 1.94e+01 2lbd a.123.1.1 19282 1icfI 65 1.95e+01 1icfI g.28.1.1 44958 1wzlA 585 1.96e+01 1a6m 151 1.98e+01 1a6m a.1.1.2 15018 1y4tA 322 2.08e+01 1zrn 232 2.16e+01 1qq5A c.108.1.1 43323 1fjnA 39 2.18e+01 1fjnA g.3.7.3 44171 1xzoA 174 2.19e+01 1dqzA 280 2.20e+01 1dqyA c.69.1.3 34638 1gwiA 411 2.30e+01 a.104.1.1 76364 2bzvA 181 2.34e+01 2eutA 294 2.37e+01 1lm8C 96 2.38e+01 d.42.1.1 74034 1j8bA 112 2.38e+01 d.222.1.1 77101 2bsxA 253 2.38e+01 2if1 126 2.43e+01 2if1 d.64.1.1 39547 2a65A 519 2.45e+01 1w85A 368 2.47e+01 1s9uA 207 2.47e+01 a.184.1.1 105390 1b0nA 111 2.48e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 1eiwA 111 2.59e+01 1eiwA c.23.3.1 31130 1seiA 130 2.62e+01 1seiA d.140.1.1 41463 1dzkA 157 2.63e+01 1obpA b.60.1.1 27096 1on2A 142 2.65e+01 a.4.5.24,a.76.1.1 87103,87104 1nvvS 481 2.66e+01 a.117.1.1 86279 1mbmA 198 2.66e+01 b.47.1.3 78916 1ug7A 128 2.69e+01 a.24.24.1 107824 1fjgK 129 2.70e+01 1fjfK c.55.4.1 33733 2aaxA 275 2.73e+01 1f0nA 285 2.73e+01 1dqyA c.69.1.3 34636 1iujA 106 2.74e+01 d.58.4.5 90701 1vr5A 547 2.77e+01 1v93A 296 2.80e+01 c.1.23.1 100532 1z6oM 191 2.82e+01 1m45A 148 2.82e+01 a.39.1.5 78598 1pn0A 665 2.83e+01 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 2aqaA 63 2.85e+01 1s2oA 244 2.88e+01 1l4dB 122 2.89e+01 d.15.5.1 77684 1s8nA 205 2.94e+01 c.23.1.1 105374 1dvpA 220 2.94e+01 1dvpA a.118.9.2,g.50.1.1 19216,45358 1wtaA 275 2.96e+01 1tp9A 162 3.00e+01 1lktA 104 3.03e+01 1lktA b.90.1.1 28398 1us0A 316 3.07e+01 c.1.7.1 99850 1pii 452 3.08e+01 1pii c.1.2.4,c.1.2.4 28559,28563 1zklA 353 3.08e+01 1ht6A 405 3.09e+01 b.71.1.1,c.1.8.1 83629,83630 1ucnA 152 3.13e+01 d.58.6.1 99183 1mvcA 240 3.15e+01 a.123.1.1 79499 1zvtA 256 3.19e+01 1m65A 245 3.20e+01 c.6.3.1 84847 1nzjA 298 3.22e+01 c.26.1.1 92377 1yuzA 202 3.23e+01 1gt1A 159 3.24e+01 b.60.1.1 90515 1mlwA 301 3.24e+01 d.178.1.1 79289 1nw1A 429 3.30e+01 d.144.1.8 86286 1psrA 100 3.31e+01 1psrA a.39.1.2 17180 2a6hE 99 3.31e+01 1vfsA 386 3.32e+01 b.49.2.2,c.1.6.1 108584,108585 2fnaA 357 3.32e+01 1m0kA 262 3.34e+01 f.13.1.1 78344 2carA 196 3.36e+01 1dk8A 147 3.42e+01 1agrE a.91.1.1 18548 1vp4A 425 3.44e+01 1y81A 138 3.44e+01 1mzgA 146 3.45e+01 d.224.1.1 79696 1wzcA 249 3.47e+01 2gz4A 207 3.49e+01 1bm9A 122 3.50e+01 1bm9A a.4.5.7 16116 1djtA 64 3.56e+01 1aho g.3.7.1 44132 1f20A 435 3.56e+01 b.43.4.1,c.25.1.4 64932,64933 1xyiA 66 3.69e+01 1sv0C 82 3.72e+01 a.60.1.1 106037 1ub1A 133 3.73e+01 d.10.1.3 99140 2bneA 241 3.79e+01 1uw4A 91 3.83e+01 d.58.7.4 100071 1wvfA 520 3.85e+01 1uvjA 664 3.85e+01 e.8.1.6 100045 1umdA 367 3.89e+01 c.36.1.11 99599 2frfA 153 3.95e+01 1oq9A 363 3.96e+01 a.25.1.2 87257 1t5oA 351 3.97e+01 c.124.1.5 106459 1u24A 337 4.01e+01 1ib2A 349 4.01e+01 1ib2A a.118.1.8 62141 1r8oA 96 4.03e+01 b.42.4.1 104852 1dxsA 80 4.04e+01 1cokA a.60.1.2 17944 1snrA 341 4.06e+01 b.6.1.3,b.6.1.3 105823,105824 1gqzA 274 4.08e+01 d.21.1.1,d.21.1.1 83311,83312 1wz3A 96 4.09e+01 1rxqA 178 4.15e+01 a.213.1.1 105118 2fbqA 235 4.16e+01 1v25A 541 4.23e+01 e.23.1.1 108275 1c7sA 858 4.27e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21812,22408,29011,40410 2a6sA 84 4.29e+01 1k0mA 241 4.33e+01 a.45.1.1,c.47.1.5 67949,67950 1vchA 175 4.35e+01 1dl5A 317 4.36e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 2bw4A 340 4.40e+01 1regX 122 4.42e+01 1regX d.58.27.1 39406 1dmgA 225 4.43e+01 1dmgA c.22.1.1 31036 1yewC 289 4.49e+01 1twuA 139 4.52e+01 d.32.1.8 107413 1cs1A 386 4.58e+01 1ibjA c.67.1.3 34399 1n7kA 234 4.59e+01 c.1.10.1 85374 1vraB 215 4.59e+01 1r8eA 278 4.60e+01 a.6.1.3,d.60.1.1 104843,104844 1dp4A 435 4.60e+01 1dp4A c.93.1.1 35710 1whzA 70 4.62e+01 1x74A 360 4.66e+01 1xtmA 175 4.71e+01 1ff9A 450 4.71e+01 1ff9A c.2.1.3,d.81.1.2 30039,39954 1q0gA 117 4.72e+01 a.24.22.1 104428 1bjt 793 4.73e+01 1bjt e.11.1.1 43249 1pu1A 94 4.75e+01 d.266.1.1 104307 1xi7A 61 4.77e+01 1xvsA 126 4.78e+01 2cmwA 310 4.79e+01 1zsqA 528 4.85e+01 1ltqA 301 4.86e+01 c.108.1.9,c.37.1.1 78208,78209 1u69A 163 4.86e+01 d.32.1.7 107699 1ngnA 155 4.86e+01 a.96.1.2 85697 1f1uA 323 4.89e+01 d.32.1.3,d.32.1.3 83200,83201 1gmeA 151 4.95e+01 b.15.1.1 65305 1h5rA 293 4.96e+01 c.68.1.6 65623 1wzzA 334 4.99e+01 1v0eA 666 5.03e+01 1gjnA 153 5.05e+01 a.1.1.2 70191 1u3eM 174 5.06e+01 d.4.1.3,d.285.1.1 107640,107641 1t4wA 196 5.08e+01 b.2.5.2 106427 2etgA 296 5.11e+01 1avsA 90 5.15e+01 1cll a.39.1.5 17226 1cnv 299 5.17e+01 1cnv c.1.8.5 28989 1z64A 26 5.17e+01 1qo2A 241 5.19e+01 1qo2A c.1.2.1 28533 2a8yA 270 5.23e+01 2h1tA 188 5.30e+01 2fdbM 164 5.31e+01 1vcoA 550 5.34e+01 c.23.16.1,c.37.1.10 108508,108509 1f9zA 135 5.35e+01 1qipA d.32.1.1 38484 1yhvA 297 5.35e+01 1vpmA 169 5.44e+01 1yemA 179 5.45e+01 1ef8A 261 5.49e+01 1ef8A c.14.1.3 30921 1xpcA 248 5.51e+01 1gntA 553 5.51e+01 e.26.1.1 70290 1k4nA 192 5.52e+01 d.32.1.5 72059 1lm8V 160 5.53e+01 b.3.3.1 74035 1q7zA 566 5.64e+01 c.1.21.2,c.1.26.1 96090,96091 2bl0B 145 5.65e+01 1zfuA 40 5.71e+01 2cb5A 453 5.74e+01 3gcb d.3.1.1 37035 2frnA 278 5.76e+01 1zxtA 76 5.76e+01 1yaxA 153 5.76e+01 2fwhA 134 5.77e+01 1yz4A 160 5.80e+01 1mw9X 592 5.83e+01 e.10.1.1 91480 1wnyA 186 5.83e+01 1q7fA 286 5.87e+01 b.68.9.1 96036 1oc2A 348 5.93e+01 c.2.1.2 92765 1my6A 199 5.93e+01 a.2.11.1,d.44.1.1 85232,85233 1xqoA 256 5.94e+01 2bgkA 278 6.00e+01 1nrjA 158 6.03e+01 d.110.4.4 86124 2a2pA 129 6.06e+01 1mqvA 125 6.07e+01 a.24.3.2 79415 1qb5D 99 6.09e+01 b.40.2.1 88357 1cby 259 6.14e+01 1cby d.103.1.1 40705 2gs5A 198 6.16e+01 1byi 224 6.17e+01 1byi c.37.1.10 32199 1vk6A 269 6.20e+01 d.113.1.4,d.113.1.4 100851,100852 1xdpA 687 6.22e+01 1wmhA 89 6.24e+01 1g3qA 237 6.24e+01 1hyqA c.37.1.10 60237 2arzA 247 6.31e+01 1t95A 240 6.33e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1e7wA 291 6.34e+01 c.2.1.2 59373 1dbwA 126 6.38e+01 1dbwA c.23.1.1 31095 1mkiA 330 6.40e+01 e.3.1.2 84994 1fr2B 134 6.44e+01 d.4.1.1 83257 1xvxA 312 6.52e+01 1iqzA 81 6.53e+01 d.58.1.4 66281 1dyoA 160 6.55e+01 1dyoA b.18.1.7 23771 1tc5A 194 6.56e+01 c.110.1.1 106752 2g09A 297 6.59e+01 1alu 186 6.61e+01 1alu a.26.1.1 16826 2afaA 425 6.62e+01 2cy5A 140 6.64e+01 1tu1A 148 6.65e+01 d.107.1.3 107316 1m1nB 522 6.70e+01 c.92.2.3 78418 1s1pA 331 6.75e+01 c.1.7.1 98350 1c30B 382 6.76e+01 c.8.3.1,c.23.16.1 30736,31413 1a9xB 379 6.82e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 1r1hA 696 6.86e+01 d.92.1.4 104756 1segA 64 6.93e+01 g.3.7.1 105453 1vlmA 219 6.93e+01 c.66.1.41 108836 1nuuA 252 6.95e+01 c.26.1.3 86209 1pylA 97 6.96e+01 d.1.1.2 104391 1zkrA 153 6.97e+01 1s1hD 179 6.99e+01 i.1.1.1 105157 2f06A 144 7.03e+01 2gl5A 410 7.06e+01 1xhnA 184 7.09e+01 1bea 127 7.12e+01 1bea a.52.1.2 17826 1a62 130 7.16e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1zv9A 172 7.28e+01 2gkeA 274 7.29e+01 1aho 64 7.32e+01 1aho g.3.7.1 44127 1yj7A 171 7.33e+01 1uc7A 125 7.34e+01 c.47.1.1 99163 2fswA 107 7.37e+01 1qgoA 264 7.40e+01 1qgoA c.92.1.2 35596 2a4dA 160 7.41e+01 2bfdA 400 7.42e+01 1a0cA 438 7.45e+01 1a0cA c.1.15.3 29529 1dsxA 87 7.45e+01 1t1dA d.42.1.2 38644 1st9A 143 7.46e+01 c.47.1.10 98987 2g8mA 264 7.47e+01 2ftwA 521 7.51e+01 1oshA 232 7.56e+01 a.123.1.1 93496 2gdqA 382 7.57e+01 2bs3A 656 7.58e+01 1ve6A 582 7.64e+01 2f96A 224 7.65e+01 1o26A 232 7.66e+01 d.207.1.1 86566 1vlbA 907 7.66e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 1uzmA 247 7.75e+01 2g5cA 281 7.86e+01 1e0nA 27 7.88e+01 b.72.1.1 27807 1j96A 323 7.89e+01 c.1.7.1 71616 1zpdA 568 7.98e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31741,31785,31786 1lkoA 191 7.98e+01 a.25.1.1,g.41.5.1 78063,78064 1qznA 173 7.99e+01 b.2.2.2 104669 2azpA 318 8.00e+01 1kqfC 217 8.02e+01 f.21.1.1 72874 2pia 321 8.04e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1nkiA 135 8.05e+01 d.32.1.2 91941 1tedA 393 8.05e+01 c.95.1.2 106807 1twfB 1224 8.06e+01 1i19A 561 8.08e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 2aukA 190 8.12e+01 1eaiC 61 8.17e+01 1eaiC g.22.1.1 44894 1m33A 258 8.20e+01 c.69.1.26 78514 1x7yA 400 8.21e+01 1zxfA 155 8.26e+01 1v72A 356 8.26e+01 1rypL 212 8.32e+01 d.153.1.4 41880 1b79A 119 8.34e+01 1b79A a.81.1.1 18451 1yn8A 59 8.35e+01 2f9sA 151 8.36e+01 1o20A 427 8.40e+01 c.82.1.1 86556 1a2pA 110 8.40e+01 1b20A d.1.1.2 36140 1q9uA 130 8.46e+01 d.129.7.1 96314 1jb0A 755 8.47e+01 1jb0A f.29.1.1 62820 2fnjC 96 8.53e+01 1fp2A 352 8.53e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1mxgA 435 8.71e+01 b.71.1.1,c.1.8.1 85193,85194 1qd9A 124 8.71e+01 1qu9A d.79.1.1 39758 1vcc 77 8.71e+01 1vcc d.121.1.1 41092 2ct9A 208 8.71e+01 2evaA 307 8.73e+01 1guxA 218 8.74e+01 1guxA a.74.1.3 18388 1ktbA 405 8.75e+01 b.71.1.1,c.1.8.1 72960,72961 2freA 200 8.79e+01 1vl5A 260 8.80e+01 c.66.1.41 108720 2cz1A 206 8.80e+01 1k66A 149 8.86e+01 c.23.1.1 90941 1px5A 349 8.87e+01 a.160.1.2,d.218.1.6 95277,95278 2arpA 116 8.88e+01