# 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 1oneA 436 2.85e-01 4enl c.1.11.1,d.54.1.1 29200,38844 2al1A 436 3.51e-01 2al2A 436 3.53e-01 1khdA 345 4.92e-01 a.46.2.1,c.27.1.1 77400,77401 1q8bA 105 6.26e-01 d.58.4.6 96201 3nul 130 8.94e-01 3nul d.110.1.1 40891 1nxmA 197 9.86e-01 b.82.1.1 86385 1kyqA 274 1.41e+00 c.2.1.11,e.37.1.1 73281,73282 1h0hB 214 1.42e+00 d.58.1.5 76437 1ri6A 343 1.43e+00 b.69.11.1 97503 1f9zA 135 1.45e+00 1qipA d.32.1.1 38484 1tqzA 133 1.67e+00 2fuvA 549 1.68e+00 1xfsA 178 1.94e+00 d.129.3.5 109589 2cy2A 174 1.97e+00 1acf 125 2.21e+00 3nul d.110.1.1 40882 1qipA 183 2.21e+00 1qipA d.32.1.1 38470 2gupA 292 2.35e+00 2as0A 396 2.66e+00 1cojA 212 2.72e+00 1avmA a.2.11.1,d.44.1.1 15737,38734 1vavA 222 2.79e+00 b.29.1.18 108472 1vquA 374 2.84e+00 1dq3A 454 2.86e+00 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1ijtA 128 2.88e+00 1bfg b.42.1.1 62510 1eo1A 124 2.97e+00 1eo1A c.55.5.1 33739 1nziA 159 2.99e+00 b.23.1.1,g.3.11.1 86449,86450 2fymA 431 3.03e+00 1u9aA 160 3.10e+00 1u9aA d.20.1.1 38333 2gwdA 449 3.16e+00 1fvuB 125 3.21e+00 1ixxB d.169.1.1 42346 1m93B 245 3.23e+00 1kyfA 247 3.35e+00 b.1.10.1,d.105.1.1 73220,73221 2grrA 161 3.91e+00 1w8oA 601 4.08e+00 2cr9A 139 4.10e+00 1ww9A 392 4.16e+00 1ojqA 212 4.20e+00 d.166.1.1 93146 1olzA 663 4.24e+00 b.1.1.4,b.69.12.1,g.16.2.1 93341,93342,93343 1svpA 161 4.29e+00 1svpA b.47.1.3 26384 1jtdB 273 4.47e+00 b.69.5.2 67265 1wm1A 317 4.48e+00 c.69.1.7 109405 1voqa 90 4.53e+00 1f89A 291 4.56e+00 d.160.1.1 64988 1u2cA 246 4.63e+00 b.1.6.2,d.272.1.1 107610,107611 1tq5A 242 4.79e+00 1pm3A 78 5.03e+00 b.41.1.2 94889 1zc3B 113 5.24e+00 1ee8A 266 5.59e+00 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1zn6A 227 5.91e+00 2gqrA 237 5.96e+00 1khiA 176 5.98e+00 b.34.5.2,b.40.4.5 77408,77409 1m98A 317 6.01e+00 a.175.1.1,d.17.4.6 78866,78867 1qwyA 291 6.01e+00 b.84.3.2 96509 2f5tX 233 6.03e+00 1yqzA 438 6.18e+00 1o13A 136 6.54e+00 c.55.5.1 80762 1fzvA 132 6.64e+00 1vpfA g.17.1.1 60159 1pot 325 6.75e+00 1pot c.94.1.1 35807 1lfdA 87 6.77e+00 1lfdA d.15.1.5 37622 1hd2A 161 6.89e+00 c.47.1.10 60962 1juhA 350 7.09e+00 b.82.1.5 71884 1txkA 498 7.22e+00 b.1.18.2,b.30.5.9 107425,107426 1v0aA 178 7.27e+00 1o97C 264 7.43e+00 c.26.2.3 81232 1dxrH 258 7.69e+00 6prcH b.41.1.1,f.23.10.1 25456,43433 1y0gA 191 7.83e+00 1ctt 294 8.08e+00 1ctt c.97.1.1,c.97.1.1 36022,36023 1ts9A 102 8.15e+00 2biwA 490 8.17e+00 1lj5A 379 8.27e+00 e.1.1.1 73928 1qz8A 113 8.28e+00 b.140.1.1 96619 2gdnA 267 8.29e+00 2avtA 378 9.06e+00 1zhhB 242 9.10e+00 1wwrA 171 9.25e+00 1df7A 159 9.46e+00 3dfr c.71.1.1 34885 2bw8A 227 9.64e+00 1p1mA 406 9.94e+00 b.92.1.4,c.1.9.9 87696,87697 1syxB 86 1.00e+01 1jofA 365 1.01e+01 b.69.10.1 71775 1qv1A 195 1.02e+01 a.39.1.5 96347 1tzfA 259 1.04e+01 c.68.1.13 107476 1n71A 180 1.07e+01 d.108.1.1 85370 2ge3A 170 1.08e+01 1rzhH 260 1.09e+01 b.41.1.1,f.23.10.1 98162,98163 1dx5I 118 1.11e+01 1dx5I g.3.11.1,g.3.11.1,g.3.11.1 44302,44303,44304 4ubpA 101 1.12e+01 1ubpA d.8.1.1 37352 1o12A 376 1.12e+01 b.92.1.5,c.1.9.10 80758,80759 1wba 175 1.13e+01 1wba b.42.4.1 25591 1s4bP 674 1.13e+01 d.92.1.5 105252 2d7nA 93 1.13e+01 2fnjA 226 1.15e+01 1vrmA 325 1.21e+01 1w1hA 151 1.21e+01 2bpqA 373 1.22e+01 1a2pA 110 1.23e+01 1b20A d.1.1.2 36140 1vzqH 250 1.24e+01 2bryA 497 1.26e+01 2bepA 159 1.26e+01 1mkkA 96 1.27e+01 g.17.1.1 79240 1vphA 149 1.32e+01 1h8dH 260 1.32e+01 5ptp 2b5nA 323 1.33e+01 1noyA 388 1.33e+01 1clqA c.55.3.5 33713 2cf8H 257 1.34e+01 1r26A 125 1.37e+01 c.47.1.1 96847 2akzA 439 1.37e+01 2napA 723 1.39e+01 2napA b.52.2.2,c.81.1.1 26926,35334 1vmjA 151 1.41e+01 1nw3A 416 1.43e+01 c.66.1.31 86288 1vmfA 145 1.44e+01 1vk0A 206 1.45e+01 c.55.3.5 100839 1qmyA 167 1.45e+01 1qmyA d.3.1.2 37094 1vqoW 154 1.46e+01 2cdcA 366 1.47e+01 2c4bA 143 1.47e+01 1j1qA 261 1.50e+01 d.165.1.1 90768 2d93A 134 1.53e+01 1ejxA 100 1.55e+01 d.8.1.1 83182 1svvA 359 1.57e+01 c.67.1.1 106054 1gcqC 70 1.59e+01 1gcpA b.34.2.1 60436 2f4wA 187 1.59e+01 1z47A 355 1.60e+01 1woqA 267 1.62e+01 c.55.1.10,c.55.1.10 109462,109463 1npuA 117 1.62e+01 b.1.1.1 92038 1zgkA 308 1.63e+01 1vr3A 191 1.64e+01 2c9wA 169 1.65e+01 1cv8 174 1.66e+01 1cv8 d.3.1.1 37089 1q8fA 313 1.68e+01 c.70.1.1 96203 1cruA 454 1.68e+01 1c9uA b.68.2.1 27617 1w9sA 142 1.70e+01 1kw3B 292 1.70e+01 d.32.1.3,d.32.1.3 77549,77550 1yhfA 115 1.72e+01 2b8mA 117 1.72e+01 1o5uA 101 1.73e+01 b.82.1.8 92518 1jatA 155 1.74e+01 1u9aA d.20.1.1 62818 1q5hA 147 1.74e+01 b.85.4.1 95893 1x31C 206 1.76e+01 2g84A 197 1.76e+01 4ubpC 570 1.76e+01 1ubpC b.92.1.1,c.1.9.2 28431,29053 1vkdA 338 1.81e+01 b.67.2.4 108644 1xtoA 311 1.81e+01 1wkt 88 1.83e+01 1wkt b.11.1.2 23630 1wkqA 164 1.83e+01 c.97.1.2 109393 1m1fA 110 1.90e+01 b.34.6.2 78401 1yfuA 174 1.90e+01 1jmxB 349 1.91e+01 b.69.2.2 66906 1dkzA 219 1.93e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1eaxA 241 1.94e+01 b.47.1.2 64889 1s5aA 150 1.97e+01 d.17.4.10 98525 1d4tA 104 1.98e+01 1d4tA d.93.1.1 40537 1umgA 362 1.99e+01 d.280.1.1 107956 1ecsA 126 2.02e+01 1ecsA d.32.1.2 59407 1v04A 355 2.05e+01 b.68.6.2 100240 1ne8A 117 2.06e+01 b.34.6.2 80424 1q8iA 783 2.07e+01 c.55.3.5,e.8.1.1 96208,96209 1dytA 133 2.07e+01 7rsa d.5.1.1 37288 1l8bA 190 2.07e+01 d.86.1.1 73683 1pguA 615 2.10e+01 b.69.4.1,b.69.4.1 88069,88070 1f1uA 323 2.12e+01 d.32.1.3,d.32.1.3 83200,83201 2he7A 283 2.15e+01 1ryaA 160 2.17e+01 d.113.1.5 105122 1o0xA 262 2.17e+01 d.127.1.1 80755 1q40B 219 2.19e+01 d.17.4.2 95771 1ytaA 180 2.21e+01 2cbp 96 2.22e+01 2cbp b.6.1.1 22895 2pia 321 2.22e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1uq5A 263 2.23e+01 d.165.1.1 99778 1ydwA 362 2.23e+01 1i4uA 181 2.24e+01 b.60.1.1 61732 2al3A 90 2.25e+01 1lcyA 325 2.25e+01 b.36.1.4,b.47.1.1 73834,73835 2cw9A 194 2.26e+01 1icfI 65 2.27e+01 1icfI g.28.1.1 44958 1mswD 883 2.31e+01 e.8.1.3 79427 1gr3A 160 2.35e+01 b.22.1.1 65476 1y0yA 353 2.40e+01 1lvoA 302 2.43e+01 b.47.1.4 74284 1vpkA 378 2.46e+01 2c2xA 281 2.46e+01 1t0hA 132 2.50e+01 b.34.2.1 106207 1dynA 125 2.54e+01 1dynA b.55.1.1 26955 1un7A 400 2.61e+01 b.92.1.5,c.1.9.10 99657,99658 1b5fA 239 2.62e+01 1smrA b.50.1.2 26836 2aiqA 231 2.63e+01 2gfaA 119 2.63e+01 1ti6A 875 2.64e+01 b.52.2.2,c.81.1.1 106974,106975 1dgwA 178 2.65e+01 1dgwA b.82.1.2 28090 1r9cA 139 2.65e+01 d.32.1.2 97255 1w7jA 795 2.67e+01 1cs6A 382 2.72e+01 1cs6A b.1.1.4,b.1.1.4,b.1.1.4,b.1.1.4 21760,21761,21762,21763 2bhuA 602 2.73e+01 1frrA 95 2.77e+01 1awd d.15.4.1 37674 1wosA 364 2.79e+01 b.44.2.1,d.250.1.1 109468,109469 1gl4B 98 2.80e+01 b.1.1.4 65288 1mvfD 82 2.80e+01 b.129.1.1 85143 1xy7A 166 2.81e+01 1pcfA 66 2.85e+01 1pcfA d.18.1.1 38142 1u04A 771 2.85e+01 b.34.14.1,c.55.3.10 107539,107540 1ufkA 254 2.88e+01 c.66.1.39 99340 1fl2A 310 2.90e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1mugA 168 2.95e+01 1mugA c.18.1.2 31030 2c27A 315 2.98e+01 1vqoQ 96 2.99e+01 1zc1A 208 3.06e+01 1i1qB 192 3.09e+01 1qdlB c.23.16.1 61544 1npsA 88 3.11e+01 1prs b.11.1.1 23622 2fhzB 108 3.12e+01 1ro5A 201 3.16e+01 d.108.1.3 105023 1lk2A 274 3.18e+01 b.1.1.2,d.19.1.1 91056,91057 1z4rA 168 3.18e+01 1kjkA 64 3.19e+01 d.10.1.4 72613 1rg9A 383 3.19e+01 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1gpiA 431 3.21e+01 b.29.1.10 65450 1ijaA 148 3.22e+01 1ijaA b.100.1.1 62484 1n7zA 334 3.23e+01 b.127.1.1 85380 1m40A 263 3.24e+01 e.3.1.1 74437 2ffsA 157 3.29e+01 1uoyA 64 3.30e+01 g.3.19.1 99709 1tuhA 156 3.35e+01 d.17.4.11 107345 2fqpA 97 3.35e+01 2b4wA 315 3.36e+01 1uxxX 133 3.36e+01 b.18.1.10 100169 1mwqA 101 3.37e+01 d.58.4.7 91481 1urrA 102 3.37e+01 d.58.10.1 107998 1p6oA 161 3.38e+01 c.97.1.2 94185 1hp1A 516 3.42e+01 d.114.1.1,d.159.1.2 70976,70977 1hzoA 271 3.44e+01 e.3.1.1 71092 1ws0A 156 3.44e+01 2ck3D 482 3.44e+01 1vloA 381 3.45e+01 b.44.2.1,d.250.1.1 108838,108839 1c4rA 182 3.46e+01 1c4rA b.29.1.4 24229 2arcA 164 3.50e+01 2arcA b.82.4.1 28148 1kdgA 546 3.55e+01 c.3.1.2,d.16.1.1 77337,77338 1ihkA 174 3.57e+01 1bfg b.42.1.1 62384 2cn3A 737 3.61e+01 1fxkC 133 3.65e+01 1fxkC a.2.5.1 15702 2cohA 202 3.66e+01 1h6lA 353 3.66e+01 b.68.3.1 60687 1wstA 417 3.66e+01 1oalA 151 3.66e+01 b.1.8.1 86739 1q67A 231 3.67e+01 b.55.1.7 95960 1qfoA 119 3.67e+01 1qfoA b.1.1.1 19708 1jy4A 35 3.68e+01 k.35.1.1 71938 2a38A 194 3.68e+01 2bs3A 656 3.71e+01 1vbkA 307 3.71e+01 1nuyA 337 3.74e+01 e.7.1.1 86213 1nnwA 252 3.74e+01 d.159.1.5 80674 2fvhA 120 3.77e+01 1zxxA 319 3.79e+01 1q1uA 144 3.80e+01 b.42.1.1 95608 1h12A 405 3.84e+01 a.102.1.2 83447 2ftwA 521 3.85e+01 1t2wA 145 3.88e+01 b.100.1.1 106289 1kxqE 120 3.88e+01 b.1.1.1 73171 1zn8A 180 3.92e+01 2gjdA 157 3.96e+01 2biqA 219 3.97e+01 1p5zB 263 3.98e+01 c.37.1.1 87815 1n9bA 265 3.99e+01 e.3.1.1 85463 1wwzA 159 4.01e+01 1s6lA 212 4.02e+01 1xk5A 204 4.02e+01 1qfhA 212 4.08e+01 1qfhA b.1.18.10,b.1.18.10 21893,21894 1yopA 83 4.10e+01 1h7sA 365 4.20e+01 d.14.1.3,d.122.1.2 65705,65706 1zvdA 380 4.22e+01 1yn8A 59 4.23e+01 1fyeA 229 4.24e+01 1fyeA c.23.16.4 31477 1sjyA 159 4.25e+01 d.113.1.1 98900 1zgoA 223 4.30e+01 1i3zA 103 4.34e+01 d.93.1.1 83667 1yifA 533 4.34e+01 1o50A 157 4.38e+01 d.37.1.1,d.37.1.1 92478,92479 2fb0A 94 4.42e+01 1w4vA 119 4.42e+01 1rb9 53 4.42e+01 1rb9 g.41.5.1 45214 1gteA 1025 4.42e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70440,70441,70442,70443,70444 1gmiA 136 4.49e+01 b.7.1.1 65309 1ym0A 238 4.50e+01 2ac0A 200 4.52e+01 2ayh 214 4.53e+01 1axkA b.29.1.2 24172 1jmsA 381 4.60e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1l3lA 234 4.62e+01 a.4.6.2,d.110.5.1 73541,73542 1fjgE 162 4.62e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 2axtO 247 4.62e+01 1ztuA 341 4.63e+01 1r45A 204 4.63e+01 1uy4A 145 4.63e+01 b.18.1.10 108131 2fsrA 195 4.63e+01 1gvhA 396 4.66e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1k47A 337 4.70e+01 d.14.1.5,d.58.26.4 72040,72041 1cvrA 435 4.73e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 1qy6A 274 4.74e+01 b.47.1.1 96574 1gbg 214 4.77e+01 1axkA b.29.1.2 24171 2giyA 191 4.77e+01 1w9iA 770 4.79e+01 1w0dA 337 4.85e+01 1gw5S 142 4.86e+01 d.110.4.2 70633 1khoA 370 4.87e+01 a.124.1.1,b.12.1.3 72489,72490 1v2bA 177 4.93e+01 d.107.1.2 108279 1o8xA 146 5.00e+01 c.47.1.10 86681 1oboA 169 5.01e+01 c.23.5.1 86776 1ca1 370 5.03e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1bqk 124 5.08e+01 1bqk b.6.1.1 22889 1v9yA 167 5.09e+01 d.110.3.2 108454 1lkdA 297 5.11e+01 d.32.1.3,d.32.1.3 78059,78060 2fdbM 164 5.20e+01 1nscA 390 5.20e+01 2qwc b.68.1.1 27591 1ywqA 200 5.22e+01 1h6hA 143 5.26e+01 d.189.1.1 65681 2iwaA 266 5.28e+01 1pzsA 208 5.30e+01 b.1.8.1 104397 2et1A 201 5.31e+01 1pbyB 337 5.42e+01 b.69.2.2 94422 1ckaA 57 5.42e+01 1ckaA b.34.2.1 24459 2b18A 164 5.42e+01 1mml 265 5.43e+01 1mml e.8.1.2 43015 1pieA 419 5.47e+01 d.14.1.5,d.58.26.7 94706,94707 2gmqA 118 5.48e+01 1l7mA 211 5.48e+01 c.108.1.4 73664 1u9kA 114 5.52e+01 1m0wA 491 5.54e+01 c.30.1.4,d.142.1.6 78363,78364 1s21A 206 5.55e+01 d.166.1.4 105222 1f1xA 322 5.56e+01 d.32.1.3,d.32.1.3 83208,83209 1t3tA 1303 5.63e+01 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 1y9wA 140 5.63e+01 1h8eD 482 5.64e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 2fp8A 322 5.65e+01 1c7sA 858 5.66e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21812,22408,29011,40410 1wz4A 23 5.71e+01 2d28C 149 5.73e+01 1ad2 228 5.76e+01 1ad2 e.24.1.1 43353 1gtkA 313 5.78e+01 c.94.1.1,d.50.2.1 76346,76347 2fhfA 1083 5.79e+01 1pl8A 356 5.79e+01 b.35.1.2,c.2.1.1 94878,94879 1ex2A 189 5.81e+01 1ex2A c.51.4.2 33225 1pj5A 830 5.81e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1d3bA 75 5.84e+01 1d3bA b.38.1.1 24798 1r31A 428 5.85e+01 d.58.20.1,d.179.1.1 96897,96898 1wriA 93 5.93e+01 2ixiA 184 5.96e+01 1zvhA 134 6.00e+01 1io1A 398 6.02e+01 1io1A e.32.1.1 62611 1mjfA 281 6.02e+01 c.66.1.17 79198 1lkkA 105 6.09e+01 1lckA d.93.1.1 40412 1d2oA 187 6.10e+01 1d2oA b.3.5.1,b.3.5.1 22625,22626 1kv7A 488 6.14e+01 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 1vq2A 193 6.22e+01 1ywfA 296 6.25e+01 1uwcA 261 6.30e+01 c.69.1.17 100101 1p0hA 318 6.40e+01 d.108.1.1 93866 1wxcB 134 6.41e+01 1upsA 420 6.43e+01 1lj2C 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