# List of top-scoring protein chains for t04-100-30-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 1q8bA 105 4.04e-01 d.58.4.6 96201 1oneA 436 5.17e-01 4enl c.1.11.1,d.54.1.1 29200,38844 4enl 436 7.18e-01 4enl c.1.11.1,d.54.1.1 29202,38846 1khdA 345 8.17e-01 a.46.2.1,c.27.1.1 77400,77401 2al1A 436 8.21e-01 2al2A 436 8.25e-01 1h0hB 214 1.06e+00 d.58.1.5 76437 1nxmA 197 1.46e+00 b.82.1.1 86385 1qipA 183 1.51e+00 1qipA d.32.1.1 38470 1dq3A 454 1.54e+00 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1khiA 176 1.56e+00 b.34.5.2,b.40.4.5 77408,77409 1zc3B 113 1.64e+00 1ri6A 343 1.68e+00 b.69.11.1 97503 1xygD 359 1.73e+00 1ijtA 128 1.74e+00 1bfg b.42.1.1 62510 1xfsA 178 1.95e+00 d.129.3.5 109589 1ww9A 392 2.35e+00 2cy2A 174 2.40e+00 1yqzA 438 2.41e+00 1kyfA 247 2.62e+00 b.1.10.1,d.105.1.1 73220,73221 1cojA 212 2.67e+00 1avmA a.2.11.1,d.44.1.1 15737,38734 2fuvA 549 2.78e+00 1u2cA 246 2.89e+00 b.1.6.2,d.272.1.1 107610,107611 1tqzA 133 3.45e+00 1qtsA 247 3.62e+00 1qtsA b.1.10.1,d.105.1.1 22313,40789 1u9aA 160 3.63e+00 1u9aA d.20.1.1 38333 1nziA 159 4.05e+00 b.23.1.1,g.3.11.1 86449,86450 3nul 130 4.23e+00 3nul d.110.1.1 40891 1tq5A 242 4.54e+00 1f89A 291 4.78e+00 d.160.1.1 64988 1vavA 222 4.79e+00 b.29.1.18 108472 1wba 175 4.87e+00 1wba b.42.4.1 25591 1vquA 374 5.17e+00 2gupA 292 5.21e+00 1m93B 245 5.22e+00 1acf 125 5.42e+00 3nul d.110.1.1 40882 1svpA 161 5.44e+00 1svpA b.47.1.3 26384 1ee8A 266 5.67e+00 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1fvuB 125 5.78e+00 1ixxB d.169.1.1 42346 2biwA 490 5.85e+00 2grrA 161 5.86e+00 1juhA 350 5.95e+00 b.82.1.5 71884 1y0gA 191 5.96e+00 1h8gA 95 6.10e+00 b.109.1.1 65735 1eo1A 124 6.11e+00 1eo1A c.55.5.1 33739 1pm3A 78 6.40e+00 b.41.1.2 94889 2as0A 396 6.59e+00 2bz8A 58 6.92e+00 1eaxA 241 6.97e+00 b.47.1.2 64889 1vphA 149 7.11e+00 2bzuA 181 7.27e+00 1ts9A 102 7.28e+00 1voqa 90 7.37e+00 2fymA 431 7.37e+00 1eur 365 7.72e+00 1eut b.68.1.1 27607 2awaA 390 7.78e+00 1a7cA 379 7.80e+00 1sek e.1.1.1 42660 2gqrA 237 7.95e+00 1w8oA 601 8.12e+00 2cw9A 194 8.23e+00 1s4bP 674 8.38e+00 d.92.1.5 105252 1yfuA 174 8.45e+00 1ojqA 212 8.71e+00 d.166.1.1 93146 1hd2A 161 8.73e+00 c.47.1.10 60962 1vmfA 145 8.75e+00 1qv1A 195 8.77e+00 a.39.1.5 96347 1wwrA 171 8.79e+00 1vmjA 151 8.85e+00 2cr9A 139 9.02e+00 1el4A 195 9.02e+00 1ej3A a.39.1.5 59453 1jf2A 195 9.09e+00 1ej3A a.39.1.5 62930 1nnwA 252 9.27e+00 d.159.1.5 80674 1vr1H 261 9.35e+00 5ptp 1kyqA 274 9.36e+00 c.2.1.11,e.37.1.1 73281,73282 1o13A 136 9.55e+00 c.55.5.1 80762 1kwsA 261 9.68e+00 c.68.1.7 73083 1lj5A 379 1.01e+01 e.1.1.1 73928 1syxB 86 1.01e+01 1v04A 355 1.05e+01 b.68.6.2 100240 2bw8A 227 1.07e+01 1o5uA 101 1.08e+01 b.82.1.8 92518 1nw3A 416 1.08e+01 c.66.1.31 86288 4ubpA 101 1.09e+01 1ubpA d.8.1.1 37352 1h8dH 260 1.11e+01 5ptp 1wkt 88 1.12e+01 1wkt b.11.1.2 23630 1h0bA 256 1.13e+01 b.29.1.11 83422 1f9zA 135 1.13e+01 1qipA d.32.1.1 38484 2bepA 159 1.14e+01 1jtdB 273 1.14e+01 b.69.5.2 67265 2napA 723 1.15e+01 2napA b.52.2.2,c.81.1.1 26926,35334 1f0cA 305 1.16e+01 1c8oA e.1.1.1 42676 1lfdA 87 1.17e+01 1lfdA d.15.1.5 37622 1pot 325 1.18e+01 1pot c.94.1.1 35807 1yh6A 179 1.19e+01 1vzqH 250 1.20e+01 2b5nA 323 1.21e+01 1dar 691 1.21e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1 25707,32142,37547,39300 1xtoA 311 1.21e+01 1p1mA 406 1.22e+01 b.92.1.4,c.1.9.9 87696,87697 1fa8A 135 1.24e+01 1qipA d.32.1.1 38486 1e79D 482 1.25e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18272,26437,32317 2cf8H 257 1.27e+01 1xfoA 357 1.27e+01 1wm1A 317 1.28e+01 c.69.1.7 109405 1fzvA 132 1.30e+01 1vpfA g.17.1.1 60159 2fqpA 97 1.30e+01 2f5tX 233 1.31e+01 1yhfA 115 1.31e+01 1ctt 294 1.32e+01 1ctt c.97.1.1,c.97.1.1 36022,36023 1zhhB 242 1.33e+01 1pguA 615 1.34e+01 b.69.4.1,b.69.4.1 88069,88070 1zq4A 693 1.39e+01 2b8mA 117 1.40e+01 1ejxA 100 1.42e+01 d.8.1.1 83182 1m98A 317 1.43e+01 a.175.1.1,d.17.4.6 78866,78867 1x31C 206 1.44e+01 2pia 321 1.44e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1qtrA 317 1.46e+01 1qtrA c.69.1.7 34660 1jofA 365 1.46e+01 b.69.10.1 71775 1b87A 181 1.49e+01 1b87A d.108.1.1 40797 2fnjA 226 1.52e+01 2gwdA 449 1.52e+01 1c4rA 182 1.55e+01 1c4rA b.29.1.4 24229 1rzhH 260 1.56e+01 b.41.1.1,f.23.10.1 98162,98163 1wcqA 601 1.57e+01 1gmmA 133 1.57e+01 b.18.1.10 65314 1yuwA 554 1.62e+01 1w1hA 151 1.64e+01 1a2pA 110 1.65e+01 1b20A d.1.1.2 36140 1zn6A 227 1.65e+01 1n3gA 113 1.66e+01 d.204.1.1 79962 2c9wA 169 1.68e+01 1mswD 883 1.70e+01 e.8.1.3 79427 1tiyA 164 1.75e+01 c.97.1.2 107012 1df7A 159 1.76e+01 3dfr c.71.1.1 34885 1vk0A 206 1.76e+01 c.55.3.5 100839 1j6pA 418 1.77e+01 b.92.1.4,c.1.9.9 77089,77090 1qovH 260 1.77e+01 6prcH b.41.1.1,f.23.10.1 25464,43457 1hr6B 443 1.78e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1i1iP 681 1.80e+01 1i1iP d.92.1.5 40297 1a44 185 1.82e+01 1a44 b.17.1.1 23704 1ydwA 362 1.82e+01 1wkqA 164 1.82e+01 c.97.1.2 109393 1kw3B 292 1.84e+01 d.32.1.3,d.32.1.3 77549,77550 1r26A 125 1.85e+01 c.47.1.1 96847 1n71A 180 1.91e+01 d.108.1.1 85370 1j1qA 261 1.92e+01 d.165.1.1 90768 1w9sA 142 1.94e+01 1xbfA 140 1.94e+01 d.273.1.1 109538 1vrmA 325 1.96e+01 1o12A 376 1.97e+01 b.92.1.5,c.1.9.10 80758,80759 1qwyA 291 2.06e+01 b.84.3.2 96509 2a4nA 182 2.10e+01 2c4bA 143 2.11e+01 1jmxB 349 2.12e+01 b.69.2.2 66906 1v0aA 178 2.14e+01 1pdz 434 2.14e+01 4enl c.1.11.1,d.54.1.1 29215,38859 1tzfA 259 2.21e+01 c.68.1.13 107476 1qmyA 167 2.22e+01 1qmyA d.3.1.2 37094 1uxxX 133 2.26e+01 b.18.1.10 100169 2cbp 96 2.29e+01 2cbp b.6.1.1 22895 1umgA 362 2.29e+01 d.280.1.1 107956 2ck3D 482 2.29e+01 2f4wA 187 2.30e+01 2kfnA 605 2.32e+01 1xwl c.55.3.5,e.8.1.1 33682,42975 1ui8A 638 2.32e+01 b.30.2.1,d.17.2.1,d.17.2.1 99419,99420,99421 1dxrH 258 2.34e+01 6prcH b.41.1.1,f.23.10.1 25456,43433 1epaA 164 2.35e+01 1epaA b.60.1.1 27128 1gpiA 431 2.36e+01 b.29.1.10 65450 1q8iA 783 2.36e+01 c.55.3.5,e.8.1.1 96208,96209 4ubpC 570 2.38e+01 1ubpC b.92.1.1,c.1.9.2 28431,29053 2a8kA 108 2.38e+01 2a38A 194 2.41e+01 2g84A 197 2.41e+01 1ytaA 180 2.41e+01 1olzA 663 2.42e+01 b.1.1.4,b.69.12.1,g.16.2.1 93341,93342,93343 1o97C 264 2.44e+01 c.26.2.3 81232 1txkA 498 2.45e+01 b.1.18.2,b.30.5.9 107425,107426 1gr3A 160 2.45e+01 b.22.1.1 65476 1ecsA 126 2.46e+01 1ecsA d.32.1.2 59407 1y71A 130 2.52e+01 1o0xA 262 2.53e+01 d.127.1.1 80755 2d7nA 93 2.53e+01 2fhzB 108 2.54e+01 1gmiA 136 2.60e+01 b.7.1.1 65309 1q48A 134 2.61e+01 d.224.1.2 95783 1upsA 420 2.61e+01 1ryaA 160 2.63e+01 d.113.1.5 105122 1yr0A 175 2.66e+01 1vqoW 154 2.66e+01 1j9aA 184 2.69e+01 c.55.3.5 84135 1m40A 263 2.73e+01 e.3.1.1 74437 2axtO 247 2.73e+01 1ug1A 92 2.77e+01 b.34.2.1 99360 1i1qB 192 2.82e+01 1qdlB c.23.16.1 61544 2gdnA 267 2.83e+01 1j1bA 420 2.83e+01 d.144.1.7 90758 1gcqC 70 2.83e+01 1gcpA b.34.2.1 60436 1ermA 263 2.85e+01 1btl e.3.1.1 42690 1jatA 155 2.86e+01 1u9aA d.20.1.1 62818 1mugA 168 2.86e+01 1mugA c.18.1.2 31030 1btl 263 2.87e+01 1btl e.3.1.1 42691 1d09B 153 2.89e+01 8atcB d.58.2.1,g.41.7.1 39015,45267 1w6gA 646 2.94e+01 1a2vA 655 2.97e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24416,38059,38060 1rjoA 646 2.98e+01 2bpqA 373 2.99e+01 1y0yA 353 3.01e+01 1dx5I 118 3.01e+01 1dx5I g.3.11.1,g.3.11.1,g.3.11.1 44302,44303,44304 1q40B 219 3.03e+01 d.17.4.2 95771 1yaiA 151 3.03e+01 1yaiA b.1.8.1 22289 1mixA 206 3.05e+01 a.11.2.1,b.55.1.5 79166,79167 2ge3A 170 3.06e+01 2bryA 497 3.06e+01 1dgwA 178 3.12e+01 1dgwA b.82.1.2 28090 1ijaA 148 3.14e+01 1ijaA b.100.1.1 62484 1o8xA 146 3.14e+01 c.47.1.10 86681 1p6oA 161 3.17e+01 c.97.1.2 94185 1vr3A 191 3.20e+01 1ywfA 296 3.23e+01 1qk8A 146 3.26e+01 1ewxA c.47.1.10 33061 1ym0A 238 3.27e+01 1jy4A 35 3.34e+01 k.35.1.1 71938 2akzA 439 3.34e+01 1gyfA 62 3.36e+01 1gyfA d.76.1.1 39749 1svvA 359 3.39e+01 c.67.1.1 106054 1n9bA 265 3.39e+01 e.3.1.1 85463 2pil 159 3.45e+01 2pil d.24.1.1 38376 1un7A 400 3.48e+01 b.92.1.5,c.1.9.10 99657,99658 2avtA 378 3.51e+01 1korA 400 3.52e+01 c.26.2.1,d.210.1.1 72824,72825 1siiA 646 3.53e+01 b.30.2.1,d.17.2.1,d.17.2.1 105578,105579,105580 1b5fA 239 3.56e+01 1smrA b.50.1.2 26836 1n2fA 142 3.61e+01 d.227.1.1 79853 1xy7A 166 3.62e+01 1lvoA 302 3.65e+01 b.47.1.4 74284 1uq5A 263 3.66e+01 d.165.1.1 99778 1sjyA 159 3.69e+01 d.113.1.1 98900 1han 297 3.69e+01 1han d.32.1.3,d.32.1.3 38506,38507 2giyA 191 3.73e+01 2gfaA 119 3.75e+01 1dynA 125 3.78e+01 1dynA b.55.1.1 26955 1rg9A 383 3.78e+01 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 2fbeA 201 3.81e+01 2ffsA 157 3.82e+01 1t3tA 1303 3.90e+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 1ift 263 3.92e+01 1mrj d.165.1.1 42211 1ti6A 875 3.92e+01 b.52.2.2,c.81.1.1 106974,106975 1uoyA 64 3.96e+01 g.3.19.1 99709 1dkzA 219 3.99e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1onxA 390 4.01e+01 b.92.1.7,c.1.9.13 87176,87177 1x23A 155 4.03e+01 1f1uA 323 4.05e+01 d.32.1.3,d.32.1.3 83200,83201 2cn3A 737 4.07e+01 1vkdA 338 4.17e+01 b.67.2.4 108644 1pl8A 356 4.18e+01 b.35.1.2,c.2.1.1 94878,94879 2aiqA 231 4.20e+01 1iz0A 302 4.29e+01 b.35.1.2,c.2.1.1 83821,83822 1w2xA 758 4.29e+01 c.14.1.4,c.14.1.4 109134,109135 1gl4B 98 4.31e+01 b.1.1.4 65288 2aq5A 402 4.35e+01 1ug8A 87 4.39e+01 d.68.7.1 107825 1kexA 155 4.40e+01 b.18.1.2 77350 1c3hA 137 4.41e+01 b.22.1.1 90405 1avk 638 4.41e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24410,38047,38048 1ro5A 201 4.42e+01 d.108.1.3 105023 1pieA 419 4.45e+01 d.14.1.5,d.58.26.7 94706,94707 1frpA 335 4.45e+01 1frpA e.7.1.1 42875 1sacA 204 4.48e+01 1sacA b.29.1.5 24237 1l8bA 190 4.53e+01 d.86.1.1 73683 1o50A 157 4.54e+01 d.37.1.1,d.37.1.1 92478,92479 2bhuA 602 4.56e+01 1q47A 495 4.56e+01 b.69.12.1 104532 1lk2A 274 4.57e+01 b.1.1.2,d.19.1.1 91056,91057 1cv8 174 4.59e+01 1cv8 d.3.1.1 37089 1db3A 372 4.63e+01 1db3A c.2.1.2 29813 1ui7A 638 4.64e+01 b.30.2.1,d.17.2.1,d.17.2.1 99413,99414,99415 1h8eD 482 4.73e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 1oqkA 97 4.74e+01 b.137.1.1 93419 1s72W 154 4.76e+01 d.59.1.1 105342 1jj2V 154 4.76e+01 1ffkT d.59.1.1 63107 1g55A 343 4.86e+01 1g55A c.66.1.26 34247 1wr7A 41 5.00e+01 1iqyA 638 5.06e+01 b.30.2.1,d.17.2.1,d.17.2.1 76763,76764,76765 1i4uA 181 5.07e+01 b.60.1.1 61732 2al3A 90 5.11e+01 1zzcA 198 5.11e+01 1ws0A 156 5.12e+01 2ixiA 184 5.13e+01 1g72A 573 5.14e+01 4aahA b.70.1.1 27680 1zbfA 142 5.15e+01 1q1uA 144 5.18e+01 b.42.1.1 95608 2h4vA 320 5.29e+01 1uy4A 145 5.29e+01 b.18.1.10 108131 3pcgM 238 5.34e+01 3pchM b.3.6.1 22742 1te6A 439 5.35e+01 c.1.11.1,d.54.1.1 106797,106798 1v2bA 177 5.38e+01 d.107.1.2 108279 1vmhA 144 5.38e+01 1zbpA 273 5.44e+01 2madH 373 5.46e+01 2bbkH b.69.2.1 27639 1pk6A 133 5.47e+01 b.22.1.1 94801 2arcA 164 5.53e+01 2arcA b.82.4.1 28148 1oalA 151 5.53e+01 b.1.8.1 86739 1l3lA 234 5.53e+01 a.4.6.2,d.110.5.1 73541,73542 1prs 173 5.55e+01 1prs b.11.1.1,b.11.1.1 23625,23626 1eso 154 5.56e+01 1yaiA b.1.8.1 22293 1k6wA 426 5.59e+01 b.92.1.2,c.1.9.5 68236,68237 1u04A 771 5.59e+01 b.34.14.1,c.55.3.10 107539,107540 2ftwA 521 5.62e+01 2cdcA 366 5.63e+01 1xewY 172 5.63e+01 1w4vA 119 5.64e+01 1ex2A 189 5.64e+01 1ex2A c.51.4.2 33225 2b4wA 315 5.66e+01 1h6lA 353 5.67e+01 b.68.3.1 60687 1jlnA 297 5.70e+01 1pty c.45.1.2 63172 1vq2A 193 5.74e+01 1sgzA 389 5.77e+01 b.50.1.2 98872 1wz4A 23 5.78e+01 1m1fA 110 5.81e+01 b.34.6.2 78401 1r45A 204 5.83e+01 1uvzA 119 5.84e+01 1v9yA 167 5.85e+01 d.110.3.2 108454 2d93A 134 5.85e+01 1ufkA 254 5.89e+01 c.66.1.39 99340 1qfoA 119 5.91e+01 1qfoA b.1.1.1 19708 2gjdA 157 5.91e+01 1cruA 454 5.94e+01 1c9uA b.68.2.1 27617 2fdbM 164 6.08e+01 1zc1A 208 6.12e+01 1jbbA 153 6.13e+01 1u9aA d.20.1.1 62842 1wosA 364 6.15e+01 b.44.2.1,d.250.1.1 109468,109469 1itcA 516 6.18e+01 b.3.1.1,c.1.8.1 83705,83706 1xuvA 178 6.25e+01 1wstA 417 6.26e+01 1hv9A 456 6.28e+01 1fwyA b.81.1.4,c.68.1.5 28060,34518 1yopA 83 6.30e+01 1ad2 228 6.32e+01 1ad2 e.24.1.1 43353 1u3oA 82 6.33e+01 1xk5A 204 6.35e+01 1icfI 65 6.35e+01 1icfI g.28.1.1 44958 1tuhA 156 6.36e+01 d.17.4.11 107345 2ac0A 200 6.36e+01 1kdgA 546 6.39e+01 c.3.1.2,d.16.1.1 77337,77338 1ej1A 190 6.39e+01 1ejhA d.86.1.1 40144 1frrA 95 6.41e+01 1awd d.15.4.1 37674 2fvhA 120 6.42e+01 1lkdA 297 6.42e+01 d.32.1.3,d.32.1.3 78059,78060 1nuyA 337 6.46e+01 e.7.1.1 86213 1mkkA 96 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