# 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 1xngA 268 2.41e-02 1qwdA 177 1.57e-01 b.60.1.1 96471 2a2pA 129 2.42e-01 2cokA 113 3.13e-01 1gpmA 525 3.39e-01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1gmyA 261 3.88e-01 d.3.1.1 76236 1tif 78 4.20e-01 1tif d.15.8.1 37836 1p5dX 463 1.06e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1pmzA 86 1.16e+00 a.39.1.10 104195 1v8hA 107 1.17e+00 2gcuA 245 1.23e+00 2ew2A 316 1.46e+00 1wosA 364 1.54e+00 b.44.2.1,d.250.1.1 109468,109469 1ut7A 171 2.17e+00 b.143.1.1 99906 1xcbA 211 2.18e+00 a.4.5.38,c.2.1.12 109552,109553 1o4sA 389 2.24e+00 c.67.1.1 86620 1wdcC 156 2.28e+00 1wdcC a.39.1.5 17317 1zg2A 107 2.79e+00 1ra0A 430 2.97e+00 1xewX 182 3.01e+00 1rewC 135 3.01e+00 g.7.1.3 97336 1s3cA 141 3.03e+00 1tzyD 103 3.23e+00 a.22.1.1 107533 1iloA 77 3.28e+00 c.47.1.1 66205 1qtnA 164 3.31e+00 1pauA c.17.1.1 30999 1kqpA 271 3.43e+00 c.26.2.1 72883 1fxoA 293 3.47e+00 1g0rA c.68.1.6 34524 1u6zA 513 3.64e+00 1widA 130 3.68e+00 1r26A 125 3.68e+00 c.47.1.1 96847 1k3iA 656 3.93e+00 b.1.18.2,b.18.1.1,b.69.1.1 68113,68114,68115 1whzA 70 3.93e+00 1rypI 222 3.98e+00 d.153.1.4 41877 1wy5A 317 4.07e+00 1sglA 209 4.26e+00 d.124.1.1 105536 1zljA 78 4.68e+00 1vetA 124 4.75e+00 d.110.7.1 108553 1zo0A 126 4.82e+00 1lfpA 249 5.34e+00 e.39.1.1 73885 2blnA 305 5.51e+00 1ssxA 198 5.92e+00 b.47.1.1 98978 1g5cA 170 6.06e+00 1g5cA c.53.2.1 60264 1cdcA 99 6.28e+00 1cdcA b.1.1.1 19746 1sh0A 510 6.37e+00 e.8.1.4 98876 1jl0A 334 7.14e+00 1jenA d.156.1.1 63155 1qmeA 702 7.16e+00 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 2aotA 292 7.26e+00 1d5tA 433 7.37e+00 1gnd c.3.1.3,d.16.1.6 30422,37986 1exrA 148 7.43e+00 1cll a.39.1.5 17299 1meoA 209 7.78e+00 c.65.1.1 79035 1odkA 235 7.87e+00 c.56.2.1 86863 1ddgA 374 8.03e+00 1amoA b.43.4.1,c.25.1.4 25671,31559 1m6yA 301 8.51e+00 a.60.13.1,c.66.1.23 78716,78717 1ycoA 279 8.92e+00 2gvhA 288 9.10e+00 1uu1A 335 9.18e+00 c.67.1.1 99993 1a64A 97 9.19e+00 1cdcA b.1.1.1 19750 1hjrA 158 9.19e+00 1hjrA c.55.3.6 33727 1lvwA 295 9.28e+00 c.68.1.6 84723 1q8iA 783 9.45e+00 c.55.3.5,e.8.1.1 96208,96209 2fp4B 395 9.73e+00 1ecfA 504 9.98e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 2g76A 335 1.01e+01 1o50A 157 1.05e+01 d.37.1.1,d.37.1.1 92478,92479 1k07A 263 1.05e+01 d.157.1.1 77218 1ud9A 245 1.07e+01 d.131.1.2,d.131.1.2 107768,107769 2c30A 321 1.10e+01 1kwgA 645 1.13e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 2fd6U 276 1.13e+01 1l1eA 287 1.14e+01 c.66.1.18 73454 2g5dA 422 1.17e+01 1chmA 401 1.18e+01 1chmA c.55.2.1,d.127.1.1 33545,41142 2f3yA 148 1.19e+01 1xl3C 92 1.26e+01 1vddA 228 1.27e+01 e.49.1.1 108519 1xi1A 575 1.28e+01 1wr2A 238 1.29e+01 1w4vA 119 1.32e+01 1xer 103 1.32e+01 1xer d.58.1.3 38990 1l0bA 229 1.33e+01 c.15.1.3,c.15.1.3 73391,73392 1qw1A 121 1.36e+01 1gxuA 91 1.37e+01 d.58.10.1 76378 1h5rA 293 1.37e+01 c.68.1.6 65623 2absA 383 1.40e+01 1x0pA 143 1.40e+01 1wdtA 665 1.42e+01 1v5vA 401 1.45e+01 1nofA 383 1.46e+01 b.71.1.2,c.1.8.3 92020,92021 1sb2A 133 1.47e+01 1h72C 296 1.50e+01 d.14.1.5,d.58.26.1 60712,60713 1bb8 71 1.50e+01 2bb8 d.10.1.1 37478 1qo3C 137 1.50e+01 1qo3C d.169.1.1 42350 1y1oA 203 1.50e+01 1sur 215 1.53e+01 1sur c.26.2.2 31620 1lj5A 379 1.53e+01 e.1.1.1 73928 2bl0B 145 1.59e+01 1tjyA 316 1.59e+01 c.93.1.1 107062 2bcmA 165 1.60e+01 1knmA 130 1.64e+01 b.42.2.1 72781 1i9gA 280 1.65e+01 c.66.1.13 62090 1lucB 324 1.66e+01 1lucA c.1.16.1 29548 1pme 380 1.67e+01 1hcl d.144.1.7 41653 1yemA 179 1.69e+01 1avsA 90 1.71e+01 1cll a.39.1.5 17226 2gfaA 119 1.72e+01 1dqeA 137 1.73e+01 1dqeA a.39.2.1 17388 1wy2A 351 1.73e+01 1wu7A 434 1.75e+01 1x1rA 178 1.77e+01 1t7lA 766 1.82e+01 1el5A 389 1.82e+01 1b3mA c.3.1.2,d.16.1.3 30369,37937 2d28C 149 1.83e+01 1rifA 282 1.83e+01 c.37.1.23 97507 1juhA 350 1.83e+01 b.82.1.5 71884 2bl0C 142 1.85e+01 2gu3A 136 1.89e+01 1y5oA 115 1.91e+01 2d13A 227 1.92e+01 1cb8A 678 1.94e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1xzoA 174 1.97e+01 1j8mF 297 1.97e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1e87A 118 1.98e+01 1b6e d.169.1.1 42327 1p1mA 406 1.98e+01 b.92.1.4,c.1.9.9 87696,87697 1rkqA 282 2.02e+01 c.108.1.10 97621 1xtmA 175 2.02e+01 1dkzA 219 2.03e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1oxxK 353 2.05e+01 b.40.6.3,c.37.1.12 93715,93716 1lrzA 426 2.07e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1ifrA 121 2.08e+01 b.1.16.1 71203 1erw 105 2.13e+01 1erv c.47.1.1 32745 1zdyA 307 2.13e+01 1rhs 296 2.14e+01 1rhs c.46.1.2,c.46.1.2 32703,32704 1iow 306 2.15e+01 1iow c.30.1.2,d.142.1.1 31713,41481 1k9uA 78 2.18e+01 a.39.1.10 84348 1w85I 49 2.20e+01 1wlsA 328 2.20e+01 1kte 105 2.21e+01 1kte c.47.1.1 32771 1pbjA 125 2.23e+01 d.37.1.1,d.37.1.1 94414,94415 1nnxA 109 2.26e+01 b.40.10.1 92013 1yvcA 70 2.31e+01 1wlyA 333 2.33e+01 1cqqA 180 2.33e+01 1cqqA b.47.1.4 26422 2f9lA 199 2.36e+01 1wdcB 156 2.37e+01 1wdcB a.39.1.5 17302 1fjgP 88 2.41e+01 1emwA d.27.1.1 38444 1g0sA 209 2.42e+01 1g0sA d.113.1.1 60187 1zczA 464 2.47e+01 1g8mA 593 2.48e+01 1g8mA c.24.1.3,c.97.2.1 60371,60372 1erv 105 2.52e+01 1erv c.47.1.1 32743 1rz4A 226 2.54e+01 a.4.5.53,a.118.1.18 105131,105132 1mbmA 198 2.55e+01 b.47.1.3 78916 1oeyA 83 2.55e+01 d.15.2.2 92800 1pyaB 228 2.63e+01 1pyaB 1w1oA 534 2.65e+01 d.58.32.4,d.145.1.1 109071,109072 1vrmA 325 2.65e+01 1oo0A 147 2.67e+01 d.232.1.1 87182 2bu3A 254 2.69e+01 1wucA 250 2.72e+01 1o4wA 147 2.74e+01 c.120.1.1 86629 1xauA 122 2.75e+01 1hgxA 183 2.76e+01 1tc1A c.61.1.1 34027 1pguA 615 2.77e+01 b.69.4.1,b.69.4.1 88069,88070 1o7iA 119 2.77e+01 b.40.4.3 86642 1u24A 337 2.77e+01 1st9A 143 2.81e+01 c.47.1.10 98987 1ugnA 198 2.82e+01 b.1.1.4,b.1.1.4 107828,107829 1f89A 291 2.85e+01 d.160.1.1 64988 1jkeA 145 2.86e+01 c.110.1.1 66791 1n4kA 381 2.87e+01 a.118.22.1,b.42.6.1 79992,79993 1iueA 98 2.91e+01 d.15.4.1 90697 1vfgA 390 2.96e+01 a.173.1.1,d.218.1.4 108570,108571 1j7gA 144 2.96e+01 c.110.1.1 84130 1kk8B 139 2.98e+01 a.39.1.5 77430 1qu9A 128 2.99e+01 1qu9A d.79.1.1 39755 1k32A 1045 3.03e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1zkdA 387 3.03e+01 2ffyA 358 3.04e+01 2aioA 269 3.06e+01 1efyA 350 3.06e+01 1a26 a.41.1.1,d.166.1.2 17413,42275 1xvwA 160 3.08e+01 1hw5A 210 3.12e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 1x0vA 354 3.14e+01 1wfxA 186 3.15e+01 1jbeA 128 3.24e+01 3chy c.23.1.1 62845 1qsgA 265 3.24e+01 1eny c.2.1.2 29935 1cqmA 101 3.29e+01 1ris d.58.14.1 39321 1o9wA 177 3.38e+01 b.2.3.5 86713 1ttwA 138 3.38e+01 d.198.1.1 107308 1xfrA 128 3.39e+01 1z2lA 423 3.40e+01 2cc0A 195 3.43e+01 2cvdA 198 3.47e+01 1wn5A 130 3.49e+01 1k1eA 180 3.50e+01 c.108.1.5 67995 1iyeA 309 3.53e+01 e.17.1.1 83786 1u69A 163 3.55e+01 d.32.1.7 107699 2a6hC 1119 3.57e+01 2cyeA 133 3.58e+01 1atg 231 3.59e+01 1atg c.94.1.1 35834 1o6yA 299 3.63e+01 d.144.1.7 81106 1ws0A 156 3.71e+01 1gcyA 527 3.71e+01 1jdc b.71.1.1,c.1.8.1 27788,28775 1iyhA 198 3.75e+01 a.45.1.1,c.47.1.5 83790,83791 2coeA 120 3.77e+01 1m45A 148 3.77e+01 a.39.1.5 78598 1uwvA 433 3.79e+01 b.40.4.12,c.66.1.40 100128,100129 2fjbA 643 3.80e+01 2fug5 207 3.80e+01 1r7mA 235 3.82e+01 1rkd 309 3.83e+01 1rkd c.72.1.1 34928 1y7yA 74 3.83e+01 1ars 396 3.85e+01 1ajsA c.67.1.1 34287 2ca6A 386 3.86e+01 1j58A 385 3.87e+01 b.82.1.2 71531 2fl4A 149 3.92e+01 1jidA 128 3.94e+01 d.201.1.1 66735 1lcyA 325 3.96e+01 b.36.1.4,b.47.1.1 73834,73835 1vr9A 213 4.00e+01 1wd5A 208 4.04e+01 2fomB 185 4.05e+01 1om1A 332 4.06e+01 d.144.1.7 93347 1f1eA 154 4.13e+01 a.22.1.2 64927 1mkyA 439 4.14e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 2c46A 241 4.14e+01 2a1vA 144 4.15e+01 1vixA 420 4.18e+01 c.56.5.4,d.58.19.1 100777,100778 1rtqA 299 4.20e+01 c.56.5.4 97819 1oh4A 179 4.21e+01 b.18.1.18 92978 2f9sA 151 4.25e+01 1jnrA 643 4.26e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1qzzA 374 4.27e+01 a.4.5.29,c.66.1.12 96719,96720 1g8iA 190 4.30e+01 1rec a.39.1.5 60363 2flsA 132 4.37e+01 2axcA 264 4.38e+01 2fokA 579 4.38e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16131,16132,16133,33323 1kxvC 121 4.43e+01 b.1.1.1 73190 1t4nA 94 4.44e+01 d.50.1.1 106424 2fuvA 549 4.45e+01 2a6cA 83 4.45e+01 1wmiB 67 4.46e+01 1kpf 126 4.47e+01 1kpf d.13.1.1 37507 1p1lA 102 4.49e+01 d.58.5.2 87695 1gl4A 285 4.50e+01 d.22.1.2,g.3.11.5 65286,65287 1a4pA 96 4.52e+01 1b4cA a.39.1.2 17176 1rcwA 231 4.56e+01 a.132.1.4 97299 1mpgA 282 4.59e+01 1mpgA a.96.1.3,d.129.1.2 18747,41296 2cvlA 124 4.64e+01 2a2lA 145 4.67e+01 1rq6A 62 4.68e+01 1m32A 366 4.69e+01 c.67.1.3 78508 1z5yE 149 4.70e+01 1p4fA 293 4.73e+01 d.144.1.7 104063 1a7s 221 4.73e+01 1a7s b.47.1.2 26284 2g6bA 180 4.73e+01 2fftA 84 4.74e+01 1neyA 247 4.75e+01 c.1.1.1 80449 1wxiA 275 4.76e+01 1yx4A 132 4.76e+01 1lgpA 116 4.78e+01 b.26.1.2 73890 2a7oA 112 4.81e+01 2b7aA 293 4.82e+01 1wqsA 173 4.82e+01 1dm5A 315 4.86e+01 1avc a.65.1.1 18186 1vhcA 224 4.86e+01 c.1.10.1 100661 2fp7B 172 4.87e+01 1tzjA 338 4.88e+01 1q79A 514 4.88e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1ub3A 220 4.89e+01 c.1.10.1 88395 2f91B 35 4.89e+01 1ok0A 74 4.91e+01 b.5.1.1 93191 1tfe 145 4.92e+01 1tfe d.43.1.1 38680 1m4vA 204 4.98e+01 b.40.2.2,d.15.6.1 74459,74460 1m93C 41 4.99e+01 1bu6O 501 5.00e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1xkzA 255 5.04e+01 1tafB 70 5.07e+01 1tafB a.22.1.3 16482 2ge3A 170 5.08e+01 1omhA 293 5.13e+01 d.89.1.5 93348 1d1qA 161 5.20e+01 1dg9A c.44.1.1 32642 1kmoA 774 5.23e+01 f.4.3.3 72753 2a13A 166 5.27e+01 1z3eB 73 5.28e+01 1p0zA 131 5.29e+01 d.110.6.1 93882 2bszA 278 5.33e+01 2f57A 317 5.33e+01 1x0rA 249 5.37e+01 1jakA 512 5.37e+01 c.1.8.6,d.92.2.1 66472,66473 1dcfA 136 5.41e+01 1dcfA c.23.1.2 31124 1s5jA 847 5.45e+01 2al1A 436 5.45e+01 1eq9A 222 5.46e+01 5ptp b.47.1.2 26068 1bkb 136 5.47e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 1p9bA 442 5.56e+01 c.37.1.10 94385 1iybA 208 5.60e+01 d.124.1.1 90720 1fmtA 314 5.61e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 2d1uA 104 5.66e+01 1faaA 124 5.69e+01 1erv c.47.1.1 32738 2bxxA 134 5.71e+01 1xhkA 187 5.74e+01 2fbwA 621 5.76e+01 1jalA 363 5.76e+01 c.37.1.8,d.15.10.2 84138,84139 2bhuA 602 5.77e+01 1suuA 312 5.77e+01 b.68.10.1 99006 1vhoA 346 5.78e+01 b.49.3.1,c.56.5.4 100694,100695 1mvuB 121 5.80e+01 b.1.1.1 91475 1rgzA 363 5.85e+01 e.3.1.1 97457 1sheA 103 5.85e+01 d.274.1.1 105551 1zkpA 268 5.86e+01 1txdA 385 5.90e+01 a.87.1.1,b.55.1.1 107422,107423 1clc 639 5.90e+01 1clc a.102.1.2,b.1.18.2 18835,21872 1h05A 146 5.91e+01 c.23.13.1 76433 2b0tA 738 5.93e+01 1zmoA 244 5.93e+01 1nw3A 416 5.96e+01 c.66.1.31 86288 1gz8A 299 5.96e+01 d.144.1.7 83405 1jqlB 140 5.99e+01 c.37.1.20 63234 2acaA 189 6.04e+01 1wojA 214 6.06e+01 1vhyA 257 6.15e+01 b.122.1.2,c.116.1.5 100714,100715 1k1vA 41 6.19e+01 a.37.1.1 71999 1ka1A 357 6.23e+01 e.7.1.1 68369 1zk5A 176 6.26e+01 1i4uA 181 6.28e+01 b.60.1.1 61732 1jogA 146 6.30e+01 a.24.16.2 77142 1hkfA 122 6.31e+01 b.1.1.1 83553 1jdlA 121 6.32e+01 a.3.1.1 66557 2f5tX 233 6.40e+01 2bbeA 108 6.40e+01 1i7nA 309 6.40e+01 c.30.1.5,d.142.1.3 83681,83682 1vqoR 155 6.41e+01 1ek0A 170 6.41e+01 1ctqA c.37.1.8 32076 2al2A 436 6.43e+01 1yb3A 175 6.44e+01 2basA 431 6.47e+01 2f3nA 76 6.48e+01 1gwuA 309 6.48e+01 a.93.1.1 83351 1iq4A 179 6.50e+01 1iq4A d.77.1.1 62641 1ewnA 219 6.51e+01 1bnkA b.46.1.2 25762 1je0A 236 6.54e+01 c.56.2.1 66581 1m15A 357 6.58e+01 a.83.1.1,d.128.1.2 78368,78369 1m4rA 151 6.58e+01 a.26.1.3 84799 1mdbA 539 6.59e+01 e.23.1.1 79008 1y81A 138 6.60e+01 1d8bA 81 6.61e+01 1d8bA a.60.8.1 18094 1sx5A 244 6.63e+01 c.52.1.2 99023 1dzfA 215 6.66e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1dyr 206 6.67e+01 1aoeA c.71.1.1 34916 1lfdA 87 6.68e+01 1lfdA d.15.1.5 37622 1x8qA 184 6.72e+01 1s6lA 212 6.73e+01 1s4iA 175 6.75e+01 1dceB 331 6.78e+01 1dceB a.102.4.3 18872 2a4aA 281 6.79e+01 1vp2A 208 6.81e+01 3gcb 470 6.82e+01 3gcb d.3.1.1 37032 1w7jB 151 6.84e+01 1ni9A 338 6.86e+01 e.7.1.2 85739 1dkiA 371 6.88e+01 1dkiA d.3.1.1 37090 2gf9A 189 6.90e+01 2bw0A 329 6.92e+01 1zrjA 50 6.94e+01 1s68A 249 6.98e+01 d.142.2.4 98591 2fp3A 316 6.98e+01 2cbp 96 6.98e+01 2cbp b.6.1.1 22895 1gngX 39 7.08e+01 1s3eA 520 7.08e+01 c.3.1.2,d.16.1.5 98426,98427 1fp0A 88 7.11e+01 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119 8.60e+01 1b2pA b.78.1.1 27998 1qh5A 260 8.66e+01 1qh5A d.157.1.2 42057 1ofdA 1520 8.66e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 2a1hA 365 8.68e+01 2erxA 172 8.71e+01 1r5tA 142 8.73e+01 c.97.1.1 104812 2fyxA 143 8.78e+01 1iukA 140 8.82e+01 c.2.1.8 83712 1r45A 204 8.84e+01 5pal 109 8.86e+01 1a75A a.39.1.4 17215 1i58A 189 8.91e+01 1b3qA d.122.1.3 61773 2ghpA 292 8.91e+01