# List of top-scoring protein chains for t04-100-30-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 1a48 306 2.86e-03 1a48 1obdA 306 3.41e-03 d.143.1.1 86767 2cnqA 306 4.84e-03 d.143.1.1 130646 3proC 166 2.26e-02 3proC d.52.1.1,d.52.1.1 38812,38813 1v7cA 351 4.52e-02 c.79.1.1 100446 2gu3A 136 7.27e-02 1ykdA 398 8.72e-02 1t6sA 162 8.92e-02 a.4.5.60,a.4.5.60 112271,112272 2gnqA 336 1.16e-01 1zxzA 197 1.33e-01 2a2lA 145 1.59e-01 d.110.9.1 126035 2nr1 27 1.97e-01 1w53A 84 2.10e-01 a.186.1.2 109175 1v5xA 203 2.12e-01 c.1.2.4 100377 1s6cA 183 2.16e-01 a.39.1.5 98594 1jnyA 435 2.91e-01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1j8uA 325 2.97e-01 d.178.1.1 71611 2c2aA 258 2.99e-01 a.30.2.1,d.122.1.3 129662,129663 1914 232 3.10e-01 1914 4pah 308 3.40e-01 4pah 1o8xA 146 3.61e-01 c.47.1.10 86681 1ohtA 215 3.67e-01 d.118.1.1 87036 1s1eA 224 4.34e-01 a.39.1.5 112007 1nqkA 381 4.40e-01 c.1.16.4 92050 1qk8A 146 4.43e-01 1ewxA c.47.1.10 33061 1l0qA 391 4.53e-01 b.1.3.1,b.69.2.3 77644,77645 1kblA 873 4.68e-01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 2bwqA 129 4.69e-01 b.7.1.2 129380 1zy1B 197 4.78e-01 1yqtA 538 5.24e-01 1a9xA 1058 5.26e-01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1avbA 226 5.35e-01 1led b.29.1.1 24158 1cs0A 1073 5.38e-01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1k2yX 463 6.28e-01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1ob8A 135 6.79e-01 c.52.1.18 111627 1s5jA 847 6.79e-01 c.55.3.5,e.8.1.1 112040,112041 1dkzA 219 6.90e-01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1dhkB 223 6.90e-01 1led b.29.1.1 24157 2igd 61 6.98e-01 2igd 1i1iP 681 7.11e-01 1i1iP d.92.1.5 40297 2ax3A 502 7.37e-01 c.72.1.4,c.104.1.1 127477,127478 1aqcA 172 7.58e-01 1x11A b.55.1.2 26983 1go4A 205 7.71e-01 d.135.1.1 70292 1p5dX 463 8.33e-01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1rypK 198 8.36e-01 d.153.1.4 41879 5csmA 256 8.91e-01 5csmA a.130.1.2 19494 1hbkA 94 8.98e-01 1aca a.11.1.1 60887 2ex3B 264 9.09e-01 a.263.1.1 132500 1i2sA 282 9.32e-01 e.3.1.1 71104 1o58A 303 9.78e-01 c.79.1.1 92491 1d4oA 184 1.04e+00 1d4oA c.31.1.4 31748 2bfdA 400 1.06e+00 1ls1A 295 1.06e+00 a.24.13.1,c.37.1.10 78170,78171 1x7yA 400 1.07e+00 c.36.1.11 114944 1az9 457 1.18e+00 1az9 1bebA 162 1.21e+00 1bebA b.60.1.1 27115 1ovnA 248 1.23e+00 a.71.1.1,c.47.1.7 93602,93603 1gzcA 239 1.25e+00 b.29.1.1 70803 1olsA 400 1.25e+00 c.36.1.11 93331 2gi9A 56 1.31e+00 1v1rA 400 1.43e+00 c.36.1.11 108272 1ud0A 113 1.45e+00 a.8.4.1 99198 2fflA 756 1.48e+00 2c6cA 707 1.50e+00 a.48.2.1,c.8.4.1,c.56.5.5 129989,129990,129991 2erfA 209 1.54e+00 b.29.1.4 132287 1wq3A 322 1.54e+00 2cxcA 144 1.61e+00 1fit 147 1.90e+00 1fit 1o70A 324 1.93e+00 b.118.1.1,b.118.1.1 81115,81116 1mkeA 152 1.94e+00 b.55.1.4 79231 1u04A 771 2.12e+00 b.34.14.1,c.55.3.10 107539,107540 1pvgA 418 2.19e+00 d.14.1.3,d.122.1.2 95161,95162 2cfuA 658 2.28e+00 1n6zA 105 2.38e+00 d.263.1.1 85369 1xqoA 256 2.41e+00 a.96.1.6 115853 1zchA 255 2.43e+00 d.90.1.1 124908 2fw2A 260 2.43e+00 c.14.1.3 134231 1u00A 227 2.45e+00 a.8.4.1,b.130.1.1 112900,112901 2ng1 293 2.52e+00 1ng1 1j6qA 136 2.86e+00 b.40.9.1 77091 1t95A 240 2.91e+00 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1vr6A 350 2.96e+00 c.1.10.4 120439 1z7wA 322 2.99e+00 c.79.1.1 124674 1u84A 90 3.03e+00 a.230.1.1 113114 1tr0A 108 3.10e+00 d.58.4.4 107261 2g0wA 296 3.13e+00 c.1.15.4 134503 1v9dA 340 3.21e+00 a.207.1.1 100535 1k47A 337 3.39e+00 d.14.1.5,d.58.26.4 72040,72041 1ash 150 3.40e+00 1ash 1in0A 163 3.45e+00 d.58.49.1,d.58.49.1 83694,83695 1kugA 203 3.45e+00 d.92.1.9 73008 1ospO 257 3.50e+00 1ospO b.76.1.1 27971 1rypA 243 3.50e+00 1pmaA d.153.1.4 41932 1dq3A 454 3.62e+00 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1plq 258 3.74e+00 1plq 1ub4A 110 3.82e+00 b.34.6.2 88399 1fcjA 322 3.88e+00 1oasA c.79.1.1 35289 1i50I 122 4.13e+00 g.41.3.1,g.41.3.1 61762,61763 1adoA 363 4.24e+00 1fbaA c.1.10.1 29124 2bbkH 355 4.24e+00 2bbkH b.69.2.1 27634 1k0wA 231 4.35e+00 c.74.1.1 77220 1twfI 122 4.40e+00 g.41.3.1,g.41.3.1 112733,112734 1zaiA 363 4.43e+00 c.1.10.1 124828 1w96A 554 4.43e+00 b.84.2.1,c.30.1.1,d.142.1.2 114397,114398,114399 1g0uG 252 4.44e+00 d.153.1.4 41952 1kufA 203 4.63e+00 d.92.1.9 73007 1ykuA 136 4.65e+00 1k1xA 659 4.67e+00 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1zatA 250 4.68e+00 b.160.1.1,d.335.1.1 124845,124846 1zq1A 438 4.83e+00 b.38.3.1,c.88.1.1 125489,125490 1bazA 53 4.94e+00 1bazA a.43.1.1 17421 1q4rA 112 5.04e+00 d.58.4.4 95823 1jovA 270 5.04e+00 b.30.5.7 84192 1dgwY 93 5.29e+00 1caxB 1wy0A 342 5.33e+00 4blmA 265 5.36e+00 1btl e.3.1.1 42721 1xd3A 230 5.44e+00 d.3.1.6 115145 1obbA 480 5.46e+00 c.2.1.5,d.162.1.2 86760,86761 1i0rA 169 5.56e+00 1i0rA b.45.1.2 61489 1i0sA 169 5.79e+00 1i0rA b.45.1.2 61491 1sviA 195 5.96e+00 c.37.1.8 106048 1at0 145 5.98e+00 1at0 1iazA 179 6.05e+00 1iazA b.97.1.1 62131 1pguA 615 6.05e+00 b.69.4.1,b.69.4.1 88069,88070 1xccA 220 6.23e+00 c.47.1.10 115113 1ylxA 103 6.23e+00 d.82.5.1 123677 1iznB 277 6.24e+00 e.43.1.2 83848 1dxsA 80 6.35e+00 1cokA a.60.1.2 17944 1erjA 393 6.46e+00 1erjA b.69.4.1 27660 2erbA 125 6.46e+00 1kinA 366 6.49e+00 1mjhA 162 6.64e+00 1mjhA c.26.2.4 31639 1wgeA 83 6.78e+00 g.41.17.1 120972 1v5tA 90 6.81e+00 d.15.1.1 108385 2agyA 361 6.88e+00 1t5yA 190 6.93e+00 b.122.1.1,d.17.6.3 106495,106496 1fp1D 372 6.96e+00 1fpqA a.4.5.29,c.66.1.12 59939,59940 1ly1A 181 7.08e+00 c.37.1.1 74334 2cyjA 118 7.10e+00 c.103.1.1 131026 1ywqA 200 7.18e+00 d.90.1.1 124162 1ym5A 300 7.33e+00 1pot 325 7.43e+00 1pot 2fmpA 335 7.45e+00 a.60.6.1,a.60.12.1,d.218.1.2 133786,133787,133788 1mu5A 471 7.61e+00 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1qhiA 366 7.68e+00 1qhiA c.37.1.1 31860 1z5bA 469 7.70e+00 a.156.1.3,d.14.1.3,d.122.1.2 124464,124465,124466 1atlA 202 7.77e+00 1atlA d.92.1.9 40322 1rwiA 270 7.93e+00 b.68.9.1 97987 1c44A 123 7.98e+00 1qndA d.106.1.1 40795 1zhhB 242 8.03e+00 1h5wA 309 8.07e+00 e.27.1.1 65635 1tv9A 335 8.12e+00 a.60.6.1,a.60.12.1,d.218.1.2 112675,112676,112677 1ijgA 309 8.16e+00 1fouA e.27.1.1 62493 1p9qC 256 8.25e+00 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1sxrA 183 8.28e+00 d.118.1.1 106101 1z7yA 322 8.34e+00 c.79.1.1 124679 1dik 874 8.35e+00 1dik 1bpyA 335 8.37e+00 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 17980,75819,75820 1e2kA 331 8.38e+00 1qhiA c.37.1.1 31854 1tuaA 191 8.39e+00 d.51.1.1,d.51.1.1 107321,107322 1mc0A 368 8.48e+00 d.110.2.1,d.110.2.1 78937,78938 1pprM 312 8.54e+00 1pprM a.131.1.1,a.131.1.1 19502,19503 1g6aA 271 8.64e+00 1btl e.3.1.1 42704 1d0cA 444 8.65e+00 d.174.1.1 64769 1wznA 252 8.75e+00 c.66.1.43 121525 1rzmA 338 8.81e+00 c.1.10.4 105137 2bwvA 440 8.88e+00 c.55.2.1,d.127.1.1 129387,129388 2fbmA 291 8.89e+00 c.14.1.3 133251 1oz9A 150 9.14e+00 d.92.1.15 93808 1gxrA 337 9.61e+00 b.69.4.1 70722 1ax0 239 9.74e+00 1led 1vmbA 140 9.88e+00 d.58.14.1 113672 1uv7A 110 9.94e+00 d.67.4.1 100040 1o5zA 442 1.00e+01 c.59.1.2,c.72.2.2 92530,92531 1gwyA 175 1.00e+01 b.97.1.1 83356 2bvfA 459 1.01e+01 1yp1A 202 1.02e+01 2aq5A 402 1.02e+01 1qopB 396 1.02e+01 2tysB c.79.1.1 35270 1wr2A 238 1.04e+01 1ov9A 50 1.05e+01 a.155.1.1 93591 1dosA 358 1.05e+01 1dosA c.1.10.2 29175 1kutA 230 1.05e+01 d.143.1.1 73017 1o04A 500 1.06e+01 c.82.1.1 86508 1u9yA 284 1.09e+01 c.61.1.2,c.61.1.2 119655,119656 1uch 230 1.09e+01 1uch 1jvbA 347 1.10e+01 b.35.1.2,c.2.1.1 77181,77182 1phk 298 1.11e+01 1cdkA 1iq5B 27 1.13e+01 2b06A 155 1.16e+01 d.113.1.1 127624 2akoA 251 1.17e+01 c.73.1.3 126923 1j1iA 296 1.18e+01 c.69.1.10 83977 1bpoA 494 1.19e+01 1bpoA a.118.1.4,b.69.6.1 19143,27670 1i40A 175 1.20e+01 b.40.5.1 66024 1lfb 99 1.20e+01 1lfb 1oxxK 353 1.20e+01 b.40.6.3,c.37.1.12 93715,93716 1cdzA 96 1.22e+01 1cdzA c.15.1.1 30925 1yuwA 554 1.22e+01 b.130.1.1,c.55.1.1,c.55.1.1 124070,124071,124072 1obwA 175 1.23e+01 2prd b.40.5.1 25416 2fhi 147 1.24e+01 1fit 1vh5A 148 1.24e+01 d.38.1.5 100642 1ltqA 301 1.26e+01 c.108.1.9,c.37.1.1 78208,78209 1oxsC 353 1.26e+01 b.40.6.3,c.37.1.12 87519,87520 2c7hA 86 1.26e+01 1o22A 170 1.27e+01 d.238.1.1 86557 1r7mA 235 1.28e+01 d.95.2.1,d.95.2.1 111713,111714 1ykhB 132 1.28e+01 a.252.1.1 123519 1zbfA 142 1.30e+01 c.55.3.1 124850 1iuhA 198 1.31e+01 d.61.1.2 83711 1r2zA 274 1.31e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1vkmA 297 1.31e+01 c.138.1.1 108670 1vliA 385 1.31e+01 b.85.1.1,c.1.10.6 108830,108831 1qnxA 209 1.32e+01 1qnxA d.111.1.1 40914 1pzgA 331 1.32e+01 c.2.1.5,d.162.1.1 95425,95426 1g291 372 1.33e+01 1g291 1wlsA 328 1.33e+01 1uheA 97 1.33e+01 1pl8A 356 1.34e+01 b.35.1.2,c.2.1.1 94878,94879 1jc9A 269 1.34e+01 d.171.1.1 66490 2gk9A 426 1.34e+01 3erk 364 1.34e+01 1hcl 1t6t1 118 1.36e+01 2jdxA 385 1.39e+01 1jdw d.126.1.2 41139 1sh8A 154 1.39e+01 d.38.1.5 105549 1yaiA 151 1.41e+01 1yaiA b.1.8.1 22289 1lrwA 600 1.42e+01 b.70.1.1 91111 1nzjA 298 1.42e+01 c.26.1.1 92377 1utcA 363 1.42e+01 a.118.1.4,b.69.6.1 99914,99915 1wl9A 440 1.44e+01 c.55.2.1,d.127.1.1 120998,120999 2h4uA 145 1.48e+01 d.38.1.5 136082 1lgpA 116 1.49e+01 b.26.1.2 73890 1jcfA 344 1.50e+01 c.55.1.1,c.55.1.1 62878,62879 1p35A 299 1.54e+01 1p35A b.28.1.1 23925 1jayA 212 1.55e+01 c.2.1.6 66478 1wjtA 103 1.56e+01 a.48.3.1 114711 1usyA 275 1.57e+01 d.104.1.1 113422 1u7bA 261 1.57e+01 d.131.1.2,d.131.1.2 113083,113084 1ihuA 589 1.59e+01 c.37.1.10,c.37.1.10 62394,62395 1o7fA 469 1.60e+01 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 1zpsA 138 1.61e+01 b.168.1.1 125473 1tzjA 338 1.62e+01 c.79.1.1 112868 2bszA 278 1.63e+01 d.3.1.5 129131 1pcfA 66 1.65e+01 1pcfA d.18.1.1 38142 1nlfA 279 1.65e+01 c.37.1.11 85850 1zejA 293 1.66e+01 1oixA 191 1.67e+01 c.37.1.8 118710 1g61A 228 1.67e+01 1g61A d.126.1.1 41126 1h7sA 365 1.67e+01 d.14.1.3,d.122.1.2 65705,65706 1yhpA 212 1.68e+01 1dd9A 338 1.69e+01 1dd9A e.13.1.1 43254 1u0sA 86 1.70e+01 d.58.24.1 107565 2b33A 140 1.71e+01 d.79.1.1 127765 1fxrA 64 1.78e+01 1fxd d.58.1.4 38993 1vpkA 378 1.79e+01 d.131.1.1,d.131.1.1,d.131.1.1 113963,113964,113965 1jdw 423 1.79e+01 1jdw 2gqrA 237 1.81e+01 1xvwA 160 1.81e+01 c.47.1.10 122387 2fnjC 96 1.82e+01 d.42.1.1 133820 1yewA 382 1.82e+01 1nxqA 251 1.82e+01 c.2.1.2 86388 1s0aA 429 1.83e+01 c.67.1.4 98263 1o0pA 104 1.83e+01 d.58.7.1 86535 1qj5A 429 1.83e+01 1dtyA c.67.1.4 34493 1vkjA 285 1.84e+01 c.37.1.5 108666 1or7A 194 1.84e+01 a.4.13.2,a.177.1.1 87332,87333 2a3qA 170 1.85e+01 a.204.1.2 126092 1m6yA 301 1.87e+01 a.60.13.1,c.66.1.23 78716,78717 1f97A 212 1.87e+01 1f97A b.1.1.1,b.1.1.4 19763,21764 1txuA 273 1.87e+01 a.222.1.1 107439 1sflA 238 1.96e+01 c.1.10.1 112077 1skhA 30 2.01e+01 1n13B 113 2.01e+01 1mswD 883 2.02e+01 e.8.1.3 79427 1qsoA 149 2.02e+01 1qsmA d.108.1.1 40812 1w1kA 560 2.03e+01 d.58.32.1,d.145.1.1 109059,109060 1quqB 121 2.03e+01 1quqB b.40.4.3 25305 1po5A 476 2.08e+01 a.104.1.1 94963 2f4qA 346 2.08e+01 1zpwX 90 2.09e+01 d.58.58.1 125478 1iz6A 138 2.11e+01 b.34.5.2,b.40.4.5 76976,76977 1wvvA 265 2.11e+01 1wdjA 187 2.14e+01 c.52.1.27 114536 1x38A 602 2.14e+01 c.1.8.7,c.23.11.1 121655,121656 1wnaA 131 2.17e+01 d.319.1.1 121091 1vggA 161 2.19e+01 d.256.1.1 113647 1oglA 283 2.21e+01 a.204.1.1 92922 1lm8C 96 2.22e+01 d.42.1.1 74034 1cauB 184 2.24e+01 1caxB b.82.1.2 28103 1ex1A 605 2.25e+01 1ex1A c.1.8.7,c.23.11.1 29013,31347 1xmxA 385 2.25e+01 c.52.1.26 115568 1sfjA 238 2.25e+01 c.1.10.1 112075 1g8yA 279 2.26e+01 1g8yA c.37.1.11 32302 1l2tA 235 2.27e+01 c.37.1.12 73514 1x3zA 335 2.29e+01 d.3.1.4 121673 1l1zA 274 2.31e+01 a.156.1.2,b.113.1.1,g.39.1.8 75911,75912,75913 1rsy 152 2.32e+01 1rsy 1ppt 36 2.33e+01 1ppt 1c4zA 358 2.36e+01 1c4zA d.148.1.1 41766 1wmmA 145 2.38e+01 b.122.1.8 121049 1m0wA 491 2.45e+01 c.30.1.4,d.142.1.6 78363,78364 1f7sA 139 2.46e+01 1cof d.109.1.2 40857 1q7sA 117 2.46e+01 c.131.1.1 96055 1zk4A 251 2.47e+01 c.2.1.2 125176 2bf9A 36 2.48e+01 j.6.1.1 116717 1b7gO 340 2.48e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907 1dd3C 32 2.50e+01 1dd3C a.108.1.1 19033 1gwiA 411 2.50e+01 a.104.1.1 76364 1xfkA 336 2.51e+01 c.42.1.1 115264 1cy9A 264 2.52e+01 1ecl e.10.1.1 43236 1atiA 505 2.54e+01 1atiA c.51.1.1,d.104.1.1 33196,40745 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