# 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 1a58 177 6.94e-27 2cpl b.62.1.1 27495 1ihgA 370 7.13e-27 2cpl a.118.8.1,b.62.1.1 62380,62381 1dywA 173 8.43e-27 2cpl b.62.1.1 27505 1awsA 164 8.90e-27 2cpl b.62.1.1 27431 2bitX 165 1.02e-26 2cpl 165 1.26e-26 2cpl b.62.1.1 27420 1awqA 164 1.47e-26 2cpl b.62.1.1 27461 1yndA 165 1.96e-26 1xo7A 166 2.12e-26 2rmcA 182 2.95e-26 2cpl b.62.1.1 27491 1zcxA 178 4.40e-26 2cfeA 162 6.20e-26 1qoiA 177 7.37e-26 2cpl b.62.1.1 27490 1vdnA 162 1.19e-25 1h0pA 182 5.45e-25 b.62.1.1 76450 2a2nA 176 9.37e-25 1zkcA 197 1.36e-24 1xwnA 174 4.26e-24 2fu0A 160 2.00e-23 2b71A 196 2.35e-23 1j2aA 166 1.23e-21 b.62.1.1 90779 1v9tA 166 2.54e-21 b.62.1.1 108451 1lopA 164 2.81e-20 2cpl b.62.1.1 27510 1lq9A 112 9.87e-01 d.58.4.3 78129 1zoxA 113 1.74e+00 1wu7A 434 2.37e+00 2bf6A 449 2.67e+00 1vr0A 247 3.83e+00 2b8mA 117 4.21e+00 1gteA 1025 4.37e+00 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 1h7wA 1025 4.56e+00 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15683,28628,30324,30609,39007 1i8dA 213 5.31e+00 b.43.4.3,b.43.4.3 61953,61954 2cy7A 396 5.75e+00 1mdbA 539 6.85e+00 e.23.1.1 79008 2gefA 217 7.43e+00 2bm3A 166 7.49e+00 1pbyA 489 7.74e+00 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 1f0xA 571 8.40e+00 1f0xA d.58.32.2,d.145.1.1 39483,41746 1oa4A 222 8.91e+00 b.29.1.11 86731 1us5A 314 9.32e+00 c.94.1.1 99856 1zx8A 136 9.97e+00 2gk3A 256 1.00e+01 1do6A 124 1.02e+01 1do6A b.1.13.1 22361 1kv9A 668 1.05e+01 a.3.1.6,b.70.1.1 73056,73057 1qwgA 251 1.12e+01 c.1.27.1 96473 1khbA 625 1.13e+01 c.91.1.1,c.109.1.1 68606,68607 1fh0A 221 1.14e+01 1cs8A d.3.1.1 59832 1sq2N 113 1.16e+01 b.1.1.1 105881 1bdfA 235 1.19e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1yo8A 634 1.29e+01 2b59A 187 1.35e+01 1qmpA 130 1.35e+01 1dz3A c.23.1.1 31106 1b77A 228 1.37e+01 1b77A d.131.1.2,d.131.1.2 41362,41363 1cr5A 189 1.44e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1gggA 226 1.44e+01 1lst c.94.1.1 35817 3stdA 165 1.45e+01 3stdA d.17.4.1 38073 2bw2A 140 1.45e+01 1fvuB 125 1.47e+01 1ixxB d.169.1.1 42346 1tllA 688 1.51e+01 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1dz3A 130 1.58e+01 1dz3A c.23.1.1 31105 1tl2A 236 1.60e+01 1tl2A b.67.1.1 27541 1xewX 182 1.67e+01 2cy5A 140 1.69e+01 1o04A 500 1.71e+01 c.82.1.1 86508 2b0aA 186 1.72e+01 1xwsA 313 1.73e+01 2f71A 298 1.74e+01 1k2fA 190 1.77e+01 b.8.1.2 68054 1wchA 315 1.77e+01 2azpA 318 1.80e+01 1g7fA 298 1.80e+01 1pty c.45.1.2 60330 1ntyA 311 1.88e+01 a.87.1.1,b.55.1.1 103873,103874 1u2zA 433 1.90e+01 c.66.1.31 107626 1s55A 156 1.92e+01 1agjA 242 1.95e+01 1agjA b.47.1.1 25827 1iqaA 160 2.02e+01 b.22.1.1 71274 1ja1A 622 2.03e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1qcsA 211 2.18e+01 1qcsA b.52.2.3,d.31.1.1 26927,38461 1pmy 123 2.23e+01 1bqk b.6.1.1 22888 1q1oA 98 2.23e+01 d.15.2.2 95596 1c0pA 363 2.24e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1w96A 554 2.26e+01 1jmxA 494 2.31e+01 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 1pa1A 310 2.35e+01 c.45.1.2 94404 1djnA 729 2.42e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 1idpA 172 2.46e+01 d.17.4.1 83685 2fpqA 444 2.52e+01 1o94A 729 2.56e+01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 1f20A 435 2.60e+01 b.43.4.1,c.25.1.4 64932,64933 3cla 213 2.60e+01 3cla c.43.1.1 32610 1vj0A 380 2.63e+01 b.35.1.2,c.2.1.1 100786,100787 2aexA 346 2.67e+01 1lqtA 456 2.78e+01 c.3.1.1,c.4.1.1 74198,74199 2atpB 115 2.79e+01 1p42A 270 2.83e+01 d.14.1.7,d.14.1.7 87754,87755 1rc9A 221 2.87e+01 1c4rA 182 2.88e+01 1c4rA b.29.1.4 24229 1djqA 729 2.92e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 1dar 691 3.01e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1 25707,32142,37547,39300 1j3kA 280 3.01e+01 c.71.1.1 84070 2ar9A 278 3.08e+01 1f0iA 504 3.10e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 1q8fA 313 3.17e+01 c.70.1.1 96203 1v0wA 506 3.20e+01 d.136.1.2,d.136.1.2 108220,108221 1dkgA 197 3.21e+01 1dkgA b.73.1.1,h.1.9.1 27812,45626 1wdnA 226 3.27e+01 1lst c.94.1.1 35816 1deuA 277 3.28e+01 1theB d.3.1.1 37085 1y7bA 542 3.30e+01 1qlpA 394 3.35e+01 1ovaA e.1.1.1 42628 1oxsC 353 3.40e+01 b.40.6.3,c.37.1.12 87519,87520 1s8nA 205 3.42e+01 c.23.1.1 105374 1f1zA 273 3.49e+01 1f1zA a.4.5.27,c.52.1.16 16081,33334 1ptvA 321 3.55e+01 1pty c.45.1.2 32665 1wc9A 169 3.60e+01 1ri7A 171 3.71e+01 a.4.5.32,d.58.4.2 97504,97505 1std 172 3.78e+01 3stdA d.17.4.1 38089 1lf7A 182 3.83e+01 b.60.1.1 73878 1l4iA 206 3.94e+01 b.1.11.1,b.7.2.1 73564,73565 2bibA 547 4.02e+01 2tmdA 729 4.09e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28616,30317,30602 1w2xA 758 4.10e+01 c.14.1.4,c.14.1.4 109134,109135 1y7mA 164 4.14e+01 1y3jA 77 4.19e+01 2masA 314 4.20e+01 2masA c.70.1.1 34810 1zoiA 276 4.21e+01 1wmdA 434 4.25e+01 b.18.1.20,c.41.1.1 109408,109409 830cA 168 4.32e+01 1ck7A d.92.1.11 40400 1bqk 124 4.38e+01 1bqk b.6.1.1 22889 1oxxK 353 4.39e+01 b.40.6.3,c.37.1.12 93715,93716 1erjA 393 4.41e+01 1erjA b.69.4.1 27660 2g6yA 217 4.41e+01 1t0fA 276 4.41e+01 2awdA 323 4.44e+01 1dqiA 124 4.53e+01 1do6A b.1.13.1 22357 1ww9A 392 4.54e+01 1ygtA 111 4.56e+01 1m3iA 471 4.62e+01 f.9.1.1 91178 2bh9A 489 4.63e+01 1r64A 481 4.68e+01 b.18.1.20,c.41.1.1 97140,97141 1hn2A 159 4.71e+01 b.60.1.1 65890 1gt1A 159 4.72e+01 b.60.1.1 90515 1yoeA 322 4.75e+01 1h4xA 117 4.82e+01 1auz c.13.2.1 60626 1wi5A 119 4.82e+01 1vi2A 300 4.83e+01 c.2.1.7,c.58.1.5 100726,100727 1zdrA 164 4.83e+01 2bikB 313 4.93e+01 1s2oA 244 4.94e+01 3il8 72 4.94e+01 1tvxA d.9.1.1 37356 1l7lA 121 4.95e+01 b.18.1.16 77790 1e7uA 961 5.04e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1cjbA 231 5.07e+01 1qk3A c.61.1.1 34079 1xk7A 408 5.10e+01 1yqtA 538 5.14e+01 1wosA 364 5.28e+01 b.44.2.1,d.250.1.1 109468,109469 1h54A 754 5.28e+01 a.102.1.4,b.30.5.3 60634,60635 1gowA 489 5.29e+01 1qvbA c.1.8.4 28981 1obpA 159 5.40e+01 1obpA b.60.1.1 27092 1ew0A 130 5.44e+01 1drmA d.110.3.2 40905 1vr8A 142 5.49e+01 1wriA 93 5.54e+01 1o7iA 119 5.59e+01 b.40.4.3 86642 1wloA 136 5.60e+01 1e8yA 966 5.66e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1kskA 234 5.71e+01 d.66.1.5,d.265.1.3 72920,90389 1ul7A 102 5.81e+01 d.129.6.1 99540 1k07A 263 5.82e+01 d.157.1.1 77218 1u2cA 246 5.83e+01 b.1.6.2,d.272.1.1 107610,107611 1zxfA 155 5.85e+01 2b7aA 293 5.85e+01 1oalA 151 5.94e+01 b.1.8.1 86739 1xedA 117 5.97e+01 1g1tA 157 5.99e+01 d.169.1.1,g.3.11.1 65104,65105 1z4xA 532 6.09e+01 1npuA 117 6.18e+01 b.1.1.1 92038 1z4vA 532 6.18e+01 1befA 181 6.19e+01 1befA b.47.1.3 26419 1khvA 516 6.23e+01 e.8.1.4 68627 1tuwA 109 6.30e+01 d.58.4.8 107346 1xn5A 146 6.31e+01 1xknA 355 6.33e+01 1q5fA 156 6.39e+01 d.24.1.1 104536 1ve4A 206 6.40e+01 1j58A 385 6.44e+01 b.82.1.2 71531 2axtB 510 6.51e+01 1vdxA 184 6.51e+01 1pfo 500 6.52e+01 1pfo f.9.1.1 43826 1v9nA 360 6.60e+01 1lam 484 6.60e+01 1lam c.50.1.1,c.56.5.3 33166,33829 1qr0A 228 6.60e+01 1qr0A d.150.1.1,d.150.1.1 59038,59039 1vjhA 122 6.62e+01 d.129.3.1 100811 1g291 372 6.64e+01 1g291 1wv3A 238 6.64e+01 1whtB 153 6.82e+01 1whtB 1whsB 153 6.84e+01 1whtB 1y60A 169 6.84e+01 1zxiB 809 6.86e+01 1mpgA 282 6.89e+01 1mpgA a.96.1.3,d.129.1.2 18747,41296 1xa3A 437 6.92e+01 1kb0A 677 6.93e+01 a.3.1.6,b.70.1.1 68378,68379 1llnA 262 6.96e+01 d.165.1.1 84625 1b7gO 340 6.97e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907 1r0wA 286 7.07e+01 c.37.1.12 96754 1w0pA 781 7.07e+01 b.29.1.8,b.29.1.8,b.68.1.1 109038,109039,109040 1bcpB 199 7.07e+01 1bcpB b.40.2.1,d.169.1.2 25120,42429 1fa8A 135 7.10e+01 1qipA d.32.1.1 38486 1nykA 165 7.10e+01 b.33.1.1 86408 1paz 123 7.12e+01 1bqk b.6.1.1 22878 1koqA 253 7.16e+01 2cba b.74.1.1 27964 1bbpA 173 7.19e+01 1bbpA b.60.1.1 27147 1wggA 96 7.25e+01 2a8eA 220 7.32e+01 1b1cA 181 7.33e+01 1amoA c.23.5.2 31212 1vfjA 116 7.39e+01 1kit 757 7.40e+01 1kit b.29.1.8,b.29.1.8,b.68.1.1 24272,24273,27616 1a70 97 7.42e+01 1awd d.15.4.1 37678 1a04A 215 7.49e+01 1a04A a.4.6.2,c.23.1.1 16234,31089 2f02A 323 7.49e+01 1mh1 186 7.49e+01 1eesA c.37.1.8 32002 2bsdA 264 7.61e+01 1acf 125 7.62e+01 3nul d.110.1.1 40882 1n13B 113 7.63e+01 1cf2O 337 7.63e+01 1b7gO c.2.1.3,d.81.1.1 29994,39909 1y4jA 284 7.64e+01 1z7mA 344 7.64e+01 2fdiA 211 7.70e+01 1ec7A 446 7.80e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1ncwH 222 7.90e+01 b.1.1.1,b.1.1.2 85555,85556 1p63A 144 7.92e+01 b.42.1.1 94153 1p15A 253 7.96e+01 c.45.1.2 93894 1u0sY 118 8.02e+01 c.23.1.1 107566 2acy 98 8.03e+01 2acy d.58.10.1 39298 1tmy 120 8.06e+01 1dbwA c.23.1.1 31083 1ttuA 477 8.15e+01 b.1.18.1,b.2.5.8,b.42.7.1 107305,107306,107307 1u5uA 374 8.18e+01 1rg8A 146 8.34e+01 1jtdB 273 8.38e+01 b.69.5.2 67265 1a8p 258 8.38e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1zruA 264 8.59e+01 1u8sA 192 8.60e+01 d.58.18.5,d.58.18.5 107737,107738 4fgf 146 8.61e+01 1bfg b.42.1.1 25486 2aqjA 538 8.70e+01 2b4wA 315 8.71e+01 2bhmA 164 8.73e+01 1n62B 809 8.80e+01 d.41.1.1,d.133.1.1 80092,80093 1nytA 271 8.81e+01 c.2.1.7,c.58.1.5 86417,86418 1qv9A 283 8.88e+01 c.127.1.1 96356 1w4sA 174 8.99e+01