# List of top-scoring protein chains for t06-100-30-alpha-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 1.91e-01 1ok0A 74 2.23e-01 b.5.1.1 93191 1gmyA 261 4.24e-01 d.3.1.1 76236 2d13A 227 5.39e-01 1rsy 152 5.60e-01 1rsy b.7.1.2 23192 1tif 78 6.33e-01 1tif d.15.8.1 37836 1dq3A 454 9.59e-01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1k3iA 656 1.00e+00 b.1.18.2,b.18.1.1,b.69.1.1 68113,68114,68115 1vckA 115 1.03e+00 2ew2A 316 1.17e+00 1wosA 364 1.35e+00 b.44.2.1,d.250.1.1 109468,109469 2cokA 113 1.40e+00 1dgwA 178 1.43e+00 1dgwA b.82.1.2 28090 1odkA 235 1.50e+00 c.56.2.1 86863 1jm1A 204 1.53e+00 b.33.1.1 71745 1qmeA 702 1.88e+00 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 3pcgA 200 1.92e+00 3pchA b.3.6.1 22647 1snnA 227 1.96e+00 d.115.1.2 105821 1bb8 71 1.99e+00 2bb8 d.10.1.1 37478 1nezG 128 2.01e+00 b.1.1.1 85592 1rzfL 213 2.04e+00 b.1.1.1,b.1.1.2 98152,98153 1yu0A 381 2.11e+00 1p5dX 463 2.24e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1mbmA 198 2.30e+00 b.47.1.3 78916 1tzyD 103 2.46e+00 a.22.1.1 107533 1yllA 200 2.59e+00 1lgpA 116 2.83e+00 b.26.1.2 73890 1qhoA 686 2.87e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1f7dA 136 2.90e+00 1dun b.85.4.1 28353 1gttA 429 2.90e+00 d.177.1.1,d.177.1.1 70529,70530 1yg9A 330 2.90e+00 1cqqA 180 3.19e+00 1cqqA b.47.1.4 26422 1gpmA 525 3.19e+00 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1u24A 337 3.43e+00 2a2pA 129 3.52e+00 2f9lA 199 3.54e+00 1o9wA 177 3.56e+00 b.2.3.5 86713 1r26A 125 3.85e+00 c.47.1.1 96847 1jssA 224 3.95e+00 d.129.3.2 71844 2gjgA 248 3.96e+00 1i2aA 219 4.10e+00 e.24.1.1 90660 2gfaA 119 4.29e+00 1uwvA 433 4.54e+00 b.40.4.12,c.66.1.40 100128,100129 1ee6A 197 4.59e+00 1ee6A b.80.1.1 28024 1lucB 324 4.62e+00 1lucA c.1.16.1 29548 1cb8A 678 4.67e+00 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1el5A 389 4.72e+00 1b3mA c.3.1.2,d.16.1.3 30369,37937 1i4uA 181 4.72e+00 b.60.1.1 61732 1xwyA 264 4.77e+00 1wyxA 69 4.78e+00 1nkqA 259 4.78e+00 d.177.1.1 103862 1zczA 464 4.89e+00 1v5vA 401 4.93e+00 1s98A 107 5.01e+00 b.124.1.1 105377 1ut7A 171 5.03e+00 b.143.1.1 99906 1mhnA 59 5.14e+00 b.34.9.1 84964 1j8mF 297 5.16e+00 1ng1 a.24.13.1,c.37.1.10 62742,62743 1vqoT 120 5.33e+00 1iq4A 179 5.39e+00 1iq4A d.77.1.1 62641 1qsgA 265 5.45e+00 1eny c.2.1.2 29935 1dy9A 187 5.47e+00 1jxpA b.47.1.3 26400 2cxaA 256 5.66e+00 2f5gA 133 5.85e+00 1xcbA 211 5.88e+00 a.4.5.38,c.2.1.12 109552,109553 1w85I 49 6.02e+00 1wqsA 173 6.28e+00 2aotA 292 6.54e+00 1qw1A 121 6.65e+00 1dz3A 130 6.70e+00 1dz3A c.23.1.1 31105 1wzoA 246 6.72e+00 1v8hA 107 6.89e+00 1g5cA 170 6.93e+00 1g5cA c.53.2.1 60264 1vlmA 219 6.98e+00 c.66.1.41 108836 2g6fX 59 7.02e+00 1zvhA 134 7.13e+00 1yovA 537 7.36e+00 2absA 383 7.40e+00 1vr0A 247 7.40e+00 1yhfA 115 7.47e+00 2fyxA 143 7.66e+00 1hlvA 131 8.02e+00 a.4.1.7,a.4.1.7 65854,65855 1iloA 77 8.12e+00 c.47.1.1 66205 1ddgA 374 8.25e+00 1amoA b.43.4.1,c.25.1.4 25671,31559 1r5tA 142 8.32e+00 c.97.1.1 104812 1lcyA 325 8.66e+00 b.36.1.4,b.47.1.1 73834,73835 2fp4B 395 8.82e+00 1squA 155 8.86e+00 d.252.1.1 98971 1zkpA 268 8.86e+00 1iukA 140 8.99e+00 c.2.1.8 83712 1o5zA 442 9.01e+00 c.59.1.2,c.72.2.2 92530,92531 1gxuA 91 9.06e+00 d.58.10.1 76378 2fomB 185 9.20e+00 1obdA 306 9.22e+00 d.143.1.1 86767 2b8lA 405 9.26e+00 2abqA 306 9.36e+00 2a7mA 250 9.44e+00 1iyeA 309 9.45e+00 e.17.1.1 83786 1cxqA 162 9.51e+00 1cxqA c.55.3.2 33621 1ru4A 400 1.04e+01 b.80.1.9 97836 1s3cA 141 1.06e+01 1chmA 401 1.06e+01 1chmA c.55.2.1,d.127.1.1 33545,41142 1ekgA 127 1.06e+01 1dlxA d.82.2.1 40021 1qzzA 374 1.07e+01 a.4.5.29,c.66.1.12 96719,96720 1k07A 263 1.08e+01 d.157.1.1 77218 1l6rA 227 1.08e+01 c.108.1.10 77768 1o4sA 389 1.08e+01 c.67.1.1 86620 2a65A 519 1.11e+01 1w50A 411 1.11e+01 b.50.1.2 109173 1hgxA 183 1.16e+01 1tc1A c.61.1.1 34027 1po5A 476 1.18e+01 a.104.1.1 94963 1vr6A 350 1.21e+01 1pvdA 537 1.21e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 2g76A 335 1.23e+01 1xer 103 1.23e+01 1xer d.58.1.3 38990 1wdcB 156 1.25e+01 1wdcB a.39.1.5 17302 1qwdA 177 1.25e+01 b.60.1.1 96471 1xs1A 193 1.27e+01 2g9iA 249 1.28e+01 1vfgA 390 1.28e+01 a.173.1.1,d.218.1.4 108570,108571 1whzA 70 1.29e+01 1wy5A 317 1.29e+01 2as0A 396 1.30e+01 1ua4A 455 1.36e+01 c.72.1.3 99128 1x6oA 174 1.36e+01 b.34.5.2,b.40.4.5 109493,109494 2f5tX 233 1.37e+01 1wznA 252 1.37e+01 1nycA 111 1.38e+01 b.61.2.2 92336 1rwiA 270 1.38e+01 b.68.9.1 97987 2gtrA 261 1.41e+01 1sawA 225 1.43e+01 1wi5A 119 1.44e+01 2ge3A 170 1.46e+01 2b3nA 159 1.46e+01 1ub3A 220 1.48e+01 c.1.10.1 88395 1tyv 542 1.48e+01 1tyv b.80.1.6 28038 1vjgA 218 1.48e+01 c.23.10.6 100810 1zo0A 126 1.51e+01 1agi 125 1.54e+01 7rsa d.5.1.1 37303 1qo3C 137 1.57e+01 1qo3C d.169.1.1 42350 1vl5A 260 1.57e+01 c.66.1.41 108720 1zrjA 50 1.57e+01 1cojA 212 1.58e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1j83A 180 1.59e+01 b.18.1.12 66430 1zk5A 176 1.60e+01 1wdtA 665 1.62e+01 1pmzA 86 1.63e+01 a.39.1.10 104195 1x0vA 354 1.64e+01 1o7iA 119 1.66e+01 b.40.4.3 86642 1u2zA 433 1.69e+01 c.66.1.31 107626 1wmzA 140 1.69e+01 d.169.1.1 109422 1dzfA 215 1.71e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1v6tA 255 1.72e+01 2coeA 120 1.72e+01 1uv4A 293 1.73e+01 1ek0A 170 1.74e+01 1ctqA c.37.1.8 32076 1kte 105 1.76e+01 1kte c.47.1.1 32771 1vj7A 393 1.76e+01 a.211.1.1,d.218.1.8 100801,100802 2bl0C 142 1.79e+01 1lvwA 295 1.80e+01 c.68.1.6 84723 1qy6A 274 1.83e+01 b.47.1.1 96574 1wdnA 226 1.83e+01 1lst c.94.1.1 35816 2flsA 132 1.84e+01 2ex4A 241 1.84e+01 1wr8A 231 1.89e+01 1m2tB 263 1.92e+01 b.42.2.1,b.42.2.1 84762,84763 1wu7A 434 1.92e+01 2bcmA 165 1.93e+01 1lmmA 40 1.93e+01 g.3.6.2 91080 1zud2 66 1.94e+01 1wlyA 333 1.95e+01 1eny 268 1.96e+01 1eny c.2.1.2 29910 1neyA 247 1.97e+01 c.1.1.1 80449 1ihjA 98 1.97e+01 1pdr b.36.1.1 62382 1uu1A 335 1.99e+01 c.67.1.1 99993 2bopA 85 2.02e+01 2bopA d.58.8.1 39217 1mvfA 135 2.04e+01 b.1.1.1 85141 1t7lA 766 2.04e+01 1qtnA 164 2.05e+01 1pauA c.17.1.1 30999 1dcfA 136 2.06e+01 1dcfA c.23.1.2 31124 1agjA 242 2.07e+01 1agjA b.47.1.1 25827 1pbjA 125 2.07e+01 d.37.1.1,d.37.1.1 94414,94415 1bqfA 25 2.09e+01 j.8.1.1 46113 1qreA 247 2.10e+01 1qreA b.81.1.5 28066 1oaqL 120 2.11e+01 b.1.1.1 92708 1kl9A 182 2.13e+01 b.40.4.5 72681 1ars 396 2.13e+01 1ajsA c.67.1.1 34287 2blnA 305 2.13e+01 1hfuA 503 2.14e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1upaA 573 2.14e+01 c.31.1.3,c.36.1.5,c.36.1.9 99714,99715,99716 1l7dA 384 2.15e+01 c.2.1.4,c.23.12.2 77774,77775 1uebA 184 2.16e+01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1f89A 291 2.17e+01 d.160.1.1 64988 1h05A 146 2.17e+01 c.23.13.1 76433 1nofA 383 2.18e+01 b.71.1.2,c.1.8.3 92020,92021 1g7sA 594 2.19e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 2cyeA 133 2.20e+01 1t6t1 118 2.21e+01 2cc0A 195 2.22e+01 1goiA 499 2.23e+01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 1y81A 138 2.23e+01 1gycA 499 2.23e+01 b.6.1.3,b.6.1.3,b.6.1.3 70748,70749,70750 1v70A 105 2.24e+01 2bvbA 137 2.24e+01 1v10A 521 2.28e+01 b.6.1.3,b.6.1.3,b.6.1.3 108224,108225,108226 1aop 497 2.30e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39501,39502,41425,41426 1gzsB 165 2.31e+01 a.168.1.1 76425 1y96A 86 2.31e+01 1z5bA 469 2.32e+01 1jy4A 35 2.34e+01 k.35.1.1 71938 1k0iA 394 2.35e+01 c.3.1.2,d.16.1.2 67942,67943 1nykA 165 2.36e+01 b.33.1.1 86408 1weuA 91 2.36e+01 1yfbA 59 2.37e+01 1czfA 362 2.37e+01 1czfA b.80.1.3 28031 1b43A 340 2.43e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 1pq7A 224 2.46e+01 b.47.1.2 95002 1zvyA 136 2.48e+01 1us5A 314 2.49e+01 c.94.1.1 99856 1uaiA 224 2.53e+01 b.29.1.18 107761 1zsyA 357 2.53e+01 1xfpA 142 2.53e+01 b.1.1.1 109587 2aioA 269 2.54e+01 1v74B 87 2.56e+01 a.24.20.1 100443 2aq8A 269 2.58e+01 1mxmA 254 2.59e+01 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1m4vA 204 2.61e+01 b.40.2.2,d.15.6.1 74459,74460 2azwA 148 2.64e+01 1x99A 145 2.64e+01 2fhxA 246 2.64e+01 1x1rA 178 2.65e+01 1t64A 377 2.66e+01 c.42.1.2 106543 1kk8B 139 2.67e+01 a.39.1.5 77430 2fb7A 95 2.70e+01 1snyA 267 2.71e+01 c.2.1.2 105833 1ykjA 394 2.71e+01 1oz9A 150 2.72e+01 d.92.1.15 93808 1o4wA 147 2.76e+01 c.120.1.1 86629 1ng7A 60 2.76e+01 a.178.1.1 85671 1luzA 88 2.77e+01 b.40.4.5 74271 1s3eA 520 2.78e+01 c.3.1.2,d.16.1.5 98426,98427 1jbeA 128 2.79e+01 3chy c.23.1.1 62845 1v3yA 192 2.79e+01 1pk6A 133 2.80e+01 b.22.1.1 94801 1o9yA 84 2.80e+01 b.139.1.1 92692 1k3yA 221 2.82e+01 a.45.1.1,c.47.1.5 77245,77246 1hf2A 210 2.82e+01 1hf2A b.80.3.1,c.102.1.1 60992,60993 1vcoA 550 2.84e+01 c.23.16.1,c.37.1.10 108508,108509 1f1eA 154 2.85e+01 a.22.1.2 64927 2a8nA 144 2.85e+01 1d3cA 686 2.88e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21827,22496,27734,28721 2g6bA 180 2.90e+01 2fp7B 172 2.94e+01 1svpA 161 2.94e+01 1svpA b.47.1.3 26384 1o5uA 101 2.96e+01 b.82.1.8 92518 2cpgA 45 2.97e+01 2cpgA a.43.1.3 17455 1oygA 447 2.97e+01 b.67.2.2 93726 1bn8A 420 3.00e+01 1pcl b.80.1.1 28022 2a5jA 191 3.01e+01 1zjjA 263 3.01e+01 1su8A 636 3.08e+01 e.26.1.2 98999 1ssxA 198 3.08e+01 b.47.1.1 98978 1y96B 85 3.09e+01 1q7hA 153 3.10e+01 b.122.1.1,d.17.6.2 96042,96043 1kb0A 677 3.11e+01 a.3.1.6,b.70.1.1 68378,68379 1drw 273 3.11e+01 1drw c.2.1.3,d.81.1.3 30057,39972 1d5tA 433 3.14e+01 1gnd c.3.1.3,d.16.1.6 30422,37986 1gadO 330 3.15e+01 1dssG c.2.1.3,d.81.1.1 29950,39865 3tdt 274 3.16e+01 3tdt b.81.1.2 28053 2eifA 136 3.17e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1rc6A 261 3.19e+01 b.82.1.11 97287 1fqtA 112 3.19e+01 1fqtA b.33.1.1 24441 2fvgA 340 3.19e+01 1fvuB 125 3.20e+01 1ixxB d.169.1.1 42346 1kt6A 183 3.20e+01 b.60.1.1 84466 3proC 166 3.21e+01 3proC d.52.1.1,d.52.1.1 38812,38813 1q79A 514 3.21e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1ow1A 195 3.24e+01 b.131.1.3 93625 1vk6A 269 3.28e+01 d.113.1.4,d.113.1.4 100851,100852 1vetA 124 3.28e+01 d.110.7.1 108553 1zmaA 118 3.31e+01 1tuhA 156 3.32e+01 d.17.4.11 107345 1eziA 228 3.32e+01 1eyrA c.68.1.13 34512 2gf9A 189 3.33e+01 1fmtA 314 3.34e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 1rkqA 282 3.34e+01 c.108.1.10 97621 2dcnA 311 3.35e+01 1fdr 248 3.35e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 1viaA 175 3.36e+01 c.37.1.2 100754 1jidA 128 3.39e+01 d.201.1.1 66735 1gppA 237 3.39e+01 b.86.1.2 76262 1oeyA 83 3.44e+01 d.15.2.2 92800 2fzsA 193 3.46e+01 1w4vA 119 3.46e+01 1yhtA 367 3.47e+01 1fsgA 233 3.49e+01 1qk3A c.61.1.1 34029 1snzA 344 3.50e+01 b.30.5.4 98930 1i8nA 126 3.50e+01 1i8nA g.10.1.2 61976 1dro 122 3.55e+01 1btn b.55.1.1 26954 1l7lA 121 3.56e+01 b.18.1.16 77790 2bm5A 186 3.57e+01 1svvA 359 3.57e+01 c.67.1.1 106054 1vrbA 342 3.57e+01 1q3eA 207 3.59e+01 b.82.3.2 95669 1bkb 136 3.62e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 2gxfA 142 3.65e+01 1s68A 249 3.66e+01 d.142.2.4 98591 1w41A 101 3.67e+01 7a3hA 303 3.68e+01 7a3hA c.1.8.3 28817 1lkdA 297 3.69e+01 d.32.1.3,d.32.1.3 78059,78060 1dceB 331 3.69e+01 1dceB a.102.4.3 18872 1rq6A 62 3.70e+01 1srvA 145 3.71e+01 1derA c.8.5.1 30817 1y8tA 324 3.73e+01 1b65A 375 3.73e+01 1b65A d.154.1.1 42020 1kb9D 246 3.76e+01 a.3.1.3,f.23.11.1 77317,77318 1ppjD 241 3.77e+01 a.3.1.3,f.23.11.1 104258,104259 1yg6A 193 3.79e+01 1mk0A 97 3.79e+01 d.226.1.1 79216 1id2A 106 3.80e+01 1aac b.6.1.1 62288 1h6lA 353 3.80e+01 b.68.3.1 60687 2bu3A 254 3.81e+01 1u8fO 335 3.83e+01 1gqiA 708 3.84e+01 c.1.8.10,d.92.2.2 76279,76280 2avdA 219 3.85e+01 1b5fB 87 3.86e+01 1b5fB 1wd7A 261 3.87e+01 1vdwA 254 3.90e+01 e.7.1.1 100569 1g8kB 133 3.90e+01 1g8jB b.33.1.1 24435 1wcwA 261 3.90e+01 1rzhH 260 3.92e+01 b.41.1.1,f.23.10.1 98162,98163 1yqeA 282 3.96e+01 1rybA 212 3.98e+01 c.56.3.1 98098 1r1gA 31 3.98e+01 g.3.7.2 96816 2ltnA 181 4.00e+01 1led b.29.1.1 24024 1y2tA 142 4.01e+01 1tafB 70 4.02e+01 1tafB a.22.1.3 16482 2d4qA 257 4.09e+01 2apxA 112 4.11e+01 2fh7A 595 4.11e+01 1p3cA 215 4.12e+01 b.47.1.1 93996 2cayA 145 4.13e+01 1t6aA 126 4.13e+01 d.129.8.1 106555 1tp6A 128 4.14e+01 d.17.4.12 107184 1bywA 110 4.14e+01 1bywA d.110.3.6 40912 1wn5A 130 4.19e+01 1nkiA 135 4.21e+01 d.32.1.2 91941 1lba 146 4.21e+01 1lba d.118.1.1 41062 1p7tA 731 4.23e+01 c.1.13.1 94319 1xezA 721 4.25e+01 1p0zA 131 4.26e+01 d.110.6.1 93882 2fgtA 417 4.31e+01 2a19A 175 4.32e+01 1knmA 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