# 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 1yndA 165 9.42e-43 1ihgA 370 4.33e-42 2cpl a.118.8.1,b.62.1.1 62380,62381 1dywA 173 8.89e-42 2cpl b.62.1.1 27505 1h0pA 182 2.26e-40 b.62.1.1 76450 1lopA 164 3.22e-32 2cpl b.62.1.1 27510 3sil 379 1.42e-01 3sil b.68.1.1 27542 1gteA 1025 2.28e-01 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 1mxiA 160 2.63e-01 c.116.1.1 79646 1us5A 314 2.73e-01 c.94.1.1 99856 1rx0A 393 4.07e-01 a.29.3.1,e.6.1.1 98007,98008 1dz3A 130 6.43e-01 1dz3A c.23.1.1 31105 1h4xA 117 6.55e-01 1auz c.13.2.1 60626 1fsgA 233 9.84e-01 1qk3A c.61.1.1 34029 1dqiA 124 9.89e-01 1do6A b.1.13.1 22357 1oxxK 353 1.07e+00 b.40.6.3,c.37.1.12 93715,93716 1oalA 151 1.23e+00 b.1.8.1 86739 1ezwA 349 1.30e+00 1ezwA c.1.16.3 29558 1cliA 345 1.55e+00 1cliA d.79.4.1,d.139.1.1 39816,41459 1fs0E 138 1.55e+00 1aqt a.2.10.1,b.93.1.1 59997,59998 1h5rA 293 1.87e+00 c.68.1.6 65623 1thfD 253 1.88e+00 1thfD c.1.2.1 28535 1ewnA 219 2.33e+00 1bnkA b.46.1.2 25762 1dl5A 317 2.46e+00 1dl5A c.66.1.7,d.197.1.1 64720,64721 1e9pA 151 2.60e+00 1mfmA b.1.8.1 22215 1g291 372 2.75e+00 1g291 1llnA 262 2.79e+00 d.165.1.1 84625 1qwyA 291 2.90e+00 b.84.3.2 96509 2gk3A 256 3.06e+00 1dzlA 505 3.21e+00 1dzlA b.121.6.1 23586 1pa1A 310 3.85e+00 c.45.1.2 94404 1vfjA 116 3.90e+00 1juhA 350 4.01e+00 b.82.1.5 71884 1ejxC 567 4.10e+00 b.92.1.1,c.1.9.2 83184,83185 1o7iA 119 4.67e+00 b.40.4.3 86642 1i6aA 219 4.83e+00 c.94.1.1 61827 1fnlA 175 5.13e+00 2fcbA b.1.1.4,b.1.1.4 21783,21784 1v7wA 807 5.29e+00 a.102.1.4,b.30.5.3 108411,108412 1c96A 753 5.29e+00 1amj c.8.2.1,c.83.1.1 30727,35403 1vjvA 415 5.32e+00 d.3.1.9 108632 1gd0A 122 5.36e+00 1dptA d.80.1.3 39834 1f39A 101 5.57e+00 1umuA b.87.1.1 28386 1sgwA 214 5.73e+00 c.37.1.12 105541 1guiA 155 5.94e+00 b.18.1.14 76351 1j71A 334 6.31e+00 1eagA b.50.1.2 62669 1b77A 228 6.55e+00 1b77A d.131.1.2,d.131.1.2 41362,41363 1dg9A 157 6.75e+00 1dg9A c.44.1.1 32637 1lq9A 112 6.78e+00 d.58.4.3 78129 1vyrA 364 6.79e+00 c.1.4.1 108906 1vj2A 126 6.91e+00 b.82.1.10 100796 1zjjA 263 6.93e+00 1idpA 172 6.99e+00 d.17.4.1 83685 1hy7A 173 7.17e+00 d.92.1.11 65957 1w2wB 191 7.31e+00 1vhuA 211 7.49e+00 c.50.1.2 100703 1mqoA 227 7.57e+00 d.157.1.1 103846 1isiA 265 7.95e+00 e.4.1.1 71394 1e9rA 437 8.02e+00 c.37.1.11 64827 1icpA 376 8.06e+00 1oyc c.1.4.1 62270 1rzhH 260 8.33e+00 b.41.1.1,f.23.10.1 98162,98163 1tyv 542 8.49e+00 1tyv b.80.1.6 28038 1gotG 73 8.59e+00 1tbgE a.137.3.1 19629 1cr5A 189 9.30e+00 1cr5A b.52.2.3,d.31.1.1 26931,38465 2fneA 117 9.38e+00 1g8sA 230 9.71e+00 c.66.1.3 90507 1a0tP 413 9.98e+00 1a0tP f.4.3.2 43794 1agjA 242 1.03e+01 1agjA b.47.1.1 25827 1f7dA 136 1.07e+01 1dun b.85.4.1 28353 1ee6A 197 1.08e+01 1ee6A b.80.1.1 28024 3seb 238 1.09e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1pmhX 185 1.09e+01 b.18.1.18 104193 1pz7A 204 1.11e+01 b.29.1.4 95405 1jfbA 404 1.15e+01 a.104.1.1 66624 1g0sA 209 1.18e+01 1g0sA d.113.1.1 60187 1bjt 793 1.23e+01 1bjt e.11.1.1 43249 1lv7A 257 1.25e+01 c.37.1.20 78232 1e1oA 504 1.25e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1b6g 310 1.27e+01 1b6g c.69.1.8 34661 1ve2A 235 1.27e+01 1v6sA 390 1.29e+01 c.86.1.1 100424 1w0nA 131 1.32e+01 1itxA 419 1.33e+01 c.1.8.5,d.26.3.1 71425,71426 1kqrA 179 1.33e+01 b.29.1.14 72886 1cb0A 283 1.35e+01 1cb0A c.56.2.1 33790 1xsqA 168 1.37e+01 1ea7A 310 1.38e+01 c.41.1.1 70086 1czfA 362 1.39e+01 1czfA b.80.1.3 28031 1oflA 481 1.40e+01 b.80.1.4 103934 1i3cA 149 1.40e+01 c.23.1.1 71112 1lf7A 182 1.43e+01 b.60.1.1 73878 1acf 125 1.44e+01 3nul d.110.1.1 40882 1vlaA 150 1.44e+01 d.227.1.2 108735 1in6A 334 1.45e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 1a2zA 220 1.48e+01 1a2zA c.56.4.1 33794 1c4rA 182 1.48e+01 1c4rA b.29.1.4 24229 1el6A 219 1.49e+01 1el6B d.182.1.1 42606 1k07A 263 1.51e+01 d.157.1.1 77218 1d3gA 367 1.52e+01 1d3gA c.1.4.1 28600 2d5cA 263 1.56e+01 1fxoA 293 1.56e+01 1g0rA c.68.1.6 34524 1n40A 396 1.56e+01 a.104.1.1 79977 1nykA 165 1.57e+01 b.33.1.1 86408 1oygA 447 1.57e+01 b.67.2.2 93726 1fjgE 162 1.59e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 1xubA 298 1.60e+01 1dbhA 354 1.61e+01 1awe a.87.1.1,b.55.1.1 18514,26967 1v8hA 107 1.64e+01 1vhwA 253 1.67e+01 c.56.2.1 100706 1h9hI 36 1.67e+01 g.3.2.1 103811 1a2yB 116 1.69e+01 1gc1H b.1.1.1 19927 2bjqA 345 1.70e+01 1tt8A 164 1.74e+01 1ogiA 303 1.78e+01 b.43.4.2,c.25.1.1 92914,92915 1v54G 85 1.79e+01 f.23.2.1 100328 1h7sA 365 1.79e+01 d.14.1.3,d.122.1.2 65705,65706 1kgsA 225 1.82e+01 a.4.6.1,c.23.1.1 68596,68597 1a8s 273 1.84e+01 1brt c.69.1.12 34710 1vkpA 383 1.86e+01 d.126.1.6 108686 1a8d 452 1.86e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 1bcpB 199 1.88e+01 1bcpB b.40.2.1,d.169.1.2 25120,42429 1gr0A 367 1.89e+01 c.2.1.3,d.81.1.3 70379,70380 1byrA 155 1.90e+01 1byrA d.136.1.1 41450 1ten 90 1.92e+01 1ten b.1.2.1 21990 1nszA 347 1.93e+01 b.30.5.4 80724 1fh0A 221 1.95e+01 1cs8A d.3.1.1 59832 1g6gA 127 1.96e+01 1g6gA b.26.1.2 23916 1a70 97 2.01e+01 1awd d.15.4.1 37678 1ooyA 481 2.01e+01 c.124.1.3,c.124.1.2 93388,93389 1z2uA 150 2.03e+01 1h30A 422 2.05e+01 b.29.1.4,b.29.1.4 76604,76605 1vclA 432 2.06e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1jbeA 128 2.08e+01 3chy c.23.1.1 62845 1vrmA 325 2.10e+01 1fonA 240 2.10e+01 5ptp b.47.1.2 26231 1qreA 247 2.11e+01 1qreA b.81.1.5 28066 1g6hA 257 2.12e+01 1gajA c.37.1.12 60318 1lam 484 2.13e+01 1lam c.50.1.1,c.56.5.3 33166,33829 1es5A 262 2.16e+01 1skf e.3.1.1 42679 1mpgA 282 2.17e+01 1mpgA a.96.1.3,d.129.1.2 18747,41296 1rg8A 146 2.21e+01 1i12A 160 2.27e+01 1i21A d.108.1.1 61515 1qwgA 251 2.30e+01 c.1.27.1 96473 1uuqA 440 2.32e+01 c.1.8.3 100015 1nkiA 135 2.33e+01 d.32.1.2 91941 1l7lA 121 2.43e+01 b.18.1.16 77790 1ql0A 241 2.46e+01 1qaeA d.4.1.2 37139 1r9wA 145 2.47e+01 d.89.1.2 97264 1nkr 201 2.48e+01 1nkr b.1.1.4,b.1.1.4 21799,21800 1si6X 282 2.54e+01 1w0pA 781 2.55e+01 b.29.1.8,b.29.1.8,b.68.1.1 109038,109039,109040 1cznA 169 2.59e+01 1rcf c.23.5.1 31181 1rvkA 382 2.61e+01 c.1.11.2,d.54.1.1 97928,97929 1bfg 146 2.63e+01 1bfg b.42.1.1 25485 1pg4A 652 2.63e+01 e.23.1.1 88067 1vr8A 142 2.67e+01 1r5lA 262 2.69e+01 a.5.3.1,c.13.1.1 97099,97100 1vjpA 394 2.75e+01 c.2.1.3,d.81.1.3 100828,100829 1pcfA 66 2.76e+01 1pcfA d.18.1.1 38142 1aa6 715 2.78e+01 2napA b.52.2.2,c.81.1.1 26916,35324 1im5A 180 2.78e+01 c.33.1.3 66211 1xttA 216 2.83e+01 1dzfA 215 2.87e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1rk6A 496 2.87e+01 b.92.1.6,b.92.1.6,c.1.9.11 97599,97600,97601 1ieaB 228 2.88e+01 1iakB b.1.1.2,d.19.1.1 21632,38206 1fqtA 112 2.93e+01 1fqtA b.33.1.1 24441 1mfgA 95 2.96e+01 b.36.1.1 79043 1h54A 754 2.98e+01 a.102.1.4,b.30.5.3 60634,60635 1o9wA 177 2.99e+01 b.2.3.5 86713 1amm 174 3.01e+01 1amm b.11.1.1,b.11.1.1 23587,23588 1hq8A 123 3.02e+01 1b6e d.169.1.1 61127 1p5vA 235 3.04e+01 b.1.11.1,b.7.2.1 87812,87813 1g8lA 411 3.07e+01 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1w50A 411 3.08e+01 b.50.1.2 109173 1ut1A 148 3.10e+01 b.2.3.6 108014 1su8A 636 3.13e+01 e.26.1.2 98999 1g3p 217 3.16e+01 1g3p b.37.1.1,b.37.1.1 24788,24789 1flcA 432 3.16e+01 1flcA b.19.1.3,c.23.10.2 23837,31337 1ml4A 308 3.19e+01 c.78.1.1,c.78.1.1 79255,79256 1bhu 102 3.26e+01 1bhu b.11.1.3 23631 1j58A 385 3.28e+01 b.82.1.2 71531 8abp 306 3.35e+01 8abp c.93.1.1 35647 1opd 85 3.35e+01 1ptf d.94.1.1 40560 1nnxA 109 3.35e+01 b.40.10.1 92013 1d5tA 433 3.35e+01 1gnd c.3.1.3,d.16.1.6 30422,37986 1hgxA 183 3.36e+01 1tc1A c.61.1.1 34027 1faaA 124 3.37e+01 1erv c.47.1.1 32738 1xk7A 408 3.40e+01 1mr7A 209 3.42e+01 b.81.1.3 91430 1hdoA 206 3.42e+01 1he2A c.2.1.2 60965 1dgwX 79 3.44e+01 1caxB b.82.1.2 28091 1pmi 440 3.44e+01 1pmi b.82.1.3 28114 2gdm 153 3.47e+01 2gdm a.1.1.2 15212 1gmuA 143 3.48e+01 b.107.1.1,d.58.38.1 65335,65336 1v0wA 506 3.49e+01 d.136.1.2,d.136.1.2 108220,108221 1jovA 270 3.50e+01 b.30.5.7 84192 1qv9A 283 3.51e+01 c.127.1.1 96356 1gesA 450 3.56e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 1frrA 95 3.57e+01 1awd d.15.4.1 37674 1nkgA 508 3.57e+01 b.3.1.2,b.18.1.25,b.30.5.10 103859,103860,103861 1b9hA 388 3.59e+01 1b9hA c.67.1.4 34488 1kugA 203 3.61e+01 d.92.1.9 73008 1bkzA 135 3.65e+01 1a3k b.29.1.3 24202 2arcA 164 3.71e+01 2arcA b.82.4.1 28148 1jer 138 3.76e+01 2cbp b.6.1.1 23022 1jhfA 202 3.81e+01 a.4.5.2,b.87.1.1 63057,63058 1hxn 219 3.82e+01 1hxn b.66.1.1 27529 1g1tA 157 3.82e+01 d.169.1.1,g.3.11.1 65104,65105 1wd7A 261 3.83e+01 1yleA 342 3.83e+01 1dynA 125 3.85e+01 1dynA b.55.1.1 26955 1bteA 97 3.87e+01 1bteA g.7.1.3 44463 1s2oA 244 3.88e+01 1r29A 127 3.94e+01 d.42.1.1 96856 1ix9A 205 3.99e+01 a.2.11.1,d.44.1.1 76899,76900 1ixcA 294 4.06e+01 a.4.5.37,c.94.1.1 83764,83765 1hw1A 239 4.08e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1h03P 125 4.08e+01 g.18.1.1,g.18.1.1 83411,83412 1ejbA 168 4.11e+01 1rvv1 c.16.1.1 59417 1qe3A 489 4.15e+01 2bce c.69.1.1 34630 1eexA 554 4.20e+01 1dioA c.1.19.3 29650 1dkiA 371 4.22e+01 1dkiA d.3.1.1 37090 1jtdB 273 4.27e+01 b.69.5.2 67265 1ixkA 315 4.31e+01 c.66.1.38 90716 1uxy 340 4.32e+01 2mbr d.145.1.2,d.146.1.1 41748,41761 1oa8A 133 4.34e+01 b.145.1.1 92698 1pbyA 489 4.35e+01 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 1pbjA 125 4.40e+01 d.37.1.1,d.37.1.1 94414,94415 1js1X 324 4.41e+01 c.78.1.1,c.78.1.1 71834,71835 1h5uA 842 4.46e+01 1a8i c.87.1.4 60655 1f9zA 135 4.47e+01 1qipA d.32.1.1 38484 1bed 181 4.52e+01 1fvkA c.47.1.13 90330 1lc0A 294 4.56e+01 c.2.1.3,d.81.1.4 73823,73824 1vpt 348 4.56e+01 3mag c.66.1.25 34207 1jk7A 323 4.57e+01 1auiA d.159.1.3 63144 1jmxA 494 4.58e+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 1hqz1 141 4.59e+01 1ok0A 74 4.62e+01 b.5.1.1 93191 1ifrA 121 4.67e+01 b.1.16.1 71203 1uxzA 131 4.71e+01 b.18.1.10 100170 1ituA 369 4.73e+01 c.1.9.7 71423 2sli 679 4.73e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1fg7A 356 4.79e+01 1gewA c.67.1.1 59819 1v5dA 386 4.81e+01 1uebA 184 4.86e+01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1iznB 277 4.87e+01 e.43.1.2 83848 1lqtA 456 4.92e+01 c.3.1.1,c.4.1.1 74198,74199 1ffyA 917 4.94e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1ea5A 537 4.95e+01 2bce c.69.1.1 34592 1f20A 435 4.96e+01 b.43.4.1,c.25.1.4 64932,64933 1bd3A 243 4.96e+01 1bd3A c.61.1.1 34098 1f5mA 180 4.96e+01 1f5mB d.110.2.1 40895 1jr7A 311 4.98e+01 b.82.2.3 63255 1xe7A 203 4.99e+01 1cb8A 678 5.00e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1gtmA 419 5.01e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1h8dH 260 5.04e+01 5ptp 1i78A 297 5.04e+01 f.4.4.1 66046 1evlA 401 5.06e+01 1qf6A c.51.1.1,d.104.1.1 33202,40751 1gsmA 210 5.08e+01 b.1.1.4,b.1.1.4 65535,65536 1oi0A 124 5.10e+01 c.97.3.1 93045 1t0pB 86 5.10e+01 1lugA 259 5.12e+01 b.74.1.1 91127 1ep0A 185 5.13e+01 1dzrA b.82.1.1 28080 1j5pA 253 5.16e+01 d.81.1.3,c.2.1.3 71577,83092 1i8dA 213 5.16e+01 b.43.4.3,b.43.4.3 61953,61954 1dekA 241 5.20e+01 1dekA c.37.1.1 31842 1e5dA 402 5.23e+01 1e5dA c.23.5.1,d.157.1.3 31208,42061 1j54A 186 5.23e+01 c.55.3.5 77077 1fn9A 365 5.24e+01 1fn9A d.196.1.1 59894 1deuA 277 5.25e+01 1theB d.3.1.1 37085 1hh5A 68 5.30e+01 1new a.138.1.1 61041 1ijtA 128 5.31e+01 1bfg b.42.1.1 62510 1j7gA 144 5.34e+01 c.110.1.1 84130 1ltzA 297 5.38e+01 d.178.1.1 74254 1m4jA 142 5.39e+01 d.109.1.2 78602 1jl3A 139 5.40e+01 c.44.1.1 66826 1fiqC 763 5.45e+01 1fiqC d.41.1.1,d.133.1.1 38588,41418 1dxrH 258 5.47e+01 6prcH b.41.1.1,f.23.10.1 25456,43433 1aihA 170 5.47e+01 1aihA d.163.1.1 42149 1cg2A 393 5.47e+01 1cg2A c.56.5.4,d.58.19.1 33844,39360 2cfuA 658 5.48e+01 1gmyA 261 5.50e+01 d.3.1.1 76236 1sjwA 144 5.52e+01 d.17.4.9 98899 1jd1A 129 5.52e+01 1qu9A d.79.1.1 62890 1fh9A 312 5.53e+01 1taxA c.1.8.3 28913 1eerB 227 5.53e+01 1eerB b.1.2.1,b.1.2.1 22011,22012 1abv 134 5.54e+01 1abv a.70.1.1 18317 1npsA 88 5.57e+01 1prs b.11.1.1 23622 1uozA 315 5.57e+01 1g5bA 221 5.59e+01 1g5bA d.159.1.3 60261 1oboA 169 5.61e+01 c.23.5.1 86776 1llfA 534 5.63e+01 c.69.1.17 78094 1molA 94 5.65e+01 1molA d.17.1.1 37988 1dc1A 323 5.71e+01 1dc1A c.52.1.11 33321 1mb3A 124 5.71e+01 c.23.1.1 78907 1eljA 381 5.73e+01 4mbp c.94.1.1 35791 1jnyA 435 5.74e+01 b.43.3.1,b.44.1.1,c.37.1.8 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