# 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 1xubA 298 4.70e-05 2gkeA 274 4.67e-04 1gqzA 274 6.28e-04 d.21.1.1,d.21.1.1 83311,83312 1w61A 414 1.40e-03 1ym5A 300 8.65e-03 1o17A 345 3.69e-02 a.46.2.1,c.27.1.1 80765,80766 1dkmA 410 1.25e-01 1dklA c.60.1.2 34000 1dkqA 410 1.31e-01 1dklA c.60.1.2 33998 1bupA 386 3.48e-01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1yqfA 203 5.02e-01 1wc3A 219 5.44e-01 1ycoA 279 6.17e-01 1xtqA 177 8.66e-01 1p3dA 475 8.86e-01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1sdjA 310 8.92e-01 d.21.1.2,d.21.1.2 98807,98808 1u0kA 288 1.12e+00 d.21.1.2,d.21.1.2 107547,107548 2azpA 318 1.61e+00 1vdkA 466 1.76e+00 a.127.1.1 100561 1ubkL 534 1.94e+00 e.18.1.1 88422 1wuiL 534 1.97e+00 1sr8A 298 2.18e+00 e.54.1.1 105959 1gtzA 156 2.41e+00 c.23.13.1 70539 1n2eA 300 2.43e+00 c.26.1.4 85268 1iznB 277 2.61e+00 e.43.1.2 83848 2bw8A 227 2.70e+00 1oe4A 247 3.61e+00 c.18.1.3 86895 1vh5A 148 3.75e+00 d.38.1.5 100642 2acfA 182 3.93e+00 2a84A 300 4.10e+00 2f23A 156 4.41e+00 2gtqA 867 5.18e+00 1wtaA 275 5.37e+00 1o8bA 219 5.42e+00 c.124.1.4,d.58.40.1 81180,81181 1o0iA 138 5.70e+00 d.38.1.5 86532 1srqA 341 5.91e+00 e.55.1.1 105967 1dmhA 311 7.21e+00 1dmhA b.3.6.1 22633 1nbwA 607 7.63e+00 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1rl0A 255 7.77e+00 1hzdA 272 8.08e+00 c.14.1.3 65969 1zhhB 242 8.12e+00 1qstA 160 9.00e+00 1yghA d.108.1.1 40804 2cx7A 130 9.09e+00 1vqzA 341 9.43e+00 1zcjA 463 9.86e+00 1u9yA 284 1.06e+01 1ogsA 497 1.07e+01 b.71.1.2,c.1.8.3 86997,86998 4uagA 437 1.12e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1f08A 148 1.16e+01 1f08A d.89.1.2 59564 2aneA 125 1.17e+01 1rzuA 485 1.22e+01 c.87.1.8 105140 1qwiA 143 1.25e+01 d.227.1.1 96474 1pfsA 78 1.25e+01 1pfsA b.40.4.7 25391 1y791 680 1.26e+01 1giqA 413 1.32e+01 d.166.1.1,d.166.1.1 76224,76225 1m0wA 491 1.32e+01 c.30.1.4,d.142.1.6 78363,78364 1ab8A 220 1.35e+01 1azsA d.58.29.1 39414 1mxmA 254 1.36e+01 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1q15A 503 1.43e+01 c.26.2.1,d.153.1.1 95538,95539 1z5hA 780 1.44e+01 1qjtA 99 1.46e+01 1eh2 a.39.1.6 17335 2b3nA 159 1.47e+01 1nh1A 330 1.47e+01 e.45.1.1 91871 2b5wA 357 1.48e+01 2a8yA 270 1.50e+01 1mqvA 125 1.53e+01 a.24.3.2 79415 1josA 128 1.58e+01 d.52.7.1 84191 2fvhA 120 1.60e+01 1jc9A 269 1.61e+01 d.171.1.1 66490 2g6yA 217 1.61e+01 1mtpA 323 1.63e+01 e.1.1.1 85107 2aliA 158 1.64e+01 1q87A 221 1.65e+01 e.47.1.1 96192 1vpbA 451 1.67e+01 1h65A 270 1.68e+01 c.37.1.8 65640 1xizA 159 1.72e+01 2fkbA 180 1.73e+01 2dbbA 151 1.75e+01 1br9 194 1.85e+01 1br9 b.40.3.1 25235 1u7nA 336 1.87e+01 c.77.1.4 107726 1dp4A 435 1.88e+01 1dp4A c.93.1.1 35710 1pzsA 208 1.91e+01 b.1.8.1 104397 1prxA 224 1.92e+01 1prxA c.47.1.10 33076 1wxxA 382 1.94e+01 1gmuA 143 2.03e+01 b.107.1.1,d.58.38.1 65335,65336 1vi6A 208 2.04e+01 c.23.15.1 100736 1zkiA 133 2.05e+01 2cxcA 144 2.06e+01 1vliA 385 2.10e+01 b.85.1.1,c.1.10.6 108830,108831 1q1rA 431 2.11e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1uz5A 402 2.11e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1zvpA 133 2.13e+01 1lyqA 104 2.13e+01 b.1.18.17 78302 1z94A 147 2.19e+01 1l0wA 580 2.28e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1ghpA 258 2.29e+01 1btl e.3.1.1 60520 1xhkA 187 2.35e+01 1bywA 110 2.38e+01 1bywA d.110.3.6 40912 1tafB 70 2.41e+01 1tafB a.22.1.3 16482 1yloA 348 2.42e+01 1pyoA 167 2.45e+01 c.17.1.1 95370 1q2lA 939 2.47e+01 1h9dB 134 2.50e+01 2jhbA b.54.1.1 60822 1es9A 232 2.52e+01 1wab c.23.10.3 31340 2fs2A 151 2.60e+01 1a3aA 148 2.64e+01 1a3aA d.112.1.1 40917 1nziA 159 2.64e+01 b.23.1.1,g.3.11.1 86449,86450 1pjcA 361 2.66e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 1g2bA 62 2.66e+01 1tud b.34.2.1 24488 1iicA 422 2.70e+01 1nmtA d.108.1.2,d.108.1.2 62422,62423 1ntvA 152 2.81e+01 b.55.1.2 86168 1oruA 195 2.81e+01 b.58.1.2 93464 1ru0A 105 2.84e+01 2bbhA 269 2.84e+01 1bia 321 2.84e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1ixlA 131 2.90e+01 d.38.1.5 90717 1tueB 218 2.94e+01 b.91.1.1 107324 2gfgA 193 2.94e+01 1m2oA 768 2.95e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78480,78481,78482,78483,78484 1b7yA 350 2.97e+01 1pysA d.104.1.1 40776 1cl8A 276 2.98e+01 1ckqA c.52.1.1 33230 1bebA 162 3.07e+01 1bebA b.60.1.1 27115 1p5dX 463 3.08e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1nnsA 326 3.10e+01 c.88.1.1 85910 1umkA 275 3.18e+01 2a15A 139 3.20e+01 2f8mA 244 3.21e+01 1sefA 274 3.23e+01 b.82.1.11 105452 1q79A 514 3.23e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 2fnaA 357 3.31e+01 1h2bA 359 3.32e+01 b.35.1.2,c.2.1.1 90543,90544 2hrvA 142 3.33e+01 2hrvA b.47.1.4 26429 1ash 150 3.42e+01 1ash a.1.1.2 15622 1nh0A 99 3.51e+01 b.50.1.1 91869 1kxqE 120 3.53e+01 b.1.1.1 73171 1tuhA 156 3.54e+01 d.17.4.11 107345 2f2hA 773 3.54e+01 1hp1A 516 3.56e+01 d.114.1.1,d.159.1.2 70976,70977 1lo7A 141 3.57e+01 d.38.1.1 74144 1suuA 312 3.64e+01 b.68.10.1 99006 2c0zA 216 3.64e+01 2bmoB 194 3.65e+01 1z4rA 168 3.67e+01 1qwkA 317 3.67e+01 c.1.7.1 96482 1sg4A 260 3.72e+01 1r44A 202 3.82e+01 d.65.1.4 104787 2govA 195 3.83e+01 2fr2A 172 3.84e+01 1r5eA 115 3.86e+01 1vgjA 184 3.88e+01 1gteA 1025 4.02e+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 1bw0A 416 4.04e+01 1bw0A c.67.1.1 34385 2c8mA 262 4.09e+01 1qx4A 274 4.12e+01 b.43.4.2,c.25.1.1 104624,104625 1h4xA 117 4.16e+01 1auz c.13.2.1 60626 1yb3A 175 4.17e+01 2a74A 643 4.21e+01 1i1nA 226 4.30e+01 c.66.1.7 71102 1nnhA 294 4.35e+01 d.104.1.1 92005 2dgkA 452 4.36e+01 1nkqA 259 4.37e+01 d.177.1.1 103862 1ww7A 160 4.53e+01 1q6hA 224 4.53e+01 d.26.1.1 95975 1xhcA 367 4.56e+01 1g5cA 170 4.63e+01 1g5cA c.53.2.1 60264 2d93A 134 4.72e+01 1rsy 152 4.79e+01 1rsy b.7.1.2 23192 1lr0A 129 4.81e+01 d.212.1.1 74213 1tw7A 99 4.81e+01 2d4qA 257 4.85e+01 2eulA 156 4.89e+01 1rrmA 386 4.95e+01 e.22.1.2 105081 1w77A 228 4.96e+01 1sk4A 163 5.00e+01 d.118.1.1 105664 1fcdA 401 5.10e+01 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 1o97D 320 5.10e+01 c.26.2.3,c.31.1.2 81233,81234 1v9yA 167 5.15e+01 d.110.3.2 108454 1pmmA 466 5.17e+01 c.67.1.6 94901 1kmqA 184 5.17e+01 c.37.1.8 84412 1uebA 184 5.18e+01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1qyaA 307 5.28e+01 d.21.1.2,d.21.1.2 104653,104654 1u6zA 513 5.30e+01 1uwkA 557 5.38e+01 e.51.1.1 108065 1ynfA 458 5.41e+01 1epfA 191 5.44e+01 2ncm b.1.1.4,b.1.1.4 21694,21695 1z54A 132 5.54e+01 1lkkA 105 5.57e+01 1lckA d.93.1.1 40412 1w2tA 432 5.57e+01 2etvA 346 5.58e+01 1k8kD 300 5.59e+01 d.198.2.1,d.198.2.1 68309,68310 1jf9A 408 5.60e+01 1c0nA c.67.1.3 62931 1jihA 531 5.64e+01 d.240.1.1,e.8.1.7 90374,90375 1ryaA 160 5.64e+01 d.113.1.5 105122 1i2aA 219 5.76e+01 e.24.1.1 90660 1fi2A 201 5.81e+01 1fi2A b.82.1.2 59845 1tzjA 338 5.91e+01 1yphC 131 5.92e+01 1jcfA 344 5.93e+01 c.55.1.1,c.55.1.1 62878,62879 1wmdA 434 5.95e+01 b.18.1.20,c.41.1.1 109408,109409 2lhb 149 5.99e+01 2fal a.1.1.2 15597 1i76A 163 5.99e+01 1hfc d.92.1.11 61877 2ajgA 196 6.00e+01 2et1A 201 6.03e+01 1a9xA 1058 6.04e+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 1sxvA 172 6.11e+01 1y8qA 346 6.11e+01 1z2wA 192 6.23e+01 1ry6A 360 6.26e+01 c.37.1.9 98090 1z47A 355 6.32e+01 1yt5A 258 6.36e+01 1q1fA 151 6.39e+01 a.1.1.2 104476 1lnsA 763 6.41e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 2aioA 269 6.41e+01 1uypA 432 6.46e+01 b.29.1.19,b.67.2.3 100176,100177 1awd 94 6.47e+01 1awd d.15.4.1 37673 1dgfA 497 6.47e+01 1cf9A e.5.1.1 42782 1hbnC 248 6.50e+01 1mroC d.58.31.1 60902 2f15A 96 6.53e+01 1nnxA 109 6.56e+01 b.40.10.1 92013 2go8A 122 6.61e+01 1u7iA 136 6.65e+01 d.32.1.7 107724 1avyA 74 6.72e+01 1avyB h.1.17.1 45656 1jb0E 75 6.76e+01 1pse b.34.4.2 62824 1v33A 366 6.81e+01 d.264.1.1 100278 1zd7A 159 6.85e+01 1c7qA 445 6.92e+01 2pgi c.80.1.2 35307 1ryiA 382 6.96e+01 1kg0C 136 7.02e+01 d.169.1.1 72445 1m7bA 184 7.07e+01 c.37.1.8 74572 1s4bP 674 7.10e+01 d.92.1.5 105252 1izmA 184 7.10e+01 a.199.1.1 90725 1qi9A 556 7.11e+01 1qhbA a.111.1.2 19053 1dcoA 104 7.11e+01 1dcpA d.74.1.1 39680 1zd9A 188 7.15e+01 2ajtA 500 7.17e+01 1yfqA 342 7.18e+01 1z85A 234 7.20e+01 3cms 323 7.26e+01 1smrA b.50.1.2 26865 1wleA 501 7.26e+01 1ejeA 192 7.28e+01 1ejeA b.45.1.2 25757 1yzsA 121 7.30e+01 1w19A 160 7.30e+01 1fnnA 389 7.34e+01 1fnnA a.4.5.11,c.37.1.20 16129,32426 1o7nA 449 7.36e+01 b.33.1.2,d.129.3.3 81162,81163 1gkmA 509 7.36e+01 a.127.1.2 70228 2b61A 377 7.37e+01 1rkqA 282 7.38e+01 c.108.1.10 97621 1e4mM 501 7.40e+01 1e70M c.1.8.4 59226 2a6aA 218 7.41e+01 1e8pA 46 7.41e+01 g.55.1.1 59385 2blnA 305 7.42e+01 1rwiA 270 7.42e+01 b.68.9.1 97987 1e9gA 286 7.43e+01 1wgjA b.40.5.1 59393 2bemA 170 7.47e+01 1wqwA 235 7.48e+01 1u24A 337 7.49e+01 1y8tA 324 7.60e+01 1wi6A 88 7.61e+01 1uj6A 227 7.62e+01 c.124.1.4,d.58.40.1 107898,107899 2nlrA 234 7.64e+01 2nlrA b.29.1.11 24344 1bteA 97 7.64e+01 1bteA g.7.1.3 44463 2bm3A 166 7.68e+01 2fsjA 346 7.74e+01 1ywmA 200 7.80e+01 2gjgA 248 7.81e+01 1q25A 432 7.83e+01 b.64.1.1,b.64.1.1,b.64.1.1 104493,104494,104495 2msbA 115 7.83e+01 1rtm1 d.169.1.1 42355 1h05A 146 7.88e+01 c.23.13.1 76433 1uteA 313 7.90e+01 1uteA d.159.1.1 42078 1bdo 80 8.00e+01 1bdo b.84.1.1 28214 1bbzA 58 8.02e+01 1bbzA b.34.2.1 24477 1w8oA 601 8.04e+01 1yliA 153 8.07e+01 1ignA 246 8.13e+01 1ignA a.4.1.6,a.4.1.6 16048,16049 1q5dA 419 8.15e+01 a.104.1.1 95891 1snzA 344 8.22e+01 b.30.5.4 98930 1v8fA 276 8.22e+01 c.26.1.4 100503 1xjvA 294 8.31e+01 1z9zA 60 8.32e+01 1zl0A 311 8.35e+01 1vqoQ 96 8.36e+01 1wekA 217 8.39e+01 1m4jA 142 8.41e+01 d.109.1.2 78602 2a19A 175 8.41e+01 1rzhL 281 8.44e+01 f.26.1.1 98164 2a2cA 478 8.45e+01 1wriA 93 8.60e+01 2bz6H 254 8.69e+01 2h4uA 145 8.71e+01 1w0nA 131 8.81e+01 1mngA 203 8.81e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1mnaA 298 8.92e+01 c.69.1.22 79322 1udxA 416 8.94e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1j5wA 298 8.94e+01 d.104.1.1 71589 1o3yA 166 8.95e+01 c.37.1.8 86618 1rwrA 301 8.96e+01 b.80.1.11 97990