# 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 1xv2A 237 3.16e-04 1ys7A 233 1.05e+00 1qrrA 394 1.25e+00 1qrrA c.2.1.2 29824 2al3A 90 1.26e+00 1i24A 404 1.37e+00 c.2.1.2 83663 3aprE 325 1.41e+00 2er7E b.50.1.2 26820 2apr 325 1.42e+00 2er7E b.50.1.2 26819 1c1yB 77 1.70e+00 1c1yB d.15.1.5 37618 1zmdA 474 2.11e+00 1qcwA 410 2.61e+00 1gox c.1.4.1 28622 1ktgA 138 3.04e+00 d.113.1.1 72972 1wosA 364 3.16e+00 b.44.2.1,d.250.1.1 109468,109469 1zdrA 164 3.64e+00 1xezA 721 3.68e+00 1m1hA 248 4.32e+00 b.114.1.1,d.58.42.1 78415,78416 1kbjA 412 4.64e+00 c.1.4.1 72280 1c3mA 147 4.83e+00 1jotA b.77.3.1 27983 1hskA 326 4.88e+00 2mbr d.145.1.2,d.146.1.1 61241,61242 1n6aA 259 5.25e+00 b.76.2.1,b.85.7.1 80121,80122 1vizA 240 5.40e+00 c.1.4.1 100784 1olrA 224 6.50e+00 b.29.1.11 93330 1yasA 257 6.91e+00 1qj4A c.69.1.20 34801 2f69A 261 7.17e+00 1mpp 361 7.46e+00 2rmpA b.50.1.2 26856 1nwbA 124 7.48e+00 b.124.1.1 86296 1qj4A 257 8.04e+00 1qj4A c.69.1.20 34796 1yx1A 264 8.17e+00 1p1cA 199 8.36e+00 c.66.1.16 87669 1s1qA 145 8.55e+00 d.20.1.2 98351 1xclA 235 9.24e+00 1vcoA 550 1.01e+01 c.23.16.1,c.37.1.10 108508,108509 1qgvA 142 1.11e+01 1qgvA c.47.1.8 33056 1k2eA 156 1.13e+01 d.113.1.1 72010 1yirA 408 1.15e+01 1a6cA 513 1.16e+01 1a6cA b.121.4.2,b.121.4.2,b.121.4.2 23296,23297,23298 1q45A 391 1.23e+01 c.1.4.1 95780 1ohvA 472 1.27e+01 c.67.1.4 93031 1gutA 68 1.31e+01 b.40.6.1 65576 1gy6A 127 1.33e+01 d.17.4.2 70736 1wcdJ 441 1.35e+01 1ounA 127 1.43e+01 1ounA d.17.4.2 38090 1f3uB 171 1.49e+01 1f3uB b.65.1.1 27525 1dciA 275 1.57e+01 1dciA c.14.1.3 30918 2axwA 134 1.58e+01 1m4lA 307 1.59e+01 c.56.5.1 78604 1g291 372 1.59e+01 1g291 1yloA 348 1.62e+01 2fp7B 172 1.64e+01 1ryiA 382 1.66e+01 1te0A 318 1.66e+01 1te5A 257 1.70e+01 d.153.1.1 106795 1ptvA 321 1.70e+01 1pty c.45.1.2 32665 1ub0A 258 1.74e+01 c.72.1.2 88394 2ctc 307 1.76e+01 1aye c.56.5.1 33802 2fblA 153 1.82e+01 1fukA 165 1.82e+01 1fukA c.37.1.19 32409 2essA 248 1.83e+01 1noa 113 1.83e+01 2mcm b.1.7.1 22208 1h7mA 102 1.84e+01 d.79.3.1 83485 1qhqA 140 1.85e+01 1qhqA b.6.1.1 63326 1ng4A 390 1.85e+01 c.3.1.2,d.16.1.3 85666,85667 1h65A 270 1.88e+01 c.37.1.8 65640 1k92A 455 1.90e+01 c.26.2.1,d.210.1.1 68325,68326 1qc5A 192 1.91e+01 1aoxA c.62.1.1 34147 1q42A 201 1.98e+01 d.17.4.2 95776 1vjkA 98 2.01e+01 d.15.3.1 108631 1siqA 392 2.03e+01 a.29.3.1,e.6.1.1 105585,105586 1z9lA 128 2.05e+01 2f71A 298 2.09e+01 1g2oA 268 2.09e+01 1b8oA c.56.2.1 60228 1icpA 376 2.09e+01 1oyc c.1.4.1 62270 1jmcA 246 2.10e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 1nm1G 125 2.12e+01 d.109.1.1 80653 1gs5A 258 2.13e+01 c.73.1.2 70395 1gox 370 2.13e+01 1gox c.1.4.1 28607 7ahlA 293 2.14e+01 7ahlA f.6.1.1 43812 1wn2A 121 2.15e+01 1j3kA 280 2.18e+01 c.71.1.1 84070 1pa1A 310 2.26e+01 c.45.1.2 94404 1r77A 103 2.27e+01 1w41A 101 2.28e+01 1dl5A 317 2.30e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1x6mA 196 2.31e+01 1d4xG 126 2.33e+01 1d0nA d.109.1.1 59109 2bkyA 97 2.33e+01 1euvB 86 2.40e+01 1a5r d.15.1.1 37598 2bgcA 238 2.56e+01 1t3tA 1303 2.57e+01 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 1wm3A 72 2.58e+01 1iupA 282 2.59e+01 c.69.1.10 76815 1ckv 141 2.60e+01 1ckv d.137.1.1 41452 1uk8A 282 2.66e+01 c.69.1.10 107907 1yduA 170 2.68e+01 1d3bA 75 2.68e+01 1d3bA b.38.1.1 24798 2a0iA 330 2.76e+01 1omiA 248 2.87e+01 b.82.3.3,a.4.5.4 87079,87080 1m1nB 522 2.87e+01 c.92.2.3 78418 1iz6A 138 2.89e+01 b.34.5.2,b.40.4.5 76976,76977 1qh8B 519 2.90e+01 1qguB c.92.2.3 35634 1iyeA 309 2.93e+01 e.17.1.1 83786 1i1kA 309 2.98e+01 1daaA e.17.1.1 61533 2f7fA 494 2.98e+01 1gx3A 284 2.99e+01 d.3.1.5 70678 1pt6A 213 2.99e+01 c.62.1.1 95091 1b56 135 3.04e+01 1hmt b.60.1.2 27183 1g7fA 298 3.13e+01 1pty c.45.1.2 60330 1qexA 288 3.23e+01 1qexA b.32.1.1 24425 1f5mA 180 3.28e+01 1f5mB d.110.2.1 40895 1epfA 191 3.30e+01 2ncm b.1.1.4,b.1.1.4 21694,21695 1jg1A 235 3.46e+01 c.66.1.7 66661 2cvjA 180 3.46e+01 1r6fA 310 3.49e+01 e.46.1.1 97149 1s5uA 138 3.50e+01 d.38.1.1 98573 1wznA 252 3.55e+01 1vixA 420 3.63e+01 c.56.5.4,d.58.19.1 100777,100778 1hqsA 423 3.65e+01 1iso c.77.1.1 61154 1ogwA 76 3.65e+01 d.15.1.1 87001 1p5fA 189 3.67e+01 c.23.16.2 94142 2fp8A 322 3.71e+01 1m26A 133 3.71e+01 1v04A 355 3.71e+01 b.68.6.2 100240 2f20A 240 3.74e+01 1ugxA 133 3.78e+01 1w5rA 278 3.79e+01 1uv4A 293 3.80e+01 2a74B 188 3.83e+01 1ydwA 362 3.84e+01 2aukA 190 3.88e+01 1v5eA 590 3.89e+01 1ubi 76 4.00e+01 1ubi d.15.1.1 37584 1frpA 335 4.00e+01 1frpA e.7.1.1 42875 1p1lA 102 4.03e+01 d.58.5.2 87695 1sotA 320 4.05e+01 b.36.1.4,b.47.1.1 105852,105853 1wrvA 308 4.06e+01 1e44B 96 4.08e+01 1e44B b.101.1.1 59220 2gasA 307 4.10e+01 1nbcA 155 4.12e+01 1nbcA b.2.2.2 22390 1p9eA 331 4.16e+01 d.157.1.5 104088 1j1bA 420 4.17e+01 d.144.1.7 90758 1yhfA 115 4.20e+01 1dmhA 311 4.32e+01 1dmhA b.3.6.1 22633 1ukuA 102 4.34e+01 d.58.5.2 99533 1e9lA 377 4.35e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 1jxhA 288 4.38e+01 c.72.1.2 67415 2a3nA 355 4.38e+01 2bv5A 282 4.39e+01 1qkkA 155 4.42e+01 1dbwA c.23.1.1 31104 1nbfD 76 4.44e+01 d.15.1.1 80390 1pgl1 185 4.45e+01 1peqA 714 4.47e+01 a.98.1.1,c.7.1.2 104131,104132 2f96A 224 4.49e+01 1oywA 523 4.53e+01 a.4.5.43,c.37.1.19,c.37.1.19 93760,93761,93762 2bh8A 101 4.56e+01 2gk3A 256 4.62e+01 1nzaA 103 4.64e+01 d.58.5.2 86444 2bklA 695 4.65e+01 1kgsA 225 4.68e+01 a.4.6.1,c.23.1.1 68596,68597 1t6kA 278 4.68e+01 1a12A 413 4.72e+01 1a12A b.69.5.1 27663 1ea7A 310 4.80e+01 c.41.1.1 70086 1kv7A 488 4.81e+01 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 1t0bA 252 4.87e+01 c.23.16.6 106199 1p7hL 286 4.90e+01 b.1.18.1,b.2.5.3 94271,94272 2blcA 238 4.92e+01 1w2wB 191 5.02e+01 1xwwA 157 5.06e+01 1sffA 426 5.06e+01 c.67.1.4 105482 2b5nA 323 5.07e+01 1ek1A 554 5.08e+01 1cr6B c.69.1.11,c.108.1.2 34685,43335 1sznA 417 5.11e+01 b.71.1.1,c.1.8.1 106162,106163 1z4xA 532 5.13e+01 1lnsA 763 5.15e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1ojqA 212 5.16e+01 d.166.1.1 93146 1td5A 202 5.18e+01 d.110.2.2 106767 1h0xA 100 5.22e+01 d.68.6.1 76451 1z4vA 532 5.26e+01 1naqA 112 5.28e+01 d.58.5.2 91761 1nxjA 183 5.34e+01 c.8.7.1 86382 2a73B 991 5.36e+01 2cxxA 190 5.36e+01 1trkA 680 5.36e+01 1trkA c.36.1.10,c.36.1.6,c.48.1.1 31803,31804,33090 1kv0A 66 5.37e+01 g.3.7.1 91040 1oltA 457 5.39e+01 c.1.28.2 93334 1l6rA 227 5.44e+01 c.108.1.10 77768 2bw0A 329 5.60e+01 1dosA 358 5.64e+01 1dosA c.1.10.2 29175 2f8mA 244 5.69e+01 1qfhA 212 5.69e+01 1qfhA b.1.18.10,b.1.18.10 21893,21894 1p5tA 127 5.70e+01 b.55.1.2 94148 1np6A 174 5.71e+01 c.37.1.10 85954 3tdt 274 5.72e+01 3tdt b.81.1.2 28053 2bl9A 238 5.73e+01 2a5zA 262 5.74e+01 1fjgE 162 5.80e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 1vlpA 441 5.82e+01 d.41.2.2,d.41.2.3 108840,108841 1moq 368 5.83e+01 1moq c.80.1.1 35302 2yhx 457 5.88e+01 2yhx i.12.1.1 46024 1s3iA 310 5.91e+01 b.46.1.1,c.65.1.1 98435,98436 1gpuA 680 5.93e+01 c.36.1.10,c.36.1.6,c.48.1.1 65454,65455,65456 2hlcA 230 5.93e+01 5ptp b.47.1.2 26074 1ny4A 82 5.93e+01 b.40.4.5 92316 1gskA 513 5.98e+01 b.6.1.3,b.6.1.3,b.6.1.3 83314,83315,83316 1eqcA 394 6.00e+01 1cz1A c.1.8.3 28811 1a02N 301 6.02e+01 1a02N b.1.18.1,b.2.5.3 21923,22440 1d7qA 143 6.06e+01 1d7qA b.40.4.5 25331 1gheA 177 6.15e+01 d.108.1.1 76222 1iso 416 6.20e+01 1iso c.77.1.1 35065 1tfr 305 6.24e+01 1tfr a.60.7.1,c.120.1.2 18081,33351 1rxyA 253 6.25e+01 c.56.2.1 98065 1cqyA 99 6.27e+01 1b9zA b.3.1.1 22527 1esgA 213 6.28e+01 1bam c.52.1.3 33286 1zx0A 236 6.28e+01 1f52A 468 6.30e+01 1lgr d.15.9.1,d.128.1.1 37839,41169 2b4hA 254 6.34e+01 1q3lA 69 6.44e+01 1rocA 155 6.45e+01 b.1.22.1 97673 2b8mA 117 6.46e+01 1h7zA 194 6.53e+01 1qhvA b.21.1.1 60733 1jykA 254 6.55e+01 c.68.1.13 67458 2coaA 125 6.60e+01 1vrmA 325 6.70e+01 1bmv1 198 6.76e+01 1bmv1 1nciA 110 6.92e+01 1edhA b.1.6.1 22191 1u1wA 298 6.92e+01 1wlsA 328 6.94e+01 1xwiA 322 6.98e+01 1sczA 233 7.00e+01 c.43.1.1 98802 2bj0A 203 7.06e+01 2b0vA 153 7.07e+01 2gh1A 301 7.10e+01 2f6uA 234 7.16e+01 1od3A 168 7.16e+01 b.18.1.10 86825 1pb1A 416 7.23e+01 c.77.1.1 88014 1xpiA 231 7.28e+01 1v6fA 151 7.28e+01 d.109.1.2 108395 1rz3A 201 7.31e+01 c.37.1.6 98132 1pvmA 184 7.39e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1rloA 271 7.39e+01 1zjjA 263 7.46e+01 1ygtA 111 7.47e+01 1ek6A 348 7.53e+01 1xel c.2.1.2 29800 1zo2A 129 7.57e+01 1vjoA 393 7.61e+01 c.67.1.3 100827 2f06A 144 7.67e+01 1jy1A 464 7.68e+01 d.136.1.3,d.136.1.3 67438,67439 1bkb 136 7.73e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 2cpgA 45 7.77e+01 2cpgA a.43.1.3 17455 1p6pA 125 7.80e+01 b.60.1.2 87839 1u8sA 192 7.82e+01 d.58.18.5,d.58.18.5 107737,107738 1dg9A 157 7.84e+01 1dg9A c.44.1.1 32637 1r85A 379 7.86e+01 c.1.8.3 104839 1bi5A 389 7.87e+01 1bi5A c.95.1.2,c.95.1.2 35985,35986 1zk5A 176 7.87e+01 1w2wA 211 7.87e+01 c.124.1.5 109130 1dozA 309 7.87e+01 1ak1 c.92.1.1 35592 1soxA 466 7.90e+01 1soxA b.1.18.6,d.120.1.1,d.176.1.1 21947,41090,42563 1p5vA 235 7.93e+01 b.1.11.1,b.7.2.1 87812,87813 1erjA 393 7.93e+01 1erjA b.69.4.1 27660 1ezwA 349 7.97e+01 1ezwA c.1.16.3 29558 1mvfA 135 8.02e+01 b.1.1.1 85141 2ac4A 309 8.06e+01 1vr9A 213 8.10e+01 1nv8A 284 8.10e+01 c.66.1.30 86224 1zd7A 159 8.17e+01 1n5nA 180 8.18e+01 d.167.1.1 85336 1fsoA 139 8.19e+01 1rhoA b.1.18.8 60007 1omhA 293 8.20e+01 d.89.1.5 93348 1k77A 260 8.20e+01 c.1.15.5 72096 2a9dA 372 8.22e+01 1i8dA 213 8.22e+01 b.43.4.3,b.43.4.3 61953,61954 2ac2A 309 8.25e+01 1oqyA 368 8.27e+01 a.5.2.1,a.5.2.1,a.189.1.1,d.15.1.1 93439,93440,93441,93442 1dzfA 215 8.29e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1kte 105 8.54e+01 1kte c.47.1.1 32771 1crb 134 8.56e+01 1hmt b.60.1.2 27220 1fhgA 154 8.59e+01 1tlk b.1.1.4 21706 1jjiA 311 8.60e+01 c.69.1.2 66766 1yj1A 76 8.63e+01 1wnfA 328 8.77e+01 1ob8A 135 8.89e+01 3bamA 213 8.90e+01 1bam c.52.1.3 33288 1gt1A 159 8.92e+01 b.60.1.1 90515 1hn2A 159 8.93e+01 b.60.1.1 65890 1tlk 154 8.98e+01 1tlk b.1.1.4 21707