# List of top-scoring protein chains for t04-100-30-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 1d8wA 426 9.78e-02 1de5A c.1.15.2 29394 1vj5A 555 1.10e-01 c.108.1.2,c.69.1.11 100799,100800 1zd3A 555 1.81e-01 1ihp 438 3.22e-01 1ihp c.60.1.2 33993 1y3nA 490 3.44e-01 1jhgA 101 4.41e-01 1jhgA a.4.12.1 19009 1jpaA 312 5.02e-01 d.144.1.7 67011 1tbmA 326 5.83e-01 a.211.1.2 106744 1h6zA 913 7.10e-01 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 1ad3A 452 8.69e-01 1ad3A c.82.1.1 35335 1q18A 332 9.05e-01 c.55.1.7,c.55.1.7 104470,104471 1sz2A 332 1.02e+00 2a9iA 113 1.86e+00 1kblA 873 1.87e+00 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1zv1A 65 2.01e+00 1yzxA 226 2.19e+00 1fsu 492 2.43e+00 1auk c.76.1.2 35032 1r4wA 226 2.57e+00 c.47.1.13 97050 1dik 874 2.68e+00 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 2ccmA 191 2.78e+00 2gsfA 373 2.99e+00 1bd8 156 3.20e+00 1bd8 d.211.1.1 19157 1jakA 512 3.64e+00 c.1.8.6,d.92.2.1 66472,66473 1x7yA 400 3.76e+00 1x6vA 630 3.98e+00 2b7aA 293 4.30e+00 1qu9A 128 4.57e+00 1qu9A d.79.1.1 39755 1hp5A 512 4.61e+00 1hp4A c.1.8.6,d.92.2.1 61113,61114 2ctoA 93 4.96e+00 2fqmA 75 5.03e+00 1xioA 261 5.05e+00 2aheA 267 5.05e+00 1jb0I 38 5.11e+00 1jb0I f.23.17.1 62826 3inkC 133 5.15e+00 3inkC a.26.1.2 16881 2fiyA 309 5.17e+00 1v1rA 400 5.30e+00 c.36.1.11 108272 1qfxA 460 6.02e+00 1qfxA c.60.1.2 33994 1qd9A 124 6.27e+00 1qu9A d.79.1.1 39758 1z2nX 324 6.50e+00 1m48A 133 6.69e+00 a.26.1.2 74443 1t92A 116 7.50e+00 1ufaA 520 7.72e+00 a.8.3.3,c.6.2.4 99329,99330 1jmtB 28 7.88e+00 2bemA 170 7.89e+00 2b05A 246 8.00e+00 1x91A 153 8.30e+00 2fmcA 82 8.30e+00 2fu4A 83 8.69e+00 1ewfA 456 8.99e+00 1bp1 d.83.1.1,d.83.1.1 40024,40025 2furA 209 9.37e+00 1jmxA 494 9.75e+00 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 1m93B 245 1.02e+01 1w1oA 534 1.09e+01 d.58.32.4,d.145.1.1 109071,109072 1es5A 262 1.12e+01 1skf e.3.1.1 42679 1m98A 317 1.16e+01 a.175.1.1,d.17.4.6 78866,78867 1whrA 124 1.16e+01 1x1fA 149 1.16e+01 2afwA 329 1.16e+01 1mzbA 136 1.17e+01 a.4.5.42 91497 1n2fA 142 1.17e+01 d.227.1.1 79853 1jhdA 396 1.19e+01 b.122.1.3,c.26.1.5 66712,66713 2bjqA 345 1.21e+01 1ssqA 267 1.22e+01 b.81.1.6 105993 1cojA 212 1.24e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1esiA 262 1.25e+01 1skf e.3.1.1 42682 1zq9A 285 1.26e+01 1w07A 659 1.33e+01 1tzvA 142 1.40e+01 a.79.1.1 107526 2iu5A 195 1.41e+01 1m2kA 249 1.43e+01 c.31.1.5 84754 2gdjA 264 1.46e+01 2fpmA 322 1.48e+01 1im5A 180 1.51e+01 c.33.1.3 66211 6gsvA 217 1.54e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 1v4aA 440 1.58e+01 a.24.16.4,d.218.1.9 108350,108351 1p4cA 380 1.66e+01 c.1.4.1 94100 1m3uA 264 1.73e+01 c.1.12.8 84784 1mvlA 209 1.75e+01 c.34.1.1 85146 1ngzA 213 1.78e+01 b.1.1.1,b.1.1.2 80500,80501 1sszA 34 1.79e+01 j.35.1.1 105999 1tqxA 227 1.88e+01 1i9gA 280 1.91e+01 c.66.1.13 62090 2mtaC 147 1.93e+01 2mtaC a.3.1.1 15908 1v96A 149 1.97e+01 1rypH 205 1.98e+01 d.153.1.4 41876 1aq0A 306 2.00e+01 1aq0A c.1.8.3 28842 1dciA 275 2.01e+01 1dciA c.14.1.3 30918 1h2vC 771 2.06e+01 a.118.1.14,a.118.1.14,a.118.1.14 76592,76593,76594 2bnkA 67 2.14e+01 2c4jA 218 2.16e+01 1x23A 155 2.17e+01 1x6oA 174 2.22e+01 b.34.5.2,b.40.4.5 109493,109494 1v9jA 113 2.26e+01 d.52.6.1 100542 1z6uA 150 2.33e+01 1z2uA 150 2.36e+01 1wr7A 41 2.39e+01 1t8kA 77 2.43e+01 a.28.1.1 106666 1dbwA 126 2.44e+01 1dbwA c.23.1.1 31095 1kpsB 171 2.45e+01 a.118.12.1 68787 1ppjF 110 2.45e+01 f.27.1.1 104262 2bnfB 241 2.46e+01 2bneA 241 2.51e+01 2gsvA 80 2.51e+01 1m2oA 768 2.52e+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 2fgtA 417 2.53e+01 1jy2N 53 2.54e+01 h.1.8.1 67440 1xfsA 178 2.59e+01 d.129.3.5 109589 1nd7A 374 2.74e+01 d.148.1.1 91817 1t4gA 322 2.87e+01 a.60.4.1,c.37.1.11 106418,106419 2a7mA 250 2.96e+01 1tueA 212 3.03e+01 c.37.1.20 107323 1r6wA 322 3.03e+01 c.1.11.2,d.54.1.1 97165,97166 1rkd 309 3.08e+01 1rkd c.72.1.1 34928 1zanL 214 3.08e+01 1h3nA 878 3.16e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1xw5A 217 3.18e+01 2c7pA 327 3.20e+01 1m6jA 261 3.23e+01 c.1.1.1 78693 1wmmA 145 3.25e+01 1p2fA 220 3.28e+01 a.4.6.1,c.23.1.1 87720,87721 2ewcA 126 3.28e+01 1nddA 76 3.31e+01 1ubi d.15.1.1 37599 1sphA 88 3.33e+01 1ptf d.94.1.1 40544 1hfeL 421 3.34e+01 1fehA c.96.1.1,d.58.1.5 36018,39001 1iqcA 308 3.38e+01 a.3.1.5,a.3.1.5 66266,66267 1im8A 244 3.48e+01 c.66.1.14 66212 1sheA 103 3.49e+01 d.274.1.1 105551 1no1A 126 3.51e+01 a.179.1.1 85913 1mp8A 281 3.51e+01 d.144.1.7 91384 1jae 471 3.57e+01 1smd b.71.1.1,c.1.8.1 27773,28760 7atjA 308 3.60e+01 1bgp a.93.1.1 18673 2cqsA 842 3.61e+01 1q4mA 221 3.62e+01 a.132.1.3 95805 2gboA 104 3.65e+01 1gwuA 309 3.70e+01 a.93.1.1 83351 1x8vA 455 3.73e+01 1iuhA 198 3.75e+01 d.61.1.2 83711 1c5cL 214 3.77e+01 32c2A b.1.1.1,b.1.1.2 20474,21438 1p8xA 344 3.84e+01 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 2f2mA 113 3.85e+01 2eu8A 216 3.87e+01 1cfr 285 3.92e+01 1cfr c.52.1.7 33312 1f0cA 305 3.96e+01 1c8oA e.1.1.1 42676 2b33A 140 3.97e+01 1jk8B 190 3.98e+01 1iakB b.1.1.2,d.19.1.1 63147,63148 1p3jA 217 4.03e+01 c.37.1.1,g.41.2.1 94022,94023 1rzsA 61 4.04e+01 a.35.1.2 105139 1deeG 54 4.05e+01 1fc2C a.8.1.1 16343 2g3kA 94 4.09e+01 1pw4A 451 4.11e+01 f.38.1.1 95198 2f2gA 221 4.13e+01 1pgjA 478 4.15e+01 2pgd a.100.1.1,c.2.1.6 18783,30195 2fh1A 344 4.19e+01 2f8mA 244 4.20e+01 1mg2D 155 4.21e+01 a.3.1.1 79062 1um5L 219 4.22e+01 2b1eA 564 4.31e+01 1i37A 260 4.33e+01 1a28A a.123.1.1 61583 1qwoA 442 4.38e+01 c.60.1.2 104620 2br9A 234 4.39e+01 1hlvA 131 4.39e+01 a.4.1.7,a.4.1.7 65854,65855 1u5tC 202 4.42e+01 a.4.5.54,a.4.5.54 107688,107689 2bfdA 400 4.44e+01 1sq5A 308 4.45e+01 c.37.1.6 105882 1alvA 173 4.57e+01 1alvA a.39.1.8 17370 2fb6A 117 4.60e+01 1g8fA 511 4.62e+01 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 1z6gA 218 4.64e+01 1zbfA 142 4.64e+01 2cvlA 124 4.65e+01 1n0xL 215 4.69e+01 b.1.1.1,b.1.1.2 91532,91533 1hdiA 413 4.70e+01 16pk c.86.1.1 60964 1d2mA 665 4.70e+01 1d2mA c.37.1.19,c.37.1.19 32417,32418 1h5zA 455 4.71e+01 a.104.1.1 90622 1thg 544 4.75e+01 1thg c.69.1.17 34763 1px5A 349 4.75e+01 a.160.1.2,d.218.1.6 95277,95278 1t7rA 269 4.75e+01 a.123.1.1 106635 2givA 295 4.77e+01 1e9xA 455 4.77e+01 1ea1A a.104.1.1 18969 1ab8A 220 4.81e+01 1azsA d.58.29.1 39414 1zy9A 564 4.81e+01 2g19A 244 4.83e+01 1jgjA 217 4.91e+01 1c3wA f.13.1.1 62952 1p1mA 406 4.96e+01 b.92.1.4,c.1.9.9 87696,87697 1u13A 455 4.98e+01 a.104.1.1 107578 1wnlA 235 5.00e+01 2c5rA 67 5.01e+01 1y82A 157 5.03e+01 1j8mF 297 5.05e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1h7wA 1025 5.07e+01 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 1rmg 422 5.11e+01 1rmg b.80.1.3 28029 1u04A 771 5.12e+01 b.34.14.1,c.55.3.10 107539,107540 2hbtA 247 5.25e+01 2an3A 289 5.27e+01 1x6iA 91 5.28e+01 1azsB 212 5.34e+01 1azsA d.58.29.1 39423 1x4tA 92 5.35e+01 2fupA 168 5.35e+01 1zboA 210 5.39e+01 2f02A 323 5.42e+01 2f96A 224 5.43e+01 1zwwA 256 5.45e+01 2c2nA 339 5.52e+01 2cygA 312 5.54e+01 1olsA 400 5.63e+01 c.36.1.11 93331 1j3gA 187 5.66e+01 d.118.1.1 77075 1h99A 224 5.68e+01 a.142.1.1,a.142.1.1 60814,60815 1eyeA 280 5.74e+01 1aj2 c.1.21.1 29672 1z83A 196 5.74e+01 1u5dA 108 5.76e+01 2a2pA 129 5.80e+01 2awdA 323 5.87e+01 1gjjA 168 5.89e+01 a.140.1.1,a.140.1.1 83291,83292 1zkeA 83 5.89e+01 1qh4A 380 5.91e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 1adjA 421 5.94e+01 1adjA c.51.1.1,d.104.1.1 33188,40737 1g7oA 215 6.05e+01 1g7oA a.45.1.1,c.47.1.5 60332,60333 1m1nB 522 6.10e+01 c.92.2.3 78418 1t6uA 117 6.10e+01 a.24.22.1 106584 1dp7P 76 6.14e+01 1dp7P a.4.5.20 16159 1wjgA 137 6.18e+01 1tqyB 415 6.28e+01 c.95.1.1,c.95.1.1 107247,107248 1eyhA 144 6.29e+01 1eduA a.118.9.1 19214 1zhcA 76 6.34e+01 2fikA 287 6.35e+01 1v54J 59 6.37e+01 f.23.4.1 100331 1vls 146 6.37e+01 1vls a.24.2.1 16532 1pa7A 130 6.40e+01 a.40.1.1 94410 1n1jA 93 6.44e+01 a.22.1.3 79813 1ewqA 765 6.57e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1v73A 342 6.58e+01 1rg9A 383 6.59e+01 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1afrA 345 6.63e+01 1afrA a.25.1.2 16805 1j6pA 418 6.67e+01 b.92.1.4,c.1.9.9 77089,77090 1geeA 261 6.69e+01 c.2.1.2 90509 1hnnA 282 7.00e+01 c.66.1.15 65895 1har 216 7.01e+01 1rthA e.8.1.2 43025 1t6cA 315 7.02e+01 c.55.1.8,c.55.1.8 106558,106559 1n8vA 112 7.03e+01 a.118.21.1 85457 1sr2A 116 7.15e+01 1dfwA 25 7.30e+01 j.35.1.1 46255 1uvzA 119 7.33e+01 1w4vA 119 7.34e+01 1wqwA 235 7.35e+01 1rx0A 393 7.40e+01 a.29.3.1,e.6.1.1 98007,98008 1gteA 1025 7.46e+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 1uwdA 103 7.46e+01 1ux5A 411 7.48e+01 a.207.1.1 100144 1otsA 465 7.52e+01 f.20.1.1 87415 1vjkA 98 7.61e+01 d.15.3.1 108631 2ac5A 316 7.65e+01 1se7A 83 7.69e+01 1jmmA 377 7.69e+01 b.30.6.1 71749 1i2aA 219 7.74e+01 e.24.1.1 90660 1tkeA 224 7.75e+01 1h2sA 225 7.79e+01 f.13.1.1 76578 1l0iA 78 7.85e+01 a.28.1.1 77643 6mhtA 327 7.86e+01 6mhtA c.66.1.26 34226 2bkrB 77 7.91e+01 1c52 131 7.96e+01 1c52 a.3.1.1 15810 1pu5A 164 7.99e+01 b.95.1.1 104310 2dg5A 366 8.06e+01 1l1jA 239 8.06e+01 b.47.1.1 84516 1xqrA 296 8.11e+01 1bt0A 76 8.20e+01 1ubi d.15.1.1 37607 1sqgA 429 8.21e+01 a.79.1.3,c.66.1.38 105912,105913 2occJ 59 8.25e+01 2occJ f.23.4.1 43524 1xg2B 153 8.34e+01 1mjuL 219 8.40e+01 b.1.1.1,b.1.1.2 91304,91305 1fmtA 314 8.43e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 1uxtA 501 8.46e+01 c.82.1.1 108125 2db9A 149 8.49e+01 1w34A 304 8.50e+01 1rfeA 162 8.59e+01 1fc3A 120 8.60e+01 1fc3A a.4.6.3 16237 1repC 251 8.82e+01 1repC a.4.5.10,a.4.5.10 16125,16126 1h4vB 421 8.82e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1zin 217 8.84e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1ln4A 104 8.87e+01 d.68.4.1 74043 2esnA 310 8.91e+01 1e3pA 757 8.92e+01 1e3hA a.4.9.1,b.40.4.5,d.14.1.4,d.14.1.4,d.52.3.1,d.101.1.1,d.101.1.1 16258,25328,37574,37575,38811,40697,40698 1yozA 116 8.94e+01 1gcoA 261 8.98e+01 1ybvA c.2.1.2 29884