# List of top-scoring protein chains for t06-100-30-bys-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 1g9oA 91 1.46e-18 1pdr b.36.1.1 60400 1q3oA 109 7.80e-17 b.36.1.1 95700 1ihjA 98 1.01e-16 1pdr b.36.1.1 62382 1qauA 112 9.54e-16 1qauA b.36.1.1 24779 1mfgA 95 1.11e-15 b.36.1.1 79043 1r6jA 82 9.44e-15 b.36.1.1 97151 1fc6A 388 6.41e-11 1fc6A b.36.1.3,c.14.1.2 64738,64739 1qb7A 236 1.55e-02 1qb7A c.61.1.1 34087 1koe 172 3.61e-02 1koe d.169.1.5 42448 1t6t1 118 3.62e-02 1cq3A 233 1.85e-01 1cq3A b.27.1.1 23923 1kw4A 89 6.05e-01 a.60.1.2 73077 1fm0E 150 9.96e-01 1fmaE d.41.5.1 38629 1i4jA 110 1.00e+00 d.55.1.1 76734 1q52A 314 1.01e+00 c.14.1.3 95846 1ebfA 358 1.11e+00 1ebuA c.2.1.3,d.81.1.2 30033,39948 1yg9A 330 1.15e+00 1cliA 345 1.45e+00 1cliA d.79.4.1,d.139.1.1 39816,41459 1oxxK 353 1.91e+00 b.40.6.3,c.37.1.12 93715,93716 1w99A 558 1.94e+00 1rutX 188 2.01e+00 1gky 187 2.08e+00 1gky c.37.1.1 31839 1r62A 160 2.16e+00 d.122.1.3 104816 1mkkA 96 2.22e+00 g.17.1.1 79240 1eyqA 222 2.39e+00 1eypA d.36.1.1 38534 1ojhA 65 2.96e+00 a.214.1.1 103976 1ci9A 392 3.29e+00 e.3.1.1 64767 1rhcA 330 3.37e+00 c.1.16.3 97468 1fjgK 129 3.50e+00 1fjfK c.55.4.1 33733 1xdnA 277 3.58e+00 1gjjA 168 4.15e+00 a.140.1.1,a.140.1.1 83291,83292 1hnjA 317 4.32e+00 1hn9A c.95.1.2,c.95.1.2 35969,35970 1g57A 217 4.45e+00 1g57A d.115.1.2 60253 1eceA 358 4.66e+00 1eceA c.1.8.3 28813 1dljA 402 4.69e+00 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1fs0E 138 4.96e+00 1aqt a.2.10.1,b.93.1.1 59997,59998 1iv3A 152 5.11e+00 d.79.5.1 76828 1csh 435 5.17e+00 1csh a.103.1.1 18880 1fxlA 167 5.53e+00 1b7fA d.58.7.1,d.58.7.1 39183,39184 1earA 147 5.75e+00 b.107.1.1,d.58.38.1 64875,64876 1bouA 139 6.30e+00 1bouA a.88.1.1 18521 1tif 78 6.33e+00 1tif d.15.8.1 37836 1rwrA 301 6.48e+00 b.80.1.11 97990 1at0 145 6.99e+00 1at0 b.86.1.1 28374 1n6aA 259 7.08e+00 b.76.2.1,b.85.7.1 80121,80122 1ec7A 446 7.56e+00 1bqg c.1.11.2,d.54.1.1 29218,38862 1mfmA 153 8.31e+00 1mfmA b.1.8.1 22246 1eu1A 780 8.51e+00 1dmr b.52.2.2,c.81.1.1 26903,35311 1mzbA 136 8.52e+00 a.4.5.42 91497 2g7jA 124 8.52e+00 1m65A 245 8.64e+00 c.6.3.1 84847 1a8y 367 8.85e+00 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1egpA 45 8.85e+00 1egpA d.40.1.1 38561 1x8vA 455 8.96e+00 1fkqA 124 9.13e+00 3lzt d.2.1.2 36601 1h05A 146 9.14e+00 c.23.13.1 76433 1fr3A 67 9.16e+00 1fr3A b.40.6.1 25436 1i27A 73 9.25e+00 1i27A a.4.5.30 61555 1eaxA 241 9.38e+00 b.47.1.2 64889 1rrmA 386 9.38e+00 e.22.1.2 105081 1h30A 422 9.39e+00 b.29.1.4,b.29.1.4 76604,76605 1hw1A 239 9.89e+00 1e2xA a.4.5.6,a.78.1.1 16111,18441 1g0cA 364 9.90e+00 7a3hA c.1.8.3 60165 1g31A 111 1.03e+01 1g31A b.35.1.1 24656 1o7iA 119 1.07e+01 b.40.4.3 86642 1dkuA 317 1.08e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1xkzA 255 1.13e+01 1f28A 297 1.14e+01 1bkpA d.117.1.1 59608 1q8fA 313 1.17e+01 c.70.1.1 96203 1sfdA 105 1.18e+01 b.6.1.1 105480 1oqvA 192 1.19e+01 d.24.1.2 87320 1eexA 554 1.24e+01 1dioA c.1.19.3 29650 1fgkA 310 1.29e+01 1fgkA d.144.1.7 41693 1n0qA 93 1.30e+01 k.37.1.1 79754 1g3qA 237 1.30e+01 1hyqA c.37.1.10 60237 1h6kA 757 1.34e+01 a.118.1.14,a.118.1.14,a.118.1.14 60675,60676,60677 1tmxA 293 1.38e+01 1bu6O 501 1.41e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1pvmA 184 1.42e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1st9A 143 1.43e+01 c.47.1.10 98987 1fjrA 195 1.55e+01 1fjrA b.102.1.1 59855 1h3gA 601 1.57e+01 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1dekA 241 1.69e+01 1dekA c.37.1.1 31842 1y0yA 353 1.71e+01 1jyhA 157 1.74e+01 d.60.1.3 71956 1qwgA 251 1.77e+01 c.1.27.1 96473 1h1dA 221 1.78e+01 c.66.1.1 83452 1ji7A 89 1.82e+01 a.60.1.1 71682 1e5kA 201 1.83e+01 1fr9A c.68.1.8 34578 1m9xC 146 1.85e+01 a.73.1.1 84907 1px5A 349 1.87e+01 a.160.1.2,d.218.1.6 95277,95278 1dg6A 191 1.87e+01 1d4vB b.22.1.1 23883 1lam 484 1.90e+01 1lam c.50.1.1,c.56.5.3 33166,33829 1m45A 148 1.93e+01 a.39.1.5 78598 1yc5A 246 1.94e+01 1augA 215 1.96e+01 1a2zA c.56.4.1 33798 1ctf 74 1.99e+01 1ctf d.45.1.1 38759 1hxhA 253 2.03e+01 c.2.1.2 76725 1yllA 200 2.03e+01 1f3uB 171 2.04e+01 1f3uB b.65.1.1 27525 1qveA 126 2.04e+01 d.24.1.1 104594 1rm6A 769 2.15e+01 1iirA 415 2.17e+01 1iirA c.87.1.5 62453 1h2bA 359 2.25e+01 b.35.1.2,c.2.1.1 90543,90544 1g2qA 187 2.27e+01 c.61.1.1 65117 1h6kZ 98 2.27e+01 d.58.7.1 60686 1jm1A 204 2.27e+01 b.33.1.1 71745 1g38A 393 2.34e+01 2admA c.66.1.27 60235 1d0qA 103 2.35e+01 1d0qA g.41.3.2 45208 1sw5A 275 2.41e+01 c.94.1.1 106069 1vybA 238 2.42e+01 d.151.1.1 108897 1ggzA 148 2.43e+01 a.39.1.5 70176 1g8aA 227 2.48e+01 c.66.1.3 90506 1f1gA 154 2.50e+01 b.1.8.1 76153 1oxdA 227 2.51e+01 d.22.1.1 93687 1b25A 619 2.52e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1d7oA 297 2.52e+01 1enp c.2.1.2 29907 2pvbA 107 2.54e+01 1a75A a.39.1.4 17205 1t3iA 420 2.55e+01 c.67.1.3 106354 1bxvA 91 2.55e+01 1aac b.6.1.1 22875 1gvp 87 2.56e+01 1gvp b.40.4.7 25369 1se8A 301 2.56e+01 b.40.4.3 105448 1e0nA 27 2.56e+01 b.72.1.1 27807 1am2 199 2.66e+01 1am2 b.86.1.2 28381 1dysA 348 2.66e+01 1bvwA c.6.1.1 30669 1nqzA 194 2.69e+01 d.113.1.1 86077 1hgxA 183 2.73e+01 1tc1A c.61.1.1 34027 1a8l 226 2.83e+01 1a8l c.47.1.2,c.47.1.2 32777,32778 1jidA 128 2.87e+01 d.201.1.1 66735 1q0pA 223 2.91e+01 c.62.1.1 95507 1pu6A 218 2.96e+01 a.96.1.5 95123 1bqcA 302 2.99e+01 1bqcA c.1.8.3 28831 1xu9A 286 3.02e+01 1pwgA 349 3.05e+01 e.3.1.1 104340 1nulA 152 3.07e+01 1nulA c.61.1.1 34011 1oz2A 331 3.07e+01 b.34.9.3,b.34.9.3,b.34.9.3 93781,93782,93783 1b9oA 123 3.12e+01 3lzt d.2.1.2 36597 1bkzA 135 3.13e+01 1a3k b.29.1.3 24202 1pg4A 652 3.15e+01 e.23.1.1 88067 1rkuA 206 3.25e+01 c.108.1.11 97627 1a62 130 3.26e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1wwzA 159 3.28e+01 1e0bA 68 3.29e+01 1e0bA b.34.13.2 37476 1cv8 174 3.30e+01 1cv8 d.3.1.1 37089 1c75A 71 3.36e+01 451c a.3.1.1 15796 1rm6B 324 3.39e+01 1s3cA 141 3.40e+01 1q7zA 566 3.41e+01 c.1.21.2,c.1.26.1 96090,96091 1t4bA 367 3.41e+01 c.2.1.3,d.81.1.1 106406,106407 1hbkA 94 3.43e+01 1aca a.11.1.1 60887 1o54A 277 3.44e+01 c.66.1.13 92482 1nykA 165 3.45e+01 b.33.1.1 86408 1jnrA 643 3.45e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1k3xA 262 3.47e+01 a.156.1.2,b.113.1.1,g.39.1.8 77242,77243,77244 1zceA 155 3.48e+01 1uteA 313 3.50e+01 1uteA d.159.1.1 42078 1f8fA 371 3.52e+01 b.35.1.2,c.2.1.1 83246,83247 1wvfA 520 3.58e+01 1m15A 357 3.58e+01 a.83.1.1,d.128.1.2 78368,78369 1ef8A 261 3.64e+01 1ef8A c.14.1.3 30921 1xpcA 248 3.68e+01 1eswA 500 3.71e+01 1cwyA c.1.8.1 59500 1efyA 350 3.72e+01 1a26 a.41.1.1,d.166.1.2 17413,42275 1gmuA 143 3.73e+01 b.107.1.1,d.58.38.1 65335,65336 1rvkA 382 3.74e+01 c.1.11.2,d.54.1.1 97928,97929 1nr0A 611 3.75e+01 b.69.4.1,b.69.4.1 86078,86079 1tp6A 128 3.76e+01 d.17.4.12 107184 1yb3A 175 3.78e+01 1bia 321 3.83e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1bh9B 89 3.84e+01 1bh9B a.22.1.3 16485 1ja9A 274 3.84e+01 c.2.1.2 62817 1k1eA 180 3.93e+01 c.108.1.5 67995 1rk6A 496 3.96e+01 b.92.1.6,b.92.1.6,c.1.9.11 97599,97600,97601 1ecfA 504 3.98e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 2arcA 164 4.00e+01 2arcA b.82.4.1 28148 1fm0D 81 4.01e+01 1fmaD d.15.3.1 37642 1ye8A 178 4.08e+01 1ut1A 148 4.09e+01 b.2.3.6 108014 1cc8A 73 4.11e+01 1cc8A d.58.17.1 39343 1kqpA 271 4.15e+01 c.26.2.1 72883 1mb3A 124 4.15e+01 c.23.1.1 78907 1dcfA 136 4.16e+01 1dcfA c.23.1.2 31124 1goiA 499 4.25e+01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 1h6fA 193 4.25e+01 b.2.5.4 70901 1fxkC 133 4.32e+01 1fxkC a.2.5.1 15702 1bn8A 420 4.39e+01 1pcl b.80.1.1 28022 1vpjA 192 4.49e+01 1s29A 92 4.49e+01 a.4.5.46 98373 1oalA 151 4.49e+01 b.1.8.1 86739 1evlA 401 4.53e+01 1qf6A c.51.1.1,d.104.1.1 33202,40751 1f7lA 121 4.55e+01 1f7lA d.150.1.2 59666 1c7gA 456 4.56e+01 c.67.1.2 90415 1fp2A 352 4.64e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1oq1A 223 4.65e+01 b.29.1.17 93408 2sli 679 4.66e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1em2A 229 4.68e+01 1em2A d.129.3.2 41321 1h9dB 134 4.79e+01 2jhbA b.54.1.1 60822 1dvoA 152 4.79e+01 1dvoA a.136.1.1 19623 1oaiA 59 4.81e+01 a.5.2.3 81255 1euwA 152 4.86e+01 1dupA b.85.4.1 28349 1f5nA 592 4.95e+01 1dg3A a.114.1.1,c.37.1.8 19077,32152 1cl1A 395 4.96e+01 1cl2A c.67.1.3 34395 1h2eA 207 4.96e+01 c.60.1.1 70857 1f9yA 158 4.99e+01 d.58.30.1 83249 1vioA 243 5.02e+01 d.265.1.3,d.66.1.5 100762,100763 1nz0A 118 5.02e+01 d.14.1.2 86433 1avaC 181 5.04e+01 1avaC b.42.4.1 25604 1woqA 267 5.05e+01 c.55.1.10,c.55.1.10 109462,109463 1f00I 282 5.06e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1fpzA 212 5.12e+01 1fpzA c.45.1.1 59976 1f60A 458 5.14e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1cs0A 1073 5.16e+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 18558,31487,31673,31674,41518,41519 1dfuP 94 5.18e+01 1dfuP b.53.1.1 26936 1s2oA 244 5.18e+01 1lycA 343 5.21e+01 a.93.1.1 74344 1qqqA 264 5.28e+01 1bkpA d.117.1.1 40931 1g8kA 825 5.32e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 1y0bA 197 5.33e+01 1tbfA 347 5.36e+01 a.211.1.2 106743 1n8kA 374 5.37e+01 b.35.1.2,c.2.1.1 80298,80299 1h3fA 432 5.43e+01 c.26.1.1,d.66.1.4 76631,76632 1vyiA 112 5.43e+01 1q74A 303 5.46e+01 c.134.1.1 96019 1oruA 195 5.46e+01 b.58.1.2 93464 1k2eA 156 5.51e+01 d.113.1.1 72010 1vqqA 646 5.51e+01 1xsvA 113 5.54e+01 1dzlA 505 5.69e+01 1dzlA b.121.6.1 23586 1gkpA 458 5.73e+01 b.92.1.3,c.1.9.6 70231,70232 1xjvA 294 5.76e+01 1pqhA 143 5.91e+01 b.52.2.1 95017 1gg4A 452 5.93e+01 1gg4A c.59.1.1,c.98.1.1,c.72.2.1 33957,58985,58986 1kgdA 180 5.95e+01 c.37.1.1 68582 1c9oA 66 5.95e+01 1mjc b.40.4.5 25325 1lf7A 182 5.97e+01 b.60.1.1 73878 1mgqA 83 6.01e+01 b.38.1.1 79099 1aohA 147 6.04e+01 1aohA b.2.2.2 22401 1jykA 254 6.08e+01 c.68.1.13 67458 1b8aA 438 6.18e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1dzfA 215 6.20e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1c0pA 363 6.25e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1txgA 335 6.27e+01 1yrcA 414 6.32e+01 1n2eA 300 6.37e+01 c.26.1.4 85268 1yn9A 169 6.41e+01 1qmvA 197 6.41e+01 1qq2A c.47.1.10 33066 1cydA 244 6.50e+01 1cydA c.2.1.2 29825 1g5tA 196 6.53e+01 1g5rA c.37.1.11 32366 1j27A 102 6.55e+01 d.58.50.1 90778 1kicA 339 6.56e+01 c.70.1.1 72510 1k4iA 233 6.60e+01 d.115.1.2 72056 1v4vA 376 6.61e+01 c.87.1.3 100313 1agi 125 6.61e+01 7rsa d.5.1.1 37303 1wr8A 231 6.62e+01 1qd1A 325 6.63e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1ako 268 6.69e+01 1ako d.151.1.1 41779 1bkpA 278 6.70e+01 1bkpA d.117.1.1 41029 1orc 71 6.71e+01 1orc a.35.1.2 17054 1vhuA 211 6.71e+01 c.50.1.2 100703 1d4oA 184 6.73e+01 1d4oA c.31.1.4 31748 1dkiA 371 6.75e+01 1dkiA d.3.1.1 37090 1uscA 178 6.79e+01 b.45.1.2 99860 1gu9A 177 6.80e+01 a.152.1.1 65540 1g60A 260 6.86e+01 c.66.1.11 70151 1vmgA 95 6.88e+01 1u8vA 490 6.93e+01 1frb 315 6.94e+01 1frb c.1.7.1 28665 1f20A 435 7.00e+01 b.43.4.1,c.25.1.4 64932,64933 1kqwA 134 7.03e+01 b.60.1.2 72887 1hq1A 105 7.05e+01 1dulA a.36.1.1 17120 1h54A 754 7.07e+01 a.102.1.4,b.30.5.3 60634,60635 1h70A 255 7.10e+01 1h70A d.126.1.3 60711 1oh0A 131 7.18e+01 d.17.4.3 87004 1es9A 232 7.22e+01 1wab c.23.10.3 31340 1jndA 420 7.33e+01 c.1.8.5,d.26.3.1 71757,71758 1dcjA 81 7.38e+01 1dcjA d.68.3.3 59115 1akz 223 7.43e+01 3eugA c.18.1.1 31007 1xyiA 66 7.44e+01 16pk 415 7.45e+01 16pk c.86.1.1 35454 1p5vB 147 7.45e+01 b.2.3.2 87814 1k5cA 335 7.50e+01 b.80.1.3 72076 1upqA 123 7.63e+01 1j2rA 199 7.67e+01 c.33.1.3 90788 1gcqC 70 7.73e+01 1gcpA b.34.2.1 60436 1oi2A 366 7.73e+01 c.119.1.2 103802 1e3dA 266 7.75e+01 2frvA e.19.1.1 59188 1llnA 262 7.79e+01 d.165.1.1 84625 1g2bA 62 7.81e+01 1tud b.34.2.1 24488 1s2wA 295 7.85e+01 c.1.12.7 98407 1qw2A 102 7.91e+01 d.249.1.1 96456 1vkfA 188 8.03e+01 c.1.29.1 108656 1vcaA 202 8.06e+01 1vcaA b.1.1.3,b.1.1.4 21649,21685 1y7rA 133 8.07e+01 1qksA 567 8.11e+01 1qksA a.3.1.2,b.70.2.1 15951,27710 1bebA 162 8.20e+01 1bebA b.60.1.1 27115 1gvjA 146 8.21e+01 a.4.5.21 90525 1ytlA 174 8.33e+01 1jakA 512 8.35e+01 c.1.8.6,d.92.2.1 66472,66473 1fp1D 372 8.37e+01 1fpqA a.4.5.29,c.66.1.12 59939,59940 1n7oA 721 8.41e+01 a.102.3.2,b.24.1.1,b.30.5.2 80259,80260,80261 1nthA 458 8.41e+01 c.1.25.1 80730 1ooyA 481 8.46e+01 c.124.1.3,c.124.1.2 93388,93389 1io0A 185 8.48e+01 c.10.1.1 76753 1guqA 348 8.56e+01 1guqA d.13.1.2,d.13.1.2 37522,37523 1jf8A 131 8.59e+01 c.44.1.1 66621 1rliA 184 8.59e+01 c.23.5.6 97647 1j24A 143 8.62e+01 c.52.1.20 84008 1iooA 196 8.63e+01 d.124.1.1 71250 1giqA 413 8.63e+01 d.166.1.1,d.166.1.1 76224,76225 1te2A 226 8.70e+01 c.108.1.6 106792 1gcqA 61 8.81e+01 1ckaA b.34.2.1 60434 1gppA 237 8.81e+01 b.86.1.2 76262 1gc0A 398 8.85e+01 c.67.1.3 70168 1zelA 298 8.86e+01 1h8eA 510 8.91e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 3ezmA 101 8.98e+01 3ezmA b.89.1.1 28395 1suuA 312 8.98e+01 b.68.10.1 99006 1wp5A 323 8.98e+01