# 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 1rybA 212 5.21e-02 c.56.3.1 98098 1u69A 163 1.75e-01 d.32.1.7 107699 1k3yA 221 2.34e-01 a.45.1.1,c.47.1.5 77245,77246 1y7tA 327 2.50e-01 1womA 271 2.61e-01 1bmdA 327 2.80e-01 1bmdA c.2.1.5,d.162.1.1 30139,42106 1v7cA 351 3.51e-01 c.79.1.1 100446 2gaiA 633 3.74e-01 1zemA 262 3.74e-01 1bdmA 327 4.00e-01 1bmdA c.2.1.5,d.162.1.1 30137,42104 2b33A 140 4.71e-01 1vhmA 195 4.76e-01 d.110.2.1 100691 1y74A 57 5.03e-01 1df7A 159 6.14e-01 3dfr c.71.1.1 34885 2c0cA 362 7.11e-01 1f3aA 222 8.47e-01 1pgtA a.45.1.1,c.47.1.5 17701,32995 1i1qA 520 9.20e-01 1qdlA d.161.1.1 61543 1xd7A 145 1.13e+00 a.4.5.55 109566 1jvnA 555 1.19e+00 c.1.2.1,c.23.16.1 67355,67356 1rypC 244 1.66e+00 1rypC d.153.1.4 41934 1qxrA 189 1.67e+00 b.82.1.7 96552 1rw2A 152 1.69e+00 a.118.19.1 97961 1ox6A 555 1.72e+00 c.1.2.1,c.23.16.1 87505,87506 1vpkA 378 1.89e+00 1ysjA 404 2.06e+00 1x82A 190 2.25e+00 1yuwA 554 2.30e+00 1xygD 359 2.33e+00 2fd5A 180 2.44e+00 1wxxA 382 2.44e+00 1ryp2 233 2.52e+00 1ryp2 1vf1A 229 2.56e+00 1wwpA 119 2.64e+00 1z6oM 191 2.73e+00 1e1hA 287 2.79e+00 d.92.1.7 83167 1pkp 150 3.40e+00 1pkp d.14.1.1,d.50.1.2 37551,38787 1k3bA 119 3.43e+00 b.61.5.1 72016 1sdoA 203 3.48e+00 c.52.1.21 98809 1vcdA 126 3.53e+00 1jb0D 138 4.12e+00 1jb0D d.187.1.1 62823 1lj2A 110 4.30e+00 h.1.13.2 73926 1q2zA 120 4.87e+00 a.118.19.1 95656 1h1wA 289 5.21e+00 d.144.1.7 83460 1avoA 60 5.29e+00 1avoA a.24.8.1 16619 1eudB 396 5.57e+00 2scuB c.23.4.1,d.142.1.4 31150,41571 1ee8A 266 6.02e+00 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1zmbA 290 6.08e+00 1v2xA 194 6.57e+00 c.116.1.1 100274 2pviA 157 6.70e+00 3pviA c.52.1.6 33302 1kl7A 514 6.85e+00 c.79.1.1 72678 1mldA 314 7.21e+00 2cmd c.2.1.5,d.162.1.1 30122,42089 1lba 146 7.65e+00 1lba d.118.1.1 41062 1bupA 386 7.99e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 1y9lA 115 8.08e+00 1cojA 212 8.37e+00 1avmA a.2.11.1,d.44.1.1 15737,38734 1onqA 283 8.57e+00 b.1.1.2,d.19.1.1 93365,93366 3xis 387 8.65e+00 4xis c.1.15.3 29423 1ksqA 75 9.14e+00 g.23.1.1 91026 1phk 298 9.24e+00 1cdkA d.144.1.7 41635 1mkp 144 9.38e+00 1vhrA c.45.1.1 32654 3pviA 157 9.85e+00 3pviA c.52.1.6 33300 1avqA 228 1.01e+01 1avqA c.52.1.13 33326 1z9lA 128 1.02e+01 1w8kA 447 1.02e+01 1avwB 171 1.03e+01 1wba b.42.4.1 25599 1c6vX 81 1.03e+01 1ihvA b.34.7.1 24641 2f9sA 151 1.07e+01 1kay 381 1.10e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1st9A 143 1.13e+01 c.47.1.10 98987 1dl5A 317 1.14e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1llmC 88 1.15e+01 g.37.1.1,g.37.1.1 91059,91060 1h8mA 140 1.15e+01 1h8mA d.110.4.1 60782 1mw7A 240 1.16e+01 e.39.1.1 79557 1v9yA 167 1.20e+01 d.110.3.2 108454 1k4nA 192 1.23e+01 d.32.1.5 72059 2bmeA 186 1.24e+01 1e3dB 542 1.27e+01 1h2rL e.18.1.1 59189 1zl8A 53 1.28e+01 1qh4A 380 1.30e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 1s3sG 127 1.31e+01 d.15.1.2 98457 1uu3A 310 1.32e+01 d.144.1.7 99999 1tu7A 208 1.35e+01 1ox0A 430 1.38e+01 c.95.1.1,c.95.1.1 87495,87496 1clvI 32 1.41e+01 1qfdA g.3.2.1 44075 4xis 387 1.42e+01 4xis c.1.15.3 29421 1vrpA 381 1.43e+01 1tf1A 198 1.45e+01 d.110.2.2 106826 1y3nA 490 1.46e+01 1hnjA 317 1.50e+01 1hn9A c.95.1.2,c.95.1.2 35969,35970 1wucA 250 1.56e+01 1f5qB 252 1.57e+01 1f5qB a.74.1.1,a.74.1.1 18362,18363 256bA 106 1.57e+01 256bA a.24.3.1 16539 1nh2D 121 1.60e+01 a.32.1.1,b.56.1.1 91876,91877 1t9mA 214 1.63e+01 2mltA 27 1.66e+01 j.19.1.1 46171 1yoaA 159 1.67e+01 1uunA 184 1.70e+01 f.6.1.2 100012 1yr2A 741 1.72e+01 1oxjA 173 1.84e+01 a.60.1.2,a.118.1.13 87517,87518 1g5aA 628 1.87e+01 b.71.1.1,c.1.8.1 65152,65153 1fntc 245 1.88e+01 1muwA 386 1.89e+01 c.1.15.3 79495 1ytfD 121 1.90e+01 1ytfD a.32.1.1,b.56.1.1 16998,27011 2cs7A 55 1.92e+01 1wloA 136 2.02e+01 1omwA 689 2.03e+01 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 1osdA 72 2.04e+01 d.58.17.1 104022 1p6xA 334 2.08e+01 c.37.1.1 94195 2blkA 122 2.08e+01 1vk8A 106 2.08e+01 d.58.48.1 108636 1nowA 507 2.09e+01 c.1.8.6,d.92.2.1 85936,85937 1wgbA 159 2.11e+01 1qh8A 478 2.14e+01 1qguA c.92.2.3 35633 1j8mF 297 2.16e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 2g7uA 257 2.23e+01 2f60K 64 2.24e+01 1ujrA 110 2.24e+01 1xmbA 418 2.30e+01 1yge 839 2.35e+01 1yge a.119.1.1,b.12.1.1 19234,23634 1j8yF 297 2.36e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1rktA 205 2.40e+01 a.4.1.9,a.121.1.1 97623,97624 2cblA 305 2.40e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17380,17774,40528 1wnlA 235 2.41e+01 1xw8A 252 2.42e+01 1jogA 146 2.43e+01 a.24.16.2 77142 1zwxA 301 2.53e+01 1owfB 94 2.56e+01 a.55.1.1 87488 1v6tA 255 2.56e+01 1iugA 352 2.58e+01 c.67.1.3 90699 1wk2A 121 2.58e+01 2msbA 115 2.69e+01 1rtm1 d.169.1.1 42355 1nyoA 163 2.74e+01 b.118.1.1 92345 2f6mA 65 2.76e+01 1i7wB 151 2.77e+01 1i7wB j.71.1.1 61910 1x47A 98 2.78e+01 1lpbA 95 2.79e+01 1lpbA g.3.10.1,g.3.10.1 44189,44190 1i19A 561 2.87e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 1v5dA 386 2.88e+01 1yvhA 329 2.93e+01 1o70A 324 2.98e+01 b.118.1.1,b.118.1.1 81115,81116 2a0b 125 2.98e+01 2a0b a.24.10.1 16630 1xfsA 178 3.01e+01 d.129.3.5 109589 2ae6A 166 3.06e+01 1sxrA 183 3.07e+01 d.118.1.1 106101 1t0hA 132 3.14e+01 b.34.2.1 106207 1om2A 95 3.15e+01 1om2A a.23.4.1 16520 1sesA 421 3.16e+01 1sesA a.2.7.1,d.104.1.1 15710,40710 1e4fT 419 3.21e+01 1e4fT c.55.1.1,c.55.1.1 33453,33454 1nthA 458 3.27e+01 c.1.25.1 80730 2ftbA 125 3.32e+01 1xrkA 124 3.34e+01 2c4jA 218 3.37e+01 1gwmA 153 3.42e+01 b.18.1.19 83348 2a5jA 191 3.44e+01 1dar 691 3.47e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1 25707,32142,37547,39300 1kq6A 141 3.48e+01 d.189.1.1 91020 2g9iA 249 3.52e+01 1r77A 103 3.55e+01 1hjzA 192 3.57e+01 c.50.1.2 83520 1u20A 212 3.57e+01 1x6vA 630 3.57e+01 1lk5A 229 3.61e+01 c.124.1.4,d.58.40.1 73960,73961 1kaeA 434 3.62e+01 c.82.1.2 72247 2avpA 70 3.62e+01 1l3lA 234 3.68e+01 a.4.6.2,d.110.5.1 73541,73542 1rp4A 389 3.70e+01 a.227.1.1 105027 2ashA 381 3.70e+01 1wgzA 510 3.72e+01 1k2xA 177 3.75e+01 d.153.1.5 90929 1xw5A 217 3.79e+01 3tmkA 216 3.79e+01 3tmkA c.37.1.1 31920 1hd7A 318 3.86e+01 1bix d.151.1.1 41780 1a91 79 3.90e+01 1a91 f.17.1.1 43635 1t3uA 104 3.90e+01 d.244.1.1 99120 2ddrA 306 3.94e+01 1b1cA 181 4.04e+01 1amoA c.23.5.2 31212 1bylA 125 4.06e+01 1bylA d.32.1.2 38495 1cdzA 96 4.09e+01 1cdzA c.15.1.1 30925 1d7qA 143 4.10e+01 1d7qA b.40.4.5 25331 1fjlA 81 4.12e+01 2hddA a.4.1.1 16017 1wkvA 389 4.12e+01 2aw5A 541 4.13e+01 1v30A 124 4.14e+01 1din 236 4.17e+01 1din c.69.1.9 34682 1nxuA 333 4.20e+01 c.122.1.1 86389 1e58A 249 4.24e+01 1qhfA c.60.1.1 59262 1zi8A 236 4.29e+01 1vhuA 211 4.30e+01 c.50.1.2 100703 1g7fA 298 4.32e+01 1pty c.45.1.2 60330 1b7yB 785 4.33e+01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16301,16302,25312,39311,40780,41456 1wq6A 72 4.34e+01 1ctqA 166 4.41e+01 1ctqA c.37.1.8 31965 1eijA 80 4.45e+01 1eijA a.5.6.1 16298 1ppjJ 62 4.49e+01 f.23.14.1 104266 1b5l 172 4.51e+01 1b5l a.26.1.3 16900 1v2bA 177 4.54e+01 d.107.1.2 108279 1yw5A 177 4.59e+01 2btoA 473 4.59e+01 1kkcA 221 4.65e+01 a.2.11.1,d.44.1.1 68660,68661 1dugA 234 4.68e+01 1b8xA a.45.1.1,c.47.1.5 17718,33012 1o7kA 131 4.70e+01 d.189.1.1 81144 1fvrA 327 4.71e+01 d.144.1.7 60047 1uqrA 154 4.72e+01 c.23.13.1 99779 2dg5B 190 4.72e+01 1lqtA 456 4.75e+01 c.3.1.1,c.4.1.1 74198,74199 1ckeA 227 4.77e+01 1ckeA c.37.1.1 31846 1f60A 458 4.80e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1jksA 294 4.84e+01 d.144.1.7 71710 1jjyA 636 4.89e+01 1jjyA 2hddA 61 4.98e+01 2hddA a.4.1.1 15971 1sr4A 206 5.04e+01 b.42.2.1 105948 1zowA 313 5.08e+01 1uroA 367 5.10e+01 1uroA c.1.22.1 29675 2ethA 154 5.11e+01 2f9lA 199 5.12e+01 1su8A 636 5.21e+01 e.26.1.2 98999 1esc 306 5.24e+01 1esc c.23.10.1 31334 1x3sA 195 5.24e+01 1xfcA 384 5.24e+01 1d0cA 444 5.28e+01 d.174.1.1 64769 1rtm1 149 5.28e+01 1rtm1 1cfr 285 5.29e+01 1cfr c.52.1.7 33312 1pa1A 310 5.30e+01 c.45.1.2 94404 1z84A 351 5.31e+01 4tmkA 213 5.33e+01 5tmpA c.37.1.1 31930 1mrj 247 5.33e+01 1mrj d.165.1.1 42177 1za0A 275 5.35e+01 1ifqA 138 5.37e+01 1ifqA d.110.4.1 62350 1u2wA 122 5.39e+01 8pchA 220 5.44e+01 1cs8A 1eu1A 780 5.48e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 1zq7A 207 5.48e+01 2occA 514 5.52e+01 2occA f.24.1.1 43518 2csgA 424 5.54e+01 1dseA 292 5.54e+01 1ryc a.93.1.1 59130 1xn7A 78 5.55e+01 2ex0A 399 5.58e+01 1gg4A 452 5.64e+01 1gg4A c.59.1.1,c.98.1.1,c.72.2.1 33957,58985,58986 1i58A 189 5.68e+01 1b3qA d.122.1.3 61773 1sluA 142 5.70e+01 1sluA b.16.1.1 23685 2f71A 298 5.74e+01 1nwzA 125 5.79e+01 d.110.3.1 86370 2g64A 140 5.83e+01 1qc7A 101 5.86e+01 1qc7A a.118.14.1 18456 3pyp 125 5.88e+01 3pyp d.110.3.1 40897 1efnB 152 5.92e+01 1efnB d.102.1.1 40699 1fzqA 181 5.92e+01 1hurA c.37.1.8 32060 1hw7A 255 5.93e+01 1i7fA d.193.1.1 61297 1x3cA 73 6.05e+01 1iakA 199 6.08e+01 1iakA b.1.1.2,d.19.1.1 21625,38199 1khoA 370 6.09e+01 a.124.1.1,b.12.1.3 72489,72490 1fiwA 290 6.10e+01 5ptp 1ycqA 107 6.12e+01 1ycqA a.42.1.1 17419 1stfI 98 6.13e+01 1stfI d.17.1.2 38006 1su0B 159 6.16e+01 d.224.1.2 106015 1dfeA 37 6.17e+01 1dfeA g.42.1.1 45318 1m0uA 249 6.18e+01 a.45.1.1,c.47.1.5 78359,78360 2cvdA 198 6.23e+01 1qzgA 187 6.23e+01 b.40.4.3 96643 1wjtA 103 6.25e+01 2fjbA 643 6.25e+01 2f6sA 201 6.32e+01 1d1vA 444 6.43e+01 1nseA d.174.1.1 59101 1ed5A 444 6.45e+01 1nseA d.174.1.1 42530 6gsvA 217 6.46e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 1k5dB 201 6.53e+01 b.55.1.3 68169 2b3hA 329 6.56e+01 1gkzA 388 6.59e+01 a.29.5.1,d.122.1.4 65268,65269 1vj1A 363 6.61e+01 b.35.1.2,c.2.1.1 100794,100795 1t9hA 307 6.63e+01 1v54A 514 6.69e+01 f.24.1.1 100321 1yfnA 118 6.73e+01 1gdvA 85 6.75e+01 1ctj a.3.1.1 60458 1ug8A 87 6.82e+01 d.68.7.1 107825 1bed 181 6.90e+01 1fvkA c.47.1.13 90330 1pd21 199 6.96e+01 1pd21 1tyyA 339 6.98e+01 2a74C 343 6.99e+01 1vp2A 208 7.05e+01 1jnrA 643 7.27e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1d0qA 103 7.28e+01 1d0qA g.41.3.2 45208 1uch 230 7.30e+01 1uch d.3.1.6 37129 2govA 195 7.32e+01 1fh0A 221 7.34e+01 1cs8A d.3.1.1 59832 1y6nL 145 7.34e+01 1iy8A 267 7.34e+01 c.2.1.2 83774 1uehA 253 7.37e+01 c.101.1.1 99259 1gcvA 140 7.37e+01 1cg5B a.1.1.2 15410 1uptC 170 7.45e+01 c.37.1.8 99769 1e85A 127 7.47e+01 1bbhA a.24.3.2 16549 1knvA 293 7.48e+01 c.52.1.7 68707 1hd2A 161 7.50e+01 c.47.1.10 60962 1uteA 313 7.62e+01 1uteA d.159.1.1 42078 1binB 143 7.63e+01 2gdm a.1.1.2 15232 1z53A 294 7.63e+01 1uzpA 162 7.77e+01 g.3.11.1,g.3.11.1,g.23.1.1 100232,100233,100234 1on0A 158 7.79e+01 d.108.1.1 87095 1tffA 234 7.79e+01 d.3.1.11 106854 1gyzA 60 7.81e+01 a.144.2.1 70793 1zbyA 294 7.82e+01 3ygsP 97 7.84e+01 3ygsP a.77.1.3 18435 1xd3A 230 7.90e+01 1opd 85 7.97e+01 1ptf d.94.1.1 40560 1r3sA 367 7.99e+01 c.1.22.1 96963 1txoA 237 8.00e+01 1wd6A 123 8.00e+01 1lmeA 176 8.03e+01 d.167.1.1 84629 1dorA 311 8.10e+01 2dorA c.1.4.1 28595 1f4pA 147 8.16e+01 5nul c.23.5.1 59651 2ampA 304 8.19e+01 1z5hA 780 8.19e+01 2b5eA 504 8.25e+01 1fo0B 112 8.29e+01 1kb5B b.1.1.1 20631 1avbA 226 8.30e+01 1led b.29.1.1 24158 1y8oA 419 8.38e+01 1r2zA 274 8.40e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1go4E 100 8.40e+01 h.1.22.1 70296 2dorA 311 8.42e+01 2dorA c.1.4.1 28593 1g6uA 48 8.43e+01 1g6uA k.9.1.1 46425 1wvfA 520 8.46e+01 1z6oA 212 8.51e+01 1wqwA 235 8.55e+01 2aorA 223 8.55e+01 1b8aA 438 8.70e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1aun 208 8.71e+01 1thv b.25.1.1 23900 1rgxA 114 8.72e+01 g.77.1.1 104932 1lvoA 302 8.81e+01 b.47.1.4 74284 1qlaB 239 8.82e+01 1qlaB a.1.2.1,d.15.4.2 15679,37707 1s6bA 119 8.86e+01 a.133.1.2 98592 2b3nA 159 8.87e+01