# List of top-scoring protein chains for t06-100-30-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 4.06e-02 c.56.3.1 98098 1u69A 163 1.36e-01 d.32.1.7 107699 1k3yA 221 1.82e-01 a.45.1.1,c.47.1.5 77245,77246 1womA 271 2.02e-01 1v7cA 351 2.71e-01 c.79.1.1 100446 2gaiA 633 2.89e-01 1zemA 262 2.89e-01 1bdmA 327 3.09e-01 1bmdA c.2.1.5,d.162.1.1 30137,42104 1y74A 57 3.88e-01 1df7A 159 4.73e-01 3dfr c.71.1.1 34885 1i1qA 520 7.07e-01 1qdlA d.161.1.1 61543 1xd7A 145 8.72e-01 a.4.5.55 109566 1rypC 244 1.27e+00 1rypC d.153.1.4 41934 1vpkA 378 1.45e+00 1ysjA 404 1.57e+00 1x82A 190 1.73e+00 2fd5A 180 1.87e+00 1wxxA 382 1.87e+00 1ryp2 233 1.93e+00 1ryp2 1vf1A 229 1.96e+00 1wwpA 119 2.02e+00 1z6oM 191 2.09e+00 1e1hA 287 2.13e+00 d.92.1.7 83167 1k3bA 119 2.62e+00 b.61.5.1 72016 1sdoA 203 2.66e+00 c.52.1.21 98809 1vcdA 126 2.70e+00 1jb0D 138 3.15e+00 1jb0D d.187.1.1 62823 1lj2A 110 3.28e+00 h.1.13.2 73926 1q2zA 120 3.72e+00 a.118.19.1 95656 1avoA 60 4.03e+00 1avoA a.24.8.1 16619 1ee8A 266 4.58e+00 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1v2xA 194 5.01e+00 c.116.1.1 100274 1mldA 314 5.49e+00 2cmd c.2.1.5,d.162.1.1 30122,42089 1lba 146 5.82e+00 1lba d.118.1.1 41062 1bupA 386 6.08e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 1y9lA 115 6.15e+00 1cojA 212 6.37e+00 1avmA a.2.11.1,d.44.1.1 15737,38734 1ksqA 75 6.95e+00 g.23.1.1 91026 3pviA 157 7.48e+00 3pviA c.52.1.6 33300 1avqA 228 7.71e+00 1avqA c.52.1.13 33326 1z9lA 128 7.72e+00 1w8kA 447 7.74e+00 1avwB 171 7.80e+00 1wba b.42.4.1 25599 1c6vX 81 7.82e+00 1ihvA b.34.7.1 24641 2f9sA 151 8.11e+00 1st9A 143 8.61e+00 c.47.1.10 98987 1dl5A 317 8.65e+00 1dl5A c.66.1.7,d.197.1.1 64720,64721 1llmC 88 8.74e+00 g.37.1.1,g.37.1.1 91059,91060 1h8mA 140 8.76e+00 1h8mA d.110.4.1 60782 1mw7A 240 8.82e+00 e.39.1.1 79557 1v9yA 167 9.08e+00 d.110.3.2 108454 1k4nA 192 9.32e+00 d.32.1.5 72059 2bmeA 186 9.43e+00 1e3dB 542 9.68e+00 1h2rL e.18.1.1 59189 1qh4A 380 9.91e+00 1qh4A a.83.1.1,d.128.1.2 18462,41197 1s3sG 127 9.94e+00 d.15.1.2 98457 1uu3A 310 1.01e+01 d.144.1.7 99999 1tu7A 208 1.03e+01 1ox0A 430 1.05e+01 c.95.1.1,c.95.1.1 87495,87496 1clvI 32 1.07e+01 1qfdA g.3.2.1 44075 1tf1A 198 1.10e+01 d.110.2.2 106826 1hnjA 317 1.14e+01 1hn9A c.95.1.2,c.95.1.2 35969,35970 1wucA 250 1.18e+01 1f5qB 252 1.19e+01 1f5qB a.74.1.1,a.74.1.1 18362,18363 256bA 106 1.19e+01 256bA a.24.3.1 16539 1nh2D 121 1.21e+01 a.32.1.1,b.56.1.1 91876,91877 2mltA 27 1.26e+01 j.19.1.1 46171 1yoaA 159 1.26e+01 1uunA 184 1.29e+01 f.6.1.2 100012 1yr2A 741 1.30e+01 1oxjA 173 1.39e+01 a.60.1.2,a.118.1.13 87517,87518 1g5aA 628 1.42e+01 b.71.1.1,c.1.8.1 65152,65153 1muwA 386 1.44e+01 c.1.15.3 79495 2cs7A 55 1.45e+01 1wloA 136 1.53e+01 1osdA 72 1.55e+01 d.58.17.1 104022 1p6xA 334 1.57e+01 c.37.1.1 94195 2blkA 122 1.58e+01 1vk8A 106 1.58e+01 d.58.48.1 108636 1nowA 507 1.58e+01 c.1.8.6,d.92.2.1 85936,85937 1qh8A 478 1.62e+01 1qguA c.92.2.3 35633 1j8mF 297 1.64e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 2g7uA 257 1.69e+01 2f60K 64 1.69e+01 1xmbA 418 1.74e+01 1yge 839 1.78e+01 1yge a.119.1.1,b.12.1.1 19234,23634 1rktA 205 1.82e+01 a.4.1.9,a.121.1.1 97623,97624 1xw8A 252 1.83e+01 1jogA 146 1.84e+01 a.24.16.2 77142 1owfB 94 1.93e+01 a.55.1.1 87488 1v6tA 255 1.94e+01 1iugA 352 1.95e+01 c.67.1.3 90699 1wk2A 121 1.95e+01 2msbA 115 2.03e+01 1rtm1 d.169.1.1 42355 1nyoA 163 2.07e+01 b.118.1.1 92345 2f6mA 65 2.08e+01 1i7wB 151 2.10e+01 1i7wB j.71.1.1 61910 1x47A 98 2.10e+01 1lpbA 95 2.11e+01 1lpbA g.3.10.1,g.3.10.1 44189,44190 1i19A 561 2.17e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 1v5dA 386 2.18e+01 1yvhA 329 2.21e+01 2a0b 125 2.26e+01 2a0b a.24.10.1 16630 1xfsA 178 2.28e+01 d.129.3.5 109589 2ae6A 166 2.31e+01 1sxrA 183 2.32e+01 d.118.1.1 106101 1t0hA 132 2.38e+01 b.34.2.1 106207 1e4fT 419 2.42e+01 1e4fT c.55.1.1,c.55.1.1 33453,33454 1nthA 458 2.47e+01 c.1.25.1 80730 2ftbA 125 2.51e+01 1xrkA 124 2.53e+01 2c4jA 218 2.54e+01 1gwmA 153 2.58e+01 b.18.1.19 83348 2a5jA 191 2.60e+01 1kq6A 141 2.63e+01 d.189.1.1 91020 2g9iA 249 2.66e+01 1r77A 103 2.68e+01 1u20A 212 2.70e+01 1x6vA 630 2.70e+01 1lk5A 229 2.73e+01 c.124.1.4,d.58.40.1 73960,73961 1kaeA 434 2.73e+01 c.82.1.2 72247 1l3lA 234 2.78e+01 a.4.6.2,d.110.5.1 73541,73542 1rp4A 389 2.79e+01 a.227.1.1 105027 2ashA 381 2.79e+01 1wgzA 510 2.81e+01 1k2xA 177 2.83e+01 d.153.1.5 90929 3tmkA 216 2.86e+01 3tmkA c.37.1.1 31920 1hd7A 318 2.91e+01 1bix d.151.1.1 41780 1a91 79 2.94e+01 1a91 f.17.1.1 43635 1t3uA 104 2.95e+01 d.244.1.1 99120 2ddrA 306 2.98e+01 1cdzA 96 3.09e+01 1cdzA c.15.1.1 30925 1d7qA 143 3.09e+01 1d7qA b.40.4.5 25331 1fjlA 81 3.11e+01 2hddA a.4.1.1 16017 1wkvA 389 3.11e+01 1v30A 124 3.12e+01 1din 236 3.14e+01 1din c.69.1.9 34682 1nxuA 333 3.17e+01 c.122.1.1 86389 1e58A 249 3.20e+01 1qhfA c.60.1.1 59262 1zi8A 236 3.24e+01 1vhuA 211 3.25e+01 c.50.1.2 100703 1b7yB 785 3.27e+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 3.28e+01 1ctqA 166 3.33e+01 1ctqA c.37.1.8 31965 1ppjJ 62 3.39e+01 f.23.14.1 104266 1b5l 172 3.40e+01 1b5l a.26.1.3 16900 1v2bA 177 3.42e+01 d.107.1.2 108279 1yw5A 177 3.46e+01 2btoA 473 3.46e+01 1dugA 234 3.53e+01 1b8xA a.45.1.1,c.47.1.5 17718,33012 1uqrA 154 3.56e+01 c.23.13.1 99779 2dg5B 190 3.56e+01 1lqtA 456 3.58e+01 c.3.1.1,c.4.1.1 74198,74199 1ckeA 227 3.60e+01 1ckeA c.37.1.1 31846 1f60A 458 3.62e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1jksA 294 3.65e+01 d.144.1.7 71710 2hddA 61 3.75e+01 2hddA a.4.1.1 15971 1sr4A 206 3.80e+01 b.42.2.1 105948 1zowA 313 3.83e+01 2ethA 154 3.85e+01 2f9lA 199 3.86e+01 1su8A 636 3.93e+01 e.26.1.2 98999 1esc 306 3.95e+01 1esc c.23.10.1 31334 1x3sA 195 3.95e+01 1xfcA 384 3.95e+01 1d0cA 444 3.98e+01 d.174.1.1 64769 1cfr 285 3.99e+01 1cfr c.52.1.7 33312 1pa1A 310 4.00e+01 c.45.1.2 94404 1z84A 351 4.00e+01 4tmkA 213 4.02e+01 5tmpA c.37.1.1 31930 1mrj 247 4.02e+01 1mrj d.165.1.1 42177 1za0A 275 4.04e+01 1ifqA 138 4.05e+01 1ifqA d.110.4.1 62350 1u2wA 122 4.06e+01 1eu1A 780 4.13e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 2csgA 424 4.18e+01 1xn7A 78 4.18e+01 2ex0A 399 4.21e+01 1gg4A 452 4.25e+01 1gg4A c.59.1.1,c.98.1.1,c.72.2.1 33957,58985,58986 1i58A 189 4.28e+01 1b3qA d.122.1.3 61773 1sluA 142 4.29e+01 1sluA b.16.1.1 23685 2f71A 298 4.33e+01 1nwzA 125 4.36e+01 d.110.3.1 86370 2g64A 140 4.40e+01 1qc7A 101 4.41e+01 1qc7A a.118.14.1 18456 1efnB 152 4.46e+01 1efnB d.102.1.1 40699 1fzqA 181 4.46e+01 1hurA c.37.1.8 32060 1hw7A 255 4.47e+01 1i7fA d.193.1.1 61297 1x3cA 73 4.56e+01 1iakA 199 4.58e+01 1iakA b.1.1.2,d.19.1.1 21625,38199 1khoA 370 4.59e+01 a.124.1.1,b.12.1.3 72489,72490 1fiwA 290 4.60e+01 5ptp 1stfI 98 4.62e+01 1stfI d.17.1.2 38006 1su0B 159 4.64e+01 d.224.1.2 106015 1m0uA 249 4.66e+01 a.45.1.1,c.47.1.5 78359,78360 2cvdA 198 4.70e+01 1qzgA 187 4.70e+01 b.40.4.3 96643 1wjtA 103 4.71e+01 2fjbA 643 4.71e+01 1k5dB 201 4.92e+01 b.55.1.3 68169 2b3hA 329 4.94e+01 1vj1A 363 4.98e+01 b.35.1.2,c.2.1.1 100794,100795 1t9hA 307 4.99e+01 1v54A 514 5.04e+01 f.24.1.1 100321 1yfnA 118 5.07e+01 1gdvA 85 5.08e+01 1ctj a.3.1.1 60458 1bed 181 5.19e+01 1fvkA c.47.1.13 90330 1vp2A 208 5.31e+01 1jnrA 643 5.48e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1d0qA 103 5.48e+01 1d0qA g.41.3.2 45208 2govA 195 5.51e+01 1fh0A 221 5.52e+01 1cs8A d.3.1.1 59832 1iy8A 267 5.52e+01 c.2.1.2 83774 1uehA 253 5.55e+01 c.101.1.1 99259 1gcvA 140 5.55e+01 1cg5B a.1.1.2 15410 1e85A 127 5.62e+01 1bbhA a.24.3.2 16549 1knvA 293 5.63e+01 c.52.1.7 68707 1hd2A 161 5.65e+01 c.47.1.10 60962 1uteA 313 5.74e+01 1uteA d.159.1.1 42078 1uzpA 162 5.85e+01 g.3.11.1,g.3.11.1,g.23.1.1 100232,100233,100234 1on0A 158 5.86e+01 d.108.1.1 87095 1tffA 234 5.86e+01 d.3.1.11 106854 3ygsP 97 5.90e+01 3ygsP a.77.1.3 18435 1xd3A 230 5.95e+01 1opd 85 6.00e+01 1ptf d.94.1.1 40560 1r3sA 367 6.01e+01 c.1.22.1 96963 1txoA 237 6.02e+01 1wd6A 123 6.02e+01 1f4pA 147 6.14e+01 5nul c.23.5.1 59651 1z5hA 780 6.16e+01 2b5eA 504 6.20e+01 1fo0B 112 6.24e+01 1kb5B b.1.1.1 20631 1avbA 226 6.24e+01 1led b.29.1.1 24158 1r2zA 274 6.32e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1go4E 100 6.32e+01 h.1.22.1 70296 1g6uA 48 6.34e+01 1g6uA k.9.1.1 46425 1wvfA 520 6.37e+01 1z6oA 212 6.40e+01 1wqwA 235 6.43e+01 1b8aA 438 6.55e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1aun 208 6.55e+01 1thv b.25.1.1 23900 1rgxA 114 6.56e+01 g.77.1.1 104932 1lvoA 302 6.63e+01 b.47.1.4 74284 1s6bA 119 6.67e+01 a.133.1.2 98592 2b3nA 159 6.67e+01 1x4rA 99 6.77e+01 2eutA 294 6.78e+01 1wddS 128 6.86e+01 1z08A 170 6.88e+01 2d1pC 95 6.89e+01 2azwA 148 6.92e+01 1v3vA 333 7.00e+01 b.35.1.2,c.2.1.1 108345,108346 1n4kA 381 7.02e+01 a.118.22.1,b.42.6.1 79992,79993 1ek9A 428 7.05e+01 1ek9A f.5.1.1 43809 1vjoA 393 7.07e+01 c.67.1.3 100827 1eluA 390 7.15e+01 1elqA c.67.1.3 34434 2bkrA 212 7.15e+01 2fsqA 243 7.19e+01 1wb4A 297 7.35e+01 1m1nA 491 7.36e+01 c.92.2.3 78417 2bemA 170 7.36e+01 1ok0A 74 7.43e+01 b.5.1.1 93191 1bl0A 129 7.48e+01 1d5yA a.4.1.8,a.4.1.8 16053,16054 1vzoA 355 7.50e+01 d.144.1.7 108971 1y0zA 330 7.55e+01 1jubA 311 7.57e+01 c.1.4.1 90908 1h65A 270 7.58e+01 c.37.1.8 65640 1t7lA 766 7.59e+01 1na3A 91 7.63e+01 k.38.1.1 85481 1hyvA 166 7.64e+01 1b9dA c.55.3.2 61424 1pbyB 337 7.65e+01 b.69.2.2 94422 1o0sA 605 7.66e+01 c.2.1.7,c.58.1.3 86540,86541 1aol 228 7.72e+01 1aol b.20.1.1 23840 1q4uA 151 7.73e+01 d.38.1.5 95828 1wycA 392 7.74e+01 2ilk 160 7.76e+01 2ilk a.26.1.3 16885 1iyhA 198 7.77e+01 a.45.1.1,c.47.1.5 83790,83791 2fhpA 187 7.80e+01 1afp 51 7.83e+01 1afp g.26.1.1 44947 1x93A 55 7.87e+01 1y0gA 191 7.88e+01 1cf4B 44 7.89e+01 1cf4B 1uptA 171 7.98e+01 c.37.1.8 99767 1wurA 220 8.17e+01 1xeeA 91 8.18e+01 1go3F 107 8.20e+01 a.60.8.2 65407 1o2dA 371 8.35e+01 e.22.1.2 86591 1w19A 160 8.40e+01 1tqyA 424 8.46e+01 c.95.1.1,c.95.1.1 107245,107246 1jmtA 104 8.47e+01 d.58.7.3 63180 1yh3A 256 8.47e+01 1jigA 146 8.53e+01 a.25.1.1 71685 1tdpA 111 8.56e+01 a.29.8.1 106781 1d3yA 301 8.57e+01 1d3yA e.12.1.1 43252 1u6rA 380 8.66e+01 1g7sA 594 8.67e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1vqoH 171 8.72e+01 1vd3A 217 8.74e+01 1gxmA 332 8.81e+01 a.102.5.1 76371 1kllA 130 8.84e+01 d.32.1.2 72720 1wd7A 261 8.96e+01