# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 2cw9A 194 9.43e-01 1f7tA 122 9.84e-01 1f7lA d.150.1.2 59667 1cqxA 403 1.10e+00 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1tmxA 293 1.31e+00 1yz7A 188 1.58e+00 1c02A 166 1.83e+00 1qspA a.24.10.2 16633 1dc1A 323 2.67e+00 1dc1A c.52.1.11 33321 1uurA 473 2.69e+00 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1f7lA 121 2.98e+00 1f7lA d.150.1.2 59666 1qspA 165 3.04e+00 1qspA a.24.10.2 16639 1q6uA 245 3.48e+00 d.26.1.1 95998 1q6hA 224 4.22e+00 d.26.1.1 95975 1udxA 416 4.51e+00 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1yj7A 171 4.75e+00 1q3eA 207 5.30e+00 b.82.3.2 95669 1z7uA 112 5.39e+00 2d7vA 162 6.10e+00 1qi7A 253 6.44e+00 1qi7A d.165.1.1 42210 2ahjA 206 7.99e+00 2ahjA d.149.1.1 41772 1josA 128 8.06e+00 d.52.7.1 84191 1ugpA 203 8.25e+00 d.149.1.1 107831 2cwyA 94 8.73e+00 1ireA 204 8.76e+00 d.149.1.1 76769 2b7eA 59 9.66e+00 1bm9A 122 9.74e+00 1bm9A a.4.5.7 16116 1necA 216 1.07e+01 1vfrA d.90.1.1 40249 1ahjA 207 1.14e+01 2ahjA d.149.1.1 41774 2ahjC 206 1.15e+01 2ahjA d.149.1.1 41773 1zx4A 192 1.17e+01 1knqA 175 1.17e+01 c.37.1.17 72786 1xq8A 140 1.19e+01 1aipC 196 1.39e+01 1tfe a.5.2.2,d.43.1.1 58930,58931 1bxeA 113 1.54e+01 1bxeA d.55.1.1 38898 2ezk 99 1.54e+01 2ezk a.4.1.2 16027 1cqa 133 1.57e+01 3nul d.110.1.1 40890 1ykiA 217 1.62e+01 1yviA 149 1.63e+01 1icrA 217 1.63e+01 1vfrA d.90.1.1 62274 1cojA 212 1.68e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1m3sA 186 1.69e+01 c.80.1.3 78573 2cz1A 206 1.71e+01 1f4kA 122 1.71e+01 1bm9A a.4.5.7 59646 1fthA 122 1.73e+01 d.150.1.2 60028 1mzbA 136 1.75e+01 a.4.5.42 91497 1ig8A 486 1.76e+01 2yhx c.55.1.3,c.55.1.3 64746,64747 1i50A 1733 1.88e+01 e.29.1.2 61754 1p68A 102 1.89e+01 k.8.1.1 94158 1gqeA 365 1.91e+01 e.38.1.1 70351 1tc6A 236 1.96e+01 d.122.1.1 106756 1d5yA 292 1.96e+01 1d5yA a.4.1.8,a.4.1.8,d.60.1.2 16055,16056,39532 1g60A 260 1.98e+01 c.66.1.11 70151 1x0tA 120 1.99e+01 1x6iA 91 2.01e+01 1fx7A 230 2.04e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 1wpuA 147 2.05e+01 1bf5A 545 2.12e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 1b33A 160 2.16e+01 1qgwC a.1.1.3 15649 1allA 160 2.18e+01 1qgwC a.1.1.3 15647 1bo1A 416 2.22e+01 1bo1A d.143.1.2 41591 1g8pA 350 2.23e+01 1g8pA c.37.1.20 60376 1wwzA 159 2.26e+01 1b3oA 514 2.30e+01 1ak5 c.1.5.1 28640 1g5aA 628 2.34e+01 b.71.1.1,c.1.8.1 65152,65153 1ab4 477 2.40e+01 1ab4 e.11.1.1 43251 1vm0A 130 2.41e+01 d.68.6.2 108873 1liaA 164 2.44e+01 1cpcA a.1.1.3 15661 2gh1A 301 2.51e+01 2ezl 99 2.54e+01 2ezk a.4.1.2 16026 1wpbA 172 2.57e+01 1io1A 398 2.57e+01 1io1A e.32.1.1 62611 1ku1A 230 2.62e+01 a.118.3.1 72996 3nul 130 2.83e+01 3nul d.110.1.1 40891 1twfA 1733 2.86e+01 1kbuA 349 2.86e+01 a.60.9.1,d.163.1.1 72284,72285 1sedA 117 2.90e+01 a.219.1.1 105449 1pls 113 2.91e+01 1pls b.55.1.1 26965 1yw4A 341 2.97e+01 1a0k 131 3.00e+01 3nul d.110.1.1 40892 1quuA 250 3.01e+01 1quuA a.7.1.1,a.7.1.1 16320,16321 2bnmA 198 3.18e+01 1ihoA 283 3.20e+01 1ihoA c.26.1.4 62390 1vfgA 390 3.23e+01 a.173.1.1,d.218.1.4 108570,108571 1p5zB 263 3.29e+01 c.37.1.1 87815 1ytzT 107 3.29e+01 1g24A 211 3.33e+01 1g24A d.166.1.1 42270 9apiA 347 3.36e+01 1ovaA e.1.1.1 42630 2bmoB 194 3.37e+01 1k9uA 78 3.55e+01 a.39.1.10 84348 1ad6 185 3.60e+01 1guxA a.74.1.3 18390 1veaA 148 3.66e+01 d.275.1.1 108529 1uuzA 137 3.67e+01 d.233.1.1 100024 1twfK 120 3.82e+01 1t0tV 248 3.89e+01 d.58.4.10 106229 176lA 164 3.98e+01 1l92 d.2.1.3 36942 1y1xA 191 4.08e+01 1y7rA 133 4.10e+01 1yqyA 523 4.15e+01 1cc1L 498 4.23e+01 1h2rL e.18.1.1 43301 1a81A 254 4.24e+01 1a81A d.93.1.1,d.93.1.1 40507,40508 1vhiA 142 4.24e+01 1b3tA d.58.8.1 39230 1yoyA 175 4.26e+01 1wd6A 123 4.37e+01 1xvhA 129 4.45e+01 2trcP 217 4.45e+01 1b9yC c.47.1.6 33051 1b4pA 217 4.47e+01 a.45.1.1,c.47.1.5 83158,83159 1guxA 218 4.47e+01 1guxA a.74.1.3 18388 1czaN 917 4.51e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 1bt4A 362 4.57e+01 1bjnA c.67.1.4 34468 1zcbA 362 4.59e+01 1ofcX 304 4.60e+01 a.4.1.3,a.4.1.13,a.187.1.1 92826,92827,92828 2a9kB 223 4.71e+01 1b5sA 242 4.75e+01 1eaf c.43.1.1 32626 1oqyA 368 4.76e+01 a.5.2.1,a.5.2.1,a.189.1.1,d.15.1.1 93439,93440,93441,93442 1louA 101 4.84e+01 1ris d.58.14.1 39323 1z3xA 238 4.90e+01 1hkcA 917 4.93e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33475,33476,33477,33478 1ca9A 192 4.96e+01 1d0aB b.8.1.1,h.1.2.1 23244,45451 1m1jA 491 4.96e+01 h.1.8.1 74369 1m2kA 249 4.99e+01 c.31.1.5 84754 171l 164 5.05e+01 1l92 d.2.1.3 36962 1k3kA 158 5.11e+01 f.1.4.1 72017 1kfd 605 5.17e+01 1xwl c.55.3.5,e.8.1.1 33694,42987 2bduA 297 5.20e+01 1dgkN 917 5.25e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33487,33488,33489,33490 1ecmA 109 5.39e+01 1ecmA a.130.1.1 19492 1qf6A 642 5.41e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1ac1A 189 5.42e+01 1fvkA c.47.1.13 90326 1wlqC 201 5.43e+01 a.4.5.52 109400 1i8vA 96 5.45e+01 d.1.1.2 61985 2ga1A 106 5.46e+01 3crxA 343 5.48e+01 4crxA a.60.9.1,d.163.1.1 18101,42161 192l 164 5.49e+01 1l92 d.2.1.3 36815 1asx 159 5.55e+01 1a6dA c.8.5.2 30821 1obs 267 5.59e+01 1mrj d.165.1.1 42213 1rl0A 255 5.61e+01 1fslA 143 5.72e+01 2gdm a.1.1.2 15229 1hfoA 113 5.92e+01 d.80.1.3 61006 2auaA 224 5.94e+01 1e9gB 286 5.94e+01 1wgjA b.40.5.1 59394 2bolA 314 5.96e+01 1fvkA 189 5.96e+01 1fvkA c.47.1.13 90351 1dkvA 699 5.97e+01 1dkvA 1b3tA 147 5.99e+01 1b3tA d.58.8.1 39228 1vmbA 140 6.05e+01 1cr1A 296 6.07e+01 1cr1A c.37.1.11 32286 1dlwA 116 6.11e+01 1dlyA a.1.1.1 14982 1y4oA 104 6.14e+01 1s2xA 206 6.14e+01 a.47.3.1 105229 2sas 185 6.15e+01 2sas a.39.1.5 17258 2ezvA 269 6.17e+01 1or7A 194 6.24e+01 a.4.13.2,a.177.1.1 87332,87333 1b8dA 164 6.27e+01 1cpcA a.1.1.3 15665 1jmsA 381 6.28e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1ehyA 294 6.37e+01 1ehyA c.69.1.11 34693 2aifA 135 6.38e+01 1ib8A 164 6.38e+01 b.38.2.1,d.52.4.1 71168,71169 1d8yA 605 6.39e+01 1xwl c.55.3.5,e.8.1.1 33684,42977 2hddA 61 6.44e+01 2hddA a.4.1.1 15971 1dovA 181 6.47e+01 1dovA a.24.9.1 16627 1b8yA 167 6.52e+01 1hfc d.92.1.11 40377 1m8aA 70 6.55e+01 d.9.1.1 74579 1cr0A 296 6.58e+01 1cr1A c.37.1.11 32287 1alvA 173 6.58e+01 1alvA a.39.1.8 17370 1chuA 540 6.60e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1bsmA 201 6.64e+01 1avmA a.2.11.1,d.44.1.1 15780,38743 1hw1A 239 6.81e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 2g09A 297 7.02e+01 1hkbA 917 7.08e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33479,33480,33481,33482 8prkB 287 7.09e+01 1wgjA b.40.5.1 25396 2c0rA 362 7.26e+01 1dsbA 189 7.27e+01 1fvkA c.47.1.13 90347 1w3uA 362 7.27e+01 1gmpA 96 7.30e+01 1rgeA d.1.1.2 36036 1nh1A 330 7.32e+01 e.45.1.1 91871 1gifA 115 7.33e+01 1dptA d.80.1.3 39837 1fiqB 350 7.34e+01 1fiqB d.87.2.1,d.145.1.3 40229,41760 1q2hA 69 7.38e+01 a.34.4.1 104498 1g4uS 383 7.42e+01 1g4uS a.24.11.1,c.45.1.2 16643,32691 1lswA 131 7.53e+01 d.110.3.2 78181 1hddC 61 7.54e+01 2hddA a.4.1.1 15978 1gd0A 122 7.54e+01 1dptA d.80.1.3 39834 2d27A 149 7.57e+01 1du0A 57 7.57e+01 2hddA a.4.1.1 15974 1pyp 285 7.59e+01 1wgjA b.40.5.1 25409 1yarO 237 7.62e+01 1xqiA 195 7.72e+01 1lp8A 254 7.78e+01 d.165.1.1 91082 1zm0A 114 7.78e+01 1xmeA 568 7.81e+01 1bed 181 7.83e+01 1fvkA c.47.1.13 90330 2ffjA 300 7.91e+01 1y9qA 192 7.93e+01 1u3aA 189 7.95e+01 1g99A 408 7.97e+01 1g99A c.55.1.2,c.55.1.2 33457,33458 1v9nA 360 8.02e+01 1feuA 206 8.07e+01 1feuA b.53.1.1 59801 1oaoC 729 8.15e+01 e.26.1.3 86746 1rj1A 151 8.15e+01 a.29.6.1 97526 1acvA 189 8.23e+01 1fvkA c.47.1.13 90328 2b3oA 532 8.25e+01 1hi2A 135 8.27e+01 7rsa d.5.1.1 61057 1u0mA 382 8.27e+01 c.95.1.2,c.95.1.2 107557,107558 1mfiA 114 8.27e+01 1dptA d.80.1.3 39856 1xx0A 127 8.28e+01 1e9gA 286 8.30e+01 1wgjA b.40.5.1 59393 1qhaA 917 8.35e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33467,33468,33469,33470 1tueB 218 8.39e+01 b.91.1.1 107324 1drmA 131 8.45e+01 1drmA d.110.3.2 40908 2brcA 214 8.47e+01 1dgnA 89 8.47e+01 1dgnA a.77.1.3 18436 2b95A 106 8.63e+01 1h6qA 168 8.69e+01 1h6qA b.88.1.2 60692 1e2xA 243 8.70e+01 1e2xA a.4.5.6,a.78.1.1 16113,18443 1fzcA 87 8.84e+01 1fzcA h.1.8.1 45590 2cunA 410 8.95e+01 1klxA 138 8.98e+01 a.118.18.1 77440