# List of top-scoring protein chains for t04-100-40-40-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 1d2eA 397 1.60e-03 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 2c78A 405 3.52e-02 1ha3A 405 3.89e-02 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1exmA 405 6.54e-02 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 2fhxA 246 1.94e-01 1uebA 184 3.05e-01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1kk1A 410 3.82e-01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1m2xA 223 3.87e-01 d.157.1.1 84764 1x8hA 228 4.01e-01 1oalA 151 1.05e+00 b.1.8.1 86739 1hd7A 318 1.22e+00 1bix d.151.1.1 41780 1jjeA 222 1.29e+00 1a7tA d.157.1.1 63117 1x8gA 227 1.31e+00 1z6bA 154 1.33e+00 1hoe 74 1.91e+00 1hoe b.5.1.1 22833 1yaiA 151 2.35e+00 1yaiA b.1.8.1 22289 1jjtA 228 2.66e+00 1a7tA d.157.1.1 63139 2c5qA 240 2.94e+00 1p57B 255 2.96e+00 b.47.1.2 94126 2bz6H 254 3.05e+00 1kliH 254 3.46e+00 b.47.1.2 77435 1gpc 218 3.72e+00 1gpc b.40.4.7 25393 1u1zA 168 3.72e+00 d.38.1.6 107602 1gxuA 91 3.79e+00 d.58.10.1 76378 1owxA 121 3.93e+00 d.58.7.1 87494 1bx1A 314 4.26e+00 1fnc b.43.4.2,c.25.1.1 25629,31519 1ok0A 74 4.36e+00 b.5.1.1 93191 1danH 254 4.83e+00 5ptp b.47.1.2 26292 2as9A 210 4.97e+00 1oaqL 120 5.26e+00 b.1.1.1 92708 1hn0A 1021 5.35e+00 a.102.3.2,b.18.1.17,b.24.1.1,b.30.5.2 83616,83617,83618,83619 1fnd 314 5.61e+00 1fnc b.43.4.2,c.25.1.1 25626,31516 1ah6 220 6.83e+00 1yer d.122.1.1 41094 1cid 177 7.16e+00 1cid b.1.1.1,b.1.1.3 19740,21679 2breA 219 7.17e+00 1zo0A 126 7.24e+00 1neu 124 7.45e+00 1neu b.1.1.1 19704 1ktjA 129 7.50e+00 b.1.18.7 72974 1cd8 114 7.58e+00 1cd8 b.1.1.1 19714 1u3oA 82 8.05e+00 1vzqH 250 8.24e+00 2a1kA 233 8.25e+00 2bb6A 414 8.69e+00 1yhfA 115 8.80e+00 2alaA 391 9.00e+00 1fjgL 135 9.17e+00 1fjfL b.40.4.5 25346 1yb3A 175 9.29e+00 1sr9A 644 9.43e+00 a.5.7.1,c.1.10.5,d.270.1.1 105960,105961,105962 2fblA 153 9.68e+00 2fcbA 173 9.79e+00 2fcbA b.1.1.4,b.1.1.4 21781,21782 1lo6A 223 9.85e+00 b.47.1.2 74143 1fnc 314 9.90e+00 1fnc b.43.4.2,c.25.1.1 25627,31517 1nxzA 246 1.00e+01 b.122.1.2,c.116.1.5 86391,86392 2fs2A 151 1.03e+01 1psuA 140 1.12e+01 d.38.1.5 88285 1yhpA 212 1.13e+01 1x8mA 288 1.19e+01 b.82.1.13 109516 1fvuB 125 1.20e+01 1ixxB d.169.1.1 42346 1e3pA 757 1.20e+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 1x99A 145 1.20e+01 1xwvA 129 1.21e+01 1tbuA 118 1.22e+01 1n12A 138 1.30e+01 b.2.3.2 79779 1cqxA 403 1.32e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 2bc2A 227 1.36e+01 1a7tA d.157.1.1 42031 1xauA 122 1.36e+01 1fdr 248 1.40e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 1z9lA 128 1.40e+01 1h8dH 260 1.44e+01 5ptp 1ts9A 102 1.44e+01 2d4qA 257 1.44e+01 2fimA 276 1.60e+01 2d7nA 93 1.67e+01 1g1kA 143 1.70e+01 1aohA b.2.2.2 22404 2brcA 214 1.77e+01 1ifrA 121 1.79e+01 b.1.16.1 71203 1zn8A 180 1.82e+01 1k7iA 479 1.84e+01 b.80.7.1,d.92.1.6 77281,77282 1go7P 462 1.84e+01 b.80.7.1,d.92.1.6 76245,76246 1z8gA 372 1.87e+01 2aw2A 120 1.91e+01 1a6wL 109 1.92e+01 1mfa b.1.1.1 20252 1i7pA 274 1.93e+01 b.43.4.2,c.25.1.1 66048,66049 1dyoA 160 1.93e+01 1dyoA b.18.1.7 23771 2cwsA 237 1.93e+01 1aboA 62 1.94e+01 1bbzA b.34.2.1 24474 1yloA 348 1.96e+01 1hrhA 136 1.97e+01 1rthA c.55.3.1 33577 1iz6A 138 2.21e+01 b.34.5.2,b.40.4.5 76976,76977 1pmnA 364 2.25e+01 d.144.1.7 94907 2c60A 111 2.28e+01 1yukB 120 2.29e+01 1y55X 126 2.30e+01 1fs0E 138 2.43e+01 1aqt a.2.10.1,b.93.1.1 59997,59998 1ifqA 138 2.51e+01 1ifqA d.110.4.1 62350 1x89A 178 2.52e+01 1jmtA 104 2.52e+01 d.58.7.3 63180 1j7xA 302 2.52e+01 c.14.1.2 66425 1bbzA 58 2.53e+01 1bbzA b.34.2.1 24477 2f4lA 297 2.63e+01 2a6sA 84 2.63e+01 1nkgA 508 2.72e+01 b.3.1.2,b.18.1.25,b.30.5.10 103859,103860,103861 1kcqA 104 2.76e+01 d.109.1.1 68449 1ub1A 133 2.76e+01 d.10.1.3 99140 1mqoA 227 2.82e+01 d.157.1.1 103846 1ixmA 192 2.85e+01 1ixmA d.123.1.1 41114 1ftrA 296 2.85e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1qqsA 174 2.90e+01 1nglA b.60.1.1 27143 2eifA 136 2.92e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 2bhuA 602 3.01e+01 1yy5B 513 3.04e+01 1r9fA 136 3.09e+01 d.255.1.1 97257 1f42A 306 3.16e+01 1f42A b.1.1.4,b.1.2.1,b.1.2.1 59636,59637,59638 1que 303 3.29e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1avbA 226 3.39e+01 1led b.29.1.1 24158 1p2zA 968 3.46e+01 b.121.2.2,b.121.2.2 93962,93963 2fhzB 108 3.53e+01 2a7yA 83 3.56e+01 1qz8A 113 3.56e+01 b.140.1.1 96619 1a8rA 221 3.56e+01 1a8rA d.96.1.1 40587 2gpzA 111 3.71e+01 1xypA 190 3.71e+01 1axkA b.29.1.11 24327 1b77A 228 3.74e+01 1b77A d.131.1.2,d.131.1.2 41362,41363 1rthA 560 3.76e+01 1rthA c.55.3.1,e.8.1.2 33576,43028 1r6vA 671 3.78e+01 1q1rA 431 3.79e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1ukgA 252 3.81e+01 b.29.1.1 99489 1tidB 119 3.83e+01 c.13.2.1 107000 1gvzA 237 3.85e+01 b.47.1.2 76360 1wbiA 129 3.86e+01 1w34A 304 3.87e+01 1ycsB 239 3.92e+01 1ycsB d.211.1.1,b.34.2.1 19155,24553 1jvnA 555 3.98e+01 c.1.2.1,c.23.16.1 67355,67356 1i1qB 192 4.01e+01 1qdlB c.23.16.1 61544 1ox6A 555 4.01e+01 c.1.2.1,c.23.16.1 87505,87506 2av9A 147 4.02e+01 1go2A 304 4.04e+01 b.43.4.2,c.25.1.1 76243,76244 2an1A 292 4.12e+01 1sb2A 133 4.14e+01 1o4tA 133 4.20e+01 b.82.1.9 86622 2aaiB 262 4.25e+01 1abrB b.42.2.1,b.42.2.1 25561,25562 1zkkA 167 4.28e+01 2fytA 340 4.29e+01 1tit 98 4.30e+01 1tit b.1.1.4 21716 2cwzA 141 4.37e+01 1s0uA 408 4.40e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1lmiA 131 4.41e+01 b.1.19.1 78098 1j1tA 233 4.44e+01 b.29.1.18 90771 1ylnA 252 4.52e+01 2g1lA 104 4.58e+01 1ckaA 57 4.61e+01 1ckaA b.34.2.1 24459 1pz4A 116 4.62e+01 d.106.1.1 95400 1bqsA 209 4.66e+01 1bqsA b.1.1.4,b.1.1.4 21704,21705 1mj4A 82 4.67e+01 d.120.1.1 79189 1r4yA 136 4.69e+01 d.1.1.3 97056 1ogiA 303 4.74e+01 b.43.4.2,c.25.1.1 92914,92915 1mfa 247 4.75e+01 1mfa b.1.1.1,b.1.1.1 19888,19889 1a7tA 232 4.76e+01 1a7tA d.157.1.1 42041 1gsmA 210 4.77e+01 b.1.1.4,b.1.1.4 65535,65536 1h9sA 140 4.91e+01 1b9mA b.40.6.2,b.40.6.2 60843,60844 2bgoA 140 4.98e+01 1e7uA 961 5.13e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1rsgA 516 5.14e+01 1umhA 184 5.22e+01 b.18.1.21 99605 2bsaA 303 5.22e+01 2b3nA 159 5.24e+01 1luzA 88 5.31e+01 b.40.4.5 74271 1qlpA 394 5.33e+01 1ovaA e.1.1.1 42628 1jcv 153 5.38e+01 1mfmA b.1.8.1 22279 1rds 105 5.47e+01 9rnt d.1.1.4 36236 1vqqA 646 5.49e+01 1x71A 178 5.55e+01 1s12A 94 5.57e+01 1f1gA 154 5.58e+01 b.1.8.1 76153 2b5oA 402 5.63e+01 1mkfA 382 5.70e+01 b.116.1.1 79232 1xr4A 509 5.73e+01 1gl4B 98 5.76e+01 b.1.1.4 65288 1g38A 393 5.76e+01 2admA c.66.1.27 60235 1xo8A 151 5.80e+01 2olbA 517 5.80e+01 1jevA c.94.1.1 35721 1jetA 517 5.84e+01 1jevA c.94.1.1 35718 1shsA 147 5.93e+01 1shsA b.15.1.1 23675 3hhrB 203 5.94e+01 1axiB b.1.2.1,b.1.2.1 22005,22006 1jb9A 316 6.02e+01 1fnc b.43.4.2,c.25.1.1 62840,62841 1n3oA 252 6.03e+01 b.29.1.1 79967 1itwA 741 6.04e+01 c.77.1.2 76793 1cqkA 101 6.07e+01 1cqkA b.1.1.2 21547 1e8cA 498 6.09e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1am2 199 6.17e+01 1am2 b.86.1.2 28381 1914 232 6.19e+01 1914 d.49.1.1,d.49.1.1 83028,83029 1e5dA 402 6.20e+01 1e5dA c.23.5.1,d.157.1.3 31208,42061 1rerA 391 6.29e+01 b.1.18.4,f.10.1.1 97327,97328 2a6vA 226 6.30e+01 1gbg 214 6.31e+01 1axkA b.29.1.2 24171 1rewC 135 6.31e+01 g.7.1.3 97336 1qmyA 167 6.33e+01 1qmyA d.3.1.2 37094 1dzkA 157 6.38e+01 1obpA b.60.1.1 27096 1qx4A 274 6.44e+01 b.43.4.2,c.25.1.1 104624,104625 1earA 147 6.47e+01 b.107.1.1,d.58.38.1 64875,64876 1t0bA 252 6.51e+01 c.23.16.6 106199 2bypA 214 6.58e+01 2bivA 243 6.67e+01 1m8aA 70 6.72e+01 d.9.1.1 74579 2bw2A 140 6.80e+01 1ecfA 504 6.85e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1bkb 136 6.90e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 1f2rI 100 6.91e+01 1c9fA d.15.2.1 37641 1vc1A 110 7.03e+01 c.13.2.1 108493 1vioA 243 7.10e+01 d.265.1.3,d.66.1.5 100762,100763 1uldA 150 7.19e+01 b.29.1.3 99545 1e5pA 151 7.20e+01 1bj7 b.60.1.1 59272 1kjvB 100 7.25e+01 b.1.1.2 77423 1vcbC 160 7.27e+01 1vcbC b.3.3.1 22535 2ciaA 102 7.30e+01 1vqoA 240 7.30e+01 1ko3A 230 7.36e+01 d.157.1.1 90974 1axiB 236 7.37e+01 1axiB b.1.2.1,b.1.2.1 21997,21998 1quqB 121 7.46e+01 1quqB b.40.4.3 25305 1g0sA 209 7.53e+01 1g0sA d.113.1.1 60187 1g8mA 593 7.61e+01 1g8mA c.24.1.3,c.97.2.1 60371,60372 1tvxA 75 7.62e+01 1tvxA d.9.1.1 37441 1v6fA 151 7.65e+01 d.109.1.2 108395 1jwiB 125 7.68e+01 d.169.1.1 67384 2a6aA 218 7.69e+01 1ut1A 148 7.74e+01 b.2.3.6 108014 1rzfL 213 7.74e+01 b.1.1.1,b.1.1.2 98152,98153 1i0vA 104 7.77e+01 9rnt d.1.1.4 36054 1a7j 290 7.78e+01 1a7j c.37.1.6 31952 1kskA 234 7.78e+01 d.66.1.5,d.265.1.3 72920,90389 1iq6A 134 7.81e+01 d.38.1.4 76755 1b8kA 119 7.85e+01 1bndA g.17.1.3 44795 1i78A 297 7.85e+01 f.4.4.1 66046 1v88A 130 7.86e+01 b.55.1.1 108423 1c01A 76 7.87e+01 1c01A b.11.1.5 23633 4ubpA 101 7.87e+01 1ubpA d.8.1.1 37352 1o97C 264 7.88e+01 c.26.2.3 81232 1k5dB 201 7.90e+01 b.55.1.3 68169 1k12A 158 7.95e+01 b.18.1.15 71978 1jfmA 174 8.02e+01 d.19.1.1 66640 1pov1 302 8.12e+01 1pov1 1kwaA 88 8.16e+01 1kwaA b.36.1.1 24772 1dzaA 129 8.16e+01 7rsa d.5.1.1 37275 1i50H 146 8.19e+01 b.40.4.8 61761 1ok8A 394 8.23e+01 b.1.18.4,f.10.1.1 93236,93237 2cxkA 95 8.25e+01 1z47A 355 8.26e+01 1h5uA 842 8.27e+01 1a8i c.87.1.4 60655 1k3bA 119 8.35e+01 b.61.5.1 72016 2carA 196 8.36e+01 1mla 309 8.39e+01 1mla c.19.1.1,d.58.23.1 31031,39383 1qy6A 274 8.40e+01 b.47.1.1 96574 2cfxA 144 8.43e+01 1ng2A 193 8.53e+01 b.34.2.1,b.34.2.1 85660,85661 1oebA 62 8.60e+01 b.34.2.1 86909 2bsfA 176 8.64e+01 2ac3A 316 8.72e+01 1mdl 359 8.76e+01 2mnr c.1.11.2,d.54.1.1 29247,38891 1v58A 241 8.89e+01 c.47.1.9,d.17.3.1 108371,108372 1cs0A 1073 8.90e+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 1f60A 458 9.00e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140