# 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 1a53 247 1.39e-01 1a53 c.1.2.4 28564 1dyqA 234 4.98e-01 3seb b.40.2.2,d.15.6.1 59140,59141 2rslA 140 6.89e-01 2rslA c.53.1.1 33345 2fclA 169 9.82e-01 1sqsA 242 1.18e+00 c.23.5.5 98968 2aioA 269 1.68e+00 2fvtA 135 2.31e+00 2flsA 132 2.41e+00 1m93A 55 2.60e+00 e.1.1.1 91235 2g9iA 249 2.90e+00 1hdoA 206 2.90e+00 1he2A c.2.1.2 60965 1thg 544 2.92e+00 1thg c.69.1.17 34763 1ma3A 253 3.12e+00 c.31.1.5 78883 1q59A 172 3.18e+00 f.1.4.1 95881 1repC 251 3.40e+00 1repC a.4.5.10,a.4.5.10 16125,16126 1zpvA 91 3.46e+00 1qhlA 227 3.90e+00 1qhlA c.37.1.12 32382 1v0lA 313 4.74e+00 c.1.8.3 108207 1regX 122 4.82e+00 1regX d.58.27.1 39406 2bg5A 324 4.86e+00 1ex0A 731 5.50e+00 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1ej0A 180 5.65e+00 1ej0A c.66.1.2 34179 1qzgA 187 5.70e+00 b.40.4.3 96643 2cxcA 144 5.93e+00 1zruA 264 6.05e+00 1exg 110 6.22e+00 1exg b.2.2.1 22387 1c7qA 445 6.45e+00 2pgi c.80.1.2 35307 1iz5A 249 6.91e+00 d.131.1.2,d.131.1.2 83834,83835 1kqpA 271 7.25e+00 c.26.2.1 72883 1tf1A 198 7.32e+00 d.110.2.2 106826 1g7nA 131 7.55e+00 b.60.1.2 83274 1fl2A 310 7.58e+00 1hyuA c.3.1.5,c.3.1.5 59869,59870 2gmqA 118 7.78e+00 1y96B 85 7.79e+00 1vr0A 247 7.96e+00 1kshA 186 7.98e+00 c.37.1.8 72914 1v30A 124 9.43e+00 1o6dA 163 9.60e+00 c.116.1.3 92567 1m07A 111 9.87e+00 d.5.1.1 78328 2bwfA 77 1.07e+01 2axwA 134 1.08e+01 1s55A 156 1.13e+01 1eceA 358 1.21e+01 1eceA c.1.8.3 28813 1zthA 258 1.23e+01 1jhfA 202 1.23e+01 a.4.5.2,b.87.1.1 63057,63058 2b7eA 59 1.30e+01 2amhA 207 1.31e+01 1yr2A 741 1.31e+01 1vkuA 100 1.32e+01 a.28.1.1 108690 1b65A 375 1.32e+01 1b65A d.154.1.1 42020 1ydmA 187 1.33e+01 1xkrA 206 1.35e+01 1nijA 318 1.37e+01 c.37.1.10,d.237.1.1 85741,85742 1t0hA 132 1.46e+01 b.34.2.1 106207 1b56 135 1.47e+01 1hmt b.60.1.2 27183 1d2oA 187 1.52e+01 1d2oA b.3.5.1,b.3.5.1 22625,22626 1wrjA 156 1.54e+01 1s50A 259 1.55e+01 1sek 378 1.55e+01 1sek e.1.1.1 42675 1b25A 619 1.56e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 2aefA 234 1.58e+01 1a99A 344 1.67e+01 1pot c.94.1.1 35812 1r5lA 262 1.68e+01 a.5.3.1,c.13.1.1 97099,97100 1fh9A 312 1.71e+01 1taxA c.1.8.3 28913 1i6lA 328 1.77e+01 c.26.1.1 66041 1vddA 228 1.77e+01 e.49.1.1 108519 1h72C 296 1.79e+01 d.14.1.5,d.58.26.1 60712,60713 1g8lA 411 1.80e+01 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1n8kA 374 1.82e+01 b.35.1.2,c.2.1.1 80298,80299 1rwiA 270 1.84e+01 b.68.9.1 97987 1nf3C 128 1.90e+01 b.36.1.1 85596 1i8fA 81 1.90e+01 1i8fA b.38.1.1 61959 1epwA 1290 1.91e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1qi9A 556 1.96e+01 1qhbA a.111.1.2 19053 2cq2A 114 2.00e+01 1quqB 121 2.04e+01 1quqB b.40.4.3 25305 1y96A 86 2.06e+01 1qy1A 174 2.08e+01 b.60.1.1 96568 2d1uA 104 2.08e+01 1oa2A 218 2.09e+01 b.29.1.11 86721 1wwhA 119 2.13e+01 1vl4A 447 2.14e+01 d.283.1.1 108718 1e0tA 470 2.17e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1c52 131 2.17e+01 1c52 a.3.1.1 15810 1w9zA 283 2.19e+01 2awpA 198 2.19e+01 1wmhA 89 2.19e+01 1o0yA 260 2.20e+01 c.1.10.1 80756 1ta8A 332 2.22e+01 1kq1A 77 2.23e+01 b.38.1.2 72848 1t0aA 159 2.26e+01 1ydyA 356 2.28e+01 1bn8A 420 2.30e+01 1pcl b.80.1.1 28022 2cygA 312 2.34e+01 1u3wA 374 2.34e+01 1xwvA 129 2.37e+01 2fbyA 205 2.37e+01 1ddf 127 2.40e+01 1ddf a.77.1.2 18423 2b3wA 168 2.48e+01 1my6A 199 2.48e+01 a.2.11.1,d.44.1.1 85232,85233 1h6lA 353 2.49e+01 b.68.3.1 60687 2a2pA 129 2.50e+01 1wvqA 167 2.51e+01 1vfsA 386 2.51e+01 b.49.2.2,c.1.6.1 108584,108585 1bia 321 2.58e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1h2cA 140 2.62e+01 b.31.1.1 83462 1juvA 193 2.66e+01 c.71.1.1 90912 1cfr 285 2.76e+01 1cfr c.52.1.7 33312 2tpt 440 2.82e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17759,31623,38621 1o58A 303 2.82e+01 c.79.1.1 92491 1n91A 108 2.83e+01 d.206.1.1 80326 1xfcA 384 2.85e+01 2bbkL 125 2.90e+01 2bbkL g.21.1.1 44882 1xdpA 687 2.92e+01 1t64A 377 2.93e+01 c.42.1.2 106543 1xedA 117 2.94e+01 1zndA 174 2.95e+01 1m4jA 142 2.95e+01 d.109.1.2 78602 5nul 138 2.95e+01 5nul c.23.5.1 31191 1rf6A 427 2.96e+01 d.68.2.2 97366 1qhtA 775 3.04e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1oj4A 283 3.05e+01 d.14.1.5,d.58.26.5 93083,93084 1vcvA 226 3.07e+01 2afbA 351 3.08e+01 1vbuA 328 3.15e+01 1qavA 90 3.16e+01 1qauA b.36.1.1 24777 1wu3I 161 3.17e+01 1s9rA 410 3.17e+01 d.126.1.4 98758 1o1zA 234 3.21e+01 c.1.18.3 86555 1ois 223 3.26e+01 1a36A e.15.1.1 43267 1tt8A 164 3.30e+01 2bo4A 397 3.30e+01 2gfgA 193 3.42e+01 1fp1D 372 3.43e+01 1fpqA a.4.5.29,c.66.1.12 59939,59940 2g0uA 92 3.45e+01 2fgtA 417 3.47e+01 2f4mA 295 3.48e+01 1xcbA 211 3.55e+01 a.4.5.38,c.2.1.12 109552,109553 1xkiA 162 3.55e+01 1ockA 412 3.61e+01 c.117.1.1 86802 1nq6A 302 3.68e+01 c.1.8.3 92046 1p5vA 235 3.69e+01 b.1.11.1,b.7.2.1 87812,87813 1z0wA 207 3.79e+01 2gw6A 123 3.80e+01 1bdfA 235 3.80e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 2fcjA 119 3.82e+01 2b2aA 199 3.84e+01 1ee6A 197 3.87e+01 1ee6A b.80.1.1 28024 1udc 338 3.91e+01 1xel c.2.1.2 29785 1zhvA 134 3.92e+01 1qopB 396 3.98e+01 2tysB c.79.1.1 35270 1xttA 216 4.00e+01 1rwrA 301 4.01e+01 b.80.1.11 97990 2gkeA 274 4.05e+01 1gqzA 274 4.07e+01 d.21.1.1,d.21.1.1 83311,83312 1xdnA 277 4.12e+01 1ljoA 77 4.16e+01 b.38.1.1 73941 2fj6A 82 4.22e+01 1cojA 212 4.26e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1qlmA 316 4.28e+01 1qlmA d.147.1.1 41765 1vjjA 692 4.31e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 16pk 415 4.39e+01 16pk c.86.1.1 35454 1s0pA 176 4.40e+01 a.192.1.1 98300 1xyiA 66 4.40e+01 1vdc 333 4.43e+01 1trb c.3.1.5,c.3.1.5 30545,30546 1uc7A 125 4.44e+01 c.47.1.1 99163 1cf7B 95 4.47e+01 1cf7B a.4.5.17 16152 1idk 359 4.55e+01 1qcxA b.80.1.2 28025 1je0A 236 4.60e+01 c.56.2.1 66581 1n8jA 186 4.64e+01 c.47.1.10 85401 2cdpA 160 4.69e+01 1xnaA 183 4.69e+01 1xnaA b.18.1.8 23773 2fh7A 595 4.70e+01 1u6tA 121 4.73e+01 2etxA 209 4.79e+01 1uc2A 481 4.82e+01 d.261.1.1 99161 1v7wA 807 4.87e+01 a.102.1.4,b.30.5.3 108411,108412 1wlyA 333 4.91e+01 1qa5A 58 4.93e+01 1qa5A j.52.1.1 46335 1nf2A 268 4.95e+01 c.108.1.10 91849 1omzA 293 4.95e+01 c.68.1.15 87093 1s6lA 212 5.02e+01 1nu4A 97 5.03e+01 d.58.7.1 80731 1vqzA 341 5.07e+01 1l2tA 235 5.10e+01 c.37.1.12 73514 1v04A 355 5.16e+01 b.68.6.2 100240 1l1sA 113 5.17e+01 c.114.1.1 73484 1pbjA 125 5.30e+01 d.37.1.1,d.37.1.1 94414,94415 2axpA 173 5.30e+01 1t9bA 677 5.35e+01 1vqoL 165 5.37e+01 1id0A 152 5.44e+01 d.122.1.3 66111 1dkuA 317 5.46e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 2as9A 210 5.52e+01 1f9vA 347 5.60e+01 1bg2 c.37.1.9 59745 1cq3A 233 5.61e+01 1cq3A b.27.1.1 23923 2bm5A 186 5.67e+01 1fg7A 356 5.70e+01 1gewA c.67.1.1 59819 1tq5A 242 5.76e+01 1b43A 340 5.77e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 1h5uA 842 5.83e+01 1a8i c.87.1.4 60655 1u55A 188 5.86e+01 d.278.1.1 107677 1vmaA 306 5.90e+01 a.24.13.1,c.37.1.10 108887,108888 1rwzA 245 5.93e+01 d.131.1.2,d.131.1.2 98005,98006 1f0lA 535 5.98e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22377,42239,43382 1gyxA 76 5.99e+01 d.80.1.1 76387 1iwmA 186 6.12e+01 b.125.1.2 83758 1vknA 351 6.13e+01 c.2.1.3,d.81.1.1 108676,108677 1ugiA 84 6.14e+01 1ugiA d.17.5.1 38125 1yiyA 429 6.18e+01 1ukuA 102 6.21e+01 d.58.5.2 99533 2trcP 217 6.23e+01 1b9yC c.47.1.6 33051 1b93A 152 6.23e+01 1b93A c.24.1.2 31507 1tygB 87 6.25e+01 d.15.3.2 107455 1fhgA 154 6.27e+01 1tlk b.1.1.4 21706 1x8dA 104 6.32e+01 1q3iA 214 6.34e+01 d.220.1.1 104524 1u7eB 154 6.38e+01 1ns5A 155 6.44e+01 c.116.1.3 80705 1pm1X 180 6.54e+01 b.60.1.1 104189 1uheA 97 6.56e+01 2ga9D 469 6.58e+01 1wohA 305 6.68e+01 c.42.1.1 109446 1hm9A 468 6.68e+01 b.81.1.4,c.68.1.5 65866,65867 1zetA 388 6.72e+01 1vjpA 394 6.72e+01 c.2.1.3,d.81.1.3 100828,100829 1tdzA 272 6.76e+01 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 2aq4A 434 6.76e+01 1luzA 88 6.76e+01 b.40.4.5 74271 1ztsA 139 6.80e+01 1gs5A 258 6.81e+01 c.73.1.2 70395 1sr4B 261 6.84e+01 d.151.1.1 105949 1duvG 333 6.89e+01 1othA c.78.1.1,c.78.1.1 35228,35229 1jp4A 308 6.89e+01 1jp4A e.7.1.1 63223 2ez6A 221 6.91e+01 1i1rB 181 6.96e+01 1i1rB a.26.1.1 61548 1yy7A 213 7.08e+01 2fnuA 375 7.10e+01 1g291 372 7.19e+01 1g291 2nacA 393 7.27e+01 2nadA c.2.1.4,c.23.12.1 30088,31348 2ftbA 125 7.35e+01 1cxc 124 7.37e+01 1ycc a.3.1.1 15890 1mixA 206 7.45e+01 a.11.2.1,b.55.1.5 79166,79167 1svpA 161 7.48e+01 1svpA b.47.1.3 26384 1i8dA 213 7.49e+01 b.43.4.3,b.43.4.3 61953,61954 1jy5A 212 7.53e+01 d.124.1.1 71940 1z5sD 83 7.63e+01 1trb 320 7.72e+01 1trb c.3.1.5,c.3.1.5 30529,30530 1yoaA 159 7.78e+01 1azsA 220 7.78e+01 1azsA d.58.29.1 39416 2gi3A 476 7.78e+01 1vicA 262 7.79e+01 c.68.1.13 100756 1p3dA 475 7.86e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1wb4A 297 7.87e+01 1whvA 100 7.94e+01 2ftzA 284 7.96e+01 1zc1A 208 7.96e+01 2biiA 424 7.98e+01 1kkhA 317 8.00e+01 d.14.1.5,d.58.26.3 72645,72646 1jlyA 304 8.01e+01 1jlyA b.42.3.1,b.42.3.1 25587,25588 1zpsA 138 8.05e+01 1jer 138 8.07e+01 2cbp b.6.1.1 23022 2a41C 32 8.08e+01 1njhA 119 8.11e+01 b.128.1.1 85787 2gjlA 328 8.11e+01 1bg6 359 8.12e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 2f6hX 419 8.14e+01 1gntA 553 8.17e+01 e.26.1.1 70290 1fzqA 181 8.24e+01 1hurA c.37.1.8 32060 1tzzA 392 8.25e+01 1iwdA 215 8.28e+01 d.3.1.1 83756 1c7nA 399 8.30e+01 1d2fA c.67.1.3 34413 1z90A 469 8.30e+01 1l0wA 580 8.34e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1fecA 490 8.36e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1zp4A 304 8.37e+01 1ukkA 142 8.39e+01 d.227.1.1 99491 1tuaA 191 8.40e+01 d.51.1.1,d.51.1.1 107321,107322 1ur1A 378 8.40e+01 c.1.8.3 99804 1wyxA 69 8.42e+01 1ztdA 133 8.49e+01 1ny4A 82 8.51e+01 b.40.4.5 92316 2gk3A 256 8.52e+01 1ri6A 343 8.66e+01 b.69.11.1 97503 1mzgA 146 8.72e+01 d.224.1.1 79696 2fmpA 335 8.72e+01 1smd 496 8.77e+01 1smd b.71.1.1,c.1.8.1 27768,28755 1ze3C 205 8.78e+01 1r6jA 82 8.81e+01 b.36.1.1 97151 1wckA 220 8.90e+01 1o22A 170 8.95e+01 d.238.1.1 86557 1eu1A 780 8.95e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 3grs 478 8.97e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30441,30442,40152