# 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 2ct7A 86 5.99e-02 1vqoZ 83 8.94e-02 1vk6A 269 1.43e-01 d.113.1.4,d.113.1.4 100851,100852 1odhA 174 1.64e-01 d.239.1.1 86850 1ww8A 439 1.64e-01 1vckA 115 2.19e-01 1wrvA 308 2.35e-01 1kmtA 141 4.57e-01 b.1.18.8 77442 1k7cA 233 4.61e-01 c.23.10.4 68267 1qqqA 264 6.14e-01 1bkpA d.117.1.1 40931 1x75A 132 6.40e-01 2cklB 165 6.40e-01 1ur6B 52 7.28e-01 g.44.1.1 99812 2g2kA 170 9.13e-01 1ifqA 138 1.05e+00 1ifqA d.110.4.1 62350 1vd4A 62 1.10e+00 2aq6A 147 1.13e+00 1ji1A 637 1.25e+00 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 1ypvA 313 1.25e+00 2g8mA 264 1.32e+00 2g8oA 264 1.33e+00 1jm1A 204 1.36e+00 b.33.1.1 71745 1ee8A 266 1.44e+00 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1w9aA 147 1.45e+00 1d0qA 103 1.49e+00 1d0qA g.41.3.2 45208 1k8kA 418 1.61e+00 c.55.1.1,c.55.1.1 68305,68306 1l8dA 112 1.77e+00 h.4.12.1 73687 1uh4A 637 1.78e+00 b.1.18.2,b.71.1.1,c.1.8.1 99391,99392,99393 2csvA 72 1.89e+00 1u79A 129 2.10e+00 d.26.1.1 107714 1jx4A 352 2.14e+00 d.240.1.1,e.8.1.7 90378,90379 1r6lA 239 2.32e+00 d.14.1.4,d.101.1.1 97153,97154 3daaA 277 2.38e+00 1daaA e.17.1.1 43272 2aq4A 434 2.39e+00 1mswD 883 2.58e+00 e.8.1.3 79427 1upiA 225 2.60e+00 b.82.1.1 99757 1qz5A 375 2.64e+00 c.55.1.1,c.55.1.1 96614,96615 1lm5A 214 2.67e+00 d.211.2.1 74029 1rfs 139 2.69e+00 1rfs b.33.1.1 24434 2fxuA 375 2.74e+00 1rmd 116 3.09e+00 1rmd g.37.1.1,g.44.1.1 45025,45322 1wfeA 86 3.21e+00 1iyeA 309 3.60e+00 e.17.1.1 83786 1pfvA 551 3.74e+00 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1rb9 53 3.96e+00 1rb9 g.41.5.1 45214 2a20A 62 4.12e+00 1wd2A 60 4.18e+00 g.44.1.1 109232 2fqpA 97 4.23e+00 1weoA 93 4.26e+00 1o12A 376 4.32e+00 b.92.1.5,c.1.9.10 80758,80759 1fp0A 88 4.32e+00 1fp0A g.50.1.2 45361 2cklA 108 4.39e+00 1tr9A 341 4.49e+00 1ptq 50 4.55e+00 1ptq g.49.1.1 45349 1z60A 59 4.57e+00 1nv8A 284 4.63e+00 c.66.1.30 86224 2a8jA 420 4.74e+00 1u8bA 133 4.98e+00 1lvoA 302 4.98e+00 b.47.1.4 74284 1l1oC 181 5.16e+00 b.40.4.3 73480 1inp 400 5.23e+00 1inp e.7.1.1 42972 1brfA 53 5.30e+00 1rb9 g.41.5.1 45236 2dasA 62 5.39e+00 1z90A 469 5.49e+00 1vphA 149 5.92e+00 1yk4A 52 5.99e+00 1afp 51 6.09e+00 1afp g.26.1.1 44947 1mr1C 99 6.13e+00 d.217.1.2 79420 1m22A 503 6.17e+00 c.117.1.1 78464 1rutX 188 6.27e+00 1zd9A 188 6.28e+00 2a1rA 430 6.37e+00 1mea 28 6.51e+00 g.41.1.1 45176 1rdg 53 6.62e+00 1rb9 g.41.5.1 45221 2cjsC 62 6.75e+00 1g38A 393 6.88e+00 2admA c.66.1.27 60235 1g6aA 271 7.15e+00 1btl e.3.1.1 42704 2bwfA 77 7.36e+00 2g8yA 385 7.56e+00 1r5mA 425 7.82e+00 2bx9A 53 8.03e+00 1m2tB 263 8.51e+00 b.42.2.1,b.42.2.1 84762,84763 1dl0A 37 8.62e+00 1dl0A g.3.6.2 44112 1q35A 320 8.70e+00 c.94.1.1 95661 1twfL 70 8.83e+00 1z6uA 150 8.96e+00 830cA 168 9.07e+00 1ck7A d.92.1.11 40400 1w2lA 99 9.21e+00 1lv3A 68 9.28e+00 g.39.1.9 78231 7taa 478 9.28e+00 7taa b.71.1.1,c.1.8.1 27778,28765 1nigA 152 9.62e+00 a.25.2.1 85740 1o7eA 276 1.03e+01 e.3.1.1 92622 1lj5A 379 1.05e+01 e.1.1.1 73928 1q68B 29 1.07e+01 j.108.1.1 95963 1x31D 99 1.09e+01 1ywmA 200 1.10e+01 1s9rA 410 1.10e+01 d.126.1.4 98758 1un3A 123 1.13e+01 d.5.1.1 99646 2bwkA 121 1.15e+01 1e7lA 157 1.19e+01 1en7A a.140.4.1,d.4.1.5 64728,64729 6rxn 46 1.20e+01 1rb9 g.41.5.1 45222 1fjgS 93 1.20e+01 1qkfA d.28.1.1 38451 2cszA 76 1.27e+01 1iro 54 1.31e+01 1rb9 g.41.5.1 45223 1ew4A 106 1.33e+01 1ew4A d.82.2.1 40023 1ldjB 90 1.34e+01 g.44.1.1 73850 1p32A 209 1.36e+01 1p32A d.25.1.1 38379 2awpA 198 1.38e+01 1k0mA 241 1.39e+01 a.45.1.1,c.47.1.5 67949,67950 1o7iA 119 1.39e+01 b.40.4.3 86642 1a78A 134 1.41e+01 1c1lA b.29.1.3 24212 2fiyA 309 1.41e+01 1ww9A 392 1.46e+01 1ywzA 175 1.46e+01 1hw5A 210 1.52e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 2an1A 292 1.56e+01 1h3nA 878 1.58e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1o5uA 101 1.60e+01 b.82.1.8 92518 1pu6A 218 1.62e+01 a.96.1.5 95123 1m1qA 91 1.64e+01 a.138.1.3 74419 1hl9A 449 1.65e+01 b.71.1.3,c.1.8.11 90650,90651 1k7hA 476 1.66e+01 c.76.1.1 72101 2fe5A 94 1.67e+01 1dxgA 36 1.68e+01 1dxgA g.41.5.2 45247 1vekA 84 1.70e+01 1sefA 274 1.72e+01 b.82.1.11 105452 1gvjA 146 1.74e+01 a.4.5.21 90525 2fs3A 282 1.74e+01 1zkkA 167 1.76e+01 1cqmA 101 1.77e+01 1ris d.58.14.1 39321 1g8kB 133 1.79e+01 1g8jB b.33.1.1 24435 1rlyA 60 1.79e+01 g.41.3.1 104988 2etxA 209 1.79e+01 1xakA 83 1.80e+01 1zu1A 127 1.82e+01 1nykA 165 1.82e+01 b.33.1.1 86408 1y9uA 323 1.82e+01 1u00A 227 1.83e+01 1yc5A 246 1.86e+01 1ogdA 131 1.87e+01 c.133.1.1 92893 1yovA 537 1.89e+01 1w6sB 74 1.90e+01 1t0fA 276 1.91e+01 1s1dA 331 1.92e+01 b.67.3.1 98344 1vq0A 302 1.92e+01 1utyA 187 1.94e+01 b.147.1.1 108036 1i6pA 220 1.94e+01 1ddzA c.53.2.1 61848 1woyA 500 1.95e+01 1t0bA 252 1.96e+01 c.23.16.6 106199 1iugA 352 1.96e+01 c.67.1.3 90699 2fclA 169 1.98e+01 1yp8A 33 1.98e+01 1fl2A 310 1.99e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1m07A 111 2.01e+01 d.5.1.1 78328 1twfI 122 2.05e+01 2bhvA 246 2.08e+01 1vrmA 325 2.08e+01 1wjvA 79 2.10e+01 2eifA 136 2.16e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1i76A 163 2.16e+01 1hfc d.92.1.11 61877 1guiA 155 2.19e+01 b.18.1.14 76351 1q33A 292 2.20e+01 d.113.1.1 95657 2c1xA 456 2.21e+01 2sak 121 2.24e+01 2sak d.15.5.1 37711 2ct0A 74 2.31e+01 1kdj 102 2.33e+01 1plc b.6.1.1 22864 1qxfA 66 2.36e+01 g.41.8.4 96527 2apoB 60 2.36e+01 1ty9A 222 2.39e+01 1wflA 74 2.40e+01 4eugA 229 2.43e+01 3eugA c.18.1.1 31019 1fn9A 365 2.45e+01 1fn9A d.196.1.1 59894 1wjpA 107 2.47e+01 1yhfA 115 2.48e+01 1wxiA 275 2.50e+01 2cw8A 537 2.52e+01 1qd1A 325 2.52e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1gvzA 237 2.57e+01 b.47.1.2 76360 2eng 210 2.63e+01 2eng b.52.1.1 26895 2d8vA 67 2.64e+01 1erd 40 2.70e+01 1erd a.10.1.1 16362 1m2kA 249 2.75e+01 c.31.1.5 84754 2dg5B 190 2.78e+01 1ubkS 267 2.89e+01 e.19.1.1 88423 1cv8 174 2.89e+01 1cv8 d.3.1.1 37089 1nepA 130 2.90e+01 b.1.18.7 80440 1pszA 303 2.91e+01 1toaA c.92.2.2 35600 1e19A 314 2.92e+01 1b7bA c.73.1.1 34967 1qtwA 285 2.92e+01 1qumA c.1.15.1 29392 1wuiS 267 2.95e+01 2f6eA 127 2.97e+01 1ayoA 130 3.06e+01 1ayoA b.2.4.1 22431 1o7sA 127 3.08e+01 b.1.1.1 86644 1sur 215 3.14e+01 1sur c.26.2.2 31620 1hyeA 313 3.23e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 2sicI 107 3.23e+01 3ssi d.84.1.1 40031 2fgtA 417 3.24e+01 1xk5A 204 3.31e+01 2iv2X 715 3.33e+01 1xkwA 665 3.33e+01 1lw7A 365 3.36e+01 c.26.1.3,c.37.1.1 74295,74296 1oxdA 227 3.47e+01 d.22.1.1 93687 2cy2A 174 3.48e+01 2cohA 202 3.51e+01 1dgwA 178 3.60e+01 1dgwA b.82.1.2 28090 1mldA 314 3.60e+01 2cmd c.2.1.5,d.162.1.1 30122,42089 1vm9A 111 3.60e+01 b.33.1.1 108886 1hdlA 55 3.62e+01 g.68.1.2 65808 1pk6C 129 3.65e+01 b.22.1.1 94803 2c43A 323 3.68e+01 1i6aA 219 3.68e+01 c.94.1.1 61827 1dxsA 80 3.69e+01 1cokA a.60.1.2 17944 1rh6A 55 3.71e+01 a.6.1.7 104935 1shuX 182 3.72e+01 c.62.1.1 98882 1y4tA 322 3.74e+01 1wraA 308 3.75e+01 1gqpA 221 3.84e+01 b.18.1.9 70372 1o9iA 266 3.91e+01 a.25.1.3 92671 1v54F 98 3.94e+01 g.41.5.3 100327 2as9A 210 3.96e+01 1erjA 393 3.98e+01 1erjA b.69.4.1 27660 1xebA 150 4.01e+01 1qjpA 171 4.02e+01 1bxwA f.4.1.1 43742 1xfkA 336 4.04e+01 1vfyA 73 4.12e+01 1vfyA g.50.1.1 45357 1am2 199 4.12e+01 1am2 b.86.1.2 28381 1qwtA 255 4.14e+01 b.26.1.3 96501 1vqoU 66 4.17e+01 1zin 217 4.20e+01 1zin c.37.1.1,g.41.2.1 31915,45178 2fn4A 181 4.24e+01 2cyeA 133 4.25e+01 1u24A 337 4.27e+01 2bmoA 447 4.30e+01 1x4sA 59 4.31e+01 2awkA 228 4.32e+01 1ud9A 245 4.32e+01 d.131.1.2,d.131.1.2 107768,107769 1nkoA 132 4.36e+01 b.1.1.1 85829 1g9pA 45 4.44e+01 g.3.6.2 65171 2gatA 66 4.46e+01 1gatA g.39.1.1 45102 1yuiA 54 4.62e+01 1yuiA g.37.1.1 45073 2a5sA 284 4.62e+01 1r85A 379 4.66e+01 c.1.8.3 104839 2axcA 264 4.71e+01 1aa6 715 4.73e+01 2napA b.52.2.2,c.81.1.1 26916,35324 2cx1A 187 4.76e+01 1xd3A 230 4.76e+01 1dgfA 497 4.78e+01 1cf9A e.5.1.1 42782 2bngA 149 4.83e+01 1htrB 329 4.86e+01 1smrA 1rgyA 360 4.91e+01 e.3.1.1 97456 1v6pA 62 4.95e+01 1c9kA 180 4.95e+01 1c9kB c.37.1.11 32363 1e0eA 55 4.96e+01 1wjcA a.4.10.1 59147 1r61A 207 4.98e+01 c.8.8.1 97138 1t71A 281 5.02e+01 1ukkA 142 5.04e+01 d.227.1.1 99491 1srkA 35 5.04e+01 g.37.1.1 105966 1kk1A 410 5.12e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1ri6A 343 5.14e+01 b.69.11.1 97503 1wimA 94 5.17e+01 2cs3A 93 5.18e+01 1h4rA 314 5.19e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1vj2A 126 5.23e+01 b.82.1.10 100796 2bibA 547 5.28e+01 1v7lA 163 5.46e+01 1xlqA 106 5.47e+01 2erxA 172 5.49e+01 1nwwA 149 5.50e+01 d.17.4.8 86306 1se7A 83 5.55e+01 1njqA 39 5.58e+01 g.37.1.3 85822 1uv4A 293 5.60e+01 1k82A 268 5.63e+01 a.156.1.2,b.113.1.1,g.39.1.8 75866,75867,75868 1wmaA 276 5.63e+01 1qhfA 240 5.65e+01 1qhfA c.60.1.1 33960 1ihoA 283 5.65e+01 1ihoA c.26.1.4 62390 1io1A 398 5.67e+01 1io1A e.32.1.1 62611 1vl2A 421 5.69e+01 c.26.2.1,d.210.1.1 108708,108709 2bf6A 449 5.71e+01 1cl4A 60 5.71e+01 1cl4A g.40.1.1 45171 1uq5A 263 5.77e+01 d.165.1.1 99778 1gpc 218 5.77e+01 1gpc b.40.4.7 25393 1qg3A 195 5.79e+01 1qg3A b.1.2.1,b.1.2.1 21993,21994 2a74A 643 5.80e+01 1llmC 88 5.82e+01 g.37.1.1,g.37.1.1 91059,91060 1a7i 81 5.82e+01 1b8tA g.39.1.3,g.39.1.3 45143,45144 1z4rA 168 5.84e+01 1fus 106 5.84e+01 9rnt d.1.1.4 36050 1cojA 212 5.87e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1fvkA 189 5.88e+01 1fvkA c.47.1.13 90351 1y88A 199 5.91e+01 1vziA 126 5.93e+01 b.1.13.1,g.41.5.2 108967,108968 1agi 125 5.95e+01 7rsa d.5.1.1 37303 1u3eM 174 5.98e+01 d.4.1.3,d.285.1.1 107640,107641 2a6sA 84 5.98e+01 1eaxA 241 6.22e+01 b.47.1.2 64889 1xgsA 295 6.25e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1yp2A 451 6.26e+01 2bhuA 602 6.32e+01 1tuaA 191 6.37e+01 d.51.1.1,d.51.1.1 107321,107322 1lp9E 194 6.39e+01 b.1.1.1,b.1.1.2 91086,91087 1oqqA 106 6.54e+01 d.15.4.1 93422 1t6lA 290 6.54e+01 d.131.1.2,d.131.1.2 106574,106575 2aheA 267 6.61e+01 1ovxA 67 6.62e+01 g.39.1.11 93622 2fvhA 120 6.63e+01 2ctdA 96 6.68e+01 1i1qA 520 6.74e+01 1qdlA d.161.1.1 61543 1e8rA 50 6.77e+01 1e8rA g.29.1.1 44960 1td4A 115 6.79e+01 1m0gA 30 6.83e+01 g.46.1.1 84743 2cxkA 95 6.83e+01 2fctA 313 6.85e+01 1qd6C 240 6.89e+01 1qd5A 1txoA 237 6.90e+01 1i5pA 633 6.91e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 1ku1A 230 6.96e+01 a.118.3.1 72996 2gpyA 233 6.99e+01 1f0xA 571 7.00e+01 1f0xA d.58.32.2,d.145.1.1 39483,41746 1se0A 116 7.03e+01 g.52.1.1 98814 1zud1 251 7.04e+01 1juvA 193 7.06e+01 c.71.1.1 90912 1ti6B 274 7.08e+01 b.3.5.1,d.58.1.5 106976,106977 1jbwA 428 7.08e+01 c.59.1.2,c.72.2.2 62860,62861 1kqfB 294 7.09e+01 d.58.1.5,f.23.22.1 75900,75901 1ej6B 1275 7.14e+01 i.7.1.1 45968 2c3vA 102 7.15e+01 1ua4A 455 7.18e+01 c.72.1.3 99128 1n2sA 299 7.20e+01 c.2.1.2 79857 2avuE 192 7.20e+01 2fqaA 27 7.21e+01 1zyoA 191 7.22e+01 2azpA 318 7.22e+01 2d1pB 119 7.23e+01 1yqbA 100 7.29e+01 2g1lA 104 7.30e+01 1dekA 241 7.36e+01 1dekA c.37.1.1 31842 1t64A 377 7.36e+01 c.42.1.2 106543 1tpm 50 7.37e+01 1tpg g.27.1.1 44957 1t2jA 116 7.40e+01 2cfuA 658 7.41e+01 1b9wA 89 7.44e+01 1b9wA g.3.11.4,g.3.11.4 44334,44335 2ctoA 93 7.44e+01 1m65A 245 7.59e+01 c.6.3.1 84847 1bs0A 384 7.60e+01 1bs0A c.67.1.4 34490 1sr8A 298 7.63e+01 e.54.1.1 105959 1ys4A 354 7.69e+01 1cr1A 296 7.69e+01 1cr1A c.37.1.11 32286 2au3A 407 7.70e+01 1e0nA 27 7.70e+01 b.72.1.1 27807 2d0oA 610 7.74e+01 1ym0A 238 7.77e+01 1yd0A 96 7.78e+01 1ia9A 280 7.78e+01 1ia9A d.144.1.5 62113 1yaxA 153 7.79e+01 1hfc 169 7.79e+01 1hfc d.92.1.11 40335 1kmoA 774 7.79e+01 f.4.3.3 72753 1ykdA 398 7.80e+01 1rz2A 254 7.85e+01 b.100.1.1 105130 1vhqA 232 7.87e+01 c.23.16.2 100696 1tl2A 236 7.87e+01 1tl2A b.67.1.1 27541 1vheA 373 7.92e+01 b.49.3.1,c.56.5.4 100669,100670 1p5vA 235 7.97e+01 b.1.11.1,b.7.2.1 87812,87813 1pj5A 830 8.02e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1nox 205 8.05e+01 1nox d.90.1.1 40242 1eyeA 280 8.06e+01 1aj2 c.1.21.1 29672 1qs1A 462 8.07e+01 1qs1A d.166.1.1,d.166.1.1 42260,42261 1rsy 152 8.11e+01 1rsy b.7.1.2 23192 1euvB 86 8.11e+01 1a5r d.15.1.1 37598 1tmxA 293 8.16e+01 1j05A 111 8.19e+01 b.1.1.1 90735 2bayA 61 8.20e+01 2eu8A 216 8.24e+01 1qjtA 99 8.24e+01 1eh2 a.39.1.6 17335 1wr8A 231 8.27e+01 2fo3A 125 8.29e+01 1rrmA 386 8.34e+01 e.22.1.2 105081 1r4pB 70 8.39e+01 b.40.2.1 97026 1s3eA 520 8.44e+01 c.3.1.2,d.16.1.5 98426,98427 1qamA 244 8.54e+01 2ercA c.66.1.24 34220 1l0sA 90 8.54e+01 b.81.2.1 73408 1aly 146 8.55e+01 1aly b.22.1.1 23856 2cy5A 140 8.63e+01 1vdwA 254 8.66e+01 e.7.1.1 100569 2booA 247 8.68e+01 1nnhA 294 8.69e+01 d.104.1.1 92005 1pk6A 133 8.72e+01 b.22.1.1 94801 1s5aA 150 8.75e+01 d.17.4.10 98525 2frnA 278 8.80e+01 1bueA 265 8.80e+01 1btl e.3.1.1 42727 1dvpA 220 8.84e+01 1dvpA a.118.9.2,g.50.1.1 19216,45358 1exqA 154 8.89e+01 1b9dA c.55.3.2 33646 1vk9A 151 8.92e+01 c.139.1.1 108640 1ejxA 100 8.92e+01 d.8.1.1 83182 1uwcA 261 8.95e+01 c.69.1.17 100101 1zxuA 217 8.96e+01 1mxiA 160 9.00e+01 c.116.1.1 79646