# List of top-scoring protein chains for t04-100-30-dssp-ebghstl-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 3proC 166 1.05e+00 3proC d.52.1.1,d.52.1.1 38812,38813 1obdA 306 1.29e+00 d.143.1.1 86767 2cnqA 306 1.50e+00 d.143.1.1 130646 1s5jA 847 1.56e+00 c.55.3.5,e.8.1.1 112040,112041 1ospO 257 2.08e+00 1ospO b.76.1.1 27971 1zbfA 142 2.39e+00 c.55.3.1 124850 1kveB 77 2.42e+00 1kveB 1a48 306 2.54e+00 1a48 2gu3A 136 2.77e+00 1f1xA 322 2.95e+00 d.32.1.3,d.32.1.3 83208,83209 1n91A 108 3.01e+00 d.206.1.1 80326 1v5xA 203 3.16e+00 c.1.2.4 100377 1yzsA 121 3.70e+00 1f1uA 323 3.88e+00 d.32.1.3,d.32.1.3 83200,83201 1vpkA 378 4.52e+00 d.131.1.1,d.131.1.1,d.131.1.1 113963,113964,113965 1phk 298 4.58e+00 1cdkA 1i1iP 681 5.14e+00 1i1iP d.92.1.5 40297 1qcsA 211 5.36e+00 1qcsA b.52.2.3,d.31.1.1 26927,38461 1c44A 123 5.55e+00 1qndA d.106.1.1 40795 1ylxA 103 5.71e+00 d.82.5.1 123677 1r8gA 372 5.85e+00 d.128.1.3 104845 1a9xA 1058 6.13e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1lm4A 194 6.41e+00 d.167.1.1 84626 1cs0A 1073 6.62e+00 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 1914 232 6.68e+00 1914 1rypK 198 6.83e+00 d.153.1.4 41879 1w53A 84 6.90e+00 a.186.1.2 109175 2gu2A 312 6.91e+00 1k2yX 463 7.28e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1t6sA 162 7.37e+00 a.4.5.60,a.4.5.60 112271,112272 2nr1 27 8.12e+00 1vjvA 415 8.14e+00 d.3.1.9 108632 2gk9A 426 8.17e+00 1ii2A 524 8.40e+00 c.91.1.1,c.109.1.1 66146,66147 1z5bA 469 9.81e+00 a.156.1.3,d.14.1.3,d.122.1.2 124464,124465,124466 1s6cA 183 9.83e+00 a.39.1.5 98594 1vm6A 228 1.03e+01 d.81.1.3,c.2.1.3 108877,118631 1mu5A 471 1.08e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 830cA 168 1.12e+01 1ck7A d.92.1.11 40400 1ob8A 135 1.12e+01 c.52.1.18 111627 2fckA 181 1.13e+01 d.108.1.1 133272 1ifqA 138 1.14e+01 1ifqA d.110.4.1 62350 1wq3A 322 1.14e+01 1crzA 403 1.14e+01 1crzA b.68.4.1,c.51.2.1 27629,33211 1wr2A 238 1.16e+01 1ohtA 215 1.16e+01 d.118.1.1 87036 1xw4X 110 1.17e+01 1v7cA 351 1.19e+01 c.79.1.1 100446 1iuhA 198 1.19e+01 d.61.1.2 83711 1xw3A 110 1.19e+01 1iujA 106 1.20e+01 d.58.4.5 90701 1zceA 155 1.20e+01 b.122.1.8 124907 1in0A 163 1.24e+01 d.58.49.1,d.58.49.1 83694,83695 1zchA 255 1.26e+01 d.90.1.1 124908 1k8tA 510 1.26e+01 e.41.1.1 68316 1p5dX 463 1.29e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 2ajrA 331 1.32e+01 c.72.1.1 126892 1ykdA 398 1.34e+01 1kugA 203 1.36e+01 d.92.1.9 73008 1kufA 203 1.38e+01 d.92.1.9 73007 1nqkA 381 1.41e+01 c.1.16.4 92050 1o8xA 146 1.46e+01 c.47.1.10 86681 2bvfA 459 1.48e+01 1u04A 771 1.54e+01 b.34.14.1,c.55.3.10 107539,107540 1mixA 206 1.55e+01 a.11.2.1,b.55.1.5 79166,79167 2bwqA 129 1.55e+01 b.7.1.2 129380 1nw1A 429 1.56e+01 d.144.1.8 86286 2cunA 410 1.56e+01 1t9mA 214 1.56e+01 b.45.1.1 112364 1j3bA 529 1.57e+01 c.91.1.1,c.109.1.1 77071,77072 1g0uG 252 1.58e+01 d.153.1.4 41952 2bgkA 278 1.60e+01 c.2.1.2 128480 1v74A 107 1.63e+01 d.243.1.1 100442 2ewrA 170 1.64e+01 d.218.1.11 132493 2fclA 169 1.65e+01 d.218.1.11 133273 1p4fA 293 1.66e+01 d.144.1.7 104063 1e0cA 271 1.68e+01 1e0cA c.46.1.2,c.46.1.2 32717,32718 1s1eA 224 1.69e+01 a.39.1.5 112007 1xr4A 509 1.69e+01 c.124.1.2,c.124.1.2 115860,115861 1mjhA 162 1.70e+01 1mjhA c.26.2.4 31639 2c7hA 86 1.70e+01 1rypA 243 1.73e+01 1pmaA d.153.1.4 41932 1vk8A 106 1.75e+01 d.58.48.1 108636 1fit 147 1.76e+01 1fit 2essA 248 1.77e+01 d.38.1.8,d.38.1.8 132346,132347 2g3aA 152 1.85e+01 d.108.1.1 134557 1em2A 229 1.86e+01 1em2A d.129.3.2 41321 1az9 457 1.88e+01 1az9 2cyjA 118 1.93e+01 c.103.1.1 131026 1vkkA 154 1.96e+01 d.109.1.2 108669 2c6cA 707 2.03e+01 a.48.2.1,c.8.4.1,c.56.5.5 129989,129990,129991 1txvA 452 2.09e+01 b.69.8.1 112783 1o0pA 104 2.09e+01 d.58.7.1 86535 1qk8A 146 2.12e+01 1ewxA c.47.1.10 33061 1sh8A 154 2.12e+01 d.38.1.5 105549 1a0p 290 2.13e+01 1a0p 1yewA 382 2.14e+01 1o70A 324 2.15e+01 b.118.1.1,b.118.1.1 81115,81116 1ebfA 358 2.17e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1bif 469 2.17e+01 1bif 2b9hA 353 2.19e+01 1oo0A 147 2.19e+01 d.232.1.1 87182 1ash 150 2.23e+01 1ash 1jovA 270 2.32e+01 b.30.5.7 84192 1jnyA 435 2.34e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1p9qC 256 2.38e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1gw5S 142 2.41e+01 d.110.4.2 70633 1gxrA 337 2.48e+01 b.69.4.1 70722 1dkzA 219 2.49e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1rypD 241 2.50e+01 1rypD d.153.1.4 41935 1aqcA 172 2.51e+01 1x11A b.55.1.2 26983 2afbA 351 2.51e+01 c.72.1.1 126674 1o26A 232 2.53e+01 d.207.1.1 86566 1j6qA 136 2.54e+01 b.40.9.1 77091 1xqoA 256 2.56e+01 a.96.1.6 115853 1pz4A 116 2.57e+01 d.106.1.1 95400 2es7A 142 2.57e+01 c.47.1.20 132314 1tr0A 108 2.60e+01 d.58.4.4 107261 2igd 61 2.63e+01 2igd 1mi3A 322 2.64e+01 c.1.7.1 91274 1xv2A 237 2.64e+01 d.290.1.1 116076 1dq3A 454 2.65e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1gzcA 239 2.70e+01 b.29.1.1 70803 1oivA 191 2.79e+01 c.37.1.8 93076 1j5vA 351 2.84e+01 1pguA 615 2.85e+01 b.69.4.1,b.69.4.1 88069,88070 1zy1B 197 2.87e+01 2gi9A 56 2.90e+01 1qmvA 197 2.92e+01 1qq2A c.47.1.10 33066 2f9lA 199 2.92e+01 c.37.1.8 133166 2a2lA 145 2.96e+01 d.110.9.1 126035 1bywA 110 3.02e+01 1bywA d.110.3.6 40912 1atlA 202 3.03e+01 1atlA d.92.1.9 40322 1nwzA 125 3.05e+01 d.110.3.1 86370 3pyp 125 3.05e+01 3pyp 1ym5A 300 3.06e+01 1u84A 90 3.06e+01 a.230.1.1 113114 2fhi 147 3.06e+01 1fit 1hbkA 94 3.07e+01 1aca a.11.1.1 60887 2aq4A 434 3.11e+01 1m7xA 617 3.12e+01 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 1zwyA 185 3.13e+01 c.51.4.3 125753 1d4oA 184 3.19e+01 1d4oA c.31.1.4 31748 1rwiA 270 3.22e+01 b.68.9.1 97987 1iazA 179 3.24e+01 1iazA b.97.1.1 62131 1sviA 195 3.25e+01 c.37.1.8 106048 1r7aA 504 3.26e+01 b.71.1.1,c.1.8.1 97192,97193 1a64A 97 3.31e+01 1cdcA b.1.1.1 19750 1utcA 363 3.32e+01 a.118.1.4,b.69.6.1 99914,99915 2bo9A 308 3.32e+01 c.56.5.1 128897 1d1vA 444 3.33e+01 1nseA d.174.1.1 59101 1xwl 580 3.34e+01 1xwl 1yarH 217 3.37e+01 d.153.1.4 122844 1rypB 250 3.39e+01 1rypB d.153.1.4 41933 1qh3A 260 3.43e+01 1qh5A d.157.1.2 42059 1qh5A 260 3.45e+01 1qh5A d.157.1.2 42057 1ad2 228 3.46e+01 1ad2 1mzbA 136 3.47e+01 a.4.5.42 91497 2bklA 695 3.49e+01 1go4A 205 3.53e+01 d.135.1.1 70292 1l3sA 580 3.56e+01 c.55.3.5,e.8.1.1 84521,84522 1e8gA 560 3.58e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1iybA 208 3.58e+01 d.124.1.1 90720 1u14A 172 3.61e+01 c.51.4.3 107579 2amyA 246 3.62e+01 c.108.1.10 127026 1l1zA 274 3.76e+01 a.156.1.2,b.113.1.1,g.39.1.8 75911,75912,75913 1o04A 500 3.77e+01 c.82.1.1 86508 1vh5A 148 3.82e+01 d.38.1.5 100642 1bf6A 291 3.83e+01 1pscA c.1.9.3 29065 1t95A 240 3.84e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1psdA 409 3.86e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1cdcA 99 3.87e+01 1cdcA b.1.1.1 19746 2g0wA 296 3.88e+01 c.1.15.4 134503 1u4bA 580 3.89e+01 c.55.3.5,e.8.1.1 107664,107665 1nk4A 580 3.90e+01 c.55.3.5,e.8.1.1 91923,91924 1q7sA 117 3.92e+01 c.131.1.1 96055 1ukkA 142 3.92e+01 d.227.1.1 99491 1xh9A 350 3.93e+01 1mkeA 152 3.96e+01 b.55.1.4 79231 1squA 155 3.97e+01 d.252.1.1 98971 1yduA 170 3.98e+01 b.162.1.1 123003 1zxzA 197 3.98e+01 1scfA 273 4.12e+01 1exzA a.26.1.2 16873 1u00A 227 4.13e+01 a.8.4.1,b.130.1.1 112900,112901 1mngA 203 4.14e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1k3xA 262 4.15e+01 a.156.1.2,b.113.1.1,g.39.1.8 77242,77243,77244 1gwyA 175 4.16e+01 b.97.1.1 83356 1vggA 161 4.23e+01 d.256.1.1 113647 1mdwA 328 4.26e+01 d.3.1.3 84934 1zjcA 418 4.27e+01 e.60.1.1 125147 1oixA 191 4.27e+01 c.37.1.8 118710 1bpoA 494 4.28e+01 1bpoA a.118.1.4,b.69.6.1 19143,27670 1c4zA 358 4.36e+01 1c4zA d.148.1.1 41766 1yb2A 275 4.40e+01 c.66.1.13 122868 1adoA 363 4.41e+01 1fbaA c.1.10.1 29124 2cfuA 658 4.47e+01 1ta8A 332 4.49e+01 d.142.2.2 112375 1f2tB 148 4.49e+01 1f2tB 1x7yA 400 4.50e+01 c.36.1.11 114944 1zaiA 363 4.54e+01 c.1.10.1 124828 1vkcA 158 4.60e+01 d.108.1.1 113663 1tn6B 437 4.61e+01 a.102.4.3 112528 1gqzA 274 4.63e+01 d.21.1.1,d.21.1.1 83311,83312 1quqB 121 4.63e+01 1quqB b.40.4.3 25305 1fj2A 232 4.75e+01 1auoA c.69.1.14 34720 1ekeA 230 4.82e+01 1ekeA c.55.3.1 33572 1ed5A 444 4.82e+01 1nseA d.174.1.1 42530 1zatA 250 4.86e+01 b.160.1.1,d.335.1.1 124845,124846 1zq1A 438 4.91e+01 b.38.3.1,c.88.1.1 125489,125490 1v3wA 173 4.91e+01 b.81.1.5 100291 2bfdA 400 4.93e+01 1vlaA 150 4.97e+01 d.227.1.2 108735 1a1x 108 4.97e+01 1a1x 1jayA 212 5.00e+01 c.2.1.6 66478 1gnlA 544 5.00e+01 e.26.1.1 70287 1r2zA 274 5.05e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1x3mA 415 5.11e+01 c.55.1.2,c.55.1.2 121664,121665 1yarA 233 5.14e+01 d.153.1.4 122837 2gkeA 274 5.18e+01 d.21.1.1,d.21.1.1 135329,135330 1u5uA 374 5.19e+01 e.5.1.2 113052 2aeuA 374 5.21e+01 c.67.1.8 126646 1ehiA 377 5.24e+01 1iow c.30.1.2,d.142.1.1 31716,41484 1auvA 311 5.26e+01 1auvA c.30.1.5,d.142.1.3 31723,41558 1bwzA 274 5.26e+01 1bwzA d.21.1.1,d.21.1.1 38337,38338 1vd3A 217 5.27e+01 1cby 259 5.28e+01 1cby 1d0cA 444 5.37e+01 d.174.1.1 64769 2ax3A 502 5.38e+01 c.72.1.4,c.104.1.1 127477,127478 1fc6A 388 5.50e+01 1fc6A b.36.1.3,c.14.1.2 64738,64739 2b06A 155 5.50e+01 d.113.1.1 127624 1a5t 334 5.51e+01 1a5t 1jksA 294 5.51e+01 d.144.1.7 71710 1ummA 172 5.52e+01 1nscA 390 5.52e+01 2qwc b.68.1.1 27591 2c8sA 172 5.53e+01 a.3.1.1 130123 3erk 364 5.59e+01 1hcl 1zj8A 566 5.59e+01 1trb 320 5.60e+01 1trb 1ud0A 113 5.61e+01 a.8.4.1 99198 1z2nX 324 5.62e+01 1u07A 90 5.65e+01 d.212.1.2 112902 1enp 312 5.66e+01 1enp 1b66A 140 5.69e+01 1b66A d.96.1.2 40657 1tuaA 191 5.69e+01 d.51.1.1,d.51.1.1 107321,107322 1t1uA 639 5.72e+01 c.43.1.3,c.43.1.3 119110,119111 1uy4A 145 5.73e+01 b.18.1.10 108131 1mmsA 140 5.73e+01 1mmsA a.4.7.1,d.47.1.1 16247,38766 1ng4A 390 5.73e+01 c.3.1.2,d.16.1.3 85666,85667 2cdnA 201 5.74e+01 c.37.1.1 130289 1u9yA 284 5.81e+01 c.61.1.2,c.61.1.2 119655,119656 1go7P 462 5.85e+01 b.80.7.1,d.92.1.6 76245,76246 1edqA 540 5.85e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1weyA 104 5.88e+01 d.58.7.1 114569 1bazA 53 5.94e+01 1bazA a.43.1.1 17421 1a99A 344 5.99e+01 1pot c.94.1.1 35812 1qd1A 325 5.99e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1ls1A 295 6.01e+01 a.24.13.1,c.37.1.10 78170,78171 1nekA 588 6.01e+01 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 1oxwA 373 6.07e+01 c.19.1.3 87539 1nrlA 316 6.09e+01 a.123.1.1 92091 2bw4A 340 6.12e+01 b.6.1.3,b.6.1.3 129320,129321 2ex3B 264 6.12e+01 a.263.1.1 132500 1hwxA 501 6.14e+01 1hwyA c.2.1.7,c.58.1.1 30250,33898 1k7iA 479 6.15e+01 b.80.7.1,d.92.1.6 77281,77282 1wvqA 167 6.15e+01 1v1rA 400 6.16e+01 c.36.1.11 108272 1yvhA 329 6.19e+01 a.39.1.7,a.48.1.1,d.93.1.1 124096,124097,124098 1iyxA 432 6.25e+01 c.1.11.1,d.54.1.1 83815,83816 1vclA 432 6.28e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1olsA 400 6.30e+01 c.36.1.11 93331 1apmE 350 6.33e+01 1cdkA d.144.1.7 41628 1tvoA 368 6.34e+01 1cdzA 96 6.37e+01 1cdzA c.15.1.1 30925 2cblA 305 6.38e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17380,17774,40528 1lm6A 215 6.42e+01 d.167.1.1 84628 1cyj 90 6.42e+01 1ctj 1usyA 275 6.45e+01 d.104.1.1 113422 1nffA 260 6.48e+01 c.2.1.2 80457 1plq 258 6.50e+01 1plq 1r7mA 235 6.59e+01 d.95.2.1,d.95.2.1 111713,111714 1y6zA 263 6.61e+01 1u6bA 98 6.65e+01 d.58.7.1 107703 2cfxA 144 6.66e+01 a.4.5.32,d.58.4.2 130395,130396 1bo1A 416 6.74e+01 1bo1A d.143.1.2 41591 1fcdA 401 6.81e+01 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 1ryp1 222 6.83e+01 1ryp1 1rdqE 350 6.88e+01 d.144.1.7 97314 1ctn 540 6.89e+01 1ctn 1usuA 260 6.90e+01 d.14.1.8 99885 1ksiA 642 6.91e+01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24408,38043,38044 2gqrA 237 6.92e+01 1vl2A 421 6.93e+01 c.26.2.1,d.210.1.1 108708,108709 1dixA 208 6.96e+01 1bk7A d.124.1.1 41122 1u6zA 513 6.97e+01 a.211.1.5,c.55.1.8,c.55.1.8 119608,119609,119610 1q4rA 112 7.00e+01 d.58.4.4 95823 1xhdA 173 7.08e+01 b.81.1.5 115295 1k0wA 231 7.09e+01 c.74.1.1 77220 1skhA 30 7.10e+01 1n9lA 109 7.11e+01 d.110.3.6 85468 1kutA 230 7.15e+01 d.143.1.1 73017 1ovnA 248 7.17e+01 a.71.1.1,c.47.1.7 93602,93603 2fflA 756 7.19e+01 1e2kA 331 7.21e+01 1qhiA c.37.1.1 31854 1lfb 99 7.23e+01 1lfb 1th5A 74 7.24e+01 d.52.8.1 119263 2aorA 223 7.28e+01 1vfrA 218 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