# 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 2ap1A 327 2.85e-02 1fezA 256 3.14e-01 1fezA c.108.1.3 43343 1swvA 267 5.21e-01 1rqlA 267 5.55e-01 c.108.1.3 97750 1rypA 243 8.44e-01 1pmaA d.153.1.4 41932 1g0uG 252 1.01e+00 d.153.1.4 41952 1u2eA 289 1.10e+00 1yrvA 169 1.24e+00 1zoyC 140 1.35e+00 2h88C 140 1.54e+00 1zd9A 188 1.61e+00 1pysA 350 1.79e+00 1pysA d.104.1.1 40775 1fseA 74 1.98e+00 1fseA a.4.6.2 60000 1h2kA 349 2.02e+00 b.82.2.6 76572 1jl5A 454 2.14e+00 c.10.2.6 66830 2fbwC 141 2.37e+00 1ofgA 381 2.40e+00 1ofgA c.2.1.3,d.81.1.5 30064,39979 1u9aA 160 2.47e+00 1u9aA d.20.1.1 38333 1h6dA 433 2.54e+00 c.2.1.3,d.81.1.5 65656,65657 1gu7A 364 2.59e+00 b.35.1.2,c.2.1.1 83321,83322 1r0pA 312 2.67e+00 d.144.1.7 96734 1b5pA 385 2.72e+00 c.67.1.1 90403 1w77A 228 2.81e+00 1r8sA 164 3.20e+00 c.37.1.8 97247 1b7yA 350 3.24e+00 1pysA d.104.1.1 40776 2ahqA 76 3.30e+00 1z5bA 469 3.51e+00 1nepA 130 3.80e+00 b.1.18.7 80440 1wf9A 107 3.91e+00 1nrjA 158 4.00e+00 d.110.4.4 86124 1bjwA 382 4.27e+00 1bjwA c.67.1.1 34349 2grrA 161 4.70e+00 1ajsA 412 4.73e+00 1ajsA c.67.1.1 34276 1f20A 435 4.90e+00 b.43.4.1,c.25.1.4 64932,64933 1l9hA 349 4.96e+00 f.13.1.2 73720 1yirA 408 5.18e+00 1z8uA 102 5.18e+00 2b20A 403 5.36e+00 1u19A 349 5.61e+00 1jsdA 319 5.68e+00 b.19.1.2 63258 1wg8A 285 6.02e+00 2a3qA 170 6.22e+00 1ymmA 191 6.37e+00 1r85A 379 6.39e+00 c.1.8.3 104839 1sxjE 354 6.65e+00 a.80.1.1,c.37.1.20 106089,106090 2a5lA 200 6.87e+00 1tllA 688 7.12e+00 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1ufiA 64 7.24e+00 a.30.4.1 99336 1jy2O 56 7.32e+00 h.1.8.1 67441 1hzxA 349 7.37e+00 1f88A f.13.1.2 61466 1w0bA 102 7.41e+00 a.7.11.1 108985 2ddrA 306 7.62e+00 1a8y 367 7.77e+00 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1kxoA 184 7.79e+00 b.60.1.1 84475 1uj8A 77 7.81e+00 1kvkA 395 7.92e+00 d.14.1.5,d.58.26.3 73060,73061 1gg3A 279 8.77e+00 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16372,27007,37615 1kveB 77 8.86e+00 1kveB 1bbpA 173 9.13e+00 1bbpA b.60.1.1 27147 2bjkA 516 9.15e+00 1yx1A 264 9.19e+00 1onwA 390 9.32e+00 b.92.1.7,c.1.9.13 87172,87173 1sjiA 350 9.76e+00 1uzbA 516 9.92e+00 c.82.1.1 100220 1rdfA 267 1.03e+01 c.108.1.3 104884 1a8d 452 1.04e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 1ois 223 1.06e+01 1a36A e.15.1.1 43267 1exrA 148 1.06e+01 1cll a.39.1.5 17299 1rm4A 337 1.10e+01 c.2.1.3,d.81.1.1 105000,105001 1wzvA 155 1.12e+01 1stzA 338 1.12e+01 a.4.5.51,d.110.2.3 106009,106010 1wijA 140 1.13e+01 1q1vA 70 1.16e+01 a.159.4.1 104479 1qsdA 106 1.17e+01 1qsdA a.7.5.1 16335 2g7jA 124 1.17e+01 1k3tA 359 1.25e+01 c.2.1.3,d.81.1.1 72022,72023 1mlwA 301 1.26e+01 d.178.1.1 79289 2afdA 88 1.27e+01 1wgxA 73 1.27e+01 1sziA 247 1.34e+01 a.24.23.1 106159 1xqaA 113 1.36e+01 1gqeA 365 1.37e+01 e.38.1.1 70351 1jchA 551 1.37e+01 b.101.1.1,b.110.1.1,h.4.9.1 66491,66492,66493 2ajrA 331 1.38e+01 1z08A 170 1.39e+01 1td6A 306 1.39e+01 1ztpA 251 1.44e+01 1ujwB 135 1.46e+01 h.4.9.1 99472 1s1qA 145 1.51e+01 d.20.1.2 98351 2bogX 286 1.55e+01 1o5iA 249 1.60e+01 c.2.1.2 92499 1fzqA 181 1.61e+01 1hurA c.37.1.8 32060 1ufzA 83 1.64e+01 a.5.9.1 107821 1o5kA 306 1.68e+01 c.1.10.1 92504 1lvfA 110 1.73e+01 a.47.2.1 74280 1ug0A 88 1.77e+01 a.217.1.1 107822 2fjlA 150 1.79e+01 1gypA 358 1.82e+01 1dssG c.2.1.3,d.81.1.1 30004,39919 1q2hA 69 1.83e+01 a.34.4.1 104498 2fi9A 128 1.84e+01 2bwfA 77 1.91e+01 1xttA 216 2.01e+01 2fa8A 105 2.04e+01 1wxcB 134 2.05e+01 1zwwA 256 2.07e+01 2b6hA 192 2.07e+01 1lox 662 2.07e+01 1lox a.119.1.2,b.12.1.1 19238,23638 1uujA 88 2.12e+01 a.221.1.1 108046 2cglA 489 2.13e+01 1lkkA 105 2.17e+01 1lckA d.93.1.1 40412 1lre 81 2.23e+01 1lre a.13.1.1 16376 1shuX 182 2.24e+01 c.62.1.1 98882 1yovA 537 2.26e+01 1aj8A 371 2.32e+01 1aj8A a.103.1.1 18900 1jj2L 194 2.33e+01 1ffkI d.12.1.2 63097 1s72M 194 2.36e+01 d.12.1.2 105332 1eu8A 409 2.44e+01 1eu8A c.94.1.1 59502 1yg2A 179 2.44e+01 1vqoM 195 2.45e+01 1sz2A 332 2.46e+01 1u7kA 131 2.47e+01 1q18A 332 2.48e+01 c.55.1.7,c.55.1.7 104470,104471 1pzlA 237 2.53e+01 a.123.1.1 104393 1g8iA 190 2.55e+01 1rec a.39.1.5 60363 1go4A 205 2.57e+01 d.135.1.1 70292 1k1fA 72 2.62e+01 a.147.1.1 68007 1iyjB 817 2.63e+01 a.170.1.1,a.171.1.1,b.40.4.3,b.40.4.3,b.40.4.3 76948,76949,76950,76951,76952 2glzA 153 2.75e+01 1zmtA 254 2.83e+01 1o6zA 303 2.97e+01 c.2.1.5,d.162.1.1 81107,81108 1vmiA 355 2.97e+01 1g4yR 148 3.01e+01 1cll a.39.1.5 60252 1ov2A 99 3.04e+01 a.13.1.1 93580 1ytw 306 3.04e+01 1ytw c.45.1.2 32689 1wpiA 133 3.08e+01 1rgxA 114 3.08e+01 g.77.1.1 104932 1wx1A 335 3.11e+01 1kr4A 125 3.14e+01 d.58.5.2 72889 1sk4A 163 3.14e+01 d.118.1.1 105664 2bpsA 81 3.20e+01 1m0wA 491 3.21e+01 c.30.1.4,d.142.1.6 78363,78364 1w23A 360 3.24e+01 1ul7A 102 3.26e+01 d.129.6.1 99540 1ev0A 58 3.27e+01 1ev0A d.71.1.1 39594 1z02A 446 3.27e+01 1jpzA 473 3.28e+01 a.104.1.1 67069 1vjeA 166 3.31e+01 d.185.1.2 100807 1ggzA 148 3.31e+01 a.39.1.5 70176 1zvkA 358 3.33e+01 2fupA 168 3.33e+01 1m3qA 317 3.33e+01 a.96.1.3,d.129.1.2 91184,91185 1rec 201 3.38e+01 1rec a.39.1.5 17326 1ebmA 317 3.40e+01 1ebmA a.96.1.3,d.129.1.2 18751,41300 1tn4 159 3.40e+01 1ncx a.39.1.5 17248 1d9cA 121 3.40e+01 1d9cA a.26.1.3 16901 1innA 166 3.40e+01 1j98A d.185.1.2 62608 2b8iA 77 3.56e+01 2a2pA 129 3.57e+01 1qqgA 264 3.59e+01 1qqgA b.55.1.2,b.55.1.2 26987,26988 1ukxA 137 3.61e+01 d.20.1.3 107919 1fi2A 201 3.66e+01 1fi2A b.82.1.2 59845 1uqvA 85 3.70e+01 a.60.1.2 99798 1gk8I 140 3.72e+01 d.73.1.1 65242 1wmhA 89 3.76e+01 1xn9A 101 3.82e+01 1xkrA 206 3.83e+01 1lyvA 306 3.86e+01 c.45.1.2 74348 1kshA 186 3.89e+01 c.37.1.8 72914 1eqfA 280 3.90e+01 1eqfA a.29.2.1,a.29.2.1 16972,16973 1jggA 60 3.92e+01 2hddA a.4.1.1 62950 2bodX 286 3.93e+01 1zb1A 392 3.97e+01 1q02A 52 3.98e+01 a.5.2.1 95490 1uyrA 737 3.99e+01 c.14.1.4,c.14.1.4 100188,100189 1xdfA 157 3.99e+01 2f3yA 148 4.04e+01 2aegA 268 4.06e+01 8rucI 123 4.08e+01 1rboC d.73.1.1 39629 2viuA 328 4.11e+01 1hgeA b.19.1.2 23797 2et1A 201 4.14e+01 1sq5A 308 4.16e+01 c.37.1.6 105882 1cuk 203 4.17e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1j33A 335 4.18e+01 c.39.1.1 77069 1gd8A 118 4.18e+01 d.188.1.1 60445 1v5sA 126 4.18e+01 d.129.6.1 108384 1ax8 146 4.23e+01 1ax8 a.26.1.1 16844 2b0tA 738 4.23e+01 1yf9A 171 4.23e+01 2a0iA 330 4.25e+01 1pwxA 254 4.29e+01 c.2.1.2 95262 1yz4A 160 4.38e+01 1qgtA 149 4.38e+01 1qgtA a.62.1.1 18135 1iapA 211 4.49e+01 a.91.1.1 62119 1kr7A 110 4.55e+01 a.1.1.4 72890 1nqzA 194 4.56e+01 d.113.1.1 86077 2gokA 429 4.58e+01 1ayaA 101 4.65e+01 1qadA d.93.1.1 40460 1uzcA 71 4.72e+01 a.159.2.1 100222 1yvhA 329 4.75e+01 1p5fA 189 4.76e+01 c.23.16.2 94142 2mev1 277 4.80e+01 2mev1 1w9yA 319 4.88e+01 1xawA 140 4.89e+01 2dgkA 452 4.94e+01 1r1qA 100 5.03e+01 d.93.1.1 104763 1y8qB 640 5.05e+01 2iugA 120 5.11e+01 1ni5A 433 5.15e+01 c.26.2.5,d.229.1.1 80533,80534 1p8xA 344 5.16e+01 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 2c0rA 362 5.18e+01 1yruB 74 5.21e+01 1w3uA 362 5.21e+01 1woqA 267 5.33e+01 c.55.1.10,c.55.1.10 109462,109463 7aatA 401 5.34e+01 1ajsA c.67.1.1 34250 1o04A 500 5.41e+01 c.82.1.1 86508 1auiA 521 5.43e+01 1auiA d.159.1.3 42085 1b3uA 588 5.47e+01 1b3uA a.118.1.2 19135 2gp5A 349 5.60e+01 2aobA 99 5.64e+01 2gd5A 179 5.65e+01 1n82A 331 5.66e+01 c.1.8.3 91703 1h0hA 977 5.68e+01 b.52.2.2,c.81.1.1 76435,76436 2gkpA 167 5.72e+01 1xiuA 230 5.76e+01 1yf2A 425 5.77e+01 1zg2A 107 5.82e+01 1wqgA 185 5.83e+01 2bydA 323 5.85e+01 1u9jA 358 5.91e+01 1f5aA 513 5.94e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39337,75835,75836 1kllA 130 5.95e+01 d.32.1.2 72720 1vkkA 154 6.02e+01 d.109.1.2 108669 1q79A 514 6.06e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1vgmA 378 6.07e+01 1sxrA 183 6.09e+01 d.118.1.1 106101 1akz 223 6.11e+01 3eugA c.18.1.1 31007 1o5oA 221 6.19e+01 c.61.1.1 92509 2db9A 149 6.28e+01 1zwxA 301 6.29e+01 1omrA 201 6.32e+01 a.39.1.5 93349 2fh1A 344 6.35e+01 1sur 215 6.41e+01 1sur c.26.2.2 31620 2f2hA 773 6.43e+01 1yh6A 179 6.44e+01 1s62A 106 6.45e+01 2g0uA 92 6.46e+01 1avsA 90 6.46e+01 1cll a.39.1.5 17226 1qlnA 883 6.46e+01 1cezA e.8.1.3 43111 1g03A 134 6.50e+01 1qrjB a.73.1.1 60162 1sg7A 96 6.53e+01 1dhpA 292 6.55e+01 1dhpA c.1.10.1 29097 1qx2A 76 6.57e+01 a.39.1.1 104622 1y8tA 324 6.65e+01 1tuoA 464 6.67e+01 1r5zA 323 6.70e+01 f.40.1.1 97135 1xsjA 778 6.76e+01 1q33A 292 6.77e+01 d.113.1.1 95657 1goiA 499 6.77e+01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 1pa2A 306 6.79e+01 1bgp a.93.1.1 18693 1z21A 112 6.79e+01 2g7uA 257 6.80e+01 2eueA 279 6.82e+01 2f02A 323 6.82e+01 2ck3A 510 6.86e+01 1ej1A 190 6.89e+01 1ejhA d.86.1.1 40144 1f24A 402 6.90e+01 1rom a.104.1.1 18953 1tkeA 224 6.95e+01 1xqoA 256 7.01e+01 1w4tA 299 7.02e+01 1p5zB 263 7.03e+01 c.37.1.1 87815 1l8bA 190 7.03e+01 d.86.1.1 73683 1womA 271 7.05e+01 2f6uA 234 7.07e+01 2a6lA 292 7.09e+01 2pth 193 7.13e+01 2pth c.56.3.1 33793 2a6nA 292 7.19e+01 1dat 174 7.20e+01 2fha a.25.1.1 16677 1sauA 115 7.30e+01 1jsmA 325 7.34e+01 b.19.1.2 63264 1jfbA 404 7.34e+01 a.104.1.1 66624 1yxcA 292 7.36e+01 1onxA 390 7.40e+01 b.92.1.7,c.1.9.13 87176,87177 1e79A 510 7.46e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 1gvfA 286 7.55e+01 c.1.10.2 70599 1uvqA 197 7.55e+01 b.1.1.2,d.19.1.1 100062,100063 1ei7A 158 7.55e+01 1rmvA a.24.5.1 16584 1rktA 205 7.60e+01 a.4.1.9,a.121.1.1 97623,97624 1xtnA 120 7.65e+01 1jr7A 311 7.66e+01 b.82.2.3 63255 2c5rA 67 7.73e+01 1pea 385 7.74e+01 1pea c.93.1.1 35662 1fjgP 88 7.74e+01 1emwA d.27.1.1 38444 2h1nA 567 7.75e+01 2awdA 323 7.82e+01 1py5A 326 7.84e+01 d.144.1.7 104389 1em8B 112 7.87e+01 c.126.1.1 90458 1wpaA 114 7.87e+01 1opjA 293 7.90e+01 d.144.1.7 87230 2bllA 345 7.95e+01 1k4nA 192 7.99e+01 d.32.1.5 72059 1mdyA 68 8.01e+01 1mdyA a.38.1.1 17132 1vs0A 310 8.06e+01 1adn 92 8.06e+01 1adn g.48.1.1 45348 1a17 166 8.06e+01 1a17 a.118.8.1 19206 4bcl 366 8.09e+01 4bcl b.75.1.1 27968 1xteA 154 8.13e+01 2tmnE 316 8.16e+01 1hyt d.92.1.2 59055 1cpcA 162 8.17e+01 1cpcA a.1.1.3 15643 1qnrA 344 8.20e+01 1qnoA c.1.8.3 28834 1a02F 56 8.23e+01 1a02F h.1.3.1 45534 1bs0A 384 8.28e+01 1bs0A c.67.1.4 34490 2c0wA 50 8.36e+01 1zfpE 98 8.45e+01 1griA d.93.1.1 40465 1wddS 128 8.49e+01 1vcbA 118 8.53e+01 1vcbA d.15.1.1 37603 3nul 130 8.56e+01 3nul d.110.1.1 40891 1pmmA 466 8.57e+01 c.67.1.6 94901 1o0uA 429 8.57e+01 c.118.1.1 80743 2b8nA 429 8.61e+01 1sfcD 87 8.66e+01 1sfcD h.1.15.1 45646 1ail 73 8.77e+01 1ail a.16.1.1 16381 2d81A 318 8.77e+01 1y1uA 585 8.79e+01 1obfO 335 8.91e+01 c.2.1.3,d.81.1.1 86768,86769 2ga9D 469 8.95e+01 8tlnE 316 8.95e+01 1hyt d.92.1.2 59075 2d7vA 162 8.96e+01 2dfkA 402 8.96e+01 1s9kD 53 8.98e+01