# List of top-scoring protein chains for t06-80-60-80-str2+near-backbone-11-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 2a84A 300 2.24e-02 1n2eA 300 3.97e-02 c.26.1.4 85268 1v8fA 276 6.20e-02 c.26.1.4 100503 1qwzA 235 9.71e-02 b.100.1.1 96510 2b20A 403 1.22e-01 1y7rA 133 1.37e-01 1jae 471 1.44e-01 1smd b.71.1.1,c.1.8.1 27773,28760 1smd 496 1.80e-01 1smd b.71.1.1,c.1.8.1 27768,28755 1iwmA 186 2.00e-01 b.125.1.2 83758 1q33A 292 2.43e-01 d.113.1.1 95657 1vr3A 191 2.84e-01 1wgkA 114 3.03e-01 1tiqA 180 3.69e-01 d.108.1.1 107010 1cojA 212 3.97e-01 1avmA a.2.11.1,d.44.1.1 15737,38734 1e19A 314 5.97e-01 1b7bA c.73.1.1 34967 1ebfA 358 5.99e-01 1ebuA c.2.1.3,d.81.1.2 30033,39948 2a74A 643 6.04e-01 1dmhA 311 6.58e-01 1dmhA b.3.6.1 22633 2b18A 164 6.96e-01 2as0A 396 7.21e-01 1w44A 331 7.38e-01 1rz2A 254 7.41e-01 b.100.1.1 105130 1hx0A 496 8.45e-01 b.71.1.1,c.1.8.1 61346,61347 2a2lA 145 9.19e-01 1sqwA 188 9.48e-01 1v25A 541 1.30e+00 e.23.1.1 108275 1xs0A 136 1.45e+00 2dbbA 151 1.52e+00 1xzzA 246 1.64e+00 3pcgA 200 1.68e+00 3pchA b.3.6.1 22647 3proC 166 1.71e+00 3proC d.52.1.1,d.52.1.1 38812,38813 1ohpA 125 1.78e+00 1cl8A 276 1.80e+00 1ckqA c.52.1.1 33230 1djrD 103 1.90e+00 3chbD b.40.2.1 24865 1qwtA 255 2.01e+00 b.26.1.3 96501 1jkxA 212 2.33e+00 c.65.1.1 66813 1ti6B 274 2.61e+00 b.3.5.1,d.58.1.5 106976,106977 1ugjA 141 2.66e+00 b.41.1.3 107826 3gcb 470 2.78e+00 3gcb d.3.1.1 37032 1tu1A 148 2.87e+00 d.107.1.3 107316 1rgxA 114 2.89e+00 g.77.1.1 104932 7taa 478 2.92e+00 7taa b.71.1.1,c.1.8.1 27778,28765 2bjfA 329 3.00e+00 1vetA 124 3.07e+00 d.110.7.1 108553 1ki0A 253 3.11e+00 g.14.1.1,g.14.1.1,g.14.1.1 72493,72494,72495 3chbD 104 3.21e+00 3chbD b.40.2.1 24970 1n71A 180 3.22e+00 d.108.1.1 85370 1zpvA 91 3.34e+00 1fzqA 181 3.41e+00 1hurA c.37.1.8 32060 1bcpF 99 3.50e+00 1prtF b.40.2.1 25142 1qipA 183 3.59e+00 1qipA d.32.1.1 38470 1y12A 165 3.67e+00 1kao 167 3.77e+00 1ctqA c.37.1.8 32014 1qhtA 775 3.89e+00 1tgoA c.55.3.5,e.8.1.1 33722,43011 2bmoB 194 3.93e+00 1wz9A 375 3.93e+00 1v3yA 192 4.01e+00 1quqB 121 4.06e+00 1quqB b.40.4.3 25305 1g94A 448 4.46e+00 b.71.1.1,c.1.8.1 65169,65170 1pea 385 4.48e+00 1pea c.93.1.1 35662 1x4rA 99 4.56e+00 2atrA 138 4.67e+00 1x6oA 174 4.76e+00 b.34.5.2,b.40.4.5 109493,109494 1uw4A 91 4.89e+00 d.58.7.4 100071 1qb5D 99 4.90e+00 b.40.2.1 88357 2f4iA 197 4.95e+00 1ecrA 309 5.51e+00 1ecrA e.2.1.1 42678 1luzA 88 5.56e+00 b.40.4.5 74271 1bsmA 201 5.64e+00 1avmA a.2.11.1,d.44.1.1 15780,38743 1qstA 160 5.81e+00 1yghA d.108.1.1 40804 1zldA 120 5.83e+00 2biiA 424 6.18e+00 1fjrA 195 6.34e+00 1fjrA b.102.1.1 59855 1vl4A 447 6.40e+00 d.283.1.1 108718 1c44A 123 6.65e+00 1qndA d.106.1.1 40795 1ogdA 131 6.68e+00 c.133.1.1 92893 1zkdA 387 6.69e+00 1xk7A 408 6.75e+00 2c5lC 117 6.82e+00 1vjvA 415 6.94e+00 d.3.1.9 108632 1opd 85 6.99e+00 1ptf d.94.1.1 40560 1mw9X 592 7.09e+00 e.10.1.1 91480 1bcpD 110 7.11e+00 1bcpD b.40.2.1 25132 1fjjA 159 7.12e+00 1fjjA b.17.1.2 59852 2erxA 172 7.12e+00 2a90A 240 7.28e+00 1rg9A 383 7.32e+00 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1wddS 128 7.36e+00 1wtaA 275 7.43e+00 2gj8A 172 7.44e+00 1y51A 88 7.52e+00 1lcyA 325 7.58e+00 b.36.1.4,b.47.1.1 73834,73835 1ckmA 330 7.99e+00 1ckmA b.40.4.6,d.142.2.3 25358,41585 1o54A 277 8.20e+00 c.66.1.13 92482 2basA 431 8.37e+00 1fl2A 310 8.46e+00 1hyuA c.3.1.5,c.3.1.5 59869,59870 1voqa 90 8.83e+00 2bukA 196 8.94e+00 1wwjA 105 8.97e+00 1ei6A 406 9.19e+00 c.76.1.4 90443 1yhfA 115 9.22e+00 2h3bA 494 9.24e+00 1u04A 771 9.25e+00 b.34.14.1,c.55.3.10 107539,107540 2fr5A 146 9.30e+00 3tdt 274 9.44e+00 3tdt b.81.1.2 28053 2a5jA 191 9.48e+00 1yj7A 171 9.79e+00 1e2wA 251 9.83e+00 1hcz b.2.6.1,b.84.2.2 22466,28252 2cyeA 133 9.90e+00 1pl4A 198 9.91e+00 a.2.11.1,d.44.1.1 94854,94855 2iwrA 178 1.02e+01 2essA 248 1.02e+01 2cy2A 174 1.03e+01 2exnA 136 1.04e+01 1r45A 204 1.05e+01 1meoA 209 1.05e+01 c.65.1.1 79035 1ex2A 189 1.05e+01 1ex2A c.51.4.2 33225 1x9mA 698 1.06e+01 1wchA 315 1.08e+01 1q8iA 783 1.10e+01 c.55.3.5,e.8.1.1 96208,96209 1pzxA 289 1.10e+01 c.119.1.1 95484 1tedA 393 1.11e+01 c.95.1.2 106807 1lj5A 379 1.13e+01 e.1.1.1 73928 1jsuC 84 1.13e+01 1jsuC j.55.1.1 46339 1lc5A 364 1.13e+01 c.67.1.1 73827 1zbpA 273 1.17e+01 1sc6A 404 1.17e+01 1rzhH 260 1.18e+01 b.41.1.1,f.23.10.1 98162,98163 2bzvA 181 1.18e+01 2a8jA 420 1.19e+01 1eluA 390 1.20e+01 1elqA c.67.1.3 34434 2fug7 129 1.21e+01 1vkiA 181 1.21e+01 d.116.1.1 108664 1t6aA 126 1.23e+01 d.129.8.1 106555 2gkpA 167 1.24e+01 2nlrA 234 1.24e+01 2nlrA b.29.1.11 24344 1pq4A 291 1.25e+01 c.92.2.2 94995 1tvxA 75 1.25e+01 1tvxA d.9.1.1 37441 1q1oA 98 1.27e+01 d.15.2.2 95596 2fvhA 120 1.27e+01 1fc4A 401 1.27e+01 1bs0A c.67.1.4 59760 1x99A 145 1.27e+01 1dkiA 371 1.29e+01 1dkiA d.3.1.1 37090 1xeeA 91 1.33e+01 2carA 196 1.34e+01 1toaA 313 1.36e+01 1toaA c.92.2.2 35598 1aly 146 1.37e+01 1aly b.22.1.1 23856 2evwX 166 1.38e+01 1ogaE 252 1.39e+01 b.1.1.1,b.1.1.2 86992,86993 1ir21 140 1.42e+01 1v74A 107 1.43e+01 d.243.1.1 100442 1unnC 115 1.44e+01 d.240.1.1 99680 1olrA 224 1.48e+01 b.29.1.11 93330 1vk0A 206 1.50e+01 c.55.3.5 100839 1h8eH 146 1.51e+01 1e79H b.93.1.1 60757 1vjfA 180 1.51e+01 d.116.1.1 100809 1z4rA 168 1.51e+01 1ig8A 486 1.52e+01 2yhx c.55.1.3,c.55.1.3 64746,64747 1cqxA 403 1.52e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1vj0A 380 1.52e+01 b.35.1.2,c.2.1.1 100786,100787 4ubpA 101 1.53e+01 1ubpA d.8.1.1 37352 1b06A 210 1.53e+01 1avmA a.2.11.1,d.44.1.1 15740,38737 1mtpA 323 1.53e+01 e.1.1.1 85107 2c9wA 169 1.54e+01 1x9pA 523 1.54e+01 2blnA 305 1.55e+01 1bg2 325 1.58e+01 1bg2 c.37.1.9 32189 2bidA 197 1.59e+01 2bidA f.1.4.1 43398 2ff4A 388 1.59e+01 1wznA 252 1.60e+01 1je5A 206 1.61e+01 1je5A b.40.4.7 62909 1p0zA 131 1.62e+01 d.110.6.1 93882 2b06A 155 1.63e+01 1tmxA 293 1.63e+01 1y9lA 115 1.65e+01 2bjuA 453 1.70e+01 1s68A 249 1.72e+01 d.142.2.4 98591 1b34B 118 1.73e+01 1b34B b.38.1.1 24797 1mkmA 249 1.76e+01 a.4.5.33,d.110.2.2 79242,79243 1s3cA 141 1.77e+01 2ew2A 316 1.78e+01 1mixA 206 1.78e+01 a.11.2.1,b.55.1.5 79166,79167 1lp9E 194 1.79e+01 b.1.1.1,b.1.1.2 91086,91087 2cx7A 130 1.79e+01 1jmcA 246 1.81e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 1qtqA 553 1.82e+01 1gtrA b.53.1.2,c.26.1.1 26940,31579 1x9gA 200 1.87e+01 c.33.1.3 109527 1o75A 415 1.87e+01 b.1.20.1,b.1.20.1,b.120.1.1 81117,81118,81119 1g9oA 91 1.88e+01 1pdr b.36.1.1 60400 1k7kA 221 1.89e+01 c.51.4.1 72104 1ycoA 279 1.89e+01 1obbA 480 1.91e+01 c.2.1.5,d.162.1.2 86760,86761 1tueA 212 1.92e+01 c.37.1.20 107323 1mai 131 1.93e+01 1mai b.55.1.1 26951 2d1sA 548 1.94e+01 1ryaA 160 1.96e+01 d.113.1.5 105122 1yfnA 118 1.96e+01 1t4wA 196 1.97e+01 b.2.5.2 106427 1cv8 174 1.98e+01 1cv8 d.3.1.1 37089 1yd0A 96 1.99e+01 1ejxA 100 2.00e+01 d.8.1.1 83182 1w15A 153 2.02e+01 b.7.1.2 109041 1gcqC 70 2.03e+01 1gcpA b.34.2.1 60436 1u58A 253 2.04e+01 2ajgA 196 2.04e+01 1zjcA 418 2.05e+01 2glfA 450 2.05e+01 1fvuA 133 2.06e+01 1ixxB d.169.1.1 42345 1d3bB 91 2.07e+01 1d3bB b.38.1.1 24804 1q67A 231 2.09e+01 b.55.1.7 95960 1r8gA 372 2.14e+01 d.128.1.3 104845 1h6lA 353 2.16e+01 b.68.3.1 60687 1ptf 88 2.16e+01 1ptf d.94.1.1 40549 1ako 268 2.16e+01 1ako d.151.1.1 41779 1u07A 90 2.17e+01 1whzA 70 2.17e+01 1jkmB 361 2.18e+01 1jkmA c.69.1.2 34634 2bdeA 470 2.20e+01 1ytqA 204 2.21e+01 1q40B 219 2.22e+01 d.17.4.2 95771 1z6nA 167 2.23e+01 1vhxA 150 2.24e+01 c.55.3.8 100712 1up7A 417 2.25e+01 1b5pA 385 2.25e+01 c.67.1.1 90403 1jyhA 157 2.27e+01 d.60.1.3 71956 2bw3A 534 2.28e+01 2cttA 104 2.28e+01 2aukA 190 2.30e+01 1cr5A 189 2.31e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1pa1A 310 2.34e+01 c.45.1.2 94404 1nrlA 316 2.34e+01 a.123.1.1 92091 1vl2A 421 2.37e+01 c.26.2.1,d.210.1.1 108708,108709 1ou8A 111 2.38e+01 b.136.1.1 93543 2bmjA 178 2.40e+01 1k2xA 177 2.40e+01 d.153.1.5 90929 1n8yC 608 2.41e+01 c.10.2.5,c.10.2.5,g.3.9.1,g.3.9.1 80314,80315,80316,80317 1vdc 333 2.42e+01 1trb c.3.1.5,c.3.1.5 30545,30546 2db9A 149 2.46e+01 1vqoE 178 2.47e+01 1s5jA 847 2.47e+01 1y0zA 330 2.48e+01 2aotA 292 2.48e+01 2he7A 283 2.51e+01 1suwA 249 2.51e+01 e.52.1.1 106027 1x82A 190 2.51e+01 2aheA 267 2.51e+01 1yleA 342 2.51e+01 1aqcA 172 2.54e+01 1x11A b.55.1.2 26983 1a8l 226 2.55e+01 1a8l c.47.1.2,c.47.1.2 32777,32778 1yfuA 174 2.56e+01 1wc3A 219 2.59e+01 2fsqA 243 2.59e+01 1gpqA 135 2.61e+01 d.233.1.1 83295 1th7A 81 2.64e+01 1x88A 359 2.67e+01 1molA 94 2.74e+01 1molA d.17.1.1 37988 1f08A 148 2.77e+01 1f08A d.89.1.2 59564 1vqoH 171 2.82e+01 2d28C 149 2.83e+01 1v54B 227 2.84e+01 b.6.1.2,f.17.2.1 100322,100323 1ecfA 504 2.90e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1ykdA 398 2.90e+01 1i12A 160 2.91e+01 1i21A d.108.1.1 61515 1cozA 129 2.97e+01 1cozA c.26.1.2 31598 1njhA 119 2.98e+01 b.128.1.1 85787 1cjwA 166 2.98e+01 1cjwA d.108.1.1 40818 2bnmA 198 2.98e+01 1zsqA 528 3.01e+01 1u4nA 310 3.02e+01 1v60A 123 3.02e+01 1wvqA 167 3.03e+01 1nqzA 194 3.04e+01 d.113.1.1 86077 1wmmA 145 3.06e+01 2aq4A 434 3.06e+01 1x1rA 178 3.08e+01 1fgkA 310 3.09e+01 1fgkA d.144.1.7 41693 2bkrA 212 3.10e+01 1svdM 110 3.12e+01 1f35A 162 3.12e+01 1f35A b.94.1.1 59628 1kshB 152 3.12e+01 b.1.18.8 72915 1xizA 159 3.13e+01 1f06A 320 3.18e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 1vggA 161 3.18e+01 2tnfA 156 3.18e+01 2tnfA b.22.1.1 23880 1e7uA 961 3.18e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 2d4qA 257 3.24e+01 1ifrA 121 3.27e+01 b.1.16.1 71203 1chd 203 3.28e+01 1chd c.40.1.1 32478 1zhsA 113 3.31e+01 1r75A 141 3.34e+01 b.134.1.1 97189 2g29A 417 3.35e+01 1cewI 108 3.36e+01 1cewI d.17.1.2 37999 1no5A 114 3.36e+01 d.218.1.5 92014 1h2wA 710 3.37e+01 b.69.7.1,c.69.1.4 76596,76597 1erw 105 3.38e+01 1erv c.47.1.1 32745 2b49A 287 3.39e+01 1fm0D 81 3.39e+01 1fmaD d.15.3.1 37642 1rsy 152 3.40e+01 1rsy b.7.1.2 23192 1u8zA 168 3.41e+01 1l5xA 280 3.41e+01 c.106.1.1 77718 1d8hA 311 3.45e+01 1d8iA d.63.1.1 39544 1z2mA 155 3.46e+01 1xqbA 247 3.47e+01 1i9gA 280 3.48e+01 c.66.1.13 62090 2axcA 264 3.50e+01 1umwA 237 3.50e+01 d.223.1.2,d.223.1.2 99631,99632 1dwkA 156 3.51e+01 1dw9A a.35.1.4,d.72.1.1 17075,39606 1w2lA 99 3.51e+01 1pbyB 337 3.53e+01 b.69.2.2 94422 1b65A 375 3.53e+01 1b65A d.154.1.1 42020 2cu6A 103 3.55e+01 1va6A 518 3.60e+01 2gu3A 136 3.62e+01 1rjcA 137 3.64e+01 2fytA 340 3.64e+01 1sjyA 159 3.65e+01 d.113.1.1 98900 1m4iA 181 3.66e+01 d.108.1.1 74457 1gk8I 140 3.66e+01 d.73.1.1 65242 1who 96 3.66e+01 1who b.7.3.1 23215 1wlgA 299 3.73e+01 1ejeA 192 3.73e+01 1ejeA b.45.1.2 25757 1t4aA 84 3.75e+01 d.284.1.1 106404 1y8tA 324 3.77e+01 1wlsA 328 3.83e+01 2faoA 309 3.84e+01 1yumA 242 3.84e+01 1yi9A 309 3.85e+01 1ewfA 456 3.86e+01 1bp1 d.83.1.1,d.83.1.1 40024,40025 1qh8A 478 3.87e+01 1qguA c.92.2.3 35633 1vioA 243 3.87e+01 d.265.1.3,d.66.1.5 100762,100763 1y9qA 192 3.89e+01 1wxcB 134 3.91e+01 1uocA 289 3.91e+01 c.55.3.9 99686 1hleA 345 3.93e+01 1ovaA e.1.1.1 42618 1nnvA 110 3.93e+01 d.17.7.1 92012 1q87A 221 3.95e+01 e.47.1.1 96192 2a9dA 372 3.97e+01 1zceA 155 3.97e+01 2bj7A 138 3.98e+01 1j7gA 144 3.98e+01 c.110.1.1 84130 1epfA 191 3.98e+01 2ncm b.1.1.4,b.1.1.4 21694,21695 1fiuA 286 4.03e+01 1fiuA c.52.1.10 33317 2yhx 457 4.05e+01 2yhx i.12.1.1 46024 1koe 172 4.09e+01 1koe d.169.1.5 42448 1fvuB 125 4.12e+01 1ixxB d.169.1.1 42346 1uekA 275 4.15e+01 d.14.1.5,d.58.26.5 88483,88484 2arrA 382 4.19e+01 1wloA 136 4.20e+01 2amhA 207 4.21e+01 1fs0E 138 4.22e+01 1aqt a.2.10.1,b.93.1.1 59997,59998 1oa4A 222 4.27e+01 b.29.1.11 86731 1kdj 102 4.28e+01 1plc b.6.1.1 22864 2bbkH 355 4.30e+01 2bbkH b.69.2.1 27634 1nnwA 252 4.30e+01 d.159.1.5 80674 1p7gA 222 4.36e+01 a.2.11.1,d.44.1.1 94223,94224 1o7zA 77 4.38e+01 d.9.1.1 86660 1o5uA 101 4.38e+01 b.82.1.8 92518 1f0xA 571 4.39e+01 1f0xA d.58.32.2,d.145.1.1 39483,41746 1m5q1 130 4.40e+01 1rypC 244 4.40e+01 1rypC d.153.1.4 41934 1pmmA 466 4.42e+01 c.67.1.6 94901 1twuA 139 4.42e+01 d.32.1.8 107413 1yn3A 98 4.46e+01 1zowA 313 4.48e+01 1ycdA 243 4.52e+01 1div 149 4.55e+01 1div d.99.1.1,d.100.1.1 40692,40693 2b4yA 271 4.57e+01 1a8y 367 4.57e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 2iugA 120 4.58e+01 1un7A 400 4.61e+01 b.92.1.5,c.1.9.10 99657,99658 2f23A 156 4.62e+01 1c1lA 136 4.63e+01 1c1lA b.29.1.3 24219 1bu8A 452 4.66e+01 1gpl b.12.1.2,c.69.1.19 23647,34795 2g45A 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