# List of top-scoring protein chains for t04-100-40-40-str2+CB_burial_14_7-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 1dnlA 199 4.27e-14 1ci0A b.45.1.1 25753 1g79A 218 4.92e-14 1ci0A b.45.1.1 25752 1nrgA 261 1.49e-12 b.45.1.1 80694 1t9mA 214 1.55e-12 1ty9A 222 3.04e-12 2fhqA 141 1.11e-11 1rfeA 162 1.59e-11 2fg9A 178 4.51e-10 2asfA 137 6.62e-10 1vl7A 157 7.49e-10 b.45.1.1 108732 2arzA 247 2.43e-08 2aq6A 147 2.58e-08 1xxoA 147 3.76e-08 1w9aA 147 8.48e-08 2furA 209 2.39e-07 1w3oA 216 1.83e-06 1xhnA 184 3.86e-06 1flmA 122 1.02e-05 1axj b.45.1.1 25747 1ejeA 192 5.29e-04 1ejeA b.45.1.2 25757 1wgbA 159 5.79e-02 1yoaA 159 6.32e-02 1uscA 178 9.38e-02 b.45.1.2 99860 2d37A 176 1.13e-01 1rz1A 161 1.64e-01 b.45.1.2 98124 1i0sA 169 1.66e-01 1i0rA b.45.1.2 61491 1i0rA 169 1.79e-01 1i0rA b.45.1.2 61489 1ha3A 405 2.17e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1exmA 405 6.53e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1y08A 323 6.65e-01 1obpA 159 1.06e+00 1obpA b.60.1.1 27092 2bkqA 212 1.36e+00 1rlmB 271 1.62e+00 2bkrA 212 1.65e+00 1lrzA 426 1.79e+00 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1fsz 372 1.84e+00 1fsz c.32.1.1,d.79.2.1 31750,39802 2c78A 405 2.61e+00 2fp8A 322 2.61e+00 1vavA 222 2.72e+00 b.29.1.18 108472 2kfnA 605 2.73e+00 1xwl c.55.3.5,e.8.1.1 33682,42975 1ko3A 230 2.78e+00 d.157.1.1 90974 2fhfA 1083 3.16e+00 1u04A 771 3.19e+00 b.34.14.1,c.55.3.10 107539,107540 1v3eA 431 3.20e+00 b.68.1.1 100287 1tdzA 272 3.33e+00 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 1rlmA 271 3.65e+00 2cxvA 219 3.78e+00 1vlyA 338 3.90e+00 b.44.2.1,d.250.1.1 108871,108872 1nnjA 271 3.94e+00 a.156.1.2,b.113.1.1,g.39.1.8 80669,80670,80671 1pg4A 652 4.06e+00 e.23.1.1 88067 1xt9A 212 4.20e+00 1q6uA 245 4.44e+00 d.26.1.1 95998 2pooA 355 4.69e+00 1qlgA b.68.3.1 27626 1a0i 348 4.70e+00 1a0i b.40.4.6,d.142.2.1 25363,41577 1cruA 454 4.81e+00 1c9uA b.68.2.1 27617 1hn2A 159 4.88e+00 b.60.1.1 65890 1pjjA 271 5.06e+00 a.156.1.2,b.113.1.1,g.39.1.8 104164,104165,104166 1gt1A 159 5.10e+00 b.60.1.1 90515 1nlfA 279 5.44e+00 c.37.1.11 85850 1rgyA 360 5.92e+00 e.3.1.1 97456 1jhdA 396 6.02e+00 b.122.1.3,c.26.1.5 66712,66713 1nrkA 328 6.09e+00 b.44.2.1,d.250.1.1 92089,92090 1ww7A 160 6.19e+00 1bmv2 374 6.30e+00 1bmv2 1l0wA 580 6.40e+00 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1gdoA 240 6.50e+00 1gdoA 2cxcA 144 6.61e+00 2pvaA 345 6.75e+00 3pvaA d.153.1.3 41850 2ffyA 358 6.77e+00 1z4rA 168 6.79e+00 1pgl2 370 6.83e+00 1xhbA 472 6.85e+00 1llnA 262 6.86e+00 d.165.1.1 84625 1qa7A 217 7.02e+00 1havA b.47.1.4 26425 2b4yA 271 7.18e+00 1l0gA 358 7.39e+00 e.3.1.1 73400 1f0cA 305 7.48e+00 1c8oA e.1.1.1 42676 1w8oA 601 7.54e+00 1lq9A 112 7.57e+00 d.58.4.3 78129 1r2zA 274 7.60e+00 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 2bu3A 254 7.60e+00 1pi4A 358 7.82e+00 e.3.1.1 94700 2ftrA 108 7.93e+00 1m2kA 249 7.94e+00 c.31.1.5 84754 1h2wA 710 8.06e+00 b.69.7.1,c.69.1.4 76596,76597 2cwzA 141 8.06e+00 1wcqA 601 8.31e+00 1fsyA 358 8.37e+00 1gceA e.3.1.1 60016 1wubA 178 8.58e+00 1jfuA 186 8.68e+00 c.47.1.10 62940 1q6hA 224 8.86e+00 d.26.1.1 95975 1sq9A 397 8.87e+00 b.69.4.1 105889 1vclA 432 9.17e+00 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1y7bA 542 9.21e+00 2c43A 323 9.26e+00 1wosA 364 9.28e+00 b.44.2.1,d.250.1.1 109468,109469 1yt3A 375 9.30e+00 1jkgA 140 9.36e+00 d.17.4.2 66795 1d2eA 397 9.39e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1z4xA 532 9.40e+00 1ex2A 189 9.59e+00 1ex2A c.51.4.2 33225 1o0pA 104 9.63e+00 d.58.7.1 86535 1qqgA 264 9.91e+00 1qqgA b.55.1.2,b.55.1.2 26987,26988 1b8aA 438 9.92e+00 1b8aA b.40.4.1,d.104.1.1 25244,40765 1rloA 271 1.00e+01 1mdbA 539 1.01e+01 e.23.1.1 79008 1uldA 150 1.02e+01 b.29.1.3 99545 1l1zA 274 1.07e+01 a.156.1.2,b.113.1.1,g.39.1.8 75911,75912,75913 2sli 679 1.08e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1r5mA 425 1.08e+01 1l0qA 391 1.13e+01 b.1.3.1,b.69.2.3 77644,77645 1wbiA 129 1.14e+01 1sdjA 310 1.14e+01 d.21.1.2,d.21.1.2 98807,98808 1ksiA 642 1.16e+01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24408,38043,38044 2c1lA 358 1.20e+01 1eur 365 1.21e+01 1eut b.68.1.1 27607 2bkkA 264 1.28e+01 3pvaA 335 1.35e+01 3pvaA d.153.1.3 41854 1h6lA 353 1.38e+01 b.68.3.1 60687 1chuA 540 1.42e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 3mag 307 1.46e+01 3mag c.66.1.25 34205 2bydA 323 1.46e+01 1iznA 286 1.46e+01 e.43.1.1 83847 1cr5A 189 1.47e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 7ahlA 293 1.47e+01 7ahlA f.6.1.1 43812 1ylnA 252 1.48e+01 1xffA 240 1.48e+01 d.153.1.1 109580 2cveA 191 1.52e+01 2dbsA 90 1.53e+01 1qfmA 710 1.54e+01 1qfmA b.69.7.1,c.69.1.4 27673,34641 1y55X 126 1.57e+01 1jkxA 212 1.62e+01 c.65.1.1 66813 2bjfA 329 1.64e+01 1vyoA 128 1.64e+01 1rocA 155 1.67e+01 b.1.22.1 97673 2d1sA 548 1.68e+01 1vmfA 145 1.70e+01 2cwsA 237 1.70e+01 1mkyA 439 1.74e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1ha1 184 1.77e+01 1ha1 d.58.7.1,d.58.7.1 39147,39148 1xi1A 575 1.78e+01 1e6pA 499 1.79e+01 1e15A b.72.2.1,c.1.8.5,d.26.3.1 59314,59315,59316 1v39 322 1.81e+01 3mag c.66.1.25 34206 1vheA 373 1.84e+01 b.49.3.1,c.56.5.4 100669,100670 1aszB 490 1.87e+01 1b8aA b.40.4.1,d.104.1.1 25241,40762 1tvzA 388 1.88e+01 c.95.1.2,c.95.1.2 107367,107368 2bltA 361 1.89e+01 1gceA e.3.1.1 42739 1c8uA 285 1.90e+01 1c8uA d.38.1.3,d.38.1.3 38547,38548 1qfoA 119 1.90e+01 1qfoA b.1.1.1 19708 1f8eA 388 1.96e+01 2qwc b.68.1.1 59694 1iwmA 186 1.99e+01 b.125.1.2 83758 1y89A 238 2.01e+01 1t0tV 248 2.04e+01 d.58.4.10 106229 2ga9A 297 2.09e+01 1kptA 105 2.12e+01 1kptA d.70.1.1 39588 1wdtA 665 2.12e+01 1usrA 454 2.15e+01 b.68.1.1 99881 1b6rA 355 2.17e+01 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28241,31648,41493 1vp9 322 2.19e+01 3mag c.66.1.25 34210 1j7lA 264 2.22e+01 d.144.1.6 62697 2b20A 403 2.22e+01 1kvkA 395 2.23e+01 d.14.1.5,d.58.26.3 73060,73061 1cl1A 395 2.23e+01 1cl2A c.67.1.3 34395 1e8uA 454 2.24e+01 1e8tA b.68.1.1 59389 1tuvA 114 2.24e+01 1q47A 495 2.26e+01 b.69.12.1 104532 2gjgA 248 2.31e+01 1oruA 195 2.37e+01 b.58.1.2 93464 1hxn 219 2.37e+01 1hxn b.66.1.1 27529 1ii7A 333 2.38e+01 1ii7A d.159.1.4 62415 1havA 217 2.38e+01 1havA b.47.1.4 26423 2ex4A 241 2.40e+01 1g291 372 2.47e+01 1g291 1v5wA 343 2.47e+01 c.37.1.11 108387 2ebn 289 2.50e+01 2ebn c.1.8.5 28990 1in0A 163 2.51e+01 d.58.49.1,d.58.49.1 83694,83695 1l3kA 196 2.52e+01 d.58.7.1,d.58.7.1 73539,73540 2d13A 227 2.53e+01 1ct9A 553 2.57e+01 1ct9A c.26.2.1,d.153.1.1 31616,41834 2bfgA 503 2.57e+01 1vgjA 184 2.64e+01 1ecfA 504 2.64e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1g7sA 594 2.65e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1qhdA 398 2.67e+01 1qhdA a.115.1.2,b.19.1.1 63324,63325 1ga0A 364 2.69e+01 1gceA e.3.1.1 60410 1ryaA 160 2.70e+01 d.113.1.5 105122 1v7oA 165 2.70e+01 d.67.1.2 100480 1frpA 335 2.71e+01 1frpA e.7.1.1 42875 1efyA 350 2.71e+01 1a26 a.41.1.1,d.166.1.2 17413,42275 1ravA 127 2.73e+01 1swuA b.61.1.1 27409 1chmA 401 2.75e+01 1chmA c.55.2.1,d.127.1.1 33545,41142 2fibA 269 2.78e+01 3fib d.171.1.1 42457 1v73A 342 2.79e+01 1wj9A 211 2.79e+01 1dzkA 157 2.83e+01 1obpA b.60.1.1 27096 1mw7A 240 2.84e+01 e.39.1.1 79557 1mgpA 313 2.84e+01 c.119.1.1 79098 3fib 249 2.89e+01 3fib d.171.1.1 42455 1npeA 267 2.91e+01 b.68.5.1 92032 1qwrA 319 2.92e+01 b.82.1.3 96491 1qyaA 307 2.93e+01 d.21.1.2,d.21.1.2 104653,104654 1xfkA 336 2.95e+01 1ftrA 296 2.98e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1v4pA 157 3.00e+01 1yifA 533 3.03e+01 1s2kA 206 3.07e+01 b.29.1.20 98389 1goiA 499 3.09e+01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 1ihoA 283 3.10e+01 1ihoA c.26.1.4 62390 2bklA 695 3.10e+01 1n9eA 787 3.12e+01 b.30.2.1,d.17.2.1,d.17.2.1 91708,91709,91710 1ri6A 343 3.16e+01 b.69.11.1 97503 1e0tA 470 3.18e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 2ghpA 292 3.20e+01 1at0 145 3.25e+01 1at0 b.86.1.1 28374 1srqA 341 3.26e+01 e.55.1.1 105967 1vpt 348 3.27e+01 3mag c.66.1.25 34207 1rgzA 363 3.29e+01 e.3.1.1 97457 1b6a 478 3.31e+01 1bn5 a.4.5.25,d.127.1.1 16223,41160 1otjA 283 3.33e+01 b.82.2.5 93517 2f5tX 233 3.36e+01 1jalA 363 3.36e+01 c.37.1.8,d.15.10.2 84138,84139 1z90A 469 3.40e+01 1fljA 260 3.42e+01 2cba b.74.1.1 27954 1qamA 244 3.48e+01 2ercA c.66.1.24 34220 1z4vA 532 3.51e+01 1eqjA 511 3.52e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 1lml 478 3.53e+01 1lml d.92.1.3 40295 1r6yA 115 3.61e+01 1mveA 243 3.68e+01 b.29.1.2 85140 1s3rA 535 3.68e+01 1zzoA 136 3.73e+01 1t5hX 504 3.73e+01 e.23.1.1 106449 1s5jA 847 3.78e+01 1uocA 289 3.79e+01 c.55.3.9 99686 1lci 550 3.79e+01 1lci e.23.1.1 43349 2bwrA 401 3.80e+01 2erfA 209 3.83e+01 1nqnA 122 3.89e+01 b.61.1.1 86042 1s0uA 408 3.90e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1vajA 214 3.90e+01 1wq3A 322 3.92e+01 1xv2A 237 3.93e+01 1ox6A 555 3.93e+01 c.1.2.1,c.23.16.1 87505,87506 1vggA 161 3.95e+01 2dbqA 334 3.96e+01 1q4rA 112 3.97e+01 d.58.4.4 95823 1o98A 511 3.99e+01 c.105.1.1,c.76.1.3 86684,86685 2f1wA 158 4.04e+01 1wv2A 265 4.08e+01 1dpgA 485 4.11e+01 1dpgA c.2.1.3,d.81.1.5 30074,39989 1ikpA 613 4.12e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1egaA 301 4.16e+01 1egaA c.37.1.8,d.52.3.1 32150,38836 1jvnA 555 4.21e+01 c.1.2.1,c.23.16.1 67355,67356 1b93A 152 4.21e+01 1b93A c.24.1.2 31507 1i31A 314 4.22e+01 1bw8A b.2.7.1 22481 1ax4A 467 4.22e+01 1ax4A c.67.1.2 34391 1cf1A 404 4.24e+01 1cf1A b.1.18.11,b.1.18.11 21907,21908 1y0pA 571 4.27e+01 1p2hA 571 4.35e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1xipA 388 4.36e+01 2cw5A 255 4.37e+01 1wchA 315 4.37e+01 1ycoA 279 4.37e+01 9gafA 295 4.38e+01 1apyA d.153.1.5 42008 1wr2A 238 4.39e+01 1ckv 141 4.39e+01 1ckv d.137.1.1 41452 1mo7A 213 4.42e+01 d.220.1.1 85028 1nuyA 337 4.42e+01 e.7.1.1 86213 1jofA 365 4.42e+01 b.69.10.1 71775 1suwA 249 4.46e+01 e.52.1.1 106027 1ukuA 102 4.46e+01 d.58.5.2 99533 1tuhA 156 4.49e+01 d.17.4.11 107345 1wn5A 130 4.55e+01 1wmmA 145 4.56e+01 1dzfA 215 4.59e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1kr4A 125 4.61e+01 d.58.5.2 72889 2c2aA 258 4.64e+01 1tkeA 224 4.69e+01 2esrA 177 4.71e+01 1om0A 274 4.71e+01 c.1.8.5 87058 1vf8A 377 4.76e+01 1oniA 137 4.76e+01 d.79.1.1 87144 1j1qA 261 4.78e+01 d.165.1.1 90768 2axoA 270 4.79e+01 1hfoA 113 4.80e+01 d.80.1.3 61006 1nnvA 110 4.82e+01 d.17.7.1 92012 2sak 121 4.83e+01 2sak d.15.5.1 37711 1gp1A 198 4.84e+01 1gp1A c.47.1.10 33059 2bjrA 368 4.86e+01 1xpkC 388 4.88e+01 1q9iA 571 4.89e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 2gibA 103 4.91e+01 1cx4A 305 4.92e+01 b.82.3.2,b.82.3.2 59099,59100 2camA 127 4.92e+01 1swuA b.61.1.1 27407 2exrA 524 4.95e+01 1ijqA 316 4.97e+01 1ijqA b.68.5.1,g.3.11.1 62506,62507 1cyx 205 4.99e+01 1cyx b.6.1.2 23023 1v1qA 134 4.99e+01 1hskA 326 4.99e+01 2mbr d.145.1.2,d.146.1.1 61241,61242 2fgtA 417 5.00e+01 1r6vA 671 5.00e+01 2fjrA 189 5.03e+01 1vp8A 201 5.03e+01 1avqA 228 5.04e+01 1avqA c.52.1.13 33326 1dykA 394 5.04e+01 1dykA b.29.1.4,b.29.1.4 24223,24224 1ewqA 765 5.05e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1jhfA 202 5.05e+01 a.4.5.2,b.87.1.1 63057,63058 1vdxA 184 5.06e+01 1e39A 571 5.08e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1rkiA 102 5.11e+01 1w5fA 353 5.11e+01 1p4uA 153 5.15e+01 b.1.10.2 87780 1e1aA 314 5.16e+01 1e1aA b.68.6.1 59155 1z47A 355 5.18e+01 1mc0A 368 5.22e+01 d.110.2.1,d.110.2.1 78937,78938 1wjxA 122 5.22e+01 1p4kA 295 5.24e+01 d.153.1.5 87772 2dcnA 311 5.25e+01 1wsrA 375 5.26e+01 1memA 215 5.28e+01 1cs8A d.3.1.1 37069 1va0A 239 5.28e+01 1e8cA 498 5.29e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 2dlbA 80 5.30e+01 2bw3A 534 5.37e+01 2bbeA 108 5.41e+01 1w0dA 337 5.44e+01 1vpsA 289 5.51e+01 1vpsA b.121.6.1 23336 1zc1A 208 5.52e+01 1u07A 90 5.52e+01 1wf3A 301 5.55e+01 1rypI 222 5.58e+01 d.153.1.4 41877 1htwA 158 5.60e+01 c.37.1.18 71083 1x8dA 104 5.61e+01 1zboA 210 5.65e+01 2eveA 157 5.68e+01 1a6cA 513 5.72e+01 1a6cA b.121.4.2,b.121.4.2,b.121.4.2 23296,23297,23298 1ve0A 134 5.79e+01 1n08A 163 5.80e+01 b.43.5.1 79730 1kolA 398 5.85e+01 b.35.1.2,c.2.1.1 77474,77475 1l2lA 457 5.86e+01 c.72.1.3 77656 2f8aA 208 5.87e+01 1xpmA 396 5.91e+01 1mixA 206 5.95e+01 a.11.2.1,b.55.1.5 79166,79167 2gq1A 332 5.96e+01 2f8lA 344 6.00e+01 1feuA 206 6.12e+01 1feuA b.53.1.1 59801 1pjxA 314 6.16e+01 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