# List of top-scoring protein chains for t2k-100-30-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.soe.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 1cozA 129 1.17e-17 1cozA c.26.1.2 31598 1qjcA 158 3.37e-15 1b6tA c.26.1.3 63328 1b6tA 159 4.18e-15 1b6tA c.26.1.3 31600 1od6A 160 2.24e-13 c.26.1.3 86836 1kamA 194 3.01e-13 c.26.1.3 72254 1tfuA 157 2.89e-12 c.26.1.3 106859 1yumA 242 4.84e-12 1k4mA 213 1.25e-11 c.26.1.3 77258 2h29A 189 7.23e-10 1lw7A 365 5.14e-08 c.26.1.3,c.37.1.1 74295,74296 1f9aA 168 6.93e-08 1f9aA c.26.1.3 31602 2qjoA 341 8.92e-08 2qjtA 352 3.50e-07 1mrzA 293 1.58e-06 b.43.5.1,c.26.1.3 91452,91453 1m8jA 181 5.27e-06 c.26.1.3 84875 1kqnA 279 5.39e-06 c.26.1.3 77492 1ej2A 181 6.05e-06 1f9aA c.26.1.3 59414 1nuuA 252 9.14e-06 c.26.1.3 86209 1kkuA 279 1.18e-05 c.26.1.3 72661 1v8fA 276 1.76e-04 c.26.1.4 100503 1ihoA 283 2.01e-04 1ihoA c.26.1.4 62390 1n2eA 300 1.56e-03 c.26.1.4 85268 2a84A 300 5.03e-03 c.26.1.4 126389 1hybA 181 1.27e-02 1f9aA c.26.1.3 61399 1jhdA 396 5.94e-02 b.122.1.3,c.26.1.5 66712,66713 2ebjA 192 9.84e-02 1v47A 349 1.63e-01 b.122.1.3,c.26.1.5 100292,100293 2asbA 251 3.52e-01 b.40.4.5,d.52.3.1,d.52.3.1 127244,127245,127246 3bofA 566 5.34e-01 1wmhA 89 5.75e-01 d.15.2.2 114744 1s0uA 408 6.14e-01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 2z0dB 125 7.05e-01 d.15.1.3 140096 1qrrA 394 7.30e-01 1qrrA c.2.1.2 29824 1q7zA 566 7.36e-01 c.1.21.2,c.1.26.1 96090,96091 2chuA 296 8.39e-01 c.92.2.4 130485 1akyA 220 8.69e-01 c.37.1.1,g.41.2.1 31896,45197 1i2cA 404 8.79e-01 c.2.1.2 83666 1bf6A 291 8.84e-01 1pscA c.1.9.3 29065 1i24A 404 9.28e-01 c.2.1.2 83663 1r6uA 437 9.37e-01 c.26.1.1 97163 2ekpA 239 1.08e+00 1h3fA 432 1.15e+00 c.26.1.1,d.66.1.4 76631,76632 2rgxA 206 1.20e+00 2fexA 188 1.28e+00 c.23.16.2 133354 2c71A 216 1.37e+00 c.6.2.3 130017 1k0rA 366 1.41e+00 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 67961,67962,67963,67964 2qiwA 255 1.42e+00 3cjeA 167 1.42e+00 1x1eA 239 1.44e+00 1ccwA 137 1.53e+00 1be1 c.23.6.1 31238 3ciwA 348 1.57e+00 1vl8A 267 1.60e+00 c.2.1.2 108733 1yexA 186 1.61e+00 c.47.1.10 123021 1g0oA 283 1.70e+00 1ybvA c.2.1.2 60181 2pcqA 283 1.74e+00 2zjdA 130 1.90e+00 1x0rA 249 1.93e+00 c.47.1.10 121562 1ybvA 283 2.01e+00 1ybvA c.2.1.2 29948 2ph3A 245 2.08e+00 1g67A 225 2.12e+00 c.1.3.1 60311 2brxA 244 2.23e+00 c.73.1.3 129028 1tqjA 230 2.27e+00 c.1.2.2 107228 1j08A 226 2.36e+00 c.47.1.2,c.47.1.2 83855,83856 1zyeA 220 2.38e+00 c.47.1.10 125817 1vyrA 364 2.41e+00 c.1.4.1 108906 1knyA 253 2.56e+00 1knyA a.24.16.1,d.218.1.1 75896,75897 1vypX 364 2.64e+00 c.1.4.1 108905 1e6wA 260 2.64e+00 1e6wA c.2.1.2 59326 2e87A 357 2.67e+00 3b2nA 133 2.94e+00 2zctA 249 2.97e+00 1wq3A 322 3.01e+00 1r6xA 395 3.08e+00 b.122.1.3,c.26.1.5 97167,97168 1vp8A 201 3.12e+00 c.49.1.2 113947 2rffA 111 3.14e+00 1vr3A 191 3.20e+00 b.82.1.6 120431 2p10A 286 3.24e+00 2i5eA 211 3.27e+00 2gl5A 410 3.29e+00 c.1.11.2,d.54.1.1 135336,135337 1e3sA 261 3.33e+00 1e6wA c.2.1.2 59201 1v6tA 255 3.36e+00 c.6.2.5 113550 1icpA 376 3.51e+00 1oyc c.1.4.1 62270 1qmvA 197 3.96e+00 1qq2A c.47.1.10 33066 1mjhA 162 3.97e+00 1mjhA c.26.2.4 31639 1i6wA 181 3.98e+00 1i6wA c.69.1.18 61859 1ej0A 180 4.09e+00 1ej0A c.66.1.2 34179 1qqcA 773 4.10e+00 1tgoA c.55.3.5,e.8.1.1 33724,43013 2p3eA 420 4.14e+00 4ts1A 319 4.34e+00 2ts1 c.26.1.1 31565 2cybA 323 4.51e+00 2hx1A 284 4.58e+00 1v95A 130 4.58e+00 c.51.1.1 108435 1ispA 181 4.64e+00 c.69.1.18 76778 2yxnA 322 4.64e+00 1to3A 304 4.67e+00 c.1.10.1 107161 1wd7A 261 4.96e+00 c.113.1.1 114526 2abbA 364 5.14e+00 c.1.4.1 126517 1gcoA 261 5.20e+00 1ybvA c.2.1.2 29884 1cy5A 97 5.30e+00 1cy5A a.77.1.3 18430 1efdN 266 5.39e+00 1efdN c.92.2.1 35597 1qhtA 775 5.43e+00 1tgoA c.55.3.5,e.8.1.1 33722,43011 1w15A 153 5.64e+00 b.7.1.2 109041 2tpsA 227 5.66e+00 2tpsA c.1.3.1 28591 2c0dA 221 5.71e+00 1rec 201 5.81e+00 1rec 1omrA 201 6.07e+00 a.39.1.5 93349 3b9oA 440 6.13e+00 1wcwA 261 6.14e+00 1qwgA 251 6.20e+00 c.1.27.1 96473 1gz6A 319 6.21e+00 c.2.1.2 76410 1j1nA 492 6.66e+00 c.94.1.1 83978 2cmd 312 6.68e+00 2cmd 2cmdA 312 6.74e+00 c.2.1.5,d.162.1.1 30135,42102 2hmcA 344 6.79e+00 1g8fA 511 6.88e+00 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 3c3pA 210 7.06e+00 1q52A 314 7.12e+00 c.14.1.3 95846 1wehA 171 7.13e+00 c.129.1.1 114551 1mzgA 146 7.16e+00 d.224.1.1 79696 2hldG 278 7.16e+00 1w3iA 293 7.21e+00 c.1.10.1 109152 2v2gA 233 7.53e+00 1nal1 297 7.62e+00 1nal3 1pieA 419 7.63e+00 d.14.1.5,d.58.26.7 94706,94707 3cc8A 230 8.02e+00 2eu8A 216 8.05e+00 1rpxA 230 8.13e+00 1rpxA c.1.2.2 28536 2ygsA 92 8.28e+00 1cy5A a.77.1.3 18431 1y63A 184 8.33e+00 c.37.1.1 116494 2ogyA 262 8.35e+00 3bq5A 766 8.54e+00 2z08A 137 8.57e+00 2e7fA 262 8.59e+00 2qorA 204 8.76e+00 2yv5A 302 8.96e+00 1mtyG 162 9.01e+00 1mtyG a.23.3.1 16498 1p3jA 217 9.09e+00 c.37.1.1,g.41.2.1 94022,94023 1awcA 110 9.17e+00 1awcA a.4.5.21 16167 2i5uA 83 9.30e+00 3b59A 310 9.37e+00 1fdyA 297 9.38e+00 1nal3 c.1.10.1 29071 2pfsA 150 9.38e+00 1lqaA 346 9.53e+00 c.1.7.1 84674 2pljA 419 9.82e+00 3c19A 186 9.91e+00 2pezA 179 9.98e+00 1jl0A 334 1.00e+01 1jenA d.156.1.1 63155 1geeA 261 1.02e+01 c.2.1.2 90509 1zz1A 369 1.02e+01 2q3uA 383 1.03e+01 d.126.1.6 139809 1jilA 420 1.04e+01 c.26.1.1 66745 2drvA 200 1.04e+01 1a8l 226 1.08e+01 1a8l 1a8lA 226 1.08e+01 c.47.1.2,c.47.1.2 32777,32778 2qgqA 304 1.08e+01 1ve5A 311 1.09e+01 c.79.1.1 120013 1uz5A 402 1.11e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1z41A 338 1.12e+01 c.1.4.1 124421 1vlmA 219 1.12e+01 c.66.1.41 108836 1nal3 297 1.12e+01 1nal3 1qq2A 199 1.16e+01 1qq2A c.47.1.10 33064 2ez2A 456 1.18e+01 1ep3A 311 1.20e+01 2dorA c.1.4.1 28597 2j9oA 298 1.21e+01 1j09A 468 1.25e+01 a.97.1.1,c.26.1.1 77025,77026 1ax4A 467 1.25e+01 1ax4A c.67.1.2 34391 1t7lA 766 1.25e+01 2iyeA 263 1.26e+01 2it2A 200 1.26e+01 2yvuA 186 1.30e+01 1kfuS 184 1.33e+01 a.39.1.8 68574 1np8A 159 1.33e+01 a.39.1.8 92022 2gu3A 136 1.35e+01 1vkpA 383 1.36e+01 d.126.1.6 108686 1xccA 220 1.37e+01 c.47.1.10 115113 1t0yA 122 1.37e+01 d.15.1.1 99066 1g59A 468 1.38e+01 a.97.1.1,c.26.1.1 60257,60258 1kqpA 271 1.38e+01 c.26.2.1 72883 2z1nA 260 1.41e+01 2nsyA 271 1.41e+01 2nsyA c.26.2.1 31612 1n8jA 186 1.42e+01 c.47.1.10 85401 2j7vA 298 1.43e+01 1vhcA 224 1.44e+01 c.1.10.1 100661 1edoA 244 1.46e+01 1ybvA c.2.1.2 29896 1wl8A 189 1.46e+01 c.23.16.1 120997 1rhcA 330 1.47e+01 c.1.16.3 97468 1tplA 426 1.49e+01 1ax4A c.67.1.2 34387 2q5wE 149 1.49e+01 2ax3A 502 1.50e+01 c.72.1.4,c.104.1.1 127477,127478 1xqwA 293 1.51e+01 1vqtA 213 1.53e+01 c.1.2.3 120417 3bt3A 148 1.53e+01 2pjmA 226 1.54e+01 1pqsA 77 1.54e+01 d.15.2.2 88277 1gnxA 479 1.54e+01 c.1.8.4 76241 1ehiA 377 1.55e+01 1iow c.30.1.2,d.142.1.1 31716,41484 1q74A 303 1.55e+01 c.134.1.1 96019 1f6yA 262 1.56e+01 1f6yA c.1.21.2 29673 1iu8A 206 1.58e+01 c.56.4.1 71436 2ip1A 432 1.59e+01 1di2A 69 1.65e+01 1di2A d.50.1.1 38780 1gegA 256 1.66e+01 1ybvA c.2.1.2 29888 1ex2A 189 1.67e+01 1ex2A c.51.4.2 33225 1cwwA 102 1.70e+01 1cy5A a.77.1.3 18434 2i6jA 161 1.70e+01 2j41A 207 1.71e+01 3c6cA 316 1.74e+01 1alvA 173 1.80e+01 1alvA a.39.1.8 17370 3chvA 284 1.81e+01 1w7jB 151 1.82e+01 a.39.1.5 120690 1aj5A 173 1.83e+01 1alvA a.39.1.8 17367 1eywA 331 1.86e+01 1pscA c.1.9.3 29057 2pk8A 103 1.87e+01 d.274.1.1 139707 1j7lA 264 1.94e+01 d.144.1.6 62697 1reqA 727 1.94e+01 1reqA c.1.19.1,c.23.6.1 29620,31247 2qi2A 347 1.96e+01 2pn8A 211 2.02e+01 1ek6A 348 2.03e+01 1xel c.2.1.2 29800 1jkgA 140 2.05e+01 d.17.4.2 66795 2h5cA 198 2.05e+01 b.47.1.1 136145 1kfwA 435 2.06e+01 c.1.8.5,d.26.3.1 77376,77377 1xd3A 230 2.07e+01 d.3.1.6 115145 2bzsA 236 2.07e+01 c.23.5.3 129560 1o0pA 104 2.08e+01 d.58.7.1 86535 2cunA 410 2.08e+01 2nytA 190 2.09e+01 1wz7A 111 2.09e+01 d.330.1.1 121480 5reqA 727 2.09e+01 1reqA c.1.19.1,c.23.6.1 29632,31259 1im8A 244 2.12e+01 c.66.1.14 66212 2auaA 224 2.15e+01 d.166.1.6 127326 1zbqA 327 2.17e+01 c.2.1.2 124862 2j5aA 110 2.19e+01 1ghsA 306 2.19e+01 1aq0A c.1.8.3 28840 1qapA 296 2.19e+01 1qpoA c.1.17.1,d.41.2.1 29559,38595 1tfjA 219 2.20e+01 2q5cA 196 2.22e+01 1y791 680 2.22e+01 2i2xB 258 2.22e+01 1dc7A 124 2.23e+01 1dbwA c.23.1.1 31093 2ox1A 196 2.25e+01 2d1yA 256 2.25e+01 c.2.1.2 131151 2p4zA 284 2.27e+01 2cx4A 164 2.28e+01 c.47.1.10 130973 1pyfA 312 2.29e+01 c.1.7.1 95334 2hjpA 290 2.34e+01 2vc7A 314 2.35e+01 2aqjA 538 2.35e+01 2r4vA 247 2.36e+01 1ssxA 198 2.37e+01 b.47.1.1 98978 1zzmA 259 2.38e+01 c.1.9.12 125911 1vjgA 218 2.44e+01 c.23.10.6 100810 2cyaA 364 2.44e+01 1wzcA 249 2.44e+01 c.108.1.10 121491 1xeqA 103 2.47e+01 a.16.1.1 121915 1y80A 210 2.47e+01 1uch 230 2.47e+01 1uch 2aiuA 105 2.48e+01 1anjA 446 2.48e+01 1b8jA c.76.1.1 35008 1g5qA 181 2.49e+01 1g5qA c.34.1.1 60288 2ap1A 327 2.49e+01 c.55.1.10,c.55.1.10 127108,127109 2ov7A 137 2.50e+01 3bt7A 369 2.52e+01 1lucA 355 2.52e+01 1lucA c.1.16.1 29547 2qh9A 184 2.53e+01 1f74A 293 2.54e+01 1nal3 c.1.10.1 29079 1y0nA 78 2.54e+01 d.291.1.1 116305 2hjvA 163 2.55e+01 2p3yA 491 2.56e+01 2ogtA 498 2.60e+01 1szhA 161 2.63e+01 a.226.1.1 106157 2f6mB 109 2.63e+01 a.2.17.2 133052 2jgyA 279 2.63e+01 1b8jA 449 2.64e+01 1b8jA c.76.1.1 34992 2ts1 419 2.65e+01 2ts1 1qj5A 429 2.66e+01 1dtyA c.67.1.4 34493 1lnzA 342 2.67e+01 b.117.1.1,c.37.1.8 78112,78113 2o23A 265 2.68e+01 c.2.1.2 138884 1ed8A 449 2.70e+01 1b8jA c.76.1.1 34988 1jwqA 179 2.71e+01 c.56.5.6 90921 1be1 137 2.73e+01 1be1 2jabA 136 2.76e+01 1rq2A 382 2.76e+01 c.32.1.1,d.79.2.1 105048,105049 2g6tA 306 2.77e+01 c.147.1.1 134717 2anhA 446 2.78e+01 1b8jA c.76.1.1 35004 1s0aA 429 2.80e+01 c.67.1.4 98263 1wbeA 209 2.81e+01 1m7gA 211 2.82e+01 c.37.1.4 78724 2qpxA 376 2.83e+01 1v7bA 185 2.87e+01 a.4.1.9,a.121.1.1 119861,119862 1guuA 52 2.90e+01 a.4.1.3 83332 2ag6A 314 2.93e+01 1oeyA 83 2.94e+01 d.15.2.2 92800 1ajaA 449 2.98e+01 1b8jA c.76.1.1 35010 2p8eA 307 2.99e+01 3c5rA 137 3.02e+01 1j6uA 469 3.03e+01 c.5.1.1,c.59.1.1,c.72.2.1 77094,77095,77096 1j34A 129 3.04e+01 d.169.1.1 84048 2j5bA 348 3.08e+01 1wjgA 137 3.08e+01 c.26.2.4 114696 1gmlA 178 3.09e+01 c.8.5.2 70273 2dplA 308 3.10e+01 2hq1A 247 3.12e+01 1cqwA 295 3.15e+01 1b6g c.69.1.8 34679 1egaA 301 3.15e+01 1egaA c.37.1.8,d.52.3.1 32150,38836 2oap1 511 3.16e+01 2qwxA 231 3.16e+01 2ob3A 330 3.20e+01 2pidA 356 3.20e+01 1sg0A 230 3.25e+01 c.23.5.3 118955 1q1oA 98 3.29e+01 d.15.2.2 95596 1aniA 446 3.32e+01 1b8jA c.76.1.1 35018 1u5tA 233 3.34e+01 a.4.5.54,a.4.5.54 107684,107685 1xm7A 195 3.35e+01 d.159.1.8 115473 1ofuA 320 3.35e+01 c.32.1.1,d.79.2.1 86972,86973 2nmlA 104 3.35e+01 d.330.1.1 138371 1aq0A 306 3.35e+01 1aq0A c.1.8.3 28842 1r13A 148 3.36e+01 d.169.1.1,h.1.1.1 96782,96783 1n0wA 243 3.43e+01 c.37.1.11 79772 2r91A 286 3.47e+01 2v9dA 343 3.47e+01 1u1jA 765 3.51e+01 c.1.22.2,c.1.22.2 107590,107591 1colA 204 3.55e+01 1a87 f.1.1.1 43378 1fyeA 229 3.56e+01 1fyeA c.23.16.4 31477 3c8nA 356 3.57e+01 2qqyA 149 3.57e+01 1ssqA 267 3.58e+01 b.81.1.6 105993 2ax4A 198 3.58e+01 2amlA 373 3.59e+01 2qcfA 260 3.61e+01 2obbA 142 3.62e+01 1bn6A 294 3.63e+01 1bn6A c.69.1.8 34678 1vjrA 271 3.63e+01 c.108.1.14 100832 1ypxA 375 3.64e+01 2ijcA 145 3.65e+01 a.152.1.3 137465 2nq5A 755 3.67e+01 1dtyA 429 3.67e+01 1dtyA c.67.1.4 34495 1kcfA 258 3.69e+01 a.140.2.1,c.55.3.7 68434,68435 2fcoA 200 3.70e+01 1vcvA 226 3.75e+01 c.1.10.1 119988 1jjvA 206 3.77e+01 c.37.1.1 71698 2hr2A 159 3.77e+01 2yw2A 424 3.80e+01 2zatA 260 3.86e+01 2v78A 313 3.87e+01 1xn9A 101 3.88e+01 d.12.1.3 115578 2c4wA 176 3.95e+01 1qtnA 164 3.95e+01 1pauA c.17.1.1 30999 1ble 163 3.99e+01 1ble 2o4dA 165 4.03e+01 a.152.1.3 138907 2yrxA 451 4.03e+01 2b81A 323 4.07e+01 2yxoA 267 4.10e+01 1wn2A 121 4.11e+01 1gvnA 90 4.13e+01 a.8.2.1 76353 1kmmA 424 4.14e+01 1adjA c.51.1.1,d.104.1.1 33174,40723 2awfA 172 4.14e+01 d.20.1.1 127432 1mumA 295 4.20e+01 c.1.12.7 85108 2p1fA 291 4.22e+01 2rk0A 136 4.24e+01 2c4nA 250 4.26e+01 c.108.1.14 129837 1zhhB 242 4.26e+01 1i0dA 332 4.28e+01 1pscA c.1.9.3 61487 1y8cA 246 4.30e+01 c.66.1.43 116563 1gln 468 4.31e+01 1gln 1g0u1 266 4.32e+01 1zuwA 272 4.33e+01 2ebeA 106 4.36e+01 2dumA 170 4.37e+01 1b2sD 90 4.37e+01 1ay7B c.9.1.1 30837 2cpgA 45 4.39e+01 2cpgA a.43.1.3 17455 1httA 423 4.39e+01 1adjA c.51.1.1,d.104.1.1 33178,40727 1jqoA 970 4.42e+01 c.1.12.3 77160 1hslA 238 4.42e+01 1lst c.94.1.1 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