# List of top-scoring protein chains for t04-100-30-n_notor2-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 2gfhA 260 7.16e-02 1xfkA 336 4.22e-01 1uohA 226 6.22e-01 d.211.1.1 99690 1nrlA 316 7.65e-01 a.123.1.1 92091 1u3wA 374 9.01e-01 1hdhA 536 1.06e+00 c.76.1.2 65805 1rpnA 335 1.13e+00 c.2.1.2 97708 1ru3A 732 1.78e+00 e.26.1.3 97835 2bw4A 340 1.78e+00 1larA 575 2.22e+00 1larA c.45.1.2,c.45.1.2 32693,32694 1nif 340 3.30e+00 1nif b.6.1.3,b.6.1.3 23048,23049 1jofA 365 3.37e+00 b.69.10.1 71775 1n8kA 374 3.38e+00 b.35.1.2,c.2.1.1 80298,80299 2rslA 140 3.39e+00 2rslA c.53.1.1 33345 1mtyD 512 3.96e+00 1mhyD a.25.1.2 16742 1qf5A 431 4.06e+00 1adeA c.37.1.10 32212 1hetA 374 4.19e+00 2ohxA b.35.1.2,c.2.1.1 60975,60976 1xx4A 261 4.31e+00 1a0rP 245 4.50e+00 1b9yC c.47.1.6 33054 1fo3A 460 4.59e+00 1dl2A a.102.2.1 18845 1bd8 156 4.63e+00 1bd8 d.211.1.1 19157 1kcbA 340 4.70e+00 b.6.1.3,b.6.1.3 90951,90952 1tiqA 180 4.75e+00 d.108.1.1 107010 1cf2O 337 5.06e+00 1b7gO c.2.1.3,d.81.1.1 29994,39909 1ks8A 433 5.42e+00 a.102.1.2 77519 2b8nA 429 5.43e+00 1itcA 516 5.55e+00 b.3.1.1,c.1.8.1 83705,83706 1m2kA 249 5.75e+00 c.31.1.5 84754 1t8qA 336 5.80e+00 c.1.18.3 106669 1yaiA 151 6.39e+00 1yaiA b.1.8.1 22289 1j9lA 247 6.67e+00 c.106.1.1 62762 2fgtA 417 6.87e+00 1yu4A 381 6.99e+00 1ua7A 422 7.00e+00 b.71.1.1,c.1.8.1 107759,107760 1vloA 381 7.19e+00 b.44.2.1,d.250.1.1 108838,108839 2b0oE 301 7.49e+00 1riqA 465 7.56e+00 a.203.1.1,d.104.1.1 97516,97517 1ub0A 258 7.92e+00 c.72.1.2 88394 1vyfA 135 8.16e+00 b.60.1.2 108902 2aq4A 434 8.79e+00 1xel 338 8.80e+00 1xel c.2.1.2 29786 1vybA 238 8.91e+00 d.151.1.1 108897 2reb 352 8.97e+00 2reb c.37.1.11,d.48.1.1 32282,38767 2gdnA 267 9.26e+00 2gbp 309 9.64e+00 1gca c.93.1.1 35657 1ew2A 513 1.00e+01 1b8jA c.76.1.1 59525 1vj0A 380 1.01e+01 b.35.1.2,c.2.1.1 100786,100787 1yhtA 367 1.03e+01 1d2nA 272 1.04e+01 1d2nA c.37.1.20 32428 1adjA 421 1.06e+01 1adjA c.51.1.1,d.104.1.1 33188,40737 1kwfA 363 1.08e+01 a.102.1.2 73078 3pvaA 335 1.09e+01 3pvaA d.153.1.3 41854 1twdA 256 1.12e+01 c.1.30.1 107397 1sr4B 261 1.13e+01 d.151.1.1 105949 1sh7A 284 1.15e+01 1f9vA 347 1.15e+01 1bg2 c.37.1.9 59745 1e4mM 501 1.18e+01 1e70M c.1.8.4 59226 1dxeA 256 1.20e+01 1dxeA c.1.12.5 29310 1wljA 189 1.23e+01 1brmA 367 1.23e+01 1brmA c.2.1.3,d.81.1.1 30030,39945 1z82A 335 1.26e+01 2awpA 198 1.27e+01 1qrrA 394 1.28e+01 1qrrA c.2.1.2 29824 1div 149 1.28e+01 1div d.99.1.1,d.100.1.1 40692,40693 2bghA 421 1.28e+01 1c3hA 137 1.30e+01 b.22.1.1 90405 1qisA 396 1.34e+01 1ajsA c.67.1.1 34284 1u2xA 474 1.35e+01 c.72.1.3 107622 1qwgA 251 1.36e+01 c.1.27.1 96473 1gd1O 334 1.41e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 1yu1A 381 1.45e+01 1qr6A 584 1.47e+01 1qr6A c.2.1.7,c.58.1.3 30293,33941 1e55A 512 1.48e+01 1e70M c.1.8.4 28934 1x8qA 184 1.58e+01 1top 162 1.60e+01 1ncx a.39.1.5 17223 1ydyA 356 1.65e+01 1cem 363 1.69e+01 1cem a.102.1.2 18826 2cklB 165 1.69e+01 1njhA 119 1.71e+01 b.128.1.1 85787 1h49A 512 1.71e+01 c.1.8.4 83477 1q2bA 434 1.72e+01 b.29.1.10 95624 1xrtA 467 1.79e+01 2an3A 289 1.91e+01 1lzjA 292 1.97e+01 c.68.1.9 74352 1ctt 294 2.03e+01 1ctt c.97.1.1,c.97.1.1 36022,36023 2b4yA 271 2.10e+01 1vjfA 180 2.11e+01 d.116.1.1 100809 1ssqA 267 2.12e+01 b.81.1.6 105993 1amk 251 2.12e+01 1amk c.1.1.1 28503 2b81A 323 2.14e+01 1v02A 565 2.14e+01 c.1.8.4 108194 1ktaA 365 2.14e+01 e.17.1.1 77533 1lt3A 240 2.17e+01 1lt3A d.166.1.1 42230 1iz5A 249 2.17e+01 d.131.1.2,d.131.1.2 83834,83835 1oi0A 124 2.20e+01 c.97.3.1 93045 1u1wA 298 2.21e+01 1mnaA 298 2.23e+01 c.69.1.22 79322 1o6dA 163 2.24e+01 c.116.1.3 92567 1t9kA 347 2.24e+01 c.124.1.5 106721 1nnlA 225 2.25e+01 c.108.1.4 85906 1d9tA 289 2.25e+01 1deaA 1wkbA 810 2.25e+01 1ne7A 289 2.25e+01 c.124.1.1 91833 1jbwA 428 2.27e+01 c.59.1.2,c.72.2.2 62860,62861 1k28A 584 2.29e+01 b.40.8.1,b.108.1.2,d.2.1.3 68049,68050,68051 1cf7B 95 2.30e+01 1cf7B a.4.5.17 16152 1pg4A 652 2.31e+01 e.23.1.1 88067 1erxA 184 2.42e+01 1np1A b.60.1.1 27164 1zp4A 304 2.43e+01 1ynmA 247 2.46e+01 1i50A 1733 2.54e+01 e.29.1.2 61754 1y7lA 316 2.66e+01 1igwA 434 2.66e+01 c.1.12.7 62370 1kutA 230 2.68e+01 d.143.1.1 73017 2bx2L 517 2.72e+01 1zaiA 363 2.81e+01 1uheA 97 2.83e+01 1k55A 246 2.87e+01 e.3.1.1 68156 2bgiA 272 2.88e+01 1opd 85 2.88e+01 1ptf d.94.1.1 40560 1ksiA 642 2.90e+01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24408,38043,38044 1v5vA 401 2.90e+01 2cq2A 114 2.93e+01 1m93A 55 2.95e+01 e.1.1.1 91235 1c93A 265 2.95e+01 2ebn c.1.8.5 28998 1xovA 326 2.96e+01 1qwnA 1045 2.96e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1tluA 130 2.97e+01 d.156.1.2 107139 1zy9A 564 2.98e+01 1skoB 130 2.98e+01 d.110.7.1 105677 2ga9D 469 3.12e+01 2g9iA 249 3.16e+01 1snlA 103 3.18e+01 a.39.1.7 105820 2bwbA 46 3.19e+01 1vr7A 142 3.21e+01 1qgjA 300 3.21e+01 1bgp a.93.1.1 18691 1mkmA 249 3.24e+01 a.4.5.33,d.110.2.2 79242,79243 1x9mA 698 3.25e+01 1tr9A 341 3.25e+01 2adoA 196 3.25e+01 1u8fO 335 3.25e+01 1sy3A 184 3.27e+01 b.60.1.1 106110 1mrg 263 3.36e+01 1mrj d.165.1.1 42183 1up6A 416 3.36e+01 c.2.1.5,d.162.1.2 107976,107977 1mvwB 145 3.39e+01 i.15.1.1 79524 1dj0A 264 3.40e+01 1dj0A d.265.1.1 90337 1amy 403 3.44e+01 1jdc b.71.1.1,c.1.8.1 27799,28786 1hleA 345 3.44e+01 1ovaA e.1.1.1 42618 1ymtA 246 3.49e+01 1p1mA 406 3.50e+01 b.92.1.4,c.1.9.9 87696,87697 1yu3A 381 3.56e+01 1j08A 226 3.56e+01 c.47.1.2,c.47.1.2 83855,83856 1repC 251 3.62e+01 1repC a.4.5.10,a.4.5.10 16125,16126 1ur4A 399 3.63e+01 2a67A 167 3.63e+01 1h5qA 265 3.69e+01 1cydA c.2.1.2 60643 1twfA 1733 3.71e+01 1a8s 273 3.74e+01 1brt c.69.1.12 34710 1yrlA 491 3.74e+01 1v7oA 165 3.74e+01 d.67.1.2 100480 1nbwA 607 3.77e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1c52 131 3.77e+01 1c52 a.3.1.1 15810 1oyeA 1049 3.77e+01 d.58.44.1,d.58.44.1,d.58.44.1,d.58.44.1,d.225.1.1,d.225.1.1,f.35.1.1,f.35.1.1 87587,87588,87589,87590,87591,87592,87593,87594 1rypL 212 3.79e+01 d.153.1.4 41880 1b3uA 588 3.79e+01 1b3uA a.118.1.2 19135 1ede 310 3.86e+01 1b6g c.69.1.8 34662 2his 312 3.90e+01 1taxA c.1.8.3 28918 1fhgA 154 3.95e+01 1tlk b.1.1.4 21706 1x3lA 440 3.99e+01 2fclA 169 3.99e+01 1pg5A 299 4.02e+01 c.78.1.1,c.78.1.1 104146,104147 1fwkA 296 4.04e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 2gl5A 410 4.04e+01 1py5A 326 4.06e+01 d.144.1.7 104389 1cy9A 264 4.08e+01 1ecl e.10.1.1 43236 1nc5A 373 4.13e+01 a.102.1.6 85548 1wr1B 58 4.14e+01 1p2hA 571 4.16e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1xn5A 146 4.23e+01 1tvzA 388 4.24e+01 c.95.1.2,c.95.1.2 107367,107368 1vi7A 217 4.25e+01 d.14.1.11,d.58.11.2 100740,100741 1d4xG 126 4.27e+01 1d0nA d.109.1.1 59109 1e4yA 214 4.27e+01 1zin c.37.1.1,g.41.2.1 31901,45181 1je0A 236 4.30e+01 c.56.2.1 66581 1mo9A 523 4.30e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 3chbD 104 4.36e+01 3chbD b.40.2.1 24970 1h4vB 421 4.38e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1r77A 103 4.39e+01 1ht6A 405 4.40e+01 b.71.1.1,c.1.8.1 83629,83630 2b0mA 393 4.44e+01 1m98A 317 4.44e+01 a.175.1.1,d.17.4.6 78866,78867 1lurA 339 4.44e+01 b.30.5.4 84717 1nfkA 325 4.46e+01 1a3qA b.1.18.1,b.2.5.3 21929,22444 1ydnA 295 4.52e+01 1kevA 351 4.52e+01 1pedA b.35.1.2,c.2.1.1 24749,29765 1vzyA 291 4.54e+01 1pbgA 468 4.64e+01 1e70M c.1.8.4 28946 1dosA 358 4.66e+01 1dosA c.1.10.2 29175 1ecpA 238 4.66e+01 1ecpA c.56.2.1 33775 1ej0A 180 4.67e+01 1ej0A c.66.1.2 34179 1jr7A 311 4.68e+01 b.82.2.3 63255 2pvaA 345 4.69e+01 3pvaA d.153.1.3 41850 1hxxA 340 4.70e+01 2omf f.4.3.1 61385 2biqA 219 4.71e+01 1pp0A 199 4.73e+01 d.103.1.1 104211 1rfmA 344 4.84e+01 c.122.1.1 97385 1h1nA 305 4.87e+01 c.1.8.3 70855 1c96A 753 4.88e+01 1amj c.8.2.1,c.83.1.1 30727,35403 1xhfA 123 4.92e+01 1eg3A 261 4.92e+01 1eg3A a.39.1.7,a.39.1.7,b.72.1.1 17376,17377,27805 5reqA 727 4.95e+01 1reqA c.1.19.1,c.23.6.1 29632,31259 1f8yA 157 5.00e+01 1f8xA c.23.14.1 31395 1tzjA 338 5.00e+01 2cfuA 658 5.02e+01 1axiB 236 5.04e+01 1axiB b.1.2.1,b.1.2.1 21997,21998 1j5vA 351 5.04e+01 c.72.1.1 71585 2aaoA 166 5.04e+01 1rhs 296 5.04e+01 1rhs c.46.1.2,c.46.1.2 32703,32704 1vqzA 341 5.08e+01 1nb8A 353 5.08e+01 d.3.1.9 80385 1qqp1 213 5.08e+01 1qqp1 1amuA 563 5.14e+01 1amuA e.23.1.1 43351 2fflA 756 5.15e+01 1rp4A 389 5.16e+01 a.227.1.1 105027 1enfA 212 5.20e+01 3seb b.40.2.2,d.15.6.1 25198,37787 2aq8A 269 5.20e+01 1z7wA 322 5.22e+01 2liv 344 5.36e+01 2liv c.93.1.1 35708 1z5lA 285 5.41e+01 1fnuA 221 5.41e+01 3seb b.40.2.2,d.15.6.1 25212,37801 1yadA 221 5.48e+01 1yu0A 381 5.55e+01 1u6rA 380 5.63e+01 2culA 232 5.66e+01 1nm1G 125 5.70e+01 d.109.1.1 80653 1qlnA 883 5.70e+01 1cezA e.8.1.3 43111 1v8eA 224 5.71e+01 1xcbA 211 5.71e+01 a.4.5.38,c.2.1.12 109552,109553 1mq4A 272 5.73e+01 d.144.1.7 91391 1z9tA 255 5.76e+01 1eg2A 319 5.76e+01 1eg2A c.66.1.11 34249 1b6g 310 5.77e+01 1b6g c.69.1.8 34661 2flsA 132 5.78e+01 1a78A 134 5.80e+01 1c1lA b.29.1.3 24212 1g5gA 481 5.86e+01 f.12.1.1,h.3.2.1 65155,65156 1lmeA 176 5.87e+01 d.167.1.1 84629 1v4vA 376 5.92e+01 c.87.1.3 100313 1ml9A 302 5.94e+01 b.85.7.1 79282 1ogiA 303 5.95e+01 b.43.4.2,c.25.1.1 92914,92915 1ih8A 271 5.95e+01 2nsyA c.26.2.1 62377 1sflA 238 5.97e+01 1f0nA 285 6.02e+01 1dqyA c.69.1.3 34636 1ynpA 317 6.03e+01 1j5xA 342 6.06e+01 c.80.1.1 71591 1p0kA 349 6.07e+01 c.1.4.1 87648 1lt8A 406 6.07e+01 c.1.26.1 78186 1wfxA 186 6.07e+01 1mhyD 521 6.16e+01 1mhyD a.25.1.2 16780 1xttA 216 6.16e+01 1m2oA 768 6.19e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78480,78481,78482,78483,78484 1xqwA 293 6.21e+01 1hqz1 141 6.23e+01 1d3cA 686 6.27e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21827,22496,27734,28721 1yzyA 413 6.28e+01 1qg3A 195 6.30e+01 1qg3A b.1.2.1,b.1.2.1 21993,21994 1rqbA 539 6.30e+01 a.5.7.2,c.1.10.5 105057,105058 1jv1A 505 6.35e+01 c.68.1.5 71892 4ubpC 570 6.42e+01 1ubpC b.92.1.1,c.1.9.2 28431,29053 1wrjA 156 6.44e+01 1ov2A 99 6.49e+01 a.13.1.1 93580 1r5tA 142 6.49e+01 c.97.1.1 104812 1ek9A 428 6.51e+01 1ek9A f.5.1.1 43809 1yf3A 259 6.58e+01 1ns5A 155 6.63e+01 c.116.1.3 80705 1gu7A 364 6.67e+01 b.35.1.2,c.2.1.1 83321,83322 1zpvA 91 6.70e+01 1que 303 6.71e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1rr7A 129 6.74e+01 a.4.1.14 105075 1oroA 213 6.75e+01 1opr c.61.1.1 34093 1e6yA 569 6.84e+01 1mroA a.89.1.1,d.58.31.2 18529,39447 1vhqA 232 6.85e+01 c.23.16.2 100696 1oaoC 729 6.87e+01 e.26.1.3 86746 1w9hA 427 6.88e+01 1xwfA 431 6.90e+01 1h72C 296 6.91e+01 d.14.1.5,d.58.26.1 60712,60713 2f4qA 346 6.92e+01 1vjjA 692 6.93e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 1rsy 152 6.93e+01 1rsy b.7.1.2 23192 1go2A 304 6.95e+01 b.43.4.2,c.25.1.1 76243,76244 1e0wA 313 7.09e+01 1taxA c.1.8.3 59150 1sw5B 275 7.12e+01 c.94.1.1 106070 1g6aA 271 7.13e+01 1btl e.3.1.1 42704 1eg7A 557 7.13e+01 1eg7A c.37.1.10 32241 1ckiA 317 7.14e+01 1csn d.144.1.7 41660 1gntA 553 7.24e+01 e.26.1.1 70290 1t13A 158 7.25e+01 1gefA 123 7.28e+01 1gefA c.52.1.18 60465 1gj7B 253 7.29e+01 1exg 110 7.29e+01 1exg b.2.2.1 22387 2ax3A 502 7.31e+01 1z15A 344 7.32e+01 1w36C 1122 7.34e+01 2sli 679 7.35e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1cjxA 357 7.39e+01 1cjxA d.32.1.3,d.32.1.3 38516,38517 1e3dA 266 7.41e+01 2frvA e.19.1.1 59188 1khbA 625 7.41e+01 c.91.1.1,c.109.1.1 68606,68607 1uumA 372 7.48e+01 c.1.4.1 100010 2gdzA 267 7.48e+01 1efpB 252 7.53e+01 1efvB c.26.2.3 31636 2g0wA 296 7.56e+01 1r6dA 337 7.59e+01 c.2.1.2 97148 2aefA 234 7.68e+01 1gtmA 419 7.70e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1o0yA 260 7.71e+01 c.1.10.1 80756 1h6fA 193 7.73e+01 b.2.5.4 70901 1nnjA 271 7.78e+01 a.156.1.2,b.113.1.1,g.39.1.8 80669,80670,80671 1s29A 92 7.85e+01 a.4.5.46 98373 1pjjA 271 7.86e+01 a.156.1.2,b.113.1.1,g.39.1.8 104164,104165,104166 1nf2A 268 7.99e+01 c.108.1.10 91849 1b63A 333 7.99e+01 1b63A d.14.1.3,d.122.1.2 37566,41107 1f8fA 371 8.01e+01 b.35.1.2,c.2.1.1 83246,83247 1l6rA 227 8.04e+01 c.108.1.10 77768 1ymmE 249 8.08e+01 1ei6A 406 8.13e+01 c.76.1.4 90443 1wouA 123 8.18e+01 c.47.1.16 109471 1xbrA 184 8.20e+01 1xbrA b.2.5.4 22458 1s5jA 847 8.22e+01 1wzoA 246 8.22e+01 2avyC 232 8.24e+01 1vr4A 103 8.24e+01 1cl8A 276 8.28e+01 1ckqA c.52.1.1 33230 1rqwA 207 8.29e+01 b.25.1.1 97781 1ois 223 8.34e+01 1a36A e.15.1.1 43267 1ezfA 340 8.38e+01 1ezfA a.128.1.2 19440 1cnv 299 8.38e+01 1cnv c.1.8.5 28989 2a9dA 372 8.42e+01 1ydmA 187 8.46e+01 1ntyA 311 8.47e+01 a.87.1.1,b.55.1.1 103873,103874 1zh5A 195 8.49e+01 1fjgC 239 8.50e+01 1fjfC d.52.3.1,d.53.1.1 38831,38839 1ogsA 497 8.52e+01 b.71.1.2,c.1.8.3 86997,86998 1qtsA 247 8.54e+01 1qtsA b.1.10.1,d.105.1.1 22313,40789 1dgfA 497 8.55e+01 1cf9A e.5.1.1 42782 1mkaA 171 8.56e+01 1mkaA d.38.1.2 38543 1mj5A 302 8.60e+01 c.69.1.8 91285 1j6wA 175 8.62e+01 1j98A d.185.1.2 62663 2b7eA 59 8.69e+01 2ab0A 205 8.71e+01 1efyA 350 8.71e+01 1a26 a.41.1.1,d.166.1.2 17413,42275 1u9tA 354 8.72e+01 1qavA 90 8.72e+01 1qauA b.36.1.1 24777 2fxqA 264 8.75e+01 1gyxA 76 8.76e+01 d.80.1.1 76387 1d8dB 437 8.82e+01 1ft1B a.102.4.3 18866 1ars 396 8.87e+01 1ajsA c.67.1.1 34287 1g38A 393 8.88e+01 2admA c.66.1.27 60235 1f5nA 592 8.90e+01 1dg3A a.114.1.1,c.37.1.8 19077,32152 1wthD 391 8.95e+01