# 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 1xfkA 336 3.89e-01 1uohA 226 6.05e-01 d.211.1.1 99690 1nrlA 316 8.31e-01 a.123.1.1 92091 1u3wA 374 1.11e+00 2gfhA 260 1.45e+00 1rpnA 335 1.53e+00 c.2.1.2 97708 1larA 575 1.55e+00 1larA c.45.1.2,c.45.1.2 32693,32694 1ru3A 732 1.75e+00 e.26.1.3 97835 1cf2O 337 1.77e+00 1b7gO c.2.1.3,d.81.1.1 29994,39909 1qf5A 431 2.46e+00 1adeA c.37.1.10 32212 1jofA 365 2.94e+00 b.69.10.1 71775 1tluA 130 3.00e+00 d.156.1.2 107139 1n8kA 374 3.09e+00 b.35.1.2,c.2.1.1 80298,80299 1vr7A 142 3.50e+00 2ga9D 469 3.55e+00 1wljA 189 3.70e+00 1a0rP 245 3.72e+00 1b9yC c.47.1.6 33054 1hetA 374 3.77e+00 2ohxA b.35.1.2,c.2.1.1 60975,60976 2rslA 140 3.79e+00 2rslA c.53.1.1 33345 1e4mM 501 3.84e+00 1e70M c.1.8.4 59226 1fo3A 460 4.03e+00 1dl2A a.102.2.1 18845 1qh3A 260 4.57e+00 1qh5A d.157.1.2 42059 1itcA 516 4.67e+00 b.3.1.1,c.1.8.1 83705,83706 3pvaA 335 4.83e+00 3pvaA d.153.1.3 41854 1tiqA 180 4.93e+00 d.108.1.1 107010 1hdhA 536 5.06e+00 c.76.1.2 65805 1riqA 465 5.31e+00 a.203.1.1,d.104.1.1 97516,97517 1ks8A 433 5.47e+00 a.102.1.2 77519 1t8qA 336 5.73e+00 c.1.18.3 106669 1bd8 156 6.53e+00 1bd8 d.211.1.1 19157 1vloA 381 6.60e+00 b.44.2.1,d.250.1.1 108838,108839 2b0oE 301 6.76e+00 1qh5A 260 6.84e+00 1qh5A d.157.1.2 42057 1mtyD 512 6.86e+00 1mhyD a.25.1.2 16742 2fgtA 417 6.90e+00 1c3hA 137 7.43e+00 b.22.1.1 90405 1kwfA 363 7.45e+00 a.102.1.2 73078 1qr6A 584 7.72e+00 1qr6A c.2.1.7,c.58.1.3 30293,33941 1div 149 7.85e+00 1div d.99.1.1,d.100.1.1 40692,40693 1vybA 238 8.53e+00 d.151.1.1 108897 2aq4A 434 8.85e+00 1lt3A 240 8.94e+00 1lt3A d.166.1.1 42230 1adjA 421 9.83e+00 1adjA c.51.1.1,d.104.1.1 33188,40737 1dxeA 256 1.01e+01 1dxeA c.1.12.5 29310 1vyfA 135 1.02e+01 b.60.1.2 108902 1xel 338 1.03e+01 1xel c.2.1.2 29786 1twdA 256 1.04e+01 c.1.30.1 107397 2reb 352 1.04e+01 2reb c.37.1.11,d.48.1.1 32282,38767 2fxqA 264 1.04e+01 2bw4A 340 1.05e+01 1cem 363 1.06e+01 1cem a.102.1.2 18826 1xx4A 261 1.06e+01 1brmA 367 1.10e+01 1brmA c.2.1.3,d.81.1.1 30030,39945 1f9vA 347 1.14e+01 1bg2 c.37.1.9 59745 1x8qA 184 1.17e+01 1qrrA 394 1.18e+01 1qrrA c.2.1.2 29824 1d2nA 272 1.18e+01 1d2nA c.37.1.20 32428 1m2kA 249 1.20e+01 c.31.1.5 84754 1z82A 335 1.30e+01 1sr4B 261 1.31e+01 d.151.1.1 105949 1qisA 396 1.36e+01 1ajsA c.67.1.1 34284 1yhtA 367 1.36e+01 2bgiA 272 1.41e+01 1wkbA 810 1.45e+01 1gd1O 334 1.53e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 1igwA 434 1.57e+01 c.1.12.7 62370 1ctt 294 1.59e+01 1ctt c.97.1.1,c.97.1.1 36022,36023 1ub0A 258 1.60e+01 c.72.1.2 88394 1zy9A 564 1.65e+01 2bghA 421 1.66e+01 1ssqA 267 1.67e+01 b.81.1.6 105993 1ydyA 356 1.69e+01 2cklB 165 1.72e+01 1yaiA 151 1.72e+01 1yaiA b.1.8.1 22289 1njhA 119 1.76e+01 b.128.1.1 85787 1t9kA 347 1.88e+01 c.124.1.5 106721 1top 162 1.92e+01 1ncx a.39.1.5 17223 1qgjA 300 1.93e+01 1bgp a.93.1.1 18691 1u2xA 474 1.93e+01 c.72.1.3 107622 1erxA 184 1.95e+01 1np1A b.60.1.1 27164 1nbwA 607 1.96e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1v02A 565 2.01e+01 c.1.8.4 108194 1lzjA 292 2.06e+01 c.68.1.9 74352 1j9lA 247 2.06e+01 c.106.1.1 62762 1djxB 624 2.09e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17343,23160,29588 1a8s 273 2.09e+01 1brt c.69.1.12 34710 1d9tA 289 2.11e+01 1deaA 1vjfA 180 2.11e+01 d.116.1.1 100809 1ne7A 289 2.11e+01 c.124.1.1 91833 1jbwA 428 2.14e+01 c.59.1.2,c.72.2.2 62860,62861 1v4vA 376 2.19e+01 c.87.1.3 100313 1amk 251 2.22e+01 1amk c.1.1.1 28503 1zp4A 304 2.23e+01 1i50A 1733 2.25e+01 e.29.1.2 61754 1sy3A 184 2.26e+01 b.60.1.1 106110 1o6dA 163 2.27e+01 c.116.1.3 92567 1iz5A 249 2.29e+01 d.131.1.2,d.131.1.2 83834,83835 1nnlA 225 2.29e+01 c.108.1.4 85906 2pvaA 345 2.31e+01 3pvaA d.153.1.3 41850 2b4yA 271 2.34e+01 1dgfA 497 2.38e+01 1cf9A e.5.1.1 42782 1cf7B 95 2.38e+01 1cf7B a.4.5.17 16152 1kcbA 340 2.39e+01 b.6.1.3,b.6.1.3 90951,90952 2awpA 198 2.44e+01 1sjgA 112 2.48e+01 b.33.1.1 105647 1vj0A 380 2.50e+01 b.35.1.2,c.2.1.1 100786,100787 1zaiA 363 2.52e+01 2cfuA 658 2.58e+01 1nif 340 2.61e+01 1nif b.6.1.3,b.6.1.3 23048,23049 1uheA 97 2.75e+01 1oyeA 1049 2.76e+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 1m93A 55 2.77e+01 e.1.1.1 91235 1up6A 416 2.79e+01 c.2.1.5,d.162.1.2 107976,107977 2bx2L 517 2.79e+01 1w7lA 422 2.79e+01 c.67.1.1 109226 1k55A 246 2.80e+01 e.3.1.1 68156 1q2bA 434 2.84e+01 b.29.1.10 95624 1p1mA 406 2.87e+01 b.92.1.4,c.1.9.9 87696,87697 1opd 85 2.94e+01 1ptf d.94.1.1 40560 1snlA 103 3.00e+01 a.39.1.7 105820 2cq2A 114 3.01e+01 3chbD 104 3.05e+01 3chbD b.40.2.1 24970 2gl5A 410 3.07e+01 1h49A 512 3.08e+01 c.1.8.4 83477 2an3A 289 3.08e+01 1y7lA 316 3.12e+01 2bwbA 46 3.13e+01 2liv 344 3.16e+01 2liv c.93.1.1 35708 1qwgA 251 3.16e+01 c.1.27.1 96473 1ojrA 274 3.20e+01 c.74.1.1 93147 1x9mA 698 3.23e+01 1je0A 236 3.24e+01 c.56.2.1 66581 1twfA 1733 3.28e+01 2adoA 196 3.29e+01 1cy9A 264 3.29e+01 1ecl e.10.1.1 43236 1mvwB 145 3.30e+01 i.15.1.1 79524 1lmeA 176 3.37e+01 d.167.1.1 84629 1ua7A 422 3.43e+01 b.71.1.1,c.1.8.1 107759,107760 2a67A 167 3.44e+01 1ktaA 365 3.44e+01 e.17.1.1 77533 1c52 131 3.49e+01 1c52 a.3.1.1 15810 1h4vB 421 3.52e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1repC 251 3.53e+01 1repC a.4.5.10,a.4.5.10 16125,16126 1nc5A 373 3.54e+01 a.102.1.6 85548 1amuA 563 3.54e+01 1amuA e.23.1.1 43351 2g9iA 249 3.56e+01 1e55A 512 3.59e+01 1e70M c.1.8.4 28934 1hleA 345 3.62e+01 1ovaA e.1.1.1 42618 1fwkA 296 3.63e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1rqwA 207 3.66e+01 b.25.1.1 97781 1xovA 326 3.66e+01 1b3uA 588 3.67e+01 1b3uA a.118.1.2 19135 1k28A 584 3.68e+01 b.40.8.1,b.108.1.2,d.2.1.3 68049,68050,68051 1dj0A 264 3.69e+01 1dj0A d.265.1.1 90337 1ynmA 247 3.70e+01 1dosA 358 3.71e+01 1dosA c.1.10.2 29175 1lurA 339 3.72e+01 b.30.5.4 84717 1vi7A 217 3.75e+01 d.14.1.11,d.58.11.2 100740,100741 1kutA 230 3.77e+01 d.143.1.1 73017 1skoB 130 3.94e+01 d.110.7.1 105677 2his 312 3.94e+01 1taxA c.1.8.3 28918 2biqA 219 3.95e+01 1wr1B 58 3.97e+01 1sh7A 284 4.00e+01 1wrjA 156 4.00e+01 16vpA 366 4.01e+01 16vpA d.180.1.1 42601 1pg5A 299 4.08e+01 c.78.1.1,c.78.1.1 104146,104147 1c93A 265 4.11e+01 2ebn c.1.8.5 28998 1wyuB 474 4.11e+01 1py5A 326 4.12e+01 d.144.1.7 104389 1p2hA 571 4.15e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 2b8nA 429 4.17e+01 1ze3C 205 4.17e+01 1e5kA 201 4.23e+01 1fr9A c.68.1.8 34578 2sli 679 4.24e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1w0pA 781 4.27e+01 b.29.1.8,b.29.1.8,b.68.1.1 109038,109039,109040 2fclA 169 4.27e+01 1sflA 238 4.28e+01 1ek9A 428 4.30e+01 1ek9A f.5.1.1 43809 1v7oA 165 4.34e+01 d.67.1.2 100480 1jr7A 311 4.34e+01 b.82.2.3 63255 1vcdA 126 4.37e+01 1v5vA 401 4.42e+01 1cvrA 435 4.46e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 1gtmA 419 4.48e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1gntA 553 4.48e+01 e.26.1.1 70290 1v8eA 224 4.50e+01 1eg3A 261 4.52e+01 1eg3A a.39.1.7,a.39.1.7,b.72.1.1 17376,17377,27805 1pbgA 468 4.53e+01 1e70M c.1.8.4 28946 5reqA 727 4.53e+01 1reqA c.1.19.1,c.23.6.1 29632,31259 1j5vA 351 4.54e+01 c.72.1.1 71585 1fs5A 266 4.57e+01 c.124.1.1 65044 1tvzA 388 4.58e+01 c.95.1.2,c.95.1.2 107367,107368 1qwnA 1045 4.59e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1fnuA 221 4.64e+01 3seb b.40.2.2,d.15.6.1 25212,37801 1tr9A 341 4.65e+01 1r89A 437 4.69e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1xn5A 146 4.73e+01 1qqp1 213 4.75e+01 1qqp1 1tf4A 605 4.76e+01 1tf4A a.102.1.2,b.2.2.2 18827,22393 1fjgC 239 4.76e+01 1fjfC d.52.3.1,d.53.1.1 38831,38839 1ymtA 246 4.77e+01 1kevA 351 4.82e+01 1pedA b.35.1.2,c.2.1.1 24749,29765 1ede 310 4.82e+01 1b6g c.69.1.8 34662 1pe9A 361 4.87e+01 b.80.1.1 94595 1rhs 296 4.88e+01 1rhs c.46.1.2,c.46.1.2 32703,32704 1c96A 753 4.92e+01 1amj c.8.2.1,c.83.1.1 30727,35403 1nb8A 353 4.94e+01 d.3.1.9 80385 1e3dA 266 4.94e+01 2frvA e.19.1.1 59188 1tzjA 338 4.98e+01 1a78A 134 4.98e+01 1c1lA b.29.1.3 24212 1d4xG 126 5.00e+01 1d0nA d.109.1.1 59109 1f8yA 157 5.06e+01 1f8xA c.23.14.1 31395 2aq8A 269 5.08e+01 1u8fO 335 5.12e+01 1nnjA 271 5.12e+01 a.156.1.2,b.113.1.1,g.39.1.8 80669,80670,80671 1x3lA 440 5.14e+01 1mnaA 298 5.20e+01 c.69.1.22 79322 1gj7B 253 5.23e+01 1e6yA 569 5.25e+01 1mroA a.89.1.1,d.58.31.2 18529,39447 2b0mA 393 5.29e+01 1xcbA 211 5.32e+01 a.4.5.38,c.2.1.12 109552,109553 1uumA 372 5.32e+01 c.1.4.1 100010 1hxxA 340 5.39e+01 2omf f.4.3.1 61385 1yadA 221 5.39e+01 2bfgA 503 5.40e+01 1xhfA 123 5.41e+01 1pixA 587 5.42e+01 c.14.1.4 94708 1eg7A 557 5.43e+01 1eg7A c.37.1.10 32241 1rp4A 389 5.44e+01 a.227.1.1 105027 1e4yA 214 5.44e+01 1zin c.37.1.1,g.41.2.1 31901,45181 1p0kA 349 5.46e+01 c.1.4.1 87648 1mrg 263 5.51e+01 1mrj d.165.1.1 42183 1wzoA 246 5.51e+01 2aaoA 166 5.59e+01 1ckiA 317 5.62e+01 1csn d.144.1.7 41660 1ih8A 271 5.65e+01 2nsyA c.26.2.1 62377 1d0cA 444 5.65e+01 d.174.1.1 64769 2adgA 214 5.66e+01 1jv1A 505 5.69e+01 c.68.1.5 71892 1gefA 123 5.69e+01 1gefA c.52.1.18 60465 1j5xA 342 5.71e+01 c.80.1.1 71591 1oaoC 729 5.74e+01 e.26.1.3 86746 1lt8A 406 5.77e+01 c.1.26.1 78186 1ml9A 302 5.80e+01 b.85.7.1 79282 1cjxA 357 5.84e+01 1cjxA d.32.1.3,d.32.1.3 38516,38517 1ntyA 311 5.88e+01 a.87.1.1,b.55.1.1 103873,103874 1o0yA 260 5.99e+01 c.1.10.1 80756 1ov2A 99 6.02e+01 a.13.1.1 93580 1hqz1 141 6.04e+01 2culA 232 6.05e+01 1h72C 296 6.09e+01 d.14.1.5,d.58.26.1 60712,60713 1rqbA 539 6.12e+01 a.5.7.2,c.1.10.5 105057,105058 1qtsA 247 6.16e+01 1qtsA b.1.10.1,d.105.1.1 22313,40789 1wyuA 438 6.17e+01 1xqwA 293 6.18e+01 1z15A 344 6.20e+01 1ynpA 317 6.27e+01 1bu6O 501 6.29e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 2flsA 132 6.30e+01 1zpvA 91 6.32e+01 1rsy 152 6.33e+01 1rsy b.7.1.2 23192 1cl8A 276 6.36e+01 1ckqA c.52.1.1 33230 1rypL 212 6.36e+01 d.153.1.4 41880 1ys4A 354 6.37e+01 1d3gA 367 6.38e+01 1d3gA c.1.4.1 28600 1ur4A 399 6.38e+01 1r77A 103 6.44e+01 1rr7A 129 6.45e+01 a.4.1.14 105075 1ogiA 303 6.45e+01 b.43.4.2,c.25.1.1 92914,92915 1gu7A 364 6.51e+01 b.35.1.2,c.2.1.1 83321,83322 1mq4A 272 6.56e+01 d.144.1.7 91391 1t5rA 284 6.56e+01 f.6.1.1 106465 1xrtA 467 6.57e+01 1yozA 116 6.61e+01 1f0nA 285 6.61e+01 1dqyA c.69.1.3 34636 1j6wA 175 6.62e+01 1j98A d.185.1.2 62663 1yu3A 381 6.64e+01 1evfA 264 6.72e+01 1bkpA d.117.1.1 40932 1qqqA 264 6.73e+01 1bkpA d.117.1.1 40931 1ns5A 155 6.76e+01 c.116.1.3 80705 1oroA 213 6.78e+01 1opr c.61.1.1 34093 1rerA 391 6.79e+01 b.1.18.4,f.10.1.1 97327,97328 1b6g 310 6.94e+01 1b6g c.69.1.8 34661 1pvvA 315 6.94e+01 c.78.1.1,c.78.1.1 95190,95191 1h1nA 305 6.97e+01 c.1.8.3 70855 1mc0A 368 7.06e+01 d.110.2.1,d.110.2.1 78937,78938 1ll7A 392 7.07e+01 c.1.8.5,d.26.3.1 78085,78086 2as0A 396 7.09e+01 1rfmA 344 7.12e+01 c.122.1.1 97385 1r6dA 337 7.14e+01 c.2.1.2 97148 1w9hA 427 7.17e+01 1pjjA 271 7.22e+01 a.156.1.2,b.113.1.1,g.39.1.8 104164,104165,104166 1que 303 7.25e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1t94A 459 7.26e+01 d.240.1.1,e.8.1.7 106701,106702 1e0wA 313 7.31e+01 1taxA c.1.8.3 59150 1svpA 161 7.34e+01 1svpA b.47.1.3 26384 2ax3A 502 7.36e+01 1s5jA 847 7.38e+01 2aefA 234 7.43e+01 1go2A 304 7.46e+01 b.43.4.2,c.25.1.1 76243,76244 2b7eA 59 7.53e+01 1g6aA 271 7.53e+01 1btl e.3.1.1 42704 1eexA 554 7.54e+01 1dioA c.1.19.3 29650 1vhqA 232 7.55e+01 c.23.16.2 100696 1zh5A 195 7.59e+01 2g0wA 296 7.61e+01 1qavA 90 7.63e+01 1qauA b.36.1.1 24777 1axiB 236 7.73e+01 1axiB b.1.2.1,b.1.2.1 21997,21998 1nksA 194 7.73e+01 1nksA c.37.1.1 31886 1ksiA 642 7.76e+01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24408,38043,38044 1s29A 92 7.95e+01 a.4.5.46 98373 2f9cA 334 7.95e+01 1ezfA 340 8.02e+01 1ezfA a.128.1.2 19440 1wouA 123 8.10e+01 c.47.1.16 109471 1ej0A 180 8.13e+01 1ej0A c.66.1.2 34179 1ydmA 187 8.14e+01 4ubpC 570 8.20e+01 1ubpC b.92.1.1,c.1.9.2 28431,29053 1ps9A 671 8.25e+01 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 1p5dX 463 8.29e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1ars 396 8.29e+01 1ajsA c.67.1.1 34287 1eg2A 319 8.31e+01 1eg2A c.66.1.11 34249 1f8fA 371 8.32e+01 b.35.1.2,c.2.1.1 83246,83247 1efyA 350 8.35e+01 1a26 a.41.1.1,d.166.1.2 17413,42275 1bgp 309 8.36e+01 1bgp a.93.1.1 18690 1gyxA 76 8.41e+01 d.80.1.1 76387 1sw5B 275 8.44e+01 c.94.1.1 106070 2fflA 756 8.46e+01 1efpB 252 8.46e+01 1efvB c.26.2.3 31636 1u9tA 354 8.52e+01 1tqnA 486 8.54e+01 a.104.1.1 107238 1yh2A 175 8.55e+01 2av4A 162 8.64e+01 1ois 223 8.65e+01 1a36A e.15.1.1 43267 1mzyA 333 8.67e+01 b.6.1.3,b.6.1.3 103848,103849 2fbaA 492 8.70e+01 1fvgA 199 8.76e+01 1fvaA d.58.28.1 39408 1m2oA 768 8.78e+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 1mj5A 302 8.80e+01 c.69.1.8 91285 1a88A 275 8.83e+01 1brt c.69.1.12 34707 1d2kA 392 8.91e+01 1d2kA c.1.8.5,d.26.3.1 29008,38442 1j08A 226 8.92e+01 c.47.1.2,c.47.1.2 83855,83856 1b7yB 785 8.97e+01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16301,16302,25312,39311,40780,41456 1id0A 152 8.97e+01 d.122.1.3 66111