# List of top-scoring protein chains for t2k.100-30-stride-ebghtl 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 2goyA 275 1.73e-27 2oq2A 261 1.50e-25 1sur 215 6.79e-23 1sur 1surA 215 6.79e-23 c.26.2.2 31620 1zunA 325 2.34e-19 c.26.2.2 125676 2e18A 257 2.08e-07 1gpmA 525 3.30e-06 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 1xngA 268 6.66e-05 c.26.2.1 122186 2dplA 308 1.47e-04 1q15A 503 8.76e-04 c.26.2.1 95538 d.153.1.1 95539 1wy5A 317 1.72e-03 c.26.2.5 121428 d.229.1.1 121429 1ni5A 433 3.86e-03 b.153.1.2 111592 c.26.2.5 80533 d.229.1.1 111593 2pg3A 232 5.15e-03 1m1zA 513 9.51e-03 c.26.2.1 78457 d.153.1.1 78458 1k92A 455 1.32e-02 c.26.2.1 68325 d.210.1.1 68326 1ru8A 232 1.64e-02 c.26.2.1 97849 2hmaA 376 3.43e-02 2c5sA 413 5.91e-02 c.26.2.6 129950 d.308.1.1 129951 1vl2A 421 1.09e-01 c.26.2.1 108708 d.210.1.1 108709 2d13A 227 1.31e-01 c.26.2.1 131121 2nsyA 271 1.54e-01 2nsyA c.26.2.1 31612 1kqpA 271 1.57e-01 c.26.2.1 72883 1korA 400 2.14e-01 c.26.2.1 72824 d.210.1.1 72825 1pl8A 356 2.54e-01 b.35.1.2 94878 c.2.1.1 94879 1a2oA 349 3.27e-01 1chd c.23.1.1 31120 c.40.1.1 32479 1qnrA 344 3.46e-01 1qnoA c.1.8.3 28834 2b5tI 432 3.90e-01 e.1.1.1 127905 1wxiA 275 4.65e-01 c.26.2.1 121400 1qnoA 344 5.44e-01 1qnoA c.1.8.3 28838 1pwhA 327 6.49e-01 c.79.1.1 95224 1ct9A 553 6.63e-01 1ct9A c.26.2.1 31616 d.153.1.1 41834 2cb1A 412 8.33e-01 1attA 421 8.47e-01 1ovaA e.1.1.1 42638 1k0dA 260 8.68e-01 a.45.1.1 67930 c.47.1.5 67931 1n1cA 217 1.02e+00 a.184.1.1 85254 2jfnA 285 1.11e+00 1cs1A 386 1.18e+00 1ibjA c.67.1.3 34399 1vd6A 224 1.19e+00 c.1.18.3 119991 1y4iA 398 1.25e+00 c.67.1.3 122619 2v03A 303 1.29e+00 1mioA 534 1.37e+00 1qguA c.92.2.3 35601 1b74A 254 1.85e+00 1b74A c.78.2.1 35264 c.78.2.1 35265 1g6wA 261 2.13e+00 1hqoA a.45.1.1 17751 c.47.1.5 33045 2jfuA 291 2.15e+00 2ozeA 298 2.16e+00 1e5eA 404 2.26e+00 1ibjA c.67.1.3 59265 1e3jA 352 2.37e+00 1e3jA b.35.1.2 24765 c.2.1.1 29781 2i9uA 439 2.52e+00 2ox4A 403 2.57e+00 1y7lA 316 2.66e+00 c.79.1.1 122695 1vjrA 271 2.69e+00 c.108.1.14 100832 1vp8A 201 2.73e+00 c.49.1.2 113947 2gcuA 245 2.88e+00 3b8xA 390 2.88e+00 2vlbA 251 3.06e+00 2qrvB 230 3.10e+00 1zjjA 263 3.13e+00 1xbtA 193 3.14e+00 c.37.1.24 115080 g.39.1.14 115081 2gmsA 390 3.21e+00 2c6qA 351 3.26e+00 2rjnA 154 3.27e+00 2ax3A 502 3.33e+00 c.72.1.4 127477 c.104.1.1 127478 1g71A 347 3.38e+00 1g71A d.264.1.1 43268 3bcvA 240 3.64e+00 1w4rA 195 3.75e+00 1h67A 108 3.79e+00 a.40.1.1 65643 2c40A 312 3.93e+00 2ywiA 196 3.93e+00 1b0jA 754 4.10e+00 1amj c.8.2.1 30719 c.83.1.1 35395 2q3bA 313 4.15e+00 1egzA 291 4.24e+00 7a3hA c.1.8.3 28828 1rcuA 195 4.46e+00 c.129.1.1 97295 2oqrA 230 4.50e+00 2p5yA 311 4.82e+00 1b0uA 262 4.95e+00 1b0uA c.37.1.12 32370 2fnaA 357 5.21e+00 a.4.5.11 133809 c.37.1.20 133810 2gnpA 266 5.23e+00 1zh2A 121 5.25e+00 c.23.1.1 125069 1kw4A 89 5.28e+00 a.60.1.2 73077 1hqoA 258 5.38e+00 1hqoA a.45.1.1 17749 c.47.1.5 33043 3c0bA 334 5.44e+00 1u8tA 129 5.48e+00 c.23.1.1 113192 2h6eA 344 5.52e+00 2gzmA 267 5.53e+00 1ufoA 238 5.59e+00 c.69.1.27 99344 16pk 415 5.64e+00 16pk 16pkA 415 5.64e+00 c.86.1.1 35454 2a9oA 120 5.89e+00 c.23.1.1 126444 2gwgA 350 5.91e+00 c.1.9.15 135805 1jlnA 297 6.52e+00 1pty c.45.1.2 63172 1o1zA 234 6.70e+00 c.1.18.3 86555 3bzcA 785 6.79e+00 1c96A 753 7.02e+00 1amj c.8.2.1 30727 c.83.1.1 35403 1f6dA 376 7.07e+00 1f6dA c.87.1.3 35467 1ll7A 392 7.24e+00 c.1.8.5 78085 d.26.3.1 78086 1fp4A 492 7.25e+00 c.92.2.3 76187 1vgvA 384 7.28e+00 c.87.1.3 100608 1j0dA 341 7.29e+00 c.79.1.1 83902 1jsxA 207 7.55e+00 c.66.1.20 71846 1o58A 303 7.72e+00 c.79.1.1 92491 2aq4A 434 7.75e+00 2ovlA 371 8.06e+00 2f1kA 279 8.06e+00 a.100.1.12 132772 c.2.1.6 132773 2iojA 139 8.12e+00 1nbwB 117 8.35e+00 c.51.3.2 80396 2e0tA 151 8.40e+00 1jbwA 428 8.42e+00 c.59.1.2 62860 c.72.2.2 62861 1vb5A 276 8.43e+00 c.124.1.5 113604 1ws6A 171 8.70e+00 c.66.1.46 121222 1f74A 293 8.76e+00 1nal3 c.1.10.1 29079 1qq7A 253 8.93e+00 1qq5A c.108.1.1 43329 2qpxA 376 8.96e+00 1d2kA 392 9.06e+00 1d2kA c.1.8.5 29008 d.26.3.1 38442 3cetA 334 9.28e+00 1qq5A 253 9.31e+00 1qq5A c.108.1.1 43327 2b8eA 273 9.53e+00 c.108.1.7 128068 d.220.1.1 128069 7a3hA 303 9.55e+00 7a3hA c.1.8.3 28817 1wznA 252 9.55e+00 c.66.1.43 121525 2pi0A 116 9.56e+00 1h5vA 304 9.60e+00 c.1.8.3 70898 1p5jA 372 9.60e+00 c.79.1.1 104067 1aq6A 253 9.84e+00 1qq5A c.108.1.1 43331 2c4nA 250 1.02e+01 c.108.1.14 129837 1r13A 148 1.02e+01 d.169.1.1 96782 h.1.1.1 96783 2p35A 259 1.03e+01 3c6qA 311 1.03e+01 2gruA 368 1.04e+01 3berA 249 1.05e+01 1pk1B 89 1.06e+01 a.60.1.2 118712 2gn4A 344 1.07e+01 1e6mA 128 1.08e+01 3chy c.23.1.1 31039 1p77A 272 1.08e+01 c.2.1.7 94214 c.58.1.5 94215 1u32A 293 1.09e+01 d.159.1.3 107631 2pa6A 427 1.10e+01 1vliA 385 1.10e+01 b.85.1.1 108830 c.1.10.6 108831 1jk7A 323 1.10e+01 1auiA d.159.1.3 63144 1kzfA 230 1.12e+01 d.108.1.3 73354 1w9pA 433 1.18e+01 c.1.8.5 114412 d.26.3.1 114413 1h1yA 228 1.18e+01 c.1.2.2 76506 2avdA 219 1.19e+01 c.66.1.1 127377 1zjcA 418 1.24e+01 e.60.1.1 125147 2h3hA 313 1.25e+01 1eg7A 557 1.26e+01 1eg7A c.37.1.10 32241 3chy 128 1.27e+01 3chy 2qvcA 313 1.27e+01 2e55A 208 1.29e+01 1p2xA 159 1.29e+01 a.40.1.1 104062 1jqoA 970 1.29e+01 c.1.12.3 77160 1h05A 146 1.32e+01 c.23.13.1 76433 1yeyA 444 1.33e+01 c.1.11.2 116664 d.54.1.1 116665 1xr4A 509 1.34e+01 c.124.1.2 115860 c.124.1.2 115861 2idbA 505 1.34e+01 b.45.1.3 137270 d.333.1.1 137271 1tzjA 338 1.35e+01 c.79.1.1 112868 1gc0A 398 1.35e+01 c.67.1.3 70168 1lvk 762 1.36e+01 1lvk 1x19A 359 1.38e+01 7odcA 424 1.40e+01 7odcA b.49.2.3 26488 c.1.6.1 28650 1l2tA 235 1.42e+01 c.37.1.12 73514 1kgsA 225 1.43e+01 a.4.6.1 68596 c.23.1.1 68597 1w9iA 770 1.43e+01 1bn6A 294 1.45e+01 1bn6A c.69.1.8 34678 3bwxA 285 1.47e+01 2dhqA 146 1.54e+01 2dhqA c.23.13.1 31382 2i1oA 398 1.57e+01 1ta9A 450 1.57e+01 2bleA 367 1.60e+01 1ltqA 301 1.63e+01 c.108.1.9 78208 c.37.1.1 78209 1d0yA 761 1.65e+01 1lvk b.34.3.1 24581 c.37.1.9 32178 1xyfA 436 1.65e+01 1taxA b.42.2.1 25577 c.1.8.3 28909 1zp2A 235 1.66e+01 1v33A 366 1.68e+01 d.264.1.1 100278 3bn1A 373 1.69e+01 2npnA 251 1.70e+01 1sazA 381 1.70e+01 c.55.1.2 118925 c.55.1.2 118926 2ixaA 444 1.71e+01 2qdeA 397 1.72e+01 2akaA 776 1.73e+01 1t6cA 315 1.74e+01 c.55.1.8 106558 c.55.1.8 106559 2uyoA 310 1.76e+01 2qjwA 176 1.77e+01 1u4nA 310 1.78e+01 c.69.1.2 113021 2uyzB 79 1.82e+01 d.15.1.1 140039 2hcyA 347 1.87e+01 2hm7A 310 1.87e+01 1urjA 1136 1.87e+01 e.58.1.1 113410 1kk1A 410 1.89e+01 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 2dxnA 274 1.90e+01 3beoA 375 1.96e+01 2hkeA 380 1.96e+01 2ah5A 210 1.97e+01 c.108.1.6 126742 3rubS 123 1.98e+01 1rboC d.73.1.1 39616 1m1nA 491 1.99e+01 c.92.2.3 78417 1ly1A 181 2.03e+01 c.37.1.1 74334 1v71A 323 2.05e+01 c.79.1.1 119859 1ut7A 171 2.06e+01 b.143.1.1 99906 2p2vA 288 2.13e+01 1edoA 244 2.13e+01 1ybvA c.2.1.2 29896 1cl1A 395 2.14e+01 1cl2A c.67.1.3 34395 1ortA 335 2.15e+01 1othA c.78.1.1 35204 c.78.1.1 35205 2oasA 436 2.16e+01 1xwyA 264 2.18e+01 c.1.9.12 122411 1wzuA 300 2.18e+01 c.145.1.1 121528 1kxlA 199 2.20e+01 b.40.4.3 73155 2yv5A 302 2.20e+01 1ys4A 354 2.24e+01 2v9dA 343 2.25e+01 1jmsA 381 2.26e+01 a.60.6.1 66889 a.60.12.1 75862 d.218.1.2 75863 2dri 271 2.27e+01 2dri 2driA 271 2.27e+01 c.93.1.1 35637 3borA 237 2.28e+01 1exqA 154 2.28e+01 1b9dA c.55.3.2 33646 2im5A 394 2.30e+01 1f2dA 341 2.30e+01 1f2dA c.79.1.1 35298 2aeuA 374 2.31e+01 c.67.1.8 126646 1v0lA 313 2.31e+01 c.1.8.3 108207 2hrzA 342 2.33e+01 1qysA 106 2.33e+01 k.41.1.1 96603 1hl9A 449 2.34e+01 b.71.1.3 90650 c.1.8.11 90651 2cw6A 298 2.34e+01 1eaxA 241 2.35e+01 b.47.1.2 64889 1omwA 689 2.36e+01 a.91.1.1 87086 b.55.1.1 87087 d.144.1.7 87088 1zuwA 272 2.36e+01 2c1cA 312 2.36e+01 c.56.5.1 129630 1h8uA 117 2.37e+01 1h8uA d.169.1.1 60793 1ppjA 446 2.41e+01 d.185.1.1 104252 d.185.1.1 104253 1v5tA 90 2.41e+01 d.15.1.1 108385 2dtvA 397 2.42e+01 1fjmA 330 2.47e+01 1auiA d.159.1.3 42082 1wyzA 242 2.47e+01 c.90.1.1 121471 1wddS 128 2.49e+01 d.73.1.1 114532 3bzwA 274 2.49e+01 1httA 423 2.50e+01 1adjA c.51.1.1 33178 d.104.1.1 40727 2nloA 302 2.51e+01 1cqwA 295 2.51e+01 1b6g c.69.1.8 34679 1im5A 180 2.52e+01 c.33.1.3 66211 2hxtA 441 2.53e+01 2o7cA 398 2.53e+01 1ugpB 226 2.54e+01 b.34.4.4 107832 1ireB 228 2.54e+01 b.34.4.4 76770 2rgxA 206 2.55e+01 2d1zA 436 2.56e+01 1eziA 228 2.57e+01 1eyrA c.68.1.13 34512 1up7A 417 2.59e+01 c.2.1.5 113374 d.162.1.2 113375 2dskA 311 2.59e+01 1nar 290 2.59e+01 1nar 1narA 290 2.59e+01 c.1.8.5 28988 2i10A 202 2.62e+01 a.4.1.9 136960 a.121.1.1 136961 1xg5A 279 2.62e+01 c.2.1.2 115277 2g0dA 409 2.65e+01 1gu7A 364 2.65e+01 b.35.1.2 83321 c.2.1.1 83322 2yrrA 353 2.67e+01 1znbA 232 2.68e+01 1a7tA d.157.1.1 42039 1cf2O 337 2.72e+01 1b7gO c.2.1.3 29994 d.81.1.1 39909 1vdmA 153 2.73e+01 c.61.1.1 119994 1nm2A 317 2.74e+01 c.19.1.1 80654 d.58.23.1 80655 1b8qA 127 2.74e+01 1qauA b.36.1.1 24781 1ve5A 311 2.76e+01 c.79.1.1 120013 1tk9A 188 2.76e+01 c.80.1.3 107082 3c3jA 384 2.77e+01 1ble 163 2.79e+01 1ble 1jbeA 128 2.81e+01 3chy c.23.1.1 62845 1oi0A 124 2.82e+01 c.97.3.1 93045 1bn7A 294 2.86e+01 1bn6A c.69.1.8 34677 3c85A 183 2.87e+01 1z45A 699 2.89e+01 b.30.5.4 124427 c.2.1.2 124428 1gy8A 397 2.89e+01 c.2.1.2 83376 1mkzA 172 2.90e+01 c.57.1.1 84998 1fg7A 356 2.91e+01 1gewA c.67.1.1 59819 1tovA 98 2.91e+01 b.34.10.1 107179 2p1fA 291 2.92e+01 1qwjA 229 2.96e+01 c.68.1.13 96478 2pz0A 252 2.98e+01 1c0pA 363 2.98e+01 1an9A c.4.1.2 30647 d.16.1.3 37934 1lkyA 77 2.98e+01 a.60.1.1 73985 1yoeA 322 3.00e+01 1ji7A 89 3.04e+01 a.60.1.1 71682 1ab5A 125 3.07e+01 3chy c.23.1.1 31056 3cs3A 277 3.10e+01 1vg5A 73 3.10e+01 a.5.2.1 113640 1b1cA 181 3.12e+01 1amoA c.23.5.2 31212 1nqkA 381 3.12e+01 c.1.16.4 92050 1yrbA 262 3.13e+01 c.37.1.10 123915 2cvhA 220 3.13e+01 2masA 314 3.14e+01 2masA c.70.1.1 34810 1up6A 416 3.16e+01 c.2.1.5 107976 d.162.1.2 107977 1fpzA 212 3.17e+01 1fpzA c.45.1.1 59976 1tdj 514 3.21e+01 1tdj 1jztA 246 3.22e+01 c.104.1.1 63319 2bifA 469 3.24e+01 1bif c.37.1.7 31963 c.60.1.4 34009 1nnwA 252 3.25e+01 d.159.1.5 80674 1ylkA 172 3.30e+01 1q0uA 219 3.31e+01 c.37.1.19 95512 2jgyA 279 3.33e+01 2qcfA 260 3.35e+01 1gewA 356 3.38e+01 1gewA c.67.1.1 60470 1wv2A 265 3.45e+01 c.1.31.1 114910 3pmgA 561 3.48e+01 3pmgA c.84.1.1 35408 c.84.1.1 35409 c.84.1.1 35410 d.129.2.1 41301 1va4A 279 3.49e+01 c.69.1.12 108458 1sv0C 82 3.50e+01 a.60.1.1 106037 1cl2A 395 3.52e+01 1cl2A c.67.1.3 34397 1g8pA 350 3.53e+01 1g8pA c.37.1.20 60376 1dik 874 3.53e+01 1dik 2e57A 637 3.54e+01 2px0A 296 3.54e+01 1yj7A 171 3.55e+01 1kmmA 424 3.57e+01 1adjA c.51.1.1 33174 d.104.1.1 40723 1b0aA 288 3.57e+01 1a4iA c.2.1.7 30286 c.58.1.2 33934 2hneA 436 3.59e+01 1vecA 206 3.63e+01 c.37.1.19 100575 1lktA 104 3.64e+01 1lktA b.90.1.1 28398 2fq6A 415 3.65e+01 c.67.1.3 133939 2zg5A 397 3.66e+01 1ub3A 220 3.69e+01 c.1.10.1 88395 1mi3A 322 3.71e+01 c.1.7.1 91274 1h1nA 305 3.74e+01 c.1.8.3 70855 1fgs 428 3.74e+01 1fgs 1r5jA 337 3.74e+01 c.77.1.5 97097 2qv0A 143 3.77e+01 1tib 269 3.78e+01 3tgl 1tibA 269 3.78e+01 c.69.1.17 34738 2b4zA 104 3.78e+01 1p5sA 203 3.79e+01 a.40.1.1 94147 1e0tA 470 3.81e+01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1j53A 186 3.82e+01 c.55.3.5 77076 3bifA 468 3.84e+01 1bif c.37.1.7 31962 c.60.1.4 34008 1xm7A 195 3.84e+01 d.159.1.8 115473 1qwoA 442 3.86e+01 c.60.1.2 104620 1w8iA 156 3.87e+01 c.120.1.1 114368 1sdsA 117 3.88e+01 d.79.3.1 105439 1u6eA 335 3.89e+01 c.95.1.2 119568 c.95.1.2 119569 1a49A 530 3.90e+01 1a49A b.58.1.1 27026 c.1.12.1 29255 c.49.1.1 33109 1zu0A 529 3.91e+01 1o69A 394 3.95e+01 c.67.1.4 92560 1a6q 382 3.95e+01 1a6q 1tdzA 272 3.97e+01 a.156.1.2 106787 b.113.1.1 106788 g.39.1.8 106789 2it1A 362 3.97e+01 2e8oA 103 3.98e+01 2hufA 393 4.00e+01