# List of top-scoring protein chains for t2k.w0.5 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 2h6nA 312 9.60e-17 2o9kA 313 9.60e-17 2h14A 317 9.60e-17 2h9lA 329 9.60e-17 3emhA 318 9.60e-17 2gnqA 336 9.60e-17 2g9aA 311 9.61e-17 2g99A 308 9.61e-17 2cnxA 315 2.30e-16 2co0A 315 3.20e-16 2bcjB 340 1.32e-13 b.69.4.1 128289 1tbgA 340 1.32e-13 1tbgA b.69.4.1 27649 1vyhC 410 1.34e-13 b.69.4.1 144534 1gotB 340 1.37e-13 1tbgA b.69.4.1 27648 1a0rB 340 1.37e-13 1tbgA b.69.4.1 27658 1erjA 393 1.70e-13 1erjA b.69.4.1 27660 3hxjA 330 2.10e-13 2zkqa 317 3.28e-13 3dm0A 694 7.20e-13 1q7fA 286 8.68e-13 b.68.9.1 96036 2ovrB 445 2.84e-11 a.158.1.1 145735 b.69.4.1 145736 3frxA 319 2.75e-10 1trjA 314 2.75e-10 3jyvR 313 2.75e-10 3fm0A 345 7.07e-10 2pbiB 354 1.62e-09 1p22A 435 7.27e-09 a.158.1.1 87715 b.69.4.1 87716 1nexB 464 1.27e-08 a.158.1.1 80443 b.69.4.1 80444 1rwiA 270 1.52e-08 b.68.9.1 97987 1gxrA 337 7.52e-08 b.69.4.1 70722 1k8kC 372 1.34e-07 b.69.4.1 68308 3dxkC 372 1.74e-07 2aq5A 402 1.33e-06 1nr0A 611 2.28e-06 b.69.4.1 86078 b.69.4.1 86079 3fvzA 329 3.07e-06 2hesX 330 4.52e-06 3bg1A 316 1.31e-05 3ei4B 436 1.73e-05 1sq9A 397 3.72e-05 b.69.4.1 105889 1s4uX 407 3.75e-05 b.69.4.1 112027 1l0qA 391 3.99e-05 b.1.3.1 77644 b.69.2.3 77645 1r5mA 425 4.53e-05 3acpA 417 7.07e-05 3jrpA 379 8.66e-05 2pm6B 297 9.78e-05 3jroA 753 1.23e-04 2pm7B 297 1.68e-04 3fgbA 361 1.87e-04 3bwsA 433 3.38e-04 1kv9A 668 3.65e-04 a.3.1.6 73056 b.70.1.1 73057 3dwlC 377 4.27e-04 1pguA 615 9.81e-04 b.69.4.1 88069 b.69.4.1 88070 3c99A 432 1.85e-03 2dsoA 333 1.94e-03 b.68.6.1 131689 1kb0A 677 2.32e-03 a.3.1.6 68378 b.70.1.1 68379 3hrpA 409 2.58e-03 3ei3B 383 3.08e-03 3e5zA 296 3.35e-03 1n6eA 1071 4.18e-03 b.36.1.3 80149 b.68.7.1 80150 b.69.9.1 80151 c.14.1.2 80152 1k32A 1045 4.19e-03 b.36.1.3 68068 b.68.7.1 68069 b.69.9.1 68070 c.14.1.2 68071 2gvxA 314 4.20e-03 2p9wA 334 4.44e-03 1flgA 582 5.19e-03 4aahA b.70.1.1 27682 2dg1A 333 5.46e-03 b.68.6.1 131493 3gfcA 425 5.71e-03 3cfsB 414 5.88e-03 1g72A 573 5.91e-03 4aahA b.70.1.1 27680 2ad6A 571 5.91e-03 b.70.1.1 126568 4aahA 571 5.91e-03 4aahA b.70.1.1 27678 2z2nA 299 6.93e-03 2z2pA 299 7.16e-03 2iaxA 312 7.39e-03 2p4oA 306 7.76e-03 b.68.6.3 149216 3li5A 314 8.15e-03 3hliA 314 8.19e-03 3li4A 314 8.37e-03 3hlhA 314 8.79e-03 2iawA 312 9.59e-03 3i1cA 324 1.10e-02 2gvuA 314 1.43e-02 3greA 437 1.44e-02 2iapA 312 1.49e-02 1pjxA 314 1.53e-02 b.68.6.1 104167 1e1aA 314 1.53e-02 1e1aA b.68.6.1 59155 2iaoA 312 1.54e-02 2iaqA 312 1.55e-02 2iavA 312 1.76e-02 1yiqA 689 2.54e-02 3li3A 314 2.55e-02 2iasA 312 2.78e-02 2iauA 312 2.89e-02 2gopA 347 3.03e-02 2iatA 312 3.33e-02 3iaxA 438 4.29e-02 2ivzA 439 4.30e-02 b.68.4.1 137729 c.51.2.1 137730 2hqsA 415 4.30e-02 b.68.4.1 136662 c.51.2.1 136663 1crzA 403 4.31e-02 1crzA b.68.4.1 27629 c.51.2.1 33211 2w8bB 409 4.34e-02 2vduB 450 4.44e-02 2i3tA 341 4.53e-02 b.69.4.2 137034 1u4cA 349 4.53e-02 b.69.4.2 107666 2i3sA 349 4.53e-02 b.69.4.2 137031 1yfqA 342 4.53e-02 b.69.4.2 116680 2w8bA 409 4.66e-02 3g4eA 297 5.42e-02 1h4iA 599 5.49e-02 4aahA b.70.1.1 60586 1w6sA 599 5.49e-02 b.70.1.1 114284 1h4jA 599 5.50e-02 4aahA b.70.1.1 60590 2pm9A 416 5.72e-02 1lrwA 600 5.80e-02 b.70.1.1 91111 2iarA 312 6.00e-02 3i2nA 357 7.11e-02 1ri6A 343 1.00e-01 b.69.11.1 97503 3f3fA 351 1.01e-01 3eweA 349 1.06e-01 1pbyB 337 1.44e-01 b.69.2.2 94422 1jmxB 349 1.61e-01 b.69.2.2 66906 2ojhA 297 1.75e-01 3jzhA 402 1.80e-01 3ijcA 365 1.85e-01 3k26A 366 1.88e-01 3iiwA 365 1.90e-01 2qxvA 361 1.96e-01 1mg2A 390 2.74e-01 b.69.2.1 79059 2bbkH 355 2.93e-01 2bbkH b.69.2.1 27634 2d5lA 706 3.20e-01 2dcmA 706 3.29e-01 2z3zA 706 3.40e-01 3dr2A 305 3.92e-01 2hewF 152 4.65e-01 b.22.1.1 136364 1z68A 719 5.10e-01 2gc7A 386 5.26e-01 b.69.2.1 134954 2hz6A 369 6.24e-01 2cn3A 737 7.26e-01 1h3iA 293 8.05e-01 b.76.2.1 76635 b.85.7.1 76636 2biwA 490 9.14e-01 2pagA 135 9.64e-01 d.369.1.1 149343 3ettA 571 1.06e+00 2mtaH 373 1.08e+00 2bbkH b.69.2.1 27636 3elqA 571 1.13e+00 3a2kA 464 1.16e+00 3e0cA 1140 1.23e+00 3dasA 347 1.29e+00 3ei3A 1158 1.33e+00 2cn2A 737 1.38e+00 2oajA 902 1.51e+00 1mt6A 280 1.54e+00 b.76.2.1 79446 b.85.7.1 79447 1hzuA 543 1.59e+00 a.3.1.2 61460 b.70.2.1 61461 1nirA 543 1.62e+00 1qksA a.3.1.2 15939 b.70.2.1 27698 1hzvA 543 1.63e+00 a.3.1.2 61462 b.70.2.1 61463 1qniA 581 1.80e+00 1qniA b.6.1.4 23042 b.69.3.1 27642 2d0vA 597 2.04e+00 1gq1A 567 2.11e+00 a.3.1.2 76264 b.70.2.1 76265 1hj5A 567 2.11e+00 1qksA a.3.1.2 15927 b.70.2.1 27684 1qksA 567 2.16e+00 1qksA a.3.1.2 15951 b.70.2.1 27710 3hfqA 347 2.26e+00 1e2rA 567 2.28e+00 1qksA a.3.1.2 15953 b.70.2.1 27712 2ghsA 326 2.51e+00 b.68.6.1 135209 3c75H 426 2.55e+00 1jofA 365 2.59e+00 b.69.10.1 71775 3fhcA 405 2.80e+00 1jtdB 273 2.89e+00 b.69.5.2 67265 1n6cA 297 2.91e+00 b.76.2.1 80123 b.85.7.1 80124 2oitA 434 2.98e+00 3fmoA 450 2.99e+00 1bk4A 337 3.11e+00 1frpA e.7.1.1 42938 3dsmA 328 3.24e+00 2be1A 339 3.27e+00 2b5nA 323 3.42e+00 2wozA 318 3.80e+00 2zwaA 695 3.87e+00 3fyfA 176 3.93e+00 2b5lA 1140 4.00e+00 3i7kA 1143 4.11e+00 3ei4A 1158 4.35e+00 1ybqA 390 4.56e+00 1ybqB 390 4.56e+00 2qt9A 766 4.66e+00 b.70.3.1 151329 c.69.1.24 151330 1r9nA 739 4.71e+00 b.70.3.1 118745 c.69.1.24 118746 3g0bA 740 4.73e+00 2bgrA 738 4.74e+00 b.70.3.1 128496 c.69.1.24 128497 1r9mA 733 4.74e+00 b.70.3.1 104870 c.69.1.24 104871 2jidA 736 4.74e+00 b.70.3.1 148087 c.69.1.24 148088 1wcyA 740 4.74e+00 b.70.3.1 120903 c.69.1.24 120904 1pfqA 731 4.74e+00 b.70.3.1 88061 c.69.1.24 88062 2oncA 731 4.74e+00 b.70.3.1 148891 c.69.1.24 148892 2ripA 729 4.75e+00 b.70.3.1 152095 c.69.1.24 152096 2qjrA 748 4.75e+00 b.70.3.1 150830 c.69.1.24 150831 1tk3A 728 4.75e+00 b.70.3.1 107069 c.69.1.24 107070 2g63A 726 4.75e+00 b.70.3.1 134686 c.69.1.24 134687 2rguA 734 4.75e+00 b.70.3.1 152022 c.69.1.24 152023 3hacA 728 4.75e+00 1u8eA 728 4.78e+00 b.70.3.1 107733 c.69.1.24 107734 2qzpA 562 4.90e+00 b.69.7.2 151487 c.69.1.33 151488 2qr5A 582 5.31e+00 b.69.7.2 151278 c.69.1.33 151279 2ismA 352 5.34e+00 1onwA 390 5.41e+00 b.92.1.7 87172 c.1.9.13 87173 1onxA 390 5.41e+00 b.92.1.7 87176 c.1.9.13 87177 2aqvA 390 5.42e+00 2hu5A 582 5.47e+00 b.69.7.2 136763 c.69.1.33 136764 2hu8A 582 5.47e+00 b.69.7.2 136772 c.69.1.33 136773 1bwnA 169 5.48e+00 1btkA b.55.1.1 26961 1btkA 169 5.74e+00 1btkA b.55.1.1 26959 1b55A 169 5.84e+00 1btkA b.55.1.1 26963 1cruA 454 6.27e+00 1c9uA b.68.2.1 27617 1c9uA 454 6.27e+00 1c9uA b.68.2.1 27623 1lvwA 295 6.59e+00 c.68.1.6 84723 2hr7A 486 6.63e+00 1s8eA 333 7.04e+00 d.159.1.4 105368 1wp5A 323 7.58e+00 b.68.10.1 114780 1jqeA 292 7.68e+00 c.66.1.19 71789 2aotA 292 7.76e+00 c.66.1.19 127098 2yqcA 486 7.80e+00 2aouA 292 7.96e+00 c.66.1.19 127100 1i9zA 347 7.96e+00 1i9yA d.151.1.2 62102 1i9yA 347 7.96e+00 1i9yA d.151.1.2 62101 2v5hA 321 8.02e+00 2aqoA 390 8.07e+00 2dtgE 897 8.42e+00 b.1.2.1 145100 b.1.2.1 145101 b.1.2.1 145102 c.10.2.5 145103 c.10.2.5 145104 g.3.9.1 145105 2wdtA 232 8.46e+00 2qc5A 300 8.70e+00 3cbgA 232 8.76e+00 3lohE 917 8.84e+00 1ihuA 589 9.09e+00 c.37.1.10 62394 c.37.1.10 62395 1f48A 589 9.09e+00 1f48A c.37.1.10 32280 c.37.1.10 32281 2amuA 143 9.41e+00 2k3dA 87 9.69e+00 1f5mA 180 9.78e+00 1f5mB d.110.2.1 40895 2ox7A 155 9.87e+00 b.172.1.1 149054 3kciA 389 9.88e+00 1mufA 257 9.92e+00 b.76.2.1 79483 b.85.7.1 79484 1vmeA 410 1.01e+01 c.23.5.1 108893 d.157.1.3 108894 2va8A 715 1.04e+01 3dzwA 109 1.05e+01 2d04B 114 1.05e+01 2dpfA 115 1.05e+01 2j85A 122 1.08e+01 d.321.1.1 138133 2nrsA 411 1.15e+01 b.85.6.1 138539 b.103.1.1 138540 c.57.1.2 138541 1oh1A 109 1.19e+01 b.61.2.2 92977 2fdbM 164 1.31e+01 b.42.1.1 145162 3c5mA 396 1.34e+01 1senA 164 1.35e+01 c.47.1.1 105465 2k8vA 157 1.35e+01 3fk9A 188 1.37e+01 1qz9A 416 1.45e+01 c.67.1.3 96621 1jvgA 522 1.48e+01 c.68.1.5 77185 1y2yA 58 1.51e+01 g.41.16.1 122575 3ibsA 218 1.55e+01 1jv1A 505 1.60e+01 c.68.1.5 71892 2d0dA 282 1.60e+01 1eifA 135 1.61e+01 b.34.5.2 24608 b.40.4.5 25340 1uk8A 282 1.61e+01 c.69.1.10 107907 1irxA 523 1.63e+01 a.97.1.2 71378 c.26.1.1 71379 3cngA 189 1.63e+01 2eifA 136 1.64e+01 1bkb b.34.5.2 24607 b.40.4.5 25339 1dlpA 236 1.69e+01 1b2pA b.78.1.1 28000 b.78.1.1 28001 1suuA 312 1.71e+01 b.68.10.1 99006 3d3oA 178 1.74e+01 2aqaA 63 1.78e+01 g.41.16.1 127168 1cj0A 470 1.80e+01 1bj4A c.67.1.4 34473 1rv3A 483 1.82e+01 c.67.1.4 105101 1rvuA 483 1.83e+01 c.67.1.4 105106 1ls3A 483 1.83e+01 c.67.1.4 78172 2h1aA 143 1.83e+01 3c73A 140 1.84e+01 2h1bA 143 1.88e+01 1st9A 143 1.90e+01 c.47.1.10 98987 3d37A 381 1.92e+01 b.106.1.1 157269 b.106.1.1 157270 2rdpA 150 1.92e+01 2f9sA 151 1.94e+01 c.47.1.10 133168 1o54A 277 1.94e+01 c.66.1.13 92482 3c71A 143 1.95e+01 2ysqA 81 1.98e+01 1vpkA 378 1.98e+01 d.131.1.1 113963 d.131.1.1 113964 d.131.1.1 113965 2d0sA 79 2.05e+01 1exrA 148 2.06e+01 1cll a.39.1.5 17299 1clmA 148 2.09e+01 a.39.1.5 17301 2wnwA 447 2.14e+01 2jdaA 145 2.16e+01 3dxvA 452 2.17e+01 1g65K 211 2.25e+01 d.153.1.4 41907 1g0uK 212 2.25e+01 d.153.1.4 41893 1rypL 212 2.28e+01 d.153.1.4 41880 3d4rA 169 2.33e+01 2cpcA 113 2.34e+01 3er0A 167 2.39e+01 2zkra 257 2.41e+01 1gc5A 467 2.44e+01 1gc5A c.72.1.3 60429 2iwaA 266 2.48e+01 1mhyD 521 2.49e+01 1mhyD a.25.1.2 16780 2z02A 242 2.61e+01 1jpcA 109 2.64e+01 b.78.1.1 27986 2h19A 143 2.69e+01 1zkdA 387 2.70e+01 c.66.1.52 125184 2h1gA 143 2.72e+01 1v04A 355 2.73e+01 b.68.6.2 100240 1ixkA 315 2.73e+01 c.66.1.38 90716 3fzyA 234 2.75e+01 2iwgB 181 2.80e+01 b.29.1.22 145548 3eh7A 434 2.81e+01 2v3xA 440 2.83e+01 c.55.2.1 152477 d.127.1.1 152478 1gv4A 528 2.86e+01 c.3.1.5 70589 c.3.1.5 70590 d.87.1.1 70591 2joiA 118 2.94e+01 1h6lA 353 2.96e+01 b.68.3.1 60687 1qlgA 355 2.96e+01 1qlgA b.68.3.1 27627 2pooA 355 3.15e+01 1qlgA b.68.3.1 27626 2vlgA 111 3.15e+01 1g652 196 3.16e+01 3ho3A 481 3.17e+01 3gd4A 511 3.19e+01 3gd3A 535 3.23e+01 1rypH 205 3.23e+01 d.153.1.4 41876 3jtjA 253 3.29e+01 2nn6A 358 3.50e+01 d.14.1.4 148295 d.101.1.1 148296 3gcfA 394 3.50e+01 2pgnA 589 3.52e+01 2v91A 302 3.59e+01 2gagC 210 3.63e+01 3kifA 106 3.64e+01 2fp8A 322 3.65e+01 2bwxA 441 3.66e+01 c.55.2.1 129391 d.127.1.1 129392 1m6iA 493 3.74e+01 c.3.1.5 74533 c.3.1.5 74534 d.87.1.1 74535 1dcuA 357 3.81e+01 1frpA e.7.1.1 42943 1iruE 241 3.83e+01 d.153.1.4 71356 1spiA 358 3.85e+01 1frpA e.7.1.1 42939 2qyhA 258 3.91e+01 2v4iA 173 3.93e+01 2vzkA 173 3.93e+01 1vm8A 534 3.93e+01 c.68.1.5 113670 3i70A 128 3.98e+01 2bwwA 440 3.98e+01 c.55.2.1 129389 d.127.1.1 129390 2wftA 458 3.98e+01 3llpA 493 3.98e+01 1dfcA 493 3.98e+01 1dfcA b.42.5.1 25616 b.42.5.1 25617 b.42.5.1 25618 b.42.5.1 25619 2wg4B 457 3.98e+01 2wg3C 463 3.99e+01