# 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.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 1a88A 275 6.04e-19 1brt c.69.1.12 34707 1a8s 273 1.59e-18 1brt c.69.1.12 34710 1a8q 274 1.45e-14 1brt c.69.1.12 34702 1broA 277 5.03e-14 1brt c.69.1.12 34700 1a8uA 277 6.74e-14 1brt c.69.1.12 34703 1brt 277 1.14e-13 1brt c.69.1.12 34699 1qfmA 710 1.47e-13 1qfmA b.69.7.1 27673 c.69.1.4 34641 1qfsA 710 2.18e-13 1qfmA b.69.7.1 27677 c.69.1.4 34645 1e5tA 710 2.24e-13 1qfmA b.69.7.1 27676 c.69.1.4 34644 1e8nA 710 6.58e-13 1qfmA b.69.7.1 27675 c.69.1.4 34643 1c4xA 285 7.98e-13 1c4xA c.69.1.10 34684 1jfrA 262 6.72e-12 1jfrA c.69.1.16 34724 1auoA 218 9.77e-12 1auoA c.69.1.14 34716 1aurA 218 9.77e-12 1auoA c.69.1.14 34718 1evqA 310 1.77e-11 1jkmA c.69.1.2 34635 1jjiA 311 1.06e-10 c.69.1.2 66766 1cr6B 554 2.86e-10 1cr6B c.108.1.2 43338 c.69.1.11 34688 1ek1A 554 2.86e-10 1cr6B c.108.1.2 43335 c.69.1.11 34685 1cqzA 554 2.86e-10 1cr6B c.108.1.2 43339 c.69.1.11 34689 1ehyA 294 3.00e-10 1ehyA c.69.1.11 34693 1ggvA 232 7.40e-10 1din c.69.1.9 34683 1azwA 313 5.16e-09 1qtrA c.69.1.7 34658 1din 234 6.79e-09 1din c.69.1.9 34682 1jkmA 358 8.42e-09 1jkmA c.69.1.2 34633 1jkmB 361 8.48e-09 1jkmA c.69.1.2 34634 1qtrA 317 9.00e-09 1qtrA c.69.1.7 34660 1ju3A 583 2.20e-08 b.18.1.13 67300 c.69.1.21 67301 1fj2A 232 8.45e-08 1auoA c.69.1.14 34720 1c7iA 489 1.35e-07 1thg c.69.1.1 34632 1qe3A 489 2.68e-07 2bce c.69.1.1 34630 1c7jA 489 2.90e-07 2bce c.69.1.1 34631 1imjA 210 3.27e-07 1k8qA 377 4.17e-07 1hlgA 371 6.44e-07 1hlgA c.69.1.6 34656 1k4yA 534 9.32e-07 1be0 310 1.12e-06 1b6g c.69.1.8 34663 1ede 310 1.12e-06 1b6g c.69.1.8 34662 1hdeA 310 1.21e-06 1b6g c.69.1.8 34675 1b6g 310 1.36e-06 1b6g c.69.1.8 34661 1bn7A 294 1.49e-06 1bn6A c.69.1.8 34677 1bn6A 294 1.49e-06 1bn6A c.69.1.8 34678 1bez 310 1.57e-06 1b6g c.69.1.8 34666 1cqwA 295 1.59e-06 1b6g c.69.1.8 34679 1ivyA 452 3.07e-06 1ivyA c.69.1.5 34654 1b41A 539 5.82e-06 2bce c.69.1.1 34621 1jjfA 268 6.19e-06 c.69.1.2 66765 3lip 320 7.54e-06 1cvl c.69.1.18 34778 1gqsA 532 9.16e-06 1eeaA 534 9.16e-06 2bce c.69.1.1 34609 1amn 532 9.18e-06 2bce c.69.1.1 34587 1acl 537 9.27e-06 2bce c.69.1.1 34590 1vxrA 537 9.28e-06 2bce c.69.1.1 34595 1qidA 537 9.28e-06 2bce c.69.1.1 34593 1ea5A 537 9.28e-06 2bce c.69.1.1 34592 1eve 543 9.37e-06 2bce c.69.1.1 34585 1f8uA 583 9.79e-06 2bce c.69.1.1 34620 1thtA 305 1.02e-05 1thtA c.69.1.13 34711 1qgeD 222 2.05e-05 1cvl c.69.1.18 34773 2dfpA 534 3.04e-05 2bce c.69.1.1 34597 2bce 532 3.34e-05 2bce c.69.1.1 34625 1c2oA 539 3.77e-05 2bce c.69.1.1 34610 1c2bA 540 3.77e-05 2bce c.69.1.1 34614 1maaD 547 3.77e-05 2bce c.69.1.1 34618 1mahA 543 3.77e-05 2bce c.69.1.1 34619 1cvl 319 3.95e-05 1cvl c.69.1.18 34786 1tahA 318 3.96e-05 1cvl c.69.1.18 34775 1tahB 318 3.96e-05 1cvl c.69.1.18 34774 1jt2A 268 4.46e-05 1aqlA 532 7.67e-05 2bce c.69.1.1 34627 1akn 579 7.85e-05 2bce c.69.1.1 34626 1f6wA 533 1.68e-04 2bce c.69.1.1 34629 1jmyA 522 2.33e-04 c.69.1.1 63182 1bu8A 452 2.95e-04 1gpl b.12.1.2 23647 c.69.1.19 34795 1ysc 421 3.85e-04 1ivyA c.69.1.5 34652 1cpy 421 4.61e-04 1ivyA c.69.1.5 34651 1gpl 432 1.05e-03 1gpl b.12.1.2 23645 c.69.1.19 34793 1thg 544 1.08e-03 1thg c.69.1.17 34763 1lpbB 449 1.84e-03 1gpl b.12.1.2 23643 c.69.1.19 34791 1cv2A 296 2.31e-03 1bn6A c.69.1.8 34680 1g42A 296 2.31e-03 c.69.1.8 65139 1yasA 257 2.42e-03 1qj4A c.69.1.20 34801 1qj4A 257 2.42e-03 1qj4A c.69.1.20 34796 1dqyA 283 5.15e-03 1dqyA c.69.1.3 34640 1dqzA 280 5.69e-03 1dqyA c.69.1.3 34638 1tib 269 6.44e-03 3tgl c.69.1.17 34738 1qlwA 328 1.41e-02 1qlwA c.69.1.15 34722 1qlwB 328 1.46e-02 1qlwA c.69.1.15 34723 1dx4A 586 1.49e-02 2bce c.69.1.1 34622 1ex9A 285 1.82e-02 1cvl c.69.1.18 34785 1ethA 448 2.04e-02 1gpl b.12.1.2 23641 c.69.1.19 34789 1rp1 441 2.20e-02 1gpl b.12.1.2 23646 c.69.1.19 34794 1i6wA 181 2.66e-02 1i6wA c.69.1.18 61859 5tgl 269 3.20e-02 3tgl c.69.1.17 34736 4tgl 269 3.21e-02 3tgl c.69.1.17 34735 1tgl 269 3.21e-02 3tgl c.69.1.17 34734 3tgl 269 4.40e-02 3tgl c.69.1.17 34733 1cleA 534 5.27e-02 1thg c.69.1.17 34771 1ac5 483 7.12e-02 1ac5 c.69.1.5 34653 1bcsA 263 8.27e-02 1ivyA c.69.1.5 34647 1whtA 256 9.57e-02 1ivyA c.69.1.5 34646 1whsA 255 9.59e-02 1ivyA c.69.1.5 34649 1hplA 449 1.19e-01 1gpl b.12.1.2 23639 c.69.1.19 34787 1kezA 300 1.23e-01 c.69.1.22 68546 3sc2A 259 1.34e-01 1ivyA c.69.1.5 34648 1tca 317 1.49e-01 1tca c.69.1.17 34726 1dwqA 262 2.00e-01 1qj4A c.69.1.20 34808 1tia 279 2.21e-01 3tgl c.69.1.17 34737 1dxlA 470 3.19e-01 1lvl c.3.1.5 30585 c.3.1.5 30586 d.87.1.1 40214 1gklA 297 3.66e-01 c.69.1.2 65250 1crl 534 3.82e-01 1thg c.69.1.17 34765 1dwpA 262 3.90e-01 1qj4A c.69.1.20 34806 1lpp 549 3.96e-01 1thg c.69.1.17 34764 1qo7A 394 4.16e-01 1qo7A c.69.1.11 34697 2axe 207 4.37e-01 1bs9 c.23.9.1 31331 1f0nA 285 4.63e-01 1dqyA c.69.1.3 34636 1g66A 207 5.69e-01 1bs9 c.23.9.1 31329 1bs9 207 5.69e-01 1bs9 c.23.9.1 31330 1lgyA 269 5.72e-01 3tgl c.69.1.17 34758 1eb9A 262 6.44e-01 c.69.1.20 64898 1gkkA 297 6.98e-01 c.69.1.2 65248 1ddzA 496 1.24e+00 1ddzA c.53.2.1 33372 c.53.2.1 33373 1f0kA 364 1.39e+00 1f0kA c.87.1.2 35465 1j9eA 147 1.40e+00 c.23.5.1 62756 1eiwA 111 1.79e+00 1eiwA c.23.3.1 31130 1aku 147 2.23e+00 5nul c.23.5.1 31161 1c7fA 147 2.66e+00 5nul c.23.5.1 31163 1bu5A 147 2.82e+00 5nul c.23.5.1 31155 1e89A 262 2.91e+00 1qj4A c.69.1.20 59375 1gpdG 334 3.05e+00 1dssG c.2.1.3 30020 d.81.1.1 39935 1i1oA 147 3.22e+00 5nul c.23.5.1 61542 2fx2 147 3.25e+00 1rcf c.23.5.1 31158 4gpd1 333 3.35e+00 1dssG 1f4pA 147 3.48e+00 5nul c.23.5.1 59651 1j9gA 147 3.52e+00 c.23.5.1 62757 1akt 147 3.55e+00 5nul c.23.5.1 31157 1fx1 148 3.56e+00 1rcf c.23.5.1 31169 1bccE 196 4.90e+00 1rie b.33.1.1 24431 f.2.1.8 43699 1db3A 372 5.16e+00 1db3A c.2.1.2 29813 1akr 147 5.28e+00 1rcf c.23.5.1 31152 1tpt 440 5.36e+00 1brwA a.46.2.1 17763 c.27.1.1 31627 d.41.3.1 38625 1azl 147 6.00e+00 5nul c.23.5.1 31154 1bgyE 196 6.26e+00 1bgyE f.2.1.8 43683 1dbp 271 6.27e+00 2dri c.93.1.1 35639 1rie 129 6.53e+00 1rie b.33.1.1 24427 2dri 271 6.84e+00 2dri c.93.1.1 35637 1fcdA 401 6.98e+00 1fcdA c.3.1.5 30593 c.3.1.5 30594 d.87.1.1 40218 1jmkC 230 6.99e+00 1ba2A 271 7.08e+00 2dri c.93.1.1 35640 1akw 147 7.23e+00 5nul c.23.5.1 31153 1ei9A 279 7.27e+00 1ei9A c.69.1.13 34713 1mdaH 368 8.24e+00 2bbkH b.69.2.1 27637 1b0mA 753 8.52e+00 1amj c.8.2.1 30722 c.83.1.1 35398 8acn 754 8.68e+00 1amj c.8.2.1 30724 c.83.1.1 35400 1amj 754 8.69e+00 1amj c.8.2.1 30725 c.83.1.1 35401 6acn 754 8.73e+00 1amj c.8.2.1 30721 c.83.1.1 35397 1nis 754 9.10e+00 1amj c.8.2.1 30730 c.83.1.1 35406 1c97A 753 9.10e+00 1amj c.8.2.1 30731 c.83.1.1 35407 1b0jA 754 9.11e+00 1amj c.8.2.1 30719 c.83.1.1 35395 1c96A 753 9.12e+00 1amj c.8.2.1 30727 c.83.1.1 35403 1ix6A 396 9.17e+00 1qitA 396 9.21e+00 1ajsA c.67.1.1 34286 1yoo 396 9.22e+00 1ajsA c.67.1.1 34295 1ahxA 396 9.56e+00 1ajsA c.67.1.1 34293 1i7fA 292 9.98e+00 1i7fA d.193.1.1 61888 1aam 396 1.00e+01 1ajsA c.67.1.1 34347 1ars 396 1.01e+01 1ajsA c.67.1.1 34287 1art 398 1.01e+01 1ajsA c.67.1.1 34285 1arhA 396 1.03e+01 1ajsA c.67.1.1 34321 1qisA 396 1.04e+01 1ajsA c.67.1.1 34284 1mdc 133 1.10e+01 1hmt b.60.1.2 27198 1fts 295 1.10e+01 1ng1 a.24.13.1 16968 c.37.1.10 32279 1brwA 433 1.11e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1cgo 127 1.12e+01 1cpq a.24.3.2 16550 1ariA 396 1.12e+01 1ajsA c.67.1.1 34331 3aat 396 1.13e+01 1ajsA c.67.1.1 34346 1czeA 396 1.14e+01 1ajsA c.67.1.1 34301 2aat 396 1.15e+01 1ajsA c.67.1.1 34348 1qirA 396 1.17e+01 1ajsA c.67.1.1 34290 1e85A 127 1.23e+01 1bbhA a.24.3.2 16549 1aiaA 396 1.27e+01 1ajsA c.67.1.1 34306 1chd 203 1.28e+01 1chd c.40.1.1 32478 1hey 128 1.31e+01 3chy c.23.1.1 31061 1fvzA 271 1.40e+01 1fvzA d.129.3.4 60050 1bqaA 396 1.41e+01 1ajsA c.67.1.1 34298 1cqxA 403 1.43e+01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1cpb 306 1.43e+01 1aye c.56.5.1 33826 1spa 396 1.44e+01 1ajsA c.67.1.1 34291 1asf 396 1.45e+01 1ajsA c.67.1.1 34345 1qnrA 344 1.47e+01 1qnoA c.1.8.3 28834 1qnoA 344 1.47e+01 1qnoA c.1.8.3 28838 1kcmA 270 1.47e+01 1e42A 258 1.48e+01 1e42A b.1.10.1 22316 d.105.1.1 40792 1ivhA 394 1.54e+01 3mdeA a.29.3.1 16608 e.6.1.1 42869 1a2oA 349 1.57e+01 1chd c.23.1.1 31120 c.40.1.1 32479 1bqdA 396 1.63e+01 1ajsA c.67.1.1 34296 1bfvH 119 1.71e+01 1igtB b.1.1.1 20163 1eo1A 124 1.78e+01 1eo1A c.55.5.1 33739 1nsa 395 1.81e+01 1aye c.56.5.1 33825 d.58.3.1 39066 1sssA 205 1.84e+01 1avmA a.2.11.1 15738 d.44.1.1 38735 1iayA 428 1.88e+01 1b8gA c.67.1.4 62130 1fotA 318 1.88e+01 1cdkA d.144.1.1 59938 1crwG 333 1.89e+01 1dssG c.2.1.3 30026 d.81.1.1 39941 1ix8A 396 1.90e+01 1avaA 403 1.91e+01 1jdc b.71.1.1 27797 c.1.8.1 28784 1cwxA 44 2.07e+01 1cwxA j.54.1.1 46338 1g4xA 396 2.07e+01 1ajsA c.67.1.1 34313 1hw7A 255 2.07e+01 1i7fA d.193.1.1 61297 1dssG 333 2.08e+01 1dssG c.2.1.3 30022 d.81.1.1 39937 1f80D 81 2.08e+01 1acp a.28.1.1 59686 1g7xA 396 2.12e+01 1ajsA c.67.1.1 34304 1g7wA 396 2.15e+01 1ajsA c.67.1.1 34308 1qdlA 422 2.30e+01 1qdlA d.161.1.1 42088 1crzA 403 2.37e+01 1crzA b.68.4.1 27629 c.51.2.1 33211 1drk 271 2.44e+01 2dri c.93.1.1 35638 1l7vA 326 2.45e+01 1jchA 551 2.50e+01 b.101.1.1 66491 b.110.1.1 66492 h.4.9.1 66493 1hy8A 76 2.62e+01 a.28.1.1 65959 1c3uA 431 2.76e+01 1c3cA a.127.1.1 19427 1fh0A 221 2.77e+01 1cs8A d.3.1.1 59832 2yhx 457 2.81e+01 2yhx i.12.1.1 46024 4upjA 99 2.86e+01 1fmb b.50.1.1 26719 1i6pA 220 2.87e+01 1ddzA c.53.2.1 61848 1rhgA 174 2.95e+01 1bgc a.26.1.1 16812 1c3cA 429 2.97e+01 1c3cA a.127.1.1 19425 1cd9C 175 2.98e+01 1bgc a.26.1.1 16816 5eaaA 396 2.99e+01 1ajsA c.67.1.1 34328 1g4vA 396 3.07e+01 1ajsA c.67.1.1 34289 1ksgA 186 3.09e+01 1bxrA 1073 3.09e+01 a.92.1.1 18570 c.24.1.1 31499 c.30.1.1 31697 c.30.1.1 31698 d.142.1.2 41542 d.142.1.2 41543 1cs0C 1073 3.09e+01 a.92.1.1 18559 c.24.1.1 31488 c.30.1.1 31675 c.30.1.1 31676 d.142.1.2 41520 d.142.1.2 41521 1c3oA 1073 3.09e+01 1c3oA a.92.1.1 18562 c.24.1.1 31491 c.30.1.1 31681 c.30.1.1 31682 d.142.1.2 41526 d.142.1.2 41527 1c3oC 1073 3.09e+01 a.92.1.1 18563 c.24.1.1 31492 c.30.1.1 31683 c.30.1.1 31684 d.142.1.2 41528 d.142.1.2 41529 1c3oE 1073 3.09e+01 a.92.1.1 18564 c.24.1.1 31493 c.30.1.1 31685 c.30.1.1 31686 d.142.1.2 41530 d.142.1.2 41531 1c3oG 1073 3.09e+01 a.92.1.1 18565 c.24.1.1 31494 c.30.1.1 31687 c.30.1.1 31688 d.142.1.2 41532 d.142.1.2 41533 1jdbB 1073 3.09e+01 a.92.1.1 18574 c.24.1.1 31503 c.30.1.1 31705 c.30.1.1 31706 d.142.1.2 41550 d.142.1.2 41551 1ag9A 175 3.14e+01 1rcf c.23.5.1 31178 1ffkV 143 3.14e+01 1ffkV c.9.2.1 30849 1kwmA 402 3.17e+01 2masA 314 3.17e+01 2masA c.70.1.1 34810 1jyhA 157 3.18e+01 1ulb 289 3.19e+01 1b8oA c.56.2.1 33760 2ay8A 394 3.23e+01 1ajsA c.67.1.1 34359 1jj2S 119 3.51e+01 1ffkQ b.34.5.1 63104 1ffkQ 119 3.51e+01 1ffkQ b.34.5.1 24605 1kshA 186 3.54e+01 1idaA 99 3.62e+01 1fmb b.50.1.1 26715 1ksjA 186 3.65e+01 1xzi 214 3.67e+01 1cex c.23.9.1 31297 1jtb 91 3.84e+01 1rzl a.52.1.1 17813 1i6oB 220 3.97e+01 1ddzA c.53.2.1 61847