# 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 1jjiA 311 4.13e-50 c.69.1.2 66766 1evqA 310 1.20e-49 1jkmA c.69.1.2 34635 1c2oA 539 2.42e-31 2bce c.69.1.1 34610 1c2bA 540 2.42e-31 2bce c.69.1.1 34614 1mahA 543 2.44e-31 2bce c.69.1.1 34619 1maaD 547 2.45e-31 2bce c.69.1.1 34618 1jkmA 358 1.47e-30 1jkmA c.69.1.2 34633 1jkmB 361 1.47e-30 1jkmA c.69.1.2 34634 1b41A 539 2.22e-30 2bce c.69.1.1 34621 1f8uA 583 3.03e-30 2bce c.69.1.1 34620 1gqsA 532 4.65e-29 1eeaA 534 4.67e-29 2bce c.69.1.1 34609 1vxrA 537 4.72e-29 2bce c.69.1.1 34595 1qidA 537 4.72e-29 2bce c.69.1.1 34593 1ea5A 537 4.72e-29 2bce c.69.1.1 34592 1acl 537 4.74e-29 2bce c.69.1.1 34590 1eve 543 4.82e-29 2bce c.69.1.1 34585 1amn 532 6.91e-29 2bce c.69.1.1 34587 2dfpA 534 1.64e-28 2bce c.69.1.1 34597 1k4yA 534 9.98e-28 1c7jA 489 5.76e-26 2bce c.69.1.1 34631 1qe3A 489 6.89e-26 2bce c.69.1.1 34630 1c7iA 489 7.31e-26 1thg c.69.1.1 34632 1dx4A 586 1.20e-22 2bce c.69.1.1 34622 2bce 532 3.95e-22 2bce c.69.1.1 34625 1jmyA 522 4.25e-22 c.69.1.1 63182 1f6wA 533 4.88e-22 2bce c.69.1.1 34629 1akn 579 6.48e-22 2bce c.69.1.1 34626 1aqlA 532 7.11e-22 2bce c.69.1.1 34627 1thg 544 2.14e-20 1thg c.69.1.17 34763 1cleA 534 6.82e-20 1thg c.69.1.17 34771 1crl 534 1.20e-19 1thg c.69.1.17 34765 1lpp 549 1.23e-19 1thg c.69.1.17 34764 1fj2A 232 9.49e-07 1auoA c.69.1.14 34720 1auoA 218 1.07e-06 1auoA c.69.1.14 34716 1aurA 218 1.07e-06 1auoA c.69.1.14 34718 1broA 277 8.34e-06 1brt c.69.1.12 34700 1brt 277 9.16e-06 1brt c.69.1.12 34699 1a8s 273 9.85e-06 1brt c.69.1.12 34710 1a8uA 277 1.09e-05 1brt c.69.1.12 34703 1jjfA 268 1.24e-05 c.69.1.2 66765 1lpbB 449 1.73e-05 1gpl b.12.1.2 23643 c.69.1.19 34791 1rp1 441 2.14e-05 1gpl b.12.1.2 23646 c.69.1.19 34794 1qtrA 317 2.67e-05 1qtrA c.69.1.7 34660 1e5tA 710 3.63e-05 1qfmA b.69.7.1 27676 c.69.1.4 34644 1a88A 275 4.55e-05 1brt c.69.1.12 34707 1qfmA 710 4.68e-05 1qfmA b.69.7.1 27673 c.69.1.4 34641 1gpl 432 6.18e-05 1gpl b.12.1.2 23645 c.69.1.19 34793 1qfsA 710 6.43e-05 1qfmA b.69.7.1 27677 c.69.1.4 34645 1bu8A 452 8.09e-05 1gpl b.12.1.2 23647 c.69.1.19 34795 1kezA 300 1.42e-04 c.69.1.22 68546 1jt2A 268 3.61e-04 1hplA 449 3.82e-04 1gpl b.12.1.2 23639 c.69.1.19 34787 1jfrA 262 6.28e-04 1jfrA c.69.1.16 34724 1ethA 448 7.60e-04 1gpl b.12.1.2 23641 c.69.1.19 34789 1a8q 274 1.05e-03 1brt c.69.1.12 34702 1e8nA 710 1.40e-03 1qfmA b.69.7.1 27675 c.69.1.4 34643 1ggvA 232 1.79e-03 1din c.69.1.9 34683 1azwA 313 8.37e-03 1qtrA c.69.1.7 34658 1c4xA 285 2.19e-02 1c4xA c.69.1.10 34684 1gkkA 297 3.79e-02 c.69.1.2 65248 1pyaB 228 5.39e-02 1pyaB 1ibvB 229 5.55e-02 1gklA 297 5.89e-02 c.69.1.2 65250 1tia 279 7.23e-02 3tgl c.69.1.17 34737 1yasA 257 1.41e-01 1qj4A c.69.1.20 34801 1qj4A 257 1.41e-01 1qj4A c.69.1.20 34796 1cr6B 554 1.65e-01 1cr6B c.108.1.2 43338 c.69.1.11 34688 1ek1A 554 1.65e-01 1cr6B c.108.1.2 43335 c.69.1.11 34685 1cqzA 554 1.65e-01 1cr6B c.108.1.2 43339 c.69.1.11 34689 1tib 269 2.05e-01 3tgl c.69.1.17 34738 1din 234 3.35e-01 1din c.69.1.9 34682 3sc2A 259 3.81e-01 1ivyA c.69.1.5 34648 1dxlA 470 7.57e-01 1lvl c.3.1.5 30585 c.3.1.5 30586 d.87.1.1 40214 1lgyA 269 8.62e-01 3tgl c.69.1.17 34758 1ysc 421 9.41e-01 1ivyA c.69.1.5 34652 1bcsA 263 9.73e-01 1ivyA c.69.1.5 34647 5tgl 269 9.90e-01 3tgl c.69.1.17 34736 4tgl 269 9.91e-01 3tgl c.69.1.17 34735 1tgl 269 9.91e-01 3tgl c.69.1.17 34734 1whtA 256 1.07e+00 1ivyA c.69.1.5 34646 1whsA 255 1.09e+00 1ivyA c.69.1.5 34649 3tgl 269 1.27e+00 3tgl c.69.1.17 34733 1ctf 74 1.90e+00 1ctf d.45.1.1 38759 1cpy 421 2.09e+00 1ivyA c.69.1.5 34651 1g66A 207 2.18e+00 1bs9 c.23.9.1 31329 1bs9 207 2.18e+00 1bs9 c.23.9.1 31330 1ekjB 221 2.45e+00 1ekjB c.53.2.1 33365 1ekjA 221 2.45e+00 1ekjB c.53.2.1 33364 1hpgA 187 2.47e+00 1qq4A b.47.1.1 25813 1hdeA 310 2.53e+00 1b6g c.69.1.8 34675 1ede 310 2.71e+00 1b6g c.69.1.8 34662 1be0 310 2.76e+00 1b6g c.69.1.8 34663 2axe 207 2.81e+00 1bs9 c.23.9.1 31331 1b6g 310 2.86e+00 1b6g c.69.1.8 34661 2pia 321 3.05e+00 2pia b.43.4.2 25663 c.25.1.2 31553 d.15.4.2 37704 1hezE 61 3.23e+00 2ptl d.15.7.1 60991 1ojt 482 3.89e+00 1lvl c.3.1.5 30581 c.3.1.5 30582 d.87.1.1 40212 1fsz 372 4.07e+00 1fsz c.32.1.1 31750 d.79.2.1 39802 1jwhA 337 4.15e+00 1bhy 482 4.15e+00 1lvl c.3.1.5 30583 c.3.1.5 30584 d.87.1.1 40213 1ju3A 583 4.19e+00 b.18.1.13 67300 c.69.1.21 67301 1imjA 210 4.33e+00 1xgsA 295 4.39e+00 1bn5 a.4.5.25 16216 d.127.1.1 41153 1bez 310 4.75e+00 1b6g c.69.1.8 34666 1b35A 260 4.82e+00 1b35A b.10.1.3 23333 1qr0A 228 4.96e+00 1qr0A d.150.1.1 59038 d.150.1.1 59039 1gaxA 862 5.05e+00 1gaxA a.27.1.1 16928 b.51.1.1 26893 c.26.1.1 31595 1iayA 428 5.17e+00 1b8gA c.67.1.4 62130 1lnqA 336 5.21e+00 1brwA 433 5.88e+00 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1an9A 340 7.62e+00 1an9A c.4.1.2 30617 d.16.1.3 37904 1dquA 538 7.74e+00 1dquA c.1.12.6 29314 1bzlA 486 8.44e+00 3grs c.3.1.5 30521 c.3.1.5 30522 d.87.1.1 40192 1aogA 485 8.55e+00 3grs c.3.1.5 30517 c.3.1.5 30518 d.87.1.1 40190 1hnhA 317 8.93e+00 1hn9A c.95.1.1 35983 c.95.1.1 35984 1f8gA 384 9.03e+00 1sayA c.2.1.4 59695 c.23.12.2 59696 2recA 353 9.33e+00 2reb i.2.1.1 45879 1hvd 319 9.35e+00 1avc a.65.1.1 18154 2reb 352 9.37e+00 2reb c.37.1.11 32282 d.48.1.1 38767 1aa8A 347 9.46e+00 1an9A c.4.1.2 30619 d.16.1.3 37906 1eblA 317 9.77e+00 1hn9A c.95.1.1 35973 c.95.1.1 35974 1eblB 317 9.77e+00 1hn9A c.95.1.1 35975 c.95.1.1 35976 1qlwB 328 9.89e+00 1qlwA c.69.1.15 34723 1hvf 319 9.91e+00 1avc a.65.1.1 18155 1qlwA 328 9.92e+00 1qlwA c.69.1.15 34722 1iirA 415 1.00e+01 1iirA c.87.1.5 62453 1cwxA 44 1.02e+01 1cwxA j.54.1.1 46338 1ndaA 491 1.04e+01 3grs c.3.1.5 30525 c.3.1.5 30526 d.87.1.1 40194 1gs8A 336 1.04e+01 b.6.1.3 65533 b.6.1.3 65534 1gc3A 385 1.08e+01 c.67.1.1 60417 1gckA 385 1.09e+01 c.67.1.1 65177 1hnjA 317 1.09e+01 1hn9A c.95.1.1 35969 c.95.1.1 35970 1hn9A 317 1.09e+01 1hn9A c.95.1.1 35977 c.95.1.1 35978 1bkgA 385 1.12e+01 1bjwA c.67.1.1 34351 1jmkC 230 1.18e+01 1ijaA 148 1.27e+01 1ijaA b.100.1.1 62484 1f4tA 368 1.27e+01 1f4tA a.104.1.1 18973 1io7A 368 1.27e+01 1f4tA a.104.1.1 18971 1ibxB 145 1.30e+01 1c9fA d.15.2.1 62232 1iduA 609 1.37e+01 1vns a.111.1.3 62303 1io8A 368 1.46e+01 1f4tA a.104.1.1 62618 1vnf 609 1.47e+01 1vns a.111.1.3 19067 1vng 609 1.47e+01 1vns a.111.1.3 19066 1vns 609 1.47e+01 1vns a.111.1.3 19061 1vnc 609 1.47e+01 1vns a.111.1.3 19065 1vnh 609 1.48e+01 1vns a.111.1.3 19062 1ij7A 241 1.50e+01 3lip 320 1.55e+01 1cvl c.69.1.18 34778 1vne 609 1.56e+01 1vns a.111.1.3 19063 1qgeD 222 1.59e+01 1cvl c.69.1.18 34773 1tytA 487 1.65e+01 3grs c.3.1.5 30513 c.3.1.5 30514 d.87.1.1 40188 1typA 487 1.66e+01 3grs c.3.1.5 30509 c.3.1.5 30510 d.87.1.1 40186 1tytB 486 1.67e+01 3grs c.3.1.5 30515 c.3.1.5 30516 d.87.1.1 40189 1uch 230 1.75e+01 1uch d.3.1.6 37129 1cp2A 269 1.86e+01 1cp2A c.37.1.10 32269 1fecA 490 1.86e+01 3grs c.3.1.5 30489 c.3.1.5 30490 d.87.1.1 40176 1sav 320 1.88e+01 1avc a.65.1.1 18158 1ceqA 316 1.89e+01 1ceqA c.2.1.5 30163 d.162.1.1 42130 1koa 491 1.90e+01 1tkiA b.1.1.4 21712 d.144.1.1 41642 1g23A 293 1.91e+01 1g0rA c.68.1.6 34568 1fnsA 196 1.92e+01 1auq c.62.1.1 34136 2tprA 490 1.92e+01 3grs c.3.1.5 30505 c.3.1.5 30506 d.87.1.1 40184 1axdA 209 1.92e+01 1gnwA a.45.1.1 17730 c.47.1.5 33024 1bd3A 243 1.93e+01 1bd3A c.61.1.1 34098 1d5aA 733 1.94e+01 1tgoA c.55.3.5 33723 e.8.1.1 43012 1g0u1 266 1.95e+01 1byeA 213 1.98e+01 1gnwA a.45.1.1 17732 c.47.1.5 33026 1hauA 336 1.99e+01 1nif b.6.1.3 60879 b.6.1.3 60880 1ldg 316 2.00e+01 1ceqA c.2.1.5 30165 d.162.1.1 42132 1iruM 213 2.03e+01 2trcP 217 2.09e+01 1b9yC c.47.1.6 33051 1bq5 342 2.15e+01 1nif b.6.1.3 23110 b.6.1.3 23111 1h6vE 499 2.15e+01 c.3.1.5 60705 c.3.1.5 60706 d.87.1.1 60707 1gsjA 258 2.21e+01 1fs0G 230 2.22e+01 1fs0G c.49.2.1 59999 1dmuA 299 2.22e+01 1dmuA c.52.1.4 33294 1ithA 141 2.23e+01 1ithA a.1.1.2 15623 1citA 89 2.25e+01 2nllB g.39.1.2 45116 1gs7A 336 2.34e+01 b.6.1.3 65531 b.6.1.3 65532 1bg2 325 2.42e+01 1bg2 c.37.1.9 32189 1jhcA 137 2.45e+01 b.87.1.1 63054 1avhA 320 2.51e+01 1avc a.65.1.1 18159 1gpmA 525 2.51e+01 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 1cvl 319 2.52e+01 1cvl c.69.1.18 34786 1tahA 318 2.52e+01 1cvl c.69.1.18 34775 1tahB 318 2.52e+01 1cvl c.69.1.18 34774 1k52B 72 2.53e+01 d.15.7.1 68149 1anxA 319 2.64e+01 1avc a.65.1.1 18161 1hvg 319 2.74e+01 1avc a.65.1.1 18166 1avaC 181 2.75e+01 1avaC b.42.4.1 25604 1h6zA 913 2.81e+01 1eulA 994 2.84e+01 1eulA f.2.1.10 43726 1ryp2 233 2.87e+01 1ryp2 1jmlA 72 2.89e+01 d.15.7.1 66887 1gr8A 412 2.93e+01 1hzzB 384 2.93e+01 c.2.1.4 61472 c.23.12.2 61473 1bik 147 2.97e+01 1bpi g.8.1.1 44549 g.8.1.1 44550 1gs6X 336 2.98e+01 b.6.1.3 65529 b.6.1.3 65530 1gs5A 258 2.99e+01 1jlkA 147 3.03e+01 1i3cA 149 3.05e+01 1inlA 296 3.07e+01 c.66.1.17 66220 1bjwA 382 3.13e+01 1bjwA c.67.1.1 34349 1fxoA 293 3.16e+01 1g0rA c.68.1.6 34524 1g0rA 293 3.16e+01 1g0rA c.68.1.6 34532 1krcC 567 3.28e+01 1ubpC b.92.1.1 28419 c.1.9.2 29041 1dd3A 128 3.38e+01 1dd3C a.108.1.1 19031 d.45.1.1 38760 1a9xB 379 3.54e+01 1c3oB c.8.3.1 30732 c.23.16.1 31409 1ez4B 318 3.55e+01 c.2.1.5 64919 d.162.1.1 64920 1ho1A 242 3.70e+01 1ho1A c.1.24.1 61097 2sfa 191 3.74e+01 1qq4A b.47.1.1 25815 1llqA 605 3.87e+01 1reqA 727 3.87e+01 1reqA c.1.19.1 29620 c.23.6.1 31247 1e1cA 727 3.88e+01 1reqA c.1.19.1 29636 c.23.6.1 31263 1jdbF 382 3.97e+01 c.8.3.1 30757 c.23.16.1 31434 1chd 203 3.98e+01 1chd c.40.1.1 32478