# 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 1jjfA 268 1.41e-20 c.69.1.2 66765 1jt2A 268 1.95e-19 1f0nA 285 3.13e-14 1dqyA c.69.1.3 34636 1dqyA 283 7.41e-13 1dqyA c.69.1.3 34640 1dqzA 280 8.36e-13 1dqyA c.69.1.3 34638 1c4xA 285 1.22e-05 1c4xA c.69.1.10 34684 1k4yA 534 2.20e-05 1c7iA 489 1.50e-04 1thg c.69.1.1 34632 1evqA 310 3.05e-04 1jkmA c.69.1.2 34635 1c7jA 489 3.49e-04 2bce c.69.1.1 34631 1qe3A 489 3.78e-04 2bce c.69.1.1 34630 1jfrA 262 4.89e-04 1jfrA c.69.1.16 34724 1gklA 297 6.42e-04 c.69.1.2 65250 1fj2A 232 1.03e-03 1auoA c.69.1.14 34720 1gkkA 297 1.07e-03 c.69.1.2 65248 1k8qA 377 1.79e-03 1hlgA 371 1.83e-03 1hlgA c.69.1.6 34656 4tgl 269 2.09e-03 3tgl c.69.1.17 34735 1tgl 269 2.09e-03 3tgl c.69.1.17 34734 5tgl 269 2.09e-03 3tgl c.69.1.17 34736 1jjiA 311 3.71e-03 c.69.1.2 66766 1auoA 218 3.97e-03 1auoA c.69.1.14 34716 1aurA 218 3.97e-03 1auoA c.69.1.14 34718 2bce 532 1.95e-02 2bce c.69.1.1 34625 3tgl 269 2.06e-02 3tgl c.69.1.17 34733 1ehyA 294 2.09e-02 1ehyA c.69.1.11 34693 1f6wA 533 2.55e-02 2bce c.69.1.1 34629 3lip 320 2.85e-02 1cvl c.69.1.18 34778 1aqlA 532 3.33e-02 2bce c.69.1.1 34627 1akn 579 3.37e-02 2bce c.69.1.1 34626 1jmyA 522 4.16e-02 c.69.1.1 63182 1hdeA 310 6.39e-02 1b6g c.69.1.8 34675 1a8q 274 6.40e-02 1brt c.69.1.12 34702 1jkmB 361 9.75e-02 1jkmA c.69.1.2 34634 1jkmA 358 9.75e-02 1jkmA c.69.1.2 34633 1qgeD 222 9.87e-02 1cvl c.69.1.18 34773 1cr6B 554 1.10e-01 1cr6B c.108.1.2 43338 c.69.1.11 34688 1ek1A 554 1.10e-01 1cr6B c.108.1.2 43335 c.69.1.11 34685 1cqzA 554 1.10e-01 1cr6B c.108.1.2 43339 c.69.1.11 34689 1cvl 319 1.37e-01 1cvl c.69.1.18 34786 1tahA 318 1.47e-01 1cvl c.69.1.18 34775 1tahB 318 1.47e-01 1cvl c.69.1.18 34774 1crl 534 2.00e-01 1thg c.69.1.17 34765 1lpp 549 2.01e-01 1thg c.69.1.17 34764 1ggvA 232 2.06e-01 1din c.69.1.9 34683 1lgyA 269 2.08e-01 3tgl c.69.1.17 34758 1gqsA 532 2.53e-01 1acl 537 2.54e-01 2bce c.69.1.1 34590 1eeaA 534 2.54e-01 2bce c.69.1.1 34609 1vxrA 537 2.54e-01 2bce c.69.1.1 34595 1qidA 537 2.54e-01 2bce c.69.1.1 34593 1ea5A 537 2.54e-01 2bce c.69.1.1 34592 1eve 543 2.55e-01 2bce c.69.1.1 34585 1amn 532 2.56e-01 2bce c.69.1.1 34587 1bez 310 2.94e-01 1b6g c.69.1.8 34666 1fokA 568 2.94e-01 2fokA a.4.5.12 16137 a.4.5.12 16138 a.4.5.12 16139 c.52.1.12 33325 1b6g 310 3.31e-01 1b6g c.69.1.8 34661 1be0 310 3.32e-01 1b6g c.69.1.8 34663 1ede 310 3.32e-01 1b6g c.69.1.8 34662 1cleA 534 3.38e-01 1thg c.69.1.17 34771 1ivyA 452 3.40e-01 1ivyA c.69.1.5 34654 1azwA 313 3.78e-01 1qtrA c.69.1.7 34658 1gpl 432 4.10e-01 1gpl b.12.1.2 23645 c.69.1.19 34793 1bvnP 496 4.78e-01 1smd b.71.1.1 27767 c.1.8.1 28754 1jeoA 180 6.36e-01 c.80.1.3 66611 1ysc 421 6.44e-01 1ivyA c.69.1.5 34652 1pig 496 6.88e-01 1smd b.71.1.1 27764 c.1.8.1 28751 1rp1 441 7.14e-01 1gpl b.12.1.2 23646 c.69.1.19 34794 1hplA 449 7.30e-01 1gpl b.12.1.2 23639 c.69.1.19 34787 1hx0A 496 7.37e-01 b.71.1.1 61346 c.1.8.1 61347 1ppi 496 7.37e-01 1smd b.71.1.1 27763 c.1.8.1 28750 1kgwA 496 7.41e-01 b.71.1.1 68600 c.1.8.1 68601 1jfh 496 7.42e-01 1smd b.71.1.1 27762 c.1.8.1 28749 1b2yA 496 7.43e-01 1smd b.71.1.1 27772 c.1.8.1 28759 1hny 496 7.43e-01 1smd b.71.1.1 27769 c.1.8.1 28756 3cpuA 496 7.47e-01 1smd b.71.1.1 63336 c.1.8.1 63337 1kxqA 496 7.54e-01 1e5tA 710 7.58e-01 1qfmA b.69.7.1 27676 c.69.1.4 34644 1kbbA 496 7.63e-01 1qfmA 710 7.84e-01 1qfmA b.69.7.1 27673 c.69.1.4 34641 1qfsA 710 7.99e-01 1qfmA b.69.7.1 27677 c.69.1.4 34645 1kguA 496 8.02e-01 b.71.1.1 68598 c.1.8.1 68599 1kgxA 496 8.46e-01 b.71.1.1 68602 c.1.8.1 68603 1lpbB 449 9.41e-01 1gpl b.12.1.2 23643 c.69.1.19 34791 1tnm 100 9.57e-01 1wit b.1.1.4 21710 1kb3A 496 9.91e-01 1cpy 421 1.05e+00 1ivyA c.69.1.5 34651 1ose 496 1.06e+00 1smd b.71.1.1 27766 c.1.8.1 28753 1dhkA 496 1.07e+00 1smd b.71.1.1 27761 c.1.8.1 28748 1jxkA 491 1.11e+00 b.71.1.1 63316 c.1.8.1 63317 1ethA 448 1.15e+00 1gpl b.12.1.2 23641 c.69.1.19 34789 1d7kA 421 1.17e+00 7odcA b.49.2.1 26486 c.1.6.1 28648 1jxjA 496 1.17e+00 b.71.1.1 63314 c.1.8.1 63315 1smd 496 1.18e+00 1smd b.71.1.1 27768 c.1.8.1 28755 2dfpA 534 1.40e+00 2bce c.69.1.1 34597 1tib 269 1.60e+00 3tgl c.69.1.17 34738 7odcA 424 1.95e+00 7odcA b.49.2.1 26488 c.1.6.1 28650 1bia 321 2.07e+00 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1bib 321 2.07e+00 1bia a.4.5.1 16084 b.34.1.1 24448 d.104.1.2 40788 1tia 279 2.35e+00 3tgl c.69.1.17 34737 1yasA 257 2.47e+00 1qj4A c.69.1.20 34801 1qj4A 257 2.47e+00 1qj4A c.69.1.20 34796 1a88A 275 2.62e+00 1brt c.69.1.12 34707 2fokA 579 2.64e+00 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1cqwA 295 2.87e+00 1b6g c.69.1.8 34679 1i6wA 181 3.17e+00 1i6wA c.69.1.18 61859 1jt9A 266 3.36e+00 c.35.1.1 67259 1fpqA 372 3.37e+00 1fpqA a.4.5.29 59947 c.66.1.12 59948 1fs5A 266 3.43e+00 c.35.1.1 65044 1fsfA 266 3.43e+00 c.35.1.1 65047 1deaA 266 3.43e+00 1deaA c.35.1.1 31760 1bn7A 294 3.59e+00 1bn6A c.69.1.8 34677 1bn6A 294 3.59e+00 1bn6A c.69.1.8 34678 1kbkA 496 3.82e+00 1qpaA 345 3.89e+00 1arv a.93.1.1 18585 1spbS 266 3.97e+00 1gci c.41.1.1 32532 1suaA 266 4.54e+00 1gci c.41.1.1 32531 1nct 106 4.75e+00 1wit b.1.1.4 21708 1gh6A 114 5.06e+00 a.2.3.1 65191 1k9sA 237 5.14e+00 c.56.2.1 68359 1ecpA 238 5.14e+00 1ecpA c.56.2.1 33775 1a8s 273 5.26e+00 1brt c.69.1.12 34710 2madH 373 5.49e+00 2bbkH b.69.2.1 27639 1whsA 255 5.56e+00 1ivyA c.69.1.5 34649 1whtA 256 5.58e+00 1ivyA c.69.1.5 34646 1bcsA 263 5.62e+00 1ivyA c.69.1.5 34647 1rtg 210 6.11e+00 1gen b.66.1.1 27537 1gen 218 6.31e+00 1gen b.66.1.1 27536 1ex9A 285 6.39e+00 1cvl c.69.1.18 34785 1akp 114 6.48e+00 2mcm b.1.7.1 22212 2occE 109 6.61e+00 2occE a.118.11.1 19224 1egaA 301 6.62e+00 1egaA c.37.1.8 32150 d.52.3.1 38836 1suc 266 7.19e+00 1gci c.41.1.1 32521 1f75A 249 7.23e+00 1f75A c.101.1.1 59662 1lk5A 229 7.52e+00 1e8nA 710 7.74e+00 1qfmA b.69.7.1 27675 c.69.1.4 34643 1dvoA 152 7.79e+00 1dvoA a.136.1.1 19623 2spcA 107 7.80e+00 2spcA a.7.1.1 16311 1jg1A 235 7.93e+00 c.66.1.7 66661 1fiqA 219 8.87e+00 1qj2A a.56.1.1 17912 d.15.4.2 37697 1thg 544 9.75e+00 1thg c.69.1.17 34763 5gcnA 166 9.85e+00 1yghA d.108.1.1 40807 1qsrA 162 1.00e+01 1yghA d.108.1.1 40805 1j4nA 271 1.01e+01 1qstA 160 1.01e+01 1yghA d.108.1.1 40804 1e3jA 352 1.06e+01 1e3jA b.35.1.2 24765 c.2.1.1 29781 1fjjA 159 1.08e+01 1fjjA b.17.1.2 59852 1duiA 266 1.13e+01 1gci c.41.1.1 32530 1scjA 275 1.14e+01 1gci c.41.1.1 32486 1kwhA 492 1.14e+01 c.94.1.1 68876 1fp1D 372 1.14e+01 1fpqA a.4.5.29 59939 c.66.1.12 59940 1imjA 210 1.22e+01 1fyvA 161 1.23e+01 1fyvA c.23.2.1 31127 1ehiA 377 1.24e+01 1iow c.30.1.2 31716 d.142.1.1 41484 3sc2A 259 1.30e+01 1ivyA c.69.1.5 34648 1meeA 275 1.32e+01 1gci c.41.1.1 32540 1qhaA 917 1.34e+01 1qhaA c.55.1.3 33467 c.55.1.3 33468 c.55.1.3 33469 c.55.1.3 33470 1hkcA 917 1.34e+01 1qhaA c.55.1.3 33475 c.55.1.3 33476 c.55.1.3 33477 c.55.1.3 33478 1hkbA 917 1.35e+01 1qhaA c.55.1.3 33479 c.55.1.3 33480 c.55.1.3 33481 c.55.1.3 33482 1sue 266 1.37e+01 1gci c.41.1.1 32520 1czaN 917 1.43e+01 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1dgkN 917 1.44e+01 1qhaA c.55.1.3 33487 c.55.1.3 33488 c.55.1.3 33489 c.55.1.3 33490 1czfA 362 1.50e+01 1czfA b.80.1.3 28031 1gm7B 557 1.51e+01 1qo7A 394 1.51e+01 1qo7A c.69.1.11 34697 1fxhB 557 1.53e+01 1ajqB 1ajqB 557 1.54e+01 1ajqB 1gk9B 557 1.56e+01 1pnkB 557 1.56e+01 1ajqB 1gnvA 266 1.57e+01 1e3aB 560 1.57e+01 1ajqB 1ffvB 803 1.64e+01 1qj2B d.41.1.1 38591 d.133.1.1 41421 1gnzA 257 1.64e+01 b.29.1.1 65405 1hqlA 257 1.65e+01 b.29.1.1 65907 1j4aA 333 1.66e+01 1smtB 122 1.73e+01 1smtA a.4.5.5 16110 1smtA 122 1.73e+01 1smtA a.4.5.5 16109 1qgwB 67 1.76e+01 1qgwA d.184.1.1 42617 1csh 435 1.76e+01 1csh a.103.1.1 18880 6cscA 437 1.78e+01 1csh a.103.1.1 18892 1djeA 384 1.79e+01 1bs0A c.67.1.4 34491 1f8uA 583 1.79e+01 2bce c.69.1.1 34620 1b41A 539 1.80e+01 2bce c.69.1.1 34621 1djuA 388 1.82e+01 1bjwA c.67.1.1 59116 1bs0A 384 1.86e+01 1bs0A c.67.1.4 34490 1gnsA 263 1.88e+01 2tmvP 158 1.93e+01 1rmvA a.24.5.1 16586 1ei7A 158 1.93e+01 1rmvA a.24.5.1 16584 1ei7B 158 1.93e+01 1rmvA a.24.5.1 16585 1bn8A 420 2.06e+01 1pcl b.80.1.1 28022 1ck7A 631 2.06e+01 1ck7A a.20.1.2 58969 b.66.1.1 27538 d.92.1.11 58970 g.14.1.2 44674 g.14.1.2 44675 g.14.1.2 44676 1jdlA 121 2.08e+01 a.3.1.1 66557 1j49A 333 2.10e+01 1ho8A 480 2.23e+01 1ho8A a.118.1.9 61107 1eaiC 61 2.24e+01 1eaiC g.22.1.1 44894 2bbvC 363 2.26e+01 2bbvA b.10.1.3 23325 2bbvA 363 2.26e+01 2bbvA b.10.1.3 23323 1gdeA 389 2.30e+01 c.67.1.1 60456 2bspA 420 2.33e+01 1pcl b.80.1.1 28023 1jroB 777 2.34e+01 d.41.1.1 67141 d.133.1.1 67142 1ac5 483 2.36e+01 1ac5 c.69.1.5 34653 1llqA 605 2.43e+01 1k9iD 156 2.55e+01 d.169.1.1 68346 1led 243 2.57e+01 1led b.29.1.1 24039 1do0A 442 2.59e+01 1do0A c.37.1.13 32432 1g4bE 443 2.60e+01 1do0A c.37.1.13 32446 1ht1E 449 2.61e+01 c.37.1.13 65928 2btfP 139 2.68e+01 1pne d.110.1.1 40867 1e54A 332 2.69e+01 1e54A f.4.3.1 59258 1pne 140 2.69e+01 1pne d.110.1.1 40866 1sud 275 2.76e+01 1gci c.41.1.1 32526 1gkdA 163 2.77e+01 1goa 156 2.97e+01 2rn2 c.55.3.1 33564 1gkcA 163 2.98e+01 1qibA 161 3.00e+01 1ck7A d.92.1.11 40359 1kezA 300 3.09e+01 c.69.1.22 68546 1b7gO 340 3.21e+01 1b7gO c.2.1.3 29992 d.81.1.1 39907 1qs2A 401 3.34e+01 1qs1A d.166.1.1 42268 d.166.1.1 42269 1e2aA 105 3.36e+01 1e2aA a.7.2.1 16322 1ba6 40 3.36e+01 1ba6 j.42.1.1 46315 1i17A 107 3.50e+01 1i17A d.6.1.1 61519 1bg3A 919 3.59e+01 1qhaA c.55.1.3 33491 c.55.1.3 33492 c.55.1.3 33493 c.55.1.3 33494 1qs1A 462 3.59e+01 1qs1A d.166.1.1 42260 d.166.1.1 42261 1itxA 419 3.59e+01 1d7oA 297 3.60e+01 1enp c.2.1.2 29907 1eno 312 3.70e+01 1enp c.2.1.2 29905 1enp 312 3.70e+01 1enp c.2.1.2 29906 2bifA 469 3.71e+01 1bif c.37.1.7 31963 c.60.1.4 34009 1bif 469 3.71e+01 1bif c.37.1.7 31961 c.60.1.4 34003 1soxA 466 3.72e+01 1soxA b.1.1.5 21947 d.120.1.1 41090 d.176.1.1 42563 3bifA 468 3.72e+01 1bif c.37.1.7 31962 c.60.1.4 34008 1sub 275 3.72e+01 1gci c.41.1.1 32513 1zeiA 53 3.74e+01 1zeiA g.1.1.1 43963 1dy6A 267 3.74e+01 1btl e.3.1.1 42732 1l7mA 211 3.76e+01 1tif 78 3.80e+01 1tif d.15.8.1 37836 1l7oA 211 3.82e+01 2sniE 275 3.88e+01 1gci c.41.1.1 32529 1jmuA 41 3.90e+01 e.35.1.1 66891 1cliA 345 3.91e+01 1cliA d.79.4.1 39816 d.139.1.1 41459 1by8A 314 3.93e+01 1cs8A d.3.1.1 37083 1f8iA 429 3.94e+01 1dquA c.1.12.6 29321 1f8mA 429 3.95e+01 1dquA c.1.12.6 29315 1f61A 429 3.95e+01 1dquA c.1.12.6 29319 1lit 144 3.98e+01 1qddA d.169.1.1 42325 1jj2I 145 4.00e+01 1ffkG c.21.1.1 63094 1ffkG 145 4.00e+01 1ffkG c.21.1.1 31035