# List of top-scoring protein chains for t2k-100-30-str2-scores 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 1rybA 212 1.55e-01 c.56.3.1 -7858 1uc2A 481 2.69e-01 unknown_sccs -11725 1h3gA 601 3.29e-01 b.1.18.2 -2725 b.71.1.1 -4653 c.1.8.1 -5277 1uypA 432 1.57e+00 unknown_sccs -3480 unknown_sccs -4554 1utwA 432 1.57e+00 1rypE 242 2.08e+00 1rypE d.153.1.4 41936 1jhnA 424 2.83e+00 b.29.1.12 70060 b.104.1.1 66722 1s48A 609 3.31e+00 e.8.1.4 -11955 1vybA 238 3.62e+00 1bn7A 294 4.31e+00 1bn6A c.69.1.8 34677 1cqwA 295 4.33e+00 1b6g c.69.1.8 34679 1j0hA 588 4.53e+00 b.1.18.2 77027 b.71.1.1 77028 c.1.8.1 77029 1bn6A 294 4.64e+00 1bn6A c.69.1.8 34678 1m5zA 91 6.17e+00 b.36.1.1 78676 1j1bA 420 6.73e+00 d.144.1.7 -11312 1ji2A 585 6.79e+00 b.1.18.2 71672 b.71.1.1 71673 c.1.8.1 71674 1bvzA 585 6.93e+00 1bvzA b.1.18.2 21856 b.71.1.1 27783 c.1.8.1 28770 1pzdA 322 7.41e+00 unknown_sccs -2848 unknown_sccs -10778 1hn2A 159 7.71e+00 b.60.1.1 65890 1gt1A 159 7.71e+00 b.60.1.1 -4436 1obpA 159 8.00e+00 1obpA b.60.1.1 27092 1m6kA 251 8.03e+00 e.3.1.1 78695 1cof 143 8.29e+00 1cof d.109.1.2 40860 1cfyA 143 8.45e+00 1cof d.109.1.2 40858 1ii6A 368 8.71e+00 1bg2 c.37.1.9 62413 1r7aA 504 9.01e+00 b.71.1.1 -4664 c.1.8.1 -5283 1dgnA 89 9.09e+00 1dgnA a.77.1.3 18436 1keeE 1073 9.68e+00 a.92.1.1 68508 c.24.1.1 68509 c.30.1.1 68510 c.30.1.1 68511 d.142.1.2 68512 d.142.1.2 68513 1a0sP 413 9.80e+00 1a0tP f.4.3.2 43797 1keeG 1073 9.95e+00 a.92.1.1 68516 c.24.1.1 68517 c.30.1.1 68518 c.30.1.1 68519 d.142.1.2 68520 d.142.1.2 68521 1sfp 114 1.05e+01 1sfp b.23.1.1 23895 1fepA 724 1.09e+01 1fepA f.4.3.3 43808 1gjwA 637 1.09e+01 b.71.1.1 60582 c.1.8.1 60583 1i8dA 213 1.10e+01 b.43.4.3 61953 b.43.4.3 61954 1vjjA 692 1.11e+01 b.1.18.9 -2758 b.1.5.1 -2786 b.1.5.1 -2787 d.3.1.4 -8893 1hxn 219 1.12e+01 1hxn b.66.1.1 27529 1c3oE 1073 1.13e+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 1r4xA 275 1.19e+01 unknown_sccs -2846 unknown_sccs -10776 1l9mA 692 1.21e+01 b.1.18.9 73732 b.1.5.1 73733 b.1.5.1 73734 d.3.1.4 73735 1dxgA 36 1.22e+01 1dxgA g.41.5.2 45247 1kmoA 774 1.26e+01 f.4.3.3 72753 1bag 425 1.26e+01 1bag b.71.1.1 27720 c.1.8.1 28707 1c3oC 1073 1.26e+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 1po0A 751 1.27e+01 f.4.3.3 -12363 1bkb 136 1.32e+01 1bkb b.34.5.2 24609 b.40.4.5 25341 1bt4A 362 1.34e+01 1bjnA c.67.1.4 34468 1d1gA 168 1.35e+01 1d1gA c.71.1.1 34889 1qi9A 556 1.35e+01 1qhbA a.111.1.2 19053 1rllA 692 1.39e+01 1cb0A 283 1.41e+01 1cb0A c.56.2.1 33790 1c3oG 1073 1.41e+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 1iz6A 138 1.42e+01 b.34.5.2 76976 b.40.4.5 76977 1a0tP 413 1.42e+01 1a0tP f.4.3.2 43794 1aohA 147 1.44e+01 1aohA b.2.2.2 22401 1q0bA 367 1.47e+01 c.37.1.9 -7105 1j6wA 175 1.48e+01 1j98A d.185.1.2 62663 1szwA 379 1.49e+01 unknown_sccs -10164 1k28D 391 1.49e+01 b.106.1.1 68052 b.106.1.1 68053 1obbA 480 1.50e+01 c.2.1.5 86760 d.162.1.2 86761 1thg 544 1.52e+01 1thg c.69.1.17 34763 1jdbB 1073 1.54e+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 1ew3A 159 1.55e+01 1mup b.60.1.1 27114 1q41A 424 1.56e+01 d.144.1.7 -11308 1keeC 1073 1.62e+01 a.92.1.1 68500 c.24.1.1 68501 c.30.1.1 68502 c.30.1.1 68503 d.142.1.2 68504 d.142.1.2 68505 1cs0C 1073 1.63e+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 1bxrA 1073 1.64e+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 1si7A 369 1.64e+01 unknown_sccs -10163 1q38A 89 1.66e+01 b.1.2.1 -2765 1obwA 175 1.71e+01 2prd b.40.5.1 25416 1keeA 1073 1.73e+01 a.92.1.1 68492 c.24.1.1 68493 c.30.1.1 68494 c.30.1.1 68495 d.142.1.2 68496 d.142.1.2 68497 1k8kC 372 1.73e+01 b.69.4.1 68308 1cz3A 168 1.80e+01 1d1gA c.71.1.1 34891 1oi1A 221 1.80e+01 b.34.9.3 87037 b.34.9.3 87038 1s3iA 310 1.87e+01 b.46.1.1 -4111 c.65.1.1 -8042 1f1sA 814 1.89e+01 a.102.3.2 64928 b.1.18.2 64929 b.24.1.1 64930 b.30.5.2 64931 1hcz 252 1.92e+01 1hcz b.2.6.1 22464 b.84.2.2 28250 1qcnA 421 1.92e+01 1qcnA b.34.8.1 59017 d.177.1.1 59018 1c0pA 363 1.96e+01 1an9A c.4.1.2 30647 d.16.1.3 37934 2pcfB 250 1.97e+01 1hcz i.4.1.1 45911 1hsbA 270 1.99e+01 1agdA b.1.1.2 20736 d.19.1.1 38257 1aohB 147 2.03e+01 1aohA b.2.2.2 22402 1kqfB 294 2.05e+01 d.58.1.5 75900 f.23.22.1 75901 1hyoA 421 2.05e+01 1qcnA b.34.8.1 59001 d.177.1.1 59002 1js3A 486 2.06e+01 c.67.1.6 67215 1rypF 233 2.11e+01 1rypF d.153.1.4 41937 1yge 839 2.11e+01 1yge a.119.1.1 19234 b.12.1.1 23634 1ipwA 175 2.12e+01 2prd b.40.5.1 25427 2prd 174 2.14e+01 2prd b.40.5.1 25435 1ejeA 192 2.20e+01 1ejeA b.45.1.2 25757 1fs7A 485 2.20e+01 1qdbA a.138.1.3 19691 1oz2A 331 2.21e+01 b.34.9.3 -3597 b.34.9.3 -3598 b.34.9.3 -3599 1ddt 535 2.21e+01 1ddt b.2.1.1 22379 d.166.1.1 42241 f.1.2.1 43384 1gjuA 637 2.23e+01 b.71.1.1 60580 c.1.8.1 60581 1qdbA 473 2.24e+01 1qdbA a.138.1.3 19688 1m6iA 493 2.32e+01 c.3.1.5 74533 c.3.1.5 74534 d.87.1.1 74535 1ahjB 212 2.39e+01 2ahjB b.34.4.4 24601 1jihA 531 2.42e+01 unknown_sccs -10212 unknown_sccs -11922 1o54A 277 2.49e+01 c.66.1.13 -8095 1dkzA 219 2.49e+01 1dkzA unknown_sccs -445 unknown_sccs -3060 1kt8A 365 2.57e+01 e.17.1.1 77531 1n3jA 119 2.62e+01 b.85.7.2 79963 1j05B 121 2.63e+01 b.1.1.1 -2251 1fggA 261 2.64e+01 1fggA c.68.1.7 34576 1dkxA 219 2.64e+01 1dkzA unknown_sccs -446 unknown_sccs -3061 1n1mA 728 2.66e+01 b.70.3.1 79815 c.69.1.24 79816 1bh3 289 2.67e+01 3prn f.4.3.1 43766 1na3A 91 2.67e+01 k.38.1.1 85481 1qdlA 422 2.73e+01 1qdlA d.161.1.1 42088 1ekfA 365 2.76e+01 1ekfA e.17.1.1 59445 1m42A 102 2.78e+01 b.1.18.17 78597 1qauA 112 2.81e+01 1qauA b.36.1.1 24779 1f0lA 535 2.83e+01 1ddt b.2.1.1 22377 d.166.1.1 42239 f.1.2.1 43382 1qwlA 505 2.83e+01 e.5.1.1 -11823 1bj7 156 2.89e+01 1bj7 b.60.1.1 27113 2ahjB 212 2.90e+01 2ahjB b.34.4.4 24599 1nr0A 611 2.93e+01 b.69.4.1 86078 b.69.4.1 86079 2frvB 536 2.94e+01 1h2rL e.18.1.1 43291 1gotB 340 2.96e+01 1tbgA b.69.4.1 27648 1pxfA 111 3.01e+01 b.40.4.4 88341 1dw9A 156 3.11e+01 1dw9A a.35.1.4 17065 d.72.1.1 39596 1dtyA 429 3.13e+01 1dtyA c.67.1.4 34495 1gweA 503 3.14e+01 e.5.1.1 70667 1au1A 166 3.15e+01 1ifa a.26.1.3 16889 1oi0A 124 3.16e+01 unknown_sccs -8782 8prn 289 3.18e+01 3prn f.4.3.1 43767 1qcoA 423 3.19e+01 1qcnA b.34.8.1 59021 d.177.1.1 59022 1dg3A 592 3.26e+01 1dg3A a.114.1.1 19078 c.37.1.8 32153 7catA 506 3.26e+01 1cf9A e.5.1.1 42781 1dghB 498 3.26e+01 1cf9A e.5.1.1 42791 1a8q 274 3.29e+01 1brt c.69.1.12 34702 1iv8A 720 3.30e+01 b.71.1.1 76842 c.1.8.1 76843 1i40A 175 3.35e+01 b.40.5.1 66024 1jnrA 643 3.39e+01 a.7.3.1 66966 c.3.1.4 66967 d.168.1.1 66968 1g0uE 234 3.39e+01 d.153.1.4 41950 1lckA 175 3.42e+01 1lckA b.34.2.1 24552 d.93.1.1 40421 1bob 320 3.42e+01 1bob d.108.1.1 40816 1vj1A 363 3.45e+01 b.35.1.2 -3728 c.2.1.1 -5752 1p5sA 203 3.47e+01 a.40.1.1 -900 1n9pA 207 3.49e+01 b.1.18.16 80343 1hbzA 498 3.54e+01 1cf9A e.5.1.1 60937 1fzvA 132 3.55e+01 1vpfA g.17.1.1 60159 1i1jA 108 3.57e+01 1i1jA b.34.2.1 61531 1cc1L 498 3.60e+01 1h2rL e.18.1.1 43301 1c3oA 1073 3.60e+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 1ipd 345 3.62e+01 1cnzA c.77.1.1 35038 3prn 289 3.66e+01 3prn f.4.3.1 43761 1oe9A 795 3.73e+01 b.34.3.1 -3581 c.37.1.9 -7103 1dr8B 344 3.77e+01 1cnzA c.77.1.1 35052 1qhuA 460 3.79e+01 1qhuA b.66.1.1 27530 b.66.1.1 27531 1pcxA 810 3.81e+01 a.71.2.1 -1098 b.2.8.1 -2910 c.62.1.2 -7984 d.109.2.1 -10823 g.41.10.1 -12792 1khiA 176 3.81e+01 b.34.5.2 77408 b.40.4.5 77409 1dwkA 156 3.86e+01 1dw9A a.35.1.4 17075 d.72.1.1 39606 1cxyA 90 3.89e+01 1cyo d.120.1.1 41085 1vjeA 166 3.93e+01 d.185.1.2 -10261 7taa 478 3.94e+01 7taa b.71.1.1 27778 c.1.8.1 28765 1ux6A 350 3.96e+01 unknown_sccs -3451 unknown_sccs -12886