# 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 1fxkC 133 2.12e-01 1fxkC a.2.5.1 15702 1hyeA 313 3.42e-01 2cmd c.2.1.5 61400 d.162.1.1 61401 1jmyA 522 7.84e-01 c.69.1.1 63182 1f6wA 533 8.14e-01 2bce c.69.1.1 34629 1aqlA 532 1.42e+00 2bce c.69.1.1 34627 1akn 579 1.46e+00 2bce c.69.1.1 34626 1rgs 288 2.23e+00 1rgs b.82.3.2 28146 b.82.3.2 28147 1lk5A 229 2.51e+00 1b1cA 181 3.34e+00 1amoA c.23.5.2 31212 1jgtA 513 3.52e+00 c.26.2.1 66684 d.153.1.1 66685 1hbnB 442 3.70e+00 1mroB a.89.1.1 60900 d.58.31.2 60901 1mroB 442 3.70e+00 1mroB a.89.1.1 18531 d.58.31.2 39449 1i6zA 135 4.15e+00 a.7.7.1 61861 1hg3A 225 4.24e+00 1hg3A c.1.1.1 61025 1gowA 489 4.71e+00 1qvbA c.1.8.4 28981 1a5z 319 4.93e+00 1ceqA c.2.1.5 30181 d.162.1.1 42148 1fwxA 595 4.99e+00 b.6.1.4 60069 b.69.3.1 60070 1b43A 340 5.00e+00 1a76 a.60.7.1 18092 c.53.1.2 33362 1edzA 320 5.65e+00 1ee9A c.2.1.7 30287 c.58.1.2 33935 1ee9A 320 5.65e+00 1ee9A c.2.1.7 30288 c.58.1.2 33936 1f5mB 180 5.92e+00 1f5mB d.110.2.1 40896 1f5mA 180 5.92e+00 1f5mB d.110.2.1 40895 1jmxA 494 6.15e+00 a.3.1.7 66901 a.3.1.7 66902 b.1.1.6 66903 b.1.1.6 66904 b.61.4.1 66905 1qniA 581 6.21e+00 1qniA b.6.1.4 23042 b.69.3.1 27642 1ja0A 620 7.66e+00 1amoA b.43.4.1 62798 c.23.5.2 62799 c.25.1.4 62800 1j9zA 622 7.70e+00 1amoA b.43.4.1 62792 c.23.5.2 62793 c.25.1.4 62794 1ja1A 622 7.92e+00 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1amoA 615 8.64e+00 1amoA b.43.4.1 25669 c.23.5.2 31210 c.25.1.4 31557 1e2tA 284 9.18e+00 1e2tA d.3.1.5 37121 1xlaA 394 9.93e+00 4xis c.1.15.3 29445 1xlmA 394 1.04e+01 4xis c.1.15.3 29441 1srvA 145 1.07e+01 1derA c.8.5.1 30817 1jssA 224 1.07e+01 2pia 321 1.14e+01 2pia b.43.4.2 25663 c.25.1.2 31553 d.15.4.2 37704 1vdc 333 1.16e+01 1trb c.3.1.5 30545 c.3.1.5 30546 4xiaA 393 1.20e+01 4xis c.1.15.3 29439 1fpqA 372 1.27e+01 1fpqA a.4.5.29 59947 c.66.1.12 59948 1oelA 547 1.28e+01 1derA a.129.1.1 19452 c.8.5.1 30781 d.56.1.1 38900 1oakA 196 1.30e+01 1auq c.62.1.1 34138 1fnsA 196 1.30e+01 1auq c.62.1.1 34136 1grl 548 1.33e+01 1derA a.129.1.1 19487 c.8.5.1 30816 d.56.1.1 38935 2ldx 331 1.33e+01 3ldh c.2.1.5 30159 d.162.1.1 42126 1ioiA 208 1.36e+01 1a2zA c.56.4.1 62629 1auq 208 1.40e+01 1auq c.62.1.1 34137 1hh2P 344 1.42e+01 b.40.4.5 65835 d.52.3.1 65836 d.52.3.1 65837 d.202.1.1 65838 1c2oA 539 1.52e+01 2bce c.69.1.1 34610 1c2bA 540 1.52e+01 2bce c.69.1.1 34614 1edsA 31 1.56e+01 1edsA j.35.1.1 46240 1mahA 543 1.58e+01 2bce c.69.1.1 34619 1maaD 547 1.58e+01 2bce c.69.1.1 34618 1php 394 1.59e+01 16pk c.86.1.1 35452 1sieB 383 1.59e+01 1vpsA b.10.1.4 23358 1b63A 333 1.65e+01 1b63A d.14.1.3 37566 d.122.1.2 41107 1bknA 352 1.65e+01 1b63A d.14.1.3 37568 d.122.1.2 41109 1ez4B 318 1.65e+01 c.2.1.5 64919 d.162.1.1 64920 1lnqA 336 1.67e+01 4pfk 319 1.67e+01 3pfk c.89.1.1 35582 3pfk 319 1.67e+01 3pfk c.89.1.1 35581 6chyB 128 1.72e+01 3chy c.23.1.1 31063 2fnbA 95 1.75e+01 2fnbA b.1.2.1 21979 1iofA 208 1.76e+01 1a2zA c.56.4.1 62625 1b62A 349 1.76e+01 1b63A d.14.1.3 37567 d.122.1.2 41108 1vlzA 128 1.77e+01 3chy c.23.1.1 31048 1hyuA 521 1.79e+01 1hyuA c.3.1.5 30547 c.3.1.5 30548 c.47.1.2 32779 c.47.1.2 32780 1sesA 421 1.81e+01 1sesA a.2.7.1 15710 d.104.1.1 40710 1lpp 549 1.89e+01 1thg c.69.1.17 34764 1crl 534 1.89e+01 1thg c.69.1.17 34765 6pfkA 319 1.89e+01 3pfk c.89.1.1 35583 1im2A 444 1.91e+01 1do0A c.37.1.13 62564 1bkpA 278 1.91e+01 1bkpA d.117.1.1 41029 1b02A 279 1.92e+01 1bkpA d.117.1.1 41035 1hneE 218 1.92e+01 1a7s b.47.1.2 26235 2dfpA 534 1.92e+01 2bce c.69.1.1 34597 1ii8B 174 1.94e+01 1f2tB 1ppgE 218 2.00e+01 1a7s b.47.1.2 26236 1ppfE 218 2.00e+01 1a7s b.47.1.2 26234 1jer 138 2.00e+01 2cbp b.6.1.1 23022 1gsjA 258 2.02e+01 1d4zA 128 2.03e+01 3chy c.23.1.1 31047 1qopA 268 2.05e+01 2tysA c.1.2.4 28570 1b0fA 218 2.09e+01 1a7s b.47.1.2 26237 1hnnA 282 2.12e+01 c.66.1.15 65895 1fp1D 372 2.16e+01 1fpqA a.4.5.29 59939 c.66.1.12 59940 1a5aA 268 2.19e+01 2tysA c.1.2.4 28576 1i36A 264 2.21e+01 1kj6A 45 2.21e+01 3cox 507 2.25e+01 1b8sA c.3.1.2 30332 d.16.1.1 37863 1rlaA 323 2.27e+01 1d3vA c.42.1.1 32561 1d3vA 323 2.27e+01 1d3vA c.42.1.1 32559 1hqxA 323 2.27e+01 1d3vA c.42.1.1 61161 2tysA 268 2.28e+01 2tysA c.1.2.4 28572 1bksA 268 2.28e+01 2tysA c.1.2.4 28585 2wsyA 268 2.28e+01 2tysA c.1.2.4 28588 2rlaA 323 2.28e+01 1d3vA c.42.1.1 32573 1lxa 262 2.29e+01 1lxa b.81.1.1 28052 1ab5A 125 2.32e+01 3chy c.23.1.1 31056 3rlaA 323 2.35e+01 1d3vA c.42.1.1 32564 1dd3A 128 2.37e+01 1dd3C a.108.1.1 19031 d.45.1.1 38760 1dywA 173 2.39e+01 2cpl b.62.1.1 27505 1gruA 547 2.46e+01 i.16.1.1 65508 1gr5A 547 2.49e+01 i.16.1.1 65478 1derA 547 2.49e+01 1derA a.129.1.1 19459 c.8.5.1 30788 d.56.1.1 38907 1prxA 224 2.59e+01 1prxA c.47.1.10 33076 1prxB 224 2.59e+01 1prxA c.47.1.10 33077 1g41A 444 2.60e+01 1do0A c.37.1.13 32450 1xyaA 386 2.62e+01 4xis c.1.15.3 29411 1gs5A 258 2.68e+01 1hx1B 114 2.75e+01 1hx1B a.7.7.1 61350 1hqgA 323 2.77e+01 1d3vA c.42.1.1 61136 2ldb 317 2.77e+01 1hyhA c.2.1.5 30175 d.162.1.1 42142 1ldnA 316 2.78e+01 1hyhA c.2.1.5 30166 d.162.1.1 42133 1qmgA 524 2.90e+01 1qmgA a.100.1.2 18785 c.2.1.6 30182 1yveI 524 2.90e+01 1qmgA a.100.1.2 18789 c.2.1.6 30186 1yveJ 524 2.90e+01 1qmgA a.100.1.2 18790 c.2.1.6 30187 1itpA 77 2.91e+01 d.58.3.2 66371 1a5cA 368 2.96e+01 1fbaA c.1.10.1 29148 1bmtA 246 2.99e+01 1bmtA a.46.1.1 17757 c.23.6.1 31235 5chy 128 3.07e+01 3chy c.23.1.1 31050 1ebbA 202 3.08e+01 c.60.1.1 64900 1bouB 302 3.11e+01 1bouB c.56.6.1 33859 1djmA 129 3.13e+01 3chy c.23.1.1 31078 1cye 129 3.15e+01 3chy c.23.1.1 31077 1cey 128 3.16e+01 3chy c.23.1.1 31082 3chy 128 3.17e+01 3chy c.23.1.1 31038 1fvsA 72 3.19e+01 1aw0 d.58.17.1 60049 1xymA 386 3.22e+01 4xis c.1.15.3 29415 1dxiA 388 3.25e+01 4xis c.1.15.3 29407 1f2tB 148 3.26e+01 1f2tB 1udrA 129 3.27e+01 3chy c.23.1.1 31041 1eg0B 148 3.27e+01 1pkp i.1.1.1 45808 1pkp 150 3.28e+01 1pkp d.14.1.1 37551 d.50.1.2 38787 2tsyA 262 3.43e+01 2tysA c.1.2.4 28583 2che 128 3.43e+01 3chy c.23.1.1 31080 1ehc 128 3.44e+01 3chy c.23.1.1 31053 1brwA 433 3.53e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1e6kA 130 3.54e+01 3chy c.23.1.1 59306 1dv4E 145 3.55e+01 i.1.1.3 45875 1qnlA 385 3.57e+01 1pea c.93.1.1 35665 1je0A 236 3.63e+01 c.56.2.1 66581 2cevA 299 3.69e+01 1d3vA c.42.1.1 32576 1phk 298 3.74e+01 1cdkA d.144.1.1 41635 1amn 532 3.74e+01 2bce c.69.1.1 34587 1gqsA 532 3.75e+01 1eeaA 534 3.75e+01 2bce c.69.1.1 34609 1vxrA 537 3.75e+01 2bce c.69.1.1 34595 1qidA 537 3.75e+01 2bce c.69.1.1 34593 1ea5A 537 3.75e+01 2bce c.69.1.1 34592 1acl 537 3.75e+01 2bce c.69.1.1 34590 1eve 543 3.77e+01 2bce c.69.1.1 34585 1e6lA 127 3.82e+01 3chy c.23.1.1 59307 1f48A 589 3.87e+01 1f48A c.37.1.10 32280 c.37.1.10 32281 1ihuA 589 3.87e+01 c.37.1.10 62394 c.37.1.10 62395 1ex2A 189 3.87e+01 1ex2A c.51.4.2 33225 1ql6A 298 3.95e+01 1cdkA d.144.1.1 41636