# List of top-scoring protein chains for T0353.t04-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 1y8qA 346 8.45e-01 2cthA 107 3.13e+00 3cyr a.138.1.1 19652 1mdvA 107 3.13e+00 3cyr a.138.1.1 19655 1wr5A 108 3.42e+00 1j0oA 107 3.42e+00 a.138.1.1 90742 2cdv 107 3.46e+00 3cyr a.138.1.1 19651 1j0pA 108 4.24e+00 a.138.1.1 90743 1pzwA 80 4.33e+00 g.39.1.10 95483 1efyA 350 5.03e+00 1a26 a.41.1.1,d.166.1.2 17413,42275 1a26 361 5.08e+00 1a26 a.41.1.1,d.166.1.2 17412,42274 1vd4A 62 5.17e+00 1wtbA 79 5.41e+00 1iqtA 75 5.55e+00 d.58.7.1 71279 1ffkI 194 5.96e+00 1ffkI d.12.1.2 37494 2mtaC 147 9.20e+00 2mtaC a.3.1.1 15908 2drpA 66 9.31e+00 2drpA g.37.1.1,g.37.1.1 45026,45027 1mg2D 155 9.41e+00 a.3.1.1 79062 2d8sA 80 9.84e+00 1es6A 296 1.06e+01 1es6A b.31.1.1,b.31.1.1 83048,83049 1b25A 619 1.10e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 2mhr 118 1.12e+01 2mhr a.24.4.1 16581 1fovA 82 1.31e+01 1qfnA c.47.1.1 32770 1io8A 368 1.39e+01 1f4tA a.104.1.1 62618 1io7A 368 1.39e+01 1f4tA a.104.1.1 18971 1uk0A 350 1.41e+01 a.41.1.1,d.166.1.2 99477,99478 2ff0A 102 1.45e+01 2c8sA 172 1.47e+01 1n9lA 109 1.48e+01 d.110.3.6 85468 155c 135 1.49e+01 1ycc a.3.1.1 15900 1a7e 118 1.49e+01 2mhr a.24.4.1 16583 1a0i 348 1.56e+01 1a0i b.40.4.6,d.142.2.1 25363,41577 1t0hB 224 1.70e+01 c.37.1.1 106208 1k0vA 73 1.81e+01 d.58.17.1 67986 2fn2 59 1.90e+01 1e8bA g.14.1.2 44668 1vyuA 351 1.90e+01 b.34.2.1,c.37.1.1 108914,108915 1udzA 182 2.07e+01 b.51.1.1 99239 1gz7A 534 2.08e+01 c.69.1.17 83401 1ta3B 303 2.11e+01 c.1.8.3 106732 1ue0A 182 2.13e+01 b.51.1.1 99241 2fwtA 125 2.28e+01 1r1dA 247 2.39e+01 c.69.1.29 96813 1vyvA 359 2.47e+01 b.34.2.1,c.37.1.1 108918,108919 1vqoU 66 2.49e+01 1hjaI 51 2.72e+01 2ovo g.68.1.1 44691 2a3mA 130 2.78e+01 3ovo 56 2.85e+01 2ovo g.68.1.1 44696 1ue8A 367 2.92e+01 a.104.1.1 107781 1citA 89 3.04e+01 2nllB g.39.1.2 45116 1sgeI 51 3.06e+01 g.68.1.1 98854 1sgyI 51 3.12e+01 g.68.1.1 98871 2sgqI 51 3.14e+01 g.68.1.1 100864 1t3lA 337 3.22e+01 b.34.2.1,c.37.1.1 106358,106359 2sgfI 51 3.34e+01 g.68.1.1 100862 1sgdI 51 3.35e+01 g.68.1.1 98852 1y6jA 318 3.38e+01 2sgpI 51 3.39e+01 2ovo g.68.1.1 44689 1ct0I 51 3.39e+01 2ovo g.68.1.1 44688 1sgnI 51 3.40e+01 g.68.1.1 98856 1bg7 176 3.40e+01 2fha a.25.1.1 16686 1ds2I 51 3.44e+01 2ovo g.68.1.1 44687 1sgpI 51 3.48e+01 2ovo g.68.1.1 44678 1ct2I 51 3.52e+01 2ovo g.68.1.1 44683 1sgqI 51 3.54e+01 2ovo g.68.1.1 44682 1faxL 96 3.54e+01 1hcgB g.3.11.1 44238 2d9nA 77 3.55e+01 1tqhA 247 3.64e+01 c.69.1.29 107225 1r0rI 51 3.67e+01 g.68.1.1 96736 2fb6A 117 3.71e+01 1c2n 137 3.72e+01 1ycc a.3.1.1 15889 2bgvX 134 3.73e+01 2bh4X 134 3.77e+01 1iy5A 54 3.82e+01 g.68.1.1 83772 2ovo 56 3.93e+01 2ovo g.68.1.1 44701 3sgbI 56 3.94e+01 2ovo g.68.1.1 44679 1cdoA 374 4.07e+01 2ohxA b.35.1.2,c.2.1.1 24747,29763 1m8bA 56 4.12e+01 g.68.1.1 78768 2a66A 113 4.25e+01 1cot 129 4.28e+01 1ycc a.3.1.1 15899 1ovb 159 4.37e+01 1nnt c.94.1.2 35875 2cevA 299 4.39e+01 1d3vA c.42.1.1 32576 1dszA 86 4.40e+01 2nllB g.39.1.2 45129 1m6xA 423 4.50e+01 a.60.9.1,d.163.1.1 78708,78709 1m6xC 423 4.50e+01 a.60.9.1,d.163.1.1 78712,78713 1csoI 51 4.56e+01 2ovo g.68.1.1 44690 1ct4I 51 4.61e+01 2ovo g.68.1.1 44681 1jnuA 104 4.69e+01 d.110.3.6 71762 1vydA 116 4.73e+01 a.3.1.1 108900 1c2rA 116 4.73e+01 1ycc a.3.1.1 15887 1mfrA 176 4.82e+01 2fha a.25.1.1 16692 1srb 21 4.90e+01 j.28.1.1 46201 1rpxA 230 5.03e+01 1rpxA c.1.2.2 28536 1hyeA 313 5.05e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 1hdj 77 5.11e+01 1bqz a.2.3.1 15696 1gqpA 221 5.32e+01 b.18.1.9 70372 1p4eA 429 5.36e+01 a.60.9.1,d.163.1.1 87764,87765 1p4eC 429 5.37e+01 a.60.9.1,d.163.1.1 87768,87769 1uvfA 61 5.42e+01 1k2eA 156 5.43e+01 d.113.1.1 72010 2d9aA 60 5.43e+01 1ds3I 51 5.50e+01 2ovo g.68.1.1 44685 1u6pA 56 5.67e+01 1q57A 503 5.69e+01 c.37.1.11,e.13.1.2 95867,95868 1hra 80 5.69e+01 2nllB g.39.1.2 45130 1iy6A 54 5.69e+01 g.68.1.1 83773 1c6s 87 5.79e+01 1ctj a.3.1.1 15806 1uvgA 78 5.95e+01 1a99A 344 6.08e+01 1pot c.94.1.1 35812 1vrnC 332 6.21e+01 1h2vZ 156 6.29e+01 d.58.7.1 76595 1rxr 83 6.35e+01 2nllB g.39.1.2 45114 1ldkA 396 6.38e+01 a.118.17.1 73851 1dxrC 336 6.38e+01 6prcC a.138.1.2 19670 1smqA 399 6.43e+01 a.25.1.2 105766 1wnyA 186 6.46e+01 1edn 21 6.47e+01 j.28.1.1 46197 1a6bB 40 6.54e+01 1a6bB g.40.1.1 45172 1jk0A 419 6.63e+01 a.25.1.2 63142 2ffwA 78 6.79e+01 1x4tA 92 7.04e+01 2cbuA 468 7.04e+01 2gryA 420 7.08e+01 1edsA 31 7.08e+01 1edsA j.35.1.1 46240 2c6jA 338 7.12e+01 2f08A 129 7.45e+01 1wk8A 194 7.47e+01 1cyj 90 7.50e+01 1ctj a.3.1.1 15805 1xr5A 466 7.76e+01 1jiwI 106 7.86e+01 1smpI b.61.2.1 63078 1eysC 382 7.90e+01 6prcC a.138.1.2 19678 1howA 373 7.92e+01 1hcl d.144.1.7 41679 1q8yA 373 7.95e+01 d.144.1.7 96234 1ykbA 142 7.99e+01 1sqiA 393 7.99e+01 d.32.1.3,d.32.1.3 105914,105915 2atcB 152 8.01e+01 8atcB d.58.2.1,g.41.7.1 39062,45314 1a6yA 94 8.13e+01 2nllB g.39.1.2 45131 1z6zA 282 8.17e+01 1xwvA 129 8.43e+01 1njqA 39 8.48e+01 g.37.1.3 85822 1n8yC 608 8.61e+01 c.10.2.5,c.10.2.5,g.3.9.1,g.3.9.1 80314,80315,80316,80317 1tpm 50 8.65e+01 1tpg g.27.1.1 44957 1t11A 392 8.76e+01 a.223.1.1,d.241.2.1,d.26.1.1 106236,106237,106238 1ctj 89 8.89e+01 1ctj a.3.1.1 15798 6cmhA 21 8.97e+01 j.28.1.1 46200