# List of top-scoring protein chains for T0353.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 1y8qA 346 1.28e+00 1pzwA 80 1.96e+00 g.39.1.10 95483 1mdvA 107 3.13e+00 3cyr a.138.1.1 19655 2cthA 107 3.13e+00 3cyr a.138.1.1 19652 1wr5A 108 3.40e+00 1j0oA 107 3.42e+00 a.138.1.1 90742 2cdv 107 3.45e+00 3cyr a.138.1.1 19651 1efyA 350 4.29e+00 1a26 a.41.1.1,d.166.1.2 17413,42275 1j0pA 108 4.30e+00 a.138.1.1 90743 1a26 361 4.35e+00 1a26 a.41.1.1,d.166.1.2 17412,42274 1ffkI 194 4.99e+00 1ffkI d.12.1.2 37494 1wtbA 79 5.04e+00 1vd4A 62 5.04e+00 1iqtA 75 5.22e+00 d.58.7.1 71279 1a0i 348 5.41e+00 1a0i b.40.4.6,d.142.2.1 25363,41577 2mtaC 147 6.37e+00 2mtaC a.3.1.1 15908 1mg2D 155 6.56e+00 a.3.1.1 79062 1es6A 296 7.48e+00 1es6A b.31.1.1,b.31.1.1 83048,83049 1b25A 619 7.73e+00 1b25A a.110.1.1,d.152.1.1 19044,41796 2mhr 118 8.12e+00 2mhr a.24.4.1 16581 2drpA 66 8.50e+00 2drpA g.37.1.1,g.37.1.1 45026,45027 1io8A 368 9.30e+00 1f4tA a.104.1.1 62618 1io7A 368 9.33e+00 1f4tA a.104.1.1 18971 1vyuA 351 9.44e+00 b.34.2.1,c.37.1.1 108914,108915 1a7e 118 1.11e+01 2mhr a.24.4.1 16583 1uk0A 350 1.23e+01 a.41.1.1,d.166.1.2 99477,99478 1fovA 82 1.24e+01 1qfnA c.47.1.1 32770 2d8sA 80 1.29e+01 1t0hB 224 1.36e+01 c.37.1.1 106208 2ff0A 102 1.37e+01 1n9lA 109 1.43e+01 d.110.3.6 85468 155c 135 1.51e+01 1ycc a.3.1.1 15900 1k0vA 73 1.53e+01 d.58.17.1 67986 2fn2 59 1.54e+01 1e8bA g.14.1.2 44668 2c8sA 172 1.58e+01 1vyvA 359 1.99e+01 b.34.2.1,c.37.1.1 108918,108919 1ue8A 367 2.12e+01 a.104.1.1 107781 1ta3B 303 2.27e+01 c.1.8.3 106732 2fwtA 125 2.33e+01 1gz7A 534 2.50e+01 c.69.1.17 83401 1t3lA 337 2.59e+01 b.34.2.1,c.37.1.1 106358,106359 1vqoU 66 2.66e+01 1citA 89 2.67e+01 2nllB g.39.1.2 45116 1r1dA 247 2.72e+01 c.69.1.29 96813 1hjaI 51 2.79e+01 2ovo g.68.1.1 44691 1y6jA 318 2.81e+01 3ovo 56 2.82e+01 2ovo g.68.1.1 44696 1udzA 182 3.04e+01 b.51.1.1 99239 1bg7 176 3.05e+01 2fha a.25.1.1 16686 1ue0A 182 3.10e+01 b.51.1.1 99241 2d9nA 77 3.15e+01 1sgeI 51 3.20e+01 g.68.1.1 98854 1sgyI 51 3.21e+01 g.68.1.1 98871 2sgqI 51 3.25e+01 g.68.1.1 100864 2a3mA 130 3.26e+01 2sgfI 51 3.41e+01 g.68.1.1 100862 1sgdI 51 3.47e+01 g.68.1.1 98852 2sgpI 51 3.50e+01 2ovo g.68.1.1 44689 1ct0I 51 3.51e+01 2ovo g.68.1.1 44688 1ds2I 51 3.51e+01 2ovo g.68.1.1 44687 1sgnI 51 3.52e+01 g.68.1.1 98856 1smqA 399 3.54e+01 a.25.1.2 105766 1sgpI 51 3.55e+01 2ovo g.68.1.1 44678 1ct2I 51 3.60e+01 2ovo g.68.1.1 44683 1jk0A 419 3.65e+01 a.25.1.2 63142 1faxL 96 3.66e+01 1hcgB g.3.11.1 44238 1r0rI 51 3.67e+01 g.68.1.1 96736 1sgqI 51 3.67e+01 2ovo g.68.1.1 44682 1iy5A 54 3.83e+01 g.68.1.1 83772 1mfrA 176 3.93e+01 2fha a.25.1.1 16692 3sgbI 56 3.94e+01 2ovo g.68.1.1 44679 2ovo 56 3.97e+01 2ovo g.68.1.1 44701 1c2n 137 3.98e+01 1ycc a.3.1.1 15889 1dszA 86 4.01e+01 2nllB g.39.1.2 45129 1m8bA 56 4.02e+01 g.68.1.1 78768 2a66A 113 4.04e+01 1cdoA 374 4.17e+01 2ohxA b.35.1.2,c.2.1.1 24747,29763 1tqhA 247 4.19e+01 c.69.1.29 107225 1rpxA 230 4.21e+01 1rpxA c.1.2.2 28536 1jnuA 104 4.27e+01 d.110.3.6 71762 2cevA 299 4.29e+01 1d3vA c.42.1.1 32576 2bgvX 134 4.30e+01 2bh4X 134 4.35e+01 1csoI 51 4.41e+01 2ovo g.68.1.1 44690 1ct4I 51 4.46e+01 2ovo g.68.1.1 44681 2fb6A 117 4.74e+01 1edsA 31 4.75e+01 1edsA j.35.1.1 46240 1cot 129 5.08e+01 1ycc a.3.1.1 15899 1c2rA 116 5.09e+01 1ycc a.3.1.1 15887 1hra 80 5.12e+01 2nllB g.39.1.2 45130 1vydA 116 5.17e+01 a.3.1.1 108900 1ds3I 51 5.19e+01 2ovo g.68.1.1 44685 1srb 21 5.29e+01 j.28.1.1 46201 1ovb 159 5.40e+01 1nnt c.94.1.2 35875 1k2eA 156 5.61e+01 d.113.1.1 72010 1iy6A 54 5.77e+01 g.68.1.1 83773 1u6pA 56 5.79e+01 1m6xA 423 5.82e+01 a.60.9.1,d.163.1.1 78708,78709 1m6xC 423 5.82e+01 a.60.9.1,d.163.1.1 78712,78713 1h2vZ 156 5.96e+01 d.58.7.1 76595 1q57A 503 6.08e+01 c.37.1.11,e.13.1.2 95867,95868 1c6s 87 6.16e+01 1ctj a.3.1.1 15806 1rxr 83 6.28e+01 2nllB g.39.1.2 45114 1uvfA 61 6.35e+01 1edn 21 6.56e+01 j.28.1.1 46197 1a6yA 94 6.60e+01 2nllB g.39.1.2 45131 2ffwA 78 6.75e+01 1a6bB 40 6.75e+01 1a6bB g.40.1.1 45172 2c6jA 338 6.77e+01 1vrnC 332 6.77e+01 1pq4A 291 6.84e+01 c.92.2.2 94995 1dxrC 336 7.00e+01 6prcC a.138.1.2 19670 1p4eA 429 7.02e+01 a.60.9.1,d.163.1.1 87764,87765 1p4eC 429 7.02e+01 a.60.9.1,d.163.1.1 87768,87769 1mjoA 104 7.07e+01 1cmbA a.43.1.5 17466 1uvgA 78 7.08e+01 1xr5A 466 7.10e+01 2f08A 129 7.13e+01 1cmcA 104 7.14e+01 1cmbA a.43.1.5 17462 1gqpA 221 7.23e+01 b.18.1.9 70372 1jiwI 106 7.24e+01 1smpI b.61.2.1 63078 2atcB 152 7.27e+01 8atcB d.58.2.1,g.41.7.1 39062,45314 1ykbA 142 7.29e+01 1j1uA 306 7.50e+01 c.26.1.1 83980 1e5dA 402 7.66e+01 1e5dA c.23.5.1,d.157.1.3 31208,42061 1n3lA 372 7.83e+01 c.26.1.1 79966 1cyj 90 7.92e+01 1ctj a.3.1.1 15805 2cbuA 468 8.01e+01 1xwvA 129 8.02e+01 1iy9A 275 8.14e+01 c.66.1.17 76943 1x4tA 92 8.34e+01 1ri5A 298 8.34e+01 c.66.1.34 97502 1howA 373 8.62e+01 1hcl d.144.1.7 41679 1eysC 382 8.64e+01 6prcC a.138.1.2 19678 1q8yA 373 8.65e+01 d.144.1.7 96234 1z6zA 282 8.68e+01 1njqA 39 8.75e+01 g.37.1.3 85822 1tpm 50 9.00e+01 1tpg g.27.1.1 44957