# List of top-scoring protein chains for T0353.t06-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 9.00e-01 1mdvA 107 3.53e+00 3cyr a.138.1.1 19655 2cthA 107 3.53e+00 3cyr a.138.1.1 19652 1wr5A 108 3.77e+00 1j0oA 107 3.77e+00 a.138.1.1 90742 2cdv 107 3.81e+00 3cyr a.138.1.1 19651 1pzwA 80 4.49e+00 g.39.1.10 95483 1j0pA 108 4.59e+00 a.138.1.1 90743 1efyA 350 5.49e+00 1a26 a.41.1.1,d.166.1.2 17413,42275 1a26 361 5.55e+00 1a26 a.41.1.1,d.166.1.2 17412,42274 1wtbA 79 5.82e+00 1vd4A 62 5.84e+00 1iqtA 75 5.98e+00 d.58.7.1 71279 1ffkI 194 7.70e+00 1ffkI d.12.1.2 37494 2drpA 66 1.08e+01 2drpA g.37.1.1,g.37.1.1 45026,45027 2mtaC 147 1.08e+01 2mtaC a.3.1.1 15908 1mg2D 155 1.11e+01 a.3.1.1 79062 2d8sA 80 1.16e+01 1es6A 296 1.26e+01 1es6A b.31.1.1,b.31.1.1 83048,83049 2mhr 118 1.28e+01 2mhr a.24.4.1 16581 1b25A 619 1.35e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1fovA 82 1.39e+01 1qfnA c.47.1.1 32770 1uk0A 350 1.50e+01 a.41.1.1,d.166.1.2 99477,99478 1a0i 348 1.58e+01 1a0i b.40.4.6,d.142.2.1 25363,41577 1io8A 368 1.58e+01 1f4tA a.104.1.1 62618 1io7A 368 1.58e+01 1f4tA a.104.1.1 18971 2c8sA 172 1.62e+01 2ff0A 102 1.62e+01 155c 135 1.67e+01 1ycc a.3.1.1 15900 1a7e 118 1.69e+01 2mhr a.24.4.1 16583 1n9lA 109 1.76e+01 d.110.3.6 85468 1udzA 182 1.83e+01 b.51.1.1 99239 1ue0A 182 1.87e+01 b.51.1.1 99241 2fn2 59 2.00e+01 1e8bA g.14.1.2 44668 1k0vA 73 2.02e+01 d.58.17.1 67986 1t0hB 224 2.08e+01 c.37.1.1 106208 1vyuA 351 2.30e+01 b.34.2.1,c.37.1.1 108914,108915 1ta3B 303 2.44e+01 c.1.8.3 106732 2fwtA 125 2.48e+01 1vqoU 66 2.68e+01 1ue8A 367 2.76e+01 a.104.1.1 107781 1r1dA 247 2.83e+01 c.69.1.29 96813 1hjaI 51 2.88e+01 2ovo g.68.1.1 44691 1vyvA 359 2.94e+01 b.34.2.1,c.37.1.1 108918,108919 3ovo 56 2.99e+01 2ovo g.68.1.1 44696 2a3mA 130 3.22e+01 1sgeI 51 3.23e+01 g.68.1.1 98854 1gz7A 534 3.26e+01 c.69.1.17 83401 1citA 89 3.27e+01 2nllB g.39.1.2 45116 2fb6A 117 3.30e+01 2sgqI 51 3.32e+01 g.68.1.1 100864 1sgyI 51 3.32e+01 g.68.1.1 98871 1bg7 176 3.44e+01 2fha a.25.1.1 16686 1sgdI 51 3.54e+01 g.68.1.1 98852 2sgfI 51 3.54e+01 g.68.1.1 100862 2sgpI 51 3.57e+01 2ovo g.68.1.1 44689 1ct0I 51 3.58e+01 2ovo g.68.1.1 44688 1sgnI 51 3.59e+01 g.68.1.1 98856 1ds2I 51 3.64e+01 2ovo g.68.1.1 44687 2d9nA 77 3.66e+01 1sgpI 51 3.66e+01 2ovo g.68.1.1 44678 1ct2I 51 3.70e+01 2ovo g.68.1.1 44683 1sgqI 51 3.73e+01 2ovo g.68.1.1 44682 1t3lA 337 3.77e+01 b.34.2.1,c.37.1.1 106358,106359 1r0rI 51 3.86e+01 g.68.1.1 96736 1faxL 96 3.90e+01 1hcgB g.3.11.1 44238 1iy5A 54 4.00e+01 g.68.1.1 83772 1c2n 137 4.02e+01 1ycc a.3.1.1 15889 1y6jA 318 4.03e+01 1cdoA 374 4.04e+01 2ohxA b.35.1.2,c.2.1.1 24747,29763 2ovo 56 4.13e+01 2ovo g.68.1.1 44701 3sgbI 56 4.13e+01 2ovo g.68.1.1 44679 1tqhA 247 4.30e+01 c.69.1.29 107225 2bgvX 134 4.30e+01 1m8bA 56 4.30e+01 g.68.1.1 78768 1m6xA 423 4.35e+01 a.60.9.1,d.163.1.1 78708,78709 1m6xC 423 4.35e+01 a.60.9.1,d.163.1.1 78712,78713 2bh4X 134 4.35e+01 1dszA 86 4.54e+01 2nllB g.39.1.2 45129 2a66A 113 4.56e+01 2cevA 299 4.62e+01 1d3vA c.42.1.1 32576 1ovb 159 4.66e+01 1nnt c.94.1.2 35875 1csoI 51 4.76e+01 2ovo g.68.1.1 44690 1mfrA 176 4.79e+01 2fha a.25.1.1 16692 1ct4I 51 4.82e+01 2ovo g.68.1.1 44681 1rpxA 230 4.91e+01 1rpxA c.1.2.2 28536 1c2rA 116 5.03e+01 1ycc a.3.1.1 15887 1cot 129 5.04e+01 1ycc a.3.1.1 15899 1vydA 116 5.12e+01 a.3.1.1 108900 1p4eC 429 5.17e+01 a.60.9.1,d.163.1.1 87768,87769 1p4eA 429 5.17e+01 a.60.9.1,d.163.1.1 87764,87765 1srb 21 5.22e+01 j.28.1.1 46201 1hyeA 313 5.26e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 1q57A 503 5.28e+01 c.37.1.11,e.13.1.2 95867,95868 1k2eA 156 5.42e+01 d.113.1.1 72010 1wnyA 186 5.43e+01 1smqA 399 5.59e+01 a.25.1.2 105766 1jnuA 104 5.62e+01 d.110.3.6 71762 1ds3I 51 5.71e+01 2ovo g.68.1.1 44685 1jk0A 419 5.76e+01 a.25.1.2 63142 1hra 80 5.82e+01 2nllB g.39.1.2 45130 1iy6A 54 5.92e+01 g.68.1.1 83773 1u6pA 56 5.99e+01 1c6s 87 6.17e+01 1ctj a.3.1.1 15806 1hdj 77 6.20e+01 1bqz a.2.3.1 15696 1uvfA 61 6.21e+01 1rxr 83 6.53e+01 2nllB g.39.1.2 45114 1vrnC 332 6.54e+01 1x4tA 92 6.56e+01 1tpm 50 6.66e+01 1tpg g.27.1.1 44957 1wk8A 194 6.69e+01 1dxrC 336 6.75e+01 6prcC a.138.1.2 19670 1uvgA 78 6.80e+01 1h2vZ 156 6.80e+01 d.58.7.1 76595 2cbuA 468 6.83e+01 1edn 21 6.84e+01 j.28.1.1 46197 1a6bB 40 6.90e+01 1a6bB g.40.1.1 45172 1ldkA 396 7.14e+01 a.118.17.1 73851 2d9aA 60 7.15e+01 1edsA 31 7.25e+01 1edsA j.35.1.1 46240 1t11A 392 7.41e+01 a.223.1.1,d.241.2.1,d.26.1.1 106236,106237,106238 1gqpA 221 7.43e+01 b.18.1.9 70372 2ffwA 78 7.44e+01 2c6jA 338 7.57e+01 1ykbA 142 7.71e+01 1cyj 90 7.77e+01 1ctj a.3.1.1 15805 1a99A 344 7.79e+01 1pot c.94.1.1 35812 1sqiA 393 7.96e+01 d.32.1.3,d.32.1.3 105914,105915 2f08A 129 8.03e+01 1a6yA 94 8.04e+01 2nllB g.39.1.2 45131 1howA 373 8.10e+01 1hcl d.144.1.7 41679 1q8yA 373 8.14e+01 d.144.1.7 96234 1jiwI 106 8.30e+01 1smpI b.61.2.1 63078 1z6zA 282 8.50e+01 2atcB 152 8.61e+01 8atcB d.58.2.1,g.41.7.1 39062,45314 1n8yC 608 8.62e+01 c.10.2.5,c.10.2.5,g.3.9.1,g.3.9.1 80314,80315,80316,80317 1ri5A 298 8.65e+01 c.66.1.34 97502 2cvlA 124 8.72e+01 1eysC 382 8.79e+01 6prcC a.138.1.2 19678 1njqA 39 8.84e+01 g.37.1.3 85822 1gc7A 297 8.97e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16370,27005,37613