# List of top-scoring protein chains for T0209.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 1rz3A 201 2.77e-01 c.37.1.6 -7048 1r2zA 274 1.39e+00 a.156.1.2 -370 b.113.1.1 -5094 g.39.1.8 -12748 1l1zA 274 1.39e+00 a.156.1.2 75911 b.113.1.1 75912 g.39.1.8 75913 1n71A 180 1.67e+00 d.108.1.1 85370 1b87A 181 1.68e+00 1b87A d.108.1.1 40797 1nepA 130 1.71e+00 b.1.18.7 80440 1chwA 389 1.84e+00 1bi5A c.95.1.2 35997 c.95.1.2 35998 1cmlA 389 1.97e+00 1bi5A c.95.1.2 35989 c.95.1.2 35990 1i86A 389 2.32e+00 c.95.1.2 66068 c.95.1.2 66069 1i88A 389 2.33e+00 c.95.1.2 66070 c.95.1.2 66071 1i89A 389 2.34e+00 c.95.1.2 66074 c.95.1.2 66075 1i8bA 389 2.34e+00 c.95.1.2 66078 c.95.1.2 66079 1bq6A 388 2.35e+00 1bi5A c.95.1.2 35987 c.95.1.2 35988 1bi5A 389 2.35e+00 1bi5A c.95.1.2 35985 c.95.1.2 35986 1jwxA 389 2.35e+00 c.95.1.2 71920 c.95.1.2 71921 1d6iA 388 2.53e+00 1bi5A c.95.1.2 36001 c.95.1.2 36002 1udxA 416 2.62e+00 b.117.1.1 -3546 c.37.1.8 -7101 unknown_sccs -9009 1nmmA 123 3.55e+00 d.2.1.2 80661 1d6hA 387 3.96e+00 1bi5A c.95.1.2 36005 c.95.1.2 36006 1nldH 215 4.54e+00 1igtB b.1.1.1 20111 b.1.1.2 21141 1p6gS 91 4.90e+00 i.1.1.1 87837 1r13A 148 5.54e+00 d.169.1.1 -11646 h.1.1.1 -12895 1jsg 114 6.12e+00 1a1x b.63.1.1 27513 1qvbA 481 6.52e+00 1qvbA c.1.8.4 28983 1dun 134 7.12e+00 1dun b.85.4.1 28371 1o6xA 81 7.33e+00 d.58.3.1 81105 1jhnA 424 1.02e+01 b.29.1.12 70060 b.104.1.1 66722 1o7tA 309 1.20e+01 c.94.1.1 86645 1d9yA 309 1.21e+01 1mrp c.94.1.1 35798 1r1nA 309 1.22e+01 c.94.1.1 -8659 1shsA 147 1.38e+01 1shsA b.15.1.1 23675 1pmd 675 1.39e+01 1pmd d.11.1.1 37491 d.11.1.1 37492 d.175.1.1 42562 e.3.1.1 42771 1pyyA 702 1.39e+01 d.11.1.1 -8970 d.11.1.1 -8971 d.175.1.1 -11704 e.3.1.1 -11781 1qmeA 702 1.39e+01 1pmd d.11.1.1 37487 d.11.1.1 37488 d.175.1.1 42560 e.3.1.1 42769 1fkvA 124 1.45e+01 3lzt d.2.1.2 36602 1fkqA 124 1.51e+01 3lzt d.2.1.2 36601 1hmkA 124 1.53e+01 3lzt d.2.1.2 36603 1i9sA 210 1.54e+01 1i9sA c.45.1.1 62099 1ux6A 350 1.61e+01 unknown_sccs -3451 unknown_sccs -12886 1qcrI 28 1.62e+01 1pdgA 109 1.68e+01 1pdgA g.17.1.1 44748 1hfyA 123 1.74e+01 3lzt d.2.1.2 36604 1mugA 168 1.90e+01 1mugA c.18.1.2 31030 1udkA 51 2.00e+01 g.3.14.1 -12520 1rv6V 101 2.05e+01 g.17.1.1 -12598 1hplA 449 2.11e+01 1gpl b.12.1.2 23639 c.69.1.19 34787 1fzvA 132 2.14e+01 1vpfA g.17.1.1 60159 1kgiA 127 2.34e+01 b.3.4.1 77388 1s2lA 167 2.44e+01 c.23.14.1 -6478 1pnuB 205 2.49e+01 i.1.1.1 88199 1lfuP 82 2.50e+01 a.4.1.1 77939 1uemA 117 2.52e+01 b.1.2.1 -2772 1nkwB 211 2.53e+01 i.1.1.2 80587 1as4A 341 2.55e+01 1sek e.1.1.1 42623 1f7dA 136 2.68e+01 1dun b.85.4.1 28353 1pca 403 2.75e+01 1aye c.56.5.1 33822 d.58.3.1 39063 1uenA 125 2.77e+01 b.1.2.1 -2776 1e33P 488 2.84e+01 1auk c.76.1.2 59186 1lpbB 449 2.84e+01 1gpl b.12.1.2 23643 c.69.1.19 34791 1e3cP 489 2.90e+01 1auk c.76.1.2 59187 1od5A 492 2.93e+01 b.82.1.2 86832 b.82.1.2 86833 1e2sP 489 2.93e+01 1auk c.76.1.2 35031 1e1zP 489 2.93e+01 1auk c.76.1.2 59158 3caaA 341 2.99e+01 1c8oA e.1.1.1 42625 1auk 488 3.08e+01 1auk c.76.1.2 35030 1qmnA 401 3.09e+01 1ovaA e.1.1.1 42624 4caaA 341 3.11e+01 1sek e.1.1.1 42627 2achA 360 3.20e+01 1c8oA e.1.1.1 42626 1k23A 309 3.21e+01 c.107.1.1 68029 1hfzA 124 3.27e+01 3lzt d.2.1.2 36618 1rdqE 350 3.45e+01 d.144.1.7 -11336 1rsoA 60 3.53e+01 unknown_sccs -1184 1hfx 123 3.61e+01 3lzt d.2.1.2 36600 1f6rA 123 3.64e+01 3lzt d.2.1.2 36606 1apmE 350 3.74e+01 1cdkA d.144.1.7 41628 1l3rE 350 3.74e+01 d.144.1.7 73552 1ntmI 57 3.90e+01 d.184.1.3 -11742 1ab6A 125 3.92e+01 3chy c.23.1.1 31054 1hfuA 503 3.96e+01 b.6.1.3 65827 b.6.1.3 65828 b.6.1.3 65829 1nz2A 153 3.97e+01 a.1.1.2 86437 1a65A 504 3.99e+01 1a65A b.6.1.3 23148 b.6.1.3 23149 b.6.1.3 23150