# List of top-scoring protein chains for t2k-100-30-str 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 1oqcA 125 1.40e-29 1jraA 117 9.40e-26 a.24.15.1 67117 1jr8A 117 1.44e-25 a.24.15.1 67115 1euvA 221 2.72e-02 1euvA d.3.1.7 37133 1ku1A 230 7.82e-02 a.118.3.1 72996 1eyvA 156 9.36e-02 1eyvA a.79.1.1 18446 1dgjA 907 9.70e-02 1alo a.56.1.1 17909 d.15.4.2 37694 d.41.1.1 38585 d.133.1.1 41415 1g8lA 411 3.49e-01 1g8lA b.85.6.1 60365 b.103.1.1 60366 c.57.1.2 60367 1jvr 137 4.35e-01 1jvr a.61.1.2 18132 1ngkA 128 6.51e-01 1iwhA 141 7.47e-01 a.1.1.2 76882 1hlrA 907 1.11e+00 a.56.1.1 65850 d.15.4.2 65851 d.41.1.1 65852 d.133.1.1 65853 1je8A 82 1.25e+00 a.4.6.2 77108 1fd8A 73 1.39e+00 1cc8A d.58.17.1 59770 2abk 211 1.57e+00 2abk a.96.1.1 18743 1ciy 590 1.64e+00 1ciy b.18.1.3 23720 b.77.2.1 27977 f.1.3.1 43392 1agi 125 1.90e+00 7rsa d.5.1.1 37303 1jjfA 268 2.21e+00 c.69.1.2 66765 1mlwA 301 2.23e+00 d.178.1.1 79289 1a32 88 2.57e+00 1a32 a.16.1.2 16384 1g4yR 148 2.58e+00 1cll a.39.1.5 60252 1gg3A 279 2.68e+00 1ef1A a.11.2.1 16372 b.55.1.5 27007 d.15.1.4 37615 1fxxA 482 3.02e+00 1fxxA c.55.3.5 33726 1cc8A 73 3.14e+00 1cc8A d.58.17.1 39343 1bev1 281 3.24e+00 1aym1 1m6bA 621 3.33e+00 c.10.2.5 74521 c.10.2.5 74522 g.3.9.1 74523 g.3.9.1 74524 4enl 436 3.45e+00 4enl c.1.11.1 29202 d.54.1.1 38846 1jroB 777 3.81e+00 d.41.1.1 67141 d.133.1.1 67142 1irdA 141 4.09e+00 a.1.1.2 66286 1pbwA 216 4.22e+00 1pbwA a.116.1.1 19103 1f7tA 122 4.80e+00 1f7lA d.150.1.2 59667 1abwA 283 4.80e+00 1abwA a.1.1.2 15288 a.1.1.2 15289 1j7yA 141 4.87e+00 a.1.1.2 66426 1babA 143 4.92e+00 1abwA a.1.1.2 15235 1g8iA 190 5.43e+00 1rec a.39.1.5 60363 1o6eA 235 5.50e+00 b.57.1.1 81083 1itg 166 5.67e+00 1b9dA c.55.3.2 33661 1a04A 215 5.81e+00 1a04A a.4.6.2 16234 c.23.1.1 31089 1pyp 285 6.59e+00 1wgjA b.40.5.1 25409 1e8nA 710 6.98e+00 1qfmA b.69.7.1 27675 c.69.1.4 34643 1h2wA 710 7.16e+00 b.69.7.1 76596 c.69.1.4 76597 1h2xA 710 7.18e+00 b.69.7.1 76598 c.69.1.4 76599 1qfmA 710 7.26e+00 1qfmA b.69.7.1 27673 c.69.1.4 34641 1if1A 113 7.26e+00 2irfG a.4.5.23 16183 1hyvA 166 7.70e+00 1b9dA c.55.3.2 61424 1eqjA 511 8.02e+00 1ejjA c.105.1.1 59495 c.76.1.3 59496 1ky9A 448 8.16e+00 b.36.1.4 73198 b.47.1.1 73199 1b9dA 163 8.50e+00 1b9dA c.55.3.2 33649 1ejjA 511 8.67e+00 1ejjA c.105.1.1 59422 c.76.1.3 59423 1o98A 511 8.90e+00 1jenB 67 9.45e+00 1jenB d.156.1.1 42029 1f4tA 368 9.77e+00 1f4tA a.104.1.1 18973 1gio 125 9.89e+00 7rsa d.5.1.1 37304 1bl3A 160 1.04e+01 1b9dA c.55.3.2 33655 1b9xB 68 1.06e+01 1tbgE a.137.3.1 19638 1vaoA 560 1.06e+01 1qltA d.58.32.1 39461 d.145.1.1 41724 1ixh 321 1.08e+01 1ixh c.94.1.1 35761 1dwtA 153 1.16e+01 1a6m a.1.1.2 15190 1toh 343 1.17e+01 4pah d.178.1.1 42573 2oneA 436 1.19e+01 4enl c.1.11.1 29203 d.54.1.1 38847 1ystH 260 1.21e+01 6prcH b.41.1.1 25482 f.23.10.1 43511 4rnpA 883 1.22e+01 1cezA e.8.1.3 43113 1kw4A 89 1.25e+01 a.60.1.2 73077 1qovH 260 1.26e+01 6prcH b.41.1.1 25464 f.23.10.1 43457 1gjnA 153 1.27e+01 a.1.1.2 70191 1jwwA 80 1.29e+01 d.58.17.1 71919 1ltzA 297 1.30e+01 d.178.1.1 74254 1itf 165 1.33e+01 1b5l a.26.1.3 16899 1kgnA 329 1.34e+01 a.25.1.2 68584 1iapA 211 1.34e+01 a.91.1.1 62119 1b75A 94 1.37e+01 1dfuP b.53.1.1 26937 1oneA 436 1.38e+01 4enl c.1.11.1 29200 d.54.1.1 38844 1tbgE 68 1.40e+01 1tbgE a.137.3.1 19630 1mhqA 148 1.53e+01 1hxs1 302 1.59e+01 1gotG 73 1.62e+01 1tbgE a.137.3.1 19629 1myf 153 1.68e+01 1a6m a.1.1.2 15147 1aw0 72 1.73e+01 1aw0 d.58.17.1 39342 1jflA 228 1.74e+01 c.78.2.1 71656 c.78.2.1 71657 1ysc 421 1.76e+01 1ivyA c.69.1.5 34652 1dszA 86 1.80e+01 2nllB g.39.1.2 45129 1pov1 302 1.85e+01 1pov1 1h0hA 977 1.89e+01 b.52.2.2 76435 c.81.1.1 76436 3cln 148 2.06e+01 1cll a.39.1.5 17286 1mkaA 171 2.07e+01 1mkaA d.38.1.2 38543 1auk 489 2.07e+01 1auk c.76.1.2 35030 1a0sP 413 2.14e+01 1a0tP f.4.3.2 43797 1ha2A 585 2.21e+01 1bj5 a.126.1.1 60866 a.126.1.1 60867 a.126.1.1 60868 1ebmA 317 2.24e+01 1ebmA a.96.1.3 18751 d.129.1.2 41300 1dxsA 80 2.25e+01 1cokA a.60.1.2 17944 1ko9A 345 2.31e+01 a.96.1.3 68717 d.129.1.2 68718 1mgn 154 2.33e+01 1a6m a.1.1.2 15097 1sw6A 327 2.37e+01 1sw6A d.211.1.1 19176 1qhtA 775 2.41e+01 1tgoA c.55.3.5 33722 e.8.1.1 43011 1cokA 68 2.42e+01 1cokA a.60.1.2 17945 5pal 109 2.50e+01 1a75A a.39.1.4 17215 1cjwA 166 2.52e+01 1cjwA d.108.1.1 40818 1lwyA 324 2.53e+01 a.96.1.3 78285 d.129.1.2 78286 1aueA 100 2.54e+01 1nsgB a.24.7.1 16615 4rxn 54 2.59e+01 1rb9 g.41.5.1 45226 1ezvD 245 2.67e+01 1be3D a.3.1.3 59546 f.23.11.1 59547 1dw9A 156 2.68e+01 1dw9A a.35.1.4 17065 d.72.1.1 39596 1iu8A 206 2.68e+01 c.56.4.1 71436 1dwkA 156 2.79e+01 1dw9A a.35.1.4 17075 d.72.1.1 39606 1bba 36 2.81e+01 1bba j.6.1.1 46088 1j5sA 463 2.81e+01 c.1.9.8 71580 1exqA 154 2.83e+01 1b9dA c.55.3.2 33646 1ka3A 90 2.87e+01 a.150.1.1 72239 1cg5B 141 2.90e+01 1cg5B a.1.1.2 15585 2spo 154 2.92e+01 1a6m a.1.1.2 15053 1kyoD 248 2.92e+01 a.3.1.3 73254 f.23.11.1 73255 3kvt 115 2.93e+01 1t1dA d.42.1.2 38642 1tgoA 773 2.97e+01 1tgoA c.55.3.5 33721 e.8.1.1 43010 1fe0A 68 2.99e+01 1cc8A d.58.17.1 39345 1kb9D 246 3.00e+01 a.3.1.3 77317 f.23.11.1 77318 1iro 54 3.07e+01 1rb9 g.41.5.1 45223 3lynA 136 3.07e+01 1lis a.19.1.1 16413 1ez3A 127 3.11e+01 1dn1B a.47.2.1 17768 1jwgA 147 3.16e+01 a.118.9.2 71911 1e9rA 437 3.21e+01 c.37.1.11 64827 1j5rA 371 3.22e+01 e.22.1.2 71578 1oaa 259 3.22e+01 1oaa c.2.1.2 29829 1sep 261 3.26e+01 1oaa c.2.1.2 29830 1vrtA 560 3.27e+01 1rthA c.55.3.1 33574 e.8.1.2 43023 1e4uA 78 3.28e+01 1e4uA g.44.1.1 59231 1f3vA 179 3.28e+01 1f3vA d.58.22.1 39382 1hra 81 3.29e+01 2nllB g.39.1.2 45130 1lpuA 332 3.31e+01 d.144.1.1 74177 1dn1B 267 3.31e+01 1dn1B a.47.2.1 17771 1ks2A 219 3.37e+01 c.35.1.2 72908 d.58.40.1 72909 1iweA 457 3.45e+01 c.37.1.10 71486 1k59A 123 3.46e+01 d.5.1.1 72073 1fl0A 171 3.48e+01 1eujA b.40.4.4 25315 1qltA 560 3.51e+01 1qltA d.58.32.1 39457 d.145.1.1 41720 1c1dA 355 3.53e+01 1bw9A c.2.1.7 30270 c.58.1.1 33918 1avmA 201 3.57e+01 1avmA a.2.11.1 15782 d.44.1.1 38745 1m1eB 81 3.59e+01 a.161.1.1 78400 1qsdA 106 3.59e+01 1qsdA a.7.5.1 16335 1isuA 62 3.59e+01 1isuA g.35.1.1 44978 1kuxA 207 3.61e+01 d.108.1.1 73021 1no1A 126 3.61e+01 2occM 46 3.66e+01 2occM f.23.7.1 43527 1hbyA 123 3.73e+01 7rsa d.5.1.1 60936 2itg 163 3.76e+01 1b9dA c.55.3.2 33669 1mbd 153 3.76e+01 1a6m a.1.1.2 15033 1hdlA 55 3.82e+01 g.57.1.1 65808 1dmhA 311 3.83e+01 1dmhA b.3.6.1 22633 1ee8A 266 3.85e+01 1ee8A a.156.1.2 75823 b.113.1.1 75824 g.39.1.8 75825 1sbp 310 3.85e+01 1sbp c.94.1.1 35760 1bsmA 201 3.91e+01 1avmA a.2.11.1 15780 d.44.1.1 38743 1m13A 316 3.92e+01 1cmkE 350 3.92e+01 1cdkA d.144.1.1 41623 1gzsB 165 3.97e+01 a.168.1.1 76425 1a4yB 123 3.98e+01 7rsa d.5.1.1 37296 1jj2P 95 3.99e+01 1ffkN b.34.5.1 63101