# List of top-scoring protein chains for T0348.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 1pft 50 2.07e-02 1pft g.41.3.1 45206 1s72Z 73 1.06e+00 g.41.8.1 105345 2ct7A 86 1.12e+00 1vqoZ 83 1.26e+00 1tr9A 341 1.53e+00 1y65A 342 1.53e+00 1ww8A 439 2.76e+00 1f4dA 264 3.31e+00 1bkpA d.117.1.1 40972 1y88A 199 3.36e+00 2ct2A 88 3.54e+00 1r4mA 529 3.71e+00 c.111.1.2 96999 1tt5A 531 3.72e+00 c.111.1.2 107291 1yovA 537 3.74e+00 1edyA 134 4.56e+00 1ayoA b.2.4.1 22428 1wd2A 60 5.42e+00 g.44.1.1 109232 1so2A 420 5.72e+00 a.211.1.2 98936 1gnf 46 5.73e+00 1gatA g.39.1.1 45107 2aq6A 147 5.77e+00 1sojI 420 5.78e+00 a.211.1.2 98950 1yqwA 264 6.81e+00 1yrqA 264 6.84e+00 1frfS 264 7.02e+00 2frvA e.19.1.1 43312 2fqpA 97 7.44e+00 1z1zA 131 8.01e+00 1e4uA 78 9.09e+00 1e4uA g.44.1.1 59231 1fl1A 230 1.03e+01 1at3A b.57.1.1 27023 1ffkW 73 1.08e+01 1ffkW g.41.8.1 45315 1p9rA 418 1.16e+01 c.37.1.11 94399 1dx8A 70 1.16e+01 1rb9 g.41.5.1 45243 1z6uA 150 1.16e+01 1wfeA 86 1.24e+01 1lm5A 214 1.24e+01 d.211.2.1 74029 1vdwA 254 1.27e+01 e.7.1.1 100569 1n9dA 199 1.29e+01 a.26.1.1 85464 1p91A 269 1.31e+01 c.66.1.33 94378 1jagA 241 1.32e+01 c.37.1.1 66463 1dsvA 31 1.33e+01 1dsvA g.40.1.1 45174 1fl2A 310 1.34e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1ydfA 257 1.39e+01 2a66A 113 1.42e+01 1sur 215 1.43e+01 1sur c.26.2.2 31620 1odhA 174 1.44e+01 d.239.1.1 86850 1zsqA 528 1.45e+01 2ff0A 102 1.50e+01 1bc8C 93 1.52e+01 1awcA a.4.5.21 16168 1ur6B 52 1.54e+01 g.44.1.1 99812 1ujvA 96 1.60e+01 b.36.1.1 99470 1jm7A 112 1.64e+01 g.44.1.1 66880 1zxzA 197 1.76e+01 1t9oA 54 1.82e+01 1lw3A 657 1.85e+01 b.55.1.8,c.45.1.3 91152,91153 5reqA 727 1.85e+01 1reqA c.1.19.1,c.23.6.1 29632,31259 1reqA 727 1.86e+01 1reqA c.1.19.1,c.23.6.1 29620,31247 1e1cA 727 1.86e+01 1reqA c.1.19.1,c.23.6.1 29636,31263 1yqdA 366 1.92e+01 1h7vA 60 2.08e+01 g.41.5.1 65713 1faq 52 2.26e+01 1far g.49.1.1 45352 1u79A 129 2.30e+01 d.26.1.1 107714 1sp1 29 2.33e+01 g.37.1.1 45051 2a62A 322 2.44e+01 1wiiA 85 2.45e+01 1spwA 39 2.50e+01 1pw4A 451 2.76e+01 f.38.1.1 95198 1bor 56 2.80e+01 1bor g.44.1.1 45324 1ek9A 428 2.83e+01 1ek9A f.5.1.1 43809 1jj2Y 73 2.84e+01 1ffkW g.41.8.1 63110 1rjwA 339 2.87e+01 b.35.1.2,c.2.1.1 97582,97583 1iq3A 110 2.92e+01 1iq3A a.39.1.6 62640 2a1rA 430 2.95e+01 1dl6A 58 2.95e+01 1dl6A g.41.3.1 45207 1g4mA 393 2.98e+01 b.1.18.11,b.1.18.11 65143,65144 1rlyA 60 2.99e+01 g.41.3.1 104988 1tqqA 471 3.05e+01 f.5.1.1 107242 2a8jA 420 3.07e+01 2a8mA 420 3.07e+01 2a8lA 420 3.07e+01 1hbxG 157 3.07e+01 1awcA a.4.5.21 60934 1eqbA 417 3.18e+01 1bj4A c.67.1.4 34484 1dfoA 417 3.18e+01 1bj4A c.67.1.4 34480 1jsyA 418 3.19e+01 b.1.18.11,b.1.18.11 71847,71848 1xfkA 336 3.21e+01 1qyp 57 3.21e+01 1qyp g.41.3.1 45205 1hvyA 288 3.21e+01 1bkpA d.117.1.1 41049 1hzwA 290 3.26e+01 1bkpA d.117.1.1 61464 1l8dA 112 3.27e+01 h.4.12.1 73687 2fymB 18 3.35e+01 1yk4A 52 3.36e+01 1t9pA 54 3.36e+01 1wjvA 79 3.37e+01 1erd 40 3.39e+01 1erd a.10.1.1 16362 1hyuA 521 3.43e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1ev5A 264 3.43e+01 1bkpA d.117.1.1 40935 2aw2B 108 3.46e+01 1ypvA 313 3.47e+01 1pt4A 29 3.49e+01 g.3.3.1 104306 2avyS 91 3.49e+01 8rxnA 52 3.50e+01 1rb9 g.41.5.1 45215 1rb9 53 3.52e+01 1rb9 g.41.5.1 45214 1ju6A 313 3.53e+01 d.117.1.1 63289 1brfA 53 3.55e+01 1rb9 g.41.5.1 45236 1bq8A 54 3.57e+01 1rb9 g.41.5.1 45237 1vd4A 62 3.63e+01 1rdg 53 3.77e+01 1rb9 g.41.5.1 45221 1zpuA 534 3.98e+01 1e8jA 52 3.98e+01 g.41.5.1 64796 1hw4A 355 4.07e+01 1bkpA d.117.1.1 41054 1us5A 314 4.13e+01 c.94.1.1 99856 1yk5A 53 4.15e+01 1ichA 112 4.21e+01 a.77.1.2 71182 1jmaB 167 4.23e+01 g.24.1.1,g.24.1.1 63178,63179 1h7kA 483 4.27e+01 e.5.1.1 90624 2cjsC 62 4.28e+01 1vckA 115 4.34e+01 1bq2 264 4.34e+01 1bkpA d.117.1.1 40971 2tsrA 307 4.40e+01 1bkpA d.117.1.1 41043 1m1qA 91 4.55e+01 a.138.1.3 74419 1dq3A 454 4.55e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1weoA 93 4.59e+01 2al7A 186 4.63e+01 1ywzA 175 4.63e+01 1v6eA 95 4.73e+01 1wxvA 92 4.75e+01 1xi6A 262 4.80e+01 1zd9A 188 4.85e+01 1vor2 58 4.88e+01 1mo2A 294 4.95e+01 c.69.1.22 79331 1nwyZ 59 4.96e+01 i.1.1.2 86369 1rikA 31 4.98e+01 k.12.1.1 104952 1jmh 316 5.00e+01 1bkpA d.117.1.1 41009 1g25A 65 5.02e+01 1g25A g.44.1.1 45325 1t1jA 125 5.04e+01 c.137.1.1 106249 1yl35 60 5.04e+01 1uufA 369 5.05e+01 b.35.1.2,c.2.1.1 100006,100007 1kezA 300 5.05e+01 c.69.1.22 68546 1q35A 320 5.06e+01 c.94.1.1 95661 1c0fA 368 5.08e+01 1yagA c.55.1.1,c.55.1.1 33447,33448 1mea 28 5.19e+01 g.41.1.1 45176 1c09A 54 5.21e+01 1rb9 g.41.5.1 45228 1nnqA 171 5.26e+01 a.25.1.1,g.41.5.1 92006,92007 2h18A 193 5.28e+01 1jcoB 30 5.29e+01 g.1.1.1 66503 1exkA 79 5.35e+01 1exkA g.54.1.1 45384 1frvA 264 5.39e+01 2frvA e.19.1.1 43308 1pkhA 204 5.40e+01 b.85.4.1 94832 1cqjA 286 5.58e+01 2scuA c.2.1.8,c.23.4.1 30305,31133 1ifqA 138 5.61e+01 1ifqA d.110.4.1 62350 2scuA 288 5.61e+01 2scuA c.2.1.8,c.23.4.1 30303,31131 1yq9A 264 5.64e+01 1iu5A 53 5.64e+01 g.41.5.1 71434 1yc5A 246 5.65e+01 2cu8A 76 5.66e+01 2d8iA 114 5.69e+01 1mm3A 61 5.82e+01 g.50.1.2 85016 1ee0A 402 5.82e+01 1bi5A c.95.1.2,c.95.1.2 36007,36008 1jkgB 250 5.84e+01 d.17.4.2 66796 1gatA 60 6.12e+01 1gatA g.39.1.1 45106 1p9hA 226 6.28e+01 b.81.3.1 94389 2gatA 66 6.43e+01 1gatA g.39.1.1 45102 1vzv 221 6.49e+01 1at3A b.57.1.1 27025 2gpyA 233 6.55e+01 1se7A 83 6.58e+01 2a6hD 1524 6.60e+01 1wijA 140 6.63e+01 1uucA 55 6.80e+01 g.68.1.2 108045 1k7cA 233 6.83e+01 c.23.10.4 68267 1a90 108 6.88e+01 1cewI d.17.1.2 38001 2rdvA 52 6.89e+01 1rb9 g.41.5.1 45217 2bx9A 53 6.99e+01 1zprA 264 7.02e+01 1bkpA d.117.1.1 40978 1ixrC 312 7.04e+01 a.4.5.11,c.37.1.20 76930,76931 1h6nA 484 7.09e+01 e.5.1.1 90623 1rimA 35 7.09e+01 k.12.1.1 104953 2g8mA 264 7.11e+01 1axwA 265 7.12e+01 1bkpA d.117.1.1 40938 2g8oA 264 7.14e+01 1ixsB 318 7.14e+01 a.4.5.11,c.37.1.20 76933,76934 2ftnA 264 7.14e+01 1aiqA 264 7.16e+01 1bkpA d.117.1.1 40967 1jg0A 264 7.19e+01 d.117.1.1 66659 1qqqA 264 7.19e+01 1bkpA d.117.1.1 40931 1m85A 484 7.21e+01 e.5.1.1 74578 2h0dB 100 7.21e+01 1e93A 484 7.24e+01 e.5.1.1 64802 1kzjA 264 7.35e+01 d.117.1.1 73365 2tscA 264 7.35e+01 1bkpA d.117.1.1 40952 2cklB 165 7.38e+01 1evfA 264 7.48e+01 1bkpA d.117.1.1 40932 1yvoA 172 7.55e+01 1cewI 108 7.56e+01 1cewI d.17.1.2 37999 1y9wA 140 7.60e+01 2bl1A 172 7.61e+01 1v9kA 228 7.67e+01 d.265.1.3 108449 1hqcA 324 7.69e+01 1hqcA a.4.5.11,c.37.1.20 16127,32424 1yvbI 111 7.94e+01 1y1cA 48 7.99e+01 1mm2A 61 8.03e+01 g.50.1.2 85015 5rxn 54 8.15e+01 1rb9 g.41.5.1 45225 1xpiA 231 8.18e+01 1dnaA 264 8.23e+01 1bkpA d.117.1.1 40956 1cteA 254 8.24e+01 1theB d.3.1.1 37058 1iml 76 8.25e+01 1iml g.39.1.3,g.39.1.3 45145,45146 1theA 260 8.30e+01 1theB d.3.1.1 37056 2gf0A 199 8.36e+01 1ln1A 214 8.36e+01 d.129.3.2 74038 1cdoA 374 8.40e+01 2ohxA b.35.1.2,c.2.1.1 24747,29763 1s7bA 110 8.61e+01 f.39.1.1 98634 1ev8A 264 8.68e+01 1bkpA d.117.1.1 40989 2f2mA 113 8.79e+01 1iro 54 8.91e+01 1rb9 g.41.5.1 45223 1ynjD 1524 8.92e+01