# List of top-scoring protein chains for T0348.t04-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 1.08e-02 1pft g.41.3.1 45206 2ct7A 86 1.23e+00 1s72Z 73 1.50e+00 g.41.8.1 105345 1vqoZ 83 1.78e+00 1tr9A 341 2.68e+00 1y65A 342 2.69e+00 2ct2A 88 3.11e+00 1y88A 199 3.27e+00 2aq6A 147 3.48e+00 1wd2A 60 4.66e+00 g.44.1.1 109232 1f4dA 264 5.49e+00 1bkpA d.117.1.1 40972 1edyA 134 5.57e+00 1ayoA b.2.4.1 22428 1gnf 46 6.09e+00 1gatA g.39.1.1 45107 1e4uA 78 6.22e+00 1e4uA g.44.1.1 59231 1z1zA 131 6.82e+00 1ww8A 439 7.08e+00 1yqwA 264 7.57e+00 1yrqA 264 7.61e+00 1frfS 264 7.90e+00 2frvA e.19.1.1 43312 1r4mA 529 7.96e+00 c.111.1.2 96999 1yovA 537 7.96e+00 1tt5A 531 7.98e+00 c.111.1.2 107291 1p91A 269 8.45e+00 c.66.1.33 94378 2avyS 91 8.85e+00 2fqpA 97 8.92e+00 1n9dA 199 9.08e+00 a.26.1.1 85464 2ff0A 102 9.10e+00 2a66A 113 9.23e+00 1fl2A 310 9.46e+00 1hyuA c.3.1.5,c.3.1.5 59869,59870 1bc8C 93 9.54e+00 1awcA a.4.5.21 16168 2a8lA 420 9.82e+00 2a8mA 420 9.82e+00 2a8jA 420 9.82e+00 1jm7A 112 1.08e+01 g.44.1.1 66880 1p9rA 418 1.12e+01 c.37.1.11 94399 1dx8A 70 1.14e+01 1rb9 g.41.5.1 45243 1ur6B 52 1.16e+01 g.44.1.1 99812 1ujvA 96 1.17e+01 b.36.1.1 99470 1odhA 174 1.18e+01 d.239.1.1 86850 1so2A 420 1.19e+01 a.211.1.2 98936 1sojI 420 1.20e+01 a.211.1.2 98950 1lm5A 214 1.21e+01 d.211.2.1 74029 1jagA 241 1.28e+01 c.37.1.1 66463 1u79A 129 1.36e+01 d.26.1.1 107714 1fl1A 230 1.36e+01 1at3A b.57.1.1 27023 1ffkW 73 1.37e+01 1ffkW g.41.8.1 45315 1zsqA 528 1.40e+01 1z6uA 150 1.42e+01 1vdwA 254 1.43e+01 e.7.1.1 100569 1ydfA 257 1.44e+01 1wfeA 86 1.51e+01 2a62A 322 1.59e+01 1iq3A 110 1.61e+01 1iq3A a.39.1.6 62640 1us5A 314 1.68e+01 c.94.1.1 99856 1yqdA 366 1.69e+01 1h7vA 60 1.70e+01 g.41.5.1 65713 1l8dA 112 1.74e+01 h.4.12.1 73687 1dsvA 31 1.76e+01 1dsvA g.40.1.1 45174 1lw3A 657 1.85e+01 b.55.1.8,c.45.1.3 91152,91153 1hbxG 157 1.87e+01 1awcA a.4.5.21 60934 1hvyA 288 1.92e+01 1bkpA d.117.1.1 41049 2a6hD 1524 1.92e+01 1zd9A 188 1.93e+01 1hzwA 290 1.95e+01 1bkpA d.117.1.1 61464 5reqA 727 2.02e+01 1reqA c.1.19.1,c.23.6.1 29632,31259 1reqA 727 2.02e+01 1reqA c.1.19.1,c.23.6.1 29620,31247 1e1cA 727 2.02e+01 1reqA c.1.19.1,c.23.6.1 29636,31263 1g4mA 393 2.05e+01 b.1.18.11,b.1.18.11 65143,65144 1ju6A 313 2.05e+01 d.117.1.1 63289 1vd4A 62 2.05e+01 1ypvA 313 2.09e+01 2al7A 186 2.11e+01 2h18A 193 2.12e+01 1sur 215 2.12e+01 1sur c.26.2.2 31620 1jsyA 418 2.20e+01 b.1.18.11,b.1.18.11 71847,71848 1bor 56 2.28e+01 1bor g.44.1.1 45324 1dl6A 58 2.30e+01 1dl6A g.41.3.1 45207 1rlyA 60 2.32e+01 g.41.3.1 104988 1wiiA 85 2.34e+01 1t9oA 54 2.37e+01 1hw4A 355 2.49e+01 1bkpA d.117.1.1 41054 1hyuA 521 2.52e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 2a1rA 430 2.56e+01 1ynjD 1524 2.57e+01 1xfkA 336 2.75e+01 1zpuA 534 2.76e+01 1spwA 39 2.77e+01 2d8iA 114 2.92e+01 1erd 40 3.07e+01 1erd a.10.1.1 16362 1m1qA 91 3.08e+01 a.138.1.3 74419 1jj2Y 73 3.09e+01 1ffkW g.41.8.1 63110 1ichA 112 3.12e+01 a.77.1.2 71182 1vckA 115 3.12e+01 2scuA 288 3.13e+01 2scuA c.2.1.8,c.23.4.1 30303,31131 1cqjA 286 3.13e+01 2scuA c.2.1.8,c.23.4.1 30305,31133 1sp1 29 3.15e+01 g.37.1.1 45051 2fymB 18 3.15e+01 1mm3A 61 3.15e+01 g.50.1.2 85016 1cteA 254 3.20e+01 1theB d.3.1.1 37058 2aw2B 108 3.20e+01 1yk4A 52 3.22e+01 1theA 260 3.22e+01 1theB d.3.1.1 37056 8rxnA 52 3.40e+01 1rb9 g.41.5.1 45215 1faq 52 3.43e+01 1far g.49.1.1 45352 1rb9 53 3.46e+01 1rb9 g.41.5.1 45214 1t9pA 54 3.48e+01 1wjvA 79 3.64e+01 1zxzA 197 3.73e+01 1brfA 53 3.74e+01 1rb9 g.41.5.1 45236 1bq8A 54 3.77e+01 1rb9 g.41.5.1 45237 1ee0A 402 3.81e+01 1bi5A c.95.1.2,c.95.1.2 36007,36008 1jmaB 167 3.90e+01 g.24.1.1,g.24.1.1 63178,63179 1v6eA 95 3.91e+01 1pw4A 451 3.91e+01 f.38.1.1 95198 1eqbA 417 3.97e+01 1bj4A c.67.1.4 34484 1mirA 322 3.97e+01 1theB d.3.1.1 37062 1dfoA 417 3.97e+01 1bj4A c.67.1.4 34480 1rdg 53 4.03e+01 1rb9 g.41.5.1 45221 1yk5A 53 4.06e+01 1e8jA 52 4.23e+01 g.41.5.1 64796 1q35A 320 4.29e+01 c.94.1.1 95661 2cjsC 62 4.30e+01 1jcoB 30 4.48e+01 g.1.1.1 66503 1weoA 93 4.49e+01 1mm2A 61 4.50e+01 g.50.1.2 85015 1uufA 369 4.75e+01 b.35.1.2,c.2.1.1 100006,100007 2a03A 206 4.78e+01 1f62A 51 4.80e+01 1f62A g.50.1.2 45360 2awpA 198 4.88e+01 1ev5A 264 4.93e+01 1bkpA d.117.1.1 40935 1uucA 55 4.94e+01 g.68.1.2 108045 2tsrA 307 5.05e+01 1bkpA d.117.1.1 41043 2cu8A 76 5.12e+01 2gf0A 199 5.14e+01 1vor2 58 5.24e+01 1nwyZ 59 5.31e+01 i.1.1.2 86369 1fiuA 286 5.36e+01 1fiuA c.52.1.10 33317 1ek9A 428 5.38e+01 1ek9A f.5.1.1 43809 1yl35 60 5.39e+01 1xi6A 262 5.47e+01 1ywzA 175 5.50e+01 1pt4A 29 5.56e+01 g.3.3.1 104306 1x4wA 67 5.57e+01 2dasA 62 5.61e+01 1wijA 140 5.68e+01 1c09A 54 5.69e+01 1rb9 g.41.5.1 45228 1jbjA 186 5.70e+01 b.1.1.4,b.1.1.4 66482,66483 1qyp 57 5.71e+01 1qyp g.41.3.1 45205 1tqqA 471 5.76e+01 f.5.1.1 107242 1iu5A 53 5.80e+01 g.41.5.1 71434 1wxvA 92 5.95e+01 1g25A 65 5.96e+01 1g25A g.44.1.1 45325 1vzv 221 6.00e+01 1at3A b.57.1.1 27025 1rikA 31 6.01e+01 k.12.1.1 104952 1rjwA 339 6.48e+01 b.35.1.2,c.2.1.1 97582,97583 1yc5A 246 6.73e+01 1bq2 264 6.76e+01 1bkpA d.117.1.1 40971 1jmh 316 6.85e+01 1bkpA d.117.1.1 41009 1h7kA 483 6.94e+01 e.5.1.1 90624 2a4eA 215 7.01e+01 1p9hA 226 7.01e+01 b.81.3.1 94389 2gpyA 233 7.02e+01 2cklB 165 7.02e+01 1pkhA 204 7.02e+01 b.85.4.1 94832 2h0dB 100 7.05e+01 2rdvA 52 7.06e+01 1rb9 g.41.5.1 45217 1ee8A 266 7.08e+01 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1mea 28 7.13e+01 g.41.1.1 45176 1a90 108 7.24e+01 1cewI d.17.1.2 38001 1y9wA 140 7.24e+01 1exkA 79 7.26e+01 1exkA g.54.1.1 45384 1nnqA 171 7.37e+01 a.25.1.1,g.41.5.1 92006,92007 1iml 76 7.53e+01 1iml g.39.1.3,g.39.1.3 45145,45146 1dq3A 454 7.54e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1s7bA 110 7.57e+01 f.39.1.1 98634 1ejxA 100 7.62e+01 d.8.1.1 83182 1ajw 145 7.62e+01 1rhoA b.1.18.8 21905 2f2mA 113 7.76e+01 5rxn 54 7.79e+01 1rb9 g.41.5.1 45225 1k7cA 233 7.80e+01 c.23.10.4 68267 1ifqA 138 7.84e+01 1ifqA d.110.4.1 62350 1xbfA 140 7.84e+01 d.273.1.1 109538 1mo2A 294 7.90e+01 c.69.1.22 79331 1kezA 300 8.08e+01 c.69.1.22 68546 1cewI 108 8.09e+01 1cewI d.17.1.2 37999 1t1jA 125 8.09e+01 c.137.1.1 106249 1rimA 35 8.16e+01 k.12.1.1 104953 2bx9A 53 8.28e+01 2bwfA 77 8.31e+01 1jkgB 250 8.35e+01 d.17.4.2 66796 1ng0A 253 8.40e+01 b.121.4.7 80475 1ctl 85 8.46e+01 g.39.1.3,g.39.1.3 45133,45134 1xmwA 178 8.51e+01 1yvbI 111 8.52e+01 1iro 54 8.54e+01 1rb9 g.41.5.1 45223 1hdlA 55 8.62e+01 g.68.1.2 65808 1chc 68 8.80e+01 1chc g.44.1.1 45323 1vmhA 144 8.82e+01