# 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 1.57e-02 1pft g.41.3.1 45206 1tr9A 341 9.73e-01 1y65A 342 9.75e-01 2ct7A 86 1.26e+00 1ww8A 439 2.56e+00 1y88A 199 2.82e+00 1s72Z 73 2.91e+00 g.41.8.1 105345 2ct2A 88 3.00e+00 1edyA 134 3.09e+00 1ayoA b.2.4.1 22428 1vqoZ 83 3.43e+00 1f4dA 264 3.59e+00 1bkpA d.117.1.1 40972 1frfS 264 4.20e+00 2frvA e.19.1.1 43312 1yqwA 264 4.21e+00 1yrqA 264 4.23e+00 1r4mA 529 4.29e+00 c.111.1.2 96999 1yovA 537 4.30e+00 1tt5A 531 4.30e+00 c.111.1.2 107291 2aq6A 147 4.48e+00 1e4uA 78 5.53e+00 1e4uA g.44.1.1 59231 1wd2A 60 5.64e+00 g.44.1.1 109232 1gnf 46 6.62e+00 1gatA g.39.1.1 45107 1p91A 269 6.77e+00 c.66.1.33 94378 1e1cA 727 6.92e+00 1reqA c.1.19.1,c.23.6.1 29636,31263 5reqA 727 6.93e+00 1reqA c.1.19.1,c.23.6.1 29632,31259 1reqA 727 6.93e+00 1reqA c.1.19.1,c.23.6.1 29620,31247 1odhA 174 7.88e+00 d.239.1.1 86850 2a66A 113 7.91e+00 1z1zA 131 8.34e+00 2ff0A 102 8.40e+00 1ur6B 52 8.78e+00 g.44.1.1 99812 1so2A 420 8.81e+00 a.211.1.2 98936 1sojI 420 8.87e+00 a.211.1.2 98950 2fqpA 97 9.56e+00 1ydfA 257 9.66e+00 1dx8A 70 9.93e+00 1rb9 g.41.5.1 45243 1lm5A 214 1.06e+01 d.211.2.1 74029 1sur 215 1.11e+01 1sur c.26.2.2 31620 1z6uA 150 1.19e+01 1jm7A 112 1.21e+01 g.44.1.1 66880 1fl2A 310 1.21e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1h7kA 483 1.24e+01 e.5.1.1 90624 1p9rA 418 1.25e+01 c.37.1.11 94399 1fl1A 230 1.38e+01 1at3A b.57.1.1 27023 1vdwA 254 1.42e+01 e.7.1.1 100569 1yqdA 366 1.43e+01 1dsvA 31 1.45e+01 1dsvA g.40.1.1 45174 1ffkW 73 1.52e+01 1ffkW g.41.8.1 45315 1h7vA 60 1.53e+01 g.41.5.1 65713 2gpyA 233 1.54e+01 1wfeA 86 1.57e+01 1mo2A 294 1.67e+01 c.69.1.22 79331 1kezA 300 1.70e+01 c.69.1.22 68546 1u79A 129 1.73e+01 d.26.1.1 107714 1zsqA 528 1.76e+01 1jagA 241 1.80e+01 c.37.1.1 66463 1g4mA 393 1.81e+01 b.1.18.11,b.1.18.11 65143,65144 1t9oA 54 1.82e+01 1jsyA 418 1.91e+01 b.1.18.11,b.1.18.11 71847,71848 1cqjA 286 1.97e+01 2scuA c.2.1.8,c.23.4.1 30305,31133 1vd4A 62 1.98e+01 2a1rA 430 1.98e+01 2scuA 288 1.98e+01 2scuA c.2.1.8,c.23.4.1 30303,31131 1l8dA 112 1.99e+01 h.4.12.1 73687 1spwA 39 2.05e+01 2avyS 91 2.08e+01 1h6nA 484 2.15e+01 e.5.1.1 90623 1e93A 484 2.16e+01 e.5.1.1 64802 1m85A 484 2.16e+01 e.5.1.1 74578 1rjwA 339 2.17e+01 b.35.1.2,c.2.1.1 97582,97583 1lw3A 657 2.33e+01 b.55.1.8,c.45.1.3 91152,91153 1n9dA 199 2.35e+01 a.26.1.1 85464 1faq 52 2.36e+01 1far g.49.1.1 45352 1uufA 369 2.36e+01 b.35.1.2,c.2.1.1 100006,100007 2cjsC 62 2.39e+01 1yk4A 52 2.53e+01 1pt4A 29 2.54e+01 g.3.3.1 104306 1sp1 29 2.56e+01 g.37.1.1 45051 1erd 40 2.71e+01 1erd a.10.1.1 16362 1us5A 314 2.76e+01 c.94.1.1 99856 1ichA 112 2.80e+01 a.77.1.2 71182 2fymB 18 2.81e+01 2a8jA 420 2.92e+01 2a8mA 420 2.92e+01 2a8lA 420 2.92e+01 1ujvA 96 2.95e+01 b.36.1.1 99470 8rxnA 52 3.00e+01 1rb9 g.41.5.1 45215 1iq3A 110 3.00e+01 1iq3A a.39.1.6 62640 1brfA 53 3.01e+01 1rb9 g.41.5.1 45236 1yk5A 53 3.01e+01 1bc8C 93 3.02e+01 1awcA a.4.5.21 16168 1bq8A 54 3.02e+01 1rb9 g.41.5.1 45237 1rb9 53 3.04e+01 1rb9 g.41.5.1 45214 1cteA 254 3.07e+01 1theB d.3.1.1 37058 1t9pA 54 3.09e+01 1theA 260 3.09e+01 1theB d.3.1.1 37056 1hyuA 521 3.17e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1ek9A 428 3.18e+01 1ek9A f.5.1.1 43809 1rdg 53 3.23e+01 1rb9 g.41.5.1 45221 1ifqA 138 3.24e+01 1ifqA d.110.4.1 62350 1m1qA 91 3.31e+01 a.138.1.3 74419 1e8jA 52 3.34e+01 g.41.5.1 64796 1tqqA 471 3.41e+01 f.5.1.1 107242 1dfoA 417 3.43e+01 1bj4A c.67.1.4 34480 1eqbA 417 3.43e+01 1bj4A c.67.1.4 34484 1xfkA 336 3.52e+01 1vzv 221 3.53e+01 1at3A b.57.1.1 27025 2d8iA 114 3.56e+01 1mirA 322 3.61e+01 1theB d.3.1.1 37062 1bor 56 3.66e+01 1bor g.44.1.1 45324 2aw2B 108 3.69e+01 1zxzA 197 3.70e+01 1hvyA 288 3.75e+01 1bkpA d.117.1.1 41049 1wjvA 79 3.77e+01 1hzwA 290 3.80e+01 1bkpA d.117.1.1 61464 1ev5A 264 3.82e+01 1bkpA d.117.1.1 40935 2a62A 322 3.86e+01 1wiiA 85 3.86e+01 1ywzA 175 4.02e+01 1ypvA 313 4.05e+01 1yc5A 246 4.06e+01 1q35A 320 4.08e+01 c.94.1.1 95661 1ju6A 313 4.09e+01 d.117.1.1 63289 1dl6A 58 4.12e+01 1dl6A g.41.3.1 45207 1mm3A 61 4.14e+01 g.50.1.2 85016 2cu8A 76 4.15e+01 1rlyA 60 4.18e+01 g.41.3.1 104988 1jcoB 30 4.23e+01 g.1.1.1 66503 1jj2Y 73 4.28e+01 1ffkW g.41.8.1 63110 1g25A 65 4.36e+01 1g25A g.44.1.1 45325 1bq2 264 4.44e+01 1bkpA d.117.1.1 40971 1iml 76 4.54e+01 1iml g.39.1.3,g.39.1.3 45145,45146 1jmaB 167 4.62e+01 g.24.1.1,g.24.1.1 63178,63179 1rikA 31 4.74e+01 k.12.1.1 104952 1hw4A 355 4.75e+01 1bkpA d.117.1.1 41054 1v6eA 95 4.78e+01 1cdoA 374 4.82e+01 2ohxA b.35.1.2,c.2.1.1 24747,29763 1c09A 54 4.92e+01 1rb9 g.41.5.1 45228 1pw4A 451 4.98e+01 f.38.1.1 95198 1x4wA 67 5.09e+01 1vor2 58 5.12e+01 1qyp 57 5.18e+01 1qyp g.41.3.1 45205 2al7A 186 5.18e+01 1oy0A 281 5.19e+01 c.1.12.8 87543 2gf0A 199 5.20e+01 1nwyZ 59 5.22e+01 i.1.1.2 86369 1zd9A 188 5.23e+01 1yl35 60 5.30e+01 2g8yA 385 5.39e+01 1exkA 79 5.42e+01 1exkA g.54.1.1 45384 1jkgB 250 5.51e+01 d.17.4.2 66796 1hbxG 157 5.53e+01 1awcA a.4.5.21 60934 1iu5A 53 5.54e+01 g.41.5.1 71434 2h18A 193 5.62e+01 1t1jA 125 5.81e+01 c.137.1.1 106249 2awpA 198 5.91e+01 1mm2A 61 5.92e+01 g.50.1.2 85015 1uucA 55 6.09e+01 g.68.1.2 108045 2tsrA 307 6.11e+01 1bkpA d.117.1.1 41043 1sjxA 122 6.18e+01 2gatA 66 6.21e+01 1gatA g.39.1.1 45102 1a90 108 6.25e+01 1cewI d.17.1.2 38001 1a9xB 379 6.25e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 2h0dB 100 6.25e+01 1jdbC 382 6.27e+01 c.8.3.1,c.23.16.1 30756,31433 2cklB 165 6.28e+01 1m6vB 382 6.32e+01 c.8.3.1,c.23.16.1 74542,74543 1vk4A 298 6.36e+01 c.72.1.1 100850 2rdvA 52 6.41e+01 1rb9 g.41.5.1 45217 1gatA 60 6.52e+01 1gatA g.39.1.1 45106 1rimA 35 6.71e+01 k.12.1.1 104953 1mea 28 6.83e+01 g.41.1.1 45176 2cuqA 80 6.84e+01 1dq3A 454 6.97e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1qvbA 481 6.98e+01 1qvbA c.1.8.4 28983 1pkhA 204 7.02e+01 b.85.4.1 94832 1xi6A 262 7.04e+01 1g0dA 695 7.15e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 60166,60167,60168,60169 5rxn 54 7.19e+01 1rb9 g.41.5.1 45225 2a03A 206 7.28e+01 1cewI 108 7.28e+01 1cewI d.17.1.2 37999 1ile 821 7.29e+01 1ile a.27.1.1,b.51.1.1,c.26.1.1 16924,26889,31591 1p9hA 226 7.38e+01 b.81.3.1 94389 1wxvA 92 7.42e+01 1gqpA 221 7.43e+01 b.18.1.9 70372 2aq4A 434 7.47e+01 2bx9A 53 7.51e+01 1wijA 140 7.61e+01 1cokA 68 7.69e+01 1cokA a.60.1.2 17945 1fiuA 286 7.72e+01 1fiuA c.52.1.10 33317 1yvbI 111 7.74e+01 1iro 54 7.89e+01 1rb9 g.41.5.1 45223 1zpuA 534 7.92e+01 1zprA 264 8.02e+01 1bkpA d.117.1.1 40978 1y1cA 48 8.09e+01 1poiA 317 8.12e+01 1poiA c.124.1.2 34153 2ftnA 264 8.19e+01 2g8mA 264 8.20e+01 1axwA 265 8.20e+01 1bkpA d.117.1.1 40938 2g8oA 264 8.20e+01 1frvA 264 8.20e+01 2frvA e.19.1.1 43308 1qqqA 264 8.22e+01 1bkpA d.117.1.1 40931 1jg0A 264 8.22e+01 d.117.1.1 66659 1aiqA 264 8.26e+01 1bkpA d.117.1.1 40967 2tscA 264 8.31e+01 1bkpA d.117.1.1 40952 1vckA 115 8.33e+01 1kzjA 264 8.34e+01 d.117.1.1 73365 1v9kA 228 8.41e+01 d.265.1.3 108449 1chc 68 8.46e+01 1chc g.44.1.1 45323 1vk6A 269 8.46e+01 d.113.1.4,d.113.1.4 100851,100852 1evfA 264 8.63e+01 1bkpA d.117.1.1 40932 1yq9A 264 8.64e+01 1x75A 132 8.64e+01 1ajw 145 8.71e+01 1rhoA b.1.18.8 21905 2cbnA 306 8.79e+01 1se7A 83 8.85e+01 1t36B 382 8.88e+01 c.8.3.1,c.23.16.1 106307,106308 1ee8A 266 8.99e+01 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825