# List of top-scoring protein chains for T0348.t06-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 4.24e-03 1pft g.41.3.1 45206 1tr9A 341 1.16e+00 1y65A 342 1.16e+00 2ct2A 88 1.65e+00 2aq6A 147 2.13e+00 2ct7A 86 2.27e+00 1e4uA 78 2.76e+00 1e4uA g.44.1.1 59231 1y88A 199 4.84e+00 1s72Z 73 4.86e+00 g.41.8.1 105345 1edyA 134 5.12e+00 1ayoA b.2.4.1 22428 1ur6B 52 5.37e+00 g.44.1.1 99812 1vqoZ 83 5.56e+00 1yqwA 264 6.06e+00 1yrqA 264 6.12e+00 2ff0A 102 6.21e+00 2a66A 113 6.28e+00 1frfS 264 6.30e+00 2frvA e.19.1.1 43312 1p91A 269 6.32e+00 c.66.1.33 94378 1gnf 46 7.23e+00 1gatA g.39.1.1 45107 1n9dA 199 7.84e+00 a.26.1.1 85464 2a8jA 420 8.15e+00 2a8mA 420 8.18e+00 2a8lA 420 8.27e+00 1odhA 174 8.36e+00 d.239.1.1 86850 1z1zA 131 8.46e+00 2a62A 322 8.57e+00 1f4dA 264 8.59e+00 1bkpA d.117.1.1 40972 1u79A 129 8.72e+00 d.26.1.1 107714 1us5A 314 8.74e+00 c.94.1.1 99856 1rlyA 60 9.31e+00 g.41.3.1 104988 1wd2A 60 9.41e+00 g.44.1.1 109232 1dl6A 58 9.42e+00 1dl6A g.41.3.1 45207 1jm7A 112 9.69e+00 g.44.1.1 66880 1yovA 537 1.14e+01 1r4mA 529 1.14e+01 c.111.1.2 96999 1zsqA 528 1.14e+01 1tt5A 531 1.15e+01 c.111.1.2 107291 1ww8A 439 1.18e+01 1fl2A 310 1.19e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1z6uA 150 1.22e+01 5reqA 727 1.24e+01 1reqA c.1.19.1,c.23.6.1 29632,31259 1reqA 727 1.25e+01 1reqA c.1.19.1,c.23.6.1 29620,31247 1e1cA 727 1.25e+01 1reqA c.1.19.1,c.23.6.1 29636,31263 1p9rA 418 1.46e+01 c.37.1.11 94399 2fqpA 97 1.46e+01 1cqjA 286 1.46e+01 2scuA c.2.1.8,c.23.4.1 30305,31133 2scuA 288 1.47e+01 2scuA c.2.1.8,c.23.4.1 30303,31131 1wfeA 86 1.53e+01 1dx8A 70 1.56e+01 1rb9 g.41.5.1 45243 2a1rA 430 1.57e+01 1ichA 112 1.59e+01 a.77.1.2 71182 1so2A 420 1.59e+01 a.211.1.2 98936 1sojI 420 1.59e+01 a.211.1.2 98950 1ujvA 96 1.65e+01 b.36.1.1 99470 2avyS 91 1.67e+01 1zd9A 188 1.68e+01 1vd4A 62 1.70e+01 1lw3A 657 1.75e+01 b.55.1.8,c.45.1.3 91152,91153 1l8dA 112 1.76e+01 h.4.12.1 73687 1bc8C 93 1.78e+01 1awcA a.4.5.21 16168 2h18A 193 1.80e+01 2al7A 186 1.83e+01 1ffkW 73 1.87e+01 1ffkW g.41.8.1 45315 1wiiA 85 1.88e+01 1h7vA 60 1.92e+01 g.41.5.1 65713 1h7kA 483 2.02e+01 e.5.1.1 90624 1lm5A 214 2.04e+01 d.211.2.1 74029 1vdwA 254 2.06e+01 e.7.1.1 100569 1bor 56 2.10e+01 1bor g.44.1.1 45324 1hzwA 290 2.17e+01 1bkpA d.117.1.1 61464 1hvyA 288 2.19e+01 1bkpA d.117.1.1 41049 1ju6A 313 2.23e+01 d.117.1.1 63289 1yqdA 366 2.29e+01 1dsvA 31 2.33e+01 1dsvA g.40.1.1 45174 1ypvA 313 2.35e+01 1ydfA 257 2.38e+01 2gpyA 233 2.43e+01 1mm3A 61 2.45e+01 g.50.1.2 85016 2fymB 18 2.51e+01 1m1qA 91 2.57e+01 a.138.1.3 74419 2d8iA 114 2.64e+01 1hyuA 521 2.74e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1hw4A 355 2.78e+01 1bkpA d.117.1.1 41054 1t9oA 54 2.79e+01 1erd 40 2.86e+01 1erd a.10.1.1 16362 1jagA 241 2.88e+01 c.37.1.1 66463 2g2kA 170 3.11e+01 1g4mA 393 3.17e+01 b.1.18.11,b.1.18.11 65143,65144 1o6bA 169 3.18e+01 c.26.1.3 92564 1mm2A 61 3.18e+01 g.50.1.2 85015 1sp1 29 3.24e+01 g.37.1.1 45051 1yk4A 52 3.36e+01 1jsyA 418 3.39e+01 b.1.18.11,b.1.18.11 71847,71848 1iq3A 110 3.43e+01 1iq3A a.39.1.6 62640 1faq 52 3.49e+01 1far g.49.1.1 45352 1iml 76 3.51e+01 1iml g.39.1.3,g.39.1.3 45145,45146 1hbxG 157 3.53e+01 1awcA a.4.5.21 60934 1vor2 58 3.54e+01 1nwyZ 59 3.58e+01 i.1.1.2 86369 1sur 215 3.58e+01 1sur c.26.2.2 31620 2gf0A 199 3.63e+01 1x4wA 67 3.63e+01 1yl35 60 3.63e+01 1pt4A 29 3.67e+01 g.3.3.1 104306 1fl1A 230 3.71e+01 1at3A b.57.1.1 27023 1ee8A 266 3.75e+01 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 8rxnA 52 3.75e+01 1rb9 g.41.5.1 45215 1rb9 53 3.81e+01 1rb9 g.41.5.1 45214 1jcoB 30 3.82e+01 g.1.1.1 66503 2tsrA 307 3.92e+01 1bkpA d.117.1.1 41043 1t9pA 54 3.99e+01 1spwA 39 4.03e+01 1fiuA 286 4.10e+01 1fiuA c.52.1.10 33317 1e93A 484 4.18e+01 e.5.1.1 64802 2a4eA 215 4.18e+01 1h6nA 484 4.19e+01 e.5.1.1 90623 1m85A 484 4.21e+01 e.5.1.1 74578 1jj2Y 73 4.27e+01 1ffkW g.41.8.1 63110 1ctl 85 4.29e+01 g.39.1.3,g.39.1.3 45133,45134 1jbjA 186 4.35e+01 b.1.1.4,b.1.1.4 66482,66483 1vckA 115 4.39e+01 1uucA 55 4.44e+01 g.68.1.2 108045 1wijA 140 4.56e+01 1yk5A 53 4.58e+01 1q35A 320 4.60e+01 c.94.1.1 95661 2cu8A 76 4.76e+01 1r6lA 239 4.84e+01 d.14.1.4,d.101.1.1 97153,97154 1ajw 145 4.91e+01 1rhoA b.1.18.8 21905 2a6hD 1524 5.00e+01 1ptq 50 5.09e+01 1ptq g.49.1.1 45349 1sezA 504 5.09e+01 c.3.1.2,d.16.1.5 98822,98823 1pkhA 204 5.20e+01 b.85.4.1 94832 1cteA 254 5.25e+01 1theB d.3.1.1 37058 1theA 260 5.28e+01 1theB d.3.1.1 37056 1inp 400 5.29e+01 1inp e.7.1.1 42972 1nigA 152 5.60e+01 a.25.2.1 85740 1uufA 369 5.69e+01 b.35.1.2,c.2.1.1 100006,100007 1zxzA 197 5.70e+01 1xmwA 178 5.77e+01 1vzv 221 5.82e+01 1at3A b.57.1.1 27025 1v87A 114 5.86e+01 g.44.1.1 108422 1rikA 31 5.93e+01 k.12.1.1 104952 2aq4A 434 5.94e+01 1xtqA 177 5.94e+01 1qyp 57 5.97e+01 1qyp g.41.3.1 45205 1f62A 51 6.04e+01 1f62A g.50.1.2 45360 1xfkA 336 6.13e+01 1ee0A 402 6.16e+01 1bi5A c.95.1.2,c.95.1.2 36007,36008 1brfA 53 6.17e+01 1rb9 g.41.5.1 45236 1rdg 53 6.18e+01 1rb9 g.41.5.1 45221 1ynjD 1524 6.20e+01 1bq8A 54 6.20e+01 1rb9 g.41.5.1 45237 1eqbA 417 6.24e+01 1bj4A c.67.1.4 34484 1dfoA 417 6.25e+01 1bj4A c.67.1.4 34480 1c09A 54 6.29e+01 1rb9 g.41.5.1 45228 1gl9B 1054 6.33e+01 c.37.1.16,c.37.1.16,e.10.1.1 65291,65292,65293 1e8jA 52 6.37e+01 g.41.5.1 64796 1weoA 93 6.38e+01 1g25A 65 6.55e+01 1g25A g.44.1.1 45325 1exkA 79 6.57e+01 1exkA g.54.1.1 45384 1lv3A 68 6.58e+01 g.39.1.9 78231 1dq3A 454 6.66e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1v6eA 95 6.74e+01 1ifqA 138 6.76e+01 1ifqA d.110.4.1 62350 2cklB 165 6.83e+01 2bx9A 53 6.88e+01 2h0dB 100 6.89e+01 1wjvA 79 6.94e+01 2awpA 198 6.99e+01 1xi6A 262 6.99e+01 1gqpA 221 7.02e+01 b.18.1.9 70372 1chc 68 7.07e+01 1chc g.44.1.1 45323 1ek9A 428 7.35e+01 1ek9A f.5.1.1 43809 2gy5A 423 7.36e+01 1mirA 322 7.40e+01 1theB d.3.1.1 37062 2aw2B 108 7.44e+01 1rimA 35 7.45e+01 k.12.1.1 104953 1kmtA 141 7.47e+01 b.1.18.8 77442 1hdlA 55 7.50e+01 g.68.1.2 65808 1yvnA 375 7.62e+01 1yagA c.55.1.1,c.55.1.1 33451,33452 1yagA 375 7.65e+01 1yagA c.55.1.1,c.55.1.1 33449,33450 1qxfA 66 7.65e+01 g.41.8.4 96527 1xwhA 66 7.66e+01 2a03A 206 7.68e+01 1s7bA 110 7.84e+01 f.39.1.1 98634 2rdvA 52 7.95e+01 1rb9 g.41.5.1 45217 1tqqA 471 7.97e+01 f.5.1.1 107242 1ile 821 8.04e+01 1ile a.27.1.1,b.51.1.1,c.26.1.1 16924,26889,31591 2f2mA 113 8.05e+01 1doaB 219 8.06e+01 1rhoA b.1.18.8 21904 5rxn 54 8.07e+01 1rb9 g.41.5.1 45225 1nypA 66 8.11e+01 g.39.1.3,g.39.1.3 86411,86412 1gvzA 237 8.11e+01 b.47.1.2 76360 2cjsC 62 8.11e+01 1rjwA 339 8.17e+01 b.35.1.2,c.2.1.1 97582,97583 1k8kA 418 8.20e+01 c.55.1.1,c.55.1.1 68305,68306 1c0fA 368 8.25e+01 1yagA c.55.1.1,c.55.1.1 33447,33448 1cokA 68 8.42e+01 1cokA a.60.1.2 17945 1b8tA 192 8.43e+01 1b8tA g.39.1.3,g.39.1.3,g.39.1.3,g.39.1.3 45135,45136,45137,45138 1mea 28 8.43e+01 g.41.1.1 45176 1poiA 317 8.43e+01 1poiA c.124.1.2 34153 2bqzA 161 8.51e+01 1jmaB 167 8.54e+01 g.24.1.1,g.24.1.1 63178,63179 1a90 108 8.57e+01 1cewI d.17.1.2 38001 1ng0A 253 8.64e+01 b.121.4.7 80475 1ku1A 230 8.73e+01 a.118.3.1 72996 1zkkA 167 8.78e+01 1fsoA 139 8.91e+01 1rhoA b.1.18.8 60007 1nkpA 88 8.96e+01 a.38.1.1 80573